Biology subjects

Gautier, M.

Publications and source records attributed to Gautier, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2023

The Tabulae Paralytica: Multimodal single-cell and spatial atlases of spinal cord injury

Here, we introduce the Tabulae Paralytica--a compilation of four atlases of spinal cord injury (SCI) comprising a single-nucleus transcriptome atlas of half a million cells; a multiome atlas pairing transcriptomic and epigenomic measurements within the same nuclei; and two spatial transcriptomic atlases of the injured spinal cord spanning four spatial and temporal dimensions. We integrated these atlases into a common framework to dissect the molecular logic that governs the responses to injury within the spinal cord. The Tabulae Paralytica exposed new biological principles that dictate the consequences of SCI, including conserved and divergent neuronal responses to injury; the priming of specific neuronal subpopulations to become circuit-reorganizing neurons after injury; an inherent trade-off between neuronal stress responses and the activation of circuit reorganization programs; the necessity of reestablishing a tripartite neuroprotective barrier between immune-privileged and extra-neural environments after SCI; and a catastrophic failure to form this barrier in old mice. We leveraged the Tabulae Paralytica to develop a rejuvenative gene therapy that reestablished this tripartite barrier, and restored the natural recovery of walking after paralysis in old mice. The Tabulae Paralytica provides an unprecedented window into the pathobiology of SCI, while establishing a framework for integrating multimodal, genome-scale measurements in four dimensions to study biology and medicine.

genomics↗

bioRxiv2023

Efficient k-mer based curation of raw sequence data: application in Drosophila suzukii

Several studies have highlighted the presence of contaminated entries in public sequence repositories, calling for special attention to the associated metadata. Here, we propose and evaluate a fast and efficient k-mer-based approach to assess the degree of mislabeling or contamination. We applied it to high-throughput whole-genome raw sequence data for 236 Ind-Seq and 22 Pool-Seq samples of the invasive species Drosophila suzukii. We first used CLARK software to build a dictionary of species-discriminating k-mers from the curated assemblies of 29 target drosophilid species (including D. melanogaster, D. simulans, D. subpulchrella, or D. biarmipes) and 12 common drosophila pathogens and commensals (including Wolbachia). Counting the number of k-mers composing each query sample sequence that matched a discriminating k-mer from the dictionary provided a simple criterion for assignment to target species and evaluation of the entire sample. Analyses of a wide range of samples, representative of both target and other drosophilid species, demonstrated very good performance of the proposed approach, both in terms of run time and accuracy of sequence assignment. Of the 236 D. suzukii individuals, five were re-assigned to D. simulans and eleven to D. subpulchrella. Another four showed moderate to substantial microbial contamination. Similarly, among the 22 Pool-Seq samples analyzed, two from the native range were found to be contaminated with 1 and 7 D. subpulchrella individuals, respectively (out of 50), and one from Europe was found to be contaminated with 5 to 6 D. immigrans individuals (out of 100). Overall, the present analysis allowed the definition of a large curated dataset consisting of > 60 population samples representative of the worldwide genetic diversity, which may be valuable for further population genetics studies on D. suzukii. More generally, while we advocate careful sample identification and verification prior to sequencing, the proposed framework is simple and computationally efficient enough to be included as a routine post-hoc quality check prior to any data analysis and prior to data submission to public repositories.

bioinformatics↗

bioRxiv2022

Environmental drivers of earthworm communities along an altitudinal gradient in the French Alps

The study of elevational diversity gradients is a central topic in biodiversity research. In this study, we tested for the effect of climate, resource quality and habitat heterogeneity on earthworm communities along an altitudinal gradient and around the treeline in the French Alps. Earthworm communities and environmental properties (i.e. climate, soil properties and vegetation structure and composition) were sampled in six altitudinal stages from 1400 to 2400 m. Results were analysed through multi-table factorial analyses and structural equation modelling. We found average density, biomass and species richness in the range of what is usually reported in comparable ecosystems. We found no monotonic decrease in species richness along the altitudinal gradient, which we explain by the species pool being dominated by taxa with high environmental tolerance and dispersal capacities. Instead, we highlighted the ecotone associated with the treeline as the primary driving factor of earthworm communities: at 1800-2000m altitude, communities were more abundant and diverse, and had a greater variability in body mass. This result was largely explained by the structure and composition of the vegetation, whereas soil and climate appeared to have only indirect effects. Therefore, the treeline effect on earthworm communities can be explained both by the effect of environmental heterogeneity and of trophic resource quality which increases at the ecotone level.

ecology↗

bioRxiv2022

Divergence of olfactory receptors associated with the evolution of assortative mating and reproductive isolation in mice

AO_SCPLOWBSTRACTC_SCPLOWDeciphering the genetic bases of behavioural traits is essential to understanding how they evolve and contribute to adaptation and biological diversification, but it remains a substantial challenge, especially for behavioural traits with polygenic architectures. In this study, we developed a population genomics approach coupled with functional predictions to address the evolution and genetic basis of olfactory-based assortative mate preferences in the house mouse, suspected to have evolved as a response to selection against hybridisation. We used whole genome resequencing data and the C2 statistic of the program BO_SCPLOWAYC_SCPLOWPO_SCPLOWASSC_SCPLOW, which contrasts allele frequencies corrected for population structure, to characterize genetic differentiation between sets of populations with strong contrast in behaviour (expressing or not assortative mate preferences) and we identified some regions of the genome showing the expected significant and consistent association with behavioural divergence. A series of Olfactory and Vomeronasal Receptor genes, among the most differentiated genomic regions and in line with functional predictions, stand out as the prime candidates underlying this olfactory-based behavioural divergence. These genes form large gene clusters in the genome, with two main candidate clusters extending up to 1.8 Mb. Variant analyses indicate a potential dual role of regulatory and protein-coding changes in the evolution of choosiness. This study shows that combining expectations on the genomic patterns of divergence with functional expectations represents a promising route to unravelling the genetic architecture of complex trait variation and provides novel insights into the role of olfactory and vomeronasal receptors in mammal adaptation and speciation.

evolutionary biology↗

bioRxiv2022

Rapid and transient evolution of local adaptation to seasonal host fruits in an invasive fly

Both local adaptation and adaptive phenotypic plasticity can influence the match between phenotypic traits and local environmental conditions. Theory predicts that environments stable for multiple generations promote local adaptation, while highly heterogeneous environments favor adaptive phenotypic plasticity. However, when environments have periods of stability mixed with heterogeneity, the relative importance of local adaptation and adaptive phenotypic plasticity is unclear. Here, we used Drosophila suzukii as a model system to evaluate the relative influence of genetic and plastic effects on the match of populations to environments with periods of stability from three to four generations. This invasive pest insect can develop within different fruits, and persists throughout the year in a given location on a succession of distinct host fruits, each one being available for only a few generations. Using reciprocal common environment experiments of natural D. suzukii populations collected from cherry, strawberry and blackberry, we found that both oviposition preference and offspring performance were higher on medium made with the fruit from which the population originated, than on media made with alternative fruits. This pattern, which remained after two generations in the laboratory, was analyzed using a statistical method we developed to quantify the contributions of local adaptation and adaptive plasticity in determining fitness. Altogether, we found that genetic effects (local adaptation) dominate over plastic effects (adaptive phenotypic plasticity). Our study demonstrates that spatially and temporally variable selection does not prevent the rapid evolution of local adaptation in natural populations. The speed and strength of adaptation may be facilitated by several mechanisms including a large effective population size and strong selective pressures imposed by host plants. Impact SummaryNatural populations often exhibit good "fit" to the environment they are in. However, environments change over time and space, and following change, the fit between a population and its environment may be poor. A question of long-standing interest is how do populations track changing environments to maintain fitness? Two main mechanisms are known: (i) genetic shifts in the form of local adaptation, in which traits evolve over time through differences in fitness of individuals harboring different genetic variants, and (ii) plastic shifts, or adaptive phenotypic plasticity, in which traits immediately change in response to environmental change. Adaptation is common when environments change over multiple generations, while plasticity is common when environments change over an individuals lifetime. However, it remains unclear whether plasticity or adaptation is more vital to maintaining fitness when environments change at an intermediate pace. Drosophila suzukii is well-suited to evaluating the relative importance of plasticity and adaptation in response to an intermediate pace of environmental change. This invasive pest species experiences an environment that shifts every 1-4 generations as host fruits change over time and space. Here, we studied natural populations of D. suzukii collected from different hosts. Using reciprocal common environment experiments, we evaluated their fitness on their source and alternative hosts. Drosophila suzukii populations were most fit on their source host, successfully tracking an intermediate pace of environmental change. We developed a statistical method to quantify the contributions of adaptive plasticity and local adaptation in determining fitness. We found that fitness was mainly maintained through local adaptation to each new host in succession. This study highlights that spatially and temporally variable selection does not prevent local adaptation and, on the contrary, illustrates how rapid the adaptive process can be. It also provides a novel statistical tool that can be applied to other systems

evolutionary biology↗

bioRxiv2021

The genetic history of Mayotte and Madagascar cattle breeds mirrors the complex pattern of human exchanges in Western Indian Ocean

Despite their central economic and cultural role, the origin of cattle populations living in Indian Ocean islands still remains poorly documented. Here, we unravel the demographic and adaptive histories of the extant Zebus from the Mayotte and Madagascar islands using high-density SNP genotyping data. We found that these populations are very closely related and both display a predominant indicine ancestry. They diverged in the 16th century at the arrival of European people who transformed the trade network in the area. Their common ancestral cattle population originates from an admixture between an admixed African zebu population and an Indian zebu that occurred around the 12th century at the time of the earliest contacts between human African populations of the Swahili corridor and Austronesian people from Southeast Asia in Comoros and Madagascar. A steep increase of the estimated population sizes from the beginning of the 16th to the 17th century coincides with the expansion of the cattle trade. By carrying out genome scans for recent selection in the two cattle populations from Mayotte and Madagascar, we identified sets of candidate genes involved in biological functions (cancer, skin structure and UV-protection, nervous system and behavior, organ development, metabolism and immune response) broadly representative of the physiological adaptation to tropical conditions. Overall, the origin of the cattle populations from Western Indian Ocean islands mirrors the complex history of human migrations and trade in this area.

evolutionary biology↗

bioRxiv2021

f-statistics estimation and admixture graph construction with Pool-Seq or allele count data using the R package poolfstat

By capturing various patterns of the structuring of genetic variation across populations, f -statistics have proved highly effective for the inference of demographic history. Such statistics are defined as covariance of SNP allele frequency differences among sets of populations without requiring haplotype information and are hence particularly relevant for the analysis of pooled sequencing (Pool-Seq) data. We here propose a reinterpretation of the F (and D) parameters in terms of probability of gene identity and derive from this unified definition unbiased estimators for both Pool-Seq and standard allele count data obtained from individual genotypes. We implemented these estimators in a new version of the R package poolfstat, which now includes a wide range of inference methods: (i) three-population test of admixture; (ii) four-population test of treeness; (iii) F4-ratio estimation of admixture rates; and (iv) fitting, visualization and (semi-automatic) construction of admixture graphs. A comprehensive evaluation of the methods implemented in poolfstat on both simulated Pool-Seq (with various sequencing coverages and error rates) and allele count data confirmed the accuracy of these approaches, even for the most cost-effective Pool-Seq design involving low sequencing coverages. We further analyzed a real Pool-Seq data made of 14 populations of the invasive species Drosophila suzukii which allowed refining both the demographic history of native populations and the invasion routes followed by this emblematic pest. Our new package poolfstat provides the community with a user-friendly and efficient all-in-one tool to unravel complex population genetic histories from large-size Pool-Seq or allele count SNP data.

evolutionary biology↗

bioRxiv2021

An improved hidden Markov model for the characterization of homozygous-by-descent segments in individual genomes

Inbreeding results from the mating of related individuals and has negative consequences because it brings together deleterious variants in one individual. Genomic estimates of the inbreeding coefficients are preferred to pedigree-based estimators as they measure the realized inbreeding levels and they are more robust to pedigree errors. Several methods identifying homozygous-by-descent (HBD) segments with hidden Markov models (HMM) have been recently developed and are particularly valuable when the information is degraded or heterogeneous (e.g., low-fold sequencing, low marker density, heterogeneous genotype quality or variable marker spacing). We previously developed a multiple HBD class HMM where HBD segments are classified in different groups based on their length (e.g., recent versus old HBD segments) but we recently observed that for high inbreeding levels with many HBD segments, the estimated contributions might be biased towards more recent classes (i.e., associated with large HBD segments) although the overall estimated level of inbreeding remained unbiased. We herein propose a new model in which the HBD classification is modeled in successive nested levels with decreasing expected HBD segment lengths, the underlying exponential rates being directly related to the number of generations to the common ancestor. The non-HBD classes are now modeled as a mixture of HBD segments from later generations and shorter non-HBD segments (i.e., both with higher rates). The new model has improved statistical properties and performs better on simulated data compared to our previous version. We also show that the parameters of the model are easier to interpret and that the model is more robust to the choice of the number of classes. Overall, the new model results in an improved partitioning of inbreeding in different HBD classes and should be preferred.

genetics↗

bioRxiv2021

Confronting false discoveries in single-cell differential expression

Differential expression analysis in single-cell transcriptomics enables the dissection of cell-type-specific responses to perturbations such as disease, trauma, or experimental manipulation. While many statistical methods are available to identify differentially expressed genes, the principles that distinguish these methods and their performance remain unclear. Here, we show that the relative performance of these methods is contingent on their ability to account for variation between biological replicates. Methods that ignore this inevitable variation are biased and prone to false discoveries. Indeed, the most widely used methods can discover hundreds of differentially expressed genes in the absence of biological differences. Our results suggest an urgent need for a paradigm shift in the methods used to perform differential expression analysis in single-cell data.

bioinformatics↗

bioRxiv2020

The worldwide invasion of Drosophila suzukii isaccompanied by a large increase of transposable elementload and a small number of putatively adaptive insertions

Transposable Elements (TEs) are ubiquitous and mobile repeated sequences. They are major determinants of host fitness. Here, we portrayed the TE content of the spotted wing fly Drosophila suzukii. Using a recently improved genome assembly, we reconstructed TE sequences de novo, and found that TEs occupy 47% of the genome and are mostly located in gene poor regions. The majority of TE insertions segregate at low frequencies, indicating a recent and probably ongoing TE activity. To explore TE dynamics in the context of biological invasions, we studied variation of TE abundance in genomic data from 16 invasive and six native populations (of D. suzukii). We found a large increase of the TE load in invasive populations correlated with a reduced Watterson estimate of genetic diversity [Formula] a proxy of effective population size. We did not find any correlation between TE contents and bio-climatic variables, indicating a minor effect of environmentally induced TE activity. A genome-wide association study revealed that ca. 5,000 genomic regions are associated with TE abundance. We did not find, however, any evidence in such regions of an enrichment for genes known to interact with TE activity (e.g. transcription factor encoding genes or genes of the piRNA pathway). Finally, the study of TE insertion frequencies revealed 15 putatively adaptive TE insertions, six of them being likely associated with the recent invasion history of the species.

evolutionary biology↗

bioRxiv2020

Exploring systematic biases, rooting methods and morphological evidence to unravel the evolutionary history of the genus Ficus (Moraceae)

Despite their ecological and evolutionary importance as key components of tropical ecosystems, the phylogeny of fig trees is still unresolved. We use restriction-site-associated DNA (RAD) sequencing (ca 420kb) and 102 morphological characters to elucidate the relationships between 70 species of Ficus representing all known subgenera and sections and five outgroups. We compare morphological and molecular results to highlight discrepancies and reveal possible inference bias. We analyse marker and taxon properties that may bias molecular inferences, with existing softwares and a new approach based on iterative principal component analysis to reduce variance between clusters of samples. For the first time, with both molecular and morphological data, we recover a monophyletic subgenus Urostigma and a clade with all gynodioecious fig trees. However, our analyses show that it is not possible to homogenize evolutionary rates and GC content for all taxa prior to phylogenetic inference and that four competing positions for the root of the molecular tree are possible. The placement of the long-branched section Pharmacosycea as sister to all other fig trees is not supported by morphological data and considered as a result of a long branch attraction artefact to the outgroups. Regarding morphological features and indirect evidence from the pollinator tree of life, the topology that divides the genus Ficus into monoecious versus gynodioecious species appears most likely. Active pollination is inferred as the ancestral state for all topologies, ambiguity remains for ancestral breeding system including for the favored topology, and it appears most likely that the ancestor of fig trees was a freestanding tree. Increasing sampling may improve results and would be at least as relevant as maximizing the number of sequenced regions given the strong heterogeneity in evolutionary rates, and to a lesser extent, base composition among species. Despite morphological plasticity and frequent homoplasy of multiple characters, we advocate giving a central role to morphology in our understanding of the evolution of Ficus, especially as it can help detect insidious systematic errors that tend to become more pronounced with larger molecular data sets.

evolutionary biology↗

bioRxiv2020

Near-chromosome level genome assembly of the fruit pest Drosophila suzukii using long-read sequencing

Over the past decade, the spotted wing Drosophila, Drosophila suzukii, has invaded Europe and America and has become a major agricultural pest in these areas, thereby prompting intense research activities to better understand its biology. Two draft genome assemblies based on short-read sequencing were released in 2013 for this species. Although valuable, these resources contain pervasive assembly errors and are highly fragmented, two features limiting their values. Our purpose here was to improve the assembly of the D. suzukii genome. For this, we generated PacBio long-read sequencing data at 160X sequence coverage and assembled a novel, contiguous D. suzukii genome. We obtained a high-quality assembly of 270 Mb (with 546 contigs, a N50 of 2.6Mb, a L50 of 15, and a BUSCO score of 95%) that we called WT3-2.0. We found that despite 16 rounds of full-sib crossings the D. suzukii strain that we sequenced has maintained high levels of polymorphism in some regions of its genome (ca. 19Mb). As a consequence, the quality of the assembly of these regions was reduced. We explored possible origins of this high residual diversity, including the presence of structural variants and a possible heterogeneous admixture pattern of North American and Asian ancestry. Overall, our WT3-2.0 assembly provides a higher quality genomic resource compared to the previous one in terms of general assembly statistics, sequence quality and gene annotation. This new D. suzukii genome assembly is therefore an improved resource for high-throughput sequencing approaches, as well as manipulative genetic technologies to study D. suzukii.

ecology↗

bioRxiv2019

Cell type prioritization in single-cell data

We present a machine-learning method to prioritize the cell types most responsive to biological perturbations within high-dimensional single-cell data. We validate our method, Augur (https://github.com/neurorestore/Augur), on a compendium of single-cell RNA-seq, chromatin accessibility, and imaging transcriptomics datasets. We apply Augur to expose the neural circuits that enable walking after paralysis in response to spinal cord neurostimulation.

genomics↗

bioRxiv2019

A whole-genome scan for association with invasion success in the fruit fly Drosophila suzukii using contrasts of allele frequencies corrected for population structure

Evidence is accumulating that evolutionary changes are not only common during biological invasions but may also contribute directly to invasion success. The genomic basis of such changes is still largely unexplored. Yet, understanding the genomic response to invasion may help to predict the conditions under which invasiveness can be enhanced or suppressed. Here we characterized the genome response of the spotted wing drosophila Drosophila suzukii during the worldwide invasion of this pest insect species, by conducting a genome-wide association study to identify genes involved in adaptive processes during invasion. Genomic data from 22 population samples were analyzed to detect genetic variants associated with the status (invasive versus native) of the sampled populations based on a newly developed statistic, we called C2, that contrasts allele frequencies corrected for population structure. This new statistical framework has been implemented in an upgraded version of the program BO_SCPLOWAYC_SCPLOWPO_SCPLOWASSC_SCPLOW. We identified a relatively small set of single nucleotide polymorphisms (SNPs) that show a highly significant association with the invasive status of populations. In particular, two genes RhoGEF64C and cpo, the latter contributing to natural variation in several life-history traits (including diapause) in Drosophila melanogaster, contained SNPs significantly associated with the invasive status in the two separate main invasion routes of D. suzukii. Our methodological approaches can be applied to any other invasive species, and more generally to any evolutionary model for species characterized by non-equilibrium demographic conditions for which binary covariables of interest can be defined at the population level.

evolutionary biology↗

bioRxiv2019

Evolution of trade-offs across environments following experimental evolution of the generalist Drosophila suzukii to different fruit media

The process of local adaptation involves differential changes in fitness over time across different environments. While experimental evolution studies have extensively tested for patterns of local adaptation at a single time point, there is relatively little research that examines fitness more than once during the time course of adaptation. We allowed replicate populations of the fruit pest Drosophila suzukii to evolve in one of eight different fruit media. After five generations, populations with the highest initial levels of maladaptation had mostly gone extinct, whereas experimental populations evolving on cherry, strawberry and cranberry media had survived. We measured the fitness of each surviving population in each of the three fruit media after five and after 26 generations of evolution. After five generations, adaptation to each medium was associated with increased fitness in the two other media. This was also true after 26 generations, except when populations that evolved on cranberry medium developed on cherry medium. These results suggest that, in the theoretical framework of a fitness landscape, the fitness optima of cherry and cranberry media are the furthest apart. Our results show that studying how fitness changes across several environments and across multiple generations provides insights into the dynamics of local adaptation that would not be evident if fitness were analyzed at a single point in time. By allowing a qualitative mapping of an experimental fitness landscape, our approach will improve our understanding of the ecological factors that drive the evolution of local adaptation in D. suzukii.

evolutionary biology↗

bioRxiv2018

The genomic basis of colour pattern polymorphism in the harlequin ladybird

Many animal species are comprised of discrete phenotypic forms. Understanding the genetic mechanisms generating and maintaining such phenotypic variation within species is essential to comprehending morphological diversity. A common and conspicuous example of discrete phenotypic variation in natural populations of insects is the occurrence of different colour patterns, which has motivated a rich body of ecological and genetic research1-6. The occurrence of dark, i.e. melanic, forms, displaying discrete colour patterns, is found across multiple taxa, but the underlying genomic basis remains poorly characterized. In numerous ladybird species (Coccinellidae), the spatial arrangement of black and orange patches on adult elytra varies wildly within species, forming strikingly different complex colour patterns7,8. In the harlequin ladybird Harmonia axyridis, more than 200 distinct colour forms have been described, which classic genetic studies suggest result from allelic variation at a single, unknown, locus9,10. Here, we combined whole-genome sequencing, population genomics, gene expression and functional analyses, to establish that the gene pannier controls melanic pattern polymorphism in H. axyridis. We show that pannier, which encodes an evolutionary conserved transcription factor, is necessary for the formation of melanic elements on the elytra. Allelic variation in pannier leads to protein expression in distinct domains on the elytra, and thus determines the distinct colour patterns in H. axyridis. Recombination between pannier alleles may be reduced by a highly divergent sequence of ca. 170 kb in the cis-regulatory regions of pannier with a 50 kb inversion between colour forms. This likely helps maintaining the distinct alleles found in natural populations. Thus we propose that highly variable discrete colour forms can arise in natural populations through cis-regulatory allelic variation of a single gene.

evolutionary biology↗

bioRxiv2018

Measuring genetic differentiation from Pool-seq data

The recent advent of high throughput sequencing and genotyping technologies enables the comparison of patterns of polymorphisms at a very large number of markers. While the characterization of genetic structure from individual sequencing data remains expensive for many non-model species, it has been shown that sequencing pools of individual DNAs (Pool-seq) represents an attractive and cost-effective alternative. However, analyzing sequence read counts from a DNA pool instead of individual genotypes raises statistical challenges in deriving correct estimates of genetic differentiation. In this article, we provide a method-of-moments estimator of FST for Pool-seq data, based on an analysis-of-variance framework. We show, by means of simulations, that this new estimator is unbiased, and outperforms previously proposed estimators. We evaluate the robustness of our estimator to model misspecification, such as sequencing errors and uneven contributions of individual DNAs to the pools. Last, by reanalyzing published Pool-seq data of different ecotypes of the prickly sculpin Cottus asper, we show how the use of an unbiased FST estimator may question the interpretation of population structure inferred from previous analyses.

evolutionary biology↗

bioRxiv2017

Species composition and environmental adaptation of indigenous Chinese cattle

Indigenous Chinese cattle combine taurine and indicine origins and occupy a broad range of different environments. By 50K SNP genotyping we found a discontinuous distribution of taurine and indicine cattle ancestries with extremes of less than 10% indicine cattle in the north and more than 90% in the far south and southwest China. Model-based clustering and f4-statistics indicate introgression of both banteng and gayal into southern Chinese cattle while the sporadic yak influence in cattle in or near Tibetan area validate earlier findings of mitochondrial DNA analysis. Geographic patterns of taurine and indicine mitochondrial and Y-chromosomal DNA diversity largely agree with the autosomal cline. The geographic distribution of the genomic admixture of different bovine species is proposed to be the combined effect of prehistoric immigrations, gene flow, major rivers acting as genetic barriers, local breeding objectives and environmental adaptation. Whole-genome scan for genetic differentiation and association analyses with both environmental and morphological covariables are remarkably consistent with previous studies and identify a number of genes implicated in adaptation, which include TNFRSF19, RFX4, SP4 and several coat color genes. We propose indigenous Chinese cattle as a unique and informative resource for gene-level studies of climate adaptation in mammals.

evolutionary biology↗