Analyses of Wheat Yellow Rust Populations Reveal Sexual Recombination and Seasonal Migration Pattern of Puccinia striiformis f. sp. tritici in Gangu, Northwestern China

Puccinia striiformis f. sp. tritici is the causal agent of wheat yellow rust with records of regular and severe epidemics in China. This study explored the population dynamics of the yellow rust pathogen in Gangu, northwestern China. In Gangu, the Weihe River runs from west to east and divides Gangu into three regions: North and South mountain, with the valley in between. To study the genetic structure of the pathogen in local populations, samples were collected over 3 years from the three regions at different altitudes both within and between the wheat cropping seasons. A total of 811 P. striiformis f. sp. tritici isolates were successfully genotyped using 16 simple sequence repeat markers. The results suggest that P. striiformis f. sp. tritici can survive year-round in Gangu. The P. striiformis f. sp. tritici populations migrated among the regions, and the migration pattern was not related to altitude. The oversummering populations in the North and South mountain regions were genetically different from each other; and the P. striiformis f. sp. tritici populations collected from the lower altitude in the valley had no relationship with any of the populations collected in the spring or fall, indicating that they too have a different origin. Signatures of random mating were found in the populations collected in both North and South mountain regions, but not in the valley populations.

The role of sexual isolation during rapid ecological divergence: evidence for a new dimension of isolation in Rhagoletis pomonella

The pace of divergence and likelihood of complete speciation may depend how and when different types of reproductive barriers evolve. After initial reproductive barriers evolve, questions remain about how subsequently evolving barriers may facilitate additional divergence and potential speciation. We tested for the presence of sexual isolation (reduced mating between populations due to divergent mating preferences and traits) in Rhagoletis pomonella flies, a model system for incipient ecological speciation. We measured the strength of sexual isolation between two very recently diverged (~170 years) sympatric populations, adapted to different host fruits. We found that sexual isolation was significantly stronger than expectations of random mating. Thus, sexual isolation may play an important role in reducing gene flow allowed by earlier-acting ecological barriers. We also found that sexual isolation was markedly asymmetric between the sexes of each population. Lastly, we tested how warmer temperatures predicted under climate change could alter sexual isolation and found that mating interactions were sensitive to temperature experienced during development. Our findings provide a window into the early divergence process and the role of sexual isolation after initial ecological divergence, in addition to examining multiple factors that could shape the likelihood of further divergence.

Gene drives and population persistence vs elimination: the impact of spatial structure and inbreeding at low density

Synthetic gene drive constructs are being developed to control disease vectors, invasive species, and other pest species. In a well-mixed random mating population a sufficiently strong gene drive is expected to eliminate a target population, but it is not clear whether the same is true when spatial processes play a role. In species with an appropriate biology it is possible that drive-induced reductions in density might lead to increased inbreeding, reducing the efficacy of drive, eventually leading to suppression rather than elimination, regardless of how strong the drive is. To investigate this question we analyse a series of explicitly solvable stochastic models considering a range of scenarios for the relative timing of mating, reproduction, and dispersal and analyse the impact of two different types of gene drive, a Driving Y chromosome and a homing construct targeting an essential gene. We find in all cases a sufficiently strong Driving Y will go to fixation and the population will be eliminated, except in the one life history scenario (reproduction and mating in patches followed by dispersal) where low density leads to increased inbreeding, in which case the population persists indefinitely, tending to either a stable equilibrium or a limit cycle. These dynamics arise because Driving Y males have reduced mating success, particularly at low densities, due to having fewer sisters to mate with. Increased inbreeding at low densities can also prevent a homing construct from eliminating a population. For both types of drive, if there is strong inbreeding depression, then the population cannot be rescued by inbreeding and it is eliminated. These results highlight the potentially critical role that low-density-induced inbreeding and inbreeding depression (and, by extension, other sources of Allee effects) can have on the eventual impact of a gene drive on a target population.

Hopping or Jumping on the Cliffs: The Unusual Phylogeographical and Demographic Structure of an Extremely Narrow Endemic Mediterranean Plant

Several past and recent climatic and geological events have greatly influenced the current distribution of coastal species around the Mediterranean Basin. As a consequence, the reconstruction of the distributional history of these species is challenging. In this study, we used both chloroplast and nuclear SNPs to assess the levels of genetic differentiation, contemporary/historical levels of gene flow, and demographic history for the three only known (one mainland and two insular) populations of Eokochia saxicola, a rare Mediterranean coastal rocky halophyte. Plastid genome analysis revealed very low intraspecific haplotype variation and partial admixture among Capri and Palinuro populations with at least two independent colonization events for the Strombolicchio islet. Nuclear SNPs variation consistently identified three distinct genetic clusters corresponding to our sampling localities. Furthermore, strong genetic isolation was confirmed by both historical and contemporary levels of migration among the three populations. The DIYABC analysis identified two introductions temporally separated from Palinuro to Capri (ca.25 Mya) and subsequently to Strombolicchio (ca.09 Mya) as the most likely hypothesis for the current distribution of E. saxicola. Regardless of their small population sizes, all study sites supported high-genetic diversity maintained by outcrossing and random mating between individuals owing largely to wind pollination, an exclusive trait among Mediterranean narrow endemics. In conclusion, the patterns observed confirm that some Mediterranean endemics are not necessarily “evolutionary dead-ends” but rather represent species that have extensive demographic stability and a strong evolutionary legacy.

From group to individual - Genotyping by pool sequencing eusocial colonies

Background: Eusocial insects play a central role in many ecosystems, and particularly the important pollinator honeybee (Apis mellifera). One approach to facilitate their study in molecular genetics, is to consider whole colonies as single individuals by combining DNA of multiple individuals in a single pool sequencing experiment. Such a technique comes with the drawback of producing data requiring dedicated analytical methods to be fully exploited. Despite this limitation, pool sequencing data has been shown to be informative and cost-effective when working on random mating populations. Here, we present new statistical methods for exploiting pool sequencing data of eusocial colonies in order to reconstruct the genotype of the colony founder, the queen. This leverages the possibility to monitor genetic diversity, perform genomic-based studies or implement selective breeding. Results: Using simulations and honeybee real data, we show that the methods allow for a fast and accurate estimation of the genetic ancestry, with correlations of 0.9 with that obtained from individual genotyping, and for an accurate reconstruction of the queen genotype, with 2% genotyping error. We further validate the inference using experimental data on colonies with both pool sequencing and individual genotyping of drones. Conclusion: In this study we present statistical models to accurately estimate the genetic ancestry and reconstruct the genotype of the queen from pool sequencing data from workers of an eusocial colony. Such information allows to exploit pool sequencing for traditional population genetics, association studies and selective breeding. While validated in Apis mellifera, these methods are applicable to other eusocial hymenoptera species.

The distribution of mutational effects on fitness in Caenorhabditis elegans inferred from standing genetic variation

The distribution of fitness effects for new mutations is one of the most theoretically important but difficult to estimate properties in population genetics. A crucial challenge to inferring the distribution of fitness effects (DFE) from natural genetic variation is the sensitivity of the site frequency spectrum to factors like population size change, population substructure, genome structure, and non-random mating. Although inference methods aim to control for population size changes, the influence of non-random mating remains incompletely understood, despite being a common feature of many species. We report the distribution of fitness effects estimated from 326 genomes of Caenorhabditis elegans, a nematode roundworm with a high rate of self-fertilization. We evaluate the robustness of DFE inferences using simulated data that mimics the genomic structure and reproductive life history of C. elegans. Our observations demonstrate how the combined influence of self-fertilization, genome structure, and natural selection on linked sites can conspire to compromise estimates of the DFE from extant polymorphisms with existing methods. These factors together tend to bias inferences towards weakly deleterious mutations, making it challenging to have full confidence in the inferred DFE of new mutations as deduced from standing genetic variation in species like C. elegans. Improved methods for inferring the distribution of fitness effects are needed to appropriately handle strong linked selection and selfing. These results highlight the importance of understanding the combined effects of processes that can bias our interpretations of evolution in natural populations.

Drop of Prevalence after Population Expansion: A lower prevalence for recessive disorders in a random mating population is a transient phenomenon during and after a growth phase

Despite increasing data from population-wide sequencing studies, the risk for recessive disorders in consanguineous partnerships is still heavily debated. An important aspect that has not sufficiently been investigated theoretically, is the influence of inbreeding on mutation load and incidence rates when the population sizes change. We therefore developed a model to study these dynamics for a wide range of growth and mating conditions. In the phase of population expansion and shortly afterwards, our simulations show that there is a drop of diseased individuals at the expense of an increasing mutation load for random mating, while both parameters remain almost constant in highly consanguineous partnerships. This explains the empirical observation in present times that a high degree of consanguinity is associated with an increased risk of autosomal recessive disorders. However, it also states that the higher frequency of severe recessive disorders with developmental delay in inbred populations is a transient phenomenon before a mutation-selection balance is reached again.

Genetic purging in captive endangered ungulates with extremely low effective population sizes

Inbreeding threatens the survival of small populations by producing inbreeding depression, but also exposes recessive deleterious effects in homozygosis allowing for genetic purging. Using inbreeding-purging theory, we analyze early survival in four pedigreed captive breeding programs of endangered ungulates where population growth was prioritized so that most adult females were allowed to contribute offspring according to their fitness. We find evidence that purging can substantially reduce inbreeding depression in Gazella cuvieri (with effective population size Ne = 14) and Nanger dama (Ne = 11). No purging is detected in Ammotragus lervia (Ne = 4), in agreement with the notion that drift overcomes purging under fast inbreeding, nor in G. dorcas (Ne = 39) where, due to the larger population size, purging is slower and detection is expected to require more generations. Thus, although smaller populations are always expected to show smaller fitness (as well as less adaptive potential) than larger ones due to higher homozygosis and deleterious fixation, our results show that a substantial fraction of their inbreeding load and inbreeding depression can be purged when breeding contributions are governed by natural selection. Since management strategies intended to maximize the ratio from the effective to the actual population size tend to reduce purging, the search for a compromise between these strategies and purging could be beneficial in the long term. This could be achieved either by allowing some level of random mating and some role of natural selection in determining breeding contributions, or by undertaking reintroductions into the wild at the earliest opportunity.

Double reduction estimation and equilibrium tests in natural autopolyploid populations

Many bioinformatics pipelines include tests for equilibrium. Tests for diploids are well studied and widely available, but extending these approaches to autopolyploids is hampered by the presence of double reduction, the co-migration of sister chromatid segments into the same gamete during meiosis. Though a hindrance for equilibrium tests, double reduction rates are quantities of interest in their own right, as they provide insights about the meiotic behavior of autopolyploid organisms. Here, we develop procedures to (i) test for equilibrium while accounting for double reduction, and (ii) estimate double reduction given equilibrium. To do so, we take two approaches: a likelihood approach, and a novel U-statistic minimization approach that we show generalizes the classical equilibrium χ2 test in diploids. For small sample sizes and uncertain genotypes, we further develop a bootstrap procedure based on our U-statistic to test for equilibrium. Finally, we highlight the difficulty in distinguishing between random mating and equilibrium in tetraploids at biallelic loci. Our methods are implemented in the hwep R package on GitHub https://github.com/dcgerard/hwep.

Temporal trends in performance and hatchability traits of eight strains of hens covered by the gene pool protection programme in Poland

The aim of the study was to determine trends in performance and hatchability traits of eight strains of hens that have been covered by the gene pool protection programme in Poland over ten years/generations. The study involved conservation populations of laying hens: Greenleg Partridge (Z-11), Yellowleg Partridge (Ż-33), Sussex (S-66), Leghorn (H-22, G99), Rhode Island Red (R-11, K-22) and Rhode Island White (A-33), which were maintained at the Experimental Station of the National Research Institute of Animal Production in Chorzelów. The following productive traits were analysed for each population: body weight at 20 wk (g), egg weight at 33 and 53 wk, sexual maturity and number of eggs laid per hen up to 56 wk of age. Mortality and culling were also recorded during rearing and production periods. Furthermore, effective population size (Ne) and inbreeding coefficient in the population (Fx) were calculated for each strain. The analysis of the performance results of the eight strains of hens and their trends indicate that the methods of conservation breeding adopted for these populations enable effective implementation of the conservation programme. The strains were found to differ in all the performance traits subjected to evaluation. Over the 10 generations, the strains examined showed high survival and hatchability parameters during both rearing and production periods. The currently used random mating system proved effective to prevent the populations from an increase of inbreeding. However, a worrying downward trend in body weight was observed in some strains.