Generalizing Bayesian phylogenetics to infer shared evolutionary events DOI Creative Commons
Jamie R. Oaks, Perry L. Wood, Cameron D. Siler

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2021, Номер unknown

Опубликована: Июль 26, 2021

Abstract Many processes of biological diversification can simultaneously affect multiple evolutionary lineages. Examples include members a gene family diverging when region chromosome is duplicated, viral strains at “super-spreading” event, and geological event fragmenting whole communities species. It difficult to test for patterns shared divergences predicted by such processes, because all phylogenetic methods assume that lineages diverge independently. We introduce Bayesian approach relax the assumption independent, bifurcating expanding space topologies trees with multifurcating divergences. This allows us jointly infer relationships, divergence times, or lead more than two descendant Using simulations, we find new method accurately infers events they occur, performs as well current are independent bifurcating. apply our genomic data from genera geckos across Philippines if past changes islands’ landscape caused bursts speciation. Unlike previous analyses restricted only pairs gecko populations, evidence By generalizing in way likelihood model, opens many avenues future research into life sciences. Significance statement Phylogenetic models have long assumed Processes interest biogeography, epidemiology, genome evolution, violate this affecting To conceptualizing, modeling, inferring trees. distributed Philippines, support repeated fragmentation archipelago interglacial rises sea level.

Язык: Английский

Hiding on jagged karst pinnacles: A new microendemic genus and species of a limestone-dwelling agamid lizard (Squamata: Agamidae: Draconinae) from Khammouan Province, Laos DOI Open Access
Saly Sitthivong, Peter Brakels, Santi Xayyasith

и другие.

动物学研究, Год журнала: 2023, Номер 44(6), С. 1039 - 1051

Опубликована: Янв. 1, 2023

We describe a unique new species and genus of agamid lizard from the karstic massifs Khammouan Province, central Laos. Laodracon carsticola Gen. et sp. nov. is an elusive medium-sized (maximum snout-vent length 101 mm) specifically adapted to life on limestone rocks pinnacles. To assess phylogenetic position amongst other agamids, we generated DNA sequences two mitochondrial gene fragments (16S rRNA ND2) three nuclear loci (BDNF, RAG1 c-mos), with final alignment comprising 7 418 base pairs for 64 species. Phylogenetic analyses unambiguously place in mainland Asia subfamily Draconinae, where it forms clade sister Diploderma East northern part Southeast Asia. Morphologically, distinguished all genera Draconinae by possessing notably swollen tail enlarged scales its dorsal ventral surfaces. Our work provides further evidence that regions Indochina represent "arks biodiversity" harbor numerous relict lineages. date, known only adult male specimens distribution seems be restricted narrow massif border Bolikhamxai provinces Additional studies are required understand history, distribution, conservation status.

Язык: Английский

Процитировано

6
A new species of the Cyrtodactylus brevipalmatus group (Squamata: Gekkonidae) from Phuket Island, Thailand with a discussion of the group’s potential biogeography DOI
L. Lee Grismer, Parinya Pawangkhanant, Andrey M. Bragin

и другие.

Zootaxa, Год журнала: 2024, Номер 5437(2), С. 193 - 222

Опубликована: Апрель 11, 2024

Model based integrative analyses supports the recognition of a new species Cyrtodactylus brevipalmatus group from Phuket Island, Thailand. thalang sp. nov. is most closely related to sister C. Thai-Malay Peninsula and cf. Langkawi Kedah State, Peninsular Malaysia. Based on mitochondrial gene ND2, bears an uncorrected pairwise sequence divergence 14.7% 15.1% brevipalmatus, respectively, significantly different (p<0.05) mean values meristic morphometric characters, discrete categorical morphological differences. A multiple factor analysis morphospatially statistically placed well outside all other group. The BAYAREALIKE model BioGeoBEARS indicated origin was in western Indochina with subsequent south north speciation along Tenasserim Mountains followed by west east invasion northern Thailand, Laos, northwestern Vietnam northeast Chao Phraya Basin Khorat Plateau.

Язык: Английский

Процитировано

2
Establishing species boundaries in Bornean geckos DOI
Hayden R. Davis,

Henry T. Sanford,

Indraneil Das

и другие.

Biology Letters, Год журнала: 2024, Номер 20(8)

Опубликована: Авг. 1, 2024

Species delimitation using mitochondrial DNA (mtDNA) remains an important and accessible approach for discovering delimiting species. However, species with a single locus (e.g. barcoding) is biased towards overestimating diversity. The highly diverse gecko genus Cyrtodactylus one such group where mtDNA the paradigm. In this study, we use genomic data to test putative boundaries established within three recognized of on island Borneo. We predict that multi-locus will estimate fewer than mtDNA, which could have ramifications diversity genus. aim (i) investigate correspondence between delimitations data, (ii) infer trees each target species, (iii) quantify gene flow identify migration patterns assess population connectivity. find overestimated differ nuclear data. This underscores value reassess mtDNA-based taxa lacking clear boundaries. expect number continue increasing, but, when possible, should be included inform more accurate

Язык: Английский

Процитировано

2
A new species in the Cyrtodactylus oldhami group (Squamata, Gekkonidae) from Kanchanaburi Province, western Thailand DOI Creative Commons
Siriporn Yodthong, Attapol Rujirawan,

Bryan L. Stuart

и другие.

ZooKeys, Год журнала: 2022, Номер 1103, С. 139 - 169

Опубликована: Июнь 2, 2022

Cyrtodactylusmonilatussp. nov. is described from Si Sawat District, Kanchanaburi Province, in western Thailand. The new species superficially resembles C.zebraicus Taylor, 1962 southern However, differences between the and other congeners were supported by an integrative taxonomic analysis of molecular morphological data. Phylogenetic analyses based on mitochondrial NADH dehydrogenase subunit 2 (ND2) gene showed that a member C.oldhami group closely related to Cyrtodactylus sp. MT468911 Thong Pha Phum National Park, Province. Uncorrected pairwise genetic divergences (p-distances) its congeners, including C.zebraicus, ranged 7.7-17.7%. can also be distinguished all members having unique combination characters, snout vent length 53.7-63.3 mm adult males 58.6-75.8 females; 22-34 paravertebral tubercles; 34-42 ventral scales; 30-39 enlarged contiguous femoroprecloacal femoral pores precloacal absent both sexes; four or five rows postprecloacal median subcaudal scales absent; weak ventrolateral folds present; 4-7 paired, paravertebral, dark-brown blotches edged yellow yellowish white; two small, diffuse, white spots flanks. occurs narrow range forest at mid low elevations associated with karst landscapes Tenasserim mountain range.

Язык: Английский

Процитировано

9
Scratching the surface: a new species of Bent-toed gecko (Squamata, Gekkonidae, Cyrtodactylus) from Timor-Leste of the darmandvillei group marks the potential for future discoveries DOI Creative Commons
Kin Onn Chan, L. Lee Grismer, Fernando Santana

и другие.

ZooKeys, Год журнала: 2023, Номер 1139, С. 107 - 126

Опубликована: Янв. 11, 2023

A new species of limestone-dwelling Bent-toed gecko (genus Cyrtodactylus) is described from Nino Konis Santana National Park in the far-east region Timor-Leste. Both genetic and morphological data strongly support evolutionary distinctness species, which we describe herein as Cyrtodactylussantanasp. nov. Phylogenetic analysis based on ND2 mitochondrial gene inferred part C.darmandvillei group with close affinities to C.batucolus, C.seribuatensis, C.petani, C.sadleiri, two undescribed lineages Moluccas Indonesia. The represents first Cyrtodactylus identified at level Timor-Leste fills an important gap our understanding biogeography history especially Wallacean region. Our results suggest that diversity Wallacea still underestimated many more unnamed remain be described.

Язык: Английский

Процитировано

5
Ecologically‐related variation of digit morphology in Cyrtodactylus (Gekkota, Squamata) reveals repeated origins of incipient adhesive toepads DOI Creative Commons
Jendrian Riedel,

K Eisele,

Mariam Gabelaia

и другие.

Functional Ecology, Год журнала: 2024, Номер 38(7), С. 1630 - 1648

Опубликована: Май 30, 2024

Abstract Exploitation of different locomotor substrates in ecological niches has driven the evolution specialized morphological structures, and similar demands, such as structure microhabitat, often lead to convergent or parallel evolution. The adhesive toepads geckos remains understudied because paucity phylogenetically‐informed investigations candidate clades exhibiting purported incipient expression these (i.e. species having evolved some, but not all, parts complex system pad‐bearing geckos). Using Cyrtodactylus , a speciose genus with well‐established ecotypes, we tested hypothesis that microhabitats require more climbing will acquisition morphology. We measured subdigital scale area, proxy for toepad evolution, quantified shape 77 354 described species, including at least one representative each ecotype. Subdigital area increased from terrestrial through generalist saxicoline (rock‐dwelling) arboreal evolving ancestral conditions padless lizards lateromedially expanded lamella‐like scales only ecotypes. This significant link between phenotype environment supports contention scansorial, particularly arboreal, ecotypes have incipiently expressed toepads. highlights suitability this model studying ecology well being promising research on adaptive radiations. Read free Plain Language Summary article Journal blog.

Язык: Английский

Процитировано

1
A New Species of Cyrtodactylus tibetanus Group (Reptilia: Squamata: Gekkonidae) from Xizang Autonomous Region, China DOI Creative Commons
Shun Ma, Shengchao Shi, Tianyu Qian

и другие.

Animals, Год журнала: 2024, Номер 14(16), С. 2384 - 2384

Опубликована: Авг. 17, 2024

A new

Язык: Английский

Процитировано

1
A multi-gene phylogeny of the Asian kukri snakes (Oligodon Fitzinger, 1826): Sharpening the blade of the second largest serpent radiation (Reptilia: Squamata: Colubridae) DOI
Justin L. Lee, Platon V. Yushchenko,

Chatmongkon Suwannapoom

и другие.

Molecular Phylogenetics and Evolution, Год журнала: 2024, Номер 201, С. 108215 - 108215

Опубликована: Окт. 11, 2024

Язык: Английский

Процитировано

1
Generalizing Bayesian phylogenetics to infer shared evolutionary events DOI Creative Commons
Jamie R. Oaks, Perry L. Wood, Cameron D. Siler

и другие.

Proceedings of the National Academy of Sciences, Год журнала: 2022, Номер 119(29)

Опубликована: Июль 15, 2022

Many processes of biological diversification can simultaneously affect multiple evolutionary lineages. Examples include members a gene family diverging when region chromosome is duplicated, viral strains at “super-spreading” event, and geological event fragmenting whole communities species. It difficult to test for patterns shared divergences predicted by such because all phylogenetic methods assume that lineages diverge independently. We introduce Bayesian approach relax the assumption independent, bifurcating expanding space topologies trees with multifurcating divergences. This allows us jointly infer relationships, divergence times, or lead more than two descendant Using simulations, we find method accurately infers events they occur performs as well current are independent bifurcating. apply our genomic data from genera geckos across Philippines if past changes islands’ landscape caused bursts speciation. Unlike previous analyses restricted only pairs gecko populations, evidence By generalizing in way likelihood model, opens many avenues future research into life sciences.

Язык: Английский

Процитировано

6
Genetic and morphological concordance and discordance within the Cyrtodactylus brevipalmatus group (Squamata: Gekkonidae) DOI
L. Lee Grismer, Shahrul Anuar Mohd Sah,

Mohd Abdul Muin

и другие.

Zootaxa, Год журнала: 2023, Номер 5353(3), С. 265 - 275

Опубликована: Окт. 9, 2023

We use data sets from the Cyrtodactylus brevipalmatus group with limited genetic and morphological sampling to demonstrate that not accounting for error may adversely influence decisions regarding species delimitation diagnosis. Lack of geographic between endpoints a species’ range recover notable interpopulational differentiation consistent species-level differentiation. Additionally, small population sample sizes fail statistically different diagnostic differences. Combined, these types can produce results seemingly recognition cryptic species—genetically delimited populations lacking characters. This is current situation within some lineages C. whereas in others, less problematic does jeopardize their taxonomy. note potential negative effects comparative biology as whole if taken into consideration prior constructing taxonomies.

Язык: Английский

Процитировано

1