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1.
Zootaxa ; 4638(2): zootaxa.4638.2.1, 2019 Jul 16.
Artigo em Inglês | MEDLINE | ID: mdl-31712473

RESUMO

An integrative taxonomic analysis of the Ptychozoon lionotum group across its range in Indochina and Sundaland recovers P. lionotum sensu lato Annandale, 1905 as paraphyletic with respect to P. popaense Grismer, Wood, Thura, Grismer, Brown, Stuart, 2018a and composed of four allopatric, genetically divergent, ND2 mitochondrial lineages. Multivariate and univariate analyses of continuous and discrete morphological and color pattern characters statistically and discretely diagnose each lineage from one another and together, with maximum likelihood and Bayesian inference analyses, provide the foundation for the recognition of each lineage as a new species-hypotheses corroborated with a Generalized Mixed Yule Coalescent species delimitation analysis. Ptychozoon cicakterbang sp. nov. ranges throughout Peninsular Malaysia to Pulau Natuna Besar, Indonesia; P. kabkaebin sp. nov. is endemic to northern and central Laos; and P. tokehos sp. nov. ranges from southern Thailand south of the Isthmus of Kra northward to Chiang Mai, fringing the Chao Phraya Basin and ranging southward through Cambodia to southern Vietnam. Ptychozoon lionotum sensu stricto ranges from northwestern Laos through southern Myanmar to eastern India. The phylogeographic structure within each species varies considerably with P. lionotum s.s. showing no genetic divergence across its 1,100 km range compared to P. cicakterbang sp. nov. showing upwards of 8.2% sequence divergence between syntopic individuals. Significant phylogeographic structure exists within P. tokehos sp. nov. and increased sampling throughout Thailand may require additional taxonomic changes within this species.


Assuntos
Lagartos , Filogenia , Animais , Ásia , Teorema de Bayes , Variação Genética , Indochina
2.
Zootaxa ; 4661(1): zootaxa.4661.1.2, 2019 Aug 27.
Artigo em Inglês | MEDLINE | ID: mdl-31716716

RESUMO

We report the first occurrence of the Asian Rock Gecko genus Cnemaspis Strauch, 1887 from mainland Myanmar based on a series of specimens recently collected from the Tanintharyi Region. These records come from several localities in the Tanintharyi Region and fill a significant sampling gap for the genus. Molecular phylogenetic analyses using the mitochondrial gene ND2 identify two distinct clades, the first includes Cnemaspis siamensis of the Southeast Asian Cnemaspis group and the second includes two new species belonging to the South Asian Cnemaspis kandiana group. These two species are morphologically distinct and are distinguished from all other members in the C. kandiana group by a combination of character states. The first species, Cnemaspis tanintharyi sp. nov. occurs on the mainland in southern Tanintharyi and is distinguished from all congeners by the possession of keeled pectoral scales; smooth ventral scales and abdominal scales; 2-4 precloacal pores; 4-5 femoral pores on each leg; smooth subcaudal scales with the median row enlarged; coloration of the gular region beige, dark gray-brown with dark blue hueing towards throat; 15-18 subdigital lamellae on the 4th toe; and 21-23 ventral scales at midbody. The other, Cnemaspis thayawthadangyi sp. nov. is known only from the island group of Thayawthadangyi, in the Myeik Archipelago and is distinguished from all congeners by the possession of keeled pectoral scales; keeled ventral scales and abdominal scales; three precloacal pores; four femoral pores on each leg; smooth subcaudal scales, scales on median row enlarged; coloration of the gular region silver with dark-gray irregularly shaped streaks; 16-18 subdigital lamellae on the 4th toe; and 18-20 ventral scales at midbody. In addition, we address the taxonomic status of populations referred to as C. kandiana (a species now restricted to Sri Lanka) found in peninsular Thailand and provisionally assign them as C. cf. tanintharyi sp. nov. until further analysis can be conducted. Finally, we briefly discuss the biogeography of the South Asian clade of Cnemaspis.


Assuntos
Lagartos , Distribuição Animal , Estruturas Animais , Animais , Ecossistema , Ilhas , Mianmar , Filogenia , Sri Lanka , Tailândia
3.
Zookeys ; (757): 85-152, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29780268

RESUMO

Despite threats of species extinctions, taxonomic crises, and technological advances in genomics and natural history database informatics, we are still distant from cataloguing all of the species of life on earth. Amphibians and reptiles are no exceptions; in fact new species are described nearly every day and many species face possible extinction. The number of described species continues to climb as new areas of the world are explored and as species complexes are examined more thoroughly. The use of DNA barcoding provides a mechanism for rapidly estimating the number of species at a given site and has the potential to record all of the species of life on Earth. Though DNA barcoding has its caveats, it can be useful to estimate the number of species in a more systematic and efficient manner, to be followed in combination with more traditional, morphology-based identifications and species descriptions. Herein, we report the results of a voucher-based herpetological expedition to the Tanintharyi (Tenasserim) Region of Myanmar, enhanced with DNA barcode data. Our main surveys took place in the currently proposed Tanintharyi National Park. We combine our results with photographs and observational data from the Chaung-nauk-pyan forest reserve. Additionally, we provide the first checklist of amphibians and reptiles of the region, with species based on the literature and museum. Amphibians, anurans in particular, are one of the most poorly known groups of vertebrates in terms of taxonomy and the number of known species, particularly in Southeast Asia. Our rapid-assessment program combined with DNA barcoding and use of Barcode Index Numbers (BINs) of voucher specimens reveals the depth of taxonomic diversity in the southern Tanintharyi herpetofauna even though only a third of the potential amphibians and reptiles were seen. A total of 51 putative species (one caecilian, 25 frogs, 13 lizards, 10 snakes, and two turtles) were detected, several of which represent potentially undescribed species. Several of these species were detected by DNA barcode data alone. Furthermore, five species were recorded for the first time in Myanmar, two amphibians (Ichthyophis cf. kohtaoensis and Chalcorana eschatia) and three snakes (Ahaetulla mycterizans, Boiga dendrophila, and Boiga drapiezii).

4.
Curr Opin Insect Sci ; 25: 91-98, 2018 02.
Artigo em Inglês | MEDLINE | ID: mdl-29602368

RESUMO

Genome sequencing initiatives like the Arthropod i5k project and other biodiversity genomics research rely on access to high quality DNA and/or tissue. Global collection initiatives such as the Smithsonian Global Genome Initiative (GGI) and its partner network, the Global Genome Biodiversity Network (GGBN) aim to provide access to these resources at high-quality standards. Here, we review progress toward providing genomic resources (tissues, DNA, genomes) for terrestrial arthropods, a megadiverse animal group, and compare progress in genome sequencing to all other animals.


Assuntos
Artrópodes/genética , Genoma , Animais , Biodiversidade , Bases de Dados Genéticas
5.
Zootaxa ; 4347(2): 301-315, 2017 Nov 13.
Artigo em Inglês | MEDLINE | ID: mdl-29245596

RESUMO

The taxonomic identity of the Trimeresurus (Popeia) popeiorum complex from the Isthmus of Kra and to the north was investigated. Several studies over the last decade have produced several specimens and associated mtDNA sequence data for a variety of individuals of the T. popeiorum and "T. sabahi" complexes. Here, we combine four mitochondrial genes (12S, 16S, ND4, and CytB) from all available specimens in GenBank with the addition of five new specimens collected from the mainland, Tanintharyi Region of Myanmar. Maximum Likelihood and Bayesian analyses identified that T. popeiorum sensu lato is paraphyletic with two geographically distinct clades: a northern clade representing populations from northern Myanmar, Laos and northern Thailand and a southern clade representing samples from the Tanintharyi Region and adjacent west Thailand. While the two clades have considerable genetic distance, they appear to be morphologically identical, leading to the hypothesis that the southern clade represents a cryptic, undescribed species. Because they appear to be cryptic species and the limitation of only five specimens from the southern lineage, this does not permit us to formally describe the new species. In accordance to past molecular studies, we uncovered paraphyly and lack of genetic support for the validity of taxa within the T. sabahi complex. However, we suggest recognizing these populations as subspecies within T. sabahi.


Assuntos
Trimeresurus , Animais , Teorema de Bayes , DNA Mitocondrial , Laos , Mianmar , Filogenia , Análise de Sequência de DNA , Tailândia
6.
PhytoKeys ; (88): 119-122, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-29118648

RESUMO

The Global Genome Initiative has sequenced and released 1961 DNA barcodes for genetic samples obtained as part of the Global Genome Initiative for Gardens Program. The dataset includes barcodes for 29 plant families and 309 genera that did not have sequences flagged as barcodes in GenBank and sequences from officially recognized barcoding genetic markers meet the data standard of the Consortium for the Barcode of Life. The genetic samples were deposited in the Smithsonian Institution's National Museum of Natural History Biorepository and their records were made public through the Global Genome Biodiversity Network's portal. The DNA barcodes are now available on GenBank.

7.
PLoS One ; 12(11): e0187283, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-29131846

RESUMO

Development projects in west Central Africa are proceeding at an unprecedented rate, often with little concern for their effects on biodiversity. In an attempt to better understand potential impacts of a road development project on the anuran amphibian community, we conducted a biodiversity assessment employing multiple methodologies (visual encounter transects, auditory surveys, leaf litter plots and pitfall traps) to inventory species prior to construction of a new road within the buffer zone of Moukalaba-Doudou National Park, Gabon. Because of difficulties in morphological identification and taxonomic uncertainty of amphibian species observed in the area, we integrated a DNA barcoding analysis into the project to improve the overall quality and accuracy of the species inventory. Based on morphology alone, 48 species were recognized in the field and voucher specimens of each were collected. We used tissue samples from specimens collected at our field site, material available from amphibians collected in other parts of Gabon and the Republic of Congo to initiate a DNA barcode library for west Central African amphibians. We then compared our sequences with material in GenBank for the genera recorded at the study site to assist in identifications. The resulting COI and 16S barcode library allowed us to update the number of species documented at the study site to 28, thereby providing a more accurate assessment of diversity and distributions. We caution that because sequence data maintained in GenBank are often poorly curated by the original submitters and cannot be amended by third-parties, these data have limited utility for identification purposes. Nevertheless, the use of DNA barcoding is likely to benefit biodiversity inventories and long-term monitoring, particularly for taxa that can be difficult to identify based on morphology alone; likewise, inventory and monitoring programs can contribute invaluable data to the DNA barcode library and the taxonomy of complex groups. Our methods provide an example of how non-taxonomists and parataxonomists working in understudied parts of the world with limited geographic sampling and comparative morphological material can use DNA barcoding and publicly available sequence data (GenBank) to rapidly identify the number of species and assign tentative names to aid in urgent conservation management actions and contribute to taxonomic resolution.


Assuntos
Anfíbios/genética , Conservação dos Recursos Naturais , Código de Barras de DNA Taxonômico , África Central , Anfíbios/classificação , Animais , Especificidade da Espécie , Incerteza
8.
PLoS One ; 12(4): e0174432, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28403189

RESUMO

Myanmar's recent transition from military rule towards a more democratic government has largely ended decades of political and economic isolation. Although Myanmar remains heavily forested, increased development in recent years has been accompanied by exceptionally high rates of forest loss. In this study, we document the rapid progression of deforestation in and around the proposed Lenya National Park, which includes some of the largest remaining areas of lowland evergreen rainforest in mainland Southeast Asia. The globally unique forests in this area are rich in biodiversity and remain a critical stronghold for many threatened and endangered species, including large charismatic fauna such as tiger and Asian elephant. We also conducted a rapid assessment survey of the herpetofauna of the proposed national park, which resulted in the discovery of two new species of bent-toed geckos, genus Cyrtodactylus. We describe these new species, C. lenya sp. nov. and C. payarhtanensis sp. nov., which were found in association with karst (i.e., limestone) rock formations within mature lowland wet evergreen forest. The two species were discovered less than 35 km apart and are each known from only a single locality. Because of the isolated nature of the karst formations in the proposed Lenya National Park, these geckos likely have geographical ranges restricted to the proposed protected area and are threatened by approaching deforestation. Although lowland evergreen rainforest has vanished from most of continental Southeast Asia, Myanmar can still take decisive action to preserve one of the most biodiverse places on Earth.


Assuntos
Conservação dos Recursos Naturais , Espécies em Perigo de Extinção , Lagartos/genética , Distribuição Animal , Animais , Feminino , Florestas , Variação Genética , Lagartos/anatomia & histologia , Masculino , Mianmar , Parques Recreativos , Filogenia , Análise de Sequência de DNA
9.
Zookeys ; (657): 141-156, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28331413

RESUMO

Recent fieldwork in southern Tanintharyi revealed the presence of a small Green Crested Lizard in the wet evergreen forest. We generated mtDNA sequence data (ND2) that demonstrates that this population's nearest relative is Bronchocela rayaensis Grismer et al., 2015 of Pulau Langkawi, northwestern Peninsular Malaysia and Phuket Island. Morphologically the Burmese Bronchocela shares many features with Bronchocela rayaensis, which potentially would make this recently described Thai-Malay species a synonym of Bronchocela burmana Blanford, 1878; however, we interpret the genetic and morphological differences to reflect evolutionary divergence and recommend the recognition of both species.

10.
PeerJ ; 4: e2528, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27761327

RESUMO

Advances in biodiversity genomic sequencing will increasingly depend on the availability of DNA samples-and their quantifiable metadata-preserved in large institutional biorepositories that are discoverable to the scientific community. Improvements in sequencing technology constantly provide longer reads, such that longer fragment length, higher molecular weight, and overall "genome-quality" DNA (gDNA) will be desirable. Ideally, biorepositories should publish numerical scale measurements of DNA quality useful to the user community. However, the most widely used technique to evaluate DNA quality, the classic agarose gel, has yet to be quantified. Here we propose a simple and economical method using open source image analysis software to make gDNA gel images quantifiable, and propose percentage of gDNA "greater than X kb" as a standard of comparison, where X is a band from any widely used DNA ladder with desirably large band sizes. We employ two metadata standards ("DNA Threshold" and "Percent above Threshold") introduced as part of the Global Genome Biodiversity Network (GGBN) Darwin Core extension. We illustrate the method using the traditionally used HindIII ladder and the 9,416 base-pair (bp) band as a standard. We also present data, for two taxa, a vertebrate (fish) and an invertebrate (crab), on how gDNA quality varies with seven tissue preservation methods, time since death, preservation method (i.e. buffers vs. cold temperatures), and storage temperature of various buffers over time. Our results suggest that putting tissue into a buffer prior to freezing may be better than directly into ultra-cold conditions.

11.
Ecography (Cop.) ; 39(5): 437-448, 2016 May.
Artigo em Inglês | MEDLINE | ID: mdl-27231410

RESUMO

During climate change, species are often assumed to shift their geographic distributions (geographic ranges) in order to track environmental conditions - niches - to which they are adapted. Recent work, however, suggests that the niches do not always remain conserved during climate change but shift instead, allowing populations to persist in place or expand into new areas. We assessed the extent of range and niche shifts in response to the warming climate after the Last Glacial Maximum (LGM) in the desert horned lizard (Phrynosoma platyrhinos), a species occupying the western deserts of North America. We used a phylogeographic approach with mitochondrial DNA sequences to approximate the species range during the LGM by identifying populations that exhibit a genetic signal of population stability versus those that exhibit a signal of a recent (likely post-LGM) geographic expansion. We then compared the climatic niche that the species occupies today with the niche it occupied during the LGM using two models of simulated LGM climate. The genetic analyses indicated that P. platyrhinos persisted within the southern Mojave and Sonoran deserts throughout the latest glacial period and expanded from these deserts northwards, into the western and eastern Great Basin, after the LGM. The climatic niche comparisons revealed that P. platyrhinos expanded its climatic niche after the LGM towards novel, warmer and drier climates that allowed it to persist within the southern deserts. Simultaneously, the species shifted its climatic niche towards greater temperature and precipitation fluctuations after the LGM. We concluded that climatic changes at the end of the LGM promoted both range and niche shifts in this lizard. The mechanism that allowed the species to shift its niche remains unknown, but phenotypic plasticity likely contributes to the species ability to adjust to climate change.

12.
Conserv Biol ; 30(1): 72-81, 2016 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-26243724

RESUMO

Phylogenetic analysis of extinction threat is an emerging tool in the field of conservation. However, there are problems with the methods and data as commonly used. Phylogenetic sampling usually extends to the level of family or genus, but International Union for Conservation of Nature (IUCN) rankings are available only for individual species, and, although different species within a taxonomic group may have the same IUCN rank, the species may have been ranked as such for different reasons. Therefore, IUCN rank may not reflect evolutionary history and thus may not be appropriate for use in a phylogenetic context. To be used appropriately, threat-risk data should reflect the cause of extinction threat rather than the IUCN threat ranking. In a case study of the toad genus Incilius, with phylogenetic sampling at the species level (so that the resolution of the phylogeny matches character data from the IUCN Red List), we analyzed causes of decline and IUCN threat rankings by calculating metrics of phylogenetic signal (such as Fritz and Purvis' D). We also analyzed the extent to which cause of decline and threat ranking overlap by calculating phylogenetic correlation between these 2 types of character data. Incilius species varied greatly in both threat ranking and cause of decline; this variability would be lost at a coarser taxonomic resolution. We found far more phylogenetic signal, likely correlated with evolutionary history, for causes of decline than for IUCN threat ranking. Individual causes of decline and IUCN threat rankings were largely uncorrelated on the phylogeny. Our results demonstrate the importance of character selection and taxonomic resolution when extinction threat is analyzed in a phylogenetic context.


Assuntos
Biodiversidade , Bufonidae , Conservação dos Recursos Naturais , Espécies em Perigo de Extinção , Animais , Filogenia
13.
PLoS One ; 10(3): e0118199, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-25803280

RESUMO

Squamate reptiles (lizards and snakes) are a pivotal group whose relationships have become increasingly controversial. Squamates include >9000 species, making them the second largest group of terrestrial vertebrates. They are important medicinally and as model systems for ecological and evolutionary research. However, studies of squamate biology are hindered by uncertainty over their relationships, and some consider squamate phylogeny unresolved, given recent conflicts between molecular and morphological results. To resolve these conflicts, we expand existing morphological and molecular datasets for squamates (691 morphological characters and 46 genes, for 161 living and 49 fossil taxa, including a new set of 81 morphological characters and adding two genes from published studies) and perform integrated analyses. Our results resolve higher-level relationships as indicated by molecular analyses, and reveal hidden morphological support for the molecular hypothesis (but not vice-versa). Furthermore, we find that integrating molecular, morphological, and paleontological data leads to surprising placements for two major fossil clades (Mosasauria and Polyglyphanodontia). These results further demonstrate the importance of combining fossil and molecular information, and the potential problems of estimating the placement of fossil taxa from morphological data alone. Thus, our results caution against estimating fossil relationships without considering relevant molecular data, and against placing fossils into molecular trees (e.g. for dating analyses) without considering the possible impact of molecular data on their placement.


Assuntos
Fósseis , Lagartos/classificação , Serpentes/classificação , Animais , Evolução Biológica , Bases de Dados Factuais , Bases de Dados Genéticas , Lagartos/genética , Filogenia , Serpentes/genética
14.
PLoS One ; 9(5): e97682, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-24837300

RESUMO

Vertebrates are currently going extinct at an alarming rate, largely because of habitat loss, global warming, infectious diseases, and human introductions. Island ecosystems are particularly vulnerable to invasive species and other ecological disturbances. Properly documenting historic and current species distributions is critical for quantifying extinction events. Museum specimens, field notes, and other archived materials from historical expeditions are essential for documenting recent changes in biodiversity. The Islas Revillagigedo are a remote group of four islands, 700-1100 km off the western coast of mainland México. The islands are home to many endemic plants and animals recognized at the specific- and subspecific-levels, several of which are currently threatened or have already gone extinct. Here, we recount the initial discovery of an endemic snake Hypsiglena ochrorhyncha unaocularus Tanner on Isla Clarión, the later dismissal of its existence, its absence from decades of field surveys, our recent rediscovery, and recognition of it as a distinct species. We collected two novel complete mitochondrial (mt) DNA genomes and up to 2800 base-pairs of mtDNA from several other individuals, aligned these with previously published mt-genome data from samples throughout the range of Hypsiglena, and conducted phylogenetic analyses to infer the biogeographic origin and taxonomic status of this population. We found the Isla Clarión population to be most closely related to populations in the Sonora-Sinaloa state border area of mainland México and Isla Santa Catalina, in the Gulf of California. Based on genetics, morphology, and geographic distributions, we also recognize these two other lineages as distinct species. Our study shows the importance of museum specimens, field notes, and careful surveys to accurately document biodiversity and brings these island endemics (Clarión and Santa Catalina nightsnakes) and mainland population near the Sonora-Sinaloa state border to the attention of conservation biologists currently monitoring biodiversity in these fragile subtropical ecosystems.


Assuntos
Serpentes/classificação , Serpentes/genética , Animais , Biodiversidade , California , DNA Mitocondrial , Genoma Mitocondrial , Ilhas , México , Oceano Pacífico , Filogenia
15.
Zootaxa ; 3626: 77-93, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-26176127

RESUMO

The salamander family Hynobiidae contains over 50 species and has been the subject of a number of molecular phylogenetic investigations aimed at reconstructing branches across the entire family. In general, studies using the greatest amount of sequence data have used reduced taxon sampling, while the study with the greatest taxon sampling has used a limited sequence data set. Here, we provide insights into the phylogenetic history of the Hynobiidae using both dense taxon sampling and a large mitochondrial DNA sequence data set. We report exclusive new mitochondrial DNA data of 2566 aligned bases (with 151 excluded sites, of included sites 1157 are variable with 957 parsimony informative). This is sampled from two genic regions encoding a 12S-16S region (the 3' end of 12S rRNA, tRNA(VAI), and the 5' end of 16S rRNA), and a ND2-COI region (ND2, tRNA(Trp), tRNA(Ala), tRNA(Asn), the origin for light strand replication--O(L), tRNA(Cys), tRNAT(Tyr), and the 5' end of COI). Analyses using parsimony, Bayesian, and maximum likelihood optimality criteria produce similar phylogenetic trees, with discordant branches generally receiving low levels of branch support. Monophyly of the Hynobiidae is strongly supported across all analyses, as is the sister relationship and deep divergence between the genus Onychodactylus with all remaining hynobiids. Within this latter grouping our phylogenetic results identify six clades that are relatively divergent from one another, but for which there is minimal support for their phylogenetic placement. This includes the genus Batrachuperus, the genus Hynobius, the genus Pachyhynobius, the genus Salamandrella, a clade containing the genera Ranodon and Paradactylodon, and a clade containing the genera Liua and Pseudohynobius. This latter clade receives low bootstrap support in the parsimony analysis, but is consistent across all three analytical methods. Our results also clarify a number of well-supported relationships within the larger Batrachuperus and Hynobius clades. While the relationships identified in this study do much to clarify the phylogenetic history of the Hynobiidae, the poor resolution among major hynobiid clades, and the contrast of mtDNA-derived relationships with recent phylogenetic results from a small number of nuclear genes, highlights the need for continued phylogenetic study with larger numbers of nuclear loci.


Assuntos
Proteínas de Anfíbios/genética , DNA Mitocondrial/genética , Filogenia , Urodelos/classificação , Urodelos/genética , Animais , Ásia , Teorema de Bayes , Proteínas Mitocondriais/genética , Dados de Sequência Molecular , Análise de Sequência de DNA
16.
Biol Lett ; 8(6): 1043-6, 2012 Dec 23.
Artigo em Inglês | MEDLINE | ID: mdl-22993238

RESUMO

Squamate reptiles (lizards and snakes) are one of the most diverse groups of terrestrial vertebrates. Recent molecular analyses have suggested a very different squamate phylogeny relative to morphological hypotheses, but many aspects remain uncertain from molecular data. Here, we analyse higher-level squamate phylogeny with a molecular dataset of unprecedented size, including 161 squamate species for up to 44 nuclear genes each (33 717 base pairs), using both concatenated and species-tree methods for the first time. Our results strongly resolve most squamate relationships and reveal some surprising results. In contrast to most other recent studies, we find that dibamids and gekkotans are together the sister group to all other squamates. Remarkably, we find that the distinctive scolecophidians (blind snakes) are paraphyletic with respect to other snakes, suggesting that snakes were primitively burrowers and subsequently re-invaded surface habitats. Finally, we find that some clades remain poorly supported, despite our extensive data. Our analyses show that weakly supported clades are associated with relatively short branches for which individual genes often show conflicting relationships. These latter results have important implications for all studies that attempt to resolve phylogenies with large-scale phylogenomic datasets.


Assuntos
Lagartos/genética , Filogenia , Serpentes/genética , Animais , Sequência de Bases , Teorema de Bayes , Genes/genética , Funções Verossimilhança , Modelos Genéticos , Dados de Sequência Molecular , Análise de Sequência de DNA , Especificidade da Espécie
17.
Mol Phylogenet Evol ; 65(3): 974-91, 2012 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-22982760

RESUMO

Recently, phylogenetics has expanded to routinely include estimation of clade ages in addition to their relationships. Various dating methods have been used, but their relative performance remains understudied. Here, we generate and assemble an extensive phylogenomic data set for squamate reptiles (lizards and snakes) and evaluate two widely used dating methods, penalized likelihood in r8s (r8s-PL) and Bayesian estimation with uncorrelated relaxed rates among lineages (BEAST). We obtained sequence data from 25 nuclear loci (∼500-1,000 bp per gene; 19,020bp total) for 64 squamate species and nine outgroup taxa, estimated the phylogeny, and estimated divergence dates using 14 fossil calibrations. We then evaluated how well each method approximated these dates using random subsets of the nuclear loci (2, 5, 10, 15, and 20; replicated 10 times each), and using ∼1 kb of the mitochondrial ND2 gene. We find that estimates from r8s-PL based on 2, 5, or 10 loci can differ considerably from those based on 25 loci (mean absolute value of differences between 2-locus and 25-locus estimates were 9.0 Myr). Estimates from BEAST are somewhat more consistent given limited sampling of loci (mean absolute value of differences between 2 and 25-locus estimates were 5.0 Myr). Most strikingly, age estimates using r8s-PL for ND2 were ∼68-82 Myr older (mean=73.1) than those using 25 nuclear loci with r8s-PL. These results show that dates from r8s-PL with a limited number of loci (and especially mitochondrial data) can differ considerably from estimates derived from a large number of nuclear loci, whereas estimates from BEAST derived from fewer nuclear loci or mitochondrial data alone can be surprisingly similar to those from many nuclear loci. However, estimates from BEAST using relatively few loci and mitochondrial data could still show substantial deviations from the full data set (>50 Myr), suggesting the benefits of sampling many nuclear loci. Finally, we found that confidence intervals on ages from BEAST were not significantly different when sampling 2 vs. 25 loci, suggesting that adding loci decreased errors but did not increase confidence in those estimates.


Assuntos
Evolução Molecular , Lagartos/classificação , Modelos Genéticos , Filogenia , Serpentes/classificação , Animais , Teorema de Bayes , Núcleo Celular/genética , DNA Mitocondrial/genética , Fósseis , Funções Verossimilhança , Lagartos/genética , Análise de Sequência de DNA , Serpentes/genética
18.
PLoS One ; 6(8): e23179, 2011.
Artigo em Inglês | MEDLINE | ID: mdl-21887238

RESUMO

The disease chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis (Bd), has caused dramatic amphibian population declines and extinctions in Australia, Central and North America, and Europe. Bd is associated with >200 species extinctions of amphibians, but not all species that become infected are susceptible to the disease. Specifically, Bd has rapidly emerged in some areas of the world, such as in Australia, USA, and throughout Central and South America, causing population and species collapse. The mechanism behind the rapid global emergence of the disease is poorly understood, in part due to an incomplete picture of the global distribution of Bd. At present, there is a considerable amount of geographic bias in survey effort for Bd, with Asia being the most neglected continent. To date, Bd surveys have been published for few Asian countries, and infected amphibians have been reported only from Indonesia, South Korea, China and Japan. Thus far, there have been no substantiated reports of enigmatic or suspected disease-caused population declines of the kind that has been attributed to Bd in other areas. In order to gain a more detailed picture of the distribution of Bd in Asia, we undertook a widespread, opportunistic survey of over 3,000 amphibians for Bd throughout Asia and adjoining Papua New Guinea. Survey sites spanned 15 countries, approximately 36° latitude, 111° longitude, and over 2000 m in elevation. Bd prevalence was very low throughout our survey area (2.35% overall) and infected animals were not clumped as would be expected in epizootic events. This suggests that Bd is either newly emerging in Asia, endemic at low prevalence, or that some other ecological factor is preventing Bd from fully invading Asian amphibians. The current observed pattern in Asia differs from that in many other parts of the world.


Assuntos
Anfíbios/microbiologia , Quitridiomicetos/fisiologia , Doenças Transmissíveis/epidemiologia , Micoses/epidemiologia , Animais , Ásia/epidemiologia , Geografia , Modelos Biológicos , Especificidade da Espécie
19.
Mol Phylogenet Evol ; 61(3): 823-33, 2011 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-21907812

RESUMO

We investigated the evolutionary relationships among populations of two threatened Red Data Book fossorial skinks, Scelotes gronovii and Scelotes kasneri, along the Western Cape Coast of South Africa. The genus Scelotes shows considerable variation in limb and digit reduction. We sampled four localities purported to contain S. gronovii and seven of S. kasneri, encompassing all of each species' limited distribution. Each of these species lack forelimbs, and differ by the number of digits on the hind limbs, among other morphological characters; S. gronovii bears a single digit and S. kasneri bears two digits on the hind limbs. Sequence data obtained from three mtDNA (16S ribosomal RNA, cytochrome b, and nicotinamide adenine dinucleotide dehydrogenase 1 unit; 2035 bp ttl.) and two nuclear (dynein axonemal heavy chain 3 and the natural killer tumor recognition; 1848 bp ttl.) gene regions were used to reconstruct the evolutionary relationships among the two focal species and several other co-distributed species (Scelotes bipes, Scelotes montispectus, and Scelotes sexlineatus). Phylogenetic results (Bayesian and parsimony) revealed that several populations previously considered S. kasneri actually belong to other species, and others are paraphyletic with respect to one another. Additionally, populations of S. gronovii were also found to be paraphyletic, with populations south of the Berg River supported as sister to S. bipes, and populations north of the Berg River sister the remaining sampled species. Our results require a redefinition of S. sexlineatus to encompass populations morphologically convergent with S. kasneri and restrict the ranges of the already threatened S. kasneri and S. gronovii even further. The paraphyly of S. gronovii and the placement of each clade as sister to clades of species bearing two digits on the hind limbs suggests that digit loss has occurred at least twice in this group.


Assuntos
Evolução Biológica , Espécies em Perigo de Extinção , Variação Genética , Lagartos/anatomia & histologia , Lagartos/genética , Dedos do Pé/anatomia & histologia , Animais , Teorema de Bayes , Núcleo Celular/genética , Citocromos b/genética , DNA Mitocondrial/genética , Membro Anterior , Loci Gênicos/genética , Geografia , Filogenia , África do Sul , Especificidade da Espécie
20.
Mol Phylogenet Evol ; 61(2): 363-80, 2011 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-21787873

RESUMO

Iguanian lizards form a diverse clade whose members have been the focus of many comparative studies of ecology, behavior, and evolution. Despite the importance of phylogeny to such studies, interrelationships among many iguanian clades remain uncertain. Within the Old World clade Acrodonta, Agamidae is sometimes found to be paraphyletic with respect to Chamaeleonidae, and recent molecular studies have produced conflicting results for many major clades. Within the largely New World clade Pleurodonta, relationships among the 12 currently recognized major subclades (mostly ranked as families) have been largely unresolved or poorly supported in previous studies. To clarify iguanian evolutionary history, we first infer phylogenies using concatenated maximum-likelihood (ML) and Bayesian analyses of DNA sequence data from 29 nuclear protein-coding genes for 47 iguanian and 29 outgroup taxa. We then estimate a relaxed-clock Bayesian chronogram for iguanians using BEAST. All three methods produce identical topologies. Within Acrodonta, we find strong support for monophyly of Agamidae with respect to Chamaeleonidae, and for almost all relationships within agamids. Within Pleurodonta, we find strong Bayesian support for almost all relationships, and strong ML support for some interfamilial relationships and for monophyly of almost all families (excepting Polychrotidae). Our phylogenetic results suggest a non-traditional biogeographic scenario in which pleurodonts originated in the Northern Hemisphere and subsequently spread southward into South America. The pleurodont portion of the tree is characterized by several very short, deep branches, raising the possibility of deep coalescences that may confound concatenated analyses. We therefore also use 27 of these genes to implement a coalescent-based species-tree approach for pleurodonts. Although this analysis strongly supports monophyly of the pleurodont families, interfamilial relationships are generally different from those in the concatenated tree, and support is uniformly poor. However, a species-tree analysis using only the seven most variable loci yields higher support and more congruence with the concatenated tree. This suggests that low support in the 27-gene species-tree analysis may be an artifact of the many loci that are uninformative for very short branches. This may be a general problem for the application of species-tree methods to rapid radiations, even with phylogenomic data sets. Finally, we correct the non-monophyly of Polychrotidae by recognizing the pleurodont genus Anolis (sensu lato) as a separate family (Dactyloidae), and we correct the non-monophyly of the agamid genus Physignathus by resurrection of the genus Istiurus for the former Physignathus lesueurii.


Assuntos
Evolução Molecular , Lagartos/genética , Filogenia , Animais , Teorema de Bayes , Núcleo Celular/genética , Funções Verossimilhança , Lagartos/classificação , Modelos Genéticos , Filogeografia , Análise de Sequência de DNA
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