Polymorphisms in the bovine hemoglobin‐beta gene provide evidence for gene‐flow between wild species of <i>Bos</i> (<i>Bibos</i>) and domestic cattle in Southeast Asia

Tanaka, Kazuaki; Takizawa, Takeo; Dorji, Tashi; Amano, Takashi; Mannen, Hideyuki; Maeda, Yoshizane; Yamamoto, Yoshio; Namikawa, Takao

doi:10.1111/j.1740-0929.2010.00808.x

Cited by 6 publications

(5 citation statements)

References 24 publications

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“…2017), and thus facilitate the adaptive response to hypoxia. Additionally, the introgression of the HBB gene from wild to domestic animals has been observed in several species such as cattle ( Bos taurus ) (Tanaka et al. 2011) and Tibetan mastiff ( Canis lupus familiaris ) (Miao et al.…”

Section: Resultsmentioning

confidence: 99%

The Genome Landscape of Tibetan Sheep Reveals Adaptive Introgression from Argali and the History of Early Human Settlements on the Qinghai–Tibetan Plateau

Yang

Xie

et al. 2018

Molecular Biology and Evolution

105

121

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Tibetan sheep are the most common and widespread domesticated animals on the Qinghai–Tibetan Plateau (QTP) and have played an essential role in the permanent human occupation of this high-altitude region. However, the precise timing, route, and process of sheep pastoralism in the QTP region remain poorly established, and little is known about the underlying genomic changes that occurred during the process. Here, we investigate the genomic variation in Tibetan sheep using whole-genome sequences, single nucleotide polymorphism arrays, mitochondrial DNA, and Y-chromosomal variants in 986 samples throughout their distribution range. We detect strong signatures of selection in genes involved in the hypoxia and ultraviolet signaling pathways (e.g., HIF-1 pathway and HBB and MITF genes) and in genes associated with morphological traits such as horn size and shape (e.g., RXFP2). We identify clear signals of argali (Ovis ammon) introgression into sympatric Tibetan sheep, covering 5.23–5.79% of their genomes. The introgressed genomic regions are enriched in genes related to oxygen transportation system, sensory perception, and morphological phenotypes, in particular the genes HBB and RXFP2 with strong signs of adaptive introgression. The spatial distribution of genomic diversity and demographic reconstruction of the history of Tibetan sheep show a stepwise pattern of colonization with their initial spread onto the QTP from its northeastern part ∼3,100 years ago, followed by further southwest expansion to the central QTP ∼1,300 years ago. Together with archeological evidence, the date and route reveal the history of human expansions on the QTP by the Tang–Bo Ancient Road during the late Holocene. Our findings contribute to a depth understanding of early pastoralism and the local adaptation of Tibetan sheep as well as the late-Holocene human occupation of the QTP.

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Section: Resultsmentioning

confidence: 99%

The Genome Landscape of Tibetan Sheep Reveals Adaptive Introgression from Argali and the History of Early Human Settlements on the Qinghai–Tibetan Plateau

Yang

Xie

et al. 2018

Molecular Biology and Evolution

105

121

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“…The structure output also revealed the same genetic architecture in the two zebu populations, with some introgressions of genes from domestic cattle (i.e., zebu) to the gayal population and vice versa. This might be due to inter-specific hybridization among the Bos species (zebu, taurine, gayal, and yak) which has been documented in South and Southeast Asian cultures (Tanaka et al, 2011). The admixed zebu and gayal individuals in the studied population might be due to sampling errors despite they have the phenotypic resemblance and every precautions were taken during sampling.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide Single Nucleotide Polymorphism Analyses Reveal Genetic Diversity and Structure of Wild and Domestic Cattle in Bangladesh

Uzzaman

Edea

Bhuiyan

et al. 2014

Asian Australas. J. Anim. Sci

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In spite of variation in coat color, size, and production traits among indigenous Bangladeshi cattle populations, genetic differences among most of the populations have not been investigated or exploited. In this study, we used a high-density bovine single nucleotide polymorphism (SNP) 80K Bead Chip derived from Bos indicus breeds to assess genetic diversity and population structure of 2 Bangladeshi zebu cattle populations (red Chittagong, n = 28 and non-descript deshi, n = 28) and a semi-domesticated population (gayal, n = 17). Overall, 95% and 58% of the total SNPs (69,804) showed polymorphisms in the zebu and gayal populations, respectively. Similarly, the average minor allele frequency value was as high 0.29 in zebu and as low as 0.09 in gayal. The mean expected heterozygosity varied from 0.42±0.14 in zebu to 0.148±0.14 in gayal with significant heterozygosity deficiency of 0.06 (FIS) in the latter. Coancestry estimations revealed that the two zebu populations are weakly differentiated, with over 99% of the total genetic variation retained within populations and less than 1% accounted for between populations. Conversely, strong genetic differentiation (FST = 0.33) was observed between zebu and gayal populations. Results of population structure and principal component analyses suggest that gayal is distinct from Bos indicus and that the two zebu populations were weakly structured. This study provides basic information about the genetic diversity and structure of Bangladeshi cattle and the semi-domesticated gayal population that can be used for future appraisal of breed utilization and management strategies.

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“…Reports on the phylogeny of Primata (Chatterjee et al 2009; Fabre et al 2009), Cetartiodactyla (Arnason et al 2004; Hernández Fernández and Vrba 2005; Price et al 2005; Steiner et al 2005; Tanaka et al 2011), Carnivora (Higdon et al. 2007), Chiroptera (Jones et al 2002, 2005), Metatheria (Nilsson et al 2010), Aves (Dimcheff et al 2002; Livezey and Zusi 2007), Crocodylidae (Meganathan et al 2010), Testudines (Krenz et al 2005; Naro-Maciel et al 2008; Barley et al 2010), Amphibia (Zardoya and Meyer 2001), Sarcopterygii (Zardoya and Meyer 1996), Actinopterygii (Meyer et al 1994; Westneat and Alfaro 2005; Mabuchi et al 2007; Espiñeira et al 2008; Chiba et al 2009; Gaubert et al 2009; Little et al 2010; Tang et al 2010), Chondrichthyes (Rocco et al 2007; Inoue et al 2010; Vélez-Zuazo and Agnarsson 2011), and Vertebrata (Meyer and Zardoya 2003) were used to create the global phylogeny that included all species in our sample (supplementary information, Supplementary Material online).…”

Section: Methodsmentioning

confidence: 99%

Estimating the Rate of Irreversibility in Protein Evolution

Söylemez

Kondrashov

2012

Genome Biology and Evolution

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Whether or not evolutionary change is inherently irreversible remains a controversial topic. Some examples of evolutionary irreversibility are known; however, this question has not been comprehensively addressed at the molecular level. Here, we use data from 221 human genes with known pathogenic mutations to estimate the rate of irreversibility in protein evolution. For these genes, we reconstruct ancestral amino acid sequences along the mammalian phylogeny and identify ancestral amino acid states that match known pathogenic mutations. Such cases represent inherent evolutionary irreversibility because, at the present moment, reversals to these ancestral amino acid states are impossible for the human lineage. We estimate that approximately 10% of all amino acid substitutions along the mammalian phylogeny are irreversible, such that a return to the ancestral amino acid state would lead to a pathogenic phenotype. For a subset of 51 genes with high rates of irreversibility, as much as 40% of all amino acid evolution was estimated to be irreversible. Because pathogenic phenotypes do not resemble ancestral phenotypes, the molecular nature of the high rate of irreversibility in proteins is best explained by evolution with a high prevalence of compensatory, epistatic interactions between amino acid sites. Under such mode of protein evolution, once an amino acid substitution is fixed, the probability of its reversal declines as the protein sequence accumulates changes that affect the phenotypic manifestation of the ancestral state. The prevalence of epistasis in evolution indicates that the observed high rate of irreversibility in protein evolution is an inherent property of protein structure and function.

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Polymorphisms in the bovine hemoglobin‐beta gene provide evidence for gene‐flow between wild species of Bos (Bibos) and domestic cattle in Southeast Asia

Cited by 6 publications

References 24 publications

The Genome Landscape of Tibetan Sheep Reveals Adaptive Introgression from Argali and the History of Early Human Settlements on the Qinghai–Tibetan Plateau

The Genome Landscape of Tibetan Sheep Reveals Adaptive Introgression from Argali and the History of Early Human Settlements on the Qinghai–Tibetan Plateau

Genome-wide Single Nucleotide Polymorphism Analyses Reveal Genetic Diversity and Structure of Wild and Domestic Cattle in Bangladesh

Estimating the Rate of Irreversibility in Protein Evolution

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