Genomic divergence and mutation load in the Begonia masoniana complex from limestone karsts

Understanding genome-wide diversity,inbreeding,and the burden of accumulated deleterious mutations in small and isolated populations is essential for predicting and enhancing population persistence and resilience.However,these effects are rarely studied in limestone karst plants.Here,we re-sequenced the nuclear genomes of 62 individuals of the Begonia masoniana complex(B.liuyanii,B.longgangensis,B.masoniana and B.variegata)and investigated genomic divergence and genetic load for these four species.Our analyses revealed four distinct clusters corresponding to each species within the complex.Notably,there was only limited admixture between B.liuyanii and B.longgangensis occurring in overlapping geographic regions.All species experienced historical bottlenecks during the Pleistocene,which were likely caused by glacial climate fluctuations.We detected an asymmetric historical gene flow between group pairs within this timeframe,highlighting a distinctive pattern of interspecific divergence attributable to karst geographic isolation.We found that isolated populations of B.masoniana have limited gene flow,the smallest recent population size,the highest inbreeding coefficients,and the greatest accumulation of recessive deleterious mutations.These findings underscore the urgency to prioritize conservation efforts for these isolated population.This study is among the first to disentangle the genetic differentiation and specific demographic history of karst Begonia plants at the whole-genome level,shedding light on the potential risks associated with the accumulation of deleterious mutations over generations of inbreeding.Moreover,our findings may facilitate conservation planning by providing critical baseline genetic data and a better understanding of the historical events that have shaped current population structure of rare and endangered karst plants.

Using non-destructive sampling to evaluate the population genomic status of captive Brown Eared Pheasants

Evaluating the genetic status of threatened species is an essential task in conservation genetics.However,the genetic status of threatened species has been mostly evaluated through techniques that fail to estimate genetic diversity at the whole genomic level.Next generation sequencing can meet this demand,but high quality samples such as blood or muscle tissues are required.However,it is difficult to collect such samples from threatened species because sampling work may impact their health.Therefore,it is essential to design a workflow to evaluate the whole genomic status of threatened species using non-destructive sampling.Even though non-destructive sampling has been used in traditional barcoding technique,the barcoding technique cannot evaluate the whole genomic status.Brown Eared Pheasant(Crossoptilon mantchuricum)is an endangered species,with captive populations maintained in Taiyuan Zoo,China,and Europe.However,the genetic diversity,inbreeding pattern,and mutation load of these two populations are unclear.To uncover the genetic status of these two captive populations,we applied 2b-RAD technology to evaluate the genomic status of these populations using feathers as samples.The feathers could be collected by non-destructive sampling.The results indicate that the Taiyuan Zoo population has a lower genetic diversity and higher inbreeding coefficient than the European population.The Taiyuan Zoo population has lethal mutations when homozygous.The current project uses a non-destructive sampling technique to evaluate the whole genomic status of the two captive populations,providing a paradigm for conservation genetics,which will facilitate the development of conservation biology.

Using MutPred derived mtDNA load scores to evaluate mtDNA variation in hypertension and diabetes in a two-population cohort：The SABPA study

Mitochondrial DNA（mt DNA） variation has been implicated in many common complex diseases, but inconsistent and contradicting results are common. Here we introduce a novel mutational load hypothesis, which also considers the collective effect of mainly rare variants, utilising the Mut Pred Program.We apply this new methodology to investigate the possible role of mt DNA in two cardiovascular disease（CVD） phenotypes（hypertension and hyperglycaemia）, within a two-population cohort（n = 363; mean age 45 ± 9 yrs）. Very few studies have looked at African mt DNA variation in the context of complex disease, and none using complete sequence data in a well-phenotyped cohort. As such, our study will also extend our knowledge of African mt DNA variation, with complete sequences of Southern Africans being especially under-represented. The cohort showed prevalence rates for hypertension（58.6%） and prediabetes（44.8%）. We could not identify a statistically significant role for mt DNA variation in association with hypertension or hyperglycaemia in our cohort. However, we are of the opinion that the method described will find wide application in the field, being especially useful for cohorts from multiple locations or with a variety of mt DNA lineages, where the traditional haplogroup association method has been particularly likely to generate spurious results in the context of association with common complex disease.

Mating behavior as an indicator of quality of Drosophila subobscura males？

According to current theoretical predictions, any deleterious mutations that reduce nonsexual fitness may have a negative influence on mating success. This means that sexual selection may remove deleterious mutations from the populations. Males of good genetic quality should be more successful in mating, compared to the males of lower genetic quality. As mating success is a condition dependent trait, large fractions of the genome may be a target of sexual selection and many behavioral traits are likely to be condition dependent. We manipulated the genetic quality of Drosophila subobscura males by inducing mutations with ionizing radiation and observed the effects of the obtained heterozygous mutations on male mating behavior： courtship occurrence, courtship latency, mating occurrence, latency to mating and duration of mating. We found possible effects of mutations. Females mated more frequently with male progeny of nonirradiated males and that these males courted females faster compared to the male progeny of irradiated males. Our findings indicate a possible important role of sexual selection in purging deleterious mutations.