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Recovering the evolutionary history of crowned pigeons (Columbidae: Goura): Implications for the biogeography and conservation of New Guinean lowland birds

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Assessing the relative contributions of immigration and diversification into the buildup of species diversity is key to understanding the role of historical processes in driving biogeographical and diversification patterns in species-rich regions. Here, we investigated how colonization, in situ speciation, and extinction history may have generated the present-day distribution and diversity of Goura crowned pigeons (Columbidae), a group of large forest-dwelling pigeons comprising four recognized species that are all endemic to New Guinea. We used a comprehensive geographical and taxonomic sampling based mostly on historical museum samples, and shallow shotgun sequencing, to generate complete mitogenomes, nuclear ribosomal clusters and independent nuclear conserved DNA elements. We used these datasets independently to reconstruct molecular phylogenies. Divergence time estimates were obtained using mitochondrial data only. All analyses revealed similar genetic divisions within the genus Goura and recovered as monophyletic groups the four species currently recognized, providing support for recent taxonomic changes based on differences in plumage characters. These four species are grouped into two pairs of strongly supported sister species, which were previously not recognized as being close relatives: Goura sclaterii with Goura cristata, and Goura victoria with Goura scheepmakeri. While the geographical origin of the Goura lineage remains elusive, the crown age of 5.73 Ma is consistent with present-day species diversity being the result of a recent diversification within New Guinea. Although the orogeny of New Guinea's central cordillera must have played a role in driving diversification in Goura, cross-barrier dispersal seems more likely than vicariance to explain the speciation events having led to the four current species. Our results also have important conservation implications. Future assessments of the conservation status of Goura species should consider threat levels following the taxonomic revision proposed by del Hoyo and Collar (HBW and BirdLife International illustrated checklist of the birds of the world 1: non-passerines, 2014), which we show to be fully supported by genomic data. In particular, by distinguishing G. sclaterii from G. scheepmakeri seems to be particularly relevant.
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... Toussaint et al., 2014Toussaint et al., , 2021. This is important in the context of speciation and phylogeography, because the Central Range has been suggested to play a key role in the diversification of several taxonomic groups on the island, namely water beetles (Toussaint et al., 2014(Toussaint et al., , 2021, rainbow fishes (Unmack et al., 2013), green pythons (Rawlings & Donnellan, 2003;Natusch et al., 2020Natusch et al., , 2021, freshwater turtles (Georges et al., 2014), lizards (Tallowin et al., 2018), skinks (Slavenko et al., 2020), toxic birds of the genus Pitohui Lesson, 1831 (Dumbacher & Fleischer, 2001), crown pigeons (Bruxaux et al., 2018) and tree-kangaroos (Eldridge et al., 2018). ...
... Toussaint et al., 2014), emphasizing the importance of geography and orogeny on early speciation in this group (see also : Irestedt et al., 2009). Similar temporal discrepancies between a Miocene origin and a Pleistocene onset of diversification have also been observed, for example, in water beetles, birds and mammals (Toussaint et al., 2014;Schweizer et al., 2015;Bruxaux et al., 2018;Eldridge et al., 2018;Joseph et al. 2020). However, it remains uncertain whether diversification was solely triggered by climatic processes in the Pleistocene as suggested for other groups. ...
... Our data suggest a Pleistocene origin for the apoda-minorraggiana clade, which postdates both the Central Range's uplift that started c. 5 Mya (Toussaint et al., 2021) and the formation of Bird's Neck isthmus c. 5-3 Mya (Charlton, 2000) that may have directly promoted diversification and geographical separation in Paradisaea as in other groups (see e.g. Bruxaux et al., 2018;Natusch et al., 2020;Toussaint et al., 2021). Moreover, the reconstruction of ancestral areas shows a westward range expansion along the eastern Central Range within the apoda-minor-raggiana clade. ...
Article
IN PRESS: Birds-of-paradise represent a textbook example for geographical speciation and sexual selection. Perhaps the most iconic genus is Paradisaea, which is restricted to New Guinea and a few surrounding islands. Although several species concepts have been applied in the past to disentangle the different entities within this genus, no attempt has been made so far to uncover phylogeographical patterns based on a genetic dataset that includes multiple individuals per species. Here, we applied amplicon sequencing for the mitochondrial fragment Cytb for a total of 69 museum specimens representing all seven Paradisaea species described and inferred both phylogenetic relationships and colonization pathways across the island. Our analyses show that the most recent common ancestor of the diverging lineages within Paradisaea probably originated in the Late Miocene in the eastern part of the Central Range and suggest that tectonic processes played a key role in shaping the diversification and distribution of species. All species were recovered as monophyletic, except for those within the apoda–minor–raggiana clade, which comprises the allopatric and parapatric species P. apoda, P. minor and P. raggiana. The comparatively young divergence times, together with possible instances of mitochondrial introgression and incomplete lineage sorting, suggest recent speciation in this clade.
... A conventional method was used to determine the complete mitogenome sequence. To amplify the complete mitogenome of C. hodgsonii, PCR primers were designed based on the mitogenomic sequence of other Columbidaes [4,6,9,15,19,31] (Table S1). Amplifications were performed with an Eppendorf AG 22331 Thermal Cycler (Berlin) in a total volume of 50 μL containing 25 μL of 2X Taq PCR Master Mix (Sangon Biotech, Shanghai, China), 3 μL of DNA template, 1.5 μL of each primer, and 19 μL of sterilized ddH 2 O. PCR was performed under the following conditions: pre-denaturation at 94 °C for 5 min; 30-35 cycles of denaturation at 94 °C for 30 s, annealing at 50-60 °C (depending on primer combination) for 30 s, and extension at 72 °C for 2-4 min (depending on the fragment length), followed by extension at 72 °C for 10 min. ...
... The complete mitogenome of C. hodgsonii is 17,477 base pairs (bp) in length, which is consistent with the length of other sequenced Columbidae species [13,14,19]. This species has the longest mitogenome of any Columbidae species [6,15,31]. The C. hodgsonii mitogenome was a closed circular molecule and contained 13 PCGs, 22 tRNAs, two rRNAs, and one CR. ...
... In addition, 19 intergenic spacers ranging from 1 to 15 bp in length were observed between mitochondrial regions, with the longest space found between ND1 and tRNA-Ile. These features are highly similar to those of other birds of the family Columbidae [6,9,19,31]. ...
Article
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The speckled wood-pigeon, Columba hodgsonii, is mainly distributed in Bhutan, China, India, Laos, Myanmar, Nepal, Pakistan, and Thailand. Although there are several studies on birds in the family Columbidae, no study has focused on C. hodgsonii, a member of this family. Therefore, this study aimed to clarify the phylogenetic status of C. hodgsonii. The complete mitochondrial genome (mitogenome) of C. hodgsonii was sequenced and characterized and compared with those of other Columba species. The C. hodgsonii mitogenome was found to be 17,477 bp in size and contained 13 PCGs, two rRNAs, 22 tRNAs, and one CR. Of the 37 genes encoded by the C. hodgsonii mitogenome, 28 were on the heavy strand and nine were on the light strand. Twelve PCGs were initiated by ATN codons and one PCG harbored an incomplete termination codon (T-). The base composition of C. hodgsonii PCGs was A = 29.44%, T = 24.37%, G = 12.43%, and C = 33.76%. For the whole mitogenome, including PCGs, rRNAs, tRNAs, and the control region, the AT-skew was positive, and the GC-skew was negative. Phylogenetic analysis based on the base sequences of 13 PCGs from 28 Columbidae species and one outgroup using maximum likelihood and Bayesian inference indicated that C. hodgsonii belongs to the genus Columba and that the family Columbidae is monophyletic.
... Unlike de novo whole genome sequencing, this approach is suitable when there are limited amounts of DNA, such as degraded DNA from museum specimens. However, with very few exceptions (e.g., Bruxaux et al., 2018), most studies have only obtained mitochondrial genomes and/or a small number of nuclear loci from low coverage shotgun sequencing of museum specimens (e.g., Besnard et al., 2016;Hung et al., 2013;Kanda et al., 2016). This is likely due to the high copy number of the mitochondrial genome in eukaryotic cells in many taxa, making coverage of mitochondrial sequences much greater than nuclear sequences which can allow assembly of mitochondria from low coverage shotgun sequencing, even from degraded DNA (Besnard et al., 2016). ...
... Furthermore, low coverage shotgun sequencing from fresh tissue can also be used to extract many different data types (e.g., Zimmer and Wen, 2015). However, the extremely low DNA quantity (2.8 ng) and quality (fragment size could not be determined) of T. charltonii (Fig. S1) appeared to result in uneven coverage of that genome (see also Bruxaux et al., 2018). While we were able to recover the complete mitochondrial genome for T. charltonii, coverage elsewhere was sporadic. ...
... In spite of this, we were still able to place this species robustly with all of our datasets. Deeper sequencing might increase the recovery of nuclear regions, but it seems likely that the low amounts of input DNA created biases in library construction and that deeper coverage would not substantially improve our results (Bruxaux et al., 2018). Instead, for such extremely low quantity and quality DNA, sequence capture for targeted nuclear regions may work better (Blaimer et al., 2016;Knapp and Hofreiter, 2010), even if sequence capture is not always ideal (as discussed above). ...
Article
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Next-generation DNA sequencing (NGS) offers a promising way to obtain massive numbers of orthologous loci to understand phylogenetic relationships among organisms. Of particular interest are old museum specimens and other samples with degraded DNA, where traditional sequencing methods have proven to be challenging. Low coverage shotgun sequencing and sequence capture are two widely used NGS approaches for degraded DNA. Sequence capture can yield sequence data for large numbers of orthologous loci, but it can only be used to sequence genomic regions near conserved sequences that can be used as probes. Low coverage shotgun sequencing has the potential to yield different data types throughout the genome. However, many studies using this method have often generated mitochondrial sequences, and few nuclear sequences, suggesting orthologous nuclear sequences are likely harder to recover. To determine the phylogenetic position of the galliform genus Tropicoperdix, whose phylogenetic position is currently uncertain, we explored two strategies to maximize data extraction from low coverage shotgun sequencing from approximately 100-year-old museum specimens from two species of Tropicoperdix. One approach, a simple read mapping strategy, outperformed the other (a reduced complexity assembly approach), and allowed us to obtain a large number of ultraconserved element (UCE) loci, relatively conserved exons, more variable introns, as well as mitochondrial genomes. Additionally, we demonstrated some simple approaches to explore possible artifacts that may result from the use of degraded DNA. Our data placed Tropicoperdix within a clade that includes many taxa characterized with ornamental eyespots (peafowl, argus pheasants, and peacock pheasants), and established relationships among species within the genus. Therefore, our study demonstrated that low coverage shotgun sequencing can easily be leveraged to yield substantial amounts and varying types of data, which opens the door for many research questions that might require information from different data types from museum specimens.
... Johnson & Clayton, 2000;Johnson, 2004; or just focused on few lineages Jønsson et al., 2011;. Bruxaux et al., 2018). The only study so far having a rather consequent sampling (39 among the 41 genera) and using a few nuclear and mitochondrial markers allowed inferring a biogeographical scenario involving an ancestral distribution in Gondwanaland with an initial radiation around 54.4 Ma (million years ago). ...
... Table 2) and established the sampling to obtain at least one species per genus, and at least one species per intra-genus clade when the monophyly of the genus was discussed. Extractions and sequencing were performed as previously described (Bruxaux et al., 2018; KX902237 and NC_001323, respectively) as outgroups for mitochondrial analyses. Pterocles belongs to Pteroclididae that is known as a putatively close relative family of Columbidae, while Gallus (Phasianidae) belongs to a more distant lineage . ...
... Mitogenomes were reconstructed as described in Bruxaux et al. (2018; Chapter 2), and MapDamage was not used for mitochondrial DNA as it was found to not change consensus results in this study. ...
Thesis
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Pigeons and doves (Columbidae) belong to a species-rich worldwide-distributed family and are of major historical and ecological importance. We generated phylogenetic hypotheses from museum samples to clarify the diversification of the family, which probably took place between mid-Eocene and mid-Miocene, where all extant clades were already established. Almost 60% of species are present on islands, and these entities probably played a role in the dispersal through stepping-stones movement between continents. On the other side, speciation rates vary following a normal distribution and islands do not seem to have played an important role in diversification. Nevertheless, the highest Columbidae species-richness is reached in South-East Asia and Australasia, regions especially rich in islands. New Guinea, in particular, hosts an impressive diversity. The biggest Columbidae, belonging to the genus Goura (crowned pigeons), are endemic to this island. Our analyses suggest that their diversification probably started within New Guinea around 5.73 Ma. Geological events such as the cordillera orogeny probably played a major role by splitting ancestral distribution, while more recent dispersals over barriers may have also led to the settlement of isolated populations that promoted diversification. This work allowed the generation of phylogenetic hypotheses, which will allow answering numerous questions regarding Columbidae biogeography and diversification.
... A series of recent papers on different groups of animals (e.g., [13,[21][22][23][24][25][26][27][28][29][30][31][32][33][34][35][36][37][38][39][40]; summaries in [33] and [41]) and plants (see e.g., [42] and references therein) identifies three major processes fueling biological diversification in New Guinea: (1) ancient diversification events on smaller proto Papuan islands including a proto Papuan Peninsula, or on the northern part of the Australian craton (see [27,33,[43][44][45]), (2) more recent but substantial lineage diversification connected to the New Guinea orogeny (e.g., [41,46]), or (3) formation of land in the north and south of the central highlands by various processes (volcanism, accretion/uplift of island arcs and ophiolites). The latter includes complex phylogeographic processes across the New Guinea lowland rainforest belts that led to the formation of allopatric species pairs (e.g., crowned pigeons: [47]) and orogeny related vicariance [48] (see Table 4). ...
... In a series of innovative papers, biogeographers sought to directly link distribution patterns to such geological events, strongly motivating increased exchange between biologists and geologists over the past two decades (e.g., [39,41,[49][50][51][52]). This is certainly the case to a large extent, but many clade diversification events might also result from biotic exchange across a more or less existing landmass, although composite and gaining altitude, as suggested by few recent analyses of insects [26,41], frogs [32] and birds [25,29,47]. In that case, and related to the above process (3), the extant geography of the island might be structuring clades of species more than the geological formation on which they occur (see [41]). ...
Article
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Background The New Guinean archipelago has been shaped by millions of years of plate tectonic activity combined with long-term fluctuations in climate and sea level. These processes combined with New Guinea’s location at the tectonic junction between the Australian and Pacific plates are inherently linked to the evolution of its rich endemic biota. With the advent of molecular phylogenetics and an increasing amount of geological data, the field of New Guinean biogeography begins to be reinvigorated. Results We inferred a comprehensive dated molecular phylogeny of endemic diving beetles to test historical hypotheses pertaining to the evolution of the New Guinean biota. We used geospatial analysis techniques to compare our phylogenetic results with a newly developed geological terrane map of New Guinea as well as the altitudinal and geographic range of species ( https://arcg.is/189zmz ). Our divergence time estimations indicate a crown age (early diversification) for New Guinea Exocelina beetles in the mid-Miocene ca. 17 Ma, when the New Guinean orogeny was at an early stage. Geographic and geological ancestral state reconstructions suggest an origin of Exocelina ancestors on the eastern part of the New Guinean central range on basement rocks (with a shared affinity with the Australian Plate). Our results do not support the hypothesis of ancestors migrating to the northern margin of the Australian Plate from Pacific terranes that incrementally accreted to New Guinea over time. However, our analyses support to some extent a scenario in which Exocelina ancestors would have been able to colonize back and forth between the amalgamated Australian and Pacific terranes from the Miocene onwards. Our reconstructions also do not support an origin on ultramafic or ophiolite rocks that have been colonized much later in the evolution of the radiation. Macroevolutionary analyses do not support the hypothesis of heterogeneous diversification rates throughout the evolution of this radiation, suggesting instead a continuous slowdown in speciation. Conclusions Overall, our geospatial analysis approach to investigate the links between the location and evolution of New Guinea’s biota with the underlying geology sheds a new light on the patterns and processes of lineage diversification in this exceedingly diverse region of the planet.
... A D-loop was found between tRNA-Glu and tRNA-Phe, and was 1,862 bp in length, with a A+T content of 61.76%, an AT-skew of -0.0139, and a GC-skew of -0.3764 (Table 5). Duplication and rearrangement of the avian mitochondrial genomes is common, but T. curvirostra had only one D-loop, which is similar to that present in other known mitogenomes of Columbidae (Pacheco et al. 2011;Eberhard and Wright 2016;Bruxaux et al. 2018). ...
Article
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Members of the genus Treron (Columbidae) are widely distributed in southern Asia and the Indo-Malayan Region but their relationships are poorly understood. Better knowledge of the systematic status of this genus may help studies of historical biogeography and taxonomy. The complete mitochondrial genome of T. curvirostra was characterized, a first for the genus. It is 17,414 base pairs in length, containing two rR-NAs, 22 tRNAs, 13 protein coding genes (PCGs), and one D-loop with a primary structure that is similar to that found in most members of Columbidae. Most PCGs start with the common ATG codon but are terminated by different codons. The highest value of the Ka/Ks ratio within 13 PCGs was found in ATP8 with 0.1937, suggesting that PCGs of the mitochondrial genome tend to be conservative in Columbidae. Moreover, the phylogenetic relationships within Columbidae, which was based on sequences of 13 PCGs, showed that (T. curvirostra + Hemiphaga novaeseelandiae) were clustered in one clade, suggesting a potentially close relationship between Treron and Hemiphaga. However, the monophyly of the subfamilies of Columbidae recognized by the Interagency Taxonomic Information System could not be corroborated. Hence, the position of the genus Treron in the classification of Columbidae may have to be revised.
... Thus far, limited amounts of phylogenomic data have been used in megaphylogenies, although it is clear that "phylogenomic megaphylogenies" have the potential to yield a strongly supported tree when genome-scale data become available for a sufficient number of species. [55] loci Jarvis et al. [37] NEORNITHES 48 YES Whole genomes Sun et al. [40] Phasianidae (peafowl) 15 5k UCE probe set Prum et al. [38] NEORNITHES 197 YES AHE probe set Bryson et al. [57] Passerellidae 30 YES 5k UCE probe set Hosner et al. [58] Cracidae 23 5k UCE probe set Hosner et al. [21] Phasianidae 90 5k UCE probe set Manthey et al. [59] Piranga 11 YES 5k UCE probe set McCormack et al. [22] Aphelocoma 1 (3) 5k UCE probe set Meiklejohn et al. [60] Phasianidae (gallopheasants) 18 5k UCE probe set Ottenburghs et al. [61] Anatidae-Anserini 19 YES Whole genomes Persons et al. [62] Phasianidae (grouse) 11 5k UCE probe set Zarza et al. [63] Aphelocoma 3 YES 5k UCE probe set Burga et al. [64] Phalacrocorax 7 YES Whole genomes Hosner et al. [42] Phasianidae 115 YES 5k UCE probe set Reddy et al. [39] NEORNITHES 235 YES legacy with data mining Wang et al. [65] Phasianidae 20 YES 5k UCE probe set White et al. [66] Nyctibiidae 12 YES 5k UCE probe set Yonezawa et al. [67] PALAEOGNATHAE YES legacy with data mining Andersen et al. [68] Alcedinidae 21 YES 5k UCE probe set Bruxaux et al. [69] Goura 6 YES Subset of UCE and AHE loci Campillo et al. [70] Arachnothera 17 YES 5k UCE probe set Chen et al. [71] Phasianidae 27 YES 5k UCE probe set Musher & Cracraft [72] Pachyramphus 18 YES 2.5K/5k UCE probe set Smith et al. 2018 [73] Psittaculidae-Loriini 54 YES 5k UCE probe set Younger et al. [74] Newtonia 4 YES 5k UCE probe set Sackton et al. [75] PALAEOGNATHAE 15 YES Whole genomes 1 Redundant trees were omitted. 2 UCE (Ultraconserved Element) probe sets are described at https://www. ultraconserved.org/; ...
Article
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It has long been appreciated that analyses of genomic data (e.g., whole genome sequencing or sequence capture) have the potential to reveal the tree of life, but it remains challenging to move from sequence data to a clear understanding of evolutionary history, in part due to the computational challenges of phylogenetic estimation using genome-scale data. Supertree methods solve that challenge because they facilitate a divide-and-conquer approach for large-scale phylogeny inference by integrating smaller subtrees in a computationally efficient manner. Here, we combined information from sequence capture and whole-genome phylogenies using supertree methods. However, the available phylogenomic trees had limited overlap so we used taxon-rich (but not phylogenomic) megaphylogenies to weave them together. This allowed us to construct a phylogenomic supertree, with support values, that included 707 bird species (~7% of avian species diversity). We estimated branch lengths using mitochondrial sequence data and we used these branch lengths to estimate divergence times. Our time-calibrated supertree supports radiation of all three major avian clades (Palaeognathae, Galloanseres, and Neoaves) near the Cretaceous-Paleogene (K-Pg) boundary. The approach we used will permit the continued addition of taxa to this supertree as new phylogenomic data are published, and it could be applied to other taxa as well.
... Yet only one study analysing genetic population structure of this species has been conducted [7]. Previous genetic studies of the Columbidae family of birds primarily focused on phylogeny reconstruction [8][9][10]. Also, intraspecific genetic variation of the Feral Pigeon Columba livia, was extensively examined [11][12][13][14]. ...
... Mitochondrial genomes (mitogenomes), because of their advantageous characteristics (small size, simple organization, lack of recombination, rapid nucleotide substitution), have been extensively applied in phylogenetic studies of birds since the report of chicken mitogenome (e.g. Desjardins et al., 1990;Cooper et al., 2001;Paton et al., 2002;Morgan-Richards et al., 2008;Pratt et al., 2009;Nabholz et al., 2010;Pacheco et al., 2011;Zhou et al., 2014;Bruxaux et al., 2018;Tamashiro et al., 2019). Some researchers proposed that the molecular studies using only mtDNA markers have limitations in testing phylogenetic hypotheses, because incomplete lineage sorting, adaptive introgression, demographic disparities or sex-biased asymmetries exist in many animal systems (Toews and Brelsford, 2012). ...
Article
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Coraciiformes contains more than 200 species with great differences on external morphology and life-style. The evolutionary relationships within Coraciiformes and the phylogenetic placement of Coraciiformes in Aves are still questioned. Mitochondrial genome (mitogenome) sequences are popular markers in molecular phylogenetic studies of birds. This study presented the genome characteristics of three new mitogenomes in Coraciiformes and explored the phylogenetic relationships among Coraciiformes and other five related orders with mitogenome data of 30 species. The sizes of three mitogenomes were 17,383 bp (Alcedo atthis), 17,892 bp (Halcyon smyrnensis) and 17,223 bp (Megaceryle lugubris). Each mitogenome contained one control region and 37 genes that were common in vertebrate mitogenomes. The organization of three mitogenomes was identical to the putative ancestral gene order in Aves. Among 13 available Coraciiform mitogenomes, 12 protein coding genes showed indications of negative selection, while the MT-ND6 presented sign of positive selection or relaxed purifying selection. The phylogenetic results supported that Upupidae and Bucerotidae should be separated from Coraciiformes, and that Coraciiformes is more closely related to Piciformes than to Strigiformes, Trogoniformes and Cuculiformes. Our study provide valuable data for further phylogenetic investigation of Coraciiformes.
... The island of New Guinea is a region of immense biodiversity and complex topography with numerous areas of endemism (Beehler, 2007;Polhemus, 2007). However, the island is large, remote, and topographically complex, so sampling across the geographic range of some widespread species has been limited (Bruxaux et al., 2018). For https://doi.org/10. ...
Article
The large and enigmatic New Guinean pythons in the genus Leiopython are harvested from the wild to supply the international trade in pets. Six species are currently recognized (albertisii, biakensis, fredparkeri, huonensis, meridionalis, montanus) but the taxonomy of this group has been controversial. We combined analysis of 421 nuclear loci and complete mitochondrial genomes with morphological data to construct a detailed phylogeny of this group, understand their biogeographic patterns and establish the systematic diversity of this genus. Our molecular genetic data support two major clades, corresponding to L. albertisii and L. fredparkeri, but offer no support for the other four species. Our morphological data also only support two species. We therefore recognize L. albertisii and L. fredparkeri as valid species and place L. biakensis, L. meridionalis, L. huonensis and L. montanus into synonymy. We found that L. albertisii and L. fredparkeri are sympatric in western New Guinea; an atypical pattern compared to other Papuan species complexes in which the distributions of sister taxa are partitioned to the north and south of the island’s central mountain range. For the purpose of conservation management, overestimation of species diversity within Leiopython has resulted in the unnecessary allocation of resources that could have been expended elsewhere. We strongly caution against revising the taxonomy of geographically widespread species groups when little or no molecular genetic data and only small morphological samples are available.
... Since UCEs are highly conserved, they are used as target to probes so that the polymorphic flanking regions can be used to reconstruct phylogenies. Therefore, UCEs have been used at many comparison levels among organisms, from population to large groups, for all sort of animals, as for example invertebrates Zhang et al., 2018a,b), amphibians (Streicher et al., 2018), fishes (Faircloth et al., 2013;Alfaro et al., 2018;Roxo et al., 2019), non-avian reptiles (Crawford et al., , 2015, birds (Barker, 2017;Bruxaux et al., 2018;Smith et al., 2014), and mammals , proving to be highly resolute and allowing the construction of strongly supported phylogenies. Studies with fishes had shown high resolution in both ancient and recent clades, as for actinopterygians (Faircloth et al., 2013), Neotropical cichlids (Burress et al., 2018), acantomorphs (Alfaro et al., 2018), and siluriforms (Roxo et al., 2019;Ochoa et al. 2020). ...
Article
The Neotropical fish family Serrasalmidae comprises 16 extant genera and 101 species widespread through major Neotropical rivers with relevant importance for regional fisheries and aquaculture. The monophyly of Serrasalmidae and the recognition of three main clades are recurrent between morphological and molecular phylogenies. However, both intergeneric and interspecific relationships within each of those clades remain uncertain. Here, we used 81 terminals of 69 species (70%) and all 16 genera of Serrasalmidae to sequence 1,553 loci of ultraconserved elements (UCEs), multiple nuclear loci widely applied in phylogenetic studies, and performed maximum likelihood, Bayesian, and species tree analyses. We obtained highly supported phylogenies in all applied methods corroborating the monophyly of Serrasalmidae and the three-clade hypotheses herein proposed as two subfamilies and two tribes: (Colossomatinae (Serrasalminae (Myleini + Serrasalmini))). Morphological features for each subfamily involve the absence (Colossomatinae) or presence (Serrasalminae) of a pre-dorsal spine. Morphological diagnoses among tribes include the pre-dorsal spine being continuous (Myleini) or discontinuous (Serrasalmini) relative to the first unbranched dorsal-fin ray. Our results highlight the complexity of the relationships especially the non-monophyly of Myleus, Mylesinus, Myloplus, Tometes, and Utiaritichthys within Myleini, as well as of Serrasalmus and Pristobrycon within Serrasalmini.
... Instead, the conserved nature of the sequences allows probes that hybridize to UCEs to be used for sequence capture in many different vertebrates; most or all of the phylogenetic information in UCE datasets actually reflects the less-conserved sequences that flank the conserved core of the UCE Faircloth et al. 2012;McCormack et al. 2012McCormack et al. , 2013. Analyses of UCEs have begun to advance our understanding of avian systematics Smith et al. (2014) Passeriformes 5 Bruxaux et al. (2017) used genome skimming followed by bioinformatic extraction of UCE loci (and other loci) rather than sequence capture at all levels, from the deepest branches (e.g., McCormack et al. 2013;Gilbert et al. 2018) to the tips of the tree (Table 2). UCEs even appear to be useful at phylogeographic scales (Harvey et al. 2016;Smith et al. 2014). ...
Chapter
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Reconstructing relationships among extant birds (Neornithes) has been one of the most difficult problems in phylogenetics, and, despite intensive effort, the avian tree of life remains (at least partially) unresolved. Thus far, the most difficult problem is the relationship among the orders of Neoaves, the major clade that includes the most (~95%) named bird species. This clade appears to have undergone a rapid radiation near the end Cretaceous mass extinction (the K-Pg boundary). On the other hand, if one embraces a “glass half full” view, the fact that most orders in Neoaves can be placed into seven clades, recently designated the “magnificent seven,” could be viewed as remarkable progress. We propose that the dawning era of whole-genome phylogenetics will only resolve the remaining relationships, if we improve data quality, exploit information from other sources (i.e., rare genomic changes), and learn more about the functional and evolutionary landscape of avian genomes. Of course, it is possible that the remaining unresolved relationships are unresolvable regardless of the data available, but we suggest that the community should avoid this conclusion until more data collection has been completed and improved analyses have been conducted. We say this because there is ample evidence that estimates of avian phylogeny based on large-scale datasets may be affected by well-characterized artifacts (e.g., long-branch attraction, heterotachy, and discordance among gene trees) and by subtle “data-type effects” that reflect poor fit to empirical data for available models of sequence evolution. Even if these analytical challenges can be addressed, we need to integrate phylogenomic and fossil data. Finally, we also emphasize that, regardless of the resolution (or lack thereof) for relationships among major avian clades, we are only at the dawn of the phylogenomics of birds. Large-scale molecular data remain unavailable for the vast majority of the ~10,000 named bird species, and those named bird species probably represent an underestimate of the true number of distinct evolutionary lineages of birds (whether or not those lineages are assigned the rank of species) by as much as threefold. A true biodiversity genomics effort in birds is likely to reveal many additional examples of cases where it is very difficult to resolve relationships; the effort to resolve as many of those relationships as possible will represent a major scientific achievement and provide lessons for phylogenomic studies in other parts of the tree of life.
... This is supported by increasingly detailed paleotectonic data and geological evidence that dates substantial landmass formation to <10 Ma [72][73]. Moreover, timing and sequence of (specific) collision events and their impact on the evolution of a host of other faunal which dispersed across the region is increasingly well documented [29,[74][75]. Following formative studies by Hall [72][73]76] on the geological evolution of the region, [30] recently published a synthesis on the historical assembly of the flora of the region, highlighting enduring gaps in our understanding. ...
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Natural history collections and tropical tree diversity are both treasure troves of biological and evolutionary information, but their accessibility for scientific study is impeded by a number of properties. DNA in historical specimens is generally highly fragmented, complicating the recovery of high-grade genetic material. Furthermore, our understanding of hyperdi-verse, widespread tree assemblages is obstructed by extensive species ranges, fragmented knowledge of tropical tree diversity and phenology, and a widespread lack of species-level diagnostic characters, prohibiting the collecting of readily identifiable specimens which can be used to build, revise or strengthen taxonomic frameworks. This, in turn, delays the application of downstream conservation action. A sizable component of botanical collections are sterile-thus eluding identification and are slowing down progress in systematic treatments of tropical biodiversity. With rapid advances in genomics and bioinformatic approaches to biodiversity research, museomics is emerging as a new field breathing life into natural collections that have been built up over centuries. Using MIGseq (multiplexed ISSR genotyping by sequencing), we generated 10,000s of short loci, for both freshly collected materials and museum specimens (aged >100 years) of Lithocarpus-a widespread tropical tree genus endemic to the Asian tropics. Loci recovery from historical and recently collected samples was not affected by sample age and preservation history of the study material, underscoring the reliability and flexibility of the MIGseq approach. Phylogenomic inference and biogeographic reconstruction across insular Asia, highlights repeated migration and diversification patterns between continental regions and islands. Results indicate that co-occurring insular species at the extremity of the distribution range are not PLOS ONE PLOS ONE | https://doi.org/10.1371/journal.pone.
... Yet only one study analysing genetic population structure of this species has been conducted [7]. Previous genetic studies of the Columbidae family of birds primarily focused on phylogeny reconstruction [8][9][10]. Also, intraspecific genetic variation of the Feral Pigeon Columba livia, was extensively examined [11][12][13][14]. ...
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The European Turtle Dove, Streptopelia turtur, a long-distance migrant wintering in Africa, is a widespread Palearctic species. This species is classified as vulnerable and is undergoing a long-term demographic decline. The results of the previous study (based on mitochondrial (mtDNA) cytochrome-b (cytb) sequences of birds from Western and Southern Europe) indicated that the species was not genetically structured. We analysed the mtDNA cytb and D-loop of 258 birds collected from Morocco, Spain, and Ukraine. High genetic variability, expressed by haplotype diversity and nucleotide diversity, was revealed in both cytb (Hd = 0.905 ± 0.009, π = 0.00628 ± 0.00014) and the D-loop (Hd = 0.937 ± 0.009, π = 0.01502 ± 0.00034). SAMOVA and principal coordinates analysis revealed the birds belonged to two genetically distinct groups. One group included birds collected in Spain, while birds sampled in Morocco and Ukraine formed another group. Furthermore, significant genetic differentiation was identified between Turtle Doves from Morocco and Ukraine, and certain Spanish samples. The present results indicate that specific management and conservation plans relevant for the species in various regions should be applied. However, further nuclear DNA research and new studies (particularly in Eastern Europe) are necessary for the decisive results on genetic structure of this species.
... Almost all the PCGs use ATN as the initiation codon except for COI starting with GTG. Ten genes (ATP6, ATP8, COI, COII, Cyt b, ND1, ND3, ND4L, ND5, ND6) end with the typical stop codon TAA, TAG, AGA, or AGG, whereas the remaining three genes (COIII, ND2, and ND4) used the incomplete T. The gene arrangement in G. cuneata mitogenome was identical to other Columbidae species (Zhang et al. 2015;Huang et al. 2016;Soares et al. 2016;Bruxaux et al. 2018). Phylogenetic analysis of Columbidae species was performed based on the concatenated datasets of 13 PCGs using the maximum-likelihood method in IQ-tree (Nguyen et al. 2015). ...
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The complete mitochondrial genome (mitogenome) of diamond dove (Geopelia cuneata) was first determined in this study. The mitogenome is 17,880 bp in size and composed of 22 transfer RNA genes, 13 protein-coding genes, two ribosomal RNA genes, and a control region. The overall nucleotide composition is 30.11% of A, 13.66% of G, 25.11% of T, and 31.13% of C. The mitochondrial structure and gene order were similar to other Columbidae species. Phylogenetic analysis suggested that G. cuneata was placed as sister to G. striata of the same genus. The data could provide valuable information for further studies on conservation genetics and evolution of G. cuneata.
... In the eastern portion of its range where elevations are < 2000 m, M. viridis occurs throughout the Owen Stanley Ranges north to the coast of Milne Bay, Oro and Morobe provinces (Fig. 1), a pattern that has been observed in several species (Beehler 2007). Although the Vogelkop Isthmus is a well-known barrier to gene flow (Beehler, 2007;Bruxaux et al., 2018;Eldridge et al., 2018), several other zones of contact between the putative green python taxa are significant. For example, the ranges of M. azurea and M. viridis approach each other in the vicinity of the Bwussi River near Schneider Point, approximately 20 -km south of Lae, where green pythons exhibit features typical of M. viridis, (which is confirmed by our mtDNA phylogeny; Fig. 2). ...
... In the eastern portion of its range where elevations are < 2000 m, M. viridis occurs throughout the Owen Stanley Ranges north to the coast of Milne Bay, Oro and Morobe provinces (Fig. 1), a pattern that has been observed in several species (Beehler 2007). Although the Vogelkop Isthmus is a well-known barrier to gene flow (Beehler, 2007;Bruxaux et al., 2018;Eldridge et al., 2018), several other zones of contact between the putative green python taxa are significant. For example, the ranges of M. azurea and M. viridis approach each other in the vicinity of the Bwussi River near Schneider Point, approximately 20 -km south of Lae, where green pythons exhibit features typical of M. viridis, (which is confirmed by our mtDNA phylogeny; Fig. 2). ...
... We demonstrated that allele frequency estimates and associated confidence intervals improved with the addition of traditional museum samples ( Figure 4) (Bi et al., 2013;Wandeler et al., 2007). Current studies based on next-generation sequencing data from traditional museum samples generally rely on hybridization capture systems or whole-genome sequencing techniques (Ali et al., 2016;Bragg et al., 2016;Bruxaux et al., 2018;Hoffberg et al., 2016;Suchan et al., 2016). We have demonstrated the utility of a RADseq-based platform to generate genome-wide SNP data in low-template traditional museum specimens, some of which are over 100 years old. ...
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Pigeons are showing remarkable progress with more profit. This sector has many potential markets in the country. After visiting some pigeon houses, many limitations have been come out. Many rearers collect pigeons based on only physical appearance, and in the long run, they cannot get pure offspring. King pigeon is considered a table breed in the world but in Bangladesh rearers keep them as a common fancy item. Pigeons do not get their nutritious food from the owners. Result suggests that many rare pigeons are caught by predators and due to unwanted dirt in those lofts birds are affected by many diseases. Some remarkable farms are showing quality environment in their lofts and getting desirable profit.
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Museum specimens play a crucial role in addressing key questions in systematics, evolution, ecology, and conservation. With the advent of high‐throughput sequencing technologies, specimens that have long been the foundation of important biological discoveries can inform new perspectives as sources of genomic data. Despite the many possibilities associated with analyzing DNA from historical specimens, several challenges persist. Using avian systems as a model, we review DNA extraction protocols, sequencing technologies, and capture methods that are helping researchers overcome some of these difficulties. We highlight empirical examples in which researchers have used these technologies to address fundamental questions related to avian conservation and evolution. Increasing accessibility to new sequencing technologies will provide researchers with tools to tap into the wealth of information contained within our valuable natural history collections. This article is protected by copyright. All rights reserved.
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Species are fundamental to biology, conservation, and environmental legislation; yet, there is often disagreement on how and where species limits should be drawn. Even sophisticated molecular methods have limitations, particularly in the context of geographically isolated lineages or inadequate sampling of loci. With extinction rates rising, methods are needed to assess species limits rapidly but robustly. Tobias et al. devised a points-based system to compare phenotypic divergence between taxa against the level of divergence in sympatric species, establishing a threshold to guide taxonomic assessments at a global scale. The method has received a mixed reception. To evaluate its performance, we identified 397 novel taxonomic splits from 328 parent taxa made by application of the criteria (in 2014‒2016) and searched for subsequent publications investigating the same taxa with molecular and/or phenotypic data. Only 71 (18%) novel splits from 60 parent taxa have since been investigated by independent studies, suggesting that publication of splits underpinned by the criteria in 2014–2016 accelerated taxonomic decisions by at least 33 years. In the evaluated cases, independent analyses explicitly or implicitly supported species status in 62 (87.3%) of 71 splits, with the level of support increasing to 97.2% when excluding subsequent studies limited only to molecular data, and reaching 100% when the points-based criteria were applied using recommended sample sizes. Despite the fact that the training set used to calibrate the criteria was heavily weighted toward passerines, splits of passerines and non-passerines received equally strong support from independent research. We conclude that the method provides a useful tool for quantifying phenotypic divergence and fast-tracking robust taxonomic decisions at a global scale.
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Recent theoretical advances have hypothesized a central role of habitat persistence on population genetic structure and resulting biodiversity patterns of freshwater organisms. Here, we address the hypothesis that lotic species, or lineages adapted to comparably geologically stable running water habitats (streams and their marginal habitats), have high levels of endemicity and phylogeographic structure due to the persistent nature of their habitat. We use a nextRAD DNA sequencing approach to investigate the population structure and phylogeography of a putatively widespread New Guinean species of diving beetle, Philaccolilus ameliae (Dytiscidae). We find that P. ameliae is a complex of morphologically cryptic, but geographically and genetically well-differentiated clades. The pattern of population connectivity is consistent with theoretical predictions associated with stable lotic habitats. However, in two clades, we find a more complex pattern of low population differentiation, revealing dispersal across rugged mountains and watersheds of New Guinea up to 430 km apart. These results, while surprising, were also consistent with the original formulation of the habitat template concept by Southwood, involving lineage-idiosyncratic evolution in response to abiotic factors. In our system, low population differentiation might reflect a young species in a phase of range expansion utilizing vast available habitat. We suggest that predictions of life history variation resulting from the dichotomy between lotic and lentic organisms require more attention to habitat characterization and microhabitat choice. Our results also underpin the necessity to study fine-scale processes but at a larger geographical scale, as compared to solely documenting macroecological patterns, to understand ecological drivers of regional biodiversity. Comprehensive sampling especially of tropical lineages in complex and threatened environments such as New Guinea remains a critical challenge.
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Kingfishers are the most species-rich family in the avian order, Coraciiformes. Their modern distribution is largely pantropical; however, global species diversity is unevenly distributed. For example, 19 of the 114 kingfisher species occur in New Guinea, whereas only six species occur in the entire New World. This disparity in diversity suggests regions with high species richness could represent the ancestral range of the family. Furthermore, some clades of kingfishers (Ceyx, Todiramphus) are thought to be the product of rapid insular radiations. Here, we investigated the biogeographical history and speciation dynamics of the Alcedinidae using a fully sampled molecular phylogeny.
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The first-ever Illustrated Checklist of the Birds of the World is really two works in one. It is a complete checklist whose taxonomy incorporates the most up-to-date information and an exhaustive methodology (Tobias et al. 2010) in an entirely systematic and consistent way. At the same time, it contains illustrations and distribution maps for every bird species in the world. This includes the original artwork from the HBW series, as well as hundreds of new illustrations, all in two compact volumes (Volume 1: Non-passerines & Volume 2: Passerines).
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Physiological novelties are often studied at macro-evolutionary scales such that their micro-evolutionary origins remain poorly understood. Here, we test the hypothesis that key components of a complex trait can evolve in isolation and later be combined by gene flow. We use C4 photosynthesis as a study system, a derived physiology that increases plant productivity in warm, dry conditions. The grass Alloteropsis semialata includes C4 and non-C4 genotypes, with some populations using laterally acquired C4-adaptive loci, providing an outstanding system to track the spread of novel adaptive mutations. Using genome data from C4 and non-C4 A. semialata individuals spanning the species’ range, we infer and date past migrations of different parts of the genome. Our results show that photosynthetic types initially diverged in isolated populations, where key C4 components were acquired. However, rare but recurrent subsequent gene flow allowed the spread of adaptive loci across genetic pools. Indeed, laterally acquired genes for key C4 functions were rapidly passed between populations with otherwise distinct genomic backgrounds. Thus, our intraspecific study of C4-related genomic variation indicates that components of adaptive traits can evolve separately and later be combined through secondary gene flow, leading to the assembly and optimization of evolutionary innovations.
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Physiological novelties are often studied at macro-evolutionary scales such that their microevolutionary origins remain poorly understood. Here, we test the hypothesis that key components of a complex trait can evolve in isolation and later be combined by gene flow. We use C4 photosynthesis as a study system, a derived physiology that increases plant productivity in warm, dry conditions. The grass Alloteropsis semialata includes C4 and non-C4 genotypes, with some populations using laterally-acquired C4-adaptive loci, providing an outstanding system to track the spread of novel adaptive mutations. Using genome data from C4 and non-C4 A. semialata individuals spanning the species’ range, we infer and date past migrations of different parts of the genome. Our results show that photosynthetic types initially diverged in isolated populations, where key C4 components were acquired. However, rare but recurrent subsequent gene flow allowed the spread of adaptive loci across genetic pools. Indeed, laterally-acquired genes for key C4 functions were rapidly passed between populations with otherwise distinct gene pools. Thus, our intraspecific study of C4-related genomic variation indicates that components of adaptive traits can evolve separately and later be combined through secondary gene flow, leading to the assembly and optimization of evolutionary innovations.
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Background Pigeons and doves (Columbiformes) are one of the oldest and most diverse extant lineages of birds. However, the nature and timing of the group’s evolutionary radiation remains poorly resolved, despite recent advances in DNA sequencing and assembly and the growing database of pigeon mitochondrial genomes. One challenge has been to generate comparative data from the large number of extinct pigeon lineages, some of which are morphologically unique and therefore difficult to place in a phylogenetic context. Results We used ancient DNA and next generation sequencing approaches to assemble complete mitochondrial genomes for eleven pigeons, including the extinct Ryukyu wood pigeon (Columba jouyi), the thick-billed ground dove (Alopecoenas salamonis), the spotted green pigeon (Caloenas maculata), the Rodrigues solitaire (Pezophaps solitaria), and the dodo (Raphus cucullatus). We used a Bayesian approach to infer the evolutionary relationships among 24 species of living and extinct pigeons and doves. Conclusions Our analyses indicate that the earliest radiation of the Columbidae crown group most likely occurred during the Oligocene, with continued divergence of major clades into the Miocene, suggesting that diversification within the Columbidae occurred more recently than has been reported previously. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0800-3) contains supplementary material, which is available to authorized users.
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Summary: 1. Describing spatial patterns of phenotypic traits can be important for evolutionary and ecological studies. However, traditional approaches, such as fieldwork, can be time-consuming and expensive. Information technologies, such as Internet search engines, could facilitate the collection of these data. Google Images is one such technology that might offer an opportunity to rapidly collect information on spatial patterns of phenotypic traits. 2. We investigated the use of Google Images in extracting data on geographical variation in phenotypic traits visible from photographs. We compared the distribution of visual traits obtained from Google Images with four previous studies: colour morphs of black bear (Ursus americanus); colouration and spottiness in barn owl (Tyto alba); colour morphs of black sparrowhawk (Accipiter melanoleucus) and the distribution of hooded (Corvus corone) and carrion crows (Corvus cornix) across their European hybrid zone. Additionally, we develop and present a web application (morphic), which facilitates the human data capture process of this method. 3. We found good agreement between fieldwork data and Google Images data across all studies. Indeed, there was strong agreement between the data obtained from the original study and from the Google Images method for the colour morphs of black bear (R2 = 80%) and for two barn owl plumage traits (R2 = 64% and 53%). Our approach also successfully matched the clinal variation of black sparrowhawks morphs across South Africa. Our method also gave a good agreement between the distribution of hooded and carrion crows (with 86% placed on the correct side of the hybrid zone line). 4. Our results suggest that this method can work well for visible traits of common and widespread species that are objective, binary, and easy to see irrespective of angle. The Google Images method is cost-effective and rapid and can be used with some confidence when investigating patterns of geographical variation, as well as a range of other applications. In many cases, it could therefore supplement or replace fieldwork.
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Determining the timing of diversification of modern birds has been difficult. We combined DNA sequences of clock-like genes for most avian families with 130 fossil birds to generate a new time tree for Neornithes and investigated their biogeographic and diversification dynamics. We found that the most recent common ancestor of modern birds inhabited South America around 95 million years ago, but it was not until the Cretaceous-Paleogene transition (66 million years ago) that Neornithes began to diversify rapidly around the world. Birds used two main dispersion routes: reaching the Old World through North America, and reaching Australia and Zealandia through Antarctica. Net diversification rates increased during periods of global cooling, suggesting that fragmentation of tropical biomes stimulated speciation. Thus, we found pervasive evidence that avian evolution has been influenced by plate tectonics and environmental change, two basic features of Earth's dynamics.
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The fate of newly settled dispersers on freshly colonized oceanic islands is a central theme of island biogeography. The emergence of increasingly sophisticated methods of macroevolutionary pattern inference paves the way for a deeper understanding of the mechanisms governing these diversification patterns on lineages following their colonization of oceanic islands. Here we infer a comprehensive molecular phylogeny for Melanesian Exocelina diving beetles. Recent methods in historical biogeography and diversification rate inference were then used to investigate the evolution of these insects in space and time. An Australian origin in the mid-Miocene was followed by independent colonization events towards New Guinea and New Caledonia in the late Miocene. One colonization of New Guinea led to a large radiation of >150 species and 3 independent colonizations of New Caledonia gave rise to about 40 species. The comparably late colonizations of Vanuatu, Hawaii and China left only one or two species in each region. The contrasting diversification trajectories of these insects on Melanesian islands are likely accounted for by island size, age and availability of ecological opportunities during the colonization stage.
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Although reconstruction of the phylogeny of living birds has progressed tremendously in the last decade, the evolutionary history of Neoaves-a clade that encompasses nearly all living bird species-remains the greatest unresolved challenge in dinosaur systematics. Here we investigate avian phylogeny with an unprecedented scale of data: >390,000 bases of genomic sequence data from each of 198 species of living birds, representing all major avian lineages, and two crocodilian outgroups. Sequence data were collected using anchored hybrid enrichment, yielding 259 nuclear loci with an average length of 1,523 bases for a total data set of over 7.8 × 10(7) bases. Bayesian and maximum likelihood analyses yielded highly supported and nearly identical phylogenetic trees for all major avian lineages. Five major clades form successive sister groups to the rest of Neoaves: (1) a clade including nightjars, other caprimulgiforms, swifts, and hummingbirds; (2) a clade uniting cuckoos, bustards, and turacos with pigeons, mesites, and sandgrouse; (3) cranes and their relatives; (4) a comprehensive waterbird clade, including all diving, wading, and shorebirds; and (5) a comprehensive landbird clade with the enigmatic hoatzin (Opisthocomus hoazin) as the sister group to the rest. Neither of the two main, recently proposed Neoavian clades-Columbea and Passerea-were supported as monophyletic. The results of our divergence time analyses are congruent with the palaeontological record, supporting a major radiation of crown birds in the wake of the Cretaceous-Palaeogene (K-Pg) mass extinction.
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New DNA sequencing technologies are allowing researchers to explore the genomes of the millions of natural history specimens collected prior to the molecular era. Yet, we know little about how well specific next-generation sequencing (NGS) techniques work with the degraded DNA typically extracted from museum specimens. Here, we use one type of NGS approach, sequence capture of ultraconserved elements (UCEs), to collect data from bird museum specimens as old as 120 years. We targeted 5,060 UCE loci in 27 Western Scrub-Jays (Aphelocoma californica) representing three evolutionary lineages that could be species, and we collected an average of 3,749 UCE loci containing 4,460 single nucleotide polymorphisms (SNPs). Despite older specimens producing fewer and shorter loci in general, we collected thousands of markers from even the oldest specimens. More sequencing reads per individual helped to boost the number of UCE loci we recovered from older specimens, but more sequencing was not as successful at increasing the length of loci. We detected contamination in some samples and determined that contamination was more prevalent in older samples that were subject to less sequencing. For the phylogeny generated from concatenated UCE loci, contamination led to incorrect placement of some individuals. In contrast, a species tree constructed from SNPs called within UCE loci correctly placed individuals into three monophyletic groups, perhaps because of the stricter analytical procedures we used for SNP calling. This study and other recent studies on the genomics of museums specimens have profound implications for natural history collections, where millions of older specimens should now be considered genomic resources. This article is protected by copyright. All rights reserved.
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The northern Australian margin includes the island of New Guinea, which records a complex structural and tectonic evolution, largely masked by Mlo-Pliocene orogenesis and the Pleistocene onset of tectonic collapse. In the Palaeozoic, New Guinea contained the boundary between a Late Palaeozoic active margin In the east and a region of extension associated with Gondwana breakup along the western margin of Australia. In the Permian and Early Triasslc, New Guinea was an active margin resulting in widespread Middle Triasslc granite Intrusions. The Mesozolc saw Triasslc and Jurassic rifting followed by Cretaceous passive margin subsidence and renewed rifting in the Late Cretaceous and Paleocene. Since the Eocene, New Guinea tectonics have been driven by rapid northward movement of the Australian Plate and later sinistral oblique convergence with the Pacific Plate, resulting in Mio-Pliocene arc-continent collision. Neogene deformation along the margin, however, has been the result of direct interaction with the Philippine and Caroline Plates. Collision with the Philippine-Caroline Arc commenced in the Late Oligocene and orogenesis continues today. We suggest that the New Guinea Mobile Belt comprises a collision zone between a north-facing Cretaceous Indented margin and a south-facing Palaeogene accretionary prism, subsequently cut by a Neogene strike-slip fault system with well over 1000 km sinistral displacement that has alternated between extension and compression. The change In character of the llthosphere in New Guinea, from thick and strong in the west to thin and weak north and east of the Tasman Line, was also an important influence on the style and location of Mesozolc and Cenozoic deformation.
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Museum specimens are of particular importance for investigating systematics and the biogeography as well as other aspects of the evolution of biodiversity. They are also a depository of specimens accumulated over recent historical times and often the only way to study recently extinct or rare species. Unfortunately, most museum specimens yield low-quality DNA limiting their generalized use in phylogenetic and population genetic studies. Advances in sequencing technologies now offer opportunities to analyse such material even from very small tissue. Here, we applied the Illumina technology (HiSeq) on three specimens of crowned pigeon (Goura spp.) collected in New Guinea between 1879 and 1934. A shotgun strategy allowed us to quickly and reliably assemble complete mitochondrial genomes and fragments of three single-copy gene phylogenetic markers even with low double-stranded DNA quantity (9 to 69 ng). Phylogenetic assignments of these new sequences confirmed them as Goura sequences. Therefore, our study confirms the power of using next-generation sequencing methods to investigate the evolutionary history of species for which access to fresh samples is limited but museum collections are available. These approaches are considerably increasing the value of many natural history collections for genetic investigations, particularly from biodiversity hotspots that are presently difficult to prospect. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, ●●, ●●–●●.
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The continental core of Southeast (SE) Asia, Sundaland, was assembled from Gondwana fragments by the Early Mesozoic. Continental blocks rifted from Australia in the Jurassic [South West (SW) Borneo, East Java-West Sulawesi-Sumba], and the Woyla intraoceanic arc of Sumatra, were added to Sundaland in the Cretaceous. These fragments probably included emergent areas and could have carried a terrestrial flora and fauna. Sarawak, the offshore Luconia-Dangerous Grounds areas, and Palawan include Asian continental material. These probably represent a wide accretionary zone at the Asia-Pacific boundary, which was an active continental margin until the mid Cretaceous. Subduction ceased around Sundaland in the Late Cretaceous, and from about 80 Ma most of Sundaland was emergent, physically connected to Asia, but separated by deep oceans from India and Australia. India moved rapidly north during the Late Cretaceous and Early Cenozoic but there is no evidence that it made contact with SE Asia prior to collision with Asia. One or more arc-India collisions during the Eocene may have preceded India-Asia collision. The arcs could have provided dispersal pathways from India into SE Asia before final suturing of the two continents. During the Late Cretaceous and Early Cenozoic there was no significant subduction beneath Sumatra, Java and Borneo. At about 45 Ma Australia began to move north, subduction resumed and there was widespread rifting within Sundaland. During the Paleogene east and north Borneo were largely submerged, the Makassar Straits became a wide marine barrier within Sundaland, and West Sulawesi was separated from Sundaland but included land. By the Early Miocene the proto-South China Sea had been eliminated by subduction leading to emergence of land in central Borneo, Sabah and Palawan. Australia-SE Asia collision began, eliminating the former deep ocean separating the two continents, and forming the region now known as Wallacea. The microplate or terrane concept of slicing fragments from New Guinea followed by multiple collisions in Wallacea is implausible. Neogene subduction drove extension and fragmentation of Wallacea that caused both subsidence of deep marine basins and elevation of land; topography and bathymetry changed very rapidly, especially during the Pliocene, but the detailed palaeogeography of this region remains uncertain.
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Background High-throughput DNA sequencing technologies are generating vast amounts of data. Fast, flexible and memory efficient implementations are needed in order to facilitate analyses of thousands of samples simultaneously.ResultsWe present a multithreaded program suite called ANGSD. This program can calculate various summary statistics, and perform association mapping and population genetic analyses utilizing the full information in next generation sequencing data by working directly on the raw sequencing data or by using genotype likelihoods.Conclusions The open source c/c++ program ANGSD is available at http://www.popgen.dk/angsd. The program is tested and validated on GNU/Linux systems. The program facilitates multiple input formats including BAM and imputed beagle genotype probability files. The program allow the user to choose between combinations of existing methods and can perform analysis that is not implemented elsewhere.
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Background The closely related and extinct Dodo (Raphus cucullatus) and Rodrigues Solitaire (Pezophaps solitaria), both in the subfamily Raphinae, are members of a clade of morphologically very diverse pigeons. Genetic analyses have revealed that the Nicobar Pigeon (Caloenas nicobarica) is the closest living relative of these birds, thereby highlighting their ancestors’ remarkable migration and morphological evolution. The Spotted Green Pigeon (Caloenas maculata) was described in 1783 and showed some similarities to the Nicobar Pigeon. Soon however the taxon fell into obscurity, as it was regarded as simply an abnormal form of the Nicobar Pigeon. The relationship between both taxa has occasionally been questioned, leading some ornithologists to suggest that the two may in fact be different taxa. Today only one of the original two specimens survives and nothing is known about the origin of the taxon. Due to its potential close relationship, the Spotted Green Pigeon may hold clues to the historical migration, isolation and morphological evolution of the Dodo and its kindred. Results We use ancient DNA methodologies to investigate the phylogeny and authenticity of the Spotted Green Pigeon. A novel extraction method with the ability to retain and purify heavily fragmented DNA is used to investigate two feathers from the sole surviving specimen. Maximum Likelihood phylogenetic analyses reveal that the Spotted Green Pigeon is a unique lineage and together with the Nicobar Pigeon, is basal to the Dodo and Rodrigues Solitaire. Conclusions The distance observed for the Spotted Green Pigeon and Nicobar Pigeon is larger than that observed within other Pigeon species, indicating that the Spotted Green pigeon is a unique taxon, thereby also indicating it is a genuine addition to the list of extinct species. The phylogenetic placement of the Spotted Green Pigeon indicates that the ancestors of both Caloenas and therefore Raphinae displayed and shared the following traits: ability of flight, semi-terrestrial habits and an affinity towards islands. This set of traits supports the stepping stone hypothesis, which states that the Raphinae got to their respective localities by island hopping from India or Southeast Asia.
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Early studies on Melanesian mountain systems provided insights for fundamental evolutionary and ecological concepts. These island-like systems are thought to provide opportunities in the form of newly formed, competition-free niches. Here we show that a hyperdiverse radiation of freshwater arthropods originated in the emerging central New Guinea orogen, out of Australia, about 10 million years ago. Further diversification was mainly allopatric, with repeated more recent colonization of lowlands as they emerged in the form of colliding oceanic island arcs, continental fragments and the Papuan Peninsula, as well as recolonization of the central orogen. We unveil a constant and ongoing process of lineage accumulation while the carrying capacity of the island is about to be reached, suggesting that lineage diversification speed now exceeds that of landmass/new ecological opportunity formation. Therefore, the central orogeny of New Guinea acts as a motor of diversification for the entire region.
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A number of hitherto unrecognized, deeply divergent taxa of Australasian songbirds have been revealed by DNA sequence studies in the last decade. Differentiation among them is at levels equivalent to family and subfamily rank among songbirds generally. Accordingly, the purpose of this paper is to name and describe eleven of them formally under Articles 13.1, 13.2, 16.1 and 16.2 of the International Code of Zoological Nomenclature so that they are made available for use in zoology. The taxa are: families Oreoicidae, Eulacestomatidae, Rhagologidae, Ifritidae and Melampittidae, and subfamilies Pachycareinae, Oreoscopinae, Toxorhamphinae, Oedistomatinae, Peltopsinae and Lamproliinae. The families to which the subfamilies belong are documented. Morphological and behavioural traits of the new family-group taxa are discussed; reasons for taxonomic rankings are summarized; and grounds for the geographic origin of corvoid songbirds, to which all the new families belong, are briefly addressed. One new genus,Megalampitta in Melampittidae, is also described.
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We present a new open source, extensible and flexible software platform for Bayesian evolutionary analysis called BEAST 2. This software platform is a re-design of the popular BEAST 1 platform to correct structural deficiencies that became evident as the BEAST 1 software evolved. Key among those deficiencies was the lack of post-deployment extensibility. BEAST 2 now has a fully developed package management system that allows third party developers to write additional functionality that can be directly installed to the BEAST 2 analysis platform via a package manager without requiring a new software release of the platform. This package architecture is showcased with a number of recently published new models encompassing birth-death-sampling tree priors, phylodynamics and model averaging for substitution models and site partitioning. A second major improvement is the ability to read/write the entire state of the MCMC chain to/from disk allowing it to be easily shared between multiple instances of the BEAST software. This facilitates checkpointing and better support for multi-processor and high-end computing extensions. Finally, the functionality in new packages can be easily added to the user interface (BEAUti 2) by a simple XML template-based mechanism because BEAST 2 has been re-designed to provide greater integration between the analysis engine and the user interface so that, for example BEAST and BEAUti use exactly the same XML file format.
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Although many NGS read pre-processing tools already existed, we could not find any tool or combination of tools which met our requirements in terms of flexibility, correct handling of paired-end data, and high performance. We have developed Trimmomatic as a more flexible and efficient pre-processing tool, which could correctly handle paired-end data. The value of NGS read pre-processing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output which is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available from http://www.usadellab.org/cms/index.php?page=trimmomatic CONTACT: usadel@bio1.rwth-aachen.de SUPPLEMENTARY INFORMATION: Manual and source code are available from http://www.usadellab.org/cms/index.php?page=trimmomatic.
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Whole genome sequencing is helping generate robust phylogenetic hypotheses for a range of taxonomic groups that were previously recalcitrant to classical molecular phylogenetic approaches. As a case study, we performed a shallow shotgun sequencing of eight species in the tropical tree family Chrysobalanaceae to retrieve large fragments of high-copy number DNA regions and test the potential of these regions for phylogeny reconstruction. We were able to assemble the nuclear ribosomal cluster (nrDNA), the complete plastid genome (ptDNA) and a large fraction of the mitochondrial genome (mtDNA) with approximately 1000x, 450x and 120x sequencing depth respectively. The phylogenetic tree obtained with ptDNA resolved five of the seven internal nodes. In contrast, the tree obtained with mtDNA and nrDNA data were largely unresolved. This study demonstrates that genome skimming is a cost-effective approach and shows potential in plant molecular systematics within Chrysobalanaceae and other understudied groups. This article is protected by copyright. All rights reserved.
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Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. I present some of the most notable new features and extensions of RAxML, such as, a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX, and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date, 50 page user manual covering all new RAxML options is available. The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Alexandros.Stamatakis@h-its.org.
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The island of New Guinea lies in one of the most tectonically active regions in the world and has long provided outstanding opportunity for studies of biogeography. Several chelid turtles, of clear Gondwanal origin, occur in New Guinea; all species except one, the endemic Elseya novaeguineae, are restricted to the lowlands south of the Central Ranges. Elseya novaeguineae is found throughout New Guinea. We use mitochondrial and nuclear gene variation among populations of E. novaeguineae throughout its range to test hypotheses of recent extensive dispersal versus more ancient persistence in New Guinea. Its genetic structure bears the signature of Miocene vicariance events. The date of the divergence between a Birds Head (Kepala Burung) clade and clades north and south of the Central Ranges is estimated to be 19.8 Mya [95% highest posterior density (HPD) interval of 13.3–26.8 Mya] and the date between the northern and southern clades is estimated to be slightly more recent at 17.4 Mya (95% HPD interval of 11.0–24.5 Mya). The distribution of this endemic species is best explained by persistent occupation (or early invasion and dispersal) and subsequent isolation initiated by the dramatic landform changes that were part of the Miocene history of the island of New Guinea, rather than as a response to the contemporary landscape of an exceptionally effective disperser. The driving influence on genetic structure appears to have been isolation arising from a combination of: (1) the early uplift of the Central Ranges and establishment of a north-south drainage divide; (2) development of the Langguru Fold Belt; (3) the opening of Cenderawasih Bay; and (4) the deep waters of the Aru Trough and Cenderawasih Bay that come close to the current coastline to maintain isolation of the Birds Head through periods of sea level minima (−135 m). The dates of divergence of turtle populations north and south of the ranges predate the telescopic uplift of the central ranges associated with oblique subduction of the Australian Plate beneath the Pacific Plate. Their isolation was probably associated with earlier uplift and drainage isolation driven by the accretion of island terranes to the northern boundary of the Australian craton that occurred earlier than the oblique subduction. The opening of Cenderawasih Bay is too recent (6 Mya) to have initiated the isolation of the Birds Head populations from those of the remainder of New Guinea, although its deep waters will have served to sustain the isolation through successive sea level changes. The molecular evidence suggests that the Birds Head docked with New Guinea some time before the Central Ranges emerged as a barrier to turtle dispersal. Overall, deep genetic structure of the species complex reflects events and processes that occurred during Miocene, whereas structure within each clade across the New Guinea landscape relates to Pliocene and Pleistocene times.
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Motivation: Ancient DNA (aDNA) molecules in fossilized bones and teeth, coprolites, sediments, mummified specimens and museum collections represent fantastic sources of information for evolutionary biologists, revealing the agents of past epidemics and the dynamics of past populations. However, the analysis of aDNA generally faces two major issues. Firstly, sequences consist of a mixture of endogenous and various exogenous backgrounds, mostly microbial. Secondly, high nucleotide misincorporation rates can be observed as a result of severe post-mortem DNA damage. Such misincorporation patterns are instrumental to authenticate ancient sequences versus modern contaminants. We recently developed the user-friendly mapDamage package that identifies such patterns from next-generation sequencing (NGS) sequence datasets. The absence of formal statistical modeling of the DNA damage process, however, precluded rigorous quantitative comparisons across samples. Results: Here, we describe mapDamage 2.0 that extends the original features of mapDamage by incorporating a statistical model of DNA damage. Assuming that damage events depend only on sequencing position and post-mortem deamination, our Bayesian statistical framework provides estimates of four key features of aDNA molecules: the average length of overhangs (λ), nick frequency (ν) and cytosine deamination rates in both double-stranded regions () and overhangs (). Our model enables rescaling base quality scores according to their probability of being damaged. mapDamage 2.0 handles NGS datasets with ease and is compatible with a wide range of DNA library protocols. Availability: mapDamage 2.0 is available at ginolhac.github.io/mapDamage/ as a Python package and documentation is maintained at the Centre for GeoGenetics Web site (geogenetics.ku.dk/publications/mapdamage2.0/). Contact: jonsson.hakon@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.
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Although reconstruction of the phylogeny of living birds has progressed tremendously in the last decade, the evolutionary history of Neoaves—a clade that encompasses nearly all living bird species—remains the greatest unresolved challenge in dinosaur systematics. Here we investigate avian phylogeny with an unprecedented scale of data: >390,000 bases of genomic sequence data from each of 198 species of living birds, representing all major avian lineages, and two crocodilian outgroups. Sequence data were collected using anchored hybrid enrichment, yielding 259 nuclear loci with an average length of 1,523 bases for a total data set of over 7.8 × 10⁷ bases. Bayesian and maximum likelihood analyses yielded highly supported and nearly identical phylogenetic trees for all major avian lineages. Five major clades form successive sister groups to the rest of Neoaves: (1) a clade including nightjars, other caprimulgiforms, swifts, and hummingbirds; (2) a clade uniting cuckoos, bustards, and turacos with pigeons, mesites, and sandgrouse; (3) cranes and their relatives; (4) a comprehensive waterbird clade, including all diving, wading, and shorebirds; and (5) a comprehensive landbird clade with the enigmatic hoatzin (Opisthocomus hoazin) as the sister group to the rest. Neither of the two main, recently proposed Neoavian clades—Columbea and Passerea—were supported as monophyletic. The results of our divergence time analyses are congruent with the palaeontological record, supporting a major radiation of crown birds in the wake of the Cretaceous–Palaeogene (K–Pg) mass extinction.
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PartitionFinder 2 is a program for automatically selecting best-fit partitioning schemes and models of evolution for phylogenetic analyses. PartitionFinder 2 is substantially faster and more efficient than version 1, and incorporates many new methods and features. These include the ability to analyze morphological datasets, new methods to analyze genome-scale datasets, new output formats to facilitate interoperability with downstream software, and many new models of molecular evolution. PartitionFinder 2 is freely available under an open source license and works on Windows, OSX, and Linux operating systems. It can be downloaded from www.robertlanfear.com/partitionfinder The source code is available at https://github.com/brettc/partitionfinder.
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Mitochondrial DNA remains one of the most widely used molecular markers to reconstruct the phylogeny and phylogeography of closely-related birds. It has been proposed that bird mitochondrial genomes evolve at a constant rate of ~0.01 substitution per site per Million years, i.e. that they evolve according to a strict molecular clock. This molecular clock is often used in studies of bird mitochondrial phylogeny and molecular dating. However, rates of mitochondrial genome evolution vary among bird species, and correlate with life-history traits such as body mass and generation time. These correlations could cause systematic biases in molecular dating studies that assume a strict molecular clock. In this study, we overcome this issue by estimating corrected molecular rates for birds. Using complete or nearly complete mitochondrial genomes of 475 species, we show that there are strong relationships between body mass and substitution rates across birds. We use this information to build models that use bird species’ body mass to estimate their substitution rates across a wide range of common mitochondrial markers. We demonstrate the use of these corrected molecular rates on two recently-published datasets. In one case, we obtained molecular dates that are twice as old as the estimates obtained using the strict molecular clock. We hope that this method to estimate molecular rates will increase the accuracy of future molecular dating studies in birds. This article is protected by copyright. All rights reserved.
Article
The Vermilion Flycatcher (Pyrocephalus rubinus) is a widespread species found in North and South America and the Galápagos. Its 12 recognized subspecies vary in degree of geographic isolation, phenotypic distinctness, and migratory status. Some authors suggest that Galápagos subspecies nanus and dubius constitute one or more separate species. Observational reports of distinct differences in song also suggest separate species status for the austral migrant subspecies rubinus. To evaluate geographical patterns of diversification and taxonomic limits within this species complex, we carried out a molecular phylogenetic analysis encompassing 10 subspecies and three outgroup taxa using mitochondrial (ND2, Cyt b) and nuclear loci (ODC introns 6 through 7, FGB intron 5). We used samples of preserved tissues from museum collections as well as toe pad samples from museum skins. Galápagos and continental clades were recovered as sister groups, with initial divergence at ∼1 mya. Within the continental clade, North and South American populations were sister groups. Three geographically distinct clades were recovered within South America. We detected no genetic differences between two broadly intergrading North American subspecies, mexicanus and flammeus, suggesting they should not be recognized as separate taxa. Four western South American subspecies were also indistinguishable on the basis of loci that we sampled, but occur in a region with patchy habitat, and may represent recently isolated populations. The austral migrant subspecies, rubinus, comprised a monophyletic mitochondrial clade and had many unique nuclear DNA alleles. In combination with its distinct song, exclusive song recognition behavior, different phenology, and an isolated breeding range, our data suggests that this taxon represents a separate species from other continental populations. Mitochondrial and nuclear genetic data, morphology, and behavior suggest that Galápagos forms should be elevated to two full species corresponding to the two currently recognized subspecies, nanus and dubius. The population of dubius is presumed to be extinct, and thus would represent the first documented extinction of a Galápagos-endemic bird species. Two strongly supported mitochondrial clades divide Galápagos subspecies nanus in a geographic pattern that conflicts with previous hypotheses that were based on plumage color. Several populations of nanus have recently become extinct or are in serious decline. Urgent conservation measures should seek to preserve the deep mitochondrial DNA diversity within nanus, and further work should explore whether additional forms should be recognized within nanus. Ancestral states analysis based on our phylogeny revealed that the most recent common ancestor of extant Vermilion Flycatcher populations was migratory, and that migratory behavior was lost more often than gained within Pyrocephalus and close relatives, as has been shown to be the case within Tyrannidae as a whole.
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Abstract Late Pliocene and Pleistocene climatic instability has been invoked to explain the buildup of Neotropical biodiversity, although other theories date Neotropical diversification to earlier periods. If these climatic fluctuations drove Neotropical diversification, then a large proportion of species should date to this period and faunas should exhibit accelerated rates of speciation. However, the unique role of recent climatic fluctuations in promoting diversification could be rejected if late Pliocene and Pleistocene rates declined. To test these temporal predictions, dateable molecular phylogenies for 27 avian taxa were used to contrast the timing and rates of diversification in lowland and highland Neotropical faunas. Trends in diversification rates were analyzed in two ways. First, rates within taxa were analyzed for increasing or decreasing speciation rates through time. There was a significant trend within lowland taxa towards decreasing speciation rates, but no significant trend was observed within most highland taxa. Second, fauna wide diversification rates through time were estimated during one-million-year intervals by combining rates across taxa. In the lowlands, rates were highest during the late Miocene and then decreased towards the present. The decline in rates observed both within taxa and for the fauna as a whole probably resulted from density dependent cladogenesis. In the highlands, faunawide rates did not vary greatly before the Pleistocene but did increase significantly during the last one million years of the Pleistocene following the onset of severe glacial cycles in the Andes. These contrasting patterns of species accumulation suggest that lowland and highland regions were affected differently by recent climatic fluctuations. Evidently, habitat alterations associated with global climate change were not enough to promote an increase in the rate of diversification in lowland faunas. In contrast, direct fragmentation of habitats by glaciers and severe altitudinal migration of montane vegetation zones during climatic cycles may have resulted in the late Pleistocene increase in highland diversification rates. This increase resulted in a fauna with one third of its species dating to the last one million years.
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The Australo-Papuan catbird genus Ailuroedus has a complex distribution and a contested taxonomy. Here, we integrate phylogenetic analysis of DNA data and morphology to study the group's biogeography and to re-examine its taxonomy. We couple phylogeographic and abiotic data to examine differences between the major groups defined in our phylogenetic analysis. Our results are consistent with Ailuroedus catbirds being divided into two species complexes, one distributed in humid forests in the lowlands on New Guinea and another in comparably drier and colder forests mainly in mid-mountains on New Guinea and Australia. Vicariant events during the Pliocene are surmised to have been the major force in shaping the contemporary phylogeographical signature of this genus. Several previously suggested vicariant events, such as fragmentation of xeric forests in Australia and the uplift of the central mountain range on New Guinea, are reinforced as important Pliocene barriers for tropical forest taxa in this region. Interaction between Pleistocene climatic fluctuations and differences in habitat requirements may explain a higher and more recent population structures in the mid-mountain catbird complex and the lack of representatives from the lowland clade in the comparably drier Australia. Phylogeographical patterns in both catbird complexes, respectively, both comply and deviate from other lowland and mid-mountain taxa in the region. This highlights that taxon-specific properties, such as their historical spatial and ecological distributions, capacity to disperse and tolerance to habitat changes, affect the phylogeographical histories of organisms. Within both species complexes, the genetic differentiation between several geographically isolated populations was found to exceed those commonly observed for avian sister species. As these genetically distinct taxa also were found to be morphological diagnosable, we suggest a revised classification of the genus Ailuroedus, where we recognize three species within the lowland complex and seven species within the mid-mountain complex. Zoologica Scripta
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Research involving ancient DNA (aDNA) has experienced a true technological revolution in recent years through advances in the recovery of aDNA and, particularly, through applications of high-throughput sequencing. Formerly restricted to the analysis of only limited amounts of genetic information, aDNA studies have now progressed to whole-genome sequencing for an increasing number of ancient individuals and extinct species, as well as to epigenomic characterization. Such advances have enabled the sequencing of specimens of up to 1 million years old, which, owing to their extensive DNA damage and contamination, were previously not amenable to genetic analyses. In this Review, we discuss these varied technical challenges and solutions for sequencing ancient genomes and epigenomes.
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Relationships and species limits among the colourful Australian parrots known as rosellas (Platycercus) are contentious because of poorly understood patterns of parapatry, sympatry and hybridization as well as complex patterns of geographical replacement of phenotypic forms. Two subgenera are, however, conventionally recognized: Platycercus comprises the blue-cheeked crimson rosella complex (Crimson Rosella P. elegans and Green Rosella P. caledonicus), and Violania contains the remaining four currently recognized species (Pale-headed Rosella P. adscitus, Eastern Rosella P. eximius, Northern Rosella P. venustus, and Western Rosella P. icterotis). We used phylogenetic analysis of ten loci (one mitochondrial, eight autosomal and one Z-linked) and several individuals per nominal species primarily to examine relationships within the subgenera, especially the relationships and species limits within Violania. Of these, P. adscitus and P. eximius have long been considered sister species or conspecific due to a morphology-based hybrid zone and an early phylogenetic analysis of mitochondrial DNA restriction fragment length polymorphisms. The multilocus phylogenetic analysis presented here supports an alternative hypothesis aligning P. adscitus and P. venustus as sister species. Using divergence rates published in other avian studies, we estimated the divergence between P. venustus and P. adscitus at 0.0148 - 0.6124 MYA and that between the P. adscitus / P. venustus ancestor and P. eximius earlier at 0.1617 - 1.0816 MYA, both within the Pleistocene. Discordant topologies among gene and species trees are discussed and proposed to be the result of historical gene flow and/or incomplete lineage sorting (ILS). In particular, we suggest that discordance between mitochondrial and nuclear data may be the result of asymmetrical mitochondrial introgression from P. adscitus into P. eximius. The biogeographical implications of our findings are discussed relative to similarly distributed groups of birds. Copyright © 2015 Elsevier Inc. All rights reserved.
Article
Major hydrocarbon discoveries have been made in eastern and westernmost New Guinea, and there is great potential for additional discoveries. Although the island is a type locality for arc-continent collision during the Cenozoic, the age, number, and plate kinematics of the events that formed the island are vigorously argued. The northern part of the island is underlain by rocks with oceanic island arc affinities, and the southern part is underlain by the Australian continental crust. Based on regional sedimentation patterns, it is argued herein that the Cenozoic tectonic history of the island involves two distinct collisional orogenic events. The first Cenozoic event, the Peninsular orogeny of Oligocene age (∼35-30 Ma), was restricted to easternmost New Guinea. Emergent uplifts that shed abundant detritus resulted from the subduction of the northeastern corner of the Australian continent beneath part of the Inner Melanesian arc. This collision uplifted the Papuan ophiolite and formed the associated mountainous uplift that was the primary source of siliciclastic sediments that largely filled the Aure trough. Between the Oligocene and Miocene, the paleogeography of the region was similar to present-day New Caledonia. The continental crust under central and western New Guinea remained a passive margin. The second event, the Central Range orogeny, began in the latest middle Miocene, when the bulldozing of Australian passive-margin strata first created emergent uplifts above a north-dipping subduction zone beneath the western part of the Outer Melanesian arc. The cessation of carbonate shelf sedimentation and widespread initiation of siliciclastic sedimentation on top of the Australian continental basement is dated at about 12 Ma. This collision emplaced the Irian ophiolite and created the present mountainous topography forming the spine of the island. Copyright ©2005. The American Association of Petroleum Geologists. All rights reserved.
Article
A 646bp fragment of the mitochondrial cytochrome b gene and a 293bp fragment of the 18S ribosomal RNA gene were sequenced from 20 species of the Passeriformes, primarily of the family Muscicapidae. Phylogenetic trees of the cytochrome b gene indicated monophyly of the genus Turdus except T. dauma and close relationships among T. chrysollaus, T. obscurus and T. pallidus with a high bootstrap probability. The tree showed an early divergence of Corvus macrorhynchos from the other Passeriformes. Sturnus cineraceus was not closely related to Corvus macrorhynchos and included in the branch of Muscicapidae with a relatively high bootstrap probability. Although the trees suggested monophyly of the families Emberizidae, Ploceidae and Zosteropidae, the relationships among the families of Passeriformes were unclear. The sequences of the 18S ribosomal RNA gene were the same in the Passeriformes examined except the Tarsiger cyanurus, Monticola solitarius and Ficedula narcissina. These three species shared a single substitution at the same position, suggesting monophyly of the three species.
Article
Phylogenetic relationships among genera of pigeons and doves (Aves, Columbiformes) have not been fully resolved because of limited sampling of taxa and characters in previous studies. We therefore sequenced multiple nuclear and mitochondrial DNA genes totaling over 9000 bp from 33 of 41 genera plus 8 outgroup taxa, and, together with sequences from 5 other pigeon genera retrieved from GenBank, recovered a strong phylogenetic hypothesis for the Columbiformes. Three major clades were recovered with the combined data set, comprising the basally branching New World pigeons and allies (clade A) that are sister to Neotropical ground doves (clade B), and the Afro-Eurasian and Australasian taxa (clade C). None of these clades supports the monophyly of current families and subfamilies. The extinct, flightless dodo and solitaires (Raphidae) were embedded within pigeons and doves (Columbidae) in clade C, and monophyly of the subfamily Columbinae was refuted because the remaining subfamilies were nested within it. Divergence times estimated using a Bayesian framework suggest that Columbiformes diverged from outgroups such as Apodiformes and Caprimulgiformes in the Cretaceous before the mass extinction that marks the end of this period. Bayesian and maximum likelihood inferences of ancestral areas, accounting for phylogenetic uncertainty and divergence times, respectively, favor an ancient origin of Columbiformes in the Neotropical portion of what was then Gondwana. The radiation of modern genera of Columbiformes started in the Early Eocene to the Middle Miocene, as previously estimated for other avian groups such as ratites, tinamous, galliform birds, penguins, shorebirds, parrots, passerine birds, and toucans. Multiple dispersals of more derived Columbiformes between Australasian and Afro-Eurasian regions are required to explain current distributions.
Article
On tropical Pacific islands, a human-caused "biodiversity crisis" began thousands of years ago and has nearly run its course. Bones identified from archaeological sites show that most species of land birds and populations of seabirds on those islands were exterminated by prehistoric human activities. The loss of birdlife in the tropical Pacific may exceed 2000 species (a majority of which were species of flightless rails) and thus represents a 20 percent worldwide reduction in the number of species of birds. The current global extinction crisis therefore has historic precedent.