The Koṅkaṇ region on the west coast of India is a hotspot of culture, folklore and ethnolinguistic diversity, yet its maternal genetic landscape remains largely unresolved. The present study captures the genetic affinities of the Koṅkaṇī population, residing along the Koṅkaṇ Malabar coast by analysing complete mitochondrial genomes (n = 85) and control region hypervariable sequences (n = 210). Our results reveal divergent maternal histories between the Sārasvata and the non-Sārasvata groups. Comparative analysis against over 5000 mitochondrial genomes from Eurasia demonstrates that the Koṅkaṇī maternal gene pool is shaped by both deep-rooted South Asian (macro-haplogroup M) and West Eurasian lineages. Demographic modelling identifies a pre-Last Glacial Maximum (LGM) expansion and a post-LGM recovery, with macro-haplogroup N lineages serving as the primary drivers of internal genetic structuring. At the subpopulation level, occupational groups such as the Khārvi and Kuḍubi exhibit genetic signatures that are consistent with historic founder events followed by increased genetic drift relative to Gauḍa Sārasvata Brahmins and Roman Catholics, where populations display higher haplotype diversity. Social practices, including endogamy, may contribute to the differences observed between these populations. While the non-Sārasvata group clusters with autochthonous tribes, the Sārasvata groups share genetic affinities with West Eurasian and Steppe-linked lineages, suggesting that the Bronze Age migrations into South Asia were not exclusively male-mediated. Overall, this study highlights the Koṅkaṇ coast as a genetic confluence, where Late Pleistocene migrations, LGM refugia, and Holocene admixture collectively shaped its maternal ancestry. It also illustrates how climate and social shifts moulded the extant genetic diversity along western India.
Transposable elements (TEs) are dispersed repetitive DNA sequences that constitute a major component of vertebrate genomes. TEs can influence genome organisation by inserting into new sites and by promoting rearrangements through recombination between repeat copies, which can contribute to gene innovation and chromosomal rearrangements. However, such changes may compromise genomic integrity and promote immune-related diseases through persistent activation of inflammatory and carcinogenic pathways. In this context, epigenetic control and immune surveillance are key mechanisms that restrain TE activity in vertebrates. Teleosts represent an early vertebrate lineage in which immune architecture is largely conserved relative to mammals. To date, however, data concerning fish TEs still remain largely unexplored. In this study, we combined a literature review with an extensive BLASTn screening of TE consensus sequences against Actinopterygii entries in GenBank to explore TE sequence matches with immune-related genes in teleost fish. Results revealed frequent TE sequence matches to immune-related loci, including inflammatory molecules, cell-surface and signalling receptors, and antiviral genes. EggNOG annotation and enrichment analysis supported a recurrent association between TE sequences and immune-related annotations, with significant enrichment of immune-related TE-gene associations in six of the eight species analysed. Furthermore, we discuss future directions integrating TE annotation with genomic mapping, epigenetic analyses, TE transcription and immune gene expression to clarify the biological relevance of TE-immune associations in fish. Overall, this systematic review provides a comprehensive perspective on the intricate relationship between TEs, epigenetic regulation, and immune system dynamics in teleost fish, supporting their inclusion in future studies of fish immune regulation, health and aquaculture.
Among-individual correlations between labile traits stem from either shared genetic architectures or developmental processes that shape trait expression. While these correlations have been extensively studied in behavioural ecology over the past two decades, the specific mechanisms driving age-related changes in among-individual trait correlations remain unclear. Given that trait correlations can significantly constrain or facilitate evolutionary trajectories, identifying how these associations—and their underlying genetic basis—evolve with age is essential for accurately predicting evolutionary responses alongside age-specific selection. Here, using field cricket Gryllus bimaculatus males from a pedigreed population, we investigated how age-related changes in (1) genetic and (2) nongenetic bases of among-individual aggression-exploration correlations, as well as (3) survival selection, explain age-related variation in an aggression-exploration correlations. Our findings indicate that the magnitudes of both the positive among-individual and genetic correlations were maintained across nymph and young adult stages, but significantly decreased with age during adulthood. This decrease was due to both survival selection and genetic variation in age-related behavioural plasticity. Survival selection tended to favour less explorative males at the young adult stage, which may have eroded the genetic correlations. In addition, genetic variation in age-related plasticity in exploration contributed to a decrease in the magnitude of genetic correlations during the adult stage. The similarity of age-related changes in among-individual and genetic correlations resulted from the absence of short-term permanent environmental correlations. Therefore, the findings of this study suggest that age-related changes in among-individual behavioural correlations are not caused by a single mechanism, but rather a combination of mechanisms, such as genetic variation in age-related behavioural plasticity and survival selection.
The Scandinavian wolf population (Norway and Sweden) is intensively managed at a population size considered sustainable by managing authorities. As these authorities have decided to reduce the population to only 170 individuals, it is timely to evaluate this population size goal and to scrutinize underlying assumptions of recent simulation studies that inform population management. The effective size of a population determines the pace at which genetic diversity declines and inbreeding increases and plays a crucial role in short- and long-term extinction risks. Here, we use the complete published pedigree of the Scandinavian wolf population to precisely calculate the effective size Ne since the founding of the population, per year. Our results indicate the Ne is unsustainably low. Moreover, we find that recent simulation studies commissioned by the managing authorities greatly overestimate the effective size of the Scandinavian wolf population, questioning their usefulness to inform population management.
Understanding recent change in effective population size is crucial to evaluate how specie respond to environmental modifications and their ability to adapt to global changes. However, the impact of past environmental change on the demography history of species communities has rarely been studied across multiple species, members of the same community sharing the same habitat. In this study, we compare historical change in effective population size across eight species of coastal sand dune plant communities along the coastal dune in Southwest France. We developed and sequenced species-specific microsatellite markers to genotype 3116 individuals. In an attempt to increase temporal resolution, we integrate both fast (microsatellite repeat number) and slow (substitution in flanking sequence) mutating polymorphisms to infer demographic parameters of a simple model of a single population size change in the past using coalescent simulations and approximate Bayesian computations. Recent and ancient effective population sizes were well inferred and informed by allelic richness at microsatellites and heterozygosity at flanking sequence respectively. The timing of event was more difficult to estimate, but benefit from summary statistics combining microsatellite variation and flanking substitutions. Most species showed a synchronous and strong decline dating back from 135 to 450 years ago, overlapping with the Little Ice Age during which high storminess caused sand drift that probably wiped out most of the open sand dune vegetation, which is now restricted along the shoreline. Historical habitat loss led to community level decline in effective population size that will constrain future sand dune plant responses.
