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2.
Science ; 383(6685): 918-923, 2024 Feb 23.
Artigo em Inglês | MEDLINE | ID: mdl-38386744

RESUMO

Snakes and lizards (Squamata) represent a third of terrestrial vertebrates and exhibit spectacular innovations in locomotion, feeding, and sensory processing. However, the evolutionary drivers of this radiation remain poorly known. We infer potential causes and ultimate consequences of squamate macroevolution by combining individual-based natural history observations (>60,000 animals) with a comprehensive time-calibrated phylogeny that we anchored with genomic data (5400 loci) from 1018 species. Due to shifts in the dynamics of speciation and phenotypic evolution, snakes have transformed the trophic structure of animal communities through the recurrent origin and diversification of specialized predatory strategies. Squamate biodiversity reflects a legacy of singular events that occurred during the early history of snakes and reveals the impact of historical contingency on vertebrate biodiversity.


Assuntos
Evolução Biológica , Serpentes , Animais , Biodiversidade , Genômica , Lagartos/classificação , Locomoção , Filogenia , Serpentes/classificação , Serpentes/genética
3.
Sci Data ; 11(1): 32, 2024 Jan 04.
Artigo em Inglês | MEDLINE | ID: mdl-38177140

RESUMO

National parks and other protected areas are important for preserving landscapes and biodiversity worldwide. An essential component of the mission of the United States (U.S.) National Park Service (NPS) requires understanding and maintaining accurate inventories of species on protected lands. We describe a new, national-scale synthesis of amphibian species occurrence in the NPS system. Many park units have a list of amphibian species observed within their borders compiled from various sources and available publicly through the NPSpecies platform. However, many of the observations in NPSpecies remain unverified and the lists are often outdated. We updated the amphibian dataset for each park unit by collating old and new park-level records and had them verified by regional experts. The new dataset contains occurrence records for 292 of the 424 NPS units and includes updated taxonomy, international and state conservation rankings, hyperlinks to a supporting reference for each record, specific notes, and related fields which can be used to better understand and manage amphibian biodiversity within a single park or group of parks.


Assuntos
Biodiversidade , Parques Recreativos , Animais , Anfíbios , Conservação dos Recursos Naturais , Estados Unidos
4.
Sci Rep ; 13(1): 22124, 2024 01 11.
Artigo em Inglês | MEDLINE | ID: mdl-38212342

RESUMO

Tyrannosaurid dinosaurs dominated as predators in the Late Cretaceous of Laurasia, culminating in the evolution of the giant Tyrannosaurus rex, both the last and largest tyrannosaurid. Where and when Tyrannosaurini (T. rex and kin) originated remains unclear. Competing hypotheses place tyrannosaurin origins in Asia, or western North America (Laramidia). We report a new tyrannosaurin, Tyrannosaurus mcraeensis, from the Campanian-Maastrichtian Hall Lake Formation of New Mexico, based on a fossil previously referred to T. rex. T. mcraeensis predates T. rex by ~ 6-7 million years, yet rivaled it in size. Phylogenetic analysis recovers T. mcraeensis as sister to T. rex and suggests Tyrannosaurini originated in southern Laramidia. Evolution of giant tyrannosaurs in southern North America, alongside giant ceratopsians, hadrosaurs, and titanosaurs suggests large-bodied dinosaurs evolved at low latitudes in North America.


Assuntos
Dinossauros , Gigantismo , Animais , Filogenia , Fósseis , América do Norte , New Mexico , Dinossauros/anatomia & histologia , Evolução Biológica
5.
Mol Ecol ; 33(2): e17219, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-38015012

RESUMO

Numerous mechanisms can drive speciation, including isolation by adaptation, distance, and environment. These forces can promote genetic and phenotypic differentiation of local populations, the formation of phylogeographic lineages, and ultimately, completed speciation. However, conceptually similar mechanisms may also result in stabilizing rather than diversifying selection, leading to lineage integration and the long-term persistence of population structure within genetically cohesive species. Processes that drive the formation and maintenance of geographic genetic diversity while facilitating high rates of migration and limiting phenotypic differentiation may thereby result in population genetic structure that is not accompanied by reproductive isolation. We suggest that this framework can be applied more broadly to address the classic dilemma of "structure" versus "species" when evaluating phylogeographic diversity, unifying population genetics, species delimitation, and the underlying study of speciation. We demonstrate one such instance in the Seepage Salamander (Desmognathus aeneus) from the southeastern United States. Recent studies estimated up to 6.3% mitochondrial divergence and four phylogenomic lineages with broad admixture across geographic hybrid zones, which could potentially represent distinct species supported by our species-delimitation analyses. However, while limited dispersal promotes substantial isolation by distance, microhabitat specificity appears to yield stabilizing selection on a single, uniform, ecologically mediated phenotype. As a result, climatic cycles promote recurrent contact between lineages and repeated instances of high migration through time. Subsequent hybridization is apparently not counteracted by adaptive differentiation limiting introgression, leaving a single unified species with deeply divergent phylogeographic lineages that nonetheless do not appear to represent incipient species.


Assuntos
DNA Mitocondrial , Urodelos , Animais , Urodelos/genética , DNA Mitocondrial/genética , Filogeografia , Filogenia , Fenótipo , Demografia , Especiação Genética
6.
Evolution ; 77(12): 2619-2630, 2023 Dec 02.
Artigo em Inglês | MEDLINE | ID: mdl-37797261

RESUMO

Iridescent ultraviolet (IUV) patterns on pierid butterfly wings are phenotypic adaptations commonly used as sexual signals, generated by scales with ultrastructural modifications. Pierid IUV patterns are sexually dichromatic, with reduced size in females, where conspicuous sexual signaling balances courtship against ecological predation. There have been no phylogenetic reconstructions of IUV within Pieridae and little morphological characterization of phenotypic diversity. Our genus-wide characterization of IUV revealed the uniform similarity of stacked lamellar ridges on the dorsal surface of cover scales. We tested a hypothesis of single versus multiple origins by reconstructing a phylogeny of 534 species (~43.2% described species), with all genera represented, and a trait matrix of 734 species (~59.4%) screened for IUV. A single, early dimorphic origin of IUV followed by several losses and gains received strong support, concluding that IUV patterns and structural coloration are old traits. Collectively, these results support the homology of IUV scales and patterns that diversified within several lineages, suggesting an interplay between female-mediated sexual selection and ecological predatory selection.


Assuntos
Borboletas , Animais , Feminino , Borboletas/genética , Borboletas/anatomia & histologia , Filogenia , Asas de Animais/anatomia & histologia , Seleção Sexual , Fenótipo
7.
Pathog Dis ; 812023 Jan 17.
Artigo em Inglês | MEDLINE | ID: mdl-37715299

RESUMO

Bald sea urchin disease (BSUD) is most likely a bacterial infection that occurs in a wide range of sea urchin species and causes the loss of surface appendages. The disease has a variety of additional symptoms, which may be the result of the many bacteria that are associated with BSUD. Previous studies have investigated causative agents of BSUD, however, there are few reports on the surface microbiome associated with the infection. Here, we report changes to the surface microbiome on purple sea urchins in a closed marine aquarium that contracted and then recovered from BSUD in addition to the microbiome of healthy sea urchins in a separate aquarium. 16S rRNA gene sequencing shows that microhabitats of different aquaria are characterized by different microbial compositions, and that diseased, recovered, and healthy sea urchins have distinct microbial compositions, which indicates that there is a correlation between microbial shifts and recovery from disease.

8.
Zootaxa ; 5270(2): 262-280, 2023 Apr 20.
Artigo em Inglês | MEDLINE | ID: mdl-37518165

RESUMO

Shovel-nosed Salamanders, Desmognathus marmoratus (Moore, 1899), were long thought to represent a single species from the southern Appalachian Mountains of the eastern United States, ranging from northeastern Georgia to extreme southwestern Virginia. These populations have a highly derived ecomorphology, being fully aquatic with a specialized flattened and elongated phenotype adapted to rocky riffle zones in fast-flowing, high-gradient mountain streams. Because of this, they were originally described in a separate genus, Leurognathus Moore, 1899. Four additional species or subspecies were described from 1928-1956 based on regional geographic variation in phenotype before being synonymized with L. marmoratus in 1962, which was reassigned to Desmognathus in 1996. Molecular analyses subsequently revealed four distinct candidate lineages in two distantly related clades, which were recently re-delimited into three species. These are D. aureatus (Martof, 1956) from northeastern Georgia, D. intermedius (Pope, 1928) from western North Carolina, and D. marmoratus from northwestern North Carolina. We provide a systematic revision of these taxa, which do not represent a natural group but instead exhibit convergent phenotypes across multiple species, potentially driven by ancient episodes of adaptive introgression between ancestral lineages. Our recent fieldwork revealed an astonishingly disjunct and morphologically distinct population of D. marmoratus in the New River Gorge of West Virginia, which were previously confused with D. kanawha Pyron and Beamer, 2022. This locality is ~120 airline km away from the nearest populations of D. marmoratus in Virginia. No Shovel-nosed Salamanders have ever been found in the New River drainage during our extensive previous explorations or credibly reported in museum specimens or the literature. Additional cryptic populations of these taxa may remain.

9.
Zootaxa ; 5311(4): 451-504, 2023 Jul 03.
Artigo em Inglês | MEDLINE | ID: mdl-37518633

RESUMO

Spotted and Northern Dusky Salamanders (Desmognathus conanti and D. fuscus) have a long and complex taxonomic history. At least 10 other currently recognized species in the genus were either described from populations previously considered D. fuscus, described as or later considered subspecies thereof, or later considered synonyms thereof, before ultimately being recognized as distinct. Recent molecular analyses have also revealed extensive cryptic diversity within both species, which are polyphyletic assemblages of 13 distinct mitochondrial lineages with 5.7-10.3% uncorrected 'p' distances in the COI barcode locus. Based on phylogenomic data and population-clustering analyses considering admixture between lineages, 11 candidate species were circumscribed by recent authors. Those within D. conanti are also ecomorphologically variable, comprising both large, robust, keel-tailed populations, and small, gracile, round-tailed forms. Evaluating their distinctiveness based on genetic, geographic, and morphological evidence, we conclude that six of the candidates represent new species: Desmognathus anicetus sp. nov., D. bairdi sp. nov., D. campi sp. nov., D. catahoula sp. nov., D. lycos sp. nov., and D. tilleyi sp. nov. Consequently, we recognize eight total species from populations formerly associated with the nominal species D. conanti and D. fuscus, the re-delimited concepts of which also contain additional phylogeographic lineage diversity that may represent further distinct species. In addition to existing mitochondrial and nuclear phylogenetic, network, and clustering results, we present preliminary analyses of linear morphometrics to bolster diagnostic specificity based on phenotypic characteristics. These changes stabilize the previously paraphyletic taxonomy of species-level lineages within Desmognathus, though additional cryptic diversity may exist both within the species considered here, and elsewhere in the genus.

10.
Zookeys ; 1145: 131-167, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37234698

RESUMO

A new species of Dipsas Laurenti, 1768, from Central Panama is described based on molecular analyses, hemipenial morphology, and external characters. This is the sixth species of Dipsas to be described for the country; the snake has been suspected to exist since 1977 and has not been thoroughly studied until now. Additionally, morphological comparations including scale counts are done with other species within the genus, and the current geographic distribution of Dipsastemporalis (Werner, 1909), the sister species, is updated. Finally, a key to the species of Dipsas currently known from Middle America is presented.


ResumenDescribimos una nueva especies de Dipsas Laurenti, 1768 de la región central de Panamá en base a análisis moleculares, morfología hemipenial y caracteres de morfología externa. Esta es la sexta especie del género Dipsas descrita para el país. Se sospechaba su existencia desde 1977 pero no había sido estudiada exhaustivamente hasta ahora. Adicionalmente, presentamos comparaciones morfológicas (incluyendo lepidosis) con otras especies del género y actualizamos la distribución geográfica de su especie hermana Dipsastemporalis (Werner, 1909). Finalmente, presentamos una clave para las especies de Dipsas distribuidas en Centroamérica.

11.
Syst Biol ; 72(1): 179-197, 2023 05 19.
Artigo em Inglês | MEDLINE | ID: mdl-36169600

RESUMO

Significant advances have been made in species delimitation and numerous methods can test precisely defined models of speciation, though the synthesis of phylogeography and taxonomy is still sometimes incomplete. Emerging consensus treats distinct genealogical clusters in genome-scale data as strong initial evidence of speciation in most cases, a hypothesis that must therefore be falsified under an explicit evolutionary model. We can now test speciation hypotheses linking trait differentiation to specific mechanisms of divergence with increasingly large data sets. Integrative taxonomy can, therefore, reflect an understanding of how each axis of variation relates to underlying speciation processes, with nomenclature for distinct evolutionary lineages. We illustrate this approach here with Seal Salamanders (Desmognathus monticola) and introduce a new unsupervised machine-learning approach for species delimitation. Plethodontid salamanders are renowned for their morphological conservatism despite extensive phylogeographic divergence. We discover 2 geographic genetic clusters, for which demographic and spatial models of ecology and gene flow provide robust support for ecogeographic speciation despite limited phenotypic divergence. These data are integrated under evolutionary mechanisms (e.g., spatially localized gene flow with reduced migration) and reflected in emergent properties expected under models of reinforcement (e.g., ethological isolation and selection against hybrids). Their genetic divergence is prima facie evidence for species-level distinctiveness, supported by speciation models and divergence along axes such as behavior, geography, and climate that suggest an ecological basis with subsequent reinforcement through prezygotic isolation. As data sets grow more comprehensive, species-delimitation models can be tested, rejected, or corroborated as explicit speciation hypotheses, providing for reciprocal illumination of evolutionary processes and integrative taxonomies. [Desmognathus; integrative taxonomy; machine learning; species delimitation.].


Assuntos
Especiação Genética , Urodelos , Animais , Filogeografia , Filogenia , Urodelos/genética , Evolução Biológica
12.
Zootaxa ; 5134(2): 151-196, 2022 May 10.
Artigo em Inglês | MEDLINE | ID: mdl-36101070

RESUMO

John Edwards Holbrook published North American Herpetology in 11 volumes from 18361842, authoring the first accounts of numerous amphibians and reptiles from the eastern and central United States, including 32 salamanders (Urodela). We reviewed these and located 51 extant salamander specimens from Holbrook in the Academy of Natural Sciences (Philadelphia), Museum of Comparative Zoology (Cambridge), and Musum national dHistoire naturelle (Paris), six of which are types. We identified four other specimens figured by Holbrook in the MNHN and National Museum of Natural History (Washington), all of which are types from descriptions by other authors. We designate lectotypes for S. porpyhritica Green, 1827 (USNM 3840; reversing neotype MCZ A-35778), Salamandra gutto-lineata Holbrook, 1838a (ANSP 716), S. auriculata Holbrook, 1838b (MNHN-RA 0.4675), S. maculo-quadrata Holbrook, 1840 (ANSP 821), S. granulata De Kay in Holbrook, 1842e (USNM 3981), S. quadridigitata Holbrook, 1842e (ANSP 490; reversing neotype UF 178833), and Plethodon variolosum Dumril, Bibron, and Dumril, 1854 (MNHN-RA 0.4666). Allocation of S. auriculata Holbrook, 1838b, S. Haldemani Holbrook, 1840, and P. variolosum Dumril, Bibron, and Dumril, 1854 is still ambiguous. We consider S. maculo-quadrata Holbrook, 1840 to be a junior subjective synonym of S. fusca Green, 1818; no valid name has ever been applied to Black-bellied Salamanders (Desmognathus sp. quadramaculatus) at the species level, and up to five candidate species require new names. Additional discoveries of data and specimens pertaining to Holbrooks names may remain to be made among his surviving papers and collections.


Assuntos
Anfíbios , Urodelos , Animais , Museus
13.
Zootaxa ; 5133(1): 53-82, 2022 May 03.
Artigo em Inglês | MEDLINE | ID: mdl-36101111

RESUMO

We describe a new, narrowly endemic species of swamp-dwelling dusky salamander (Plethodontidae: Desmognathus pascagoula sp. nov.) from the Gulf Coastal Plain of southeastern Mississippi and southwestern Alabama based on linear morphometrics, mitochondrial DNA, and single nucleotide polymorphisms from 881 loci produced using genotype-by-sequencing. Some populations of the new species were historically referred to as D. auriculatus, a polyphyletic assemblage of at least three species in the Atlantic and Gulf Coastal Plain from Texas to North Carolina. Populations of D. auriculatus from the Gulf Coastal Plain in Louisiana and Mississippi were recently described as D. valentinei. The new species includes populations that were tentatively referred to D. valentinei, but we find it is morphologically, genetically, and geographically distinct. It is smaller, has a more defined dorsal color pattern, more irregular whitish portholes in up to three rows on the lateral surfaces of the body and tail, and a brighter orange or yellowish orange postocular stripe. At present, the new species is known from only six extant populations in the lower Pascagoula, Escatawpa, and Mobile drainages. The latter represents a distinct phylogeographic lineage. We also refer a historical collection from the northeastern side of the Mobile-Tensaw River Delta to this species, suggesting a much broader range in the past. We suspect that more populations remain to be discovered in the area, and their potential species-level distinctiveness should be tested further. This discovery increases knowledge of the biodiversity in the southeastern United States Coastal Plain, a candidate region meeting the global criteria for a biodiversity hotspot, and underscores the amount of cryptic diversity likely remaining to be discovered and described in Nearctic salamanders.


Assuntos
Urodelos , Áreas Alagadas , Alabama , Animais , Mississippi , Filogenia , Urodelos/genética
14.
Zootaxa ; 5188(6): 587-595, 2022 Sep 22.
Artigo em Inglês | MEDLINE | ID: mdl-37044758

RESUMO

Most swamp-dwelling dusky salamanders of the genus Desmognathus from the Coastal Plain were long treated as a single species (Desmognathus auriculatus) ranging from east Texas to southeastern Virginia. This taxon concept was based on the name Salamandra auriculata Holbrook, 1838 with type locality Riceboro, Liberty County, Georgia and a type series that could not be located by later authors. Recent workers have been unable to locate or verify swamp-dwelling populations from east Texas and western Louisiana, which appear to be extirpated and may not have represented a distinct taxon from co-occurring lineages of D. conanti. Recent molecular phylogenies have supported at least four distinct species-level taxa within D. auriculatus. Populations from the Gulf Coastal Plain in eastern Louisiana, Mississippi, and southwestern Alabama were recently described as D. valentinei Means, Lamb, and Bernardo, 2017 and D. pascagoula Pyron, O'Connell, Lamb, and Beamer, 2022. This leaves two remaining species-level lineages with uncertain taxonomy and nomenclature: D. auriculatus A (Alabama, Florida, and Georgia), and D. auriculatus B/C (Georgia, South Carolina, and North Carolina), both of which occur near the type locality. We recently located a specimen at the Muséum national d'Histoire naturelle in Paris (MNHN 0.4675) that we concluded is one of Holbrook's syntypes and designated it as the lectotype, but without allocation. Here, we use linear morphometrics to confidently allocate it to D. auriculatus A, bolstered by examination of three historical topotypic collections. This requires a new name for D. auriculatus B/C, which we describe as D. valtos sp. nov. (suggested common name: Carolina Swamp Dusky Salamander) from Otter Creek, Craven County, North Carolina. Other related and sympatric species of Desmognathus remain to be described from the Atlantic Coastal Plain and adjacent Piedmont of the southeastern United States.


Assuntos
Salamandra , Animais , Urodelos/genética , Áreas Alagadas
15.
Zootaxa ; 5190(2): 207-240, 2022 Sep 28.
Artigo em Inglês | MEDLINE | ID: mdl-37045172

RESUMO

The "mountain" dusky is a charismatic ecomorph of Dusky Salamander (Desmognathus): smaller (~20-50mm SVL), more terrestrial and montane woodland species, typically with round tails and extremely variable, often colorful patterns. Originally considered a single species (D. ochrophaeus), populations across the Appalachians are now divided into D. abditus, D. carolinensis, D. ochrophaeus, D. ocoee, and D. orestes, which do not form a clade but are instead scattered across the phylogeny of Desmognathus. A Coastal Plain species with a mountain dusky phenotype (D. apalachicolae) is also nested within a lineage related to D. ocoee. Within the current concept of D. ocoee, there are up to 8 genetically distinct geographic lineages which display significantly different but substantially overlapping morphologies. Recent studies have suggested that as many as six species could reasonably be delimited based on genetic data. We evaluate the strength of that evidence here and find support for five species in the D. apalachicolae + D. ocoee group. The first is D. apalachicolae in essentially its originally described form from the Coastal Plain. The second and third are D. adatsihi sp. nov. and D. balsameus sp. nov., endemic to the Great Smoky/Plott Balsam and Great Balsam Mountains, respectively. The fourth corresponds to the resurrected D. perlapsus for populations from the Alarka and Cowee Mountains in North Carolina, through the Chattahoochee River drainage to the Fall Line in the Piedmont of Georgia and Alabama. The fifth is D. ocoee, here restricted to populations in the Nantahala and Unicoi Mountains and southernmost Blue Ridge escarpment, along with previously recognized populations from the Cumberland Escarpment and Cumberland Plateau of south-central Tennessee and northeastern Alabama. This taxon concept of D. ocoee includes three deeply divergent geographic genetic segments that hybridize across two contact zones, while D. apalachicolae may be nested within some southern Blue Ridge populations of D. ocoee. The resurrected form of D. perlapsus also exhibits some admixture with the newly restricted D. ocoee. While this taxonomic arrangement is robust and stably derived from mitochondrial, morphological, and nuclear data, more sophisticated future analyses sampling additional populations and loci to estimate relationships may reach more subtle conclusions regarding the identity of some lineages within D. ocoee.


Assuntos
Bálsamos , Urodelos , Animais , Urodelos/genética , Filogenia
16.
Ecol Lett ; 24(11): 2464-2476, 2021 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-34510687

RESUMO

The Tree of Life will be irrevocably reshaped as anthropogenic extinctions continue to unfold. Theory suggests that lineage evolutionary dynamics, such as age since origination, historical extinction filters and speciation rates, have influenced ancient extinction patterns - but whether these factors also contribute to modern extinction risk is largely unknown. We examine evolutionary legacies in contemporary extinction risk for over 4000 genera, representing ~30,000 species, from the major tetrapod groups: amphibians, birds, turtles and crocodiles, squamate reptiles and mammals. We find consistent support for the hypothesis that extinction risk is elevated in lineages with higher recent speciation rates. We subsequently test, and find modest support for, a primary mechanism driving this pattern: that rapidly diversifying clades predominantly comprise range-restricted, and extinction-prone, species. These evolutionary patterns in current imperilment may have important consequences for how we manage the erosion of biological diversity across the Tree of Life.


Assuntos
Biodiversidade , Evolução Biológica , Anfíbios , Animais , Extinção Biológica , Especiação Genética , Filogenia , Répteis
17.
Am Nat ; 198(3): E68-E79, 2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-34403310

RESUMO

AbstractContinental mountain areas cover <15% of global land surface, yet these regions concentrate >80% of global terrestrial diversity. One prominent hypothesis to explain this pattern proposes that high mountain diversities could be explained by higher diversification rates in regions of high topographic complexity (HTC). While high speciation in mountains has been detected for particular clades and regions, the global extent to which lineages experience faster speciation in mountains remains unknown. Here we addressed this issue using amphibians as a model system (>7,000 species), and we found that families showing high speciation rates contain a high proportion of species distributed in mountains. Moreover, we found that lineages inhabiting areas of HTC speciate faster than lineages occupying areas that are topographically less complex. When comparing across regions, we identified the same pattern in five biogeographical realms where higher speciation rates are associated with higher levels of complex topography. Low-magnitude differences in speciation rates between some low and high complex topographies suggest that high mountain diversity is also affected by low extinction and/or high colonization rates. Nevertheless, our results bolster the importance of mountains as engines of speciation at different geographical scales and highlight their importance for the conservation of global biodiversity.


Assuntos
Biodiversidade , Especiação Genética , Anfíbios , Animais , Humanos , Filogenia
18.
Syst Biol ; 70(3): 542-557, 2021 04 15.
Artigo em Inglês | MEDLINE | ID: mdl-32681800

RESUMO

Genome-scale data have the potential to clarify phylogenetic relationships across the tree of life but have also revealed extensive gene tree conflict. This seeming paradox, whereby larger data sets both increase statistical confidence and uncover significant discordance, suggests that understanding sources of conflict is important for accurate reconstruction of evolutionary history. We explore this paradox in squamate reptiles, the vertebrate clade comprising lizards, snakes, and amphisbaenians. We collected an average of 5103 loci for 91 species of squamates that span higher-level diversity within the clade, which we augmented with publicly available sequences for an additional 17 taxa. Using a locus-by-locus approach, we evaluated support for alternative topologies at 17 contentious nodes in the phylogeny. We identified shared properties of conflicting loci, finding that rate and compositional heterogeneity drives discordance between gene trees and species tree and that conflicting loci rarely overlap across contentious nodes. Finally, by comparing our tests of nodal conflict to previous phylogenomic studies, we confidently resolve 9 of the 17 problematic nodes. We suggest this locus-by-locus and node-by-node approach can build consensus on which topological resolutions remain uncertain in phylogenomic studies of other contentious groups. [Anchored hybrid enrichment (AHE); gene tree conflict; molecular evolution; phylogenomic concordance; target capture; ultraconserved elements (UCE).].


Assuntos
Lagartos , Serpentes , Animais , Evolução Biológica , Genoma/genética , Lagartos/genética , Filogenia , Serpentes/genética
19.
Syst Biol ; 70(1): 49-66, 2021 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-32359157

RESUMO

Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting hundreds of conserved exons which are effective across the class. After obtaining data from 220 loci for 286 species (representing 94% of the families and 44% of the genera), we estimate a phylogeny for extant amphibians and identify gene tree-species tree conflict across the deepest branches of the amphibian phylogeny. We perform locus-by-locus genealogical interrogation of alternative topological hypotheses for amphibian monophyly, focusing on interordinal relationships. We find that phylogenetic signal deep in the amphibian phylogeny varies greatly across loci in a manner that is consistent with incomplete lineage sorting in the ancestral lineage of extant amphibians. Our results overwhelmingly support amphibian monophyly and a sister relationship between frogs and salamanders, consistent with the Batrachia hypothesis. Species tree analyses converge on a small set of topological hypotheses for the relationships among extant amphibian families. These results clarify several contentious portions of the amphibian Tree of Life, which in conjunction with a set of vetted fossil calibrations, support a surprisingly younger timescale for crown and ordinal amphibian diversification than previously reported. More broadly, our study provides insight into the sources, magnitudes, and heterogeneity of support across loci in phylogenomic data sets.[AIC; Amphibia; Batrachia; Phylogeny; gene tree-species tree discordance; genomics; information theory.].


Assuntos
Fósseis , Genômica , Animais , Anuros , Humanos , Filogenia
20.
Zootaxa ; 4779(2): zootaxa.4779.2.2, 2020 May 19.
Artigo em Inglês | MEDLINE | ID: mdl-33055786

RESUMO

A recent molecular phylogenetic revision of the snake-eyed skinks (genus Panaspis Cope, 1868) uncovered extensive cryptic diversity, including several new species from throughout sub-Saharan Africa. Here, we describe one of these from Ethiopia as Panaspis annettesabinae sp. nov. This description is based on a previous molecular phylogeny and morphological, scalation, and coloration data collected from the type specimen. Phylogenetic analyses place the species alone in what we term the P. annettesabinae species group from Ethiopia. This group forms the sister lineage to a large southern African radiation and suggests a potential northern origin for much of the extant diversity of Panaspis. Many new taxa have recently been discovered in the genus and region, and there are several historical records of Panaspis from elsewhere in Ethiopia. Thus, we suggest that the range of this new species (known only from a single specimen at present) may be much larger, and that additional undescribed species may exist in northern sub-Saharan Africa.


Assuntos
Lagartos , Serpentes , Animais , Etiópia , Filogenia
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