Private haplotypes can reveal local adaptation

Population structure and selective signature of Kirghiz sheep by Illumina Ovine SNP50 BeadChip

Objective

By assessing the genetic diversity and associated selective traits of Kirghiz sheep (KIR), we aim to uncover the mechanisms that contribute to sheep's adaptability to the Pamir Plateau environment.

Methods

This study utilized Illumina Ovine SNP50 BeadChip data from KIR residing in the Pamir Plateau, Qira Black sheep (QBS) inhabiting the Taklamakan Desert, and commonly introduced breeds including Dorper sheep (DOR), Suffolk sheep (SUF), and Hu sheep (HU). The data was analyzed using principal component analysis, phylogenetic analysis, population admixture analysis, kinship matrix analysis, linkage disequilibrium analysis, and selective signature analysis. We employed four methods for selective signature analysis: fixation index (Fst), cross-population extended homozygosity (XP-EHH), integrated haplotype score (iHS), and nucleotide diversity (Pi). These methods aim to uncover the genetic mechanisms underlying the germplasm resources of Kirghiz sheep, enhance their production traits, and explore their adaptation to challenging environmental conditions.

Results

The test results unveiled potential selective signals associated with adaptive traits and growth characteristics in sheep under harsh environmental conditions, and annotated the corresponding genes accordingly. These genes encompass various functionalities such as adaptations associated with plateau, cold, and arid environment (ETAA1, UBE3D, TLE4, NXPH1, MAT2B, PPARGC1A, VEGFA, TBX15 and PLXNA4), wool traits (LMO3, TRPS1, EPHA5), body size traits (PLXNA2, EFNA5), reproductive traits (PPP3CA, PDHA2, NTRK2), and immunity (GATA3).

Conclusion

Our study identified candidate genes associated with the production traits and adaptation to the harsh environment of the Pamir Plateau in Kirghiz sheep. These findings provide valuable resources for local sheep breeding programs. The objective of this study is to offer valuable insights for the sustainable development of the Kirghiz sheep industry.

Whole-genome resequencing deciphers patterns of genetic diversity, phylogeny, and evolutionary dynamics in Kashmir cattle

Kashmir cattle, which were kept by local pastoralists for centuries, are exceptionally resilient and adaptive to harsh environments. Despite its significance, the genomic characteristics of this cattle breed remain elusive. This study utilized whole genome sequences of Kashmir cattle (n = 20; newly sequenced) alongside published whole genomes of 32 distinct breeds and seven core cattle populations (n = 135). The analysis identified ~25.87 million biallelic single nucleotide polymorphisms in Kashmir cattle, predominantly in intergenic and intron regions. Population structure analyses revealed distinct clustering patterns of Kashmir cattle with proximity to the South Asian, African and Chinese indicine cattle populations. Genetic diversity analysis of Kashmir cattle demonstrated lower inbreeding and greater nucleotide diversity than analyzed global breeds. Homozygosity runs indicated less consanguineous mating in Kashmir cattle compared with European taurine breeds. Furthermore, six selection sweep detection methods were used within Kashmir cattle and other cattle populations to identify genes associated with vital traits, including immunity (BOLA-DQA5, BOLA-DQB, TNFAIP8L, FCRL4, AOAH, HIF1AN, FBXL3, MPEG1, CDC40, etc.), reproduction (GOLGA4, BRWD1, OSBP2, LEO1 ADCY5, etc.), growth (ADPRHL1, NRG2, TCF12, TMOD4, GBP4, IGF2, RSPO3, SCD, etc.), milk composition (MRPS30 and CSF1) and high-altitude adaptation (EDNRA, ITPR2, AGBL4 and SCG3). These findings provide essential genetic insights into the characteristics and establish the foundation for the scientific conservation and utilization of Kashmir cattle breed.

Limited introgression from non-native commercial strains and signatures of adaptation in the key pollinator Bombus terrestris

Insect pollination is fundamental for natural ecosystems and agricultural crops. The bumblebee species Bombus terrestris has become a popular choice for commercial crop pollination worldwide due to its effectiveness and ease of mass rearing. Bumblebee colonies are mass produced for the pollination of more than 20 crops and imported into over 50 countries including countries outside their native ranges, and the risk of invasion by commercial non-native bumblebees is considered an emerging issue for global conservation and biological diversity. Here, we use genome-wide data from seven wild populations close to and far from farms using commercial colonies, as well as commercial populations, to investigate the implications of utilizing commercial bumblebee subspecies in the UK. We find evidence for generally low levels of introgression between commercial and wild bees, with higher admixture proportions in the bees occurring close to farms. We identify genomic regions putatively involved in local and global adaptation, and genes in locally adaptive regions were found to be enriched for functions related to taste receptor activity, oxidoreductase activity, fatty acid and lipid biosynthetic processes. Despite more than 30 years of bumblebee colony importation into the UK, we observe low impact on the genetic integrity of local B. terrestris populations, but we highlight that even limited introgression might negatively affect locally adapted populations.

Estimating the genetic diversity of Pacific salmon and trout using multigene eDNA metabarcoding

Genetic diversity underpins species conservation and management goals, and ultimately determines a species' ability to adapt. Using freshwater environmental DNA (eDNA) samples, we examined mitochondrial genetic diversity using multigene metabarcode sequence data from four Oncorhynchus species across 16 sites in Oregon and northern California. Our multigene metabarcode panel included targets commonly used in population genetic NADH dehydrogenase 2 (ND2), phylogenetic cytochrome c oxidase subunit 1 (COI) and eDNA (12S ribosomal DNA) screening. The ND2 locus showed the greatest within-species haplotype diversity for all species, followed by COI and then 12S rDNA for all species except Oncorhynchus kisutch. Sequences recovered for O. clarkii clarkii were either identical to, or one mutation different from, previously characterized haplotypes (95.3% and 4.5% of reads, respectively). The greatest diversity in O. c. clarkii was among coastal watersheds, and subsets of this diversity were shared with fish in inland watersheds. However, coastal streams and the Umpqua River watershed appear to harbour unique haplotypes. Sequences from O. mykiss revealed a disjunction between the Willamette watershed and southern watersheds suggesting divergent histories. We also identified similarities between populations in the northern Deschutes and southern Klamath watersheds, consistent with previously hypothesized connections between the two via inland basins. Oncorhynchus kisutch was only identified in coastal streams and the Klamath River watershed, with most diversity concentrated in the coastal Coquille watershed. Oncorhynchus tshawytscha was only observed at one site, but contained multiple haplotypes at each locus. The characterization of genetic diversity at multiple loci expands the knowledge gained from eDNA sampling and provides crucial information for conservation actions and genetic management.

Applying Population Viability Analysis to Inform Genetic Rescue That Preserves Locally Unique Genetic Variation in a Critically Endangered Mammal

Genetic rescue can reduce the extinction risk of inbred populations, but it has the poorly understood risk of ‘genetic swamping’—the replacement of the distinctive variation of the target population. We applied population viability analysis (PVA) to identify translocation rates into the inbred lowland population of Leadbeater’s possum from an outbred highland population that would alleviate inbreeding depression and rapidly reach a target population size (N) while maximising the retention of locally unique neutral genetic variation. Using genomic kinship coefficients to model inbreeding in Vortex, we simulated genetic rescue scenarios that included gene pool mixing with genetically diverse highland possums and increased the N from 35 to 110 within ten years. The PVA predicted that the last remaining population of lowland Leadbeater’s possum will be extinct within 23 years without genetic rescue, and that the carrying capacity at its current range is insufficient to enable recovery, even with genetic rescue. Supplementation rates that rapidly increased population size resulted in higher retention (as opposed to complete loss) of local alleles through alleviation of genetic drift but reduced the frequency of locally unique alleles. Ongoing gene flow and a higher N will facilitate natural selection. Accordingly, we recommend founding a new population of lowland possums in a high-quality habitat, where population growth and natural gene exchange with highland populations are possible. We also recommend ensuring gene flow into the population through natural dispersal and/or frequent translocations of highland individuals. Genetic rescue should be implemented within an adaptive management framework, with post-translocation monitoring data incorporated into the models to make updated predictions.

Anthropometric, biochemical and hormonal profiles of the partially admixed pygmoid group in Rampasasa (Flores, Indonesia)

OBJECTIVES

We performed a cross-sectional study on anthropometric and laboratory characteristics of inhabitants of Rampasasa (Flores, Indonesia). Adults were categorised according to ancestry into three groups: pygmoid (P/P, offspring of pygmoid parents, n=8), mixed pygmoid (P/N, offspring of pygmoid and non-pygmoid parents, n=12) and non-pygmoid (N/N, n=10). Children (n=28) were P/N.

METHODS

Measurements included height, weight, sitting height, arm span, head circumference, haematological analysis and serum albumin, calcium, vitamin D, insulin-like growth factor-I (IGF-I) and IGF binding protein 3 (IGFBP-3). Pubertal stage and bone age was assessed in children. Anthropometric data were expressed as standard deviation score (SDS) for age. IGF-I, IGFBP-3 and IGF-I/IGFBP-3 ratio were expressed as SDS for age, bone age and pubertal stage.

RESULTS

Mean height SDS showed a gradient from P/P (-4.0) via P/N (-3.2) to N/N (-2.3) (-3.4, -3.1 and -2.2 adjusted for age-associated shrinking). Sitting height and head circumference showed similar gradients. Serum IGF-I SDS was similar among groups (approximately -1 SDS). IGFBP-3 SDS tended toward a gradient from P/P (-1.9) via P/N (-1.5) to N/N (-1.1), but IGF-I/IGFBP-3 ratio was normal in all groups. In P/P and P/N, mean head circumference SDS was >2 SD greater than mean height SDS. Children showed a progressive growth failure and bone age delay, delayed female pubertal onset and an initial low serum IGF-I, normal IGFBP-3 and low IGF-I/IGFBP-3 ratio.

CONCLUSIONS

P/P showed proportionate short stature with relative macrocephaly and relatively low IGFBP-3; P/N presented an intermediate pattern. P/N children were progressively short, showed delayed skeletal maturation, delayed puberty in girls and low IGF-I and IGF-I/IGFBP-3.

Genetic diversity and structure of the narrow endemic Seseli farrenyi (Apiaceae): implications for translocation

Seseli farrenyi (Apiaceae) is an extremely narrow endemic plant, which is considered as one of the species of most conservation concern in Catalonia (NW Mediterranean Basin). Given the accelerated fragmentation and reduction of population size (of over 90%), the environmental agency of Catalonia is currently preparing a recovery plan that includes reinforcements of the extant populations. The present study is aimed at providing the necessary knowledge to carry out genetically-informed translocations, by using microsatellites as genetic markers. Fourteen microsatellites have been specifically developed for S. farrenyi, of which nine have been used. Besides the extant natural populations, the three ex situ collections that are known to exist of this species have also been studied, as they would be the donor sources for translocation activities. Our main finding is that levels of genetic diversity in the natural populations of S. farrenyi are still high (H_e = 0.605), most likely as a result of a predominantly outcrossing mating system in combination with the limited time elapsed since the population decline. However, population fragmentation is showing the first genetic signs, as the values of genetic differentiation are relatively high, and two well-differentiated genetic lineages have been found even in such a narrow geographic range. These genetic results provide important information when designing conservation management measures.

Genetic analyses reveal cryptic diversity in the widely distributed Styela canopus (Ascidiacea:Styelidae)

The routine use of DNA sequencing techniques and phylogenetic analysis has resulted in the discovery of many cryptic species, especially in the oceans. The common, globally introduced species Styela canopus is suspected to be a complex of cryptic species because of its widespread distribution and variable external morphology. We tested this possibility using COI and ANT marker sequences to uncover the phylogenetic relationship among 19 populations, and to examine genetic variability as well as gene flow. We obtained 271 COI and 67 ANT sequences and found surprising diversity among the 19 populations (COI: π = 0.18, hd = 0.99; ANT: π = 0.13, hd = 0.95). Corresponding topologies were found using Bayesian inference and maximum likelihood for both simple locus (COI) and multilocus (COI + ANT) analyses and so the clades received strong support. We used simple (ABGD, bPTP, GMYC) and multiple (BSD) locus methods to delimit species. The simple locus methods indicated that the current Styela canopus comprises at least 15 species. The BSD method for concatenated data supported 7 of the 15 species. We suggest that S. canopus should be treated as the Styela canopus complex. The large number of cryptic species found, often with more than one clade found in sympatry, creates opportunities for better understanding reproductive isolation, hybridisation or speciation. As several lineages have already been introduced widely around the world, we must quickly understand their diversity and invasive abilities.

Population Genetics of Phlebotomus papatasi from Endemic and Nonendemic Areas for Zoonotic Cutaneous Leishmaniasis in Morocco, as Revealed by Cytochrome Oxidase Gene Subunit I Sequencing

Zoonotic cutaneous leishmaniasis (ZCL) caused by Leishmania major Yakimoff & Shokhor and transmitted by Phlebotomus papatasi (Scopoli) is a public health concern in Morocco. The disease is endemic mainly in pre-Saharan regions on the southern slope of the High Atlas Mountains. The northern slope of the High Atlas Mountains and the arid plains of central Morocco remain non-endemic and are currently considered high risk for ZCL. Here we investigate and compare the population genetic structure of P. papatasi populations sampled in various habitats in historical foci and non-endemic ZCL areas. A fragment of the mtDNA cytochrome oxidase I (COI) gene was amplified and sequenced in 59 individuals from 10 P. papatasi populations. Haplotype diversity was probed, a median-joining network was generated (F_ST) and molecular variance (AMOVA) were analyzed. Overall, we identified 28 haplotypes with 32 distinct segregating sites, of which seven are parsimony informative. The rate of private haplotypes was high; 20 haplotypes (71.4%) are private ones and exclusive to a single population. The phylogenetic tree and the network reconstructed highlight a genetic structuration of these populations in two well defined groups: Ouarzazate (or endemic areas) and Non-Ouarzazate (or nonendemic areas). These groups are separated by the High Atlas Mountains. Overall, our study highlights differences in terms of population genetics between ZCL endemic and non-endemic areas. To what extent such differences would impact the transmission of L. major by natural P. papatasi population remains to be investigated.

Genetic integrity and individual identification-based population size estimate of the endangered long-tailed goral, Naemorhedus caudatus from Seoraksan National Park in South Korea, based on a non-invasive genetic approach

The long-tailed goral (also called the Amur goral) Naemorhedus caudatus (subfamily Caprinae), a vulnerable and protected species designated by IUCN and CITES, has sharply been declining in the population size and is now becoming critically endangered in South Korea. This species has been conserved as a natural monument by the Korean Cultural Heritage Administration since 1968. In this study, using 78 fecal DNA samples with a non-invasive genetic approach, we assessed the genetic integrity and individual identification-based population size for the goral population from Seoraksan National Park representing the largest wild population in Korea. Using the successfully isolated 38 fecal DNA, phylogeographic and population genetic analyses were performed with mitochondrial DNA control region (CR) sequences and nine microsatellite loci. We found seven CR haplotypes, of which five were unique to the Seoraksan population, considering previously determined haplotypes in Korean populations. The Seoraksan population showed higher haplotype diversity (0.777 ± 0.062) and mean number of alleles (4.67 ± 1.563) relative to southern populations in Korea reported from previous studies, with no signal of a population bottleneck. Microsatellite-based individual identification estimate based on probability of identity (PID) indicated a population size of ≥30 in this population. Altogether, we suggest that for future management efforts of this species in the Seoraksan National Park, conserving its genetic integrity as an ‘endemic’ lineage, and curbing a decrease in its number through mitigating habitat destruction might be key to secure the population for the long term.

Genetic diversity and phylogenetic relationships of tsetse flies of the palpalis group in Congo Brazzaville based on mitochondrial cox1 gene sequences

BACKGROUND

Despite the morphological characterization established in the 1950s and 1960s, the identity of extant taxa that make up Glossina fuscipes (s.l.) in the Congo remains questionable. Previous claims of overlap between G. fuscipes (believed to be G. f. quanzensis) and G. palpalis palpalis around Brazzaville city further complicate the taxonomic status and population dynamics of the two taxa. This study aimed to determine the phylogenetic relationships between G. fuscipes (s.l.) and G. p. palpalis and to assess genetic variation among G. fuscipes (s.l.) populations in Congo Brazzaville.

METHODS

We collected 263 G. fuscipes (s.l.) from northern and central regions, and 65 G. p. palpalis from southern part of the country. The mitochondrial cytochrome c oxidase subunit 1 (cox1) gene was amplified using taxa-specific primer pairs. Sequence data were analyzed in DnaSP and Arlequin to assess the genetic diversity, differentiation and demographic history of G. fuscipes (s.l.) populations.

RESULTS

The general BLAST analysis yielded a similarity of 99% for G. fuscipes (s.l.) and G. p. palpalis. BLASTn analysis for G. fuscipes (s.l.) showed > 98% identity with GenBank sequences for G. fuscipes (s.l.), with BEMB population showing 100% similarity with G. f. fuscipes. Glossina fuscipes (s.l.) populations showed high haplotype diversity (H = 46, Hd = 0.884), moderate nucleotide diversity ( = 0.012) and moderate (FST = 0.072) to high (FST = 0.152) genetic differentiation. Most of the genetic variation (89.73%) was maintained within populations. The mismatch analysis and neutrality tests indicated recent tsetse population expansions.

CONCLUSIONS

Phylogenetic analysis revealed minor differences between G. fuscipes (s.l.) and G. p. palpalis. Genetic diversity of G. fuscipes (s.l.) was high in the populations sampled except one. Genetic differentiation ranged from moderate to high among subpopulations. There was a restricted gene flow between G. fuscipes (s.l.) populations in the north and central part of the country. Genetic signatures based on cox1 showed recent expansion and recovery of G. fuscipes (s.l.) populations from previous bottlenecks. To fully understand the species distribution limits, we recommend further studies involving a wider sampling scheme including the swampy Mossaka focus for G. fuscipes (s.l.) and the entire range of G. p. palpalis in South Congo.

Post-glacial phylogeography and variation in innate immunity loci in a sylvatic rodent, bank vole Myodes glareolus

In the northern hemisphere, the spatial structure of many taxa has been shaped by migration patterns after the last glaciation, and phylogeography based on mtDNA variation may reflect the post-glacial demography. The mtDNA lineages are expected to differ in their adaptations to local conditions but little is known about the impact of these conditions on functional genetic variation. Here, we answer this question through an analysis of geographic variation and selection patterns in seven innate immunity genes in free-living bank voles Myodes glareolus from 10 localities across species range assigned to different lineages based on mtDNA. We found clear discrepancies between population structure in mtDNA and each of the studied innate immunity genes. There was no uniform pattern of spatial variation at immunity loci, they differed in the levels of polymorphism, and the results of neutrality tests were not consistent over loci. Each locus comprised a few common haplotypes shared between mitochondrial lineages and studied locations, plus numerous haplotypes unique for each studied site. Our results suggest that the diversity of innate immunity genes cannot be explained solely in terms of demographic processes, and that the observed polymorphism may be attributed to local selection. The strength and direction of selection differed between loci, even within the same gene family, which underlines how crucial it is to take a complex approach while studying the selection patterns acting on immune-related genes.

The Relationship Between Haplotype-Based FST and Haplotype Length

The population-genetic statistic [Formula: see text] is used widely to describe allele frequency distributions in subdivided populations. The increasing availability of DNA sequence data has recently enabled computations of [Formula: see text] from sequence-based "haplotype loci." At the same time, theoretical work has revealed that [Formula: see text] has a strong dependence on the underlying genetic diversity of a locus from which it is computed, with high diversity constraining values of [Formula: see text] to be low. In the case of haplotype loci, for which two haplotypes that are distinct over a specified length along a chromosome are treated as distinct alleles, genetic diversity is influenced by haplotype length: longer haplotype loci have the potential for greater genetic diversity. Here, we study the dependence of [Formula: see text] on haplotype length. Using a model in which a haplotype locus is sequentially incremented by one biallelic locus at a time, we show that increasing the length of the haplotype locus can either increase or decrease the value of [Formula: see text], and usually decreases it. We compute [Formula: see text] on haplotype loci in human populations, finding a close correspondence between the observed values and our theoretical predictions. We conclude that effects of haplotype length are valuable to consider when interpreting [Formula: see text] calculated on haplotypic data.

Mitochondrial DNA, a Powerful Tool to Decipher Ancient Human Civilization from Domestication to Music, and to Uncover Historical Murder Cases

Mitochondria are unique organelles carrying their own genetic material, independent from that in the nucleus. This review will discuss the nature of mitochondrial DNA (mtDNA) and its levels in the cell, which are the key elements to consider when trying to achieve molecular identification in ancient and degraded samples. mtDNA sequence analysis has been appropriately validated and is a consistent molecular target for the examination of biological evidence encountered in forensic cases—and profiling, in certain conditions—especially for burnt bodies and degraded samples of all types. Exceptional cases and samples will be discussed in this review, such as mtDNA from leather in Beethoven’s grand piano, mtDNA in mummies, and solving famous historical criminal cases. In addition, this review will be discussing the use of ancient mtDNA to understand past human diet, to trace historical civilizations and ancient trade routes, and to uncover geographical domestication origins and lineage relationships. In each topic, we will present the power of mtDNA and how, in many cases, no nuclear DNA was left, leaving mitochondrial DNA analysis as a powerful alternative. Exploring this powerful tool further will be extremely useful to modern science and researchers, due to its capabilities in providing us with previously unattainable knowledge.

Localization of adaptive variants in human genomes using averaged one-dependence estimation

Statistical methods for identifying adaptive mutations from population genetic data face several obstacles: assessing the significance of genomic outliers, integrating correlated measures of selection into one analytic framework, and distinguishing adaptive variants from hitchhiking neutral variants. Here, we introduce SWIF(r), a probabilistic method that detects selective sweeps by learning the distributions of multiple selection statistics under different evolutionary scenarios and calculating the posterior probability of a sweep at each genomic site. SWIF(r) is trained using simulations from a user-specified demographic model and explicitly models the joint distributions of selection statistics, thereby increasing its power to both identify regions undergoing sweeps and localize adaptive mutations. Using array and exome data from 45 ‡Khomani San hunter-gatherers of southern Africa, we identify an enrichment of adaptive signals in genes associated with metabolism and obesity. SWIF(r) provides a transparent probabilistic framework for localizing beneficial mutations that is extensible to a variety of evolutionary scenarios.

Genetic diversity and spatial structure of the Rufous-throated Antbird (Gymnopithys rufigula), an Amazonian obligate army-ant follower

Amazonian understory antbirds are thought to be relatively sedentary and to have limited dispersal ability; they avoid crossing forest gaps, and even narrow roads through a forest may limit their territories. However, most evidence for sedentariness in antbirds comes from field observations and plot‐based recapture of adult individuals, which do not provide evidence for lack of genetic dispersal, as this often occurs through juveniles. In this study, we used microsatellite markers and mitochondrial control‐region sequences to investigate contemporary and infer historical patterns of genetic diversity and structure of the Rufous‐throated Antbird (Gymnopithys rufigula) within and between two large reserves in central Amazonia. Analyses based on microsatellites suggested two genetically distinct populations and asymmetrical gene flow between them. Within a population, we found a lack of genetic spatial autocorrelation, suggesting that genotypes are randomly distributed and that G. rufigula may disperse longer distances than expected for antbirds. Analyses based on mitochondrial sequences did not recover two clear genetic clusters corresponding to the two reserves and indicated the whole population of the Rufous‐throated Antbird in the region has been expanding over the last 50,000 years. Historical migration rates were low and symmetrical between the two reserves, but we found evidence for a recent unilateral increase in gene flow. Recent differentiation between individuals of the two reserves and a unilateral increase in gene flow suggest that recent urban expansion and habitat loss may be driving changes and threatening populations of Rufous‐throated Antbird in central Amazonia. As ecological traits and behavioral characteristics affect patterns of gene flow, comparative studies of other species with different behavior and ecological requirements will be necessary to better understand patterns of genetic dispersal and effects of urban expansion on Amazonian understory antbirds.

High light intensity plays a major role in emergence of population level variation in Arabidopsis thaliana along an altitudinal gradient

Environmental conditions play an important role in the emergence of genetic variations in natural populations. We identified genome-wide patterns of nucleotide variations in the coding regions of natural Arabidopsis thaliana populations. These populations originated from 700 m to 3400 m a.m.s.l. in the Western Himalaya. Using a pooled RNA-Seq approach, we identified the local and global level population-specific SNPs. The biological functions of the SNP-containing genes were primarily related to the high light intensity prevalent at high-altitude regions. The novel SNPs identified in these genes might have arisen de novo in these populations. In another approach, the F_STs of SNP-containing genes were correlated with the corresponding climatic factors. ‘Radiation in the growing season’ was the only environmental factor found to be strongly correlated with the gene-level F_STs. In both the approaches, the high light intensity was identified as the primary abiotic stress associated with the variations in these populations. The differential gene expression analysis between field and controlled condition grown plants also showed high light intensity as the primary abiotic stress, particularly for the high altitude populations. Our results provide a genome-wide perspective of nucleotide variations in populations along altitudinal gradient and their putative role in emergence of these variations.

Fifteen years of genomewide scans for selection: trends, lessons and unaddressed genetic sources of complication

Genomewide scans for natural selection (GWSS) have become increasingly common over the last 15 years due to increased availability of genome-scale genetic data. Here, we report a representative survey of GWSS from 1999 to present and find that (i) between 1999 and 2009, 35 of 49 (71%) GWSS focused on human, while from 2010 to present, only 38 of 83 (46%) of GWSS focused on human, indicating increased focus on nonmodel organisms; (ii) the large majority of GWSS incorporate interpopulation or interspecific comparisons using, for example F(ST), cross-population extended haplotype homozygosity or the ratio of nonsynonymous to synonymous substitutions; (iii) most GWSS focus on detection of directional selection rather than other modes such as balancing selection; and (iv) in human GWSS, there is a clear shift after 2004 from microsatellite markers to dense SNP data. A survey of GWSS meant to identify loci positively selected in response to severe hypoxic conditions support an approach to GWSS in which a list of a priori candidate genes based on potential selective pressures are used to filter the list of significant hits a posteriori. We also discuss four frequently ignored determinants of genomic heterogeneity that complicate GWSS: mutation, recombination, selection and the genetic architecture of adaptive traits. We recommend that GWSS methodology should better incorporate aspects of genomewide heterogeneity using empirical estimates of relevant parameters and/or realistic, whole-chromosome simulations to improve interpretation of GWSS results. Finally, we argue that knowledge of potential selective agents improves interpretation of GWSS results and that new methods focused on correlations between environmental variables and genetic variation can help automate this approach.