Genomes reveal selective sweeps in kiang and donkey for high-altitude adaptation

Zeng, Lin; Liu, He-Qun; Tu, Xiaolong; Ji, Changmian; Gou, Xin; Esmailizadeh, Ali; Wang, Sheng; Wang, Mingshan; Wang, Mingcheng; Li, Xiaolong; Charati, Hadi; Adeola, Adeniyi C.; Adedokun, R. A. M.; Oladipo, Olatunbosun; Olaogun, Sunday Charles; Sanke, Oscar J; Godwin, F Mangbon; Ommeh, Sheila; Agwanda, Bernard; Lichoti, Jacqueline Kasiiti; Han, Jianlin; Zheng, Hongkun; Wang, Changfa; Zhang, Yaping; Frantz, Laurent; Wu, Dongdong

doi:10.24272/j.issn.2095-8137.2021.095

Cited by 14 publications

(8 citation statements)

References 55 publications

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“…This category includes studies that have not found any signs of hybridization in the populations studied or found only very limited evidence e.g., [ 154 , 208 , 209 , 210 , 211 , 212 , 213 , 214 , 215 ]. We found 24 studies that fitted this category.…”

Section: Discussionmentioning

confidence: 99%

Consequences of Hybridization in Mammals: A Systematic Review

Adavoudi¹,

Pilot²

2021

Genes

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Hybridization, defined as breeding between two distinct taxonomic units, can have an important effect on the evolutionary patterns in cross-breeding taxa. Although interspecific hybridization has frequently been considered as a maladaptive process, which threatens species genetic integrity and survival via genetic swamping and outbreeding depression, in some cases hybridization can introduce novel adaptive variation and increase fitness. Most studies to date focused on documenting hybridization events and analyzing their causes, while relatively little is known about the consequences of hybridization and its impact on the parental species. To address this knowledge gap, we conducted a systematic review of studies on hybridization in mammals published in 2010–2021, and identified 115 relevant studies. Of 13 categories of hybridization consequences described in these studies, the most common negative consequence (21% of studies) was genetic swamping and the most common positive consequence (8%) was the gain of novel adaptive variation. The total frequency of negative consequences (49%) was higher than positive (13%) and neutral (38%) consequences. These frequencies are biased by the detection possibilities of microsatellite loci, the most common genetic markers used in the papers assessed. As negative outcomes are typically easier to demonstrate than positive ones (e.g., extinction vs hybrid speciation), they may be over-represented in publications. Transition towards genomic studies involving both neutral and adaptive variation will provide a better insight into the real impacts of hybridization.

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Section: Discussionmentioning

confidence: 99%

Consequences of Hybridization in Mammals: A Systematic Review

Adavoudi¹,

Pilot²

2021

Genes

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“…To detect signal of potential genetic introgression from other tiger subspecies into the South China tigers, we applied several population genetic analyses, including the ABBA-BABA test 28,29 , f4-ratio 30 , and TreeMix method 31 . The results clearly indicated that the South China tiger sequenced by Liu et al 1 displayed the highest admixture signal of hybrid origin from other subspecies (Fig.…”

Section: Limited Gene Flow From Other Tiger Subspecies To Extant South China Tigersmentioning

confidence: 99%

Population genomic analysis provides strong evidence of the past success and future strategies of South China tiger breeding

Wang

Yuán³

et al. 2021

Preprint

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The South China tigers (Panthera tigris amoyensis) are extinct in the wild, but viable populations remain in breeding centers and zoos after 60 years of effective conservation efforts. At present, however, the existing genetic variation of these tigers remains unknown. In this study, we assembled a high-quality chromosome-level genome using long-read sequences and re-sequenced 29 high-depth genomes of the South China tigers. We identified two significantly differentiated genomic ancestries in the extant populations, which also harbored some rare genetic variants introgressed from other subspecies, suggesting limited but essential genetic diversity to sustain the South China tigers. The unique pattern of dual ancestry and the genomic resources generated in our study pay the way for a genomics-informed conservation, following the real-time monitoring and controlled exchange of all reproductive South China tigers.

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“…Data analysis was completed using Vcftools (0.1.15) [ 19 ] software. In brief, the Fst value in the chromosome was calculated with 500 kb as the sliding window and 50 kb as the step window [ 20 , 21 ], followed by extraction of the sites in the window where the Fst and θπ ratio were in the top 5% [ 22 ]. These sites were regarded as significant SNP candidate sites for the selective signatures.…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Selective Signatures Reveal Candidate Genes Associated with Hair Follicle Development and Wool Shedding in Sheep

Lei

Sun

Guo

et al. 2021

Genes

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Hair follicle development and wool shedding in sheep are poorly understood. This study investigated the population structures and genetic differences between sheep with different wool types to identify candidate genes related to these traits. We used Illumina ovine SNP 50K chip genotyping data of 795 sheep populations comprising 27 breeds with two wool types, measuring the population differentiation index (Fst), nucleotide diversity (θπ ratio), and extended haplotype homozygosity among populations (XP-EHH) to detect the selective signatures of hair sheep and fine-wool sheep. The top 5% of the Fst and θπ ratio values, and values of XP-EHH < −2 were considered strongly selected SNP sites. Annotation showed that the PRX, SOX18, TGM3, and TCF3 genes related to hair follicle development and wool shedding were strongly selected. Our results indicated that these methods identified important genes related to hair follicle formation, epidermal differentiation, and hair follicle stem cell development, and provide a meaningful reference for further study on the molecular mechanisms of economically important traits in sheep.

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Genomes reveal selective sweeps in kiang and donkey for high-altitude adaptation

Cited by 14 publications

References 55 publications

Consequences of Hybridization in Mammals: A Systematic Review

Consequences of Hybridization in Mammals: A Systematic Review

Population genomic analysis provides strong evidence of the past success and future strategies of South China tiger breeding

Genome-Wide Selective Signatures Reveal Candidate Genes Associated with Hair Follicle Development and Wool Shedding in Sheep

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