Comparing genome scans among species of the stickleback order reveals three different patterns of genetic diversity

Comparing genome scans among species is a powerful approach for investigating the patterns left by evolutionary processes. In particular, this offers a way to detect candidate genes that drive convergent evolution. We compared genome scan results to investigate if patterns of genetic diversity and divergence are shared among divergent species within the stickleback order (Gasterosteiformes): the threespine stickleback (Gasterosteus aculeatus), ninespine stickleback (Pungitius pungitus), and tubesnout (Aulorhynchus flavidus). Populations were sampled from the southern and northern edges of each species’ range, to identify patterns associated with latitudinal changes in genetic diversity. Weak correlations in genetic diversity (FST and expected heterozygosity) and three different patterns in the genomic landscape were found among these species. Additionally, no candidate genes for convergent evolution were detected. This is a counterexample to the growing number of studies that have shown overlapping genetic patterns, demonstrating that genome scan comparisons can be noisy due to the effects of several interacting evolutionary forces

Increased heterozygosity in low-pass sequencing data allows identification of blood chimeras in cattle.

In about 90% of multiple pregnancies in cattle, shared blood circulation between fetuses leads to genetic chimerism in peripheral blood and can reduce reproductive performance in heterosexual co-twins. However, the early detection of heterosexual chimeras requires specialized tests. Here, we used low-pass sequencing data with a median coverage of 0.64× generated from blood samples of 322 F1 crosses between beef and dairy cattle and identified 20 putative blood chimeras through increased levels of genome-wide heterozygosity. In contrast, for 77 samples with routine SNP microarray data generated from hair bulbs of the same F1s, we found no evidence of chimerism, simultaneously observing high levels of genotype discordance with sequencing data. Fifteen out of 18 reported twins showed signs of blood chimerism, in line with previous reports, whereas the presence of five alleged singletons with strong signs of chimerism suggests that the in-utero death rate of co-twins is at the upper limit of former estimates. Together, our results show that low-pass sequencing data allow reliable screening for blood chimeras. They further affirm that blood is not recommended as a source of DNA for the detection of germline variants

Unexpected ancestry of Populus seedlings from a hybrid zone implies a large role for postzygotic selection in the maintenance of species

In the context of potential interspecific gene flow, the integrity of species will be maintained by reproductive barriers that reduce genetic exchange, including traits associated with prezygotic isolation or poor performance of hybrids. Hybrid zones can be used to study the importance of different reproductive barriers, particularly when both parental species and hybrids occur in close spatial proximity. We investigated the importance of barriers to gene flow that act early versus late in the life cycle of European Populus by quantifying the prevalence of homospecific and hybrid matings within a mosaic hybrid zone. We obtained genotypic data for 11,976 loci from progeny and their maternal parents and constructed a Bayesian model to estimate individual admixture proportions and hybrid classes for sampled trees, and for the unsampled pollen parent. Matings that included one or two hybrid parents were common, resulting in admixture proportions of progeny that spanned the whole range of potential ancestries between the two parental species. This result contrasts strongly with the distribution of admixture proportions in adult trees, where intermediate hybrids and each of the parental species are separated into three discrete ancestry clusters. The existence of the full range of hybrids in seedlings is consistent with weak reproductive isolation early in the life cycle of Populus. Instead, a considerable amount of selection must take place between the seedling stage and maturity to remove many hybrid seedlings. Our results highlight that high hybridization rates and appreciable hybrid fitness do not necessarily conflict with the maintenance of species integrity

Causes and consequences of large clonal assemblies in a poplar hybrid zone

Asexual reproduction is a common and fundamental mode of reproduction in plants. Although persistence in adverse conditions underlies most known cases of clonal dominance, proximal genetic drivers remain unclear, in particular for populations dominated by a few large clones. In this study, we studied a clonal population of the riparian tree Populus alba in the Douro river basin (northwestern Iberian Peninsula) where it hybridizes with Populus tremula, a species that grows in highly contrasted ecological conditions. We used 73 nuclear microsatellites to test whether genomic background (species ancestry) is a relevant cause of clonal success, and to assess the evolutionary consequences of clonal dominance by a few genets. Additional genotyping-by-sequencing data were produced to estimate the age of the largest clones. We found that a few ancient (over a few thousand years old) and widespread genets dominate the population, both in terms of clone size and number of sexual offspring produced. Interestingly, large clones possessed two genomic regions introgressed from P. tremula, which may have favoured their spread under stressful environmental conditions. At the population level, the spread of large genets was accompanied by an overall ancient (>0.1 Myr) but soft decline of effective population size. Despite this decrease, and the high clonality and dominance of sexual reproduction by large clones, the Douro hybrid zone still displays considerable genetic diversity and low inbreeding. This suggests that even in extreme cases as in the Douro, asexual and sexual dominance of a few large, geographically extended individuals does not threaten population survival

Local adaptation and the evolution of genome architecture in threespine stickleback.

Theory predicts that local adaptation should favour the evolution of a concentrated genetic architecture, where the alleles driving adaptive divergence are tightly clustered on chromosomes. Adaptation to marine vs. freshwater environments in threespine stickleback has resulted in an architecture that seems consistent with this prediction: divergence among populations is mainly driven by a few genomic regions harbouring multiple quantitative trait loci (QTL) for environmentally adapted traits, as well as candidate genes with well-established phenotypic effects. One theory for the evolution of these "genomic islands" is that rearrangements remodel the genome to bring causal loci into tight proximity, but this has not been studied explicitly. We tested this theory using synteny analysis to identify micro- and macro-rearrangements in the stickleback genome and assess their potential involvement in the evolution of genomic islands. To identify rearrangements, we conducted a de novo assembly of the closely-related tubesnout (Aulorhyncus flavidus) genome and compared this to the genomes of threespine stickleback and two other closely related species. We found that small rearrangements, within-chromosome duplications, and Lineage-Specific Genes (LSGs) were enriched around genomic islands, and that all three chromosomes harbouring large genomic islands have experienced macro-rearrangements. We also found that duplicates and micro-rearrangements are 9.9x and 2.9x more likely to involve genes differentially expressed between marine and freshwater genotypes. While not conclusive, these results are consistent with the explanation that strong divergent selection on candidate genes drove the recruitment of rearrangements to yield clusters of locally adaptive loci

FHA_assignments.csv

PCA cluster and STRUCTURE karyotype assignments and PCA outlier individuals for population FH

Input_Combined21pop.tar.gz

Input files for various analyses for the combined set of 21 Timema cristinae population

FHA_samplePhenotypes.csv

Information on phenotype for samples from population FH

selectionmodels.tar.gz

Files and scripts for testing different models of selection and mating preferences for generating observed karyotype frequencies in Timema cristinae population

N1_assignments.csv

PCA cluster and STRUCTURE karyotype assignments and PCA outlier individuals for population N