Figure - uploaded by Elsa Call
Content may be subject to copyright.
Source publication
Billions of specimens can be found in natural history museum collections around the world, holding potential molecular secrets to be unveiled. Among them are intriguing specimens of rare families of moths that, while represented in morphology-based works, are only beginning to be included in genomic studies: Pseudobistonidae, Sematuridae, and Epico...
Contexts in source publication
Context 1
... addition, we sampled two species of Sematuridae (Anurapteryx interlineata and Mania empedocles) and two specimens of Pseudobistonidae (Pseudobiston pinratanai) to investigate the relationships between these three families. In total, 33 museum specimens collected between 1892 and 2001 were included (Table 1). The oldest sample is a Parabraxas davidi (Oberthür, 1885) specimen from 1892, whereas the most recent one is Parabraxas flavomarginaria (Leech, 1897) from 2001 ( Table 1). ...Context 2
... total, 33 museum specimens collected between 1892 and 2001 were included (Table 1). The oldest sample is a Parabraxas davidi (Oberthür, 1885) specimen from 1892, whereas the most recent one is Parabraxas flavomarginaria (Leech, 1897) from 2001 ( Table 1). We were not able to acquire samples of the genera Chatamla (Moore, 1881), Burmeia (Minet, 2002), Mimaporia (Wei and Yen, 2017), or Amana (Walker, 1855), or samples of Heracula discivitta, which was recently moved to the family Pseudobistonidae ( Wang et al. 2019). ...Context 3
... and sequencing were done at StarSEQ GmbH (Mainz, Germany) on Illumina Nextseq 500 Systems with a read length of 150 bp. Exons found in at least 20 of the 33 specimens (with an average of 254 loci per specimen) were used for downstream phylogenetic analyses (Table 1). Sequencing data is available at the NCBI under Bioproject PRJNA684488. ...Context 4
... obtained on average 254 loci and a median of 353 loci per specimen (Table 1). For our phylogenetic analyses, we first used all the 31 specimens that produced some data, including the 6 from Mayer et al. (2021). ...Context 5
... Epicopeiidae, specimens with few loci explain most branches with low support (the exception being Schistomitra described above). When we removed the four specimens with less than 10 loci (see Table 1) from our analyses, the relationships do not change, while the support greatly improved to reach the maximum value of 100/100 on some branches, like for N. moorei and N. nagaensis, or for the relationships between Epicopeia hainseii and E. polydora (Supp Material 1 [online only]). This would indicate that specimens with few loci are only affecting the support values, but not the general topology. ...Context 6
... addition, our E. polydora specimens were found to be genetically identical to E. hainseii, in stark contrast to Zhang et al. (2020). One of our specimens (S47) yielded 1,270 raw loci (Table 1), suggesting large amounts of DNA in the extract. The two species cannot be confused morphologically (see doi:10.5281/zenodo.3769000). ...Similar publications
Although several methods exist for extracting and sequencing historical DNA originating from dry-preserved insect specimens deposited in natural history museums, no consensus exists as to what is the optimal approach. We demonstrate that a customized, low-cost archival DNA extraction protocol (∼€10 per sample), in combination with Ultraconserved El...
Citations
... Within museomics studies, more cost-effective genome reduction methods, such as Ultra Conserved Elements (UCEs) and Anchored Hybrid Enrichment (AHE) are rising in popularity due to their ability to target specific informative loci within a focal group [17][18][19][20]. While standard extraction from dry-preserved specimens may yield adequate DNA for UCE and AHE sequencing [20,21], its success varies based upon specimen preservation. ...
... While standard extraction from dry-preserved specimens may yield adequate DNA for UCE and AHE sequencing [20,21], its success varies based upon specimen preservation. Therefore, exploring the effectiveness of more sensitive DNA extraction methods is essential, especially since their application in entomological collections remains poorly investigated [18]. ...
Although several methods exist for extracting and sequencing historical DNA originating from dry-preserved insect specimens deposited in natural history museums, no consensus exists as to what is the optimal approach. We demonstrate that a customized, low-cost archival DNA extraction protocol (∼€10 per sample), in combination with Ultraconserved Elements (UCEs), is an effective tool for insect phylogenomic studies. We successfully tested our approach by sequencing DNA from scarab dung beetles preserved in both wet and dry collections, including unique primary type and rare historical specimens from internationally important natural history museums in London, Paris and Helsinki. The focal specimens comprised of enigmatic dung beetle genera (Nesosisyphus, Onychothecus and Helictopleurus) and varied in age and preservation. The oldest specimen, the holotype of the now possibly extinct Mauritian endemic Nesosisyphus rotundatus, was collected in 1944. We obtained high-quality DNA from all studied specimens to enable the generation of a UCE-based dataset that revealed an insightful and well-supported phylogenetic tree of dung beetles. The resulting phylogeny propounded the reclassification of Onychothecus (previously incertae sedis) within the tribe Coprini. Our approach demonstrates the feasibility and effectiveness of combining DNA data from historic and recent museum specimens to provide novel insights. The proposed archival DNA protocol is available at DOI 10.17504/protocols.io.81wgbybqyvpk/v3.
... Similar cases abound in other groups of Lepidoptera (e.g. Call et al. 2021). The radiation of Nivaliodes occurred mostly throughout the Pleistocene and was likely to be related to consecutive climatic shifts, dispersal, and local adaptations to high puna habitats in central Peru. ...
A new genus of satyrine butterflies, Nivaliodes gen. nov., is described for three species, all new: Nivaliodes negrobueno sp. nov., Nivaliodes viracocha sp. nov., and Nivaliodes puriq sp. nov. (Lepidoptera: Nymphalidae), with the support of molecular data and adult morphology. A target enrichment-based phylogeny indicates that Nivaliodes gen. nov. is sister to the genus Pherepedaliodes within an extremely diverse Pedaliodes clade of the predominantly Andean subtribe Pronophilina. Although an overwhelming majority of species of this group occur in tropical montane forests, N. negrobueno sp. nov. was discovered in a central Peruvian desert puna at some 4600–4800 m a.s.l., the highest elevation reported for any species of the Pronophilina. Individuals were observed overflying rocky slopes and resting directly on snow-covered surfaces, which is an exceptionally unusual behaviour among butterflies. The other two species of the new genus were found at lower elevations, some 3300–4200 m a.s.l., at the timberline and in puna grassland.
... The field is heavily DNA-driven, but purely molecular approaches can be seen as "reductionistically mistaken" (Casacci et al. 2014). Further, even though studying 'historical' or 'ancient' DNA from old specimen from various collections is more and more promising recently, such approaches are not always straightforward and easy to adopt for every potential study object (Anderung et al. 2008;Ellis 2008;Lis et al. 2011;Call et al. 2021;Raxworthy and Smith 2021). Morphology represents the primary data we use to infer species boundaries and to describe biodiversity (Schlick- Steiner et al. 2007;Steiner et al. 2009;Yazdi et al. 2012), and morphological trait variation shows the highest heritability among various trait types (e.g. ...
For effective conservation management of endangered taxa, it is important to define operational units for conservation. In the absence of detailed genetic analyses, morphology-based taxonomy is often used as a surrogate. The Apollo butterfly, Parnassius apollo, is one of the most endangered butterfly species in Europe (considered as a flagship species) with 26 subspecies rank taxa described from the Carpatho-Pannonian region (Central Europe), often based on old, one-by-one descriptions. We applied landmark-based geometric morphometrics on wing shape to determine the number of morphologically distinguishable groups in the region, based on 949 males and 477 females from 20 Carpatho-Pannonian putative subspecies (both extant and potentially extinct). We found a single division between the Eastern Carpathian populations (described as two subspecies: ssp. transsylvanicus and ssp. rosenius) and the rest of the populations (including our outgroup from the Swiss Alps). Since P. apollo was not observed in the Eastern Carpathians in the last two decades, and the currently known extant populations in the Carpatho-Pannonian region are all located in the Northern Carpathians, our results support a single conservation unit in the region. We suggest that (i) extensive monitoring is needed to reveal whether the unique Eastern Carpathian populations have really gone extinct and (ii) more taxonomical/phylogenetic studies on Central European P. apollo are needed for establishing the taxonomy of the species and efficient conservation strategies. We emphasize that modern integrative taxonomy is not only important for clarifying taxonomical issues, but also for providing basis for sound conservation management.
... Furthermore, smaller specimens may need to be pooled together to attain sufficient amounts of mRNA, and such practice risks mixing up individuals with undetected genetic variation. Unfortunately, a large amount of collected specimens only exist in natural history museum collections, and most of these are ethanol preserved and thus not usable for transcriptomic studies (Call et al. 2021). As taxon sampling is considered one of the most important factors for accurate phylogenetic tree reconstruction (Heath et al. 2008), it would be missing an opportunity to leave the potential of natural history collections untapped. ...
Low-coverage whole-genome sequencing (also known as “genome skimming”) is becoming an increasingly affordable approach to large-scale phylogenetic analyses. While already routinely used to recover organellar genomes, genome skimming is rather rarely utilized for recovering single-copy nuclear markers. One reason might be that only few tools exist to work with this data type within a phylogenomic context, especially to deal with fragmented genome assemblies. We here present a new software tool called Patchwork for mining phylogenetic markers from highly fragmented short-read assemblies as well as directly from sequence reads. Patchwork is an alignment-based tool that utilizes the sequence aligner DIAMOND and is written in the programming language Julia. Homologous regions are obtained via a sequence similarity search, followed by a “hit stitching” phase, in which adjacent or overlapping regions are merged into a single unit. The novel sliding window algorithm trims away any noncoding regions from the resulting sequence. We demonstrate the utility of Patchwork by recovering near-universal single-copy orthologs within a benchmarking study, and we additionally assess the performance of Patchwork in comparison with other programs. We find that Patchwork allows for accurate retrieval of (putatively) single-copy genes from genome skimming data sets at different sequencing depths with high computational speed, outperforming existing software targeting similar tasks. Patchwork is released under the GNU General Public License version 3. Installation instructions, additional documentation, and the source code itself are all available via GitHub at https://github.com/fethalen/Patchwork.
... In phylogenetic studies with historical DNA, cost-effective methods such as Ultra Conserved Elements (UCEs) and Anchored Hybrid Enrichment (AHE) are rising in popularity due to their ability to target specific informative loci within a focal group (Faircloth, 2017;Call et al., 2021;Faircloth et al., 2012;Mayer et al., 2021). While standard extraction from dry-preserved specimens may yield adequate DNA for UCE and AHE sequencing (Gustafson et al., 2020;Mayer et al., 2021), its success varies based on preservation. ...
Although several methods exist for extracting and sequencing historical DNA originating from drypreserved insect specimens deposited in natural history museums, no consensus exists as to what is the optimal approach. We demonstrate that a customized, low-cost archival DNA extraction protocol (∼ €10 per sample), in combination with Ultraconserved Elements (UCEs), is an effective tool for insect phylogenomic studies. We successfully tested our approach by sequencing DNA from scarab dung beetles preserved in both wet and dry collections, including unique primary type and rare historical specimens from internationally important natural history museums in London, Paris and Helsinki. The focal specimens comprise enigmatic dung beetle genera ( Nesosisyphus, Onychotechus and Helictopleurus ) that varied in age and preservation. The oldest specimen, the holotype of the now possibly extinct Mauritian endemic Nesosisyphus rotundatus , was collected in 1944. We obtained high-quality DNA from all studied specimens to enable the generation of a UCE-based dataset that revealed an insightful and well-supported phylogenetic tree of dung beetles. The resulting phylogeny suggested the reclassification of Onychotechus (previously incertae sedis ) within the tribe Coprini. Our approach demonstrates the feasibility and effectiveness of combining DNA data from historic and recent museum specimens to provide novel insights. The proposed archival DNA protocol is available at DOI 10.17504/protocols.io.81wgbybqyvpk/v1
Highlights
We combined custom low-cost archival DNA extractions and Ultraconserved Element phylogenomics
DNA from rare museum specimens of enigmatic dung beetles revealed their phylogenetic connections
Genomic data was obtained from the holotype of a potentially extinct monoinsular endemic species
Genomic data allowed a rare and enigmatic species of previously unknown affinity to be classified
The morphology of museum specimens remained intact following non-destructive DNA extraction
Abstract Figure
... These methods are particularly useful in phylogenomics, as they focus on specific genomic regions that have been shown to be phylogenetically informative (Kadlec et al. 2017;Toussaint et al. 2018). In particular, TE has been successfully applied to phylogenomics of butterflies and moths Espeland et al. 2019;Homziak et al. 2019;Mayer et al. 2021). ...
... The resulting reads tend to range from 50 to 150 bp (Sproul and Maddision 2017;Korlević et al. 2021;Mullin et al. 2022), leading to difficulties with assembly. Recent studies have shown that it is possible to extract phylogenetically useful data from such fragmented genomes using both TE St Laurent et al. 2018;Espeland et al. 2019;Call et al. 2021) and WGS (Cong et al. 2017;Sproul and Maddision 2017;Li et al. 2019;Zhang et al. 2019;Cong et al. 2021;Grewe et al. 2021;Twort et al. 2021;Mullin et al. 2022). However, as museomics is such a young field, there is no consensus on which method to access genomic information is the most suitable. ...
... The relationships, not only within these two clades but also between them and Pseudobistonidae, a close family, were unclear until recently (Minet 2002;Rajaei et al. 2015;Wei and Yen 2017;Wang et al. 2019;Zhang et al. 2020). In a previous study, we conducted a phylogenetic analysis using TE on museum specimens of Epicopeiidae, Sematuridae and Pseudobistonidae (Call et al. 2021). Here, we performed a WGS study on Epicopeiidae and Sematuridae. ...
There are various possibilities for sequencing highly degraded DNA, such as target enrichment (TE), or whole-genome sequencing (WGS). Here we compare TE and WGS methods using old museum specimens of two families of moths in the superfamily Geometroidea: Epicopeiidae and Sematuridae. Until recently, the relationships of these two families were unclear, as few studies had been done. Recently two studies used the TE approach, either on relatively fresh specimens, or on old museum specimens. Here, we aim to increase the sampling of the families Epicopeiidae and Sematuridae from museum specimens using the WGS method. We show that both sequencing methods give comparable results, but, unsurprisingly, WGS recovers more data. By combining TE and WGS data, we confirm that Sematuridae are sister to Pseudobistonidae+Epicopeiidae. Relationships of genera within the families are well supported. With the costs of WGS decreasing, we suggest that using low-coverage whole genome sequencing is becoming an increasingly viable option in the phylogenomics of insects.
... Consequently, molecular approaches have been restricted, on one hand, to sequencing technologies (e.g., Sanger sequencing) (Hajibabaei et al., 2006;Hebert et al., 2013) and, on the other hand, were limited to quality materials (e.g., freshly collected samples, proper killing agent, etc.). However, recently, next-generation sequencing (NGS) technologies have made the DNA in museum specimens more accessible, either through whole-genome sequencing (WGS) (Allio et al., 2020;Call et al., 2021;Sproul & Maddison, 2017;Twort et al., 2021) or genome reduction methods (Breinholt et al., 2018;Mayer et al., 2021;Suchan et al., 2016). These advanced sequencing approaches have opened a new field with great potential for studying the evolutionary history of taxa that are difficult to collect: museomics . ...
Here, we present multi-locus sequencing results from the enigmatic Afrotropical monotypic genus Egybolis Boisduval (occurring in East-and South Africa-previously placed in the subfamily Catocalinae, Noctuidae). Model-based phylogenetic analysis places Egybolis within a strongly supported clade comprising four Old World Tropical genera Cocytia Boisduval, Avatha Walker, Anereuthina Hübner, and Serrodes Guenée from the family Erebidae, subfamily Erebinae. Hence, we propose to formally assign the monotypic genus Egybolis to the subfamily Erebinae and the tribe Cocytiini. Timing of divergence analysis reveals the late Oligocene origin around 25 million years ago (Ma) for the tribe Cocytiini, and an early Miocene (~21 Ma) for the split between Cocytia and Egybolis.
... However, numerous DNA extraction techniques for old insect specimens have been developed (Gilbert et al. 2007;Thomsen et al. 2009;Ballare et al. 2019). Next generation sequencing would help to obtain DNA sequences from historical specimens (Nazari et al. 2016;Prosser et al. 2016;Sproul and Maddison 2017;Call et al. 2021), but a high DNA quantity is required (Goodwin et al. 2016). According to our results, the DNA concentration of the samples in this study was not high enough for the sequencing requirement. ...
Bombus flavescens Smith is one of the most widespread bumblebee species in the Oriental region. Due to colour polymorphisms, this species or species-complex has been a challenge for taxonomy. This study aims to assess the taxonomic status of the flavescens-complex using evidence from COI barcodes and morphology. We then reconstruct its biogeographic history from a phylogenetic analysis of populations across the current range, combining COI with 16S and nuclear PEPCK data. Despite a large range of polymor-phisms across its distribution, the results show that B. flavescens is a single species based on algorithmic species delimitation methods, and it is clearly separated from its sister species, B. rotundiceps Friese. We suggest that B. flavescens diverged from its sister lineage in the Himalaya and dispersed into Southeast Asia in the Pleistocene. Conservation of the widespread B. flavescens will need to consider its several unique island populations.
... In previous studies, only a few genetic markers on these taxa were successfully sequenced, and the genetic information was not conclusive. However, new protocols for generating whole-genome sequencing data from museum samples and old DNA extracts have been successfully implemented for other Lepidoptera (Call et al., 2021). These developments have paved the way towards increasing the available genetic information for museum specimens, including taxa that are rare, extinct, or otherwise difficult to collect. ...
Geometrid moths, the second largest radiation of Lepidoptera, have been the target of extensive phylogenetic studies. Those studies have flagged several problems in tree topol-ogy that have remained unanswered. We address three of those: (i) deep nodes of Geome-tridae (subfamilies Sterrhinae + Larentiinae, or Sterrhinae alone as sister to all other subfamilies), (ii) the taxonomic status of subfamily Orthostixinae and (iii) the systematic position of the genus Eumelea (classified in Desmobathrinae: Eumeleini or incertae sedis earlier). We address these questions by using a phylogenomic approach, a novel method on these moths, with up to 1000 protein-coding genes extracted from whole-genome shotgun sequencing data. Our datasets include representatives from all geometrid subfamilies and we analyse the data by using three different tree search strategies: partitioned models, GHOST model and multispecies coalescent analysis. Despite the extensive data, we found incongruences in tree topologies. Eumelea did not associate with Desmobathrinae as suggested earlier, but instead, it was recovered in three different phylogenetic positions, either as sister to Oenochrominae, Geometrinae or as sister to Oenochrominae + Geometrinae. Orthostixinae, represented by its type species, falls within Desmobathrinae. We propose the following taxonomic changes: we raise Eumeleini to subfamily rank as Eumeleinae stat. nov. and we treat Orthostixinae as a junior synonym of Desmobathrinae syn. nov. K E Y W O R D S
... When targeting species with populations that are either locally extinct or severely threatened, museum specimens might still be available, and their genomic information is possible to access with highthroughput sequencing techniques that do not rely on PCR and that are amenable with highly fragmented DNA (Call et al., 2021;Twort et al., 2021). Such data are valuable because they can be used as baseline for the analyses of additional contemporary samples from surrounding thriving populations (Bakker et al., 2020). ...
... Alternatively, target sequence capture uses probe baits designed to extract and sequence targeted genomic regions in the laboratory, even from old and degraded samples (Call et al., 2021). However, the design of probes requires a good genomic knowledge of the study taxa and synthesising the probe baits can be expensive for small-scale studies (Andermann et al., 2020). ...
1. Genomic data are not yet widely used in insect conservation practice. Here, with a focus on butterflies, we aim to identify the strengths, limitations and remaining gaps between the fields of population genomics and insect conservation management. Based on a literature search complemented with expert opinion, we discuss avenues for translating research into practice.
2. We found that current genomic methodologies available for insect management enhance the assessment of cryptic diversity and facilitate the inference of historical population trends (temporal monitoring) by using even degraded material from historical collections.
3. Discovering and tracking adaptive genetic variation linked to increased survival and fitness is a relatively young research field, but we highlight it as a promising tool in future insect management actions.
4. We highlight recent case studies where population genomics have guided butterfly conservation. One conclusion from our advice from our non-exhaustive survey of expert opinion is to establish meaningful partnerships between researchers and practitioners, starting at the stage of project planning. Genomics is an informative tool for securing legal protection of unique populations and may offer guidance in future conservation translocations and captive breeding programmes.
5. Although insect conservation usually targets habitats, genomic guidance focusing on populations of flagship and umbrella taxa is a straightforward path to connect species-specific and habitat conservation initiatives. We conclude that there is urgency in reporting insect conservation actions guided by genomic data, both successful and unsuccessful. This will lead to constructive feedback between fields and the establishment of standardised methodologies.
