A Population Genomics Lexicon

South African indigenous chickens' genetic diversity, and the adoption of ecological niche modelling and landscape genomics as strategic conservation techniques

Selection pressures found in the prevailing production environments have shaped the genetic structure of indigenous chickens we see today. Indigenous chickens, raised in villages, provide essential genetic resources and income for poverty alleviation by providing affordable protein. However, they are threatened by predators, emerging diseases, and market demand for ideal breeds and fast production which causes loss of their valuable traits. The lack of knowledge about genetic diversity and genetic mechanisms underlying adaptive variants may compromise the goal of conserving indigenous chicken breeds. The main insights of the study are that indigenous chickens are highly diversified, and environmental factors play a key role in enabling chicken adaptation and distribution. Genomic and spatial technologies have made it possible to explore the genetic structure and fully comprehend the mechanism underlying the local adaptation of indigenous chickens. These technologies can aid in creating programs that enhance productivity and promote climate-resilient breeds. This review explores the impact of natural selection on indigenous chicken, genetic diversity, population size, and the advancement of technologies in understanding local adaptation drivers. In conclusion, this review highlights the importance of studying the habitats and how this will guide in conserving local breeds in their intended production environment.

Comparative Evolutionary Genomics Reveals Genetic Diversity and Differentiation in Bacteroides fragilis

BACKGROUND/OBJECTIVES

Bacteroides fragilis is the pathogenic anaerobe most commonly isolated from intra-abdominal infections, abscesses, and blood. Despite its clinical importance, research on its pan-genome-scale evolution is still limited.

METHODS

Herein, we analyzed the pan-genome architecture of 374 B. fragilis strains to explore their intra-species genomic diversity and evolutionary patterns.

RESULTS

Our analysis revealed an open pan-genome with a high proportion of accessory genomes, indicating high genetic variability. Accessory genome genes were substantially enriched in the functions of "Replication, Recombination, and Repair" suggesting their roles in gene transfer and divergence. Phylogenomic analysis divided B. fragilis into two distinct clades: divisions I and II, differing in gene content, antimicrobial resistance genes, and mobile genetic elements. Division II revealed higher Tajima's D values, suggesting that it separated after B. fragilis's recent species diversification. The extreme shift in the distribution of gene-wise Hudson's fixation index (Fst) values for each division suggested that several genes are highly differentiated or evolved between the two clades. Average nucleotide identity and 16S rRNA analyses showed that B. fragilis division II represents a distinct species, Bacteroides hominis. Additionally, a considerable depletion of recombination in genes with Fst values > 0.99 was noted, suggesting that the highest Fst genes with little recombination are the basis for differentiation between divisions.

CONCLUSIONS

Overall, this study enhances the understanding of B. fragilis's genomic diversity, evolutionary dynamics, and potential role in pathogenesis, shedding light on its adaptation and diversification.

Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers

Increasing habitat fragmentation leads to wild populations becoming small, isolated, and threatened by inbreeding depression. However, small populations may be able to purge recessive deleterious alleles as they become expressed in homozygotes, thus reducing inbreeding depression and increasing population viability. We used whole-genome sequences from 57 tigers to estimate individual inbreeding and mutation load in a small-isolated and two large-connected populations in India. As expected, the small-isolated population had substantially higher average genomic inbreeding (FROH = 0.57) than the large-connected (FROH = 0.35 and FROH = 0.46) populations. The small-isolated population had the lowest loss-of-function mutation load, likely due to purging of highly deleterious recessive mutations. The large populations had lower missense mutation loads than the small-isolated population, but were not identical, possibly due to different demographic histories. While the number of the loss-of-function alleles in the small-isolated population was lower, these alleles were at higher frequencies and homozygosity than in the large populations. Together, our data and analyses provide evidence of 1) high mutation load, 2) purging, and 3) the highest predicted inbreeding depression, despite purging, in the small-isolated population. Frequency distributions of damaging and neutral alleles uncover genomic evidence that purifying selection has removed part of the mutation load across Indian tiger populations. These results provide genomic evidence for purifying selection in both small and large populations, but also suggest that the remaining deleterious alleles may have inbreeding-associated fitness costs. We suggest that genetic rescue from sources selected based on genome-wide differentiation could offset any possible impacts of inbreeding depression.

Defining coalescent genes: Theory meets practice in organelle phylogenomics

The species tree paradigm that dominates current molecular systematic practice infers species trees from collections of sequences under assumptions of the multispecies coalescent (MSC), i.e., that there is free recombination between the sequences and no (or very low) recombination within them. These coalescent genes (c-genes) are thus defined in an historical rather than molecular sense, and can in theory be as large as an entire genome or as small as a single nucleotide. A debate about how to define c-genes centers on the contention that nuclear gene sequences used in many coalescent analyses undergo too much recombination, such that their introns comprise multiple c-genes, violating a key assumption of the MSC. Recently a similar argument has been made for the genes of plastid (e.g., chloroplast) and mitochondrial genomes, which for the last 30 or more years have been considered to represent a single c-gene for the purposes of phylogeny reconstruction because they are non-recombining in a historical sense. Consequently, it has been suggested that these genomes should be analyzed using coalescent methods that treat their genes-over 70 protein-coding genes in the case of most plastid genomes (plastomes)-as independent estimates of species phylogeny, in contrast to the usual practice of concatenation, which is appropriate for generating gene trees. However, although recombination certainly occurs in the plastome, as has been recognized since the 1970's, it is unlikely to be phylogenetically relevant. This is because such historically effective recombination can only occur when plastomes with incongruent histories are brought together in the same plastid. However, plastids sort rapidly into different cell lineages and rarely fuse. Thus, because of plastid biology, the plastome is a more canonical c-gene than is the average multi-intron mammalian nuclear gene. The plastome should thus continue to be treated as a single estimate of the underlying species phylogeny, as should the mitochondrial genome. The implications of this long-held insight of molecular systematics for studies in the phylogenomic era are explored.