Density-Dependent Selection during Range Expansion Affects Expansion Load in Life History Traits

AbstractModels of range expansion have independently explored fitness consequences of life history trait evolution and increased rates of genetic drift-or "allele surfing"-during spatial spread, but no previous model has examined the interactions between these two processes. Here, using spatially explicit simulations, we explore an ecologically complex range expansion scenario that combines density-dependent selection with allele surfing to asses the genetic and fitness consequences of density-dependent selection on the evolution of life history traits. We demonstrate that density-dependent selection on the range edge acts differently depending on the life history trait and can either diminish or enhance allele surfing. Specifically, we show that selection at the range edge is always weaker at sites affecting competitive ability (K-selected traits) than at sites affecting birth rate (r-selected traits). We then link differences in the frequency of deleterious mutations to differences in the efficacy of selection and rate of mutation accumulation across distinct life history traits. Finally, we demonstrate that the observed fitness consequences of allele surfing depend on the population density in which expansion load is measured. Our work highlights the complex relationship between ecology and expressed genetic load, which will be important to consider when interpreting both experimental and field studies of range expansion.

Blood Metabolite Profiling of Antarctic Expedition Members: An 1H NMR Spectroscopy-Based Study

Serum samples from eight participants during the XV winter-over at Concordia base (Antarctic expedition) collected at defined time points, including predeparture, constituted the key substrates for a specific metabolomics study. To ascertain acute changes and chronic adaptation to hypoxia, the metabolic profiles of the serum samples were analyzed using NMR spectroscopy, with principal components analysis (PCA) followed by partial least squares and orthogonal partial least squares discriminant analyses (PLS-DA and OPLS-DA) used as supervised classification methods. Multivariate data analyses clearly highlighted an adaptation period characterized by an increase in the levels of circulating glutamine and lipids, mobilized to supply the body energy needs. At the same time, a reduction in the circulating levels of glutamate and N-acetyl glycoproteins, stress condition indicators, and proinflammatory markers were also found in the NMR data investigation. Subsequent pathway analysis showed possible perturbations in metabolic processes, potentially related to the physiological adaptation, predominantly found by comparing the baseline (at sea level, before mission onset), the base arrival, and the mission ending collected values.

An etiology of human modernity

Following the refutation of the replacement hypothesis, which had proposed that a ‘superior’ hominin species arose in Africa and replaced all other humans existing at the time, the auto-domestication hypothesis remains the only viable explanation for the relatively abrupt change from robust to gracile humans in the Late Pleistocene. It invokes the incidental institution of the domestication syndrome in humans, most probably by newly introduced cultural practices. It also postulates that the induction of exograms compensated for the atrophy of the brain caused by domestication. This new explanation of the origins of modernity in humans elucidates practically all its many aspects, in stark contrast to the superseded replacement hypothesis, which explained virtually nothing. The first results of the domestication syndrome’s genetic exploration have become available in recent years, and they endorse the human self-domestication hypothesis.

Nonadaptive processes in primate and human evolution

Evolutionary biology has tended to focus on adaptive evolution by positive selection as the primum mobile of evolutionary trajectories in species while underestimating the importance of nonadaptive evolutionary processes. In this review, I describe evidence that suggests that primate and human evolution has been strongly influenced by nonadaptive processes, particularly random genetic drift and mutation. This is evidenced by three fundamental effects: a relative relaxation of selective constraints (i.e., purifying selection), a relative increase in the fixation of slightly deleterious mutations, and a general reduction in the efficacy of positive selection. These effects are observed in protein-coding, regulatory regions, and in gene expression data, as well as in an augmentation of fixation of large-scale mutations, including duplicated genes, mobile genetic elements, and nuclear mitochondrial DNA. The evidence suggests a general population-level explanation such as a reduction in effective population size (N(e)). This would have tipped the balance between the evolutionary forces of natural selection and random genetic drift toward genetic drift for variants having small selective effects. After describing these proximate effects, I describe the potential consequences of these effects for primate and human evolution. For example, an increase in the fixation of slightly deleterious mutations could potentially have led to an increase in the fixation rate of compensatory mutations that act to suppress the effects of slightly deleterious substitutions. The potential consequences of compensatory evolution for the evolution of novel gene functions and in potentially confounding the detection of positively selected genes are explored. The consequences of the passive accumulation of large-scale genomic mutations by genetic drift are unclear, though evidence suggests that new gene copies as well as insertions of transposable elements into genes can potentially lead to adaptive phenotypes. Finally, because a decrease in selective constraint at the genetic level is expected to have effects at the morphological level, I review studies that compare rates of morphological change in various mammalian and island populations where N(e) is reduced. Furthermore, I discuss evidence that suggests that craniofacial morphology in the Homo lineage has shifted from an evolutionary rate constrained by purifying selection toward a neutral evolutionary rate.

Density-regulated population dynamics and conditional dispersal alter the fate of mutations occurring at the front of an expanding population

There is an increasing recognition that the interplay between ecological and evolutionary processes shapes the genetic footprint of populations during and after range expansions. However, more complex ecological processes regularly considered within spatial ecology remain unexplored in models describing the population genetics of range expansion. In this study we integrate flexible descriptions of population growth and competition as well as conditional dispersal into a model that simulates the fate of mutations occurring at the wave front of an expanding population. Our results show that the survival and distribution of a mutation is not only affected by its bias (that is, whether it is deleterious, neutral or beneficial) but also by the mode of local density regulation and conditional dispersal of the simulated populations. It is in particular the chance of a mutation to establish at the front of advance and 'surf' to high frequencies that critically depends on the investigated ecological processes. This is because of the influence of these processes on demographic stochasticity in the system and the differential responses of deleterious, neutral and beneficial mutations to this stochasticity. Generally, deleterious mutations rely more on chance and thus profit the most from ecological processes that enhance demographic stochasticity during the period of establishment. Our study emphasizes the importance of incorporating more ecological realism into evolutionary models to better understand the consequences of shifting geographic ranges for the genetic structure of populations and to find efficient adaptation strategies to mitigate these effects.

Out of Africa: modern human origins special feature: explaining worldwide patterns of human genetic variation using a coalescent-based serial founder model of migration outward from Africa

Studies of worldwide human variation have discovered three trends in summary statistics as a function of increasing geographic distance from East Africa: a decrease in heterozygosity, an increase in linkage disequilibrium (LD), and a decrease in the slope of the ancestral allele frequency spectrum. Forward simulations of unlinked loci have shown that the decline in heterozygosity can be described by a serial founder model, in which populations migrate outward from Africa through a process where each of a series of populations is formed from a subset of the previous population in the outward expansion. Here, we extend this approach by developing a retrospective coalescent-based serial founder model that incorporates linked loci. Our model both recovers the observed decline in heterozygosity with increasing distance from Africa and produces the patterns observed in LD and the ancestral allele frequency spectrum. Surprisingly, although migration between neighboring populations and limited admixture between modern and archaic humans can be accommodated in the model while continuing to explain the three trends, a competing model in which a wave of outward modern human migration expands into a series of preexisting archaic populations produces nearly opposite patterns to those observed in the data. We conclude by developing a simpler model to illustrate that the feature that permits the serial founder model but not the archaic persistence model to explain the three trends observed with increasing distance from Africa is its incorporation of a cumulative effect of genetic drift as humans colonized the world.

The frequency of fitness peak shifts is increased at expanding range margins due to mutation surfing

Dynamic species' ranges, those that are either invasive or shifting in response to environmental change, are the focus of much recent interest in ecology, evolution, and genetics. Understanding how range expansions can shape evolutionary trajectories requires the consideration of nonneutral variability and genetic architecture, yet the majority of empirical and theoretical work to date has explored patterns of neutral variability. Here we use forward computer simulations of population growth, dispersal, and mutation to explore how range-shifting dynamics can influence evolution on rugged fitness landscapes. We employ a two-locus model, incorporating sign epistasis, and find that there is an increased likelihood of fitness peak shifts during a period of range expansion. Maladapted valley genotypes can accumulate at an expanding range front through a phenomenon called mutation surfing, which increases the likelihood that a mutation leading to a higher peak will occur. Our results indicate that most peak shifts occur close to the expanding front. We also demonstrate that periods of range shifting are especially important for peak shifting in species with narrow geographic distributions. Our results imply that trajectories on rugged fitness landscapes can be modified substantially when ranges are dynamic.

The revolution that didn't arrive: A review of Pleistocene Sahul

There is a "package" of cultural innovations that are claimed to reflect modern human behaviour. The introduction of the "package" has been associated with the Middle-to-Upper Palaeolithic transition and the appearance in Europe of modern humans. It has been proposed that modern humans spread from Africa with the "package" and colonised not only Europe but also southern Asia and Australia (McBrearty and Brooks, 2000; Mellars, 2006a). In order to evaluate this proposal, we explore the late Pleistocene archaeological record of Sahul, the combined landmass of Australia and Papua New Guinea, for indications of these cultural innovations at the earliest sites. It was found that following initial occupation of the continent by anatomically and behaviourally modern humans, the components were gradually assembled over a 30,000-year period. We discount the idea that the "package" was lost en route to Sahul and assess the possibility that the "package" was not integrated within the material culture of the initial colonising groups because they may not have been part of a rapid colonisation process from Africa. As the cultural innovations appear at different times and locations within Sahul, the proposed "package" of archaeologically visible traits cannot be used to establish modern human behaviour. Whilst the potential causal role of increasing population densities/pressure in the appearance of the "package" of modern human behaviour in the archaeological record is acknowledged, it is not seen as the sole explanation because the individual components of the "package" appear at sites that are widely separated in space and time.

Testing for archaic hominin admixture on the X chromosome: model likelihoods for the modern human RRM2P4 region from summaries of genealogical topology under the structured coalescent

A 2.4-kb stretch within the RRM2P4 region of the X chromosome, previously sequenced in a sample of 41 globally distributed humans, displayed both an ancient time to the most recent common ancestor (e.g., a TMRCA of approximately 2 million years) and a basal clade composed entirely of Asian sequences. This pattern was interpreted to reflect a history of introgressive hybridization from archaic hominins (most likely Asian Homo erectus) into the anatomically modern human genome. Here, we address this hypothesis by resequencing the 2.4-kb RRM2P4 region in 131 African and 122 non-African individuals and by extending the length of sequence in a window of 16.5 kb encompassing the RRM2P4 pseudogene in a subset of 90 individuals. We find that both the ancient TMRCA and the skew in non-African representation in one of the basal clades are essentially limited to the central 2.4-kb region. We define a new summary statistic called the minimum clade proportion (pmc), which quantifies the proportion of individuals from a specified geographic region in each of the two basal clades of a binary gene tree, and then employ coalescent simulations to assess the likelihood of the observed central RRM2P4 genealogy under two alternative views of human evolutionary history: recent African replacement (RAR) and archaic admixture (AA). A molecular-clock-based TMRCA estimate of 2.33 million years is a statistical outlier under the RAR model; however, the large variance associated with this estimate makes it difficult to distinguish the predictions of the human origins models tested here. The pmc summary statistic, which has improved power with larger samples of chromosomes, yields values that are significantly unlikely under the RAR model and fit expectations better under a range of archaic admixture scenarios.

Archaic admixture in the human genome

One of the enduring questions in the evolution of our species surrounds the fate of 'archaic' forms of Homo. Did Neanderthals go extinct without interbreeding with modern humans 25-40 thousand years ago or are their genes present among modern-day Europeans? Recent work suggests that Neanderthals and an as yet unidentified archaic African population contributed to at least 5% of the modern European and West African gene pools, respectively. Extensive sequencing of Neanderthal and other archaic human nuclear DNA has the potential to answer this question definitively within the next few years.

Reconstructing human origins in the genomic era

Analyses of recently acquired genomic sequence data are leading to important insights into the early evolution of anatomically modern humans, as well as into the more recent demographic processes that accompanied the global radiation of Homo sapiens. Some of the new results contradict early, but still influential, conclusions that were based on analyses of gene trees from mitochondrial DNA and Y-chromosome sequences. In this review, we discuss the different genetic and statistical methods that are available for studying human population history, and identify the most plausible models of human evolution that can accommodate the contrasting patterns observed at different loci throughout the genome.

Going east: new genetic and archaeological perspectives on the modern human colonization of Eurasia

The pattern of dispersal of biologically and behaviorally modern human populations from their African origins to the rest of the occupied world between approximately 60,000 and 40,000 years ago is at present a topic of lively debate, centering principally on the issue of single versus multiple dispersals. Here I argue that the archaeological and genetic evidence points to a single successful dispersal event, which took genetically and culturally modern populations fairly rapidly across southern and southeastern Asia into Australasia, and with only a secondary and later dispersal into Europe.

Genomics refutes an exclusively African origin of humans

Ten years ago, evidence from genetics gave strong support to the "recent African origin" view of the evolution of modern humans, which posits that Homo sapiens arose as a new species in Africa and subsequently spread, leading to the extinction of other archaic human species. Subsequent data from the nuclear genome not only fail to support this model, they do not support any simple model of human demographic history. In this paper, we study a process in which the modern human phenotype originates in Africa and then advances across the world by local demic diffusion, hybridization, and natural selection. While the multiregional model of human origins posits a number of independent single locus selective sweeps, and the "out of Africa" model posits a sweep of a new species, we study the intermediate case of a phenotypic sweep. Numerical simulations of this process replicate many of the seemingly contradictory features of the genetic data, and suggest that as much as 80% of nuclear loci have assimilated genetic material from non-African archaic humans.

Genetic diversity and genetic burden in humans

We discuss categories of genetic diversity in humans. Neutral diversity, population differences in frequencies of genetic markers that we think are invisible to natural selection, provides a passive record of population history but is otherwise of little interest in human biology. Genetic variation related to disease can be separated into mutational noise and variation due to selection, either ongoing selection else effects of a past environment. We distinguish consequences of genetic diversity for fitness, relevant to evolution, and consequences for well-being, relevant to medicine and public health. We call genetic variation that causes impairment of health or well-being of individual humans "apparent genetic burden" and variation that has effects on fitness but not well-being "unapparent genetic burden". We use "burden" to distinguish these notions from the classical concept of "genetic load" that refers to effects on population fitness, a concept formulated by Morton et al. [Morton, N.E., Crow, J.F., Muller, H.J., 1956. An estimate of the mutational damage in man from data on consanguineous marriages. Proc. Natl. Acad. Sci. U.S.A. 42, 855-863]. We distinguish adapted genes and adapted genotypes: an adapted gene is a gene that increases fitness of its bearer either in heterozygous or homozygous state or both, while an adapted genotype is a genotype that increases fitness of its bearer but is not transmitted intact to future generations. Balanced polymorphisms in which the heterozygote is superior in fitness may generate most adapted genotypes. In the face of major rapid environmental change adapted genotypes appear first but over time they are replaced by adapted genes. The presence of adapted genotypes is a good indication of recent environmental change: for example, there are apparently many polymorphisms in domestic animals of this nature, responses to domestication, and many fewer in wild animals (and in humans).

Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa

Equilibrium models of isolation by distance predict an increase in genetic differentiation with geographic distance. Here we find a linear relationship between genetic and geographic distance in a worldwide sample of human populations, with major deviations from the fitted line explicable by admixture or extreme isolation. A close relationship is shown to exist between the correlation of geographic distance and genetic differentiation (as measured by F(ST)) and the geographic pattern of heterozygosity across populations. Considering a worldwide set of geographic locations as possible sources of the human expansion, we find that heterozygosities in the globally distributed populations of the data set are best explained by an expansion originating in Africa and that no geographic origin outside of Africa accounts as well for the observed patterns of genetic diversity. Although the relationship between F(ST) and geographic distance has been interpreted in the past as the result of an equilibrium model of drift and dispersal, simulation shows that the geographic pattern of heterozygosities in this data set is consistent with a model of a serial founder effect starting at a single origin. Given this serial-founder scenario, the relationship between genetic and geographic distance allows us to derive bounds for the effects of drift and natural selection on human genetic variation.

The use of racial, ethnic, and ancestral categories in human genetics research

The global dispersal of anatomically modern humans over the past 100,000 years has produced patterns of phenotypic variation that have exerted--and continue to exert--powerful influences on the lives of individuals and the experiences of groups. The recency of our common ancestry and continued gene flow among populations have resulted in less genetic differentiation among geographically distributed human populations than is observed in many other mammalian species. Nevertheless, differences in appearance have contributed to the development of ideas about "race" and "ethnicity" that often include the belief that significant inherited differences distinguish humans. The use of racial, ethnic, and ancestral categories in genetics research can imply that group differences arise directly through differing allele frequencies, with little influence from socially mediated mechanisms. At the same time, careful investigations of the biological, environmental, social, and psychological attributes associated with these categories will be an essential component of cross-disciplinary research into the origins, prevention, and treatment of common diseases, including those diseases that differ in prevalence among groups.

Deep haplotype divergence and long-range linkage disequilibrium at xp21.1 provide evidence that humans descend from a structured ancestral population

Fossil evidence links human ancestry with populations that evolved from modern gracile morphology in Africa 130,000-160,000 years ago. Yet fossils alone do not provide clear answers to the question of whether the ancestors of all modern Homo sapiens comprised a single African population or an amalgamation of distinct archaic populations. DNA sequence data have consistently supported a single-origin model in which anatomically modern Africans expanded and completely replaced all other archaic hominin populations. Aided by a novel experimental design, we present the first genetic evidence that statistically rejects the null hypothesis that our species descends from a single, historically panmictic population. In a global sample of 42 X chromosomes, two African individuals carry a lineage of noncoding 17.5-kb sequence that has survived for >1 million years without any clear traces of ongoing recombination with other lineages at this locus. These patterns of deep haplotype divergence and long-range linkage disequilibrium are best explained by a prolonged period of ancestral population subdivision followed by relatively recent interbreeding. This inference supports human evolution models that incorporate admixture between divergent African branches of the genus Homo.

Genetic analysis of lice supports direct contact between modern and archaic humans

Parasites can be used as unique markers to investigate host evolutionary history, independent of host data. Here we show that modern human head lice, Pediculus humanus, are composed of two ancient lineages, whose origin predates modern Homo sapiens by an order of magnitude (ca. 1.18 million years). One of the two louse lineages has a worldwide distribution and appears to have undergone a population bottleneck ca. 100,000 years ago along with its modern H. sapiens host. Phylogenetic and population genetic data suggest that the other lineage, found only in the New World, has remained isolated from the worldwide lineage for the last 1.18 million years. The ancient divergence between these two lice is contemporaneous with splits among early species of Homo, and cospeciation analyses suggest that the two louse lineages codiverged with a now extinct species of Homo and the lineage leading to modern H. sapiens. If these lice indeed codiverged with their hosts ca. 1.18 million years ago, then a recent host switch from an archaic species of Homo to modern H. sapiens is required to explain the occurrence of both lineages on modern H. sapiens. Such a host switch would require direct physical contact between modern and archaic forms of Homo.