Early modern human dispersal from Africa: genomic evidence for multiple waves of migration

Early modern human dispersal from Africa: genomic evidence for multiple waves of migration
Francesca Tassi, Silvia Ghirotto, Massimo Mezzavilla, Sibelle Torres Vilaça, Lisa De Santi, Guido Barbujani
doi: http://dx.doi.org/10.1101/022889

Background. Anthropological and genetic data agree in indicating the African continent as the main place of origin for modern human. However, it is unclear whether early modern humans left Africa through a single, major process, dispersing simultaneously over Asia and Europe, or in two main waves, first through the Arab peninsula into Southern Asia and Oceania, and later through a Northern route crossing the Levant. Results. Here we show that accurate genomic estimates of the divergence times between European and African populations are more recent than those between Australo-Melanesia and Africa, and incompatible with the effects of a single dispersal. This difference cannot possibly be accounted for by the effects of hybridization with archaic human forms in Australo-Melanesia. Furthermore, in several populations of Asia we found evidence for relatively recent genetic admixture events, which could have obscured the signatures of the earliest processes. Conclusions. We conclude that the hypothesis of a single major human dispersal from Africa appears hardly compatible with the observed historical and geographical patterns of genome diversity, and that Australo-Melanesian populations seem still to retain a genomic signature of a more ancient divergence from Africa

Adaptive evolution is substantially impeded by Hill-Robertson interference in Drosophila

Adaptive evolution is substantially impeded by Hill-Robertson interference in Drosophila

David Castellano, Marta Coronado, Jose Campos, Antonio Barbadilla, Adam Eyre-Walker
doi: http://dx.doi.org/10.1101/021600

It is known that rates of mutation and recombination vary across the genome in many species. Here we investigate whether these factors affect the rate at which genes undergo adaptive evolution both individually and in combination and quantify the degree to which Hill-Robertson interference (HRi) impedes the rate of adaptive evolution. To do this we compiled a dataset of 6,141 autosomal protein coding genes from Drosophila, for which we have polymorphism data from D. melanogaster and divergence out to D. yakuba. We estimated the rate of adaptive evolution using a derivative of the McDonald-Kreitman test that controls for the slightly deleterious mutations. We find that the rate of adaptive amino acid substitution is positively correlated to both the rates of recombination and mutation. We also find that these correlations are robust to controlling for each other, synonymous codon bias and gene functions related to immune response and testes. We estimate that HRi reduces the rate of adaptive evolution by ~27%. We also show that this fraction depends on a gene’s mutation rate; genes with low mutation rates lose ~11% of their adaptive substitutions while genes with high mutation rates lose ~43%. In conclusion, we show that the mutation rate and the rate of recombination, are important modifiers of the rate of adaptive evolution in Drosophila.

Independent molecular basis of convergent highland adaptation in maize

Independent molecular basis of convergent highland adaptation in maize

Shohei Takuno, Peter Ralph, Kelly Swarts, Rob J Elshire, Jeffrey C Glaubitz, Edward S. Buckler, Matthew B Hufford, Jeffrey Ross-Ibarra
doi: http://dx.doi.org/10.1101/013607

Convergent evolution is the independent evolution of similar traits in different species or lineages of the same species; this often is a result of adaptation to similar environments, a process referred to as convergent adaptation.} We investigate here the molecular basis of convergent adaptation in maize to highland climates in Mesoamerica and South America using genome-wide SNP data. Taking advantage of archaeological data on the arrival of maize to the highlands, we infer demographic models for both populations, identifying evidence of a strong bottleneck and rapid expansion in South America. We use these models to then identify loci showing an excess of differentiation as a means of identifying putative targets of natural selection, and compare our results to expectations from recently developed theory on convergent adaptation. Consistent with predictions across a wide parameter space, we see limited evidence for convergent evolution at the nucleotide level in spite of strong similarities in overall phenotypes. Instead, we show that selection appears to have predominantly acted on standing genetic variation, and that introgression from wild teosinte populations appears to have played a role in highland adaptation in Mexican maize.

Chromosomal rearrangements as barriers to genetic homogenization between archaic and modern humans

Chromosomal rearrangements as barriers to genetic homogenization between archaic and modern humans

Rebekah L. Rogers
(Submitted on 26 May 2015)

Chromosomal rearrangements, which shuffle DNA across the genome, are an important source of divergence across taxa that can modify gene expression and function. Using a paired-end read approach with Illumina sequence data for archaic humans, I identify changes in genome structure that occurred recently in human evolution. Hundreds of rearrangements indicate genomic trafficking between the sex chromosomes and autosomes, raising the possibility of sex-specific changes. Additionally, genes adjacent to genome structure changes in Neanderthals are associated with testis-specific expression, consistent with evolutionary theory that new genes commonly form with expression in the testes. I identify one case of new-gene creation through transposition from the Y chromosome to chromosome 10 that combines the 5′ end of the testis-specific gene Fank1 with previously untranscribed sequence. This new transcript experienced copy number expansion in archaic genomes, indicating rapid genomic change. Finally, loci containing genome structure changes show diminished rates of introgression from Neanderthals into modern humans, consistent with the hypothesis that rearrangements serve as barriers to gene flow during hybridization. Together, these results suggest that this previously unidentified source of genomic variation has important biological consequences in human evolution.

Distance from Sub-Saharan Africa Predicts Mutational Load in Diverse Human Genomes

Distance from Sub-Saharan Africa Predicts Mutational Load in Diverse Human Genomes

Brenna M. Henn, Laura R Botigue, Stephan Peischl, Isabelle Dupanloup, Mikhail Lipatov, Brian K Maples, Alicia R Martin, Shaila Musharoff, Howard Cann, Michael Snyder, Laurent Excoffier, Jeffrey Kidd, Carlos D Bustamante
doi: http://dx.doi.org/10.1101/019711

The Out-of-Africa (OOA) dispersal ~50,000 years ago is characterized by a series of founder events as modern humans expanded into multiple continents. Population genetics theory predicts an increase of mutational load in populations undergoing serial founder effects during range expansions. To test this hypothesis, we have sequenced full genomes and high-coverage exomes from 7 geographically divergent human populations from Namibia, Congo, Algeria, Pakistan, Cambodia, Siberia and Mexico. We find that individual genomes vary modestly in the overall number of predicted deleterious alleles. We show via spatially explicit simulations that the observed distribution of deleterious allele frequencies is consistent with the OOA dispersal, particularly under a model where deleterious mutations are recessive. We conclude that there is a strong signal of purifying selection at conserved genomic positions within Africa, but that many predicted deleterious mutations have evolved as if they were neutral during the expansion out of Africa. Under a model where selection is inversely related to dominance, we show that OOA populations are likely to have a higher mutation load due to increased allele frequencies of nearly neutral variants that are recessive or partially recessive.

Genomic epidemiology of the current wave of artemisinin resistant malaria

Genomic epidemiology of the current wave of artemisinin resistant malaria

Roberto Amato, Olivo Miotto, Charles Woodrow, Jacob Almagro-Garcia, Ipsita Sinha, Susana Campino, Daniel Mead, Eleanor Drury, Mihir Kekre, Mandy Sanders, Alfred Amambua-Ngwa, Chanaki Amaratunga, Lucas Amenga-Etego, Tim JC Anderson, Voahangy Andrianaranjaka, Tobias Apinjoh, Elizabeth Ashley, Sarah Auburn, Gordon A Awandare, Vito Baraka, Alyssa Barry, Maciej F Boni, Steffen Borrmann, Teun Bousema, Oralee Branch, Peter C Bull, Kesinee Chotivanich, David J Conway, Alister Craig, Nicholas P Day, Abdoulaye Djimdé, Christiane Dolecek, Arjen M Dondorp, Chris Drakeley, Patrick Duffy, Diego F Echeverri-Garcia, Thomas G Egwang, Rick M Fairhurst, Md. Abul Faiz, Caterina I Fanello, Tran Tinh Hien, Abraham Hodgson, Mallika Imwong, Deus Ishengoma, Pharath Lim, Chanthap Lon, Jutta Marfurt, Kevin Marsh, Mayfong Mayxay, Victor Mobegi, Olugbenga Mokuolu, Jacqui Montgomery, Ivo Mueller, Myat Phone Kyaw, Paul N Newton, Francois Nosten, Rintis Noviyanti, Alexis Nzila, Harold Ocholla, Abraham Oduro, Marie Onyamboko, Jean-Bosco Ouedraogo, Aung Pyae Phyo, Christopher V Plowe, Ric N Price, Sasithon Pukrittayakamee, Milijaona Randrianarivelojosia, Pascal Ringwald, Lastenia Ruiz, David Saunders, Alex Shayo, Peter Siba, Shannon Takala-Harrison, Thuy-Nhien Nguyen Thanh, Vandana Thathy, Federica Verra, Nicholas J White, Ye Htut, Victoria J Cornelius, Rachel Giacomantonio, Dawn Muddyman, Christa Henrichs, Cinzia Malangone, Dushyanth Jyothi, Richard D Pearson, Julian C Rayner, Gilean McVean, Kirk Rockett, Alistair Miles, Paul Vauterin, Ben Jeffery, Magnus Manske, Jim Stalker, Bronwyn MacInnis, Dominic P Kwiatkowski, for the MalariaGEN Plasmodium falciparum Community
doi: http://dx.doi.org/10.1101/019737

Artemisinin resistant Plasmodium falciparum is advancing across Southeast Asia in a soft selective sweep involving at least 20 independent kelch13 mutations. In a large global survey, we find that kelch13 mutations which cause resistance in Southeast Asia are present at low frequency in Africa. We show that African kelch13 mutations have originated locally, and that kelch13 shows a normal variation pattern relative to other genes in Africa, whereas in Southeast Asia there is a great excess of non‐synonymous mutations, many of which cause radical amino‐acid changes. Thus, kelch13 is not currently undergoing strong selection in Africa, despite a deep reservoir of standing variation that could potentially allow resistance to emerge rapidly. The practical implications are that public health surveillance for artemisinin resistance should not rely on kelch13 data alone, and interventions to prevent resistance must account for local evolutionary conditions, shown by genomic epidemiology to differ greatly between geographical regions.

Worldwide population structure, long term demography, and local adaptation of Helicobacter pylori

Worldwide population structure, long term demography, and local adaptation of Helicobacter pylori

Valeria Montano, Xavier Didelot, Matthieu Foll, Bodo Linz, Richard Reinhardt, Sebastian Suerbaum, Yoshan Moodley, Jeffrey David Jensen
doi: http://dx.doi.org/10.1101/019430

Helicobacter pylori is an important human pathogen associated with serious gastric diseases. Owing to its medical importance and close relationship with its human host, understanding genomic patterns of global and local adaptation in H. pylori may be of particular significance for both clinical and evolutionary studies. Here we present the first such whole-genome analysis of 60 globally distributed strains, from which we inferred worldwide population structure and demographic history and shed light on interesting global and local events of positive selection, with particular emphasis on the evolution of San-associated lineages. Our results indicate a more ancient origin for the association of humans and H. pylori than previously thought. We identify several important perspectives for future clinical research on candidate selected regions that include both previously characterized genes (e.g. transcription elongation factor NusA and tumor Necrosis Factor Alpha-Inducing Protein Tipα) and hitherto unknown functional genes.