Genomewide scan for adaptive differentiation along altitudinal gradient in the Andrew's toad Bufo andrewsi

Recent studies of humans, dogs and rodents have started to discover the genetic underpinnings of high altitude adaptations, yet amphibians have received little attention in this respect. To identify possible signatures of adaptation to altitude, we performed a genome scan of 15 557 single nucleotide...

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Published inMolecular ecology Vol. 25; no. 16; pp. 3884 - 3900
Main Authors Guo, Baocheng, Lu, Di, Liao, Wen Bo, Merilä, Juha
Format Journal Article
LanguageEnglish
Published England Blackwell Publishing Ltd 01.08.2016
Subjects
adaptation
Adaptation, Physiological - genetics
Altitude
Amphibia
amphibian
Amphibians
Animals
Bufo
Bufonidae - genetics
China
dogs
genes
Genetic diversity
Genetic Drift
genetic variation
Genome
Genomics
humans
Polymorphism
Polymorphism, Single Nucleotide
RAD-seq
rodents
sequence analysis
single nucleotide polymorphism
SNP
temperature
Toads
China
altitude
RAD-seq
adaptation
SNP
amphibian
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Summary:Recent studies of humans, dogs and rodents have started to discover the genetic underpinnings of high altitude adaptations, yet amphibians have received little attention in this respect. To identify possible signatures of adaptation to altitude, we performed a genome scan of 15 557 single nucleotide polymorphisms (SNPs) obtained with restriction site‐associated DNA sequencing of pooled samples from 11 populations of Andrew's toad (Bufo andrewsi) from the edge of the Tibetan Plateau, spanning an altitudinal gradient from 1690 to 2768 m.a.s.l. We discovered significant geographic differentiation among all sites, with an average FST = 0.023 across all SNPs. Apart from clear patterns of isolation by distance, we discovered numerous outlier SNPs showing strong associations with variation in altitude (1394 SNPs), average annual temperature (1859 SNPs) or both (1051 SNPs). Levels and patterns of genetic differentiation in these SNPs were consistent with the hypothesis that they have been subject to directional selection and reflect adaptation to altitudinal variation among the study sites. Genes with footprints of selection were significantly enriched in binding and metabolic processes. Several genes potentially related to high altitude adaptation were identified, although the identity and functional significance of most genomic targets of selection remain unknown. In general, the results provide genomic support for results of earlier common garden and low coverage genetic studies that have uncovered substantial adaptive differentiation along altitudinal and latitudinal gradients in amphibians.
Bibliography:Fig. S1 Length distribution of reference sequences that resulted from de novo assembly using for alignment and SNP calling.Fig. S2 Genome-wide distribution of genetic variation. (A) Tajima's π and (B) θW across the 11 Andrew's toad populations sampled for this study. Each vertically oriented rectangle shows the median (bar), the interquartile range (box), and outlier values of 3/2 times more than upper quartile or less than lower quartile of Tajima's π or θW for a specific population. (C) Genome-wide distribution of genetic variation in each of the 11 Andrew's toad populations. Nucleotide diversity π (top panel), population mutation rate θW (middle panel), and Tajima's D (bottom panel) are plotted as functions of genomic position with a non-overlapping 200 bp sliding window.Fig. S3 Number of SNPs whose allele frequency variation are associated with variation in altitude and/or annual average temperature in Bayenv analysis across (A) all of the 11 Andrew's toad populations, (B) populations (BZG, JZG, and MYC) in the North of Sichuan Province, (C) populations (CP, DCG, and YJ) in the Middle of Sichuan Province, and (D) populations (KG, PTG, QB, and XGQ) in Yunnan Province.Fig. S4 Number of SNPs whose allele frequency variation are associated with variation in (A) altitude and (B) annual average temperature across the 11 Andrew's toad populations (Global) and different population clusters (NS, MS, and YN). Global: all of the 11 populations, NS: populations (BZG, JZG, and MYC) in the North of Sichuan Province, MS: populations (CP, DCG, and YJ) in the Middle of Sichuan Province, YN: populations (KG, PTG, QB, and XGQ) in Yunnan Province.Fig. S5 Neighbor-Joining tree of the 11 Andrew's populations based on FST values of the 454 outlier SNPs detected to be under diversifying selection. Populations from different clusters are marked in different colours (see Fig. . legend for details), and the values at nodes refer to bootstrap values of 1000 replicates.Table S1 Sampling information of populations used in this study Table S2 Pairwise geographic distances (KM) among the 11 Andrew's toad populations Table S3 Summary statistics of RAD data, including number of SNPs identified, and basic measures of genetic variability in each population Table S4 Gene harboured SNPs showing selection footprints and their GO annotation Table S5 Average pairwise FST among the 11 Andrew's toad populations based on the 15 577 SNPs identified using popoolation2
Sichuan Province Outstanding Youth Academic Technology Leaders Program - No. 2013JQ0016
istex:0B5A4AA860E00D35C727C10F38E029AE5B2EA48C
ArticleID:MEC13722
ark:/67375/WNG-R8C829B9-6
Academy of Finland - No. 129662; No. 134728
National Natural Sciences Foundation of China - No. 31471996; No. 31101633
ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 14
content type line 23
ISSN:0962-1083
1365-294X
1365-294X
DOI:10.1111/mec.13722