Yearly Archives: 2014

Demographic inference using genetic data from a single individual: separating population size variation

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Demographic inference using genetic data from a single individual: separating population size variation from population structure
Olivier Mazet, Willy Rodríguez, Lounès Chikhi
doi: http://dx.doi.org/10.1101/011866

The rapid development of sequencing technologies represents new opportunities for population genetics research. It is expected that genomic data will increase our ability to reconstruct the history of populations. While this increase in genetic information will likely help biologists and anthropologists to reconstruct the demographic history of populations, it also represents new challenges. Recent work has shown that structured populations generate signals of population size change. As a consequence it is often difficult to determine whether demographic events such as expansions or contractions (bottlenecks) inferred from genetic data are real or due to the fact that populations are structured in nature. Given that few inferential methods allow us to account for that structure, and that genomic data will necessarily increase the precision of parameter estimates, it is important to develop new approaches. In the present study we analyse two demographic models. The first is a model of instantaneous population size change whereas the second is the classical symmetric island model. We (i) re-derive the distribution of coalescence times under the two models for a sample of size two, (ii) use a maximum likelihood approach to estimate the parameters of these models (iii) validate this estimation procedure under a wide array of parameter combinations, (iv) implement and validate a model choice procedure by using a Kolmogorov-Smirnov test. Altogether we show that it is possible to estimate parameters under several models and perform efficient model choice using genetic data from a single diploid individual.

Recent Y chromosome divergence despite ancient origin of dioecy in poplars (Populus)

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Recent Y chromosome divergence despite ancient origin of dioecy in poplars (Populus)
Armando Geraldes, Charles A Hefer, Arnaud Capron, Natalia Kolosova, Felix Martinez-Nuñez, Raju Y Soolanayakanahally, Brian Stanton, Robert D Guy, Shawn D Mansfield, Carl J Douglas, Quentin C B Cronk
doi: http://dx.doi.org/10.1101/011817
Abstract

All species of the genus Populus (poplar, aspen) are dioecious, suggesting an ancient origin of this trait. Theory suggests that non-recombining sex-linked regions should quickly spread, eventually becoming heteromorphic chromosomes. In contrast, we show using whole genome scans that the sex-associated region in P. trichocarpa is small and much younger than the age of the genus. This indicates that sex-determination is highly labile in poplar, consistent with recent evidence of “turnover” of sex determination regions in animals. We performed whole genome resequencing of 52 Populus trichocarpa (black cottonwood) and 34 P. balsamifera (balsam poplar) individuals of known sex. Genome-wide association studies (GWAS) in these unstructured populations identified 650 SNPs significantly associated with sex. We estimate the size of the sex-linked region to be ∼100 Kbp. All significant SNPs were in strong linkage disequilibrium despite the fact that they were mapped to six different chromosomes (plus 3 unmapped scaffolds) in version 2.2 of the reference genome. We show that this is likely due to genome misassembly. The segregation pattern of sex associated SNPs revealed this to be an XY sex determining system. Estimated divergence times of X and Y haplotype sequences (6-7 MYA) are much more recent than the divergence of P. trichocarpa (poplar) and P. tremuloides (aspen). Consistent with this, in P. tremuloides we found no XY haplotype divergence within the P. trichocarpa sex-determining region. These two species therefore have a different genomic architecture of sex, suggestive of at least one turnover event in the recent past.

Spider web DNA: a new spin on noninvasive genetics of predator and prey

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Spider web DNA: a new spin on noninvasive genetics of predator and prey

Charles Cong Yang Xu, Ivy J Yen, Dean Bowman, Cameron R. Turner
doi: http://dx.doi.org/10.1101/011775

Noninvasive genetic approaches enable biomonitoring without the need to directly observe or disturb target organisms. Environmental DNA (eDNA) methods have recently extended this approach by assaying genetic material within bulk environmental samples without a priori knowledge about the presence of target biological material. This paper describes a novel and promising source of noninvasive spider DNA and insect eDNA from spider webs. Using black widow spiders (Latrodectus spp.) fed with house crickets (Acheta domesticus), we successfully extracted and amplified mitochondrial DNA sequences of both spider and prey from spider web. Detectability of spider DNA did not differ between assays with amplicon sizes from 135 to 497 base pairs. Spider DNA and prey eDNA remained detectable at least 88 days after living organisms were no longer present on the web. Spider web DNA may be an important tool in conservation research, pest management, biogeography studies, and biodiversity assessments.

Genetic landscape of populations along the Silk Road: admixture and migration patterns

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Genetic landscape of populations along the Silk Road: admixture and migration patterns

Massimo Mezzavilla, Diego Vozzi, Nicola Pirastu, Giorgia Girotto, Pio D’Adamo, Paolo Gasparini, Vincenza Colonna
doi: http://dx.doi.org/10.1101/011759

Background The ancient Silk Road has been a trading route between Europe and Central Asia from the 2nd century BCE to the 15th century CE. While most populations on this route have been characterized, the genetic background of others remains poorly understood, and little is known about past migration patterns. The scientific expedition “Marco Polo” has recently collected genetic and phenotypic data in six regions (Georgia, Armenia, Azerbaijan, Uzbekistan, Kazakhstan, Tajikistan) along the Silk Road to study the genetics of a number of phenotypes. Results We characterized the genetic structure of these populations within a worldwide context. We observed a West-East subdivision albeit the existence of a genetic component shared within Central Asia and nearby populations from Europe and Near East. We observed a contribution of up to 50% from Europe and Asia to most of the populations that have been analyzed. The contribution from Asia dates back to ~25 generations and is limited to the Eastern Silk Road. Time and direction of this contribution are consistent with the Mongolian expansion era. Conclusions We clarified the genetic structure of six populations from Central Asia and suggested a complex pattern of gene flow among them. We provided a map of migration events in time and space and we quantified exchanges among populations. Altogether these novel findings will support the future studies aimed at understanding the genetics of the phenotypes that have been collected during the Marco Polo campaign, they will provide insights into the history of these populations, and they will be useful to reconstruct the developments and events that have shaped modern Eurasians genomes.

Dynamic epistasis for different alleles of the same gene

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Dynamic epistasis for different alleles of the same gene

Lin Xu, Brandon Barker, Zhenglong Gu
(Submitted on 24 Nov 2014)

Epistasis refers to the phenomenon in which phenotypic consequences caused by mutation of one gene depend on one or more mutations at another gene. Epistasis is critical for understanding many genetic and evolutionary processes, including pathway organization, evolution of sexual reproduction, mutational load, ploidy, genomic complexity, speciation, and the origin of life. Nevertheless, current understandings for the genome-wide distribution of epistasis are mostly inferred from interactions among one mutant type per gene, whereas how epistatic interaction partners change dynamically for different mutant alleles of the same gene is largely unknown. Here we address this issue by combining predictions from flux balance analysis and data from a recently published high-throughput experiment. Our results show that different alleles can epistatically interact with very different gene sets. Furthermore, between two random mutant alleles of the same gene, the chance for the allele with more severe mutational consequence to develop a higher percentage of negative epistasis than the other allele is 50-70% in eukaryotic organisms, but only 20-30% in bacteria and archaea. We developed a population genetics model that predicts that the observed distribution for the sign of epistasis can speed up the process of purging deleterious mutations in eukaryotic organisms. Our results indicate that epistasis among genes can be dynamically rewired at the genome level, and call on future efforts to revisit theories that can integrate epistatic dynamics among genes in biological systems.

Tissue-specific evolution of protein coding genes in human and mouse

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Tissue-specific evolution of protein coding genes in human and mouse

Nadezda Kryuchkova, Marc Robinson-Rechavi
doi: http://dx.doi.org/10.1101/011692

Protein-coding genes evolve at different rates, and the influence of different parameters, from gene size to expression level, has been extensively studied. While in yeast gene expression level is the major causal factor of gene evolutionary rate, the situation is more complex in animals. Here we investigate these relations further, especially taking in account gene expression in different organs as well as indirect correlations between parameters. We used RNA-seq data from two large datasets, covering 22 mouse tissues and 27 human tissues. Over all tissues, evolutionary rate only correlates weakly with levels and breadth of expression. The strongest explanatory factors of strong purifying selection are GC content, expression in many developmental stages, and expression in brain tissues. While the main component of evolutionary rate is purifying selection, we also find tissue-specific patterns for sites under neutral evolution and for positive selection. We observe fast evolution of genes expressed in testis, but also in other tissues, notably liver, which are explained by weak purifying selection rather than by positive selection.

Estimating the temporal and spatial extent of gene flow among sympatric lizard populations (genus Sceloporus) in the southern Mexican highlands

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Estimating the temporal and spatial extent of gene flow among sympatric lizard populations (genus Sceloporus) in the southern Mexican highlands

Jared A Grummer, Martha L. Calderón, Adrián Nieto Montes-de Oca, Eric N Smith, Fausto Méndez-de la Cruz, Adam Leaché
doi: http://dx.doi.org/10.1101/008623

Interspecific gene flow is pervasive throughout the tree of life. Although detecting gene flow between populations has been facilitated by new analytical approaches, determining the timing and geography of hybridization has remained difficult, particularly for historical gene flow. A geographically explicit phylogenetic approach is needed to determine the ancestral population overlap. In this study, we performed population genetic analyses, species delimitation, simulations, and a recently developed approach of species tree diffusion to infer the phylogeographic history, timing and geographic extent of gene flow in lizards of the Sceloporus spinosus group. The two species in this group, S. spinosus and S. horridus, are distributed in eastern and western portions of Mexico, respectively, but populations of these species are sympatric in the southern Mexican highlands. We generated data consisting of three mitochondrial genes and eight nuclear loci for 148 and 68 individuals, respectively. We delimited six lineages in this group, but found strong evidence of mito-nuclear discordance in sympatric populations of S. spinosus and S. horridus owing to mitochondrial introgression. We used coalescent simulations to differentiate ancestral gene flow from secondary contact, but found mixed support for these two models. Bayesian phylogeography indicated more than 60% range overlap between ancestral S. spinosus and S. horridus populations since the time of their divergence. Isolation-migration analyses, however, revealed near-zero levels of gene flow between these ancestral populations. Interpreting results from both simulations and empirical data indicate that despite a long history of sympatry among these two species, gene flow in this group has only recently occurred.

Strong selection in the human-chimpanzee ancestor links the X chromosome to speciation

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Strong selection in the human-chimpanzee ancestor links the X chromosome to speciation

Julien Y Dutheil, Kasper Munch, Thomas Mailund, Kiwoong Nam, Mikkel Schierup
doi: http://dx.doi.org/10.1101/011601

The human and chimpanzee X chromosomes are less divergent than expected based on autosomal divergence. This has led to a controversial hypothesis proposing a unique role of the X chromosome in complex human-chimpanzee speciation. Here, we study incomplete lineage sorting patterns between humans, chimpanzees and gorillas to show that this low divergence is entirely due to megabase-sized regions comprising one-third of the X chromosome, where polymorphism in the human-chimpanzee ancestral species was severely reduced. Background selection can explain 10% of this reduction at most. Instead, we show that several strong selective sweeps in the ancestral species can explain these patterns. We also report evidence of population specific sweeps of a similar magnitude in extant humans that overlap the regions of low diversity in the ancestral species. These regions further correspond to chromosomal sections shown to be devoid of Neanderthal introgression into modern humans. This suggests that these X-linked regions are directly involved in forming reproductive barriers.

The seed-bank coalescent

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The seed-bank coalescent

Jochen Blath, Adrián González Casanova, Noemi Kurt, Maite Wilke-Berenguer
(Submitted on 18 Nov 2014)

We identify a new natural coalescent structure, the seed-bank coalescent, which describes the gene genealogy of populations under the influence of a strong seed-bank effect, where `dormant forms’ of individuals (such as seeds or spores) may jump a significant number of generations before joining the `active’ population. Mathematically, our seed-bank coalescent appears as scaling limit in a Wright-Fisher model with geometric seed-bank age structure if the average time of seed dormancy scales with the order of the total population size N. This extends earlier results of Kaj, Krone and Lascaux (2001) who show that the genealogy of a Wright-Fisher model in the presence of a `weak’ seed-bank effect is given by a suitably time-changed Kingman coalescent. The qualitatively new feature of the seed-bank coalescent is that ancestral lineages are independently blocked at a certain rate from taking part in coalescence events, thus strongly altering the predictions of classical coalescent models. In particular, the seed-bank coalescent `does not come down from infinity’, and the time to the most recent common ancestor of a sample of size n grows like loglogn, which is the order also observed for the Bolthausen-Sznitman coalescent. This is in line with the empirical observation that seed-banks drastically increase genetic variability in a population and indicates how they may serve as a buffer against other evolutionary forces such as genetic drift and selection.

Triticeae resources in Ensembl Plants

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Triticeae resources in Ensembl Plants

Dan M Bolser, Arnaud Kerhornou, Brandon Walts, Paul Kersey
doi: http://dx.doi.org/10.1101/011585

Recent developments in DNA sequencing have enabled the large and complex genomes of many crop species to be determined for the first time, even those previously intractable due to their polyploid nature. Indeed, over the course of the last two years, the genome sequences of several commercially important cereals, notably barley and bread wheat, have become available, as well as those of related wild species. While still incomplete, comparison to other, more completely assembled species suggests that coverage of genic regions is likely to be high. Ensembl Plants (http://plants.ensembl.org) is an integrative resource organising, analysing and visualising genome-scale information for important crop and model plants. Available data includes reference genome sequence, variant loci, gene models and functional annotation. For variant loci, individual and population genotypes, linkage information and, where available, phenotypic information, are shown. Comparative analyses are performed on DNA and protein sequence alignments. The resulting genome alignments and gene trees, representing the implied evolutionary history the gene family, are made available for visualisation and analysis. Driven by the use case of bread wheat, specific extensions to the analysis pipelines and web interface have recently been developed to support polyploid genomes. Data in Ensembl Plants is accessible through a genome browser incorporating various specialist interfaces for different data types, and through a variety of additional methods for programmatic access and data mining. These interfaces are consistent with those offered through the Ensembl interface for the genomes of non-plant species, including those of plant pathogens, pests and pollinators, facilitating the study of the plant in its environment.