Long live the alien: studying the fate of the genomic diversity along the long-term dynamics of an extremely successful invader, the crested porcupine.

Long live the alien: studying the fate of the genomic diversity along the long-term dynamics of an extremely successful invader, the crested porcupine.

Emiliano Trucchi , Benoit Facon , Paolo Gratton , Emiliano Mori , Nils Chr Stenseth , Sissel Jentoft
doi: http://dx.doi.org/10.1101/016493

Describing long-term evolutionary trajectories of alien species is a fundamental, although rarely possible, step to understand the pivotal drivers of successful invasions. Here, we tackled this task by investigating the genetic structure of the crested porcupine (Hystrix cristata), whose invasion of Italy started about 1500 years ago. Using genome-wide RAD markers, we explored the demographic processes that shaped, and are shaping, the gene pool of the expanding invasive populations and compared their genetic diversity with that of native and invasive populations of both African porcupine species (crested and Cape, H. africaeaustralis). Through coalescence-based demographic reconstructions, we demonstrated that bottleneck at introduction was mild and did not severely affect the reservoir of genetic diversity. Our data also highlighted a marked geographic structure in the invasive populations, indicating that they are likely the results of multiple introduction events. Nevertheless, both the invasive populations and its source show a lower level of diversity relative to other native populations from Sub-Saharan and South Africa, suggesting that demographic history before introduction may have played a role in forging a successful invader. Finally, we showed that the current spatial expansion at the northern boundary of the range is following a leading-edge model characterized by a general reduction of genetic diversity towards the edge of the expanding range. Consistently, random fixation of alleles through gene-surfing seems a more likely explanation than adaptive divergence for the distribution of the few outlier loci with highly divergent frequencies between core and newly colonized areas.

Cline coupling and uncoupling in a stickleback hybrid zone

Cline coupling and uncoupling in a stickleback hybrid zone
Tim Vines , Anne Dalziel , Arianne Albert , Thor Veen , Patricia Schulte , Dolph Schluter
doi: http://dx.doi.org/10.1101/016832

Strong ecological selection on a genetic locus can maintain allele frequency differences between populations in different environments, even in the face of hybridization. When alleles at divergent loci come into tight linkage disequilibria, selection acts on them as a unit and can significantly reduce gene flow. For populations interbreeding across a hybrid zone, linkage disequilibria between loci can force clines to share the same slopes and centers. However, strong ecological selection can push clines away from the others, reducing linkage disequilibria and weakening the barrier to gene flow. We looked for this ‘cline uncoupling’ effect in a hybrid zone between stream resident and anadromous sticklebacks at two genes known to be under divergent natural selection (Eda and ATP1a1) and five morphological traits that repeatedly evolve in freshwater stickleback. We used 10 anonymous SNPs to characterize the shape of the zone. We found that the clines at Eda, ATP1a1, and four morphological traits were concordant and coincident, suggesting that direct selection on each is outweighed by the indirect selection generated by linkage disequilibria. Interestingly, the cline for pectoral fin length was much steeper and displaced 200m downstream, and two anonymous SNPs also had steep clines.

Pollen-specific genes accumulate more deleterious mutations than sporophytic genes under relaxed purifying selection in Arabidopsis thaliana.

Pollen-specific genes accumulate more deleterious mutations than sporophytic genes under relaxed purifying selection in Arabidopsis thaliana.

Mark Christian Harrison , Eamonn B Mallon , Dave Twell , Robert L Hammond
doi: http://dx.doi.org/10.1101/016626

The strength of purifying selection varies among loci and leads to differing frequencies of deleterious alleles within genomes. Selection is generally stronger for highly and broadly expressed genes but can be less efficient for diploid expressed, deleterious alleles if heterozygous. In plants expression level, tissue specificity and ploidy level differ between pollen specific and sporophyte specific genes. This may explain why the reported strength and direction of the relationship between selection and the specificity of a gene to either pollen or sporophytic tissues varies between studies and species. In this study, we investigate the individual effects of expression level and tissue specificity on selection efficacy within pollen genes and sporophytic genes of Arabidopsis thaliana. Due to high homozygosity levels caused by selfing, masking is expected to play a lesser role. We find that expression level and tissue specificity independently influence selection in A. thaliana. Furthermore, contrary to expectations, pollen genes are evolving faster due to relaxed purifying selection and have accumulated a higher frequency of deleterious alleles. This suggests that high homozygosity levels resulting from high selfing rates reduce the effects of pollen competition and masking in A. thaliana, so that the high tissue specificity and expression noise of pollen genes are leading to lower selection efficacy compared to sporophyte genes.

Beyond 2/3 and 1/3: the complex signatures of sex-biased admixture on the X chromosome

Beyond 2/3 and 1/3: the complex signatures of sex-biased admixture on the X chromosome
Amy Goldberg , Noah A Rosenberg
doi: http://dx.doi.org/10.1101/016543

Sex-biased demography, in which parameters governing migration and population size differ between females and males, has been studied through comparisons of X chromosomes, which are inherited sex-specifically, and autosomes, which are not. A common form of sex bias in humans is sex-biased admixture, in which at least one of the source populations differs in its proportions of females and males contributing to an admixed population. Studies of sex-biased admixture often examine the mean ancestry for markers on the X chromosome in relation to the autosomes. A simple framework noting that in a population with equally many females and males, 2/3 of X chromosomes appear in females, suggests that the mean X-chromosomal admixture fraction is a linear combination of female and male admixture parameters, with coefficients 2/3 and 1/3, respectively. Extending a mechanistic admixture model to accommodate the X chromosome, we demonstrate that this prediction is not generally true in admixture models, though it holds in the limit for an admixture process occurring as a single event. For a model with constant ongoing admixture, we determine the mean X-chromosomal admixture, comparing admixture on female and male X chromosomes to corresponding autosomal values. Surprisingly, in reanalyzing African-American genetic data to estimate sex-specific contributions from African and European sources, we find that the range of contributions compatible with the excess African ancestry on the X chromosome compared to autosomes has a wide spread, permitting scenarios either without male-biased contributions from Europe or without female-biased contributions from Africa.

The Spatial Mixing of Genomes in Secondary Contact Zones

The Spatial Mixing of Genomes in Secondary Contact Zones
Alisa Sedghifar , Yaniv Brandvain , Peter L. Ralph , Graham Coop
doi: http://dx.doi.org/10.1101/016337

Recent genomic studies have highlighted the important role of admixture in shaping genome-wide patterns of diversity. Past admixture leaves a population genomic signature of linkage disequilibrium (LD), reflecting the mixing of parental chromosomes by segregation and recombination. The extent of this LD can be used to infer the timing of admixture. However, the results of inference can depend strongly on the assumed demographic model. Here, we introduce a theoretical framework for modeling patterns of LD in a geographic contact zone where two differentiated populations are diffusing back together. We derive expressions for the expected LD and admixture tract lengths across geographic space as a function of the age of the contact zone and the dispersal distance of individuals. We develop an approach to infer age of contact zones using population genomic data from multiple spatially sampled populations by fitting our model to the decay of LD with recombination distance. We use our approach to explore the fit of a geographic contact zone model to three human population genomic datasets from populations along the Indonesian archipelago, populations in Central Asia and populations in India.

Eight thousand years of natural selection in Europe

Eight thousand years of natural selection in Europe
Iain Mathieson , Iosif Lazaridis , Nadin Rohland , Swapan Mallick , Bastien Llamas , Joseph Pickrell , Harald Meller , Manuel A. Rojo Guerra , Johannes Krause , David Anthony , Dorcas Brown , Carles Lalueza Fox , Alan Cooper , Kurt W. Alt , Wolfgang Haak , Nick Patterson , David Reich
doi: http://dx.doi.org/10.1101/016477

The arrival of farming in Europe beginning around 8,500 years ago required adaptation to new environments, pathogens, diets, and social organizations. While evidence of natural selection can be revealed by studying patterns of genetic variation in present-day people, these pattern are only indirect echoes of past events, and provide little information about where and when selection occurred. Ancient DNA makes it possible to examine populations as they were before, during and after adaptation events, and thus to reveal the tempo and mode of selection. Here we report the first genome-wide scan for selection using ancient DNA, based on 83 human samples from Holocene Europe analyzed at over 300,000 positions. We find five genome-wide signals of selection, at loci associated with diet and pigmentation. Surprisingly in light of suggestions of selection on immune traits associated with the advent of agriculture and denser living conditions, we find no strong sweeps associated with immunological phenotypes. We also report a scan for selection for complex traits, and find two signals of selection on height: for short stature in Iberia after the arrival of agriculture, and for tall stature on the Pontic-Caspian steppe earlier than 5,000 years ago. A surprise is that in Scandinavian hunter-gatherers living around 8,000 years ago, there is a high frequency of the derived allele at the EDAR gene that is the strongest known signal of selection in East Asians and that is thought to have arisen in East Asia. These results document the power of ancient DNA to reveal features of past adaptation that could not be understood from analyses of present-day people.

PoMo: An Allele Frequency-based Approach for Species Tree Estimation

PoMo: An Allele Frequency-based Approach for Species Tree Estimation
Nicola De Maio , Dominik Schrempf , Carolin Kosiol
doi: http://dx.doi.org/10.1101/016360

Incomplete lineage sorting can cause incongruencies of the overall species-level phylogenetic tree with the phylogenetic trees for individual genes or genomic segments. If these incongruencies are not accounted for, it is possible to incur several biases in species tree estimation. Here, we present a simple maximum likelihood approach that accounts for ancestral variation and incomplete lineage sorting. We use a POlymorphisms-aware phylogenetic MOdel (PoMo) that we have recently shown to efficiently estimate mutation rates and fixation biases from within and between-species variation data. We extend this model to perform efficient estimation of species trees. We test the performance of PoMo in several different scenarios of incomplete lineage sorting using simulations and compare it with existing methods both in accuracy and computational speed. In contrast to other approaches, our model does not use coalescent theory but is allele-frequency based. We show that PoMo is well suited for genome-wide species tree estimation and that on such data it is more accurate than previous approaches.