The study of Y chromosome variation has helped reconstruct demographic events associated with the spread of languages, agriculture, and pastoralism in sub-Saharan Africa, but little attention has been given to the early history of the continent. In order to overcome this lack of knowledge, we carried out a phylogeographic analysis of haplogroups A and B in a broad data set of sub-Saharan populations. These two lineages are particularly suitable for this objective because they are the two most deeply rooted branches of the Y chromosome genealogy. Their distribution is almost exclusively restricted to sub-Saharan Africa where their frequency peaks at 65% in groups of foragers. The combined high-resolution single nucleotide polymorphism analysis with short tandem repeats variation of their subclades reveals strong geographic and population structure for both haplogroups. This has allowed us to identify specific lineages related to regional preagricultural dynamics in different areas of sub-Saharan Africa. In addition, we observed signatures of relatively recent contact, both among Pygmies and between them and Khoisan speaker groups from southern Africa, thus contributing to the understanding of the complex evolutionary relationships among African hunter-gatherers. Finally, by revising the phylogeography of the very early human Y chromosome lineages, we have obtained support for the role of southern Africa as a sink, rather than a source, of the first migrations of modern humans from eastern and central parts of the continent. These results open new perspectives on the early history of Homo sapiens in Africa, with particular attention to areas of the continent where human fossil remains and archaeological data are scant.

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 Tipa) and hitherto unknown functional genes.KEYWORDS adaptation; neutral evolution; human pathogens H ELICOBACTER pylori is a Gram-negative bacterium that infects the mucosa of the human stomach. It was first described in the 1980s, when it was initially identified in association with chronic gastritis and later causally linked to serious gastric pathologies such as gastric cancer and ulcers (Marshall and Warren 1984;Suerbaum and Michetti 2002). It infects .80% of humans in developing countries and, although its prevalence is lower in developed countries, nearly 50% of the worldwide human population is infected (Ghose et al. 2005;Salih 2009;Salama et al. 2013).Due to its clinical and evolutionary importance, there has been considerable research on mechanisms of H. pylori transmission, as well as on the population genetics and phylogenetic relationships among global isolates. Thus far, population genetic analyses have mainly focused on seven housekeeping genes (usually referred to as multilocus sequence typing or MLST), with the primary conclusions being that H. pylori strains appear highly structured, and their phylogeographic patterns correlate consistently with that of their human hosts. Given that the H. pylori-humans association is at least 100,000 years old (Moodley et al. 2012), the current population structure of H. pylori may be regarded as mirroring past human expansions and migrations Linz et al. 2007;Breurec et al. 2011) and thus help us shed light on yet unknown dynamics of local demographic processes in human evolution. However, despite the knowledge gained thus far, the long-term global demographic history of H. pylori has never been directly inferred. The long, intimate association of H. pylori with humans suggests a history of bacterial adaptation. Considerable attention has focused on specific genes involved in modulating adaptive immunity of the host (for a review see Yamaoka 2010 andSalama et al. 2013) and on genomic changes occurring during acute and chronic H. pylori infection (Kennemann et al. 2011;Linz et a...

Both anatomically modern humans and the gastric pathogen Helicobacter pylori originated in Africa, and both species have been associated for at least 100,000 years. Seven geographically distinct H. pylori populations exist, three of which are indigenous to Africa: hpAfrica1, hpAfrica2, and hpNEAfrica. The oldest and most divergent population, hpAfrica2, evolved within San hunter-gatherers, who represent one of the deepest branches of the human population tree. Anticipating the presence of ancient H. pylori lineages within all hunter-gatherer populations, we investigated the prevalence and population structure of H. pylori within Baka Pygmies in Cameroon. Gastric biopsies were obtained by esophagogastroduodenoscopy from 77 Baka from two geographically separated populations, and from 101 non-Baka individuals from neighboring agriculturalist populations, and subsequently cultured for H. pylori. Unexpectedly, Baka Pygmies showed a significantly lower H. pylori infection rate (20.8%) than non-Baka (80.2%). We generated multilocus haplotypes for each H. pylori isolate by DNA sequencing, but were not able to identify Baka-specific lineages, and most isolates in our sample were assigned to hpNEAfrica or hpAfrica1. The population hpNEAfrica, a marker for the expansion of the Nilo-Saharan language family, was divided into East African and Central West African subpopulations. Similarly, a new hpAfrica1 subpopulation, identified mainly among Cameroonians, supports eastern and western expansions of Bantu languages. An age-structured transmission model shows that the low H. pylori prevalence among Baka Pygmies is achievable within the timeframe of a few hundred years and suggests that demographic factors such as small population size and unusually low life expectancy can lead to the eradication of H. pylori from individual human populations. The Baka were thus either H. pylori-free or lost their ancient lineages during past demographic fluctuations. Using coalescent simulations and phylogenetic inference, we show that Baka almost certainly acquired their extant H. pylori through secondary contact with their agriculturalist neighbors.

The current distribution of Bantu languages is commonly considered to be a consequence of a relatively recent population expansion (3-5kya) in Central Western Africa. While there is a substantial consensus regarding the centre of origin of Bantu languages (the Benue River Valley, between South East Nigeria and Western Cameroon), the identification of the area from where the population expansion actually started, the relation between the processes leading to the spread of languages and peoples and the relevance of local migratory events remain controversial. In order to shed new light on these aspects, we studied Y chromosome variation in a broad dataset of populations encompassing Nigeria, Cameroon, Gabon and Congo. Our results evidence an evolutionary scenario which is more complex than had been previously thought, pointing to a marked differentiation of Cameroonian populations from the rest of the dataset. In fact, in contrast with the current view of Bantu speakers as a homogeneous group of populations, we observed an unexpectedly high level of interpopulation genetic heterogeneity and highlighted previously undetected diversity for lineages associated with the diffusion of Bantu languages (E1b1a (M2) sub-branches). We also detected substantial differences in local demographic histories, which concord with the hypotheses regarding an early diffusion of Bantu languages into the forest area and a subsequent demographic expansion and migration towards eastern and western Africa.

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.

Genetic estimates of effective population size (N e ) are an established means to develop informed conservation policies. Another key goal to pursue the conservation of endangered species is keeping the connectivity across fragmented environments, to which genetic inferences of gene flow and dispersal greatly contribute. Most current statistical tools for estimating such population demographic parameters are based on Kingman's coalescent (KC). However, KC is inappropriate for taxa displaying skewed reproductive variance, a property widely observed in natural species. Coalescent models that consider skewed reproductive success-called multiple merger coalescents (MMCs)-have been shown to substantially improve estimates of N e when the distribution of offspring per capita is highly skewed. MMCs predictions of standard population genetic parameters, including the rate of loss of genetic variation and the fixation probability of strongly selected alleles, substantially depart from KC predictions. These extended models also allow studying gene genealogies in a spatial continuum, providing a novel theoretical framework to investigate spatial connectivity. Therefore, development of statistical tools based on MMCs should substantially improve estimates of population demographic parameters with major conservation implications.

BackgroundThe spatial Principal Component Analysis (sPCA, Jombart (Heredity 101:92-103, 2008) is designed to investigate non-random spatial distributions of genetic variation. Unfortunately, the associated tests used for assessing the existence of spatial patterns (global and local test; (Heredity 101:92-103, 2008) lack statistical power and may fail to reveal existing spatial patterns. Here, we present a non-parametric test for the significance of specific patterns recovered by sPCA.ResultsWe compared the performance of this new test to the original global and local tests using datasets simulated under classical population genetic models. Results show that our test outperforms the original global and local tests, exhibiting improved statistical power while retaining similar, and reliable type I errors. Moreover, by allowing to test various sets of axes, it can be used to guide the selection of retained sPCA components.ConclusionsAs such, our test represents a valuable complement to the original analysis, and should prove useful for the investigation of spatial genetic patterns.Electronic supplementary materialThe online version of this article (10.1186/s12859-017-1988-y) contains supplementary material, which is available to authorized users.

Movement of species beyond their indigenous distribution can fundamentally alter the conservation status of the populations involved. If introductions are human-facilitated, introduced species could be considered pests. Characterizing the colonization history of introduced species can therefore be critical to formulating the objectives and nature of wildlife management strategies. The black swan (Cygnus atratus) is native to Australia but is considered a reintroduced species in New Zealand, where the endemic population was reported extinct during the 19th century. After the reintroduction of a small number of individuals from Australia, the New Zealand population expanded unexpectedly rapidly, which was attributed to simultaneous waves of migration fromAustralia. An alternative, but hitherto unformalized, hypothesis is that local extant populations remained and admixed with introduced individuals. To contribute to our understanding of the reintroduction history of the species, we investigated dispersal patterns and demographic histories of seven populations from Australia and New Zealand, using population genetic inferences from a microsatellite dataset. Our results on genetic structure, dispersal rates, and demographic histories provide mixed evidence on the origin of New Zealand black swans. The hypothesis that reintroduced individuals mixed with remaining local individuals and that the subsequent dramatic population expansion may have been due to genetic rescue of the inbred indigenous population cannot be discarded and needs further investigation. K E Y W O R D Sconservation, Cygnus atratus, kakianau, pest species, phylopatry