Genetic structure of Eurasian beaver in Romania: insights after two decades from the reintroduction

Once exploited for fur, meat, and extracting the yellowish exudate called castoreum, the Eurasian beaver disappeared from Romania during the eighteenth century. After, the reintroductions carried out two decades ago are currently thriving in the Danube River basin. Using nine nSSR markers, we analysed samples from 98 individuals, and we found no genetic substructure, suggesting high dispersal and gene flow capabilities. The stepwise mutation model (SMM) indicated the existence of a recent genetic bottleneck, though the Eurasian beaver retains high levels of genetic diversity and population growth facilitated variation in nSSR loci. A fine-scale spatial correlation in females was detected, contrasting with males’ dispersal on longer distances. While the movement and establishment of individuals’ new territories were made under natural predation pressure, the mix following natural expansion improved the fitness and could contribute to a higher genetic diversity than the source population. With any reintroduction, a focus on capturing individuals from various geographic origins, as well as securing many and suitable founding individuals (adults, subadults, and juveniles) with mixed origins, could secure the post-genetic bottleneck recovery and higher genetic diversity. Beyond this conservation success, future management strategies should consider building a National Action Plan (NAP) for the species, including a permanent genetic monitoring programme for Eurasian beaver.

Trunk perimeter correlates with genetic bottleneck intensity and the level of genetic diversity in populations of Taxus baccata L

Key message Taxus baccata remnants established recently tend to contribute less to the species’ overall genetic variation than historical populations because they are subjected to a greater impact of the founder effect and genetic isolation. As tree trunk perimeter is a rough indicator of genetic variation in a population, this measure should be considered in conservation programs. Context Genetic variation within Taxus baccata (L.) populations is not associated with the current census size but correlates well with the effective size, suggesting that genetic drift intensity reflects variation in demographic histories. Aims We hypothesize that recently established populations are subjected to greater bottleneck than old remnants. Using the mean trunk perimeter as a surrogate of tree age, we test whether the demographic history and genetic variation are associated with the mean tree age. Methods Using 18 microsatellite markers, we analyze the genetic diversity and demographic history of 11 yew populations in Poland to assess the relationship between the mean trunk perimeter and the inferred genetic parameters. Results Populations reveal significant differences in levels of genetic variation and in the intensity and time of genetic bottleneck. After excluding an apparent outlier, the genetic variation is significantly greater while the bottleneck intensity lower in populations with a greater perimeter. Conclusion Due to continuous species decline and increasing fragmentation, the non-uniform contribution of yew remnants to the overall genetic variation tends to decrease together with the mean tree age. Germplasm collections for the species should take into account tree perimeter as a rough indicator of the genetic variation of a population.

The paradox of retained genetic diversity of Hippocampus guttulatus in the face of demographic decline

Genetic diversity is the raw foundation for evolutionary potential. When genetic diversity is significantly reduced, the risk of extinction is heightened considerably. The long-snouted seahorse (Hippocampus guttulatus) is one of two seahorse species occurring in the North-East Atlantic. The population living in the Ria Formosa (South Portugal) declined dramatically between 2001 and 2008, prompting fears of greatly reduced genetic diversity and reduced effective population size, hallmarks of a genetic bottleneck. This study tests these hypotheses using samples from eight microsatellite loci taken from 2001 and 2013, on either side of the 2008 decline. The data suggest that the population has not lost its genetic diversity, and a genetic bottleneck was not detectable. However, overall relatedness increased between 2001 to 2013, leading to questions of future inbreeding. The effective population size has seemingly increased close to the threshold necessary for the population to retain its evolutionary potential, but whether these results have been affected by sample size is not clear. Several explanations are discussed for these unexpected results, such as gene flow, local decline due to dispersal to other areas of the Ria Formosa, and the potential that the duration of the demographic decline too short to record changes in the genetic diversity. Given the results presented here and recent evidence of a second population decline, the precise estimation of both gene flow and effective population size via more extensive genetic screening will be critical to effective population management.

Oxygen tension modulates the mitochondrial genetic bottleneck and influences the segregation of a heteroplasmic mtDNA variant in vitro

Most humans carry a mixed population of mitochondrial DNA (mtDNA heteroplasmy) affecting ~1–2% of molecules, but rapid percentage shifts occur over one generation leading to severe mitochondrial diseases. A decrease in the amount of mtDNA within the developing female germ line appears to play a role, but other sub-cellular mechanisms have been implicated. Establishing an in vitro model of early mammalian germ cell development from embryonic stem cells, here we show that the reduction of mtDNA content is modulated by oxygen and reaches a nadir immediately before germ cell specification. The observed genetic bottleneck was accompanied by a decrease in mtDNA replicating foci and the segregation of heteroplasmy, which were both abolished at higher oxygen levels. Thus, differences in oxygen tension occurring during early development likely modulate the amount of mtDNA, facilitating mtDNA segregation and contributing to tissue-specific mutation loads.

Avoiding organelle mutational meltdown across eukaryotes with or without a germline bottleneck

Mitochondrial DNA (mtDNA) and plastid DNA (ptDNA) encode vital bioenergetic apparatus, and mutations in these organelle DNA (oDNA) molecules can be devastating. In the germline of several animals, a genetic “bottleneck” increases cell-to-cell variance in mtDNA heteroplasmy, allowing purifying selection to act to maintain low proportions of mutant mtDNA. However, most eukaryotes do not sequester a germline early in development, and even the animal bottleneck remains poorly understood. How then do eukaryotic organelles avoid Muller’s ratchet—the gradual buildup of deleterious oDNA mutations? Here, we construct a comprehensive and predictive genetic model, quantitatively describing how different mechanisms segregate and decrease oDNA damage across eukaryotes. We apply this comprehensive theory to characterise the animal bottleneck with recent single-cell observations in diverse mouse models. Further, we show that gene conversion is a particularly powerful mechanism to increase beneficial cell-to-cell variance without depleting oDNA copy number, explaining the benefit of observed oDNA recombination in diverse organisms which do not sequester animal-like germlines (for example, sponges, corals, fungi, and plants). Genomic, transcriptomic, and structural datasets across eukaryotes support this mechanism for generating beneficial variance without a germline bottleneck. This framework explains puzzling oDNA differences across taxa, suggesting how Muller’s ratchet is avoided in different eukaryotes.

No severe genetic bottleneck in a rapidly range-expanding bumblebee pollinator

Genetic bottlenecks can limit the success of populations colonizing new ranges. However, successful colonizations can occur despite bottlenecks, a phenomenon known as the genetic paradox of invasion. Eusocial Hymenoptera such as bumblebees (Bombusspp.) should be particularly vulnerable to genetic bottlenecks, since homozygosity at the sex-determining locus leads to costly diploid male production (DMP). The Tree Bumblebee (Bombus hypnorum) has rapidly colonized the UK since 2001 and has been highlighted as exemplifying the genetic paradox of invasion. Using microsatellite genotyping, combined with the first genetic estimates of DMP in UKB. hypnorum, we tested two alternative genetic hypotheses (‘bottleneck’ and ‘gene flow’ hypotheses) forB. hypnorum's colonization of the UK. We found that the UK population has not undergone a recent severe genetic bottleneck and exhibits levels of genetic diversity falling between those of widespread and range-restrictedBombusspecies. Diploid males occurred in 15.4% of reared colonies, leading to an estimate of 21.5 alleles at the sex-determining locus. Overall, the findings show that this population is not bottlenecked, instead suggesting that it is experiencing continued gene flow from the continental European source population with only moderate loss of genetic diversity, and does not exemplify the genetic paradox of invasion.

Intra-Host Diversity of SARS-Cov-2 Should Not Be Neglected: Case of the State of Victoria, Australia

Since the identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as the etiological agent of the current COVID-19 pandemic, a rapid and massive effort has been made to obtain the genomic sequences of this virus to monitor (in near real time) the phylodynamic and diversity of this new pathogen. However, less attention has been given to the assessment of intra-host diversity. RNA viruses such as SARS-CoV-2 inhabit the host as a population of variants called quasispecies. We studied the quasispecies diversity in four of the main SARS-CoV-2 genes (ORF1a, ORF1b, S and N genes), using a dataset consisting of 210 next-generation sequencing (NGS) samples collected between January and early April of 2020 in the State of Victoria, Australia. We found evidence of quasispecies diversity in 68% of the samples, 76% of which was nonsynonymous variants with a higher density in the spike (S) glycoprotein and ORF1a genes. About one-third of the nonsynonymous intra-host variants were shared among the samples, suggesting host-to-host transmission. Quasispecies diversity changed over time. Phylogenetic analysis showed that some of the intra-host single-nucleotide variants (iSNVs) were restricted to specific lineages, highlighting their potential importance in the epidemiology of this virus. A greater effort must be made to determine the magnitude of the genetic bottleneck during transmission and the epidemiological and/or evolutionary factors that may play a role in the changes in the diversity of quasispecies over time.

Evaluation of Genetic Diversity in Goats of Telangana and Andhra Pradesh States of India

Background: The goat population of Andhra Pradesh and Telangana states is about five million, respectively. The goats of these two states lack phenotypic uniformity. But it is not known whether these populations have any genetically uniform group that can be registered as a breed. The study was undertaken to explore possibility of any potential new goat germplasm.Methods: Study was carried out at ICAR-NBAGR during 2017-19. Genetic diversity and differentiation was evaluated by using 22 microsatellite markers in three goat populations: Telangana Black (TB, n=26), Telangana Mixed (TM, n=49) and one Andhra Pradesh goat population (AP, n=45). Their genetic differentiation was compared with that of geographically closely distributed registered breeds viz. Bidri (n=28) and Nandidurga (n=48) of Karnatka and Ganjam (n=48) of Odisha. Result: The mean allele frequency observed was 6.59 (TB), 7.27 (TM) and 8.36 (AP). Expected number of alleles varied from 3.33 in (TB) to 3.69 in AP goats. Observed heterozygosity was lowest in the TM (0.474) followed by TB (0.504) and was highest in the AP goats (0.569). AP goat population had 6.3% heterozygote deficiency, whereas, both TB (15.4%) and TM (17.5%) had very high inbreeding coefficients. A total of 344 alleles were detected across the 22 loci in six goat groups. F-statistics, the pair-wise Nei’s genetic distance, assignment test and Baysian approach suggested that AP goats are distinct from two Telangana goat populations as well as from the other geographically closely related registered goat breeds. Genetic bottleneck analysis indicated the absence of any detectably large, recent genetic bottleneck in AP population. Altogether, the study identified Andhra Pradesh (AP) goats to be a new potential goat germplasm of India.