Phylogenomics of Psammodynastes and Buhoma (Elapoidea: Serpentes), with the description of a new Asian snake family

Scientific Reports, Год журнала: 2024, Номер 14(1)

Опубликована: Апрель 25, 2024

Abstract Asian mock vipers of the genus Psammodynastes and African forest snakes Buhoma are two genera belonging to snake superfamily Elapoidea. The phylogenetic placements within Elapoidea has been extremely unstable which resulted in their uncertain debated taxonomy. We used ultraconserved elements traditional nuclear mitochondrial markers infer relationships these with other elapoids. , for a reference genome sequenced, were found, strong branch support, be relatively early diverging split that is sister clade consisting Elapidae, Micrelapidae Lamprophiidae. Hence, we allocate its own family, Psammodynastidae new family . However, position could not resolved high degree confidence. Attempts identify possible sources conflict rapid radiation elapoid suggest both hybridisation/introgression during diversification, including ghost introgression, as well incomplete lineage sorting likely have had confounding role. usual practice combining loci genomic data appears mislead phylogeny reconstructions scenarios, especially absence scale data.

Язык: Английский

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Successful Traceability of Wildlife Samples Contributes to Wildlife Conservation: A Case Study of Tracing the Snub-Nosed Monkey (Rhinopithecus spp.)

Animals, Год журнала: 2025, Номер 15(2), С. 174 - 174

Опубликована: Янв. 10, 2025

Rapid and effective methods for tracing the geographic origin of wildlife samples are essential tackling illegal trade. Traditional morphological categorization often inadequate as relying on mitochondrial COXI barcode is insufficient determining populations. To address these limitations, we developed a bioinformatics-based pipeline rapid identification traceable nuclear genome loci. This has been applied to whole-genome sequence (WGS) data China’s flagship species, snub-nosed monkey (Rhinopithecus spp.). These species known sex-biased dispersal hybrid speciation, which complicates genealogy tracing. Using phylogenetic principles, employed Robinson Foulds (RF) distance scanned over 1,850,726 population-specific loci, identifying five pairs that can trace origins rapidly cost-effectively using PCR. Additionally, found only genetic information accurate traceability subspecies-level Our efficiently identifies loci traces individuals, providing valuable tool preservation combating approach be extended other aiding in conservation endangered criminal evidence.

Язык: Английский

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Exploration of migration directions in different populations of Eothenomys miletus in the Hengduan Mountains of Yunnan Province: a genome-based analysis

Frontiers in Ecology and Evolution, Год журнала: 2025, Номер 13

Опубликована: Янв. 28, 2025

Eothenomys miletus is an endemic species that inhabits the Hengduan Mountain regions (HDR) and serves as one of primary hosts for plague hantaviruses. While physiological characteristics E. have been extensively studied, molecular aspects, particularly migration direction , remain unclear. In present study, we utilized genomic data to investigate four populations: Ailaoshan (ALS), Jiangchuan (JC), Lijiang (LJ), Deqin (DQ), which are distributed from south north within HDR. Our results indicated ALS population positioned at base phylogenetic tree, admixture analysis revealed more closely related JC DQ populations. Integrate genetic structure, fossil records well our research, inferred may north, suggesting populations originated ALS. However, patterns origins LJ require further investigation discussion. Additionally, focused on identifying signatures selection local adaptation among different We identified three selected genes associated with olfactory placode in DQ: Six1 Six4 Sox2 . hypothesized these be linked population’s region’s microclimate. summary, study first employ genomics explore crucial future research

Язык: Английский

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GENOMIC ANALYSES REVEAL A LACK OF WIDESPREAD STRONG SELECTION IN INDIGENOUS CHICKENS

Poultry Science, Год журнала: 2025, Номер unknown, С. 105081 - 105081

Опубликована: Март 1, 2025

The study of domestication has been revolutionized with the advent molecular genetics. Chickens, their clear history, emerge as an excellent model for into paths evolution in and improvement. Here we used genomic data from wild, indigenous, commercial chickens to better understand how genetic drift selection translate differentiations. Our investigation patterns allelic change divergence reveals a polygenic architecture governing differentiation during We uncover distinctive population-specific differentiations terms genes functions among chickens. Using Runs Of Homozygosity (ROH) based mixed approach developed this study, identified only directional signatures occurring wild Notably, our findings suggest that indigenous serve reservoirs diversity, necessary rapid adaptation new environments or subsequent modern breeding. This work provides unprecedented insights chicken improvement, it illuminates understanding other animal species.

Язык: Английский

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A consequential one-night stand: Episodic historical hybridization leads to mitochondrial takeover in sympatric desert ant-eating spiders

Molecular Phylogenetics and Evolution, Год журнала: 2024, Номер 199, С. 108167 - 108167

Опубликована: Авг. 3, 2024

Язык: Английский

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Microarchitecture of the penis bone (baculum) of a seal: A 3D morphometric examination using synchrotron and laboratory micro‐computed tomography

The Anatomical Record, Год журнала: 2024, Номер 307(8), С. 2858 - 2874

Опубликована: Фев. 4, 2024

Abstract We examined the ultrastructure of mammalian os penis at high‐resolution synchrotron level. Previously, bacular microanatomy had only been investigated histologically. studied baculum harp seal ( Pagophilus groenlandicus ), in which varies more size and shape than does a mechanically constrained bone (humerus). (1) microarchitecture bacula humeri from same specimens, (2) described changes micro‐ macro‐morphology associated with age n = 15, range 1–35 years) type. analyzed cross‐sectional geometry non‐destructively through laboratory micro‐computed tomography. suggest that midshaft may resist axial compression while proximal region torsion, based on measurements cortical areas, perimeter, ratio maximum minimum moments inertia, polar moment inertia. In addition, be less mechanosensitive humeri, microstructural variables (e.g., volume, surface area, diameter lacunae porosity) across groupings. Our findings related to pinniped provide basis for further studies development, mechanical properties, functions, adaptations this other species. use multi‐modal imaging approach was minimally destructive reproducible accurate comparison three‐dimensional ultrastructure. Such methods, coupled multidisciplinary analyses, enable diverse biology, life history, evolution using museum collections.

Язык: Английский

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A Cautionary Note on Using STRUCTURE to Detect Hybridization in a Phylogenetic Context

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Фев. 8, 2024

Abstract Population genetic clustering methods are widely used to detect hybridization events between closely related populations within species, as well deeply diverged lineages across phylogenetic time-scales, although their strengths and limitations in the latter cases remain poorly explored. This study presents first systematic evaluation of performance most popular population method, STRUCTURE, under a variety cross-species scenarios, including hybrid speciation, introgression involving ghost (i.e., extinct or unsampled) otherwise. Our simulations demonstrate that STRUCTURE performs identifying hybrids parental donors only when admixture happens very recently sampled extant lineages. However, generally fails signals occurs deep time gene flow stems from We find symmetrical contribution speciation will often be revealed extremely asymmetrical especially event occurred more than some ago. results suggest population-genetic may inefficient for detecting either ancient admixtures, partly explaining why has escaped attention evolutionary biologists until recently.

Язык: Английский

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Otariid gammaherpesvirus 1 in South American fur seals (Arctocephalus australis) and a novel related herpesvirus in free-ranging South American sea lions (Otaria byronia): Prevalence and effects of age, sex, and sample type

PLoS ONE, Год журнала: 2024, Номер 19(3), С. e0299404 - e0299404

Опубликована: Март 6, 2024

Otariid gammaherpesvirus 1 (OtGHV1) is associated with high rates of urogenital carcinoma in free-ranging California sea lions (Zalophus californianus; CSL), and until recently was reported only the Northern Hemisphere. The objective this study to survey South American (Otaria byronia; SASL) fur seals (Arctocephalus australis: SAFS) Punta San Juan, Peru for OtGHV1 determine prevalence characteristics. Twenty-one percent (14/67) swabs collected over three years (2011, 2014, 2015) from live pinnipeds both species tested positive a pan-herpesvirus conventional PCR. Sequencing SAFS amplicons revealed 100% homology at DNA polymerase, glycoprotein B, viral bcl2-like genes. SASL novel related virus, herein called 8 (OtGHV8). For comparison sample sites, urogenital, conjunctival, oropharyngeal 136 Juan between 2011-2018 were then assayed using quantitative PCR segment OtGHV1/8 polymerase gene qPCR assay now determined cross-react two viruses. In total, across species, 38.6% (51/132) swabs, 5.6% (4/71) conjunctival 1.1% (1/90) OtGHV1/8, on swabs. Results complicated by finding OtGHV8, necessitating further versus OtGHV8 an alternate assay. suggest potential relationship CSL. Though necropsy surveillance very limited, geographic patterns OtGHV1-associated CSL tendency herpesviruses cause more detrimental disease aberrant hosts suggests that it possible may be definitive host OtGHV1, which gives insight into diversity phyogeography clade gammaherpesviruses.

Язык: Английский

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Homoploid Hybrid Speciation in a Marine Pelagic Fish Megalaspis cordyla (Carangidae)

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Авг. 19, 2024

Abstract Homoploid hybrid speciation (HHS) is an enigmatic evolutionary process where new species arise through hybridization of divergent lineages without changes in chromosome number. Although increasingly documented various taxa and ecosystems, convincing cases HHS marine fishes have been lacking. This study presents evidence Torpedo scad Megalaspis cordyla based on comprehensive genomic, morphological, ecological analyses. A Principal Component Analysis using thousands SNPs identified three sympatric clusters the western Pacific. Genome-wide differentiation between admixed nature a cluster others were evident from population genomic analyses, tree estimation, mitochondrial DNA divergence, tests introgression. Multiple statistical methods for detection also supported ancestry this cluster. Moreover, model-based demographic inference favored scenario over Examination occurrence data ecologically relevant morphological characters suggested differences clusters, potentially contributing to reproductive isolation niche partitioning sympatry. The are morphologically distinguishable thus can be taxonomically recognized as separate species. restricted coasts Taiwan Japan, all coexist. parental additionally found lower latitudes such Philippines, Vietnam, Thailand, Malaysia, they display non-overlapping distributions. Given geographical distributions, estimated times formation, patterns historical changes, we propose that Pleistocene glacial cycles primary driver system. Based argument, develop ecogeographic model coastal including novel hypothesis explain initial stages HHS.

Язык: Английский

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The Genetic Architecture of Local Adaptation and Reproductive Character Displacement in Scutiger boulengeri Complex (Anura: Megophryidae)

Molecular Ecology, Год журнала: 2024, Номер 34(2)

Опубликована: Дек. 16, 2024

Speciation is a continuous process driven by barriers to gene flow. Based on genome-wide SNPs (single nucleotide polymorphisms) of 190 toads from 31 sampling sites Scutiger boulengeri complex, we found evidence for monophyly which represented speciation at least six lineages in S. boulengeri, radiated and exhibited varying degrees divergence The SNP-based phylogenetic tree was largely discordant with the multilocus mitochondrial (i.e., mammatus glandulatus nested boulengeri) published before. Min Mountains (MM) Qinghai-Tibet Plateau (QTP) differ fundamentally habitat elevation) morphology SVL), detected signatures potential high-altitude cold adaptation genes QTP (vs. MM). We reproductive trait disparity SVL nuptial pads) key promoting sympatric rather than allopatric species pairs. In addition, identified selection signals related character displacement, linked obesity-related traits, spines enlarged chest pads group boulengeri). Our study provided new insight paradigm varied pattern local allopatry displacement complex.

Язык: Английский

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