A resurrection experiment finds evidence of both reduced genetic diversity and adaptive evolution in the agricultural weed Ipomoea purpurea

A resurrection experiment finds evidence of both reduced genetic diversity and adaptive evolution in the agricultural weed Ipomoea purpurea
Adam Kuester, Shu-Mei Chang, Regina Baucom
doi: http://dx.doi.org/10.1101/024950

Despite the negative economic and ecological impact of weeds, relatively little is known about the evolutionary mechanisms that influence their ability to persist and thrive in agricultural fields. Here, we use a resurrection ecology approach and compare the neutral and adaptive genetic variation of temporally sampled seed progenies of Ipomoea purpurea, an agricultural weed that is resistant to glyphosate, the most widely used herbicide in current-day agriculture. We found striking reductions in allelic diversity between cohorts sampled nine years apart, suggesting that populations of this species sampled from agricultural fields experience genetic bottleneck and/or founder events through time. We further found that populations of this species exhibit modest increases in herbicide resistance over time and evidence that this increase was due to adaptation and not genetic drift. Our results show that even in light of reduced genetic variation, populations of this noxious weed are capable of adapting to strong selection imparted by herbicide application. We likely uncovered only modest increases in resistance between sampling cohorts due to a strong and previously identified fitness cost of resistance in this species, along with the potential that non-resistant migrants germinate from the seed bank.

Neighbourhoods of phylogenetic trees: exact and asymptotic counts

Neighbourhoods of phylogenetic trees: exact and asymptotic counts

Jamie V. De Jong, Jeanette C McLeod, Mike Steel
(Submitted on 15 Aug 2015)

A central theme in phylogenetics is the reconstruction and analysis of evolutionary trees from a given set of data. To determine the optimal search methods for reconstructing trees, it is crucial to understand the size and structure of the neighbourhoods of trees under tree rearrangement operations. The diameter and size of the immediate neighbourhood of a tree has been well-studied, however little is known about the number of trees at distance two, three or (more generally) k from a given tree. In this paper we provide a number of exact and asymptotic results concerning these quantities, and identify some key aspects of tree shape that play a role in determining these quantities. We obtain several new results for two of the main tree rearrangement operations – Nearest Neighbour Interchange and Subtree Prune and Regraft — as well as for the Robinson-Foulds metric on trees.

Sex-dependent dominance at a single locus maintains variation in age at maturity in Atlantic salmon

Sex-dependent dominance at a single locus maintains variation in age at maturity in Atlantic salmon

Nicola Barson, Tutku Aykanat, Kjetil Hindar, Matthew Baranski, Geir Bolstad, Peder Fiske, Celeste Jacq, Arne Jensen, Susan E Johnston, Sten Karlsoon, Matthew Kent, Eero Niemelä, Torfinn Nome, Tor Naesje, Panu Orell, Atso Romakkaniemi, Harald Saegrov, Kurt Urdal, Jaakko Erkinaro, Sigbjorn Lien, Craig Primmer
doi: http://dx.doi.org/10.1101/024695

Males and females share many traits that have a common genetic basis, however selection on these traits often differs between the sexes leading to sexual conflict. Under such sexual antagonism, theory predicts the evolution of genetic architectures that resolve this sexual conflict. Yet, despite intense theoretical and empirical interest, the specific genetic loci behind sexually antagonistic phenotypes have rarely been identified, limiting our understanding of how sexual conflict impacts genome evolution and the maintenance of genetic diversity. Here, we identify a large effect locus controlling age at maturity in 57 salmon populations, an important fitness trait in which selection favours earlier maturation in males than females, and show it is a clear example of sex dependent dominance reducing intralocus sexual conflict and maintaining adaptive variation in wild populations. Using high density SNP data and whole genome re-sequencing, we found that vestigial-like family member 3 (VGLL3) exhibits sex-dependent dominance in salmon, promoting earlier and later maturation in males and females, respectively. VGLL3, an adiposity regulator associated with size and age at maturity in humans, explained 39.4% of phenotypic variation, an unexpectedly high effect size for what is usually considered a highly polygenic trait. Such large effects are predicted under balancing selection from either sexually antagonistic or spatially varying selection. Our results provide the first empirical example of dominance reversal permitting greater optimisation of phenotypes within each sex, contributing to the resolution of sexual conflict in a major and widespread evolutionary trade-off between age and size at maturity. They also provide key empirical evidence for how variation in reproductive strategies can be maintained over large geographical scales. We further anticipate these findings will have a substantial impact on population management in a range of harvested species where trends towards earlier maturation have been observed

A genomic region containing RNF212 is associated with sexually-dimorphic recombination rate variation in wild Soay sheep (Ovis aries).

A genomic region containing RNF212 is associated with sexually-dimorphic recombination rate variation in wild Soay sheep (Ovis aries).

Susan E Johnston, Jon Slate, Josephine M Pemberton
doi: http://dx.doi.org/10.1101/024869

Meiotic recombination breaks down linkage disequilibrium and forms new haplotypes, meaning that it is an important driver of diversity in eukaryotic genomes. Understanding the causes of variation in recombination rate is not only important in interpreting and predicting evolutionary phenomena, but also for understanding the potential of a population to respond to selection. Yet, there remains little data on if, how and why recombination rate varies in natural populations. Here, we used extensive pedigree and high-density SNP information in a wild population of Soay sheep (Ovis aries) to determine individual crossovers in 3330 gametes from 813 individuals. Using these data, we investigated the recombination landscape and the genetic architecture of individual autosomal recombination rate. The population was strongly heterochiasmic (male to female linkage map ratio = 1.31), driven by significantly elevated levels of male recombination in sub-telomeric regions. Autosomal recombination rate was heritable in both sexes (h2 = 0.16 & 0.12 in females and males, respectively), but with different genetic architectures. In females, 46.7% of heritable variation was explained by a sub-telomeric region on chromosome 6; a genome-wide association study showed the strongest associations at RNF212, with further associations observed at a nearby ~374kb region of complete linkage disequilibrium containing three additional candidate loci, CPLX1, GAK and PCGF3. This region did not affect male recombination rate. A second region on chromosome 7 containing REC8 and RNF212B explained 26.2% of heritable variation in recombination rate in both sexes, with further single locus associations identified on chromosome 3. Our findings provide a key empirical example of the genetic architecture of recombination rate in a wild mammal population with male-biased crossover frequency.

GWAS identifies a single selective sweep for age of maturation in wild and cultivated Atlantic salmon males.

GWAS identifies a single selective sweep for age of maturation in wild and cultivated Atlantic salmon males.

Fernando Ayllon, Erik Kjærner-Semb, Tomasz Furmanek, Vidar Wennevik, Monica Solberg, Harald Sægrov, Kurt Urdal, Geir Dahle, Geir Lasse Taranger, Kevin A Glover, Markus S Almén, Carl J Rubin, Rolf B Edvardsen, Anna Wargelius
doi: http://dx.doi.org/10.1101/024927

Abstract Background Sea age at sexual maturation displays large plasticity for wild Atlantic salmon males and varies between 1-5 years. This flexibility can also be observed in domesticated salmon. Previous studies have uncovered a genetic predisposition for age at maturity with moderate heritability, thus suggesting a polygenic nature of this trait. The aim with this study was to identify genomic regions and associated SNPs and genes conferring age at maturity in salmon. Results We performed a GWAS using a pool sequencing approach (n=20 per river and trait) of salmon returning as sexually mature either after one sea winter (2009) or after three sea winters (2011) in six rivers in Norway. The study revealed one major selective sweep, which covered 76 significant SNP in a 230 kb region of Chr 25. A SNP assay of other year classes of wild salmon and from cultivated fish supported this finding. The assay in cultivated fish reduced the haplotype conferring the trait to a region which covered 4 SNPs of a 2386 bp region containing the vgll3 gene. 2 of these SNPs caused miss-sense mutations in vgll3. Conclusions This study presents a single selective region in the genome for age at maturation in male Atlantic salmon. The SNPs identified may be used as QTLs to prevent early maturity in aquaculture and in monitoring programs of wild salmon. Interestingly, the identified vgll3 gene has previously been linked to time of puberty in humans, suggesting a conserved mechanism for time of puberty in vertebrates.

Genome divergence and gene flow between Drosophila simulans and D. mauritiana

Genome divergence and gene flow between Drosophila simulans and D. mauritiana
Sarah B. Kingan, Anthony J. Geneva, Jeffrey P. Vedanayagam, Daniel Garrigan
doi: http://dx.doi.org/10.1101/024711

The fruit fly Drosophila simulans and its sister species D. mauritiana are a model system for studying the genetic basis of reproductive isolation, primarily because interspecific crosses produce sterile hybrid males and their phylogenetic proximity to D. melanogaster. We present an analysis of whole-genome patterns of polymorphism and divergence that shows, on average, the genomes of the two species differ at slightly more than 1% of nucleotide positions and an estimated 40% of autosomal and 60% of X linked loci are reciprocally monophyletic. However, the analysis also identifies 21 major genomic regions, comprising ~1% of the genome, in which one species is segregating for haplotypes that are more similar to haplotypes from the other species than expected, given the levels of sequence divergence in that genomic region. This disjoint distribution of interspecific coalescence times is consistent with recent introgression between the cosmopolitan D. simulans and the island endemic D. mauritiana. We find that the putatively introgressed regions are more likely to have significantly higher rates of crossing-over and are enriched for genes with significantly slower rates of protein evolution. We also uncover instances in which genes experiencing lineage-specific positive selection closely interact with genes experiencing introgression. Finally, we find that a large introgressing region on the X chromosome has experienced a strong selective sweep in D. mauritiana and also has high levels of homozygosity in D. simulans. A detailed analysis reveals that the introgressing X chromosome haplotypes are closely associated with the presence of the MDox locus, which is the progenitor of the Winters sex-ratio meiotic drive genes. These results highlight how genetic systems that evolve rapidly in allopatry, including selfish meiotic drive elements, remain robust in natural hybrid genotypes and do not systematically promote reproductive isolation.

Life history effects on the molecular clock of autosomes and sex chromosomes

Life history effects on the molecular clock of autosomes and sex chromosomes
Guy Amster, Guy Sella
doi: http://dx.doi.org/10.1101/024281

One of the foundational results of molecular evolution is that the rate at which neutral substitutions accumulate on a lineage equals the rate at which mutations arise. Traits that affect rates of mutation therefore also affect the phylogenetic “molecular clock”. We consider the effects of sex-specific generation times and mutation rates in species with two sexes. In particular, we focus on the effects that the age of onset of male puberty and rates of spermatogenesis have likely had in extant hominines (i.e., human, chimpanzee and gorilla), considering a model that approximates features of the mutational process in most mammals and birds and some other vertebrates. As we show, this model helps explain and reconcile a number of seemingly puzzling observations. In hominines, it can explain the puzzlingly low X-to-autosome ratios of substitution rates and how the ratios and rates of autosomal substitutions differ among lineages. Importantly, it suggests how to translate pedigree-based estimates of human mutation rates into split times among apes, given sex-specific life histories. In so doing, it helps bridge the gap between estimates of split times of apes based on fossil and molecular evidence. Finally, considering these effects can help to reconcile recent evidence that changes in generation times should have small effects on mutation rates in humans with classic studies suggesting that they have had major effects on rates of evolution in the mammalian phylogeny.

Successful asexual lineages of the Irish potato Famine pathogen are triploid

Successful asexual lineages of the Irish potato Famine pathogen are triploidYing Li, Qian Zhou, Kun Qian, Theo van der Lee, Sanwen Huang
doi: http://dx.doi.org/10.1101/024596
The oomycete Phytophthora infestans was the causal agent of the Irish Great Famine and is a recurring threat to global food security. The pathogen can reproduce both sexually and asexually and has a potential to adapt both abiotic and biotic environment. Although in many regions the A1 and A2 mating types coexist, the far majority of isolates belong to few clonal, asexual lineages. As other oomycetes, P. infestans is thought to be diploid during the vegetative phase of its life cycle, but it was observed that trisomy correlated with virulence and mating type locus and that polyploidy can occur in some isolates. It remains unknown about the frequency of polyploidy occurrence in nature and the relationship between ploidy level and sexuality. Here we discovered that the sexuality of P. infestans isolates correlates with ploidy by comparison of microsatellite fingerprinting, genome-wide polymorphism, DNA quantity, and chromosome numbers. The sexual progeny of P. infestans in nature are diploid, whereas the asexual lineages are mostly triploids, including successful clonal lineages US-1 and 13_A2. This study reveals polyploidization as an extra evolutionary risk to this notorious plant destroyer.

S/HIC: Robust identification of soft and hard sweeps using machine learning

S/HIC: Robust identification of soft and hard sweeps using machine learningDaniel R Schrider, Andrew D Kern
doi: http://dx.doi.org/10.1101/024547
Detecting the targets of adaptive natural selection from whole genome sequencing data is a central problem for population genetics. However, to date most methods have shown sub-optimal performance under realistic demographic scenarios. Moreover, over the past decade there has been a renewed interest in determining the importance of selection from standing variation in adaptation of natural populations, yet very few methods for inferring this model of adaptation at the genome scale have been introduced. Here we introduce a new method, S/HIC, which uses supervised machine learning to precisely infer the location of both hard and soft selective sweeps. We show that S/HIC has unrivaled accuracy for detecting sweeps under demographic histories that are relevant to human populations, and distinguishing sweeps from linked as well as neutrally evolving regions. Moreover we show that S/HIC is uniquely robust among its competitors to model misspecification. Thus even if the true demographic model of a population differs catastrophically from that specified by the user, S/HIC still retains impressive discriminatory power. Finally we apply S/HIC to the case of resequencing data from human chromosome 18 in a European population sample and demonstrate that we can reliably recover selective sweeps that have been identified earlier using less specific and sensitive methods.

Genomic study of the Ket: a Paleo-Eskimo-related ethnic group with significant ancient North Eurasian ancestry

Genomic study of the Ket: a Paleo-Eskimo-related ethnic group with significant ancient North Eurasian ancestryPavel Flegontov, Piya Changmai, Anastassiya Zidkova, Maria D. Logacheva, Olga Flegontova, Mikhail S. Gelfand, Evgeny S. Gerasimov, Ekaterina V. Khrameeva, Olga P. Konovalova, Tatiana Neretina, Yuri V. Nikolsky, George Starostin, Vita V. Stepanova, Igor V. Travinsky, Martin Tříska, Petr Tříska, Tatiana V. Tatarinova
doi: http://dx.doi.org/10.1101/024554
The Kets, an ethnic group in the Yenisei River basin, Russia, are considered the last nomadic hunter-gatherers of Siberia, and Ket language has no transparent affiliation with any language family. We investigated connections between the Kets and Siberian and North American populations, with emphasis on the Mal’ta and Paleo-Eskimo ancient genomes, using original data from 46 unrelated samples of Kets and 42 samples of their neighboring ethnic groups (Uralic-speaking Nganasans, Enets, and Selkups). We genotyped over 130,000 autosomal SNPs, determined mitochondrial and Y-chromosomal haplogroups, and performed high-coverage genome sequencing of two Ket individuals. We established that the Kets belong to the cluster of Siberian populations related to Paleo-Eskimos. Unlike other members of this cluster (Nganasans, Ulchi, Yukaghirs, and Evens), Kets and closely related Selkups have a high degree of Mal’ta ancestry. Implications of these findings for the linguistic hypothesis uniting Ket and Na-Dene languages into a language macrofamily are discussed.