Strong Bottleneck Research Articles

On the origins of the Sakhas' paternal lineages: Reconciliation of population genetic / ancient DNA data, archaeological findings and historical narratives

Sakhas are Turkic-speaking people from Northeastern Siberia, constituting the largest ethnic population in Yakutia. According to popular legends, two heroes who arrived from the Asian Steppe during the late medieval ages, namely Elley Bootur and Omogoy Baay, are the progenitors of all Sakhas. While there is ample historical evidence towards the existence of such legendary characters, archaeological findings and ancient DNA studies provide further insights on actual Sakha ethnogenesis. This study aims to establish the genetic basis of the legendary characters Elley and Omogoy, at least through their paternal lineages, and then to reveal the prevalence of these Y-chromosomes among the contemporary Yakut population. To this end, an attempt was made to delineate fact from fiction with respect to the Sakhas’ paternal lineages through a reconciliation of population genetics data on contemporary and ancient Sakhas, along with archaeological evidence and well-recorded historical narratives. To achieve this, 17-loci Y-chromosomal STR and haplogroup analyses were conducted on a contemporary Sakha who was presumably a direct descendant of Elley’s paternal line. Furthermore, 367 Sakha Y-chromosomal STR haplotypes were compiled from the literature and elsewhere, and searched against the Y-chromosome STR Haplotype Reference Database to find potential matches with non-Sakha populations. Sakhas’ paternal lineages were found to comprise 6 major descent clusters, each corresponding to an ancient clan. The most prevalent haplotype indeed corresponded to that of the contemporary Elley descendant. Furthermore, data presented in the current work suggests a Khitan origin for this paternal line. As shown before, Sakhas’ paternal lineages were found to be very homogenous and exhibit signs of a strong population bottleneck. Reconciled genetic and archaeological data agree well with Sakhas’ historical narratives, whereby, at least from a paternal lineage perspective, only a few individuals may have arrived from Central Asia and had reproductive success that led to the Sakha Y-chromosomal diversity today.

Coalescent models characterize sources and demographic history of recent round goby colonization of Great Lakes and inland waters.

The establishment and spread of aquatic invasive species are ecologically and economically harmful and a source of conservation concern internationally. Processes of species invasion have traditionally been inferred from observational data of species presence/absence and relative abundance. However, genetic‐based approaches can provide valuable sources of inference. Restriction site‐associated DNA sequencing was used to identify and genotype single nucleotide polymorphism (SNP) loci for Round Gobies (Neogobius melanostomus) (N = 440) from 18 sampling locations in the Great Lakes and in three Michigan, USA, drainages (Flint, Au Sable, and Cheboygan River basins). Sampled rivers differed in size, accessibility, and physical characteristics including man‐made dispersal barriers. Population levels of genetic diversity and interpopulation variance in SNP allele frequency were used in coalescence‐based approximate Bayesian computation (ABC) to statistically compare models representing competing hypotheses regarding source population, postcolonization dispersal, and demographic history in the Great Lakes and inland waters. Results indicate different patterns of colonization across the three drainages. In the Flint River, models indicate a strong population bottleneck (<3% of contemporary effective population size) and a single founding event from Saginaw Bay led to the colonization of inland river segments. In the Au Sable River, analyses could not distinguish potential source populations, but supported models indicated multiple introductions from one source population. In the Cheboygan River, supported models indicated that colonization likely proceeded from east (Lake Huron source) to west among inland locales sampled in the system. Despite the recent occupancy of Great Lakes and inland habitats, large numbers of loci analyzed in an ABC framework enable statistically supported identification of source populations and reconstruction of the direction of inland spread and demographic history following establishment. Information from analyses can direct management actions to limit the spread of invasive species from identified sources and most probable vectors into additional inland aquatic habitats.

Long-term sky islands generate highly divergent lineages of a narrowly distributed stream salamander (Pachyhynobius shangchengensis) in mid-latitude mountains of East Asia

BackgroundClimate oscillation may have a profound effect on species distributions, gene flow patterns and population demography. In response to environmental change, those species restricted to montane habitats experienced expansions and contractions along elevation gradients, which can drive differentiation among sky islands.ResultsThe Shangcheng stout salamander (Pachyhynobius shangchengensis) is a cool stream amphibian restricted to high-elevation areas in the Dabie Mountains, East China. In the present study, we used mtDNA genes (Cyt b and ND2) of 193 individuals and 12 nuclear microsatellite loci genotyped on 370 individuals, representing 6 populations (JTX, KHJ, MW, TTZ, BYM and KJY) across the taxon’s distribution area, to investigate their genetic variation and evolutionary history of P. shangchengensis. Most populations showed unusually high levels of genetic diversity. Phylogenetic analyses revealed five monophyletic clades with divergence times ranging from 3.96 to 1.4 Mya. Accordingly, significant genetic differentiation was present between these populations. Bayesian skyline plot analyses provided that all populations underwent long-term population expansions since the last inter-glacial (0.13 Mya ~ 0.12 Mya). Msvar analyses found recent signals of population decline for two northern populations (JTX and KHJ) reflecting a strong bottleneck (approximately 15-fold decrease) during the mid-Holocene (about 6000 years ago). Ecological niche modelling has shown a discontinuity in suitable habitats for P. shangchengensis under different historical climatic conditions.ConclusionsOur results suggest that the niche conservatism of P. shangchengensis and sky island effects may have led to long-term isolation between populations. In sky island refuges, the mid-latitude Dabie Mountains have provided a long-term stable environment for P. shangchengensis, which has led to the accumulation of genetic diversity and has promoted genetic divergence.

Genetic rescue and the maintenance of native ancestry

Genetic rescue (GR) is an important tool in conservation biology for the management of highly inbred populations. However, GR comes at a potential cost: the reduction in native genomic content. The degree to which adaptive evolution for new immigrant alleles lead to complete or partial replacement of the native genome, depends on recombination rates, genome size, effective population sizes, and distributions of fitness effects. As one of the most well-studied examples of an inbred species that exchanged genetic material with a less inbred species, we use Neanderthals and humans as an example. Using simulations, we show that for parameters realistic for these species, the increase in fitness caused by GR is mirrored by an almost proportional reduction in the fraction of the native genome preserved. The main reason is that the effect of selection will be strongest in the first few generations during which time there is only little break-up, by recombination, of the immigrant chromosomes. We also show that in the presence of a strong and short-lived bottleneck with recessive mutations, GR leads to a stronger increase in fitness than in the presence of additive effects or a more prolonged bottleneck.

Gene pool sharing and genetic bottleneck effects in subpopulations of Eschweilera ovata (Cambess.) Mart. ex Miers (Lecythidaceae) in the Atlantic Forest of southern Bahia, Brazil.

Forest loss and fragmentation are the main threats to the maintenance of the Atlantic Forest, an important global biodiversity hotspot. Because of the current critical level of deforestation, ecological corridors are needed to facilitate species dispersion and gene flow among fragments. This study was conducted to investigate the genetic variability and gene pool sharing of Eschweilera ovata in five forest remnants in southern Bahia, Brazil using nuclear simple sequence repeat (nSSR) and plastid simple sequence repeat (cpSSR) microsatellite markers. cpSSR marker analysis revealed the domains of four haplotypes, showing that 80% of the individuals had only four maternal origins, reflecting a founder effect and/or genetic bottleneck. The results of cpSSR and nSSR analyses indicated moderate genetic diversity, particularly in conservation units with full protection, which showed the best parameters of all areas evaluated. Another indication of the susceptibility of these populations to forest loss and fragmentation was the strong genetic bottleneck observed. In contrast, genetic structure analyses (FST and discriminant analysis of principal components) revealed gene pool sharing between the subpopulations, which may reflect the historical gene flow that occurred before forest fragmentation.

Conservation genetics of a resident population of Greylag Goose (Anser anser) at the southernmost limit of the species\u2019 distribution in Europe

BackgroundConservation of small and isolated populations can be challenging since they are prone to loss of genetic diversity due to random genetic drift and inbreeding. Therefore, information from the assessment of genetic diversity and structure are needed for conservation programs to determine the appropriate management strategy for the populations. We investigated the levels of genetic variability in a resident Greylag Goose (Anser anser) population, the southernmost breeding population of the species in Europe and the sole viable population of any goose species in Greece.MethodsA fragment of mtDNA Control Region and a panel of 11 microsatellite markers were used to search for any signs of genetic impoverishment and population substructure and to reveal the underlying processes through the identification of possible past demographic events.ResultsThe population was found to be monomorphic in the amplified fragment of the mitochondrial Control Region, with all individuals sharing a single private haplotype. Analyses showed a lack of any population substructure indicating a panmictic population. Although the population seems to have experienced a strong and recent genetic bottleneck and exhibits a small effective population size, we did not find evidence of either extremely low levels of genetic diversity or inbreeding depression.ConclusionsThe recent demographic decline we detected and the combined influence of residency and anthropogenic factors have probably shaped the current genetic status. Our study population does not need emergency conservation actions but should be regarded as a discrete management unit. Future management strategies should focus on population and genetic monitoring and preventing further abundance declines that would increase the risk of genetic impoverishment.

414. The role of low-frequency variants in pre-eclampsia: Recent findings in a Finnish population

The genetic basis of pre-eclampsia and its link with increased lifetime risk of cardiovascular diseases in women with a history of pre-eclampsia and children born from pre-eclamptic pregnancies are incompletely understood. Genetic factors have been shown to account for 55% of the liability of pre-eclampsia with 35% attributed to the maternal genetic effects and 20% to the fetal genetic effects (Cnattingius et al. Am J Med Genet 2004). Genome-wide association screening in offspring from pre-eclamptic pregnancies performed by a collaboration between research groups has already proven a successful approach in finding a common sequence variant near the fms related tyrosine kinase gene (FLT1) associated with pre-eclampsia (McGinnis et al. Nat Genet 2017). The sequencing approach enables identification of both common and rare variants, but is challenging in common complex disorders like pre-eclampsia. An isolated population may offer a major advantage for genetic discovery. In Finland a strong founding bottleneck has been shown to cause enrichment of some low-frequency variants (Lim et al. PLOS Genet 2014). Centrally collected registers with lifelong medical histories can be used together with genetic data to better understand diseases associated with pre-eclampsia. We designed a targeted sequencing study to screen the coding and splicing areas of genes of interest in pre-eclampsia and found maternal low-frequency variants in FLT1 which may protect from pre-eclampsia (Lokki et al. Hypertension 2017). Using data from health registers we found that the same variants may also protect from heart failure later in life. Future studies are needed to improve our understanding of the genetic background pre-eclampsia and its links to other diseases. Any new gene discovery will highlight a known pathway or reveal a new biochemical pathway in the pathogenic process leading to pre-eclampsia and may also help in prediction and in identifying individuals with higher risk for later cardiovascular disease.

Genetic connectivity and phylogeography of the night shark (Carcharhinus signatus) in the western Atlantic Ocean: Implications for conservation management

Abstract The night shark, Carcharhinus signatus, is a mesopelagic, semi‐oceanic shark species found only in the Atlantic Ocean. It is one of the most frequently caught sharks in pelagic longline fisheries and is classified as Vulnerable by the International Union for the Conservation of Nature (IUCN). Despite their prevalence in commercial fisheries, the population genetic structure of the night shark has not been assessed. The present study investigated the genetic diversity, genetic connectivity, and phylogeography of the species throughout the western Atlantic Ocean, based on complete mitochondrial control region (mtCR) sequence data (n = 152) and genotypic data from nine nuclear microsatellites (n = 119). The mtCR sequence revealed 19 haplotypes, with overall haplotype and nucleotide diversities of 0.74 (±0.027) and 0.0034 (±0.0019), respectively, whereas the nuclear microsatellite observed and expected heterozygosities were 0.408 and 0.421, respectively. There was significant population structure (ФST = 0.429; P &lt; 0.01) and isolation by distance (r = 0.65, P = 0.03) based on mtCR sequence data, but no genetic differentiation based on nuclear microsatellite analyses. The phylogenetic analyses support the existence of two matrilineal lineages, which diverged during the Pleistocene. Mitochondrial demographic analyses indicated a historical bottleneck effect followed by population expansion during the Pleistocene, whereas nuclear microsatellites did not detect a recent or a strong bottleneck. For conservation purposes, we advocate that the species should be considered to comprise at least two management units (MUs) in the western Atlantic Ocean. MU‐specific catch quotas should be implemented throughout the range of the species given its low genetic diversity and vulnerability to overexploitation.

RAD Sequencing and a Hybrid Antarctic Fur Seal Genome Assembly Reveal Rapidly Decaying Linkage Disequilibrium, Global Population Structure and Evidence for Inbreeding.

Recent advances in high throughput sequencing have transformed the study of wild organisms by facilitating the generation of high quality genome assemblies and dense genetic marker datasets. These resources have the potential to significantly advance our understanding of diverse phenomena at the level of species, populations and individuals, ranging from patterns of synteny through rates of linkage disequilibrium (LD) decay and population structure to individual inbreeding. Consequently, we used PacBio sequencing to refine an existing Antarctic fur seal (Arctocephalus gazella) genome assembly and genotyped 83 individuals from six populations using restriction site associated DNA (RAD) sequencing. The resulting hybrid genome comprised 6,169 scaffolds with an N50 of 6.21 Mb and provided clear evidence for the conservation of large chromosomal segments between the fur seal and dog (Canis lupus familiaris). Focusing on the most extensively sampled population of South Georgia, we found that LD decayed rapidly, reaching the background level by around 400 kb, consistent with other vertebrates but at odds with the notion that fur seals experienced a strong historical bottleneck. We also found evidence for population structuring, with four main Antarctic island groups being resolved. Finally, appreciable variance in individual inbreeding could be detected, reflecting the strong polygyny and site fidelity of the species. Overall, our study contributes important resources for future genomic studies of fur seals and other pinnipeds while also providing a clear example of how high throughput sequencing can generate diverse biological insights at multiple levels of organization.

Comparing genetic diversity and demographic history in co-distributed wild South American camelids.

Vicuñas and guanacos are two species of wild South American camelids that are key ruminants in the ecosystems where they occur. Although closely related, these species feature differing ecologies and life history characters, which are expected to influence both their genetic diversity and population differentiation at different spatial scales. Here, using mitochondrial and microsatellite genetic markers, we show that vicuña display lower genetic diversity within populations than guanaco but exhibit more structure across their Peruvian range, which may reflect a combination of natural genetic differentiation linked to geographic isolation and recent anthropogenic population declines. Coalescent-based demographic analyses indicate that both species have passed through a strong bottleneck, reducing their effective population sizes from over 20,000 to less than 1000 individuals. For vicuña, this bottleneck is inferred to have taken place ~3300 years ago, but to have occurred more recently for guanaco at ~2000 years ago. These inferred dates are considerably later than the onset of domestication (when the alpaca was domesticated from the vicuña while the llama was domesticated from the guanaco), coinciding instead with a major human population expansion following the mid-Holocene cold period. As importantly, they imply earlier declines than the well-documented Spanish conquest, where major mass mortality events were recorded for Andean human and camelid populations. We argue that underlying species' differences and recent demographic perturbations have influenced genetic diversity in modern vicuña and guanaco populations, and these processes should be carefully evaluated in the development and implementation of management strategies for these important genetic resources.

Assessment of pedigree information in the Quarter Horse: Population, breeding and genetic diversity

This study aimed to evaluate population parameters and to describe the genetic diversity of Quarter Horse breed (QH) in Brazil, reported for the first time in the literature. The pedigree data comprised 131,716 animals representing the total population (TP), with records of animals born between 1747 and 2008. The reference population (RP) representing the last generation was applied in this study considering 47,861 animals born between 2000 and 2008. The average generation interval was 9.6 and 10.8 years in TP and RP, respectively. The average equivalent complete generations (EG) were 5.09 (TP) and 6.24 (RP). The inbreeding coefficient (F), average relatedness (AR) and the increase in inbreeding by generation (ΔF) was 1.07%, 0.95% and 0.24%, respectively, for TP. The effective population size (Ne) based on ΔF was 195 and 164 for TP and RP, respectively. The effective number of founders (fe) was 1045 and 811 for TP and RP, respectively, that of ancestors (fa) was 156 and 113, and that of founder genomes (fg) was 105 and 66. The fe/fa and fe/fg ratios in TP were 6.70 and 9.95, respectively, and an increase was observed in RP, indicated a strong bottleneck effect. The total genetic diversity of the QH breed was explained by 4780 ancestors, with 50% of diversity being explained by only 121 and 72 ancestors in TP and RP, respectively. The thoroughbred stallion Three Bars is the most influential ancestor with the largest marginal genetic contribution for TP (5.73) and RP (5.94%). The results demonstrate a large number of founders and ancestors, but a small ancestor group was responsible for the continuity of the QH breed in Brazil. These finding highlight the importance of monitoring genetic diversity, including follow-up by breeding programs, to permit control of the next generations.

Reactive transport under stress: Permeability evolution in deformable porous media

We study reactive transport in a stressed porous media, where dissolution of the solid matrix causes two simultaneous, competing effects: pore enlargement due to chemical deformation, and pore compaction due to mechanical weakening. We use a novel, mechanistic pore-scale model to simulate flooding of a sample under fixed confining stress. Our simulations show that increasing the stress inhibits the permeability enhancement, increasing the injected volume required to reach a certain permeability, in agreement with recent experiments. We explain this behavior by stress concentration downstream, in the less dissolved (hence stiffer) outlet region. As this region is also less conductive, even its small compaction has a strong bottleneck effect that curbs the permeability.Our results also elucidate that the impact of stress depends on the dissolution regime. Under wormholing conditions (slow injection, i.e. high Damkohler number, Da), the development of a sharp dissolution front and high porosity contrast accentuates the bottleneck effect. This reduces transport heterogeneity, promoting wormhole competition. Once the outlet starts eroding, the extreme focusing of transport and hence dissolution—characteristic of wormholing—becomes dominant, diminishing the bottleneck effect and hence the impact of stress at breakthrough. In contrast, at high flow rates (low Da), incomplete reaction upstream allows some of the reactant to traverse the sample, causing a more uniform dissolution. The continuous dissolution and its partial counteraction by compaction at the outlet provides a steady, gradual increase in the effect of stress. Consequently, the impact of stress is more pronounced at high Da during early stages (low permeability), and at low Da close breakthrough. Our work promotes understanding of the interplay between dissolution and compaction and its effect on the hydromechanical property evolution, with important implications for processes ranging from diagenesis and weathering of rocks, to well stimulation and carbon sequestration.

The ash dieback invasion of Europe was founded by two genetically divergent individuals

Accelerating international trade and climate change make pathogen spread an increasing concern. Hymenoscyphus fraxineus, the causal agent of ash dieback, is a fungal pathogen that has been moving across continents and hosts from Asian to European ash. Most European common ash trees (Fraxinus excelsior) are highly susceptible to H. fraxineus, although a minority (~5%) have partial resistance to dieback. Here, we assemble and annotate a H. fraxineus draft genome, which approaches chromosome scale. Pathogen genetic diversity across Europe and in Japan, reveals a strong bottleneck in Europe, though a signal of adaptive diversity remains in key host interaction genes. We find that the European population was founded by two divergent haploid individuals. Divergence between these haplotypes represents the ancestral polymorphism within a large source population. Subsequent introduction from this source would greatly increase adaptive potential of the pathogen. Thus, further introgression of H. fraxineus into Europe represents a potential threat and Europe-wide biological security measures are needed to manage this disease.

In-depth genome analyses of viruses from vaccine-derived rabies cases and corresponding live-attenuated oral rabies vaccines

Live-attenuated rabies virus strains such as those derived from the field isolate Street Alabama Dufferin (SAD) have been used extensively and very effectively as oral rabies vaccines for the control of fox rabies in both Europe and Canada. Although these vaccines are safe, some cases of vaccine-derived rabies have been detected during rabies surveillance accompanying these campaigns. In recent analysis it was shown that some commercial SAD vaccines consist of diverse viral populations, rather than clonal genotypes. For cases of vaccine-derived rabies, only consensus sequence data have been available to date and information concerning their population diversity was thus lacking.In our study, we used high-throughput sequencing to analyze 11 cases of vaccine-derived rabies, and compared their viral population diversity to the related oral rabies vaccines using pairwise Manhattan distances. This extensive deep sequencing analysis of vaccine-derived rabies cases observed during oral vaccination programs provided deeper insights into the effect of accidental in vivo replication of genetically diverse vaccine strains in the central nervous system of target and non-target species under field conditions. The viral population in vaccine-derived cases appeared to be clonal in contrast to their parental vaccines. The change from a state of high population diversity present in the vaccine batches to a clonal genotype in the affected animal may indicate the presence of a strong bottleneck during infection. In conclusion, it is very likely that these few cases are the consequence of host factors and not the result of the selection of a more virulent genotype. Furthermore, this type of vaccine-derived rabies leads to the selection of clonal genotypes and the selected variants were genetically very similar to potent SAD vaccines that have undergone a history of in vitro selection.

Biases of STRUCTURE software when exploring introduction routes of invasive species.

Population genetic methods are widely used to retrace the introduction routes of invasive species. The unsupervised Bayesian clustering algorithm implemented in STRUCTURE is amongst the most frequently used of these methods, but its ability to provide reliable information about introduction routes has never been assessed. We simulated microsatellite datasets to evaluate the extent to which the results provided by STRUCTURE were misleading for the inference of introduction routes. We focused on an invasion scenario involving one native and two independently introduced populations, because it is the sole scenario that can be rejected when obtaining a particular clustering with a STRUCTURE analysis at K = 2 (two clusters). Results were classified as "misleading" or "non-misleading". We investigated the influence of effective size, bottleneck severity and number of loci on the type and frequency of misleading results. We showed that misleading STRUCTURE results were obtained for 10% of all simulated datasets. Our results highlighted two categories of misleading output. The first occurs when the native population has a low level of diversity. In this case, the two introduced populations may be very similar, despite their independent introduction histories. The second category results from convergence issues in STRUCTURE for K = 2, with strong bottleneck severity and/or large numbers of loci resulting in high levels of differentiation between the three populations. Overall, the risk of being misled by STRUCTURE in the context of introduction routes inferences is moderate, but it is important to remain cautious when low genetic diversity or genuine multimodality between runs are involved.

Strong population bottleneck and repeated demographic expansions of Populus adenopoda (Salicaceae) in subtropical China.

Glacial refugia and inter-/postglacial recolonization routes during the Quaternary of tree species in Europe and North America are well understood, but far less is known about those of tree species in subtropical eastern Asia. Thus, we have examined the phylogeographic history of Populus adenopoda (Salicaceae), one of the few poplars that naturally occur in this subtropical area. Genetic variations across the range of the species in subtropical China were surveyed using ten nuclear microsatellite loci and four chloroplast fragments (matK, trnG-psbK, psbK-psbI and ndhC-trnV). Coalescent-based analyses were used to test demographic and migration hypotheses. In addition, species distribution models (SDMs) were constructed to infer past, present and future potential distributions of the species. Thirteen chloroplast haplotypes were detected, and haplotype-rich populations were found in central and southern parts of the species' range. STRUCTURE analyses of nuclear microsatellite loci suggest obvious lineage admixture, especially in peripheral and northern populations. DIYABC analysis suggests that the species might have experienced two independent rounds of demographic expansions and a strong bottleneck in the late Quaternary. SDMs indicate that the species' range contracted during the Last Glacial Maximum (LGM), and contracted northward but expanded eastward during the Last Interglacial (LIG). Chloroplast data and SDMs suggest that P. adenopoda might have survived in multiple glacial refugia in central and southern parts of its range during the LGM. Populations of the Yunnan-Guizhou Plateau in the southern part have high chloroplast DNA diversity, but may have contributed little to the postglacial recolonization of northern and eastern parts. The three major demographic events inferred by DIYABC coincide with the initiation of the LIG, start of the LGM and end of the LGM, respectively. The species may have experienced multiple rounds of range contraction during glacial periods and range expansion during interglacial periods. Our study corroborates the importance of combining multiple lines of evidence when reconstructing Quaternary population evolutionary histories.

Elevated Proportions of Deleterious Genetic Variation in Domestic Animals and Plants.

A fraction of genetic variants segregating in any population are deleterious, which negatively impacts individual fitness. The domestication of animals and plants is associated with population bottlenecks and artificial selection, which are predicted to increase the proportion of deleterious variants. However, the extent to which this is a general feature of domestic species is unclear. Here, we examine the effects of domestication on the prevalence of deleterious variation using pooled whole-genome resequencing data from five domestic animal species (dog, pig, rabbit, chicken, and silkworm) and two domestic plant species (rice and soybean) compared with their wild ancestors. We find significantly reduced genetic variation and increased proportion of nonsynonymous amino acid changes in all but one of the domestic species. These differences are observable across a range of allele frequencies, both common and rare. We find proportionally more single nucleotide polymorphisms in highly conserved elements in domestic species and a tendency for domestic species to harbor a higher proportion of changes classified as damaging. Our findings most likely reflect an increased incidence of deleterious variants in domestic species, which is most likely attributable to population bottlenecks that lead to a reduction in the efficacy of selection. An exception to this pattern is displayed by European domestic pigs, which do not show traces of a strong population bottleneck and probably continued to exchange genes with wild boar populations after domestication. The results presented here indicate that an elevated proportion of deleterious variants is a common, but not ubiquitous, feature of domestic species.

Heterozygosity-fitness correlation at the major histocompatibility complex despite low variation in Alpine ibex (Capra ibex).

Crucial for the long‐term survival of wild populations is their ability to fight diseases. Disease outbreaks can lead to severe population size reductions, which makes endangered and reintroduced species especially vulnerable. In vertebrates, the major histocompatibility complex (MHC) plays an important role in determining the immune response. Species that went through severe bottlenecks often show very low levels of genetic diversity at the MHC. Due to the known link between the MHC and immune response, such species are expected to be at particular risk in case of disease outbreaks. However, so far, only few studies have shown that low MHC diversity is correlated with increased disease susceptibility in species after severe bottlenecks. We investigated genetic variation at the MHC and its correlations with disease resistance and other fitness‐related traits in Alpine ibex (Capra ibex), a wild goat species that underwent a strong bottleneck in the last century and that is known to have extremely low genetic variability, both genome‐wide and at the MHC. We studied MHC variation in male ibex of Gran Paradiso National Park, the population used as a source for all postbottleneck reintroductions. We found that individual MHC heterozygosity (based on six microsatellites) was not correlated with genome‐wide neutral heterozygosity. MHC heterozygosity, but not genome‐wide heterozygosity, was positively correlated with resistance to infectious keratoconjunctivitis and with body mass. Our results show that genetic variation at the MHC plays an important role in disease resistance and, hence, should be taken into account for successfully managing species conservation.

Evolutionary genomics of grape (Vitis vinifera ssp. vinifera) domestication

We gathered genomic data from grapes (Vitis vinifera ssp. vinifera), a clonally propagated perennial crop, to address three ongoing mysteries about plant domestication. The first is the duration of domestication; archaeological evidence suggests that domestication occurs over millennia, but genetic evidence indicates that it can occur rapidly. We estimated that our wild and cultivated grape samples diverged ∼22,000 years ago and that the cultivated lineage experienced a steady decline in population size (Ne ) thereafter. The long decline may reflect low-intensity management by humans before domestication. The second mystery is the identification of genes that contribute to domestication phenotypes. In cultivated grapes, we identified candidate-selected genes that function in sugar metabolism, flower development, and stress responses. In contrast, candidate-selected genes in the wild sample were limited to abiotic and biotic stress responses. A genomic region of high divergence corresponded to the sex determination region and included a candidate male sterility factor and additional genes with sex-specific expression. The third mystery concerns the cost of domestication. Annual crops accumulate putatively deleterious variants, in part due to strong domestication bottlenecks. The domestication of perennial crops differs from that of annuals in several ways, including the intensity of bottlenecks, and it is not yet clear if they accumulate deleterious variants. We found that grape accessions contained 5.2% more deleterious variants than wild individuals, and these were more often in a heterozygous state. Using forward simulations, we confirm that clonal propagation leads to the accumulation of recessive deleterious mutations but without decreasing fitness.

Hidden founders? Strong bottlenecks and fine-scale genetic structure in mangrove populations of the Cameroon Estuary complex

Fine-scale genetic structure (FSGS) is common in plants, driven by several ecological and evolutionary processes, among which is gene flow. Mangrove trees rely on ocean surface currents to spread their hydrochorous propagules through space. Since pollen dispersal is generally restricted to local scales, high level of short-distance propagule dispersal is expected to result in FSGS in Rhizophora spp. We investigated FSGS, recent bottleneck events, as well as historical and contemporary expansion patterns in Rhizophora racemosa populations from the entire coast of Cameroon, using 11 polymorphic microsatellite markers. Populations of the Cameroon Estuary complex (CEC) showed significant FSGS and significant reduction in effective population sizes (recent bottlenecks), compared to the other areas. Additionally, our results indicate stark differences between historical and contemporary expansion models. These suggest that contemporary processes such as restricted propagule dispersal, bottleneck events from high indirect and direct anthropogenic pressure, and recolonization by founders from ancient local pockets/refugia most plausibly shape the patterns of FSGS in the CEC.