Dataset Information

Genome-wide SNP and population divergence of finless porpoises.

ABSTRACT: Single nucleotide polymorphisms (SNPs) are rapidly becoming the population genomic markers in addressing ecology, evolution, and conservation issues for their high capacity to access variability across the genome. We isolated a total of 140 ideal SNPs from the finless porpoise and used 78 (under Hardy-Weinberg equilibrium) of them to conduct those issues especially for addressing population genetic differentiation. Bayesian clustering and principal component analyses all suggested that finless porpoises in Chinese waters could be divided into three distinct genetic groupings. Low levels of within-population genetic variation (mean HE = 0.3405, standard deviation = 0.1188) and significant differentiation among populations (FST = 0.1050-0.1628, P < 0.01) were confirmed. Limited gene flow was found especially between the freshwater Yangtze River porpoise and the oceanic Yellow Sea and South China Sea populations, which strongly suggested that some barriers might have restricted their genetic exchange. These evidences not only support a recent subdivision of the finless porpoise into two species but also suggest a full species status for the Yangtze finless porpoise, especially considering the significant genetic divergence between freshwater and marine porpoises, in combination with the unique distribution of Yangtze finless porpoises in freshwater and their distinctness in physiological and morphological features.

SUBMITTER: Li S

PROVIDER: S-EPMC3641630 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Genome-wide SNP and population divergence of finless porpoises.

Li Shuzhen S Xu Shixia S Wan Huirong H Ji Heyi H Zhou Kaiya K Yang Gang G

Genome biology and evolution 20130101 4

Single nucleotide polymorphisms (SNPs) are rapidly becoming the population genomic markers in addressing ecology, evolution, and conservation issues for their high capacity to access variability across the genome. We isolated a total of 140 ideal SNPs from the finless porpoise and used 78 (under Hardy-Weinberg equilibrium) of them to conduct those issues especially for addressing population genetic differentiation. Bayesian clustering and principal component analyses all suggested that finless p ...[more]

PMID: 23563971

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Project description:The Yangtze finless porpoise (YFP) (Neophocaena asiaeorientalis asiaeorientalis) is a critically endangered freshwater cetacean, with about 1,249 individuals thought to be left in the wild. However, viral entities and viral diseases of YFPs remain obscure. In this study, anal swabs for virome analysis were collected during the physical examination of YFPs in the Tian-E-Zhou Oxbow (TEO) ex situ reserve. A total of 19 eukaryotic viral species belonging to 9 families, including Papillomaviridae, Herpesviridae, Picornaviridae, Picobirnaviridae, Caliciviridae, Retroviridae, Parvoviridae, Virgaviridae, and Narnaviridae, and other unclassified viruses were identified based on metasequencing. Among these detected viruses, a novel herpesvirus (NaHV), two different kobuviruses (NaKV1-2), and six different papillomaviruses (NaPV1 to -6) were considered potential risks to YFPs and confirmed by PCR or reverse transcription-PCR (RT-PCR). Most YFPs sampled were found to harbor one or more kinds of detected viral genomes (52/58 [89.7%]). Surveillance results demonstrated that kobuvirus and herpesvirus displayed obvious age distribution and PVs showed significant gender difference in YFPs. According to species demarcation criteria in individual genera in Papillomaviridae, two novel species (referred to as Omikronpapillomavirus 2 and 3) and four novel isolates of PV were identified in YFPs. Further evolutionary analysis suggested that NaPVs would occupy the mucosal niche and that virus-host codivergence mixed with duplications and host-switching events drives the evolution of cetacean PVs. Divergence times of PVs in YFP and other cetacean reflect the incipient speciation of YFPs. In summary, our findings revealed the potential viral entities, their prevalence, and their evolutionary history in YFPs, which raises an important issue regarding effects of viral infection on the fitness of YFPs. IMPORTANCE The Yangtze finless porpoise (YFP) is the only cetacean species in freshwater following the functional extinction of the baiji (Lipotes vexillifer). Health management, disease treatment, and other special measures are important for maintaining the existing YFP populations, especially in in situ and ex situ reserves. The discovery of potential viral entities and their prevalence in YFPs raises an important issue regarding the effects of viral infection on the fitness of YFPs and may contribute to the conservation of YFPs. The evolutionary history of papillomaviruses in YFP and other cetaceans reflects the phylogeny of their hosts and supports the status of incipient species, opening a window to investigate the evolutionary adaptation of cetaceans to freshwater as well as their phylogeny to remedy the deficiency of fossil evidence.

Project description:BackgroundHumpless Bos taurus cattle are one of the earliest domestic cattle in Africa, followed by the arrival of humped Bos indicus cattle. The diverse indigenous cattle breeds of Africa are derived from these migrations, with most appearing to be hybrids between Bos taurus and Bos indicus. The present study examines the patterns of admixture, diversity, and relationships among African cattle breeds.MethodsData for ~ 40 k SNPs was obtained from previous projects for 4089 animals representing 35 African indigenous, 6 European Bos taurus, 4 Bos indicus, and 5 African crossbred cattle populations. Genetic diversity and population structure were assessed using principal component analyses (PCA), admixture analyses, and Wright's F statistic. The linkage disequilibrium and effective population size (Ne) were estimated for the pure cattle populations.ResultsThe first two principal components differentiated Bos indicus from European Bos taurus, and African Bos taurus from other breeds. PCA and admixture analyses showed that, except for recently admixed cattle, all indigenous breeds are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus. The African zebu breeds had highest proportions of Bos indicus ancestry ranging from 70 to 90% or 60 to 75%, depending on the admixture model. Other indigenous breeds that were not 100% African Bos taurus, ranged from 42 to 70% or 23 to 61% Bos indicus ancestry. The African Bos taurus populations showed substantial genetic diversity, and other indigenous breeds show evidence of having more than one African taurine ancestor. Ne estimates based on r2 and r2adj showed a decline in Ne from a large population at 2000 generations ago, which is surprising for the indigenous breeds given the expected increase in cattle populations over that period and the lack of structured breeding programs.ConclusionAfrican indigenous cattle breeds have a large genetic diversity and are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus. This provides a rich resource of potentially valuable genetic variation, particularly for adaptation traits, and to support conservation programs. It also provides challenges for the development of genomic assays and tools for use in African populations.

Dataset Information

Genome-wide SNP and population divergence of finless porpoises.

Publications

Genome-wide SNP and population divergence of finless porpoises.

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