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Breeding systems vary widely in plants, but mostly cluster towards outbreeding or inbreeding extremes. Conifers, which are woody and generally long-lived perennials, are almost all classical outbreeders, but include occasional species characterised as inbreeders. The latter include some very narrow endemics, but narrow endemics include outbreeders. The inbreeders show high self-fertility, minimal inbreeding depression, typically low DNA polymorphism, and modest functional genetic variation, but self-fertilisation rates can be low. Seven such species are reviewed. It is widely (if often tacitly) assumed that inbreeders arise through severe population bottlenecks. It is proposed, more specifically, that inbreeders could arise through recessive resistance alleles of large effects being expressed, during biotic crises, through some inbreeding in the typically mixed mating systems of outbreeders. Such a crisis might produce not only a population bottleneck but also the conditions for recessive alleles to operate beneficially to make inbreeding advantageous. Avenues for probing the recessive-alleles hypothesis are: quantitative modelling to identify what are plausible conditions, examining genomic signatures of inbreeders, and empirical observation. Appropriate modelling appears challenging, as does seeking informative genomic signatures. Empirical observation, however, may be facilitated by biotic crises promoted by current global migration of pathogens and animal pests.

The evolution of selfing from outcrossing is a common transition, yet little is known about the mutations and selective factors that promote this shift. In the mustard family, single-locus self-incompatibility (SI) enforces outcrossing. In this study, we test whether mutations causing self-compatibility (SC) are linked to the self-incompatibility locus (S-locus) in Leavenworthia alabamica, a species where two selfing races (a2 and a4) co-occur with outcrossing populations. We also infer the ecological circumstances associated with origins of selfing using molecular sequence data. Genealogical reconstruction of the Lal2 locus, the putative ortholog of the SRK locus, showed that both selfing races are fixed for one of two different S-linked Lal2 sequences, whereas outcrossing populations harbor many S-alleles. Hybrid crosses demonstrated that S-linked mutations cause SC in each selfing race. These results strongly suggest two origins of selfing in this species, a result supported by population admixture analysis of 16 microsatellite loci and by a population tree built from eight nuclear loci. One selfing race (a4) shows signs of a severe population bottleneck, suggesting that reproductive assurance might have caused the evolution of selfing in this case. In contrast, the population size of race a2 cannot be distinguished from that of outcrossing populations after correcting for differences in selfing rates. Coalescent-based analyses suggest a relatively old origin of selfing in the a4 race (∼150 ka ago), whereas selfing evolved recently in the a2 race (∼12–48 ka ago). These results imply that S-locus mutations have triggered two recent shifts to selfing in L. alabamica, but that these transitions are not always associated with a severe population bottleneck, suggesting that factors other than reproductive assurance may play a role in its evolution.

Abstract Conservation genetic analyses of many endangered species have been based on genotyping of microsatellite loci and sequencing of short fragments of mtDNA. The increase in power and resolution afforded by whole genome approaches may challenge conclusions made on limited numbers of loci and maternally inherited haploid markers. Here, we provide a matched comparison of whole genome sequencing versus microsatellite and control region (CR) genotyping for Eurasian otters (Lutra lutra). Previous work identified four genetically differentiated “stronghold” populations of otter in Britain, derived from regional populations that survived the population crash of the 1950s–1980s. Using whole genome resequencing data from 45 samples from across the British stronghold populations, we confirmed some aspects of population structure derived from previous marker-driven studies. Importantly, we showed that genomic signals of the population crash bottlenecks matched evidence from otter population surveys. Unexpectedly, two strongly divergent mitochondrial lineages were identified that were undetectable using CR fragments, and otters in the east of England were genetically distinct and surprisingly variable. We hypothesize that this previously unsuspected variability may derive from past releases of Eurasian otters from other, non-British source populations in England around the time of the population bottleneck. Our work highlights that even reasonably well-studied species may harbor genetic surprises, if studied using modern high-throughput sequencing methods.

Staphylococcus aureus is a human commensal that can also cause systemic infections. This transition requires evasion of the immune response and the ability to exploit different niches within the host. However, the disease mechanisms and the dominant immune mediators against infection are poorly understood. Previously it has been shown that the infecting S. aureus population goes through a population bottleneck, from which very few bacteria escape to establish the abscesses that are characteristic of many infections. Here we examine the host factors underlying the population bottleneck and subsequent clonal expansion in S. aureus infection models, to identify underpinning principles of infection. The bottleneck is a common feature between models and is independent of S. aureus strain. Interestingly, the high doses of S. aureus required for the widely used \"survival\" model results in a reduced population bottleneck, suggesting that host defences have been simply overloaded. This brings into question the applicability of the survival model. Depletion of immune mediators revealed key breakpoints and the dynamics of systemic infection. Loss of macrophages, including the liver Kupffer cells, led to increased sensitivity to infection as expected but also loss of the population bottleneck and the spread to other organs still occurred. Conversely, neutrophil depletion led to greater susceptibility to disease but with a concomitant maintenance of the bottleneck and lack of systemic spread. We also used a novel microscopy approach to examine abscess architecture and distribution within organs. From these observations we developed a conceptual model for S. aureus disease from initial infection to mature abscess. This work highlights the need to understand the complexities of the infectious process to be able to assign functions for host and bacterial components, and why S. aureus disease requires a seemingly high infectious dose and how interventions such as a vaccine may be more rationally developed.

Genetic drift is expected to remove polymorphism from populations over long periods of time, with the rate of polymorphism loss being accelerated when species experience strong reductions in population size. Adaptive forces that maintain genetic variation in populations, or balancing selection, might counteract this process. To understand the extent to which natural selection can drive the retention of genetic diversity, we document genomic variability after two parallel species-wide bottlenecks in the genus Capsella. We find that ancestral variation preferentially persists at immunity related loci, and that the same collection of alleles has been maintained in different lineages that have been separated for several million years. By reconstructing the evolution of the disease-related locus MLO2b, we find that divergence between ancient haplotypes can be obscured by referenced based re-sequencing methods, and that trans-specific alleles can encode substantially diverged protein sequences. Our data point to long-term balancing selection as an important factor shaping the genetics of immune systems in plants and as the predominant driver of genomic variability after a population bottleneck. Capsella rubella is a small plant that is found in southern and western Europe. This plant is young in evolutionary terms: it is thought to have emerged less than 200,000 years ago from a small group of plants belonging to an older species known as Capsella grandiflora. Individuals of the same species may carry alternative versions of the same genes – known as alleles – and the total number of alleles present in a population is referred to as genetic diversity. When a few individuals form a new species, the gene pool and the genetic diversity in the new species is initially much lower than in the ancestral species, which may make the new species less robust to fluctuations in the environment. For example, alternative versions of a gene might be preferable in hot or cold climates, and loss of one of these versions would limit the species’ ability to survive in both climates. A mechanism known as balancing selection can maintain various alleles in a species, even if the population is very small. However, it was not clear how common long-lasting balancing selection was after a species had split. To address this question, Koenig et al. assembled collections of wild C. rubella and C. grandiflora plants and sequenced their genomes in search of alleles that were shared between individuals of the two species. The analysis found not just a few, but thousands of examples where the same genetic differences had been maintained in both C. rubella and C. grandiflora. Some of these allele pairs were also shared with individuals of a third species of Capsella that had split from C. rubella and C. grandiflora over a million years ago. The shared alleles did not occur randomly in the genome; genes involved in immune responses were far more likely to be targets of balancing selection than other types of genes. These findings indicate that there is strong balancing selection to maintain different alleles of immunity genes in wild populations of plants, and that some of this diversity can be maintained over hundreds of thousands, if not millions of years. The strategy developed by Koenig et al. may help to identify new versions of immunity genes from wild relatives of crop plants that could be used to combat crop diseases.

The relationship between population size, inbreeding, loss of genetic variation and evolutionary potential of fitness traits is still unresolved, and large-scale empirical studies testing theoretical expectations are surprisingly scarce. Here we present a highly replicated experimental evolution setup with 120 lines of Drosophila melanogaster having experienced inbreeding caused by low population size for a variable number of generations. Genetic variation in inbred lines and in outbred control lines was assessed by genotyping-by-sequencing (GBS) of pooled samples consisting of 15 males per line. All lines were reared on a novel stressful medium for 10 generations during which body mass, productivity, and extinctions were scored in each generation. In addition, we investigated egg-to-adult viability in the benign and the stressful environments before and after rearing at the stressful conditions for 10 generations. We found strong positive correlations between levels of genetic variation and evolutionary response in all investigated traits, and showed that genomic variation was more informative in predicting evolutionary responses than population history reflected by expected inbreeding levels. We also found that lines with lower genetic diversity were at greater risk of extinction. For viability, the results suggested a trade-off in the costs of adapting to the stressful environments when tested in a benign environment. This work presents convincing support for long-standing evolutionary theory, and it provides novel insights into the association between genetic variation and evolutionary capacity in a gradient of diversity rather than dichotomous inbred/outbred groups.

Identifying causal factors for Mendelian and common diseases is an ongoing challenge in medical genetics 1 . Population bottleneck events, such as those that occurred in the history of the Finnish population, enrich some homozygous variants to higher frequencies, which facilitates the identification of variants that cause diseases with recessive inheritance 2 , 3 . Here we examine the homozygous and heterozygous effects of 44,370 coding variants on 2,444 disease phenotypes using data from the nationwide electronic health records of 176,899 Finnish individuals. We find associations for homozygous genotypes across a broad spectrum of phenotypes, including known associations with retinal dystrophy and novel associations with adult-onset cataract and female infertility. Of the recessive disease associations that we identify, 13 out of 20 would have been missed by the additive model that is typically used in genome-wide association studies. We use these results to find many known Mendelian variants whose inheritance cannot be adequately described by a conventional definition of dominant or recessive. In particular, we find variants that are known to cause diseases with recessive inheritance with significant heterozygous phenotypic effects. Similarly, we find presumed benign variants with disease effects. Our results show how biobanks, particularly in founder populations, can broaden our understanding of complex dosage effects of Mendelian variants on disease. An analysis of biobank data from the FinnGen project examines dosage effects of genetic variants on disease, andidentifies a benefit when considering more complex inheritance in the genetics of common as well as Mendelian diseases.

Rapa Nui (also known as Easter Island) is one of the most isolated inhabited places in the world. It has captured the imagination of many owing to its archaeological record, which includes iconic megalithic statues called moai1. Two prominent contentions have arisen from the extensive study of Rapa Nui. First, the history of the Rapanui has been presented as a warning tale of resource overexploitation that would have culminated in a major population collapse-the 'ecocide' theory2 4. Second, the possibility of trans-Pacific voyages to the Americas pre-dating European contact is still debated5 7. Here, to address these questions, we reconstructed the genomic history of the Rapanui on the basis of 15 ancient Rapanui individuals that we radiocarbon dated (1670-1950 ce) and whole-genome sequenced (0.4-25.6x). We find that these individuals are Polynesian in origin and most closely related to present-day Rapanui, a finding that will contribute to repatriation efforts. Through effective population size reconstructions and extensive population genetics simulations, we reject a scenario involving a severe population bottleneck during the 1600s, as proposed by the ecocide theory. Furthermore, the ancient and present-day Rapanui carry similar proportions of Native American admixture (about 10%). Using a Bayesian approach integrating genetic and radiocarbon dates, we estimate that this admixture event occurred about 1250-1430 ce.

Demographic change lies at the core of debates on genetic inheritance and resilience to climate change of prehistoric hunter-gatherers. Here we analyze the radiocarbon record of Iberia to reconstruct long-term changes in population levels and test different models of demographic growth during the Last Glacial-Interglacial transition. Our best fitting demographic model is composed of three phases. First, we document a regime of exponential population increase during the Late Glacial warming period (c.16.6-12.9 kya). Second, we identify a phase of sustained population contraction and stagnation, beginning with the cold episode of the Younger Dryas and continuing through the first half of the Early Holocene (12.9-10.2 kya). Finally, we report a third phase of density-dependent logistic growth (10.2-8 kya), with rapid population increase followed by stabilization. Our results support a population bottleneck hypothesis during the Last Glacial-Interglacial transition, providing a demographic context to interpret major shifts of prehistoric genetic groups in south-west Europe. The archaeological record provides large ensembles of radiocarbon dates which can be used to infer long-term changes in human demography. Here, the authors analyse the radiocarbon record of the Iberian peninsula, finding support for a bottleneck during the Last Glacial-Interglacial transition