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1.
Mol Phylogenet Evol ; 141: 106627, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31539606

RESUMO

The advent of next-generation sequencing allows researchers to use large-scale datasets for species delimitation analyses, yet one can envision an inflection point where the added accuracy of including more loci does not offset the increased computational burden. One alternative to including all loci could be to prioritize the analysis of loci for which there is an expectation of high informativeness. Here, we explore the issue of species delimitation and locus selection with montane species from two anuran genera that have been isolated in sky islands across the southern Brazilian Atlantic Forest: Melanophryniscus (Bufonidae) and Brachycephalus (Brachycephalidae). To delimit species, we obtained genetic data using target enrichment of ultraconserved elements from 32 populations (13 for Melanophryniscus and 19 for Brachycephalus), and we were able to create datasets that included over 800 loci with no missing data. We ranked loci according to their number of parsimony-informative sites, and we performed species delimitation analyses using BPP with the most informative 10, 20, 40, 80, 160, 320, and 640 loci. We identified three types of phylogenetic node: nodes with either consistently high or low support regardless of the number of loci or their informativeness and nodes that were initially poorly supported where support became stronger as we included more data. When viewed across all sensitivity analyses, our results suggest that the current species richness in both genera is likely underestimated. In addition, our results show the effects of different sampling strategies on species delimitation using phylogenomic datasets.

2.
Mol Ecol Resour ; 2019 Sep 03.
Artigo em Inglês | MEDLINE | ID: mdl-31478338

RESUMO

Next-generation sequencing has greatly expanded the utility and value of museum collections by revealing specimens as genomic resources. As the field of museum genomics grows, so does the need for extraction methods that maximize DNA yields. For avian museum specimens, the established method of extracting DNA from toe pads works well for most specimens. However, for some specimens, especially those of birds that are very small or very large, toe pads can be a poor source of DNA. In this study, we apply two DNA extraction methods (phenol-chloroform and silica column) to three different sources of DNA (toe pad, skin punch and bone) from 10 historical avian museum specimens. We show that a modified phenol-chloroform protocol yielded significantly more DNA than a silica column protocol (e.g., Qiagen DNeasy Blood & Tissue Kit) across all tissue types. However, extractions using the silica column protocol contained longer fragments on average than those using the phenol-chloroform protocol, probably as a result of loss of small fragments through the silica column. While toe pads yielded more DNA than skin punches and bone fragments, skin punches proved to be a reliable alternative source of DNA and might be especially appealing when toe pad extractions are impractical. Overall, we found that historical bird museum specimens contain substantial amounts of DNA for genomic studies under most extraction scenarios, but that a phenol-chloroform protocol consistently provides the high quantities of DNA required for most current genomic protocols.

3.
BMC Res Notes ; 12(1): 456, 2019 Jul 24.
Artigo em Inglês | MEDLINE | ID: mdl-31340859

RESUMO

OBJECTIVE: Hybrid zones are geographic regions where genetically distinct taxa interbreed, resulting in offspring of mixed ancestry. California Scrub-Jays (Aphelocoma californica) and Woodhouse's Scrub-Jays (A. woodhouseii) come into secondary contact and hybridize in western Nevada. Although previous work investigated divergence and gene flow between these species using a handful of microsatellite markers, the hybrid zone has not been studied using genome-scale markers, providing an opportunity to assess genome-wide introgression, test for a genetic basis for ecomorphological traits, and compare these estimates to those derived from microsatellites. RESULTS: Using variant sites flanking ultraconserved elements (UCEs), we performed population assignment and quantified hybrid ancestry for 16 individuals across the zone of secondary contact. Our study included 2468 SNPs distributed throughout the genome, allowing discrimination of genetic affinities of hybrid individuals that were similar to estimates from microsatellites. We show a relationship between bill and wing length and the genetic composition of individuals that was not found in prior work using microsatellites, suggesting a genetic basis for these traits. Our analyses demonstrate the utility of UCEs for the analysis of hybrid zones and provide a basis for future studies to identify the genomic architecture of speciation and phenotypic differences between these incipient species.


Assuntos
Sondas de DNA , Genoma , Hibridização Genética , Passeriformes/genética , Característica Quantitativa Herdável , Animais , Bico/anatomia & histologia , Bico/metabolismo , Cruzamentos Genéticos , Feminino , Fluxo Gênico , Especiação Genética , Genética Populacional , Masculino , Repetições de Microssatélites , Passeriformes/classificação , Fenótipo , Polimorfismo de Nucleotídeo Único , Análise de Sequência de DNA , Asas de Animais/anatomia & histologia , Asas de Animais/metabolismo
4.
Syst Biol ; 68(6): 956-966, 2019 11 01.
Artigo em Inglês | MEDLINE | ID: mdl-31135028

RESUMO

Incomplete or geographically biased sampling poses significant problems for research in phylogeography, population genetics, phylogenetics, and species delimitation. Despite the power of using genome-wide genetic markers in systematics and related fields, approaches such as the multispecies coalescent remain unable to easily account for unsampled lineages. The Empidonax difficilis/Empidonax occidentalis complex of small tyrannid flycatchers (Aves: Tyrannidae) is a classic example of widely distributed species with limited phenotypic geographic variation that was broken into two largely cryptic (or "sibling") lineages following extensive study. Though the group is well-characterized north of the US Mexico border, the evolutionary distinctiveness and phylogenetic relationships of southern populations remain obscure. In this article, we use dense genomic and geographic sampling across the majority of the range of the E. difficilis/E. occidentalis complex to assess whether current taxonomy and species limits reflect underlying evolutionary patterns, or whether they are an artifact of historically biased or incomplete sampling. We find that additional samples from Mexico render the widely recognized species-level lineage E. occidentalis paraphyletic, though it retains support in the best-fit species delimitation model from clustering analyses. We further identify a highly divergent unrecognized lineage in a previously unsampled portion of the group's range, which a cline analysis suggests is more reproductively isolated than the currently recognized species E. difficilis and E. occidentalis. Our phylogeny supports a southern origin of these taxa. Our results highlight the pervasive impacts of biased geographic sampling, even in well-studied vertebrate groups like birds, and illustrate what is a common problem when attempting to define species in the face of recent divergence and reticulate evolution.


Assuntos
Marcadores Genéticos/genética , Filogenia , Aves Canoras/classificação , Aves Canoras/genética , Animais , Variação Genética , México , Viés de Seleção , Estados Unidos
5.
Mol Phylogenet Evol ; 136: 29-34, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-30930236

RESUMO

Natural history collections are increasingly valued as genomic resources. Their specimens reflect the combined efforts of collectors and curators over hundreds of years. For many rare or endangered species, specimens are the only readily available source of DNA. We leveraged specimens from a historical collection to study the evolutionary history of wood-partridges in the genus Dendrortyx. The three Dendrortyx species are found in the highlands of central Mexico and Central America south to Costa Rica. One of these species is endangered, and in general, Dendrortyx are secretive and poorly represented in tissue collections. We extracted DNA from historical museum specimens and sequenced ultraconserved elements (UCEs) and mitochondrial DNA (mtDNA) to assess their phylogeny and divergence times. Phylogenies built from hundreds to thousands of nuclear markers were well resolved and largely congruent with an mtDNA phylogeny. The divergence times revealed an unusually old avian divergence across the Isthmus of Tehuantepec in the Pliocene around 3.6 million years ago. Combined with other recent studies, our results challenge the general pattern that highland bird divergences in Mesoamerica are relatively young and influenced by the Pleistocene glacial cycles compared to the older divergences of reptiles and plants, which are thought to overlap more with periods of mountain formation. We also found evidence for monophyletic genetic lineages in mountain ranges within the widespread D. macroura, which should be investigated further with integrative taxonomic methods. Our study demonstrates the power of museum genomics to provide insight into the evolutionary histories of groups where modern samples are lacking.


Assuntos
Ecossistema , Galliformes/genética , Especiação Genética , Genômica , Museus , Madeira , Animais , Sequência de Bases , Biodiversidade , América Central , DNA Mitocondrial/genética , Florestas , México , Filogenia , Filogeografia
6.
Mol Ecol Resour ; 19(2): 349-365, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-30565862

RESUMO

With the continued adoption of genome-scale data in evolutionary biology comes the challenge of adequately harnessing the information to make accurate phylogenetic inferences. Coalescent-based methods of species tree inference have become common, and concatenation has been shown in simulation to perform well, particularly when levels of incomplete lineage sorting are low. However, simulation conditions are often overly simplistic, leaving empiricists with uncertainty regarding analytical tools. We use a large ultraconserved element data set (>3,000 loci) from rattlesnakes of the Crotalus triseriatus group to delimit lineages and estimate species trees using concatenation and several coalescent-based methods. Unpartitioned and partitioned maximum likelihood and Bayesian analysis of the concatenated matrix yield a topology identical to coalescent analysis of a subset of the data in bpp. ASTRAL analysis on a subset of the more variable loci also results in a tree consistent with concatenation and bpp, whereas the SVDquartets phylogeny differs at additional nodes. The size of the concatenated matrix has a strong effect on species tree inference using SVDquartets, warranting additional investigation on optimal data characteristics for this method. Species delimitation analyses suggest up to 16 unique lineages may be present within the C. triseriatus group, with divergences occurring during the Neogene and Quaternary. Network analyses suggest hybridization within the group is relatively rare. Altogether, our results reaffirm the Mexican highlands as a biodiversity hotspot and suggest that coalescent-based species tree inference on data subsets can provide a strongly supported species tree consistent with concatenation of all loci with a large amount of missing data.


Assuntos
Biodiversidade , Crotalus/classificação , Crotalus/genética , Filogenia , Animais , Biologia Computacional/métodos , Crotalus/crescimento & desenvolvimento , México
7.
PeerJ ; 6: e6045, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30581665

RESUMO

Molecular studies have uncovered significant diversity in the Mexican Highlands, leading to the description of many new endemic species. DNA approaches to this kind of species discovery have included both mitochondrial DNA (mtDNA) sequencing and multilocus genomic methods. While these marker types have often been pitted against one another, there are benefits to deploying them together, as linked mtDNA data can provide the bridge between uncovering lineages through rigorous multilocus genomic analysis and identifying lineages through comparison to existing mtDNA databases. Here, we apply one class of multilocus genomic marker, ultraconserved elements (UCEs), and linked mtDNA data to a species complex of frogs (Sarcohyla bistincta, Hylidae) found in the Mexican Highlands. We generated data from 1,891 UCEs, which contained 1,742 informative SNPs for S. bistincta and closely related species and captured mitochondrial genomes for most samples. Genetic analyses based on both whole loci and SNPs agree there are six to seven distinct lineages within what is currently described as S. bistincta. Phylogenies from UCEs and mtDNA mostly agreed in their topologies, and the few differences suggested a more complex evolutionary history of the mtDNA marker. Our study demonstrates that the Mexican Highlands still hold substantial undescribed diversity, making their conservation a particularly urgent goal. The Trans-Mexican Volcanic Range stands out as a significant geographic feature in Sarcohyla and may have acted as a dispersal corridor for S. bistincta to spread to the north. Combining multilocus genomic data with linked mtDNA data is a useful approach for identifying potential new species and associating them with already described taxa, which will be especially important in groups with undescribed subadult phenotypes and cryptic species.

8.
Mol Ecol ; 27(24): 5137-5153, 2018 12.
Artigo em Inglês | MEDLINE | ID: mdl-30451354

RESUMO

The formation of independent evolutionary lineages involves neutral and selective factors, and understanding their relative roles in population divergence is a fundamental goal of speciation research. Correlations between allele frequencies and environmental variability can reveal the role of selection, yet the relative contribution of drift can be difficult to establish. Recently diversified taxa like the Oregon junco (Aves, Passerellidae, Junco hyemalis oreganus) of western North America provide ideal scenarios to apply genetic-environment association analyses (GEA) while controlling for population structure. Analysis of genome-wide SNP loci revealed marked genetic structure consisting of differentiated populations in isolated, dry southern mountain ranges, and less divergent, recently expanded populations in humid northern latitudes. We used correlations between genomic and environmental variance to test for three specific modes of evolutionary divergence: (a) drift in geographic isolation, (b) differentiation along continuous selective gradients and (c) isolation-by-adaptation. We found evidence of strong drift in southern mountains, but also signals of local adaptation driven by temperature, precipitation, elevation and vegetation, especially when controlling for population history. We identified numerous variants under selection scattered across the genome, suggesting that local adaptation can promote rapid differentiation when acting over multiple independent loci.


Assuntos
Adaptação Biológica/genética , Evolução Biológica , Genética Populacional , Aves Canoras/genética , Animais , Teorema de Bayes , Meio Ambiente , Fluxo Gênico , Frequência do Gene , Deriva Genética , Genótipo , América do Norte , Polimorfismo de Nucleotídeo Único
9.
Microbiome ; 6(1): 167, 2018 09 19.
Artigo em Inglês | MEDLINE | ID: mdl-30231937

RESUMO

BACKGROUND: Darwin's finches are a clade of 19 species of passerine birds native to the Galápagos Islands, whose biogeography, specialized beak morphologies, and dietary choices-ranging from seeds to blood-make them a classic example of adaptive radiation. While these iconic birds have been intensely studied, the composition of their gut microbiome and the factors influencing it, including host species, diet, and biogeography, has not yet been explored. RESULTS: We characterized the microbial community associated with 12 species of Darwin's finches using high-throughput 16S rRNA sequencing of fecal samples from 114 individuals across nine islands, including the unusual blood-feeding vampire finch (Geospiza septentrionalis) from Darwin and Wolf Islands. The phylum-level core gut microbiome for Darwin's finches included the Firmicutes, Gammaproteobacteria, and Actinobacteria, with members of the Bacteroidetes at conspicuously low abundance. The gut microbiome was surprisingly well conserved across the diversity of finch species, with one exception-the vampire finch-which harbored bacteria that were either absent or extremely rare in other finches, including Fusobacterium, Cetobacterium, Ureaplasma, Mucispirillum, Campylobacter, and various members of the Clostridia-bacteria known from the guts of carnivorous birds and reptiles. Complementary stable isotope analysis of feathers revealed exceptionally high δ15N isotope values in the vampire finch, resembling top marine predators. The Galápagos archipelago is also known for extreme wet and dry seasons, and we observed a significant seasonal shift in the gut microbial community of five additional finch species sampled during both seasons. CONCLUSIONS: This study demonstrates the overall conservatism of the finch gut microbiome over short (< 1 Ma) divergence timescales, except in the most extreme case of dietary specialization, and elevates the evolutionary importance of seasonal shifts in driving not only species adaptation, but also gut microbiome composition.


Assuntos
Bactérias/isolamento & purificação , Tentilhões/microbiologia , Microbioma Gastrointestinal , Animais , Bactérias/classificação , Bactérias/genética , Evolução Biológica , Clima , DNA Bacteriano/genética , Equador , Fezes/microbiologia , Tentilhões/classificação , Tentilhões/genética , Trato Gastrointestinal/microbiologia , Filogenia , RNA Ribossômico 16S/genética , Estações do Ano
10.
Zookeys ; (739): 79-106, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29674883

RESUMO

Morphologically conserved taxa such as scorpions represent a challenge to delimit. We recently discovered populations of scorpions in the genus Kovarikia Soleglad, Fet & Graham, 2014 on two isolated mountain ranges in southern California. We generated genome-wide single nucleotide polymorphism data and used Bayes factors species delimitation to compare alternative species delimitation scenarios which variously placed scorpions from the two localities with geographically adjacent species or into separate lineages. We also estimated a time-calibrated phylogeny of Kovarikia and examined and compared the morphology of preserved specimens from across its distribution. Genetic results strongly support the distinction of two new lineages, which we describe and name here. Morphology among the species of Kovarikia was relatively conserved, despite deep genetic divergences, consistent with recent studies of stenotopic scorpions with limited vagility. Phylogeographic structure discovered in several previously described species also suggests additional cryptic species are probably present in the genus.

11.
Mol Phylogenet Evol ; 125: 78-84, 2018 08.
Artigo em Inglês | MEDLINE | ID: mdl-29555294

RESUMO

Mountain formation in Mexico has played an important role in the diversification of many Mexican taxa. The Trans-Mexican Volcanic Belt in particular has served as both a cradle of diversification and conduit for dispersal. We investigated the evolutionary history of the Isthmura bellii group of salamanders, a widespread amphibian across the Mexican highlands, using sequence capture of ultraconserved elements. Results suggest that the I. bellii group probably originated in southeastern Mexico in the late Miocene and later dispersed across the Trans-Mexican Volcanic Belt and into the Sierra Madre Occidental. Pre-Pleistocene uplift of the Trans-Volcanic Belt likely promoted early diversification by serving as a mesic land-bridge across central Mexico. These findings highlight the importance of the Trans-Volcanic Belt in generating Mexico's rich biodiversity.


Assuntos
Ecossistema , Filogenia , Urodelos/classificação , Urodelos/genética , Animais , Teorema de Bayes , Calibragem , México , Filogeografia , Fatores de Tempo
12.
Gene ; 628: 194-199, 2017 Sep 10.
Artigo em Inglês | MEDLINE | ID: mdl-28720533

RESUMO

Melanophryniscus is a bufonid frog genus with a broad geographic distribution over southeastern South America. In recent years, several new species of Melanophryniscus have been discovered in southern Brazil showing a distinctive life-history strategy for the genus - breeding in phytotelmata - as well as a strong association with high-altitude regions. In this study, we use mitogenomic data to infer the phylogenetic relationships among diurnal, phytotelm-breeding Melanophryniscus and to determine the timing of their divergence. We obtained the mitochondrial genomes (not including the control region) for eight individuals of Melanophryniscus representing all three described species (M. alipioi, M. milanoi, and M. xanthostomus), as well as some recently-discovered and potentially new species. Gene order was conserved in all species and corresponded to the general order found in bufonids. Although the phylogenetic relationships among the studied species was poorly supported, dating confirmed that they diverged during the Pleistocene, suggesting that phytotelm breeding could have arisen during drier periods in the glacial/interglacial cycles due to a decrease in the availability of permanent streams or ephemeral/temporary streams or ponds in which Melanophryniscus species commonly breed.


Assuntos
Bufonidae/classificação , Bufonidae/genética , Genoma Mitocondrial , Filogenia , Animais , Cruzamento , Ordem dos Genes , Genes Mitocondriais
13.
Mol Ecol Resour ; 17(4): 812-823, 2017 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-27768256

RESUMO

Arachnida is an ancient, diverse and ecologically important animal group that contains a number of species of interest for medical, agricultural and engineering applications. Despite their importance, many aspects of the arachnid tree of life remain unresolved, hindering comparative approaches to arachnid biology. Biologists have made considerable efforts to resolve the arachnid phylogeny; yet, limited and challenging morphological characters, as well as a dearth of genetic resources, have hindered progress. Here, we present a genomic toolkit for arachnids featuring hundreds of conserved DNA regions (ultraconserved elements or UCEs) that allow targeted sequencing of any species in the arachnid tree of life. We used recently developed capture probes designed from conserved regions of available arachnid genomes to enrich a sample of loci from 32 diverse arachnids. Sequence capture returned an average of 487 UCE loci for all species, with a range from 170 to 722. Phylogenetic analysis of these UCEs produced a highly resolved arachnid tree with relationships largely consistent with recent transcriptome-based phylogenies. We also tested the phylogenetic informativeness of UCE probes within the spider, scorpion and harvestman orders, demonstrating the utility of these markers at shallower taxonomic scales and suggesting that these loci will be useful for species-level differences. This probe set will open the door to phylogenomic and population genomic studies across the arachnid tree of life, enabling systematics, species delimitation, species discovery and conservation of these diverse arthropods.


Assuntos
Aracnídeos/classificação , Sondas de DNA , Filogenia , Animais , Aracnídeos/genética , Genômica , Análise de Sequência de DNA
14.
Mol Ecol ; 25(20): 5144-5157, 2016 10.
Artigo em Inglês | MEDLINE | ID: mdl-27543758

RESUMO

Genomic studies are revealing that divergence and speciation are marked by gene flow, but it is not clear whether gene flow has played a prominent role during the generation of biodiversity in species-rich regions of the world where vicariance is assumed to be the principal mode by which new species form. We revisit a well-studied organismal system in the Mexican Highlands, Aphelocoma jays, to test for gene flow among Mexican sierras. Prior results from mitochondrial DNA (mtDNA) largely conformed to the standard model of allopatric divergence, although there was also evidence for more obscure histories of gene flow in a small sample of nuclear markers. We tested for these 'hidden histories' using genomic markers known as ultraconserved elements (UCEs) in concert with phylogenies, clustering algorithms and newer introgression tests specifically designed to detect ancient gene flow (e.g. ABBA/BABA tests). Results based on 4303 UCE loci and 2500 informative SNPs are consistent with varying degrees of gene flow among highland areas. In some cases, gene flow has been extensive and recent (although perhaps not ongoing today), whereas in other cases there is only a trace signature of ancient gene flow among species that diverged as long as 5 million years ago. These results show how a species complex thought to be a model for vicariance can reveal a more reticulate history when a broader portion of the genome is queried. As more organisms are studied with genomic data, we predict that speciation-with-bouts-of-gene-flow will turn out to be a common mode of speciation.


Assuntos
Fluxo Gênico , Especiação Genética , Genética Populacional , Passeriformes/genética , Animais , DNA Mitocondrial/genética , Genômica , México , Modelos Genéticos , Filogenia , Polimorfismo de Nucleotídeo Único , Análise de Sequência de DNA
15.
Mol Ecol ; 25(15): 3731-51, 2016 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-27238387

RESUMO

The California Floristic Province (CFP) in western North America is a globally significant biodiversity hotspot. Elucidating patterns of endemism and the historical drivers of this diversity has been an important challenge of comparative phylogeography for over two decades. We generated phylogenomic data using ddRADseq to examine genetic structure in Uroctonus forest scorpions, an ecologically restricted and dispersal-limited organism widely distributed across the CFP north to the Columbia River. We coupled our genetic data with species distribution models (SDMs) to determine climatically suitable areas for Uroctonus both now and during the Last Glacial Maximum. Based on our analyses, Uroctonus is composed of two major genetic groups that likely diverged over 2 million years ago. Each of these groups itself contains numerous genetic groups that reveal a pattern of vicariance and microendemism across the CFP. Migration rates among these populations are low. SDMs suggest forest scorpion habitat has remained relatively stable over the last 21 000 years, consistent with the genetic data. Our results suggest tectonic plate rafting, mountain uplift, river drainage formation and climate-induced habitat fragmentation have all likely played a role in the diversification of Uroctonus. The intricate pattern of genetic fragmentation revealed across a temporal continuum highlights the potential of low-dispersing species to shed light on small-scale patterns of biodiversity and the underlying processes that have generated this diversity in biodiversity hotspots.


Assuntos
Evolução Biológica , Genética Populacional , Filogenia , Escorpiões/genética , Animais , California , Florestas , Genômica , Escorpiões/classificação
16.
Mol Ecol Resour ; 16(5): 1189-203, 2016 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-26391430

RESUMO

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 5060 UCE loci in 27 western scrub-jays (Aphelocoma californica) representing three evolutionary lineages that could be species, and we collected an average of 3749 UCE loci containing 4460 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 used for SNP calling. This study and other recent studies on the genomics of museum specimens have profound implications for natural history collections, where millions of older specimens should now be considered genomic resources.


Assuntos
Aves/classificação , Aves/genética , DNA/genética , DNA/isolamento & purificação , Técnicas de Genotipagem/métodos , Preservação Biológica , Manejo de Espécimes/métodos , Animais , DNA/química , Sequenciamento de Nucleotídeos em Larga Escala , Museus , Filogeografia , Polimorfismo de Nucleotídeo Único , Análise de Sequência de DNA
17.
Mol Phylogenet Evol ; 94(Pt A): 447-62, 2016 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-26518740

RESUMO

In recent articles published in Molecular Phylogenetics and Evolution, Mark Springer and John Gatesy (S&G) present numerous criticisms of recent implementations and testing of the multispecies coalescent (MSC) model in phylogenomics, popularly known as "species tree" methods. After pointing out errors in alignments and gene tree rooting in recent phylogenomic data sets, particularly in Song et al. (2012) on mammals and Xi et al. (2014) on plants, they suggest that these errors seriously compromise the conclusions of these studies. Additionally, S&G enumerate numerous perceived violated assumptions and deficiencies in the application of the MSC model in phylogenomics, such as its assumption of neutrality and in particular the use of transcriptomes, which are deemed inappropriate for the MSC because the constituent exons often subtend large regions of chromosomes within which recombination is substantial. We acknowledge these previously reported errors in recent phylogenomic data sets, but disapprove of S&G's excessively combative and taunting tone. We show that these errors, as well as two nucleotide sorting methods used in the analysis of Amborella, have little impact on the conclusions of those papers. Moreover, several concepts introduced by S&G and an appeal to "first principles" of phylogenetics in an attempt to discredit MSC models are invalid and reveal numerous misunderstandings of the MSC. Contrary to the claims of S&G we show that recent computer simulations used to test the robustness of MSC models are not circular and do not unfairly favor MSC models over concatenation. In fact, although both concatenation and MSC models clearly perform well in regions of tree space with long branches and little incomplete lineage sorting (ILS), simulations reveal the erratic behavior of concatenation when subjected to data subsampling and its tendency to produce spuriously confident yet conflicting results in regions of parameter space where MSC models still perform well. S&G's claims that MSC models explain little or none (0-15%) of the observed gene tree heterogeneity observed in a mammal data set and that MSC models assume ILS as the only source of gene tree variation are flawed. Overall many of their criticisms of MSC models are invalidated when concatenation is appropriately viewed as a special case of the MSC, which in turn is a special case of emerging network models in phylogenomics. We reiterate that there is enormous promise and value in recent implementations and tests of the MSC and look forward to its increased use and refinement in phylogenomics.


Assuntos
Simulação por Computador , Especiação Genética , Genômica/métodos , Modelos Genéticos , Filogenia , Animais , Evolução Molecular , Magnoliopsida/classificação , Magnoliopsida/genética , Mamíferos/classificação , Mamíferos/genética , Recombinação Genética
18.
Nature ; 515(7527): 406-9, 2014 Nov 20.
Artigo em Inglês | MEDLINE | ID: mdl-25209666

RESUMO

Since the recognition that allopatric speciation can be induced by large-scale reconfigurations of the landscape that isolate formerly continuous populations, such as the separation of continents by plate tectonics, the uplift of mountains or the formation of large rivers, landscape change has been viewed as a primary driver of biological diversification. This process is referred to in biogeography as vicariance. In the most species-rich region of the world, the Neotropics, the sundering of populations associated with the Andean uplift is ascribed this principal role in speciation. An alternative model posits that rather than being directly linked to landscape change, allopatric speciation is initiated to a greater extent by dispersal events, with the principal drivers of speciation being organism-specific abilities to persist and disperse in the landscape. Landscape change is not a necessity for speciation in this model. Here we show that spatial and temporal patterns of genetic differentiation in Neotropical birds are highly discordant across lineages and are not reconcilable with a model linking speciation solely to landscape change. Instead, the strongest predictors of speciation are the amount of time a lineage has persisted in the landscape and the ability of birds to move through the landscape matrix. These results, augmented by the observation that most species-level diversity originated after episodes of major Andean uplift in the Neogene period, suggest that dispersal and differentiation on a matrix previously shaped by large-scale landscape events was a major driver of avian speciation in lowland Neotropical rainforests.


Assuntos
Aves/classificação , Aves/genética , Especiação Genética , Filogenia , Floresta Úmida , Clima Tropical , Animais , Biodiversidade , Modelos Biológicos , Dados de Sequência Molecular , Panamá , Rios , América do Sul
19.
BMC Evol Biol ; 14: 135, 2014 Jun 17.
Artigo em Inglês | MEDLINE | ID: mdl-24938753

RESUMO

BACKGROUND: Haldane's Rule, the tendency for the heterogametic sex to show reduced fertility in hybrid crosses, can obscure the signal of gene flow in mtDNA between species where females are heterogametic. Therefore, it is important when studying speciation and species limits in female-heterogametic species like birds to assess the signature of gene flow in the nuclear genome as well. We studied introgression of microsatellites and mtDNA across a secondary contact zone between coastal and interior lineages of Western Scrub-Jays (Aphelocoma californica) to test for a signature of Haldane's Rule: a narrower cline of introgression in mtDNA compared to nuclear markers. RESULTS: Our initial phylogeographic analysis revealed that there is only one major area of contact between coastal and interior lineages and identified five genetic clusters with strong spatial structuring: Pacific Slope, Interior US, Edwards Plateau (Texas), Northern Mexico, and Southern Mexico. Consistent with predictions from Haldane's Rule, mtDNA showed a narrower cline than nuclear markers across a transect through the hybrid zone. This result is not being driven by female-biased dispersal because neutral diffusion analysis, which included estimates of sex-specific dispersal rates, also showed less diffusion of mtDNA. Lineage-specific plumage traits were associated with nuclear genetic profiles for individuals in the hybrid zone, indicating that these differences are under genetic control. CONCLUSIONS: This study adds to a growing list of studies that support predictions of Haldane's Rule using cline analysis of multiple loci of differing inheritance modes, although alternate hypotheses like selection on different mtDNA types cannot be ruled out. That Haldane's Rule appears to be operating in this system suggests a measure of reproductive isolation between the Pacific Slope and interior lineages. Based on a variety of evidence from the phenotype, ecology, and genetics, we recommend elevating three lineages to species level: A. californica (Pacific Slope); A. woodhouseii (Interior US plus Edwards Plateau plus Northern Mexico); A. sumichrasti (Southern Mexico). The distinctive Edwards Plateau population in Texas, which was monophyletic in mtDNA except for one individual, should be studied in greater detail given habitat threat.


Assuntos
DNA Mitocondrial/genética , Especiação Genética , Passeriformes/genética , Animais , Núcleo Celular/genética , Feminino , Fluxo Gênico , Hibridização Genética , Masculino , México , Repetições de Microssatélites , Dados de Sequência Molecular , Passeriformes/classificação , Isolamento Reprodutivo
20.
PLoS One ; 8(1): e54848, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-23382987

RESUMO

Evolutionary relationships among birds in Neoaves, the clade comprising the vast majority of avian diversity, have vexed systematists due to the ancient, rapid radiation of numerous lineages. We applied a new phylogenomic approach to resolve relationships in Neoaves using target enrichment (sequence capture) and high-throughput sequencing of ultraconserved elements (UCEs) in avian genomes. We collected sequence data from UCE loci for 32 members of Neoaves and one outgroup (chicken) and analyzed data sets that differed in their amount of missing data. An alignment of 1,541 loci that allowed missing data was 87% complete and resulted in a highly resolved phylogeny with broad agreement between the Bayesian and maximum-likelihood (ML) trees. Although results from the 100% complete matrix of 416 UCE loci were similar, the Bayesian and ML trees differed to a greater extent in this analysis, suggesting that increasing from 416 to 1,541 loci led to increased stability and resolution of the tree. Novel results of our study include surprisingly close relationships between phenotypically divergent bird families, such as tropicbirds (Phaethontidae) and the sunbittern (Eurypygidae) as well as between bustards (Otididae) and turacos (Musophagidae). This phylogeny bolsters support for monophyletic waterbird and landbird clades and also strongly supports controversial results from previous studies, including the sister relationship between passerines and parrots and the non-monophyly of raptorial birds in the hawk and falcon families. Although significant challenges remain to fully resolving some of the deep relationships in Neoaves, especially among lineages outside the waterbirds and landbirds, this study suggests that increased data will yield an increasingly resolved avian phylogeny.


Assuntos
Aves/classificação , Aves/genética , Loci Gênicos , Filogenia , Animais , Biodiversidade , Evolução Molecular , Sequenciamento de Nucleotídeos em Larga Escala
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