No full-text available
To read the full-text of this research,
you can request a copy directly from the authors.
Spider‐specific probe set for ultraconserved elements offers new perspectives on the evolutionary history of spiders (Arachnida, Araneae)
Abstract
Phylogenomic methods have proven useful for resolving deep nodes and recalcitrant groups in the spider tree of life. Across arachnids, transcriptomic approaches may generate thousands of loci, and target‐capture methods, using the previously designed arachnid‐specific probe‐set, can target a maximum of about 1,000 loci. Here, we develop a specialized target‐capture probe set for spiders that contains over 2,000 ultraconserved elements (UCEs) and then demonstrate the utility of this probe set through sequencing and phylogenetic analysis. We designed the “spider‐specific” probe set using three spider genomes (Loxosceles, Parasteatoda and Stegodyphus) and ensured that the newly designed probe‐set include UCEs from the previously designed Arachnida probe set. The new “spider‐specific” probes were used to sequence UCE loci in 51 specimens. The remaining samples included five spider genomes and taxa that were enriched using Arachnida probe set. The “spider‐specific” probes were also used to gather loci from a total of 84 representative taxa across Araneae. On mapping these 84 taxa to the Arachnida probe set, we captured at most 710 UCE loci, while the spider specific probe set captured up to 1,547 UCE loci from the same taxon sample. Phylogenetic analyses using Maximum Likelihood and coalescent methods corroborate most nodes resolved by recent transcriptomic analyses, but not all (e.g., UCE data suggests monophyly of “symphytognathoids”). Our preferred analysis based on topology tests, suggests monophyly of the “symphytognathoids” (the miniature orb‐weavers), which in previous studies has only been supported by a combination of morphological and behavioral characters.
... A handful of sets of UCE baits have been developed for arachnids in recent years, targeting from loci present across arachnids, to loci potentially present only in specific groups (Branstetter et al., 2017;Xu et al., 2021;Zhang et al., 2023). Among these, Kulkarni et al. (2020) developed a set of baits for spiders (Spider 2Kv1), which builds on the previously available arachnid set Arachnida 1.1Kv1 (Branstetter et al., 2017) but roughly duplicates the potential (2000 vs. 1000) and realized (1500 vs. 700) number of loci captured across spider groups (Kulkarni et al., 2020). Remarkably, the Spider 2Kv1 overlaps noticeably with the exon information in the transcriptomes, opening a door for incorporating transcriptomic information into UCE studies of spiders (Hedin et al., 2019;Kulkarni et al., 2020Kulkarni et al., , 2021. ...
... A handful of sets of UCE baits have been developed for arachnids in recent years, targeting from loci present across arachnids, to loci potentially present only in specific groups (Branstetter et al., 2017;Xu et al., 2021;Zhang et al., 2023). Among these, Kulkarni et al. (2020) developed a set of baits for spiders (Spider 2Kv1), which builds on the previously available arachnid set Arachnida 1.1Kv1 (Branstetter et al., 2017) but roughly duplicates the potential (2000 vs. 1000) and realized (1500 vs. 700) number of loci captured across spider groups (Kulkarni et al., 2020). Remarkably, the Spider 2Kv1 overlaps noticeably with the exon information in the transcriptomes, opening a door for incorporating transcriptomic information into UCE studies of spiders (Hedin et al., 2019;Kulkarni et al., 2020Kulkarni et al., , 2021. ...
... Among these, Kulkarni et al. (2020) developed a set of baits for spiders (Spider 2Kv1), which builds on the previously available arachnid set Arachnida 1.1Kv1 (Branstetter et al., 2017) but roughly duplicates the potential (2000 vs. 1000) and realized (1500 vs. 700) number of loci captured across spider groups (Kulkarni et al., 2020). Remarkably, the Spider 2Kv1 overlaps noticeably with the exon information in the transcriptomes, opening a door for incorporating transcriptomic information into UCE studies of spiders (Hedin et al., 2019;Kulkarni et al., 2020Kulkarni et al., , 2021. This strategy has already been successfully employed in bee (Bossert et al., 2019) and true bug (Kieran et al., 2019) studies and could allow incorporating the transcriptomic information of at least 28 theraphosid genera already available in the NCBI into future UCEbased tarantula research. ...
Although tarantulas are a widespread, highly diversified, and charismatic spider group, our understanding of their evolution remains limited. A recent transcriptome-based approach, including 16% of the nominal tarantula genera (25), provided the first robust phylogenetic hypothesis of deep tarantula relationships. However, transcriptomics has practical downsides, making it less than ideal for phylogenomic analyses. Ultraconserved Elements (UCE) sequencing, a cost-effective alternative, allows for the simultaneous reading of hundreds of loci and utilizing samples with degraded DNA, including museum material, but its utility for resolving deep tarantula relationships remains to be tested. In this study, I recovered up to ~850 unique UCE loci from publicly available individual tarantula transcriptomes. Phylogenetic estimation using these loci resulted in topologies identical to those obtained from the published complete transcriptomic datasets, with limited phylogenetic uncertainty restricted to two branches in the tarantula tree of life. I conclude that UCE information has great potential for resolving at least moderate to deep tarantula relationships and that numerous UCE loci can be harvested from tarantula transcriptomic data. Finally, I provide databases of transcripts and UCE loci for the 27 currently available tarantula genera, facilitating their inclusion in future phylogenomic studies with deeper taxon coverage.
... Phylogenomic hypotheses generated using UCEs and exons (transcriptomes) generally agree, but several studies have shown disagreement between these topologies, especially at recalcitrant nodes with low phylogenetic signal (e.g. Bossert et al., 2019;Kulkarni et al., 2020;Alda et al., 2021). Within arachnids, a notable example is the case of Symphytognathoidea, a clade of miniaturized spiders that was proposed on the basis of morphological data. ...
... Within arachnids, a notable example is the case of Symphytognathoidea, a clade of miniaturized spiders that was proposed on the basis of morphological data. While not recovered by phylotranscriptomic analyses, this group was recovered as monophyletic with strong support by UCE datasets (Kulkarni et al., 2020). These results were interpreted to mean that the phylogenetic signal in UCE datasets may be more congruent with morphological data, suggesting superior performance in comparison with phylotranscriptomic matrices. ...
... For assembly of UCE matrices, the FASTA files of transcriptomes were converted to a 2-bit format using faToTwoBit (Kent, 2002), and then recovered using PHYLUCE v.1.7 (Faircloth, 2016). The resulting FASTA files were then matched to the sequences from the Spider2Kv1 probe (Kulkarni et al., 2020). Nucleotide sequences from UCEs were assembled, aligned using MAFFT v.7.4 (--auto -anysymbol --quiet; Katoh and Standley, 2013) and trimmed using Table 1 High-level classification of scorpions proposed by Sharma et al. (2015) and modified by Santib añez-L opez et al. (2019a,b, 2020) . ...
Scorpions are ancient and historically renowned for their potent venom. Traditionally, the systematics of this group of arthro-pods was supported by morphological characters, until recent phylogenomic analyses (using RNAseq data) revealed most of the higher-level taxa to be non-monophyletic. While these phylogenomic hypotheses are stable for almost all lineages, some nodes have been hard to resolve due to minimal taxonomic sampling (e.g. family Chactidae). In the same line, it has been shown that some nodes in the Arachnid Tree of Life show disagreement between hypotheses generated using transcritptomes and other genomic sources such as the ultraconserved elements (UCEs). Here, we compared the phylogenetic signal of transcriptomes vs. UCEs by retrieving UCEs from new and previously published scorpion transcriptomes and genomes, and reconstructed phyloge-nies using both datasets independently. We reexamined the monophyly and phylogenetic placement of Chactidae, sampling an additional chactid species using both datasets. Our results showed that both sets of genome-scale datasets recovered highly similar topologies, with Chactidae rendered paraphyletic owing to the placement of Nullibrotheas allenii. As a first step toward redressing the systematics of Chactidae, we establish the family Anuroctonidae (new family) to accommodate the genus Anuroctonus.
... New molecular sequencing techniques can be used to access hundreds or thousands of loci for phylogenetic inference. Targeted enrichment approaches (e.g., Ultraconserved Elements and Anchored Hybrid Enrichment) (Faircloth et al., 2012;Lemmon and Lemmon, 2013) have been useful for inferring robust phylogenetic relationships of the non-model groups, such as Mygalomorphae spiders, such as Aphonopelma Pocock, 1901, Aptostichus Simon, 1891, Aliatypus Smith, 1908, Antrodiaetus Ausserer, 1871, Hexurella Gertsch and Platnick, 1979, Mecicobothrium Holmberg, 1882, Megahexura Kaston, 1972, Porrhothele Simon, 1892(Faircloth et al., 2012Hamilton et al., 2016b;Starrett et al., 2016;Yeates et al., 2016;Branstetter et al., 2017;Hedin et al., 2018Hedin et al., , 2019Derkarabetian et al., 2019;Zhang et al., 2019;Kulkarni et al., 2020;Xu et al., 2021). To date, there has been only one study using either of these phylogenomic approaches in tarantulas, the North American genus Aphonopelma (Hamilton et al., 2016a). ...
... To date, there has been only one study using either of these phylogenomic approaches in tarantulas, the North American genus Aphonopelma (Hamilton et al., 2016a). Kulkarni et al. (2020) designed a spider-specific UCE probe set, which has been recovering a high number of loci, contributing to several questions in different phylogenetic studies. ...
... Samples were equimolar pooled and sequenced on an SP flow cell (2 × 250 bp) or an S4 flow cell (2 × 150 bp). The resulting data were processed using Phyluce version 1.7.1 (Faircloth, 2016) and a combined arachnid-spider hybrid probeset (Starrett et al., 2016;Kulkarni et al., 2020), where match settings for minimum identity and minimum coverage of 85 and 85 (respectively) were used. Loci were then aligned using MAFFT (Katoh and Standley, 2013), with alignments externally trimmed and then internally trimmed using gblocks with b1, b2, b3, and b4 and settings of 0.5, 0.5, 5, and 10, respectively, to remove poorly aligned blocks within the sequences. ...
Theraphosinae is the most diverse subfamily of Theraphosidae spiders, but their evolutionary history remains unresolved to date. This problem is common in taxonomic groups with phylogenetic hypotheses that have often been based only on qualitative morphological characters and, rarely, on molecular analyses. Phylogenomics has significantly contributed to the understanding of the evolution of many non-model groups, such as spiders. Herein, we employed ultraconserved elements (UCEs) phylogenomics to propose a new hypothesis for a group of Theraphosinae genera, namely Lasiodoriforms: Vitalius, Lasiodora, Eupalaestrus, Pterinopelma, Proshapalopus , and Nhandu . We propose three genera and their respective morphological diagnoses are provided. Our phylogeny supports the transfer of species from the genus Vitalius to Pterinopelma and Proshapalopus and from Proshapalopus to Eupalaestrus . Finally, we describe a new species of Vitalius from Southern Brazil. Based on these three new generic descriptions and transferred species, the Lasiodoriform tarantulas comprise nine genera from Argentina, Brazil, Paraguay, and Uruguay, and the genus Vitalius now includes seven species.
... In a parsimony analysis of transcriptomic data Kallal et al. (2021) recovered Theridiosomatidae as sister to Araneidae while the other "symphytognathoid'' families formed a monophyletic group. An analysis of ultraconserved elements (UCEs) using a small sample of symphytognathoids (16 species in all families except Synaphridae and representatives of all other araneoid families) provided the first empirical support for symphytognathoid' monophyly using molecular data alone, with the analyzed low occupancy datasets (Kulkarni et al. 2020). A further integrated sampling obtained by extracting UCEs from transcriptomes found that Synaphridae too nested within symphytognathoids . ...
... The polyphyly of this group received high bootstrap support by transcriptomes. This paradox of highly supported but incongruent relationships across phylogenomic datasets was resolved through analyses of exons, ultraconserved loci, a combination of these data as amino acids and nucleotides which recovered monophyly of "symphytognathoids" (Kulkarni et al. 2020) at low occupancies. This latter study focused on the higher-level relationships of Araneae and therefore included only a handful of anapid representatives (10 out of the 58 valid genera). ...
... We included 95 terminals, some newly sequenced UCEs and others from previous studies, representing 17 Araneoidea families, two nicodamoids-Megadictyna thilenii and a Nicodamidae undetermined species, a deinopid (Deinopis sp.) and an eresid (Stegodyphus mimosarum), which was used to root the tree. In addition to our sequencing efforts, we included additional taxa from the data sets of Fernández et al. (2018), Kulkarni et al. (2020), and , Kallal et al. (2021). We compiled another data set which included 129 terminals generated by combining the UCE data set with 65 taxa represented by six publicly available Sanger sequenced loci-12S ribosomal RNA (12S), 16S ribosomal RNA (16S) and cytochrome c oxidase subunit 1 (COI) genes, three nuclear genes-the protein-coding histone H3 (H3), and small and large subunits of ribosomal RNA genes (18S and 28S, respectively). ...
The miniature orb weaving spiders (symphytognathoids) are a group of small spiders (< 2 mm), including the smallest adult spider Patu digua (0.37 mm in body length), that have been classified into five families. The species of one of its constituent lineages, the family Anapidae, build a remarkable diversity of webs (ranging from orbs to sheet webs and irregular tangles) and even include a webless kleptoparasitic species. Anapids are also exceptional because of the extraordinary diversity of their respiratory systems. The phylogenetic relationships of symphytognathoid families have been recalcitrant with different classes of data, such as, monophyletic with morphology and its concatenation with Sanger-based six markers, paraphyletic (including a paraphyletic Anapidae) with solely Sanger-based six markers, and polyphyletic with transcriptomes. In this study, we capitalized on a large taxonomic sampling of symphytognathoids, focusing on Anapidae, and using de novo sequenced ultraconserved elements (UCEs) combined with UCEs recovered from available transcriptomes and genomes. We evaluated the conflicting relationships using a variety of support metrics and topology tests. We found support for the phylogenetic hypothesis proposed using morphology to obtain the "symphytognathoids'' clade, Anterior Tracheal System (ANTS) Clade and monophyly of the family Anapidae. Anapidae can be divided into three major lineages, the Vichitra Clade (including Teutoniella, Holarchaea, Sofanapis and Acrobleps), the subfamily Micropholcommatinae and the Orb-weaving anapids (Owa) Clade. Biogeographic analyses reconstructed a hypothesis of multiple long-distance transoceanic dispersal events, potentially influenced by the Antarctic Circumpolar Current and West Wind Drift. In symphytognathoids, the ancestral anterior tracheal system transformed to book lungs four times and reduced book lungs five times. The posterior tracheal system was lost six times. The orb web structure was lost four times independently and transformed into sheet web once.
... Recent phylogenies estimated by other researchers (Dimitrov et al. 2017;Kulkarni et al. 2020;Scharff et al. 2020) agreed that these three clades are mutually monophyletic, well-defined, and informative. Kuntner et al. (2019) named this unranked group of three families Orbipurae, the archetypal orbweb spiders, preserving the family group name Araneidae for a classical, core set of diverse, coherent, widely recognized, and most studied groups of genera, including Araneus, the type genus of Araneae. ...
... Here we use subgenomic data and extensive taxon sampling of Orbipurae to confirm Paraplectanoides + Nephilidae, however, that clade is placed outside Araneidae s.s. (as in Kulkarni et al. 2020;Scharff et al. 2020). We then argue that a better supported phylogeny, and the criteria of diagnosability, information content, and utility, eclipse the arguments put forth by Kallal et al. (2020). ...
... Kallal et al.'s (2020) hypothesized relationship of Paraplectanoides + Nephilidae restated results from earlier Sanger data-based hypotheses Hormiga 2018, 2019), placing the pair inside Araneidae s.s. Developing UCE data probes for spiders, Kulkarni et al. (2020) recovered the grouping Paraplectanoides + Trichonephila outside Araneidae s.s., but the data set contained only one nephilid terminal on a long branch. As the Paraplectanoides + Trichonephila relationship might plausibly have been an artefact of long-branch attraction (Felsenstein 1978;Bergsten 2005), and as ...
Higher-level classifications often must account for monotypic taxa representing depauperate evolutionary lineages and lacking synapomorphies of their better-known, well-defined sister clades. In a ranked (Linnean) or unranked (phylogenetic) classification system, discovering such a depauperate taxon does not necessarily invalidate the rank classification of sister clades. Named higher taxa must be monophyletic to be phylogenetically valid. Ranked taxa above the species level should also maximize information content, diagnosability, and utility (e.g., in biodiversity conservation). In spider classification, families are the highest rank that is systematically catalogued, and incertae sedis is not allowed. Consequently, it is important that family level taxa be well defined and informative. We revisit the classification problem of Orbipurae, an unranked suprafamilial clade containing the spider families Nephilidae, Phonognathidae, and Araneidae sensu stricto. We argue that, to maximize diagnosability, information content, conservation utility, and practical taxonomic considerations, this "splitting" scheme is superior to its recently proposed alternative, which lumps these families together as Araneidae sensu lato. We propose to redefine Araneidae and recognize a monogeneric spider family, Paraplectanoididae fam. nov. to accommodate the depauperate lineage Paraplectanoides. We present new subgenomic data to stabilize Orbipurae topology which also supports our proposed family-level classification. Our example from spiders demonstrates why classifications must be able to accommodate depauperate evolutionary lineages, e.g., Paraplectanoides. Finally, although clade age should not be a criterion to determine rank, other things being equal, comparable ages of similarly ranked taxa do benefit comparative biology.
... McCormack et al., 2012McCormack et al., , 2013Guillory et al., 2019;Pie et al., 2019;Ochoa et al., 2020) and a variety of invertebrate groups, such as Arachnida (e.g. Starrett et al., 2017;Van Dam et al., 2018;Hedin et al., 2019;Kulkarni et al., 2020a), Pycnogonida (Ballesteros et al., 2020), Collembola (Sun et al., 2020), Hymenoptera (Faircloth et al., 2015;Branstetter et al., 2017;Cruaud et al., 2018) and Hemiptera (Forthman et al., 2019). This approach has proved to be successful for resolving both deep and shallow relationships (e.g. ...
... Probes are critical for UCE phylogenomic approach. Currently two probe sets have been widely applied in spider phylogenomics, the Arachnida probes (Faircloth, 2017;Starrett et al., 2017) and the Spider probes (Kulkarni et al., 2020a). The Arachnida probe set was designed based on 10 exemplar taxa across Arachnida, including five spider species of Theridiidae, Eresidae, Sicariidae and Theraphosidae, and contains 14 799 probes targeting 1120 loci (Faircloth, 2017). ...
... Wood et al., 2018;Hedin et al., 2019;Ram ırez et al., 2020;Maddison et al., 2020b;Azevedo et al., 2022). The Spider probe set was designed using four exemplar taxa of the spider families Theridiidae, Araneidae, Sicariidae and Eresidae, contains 15 051 probes harvesting 2021 UCEs (Kulkarni et al., 2020a), and has been used in phylogenetic studies of spiders (Kulkarni et al., 2020a, b) and Salticidae (Maddison et al., 2020a). Comparing the performance of these two probe sets, Kulkarni et al. (2020a) found that the Spider probe set captured more loci than the Arachnida probe set, and the phylogenetic tree inferred by the Spider UCEs gained higher bootstrap values for certain nodes, and therefore showed higher potential for solving some challenging relationships than the Arachnida probe set. ...
Spiders are important models for evolutionary studies of web building, sexual selection and adaptive radiation. The recent development of probes for UCE (ultra-conserved element)-based phylogenomic studies has shed light on the phylogeny and evolution of spiders. However, the two available UCE probe sets for spider phylogenomics (Spider and Arachnida probe sets) have relatively low capture efficiency within spiders, and are not optimized for the retrolateral tibial apophysis (RTA) clade, a hyperdiverse lineage that is key to understanding the evolution and diversification of spiders. In this study, we sequenced 15 genomes of species in the RTA clade, and using eight reference genomes, we developed a new UCE probe set (41 845 probes targeting 3802 loci, labelled as the RTA probe set). The performance of the RTA probes in resolving the phylogeny of the RTA clade was compared with the Spider and Arachnida probes through an in-silico test on 19 genomes. We also tested the new probe set empirically on 28 spider species of major spider lineages. The results showed that the RTA probes recovered twice and four times as many loci as the other two probe sets, and the phylogeny from the RTA UCEs provided higher support for certain relationships. This newly developed UCE probe set shows higher capture efficiency empirically and is particularly advantageous for phylogenomic and evolutionary studies of RTA clade and jumping spiders.
... The sparse genomic resources (prior to the advent of parallel sequencing) have maintained ambiguity in phylogenetic relationships of several lineages and many earlier hypotheses have been refuted with high support by these more recent genomic studies. For example, Orbiculariae, which in the past grouped cribellate and ecribellate orb weavers (e.g., Coddington 1990) has been shown not to be a natural group in multiple recent phylogenomic analyses (Bond et al., 2014;Fernández et al., 2014Fernández et al., , 2018Garrison et al., 2016;Kulkarni et al., 2020, corroborating earlier hypotheses of non monophyly based on Sanger sequencing datasets (e.g., Blackledge et al., 2009;Dimitrov et al., 2017). ...
... Wheeler et al. (2017) published a densely sampled phylogeny using six genetic markers acquired via Sanger sequencing, constrained using the transcriptomes-based phylogeny of Garrison et al., (2016), which included 932 taxa (115 out of 116 families at the time). A few studies have used genomic scale data to reconstruct the evolutionary history of a specific group of spiders, such as, Mygalomorphae Opatova et al., 2020); Leptonetidae (Ledford et al., 2021), Synspermiata (Ramírez et al., 2021), Austrochiloidea , Palpimanoidea (Wood et al., 2018), Araneoidea (Fernández et al., 2018;Kallal et al., 2020;Kulkarni et al., 2020 or Salticidae (Maddison et al., 2020). The hypotheses about relationships among different lineages of spiders have been converging to some degree, however some recalcitrant nodes remain when reconstructed using different classes of data . ...
... The ultra-conserved sequences for this study were obtained from the following sources: (1) published UCE studies: Starrett et al. (2017), Wood et al. (2018), , Kulkarni et al. (2020), , Maddison et al. (2020), Azevedo et al. (2022); (2) transcriptome based studies: Sharma et al. (2014), Zhao et al. (2014), Fernández et al. (2014Fernández et al. ( , 2018, Rix et al. (2018), Kallal et al. (2018), Shao & Li (2018), Kallal et al. (2020); (3) We analyzed 554 terminals of UCE data, representing 125 out of 132 (94.6% sampling) spider families (World Spider Catalog, 2022). The phylogenetic trees were rooted at the node containing the Xiphosura representatives, Tachypleus tridentatus and Limulus polyphemus. ...
In the last decade and a half, advances in genetic sequencing technologies have revolutionized systematics, transforming the field as studying morphological characters; a few genetic markers have given way to genomic data sets in the phylogenomic era. A plethora of molecular phylogenetic studies on many taxonomic groups have come about, converging on, or refuting prevailing morphology or legacy-marker-based hypotheses about evolutionary affinities. Spider systematics has been no exception to this transformation and the interrelationships of several groups have now been studied using genomic data. About 50,500 extant spider species have been described so far, all with a conservative body plan, but innumerable morphological and behavioral peculiarities. Inferring the spider tree of life using morphological data has been a challenging task. Molecular data have corroborated many hypotheses of higher-level relationships, but also resulted in new groups that refute previous hypotheses. In this review, we discuss recent advances in the reconstruction of the Spider Tree of Life and highlight areas where additional effort is needed with potential solutions. We base this review on the most comprehensive spider phylogeny to date, representing 131 of the currently known 132 (99%) spider families. To achieve this sampling, we combined a legacy data set of six Sanger-based markers with newly generated and publicly available genome-scale data sets. We find that some inferred relationships between major lineages of spiders (such as Austrochiloidea, Palpimanoidea, Synspermiata, etc.) are robust across different classes of data. However, several surprising new hypotheses have emerged with different classes of molecular data. We identify and discuss the robust and controversial hypotheses and compile this blueprint to design future studies targeting systematic revisions of these problematic groups. We offer an evolutionary framework to explore comparative questions such as evolution of venoms, silk, webs, morphological traits, and reproductive strategies.
... We amplified COI: cytochrome c oxidase subunit I, a mitochondrial locus. We obtained COI sequence data for seven species from GenBank for outgroups, following 148 . We included existing deinopid COI data available on DRYAD 149 and Genbank from Lin et al. 16 for additional global Deinopis samples and Asianopis samples, respectively. ...
... For UCE data, we sampled at least two individuals from each major clade and their geographic representation, including from African Menneus, Australian Menneus, African Deinopis, Australian Deinopis, Malagasy Deinopis, Asianopis, North and Central American Deinopis, and Caribbean Deinopis. UCE libraries were hybridized to the Spider probeset 148 150 bp paired-end reads were sequenced on the HiSeq4K at the University of California Davis DNA Technologies (See Supplemental Methods S1 for more detail). We obtained UCE data for four outgroup species from Kulkarni et al. 148 (NCBI Sequence Read Archive, BioProject PRJNA575576). ...
... UCE libraries were hybridized to the Spider probeset 148 150 bp paired-end reads were sequenced on the HiSeq4K at the University of California Davis DNA Technologies (See Supplemental Methods S1 for more detail). We obtained UCE data for four outgroup species from Kulkarni et al. 148 (NCBI Sequence Read Archive, BioProject PRJNA575576). UCE and COI matrices were concatenated in AMAS 152 to generate the UCE + COI combined dataset. ...
Net-casting spiders (Deinopidae) comprise a charismatic family with an enigmatic evolutionary history. There are 67 described species of deinopids, placed among three genera, Deinopis, Menneus, and Asianopis, that are distributed globally throughout the tropics and subtropics. Deinopis and Asianopis, the ogre-faced spiders, are best known for their giant light-capturing posterior median eyes (PME), whereas Menneus does not have enlarged PMEs. Molecular phylogenetic studies have revealed discordance between morphology and molecular data. We employed a character-rich ultra-conserved element (UCE) dataset and a taxon-rich cytochrome-oxidase I (COI) dataset to reconstruct a genus-level phylogeny of Deinopidae, aiming to investigate the group’s historical biogeography, and examine PME size evolution. Although the phylogenetic results support the monophyly of Menneus and the single reduction of PME size in deinopids, these data also show that Deinopis is not monophyletic. Consequently, we formally transfer 24 Deinopis species to Asianopis; the transfers comprise all of the African, Australian, South Pacific, and a subset of Central American and Mexican species. Following the divergence of Eastern and Western deinopids in the Cretaceous, Deinopis/Asianopis dispersed from Africa, through Asia and into Australia with its biogeographic history reflecting separation of Western Gondwana as well as long-distance dispersal events.
... A robust phylogenetic hypothesis is fundamental for investigating phenotypic evolution. Thus, the advent of genomic-scale sequencing and phylogenomic studies has not only provided novel views into family-level relationships within spiders (Bond et al. 2014;Garrison et al. 2016;Hamilton et al. 2016;Kallal et al. 2021;Kulkarni et al. 2020) but also shed new light on macroevolution and its link to phenotype (Fernández et al. 2018;Ramírez et al. 2021). Transcriptomes also provide a variety of genetic information underlying different traits or behaviors (Fernández et al. 2018). ...
... Phylogenomics has contributed to the resolution of ancient and rapid divergences in spiders (Bond et al. 2014;Garrison et al. 2016;Hamilton et al. 2016;Fernández et al. 2018;Kulkarni et al. 2020;Kallal et al. 2021;Ramírez et al. 2021). Despite the use of transcriptomes or target enrichment methods that have provided thousands of loci for use in phylogenetic reconstruction, limitations of their acquisition remain, such as the requirement of fresh tissue or the expensive synthesis of taxon-specific probe sets. ...
... The maximum likelihood analysis of the nucleotide data set groups the 'symphytognathoid' families and Synaphridae concordant with the UCE analysis of Kulkarni et al. (2021). Using UCE data, Kulkarni et al. (2020Kulkarni et al. ( , 2021 also showed the sister relationship between Araneidae and Synotaxidae. The discordance between different data sets is more evident in families where only one species was sampled, such as Trogloraptoridae and Synaphridae. ...
What happens when organisms actively modify their environment? Clarifying the role of construction behavior on a macroevolutionary scale is crucial to interpreting phenotypic evolution. Spiders, an extremely successful group of animals exhibiting a wide variety of functional, morphological, and behavioral diversity, are ideal candidates to test whether animal behaviors are related to their phenotypic evolution. Herein, we reconstructed the phylogenomic relationships of 303 spiders covering 105 families with 99 newly developed molecular markers that universally apply across Araneae, and explicitly tested the potential link between construction behavior and somatic evolution based on extensive morphological data from 3,342 extant species and 682 fossil species. Our dated molecular phylogeny provides the backbone for analyses, revealing the behavioral and ecological processes behind these spiders' morphological adaptations. Evolutionary model analyses showed the artifacts constructed by spiders, especially the suspending webs, expand the spider's ability to inhabit different habitats. These artifacts have more substantial impacts on their somatic traits than habitats and promote different trajectories of morphological evolution. Specifically, for spiders, silk-lined burrowing produced larger bodies, relatively shorter legs, and longer patellae, while web-building produced smaller bodies, relatively long legs, and shorter patellae, and hunting promoted an intermediate morphological size. Molecular convergence analysis showed that genes related to morphogenesis or response to stimulus and stress are enriched in spiders with construction behavior. Our study demonstrated that the construction behavior of an animal plays a crucial role in determining the direction and intensity of the selection pressure imposed on it and provides strong evidence that construction behaviors are associated with phenotypic evolution on macroevolutionary timescales.
... Despite the importance of the UCE approach in phylogenomics, the design of ad hoc probe sets remains a technical gap such that many researchers are forced to use probe sets designed for similar taxa or for different taxonomic levels. In the current study, we compared the effectiveness of an ad hoc probe set for spiders in the superfamily Araneoidea to the existing probe sets that are known to be applicable to higher taxonomic levels in arachnids [9,11]. ...
... The UCE approach was first applied to arachnids by Starrett et al. [23], and to Araneae by Kulkarni et al. [11]. Note that the order Araneae includes 49,877 species [24] in three subclades, suborder Mesothelae, infraorder Mygalomorphae, and infraorder Araneomorphae, with evolutionary time extending back to more than 300 MYA [25,26]. ...
... As data sources for our in silico testing, we employed two published probe sets for ultraconserved elements [9,11], including 14 published genomes (Table 1) and 1 de novo assembled genome (Argyrodes miniaceus). ...
Reduced-representation sequencing (RRS) has made it possible to identify hundreds to thousands of genetic markers for phylogenomic analysis for the testing of phylogenetic hypotheses in non-model taxa. The use of customized probes to capture genetic markers (i.e., ultraconserved element (UCE) approach) has further boosted the efficiency of collecting genetic markers. Three UCE probe sets pertaining to spiders (Araneae) have been published, including one for the suborder Mesothelae (an early diverged spider group), one for Araneae, and one for Arachnida. In the current study, we developed a probe set specifically for the superfamily Araneoidea in spiders. We then combined the three probe sets for Araneoidea, Araneae, and Arachnid into a fourth probe set. In testing the effectiveness of the 4 probe sets, we used the captured loci of the 15 spider genomes in silico (6 from Araneoidea). The combined probe set outperformed all other probe sets in terms of the number of captured loci. The Araneoidea probe set outperformed the Araneae and Arachnid probe sets in most of the included Araneoidea species. The reconstruction of phylogenomic trees using the loci captured from the four probe sets and the data matrices generated from 50% and 75% occupancies indicated that the node linked to the Stegodyphus + RTA (retrolateral tibial apophysis) clade has unstable nodal supports in the bootstrap values, gCFs, and sCFs. Our results strongly indicate that developing ad hoc probe sets for sub-lineages is important in the cases where the origins of a lineage are ancient (e.g., spiders ~380 MYA).
... This grade, along with the retrolateral tibial apophysis clade (RTA) constitute a monophyletic clade. Nevertheless, the interfamilial relationship of the UDOH grade remains unclear when comparing the published phylogenies (Bond et al., 2014;Dimitrov et al., 2017;Fernández et al., 2018;Kulkarni et al., 2019Kulkarni et al., , 2020. ...
... Among the spider families phylogenetically close to Deinopidae, according to the most recent phylogenies (Bond et al., 2014;Dimitrov et al., 2017;Fernández et al., 2018;Kulkarni et al., 2019Kulkarni et al., , 2020, the diploid number varies from 2n♂ = 10, in Uloborus danolius Tikader, 1969 (Uloboridae, belonging to the UDOH grade) to 2n♂ = ±52 in Agelenopsis naevia (Walckenaer, 1841) (Agelenidae, belonging to the RTA clade) (Wallace, 1909;Parida and Sharma, 1987;Sharma and Parida, 1987). The predominant chromosomal morphology is acro/telocentric and the most common sex chromosome system (SCS) is of the type ♂X 1 X 2 0 / ♀X 1 X 1 X 2 X 2 0 (Araujo et al., 2021). ...
... Recent phylogenies bring three families as close to the Deinopidae: Hersiliidae, Oecobiidae and Uloboridae (UDOH grade), and together with the RTA clade, they form a monophyletic group (Bond et al., 2014;Dimitrov et al., 2017;Fernández et al., 2018;Kulkarni et al., 2019Kulkarni et al., , 2020. Based on the few cytogenetic studies on species of the UDOH grade (see Araujo et al., 2021), the 2n♂ = 40 (36 + X 1 X 2 X 3 X 4 ) of Deinopis biaculeata and D. plurituberculata (present work) are among the highest diploid number, with Uroctea compactilis L. Kock, 1878 (Oecobiidae) presenting 2n♂ = 42 = 40 + X 1 X 2 with acro / telocentric morphology (Suzuki, 1954) being the highest diploid number within the species of the UDOH grade. ...
Here we present the first cytogentic study concerning Deinopidae and their controversial phylogenetic position. This study karyologically analyzed one population of Deinopis biaculeata Simon, 1906 and five populations of Deinopis plurituberculata Mello-Leitão, 1925. The majority of specimens of D. plurituberculata exhibited 2n♂ = 40 and 2n♀ = 44 telocentric chromosomes (however some of them showed B chromosomes, belongs to Aquidauana and Botucatu population). The Deinopis biaculeata and D. plurituberculata meiosis of males showed 18 autosomal bivalents + X1X2X3X4, n = 22 and n = 18, a rare sex chromosome system (SCS) in spiders. Some individuals of D. plurituberculata from the Campo Grande population exhibited 2n♂ = 39 and 2n♀ = 43, with a metacentric chromosome (heterozygotes for centric fusion). The D. plurituberculata males with the rearrangement exhibit diplotenes with 16 autosomal bivalents + 1 autosomal trivalent + X1X2X3X4 and metaphases II with n = 22 (18 telocentric autosomes + X1X2X3X4), n = 21 (16 telocentric autosomes + a metacentric autosome + X1X2X3X4), n = 18 (18 telocentric autosomes) and n = 17 (16 telocentric autosomes + a metacentric autosome). The Ag-NORs (silver impregnation) are terminally located in a pair, coinciding with secondary constriction, which is the most common configuration for Araneae. The relatively high diploid number in Deinopis corroborates phylogenies that place it in a basal position among Entelegynes, in the UDOH grade (Uloboridae, Deinopidae, Oecobiidae and Hersiliidae). Centric fusion in only one population of D. plurituberculata suggests low dispersion capacity of this species and an absence of homozygotes for fusion suggests their low viability or a need to increase the population sampling of D. plurituberculata exhibiting the rearrangement. B chromosomes were detected in D. plurituberculata, with interpopulacional, intrapopulacional and intraindividual numerical variation, with cells presenting 0 - 3 and 0 - 6 B chromosomes in populations of Aquidauana and Botucatu, respectively.
... The Symphytognathidae has traditionally been put together with other small size araneoids (Anapidae, Mysmenidae, and Theridiosomatidae, sometimes with synaphrids and micropholcommatids) in a group informally called the symphytognathoids (Griswold et al. 1998;Hormiga and Griswold 2014). Although phylogenetic relationships among the Symphytognathidae have not been directly studied, some representatives have been used as part of other phylogenetic studies targeting the family Mysmenidae (Lopardo et al. 2011;Feng et al. 2019), as well as a broad scope analysis of the whole order Araneae (Wheeler et al. 2017;Kulkarni et al. 2020). Symphytognathids can be separated from other relatives by the following combination of characters: the loss of the posterior median eyes, reducing eye number to six (with the further loss of the anterior median eyes in the case of the foureyed genus Anapistula), fusion of the chelicerae (but see below), extreme reduction or loss of female pedipalp, the labium being much wider than long, loss of the colulus, sternum broadly truncated posteriorly, the absence of book lungs, and the presence of one or two promarginal cheliceral teeth originating from a common base (Forster and Platnick 1977;Wunderlich 2004;Miller et al. 2009;Lopardo et al. 2011;Hormiga and Griswold 2014). ...
... The symphytognathoids were first recognized in a morphological study being formed by four putatively monophyletic families Anapidae, Symphytognathidae, Mysmenidae and Theridiosomatidae (Griswold et al. 1998). The monophyly of this clade has been tested several times using different molecular approaches targeting specific families (Rix et al. 2008;Lopardo et al. 2011;Feng et al. 2019), the Orbiculariae (Fernández et al. 2014), and the whole order Araneae (Wheeler et al. 2017;Kulkarni et al. 2020). However, only a few representatives of the family Symphytognathidae have been used rendering their position and relations largely unexplored. ...
... This has been explained by either the limited set of loci and the relatively low taxon sampling (Feng et al. 2019) or an indication of the polyphyly of the "symphytognathoids" as suggested by three broad scoped phylogenies (Dimitrov et al. 2012;Fernández et al. 2014;Wheeler et al. 2017). Nevertheless, Symphytognathoids were found to be a highly supported monophyletic group in a recent study that used ultraconserved elements (UCE) from 16 species across the four principal symphytognathoid families (Kulkarni et al. 2020) The internal relations of the Symphytognathidae in our analyses are still unresolved. Most of Lopardo's identifications (pers. ...
The family Symphytognathidae is reported from Thailand for the first time. Three new species: Anapistula choojaiae sp. nov., Crassignatha seeliam sp. nov., and Crassignatha seedam sp. nov. are described and illustrated. Distribution is expanded and additional morphological data are reported for Patu shiluensis Lin & Li, 2009. Specimens were collected in Thailand between July and August 2018. The newly described species were found in the north mountainous region of Chiang Mai, and Patu shiluensis was collected in the coastal region of Phuket. DNA sequences are provided for all the species here studied. The relations of these symphytognathid species were tested using previously published phylogenetic analyses on micro orb-weavers. Also, we used mi-cro CT analysis to build 3D models of the male genitalia and somatic characters of two species of Crassignatha Wunderlich, 1995. The molecular phylogeny and 3D models were used to discuss the taxonomy and circum-scription of the currently valid symphytognathid genera, with focus on Crassignatha and Patu Marples, 1951. Based on this, three new combinations are suggested: Crassignatha bicorniventris (Lin & Li, 2009), comb. nov., Crassignatha quadriventris (Lin & Li, 2009), comb. nov., and Crassignatha spinathoraxi (Lin & Li, 2009), comb. nov. A new record of Crassignatha danaugirangensis Miller et al. 2014 is reported from Brunei.
... Because some taxa were captured using the arachnid probeset (outgroups Attulus, Breda, Colonus, Salticus), and others using the spider probeset (remaining outgroups, and all baviines), a blended probeset file was needed to best pull out UCE contigs, because each of the arachnid and spider probesets includes loci not included by the other. Kulkarni et al.'s (2019) spider probeset includes (i) some of Starrett et al.'s (2017) arachnid probes directly, (ii) others for the same loci but modified to target spiders better, and (iii) others for new loci. Because Kulkarni et al. do not identify probes of the second category as such, we sought to identify whether spider probes are orthologous to arachnid probes. ...
... files, was taken as indicating homology between the probes. Arachnid probes that showed no such hint of homology to spider probes were then added to Kulkarni et al.'s (2019) spider probeset to generate the blended probeset (see Suppl. material 1). ...
... This resulted in resulting in a final set of 1313 loci, in which the 16 spider-probeset taxa had on average 1076 loci and 775,244 base pairs of sequence; the four arachnid-probeset taxa had on average 104 loci and 53,936 base pairs. The strong decline in arachnid-probeset taxa from 415 loci to 104 after occupancy filtering suggests that Kulkarni et al.'s (2019) incorporation of arachnid-unique probes into the spider probeset included only a portion. The 1313 loci were concatenated into a single alignment with 1,050,217 sites. ...
The systematics and taxonomy of the tropical Asian jumping spiders of the tribe Baviini is reviewed, with a molecular phylogenetic study (UCE sequence capture, traditional Sanger sequencing) guiding a reclassification of the group’s genera. The well-studied members of the group are placed into six genera: Bavia Simon, 1877, Indopadilla Caleb & Sankaran, 2019, Padillothorax Simon, 1901, Piranthus Thorell, 1895, Stagetillus Simon, 1885, and one new genus, Maripanthus Maddison, gen. nov. The identity of Padillothorax is clarified, and Bavirecta Kanesharatnam & Benjamin, 2018 synonymized with it. Hyctiota Strand, 1911 is synonymized with Stagetillus. The molecular phylogeny divides the baviines into three clades, the Piranthus clade with a long embolus (Piranthus, Maripanthus), the genus Padillothorax with a flat body and short embolus, and the Bavia clade with a higher body and (usually) short embolus (remaining genera). In general, morphological synapomorphies support or extend the molecularly delimited groups. Eighteen new species are described: Bavia nessagyna, Indopadilla bamilin, I. kodagura, I. nesinor, I. redunca, I. redynis, I. sabivia, I. vimedaba, Maripanthus draconis (type species of Maripanthus), M. jubatus, M. reinholdae, Padillothorax badut, P. mulu, Piranthus api, P. bakau, P. kohi, P. mandai, and Stagetillus irri, all sp. nov., with taxonomic authority W. Maddison. The distinctions between baviines and the astioid Nungia Żabka, 1985 are reviewed, leading to four species being moved into Nungia from Bavia and other genera. Fifteen new combinations are established: Bavia maurerae (Freudenschuss & Seiter, 2016), Indopadilla annamita (Simon, 1903), I. kahariana (Prószyński & Deeleman-Reinhold, 2013), I. sonsorol (Berry, Beatty & Prószyński, 1997), I. suhartoi (Prószyński & Deeleman-Reinhold, 2013), Maripanthus menghaiensis (Cao & Li, 2016), M. smedleyi (Reimoser, 1929), Nungia hatamensis (Thorell, 1881), N. modesta (Keyserling, 1883), N. papakula (Strand, 1911), N. xiaolonghaensis (Cao & Li, 2016), Padillothorax casteti (Simon, 1900), P. exilis (Cao & Li, 2016), P. flavopunctus (Kanesharatnam & Benjamin, 2018), Stagetillus banda (Strand, 1911), all comb. nov. One combination is restored, Bavia capistrata (C. L. Koch, 1846). Five of these new or restored combinations correct previous errors of placing species in genera that have superficially similar palps but extremely different body forms, in fact belonging in distantly related tribes, emphasizing that the general shape of male palps should be used with caution in determining relationships. A little-studied genus, Padillothorus Prószyński, 2018, is tentatively assigned to the Baviini. Ligdus Thorell, 1895 is assigned to the Ballini.
... family-level) of analyses of spider interfamilial relationships have increased (e.g. Garrison et al., 2016;Cheng and Piel, 2018;Hedin et al., 2018;Kallal et al., 2018;Shao and Li, 2018;Wood et al., 2018;Fern andez et al., 2018a;Hedin et al., 2019;Kuntner et al., 2019;Michalik et al., 2019;Kulkarni et al., 2019;Opatova et al., 2020). The increasing consensus has led to more resolved and robust trees at various phylogenetic scales, making comparative questions interpretable in new ways. ...
... Our study, with strategically increased taxon sampling to maximize web diversity across lineages and a variety of analytical methods produced a well-resolved spider tree-of-life. For the overlapping taxa, results recovered most of the phylogenetic relationships established by previous works (Garrison et al., 2016;Dimitrov et al., 2017;Wheeler et al., 2017;Cheng and Piel, 2018;Kallal et al., 2018;Shao and Li, 2018;Fern andez et al., 2018a;Hedin et al., 2019;Kulkarni et al., 2019;Michalik et al., 2019;Kulkarni et al., 2020), reinforcing several previous topologies. For this reason, we limit our discussion of relationships to highlight areas in which our results are novel. ...
... (2018a) as well as palpimanoid-specific analyses using Sanger markers and morphology (Wood et al., 2012) or UCEs (Wood et al., 2018;Kulkarni et al., 2019). Our taxon sampling is more limited than that of Wood et al. (2018), and the degree of difference suggests that sampling, data type and analysis type are very important for resolving palpimanoid relationships. ...
High throughput sequencing and phylogenomic analyses focusing on relationships among spiders have both reinforced and upturned long‐standing hypotheses. Likewise, the evolution of spider webs—perhaps their most emblematic attribute—is being understood in new ways. With a matrix including 272 spider species and close arachnid relatives, we analyze and evaluate the relationships among these lineages using a variety of orthology assessment methods, occupancy thresholds, tree inference methods and support metrics. Our analyses include families not previously sampled in transcriptomic analyses, such as Symphytognathidae, the only araneoid family absent in such prior works. We find support for the major established spider lineages, including Mygalomorphae, Araneomorphae, Synspermiata, Palpimanoidea, Araneoidea and the Retrolateral Tibial Apophysis Clade, as well as the uloborids, deinopids, oecobiids and hersiliids Grade. Resulting trees are evaluated using bootstrapping, Shimodaira–Hasegawa approximate likelihood ratio test, local posterior probabilities and concordance factors. Using structured Markov models to assess the evolution of spider webs while accounting for hierarchically nested traits, we find multiple convergent occurrences of the orb web across the spider tree‐of‐life. Overall, we provide the most comprehensive spider tree‐of‐life to date using transcriptomic data and use new methods to explore controversial issues of web evolution, including the origins and multiple losses of the orb web.
... In recent studies on the spider tree of life, phylogenies resulting from the analysis of either transcriptomes or ultraconserved elements (UCEs) have largely converged on similar topologies (e.g., Garrison et al. 2016;Fernández et al. 2018;Kulkarni et al. 2020;Dimitrov & Hormiga 2021;Kallal et al. in press). However, incongruence persists in some recalcitrant nodes, receiving high support for contradicting hypotheses. ...
... Lopardo et al.'s (2011) extensive Sanger-based data set supported "symphytognathoid" monophyly only when the nucleotide data were analyzed in combination with phenotypic data. Recently, an analysis using target enrichment methods to capture ultraconserved elements (UCEs) provided the first molecular support for the monophyly of "symphytognathoids" (ultrafast bootstrap >95), although only with the analyzed low occupancy data sets (Kulkarni et al. 2020). This result was surprising, given the lack of support for symphytognathoid monophyly in all prior molecular analyses, including phylogenomic data sets analyzed as amino acid data in a maximum likelihood framework (Kallal et al. in press). ...
... The present study aims to identify the causes of incongruence amongst transcriptomebased and UCE-based sequences in phylogenetic analyses of spiders by leveraging data from recent studies (e.g., Garrison et al. 2016;Fernández et al. 2018;Kulkarni et al. 2020;Kallal et al. in press). Our approach was to reconstruct phylogenies using sequences from transcriptomes, UCEs, and a combination of data sources, at both the amino acid and Downloaded from https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msaa251/5912541 by guest on 08 November 2020 nucleotide level. ...
Genome-scale data sets are converging on robust, stable phylogenetic hypotheses for many lineages; however, some nodes have shown disagreement across classes of data. We use spiders (Araneae) as a system to identify the causes of incongruence in phylogenetic signal between three classes of data: exons (as in phylotranscriptomics), non-coding regions (included in ultraconserved elements [UCE] analyses), and a combination of both (as in UCE analyses). Gene orthologs, coded as amino acids and nucleotides (with and without third codon positions), were generated by querying published transcriptomes for UCEs, recovering 1,931 UCE loci (codingUCEs). We expected that congeners represented in the codingUCE and UCEs data would form clades in the presence of phylogenetic signal. Non-coding regions derived from UCE sequences were recovered to test the stability of relationships. Phylogenetic relationships resulting from all analyses were largely congruent. All nucleotide data sets from transcriptomes, UCEs, or a combination of both recovered similar topologies in contrast with results from transcriptomes analyzed as amino acids. Most relationships inferred from low occupancy data sets, containing several hundreds of loci, were congruent across Araneae, as opposed to high occupancy data matrices with fewer loci, which showed more variation. Furthermore, we found that low occupancy data sets analyzed as nucleotides (as is typical of UCE data sets) can result in more congruent relationships than high occupancy data sets analyzed as amino acids (as in phylotranscriptomics). Thus, omitting data, through amino acid translation or via retention of only high occupancy loci, may have a deleterious effect in phylogenetic reconstruction.
... The design of taxon-specific UCE probes is a growing field, which is rapidly developing a body of knowledge (Branstetter et al., 2017;Gustafson et al., 2019a;Gustafson et al., 2019b;Kulkarni et al., 2020). Recent literature justified the use of tailored UCE probes as they frequently outperform general (i.e. ...
... Recent literature justified the use of tailored UCE probes as they frequently outperform general (i.e. universal) probes and should aid in locus recovery (Branstetter et al., 2017;Gustafson et al., 2019a;Gustafson et al., 2019b;Kulkarni et al., 2020). Previous molecular studies on Oestroidea (Kutty et al., 2010;Buenaventura et al., 2017;Buenaventura & Pape, 2017a;Buenaventura et al., 2019) and similar radiations predict that reconstructing a strong phylogeny would require a large increase in molecular data (Dell'Ampio et al., 2014; Giarla & Esselstyn, 2015) and the combination of information from multiple genome regions to attempt to produce accurate species tree estimates (Degnan & Rosenberg, 2009). ...
... General UCE probe sets designed to work across larger taxonomic groups have proven successful at resolving phylogeny in various groups (Faircloth et al., 2015;Starrett et al., 2016;Van Dam et al., 2017), but there is growing evidence for improved locus recovery through the use of probe sets tailored to focal taxa (Baca et al., 2017;Branstetter et al., 2017;Van Dam et al., 2019;Gustafson et al., 2019a; Gustafson et al., 2019b;Kulkarni et al., 2020). An increase in locus recovery is especially important in the study of rapid radiations (Dell'Ampio et al., 2014;Giarla & Esselstyn, 2015), such as that of Oestroidea. ...
The diverse superfamily Oestroidea with more than 15 000 known species includes among others blow flies, flesh flies, bot flies and the diverse tachinid flies. Oestroidea exhibit strikingly divergent morphological and ecological traits, but even with a variety of data sources and inferences there is no consensus on the relationships among major Oestroidea lineages. Phylogenomic inferences derived from targeted enrichment of ultraconserved elements or UCEs have emerged as a promising method for resolving difficult phylogenetic problems at varying timescales. To reconstruct phylogenetic relationships among families of Oestroidea, we obtained UCE loci exclusively derived from the transcribed portion of the genome, making them suitable for larger and more integrative phylogenomic studies using other genomic and transcriptomic resources. We analysed datasets containing 37–2077 UCE loci from 98 representatives of all oestroid families (except Ulurumyiidae and Mystacinobiidae) and seven calyptrate outgroups, with a total concatenated aligned length between 10 and 550 Mb. About 35% of the sampled taxa consisted of museum specimens (2–92 years old), of which 85% resulted in successful UCE enrichment. Our maximum likelihood and coalescent‐based analyses produced well‐resolved and highly supported topologies. With the exception of Calliphoridae and Oestridae all included families were recovered as monophyletic with the following conclusions: Oestroidea is monophyletic with Mesembrinellidae as sister to the remaining oestroid families; Oestridae is paraphyletic with respect to Sarcophagidae; Polleniidae is sister to Tachinidae; Rhinophoridae sister to (Luciliinae (Toxotarsinae (Melanomyinae + Calliphorinae))); Phumosiinae is sister to Chrysomyinae and Bengaliinae is sister to Rhiniidae. These results support the ranking of most calliphorid subfamilies as separate families.
... DNA was extracted using the Qiagen DNeasy blood and tissue kit (Qiagen, Valencia, CA, USA). UCE libraries were either prepared at the Hedin Lab (SDSU) following protocols of Starrett et al. (2017) with modifications of Kulkarni et al. (2020), or prepared by Arbor Biosciences (Ann Arbor, MI, USA) and/or RAPiD Genomics LLC (Gainesville, Fl). UCEs were captured using MYbaits (Arbor Biosciences) Spider v.1 kit (Kulkarni et al. 2020). ...
... UCE libraries were either prepared at the Hedin Lab (SDSU) following protocols of Starrett et al. (2017) with modifications of Kulkarni et al. (2020), or prepared by Arbor Biosciences (Ann Arbor, MI, USA) and/or RAPiD Genomics LLC (Gainesville, Fl). UCEs were captured using MYbaits (Arbor Biosciences) Spider v.1 kit (Kulkarni et al. 2020). Sequencing was conducted on Illumina HiSeq platforms at the U.C. Davis Genome Center (Davis, CA), RAPiD Genomics and Arbor Biosciences. ...
Karst systems have great ecological, cultural and economic importance, but are constantly threatened by human development. Northwestern Bexar County, Texas (USA), is an example of a region where urbanization threatens an essential karst landscape. Many studies have provided substantial contributions to the understanding and conservation of biodiversity in this area, including the delineation of Karst Fauna Regions (KFRs). However, no study has evaluated fundamentally important measures of genetic diversity, changes in population sizes, and gene flow for listed regional species. Here we used population genomic data derived from the sequence capture of ultraconserved elements (UCEs) to describe patterns of structure and connectivity among cave populations of Cicurina madla, and to estimate demographic and phylogeographic processes underlying those patterns. In addition, we evaluated if population genetic processes could have been influenced by human activities. Although there is weak phylogenomic differentiation between populations, the distribution of genetic diversity and patterns of gene flow within and between areas suggest important differences in population dynamics among KFRs. Our genomic data show that populations of C. madla in Bexar County currently carry comparatively low levels of heterozygosity and nucleotide diversity, and that these might have been influenced by human activities. Ultimately, we present genomic evidence for declining cave spider population sizes perhaps coincident with increases in an expanding human population and discuss implications of our findings for conservation.
... However, palpimanoids were seemingly at their zenith in the Mesozoic, when together with the Synspermiata, they were a dominant spider group until major faunal turnover in the Cenozoic (Magalhães et al. 2020). Using modern sequencing methods, palpimanoids consistently fall as the sister group to the Entelegynes (Fernández et al. 2018; Kulkarni et al. 2020;Kallal et al. 2021), which contains the bulk of modern spider species richness and contains the dominant Cenozoic groups (Magalhães et al. 2020). Using molecular clock methodology, studies have shown that palpimanoids likely emerged in the Permian or Triassic (Wood et al. 2013;Magalhães et al. 2020;Kallal et al. 2021). ...
... There currently is not consensus on extant family relationships within Palpimanoidea, and topology can change depending on the type of data (Wood et al. 2012). Using molecular data alone some, but not all, studies have recovered the "high-carapace group" (Kulkarni et al. 2020;Kallal et al. 2021;Ramírez et al. 2021). There are also some molecular studies that corroborate that Palpimanidae was the first to diverge among the extant palpimanoids (Fernández et al. 2018;Wood et al. 2018;Kulkarni et al. 2021). ...
Burmese amber is a significant source of fossils that documents the mid-Cretaceous biota. This deposit was formed around 99 Ma on the Burma Terrane, which broke away from Gondwana and later collided with Asia, although the timing is disputed. Palpimanoidea is a dispersal-limited group that was a dominant element of the Mesozoic spider fauna, and has an extensive fossil record, particularly from Burmese amber. Using morphological and molecular data, evolutionary relationships of living and fossil Palpimanoidea are examined. Divergence dating with fossils as terminal tips, followed by ancestral range estimations, shows timing of diversification is contemporaneous with continental break-up and that widespread ancestral ranges divide into lineages that inherit different Pangean fragments, consistent with vicariance. Our results suggest that the Burmese amber fauna has ties to Gondwana due to a historical connection in the Early Cretaceous, and that the Burma Terrane facilitated biotic exchange by transporting lineages from Gondwana into the Holarctic in the Cretaceous.
... Data for ultraconserved elements were produced following the (Glenn et al., 2019;BadDNA@UGA) with slight modifications on a few steps for A. isabella (for details see Derkarabetian et al., 2019). Libraries were hybridized at 60°C for 24 h to the Spider probe set (Kulkarni et al., 2020) following the version 4 chemistry protocol (Arbor Biosciences). Hybridization-enriched library pools were sequenced with 150 bp paired-end reads on the HiSeq4K at the University of California Davis DNA Technologies Core. ...
... De novo assemblies with the cleaned paired-end and single-end reads were performed using SPAdes v. 3.14.1 with the isolate option (Prjibelski et al., 2020). Scaffolds were matched with 65% identity and 65% coverage to the modified probe list from Maddison et al. (2020), which is a blend of the Arachnid (Faircloth, 2017;Starrett et al., 2017) and Spider (Kulkarni et al., 2020) probe sets. MAFFT (Katoh & Standley, 2013) was used to align individual locus datasets, and alignments with locus occupancy (i.e., completeness) minimums of 50%, 75%, and 90% were obtained. ...
Species delimitation is an imperative first step toward understanding Earth's biodiversity, yet what constitutes a species and the relative importance of the various processes by which new species arise continue to be debatable. Species delimitation in spiders has traditionally used morphological characters; however, certain mygalomorph spiders exhibit morphological homogeneity despite long periods of population-level isolation, absence of gene flow, and consequent high degrees of molecular divergence. Studies have shown strong geographic structuring and significant genetic divergence among several species complexes within the trapdoor spider genus Aptostichus, most of which are restricted to the California Floristic Province (CAFP) biodiversity hotspot. Specifically, the Aptostichus icenoglei complex, which comprises the three sibling species, A. barackobamai, A. isabella, and A. icenoglei, exhibits evidence of cryptic mitochondrial DNA diversity throughout their ranges in Northern, Central, and Southern California. Our study aimed to explicitly test species hypotheses within this assemblage by implementing a cohesion species-based approach. We used genomic-scale data (ultraconserved elements, UCEs) to first evaluate genetic exchangeability and then assessed ecological interchangeability of genetic lineages. Biogeographical analysis was used to assess the likelihood of dispersal versus vicariance events that may have influenced speciation pattern and process across the CAFP's complex geologic and topographic landscape. Considering the lack of congruence across data types and analyses, we take a more conservative approach by retaining species boundaries within A. icenoglei.
... The effectiveness of selecting UCEs for unionids with the pHylUCe pipeline is somewhat hampered because few and only distant genomes were available for molluscs (Sigwart et al., 2021;Sun et al., 2019) compared to other taxa for which UCE sets have been developed. Nevertheless, we recovered hits for 1895 (46%) of our target UCEs, which is comparable to values obtained in some previous UCE studies (e.g., Kulkarni et al., 2020;Starrett et al., 2017;Streicher et al., 2018), indicating that our design worked. As is regularly the case in UCE studies (Buenaventura et al., 2021;Faircloth et al., 2012;Kulkarni et al., 2020;Quattrini et al., 2018;Starrett et al., 2017), the number of UCEs that can eventually be included in the alignment for phylogenetic inference was restricted to a subset of UCEs with high recovery across all ingroup taxa (but see Branstetter et al., 2017). ...
... Nevertheless, we recovered hits for 1895 (46%) of our target UCEs, which is comparable to values obtained in some previous UCE studies (e.g., Kulkarni et al., 2020;Starrett et al., 2017;Streicher et al., 2018), indicating that our design worked. As is regularly the case in UCE studies (Buenaventura et al., 2021;Faircloth et al., 2012;Kulkarni et al., 2020;Quattrini et al., 2018;Starrett et al., 2017), the number of UCEs that can eventually be included in the alignment for phylogenetic inference was restricted to a subset of UCEs with high recovery across all ingroup taxa (but see Branstetter et al., 2017). Phylogenetic analysis on 276 UCEs allowed to unambiguously reconstruct the backbone phylogeny of Coelaturini and estimates of population genetic diversity from 309 UCEs were comparable to those obtained from ORFs, but more similar to the diversity at non-synonymous than at synonymous sites. ...
Despite the increasing accessibility of high‐throughput sequencing, obtaining high‐quality genomic data on non‐model organisms without proximate well‐assembled and annotated genomes remains challenging. Here we describe a workflow that takes advantage of distant genomic resources and ingroup transcriptomes to select and jointly enrich long open reading frames (ORFs) and ultraconserved elements (UCEs) from genomic samples for integrative studies of microevolutionary and macroevolutionary dynamics. This workflow is applied to samples of the African unionid bivalve tribe Coelaturini (Parreysiinae) at basin and continent‐wide scales. Our results indicate that ORFs are efficiently captured without prior identification of intron‐exon boundaries. The enrichment of UCEs was less successful, but nevertheless produced substantial datasets. Exploratory continent‐wide phylogenetic analyses with ORF supercontigs (>515,000 parsimony informative sites) resulted in a fully resolved phylogeny, the backbone of which was also retrieved with UCEs (>11,000 informative sites). Variant calling on ORFs and UCEs of Coelaturini from the Malawi Basin produced ~2,000 SNPs per population pair. Estimates of nucleotide diversity and population differentiation were similar for ORFs and UCEs. They were low compared to previous estimates in mollusks, but comparable to those in recently diversifying Malawi cichlids and other taxa at an early stage of speciation. Skimming off‐target sequence data from the same enriched libraries of Coelaturini from the Malawi Basin, we reconstructed the maternally‐inherited mitogenome, which displays the gene order inferred for the most recent common ancestor of Unionidae. Overall, our workflow and results provide exciting perspectives for integrative genomic studies of microevolutionary and macroevolutionary dynamics in non‐model organisms.
... Recently, systematic advances in spiders have relied heavily upon genomic-scale molecular data (e.g., Kulkarni et al. 2020;Ramírez 2021). While this approach has proved to be a powerful tool for resolving recalcitrant relationships, most of these studies include only molecular data in their phylogenetic matrices. ...
... To maximize morphological and genetic data overlap, we merged data from closely related species into a single terminal in the outgroup genera Stedocys, Ariadna, Althepus, and Ochyrocera (Table 1) We matched the assembled sequences to a compilation of UCE probes merging the Arachnid probe set (Starrett et al. 2017), and the Spider probe set (Kulkarni et al. 2020). Sequences were aligned using MAFFT v. 7.455 and trimmed with GBLOCKS v. 0.31b (Castresana 2000), with the default parameters implemented in PHYLUCE. ...
Recluse or violin spiders in the genus Loxosceles (Scytodoidea: Sicariidae) are a diverse group (~140 extant species) including medically important species and distributed mainly in the Americas, Africa, and the Mediterranean region. In addition, this genus includes three fossil species from Miocene Dominican amber. Here we revise the taxonomy of these fossil species by examining, imaging and re-describing their type specimens. We find that L. defecta Wunderlich, 1988 and L. deformis Wunderlich, 1988 are bona fide members of the genus and report additional characters overlooked in their original descriptions. We further study the ho-lotype of L. aculicaput Wunderlich, 2004 using synchrotron radiation micro-computed tomography to reveal previously unknown morphological details hidden by fissures in the amber. We found several characters inconsistent with Loxosceles but consistent with Drymusa (false violin spiders; Scytodoidea: Drymusidae), such as three claws, well-developed podotarsite, and a broad colulus. This suggests the species is misplaced in Loxosceles. To test this hypothesis, we estimated a total-evidence phylogeny of the superfamily Scytodoidea including extant and fossil taxa, morphological data, traditional molecular markers, and sequences of ultra-conserved elements. The results show unambiguously that L. aculicaput belongs to Drymusa and is a close relative of extant species of the genus inhabiting the Greater Antilles. Therefore, we here transfer this species to Drymusa, establishing a new combination and new family assignment. Drymusa aculicaput comb. nov. represents the first known fossil Drymusidae and shows that crown members of this genus already existed in the Miocene.
... In other spheres of evolution we recollect that the Basque and Etruscan systems of speech, which can claim kindred with no existing family of language, are excellent instances of the same phenomenon. Mello-Leitão (1946) and Lehtinen (1986) considered filistatids as the sister group of Pholcidae; Eskov and Zonshtein (1990) placed them next to mygalomorphs; the morphological data from Platnick et al. (1991) recovered them as a sister group to other spiders with simple genitalia; and NGS data recovered a close relationship to Hypochilidae (Fern andez et al., 2018;Kulkarni et al., 2020Kulkarni et al., , 2021Ram ırez et al., 2021). For a long time, they were considered closely related to the clade of spiders with simple genitalia that is now called Synspermiata (Michalik and Ram ırez, 2014), a position supported by classic characters, such as the fusion of tegulum and subtegulum and a cheliceral lamina (Platnick et al., 1991). ...
... However, filistatids present typical plesiomorphic characters, such as an M-shaped midgut (Griswold et al., 2005), retention of the posterior lungs in the first instars (Ram ırez, 2014), coenospermia (several sperm cells in the same capsule; Michalik et al., 2003), ecdysis after sexual maturity in females, copulation and spermatic web similar to that of mygalomorphs ( Barrantes and Ram ırez, 2013) and the behaviour of combing cribellate silk using leg III as support (Lopardo and Ram ırez, 2007). Finally, independent sources of NGS data strongly suggest Filistatidae are closely related to Hypochilidae, another family that has many plesiomorphic characters (Fern andez et al., 2018;Kulkarni et al., 2020Kulkarni et al., , 2021Ram ırez et al., 2021). All this suggests an adequate knowledge of the morphology and internal relationships of filistatids could have a great impact on our knowledge of the evolution of early-diverging araneomorphs. ...
Filistatids, the crevice weavers, are an ancient family of cribellate spiders without extant close relatives. As one of the first lineages of araneomorph spiders, they present a complicated mixture of primitive and derived characters that make them a key taxon to elucidate the phylogeny of spiders, as well as the evolution of phenotypic characters in this group. Their moderate diversity (187 species in 19 genera) is distributed mainly in arid and semi‐arid subtropical zones of all continents, except Antarctica. The objective of this paper is to generate a comprehensive phylogenetic hypothesis for this family to advance the understanding of its morphological evolution and biogeography, as well as lay the basis for a natural classification scheme. By studying the morphology using optical and electronic microscopy techniques, we produced a matrix of 302 morphological characters coded for a sample of 103 species of filistatids chosen to represent the phylogenetic diversity of the family. In addition, we included sequences of four molecular markers (COI, 16S, H3 and 28S; 3787 aligned positions) of 70 filistatid species. The analysis of the data (morphological, molecular, and combined) consistently indicates the separation of the Filistatidae into two subfamilies, Prithinae and Filistatinae, in addition to supporting several groups of genera: Filistata, Zaitunia and an undescribed genus from Madagascar; Sahastata and Kukulcania; all Prithinae except Filistatinella and Microfilistata; Antilloides and Filistatoides; a large Old World group including Pritha, Tricalamus, Afrofilistata, Labahitha, Yardiella, Wandella and putative new genera; and a South American group formed by Lihuelistata, Pikelinia and Misionella. Pholcoides is transferred to Filistatinae and Microfilistata is transferred to Prithinae, and each represents the sister group to the remaining genera of its own subfamily. Most genera are valid, although Pikelinia is paraphyletic with respect to Misionella, so we consider the two genera as synonyms and propose a few new generic combinations. Considering the new phylogenetic hypothesis, we discuss the evolution of some morphological character systems and the biogeography of the family. The ages of divergence between clades were estimated using a total‐evidence tip‐dating approach by including fossils of Filistatidae and early spider clades; this approach resulted in younger age estimates than those obtained with traditional node‐dating. Filistatidae is an ancient family that started diversifying in the Mesozoic and most genera date to the Cretaceous. Clades displaying transcontinental distributions were most likely affected by continental drift, but at least one clade shows unequivocal signs of transoceanic long‐distance dispersal.
... Nevertheless, we recovered hits for a total of 1,895 (46%) of our target UCEs, which is comparable to values obtained in some previous UCE studies (e.g. Kulkarni et al., 2020;Starrett et al., 2017;Streicher et al., 2018), indicating that our design worked. As is regularly the case in UCE studies (Buenaventura et al., 2021;Faircloth et al., 2012;Kulkarni et al., 2020;Quattrini et al., 2018;Starrett et al., 2017), the number of UCEs that can eventually be included in the alignment for phylogenetic inference was a restricted subset of the recovered UCEs, here n = 276 (but see Branstetter et al., 2017). ...
... Kulkarni et al., 2020;Starrett et al., 2017;Streicher et al., 2018), indicating that our design worked. As is regularly the case in UCE studies (Buenaventura et al., 2021;Faircloth et al., 2012;Kulkarni et al., 2020;Quattrini et al., 2018;Starrett et al., 2017), the number of UCEs that can eventually be included in the alignment for phylogenetic inference was a restricted subset of the recovered UCEs, here n = 276 (but see Branstetter et al., 2017). Nevertheless, this restricted set of UCEs allowed to unambiguously reconstruct the backbone phylogeny of Coelaturini. ...
Despite the increasing accessibility of high-throughput sequencing, obtaining high-quality genomic data on non-model organisms without proximate well-assembled and annotated genomes remains challenging. Here we describe a workflow that takes advantage of distant genomic resources and ingroup transcriptomes to select and jointly enrich long open reading frames (ORFs) and ultraconserved elements (UCEs) from genomic samples for integrative studies of microevolutionary and macroevolutionary dynamics. This workflow is applied to samples of the African unionid bivalve tribe Coelaturini (Parreysiinae) at basin and continent-wide scales. Our results indicate that ORFs are efficiently captured without prior identification of intron-exon boundaries. The enrichment of UCEs was less successful, but nevertheless produced a substantial dataset. Exploratory continent-wide phylogenetic analyses with ORF supercontigs (>515,000 parsimony informative sites) resulted in a fully resolved phylogeny, the backbone of which was also retrieved with UCEs (>11,000 informative sites), although some branches lack support in the latter case. Variant calling on the exome of Coelaturini from the Malawi Basin produced ~2,000 SNPs per population pair. Nucleotide diversity and population differentiation was low compared to previous estimates in mollusks, but comparable to those in recently diversifying Malawi cichlids and other taxa at an early stage of speciation. Skimming non-specific sequence data obtained for Coelaturini of the Malawi Basin, we reconstructed the maternally-inherited mitogenome, which displays an identical gene order to that of the most recent common ancestor of Unionidae. Overall, our workflow and results provide exciting perspectives for the development of integrative genomic studies on micro- and macroevolutionary dynamics in non-model organisms.
... Transcriptomic analyses of extensive taxonomic samples of araneoids and thousands of loci (Fernández et al., 2018;Kallal et al., 2021) have also refuted symphytognathoid monophyly with high nodal support values. Surprisingly, the most recent phylogenomic analyses (Kulkarni et al., 2020, using ultraconserved elements (UCEs) and up to 26 symphytognathoid representatives, suggest (and paradoxically also with high nodal support values) that when the sequence data are analyzed as nucleotides, rather than as amino acids, and when about a hundred or more loci are used, symphytognathoids are indeed monophyletic. We take this latter proposal as the best supported phylogenetic hypothesis of symphytognathoid relationships. ...
... The second hypothesis uses the interfamilial relationships of the UCE topology of Kulkarni et al. (2021: fig. 4b), which results from a dataset that included a combination of the taxon sample of UCEs recovered from the transcriptomic study of Fernández et al. (2018) and the UCEs of Kulkarni et al. (2020). This second topology is based on the same taxon sample as the first tree with the symphytognathoid intrafamilial relationships also taken from Lopardo et al. (2011: fig. ...
Spiders are unique in having a dual respiratory system with book lungs and tracheae, and most araneomorph spiders breathe simultaneously via book lungs and tracheae, or tracheae alone. The respiratory organs of spiders are diverse but relatively conserved within families. The small araneoid spiders of the symphytognathoid clade exhibit a remarkably high diversity of respiratory organs and arrangements, unparalleled by any other group of ecribellate orb weavers. In the present study, we explore and review the diversity of symphytognathoid respiratory organs. Using a phylogenetic comparative approach, we reconstruct the evolution of the respiratory system of symphytognathoids based on the most comprehensive phylogenetic frameworks to date. There are no less than 22 different respiratory system configurations in symphytognathoids. The phylogenetic reconstructions suggest that the anterior tracheal system evolved from fully developed book lungs and, conversely, reduced book lungs have originated independently at least twice from its homologous tracheal conformation. Our hypothesis suggests that structurally similar book lungs might have originated through different processes of tracheal transformation in different families. In symphytognathoids, the posterior tracheal system has either evolved into a highly branched and complex system or it is completely lost. No evident morphological or behavioral features satisfactorily explains the exceptional variation of the symphytognathoid respiratory organs.
... Phylogenomic and transcriptomic methods have (Ramírez, 2014); (b) Sanger molecular data (Wheeler et al., 2017); (c) Sanger molecular (Moradmand et al., 2014); (d) total evidence ; (e) genomic (UCE) data . also recently been applied in higher-level systematics and evolutionary studies of spiders (Fernández et al., 2018;Garrison et al., 2016;Kallal et al., 2020;Kulkarni et al., 2020;Opatova et al., 2020;Ramírez et al., 2021;Xu et al., 2020). Although some spider clades have been studied using a combined analysis of morphology and traditional molecular markers (Blackledge et al., 2009;Bond et al., 2012;Polotow et al., 2015), none have yet been explored using the combination of genomic, transcriptomic, traditional loci and morphological data. ...
... One of the key families to understanding dionychan evolution is Sparassidae. This family has been phylogenetically placed in Dionycha (Ramírez, 2014), as sister to the RTA clade (Moradmand et al., 2014), as sister to Dionycha + OCC (Wheeler et al., 2017) and as sister to marronoids (Fernández et al., 2018;Kallal et al., 2020;Kulkarni et al., 2020). Here we corroborated the latter hypothesis with strong support. ...
The importance of morphology in the phylogenomic era has recently gained attention, but relatively few studies have combined both types of information when inferring phylogenetic relationships. Sanger sequencing legacy data can also be important for understanding evolutionary relationships. The possibility of combining genomic, morphological and Sanger data in one analysis seems compelling, permitting a more complete sampling and yielding a comprehensive view of the evolution of a group. Here we used these three data types to elucidate the systematics and evolution of the Dionycha, a highly diverse group of spiders relatively underrepresented in phylogenetic studies. The datasets were analyzed separately and combined under different inference methods, including a novel approach for analyzing morphological matrices with commonly used evolutionary models. We tested alternative hypotheses of relationships and performed simulations to investigate the accuracy of our findings. We provide a comprehensive and thorough phylogenetic hypothesis for Dionycha that can serve as a robust framework to test hypotheses about the evolution of key characters. We also show that morphological data might have a phylogenetic impact, even when massively outweighed by molecular data. Our approach to analyze morphological data may serve as an alternative to the proposed practice of arbitrarily partitioning, weighting, and choosing between parsimony and stochastic models. As a result of our findings, we propose Trachycosmidae new rank for a group of Australian genera formerly included in Trochanteriidae and Gallieniellidae, and consider Ammoxenidae as a junior synonym of Gnaphosidae. We restore the family rank for Prodidomidae, but transfer the subfamily Molycriinae to Gnaphosidae. Drassinella is transferred to Liocranidae, Donuea to Corinnidae, and Mahafalytenus to Viridasiidae.
... An alternative is to target a large sample of representative loci, for example, by using hybrid enrichment to sequence ultraconserved elements (UCEs) across the genome (Faircloth et al. 2012). Although a few UCE probe sets have been designed for arachnids and spiders, these enriched only a small number of loci from the liphistiid species, Liphistius malayanus (Starrett et al. 2017;Kulkarni et al. 2020). ...
... The liphistiid-specific probe set that we have developed here has targeted a larger number of UCE loci than any existing spider-specific or Arachnida probe set (Faircloth 2017;Starrett et al. 2017;Kulkarni et al. 2020). The novel probe set is also likely to be suitable for mygalomorphs, given the UCEs targeted for seven mygalomorphs in this study. ...
The segmented trapdoor spiders (Liphistiidae) are the sole surviving family of the suborder Mesothelae, which forms the sister lineage to all other living spiders. Liphistiids have retained a number of plesiomorphic traits and their present-day distribution is limited to East and Southeast Asia. Studying this group has the potential to shed light on the deep evolutionary history of spiders, but the phylogeny and divergence times of the family have not been resolved with confidence. We performed phylogenomic and molecular dating analyses of 2,765 ultraconserved element loci from 185 liphistiid taxa. Our analyses show that the crown group of Liphistiidae appeared in the mid-Cretaceous at 102 Ma (95% credibility interval 92–113 Ma), but it was not until the Neogene that much of the diversification within the family occurred in mainland Southeast and East Asia. This diversification was coincident with tectonic events such as the extension of the East Asian continental margin, as well as geological upheavals in Indochina induced by the collision between India and Asia. Our study highlights the important role of major tectonic events in shaping the evolutionary history, present-day diversity, and geographical distribution of mesothele and liphistiid spiders.
... An alternative is to target a large sample of representative loci, for example, by using hybrid enrichment to sequence ultraconserved elements (UCEs) across the genome (Faircloth et al. 2012). Although a few UCE probe sets have been designed for arachnids and spiders, these enriched only a small number of loci from the liphistiid species, Liphistius malayanus (Starrett et al. 2017;Kulkarni et al. 2020). ...
... The liphistiid-specific probe set that we have developed here has targeted a larger number of UCE loci than any existing spider-specific or Arachnida probe set (Faircloth 2017;Starrett et al. 2017;Kulkarni et al. 2020). The novel probe set is also likely to be suitable for mygalomorphs, given the UCEs targeted for seven mygalomorphs in this study. ...
... Library preparation for a subset of the samples (n = 23) was conducted using the MYbaits Arachnida 1.1Kv1 kit (Arbor Biosciences, Ann Arbor, MI, USA) [24] (see details in electronic supplementary material, S1) and sequenced on a NovaSeq 6000 at the Bauer Core Facility at Harvard University. For the remaining samples (n = 75), the extracted DNA was dried using an Eppendorf Concentrator plus speed-vac and transported to NGS Division, Arbor Biosciences (Ann Arbor, MI, USA) for UCE library preparation using the Spider 2Kv1 kit [25]. ...
Many animals use self-built structures (extended phenotypes) to enhance body functions, such as thermoregulation, prey capture or defence. Yet, it is unclear whether the evolution of animal constructions supplements or substitutes body functions—with disparate feedbacks on trait evolution. Here, using brown spiders (Araneae: marronoid clade), we explored if the evolutionary loss and gain of silken webs as extended prey capture devices correlates with alterations in traits known to play an important role in predatory strikes—locomotor performance (sprint speed) and leg spination (expression of capture spines on front legs). We found that in this group high locomotor performance, with running speeds of over 100 body lengths per second, evolved repeatedly—both in web-building and cursorial spiders. There was no correlation with running speed, and leg spination only poorly correlated, relative to the use of extended phenotypes, indicating that web use does not reduce selective pressures on body functions involved in prey capture and defence per se . Consequently, extended prey capture devices serve as supplements rather than substitutions to body traits and may only be beneficial in conjunction with certain life-history traits, possibly explaining the rare evolution and repeated loss of trapping strategies in predatory animals.
... Creating a probe set based on a more inclusive lineage (i.e., specific orders within Arachnida) will increase specificity of the probes and ultimately the total number of loci recovered (e.g., Gustafson et al. 2019). Within arachnids, a more specific probe set was created for the order Araneae (spiders; Kulkarni et al. 2020), which targets almost twice as many UCEs as the Arachnida probe set (2021 loci versus 1120), and even more specific probe sets were made for Liphistiidae targeting 3111 loci (Xu et al. 2021) and the "RTAclade" spiders targeting 3802 loci (Zhang et al. 2023). ...
Sequence capture of ultraconserved elements (UCEs) has transformed molecular systematics across many taxa, with arachnids being no exception. The probe set available for Arachnida has been repeatedly used across multiple arachnid lineages and taxonomic levels, however more specific probe sets for spiders have demonstrated that more UCEs can be recovered with higher probe specificity. In this study, we develop an Opiliones-specific UCE probe set targeting 1915 UCEs using a combination of probes designed from genomes and transcriptomes, as well as the most useful probes from the Arachnida probe set. We demonstrate the effectiveness of this probe set across Opiliones with the most complete family-level phylogeny made to date, including representatives from 61 of 63 currently described families. We also test UCE recovery from historical specimens with degraded DNA, examine population-level data sets, and assess "backwards compatibility" with samples hybridized with the Arachnida probe set. The resulting phylogenies - which include specimens hybridized using both the Opiliones and Arachnida probe sets, historical specimens, and transcriptomes - are largely congruent with previous multi-locus and phylogenomic analyses. The probe set is also "backwards compatible", increasing the number of loci obtained in samples previously hybridized with the Arachnida probe set, and shows high utility down to shallow population-level divergences. This probe set has the potential to further transform Opiliones molecular systematics, resolving many long-standing taxonomic issues plaguing this lineage.
... Finally, representatives of all the families within the Synespermiata clade, including members of the Superfamily Dysderoidea were considered to provide fossil information for calibration. All trees were rooted, assuming a sister group relationship of the families Hypochilidae and Filistatidae with the Synespermiata clade (Garrison et al. 2016;Wheeler et al. 2017;Fernández et al. 2018;Michalik et al. 2019;Kulkarni et al. 2020Kallal et al. 2021;Ramírez et al. 2021). ...
Natural selection plays a key role in deterministic evolution, as clearly illustrated by the multiple cases of repeated evolution of ecomorphological characters observed in adaptive radiations. Unlike most spiders, Dysdera species display a high variability of cheliceral morphologies, which has been suggested to reflect different levels of specialisation to feed on isopods. In this study, we integrate geometric morphometrics and experimental trials with a fully resolved phylogeny of the highly diverse endemic species from the Canary Islands to 1) quantitatively delimit the different cheliceral morphotypes present in the archipelago, 2) test their association with trophic specialisation, as reported for continental species, 3) reconstruct the evolution of these ecomorphs throughout the diversification of the group, 4) test the hypothesis of convergent evolution of the different morphotypes, and 5) examine whether specialisation constitutes a case of evolutionary irreversibility in this group. We show the existence of nine cheliceral morphotypes and uncovered their significance for trophic ecology. Further, we demonstrate that similar ecomorphs evolved multiple times in the archipelago, providing a novel study system to explain how convergent evolution and irreversibility due to specialization may be combined to shape phenotypic diversification in adaptive radiations.
... For the UCE assembly, the transcriptome files were converted to 2-bit format using faToTwoBit (Kent, 2002), and then recovered using PHY-LUCE (Faircloth, 2016). The resulting FASTA files then were match to the reads from the Spider2Kv1 probe (Kulkarni et al., 2020) with the nucleotide sequences assembled, aligned, trimmed, and processed to obtain 1950 selected loci. Unlike in our previous scorpion phylogenomic analysis (Santibáñez-López et al., 2023), one matrix was assembled with 77 species as minimum taxon occupancy threshold. ...
In this contribution we try to unveil the diversification process of Bothriuridae in temperate Gondwana through dated phylogenomic analyses using UCE and transcriptomics, and including in the analyses species of genera Urophonius and Cercophonius, the most closely related genera of Bothriuridae from South America and Australia respectively. Additionally we explored the hypothesis that the winter activity period of some species of Urophonius, as well as the cold environmental preferences of this genus, could be related to the climatic conditions of the time frame and area in which it evolved. Genus Urophonius was recovered as sister group to Cercophonius using amino acids and UCE. The time frame obtained for the split between South American and Australian bothriurids is 94 Ma., which suggests a dispersal event through temperate Gondwana, before the final breakup of the land bridge of South America-Antarctica-Australia ca. 35 Ma. The split between summer and winter species of Urophonius, taking place at 64 Ma, is considered representative to the turnover time from the summer activity period to the winter activity period in some species of the genus. This time frame is compatible with a period of global warming of the late Cretaceous greenhouse episode that could have triggered this change.
... SDSU experiments followed standard methods as previously used for arachnids (Starrett et al. 2017). Target enrichment was performed using the myBaits UCE Spider 2Kv1 kit (Arbor Biosciences; Kulkarni et al. 2020), with libraries sequenced using 150 bp, paired-end Illumina HiSeq 4000 sequencing at the DNA Technologies Core, UC Davis, CA, USA. For the remaining experiments genomic DNA was sent to RAPID Genomics for library preparation (using the Spider 2Kv1 probe set) and Illumina sequencing. ...
The rarely encountered spider genus Hexurella Gertsch & Platnick, 1979 includes some of the smallest mygalomorph spiders in the world, with four poorly known taxa from central and southeastern montane Arizona, southern California, and northern Baja California Norte. At time of description the genus was known from fewer than 20 individuals, with sparse natural history information suggesting a vagrant, web-building, litter-dwelling natural history. Here the first published taxonomic and natural history information for this taxon is provided in more than 50 years, working from extensive new geographic sampling, consideration of male and female morphology, and sequence capture-based nuclear phylogenomics and mitogenomics. Several new species are easily diagnosed based on distinctive male morphologies, while a complex of populations from central and northern Arizona required an integrative combination of genomic algorithmic species delimitation analyses and morphological study. Four new species are described, including H. ephedra sp. nov. , H. uwiiltil sp. nov. , H. xerica sp. nov. , and H. zas sp. nov. Females of H. encina Gertsch & Platnick, 1979 are also described for the first time. It is predicted that additional new species will ultimately be found in the mountains of central and northwestern Arizona, northern mainland Mexico, and the Mojave Desert of California.
... Changes in vegetation can affect the distribution and abundance of other species of insects, birds, and mammals, and therefore also the distribution and diversity of spiders. Most studies on spiders have focused on their evolution (Coddington and Levi, 1991;Oxford and Gillespie, 1998;Kulkarni et al. 2020) and biology (Ford, 1977;Foelix, 1996;Oxford and Gillespie, 1998). Some studies have also investigated the mechanism of web construction (Tso et al., 2006) and their role in the ecosystem (Wise, 1993). ...
The study is focused on the diversity of spiders in the Central Academy
for State Forest Service Campus located in Burnihat, Assam. The
conservation-friendly non-destructive photographic identification
was the survey method in the human-dominated environment of
the campus. During the study period, 21 families and 73 genera are
recorded, among them 16% are rare, 18% are abundant, 33% are
common and 33% are occasional in terms of their occurrence status. In
this paper, occurrences status and guild types of spider are discussed.
The study is the first scientific documentation of the spider fauna in the
academy campus area.
... Comparisons to prior work. To investigate and make comparisons between Agnarsson and colleagues (2013), we had to address three types of changes that have occurred since the publication of Agnarsson and colleagues (2013) at the family level (Wunderlich 2008, Bond et al. 2012, Griswold et al. 2012, Fernández et al. 2014, Ramírez 2014, Polotow et al. 2015, Dimitrov et al. 2017, Wheeler et al. 2017, Godwin et al. 2018, Hedin et al. 2018, 2019, Ono and Ogata 2018, Kulkarni et al. 2020, Opatova et al. 2020, Ledford et al. 2021, Azevedo et al. 2022, Montes de Oca et al. 2022. Either families were split, families were merged, or new families were described. ...
Biodiversity catalogs are an invaluable resource for biological research. Efforts to scientifically document biodiversity have not been evenly applied, either because of charisma or because of ease of study. Spiders are among the most precisely cataloged and diverse invertebrates, having surpassed 50,000 described species globally. The World Spider Catalog presents a unique opportunity to assess the disproportionate documentation of spider diversity. In the present article, we develop a taxonomic ratio relating new species descriptions to other taxonomic activity as a proxy for taxonomic effort, using spiders as a case study. We use this taxonomic effort metric to examine biases along multiple axes: phylogeny, zoogeography, and socioeconomics. We also use this metric to estimate the number of species that remain to be described. This work informs arachnologists in identifying high-priority taxa and regions for species discovery and highlights the benefits of maintaining open-access taxonomic databases—a necessary step in overcoming bias and documenting the world's biodiversity.
... anchored hybrid enrichment (Lemmon et al., 2012) or the ultraconserved elements (Faircloth et al., 2012). An increasing number of studies on arachnids are demonstrating that these techniques are able to resolve both deep and shallow divergencies (Hamilton et al., 2016;Maddison et al., 2017;Starrett et al., 2017;Kuntner et al., 2019;Kulkarni et al., 2020;Xu et al., 2021;Chamberland et al., 2022;Li et al., 2022). These data should continue to be accumulated with the ultimate goal of openness and compatibility of datasets. ...
This perspective identifies the grand challenges in arachnid science: 1. Grasp the arachnid species diversity. There is a need to accelerate taxonomic research to obtain a sense of arachnid species diversity, however, at the same time, taxonomy needs to increase its quality, rigor, and repeatability. 2. Standardize arachnid systematics research. A solid phylogenetic definition and morphological diagnosis of Arachnida and its composing subgroups, usually treated at the rank of order, are needed. Studies should aim to stabilize and standardize phylogenetic efforts at all levels of hierarchy, and systematists should adopt criteria for higher level ranks in arachnid classification. 3. Interpret arachnid trait evolution through omics approaches. Among the field’s grand challenges is to define the genetic diversity encoding for the diverse arachnid traits, including developmental, morphological and ecological characteristics, biomaterials such as silks, venoms, digestive fluids, or allergens and bioproducts that cause diseases. Comparative genomics, transcriptomics, and proteomics will provide the empirical basis for biotechnology to modify arachnid genomes to fit numerous applications. 4. Facilitate biotechnological applications of arachnid molecules and biomaterials. Among the grand field challenges is to define potential applications of arachnid bioproducts from therapeutics to industry. New natural and biodegradable products, e.g. from spider silks, should ease our burden on ecosystems. 5. Utilize arachnids as models in ecological and biogeographic research. Biodiversity inventory sampling and analytical techniques should be extended from spiders to other arachnid groups. Spiders and their webs could be used as environmental DNA samplers, measuring or monitoring ecosystems’ overall biodiversity. Arachnids are excellent models to address biogeographical questions at the global to local scales. 6. Disentangle evolutionary drivers of arachnid diversity. Among the field grand challenges is a more precise evaluation to what extent the emergence of arachnid phenotypes is shaped by classical selection processes, and under what conditions, if any, sexual conflict needs to be invoked. 7. Define effective conservation measures for arachnids in the light of global changes. Effective conservation measures in arachnology should integrate the data from phylogenetic diversity, physiology, ecology, biogeography, and global change biology.
... However, the monophyly of Symphytognathidae and its relationships to the other three families are complex and inconsistent in different phylogenetic studies. Symphytognathidae has been used repeatedly as a representative clade to test the phylogenetic relationships of specific groups, such as "symphytognathoids" (Rix et al. 2008;Lopardo et al. 2011;Feng et al. 2019), the Orbiculariae (Lopardo and Hormiga 2008;Fernández et al. 2014;Rivera-Quiroz et al. 2021) and all Araneae (Dimitrov et al. 2012;Wheeler et al. 2017;Kulkarni et al. 2020) using different molecular approaches and analyses. However, these studies were limited by missing data, including species and markers. ...
Three cave-dwelling spider species belonging to the family Symphytognathidae Hickman, 1931, i.e., Anapistula sanjiao sp. nov. (♂♀), A. walayaku sp. nov. (♂♀), and A. panensis Lin, Tao & Li, 2013 (♂♀), are reported from southwest China. DNA sequences and detailed illustrations of the habitus, male palps and epigynes are provided, and their distributions are mapped. Their phylogenetic position within symphytognathids and relationships were tested and assessed using previously published phylogenetic analyses on symphytognathoids. The results showed that they form a clade with A. choojaiae Rivera-Quiroz, Petcharad & Miller, 2021 from Thailand.
... The ultraconserved sequences (UCEs) for this study were obtained from publicly available transcriptomes and UCEs (we sequenced some of these) that were targeted using Arachnida and the 'spider-specific' Spider2Kv1 probe sets (Starrett et al. 2017;Kulkarni et al. 2020). Because the aim of this study is to assess the placement of Hickmania troglodytes, we sampled lineages from the families Austrochilidae, Gradungulidae, Leptonetidae and Archoleptonetidae. ...
Hickmania troglodytes is an emblematic cave spider representing a monotypic cribellate spider genus. This is the only Australian lineage of Austrochilidae while the other members of the family are found in southern South America. In addition to being the largest spider in Tasmania, Hickmania is an oddity in Austrochilidae because this is the only lineage in the family bearing posterior book lungs, tarsal spines and an embolar process on male pedipalps. Six-gene Sanger sequences and genome scale data such as ultraconserved elements (UCEs) and transcriptomes have suggested that Hickmania troglodytes is not nested with the family of current classification, Austrochilidae. We studied the phylogenetic placement of Hickmania troglodytes using an increased taxon sample by combining publicly available UCE and UCEs recovered from transcriptomic data in a parsimony and maximum likelihood framework. Based on our phylogenetic results we formally transfer Hickmania troglodytes from Austrochilidae to the family Gradungulidae. The cladistic placement of Hickmania in the family Gradungulidae fits the geographic distribution of both gradungulids (restricted to Australia and New Zealand) and austrochilids (restricted to southern South America) more appropriately.
... Molecular studies, as well as classical morphological work and integrative "whole-evidence" analyses, are covering large parts of spider diversity with increasing density. The last years have seen the publication of several comprehensive phylogenetic studies of the entire order, based on continuously increasing species coverage and ever-larger amounts of (mostly molecular) data (e.g., Agnarsson et al. 2013;Bond et al. 2014;Dimitrov et al. 2017;Fernandez et al. 2014Fernandez et al. , 2018Garrison et al. 2016;Hedin et al. 2019;Kulkarni et al. 2020;Opatova et al. 2020;Ramírez 2014;Ramírez et al. 2019Ramírez et al. , 2021Shao & Li 2018;Wheeler et al. 2017). Subsets of the order, from superfamilies to individual groups of genera, have also been the target of various analyses (e.g., Crews et al. 2020;Godwin et al. 2018;Hedin et al. 2018;Kallal et al. 2020; and numerous publications cited below for individual families). ...
The recent accumulation of increasingly densely sampled phylogenetic analyses of spiders has greatly advanced our understanding of evolutionary relationships within this group. Here, this diverse literature is reviewed and combined with earlier morphological analyses in an attempt to reconstruct the first fully resolved phylogeny for the spider fauna of the British Isles. The resulting tree highlights parts of the group where data are still too limited for a confident assessment of relationships, proposes a number of deviations from previously suggested phylogenetic hypotheses, and can serve as a framework for evolutionary and ecological interpretations of the biology of British spiders, as well as a starting point for future studies on a larger geographical scale.
... The transcriptomic analyses of Fernández et al. (2018) and Kallal et al. (2021) support the monophyly of linyphioids but place Weintrauboa as a sister group to the linyphiid clade, rather than to Pimoa. Analyses of ultraconserved elements (Kulkarni et al. 2020 have also supported the monophyly of linyphioids, based on representation of a single pimoid genus (Pimoa). ...
We address the phylogenetic relationships of pimoid spiders (Pimoidae) using a standard target-gene approach with an extensive taxonomic sample, which includes representatives of the four currently recognized pimoid genera, 26 linyphiid genera, a sample of Physoglenidae, Cyatholipidae and one Tetragnathidae species. We test the monophyly of Pimoidae and Linyphiidae and explore the biogeographic history of the group. Nanoa Hormiga, Buckle and Scharff, 2005 and Pimoa Chamberlin & Ivie, 1943 form a clade which is the sister group of a lineage that includes all Linyphiidae, Weintrauboa Hormiga, 2003 and Putaoa Hormiga and Tu, 2008. Weintrauboa, Putaoa, Pecado and Stemonyphantes form a clade (Stemonyphantinae) sister to all remaining linyphiids. We use the resulting optimal molecular phylogenetic tree to assess hypotheses on the male palp sclerite homologies of pimoids and linyphiids. Pimoidae is redelimited to only include Pimoa and Nanoa. We formalize the transfer from Pimoidae of the genera Weintrauboa and Putaoa to Linyphiidae, re-circumscribe the linyphiid subfamily Stemonyphantinae, and offer revised morphological diagnoses for Pimoidae and Linyphiidae.
... We lacked samples of Barraina Richardson 2013, Maileus Peckham & Peckham 1907 and Prostheclina Keyserling 1882, all hypothesized members of the Saitis Clade (Zhang & Maddison (2013. We used the MYbaits Spider v.1 kit (Arbor Biosciences, Ann Arbor, MI, USA; Kulkarni et al., 2020) to capture UCE loci, using methods of library preparation as in recent publications (Starrett et al., 2017;Hedin et al., 2019). Sequencing was conducted on an Illumina HiSeq400 at the U.C. Davis Genome Center with 150-bp paired-end reads. ...
Understanding diversity has been a pursuit in evolutionary biology since its inception. A challenge arises when sexual selection has played a role in diversification. Questions of what constitutes a ‘species’, homoplasy vs. synapomorphy, and whether sexually selected traits show phylogenetic signal have hampered work on many systems. Peacock spiders are famous for sexually selected male courtship dances and peacock-like abdominal ornamentation. This lineage of jumping spiders currently includes over 90 species classified into two genera, Maratus and Saratus. Most Maratus species have been placed into groups based on secondary sexual characters, but evolutionary relationships remain unresolved. Here we assess relationships in peacock spiders using phylogenomic data (ultraconserved elements and RAD-sequencing). Analyses reveal that Maratus and the related genus Saitis are paraphyletic. Many, but not all, morphological groups within a ‘core Maratus’ clade are recovered as genetic clades but we find evidence for undocumented speciation. Based on original observations of male courtship, our comparative analyses suggest that courtship behaviour and peacock-like abdominal ornamentation have evolved sequentially, with some traits inherited from ancestors and others evolving repeatedly and independently from ‘simple’ forms. Our results have important implications for the taxonomy of these spiders, and provide a much-needed evolutionary framework for comparative studies of the evolution of sexual signal characters.
... Given the promise of this phylogenetic data class, efforts to improve the recovery of UCE data sets in sea spiders should target the generation of high-quality sea spider genomes, with downstream improvements in the design of sea spider-specific UCE probes. Such strategies have been shown to overcome limitations inherent to the arachnid UCE bait set for spiders (Kulkarni et al. 2020). ...
Despite significant advances in invertebrate phylogenomics over the past decade, the higher-level phylogeny of Pycnogonida (sea spiders) remains elusive. Due to the inaccessibility of some small-bodied lineages, few phylogenetic studies have sampled all sea spider families. Previous efforts based on a handful of genes have yielded unstable tree topologies. Here, we inferred the relationships of 89 sea spider species using targeted capture of the mitochondrial genome, 56 conserved exons, 101 ultraconserved elements, and 3 nuclear ribosomal genes. We inferred molecular divergence times by integrating morphological data for fossil species to calibrate 15 nodes in the arthropod tree of life. This integration of data classes resolved the basal topology of sea spiders with high support. The enigmatic family Austrodecidae was resolved as the sister group to the remaining Pycnogonida and the small-bodied family Rhynchothoracidae as the sister group of the robust-bodied family Pycnogonidae. Molecular divergence time estimation recovered a basal divergence of crown group sea spiders in the Ordovician. Comparison of diversification dynamics with other marine invertebrate taxa that originated in the Paleozoic suggests that sea spiders and some crustacean groups exhibit resilience to mass extinction episodes, relative to mollusk and echinoderm lineages.
... In recent years, we have seen an important increase in phylogenomic studies, and these studies are starting to converge on a relatively stable picture of the higher-level phylogenetic relationships of spiders (55,57,80,122), but relationships at a finer taxonomic scale often remain contentious; phylogenomic efforts should continue in that direction. Advances in high-throughput sequencing methods have also facilitated microbiome studies, leading to some exciting results (e.g., 124), but these studies are limited to a handful of species. ...
Spiders (Araneae) make up a remarkably diverse lineage of predators that have successfully colonized most terrestrial ecosystems. All spiders produce silk, and many species use it to build capture webs with an extraordinary diversity of forms. Spider diversity is distributed in a highly uneven fashion across lineages. This strong imbalance in species richness has led to several causal hypotheses, such as codiversification with insects, key innovations in silk structure and web architecture, and loss of foraging webs. Recent advances in spider phylogenetics have allowed testing some of these hypotheses, but results are often contradictory, highlighting the need to consider additional drivers of spider diversification. The spatial and historical patterns of diversity and diversification remain contentious. Comparative analyses of spider diversification will advance only if we continue to make progress with studies of species diversity, distribution, and phenotypic traits, together with finer-scale phylogenies and genomic data.
Expected final online publication date for the Annual Review of Entomology, Volume 66 is January 11, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Relationships among spider families that lack support through other lines of evidence (e.g., morphology) have recently been uncovered through molecular phylogenetics. One such group is the "marronoid" clade, which contains about 3,400 described species in 9 families. Marronoids run the gamut of life history strategies , with social species, species producing a variety of silk types, and species occurring in a range of extreme environments. Despite recognition of the ecological variability in the group, there remains uncertainty about family-level relationships, leaving diverse ecologies without an evolutionary context. The phylogenies produced to date have relatively low nodal support, there are few defined morphological syn-apomorphies, and the internal relationships of many families remain unclear. We use 93 exemplars from all marronoid families and ultraconserved element loci captured in silico from a combination of 48 novel low-coverage whole genomes and genomic data from the Sequence Read Archive (SRA) to produce a 50% occupancy matrix of 1,277 loci from a set of ultraconserved element probes. These loci were used to infer a phylogeny of the marronoid clade and to evaluate the familial relationships within the clade, and were combined with single-locus (Sanger) legacy data to further increase taxonomic sampling. Our results indicate a clearly defined and well-supported marronoid clade and provide evidence for both monophyly and paraphyly within the currently defined families of the clade. We propose taxonomic changes in accordance with the resulting phylogenetic hypothesis, including elevating Cicurinidae (restored status) and Macrobunidae (new rank).
In the last decade and a half, advances in genetic sequencing technologies have revolutionized systematics, transforming the field from studying morphological characters or a few genetic markers, to genomic datasets in the phylogenomic era. A plethora of molecular phylogenetic studies on many taxonomic groups have come about, converging on, or refuting prevailing morphology or legacy-marker-based hypotheses about evolutionary affinities. Spider systematics has been no exception to this transformation and the interrelationships of several groups have now been studied using genomic data. About 51 500 extant spider species have been described, all with a conservative body plan, but innumerable morphological and behavioural peculiarities. Inferring the spider tree of life using morphological data has been a challenging task. Molecular data have corroborated many hypotheses of higher-level relationships, but also resulted in new groups that refute previous hypotheses. In this review, we discuss recent advances in the reconstruction of the spider tree of life and highlight areas where additional effort is needed with potential solutions. We base this review on the most comprehensive spider phylogeny to date, representing 131 of the 132 spider families. To achieve this sampling, we combined six Sanger-based markers with newly generated and publicly available genome-scale datasets. We find that some inferred relationships between major lineages of spiders (such as Austrochiloidea, Palpimanoi-dea and Synspermiata) are robust across different classes of data. However, several new hypotheses have emerged with different classes of molecular data. We identify and discuss the robust and controversial hypotheses and compile this blueprint to design future studies targeting systematic revisions of these problematic groups. We offer an evolutionary framework to explore comparative questions such as evolution of venoms, silk, webs, morphological traits and reproductive strategies.
Advanced sequencing technologies have expedited resolving higher-level arthropod relationships. Yet, dark branches persist, principally among groups occurring in cryptic habitats. Among chelicerates, Solifugae (“camel spiders”) is the last order lacking a higher-level phylogeny and thus, historically characterized as “neglected [arachnid] cousins”. Though renowned for aggression, remarkable running speed, and xeric adaptation, inferring solifuge relationships has been hindered by inaccessibility of diagnostic morphological characters, whereas molecular investigations have been limited to one of 12 recognized families. Our phylogenomic dataset via capture of ultraconserved elements sampling all extant families recovered a well-resolved phylogeny, with two distinct groups of New World taxa nested within a broader Paleotropical radiation. Divergence times using fossil calibrations inferred Solifugae radiated by the Permian, and most families diverged pre-Paleogene-Cretaceous extinction, largely driven by continental breakup. We establish Boreosolifugae new suborder uniting five Laurasian families, and Australosolifugae new suborder uniting seven Gondwanan families using morphological and biogeographic signal.
Tailoring ultraconserved element (UCE) probe set design to focal taxa has been demonstrated to improve locus recovery and phylogenomic inference. However, beyond conducting expensive in vitro testing, it remains unclear how best to determine whether an existing UCE probe set is likely to suffice for phylogenomic inference or whether tailored probe design will be desirable. Here we investigate the utility of 8 different UCE probe sets for the in silico phylogenomic inference of scarabaeoid beetles. Probe sets tested differed in terms of (i) how phylogenetically distant from Scarabaeoidea taxa those used during probe design are, (ii) breadth of phylogenetic inference probe set was designed for, and (iii) method of probe design. As part of this study, 2 new UCE probe sets are produced for the beetle family Scarabaeidae and superfamily Hydrophiloidea. We confirm that probe set utility decreases with increasing phylogenetic distance from target taxa. In addition, narrowing the phylogenetic breadth of probe design decreases the phylogenetic capture range. We also confirm previous findings regarding ways to optimize UCE probe design. Finally, we make suggestions regarding assessment of need for de novo probe design.
This revision is based on sampling efforts over the past three decades in the southern Appalachian Mountains which have provided Nesticus (Araneae, Nesticidae) collections of approximately 2100 adult specimens from more than 475 unique collecting events. Using a “morphology first” framework we examined recently collected specimens plus museum material to formulate morphology-based species hypotheses for putative new taxa (discovery phase). Using sequence capture of nuclear ultraconserved elements (UCEs) we analyzed 801 nuclear loci to validate new (and prior) morphology-based species hypotheses (validation phase) and reconstructed a robust backbone phylogeny including all described and new species. Sanger sequencing and UCE-bycatch were also used to gather mitochondrial data for more than 240 specimens. Based on our integrative taxonomic framework ten new Nesticus species are herein described, including N. binfordae sp. nov. , N. bondi sp. nov. , N. canei sp. nov. , N. cherokeensis sp. nov. , N. dellingeri sp. nov. , N. dykemanae sp. nov. , N. jemisinae sp. nov. , N. lowderi sp. nov. , N. roanensis sp. nov. , and N. templetoni sp. nov. Previously unknown males are also described for N. bishopi Gertsch, 1984, N. crosbyi Gertsch, 1984, and N. silvanus Gertsch, 1984, as well as the previously unknown female for N. mimus Gertsch, 1984. Based on combined evidence N. cooperi Gertsch, 1984 is placed in synonymy with N. reclusus Gertsch, 1984. Overall, the montane radiation of Appalachian Nesticus reveals a general lack of species sympatry and compelling biogeographic patterns. Several regional Nesticus taxa are rare, microendemic habitat specialists that deserve conservation attention and detailed future monitoring as conservation sentinels.
Considerable progress has been achieved in resolving higher-level relationships of Arthropoda in the past two decades, largely precipitated by advances in sequencing technology. Yet, dark branches persist in the arthropod tree of life, principally among groups that are difficult to collect, occur in cryptic habitats, or are characterized by minute body size. Among chelicerates, the mesodiverse order Solifugae (commonly called camel spiders or sun spiders) is one of the last orders of Arachnida that lacks a higher-level phylogeny altogether and has long been characterized as one of the "neglected cousins", a lineage of arachnid orders that are comparatively poorly studied with respect to evolutionary relationships. Though renowned for their aggression, remarkable running speed, and adaptation to arid habitats, inferring solifuge relationships has been hindered by inaccessibility of diagnostic characters in most ontogenetic stages for morphological datasets, whereas molecular investigations to date have been limited to one of the 12 recognized families. In this study we generated a phylogenomic dataset via capture of ultraconserved elements (UCEs) and sampled all extant families. We recovered a well-resolved phylogeny of solifuge families, with two distinct groups of New World taxa nested within a broader Paleotropical radiation. To provide a temporal context to solifuge diversification, we estimated molecular divergence times using fossil calibrations within a Bayesian framework. Solifugae were inferred to have radiated by the Permian, with divergences of most families dating to the post Paleogene-Cretaceous extinction. These results accord with a diversification history largely driven by vicariance as a result of continental breakup.
The tetragnathid genus Leucauge includes some of the most common orb-weaving spiders in the tropics. Although some species in this genus have attained relevance as model systems for several aspects of spider biology, our understanding of the generic diversity and evolutionary relationships among the species is poor. In this study we present the first attempt to determine the phylogenetic structure within Leucauge and the relationship of this genus with other genera of Leucauginae. This is based on DNA sequences from the five loci commonly used and Histone H4, used for the first time in spider phylogenetics. We also assess the informativeness of the standard markers and test for base composition biases in the dataset. Our results suggest that Leucauge is not monophyletic since species of the genera Opas, Opadometa, Mecynometa and Alcimosphenus are included within the current circumscription of the genus. Based on a phylogenetic re-circumscription of the genus to fulfil the requirement for monophyly of taxa, Leucauge White, 1841 is deemed to be a senior synonym of the genera Opas Pickard-Cambridge, 1896 revalidated synonymy, Mecynometa Simon, 1894 revalidated synonymy, Opadometa Archer, 1951 new synonymy and Alcimosphenus Simon, 1895 new synonymy. We identify groups of taxa critical for resolving relationships within Leucauginae and describe the limitations of the standard loci for accomplishing these resolutions.
Synopsis
To capture prey otherwise unattainable by muscle function alone, some animal lineages have evolved movements that are driven by stored elastic energy, producing movements of remarkable speed and force. One such example that has evolved multiple times is a trap-jaw mechanism, in which the mouthparts of an animal are loaded with energy as they open to a wide gape and then, when triggered to close, produce a terrific force. Within the spiders (Araneae), this type of attack has thus far solely been documented in the palpimanoid family Mecysmaucheniidae but a similar morphology has also been observed in the distantly related araneoid subfamily Pararchaeinae, leading to speculation of a trap-jaw attack in that lineage as well. Here, using high-speed videography, we test whether cheliceral strike power output suggests elastic-driven movements in the pararchaeine Pararchaea alba. The strike speed attained places P. alba as a moderately fast striker exceeding the slowest mecysmaucheniids, but failing to the reach the most extreme high-speed strikers that have elastic-driven mechanisms. Using microcomputed tomography, we compare the morphology of P. alba chelicerae in the resting and open positions, and their related musculature, and based on results propose a mechanism for cheliceral strike function that includes a torque reversal latching mechanism. Similar to the distantly related trap-jaw mecysmaucheniid spiders, the unusual prosoma morphology in P. alba seemingly allows for highly maneuverable chelicerae with a much wider gape than typical spiders, suggesting that increasingly maneuverable joints coupled with a latching mechanism may serve as a precursor to elastic-driven movements.
Natural history collections play a crucial role in biodiversity research and museum specimens are increasingly being incorporated into modern genetics‐based studies. Sequence capture methods have proven incredibly useful for phylogenomics, providing the additional ability to sequence historical museum specimens with highly degraded DNA, which until recently have been deemed less valuable for genetic work. The successful sequencing of ultraconserved elements (UCEs) from historical museum specimens has been demonstrated on multiple tissue types including dried bird skins, formalin‐fixed squamates, and pinned insects. However, no study has thoroughly demonstrated this approach for historical ethanol‐preserved museum specimens. Alongside sequencing of “fresh” specimens preserved in >95% ethanol and stored at ‐80 ºC, we used extraction techniques specifically designed for degraded DNA coupled with sequence capture protocols to sequence UCEs from historical museum specimens preserved in 70–80% ethanol and stored at room temperature, the standard for such ethanol‐preserved museum collections. Across 35 fresh and 15 historical museum samples of the arachnid order Opiliones, an average of 345 UCE loci were included in phylogenomic matrices, with museum samples ranging from 6–495 loci. We successfully demonstrate the inclusion of historical ethanol‐preserved museum specimens in modern sequence capture phylogenomic studies, show high frequency of variant bases at the species and population‐level, and from off‐target reads successfully recover multiple loci traditionally sequenced in multi‐locus studies including mitochondrial loci and nuclear rRNA loci. The methods detailed in this study will allow researchers to potentially acquire genetic data from millions of ethanol‐preserved museum specimens held in collections worldwide. This article is protected by copyright. All rights reserved.
Instances of sexual size dimorphism (SSD) provide the context for rigorous tests of biological rules of size evolution, such as Cope's rule (phyletic size increase), Rensch's rule (allometric patterns of male and female size), as well as male and female body size optima. In certain spider groups, such as the golden orbweavers (Nephilidae), extreme female-biased SSD (eSSD, female:male body length $\ge$2) is the norm. Nephilid genera construct webs of exaggerated proportions, which can be aerial, arboricolous, or intermediate (hybrid). First, we established the backbone phylogeny of Nephilidae using 367 anchored hybrid enrichment markers, then combined these data with classical markers for a reference species-level phylogeny. Second, we used the phylogeny to test Cope and Rensch's rules, sex specific size optima, and the coevolution of web size, type, and features with female and male body size and their ratio, SSD. Male, but not female, size increases significantly over time, and refutes Cope's rule. Allometric analyses reject the converse, Rensch's rule. Male and female body sizes are uncorrelated. Female size evolution is random, but males evolve toward an optimum size (3.2-4.9 mm). Overall, female body size correlates positively with absolute web size. However, intermediate sized females build the largest webs (of the hybrid type), giant female Nephila and Trichonephila build smaller webs (of the aerial type), and the smallest females build the smallest webs (of the arboricolous type). We propose taxonomic changes based on the criteria of clade age, monophyly and exclusivity, classification information content, and diagnosability. Spider families, as currently defined, tend to be between 37 million years old and 98 million years old, and Nephilidae is estimated at 133 Ma (97-146), thus deserving family status. We, therefore, resurrect the family Nephilidae Simon 1894 that contains Clitaetra Simon 1889, the Cretaceous GeratonephilaPoinar and Buckley (2012), Herennia Thorell 1877, IndoetraKuntner 2006, new rank, Nephila Leach 1815, Nephilengys L. Koch 1872, Nephilingis Kuntner 2013, Palaeonephila Wunderlich 2004 from Tertiary Baltic amber, and TrichonephilaDahl 1911, new rank. We propose the new clade Orbipurae to contain Araneidae Clerck 1757, Phonognathidae Simon 1894, new rank, and Nephilidae. Nephilid female gigantism is a phylogenetically ancient phenotype (over 100 Ma), as is eSSD, though their magnitudes vary by lineage.
The atypoid mygalomorphs include spiders from three described families that build a diverse array of entrance web constructs, including funnel-and-sheet webs, purse webs, trapdoors, turrets and silken collars. Molecular phylogenetic analyses have generally supported the monophyly of Atypoidea, but prior studies have not sampled all relevant taxa. Here we generated a dataset of ultraconserved element loci for all described atypoid genera, including taxa (Mecicobothrium and Hexurella) key to understanding familial monophyly, divergence times, and patterns of entrance web evolution. We show that the conserved regions of the arachnid UCE probe set target exons, such that it should be possible to combine UCE and transcriptome datasets in arachnids. We also show that different UCE probes sometimes target the same protein, and under the matching parameters used here show that UCE alignments sometimes include non-orthologs. Using multiple curated phylogenomic matrices we recover a monophyletic Atypoidea, and reveal that the family Mecicobothriidae comprises four separate and divergent lineages. Fossil-calibrated divergence time analyses suggest ancient Triassic (or older) origins for several relictual atypoid lineages, with late Cretaceous/early Tertiary divergences within some genera indicating a high potential for cryptic species diversity. The ancestral entrance web construct for atypoids, and all mygalomorphs, is reconstructed as a funnel-and-sheet web.
The Infraorder Mygalomorphae is one of the three main lineages of spiders comprising over 3,000 nominal species. This ancient group has a world-wide distribution that includes among its ranks large and charismatic taxa such as tarantulas, trapdoor spiders, and highly venomous funnel web spiders. Based on past molecular studies using Sanger-sequencing approaches, numerous mygalomorph families (e.g., Hexathelidae, Ctenizidae, Cyrtaucheniidae, Dipluridae and Nemesiidae) have been identified as non-monophyletic. However, these data were unable to sufficiently resolve the higher-level (intra- and interfamilial) relationships such that the necessary changes in classification could be made with confidence. Here we present the most comprehensive phylogenomic treatment of the spider infraorder Mygalomorphae conducted to date. We employ 472 loci obtained through Anchored Hybrid Enrichment to reconstruct relationships among all the mygalomorph spider families and estimate the timeframe of their diversification. We performed an extensive generic sampling of all currently recognized families, which has allowed us to assess their status, and as a result, propose a new classification scheme. Our generic-level sampling has also provided an evolutionary framework for revisiting questions regarding silk use in mygalomorph spiders. The first such analysis for the group within a strict phylogenetic framework shows that a sheet web is likely the plesiomorphic condition for mygalomorphs, as well as providing hints to the ancestral foraging behavior for all spiders. Our divergence time estimates, concomitant with detailed biogeographic analysis, suggest that both ancient continental-level vicariance and more recent dispersal events have played an important role in shaping modern day distributional patterns. Based on our results, we relimit the generic composition of the Ctenizidae, Cyrtaucheniidae, Dipluridae and Nemesiidae. We also elevate five subfamilies to family rank: Anamidae (NEW RANK), Euagridae (NEW RANK), Ischnothelidae (NEW RANK), Pycnothelidae (NEW RANK), and Bemmeridae (NEW RANK). The three families Hermachidae (NEW FAMILY), Microhexuridae (NEW FAMILY), and Stasimopidae (NEW FAMILY) are newly proposed. Such a major rearrangement in classification, recognizing eight newly established family-level rank taxa, is the largest the group has seen in over three decades since Raven's (1985) taxonomic treatment.
The genomics revolution has initiated a new era of population genetics where genome‐wide data are frequently used to understand complex patterns of population structure and selection. However, the application of genomic tools to inform management and conservation has been somewhat rare outside a few well‐studied species. Fortunately, two recently developed approaches, amplicon sequencing and sequence capture, have the potential to significantly advance the field of conservation genomics. Here, amplicon sequencing refers to highly multiplexed PCR followed by high‐throughput sequencing (e.g. GTseq), and sequence capture refers to using capture probes to isolate loci from reduced‐representation libraries (e.g. Rapture). Both approaches allow sequencing of thousands of individuals at relatively low costs, do not require any specialized equipment for library preparation, and generate data that can be analyzed without sophisticated computational infrastructure. Here, we discuss the advantages and disadvantages of each method and provide a decision framework for geneticists who are looking to integrate these methods into their research program. While it will always be important to consider the specifics of the biological question and system, we believe that amplicon sequencing is best suited for projects aiming to genotype < 500 loci on many individuals (> 10,000) or for species where continued monitoring is anticipated (e.g. long‐term pedigrees). Sequence capture, on the other hand, is best applied to projects including fewer individuals or where > 500 loci are required. Both of these techniques should smooth the transition from traditional genetic techniques to genomics, helping to usher in the conservation genomics era.
This article is protected by copyright. All rights reserved.
Mites (Acari) are one of the most diverse groups of life on Earth, yet their evolutionary relationships are poorly understood. Also, the resolution of broader arachnid phylogeny has been hindered by an underrepresentation of mite diversity in phylogenomic analyses. To further our understanding of Acari evolution, we design targeted ultraconserved genomic elements (UCEs) probes, intended for resolving the complex relationships between mite lineages and closely related arachnids. We then test our Acari UCE baits in‐silico by constructing a phylogeny using 13 existing Acari genomes, as well as 6 additional taxa from a variety of genomic sources. Our Acari‐specific probe kit improves the recovery of loci within mites over an existing general arachnid UCE probe set. Our initial phylogeny recovers the major mite lineages, yet finds mites to be non‐monophyletic overall, with Opiliones (harvestmen) and Ricinuleidae (hooded tickspiders) rendering Parasitiformes paraphyletic.
This article is protected by copyright. All rights reserved.
Morphological, mitochondrial, and nuclear phylogenomic data were combined to address phylogenetic and species delimitation questions in cave-limited Cicurina spiders from central Texas. Special effort was focused on specimens and cave locations in the San Antonio region (Bexar County), home to four eyeless species listed as US Federally Endangered. Sequence capture experiments resulted in the recovery of ~200–400 homologous ultra-conserved element (UCE) nuclear loci across taxa, and nearly complete COI mitochondrial DNA sequences from the same set of individuals. Some of these nuclear and mitochondrial sequences were recovered from “standard” museum specimens without special preservation of DNA material, including museum specimens preserved in the 1990s. Multiple phylogenetic analyses of the UCE data agree in the recovery of two major lineages of eyeless Cicurina in Texas. These lineages also differ in mitochondrial clade membership, female genitalic morphology, degree of troglomorphy (as measured by relative leg length), and are mostly allopatric across much of Texas. Rare sympatry was confirmed in Bexar County, where members of the two major clades sometimes co-exist in the same karst feature. Both nuclear phylogenomic and mitochondrial data indicate the existence of undescribed species from the San Antonio region, although further sampling and collection of adult specimens is needed to explicitly test these hypotheses. Our data support the two following species synonymies ( Cicurinavenii Gertsch, 1992 = Cicurinamadla Gertsch, 1992; Cicurinaloftini Cokendolpher, 2004 = Cicurinavespera Gertsch, 1992), formally proposed here. Overall, our taxonomy-focused research has many important conservation implications, and again highlights the fundamental importance of robust taxonomy in conservation research.
Background:
Evolutionary histories can be discordant across the genome, and such discordances need to be considered in reconstructing the species phylogeny. ASTRAL is one of the leading methods for inferring species trees from gene trees while accounting for gene tree discordance. ASTRAL uses dynamic programming to search for the tree that shares the maximum number of quartet topologies with input gene trees, restricting itself to a predefined set of bipartitions.
Results:
We introduce ASTRAL-III, which substantially improves the running time of ASTRAL-II and guarantees polynomial running time as a function of both the number of species (n) and the number of genes (k). ASTRAL-III limits the bipartition constraint set (X) to grow at most linearly with n and k. Moreover, it handles polytomies more efficiently than ASTRAL-II, exploits similarities between gene trees better, and uses several techniques to avoid searching parts of the search space that are mathematically guaranteed not to include the optimal tree. The asymptotic running time of ASTRAL-III in the presence of polytomies is [Formula: see text] where D=O(nk) is the sum of degrees of all unique nodes in input trees. The running time improvements enable us to test whether contracting low support branches in gene trees improves the accuracy by reducing noise. In extensive simulations, we show that removing branches with very low support (e.g., below 10%) improves accuracy while overly aggressive filtering is harmful. We observe on a biological avian phylogenomic dataset of 14K genes that contracting low support branches greatly improve results.
Conclusions:
ASTRAL-III is a faster version of the ASTRAL method for phylogenetic reconstruction and can scale up to 10,000 species. With ASTRAL-III, low support branches can be removed, resulting in improved accuracy.
Here we show that the most venomous spiders in the world are phylogenetically misplaced. Australian atracine spiders (family Hexathelidae), including the notorious Sydney funnel-web spider Atrax robustus, produce venom peptides that can kill people. Intriguingly, eastern Australian mouse spiders (family Actinopodidae) are also medically dangerous, possessing venom peptides strikingly similar to Atrax hexatoxins. Based on the standing morphology-based classification, mouse spiders are hypothesized distant relatives of atracines, having diverged over 200 million years ago. Using sequence-capture phylogenomics, we instead show convincingly that hexathelids are non-monophyletic, and that atracines are sister to actinopodids. Three new mygalomorph lineages are elevated to the family level, and a revised circumscription of Hexathelidae is presented. Re-writing this phylogenetic story has major implications for how we study venom evolution in these spiders, and potentially genuine consequences for antivenom development and bite treatment research. More generally, our research provides a textbook example of the applied importance of modern phylogenomic research.
The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has been steadily adopted as an efficient alternative to SBS and other bootstrap approaches.
Here, we present UFBoot2, which substantially accelerates UFBoot and reduces the risk of overestimating branch supports due to polytomies or severe model violations. Additionally, UFBoot2 provides suitable bootstrap resampling strategies for phylogenomic data. UFBoot2 is 778 times (median) faster than SBS and 8.4 times (median) faster than RAxML rapid bootstrap on tested datasets. UFBoot2 is implemented in the IQ-TREE software package version 1.6 and freely available at http://www.iqtree.org.
We present the first genome-wide molecular phylogeny of jumping spiders (Araneae: Salticidae), inferred from Anchored Hybrid Enrichment (AHE) sequence data. From 12 outgroups plus 34 salticid taxa representing all but one subfamily and most major groups recognized in previous work, we obtained 447 loci totalling 96,946 aligned nucleotide sites. Our analyses using concatenated likelihood, parsimony, and coalescent methods (ASTRAL and SVDQuartets) strongly confirm most previous results, resolving as monophyletic the Spartaeinae, Salticinae (with the hisponines sister), Salticoida, Amycoida, Saltafresia, and Simonida. The agoriines, previously difficult to place beyond subfamily, are finally placed confidently within the saltafresians as relatives of the chrysillines and hasariines. Relationships among the baviines, astioids, marpissoids, and saltafresians remain uncertain, though our analyses tentatively conclude the first three form a clade together. Deep relationships, among the seven subfamilies, appear to be largely resolved, with spartaeines, lyssomanines, and asemoneines forming a clade. In most analyses, Onomastus (representing the onomastines) is strongly supported as sister to the hisponines plus salticines. Overall, the much-improved resolution of many deep relationships despite a relatively sparse taxon sample suggests AHE is a promising technique for salticid phylogenetics.
Background: The duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence for a large-scale duplication of genes in some chelicerate lineages including two rounds of whole genome duplication (WGD) in horseshoe crabs. To investigate this further, we sequenced and analyzed the genome of the common house spider Parasteatoda tepidariorum.
Results: We found pervasive duplication of both coding and non-coding genes in this spider, including two clusters of Hox genes. Analysis of synteny conservation across the P. tepidariorum genome suggests that there has been an ancient WGD in spiders. Comparison with the genomes of other chelicerates, including that of the newly sequenced bark scorpion Centruroides sculpturatus, suggests that this event occurred in the common ancestor of spiders and scorpions, and is probably independent of the WGDs in horseshoe crabs. Furthermore, characterization of the
sequence and expression of the Hox paralogs in P. tepidariorum suggests that many have been subject to
neo-functionalization and/or sub-functionalization since their duplication.
Conclusions: Our results reveal that spiders and scorpions are likely the descendants of a polyploid ancestor
that lived more than 450 MYA. Given the extensive morphological diversity and ecological adaptations found
among these animals, rivaling those of vertebrates, our study of the ancient WGD event in Arachnopulmonata
provides a new comparative platform to explore common and divergent evolutionary outcomes of polyploidization events across eukaryotes.
Keywords: Parasteatoda tepidariorum, Genome, Centruroides sculpturatus, Gene duplication, Evolution, Hox genes
The beetle suborder Adephaga has been the subject of many phylogenetic reconstructions utilizing a variety of data sources and inference methods. However, no strong consensus has yet emerged on the relationships among major adephagan lineages. Ultraconserved elements (UCEs) have proved useful for inferring difficult or unresolved phylogenies at varying timescales in vertebrates, arachnids and Hymenoptera. Recently, a UCE bait set was developed for Coleoptera using polyphagan genomes and a member of the order Strepsiptera as an outgroup. Here, we examine the utility of UCEs for reconstructing the phylogeny of adephagan families, in the first in vitro application a UCE bait set in Coleoptera. Our final dataset included 305 UCE loci for 18 representatives of all adephagan families except Aspidytidae, and two polyphagan outgroups, with a total concatenated length of 83 547 bp. We inferred trees using maximum likelihood analyses of the concatenated UCE alignment and coalescent species tree methods (astral ii, ASTRID, svdquartets). Although the coalescent species tree methods had poor resolution and weak support, concatenated analyses produced well-resolved, highly supported trees. Hydradephaga was recovered as paraphyletic, with Gyrinidae sister to Geadephaga and all other adephagans. Haliplidae was recovered as sister to Dytiscoidea, with Hygrobiidae and Amphizoidae successive sisters to Dytiscidae. Finally, Noteridae was recovered as monophyletic and sister to Meruidae. Given the success of UCE data for resolving phylogenetic relationships within Adephaga, we suggest the potential for further resolution of relationships within Adephaga using UCEs with improved taxon sampling, and by developing Adephaga-specific probes.
Spider silks are the toughest known biological materials, yet are lightweight and virtually invisible to the human immune system, and they thus have revolutionary potential for medicine and industry. Spider silks are largely composed of spidroins, a unique family of structural proteins. To investigate spidroin genes systematically, we constructed the first genome of an orb-weaving spider: the golden orb-weaver (Nephila clavipes), which builds large webs using an extensive repertoire of silks with diverse physical properties. We cataloged 28 Nephila spidroins, representing all known orb-weaver spidroin types, and identified 394 repeated coding motif variants and higher-order repetitive cassette structures unique to specific spidroins. Characterization of spidroin expression in distinct silk gland types indicates that glands can express multiple spidroin types. We find evidence of an alternatively spliced spidroin, a spidroin expressed only in venom glands, evolutionary mechanisms for spidroin diversification, and non-spidroin genes with expression patterns that suggest roles in silk production.