Out of Africa again and again

Range expansions across landscapes with quenched noise

When biological populations expand into new territory, the evolutionary outcomes can be strongly influenced by genetic drift, the random fluctuations in allele frequencies. Meanwhile, spatial variability in the environment can also significantly influence the competition between subpopulations vying for space. Little is known about the interplay of these intrinsic and extrinsic sources of noise in population dynamics: When does environmental heterogeneity dominate over genetic drift or vice versa, and what distinguishes their population genetics signatures? Here, in the context of neutral evolution, we examine the interplay between a population's intrinsic, demographic noise and an extrinsic, quenched random noise provided by a heterogeneous environment. Using a multispecies Eden model, we simulate a population expanding over a landscape with random variations in local growth rates and measure how this variability affects genealogical tree structure, and thus genetic diversity. We find that, for strong heterogeneity, the genetic makeup of the expansion front is to a great extent predetermined by the set of fastest paths through the environment. The landscape-dependent statistics of these optimal paths then supersede those of the population's intrinsic noise as the main determinant of evolutionary dynamics. Remarkably, the statistics for coalescence of genealogical lineages, derived from those deterministic paths, strongly resemble the statistics emerging from demographic noise alone in uniform landscapes. This cautions interpretations of coalescence statistics and raises new challenges for inferring past population dynamics.

Teeth, prenatal growth rates, and the evolution of human-like pregnancy in later Homo

Evidence of how gestational parameters evolved is essential to understanding this fundamental stage of human life. Until now, these data seemed elusive given the skeletal bias of the fossil record. We demonstrate that dentition provides a window into the life of neonates. Teeth begin to form in utero and are intimately associated with gestational development. We measured the molar dentition for 608 catarrhine primates and collected data on prenatal growth rate (PGR) and endocranial volume (ECV) for 19 primate genera from the literature. We found that PGR and ECV are highly correlated (R² = 0.93, P < 0.001). Additionally, we demonstrated that molar proportions are significantly correlated with PGR (P = 0.004) and log-transformed ECV (P = 0.001). From these correlations, we developed two methods for reconstructing PGR in the fossil record, one using ECV and one using molar proportions. Dental proportions reconstruct hominid ECV (R² = 0.81, P < 0.001), a result that can be extrapolated to PGR. As teeth dominate fossil assemblages, our findings greatly expand our ability to investigate life history in the fossil record. Fossil ECVs and dental measurements from 13 hominid species both support significantly increasing PGR throughout the terminal Miocene and Plio-Pleistocene, reflecting known evolutionary changes. Together with pelvic and endocranial morphology, reconstructed PGRs indicate the need for increasing maternal energetics during pregnancy over the last 6 million years, reaching a human-like PGR (i.e., more similar to humans than to other extant apes) and ECV in later Homo less than 1 million years ago.

Contrasting maternal and paternal genetic histories among five ethnic groups from Khyber Pakhtunkhwa, Pakistan

Northwest Pakistan has served as a point of entry to South Asia for different populations since ancient times. However, relatively little is known about the population genetic history of the people residing within this region. To better understand human dispersal in the region within the broader history of the subcontinent, we analyzed mtDNA diversity in 659 and Y-chromosome diversity in 678 individuals, respectively, from five ethnic groups (Gujars, Jadoons, Syeds, Tanolis and Yousafzais), from Swabi and Buner Districts, Khyber Pakhtunkhwa Province, Pakistan. The mtDNAs of all individuals were subject to control region sequencing and SNP genotyping, while Y-chromosomes were analyzed using 54 SNPs and 19 STR loci. The majority of the mtDNAs belonged to West Eurasian haplogroups, with the rest belonging to either South or East Asian lineages. Four of the five Pakistani populations (Gujars, Jadoons, Syeds, Yousafzais) possessed strong maternal genetic affinities with other Pakistani and Central Asian populations, whereas one (Tanolis) did not. Four haplogroups (R1a, R1b, O3, L) among the 11 Y-chromosome lineages observed among these five ethnic groups contributed substantially to their paternal genetic makeup. Gujars, Syeds and Yousafzais showed strong paternal genetic affinities with other Pakistani and Central Asian populations, whereas Jadoons and Tanolis had close affinities with Turkmen populations from Central Asia and ethnic groups from northeast India. We evaluate these genetic data in the context of historical and archeological evidence to test different hypotheses concerning their origins and biological relationships.

Human mitochondrial DNA diversity is compatible with the multiregional continuity theory of the origin of Homo sapiens

Confidence intervals for estimates of human mtDNA sequence diversity, chimpanzee-human mtDNA sequence divergence, and the time of splitting of the pongid-hominid lineages are presented. Consistent with all the data used in estimating the coalescence time for human mitochondrial lineages to a common ancestral mitochondrion is a range of dates from less than 79,000 years ago to more than 1,139,000 years ago. Consequently, the hypothesis that a migration of modern humans (Homo sapiens) out of Africa in the range of 140,000 to 280,000 years ago resulted in the complete replacement, without genetic interchange, of earlier Eurasian hominid populations (Homo erectus) is but one of several possible interpretations of the mtDNA data. The data are also compatible with the hypothesis, suggested earlier and supported by fossil evidence, of a single, more ancient expansion of the range of Homo erectus from Africa, followed by a gradual transition to Homo sapiens in Europe, Asia, and Africa.

Comparative dental study between Homo antecessor and Chinese Homo erectus: Nonmetric features and geometric morphometrics

The Chinese Middle Pleistocene fossils from Hexian, Xichuan, Yiyuan, and Zhoukoudian have been generally classified as Homo erectus s.s. These hominins share some primitive features with other Homo specimens, but they also display unique cranial and dental traits. Thus, the Chinese Middle Pleistocene hominins share with other European and Asian hominin populations the so-called 'Eurasian dental pattern'. The late Early Pleistocene hominins from Gran Dolina-TD6.2 (Spain), representing the species Homo antecessor, also exhibit the Eurasian dental pattern, which may suggest common roots. To assess phylogenetic affinities of these two taxa, we evaluated and compared nonmetric and metric dental features and interpreted morphological differences within a comparative hominin framework. We determined that the robust roots of the molars, the shelf-like protostylid, the dendrite-like pattern of the enamel-dentine junction surface of the upper fourth premolars and molars, the strongly folded dentine of the labial surface of the upper incisors, and the rare occurrence of a mid-trigonid crest in the lower molars, are all characteristic of Chinese H. erectus. With regard to H. antecessor, we observed the consistent expression of a continuous mid-trigonid crest, the absence of a cingulum in the upper canines, a complex root pattern of the lower premolars, and a rhomboidal occlusal contour and occlusal polygon and protrusion in the external outline of a large a bulging hypocone in the first and second upper molars. Using two-dimensional geometric morphometrics, we further demonstrated that H. antecessor falls outside the range of variation of Chinese H. erectus for occlusal crown outline shape, the orientation of occlusal grooves, and relative locations of anterior and posterior foveae in the P⁴s, P₃s, M¹s, M²s, and M₂s. Given their geographic and temporal separation, the differences between these two species suggest their divergence occurred at some point in the Early Pleistocene, and thereafter they followed different evolutionary paths.

The founder sociality hypothesis

In this review, we propose that the social dynamics of founder populations in novel and newly available environments can have critical effects in shaping species' sociality and can produce long-lasting changes in social structure and behavior. For founder populations which expand into an underexploited niche separated from the parent population, the necessity of bond formation with strangers, lack of clear territories, and initial abundance of resources can lead to altered initial social dynamics to which subsequent generations adapt. We call this the founder sociality hypothesis. After specifying the theoretical reasoning and mechanism of effect, we focus on three particular cases where the social dynamics of founder populations may have a central role in explaining their modern behavioral ecology. In particular, we develop and review evidence for three predictions of the founder sociality hypothesis in territorial, mixed-sex group forming species: relatively stronger social bonds in the dispersing sex with relatively weaker bonds in the nondispersing sex, reduced territoriality, and increased social tolerance. We briefly touch on the implications for human evolution given our species' evolutionary history marked by frequent expansion and adaptation to novel environments. We conclude by proposing several experiments and models with testable predictions following from the founder sociality hypothesis.

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.

The Landscape of Micro-Inversions Provide Clues for Population Genetic Analysis of Humans

Background

Variations in the human genome have been studied extensively. However, little is known about the role of micro-inversions (MIs), generally defined as small (< 100 bp) inversions, in human evolution, diversity, and health. Depicting the pattern of MIs among diverse populations is critical for interpreting human evolutionary history and obtaining insight into genetic diseases.

Results

In this paper, we explored the distribution of MIs in genomes from 26 human populations and 7 nonhuman primate genomes and analyzed the phylogenetic structure of the 26 human populations based on the MIs. We further investigated the functions of the MIs located within genes associated with human health. With hg19 as the reference genome, we detected 6968 MIs among the 1937 human samples and 24,476 MIs among the 7 nonhuman primate genomes. The analyses of MIs in human genomes showed that the MIs were rarely located in exonic regions. Nonhuman primates and human populations shared only 82 inverted alleles, and Africans had the most inverted alleles in common with nonhuman primates, which was consistent with the “Out of Africa” hypothesis. The clustering of MIs among the human populations also coincided with human migration history and ancestral lineages.

Conclusions

We propose that MIs are potential evolutionary markers for investigating population dynamics. Our results revealed the diversity of MIs in human populations and showed that they are essential to construct human population relationships and have a potential effect on human health.

Electronic supplementary material

The online version of this article (10.1007/s12539-020-00392-6) contains supplementary material, which is available to authorized users.

The Nigerian Twin and Sibling Registry: An Update

Here we provide an update of the 2013 report on the Nigerian Twin and Sibling Registry (NTSR). The major aim of the NTSR is to understand genetic and environmental influences and their interplay in psychological and mental health development in Nigerian children and adolescents. Africans have the highest twin birth rates among all human populations, and Nigeria is the most populous country in Africa. Due to its combination of large population and high twin birth rates, Nigeria has one of the largest twin populations in the world. In this article, we provide current updates on the NTSR samples recruited, recruitment procedures, zygosity assessment and findings emerging from the NTSR.

Evolutionary Perspective in Rickets and Vitamin D

Modern lifestyle limits our exposure to sunlight, which photosynthesizes vitamin D in the skin, and the incidence of nutritional rickets has been resurging. Vitamin D is one of the first hormones; it is photosynthesized in all organism from the phytoplankton to mammals. A selective sweep of the promoter of the vitamin D receptor (VDR) happened as soon as Homo sapiens migrated out of Africa; it co-adapted with skin color genes to provide adaptation to latitudes and the levels of exposure to ultraviolet (UV)B radiation along the route out of Africa. Exposure to UVB radiation balances the need for vitamin D photosynthesis and degradation of folic acid by UVB radiation. Skin color follows a latitude distribution: the darkest populations dwell in the tropical belt; and the fair-skinned populations inhabit the northern countries. Due to their greater need for calcium during their reproductive life, the skin color of women is lighter- than that of men. Vitamin D is essential for mineral homeostasis and has a wide variety of non-skeletal functions, of which the most important for natural selection is a regulatory function in the innate immune system. In the human fossil record, vitamin D deficiency coincided with bone tuberculosis. About 6,000 years ago, a diet which included cow's milk provided Neolithic humans with twice as much calcium and was more alkaline than that of its Paleolithic predecessors. Adiposity is negatively associated with the vitamin D status and obese individuals require 2-3 times more vitamin D than non-obese individuals to normalize circulating 25OHD levels. In an era of an obesity epidemic, we need more research to determine whether adiposity should be considered when determining the dietary requirements for vitamin D and calcium and the optimal serum 25OHD levels.

Spatial interference scale as a determinant of microbial range expansion

In microbial communities, social interactions such as competition occur ubiquitously across multiple spatial scales from local proximity to remote distance. However, it remains unclear how such a spatial variation of interaction contributes to the structural development of microbial populations. Here, we developed synthetic consortia, biophysical theory, and simulations to elucidate the role of spatial interference scale in governing ecosystem organization during range expansion. For consortia with unidirectional interference, we discovered that, at growing fronts, the extinction time of toxin-sensitive species is reciprocal to the spatial interference scale. In contrast, for communities with bidirectional interference, their structures diverge into distinct monoculture colonies under different initial conditions, with the corresponding separatrix set by the spatial scale of interference. Near the separatrix, ecosystem development becomes noise-driven and yields opposite structures. Our results establish spatial interaction scale as a key determinant for microbial range expansion, providing insights into microbial spatial organization and synthetic ecosystem engineering.

Intraspecific eye color variability in birds and mammals: a recent evolutionary event exclusive to humans and domestic animals

Background

Human populations and breeds of domestic animals are composed of individuals with a multiplicity of eye (= iris) colorations. Some wild birds and mammals may have intraspecific eye color variability, but this variation seems to be due to the developmental stage of the individual, its breeding status, and/or sexual dimorphism. In other words, eye colour tends to be a species-specific trait in wild animals, and the exceptions are species in which individuals of the same age group or gender all develop the same eye colour. Domestic animals, by definition, include bird and mammal species artificially selected by humans in the last few thousand years. Humans themselves may have acquired a diverse palette of eye colors, likewise in recent evolutionary time, in the Mesolithic or in the Upper Paleolithic.

Presentation of the hypothesis

We posit two previously unrecognized hypotheses regarding eye color variation: 1) eye coloration in wild animals of every species tends to be a fixed trait. 2) Humans and domestic animal populations, on the contrary, have eyes of multiple colors. Sexual selection has been invoked for eye color variation in humans, but this selection mode does not easily apply in domestic animals, where matings are controlled by the human breeder.

Testing the hypothesis

Eye coloration is polygenic in humans. We wish to investigate the genetics of eye color in other animals, as well as the ecological correlates.

Implications of the hypothesis

Investigating the origin and function of eye colors will shed light on the reason why some species may have either light-colored irises (e.g., white, yellow or light blue) or dark ones (dark red, brown or black). The causes behind the vast array of eye colors across taxa have never been thoroughly investigated, but it may well be that all Darwinian selection processes are at work: sexual selection in humans, artificial selection for domestic animals, and natural selection (mainly) for wild animals.

Electronic supplementary material

The online version of this article (10.1186/s12983-017-0243-8) contains supplementary material, which is available to authorized users.

Genetic drift and selection in many-allele range expansions

We experimentally and numerically investigate the evolutionary dynamics of four competing strains of E. coli with differing expansion velocities in radially expanding colonies. We compare experimental measurements of the average fraction, correlation functions between strains, and the relative rates of genetic domain wall annihilations and coalescences to simulations modeling the population as a one-dimensional ring of annihilating and coalescing random walkers with deterministic biases due to selection. The simulations reveal that the evolutionary dynamics can be collapsed onto master curves governed by three essential parameters: (1) an expansion length beyond which selection dominates over genetic drift; (2) a characteristic angular correlation describing the size of genetic domains; and (3) a dimensionless constant quantifying the interplay between a colony’s curvature at the frontier and its selection length scale. We measure these parameters with a new technique that precisely measures small selective differences between spatially competing strains and show that our simulations accurately predict the dynamics without additional fitting. Our results suggest that the random walk model can act as a useful predictive tool for describing the evolutionary dynamics of range expansions composed of an arbitrary number of genotypes with different fitnesses.

Population expansions occur naturally during the spread of invasive species and have played a role in our evolutionary history when humans migrated out of Africa. We use a colony of non-motile bacteria expanding into unoccupied, nutrient-rich territory on an agar plate as a model system to explore how an expanding population’s spatial structure impacts its evolutionary dynamics. Spatial structure is present in expanding microbial colonies because daughter cells migrate only a small distance away from their mothers each generation. Generally, the constituents of expansions occurring in nature and in the lab have different genetic compositions (genotypes, or alleles if a single gene differs), each instilling different fitnesses, which compete to proliferate at the frontier. Here, we show that a random-walk model can accurately predict the dynamics of four expanding strains of E. coli with different fitnesses; each strain represents a competing allele. Our results can be extended to describe any number of competing genotypes with different fitnesses in a naturally occurring expansion as long as the underlying motility of the organisms does not cause our model to break down. Our model can also be used to precisely measure small selective differences between spatially competing genotypes in controlled laboratory settings.

Reconstructing the Temporal Progression of Biological Data Using Cluster Spanning Trees

Identifying the temporal progression of a set of biological samples is crucial for comprehending the dynamics of the underlying molecular interactions. It is often also a basic step in data denoising and synchronization. Finally, identifying the progression order is crucial for problems like cell lineage identification, disease progression, tumor classification, and epidemiology and thus impacts the spectrum of disciplines spanning basic biology, drug discovery, and public health. Current methods that attempt solving this problem, face difficulty when it is necessary to factor-in complex relationships within the data, such as grouping, partial ordering or bifurcating or multifurcating progressions. We propose the notion of cluster spanning trees (CST) that can model both linear as well as the aforementioned complex progression relationships in temporally evolving data. Through a number of experimental investigations involving synthetic data sets as well as data sets from the cell cycle, cellular differentiation, phenotypic screening, and genetic variation, we show that the proposed CST approach outperforms existing methods in reconstructing the temporal progression of the data.

An ecophysiological background for biogeographic patterns of two island lizards?

Distributions of sedentary ectotherms are dependent on temperature and humidity due to their low homeostatic and dispersal abilities. Lizards are strongly conditioned by temperature, but hydric environment may be also important, at least in arid environments. Biotic interactions may also play a role in range patterns, but they are of minor importance in islands where native species monopolize well-delimited niche spaces. On the arid island of São Vicente (Cabo Verde), two endemic lizards display different spatial patterns. While the gecko Tarentola substituta is widely distributed across the island, the skink Chioninia stangeri is restricted to the NE, which is cooler, more humid, and vegetated. We hypothesized that this is due to differences in the fundamental niche, specifically in ecophysiology. We predict that C. stangeri should select for lower temperatures and lose more water by evaporation than T. substituta. We submitted adults of each species to standard experiments to assess preferred body temperatures (T_p) and evaporative water loss (EWL) rates, and examined the variation between species and through time using repeated-measures AN(C)OVAs. Results only partially supported our expectations. Contrary to the prediction, skinks attained higher Tp than geckos but in the long term showed a trend for higher EWL as predicted. Thus, while ecophysiology certainly contributes to functional interpretation of species distributions, it needs to be combined with other evidence such as habitat use and evolutionary history. These findings will be useful to perform mechanistic models to better understand the impact of climate change and habitat disturbance on these endemic species.

Phylogeographic Patterns in Africa and High Resolution Delineation of Genetic Clades in the Lion (Panthera leo)

Comparative phylogeography of African savannah mammals shows a congruent pattern in which populations in West/Central Africa are distinct from populations in East/Southern Africa. However, for the lion, all African populations are currently classified as a single subspecies (Panthera leo leo), while the only remaining population in Asia is considered to be distinct (Panthera leo persica). This distinction is disputed both by morphological and genetic data. In this study we introduce the lion as a model for African phylogeography. Analyses of mtDNA sequences reveal six supported clades and a strongly supported ancestral dichotomy with northern populations (West Africa, Central Africa, North Africa/Asia) on one branch, and southern populations (North East Africa, East/Southern Africa and South West Africa) on the other. We review taxonomies and phylogenies of other large savannah mammals, illustrating that similar clades are found in other species. The described phylogeographic pattern is considered in relation to large scale environmental changes in Africa over the past 300,000 years, attributable to climate. Refugial areas, predicted by climate envelope models, further confirm the observed pattern. We support the revision of current lion taxonomy, as recognition of a northern and a southern subspecies is more parsimonious with the evolutionary history of the lion.

Anchored pseudo-de novo assembly of human genomes identifies extensive sequence variation from unmapped sequence reads

The human genome reference (HGR) completion marked the genomics era beginning, yet despite its utility universal application is limited by the small number of individuals used in its development. This is highlighted by the presence of high-quality sequence reads failing to map within the HGR. Sequences failing to map generally represent 2-5 % of total reads, which may harbor regions that would enhance our understanding of population variation, evolution, and disease. Alternatively, complete de novo assemblies can be created, but these effectively ignore the groundwork of the HGR. In an effort to find a middle ground, we developed a bioinformatic pipeline that maps paired-end reads to the HGR as separate single reads, exports unmappable reads, de novo assembles these reads per individual and then combines assemblies into a secondary reference assembly used for comparative analysis. Using 45 diverse 1000 Genomes Project individuals, we identified 351,361 contigs covering 195.5 Mb of sequence unincorporated in GRCh38. 30,879 contigs are represented in multiple individuals with ~40 % showing high sequence complexity. Genomic coordinates were generated for 99.9 %, with 52.5 % exhibiting high-quality mapping scores. Comparative genomic analyses with archaic humans and primates revealed significant sequence alignments and comparisons with model organism RefSeq gene datasets identified novel human genes. If incorporated, these sequences will expand the HGR, but more importantly our data highlight that with this method low coverage (~10-20×) next-generation sequencing can still be used to identify novel unmapped sequences to explore biological functions contributing to human phenotypic variation, disease and functionality for personal genomic medicine.

Topological Data Analysis Generates High-Resolution, Genome-wide Maps of Human Recombination

Meiotic recombination is a fundamental evolutionary process driving diversity in eukaryotes. In mammals, recombination is known to occur preferentially at specific genomic regions. Using topological data analysis (TDA), a branch of applied topology that extracts global features from large data sets, we developed an efficient method for mapping recombination at fine scales. When compared to standard linkage-based methods, TDA can deal with a larger number of SNPs and genomes without incurring prohibitive computational costs. We applied TDA to 1,000 Genomes Project data and constructed high-resolution whole-genome recombination maps of seven human populations. Our analysis shows that recombination is generally under-represented within transcription start sites. However, the binding sites of specific transcription factors are enriched for sites of recombination. These include transcription factors that regulate the expression of meiosis- and gametogenesis-specific genes, cell cycle progression, and differentiation blockage. Additionally, our analysis identifies an enrichment for sites of recombination at repeat-derived loci matched by piwi-interacting RNAs.

Human Dispersal Out of Africa: A Lasting Debate

Unraveling the first migrations of anatomically modern humans out of Africa has invoked great interest among researchers from a wide range of disciplines. Available fossil, archeological, and climatic data offer many hypotheses, and as such genetics, with the advent of genome-wide genotyping and sequencing techniques and an increase in the availability of ancient samples, offers another important tool for testing theories relating to our own history. In this review, we report the ongoing debates regarding how and when our ancestors left Africa, how many waves of dispersal there were and what geographical routes were taken. We explore the validity of each, using current genetic literature coupled with some of the key archeological findings.

How Obstacles Perturb Population Fronts and Alter Their Genetic Structure

As populations spread into new territory, environmental heterogeneities can shape the population front and genetic composition. We focus here on the effects of an important building block of heterogeneous environments, isolated obstacles. With a combination of experiments, theory, and simulation, we show how isolated obstacles both create long-lived distortions of the front shape and amplify the effect of genetic drift. A system of bacteriophage T7 spreading on a spatially heterogeneous Escherichia coli lawn serves as an experimental model system to study population expansions. Using an inkjet printer, we create well-defined replicates of the lawn and quantitatively study the population expansion of phage T7. The transient perturbations of the population front found in the experiments are well described by a model in which the front moves with constant speed. Independent of the precise details of the expansion, we show that obstacles create a kink in the front that persists over large distances and is insensitive to the details of the obstacle's shape. The small deviations between experimental findings and the predictions of the constant speed model can be understood with a more general reaction-diffusion model, which reduces to the constant speed model when the obstacle size is large compared to the front width. Using this framework, we demonstrate that frontier genotypes just grazing the side of an isolated obstacle increase in abundance, a phenomenon we call 'geometry-enhanced genetic drift', complementary to the founder effect associated with spatial bottlenecks. Bacterial range expansions around nutrient-poor barriers and stochastic simulations confirm this prediction. The effect of the obstacle on the genealogy of individuals at the front is characterized by simulations and rationalized using the constant speed model. Lastly, we consider the effect of two obstacles on front shape and genetic composition of the population illuminating the effects expected from complex environments with many obstacles.

Evolution Arrests Invasions of Cooperative Populations

Population expansions trigger many biomedical and ecological transitions, from tumor growth to invasions of non-native species. Although population spreading often selects for more invasive phenotypes, we show that this outcome is far from inevitable. In cooperative populations, mutations reducing dispersal have a competitive advantage. Such mutations then steadily accumulate at the expansion front, bringing invasion to a halt. Our findings are a rare example of evolution driving the population into an unfavorable state, and they could lead to new strategies to combat unwelcome invaders.

Extra-long interglacial in Northern Hemisphere during MISs 15-13 arising from limited extent of Arctic ice sheets in glacial MIS 14

Knowledge of the behavior of Northern Hemisphere (NH) ice sheets over the past million years is crucial for understanding the role of orbitally driven insolation changes on glacial/interglacial cycles. Here, based on the demonstrable link between changes in Chinese loess grain-size and NH ice-sheet extent, we use loess grain-size records to confirm that northern ice-sheets were restricted during marine oxygen isotope stage (MIS) 14. Thus, an unusually long NH interglacial climate of over 100 kyr persisted during MISs 15−13, much longer than expected from marine oxygen isotope records. Taking a global view of the paleoclimate records, MIS 14 inception seems to be a response to changes in Antarctic ice-sheets rather than to NH cooling. Orbital configuration in the two Polar regions shows that the onset of MIS 14 was forced by austral insolation changes, rather than by boreal summer insolation, as Milankovitch theory proposes. Our analysis of MIS 14 raises the possibility that southern insolation forcing may have played an important role in the inception of several other glacials. We suggest that the extra-long NH interglacial climate during MISs 15−13 provided favorable conditions for the second major dispersal episode of African hominins into Eurasia.

GST M1-T1 null allele frequency patterns in geographically assorted human populations: a phylogenetic approach

Genetic diversity in drug metabolism and disposition is mainly considered as the outcome of the inter-individual genetic variation in polymorphism of drug-xenobiotic metabolizing enzyme (XME). Among the XMEs, glutathione-S-transferases (GST) gene loci are an important candidate for the investigation of diversity in allele frequency, as the deletion mutations in GST M1 and T1 genotypes are associated with various cancers and genetic disorders of all major Population Affiliations (PAs). Therefore, the present population based phylogenetic study was focused to uncover the frequency distribution pattern in GST M1 and T1 null genotypes among 45 Geographically Assorted Human Populations (GAHPs). The frequency distribution pattern for GST M1 and T1 null alleles have been detected in this study using the data derived from literatures representing 44 populations affiliated to Africa, Asia, Europe, South America and the genome of PA from Gujarat, a region in western India. Allele frequency counting for Gujarat PA and scattered plot analysis for geographical distribution among the PAs were performed in SPSS-21. The GST M1 and GST T1 null allele frequencies patterns of the PAs were computed in Seqboot, Gendist program of Phylip software package (3.69 versions) and Unweighted Pair Group method with Arithmetic Mean in Mega-6 software. Allele frequencies from South African Xhosa tribe, East African Zimbabwe, East African Ethiopia, North African Egypt, Caucasian, South Asian Afghanistan and South Indian Andhra Pradesh have been identified as the probable seven patterns among the 45 GAHPs investigated in this study for GST M1-T1 null genotypes. The patternized null allele frequencies demonstrated in this study for the first time addresses the missing link in GST M1-T1 null allele frequencies among GAHPs.

Human gephyrin is encompassed within giant functional noncoding yin-yang sequences

Gephyrin is a highly-conserved gene that is vital for the organization of proteins at inhibitory receptors, molybdenum cofactor biosynthesis, and other diverse functions. Its specific function is intricately regulated and its aberrant activities have been observed for a number of human diseases. Here we report a remarkable yin-yang haplotype pattern encompassing gephyrin. Yin-yang haplotypes arise when a stretch of DNA evolves to present two disparate forms that bear differing states for nucleotide variations along their lengths. The gephyrin yin-yang pair consists of 284 divergent nucleotide states and both variants vary drastically from their mutual ancestral haplotype, suggesting rapid evolution. Several independent lines of evidence indicate strong positive selection on the region and suggest these high-frequency haplotypes represent two distinct functional mechanisms. This discovery holds potential to deepen our understanding of variable human-specific regulation of gephyrin while providing clues for rapid evolutionary events and allelic migrations buried within human history.

Naturally rare versus newly rare: demographic inferences on two timescales inform conservation of Galápagos giant tortoises

Long-term population history can influence the genetic effects of recent bottlenecks. Therefore, for threatened or endangered species, an understanding of the past is relevant when formulating conservation strategies. Levels of variation at neutral markers have been useful for estimating local effective population sizes (N e ) and inferring whether population sizes increased or decreased over time. Furthermore, analyses of genotypic, allelic frequency, and phylogenetic information can potentially be used to separate historical from recent demographic changes. For 15 populations of Galápagos giant tortoises (Chelonoidis sp.), we used 12 microsatellite loci and DNA sequences from the mitochondrial control region and a nuclear intron, to reconstruct demographic history on shallow (past ∽100 generations, ∽2500 years) and deep (pre-Holocene, >10 thousand years ago) timescales. At the deep timescale, three populations showed strong signals of growth, but with different magnitudes and timing, indicating different underlying causes. Furthermore, estimated historical N e of populations across the archipelago showed no correlation with island age or size, underscoring the complexity of predicting demographic history a priori. At the shallow timescale, all populations carried some signature of a genetic bottleneck, and for 12 populations, point estimates of contemporary N e were very small (i.e., < 50). On the basis of the comparison of these genetic estimates with published census size data, N e generally represented ∽0.16 of the census size. However, the variance in this ratio across populations was considerable. Overall, our data suggest that idiosyncratic and geographically localized forces shaped the demographic history of tortoise populations. Furthermore, from a conservation perspective, the separation of demographic events occurring on shallow versus deep timescales permits the identification of naturally rare versus newly rare populations; this distinction should facilitate prioritization of management action.

Trend of different molecular markers in the last decades for studying human migrations

Anatomically modern humans are known to have widely migrated throughout history. Different scientific evidences suggest that the entire human population descended from just several thousand African migrants. About 85,000 years ago, the first wave of human migration was out of Africa, that followed the coasts through the Middle East, into Southern Asia via Sri Lanka, and in due course around Indonesia and into Australia. Another wave of migration between 40,000 and 12,000 years ago brought humans northward into Europe. However, the frozen north limited human expansion in Europe, and created a land bridge, "Bering land bridge", connecting Asia with North America about 25,000 years ago. Although fossil data give the most direct information about our past, it has certain anomalies. So, molecular archeologists are now using different molecular markers to trace the "most recent common ancestor" and also the migration pattern of modern humans. In this study, we have studied the trend of molecular markers and also the methodologies implemented in the last decades (2003-2014). From our observation, we can say that D-loop region of mtDNA and Y chromosome based markers are predominant. Nevertheless, mtDNA, especially the D-loop region, has some unique features, which makes it a more effective marker for tracing prehistoric footprints of modern human populations. Although, natural selection should also be taken into account in studying mtDNA based human migration. As per technology is concerned, Sanger sequencing is the major technique that is being used in almost all studies. But, the emergence of different cost-effective-and-easy-to-handle NGS platforms has increased its popularity over Sanger sequencing in studying human migration.

Population distribution and ancestry of the cancer protective MDM2 SNP285 (rs117039649)

The MDM2 promoter SNP285C is located on the SNP309G allele. While SNP309G enhances Sp1 transcription factor binding and MDM2 transcription, SNP285C antagonizes Sp1 binding and reduces the risk of breast-, ovary- and endometrial cancer. Assessing SNP285 and 309 genotypes across 25 different ethnic populations (>10.000 individuals), the incidence of SNP285C was 6-8% across European populations except for Finns (1.2%) and Saami (0.3%). The incidence decreased towards the Middle-East and Eastern Russia, and SNP285C was absent among Han Chinese, Mongolians and African Americans. Interhaplotype variation analyses estimated SNP285C to have originated about 14,700 years ago (95% CI: 8,300 – 33,300). Both this estimate and the geographical distribution suggest SNP285C to have arisen after the separation between Caucasians and modern day East Asians (17,000 - 40,000 years ago). We observed a strong inverse correlation (r = -0.805; p < 0.001) between the percentage of SNP309G alleles harboring SNP285C and the MAF for SNP309G itself across different populations suggesting selection and environmental adaptation with respect to MDM2 expression in recent human evolution. In conclusion, we found SNP285C to be a pan-Caucasian variant. Ethnic variation regarding distribution of SNP285C needs to be taken into account when assessing the impact of MDM2 SNPs on cancer risk.

Genetic variation and adaptation in Africa: implications for human evolution and disease

Because modern humans originated in Africa and have adapted to diverse environments, African populations have high levels of genetic and phenotypic diversity. Thus, genomic studies of diverse African ethnic groups are essential for understanding human evolutionary history and how this leads to differential disease risk in all humans. Comparative studies of genetic diversity within and between African ethnic groups creates an opportunity to reconstruct some of the earliest events in human population history and are useful for identifying patterns of genetic variation that have been influenced by recent natural selection. Here we describe what is currently known about genetic variation and evolutionary history of diverse African ethnic groups. We also describe examples of recent natural selection in African genomes and how these data are informative for understanding the frequency of many genetic traits, including those that cause disease susceptibility in African populations and populations of recent African descent.

A 400,000-year-old mitochondrial genome questions phylogenetic relationships amongst archaic hominins: using the latest advances in ancient genomics, the mitochondrial genome sequence of a 400,000-year-old hominin has been deciphered

By combining state-of-the-art approaches in ancient genomics, Meyer and co-workers have reconstructed the mitochondrial sequence of an archaic hominin that lived at Sierra de Atapuerca, Spain about 400,000 years ago. This achievement follows recent advances in molecular anthropology that delivered the genome sequence of younger archaic hominins, such as Neanderthals and Denisovans. Molecular phylogenetic reconstructions placed the Atapuercan as a sister group to Denisovans, although its morphology suggested closer affinities with Neanderthals. In addition to possibly challenging our interpretation of the fossil record, this study confirms that genomic information can be recovered from extremely damaged DNA molecules, even in the presence of significant levels of human contamination. Together with the recent characterization of a 700,000-year-old horse genome, this study opens the Middle Pleistocene to genomics, thereby extending the scope of ancient DNA to the last million years.

Impact of ethnicity on cardiac adaptation to exercise

The increasing globalization of sport has resulted in athletes from a wide range of ethnicities emerging onto the world stage. Fuelled by the untimely death of a number of young professional athletes, data generated from the parallel increase in preparticipation cardiovascular evaluation has indicated that ethnicity has a substantial influence on cardiac adaptation to exercise. From this perspective, the group most intensively studied comprises athletes of African or Afro-Caribbean ethnicity (black athletes), an ever-increasing number of whom are competing at the highest levels of sport and who often exhibit profound electrical and structural cardiac changes in response to exercise. Data on other ethnic cohorts are emerging, but remain incomplete. This Review describes our current knowledge on the impact of ethnicity on cardiac adaptation to exercise, starting with white athletes in whom the physiological electrical and structural changes--collectively termed the 'athlete's heart'--were first described. Discussion of the differences in the cardiac changes between ethnicities, with a focus on black athletes, and of the challenges that these variations can produce for the evaluating physician is also provided. The impact of ethnically mediated changes on preparticipation cardiovascular evaluation is highlighted, particularly with respect to false positive results, and potential genetic mechanisms underlying racial differences in cardiac adaptation to exercise are described.

Dating human cultural capacity using phylogenetic principles

Humans have genetically based unique abilities making complex culture possible; an assemblage of traits which we term “cultural capacity”. The age of this capacity has for long been subject to controversy. We apply phylogenetic principles to date this capacity, integrating evidence from archaeology, genetics, paleoanthropology, and linguistics. We show that cultural capacity is older than the first split in the modern human lineage, and at least 170,000 years old, based on data on hyoid bone morphology, FOXP2 alleles, agreement between genetic and language trees, fire use, burials, and the early appearance of tools comparable to those of modern hunter-gatherers. We cannot exclude that Neanderthals had cultural capacity some 500,000 years ago. A capacity for complex culture, therefore, must have existed before complex culture itself. It may even originated long before. This seeming paradox is resolved by theoretical models suggesting that cultural evolution is exceedingly slow in its initial stages.

Genes, Fossils, and Culture. An Overview of the Evidence for Neandertal–Modern Human Interaction and Admixture

This paper re-examines current arguments concerning the evidence for Neandertal-modern human interaction and admixture. While most researchers now agree that the ancestry of all present day humans can be traced back to African late Middle Pleistocene populations, at a time when the remainder of Eurasia was inhabited by ‘archaic humans’, most notably the Neandertals, issues that remain to be resolved are the tempo and mode of early modern human dispersal and interaction with archaic humans.

This paper focuses on what happened at the time of contact in Europe, and assesses the level of admixture that may have occurred, as well as the extent to which such level may have varied in both time and space. It explains how the available mtDNA evidence does not preclude admixture at the time of contact, and is in fact consistent, depending on a number of parameters, with a possibly substantial Neandertal contribution to the initial modern human population of Europe. It is argued that the absence of Neandertal mtDNA lineages among present Europeans is likely, on dating evidence, to be simply a particular case of generalised loss of Pleistocene mtDNA lineages. Although the full range of interaction types (mutual avoidance, hostile confrontation, full integration) is conceivable, there is plenty of archaeological evidence to suggest that admixture must have been the general rule, and that the paleontological evidence for the generalised presence of archaic traits among Europe's earliest moderns implies the transmission of genes, and indicates that mixed groups should have been reproductively viable. In this context, it would seem that the most parsimonious explanation for the disappearance of the Neandertal mtDNA lineage is genetic swamping.

Genetic drift opposes mutualism during spatial population expansion

Mutualistic interactions benefit both partners, promoting coexistence and genetic diversity. Spatial structure can promote cooperation, but spatial expansions may also make it hard for mutualistic partners to stay together, because genetic drift at the expansion front creates regions of low genetic and species diversity. To explore the antagonism between mutualism and genetic drift, we grew cross-feeding strains of the budding yeast Saccharomyces cerevisiae on agar surfaces as a model for mutualists undergoing spatial expansions. By supplying varying amounts of the exchanged nutrients, we tuned strength and symmetry of the mutualistic interaction. Strong mutualism suppresses genetic demixing during spatial expansions and thereby maintains diversity, but weak or asymmetric mutualism is overwhelmed by genetic drift even when mutualism is still beneficial, slowing growth and reducing diversity. Theoretical modeling using experimentally measured parameters predicts the size of demixed regions and how strong mutualism must be to survive a spatial expansion.

Additive genetic variation in schizophrenia risk is shared by populations of African and European descent

To investigate the extent to which the proportion of schizophrenia's additive genetic variation tagged by SNPs is shared by populations of European and African descent, we analyzed the largest combined African descent (AD [n = 2,142]) and European descent (ED [n = 4,990]) schizophrenia case-control genome-wide association study (GWAS) data set available, the Molecular Genetics of Schizophrenia (MGS) data set. We show how a method that uses genomic similarities at measured SNPs to estimate the additive genetic correlation (SNP correlation [SNP-rg]) between traits can be extended to estimate SNP-rg for the same trait between ethnicities. We estimated SNP-rg for schizophrenia between the MGS ED and MGS AD samples to be 0.66 (SE = 0.23), which is significantly different from 0 (p(SNP-rg = 0) = 0.0003), but not 1 (p(SNP-rg = 1) = 0.26). We re-estimated SNP-rg between an independent ED data set (n = 6,665) and the MGS AD sample to be 0.61 (SE = 0.21, p(SNP-rg = 0) = 0.0003, p(SNP-rg = 1) = 0.16). These results suggest that many schizophrenia risk alleles are shared across ethnic groups and predate African-European divergence.

Biological races in humans

Races may exist in humans in a cultural sense, but biological concepts of race are needed to access their reality in a non-species-specific manner and to see if cultural categories correspond to biological categories within humans. Modern biological concepts of race can be implemented objectively with molecular genetic data through hypothesis-testing. Genetic data sets are used to see if biological races exist in humans and in our closest evolutionary relative, the chimpanzee. Using the two most commonly used biological concepts of race, chimpanzees are indeed subdivided into races but humans are not. Adaptive traits, such as skin color, have frequently been used to define races in humans, but such adaptive traits reflect the underlying environmental factor to which they are adaptive and not overall genetic differentiation, and different adaptive traits define discordant groups. There are no objective criteria for choosing one adaptive trait over another to define race. As a consequence, adaptive traits do not define races in humans. Much of the recent scientific literature on human evolution portrays human populations as separate branches on an evolutionary tree. A tree-like structure among humans has been falsified whenever tested, so this practice is scientifically indefensible. It is also socially irresponsible as these pictorial representations of human evolution have more impact on the general public than nuanced phrases in the text of a scientific paper. Humans have much genetic diversity, but the vast majority of this diversity reflects individual uniqueness and not race.

Brains, innovations, tools and cultural transmission in birds, non-human primates, and fossil hominins

Recent work on birds and non-human primates has shown that taxonomic differences in field measures of innovation, tool use and social learning are associated with size of the mammalian cortex and avian mesopallium and nidopallium, as well as ecological traits like colonization success. Here, I review this literature and suggest that many of its findings are relevant to hominin intelligence. In particular, our large brains and increased intelligence may be partly independent of our ape phylogeny and the result of convergent processes similar to those that have molded avian and platyrrhine intelligence. Tool use, innovativeness and cultural transmission might be linked over our past and in our brains as operations of domain-general intelligence. Finally, colonization of new areas may have accompanied increases in both brain size and innovativeness in hominins as they have in other mammals and in birds, potentially accelerating hominin evolution via behavioral drive.

Inferring demographic history from a spectrum of shared haplotype lengths

There has been much recent excitement about the use of genetics to elucidate ancestral history and demography. Whole genome data from humans and other species are revealing complex stories of divergence and admixture that were left undiscovered by previous smaller data sets. A central challenge is to estimate the timing of past admixture and divergence events, for example the time at which Neanderthals exchanged genetic material with humans and the time at which modern humans left Africa. Here, we present a method for using sequence data to jointly estimate the timing and magnitude of past admixture events, along with population divergence times and changes in effective population size. We infer demography from a collection of pairwise sequence alignments by summarizing their length distribution of tracts of identity by state (IBS) and maximizing an analytic composite likelihood derived from a Markovian coalescent approximation. Recent gene flow between populations leaves behind long tracts of identity by descent (IBD), and these tracts give our method power by influencing the distribution of shared IBS tracts. In simulated data, we accurately infer the timing and strength of admixture events, population size changes, and divergence times over a variety of ancient and recent time scales. Using the same technique, we analyze deeply sequenced trio parents from the 1000 Genomes project. The data show evidence of extensive gene flow between Africa and Europe after the time of divergence as well as substructure and gene flow among ancestral hominids. In particular, we infer that recent African-European gene flow and ancient ghost admixture into Europe are both necessary to explain the spectrum of IBS sharing in the trios, rejecting simpler models that contain less population structure.

Spatial population expansion promotes the evolution of cooperation in an experimental Prisoner's Dilemma

Cooperation is ubiquitous in nature, but explaining its existence remains a central interdisciplinary challenge. Cooperation is most difficult to explain in the Prisoner's Dilemma game, where cooperators always lose in direct competition with defectors despite increasing mean fitness. Here we demonstrate how spatial population expansion, a widespread natural phenomenon, promotes the evolution of cooperation. We engineer an experimental Prisoner's Dilemma game in the budding yeast Saccharomyces cerevisiae to show that, despite losing to defectors in nonexpanding conditions, cooperators increase in frequency in spatially expanding populations. Fluorescently labeled colonies show genetic demixing of cooperators and defectors, followed by increase in cooperator frequency as cooperator sectors overtake neighboring defector sectors. Together with lattice-based spatial simulations, our results suggest that spatial population expansion drives the evolution of cooperation by (1) increasing positive genetic assortment at population frontiers and (2) selecting for phenotypes maximizing local deme productivity. Spatial expansion thus creates a selective force whereby cooperator-enriched demes overtake neighboring defector-enriched demes in a "survival of the fastest." We conclude that colony growth alone can promote cooperation and prevent defection in microbes. Our results extend to other species with spatially restricted dispersal undergoing range expansion, including pathogens, invasive species, and humans.

Genetic structure and demographic history reveal migration of the diamondback moth Plutella xylostella (Lepidoptera: Plutellidae) from the southern to northern regions of China

The diamondback moth Plutella xylostella (Linnaeus) (Lepidoptera: Plutellidae) is one of the most destructive insect pests of cruciferous plants worldwide. Biological, ecological and genetic studies have indicated that this moth is migratory in many regions around the world. Although outbreaks of this pest occur annually in China and cause heavy damage, little is known concerning its migration. To better understand its migration pattern, we investigated the population genetic structure and demographic history of the diamondback moth by analyzing 27 geographical populations across China using four mitochondrial genes and nine microsatellite loci. The results showed that high haplotype diversity and low nucleotide diversity occurred in the diamondback moth populations, a finding that is typical for migratory species. No genetic differentiation among all populations and no correlation between genetic and geographical distance were found. However, pairwise analysis of the mitochondrial genes has indicated that populations from the southern region were more differentiated than those from the northern region. Gene flow analysis revealed that the effective number of migrants per generation into populations of the northern region is very high, whereas that into populations of the southern region is quite low. Neutrality testing, mismatch distribution and Bayesian Skyline Plot analyses based on mitochondrial genes all revealed that deviation from Hardy-Weinberg equilibrium and sudden expansion of the effective population size were present in populations from the northern region but not in those from the southern region. In conclusion, all our analyses strongly demonstrated that the diamondback moth migrates within China from the southern to northern regions with rare effective migration in the reverse direction. Our research provides a successful example of using population genetic approaches to resolve the seasonal migration of insects.

The fate of cooperation during range expansions

Species expand their geographical ranges following an environmental change, long range dispersal, or a new adaptation. Range expansions not only bring an ecological change, but also affect the evolution of the expanding species. Although the dynamics of deleterious, neutral, and beneficial mutations have been extensively studied in expanding populations, the fate of alleles under frequency-dependent selection remains largely unexplored. The dynamics of cooperative alleles are particularly interesting because selection can be both frequency and density dependent, resulting in a coupling between population and evolutionary dynamics. This coupling leads to an increase in the frequency of cooperators at the expansion front, and, under certain conditions, the entire front can be taken over by cooperators. Thus, a mixed population wave can split into an expansion wave of only cooperators followed by an invasion wave of defectors. After the splitting, cooperators increase in abundance by expanding into new territories faster than they are invaded by defectors. Our results not only provide an explanation for the maintenance of cooperation but also elucidate the effect of eco-evolutionary feedback on the maintenance of genetic diversity during range expansions. When cooperators do not split away, we find that defectors can spread much faster with cooperators than they would be able to on their own or by invading cooperators. This enhanced rate of expansion in mixed waves could counterbalance the loss of genetic diversity due to the founder effect for mutations under frequency-dependent selection. Although we focus on cooperator-defector interactions, our analysis could also be relevant for other systems described by reaction-diffusion equations.

Cooperation is beneficial for the species as a whole, but, at the level of an individual, defection pays off. Natural selection is then expected to favor defectors and eliminate cooperation. This prediction is in stark contrast with the abundance of cooperation at all levels of biological systems: from bacterial biofilms to ecosystems and human societies. Several explanations have been proposed to resolve this paradox, including direct reciprocity and group selection. Our work, however, builds upon an observation that natural selection on cooperators might depend both on their relative frequency in the population and on the population density. We find that this feedback between the population and evolutionary dynamics can substantially increase the frequency of cooperators at the front of an expanding population, and can even lead to a splitting of cooperators from defectors. After splitting, only cooperators colonize new territories, while defectors slowly invade them from behind. Since range expansions are very common in nature, our work provides a new explanation of the maintenance of cooperation. More generally, the phenomena we describe could be of interest in other situations when coexisting entities spread in space, be it species in ecology or diffusing and reacting molecules in chemical kinetics.

Radial Domany-Kinzel models with mutation and selection

We study the effect of spatial structure, genetic drift, mutation, and selective pressure on the evolutionary dynamics in a simplified model of asexual organisms colonizing a new territory. Under an appropriate coarse-graining, the evolutionary dynamics is related to the directed percolation processes that arise in voter models, the Domany-Kinzel (DK) model, contact process, and so on. We explore the differences between linear (flat front) expansions and the much less familiar radial (curved front) range expansions. For the radial expansion, we develop a generalized, off-lattice DK model that minimizes otherwise persistent lattice artifacts. With both simulations and analytical techniques, we study the survival probability of advantageous mutants, the spatial correlations between domains of neutral strains, and the dynamics of populations with deleterious mutations. "Inflation" at the frontier leads to striking differences between radial and linear expansions. For a colony with initial radius R(0) expanding at velocity v, significant genetic demixing, caused by local genetic drift, occurs only up to a finite time t(*)=R(0)/v, after which portions of the colony become causally disconnected due to the inflating perimeter of the expanding front. As a result, the effect of a selective advantage is amplified relative to genetic drift, increasing the survival probability of advantageous mutants. Inflation also modifies the underlying directed percolation transition, introducing novel scaling functions and modifications similar to a finite-size effect. Finally, we consider radial range expansions with deflating perimeters, as might arise from colonization initiated along the shores of an island.

A multidisciplinary reconstruction of Palaeolithic nutrition that holds promise for the prevention and treatment of diseases of civilisation

Evolutionary medicine acknowledges that many chronic degenerative diseases result from conflicts between our rapidly changing environment, our dietary habits included, and our genome, which has remained virtually unchanged since the Palaeolithic era. Reconstruction of the diet before the Agricultural and Industrial Revolutions is therefore indicated, but hampered by the ongoing debate on our ancestors' ecological niche. Arguments and their counterarguments regarding evolutionary medicine are updated and the evidence for the long-reigning hypothesis of human evolution on the arid savanna is weighed against the hypothesis that man evolved in the proximity of water. Evidence from various disciplines is discussed, including the study of palaeo-environments, comparative anatomy, biogeochemistry, archaeology, anthropology, (patho)physiology and epidemiology. Although our ancestors had much lower life expectancies, the current evidence does neither support the misconception that during the Palaeolithic there were no elderly nor that they had poor health. Rather than rejecting the possibility of 'healthy ageing', the default assumption should be that healthy ageing posed an evolutionary advantage for human survival. There is ample evidence that our ancestors lived in a land-water ecosystem and extracted a substantial part of their diets from both terrestrial and aquatic resources. Rather than rejecting this possibility by lack of evidence, the default assumption should be that hominins, living in coastal ecosystems with catchable aquatic resources, consumed these resources. Finally, the composition and merits of so-called 'Palaeolithic diets', based on different hominin niche-reconstructions, are evaluated. The benefits of these diets illustrate that it is time to incorporate this knowledge into dietary recommendations.

Archaic human genomics

For much of the 20th century, the predominant view of human evolutionary history was derived from the fossil record. Homo erectus was seen arising in Africa from an earlier member of the genus and then spreading throughout the Old World and into the Oceania. A regional continuity model of anagenetic change from H. erectus via various intermediate archaic species into the modern humans in each of the regions inhabited by H. erectus was labeled the multiregional model of human evolution (MRE). A contrasting model positing a single origin, in Africa, of anatomically modern H. sapiens with some populations later migrating out of Africa and replacing the local archaic populations throughout the world with complete replacement became known as the recent African origin (RAO) model. Proponents of both models used different interpretations of the fossil record to bolster their views for decades. In the 1980s, molecular genetic techniques began providing evidence from modern human variation that allowed not only the different models of modern human origins to be tested but also the exploration demographic history and the types of selection that different regions of the genome and even specific traits had undergone. The majority of researchers interpreted these data as strongly supporting the RAO model, especially analyses of mitochondrial DNA (mtDNA). Extrapolating backward from modern patterns of variation and using various calibration points and substitution rates, a consensus arose that saw modern humans evolving from an African population around 200,000 years ago. Much later, around 50,000 years ago, a subset of this population migrated out of Africa replacing Neanderthals in Europe and western Asia as well as archaics in eastern Asia and Oceania. mtDNA sequences from more than two-dozen Neanderthals and early modern humans re-enforced this consensus. In 2010, however, the complete draft genomes of Neanderthals and of heretofore unknown hominins from Siberia, called Denisovans, demonstrated gene flow between these archaic human species and modern Eurasians but not sub-Saharan Africans. Although the levels of gene flow may be very limited, this unexpected finding does not fit well with either the RAO model or MRE model. More thorough sampling of modern human diversity, additional fossil discoveries, and the sequencing of additional hominin fossils are necessary to throw light onto our origins and our history.