Effective Population Research Articles

Bacterial lifestyle shapes pangenomes

Pangenomes vary across bacteria. Some species have fluid pangenomes, with a high proportion of genes varying between individual genomes. Other species have less fluid pangenomes, with different genomes tending to contain the same genes. Two main hypotheses have been suggested to explain this variation: differences in species' bacterial lifestyle and effective population size. However, previous studies have not been able to test between these hypotheses because the different features of lifestyle and effective population size are highly correlated with each other, and phylogenetically conserved, making it hard to disentangle their relative importance. We used phylogeny-based analyses, across 126 bacterial species, to tease apart the causal role of different factors. We found that pangenome fluidity was lower in i) host-associated compared with free-living species and ii) host-associated species that are obligately dependent on a host, live inside cells, and are more pathogenic and less motile. In contrast, we found no support for the competing hypothesis that larger effective population sizes lead to more fluid pangenomes. Effective population size appears to correlate with pangenome variation because it is also driven by bacterial lifestyle, rather than because of a causal relationship.

Insertion-deletions are depleted in protein regions with predicted secondary structure.

A fundamental goal in evolutionary biology and population genetics is to understand how selection shapes the fate of new mutations. Here we test the null hypothesis that insertion-deletion events (indels) in protein coding regions occur randomly with respect to secondary structures. We identified indels across 11,444 sequence alignments in mouse, rat, human, chimp, and dog genomes, then quantified their overlap with four different types of secondary structure - alpha helices, beta strands, protein bends, and protein turns - predicted by deep-learning methods of AlphaFold2. Indels overlapped secondary structures 54% as much as expected, and were especially under-represented over beta strands, which tend to form internal, stable regions of proteins. In contrast, indels were enriched by 155% over regions without any predicted secondary structures. These skews were stronger in the rodent lineages compared to the primate lineages, consistent with population genetic theory predicting that natural selection will be more efficient in species with larger effective population sizes. Nonsynonymous substitutions were also less common in regions of protein secondary structure, although not as strongly reduced as in indels. In a complementary analysis of thousands of human genomes, we showed that indels overlapping secondary structure segregated at significantly lower frequency than indels outside of secondary structure. Taken together, our study shows that indels are selected against if they overlap secondary structure, presumably because they disrupt the tertiary structure and function of a protein.

Divergent Aspergillus flavus corn population is composed of prolific conidium producers: Implications for saprophytic disease cycle

ABSTRACT The ascomycete fungus Aspergillus flavus infects and contaminates corn, peanuts, cottonseed, and tree nuts with toxic and carcinogenic aflatoxins. Subdivision between soil and host plant populations suggests that certain A. flavus strains are specialized to infect peanut, cotton, and corn despite having a broad host range. In this study, the ability of strains isolated from corn and/or soil in 11 Louisiana fields to produce conidia (field inoculum and male gamete) and sclerotia (resting bodies and female gamete) was assessed and compared with genotypic single-nucleotide polymorphism (SNP) differences between whole genomes. Corn strains produced upward of 47× more conidia than strains restricted to soil. Conversely, corn strains produced as much as 3000× fewer sclerotia than soil strains. Aspergillus flavus strains, typified by sclerotium diameter (small S-strains, <400 μm; large L-strains, >400 μm), belonged to separate clades. Several strains produced a mixture (M) of S and L sclerotia, and an intermediate number of conidia and sclerotia, compared with typical S-strains (minimal conidia, copious sclerotia) and L-strains (copious conidia, minimal sclerotia). They also belonged to a unique phylogenetic mixed (M) clade. Migration from soil to corn positively correlated with conidium production and negatively correlated with sclerotium production. Genetic differences correlated with differences in conidium and sclerotium production. Opposite skews in female (sclerotia) or male (conidia) gametic production by soil or corn strains, respectively, resulted in reduced effective breeding population sizes when comparing male:female gamete ratio with mating type distribution. Combining both soil and corn populations increased the effective breeding population, presumably due to contribution of male gametes from corn, which fertilize sclerotia on the soil surface. Incongruencies between aflatoxin clusters, strain morphotype designation, and whole genome phylogenies suggest a history of sexual reproduction within this Louisiana population, demonstrating the importance of conidium production, as infectious propagules and as fertilizers of the A. flavus soil population.

Genetic connectivity of the common octopus (Octopus insularis) along the southwestern Caribbean

AbstractOctopus insularis is a shallow‐water octopus distributed throughout the western Atlantic, the Gulf of Mexico and the Caribbean. To evaluate its phylogeographic pattern, mitochondrial markers (16S rRNA and COIII) and genome‐wide nuclear markers (SNP's) were analyzed in individuals from artisanal fishing in different locations of the Colombian Caribbean coast. Mitochondrial analyzes displayed novel haplotypes (16S = H2, H3 and H4; COIII = H2–H7) and haplotypes shared with distant geographic areas (16S = H1 COIII = H1). The COIII gene did not show genetic differentiation between the analyzed localities, while the 16S gene showed significant differences between Santa Marta and Isla Fuerte. COIII's demographic analysis indicated that the species' effective population size has remained constant. Inferences were made from next‐generation genomic data with restriction site‐associated DNA (ddRAD‐seq) and 6769 polymorphic loci. The pairwise FST test indicated that there are low but significant differences between localities; however, the general molecular analysis of variance (AMOVA) and the principal coordinate analysis showed a lack of spatial structure in the populations analyzed. The Mantel test found no correlation between genetic distance and geographic distance, and the genetic structure analyses showed the presence of one genetic stock. The information obtained in this study indicates the genetic connectivity of O. insularis in the southwestern Caribbean, the absence of putative biogeographic barriers that affect its gene flow, and the crucial role played by life history strategies (planktonic paralarvae) and oceanographic factors to define the current distribution of its genetic diversity in this region.

Genomics-informed captive breeding can reduce inbreeding depression and the genetic load in zoo populations.

Zoo populations of threatened species are a valuable resource for the restoration of wild populations. However, their small effective population size poses a risk to long-term viability, especially in species with high genetic load. Recent bioinformatic developments can identify harmful genetic variants in genome data. Here, we advance this approach, analysing the genetic load in the threatened pink pigeon (Nesoenas mayeri). We lifted the mutation-impact scores that had been calculated for the chicken (Gallus gallus) to estimate the genetic load in six pink pigeons. Additionally, we perform in silico crossings to predict the genetic load and realized load of potential offspring. We thus identify the optimal mate pairs that are theoretically expected to produce offspring with the least inbreeding depression. We use computer simulations to show how genomics-informed conservation can reduce the genetic load whilst reducing the loss of genome-wide diversity. Genomics-informed management is likely to become instrumental in maintaining the long-term viability of zoo populations.

Allele frequency dynamics under sex-biased demography and sex-specific inheritance in a pedigreed jay population

Abstract Sex-biased demography, including sex-biased survival or migration, can alter allele frequency changes across the genome. In particular, we can expect different patterns of genetic variation on autosomes and sex chromosomes due to sex-specific differences in life histories, as well as differences in effective population size, transmission modes, and the strength and mode of selection. Here, we demonstrate the role that sex differences in life history played in shaping short-term evolutionary dynamics across the genome. We used a 25-year pedigree and genomic dataset from a long-studied population of Florida Scrub-Jays (Aphelocoma coerulescens) to directly characterize the relative roles of sex-biased demography and inheritance in shaping genome-wide allele frequency trajectories. We used gene dropping simulations to estimate individual genetic contributions to future generations and to model drift and immigration on the known pedigree. We quantified differential expected genetic contributions of males and females over time, showing the impact of sex-biased dispersal in a monogamous system. Due to female-biased dispersal, more autosomal variation is introduced by female immigrants. However, due to male-biased transmission, more Z variation is introduced by male immigrants. Finally, we partitioned the proportion of variance in allele frequency change through time due to male and female contributions. Overall, most allele frequency change is due to variance in survival and births. Males and females make similar contributions to autosomal allele frequency change, but males make higher contributions to allele frequency change on the Z chromosome. Our work shows the importance of understanding sex-specific demographic processes in characterizing genome-wide allele frequency change in wild populations.

Genomic analysis of inbreeding level, kinship and breed relationships in Creole cattle from South America.

The conservation of animal genetic resources refers to measures taken to prevent the loss of genetic diversity in livestock populations, including the protection of breeds from extinction. Creole cattle populations have suffered a drastic reduction in recent decades owing to absorbent crosses or replacement with commercial breeds of European or Indian origin. Genetic characterization can serve as a source of information for conservation strategies to maintain genetic variation. The objective of this work was to evaluate the levels of inbreeding and kinship through the use of genomic information. A total of 903 DNAs from 13 cattle populations from Argentina, Bolivia and Uruguay were genotyped using an SNP panel of 48 K. Also, a dataset of 76 K SNPs from Peruvian Creole was included. Two inbreeding indices (FROH and Fhat2) and kinship relationships were calculated. In addition, effective population size (Ne), linkage disequilibrium, population composition and phylogenetic relationships were estimated. In Creole cattle, FROH ranged from 0.14 to 0.03, and Fhat2 was close to zero. The inferred Ne trends exhibited a decline toward the present for all populations, whereas Creole cattle presented a lower magnitude of Ne than foreign breeds. Cluster analysis clearly differentiated the taurine and Zebu components (K2) and showed that Bolivian Creole cattle presented Zebu gene introgression. Despite the population reduction, Creole populations did not present extreme values of consanguinity and kinship and maintain high levels of genetic diversity. The information obtained in this work may be useful for planning conservation programmes for these valuable local animal genetic resources.

Drift drives the evolution of chromosome number II: The impact of range size on genome evolution in Carnivora.

Chromosome number is a fundamental genomic trait that is often the first recorded characteristic of a genome. Across large clades, a common pattern emerges: many or even most lineages exhibit relative stasis, while a handful of lineages or species exhibit striking variation. Despite recent developments in comparative methods, most of this heterogeneity is still poorly understood. It is essential to understand why some lineages have rapid rates of chromosome number evolution, as it can impact a variety of other traits. Previous research suggests that biased female meiotic drive may shape rates of karyotype evolution in some mammals. However, Carnivora exhibits variation that this female meiotic drive model cannot explain. We hypothesize that variation in effective population size may underlie rate variation in Carnivora. To test this hypothesis, we estimated rates of fusions and fissions while accounting for range size, which we use as a proxy for effective population size. We reason fusions and fissions are deleterious or underdominant and that only in lineages with small range sizes will these changes be able to fix due to genetic drift. In this study, we find that the rates of fusions and fissions are elevated in taxa with small range sizes relative to those with large range sizes. Based on these findings, we conclude that 1) naturally occurring structural mutations that change chromosome number are underdominant or mildly deleterious, and 2) when population sizes are small, structural rearrangements may play an important role in speciation and reduction in gene flow among populations.

Equivalent mating system parameters in post‐mining and undisturbed native plant populations confirms restitution of bird‐pollinator function

Abstract The restoration of diverse self‐sustaining ecosystems requires re‐establishment of functional interactions among species. For plant communities, pollinators are usually essential for pollination, seed set and seed quality. A common assumption in ecological restoration for plants pollinated by animals is one of ‘build it and they will come’, which is rarely tested. Beyond seed set, there may be negative genetic consequences for seed quality if pollinators and their behaviour do not reflect those in reference populations. Here, we conduct an ecological genetic assessment of seed quality via mating system parameters in Lambertia multiflora (Proteaceae), a species dependent on nectar‐feeding birds for pollination. Four populations of L. multiflora in disturbed sites that were rehabilitated following mineral sands mining were compared with four native reference populations, near Eneabba, Western Australia. In each population, approximately 10 offspring from each of 10 maternal plants were genotyped with 11 highly polymorphic microsatellite markers. From these data, genetic diversity and mating system parameters were assessed, and found to be equivalent across all populations. Mean allelic diversity and heterozygosity across loci were very high. All populations were completely outcrossing with no bi‐parental inbreeding. Mean correlated paternity, sibship and effective population size estimates for restored and natural populations were not significantly different and reflected uniformly high paternal diversity and wide outcrossing. Equivalent genetic results for restored and natural reference populations indicate successful restitution of bird‐pollinator services for L. multiflora in these post‐mining rehabilitation sites. Synthesis and applications. Reviewing our results with other published studies to date suggests a resilience of bird‐pollinator services in restored plant communities. These findings provide some reassurance to restoration practitioners working in these global south systems where bird pollination is a feature, at least for similar landscape scenarios. Our study also highlights the global contribution of ecological genetics to the objective assessment of functional species interactions in ecological restoration, an increasingly important goal of land managers and regulators seeking to improve restoration standards.

Genealogical structure and genetic variability: A step towards conservation of white Morada Nova sheep in semi-arid region

Morada Nova breed has a low effective herd, and its white variety is in risk of extinction in Brazilian semi-arid region. This study aimed to evaluate white Morada Nova sheep’s genetic variability and population structure in four flocks. These are the only flocks in the world. The assessed parameters of pedigree integrity and a genealogy record of 219 animals. 44.74 % did not have pedigree information on their mother or father, and 50.47 % did not have available information on their grandparents. 52.97 % had a pedigree in their first ancestry (obtained through the average of known parents), 23.74 % in the second, 13.58 % in the third, and 5.33 % in the fourth. The effective size was 10.7, considering the complete equivalent generation. The effective number of founding animals (fe) and ancestors (fa) was 10, indicating the effective participation of all founding animals in the population over the generations, reducing losses of genetic variability. Out of all the ancestors, only 3 explained 50 % of the population’s genetic variability, reflecting the low values of fa and fe. The population’s average inbreeding and kinship coefficients were 2.61 and 4.54. The F statistics of Wright, Fis, Fst, and Fit, were −0.012, 0.016, and 0.003. The genetic conservation index (GCI) had an average of 2.01 ± 1.29, with minimum and maximum values of 1.0 and 6.38, respectively. Approximately, 71 % of the population had GCI below 2.0, while only 5.9 % of sheep had an GCI bigger than 5.0. This indicates the absence of sub-structures inf the population. There is no population subdivision, considering the genealogical structure of the evaluated flocks. The inbreeding and kinship coefficient values are controlled and serve as a starting point for establishing a future management plan for the genetic variability of the flock. It is recommended to use strategies to increase the effective population size, to meet the minimum number recommended by FAO and to promote the conservation and genetic improvement of the breed.

225 Genomic diversity of Katahdin sheep and impacts on genomic prediction

Abstract In the late 1950s, Katahdin hair sheep were developed as a composite breed of medium size and moderate prolificacy, with potential to express resistance to gastrointestinal nematodes. With its increasing popularity and the recent adoption of genomic prediction in the Katahdin breeding program, evaluating the genetic diversity in this breed is necessary. Prediction accuracies rely on the strength of genetic relationships. That strength often increases with selection using genomically-enhanced estimated breeding values; however, it carries the risk of decreasing diversity. We aim to characterize the genetic diversity present in the breed and the subsequent impact on the accuracies of genomic predictions. Genotypes on Katahdin sheep from member flocks in the National Sheep Improvement Program were used. Data from two medium density 50k bead chips and one high density 600k bead chip were merged and limited to shared autosomal single nucleotide polymorphisms (SNP). After quality control, there were 9,705 animals and 31,984 SNP remaining. Only for analyses of inbreeding and heterozygosity, linkage disequilibrium (LD) pruning was performed; variants with an LD score exceeding 0.8 were removed with 29,904 SNP remaining. To determine the extent of population structure, principal component (PC) analysis was conducted with PC one and PC two explaining 4.9% and 3.8% of the variation in the population, respectively. When examining subpopulations, a single ancestral population explained 99.9% of the genetic variation among animals. When clustered by identity-by-state, all animals were placed in a single cluster. Inbreeding coefficients were estimated with four methods: method of moments, variance-standardized relationship minus one, excess homozygosity, and correlation between uniting gametes. Across methods, average inbreeding coefficients ranged from 1.14% to 1.20% with Pearson and Spearman correlations ranging from -0.51 to 0.91 (Table 1). Historical effective population sizes (Ne) were estimated for earlier generations, and a linear regression fit to predict more recent Ne. At the founding of the breed, historical Ne was estimated to be 310, and the current Ne was estimated to be 150. Effects of Ne on the accuracy of genomic predictions were examined for reference population sizes ranging from 1k to 25k for traits of low (0.1), moderate (0.3), and high (0.5) heritabilities. The corresponding number of effective chromosomal segments were 2NeL, where L was the length of the genome in morgans (26M). Accuracies of genomic predictions increased as the reference population size grew, with only marginal gains once the population exceeded 15k. Overall, there were no detectable genetic subpopulations in the Katahdin breed. Current levels of inbreeding were low. With a small Ne the breed can achieve high accuracy for genomic predictions by aiming for a reference population of 15k animals. Negative impacts on genetic diversity due to genomic selection are not of immediate concern.

Understanding the genomic heterogeneity of North African Imazighen: from broad to microgeographical perspectives.

The strategic location of North Africa has led to cultural and demographic shifts, shaping its genetic structure. Historical migrations brought different genetic components that are evident in present-day North African genomes, along with autochthonous components. The Imazighen (plural of Amazigh) are believed to be the descendants of autochthonous North Africans and speak various Amazigh languages, which belong to the Afro-Asiatic language family. However, the arrival of different human groups, especially during the Arab conquest, caused cultural and linguistic changes in local populations, increasing their heterogeneity. We aim to characterize the genetic structure of the region, using the largest Amazigh dataset to date and other reference samples. Our findings indicate microgeographical genetic heterogeneity among Amazigh populations, modeled by various admixture waves and different effective population sizes. A first admixture wave is detected group-wide around the twelfth century, whereas a second wave appears in some Amazigh groups around the nineteenth century. These events involved populations with higher genetic ancestry from south of the Sahara compared to the current North Africans. A plausible explanation would be the historical trans-Saharan slave trade, which lasted from the Roman times to the nineteenth century. Furthermore, our investigation shows that assortative mating in North Africa has been rare.

Genetic predictors of population resilience: A case study of native Brook Trout in headwater streams

AbstractObjectivePopulations of eastern Brook Trout Salvelinus fontinalis face threats from several sources, such as habitat fragmentation, climate change, and competition with introduced salmonids. As a native species, understanding how these populations will respond to disturbances is paramount to their management and effective conservation. A population's ability to respond to disturbance, its resilience, is influenced by several factors. One such group of factors is population genetics.MethodsWe calculated population resilience metrics based on transient dynamics using population projection matrix models. Long‐term demographic data from 23 headwater stream Brook Trout populations were used to parameterize models. Genetic data were collected, and genetic indices were calculated. Partial redundancy analysis was then used to evaluate relationships between resilience metrics and genetic indices.ResultInbreeding coefficient, rarefied allelic richness, pairwise genetic differentiation (FST), and effective population size were all found to be important variables in predicting resilience.ConclusionOur results suggest that genetic isolation may increase the demographic resilience in Brook Trout through faster generation times and higher juvenile survival, but this likely comes at the cost of increased extinction risk and truncated size structures. Genetic indices can provide insight into gene flow between populations, thus the relationship between population connectivity and resilience. Given the importance of connectivity to population resilience, restoring and maintaining movement corridors could affect resilience in headwater Brook Trout populations.

Estimation of contemporary effective population size in plant populations: Limitations of genomic datasets.

Effective population size (N e) is a pivotal evolutionary parameter with crucial implications in conservation practice and policy. Genetic methods to estimate N e have been preferred over demographic methods because they rely on genetic data rather than time-consuming ecological monitoring. Methods based on linkage disequilibrium (LD), in particular, have become popular in conservation as they require a single sampling and provide estimates that refer to recent generations. A software program based on the LD method, GONE, looks particularly promising to estimate contemporary and recent-historical N e (up to 200 generations in the past). Genomic datasets from non-model species, especially plants, may present some constraints to the use of GONE, as linkage maps and reference genomes are seldom available, and SNP genotyping is usually based on reduced-representation methods. In this study, we use empirical datasets from four plant species to explore the limitations of plant genomic datasets when estimating N e using the algorithm implemented in GONE, in addition to exploring some typical biological limitations that may affect N e estimation using the LD method, such as the occurrence of population structure. We show how accuracy and precision of N e estimates potentially change with the following factors: occurrence of missing data, limited number of SNPs/individuals sampled, and lack of information about the location of SNPs on chromosomes, with the latter producing a significant bias, previously unexplored with empirical data. We finally compare the N e estimates obtained with GONE for the last generations with the contemporary N e estimates obtained with the programs currentNe and NeEstimator.

The Ne/N ratio in applied conservation.

Recent developments within the IUCN and the Convention on Biological Diversity have affirmed the increasingly key role that effective population size (N e) and the effective size: census size ratio (N e/N) play in applied conservation and management of global biodiversity. This paper reviews and synthesizes information regarding the definition of N e and demographic and genetic methods for estimating effective size, census size, and their ratio. Emphasis is on single-generation estimates of contemporary N e/N, which are the most informative for practical applications. It is crucial to clearly define which individuals are included in the census size (N). Defining N as the number of adults alive at a given time facilitates comparisons across species. For a wide range of applications and experimental designs, inbreeding N e is simpler to calculate and interpret than variance N e. Effects of skewed sex ratio are generally modest, so most reductions to N e/N arise from overdispersed (greater-than-Poisson) variance in offspring number (). Even when fecundity changes with age, overdispersed within-age variance generally contributes most to overall , and both random and deterministic (mediated by selection) factors can be important. Most species are age-structured, so it is important to distinguish between effective size per generation (N e) and the effective number of breeders in one season or year (N b). Both N e and N b are important for applied conservation and management. For iteroparous species, a key metric is variance in lifetime reproductive success (), which can be affected by a variety of additional factors, including variation in longevity, skip or intermittent breeding, and persistent individual differences in reproductive success. Additional factors that can be important for some species are also discussed, including mating systems, population structure, sex reversal, reproductive compensation, captive propagation, and delayed maturity.

Impact of pre-copulatory sexual cannibalism on genetic diversity and efficacy of selection.

Factors that increase reproductive variance among individuals act to reduce effective population size (Ne), which accelerates the loss of genetic diversity and decreases the efficacy of purifying selection. These factors include sexual cannibalism, offspring investment and mating system. Pre-copulatory sexual cannibalism, where the female consumes the male prior to mating, exacerbates this effect. We performed comparative transcriptomics in two spider species, the cannibalistic Trechaleoides biocellata and the non-cannibalistic T. keyserlingi, to generate genomic evidence to support these predictions. First, we estimated heterozygosity and found that genetic diversity is relatively lower in the cannibalistic species. Second, we calculated dN/dS ratios as a measure of purifying selection; a higher dN/dS ratio indicated relaxed purifying selection in the cannibalistic species. These results are consistent with the hypothesis that sexual cannibalism impacts operational sex ratio and demographic processes, which interact with evolutionary forces to shape the genetic structure of populations. However, other factors such as the mating system and life-history traits contribute to shaping Ne. Comparative analyses across multiple contrasting species pairs would be required to disentangle these effects. Our study highlights that extreme behaviours such as pre-copulatory cannibalism may have profound eco-evolutionary effects.

Historical Demography and Climate Driven Range Shifts in the Blue-spotted Salamander Under the Climate Change Scenarios

This study integrates phylogeography with distributional analysis to understand the demographic history and range dynamics of a limited dispersal capacity amphibian species, Blue-spotted Salamander (Ambystoma laterale), under several climate change scenarios. For this we used an ecological niche modeling approach, together with Bayesian based demographic analysis, to develop inferences regarding this species' demographic history and range dynamics. The current model output was mostly congruent with the present distribution of the Blue-spotted Salamander. However, under both the Last Interglacial and the Last Glacial Maximum bioclimatic conditions, the model predicted a substantially narrower distribution than the present. These predictions showed almost no suitable area in the current distribution range of the species during almost the last 22.000 y before present (ybp). The predictions indicated that the distribution of this species shifted from eastern coast of northern North America to the southern part of the current distribution range of the species. The Bayesian Skyline Plot analysis, which provided good resolution of the effective population size changes over the Blue-spotted Salamander history, was mostly congruent with ecological niche modeling predictions for this species. This study provides the first investigation of the Blue-spotted Salamander’s late-Quaternary history based on ecological niche modeling and Bayesian-based demographic analysis. In terms of the main result of this study, we found that the species' present genetic structure has been substantially affected by past climate changes, and this species has reached current distribution range almost from nothing since the Last Glacial Maximum.

Population genomic history of the endangered Anatolian and Cyprian mouflons in relation to worldwide wild, feral and domestic sheep lineages.

Once widespread in their homelands, the Anatolian mouflon (Ovis gmelini anatolica) and the Cyprian mouflon (Ovis gmelini ophion) were driven to near extinction during the 20th century and are currently listed as endangered populations by the IUCN. While the exact origins of these lineages remain unclear, they have been suggested to be close relatives of domestic sheep or remnants of proto-domestic sheep. Here, we study whole genome sequences of n = 5 Anatolian mouflons and n = 10 Cyprian mouflons in terms of population history and diversity, comparing them to eight other extant sheep lineages. We find reciprocal genetic affinity between Anatolian and Cyprian mouflons and domestic sheep, higher than all other studied wild sheep genomes, including the Iranian mouflon (Ovis gmelini). Studying diversity indices, we detect a considerable load of short runs of homozygosity (ROH) blocks (<2 Mb) in both Anatolian and Cyprian mouflons, reflecting small effective population size (Ne). Meanwhile, Ne as well as mutation load estimates are lower in Cyprian compared to Anatolian mouflons, suggesting the purging of recessive deleterious variants in Cyprian sheep under a small long-term Ne, possibly attributable to founder effects, island isolation, introgression from domestic lineages, or differences in their bottleneck dynamics. Expanding our analyses to worldwide wild and feral Ovis genomes, we observe varying viability metrics among different lineages, and a limited consistency between viability metrics and IUCN conservation status. Factors such as recent inbreeding, introgression, and unique population dynamics may have contributed to the observed disparities.

Genetic variation of English yew (Taxus baccata L.) in the Bavarian Forest National Park, Germany

AbstractTaxus baccata L. is a highly valuable species with wide distribution but scattered and locally rare occurrence. Human intervention, including forest management practices and fragmentation, can significantly impact the species’ genetic diversity, structure, and dynamics. In this study, we investigated these factors within T. baccata populations in the Bavarian Forest National Park (NP) in Germany and their implications for conservation. We used 13 EST-SSRs to assess the genetic diversity and structure of the population. Our analysis revealed a scarcity of small-diameter trees, indicating limited natural regeneration over time. However, conservation efforts, like selectively removing competitor species and using protective fencing, have improved growth conditions and promoted seedling emergence. The NP’s natural zone has no active management, which is confined to the development and management zones. Genetic diversity assessments revealed high genetic diversity (He: 0.612 and 0.614 for seedlings and adults, respectively) compared to other studies in Taxus baccata, dispelling concerns of significant inbreeding and showcasing a stable genetic structure. However, significant spatial clustering of related individuals (family structures) in both cohorts and low effective population size in the progeny hints at restricted gene flow, necessitating conservation efforts prioritizing safeguarding and promoting natural regeneration in development and management zones. Limited natural regeneration and the recent decrease in effective population size in the NP populations indicate habitat fragmentation and human interventions. Effective population size estimates emphasize the need for diverse conservation strategies. Conservation efforts should prioritize protecting natural regeneration and enhancing gene flow by actively promoting European yew, e.g., by shelterwood cutting, to ensure the long-term viability of T. baccata in the region outside the NP.

Patrilineal segmentary systems provide a peaceful explanation for the post-Neolithic Y-chromosome bottleneck

Studies have found a pronounced decline in male effective population sizes worldwide around 3000–5000 years ago. This bottleneck was not observed for female effective population sizes, which continued to increase over time. Until now, this remarkable genetic pattern was interpreted as the result of an ancient structuring of human populations into patrilineal groups (gathering closely related males) violently competing with each other. In this scenario, violence is responsible for the repeated extinctions of patrilineal groups, leading to a significant reduction in male effective population size. Here, we propose an alternative hypothesis by modelling a segmentary patrilineal system based on anthropological literature. We show that variance in reproductive success between patrilineal groups, combined with lineal fission (i.e., the splitting of a group into two new groups of patrilineally related individuals), can lead to a substantial reduction in the male effective population size without resorting to the violence hypothesis. Thus, a peaceful explanation involving ancient changes in social structures, linked to global changes in subsistence systems, may be sufficient to explain the reported decline in Y-chromosome diversity.