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1.
Syst Biol ; 72(4): 739-752, 2023 08 07.
Artigo em Inglês | MEDLINE | ID: mdl-37097104

RESUMO

In this study we detangled the evolutionary history of the Patagonian lizard clade Liolaemus kingii, coupling dense geographic sampling and novel computational analytical approaches. We analyzed nuclear and mitochondrial data (restriction site-associated DNA sequencing and cytochrome b) to hypothesize and evaluate species limits, phylogenetic relationships, and demographic histories. We complemented these analyses with posterior predictive simulations to assess the fit of the genomic data to the multispecies coalescent model. We also employed a novel approach to time-calibrate a phylogenetic network. Our results show several instances of mito-nuclear discordance and consistent support for a reticulated history, supporting the view that the complex evolutionary history of the kingii clade is characterized by extensive gene flow and rapid diversification events. We discuss our findings in the contexts of the "gray zone" of speciation, phylogeographic patterns in the Patagonian region, and taxonomic outcomes. [Model adequacy; multispecies coalescent; multispecies network coalescent; phylogenomics; species delimitation.].


Assuntos
Lagartos , Animais , Filogenia , Lagartos/genética , DNA Mitocondrial/genética , Filogeografia , Evolução Biológica
2.
Bioinformatics ; 38(13): 3361-3366, 2022 06 27.
Artigo em Inglês | MEDLINE | ID: mdl-35608310

RESUMO

MOTIVATION: Transposable elements (TEs) are ubiquitous in genomes and many remain active. TEs comprise an important fraction of the transcriptomes with potential effects on the host genome, either by generating deleterious mutations or promoting evolutionary novelties. However, their functional study is limited by the difficulty in their identification and quantification, particularly in non-model organisms. RESULTS: We developed a new pipeline [explore active transposable elements (ExplorATE)] implemented in R and bash that allows the quantification of active TEs in both model and non-model organisms. ExplorATE creates TE-specific indexes and uses the Selective Alignment (SA) to filter out co-transcribed transposons within genes based on alignment scores. Moreover, our software incorporates a Wicker-like criteria to refine a set of target TEs and avoid spurious mapping. Based on simulated and real data, we show that the SA strategy adopted by ExplorATE achieved better estimates of non-co-transcribed elements than other available alignment-based or mapping-based software. ExplorATE results showed high congruence with alignment-based tools with and without a reference genome, yet ExplorATE required less execution time. Likewise, ExplorATE expands and complements most previous TE analyses by incorporating the co-transcription and multi-mapping effects during quantification, and provides a seamless integration with other downstream tools within the R environment. AVAILABILITY AND IMPLEMENTATION: Source code is available at https://github.com/FemeniasM/ExplorATEproject and https://github.com/FemeniasM/ExplorATE_shell_script. Data available on request. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Assuntos
Elementos de DNA Transponíveis , Software , RNA-Seq , Sequenciamento do Exoma , Transcriptoma
3.
Syst Biol ; 71(2): 286-300, 2022 02 10.
Artigo em Inglês | MEDLINE | ID: mdl-34259868

RESUMO

Understanding the factors that cause heterogeneity among gene trees can increase the accuracy of species trees. Discordant signals across the genome are commonly produced by incomplete lineage sorting (ILS) and introgression, which in turn can result in reticulate evolution. Species tree inference using the multispecies coalescent is designed to deal with ILS and is robust to low levels of introgression, but extensive introgression violates the fundamental assumption that relationships are strictly bifurcating. In this study, we explore the phylogenomics of the iconic Liolaemus subgenus of South American lizards, a group of over 100 species mostly distributed in and around the Andes mountains. Using mitochondrial DNA (mtDNA) and genome-wide restriction site-associated DNA sequencing (RADseq; nDNA hereafter), we inferred a time-calibrated mtDNA gene tree, nDNA species trees, and phylogenetic networks. We found high levels of discordance between mtDNA and nDNA, which we attribute in part to extensive ILS resulting from rapid diversification. These data also reveal extensive and deep introgression, which combined with rapid diversification, explain the high level of phylogenetic discordance. We discuss these findings in the context of Andean orogeny and glacial cycles that fragmented, expanded, and contracted species distributions. Finally, we use the new phylogeny to resolve long-standing taxonomic issues in one of the most studied lizard groups in the New World.[Andes; ddRADSeq; introgression; lizards; mtDNA; reptiles; SNPs.].


Assuntos
Lagartos , Animais , DNA Mitocondrial/genética , Genoma , Lagartos/genética , Filogenia , América do Sul
4.
Mol Phylogenet Evol ; 157: 107046, 2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-33421613

RESUMO

Recent conceptual and methodological advances have enabled an increasing number of studies to address the problem of species delimitation in a comprehensive manner. This is of particular interest in cases of species whose divergence times are recent and/or effective population sizes are large, where the conclusions obtained from a single source of evidence may lead to erroneous estimations of true species numbers or incorrect assignment of individuals to species. Iguanian lizards of the Liolaemus kingii group (13 species) comprise an important component of the endemic fauna of Patagonia. The southernmost species of this group (namely L. baguali, L. escarchadosi, L. sarmientoi, and L. tari) show widely overlapping distributions across southern Patagonia, also, their phylogenetic relationships are ambiguous and species boundaries have not been explicitly tested. Here we use a comprehensive approach to assess species limits through the use of molecular and morphological information (mitochondrial cytb, nuclear sequences collected by ddRADseq, and linear, meristic and landmark-based morphometrics). We found support for the current taxonomy given that the different analyses recognized the nominal species (4 entities), also a candidate species was supported by mitochondrial and morphological data. In addition, we detected signs of admixture between some of the species. Our results indicate that the L. kingii group can serve as a model system in studies of diversification accompanied by hybridization in nature, which in turn might have been promoted by past climatic oscillations and generalist morphologies. We emphasize the importance of using multiple lines of evidence in order to solve evolutionary stories, and minimizing potential erroneous results that may arise when relying on a single source of information.


Assuntos
Lagartos/classificação , Análise de Variância , Animais , Citocromos b/genética , DNA Mitocondrial , Loci Gênicos , Geografia , Hibridização Genética , Lagartos/anatomia & histologia , Lagartos/genética , Filogenia , Polimorfismo de Nucleotídeo Único/genética , Análise de Componente Principal , Especificidade da Espécie
5.
Mol Phylogenet Evol ; 144: 106725, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-31884086

RESUMO

The clade Leiosaurae is composed of poorly-known species endemic to the southern region of South America. The difficulties of finding these lizards in the field, and their highly conserved morphology, have limited our taxonomic knowledge and understanding of their evolutionary histories. Here, we use data collected over 9 years to study the phylogenetic history, genetic diversity, and biogeographic history of almost all the southernmost species of Leiosaurae (except P. nigroigulus), including: Leiosaurus bellii, Diplolaemus darwinii, D. bibronii, D. sexcinctus and D. leopardinus. We use a fragment of the mitochondrial cytochrome-b gene to resolve general phylogeographic patterns, and add another mitochondrial gene and eight nuclear genes to perform species delimitation and phylogenetic analyses associated with divergence times. We found evidence for three putative new species-level taxa within L. bellii and five within Diplolaemus species, indicating high levels of geographic structure. We use a time-calibrated phylogeny to estimate ranges of ancestral distributions and to generate new hypotheses about their historical biogeography.


Assuntos
Ecossistema , Especiação Genética , Lagartos/classificação , Lagartos/genética , Animais , Evolução Biológica , DNA Mitocondrial/análise , DNA Mitocondrial/genética , Genes Mitocondriais , Filogenia , Filogeografia , América do Sul
6.
Mol Phylogenet Evol ; 147: 106781, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32147573

RESUMO

Phylogenomic approaches now generate hundreds of loci representative of the whole genome that can be used for phylogenetic analyses. The South American lizard genus Liolaemus is the most species-rich vertebrate radiation from temperate zones (more than 265 described species), yet most higher-level phylogenetic relationships within Liolaemus remain poorly resolved. In this study, we used 584 nuclear loci collected using targeted sequenced capture to estimate the phylogenetic relationships among 26 species representing the two subgenera within Liolaemus (Eulaemus + Liolaemus), and all major groups within Eulaemus. Previous molecular and morphological-based phylogenetic analyses of Eulaemus based on a limited number of characters resolved few higher-level relationships, although one point of agreement is that the early divergence within Eulaemus corresponds to the lineomaculatus section, followed by the diversification of eight main clades that are strongly supported and recognized. Liolaemus probably experienced relatively rapid divergences during parts of its evolutionary history, and a phylogenomic approach was used to resolve the relationships among the major groups. The new analyses presented here support the division of Liolaemus into two subgenera, and resolve relationships among many of the major clades of Eulaemus with strong support. A Bayesian divergence dating analysis using 44 protein-coding genes provides an estimation of the split of the two Liolaemus subgenera of approximately 19,7 ma (95% HPD = 16,94-23,04), while diversification within Eulaemus started at 15,05 ma (95% HPD = 12,94 - 17,59) among the L. lineomaculatus and the L. montanus series by Mid Miocene. A novel phylogenetic network analyses for SNP data identified two hybridizing edges among different groups of Eulaemus at different points in time. Having a solid phylogenetic hypothesis of the main Eulaemus clades opens new opportunities to test a variety of macroevolutionary questions for this unique radiation.


Assuntos
Lagartos/genética , Filogenia , Animais , Sequência de Bases , Teorema de Bayes , Geografia , Nucleotídeos/genética , Fatores de Tempo
7.
Mol Phylogenet Evol ; 150: 106861, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32497832

RESUMO

Southeast Asia hosts a rich concentration of biodiversity within multiple biodiversity hotspots. Indochina, a region with remarkably high levels of in situ diversification, possesses five major rivers (Ayeyarwady, Chiang Mai, Mekong, Red, and Salween), several of which coincide with phylogenetic breaks of terrestrial taxa. Draco maculatus possesses a range that stretches across Indochina, which widespread geographic distribution along with potential discrete variation within subspecies alludes to the possibility of this taxon constituting multiple divergent lineages. Using sequence data from three mitochondrial (12S, 16S, and ND2) and three nuclear (BDNF, CMOS, and PNN) genes, we provide the first estimated phylogeny of this hypothesized species complex and examine its phylogeographic architecture with maximum likelihood and Bayes factor delimitation (BFD) approaches. Our results support multiple divergent lineages with phylogenetic breaks coincident with rivers, indicating that river barriers may be contributing to the elevated levels of in situ diversification of Indochina.


Assuntos
Lagartos/classificação , Animais , Teorema de Bayes , Biodiversidade , Fator Neurotrófico Derivado do Encéfalo/classificação , Fator Neurotrófico Derivado do Encéfalo/genética , Indochina , Lagartos/genética , Mitocôndrias/genética , NADH Desidrogenase/classificação , NADH Desidrogenase/genética , Filogenia , Filogeografia , Subunidades Proteicas/classificação , Subunidades Proteicas/genética , RNA Ribossômico/classificação , RNA Ribossômico/genética
8.
Mol Phylogenet Evol ; 138: 89-101, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31128241

RESUMO

Coalescent-based algorithms coupled with the access to genome-wide data have become powerful tools for assessing questions on recent or rapid diversification, as well as delineating species boundaries in the absence of reciprocal monophyly. In southern South America, the diversification of Liolaemus lizards during the Pleistocene is well documented and has been attributed to the climatic changes that characterized this recent period of time. Past climatic changes had harsh effects at extreme latitudes, including Patagonia, but habitat changes at intermediate latitudes of South America have also been recorded, including expansion of sand fields over northern Patagonia and Pampas). In this work, we apply a coalescent-based approach to study the diversification of the Liolaemus wiegmannii species complex, a morphologically conservative clade that inhabits sandy soils across northwest and south-central Argentina, and the south shores of Uruguay. Using four standard sequence markers (mitochondrial DNA and three nuclear loci) along with ddRADseq data we inferred species limits and a time-calibrated species tree for the L. wiegmannii complex in order to evaluate the influence of Quaternary sand expansion/retraction cycles on diversification. We also evaluated the evolutionary independence of the recently described L. gardeli and inferred its phylogenetic position relative to L. wiegmannii. We find strong evidence for six allopatric candidate species within L. wiegmannii, which diversified during the Pleistocene. The Great Patagonian Glaciation (∼1 million years before present) likely split the species complex into two main groups: one composed of lineages associated with sub-Andean sedimentary formations, and the other mostly related to sand fields in the Pampas and northern Patagonia. We hypothesize that early speciation within L. wiegmannii was influenced by the expansion of sand dunes throughout central Argentina and Pampas. Finally, L. gardeli is supported as a distinct lineage nested within the L. wiegmannii complex.


Assuntos
Algoritmos , Lagartos/classificação , Animais , Argentina , Teorema de Bayes , Citocromos b/genética , DNA Mitocondrial/genética , Loci Gênicos , Variação Genética , Genoma , Geografia , Lagartos/genética , Filogenia , Análise de Componente Principal , Especificidade da Espécie , Fatores de Tempo , Uruguai
9.
Mol Phylogenet Evol ; 129: 226-241, 2018 12.
Artigo em Inglês | MEDLINE | ID: mdl-30201426

RESUMO

During the speciation process sibling lineages accumulate differences in time (e.g. genetic, morphological, and/or ecological). Phenotypic traits such as size or shape, however, could experience rapid changes or show stasis depending on their role in survival and reproduction. The clade Phymaturus patagonicus includes 26 species characterized by a conservative morphology, and all inhabit rock crevice microhabitats in arid environments. In this study we quantify levels of morphological divergence (size and shape) among the multiple species relative to interspecific molecular divergence, and show that most species have not diverged significantly in size and/or shape to permit unambiguous species diagnosis with morphological data alone. The influence of stabilizing selection for an adaptive optimum in body size and head shape was detected for 13 of the 16 variables analyzed in an Ornstein-Uhlenbeck model. The strict dependence of these species to rock-crevice microenvironments likely explains the observed morphological stasis across the many species of the Phymaturus patagonicus group.


Assuntos
Tamanho Corporal , Lagartos/anatomia & histologia , Lagartos/classificação , Filogenia , Animais , DNA Mitocondrial/genética , Lagartos/genética , Fenótipo , Análise de Componente Principal , Especificidade da Espécie
10.
Mol Phylogenet Evol ; 125: 243-254, 2018 08.
Artigo em Inglês | MEDLINE | ID: mdl-29555296

RESUMO

Rapid evolutionary radiations are difficult to resolve because divergence events are nearly synchronous and gene flow among nascent species can be high, resulting in a phylogenetic "bush". Large datasets composed of sequence loci from across the genome can potentially help resolve some of these difficult phylogenetic problems. A suitable test case is the Liolaemus fitzingerii species group of lizards, which includes twelve species that are broadly distributed in Argentinean Patagonia. The species in the group have had a complex evolutionary history that has led to high morphological variation and unstable taxonomy. We generated a sequence capture dataset for 28 ingroup individuals of 580 nuclear loci, alongside a mitogenomic dataset, to infer phylogenetic relationships among species in this group. Relationships among species were generally weakly supported with the nuclear data, and along with an inferred age of ∼2.6 million years old, indicate either rapid evolution, hybridization, incomplete lineage sorting, non-informative data, or a combination thereof. We inferred a signal of mito-nuclear discordance, indicating potential hybridization between L. melanops and L. martorii, and phylogenetic network analyses provided support for 5 reticulation events among species. Phasing the nuclear loci did not provide additional insight into relationships or suspected patterns of hybridization. Only one clade, composed of L. camarones, L. fitzingerii, and L. xanthoviridis was recovered across all analyses. Genomic datasets provide molecular systematists with new opportunities to resolve difficult phylogenetic problems, yet the lack of phylogenetic resolution in Patagonian Liolaemus is biologically meaningful and indicative of a recent and rapid evolutionary radiation. The phylogenetic relationships of the Liolaemus fitzingerii group may be best modeled as a reticulated network instead of a bifurcating phylogeny.


Assuntos
Genômica , Lagartos/genética , Filogenia , Animais , Sequência de Bases , DNA Mitocondrial/genética , Geografia , Hibridização Genética , Análise de Sequência de DNA , Especificidade da Espécie
11.
Mol Phylogenet Evol ; 127: 638-645, 2018 10.
Artigo em Inglês | MEDLINE | ID: mdl-29906606

RESUMO

The Pleistocenic Arc Hypothesis (PAH) posits that South American Seasonally Dry Tropical Forests (SDTF) were interconnected during Pleistocene glacial periods, enabling the expansion of species ranges that were subsequently fragmented in interglacial periods, promoting speciation. The lizard genus Lygodactylus occurs in Africa, Madagascar, and South America. Compared to the high diversity of African Lygodactylus, only two species are known to occur in South America, L. klugei and L. wetzeli, distributed in SDTFs and the Chaco, respectively. We use a phylogenetic approach based on mitochondrial (ND2) and nuclear (RAG-1) markers covering the known range of South American Lygodactylus to investigate (i) if they are monophyletic relative to their African congeners, (ii) if their divergence is congruent with the fragmentation of the PAH, and (iii) if cryptic diversity exists within currently recognized species. Maximum likelihood and Bayesian phylogenetic analyses recovered a well-supported monophyletic South American Lygodactylus, presumably resulting from a single trans-Atlantic dispersal event 29 Mya. Species delimitation analyses supported the existence of five putative species, three of them undescribed. Divergence times among L. klugei and the three putative undescribed species, all endemic to the SDTFs, are not congruent with the fragmentation of the PAH. However, fragmentation of the once broader and continuous SDTFs likely influenced the divergence of L. wetzeli in the Chaco and Lygodactylus sp. 3 (in a SDTF enclave in the Cerrado).


Assuntos
Evolução Biológica , Lagartos/classificação , Animais , Teorema de Bayes , Variação Genética , Geografia , Funções Verossimilhança , Lagartos/genética , Filogenia , América do Sul , Especificidade da Espécie , Fatores de Tempo
12.
J Evol Biol ; 31(6): 893-903, 2018 06.
Artigo em Inglês | MEDLINE | ID: mdl-29577500

RESUMO

Hybridization is likely to occur more often between closely related taxa that have had insufficient time to diverge to the point of reproductive incompatibility; hybridization between deeply divergent lineages is rare. In squamate reptiles, hybridization has been proposed as a possible explanation for the extensive paraphyly observed in mitochondrial gene trees in several species complexes of the South American lizard genus Liolaemus. One of the best-documented cases is within the L. boulengeri and L. rothi complexes, which diverged ~5.5 million years ago. Here, we describe a comprehensive study for approaching the hybridization hypothesis between these lizard species complexes. We explored the level of gene tree discordance using the novel 'extra lineage contribution' statistics (XLC, presented in this study) that quantifies the level of gene tree discordance contribution per individual within a species. We included molecular data (12 nuclear and two mitochondrial genes) from 127 individuals, and results of a coalescent model-based analysis show that the most likely explanation for the gene tree-species tree discordance is interspecific hybridization. Our best-supported hypothesis suggests current and past hybridization between L. rothi (rothi complex) and L. tehuelche (boulengeri complex), and independently between L. rothi and L. boulengeri and L. telsen (boulengeri complex). The hybrid descendants are characterized by intermediate phenotypes between the parental species, but are more similar to L. rothi in body size. We discuss the possible role of hybridization in Liolaemus evolution.


Assuntos
Hibridização Genética , Lagartos/genética , Animais , Especiação Genética , Variação Genética
13.
Mol Ecol ; 26(18): 4756-4771, 2017 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-28734050

RESUMO

Many studies propose that Quaternary climatic cycles contracted and/or expanded the ranges of species and biomes. Strong expansion-contraction dynamics of biomes presume concerted demographic changes of associated fauna. The analysis of temporal concordance of demographic changes can be used to test the influence of Quaternary climate on diversification processes. Hierarchical approximate Bayesian computation (hABC) is a powerful and flexible approach that models genetic data from multiple species, and can be used to estimate the temporal concordance of demographic processes. Using available single-locus data, we can now perform large-scale analyses, both in terms of number of species and geographic scope. Here, we first compared the power of four alternative hABC models for a collection of single-locus data. We found that the model incorporating an a priori hypothesis about the timing of simultaneous demographic change had the best performance. Second, we applied the hABC models to a data set of seven squamate and four amphibian species occurring in the Seasonally Dry Tropical Forests (Caatinga) in northeastern Brazil, which, according to paleoclimatic evidence, experienced an increase in aridity during the Pleistocene. If this increase was important for the diversification of associated xeric-adapted species, simultaneous population expansions should be evident at the community level. We found a strong signal of synchronous population expansion in the Late Pleistocene, supporting the increase of the Caatinga during this time. This expansion likely enhanced the formation of communities adapted to high aridity and seasonality and caused regional extirpation of taxa adapted to wet forest.


Assuntos
Anfíbios/classificação , Biota , Modelos Genéticos , Répteis/classificação , Animais , Teorema de Bayes , Brasil , Clima , Florestas , Filogenia , Filogeografia , Dinâmica Populacional
14.
Mol Phylogenet Evol ; 107: 56-63, 2017 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-27637991

RESUMO

Currently, Liolaemus is the second most species-rich reptile genus in the world (257 species), and predictions of its real diversity suggest that it may be the most diverse genus. Originally, Liolaemus species were described as widely distributed and morphologically variable taxa, but extensive sampling in previously unexplored geographic areas, coupled with molecular and more extensive morphological studies, have discovered an unexpectedly high number of previously undetected species. Here, we study the level of molecular vs. morphological divergence within the L. rothi complex, combining a total of 14 loci (2 mitochondrial and 12 nuclear loci) for 97 individuals, as well as morphological data (nine morphometric and 15 color pattern variables), that represent all six described species of the L. rothi complex, plus two candidate species. We use the multi-coalescent species delimitation program iBPP and resolve strong differences in molecular divergence; and each species is inferred as an independent lineage supported by high posterior probabilities. However, morphological differences are not that clear, and our modeling of morphological characters suggests differential selection pressures implying some level of morphological stasis. We discuss the role of natural selection on phenotypic traits, which may be an important factor in "hiding" the real diversity of the genus.


Assuntos
Lagartos/classificação , Animais , Biodiversidade , Loci Gênicos , Lagartos/anatomia & histologia , Lagartos/genética , Fenótipo , Filogenia
15.
Mol Phylogenet Evol ; 116: 157-171, 2017 11.
Artigo em Inglês | MEDLINE | ID: mdl-28887150

RESUMO

The complex orogenic history and structure of Southern South America, coupled with Pleistocene glacial cycles, have generated paleoclimatic and environmental changes that influenced the spatial distribution and genetic composition of natural populations. Despite the increased number of phylogeographic studies in this region and given the frequent idiosyncratic phylogeographic patterns, there is still the need to focus research especially on species that are currently distributed within a wide range of bioclimatic regimes, and that historically have been subject to contrasting scenarios. Liolaemus tenuis is a widely distributed lizard species inhabiting latitudinally in almost 1000km through central and southern Chile. Here we describe the geographical patterns of genetic variation and lineage diversification within L. tenuis, and their association with geography and Pleistocene glaciations, using sequences from one mitochondrial and two nuclear genes, and five microsatellite loci, and covering most of the species distributional range. Our results revealed a high diversity both within and among populations, as well as two phylogeographic breaks, which are consistent with two of the larger rivers of central Chile, the Maipo and Biobío Rivers. Liolaemus tenuis is characterized by several allopatric lineages, especially in its north and central range, which suggest a history of multiple vicariance processes. Conversely, populations found in the southern range, south of the Biobío River, show signatures of recent decreases in effective population sizes, coupled with recent range expansions and secondary contact. Niche "envelope" data are consistent with patterns of genetic variation; both suggest a history of discontinuous areas of relatively stable populations throughout all of the distribution of L. tenuis. These data are also consistent with higher probabilities of habitat suitability north of the Maipo River (ca. 33°S), in both coastal areas and the "Intermediate Depression" between 34° and 37°S, as well as in the southern Coastal Cordillera between the Biobío and Araucanía regions. Interestingly, both molecular and niche envelope modeling data suggest that some populations may have persisted in fragmented refugia in Andean valleys, within the limits of the ice sheet. Finally, our results suggest that several populations of L. tenuis colonized glaciated regions from refugial areas in lowlands and coastal regions, and in the southern distribution, historic migration events would have occurred from refugial areas within the limits of the ice sheet.


Assuntos
Evolução Biológica , Mudança Climática , Geografia , Lagartos/fisiologia , Animais , Chile , DNA Mitocondrial/genética , Ecossistema , Variação Genética , Haplótipos/genética , Lagartos/genética , Repetições de Microssatélites/genética , Filogenia , Filogeografia
17.
Mol Phylogenet Evol ; 103: 75-84, 2016 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-27395779

RESUMO

A well-known issue in phylogenetics is discordance among gene trees, species trees, morphology, and other data types. Gene-tree discordance is often caused by incomplete lineage sorting, lateral gene transfer, and gene duplication. Multispecies-coalescent methods can account for incomplete lineage sorting and are believed by many to be more accurate than concatenation. However, simulation studies and empirical data have demonstrated that concatenation and species tree methods often recover similar topologies. We use three popular methods of phylogenetic reconstruction (one concatenation, two species tree) to evaluate relationships within Teiidae. These lizards are distributed across the United States to Argentina and the West Indies, and their classification has been controversial due to incomplete sampling and the discordance among various character types (chromosomes, DNA, musculature, osteology, etc.) used to reconstruct phylogenetic relationships. Recent morphological and molecular analyses of the group resurrected three genera and created five new genera to resolve non-monophyly in three historically ill-defined genera: Ameiva, Cnemidophorus, and Tupinambis. Here, we assess the phylogenetic relationships of the Teiidae using "next-generation" anchored-phylogenomics sequencing. Our final alignment includes 316 loci (488,656bp DNA) for 244 individuals (56 species of teiids, representing all currently recognized genera) and all three methods (ExaML, MP-EST, and ASTRAL-II) recovered essentially identical topologies. Our results are basically in agreement with recent results from morphology and smaller molecular datasets, showing support for monophyly of the eight new genera. Interestingly, even with hundreds of loci, the relationships among some genera in Tupinambinae remain ambiguous (i.e. low nodal support for the position of Salvator and Dracaena).


Assuntos
Lagartos/classificação , Animais , Cromossomos/genética , Etiquetas de Sequências Expressas , Loci Gênicos , Lagartos/anatomia & histologia , Lagartos/genética , Filogenia
18.
Mol Ecol ; 22(14): 3653-5, 2013 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-24003452

RESUMO

In this issue of Molecular Ecology, Neuwald & Templeton (2013) report on a 22-year study of natural populations of Collared Lizards (Crotaphytus collaris) that evolved on isolated on rock outcrops ('glades') in the Ozark Mountains in eastern Missouri. This ecosystem was originally maintained by frequent fires that kept the forest understory open, but fire-suppression was adopted as official policy in about 1945, which led to a loss of native biodiversity, including local extinctions of some lizard populations. Policies aimed at restoring biodiversity included controlled burns and re-introductions of lizards to some glades, which began in 1984. Populations were monitored from 1984­2006, and demographic and genetic data collected from 1 679 lizards were used to documents shifts in meta-population dynamics over four distinct phases of lizard recovery: 1­an initial translocation of lizards drawn from the same source populations onto three glades that were likely part of one metapopulation; 2­a period of isolation and genetic drift associated with the absence of fires; 3­a period of rapid colonization and population increase following restoration of fire; and 4­stabilization of the meta-population under regular prescribed burning. This study system thus provides a rare opportunity to characterize the dynamics of a landscape-scale management strategy on the restoration of the meta-population of a reintroduced species; long-term case studies of the extinction, founding, increase, and stabilization of a well-defined meta-population, based on both demographic and population genetic data, are rare in the conservation, ecological, and evolutionary literature.


Assuntos
Incêndios , Variação Genética , Lagartos/genética , Animais
19.
Mol Ecol ; 22(15): 4038-54, 2013 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-23786355

RESUMO

Until recently, most phylogeographic approaches have been unable to distinguish between demographic and range expansion processes, making it difficult to test for the possibility of range expansion without population growth and vice versa. In this study, we applied a Bayesian phylogeographic approach to reconstruct both demographic and range expansion in the lizard Liolaemus darwinii of the Monte Desert in Central Argentina, during the Late Quaternary. Based on analysis of 14 anonymous nuclear loci and the cytochrome b mitochondrial DNA gene, we detected signals of demographic expansion starting at ~55 ka based on Bayesian Skyline and Skyride Plots. In contrast, Bayesian relaxed models of spatial diffusion suggested that range expansion occurred only between ~95 and 55 ka, and more recently, diffusion rates were very low during demographic expansion. The possibility of population growth without substantial range expansion could account for the shared patterns of demographic expansion during the Last Glacial Maxima (OIS 2 and 4) in fish, small mammals and other lizards of the Monte Desert. We found substantial variation in diffusion rates over time, and very high rates during the range expansion phase, consistent with a rapidly advancing expansion front towards the southeast shown by palaeo-distribution models. Furthermore, the estimated diffusion rates are congruent with observed dispersal rates of lizards in field conditions and therefore provide additional confidence to the temporal scale of inferred phylogeographic patterns. Our study highlights how the integration of phylogeography with palaeo-distribution models can shed light on both demographic and range expansion processes and their potential causes.


Assuntos
DNA Mitocondrial/genética , Evolução Molecular , Iguanas/genética , Animais , Argentina , Teorema de Bayes , Citocromos b/genética , Demografia , Clima Desértico , Ecossistema , Variação Genética , Genética Populacional , Mitocôndrias/genética , Filogeografia , Análise de Sequência de DNA
20.
Mol Phylogenet Evol ; 66(3): 694-714, 2013 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-23142698

RESUMO

The lizard genus Phymaturus is widely distributed in Argentina and along the eastern edge of Chile between 25° and 45° south. We sampled 27 of the 38 currently recognized species plus 22 candidate species using two mitochondrial genes (cytb and 12S), four protein coding nuclear genes and seven anonymous nuclear loci, and present the first comprehensive molecular phylogenetic hypothesis for the clade. We recovered two large clades (the palluma or northern group and patagonicus or southern group) previously recognized on the basis of morphological and mitochondrial sequence evidence, and compared results obtained from concatenated-gene analyses with results of a coalescent-based species-tree approach (BEST). With both methods we identified four main clades within the palluma group (mallimaccii, roigorum, verdugo, and vociferator) and five main clades within the patagonicus group (calcogaster, indistinctus, payuniae, somuncurensis, and spurcus). We found several instances of non-monophyly with cytb and cases of incongruence between mitochondrial vs nuclear data for which we discuss alternative hypotheses. Although with lower support values, combined BEST results are more congruent with concatenated nuclear data than with combined concatenated analyses, suggesting that BEST is less influenced by demographic processes than combined concatenated analyses. We discuss the taxonomic, biogeographic and conservation implications of these results and how the future integration of phylogeographic and morphological approaches will allow the further testing of demographic and biogeographic hypotheses.


Assuntos
Biodiversidade , Evolução Molecular , Lagartos/genética , Filogenia , Animais , Argentina , Sequência de Bases , Teorema de Bayes , Chile , Funções Verossimilhança , Lagartos/classificação , Modelos Genéticos , Dados de Sequência Molecular , Filogeografia , Alinhamento de Sequência , Análise de Sequência de DNA , Especificidade da Espécie
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