Genome-scale analysis of demographic history and adaptive selection

Genomic evidence for demographic fluctuations, genetic burdens and adaptive divergence in fourfinger threadfin Eleutheronema rhadinum

Declining populations and bottlenecks lead to the accumulation of deleterious mutations in fish populations. These processes also trigger genetic purging, which is a key genetic factor in reducing the deleterious burdens and increasing population viability. However, there is a lack of empirical evidence on the interaction between demographic history and the genome-wide pattern of deleterious variations. Here, we generated genome resequencing data of Eleutheronema rhadinum from China and Thailand, representing the major distribution of the species' southern regions. E. rhadinum had exceptionally low genome-wide variability and experienced dramatic population expansions followed by continuous declines. The geographical divergence, which occurred ~ 23,000 years ago, shaped different demographic trajectories and generated different regional patterns of deleterious mutations in China and Thailand populations. Several lines of evidence revealed that this geographical pattern of deleterious mutation was driven by the purging of highly deleterious mutations. We showed that purifying selection had inbreeding-associated fitness costs and was more efficient against missense mutations in the Thailand population, which had the lowest genetic burden of homozygous deleterious mutations. Multiple evolutionarily conserved protein domains were disrupted by the loss-of-function mutations, posing a high probability of gene functionality elimination. Moreover, thermal and salinity genes (Trpm3, Nek4, Gtf2f2, Cldn14) were identified in genomic divergence regions of E. rhadinum among China and Thailand populations. Our findings highlight the importance of demographic history factors shaping the geographical patterns of deleterious mutations. The results serve to deepen our understanding of the adaptive evolution and divergence of E. rhadinum with implications for other marine fish.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-024-00276-4.

The Genetic Architecture of Local Adaptation and Reproductive Character Displacement in Scutiger boulengeri Complex (Anura: Megophryidae)

Speciation is a continuous process driven by barriers to gene flow. Based on genome-wide SNPs (single nucleotide polymorphisms) of 190 toads from 31 sampling sites of Scutiger boulengeri complex, we found evidence for monophyly which represented a continuous speciation process of at least six lineages in S. boulengeri, which radiated and exhibited varying degrees of divergence and gene flow. The SNP-based phylogenetic tree was largely discordant with the multilocus mitochondrial tree (i.e., S. mammatus and S. glandulatus nested in the lineages of S. boulengeri) published before. The Min Mountains (MM) and Qinghai-Tibet Plateau (QTP) lineages differ fundamentally in habitat (i.e., elevation) and morphology (i.e., SVL), we detected signatures of potential high-altitude and cold adaptation genes in QTP (vs. MM). We found the evidence of reproductive trait disparity (i.e., SVL and nuptial pads) is key to promoting sympatric rather than allopatric species pairs. In addition, we identified selection signals for genes related to sympatric character displacement, genes linked to obesity-related traits, nuptial spines morphology and enlarged chest nuptial pads in S. mammatus (vs. QTP group of S. boulengeri). Our study provided new insight and paradigm for a varied speciation pattern from local adaptation of allopatry to sympatric character displacement in the S. boulengeri complex.

Population genomics provides insights into the genetic diversity and adaptation of the Pieris rapae in China

The cabbage white butterfly (Pieris rapae), a major agricultural pest, has become one of the most abundant and destructive butterflies in the world. It is widely distributed in a large variety of climates and terrains of China due to its strong adaptability. To gain insight into the population genetic characteristics of P. rapae in China, we resequenced the genome of 51 individuals from 19 areas throughout China. Using population genomics approaches, a dense variant map of P. rapae was observed, indicating a high level of polymorphism that could result in adaptation to a changing environment. The feature of the genetic structure suggested considerable genetic admixture in different geographical groups. Additionally, our analyses suggest that physical barriers may have played a more important role than geographic distance in driving genetic differentiation. Population history showed the effective population size of P. rapae was greatly affected by global temperature changes, with mild periods (i.e., temperatures warmer than those during glaciation but not excessively hot) leading to an increase in population size. Furthermore, by comparing populations from south and north China, we have identified selected genes related to sensing temperature, growth, neuromodulation and immune response, which may reveal the genetic basis of adaptation to different environments. Our study is the first to illustrate the genetic signatures of P. rapae in China at the population genomic level, providing fundamental knowledge of the genetic diversity and adaptation of P. rapae.

Chromosome-level genome and population genomics provide novel insights into adaptive divergence in allopatric Eleutheronema tetradactylum

Understanding the adaptive ecological divergence provides important information for revealing biodiversity generation and maintenance. Adaptive ecology divergence in populations occurs in various environments and locations, but its genetic underpinnings remain elusive. We generated a chromosome-level genome of Eleutheronema tetradactylum (~582 Mb) and re-sequenced 50 allopatric E. tetradactylum in two independent environmental axes in China and Thailand Coastal waters as well as 11 cultured relatives. A low level of whole genome-wide diversity explained their decreased adaptive potential in the wild environment. Demographic analysis showed evidence of historically high abundance followed by a continuous distinct decline, plus signs of recent inbreeding and accumulation of deleterious mutations. Extensive signals of selective sweeps with signs of local adaptation to environmental differentiation between China and Thailand at genes related to thermal and salinity adaptation were discovered, which might be the driving factors of the geographical divergence of E. tetradactylum. Many genes and pathways subjected to strong selection under artificial breeding were associated with fatty acids and immunity (ELOVL6L, MAPK, p53/NF-kB), likely contributing to the eventual adaptation of artificial selective breeding. Our comprehensive study provided crucial genetic information for E. tetradactylum, with implications for the further conservation efforts of this threatened and ecologically valuable fish.

Genomic evidence reveals intraspecific divergence of the hot-spring snake (Thermophis baileyi), an endangered reptile endemic to the Qinghai-Tibet plateau

Understanding how and why species evolve requires knowledge on intraspecific divergence. In this study, we examined intraspecific divergence in the endangered hot-spring snake (Thermophis baileyi), an endemic species on the Qinghai-Tibet Plateau (QTP). Whole-genome resequencing of 58 sampled individuals from 15 populations was performed to identify the drivers of intraspecific divergence and explore the potential roles of genes under selection. Our analyses resolved three groups, with major intergroup admixture occurring in regions of group contact. Divergence probably occurred during the Pleistocene as a result of glacial climatic oscillations, Yadong-Gulu rift, and geothermal fields differentiation, while complex gene flow between group pairs reflected a unique intraspecific divergence pattern on the QTP. Intergroup fixed loci involved selected genes functionally related to divergence and local adaptation, especially adaptation to hot spring microenvironments in different geothermal fields. Analysis of structural variants, genetic diversity, inbreeding, and genetic load indicated that the hot-spring snake population has declined to a low level with decreased diversity, which is important for the conservation management of this endangered species. Our study demonstrated that the integration of demographic history, gene flow, genomic divergence genes, and other information is necessary to distinguish the evolutionary processes involved in speciation.

Are Copy Number Variations within the FecB Gene Significantly Associated with Morphometric Traits in Goats?

The Booroola fecundity (FecB) gene is a major fertility-related gene first identified in Booroola sheep. Numerous studies have investigated whether the FecB gene is a major fecundity gene in goats or whether there are other genes that play a critical role in goat fertility. Nevertheless, little attention has been paid to the role of the FecB gene in the body morphometric traits of goats, despite the positive relationship discerned between litter size and growth. We identified five copy number variations (CNVs) within the FecB gene in 641 goats, including 318 Shaanbei white cashmere (SBWC) goats, 203 Guizhou Heima (GZHM) goats, and 120 Nubian goats, which exhibited different distributions among these populations. Our results revealed that these five CNVs were significantly associated with goat morphometric traits (p < 0.05). The normal type of CNV3 was the dominant type and displayed superior phenotypes in both litter size and morphometric traits, making it an effective marker for goat breeding. Consequently, LD blocks in the region of 10 Mb upstream and downstream from FecB and potential transcription factors (TFs) that could bind with the CNVs were analyzed via bioinformatics. Although no significant LD block was detected, our results illustrated that these CNVs could bind to growth-related TFs and indirectly affect the growth development of the goats. We identified potential markers to promote litter size and growth, and we offer a theoretical foundation for further breeding work.

Genomic landscape of the signals of positive natural selection in populations of Northern Eurasia: A view from Northern Russia

Natural selection of beneficial genetic variants played a critical role in human adaptation to a wide range of environmental conditions. Northern Eurasia, despite its severe climate, is home to lots of ethnically diverse populations. The genetic variants associated with the survival of these populations have hardly been analyzed. We searched for the genomic signatures of positive selection in (1) the genome-wide microarray data of 432 people from eight different northern Russian populations and (2) the whole-genome sequences of 250 people from Northern Eurasia from a public repository through testing the extended haplotype homozigosity (EHH) and direct comparison of allele frequency, respectively. The 20 loci with the strongest selection signals were characterized in detail. Among the top EHH hits were the NRG3 and NBEA genes, which are involved in the development and functioning of the neural system, the PTPRM gene, which mediates cell-cell interactions and adhesion, and a region on chromosome 4 (chr4:28.7-28.9 Mb) that contained several loci affiliated with different classes of non-coding RNAs (RN7SL101P, MIR4275, MESTP3, and LINC02364). NBEA and the region on chromosome 4 were novel selection targets that were identified for the first time in Western Siberian populations. Cross-population comparisons of EHH profiles suggested a particular role for the chr4:28.7-28.9 Mb region in the local adaptation of Western Siberians. The strongest selection signal identified in Siberian sequenced genomes was formed by six SNPs on chromosome 11 (chr11:124.9-125.2 Mb). This region included well-known genes SLC37A2 and PKNOX2. SLC37A2 is most-highly expressed in the gut. Its expression is regulated by vitamin D, which is often deficient in northern regions. The PKNOX2 gene is a transcription factor of the homeobox family that is expressed in the brain and many other tissues. This gene is associated with alcohol addiction, which is widespread in many Northern Eurasian populations.

Genomic evidence for two phylogenetic species and long-term population bottlenecks in red pandas

The red panda (Ailurus fulgens), an endangered Himalaya-endemic mammal, has been classified as two subspecies or even two species - the Himalayan red panda (A. fulgens) and the Chinese red panda (Ailurus styani) - based on differences in morphology and biogeography. However, this classification has remained controversial largely due to lack of genetic evidence, directly impairing scientific conservation management. Data from 65 whole genomes, 49 Y-chromosomes, and 49 mitochondrial genomes provide the first comprehensive genetic evidence for species divergence in red pandas, demonstrating substantial inter-species genetic divergence for all three markers and correcting species-distribution boundaries. Combined with morphological evidence, these data thus clearly define two phylogenetic species in red pandas. We also demonstrate different demographic trajectories in the two species: A. styani has experienced two population bottlenecks and one large population expansion over time, whereas A. fulgens has experienced three bottlenecks and one very small expansion, resulting in very low genetic diversity, high linkage disequilibrium, and high genetic load.