The contribution of Neanderthal introgression to modern human traits

Uncovering the genetic architecture and evolutionary roots of androgenetic alopecia in African men

Androgenetic alopecia is a highly heritable trait. However, much of our understanding about the genetics of male-pattern baldness comes from individuals of European descent. Here, we examined a dataset comprising 2,136 men from Ghana, Nigeria, Senegal, and South Africa that were genotyped using the Men of African Descent and Carcinoma of the Prostate Array. We first tested how genetic predictions of baldness generalize from Europe to Africa and found that polygenic scores from European genome-wide association studies (GWASs) yielded area under the curve statistics that ranged from 0.513 to 0.546, indicating that genetic predictions of baldness generalized poorly from European to African populations. Subsequently, we conducted an African GWAS of androgenetic alopecia, focusing on self-reported baldness patterns at age 45. After correcting for age at recruitment, population structure, and study site, we identified 266 moderately significant associations, 51 of which were independent (p < 10-5, r2 < 0.2). Most baldness associations were autosomal, and the X chromosome does not seem to have a large impact on baldness in African men. Although Neanderthal alleles have previously been associated with skin and hair phenotypes, within the limits of statistical power, we did not find evidence that continental differences in the genetic architecture of baldness are due to Neanderthal introgression. While most loci that are associated with androgenetic alopecia do not have large integrative haplotype scores or fixation index statistics, multiple baldness-associated SNPs near the EDA2R and AR genes have large allele frequency differences between continents. Collectively, our findings illustrate how population genetic differences contribute to the limited portability of polygenic predictions across ancestries.

The genomic legacy of aurochs hybridisation in ancient and modern Iberian cattle

Cattle (Bos taurus) play an important role in the life of humans in the Iberian Peninsula not just as a food source but also in cultural events. When domestic cattle were first introduced to Iberia, wild aurochs (Bos primigenius) were still present, leaving ample opportunity for mating (whether intended by farmers or not). Using a temporal bioarchaeological dataset covering eight millennia, we trace gene flow between the two groups. Our results show frequent hybridisation during the Neolithic and Chalcolithic, likely reflecting a mix of hunting and herding or relatively unmanaged herds, with mostly male aurochs and female domestic cattle involved. This is supported by isotopic evidence consistent with ecological niche sharing, with only a few domestic cattle possibly being managed. The proportion of aurochs ancestry in domestic cattle remains relatively constant from about 4000 years ago, probably due to herd management and selection against first generation hybrids, coinciding with other cultural transitions. The constant level of wild ancestry (~20%) continues into modern Western European breeds including Iberian cattle selected for aggressiveness and fighting ability. This study illuminates the genomic impact of human actions and wild introgression in the establishment of cattle as one of the most important domestic species today.

Archaic introgression and the distribution of shared variation under stabilizing selection

Many phenotypic traits are under stabilizing selection, which maintains a population's mean phenotypic value near some optimum. The dynamics of traits and trait architectures under stabilizing selection have been extensively studied for single populations at steady state. However, natural populations are seldom at steady state and are often structured in some way. Admixture and introgression events may be common, including over human evolutionary history. Because stabilizing selection results in selection against the minor allele at a trait-affecting locus, alleles from the minor parental ancestry will be selected against after admixture. We show that the site-frequency spectrum can be used to model the genetic architecture of such traits, allowing for the study of trait architecture dynamics in complex multi-population settings. We use a simple deterministic two-locus model to predict the reduction of introgressed ancestry around trait-contributing loci. From this and individual-based simulations, we show that introgressed-ancestry is depleted around such loci. When introgression between two diverged populations occurs in both directions, as has been inferred between humans and Neanderthals, the locations of such regions with depleted introgressed ancestry will tend to be shared across populations. We argue that stabilizing selection for shared phenotypic optima may explain recent observations in which regions of depleted human-introgressed ancestry in the Neanderthal genome overlap with Neanderthal-ancestry deserts in humans.

Human dispersal into East Eurasia: ancient genome insights and the need for research on physiological adaptations

Humans have long pondered their genesis. The answer to the great question of where Homo sapiens come from has evolved in conjunction with biotechnologies that have allowed us to more brightly illuminate our distant past. The "Multiregional Evolution" model was once the hegemonic theory of Homo sapiens origins, but in the last 30 years, it has been supplanted by the "Out of Africa" model. Here, we review the major findings that have resulted in this paradigmatic shift. These include hominin brain expansion, classical insight from the mitochondrial genome (mtDNA) regarding the timing of the divergence point between Africans and non-Africans, and next-generation sequencing (NGS) of the Neanderthal and Denisovan genomes. These findings largely bolstered the "Out of Africa" model, although they also revealed a small degree of introgression of the Neanderthal and Denisovan genomes into those of non-African Homo sapiens. We also review paleogenomic studies for which migration route, north or south, early migrants to East Eurasia most likely traversed. Whichever route was taken, the migrants moved to higher latitudes, which necessitated adaptation for lower light conditions, colder clines, and pro-adipogenic mechanisms to counteract food scarcity. Further genetic and epigenetic investigations of these physiological adaptations constitute an integral aspect of the story of human origins and human migration to East Asia.

Long-read sequencing of 945 Han individuals identifies structural variants associated with phenotypic diversity and disease susceptibility

Genomic structural variants (SVs) are a major source of genetic diversity in humans. Here, through long-read sequencing of 945 Han Chinese genomes, we identify 111,288 SVs, including 24.56% unreported variants, many with predicted functional importance. By integrating human population-level phenotypic and multi-omics data as well as two humanized mouse models, we demonstrate the causal roles of two SVs: one SV that emerges at the common ancestor of modern humans, Neanderthals, and Denisovans in GSDMD for bone mineral density and one modern-human-specific SV in WWP2 impacting height, weight, fat, craniofacial phenotypes and immunity. Our results suggest that the GSDMD SV could serve as a rapid and cost-effective biomarker for assessing the risk of cisplatin-induced acute kidney injury. The functional conservation from human to mouse and widespread signals of positive natural selection suggest that both SVs likely influence local adaptation, phenotypic diversity, and disease susceptibility across diverse human populations.

Archaic hominin admixture and its consequences for modern humans

As anatomically modern humans dispersed out of Africa, they encountered and mated with now extinct hominins, including Neanderthals and Denisovans. It is now well established that all non-African individuals derive approximately 2% of their genome from Neanderthal ancestors and individuals of Melanesian and Australian aboriginal ancestry inherited an additional 2%-5% of their genomes from Denisovan ancestors. Attention has started to shift from documenting amounts of archaic admixture and identifying introgressed segments to understanding their molecular, phenotypic, and evolutionary consequences and refining models of human history. Here, we review recent insights into admixture between modern and archaic humans, emphasizing methodological innovations and the functional and phenotypic effects Neanderthal and Denisovan sequences have in contemporary individuals.

Genomic Footprints of Hybridisation in North Atlantic Eels (Anguilla anguilla and A. rostrata)

Understanding interspecific introgressive hybridisation and the biological significance of introgressed variation remains an important goal in population genomics. European (Anguilla anguilla) and American eel (A. rostrata) represent a remarkable case of hybridisation. Both are panmictic and spawn in partial sympatry in the Sargasso Sea, occasionally producing viable, fertile hybrids, primarily found in Iceland. We studied introgressive hybridisation from American into European eel using whole-genome sequences of 78 individuals, including European, American and 21 putative hybrid eels. Previous studies using few genetic markers could not resolve whether hybridisation involved simple unidirectional backcrossing or a more complex hybrid swarm scenario. However, local ancestry inference along individual chromosomes revealed that Icelandic hybrids were primarily F1 or first-generation backcrosses towards European eel, with some showing more complex backcrossing. All European eels outside Iceland contained short chromosomal blocks from American eel, indicating a porous genome. We found no evidence for previously hypothesised geographical gradients of introgression in European eel outside Iceland. Several chromosomal regions showed high interspecific divergence, but haplotype blocks introgressed from American eel were identified both within and outside these regions. There was little correspondence between regions of high relative (FST) and absolute divergence (dXY), with the former reflecting selective sweeps within species or reduced recombination rather than barrier loci. A single genomic region showed evidence of repeated introgression from American into European eel under positive selection in both species. The study illustrates that species can maintain genetic integrity despite porous genomes and that standing variation in one species can potentially be available for future adaptive responses in the other species.

Saltational Episodes of Reticulate Evolution in the Drosophila saltans Species Group

Phylogenomics reveals reticulate evolution to be widespread across taxa, but whether reticulation is due to low statistical power or it is a true evolutionary pattern remains a field of study. Here, we investigate the phylogeny and quantify reticulation in the Drosophila saltans species group, a Neotropical clade of the subgenus Sophophora comprising 23 species whose relationships have long been problematic. Phylogenetic analyses revealed conflicting topologies between the X chromosome, autosomes and the mitochondria. We extended the ABBA-BABA test of asymmetry in phylogenetic discordance to cases where no "true" species tree could be inferred, and applied our new test (called 2A2B) to whole genome data and to individual loci. We used four strategies, two based on our new assemblies using either conserved genes or ≥50 kb-long syntenic blocks with conserved collinearity across Neotropical Sophophora, and two consisted of windows from pseudo-reference genomes aligned to either an ingroup or outgroup species. Evidence for reticulation varied among the strategies, being lowest in the synteny-based approach, where it did not exceed ∼7% of the blocks in the most conflicting species quartets. High incidences of reticulation were restricted to three nodes on the tree that coincided with major paleogeographical events in South America. Our results identify possible technical biases in quantifying reticulate evolution and indicate that episodic rapid radiations have played a major role in the evolution of a largely understudied Neotropical clade.

A history of multiple Denisovan introgression events in modern humans

The identification of a new hominin group in the Altai mountains called Denisovans was one of the most exciting discoveries in human evolution in the last decade. Unlike Neanderthal remains, the Denisovan fossil record consists of only a finger bone, jawbone, teeth and skull fragments. Leveraging the surviving Denisovan segments in modern human genomes has uncovered evidence of at least three introgression events from distinct Denisovan populations into modern humans in the past. Each of them presents different levels of relatedness to the sequenced Altai Denisovan, indicating a complex relationship between these sister lineages. Here we review the evidence suggesting that several Denisovan populations, who likely had an extensive geographical range, were adapted to distinct environments and introgressed into modern humans multiple times. We further discuss how archaic variants have been affected by demographic history, negative and positive selection and close by proposing possible new lines of future research.

Massively parallel approaches for characterizing noncoding functional variation in human evolution

The genetic differences underlying unique phenotypes in humans compared to our closest primate relatives have long remained a mystery. Similarly, the genetic basis of adaptations between human groups during our expansion across the globe is poorly characterized. Uncovering the downstream phenotypic consequences of these genetic variants has been difficult, as a substantial portion lies in noncoding regions, such as cis-regulatory elements (CREs). Here, we review recent high-throughput approaches to measure the functions of CREs and the impact of variation within them. CRISPR screens can directly perturb CREs in the genome to understand downstream impacts on gene expression and phenotypes, while massively parallel reporter assays can decipher the regulatory impact of sequence variants. Machine learning has begun to be able to predict regulatory function from sequence alone, further scaling our ability to characterize genome function. Applying these tools across diverse phenotypes, model systems, and ancestries is beginning to revolutionize our understanding of noncoding variation underlying human evolution.

The Fate of a Polygenic Phenotype Within the Genomic Landscapes of Introgression in the European Seabass Hybrid Zone

Unraveling the evolutionary mechanisms and consequences of hybridization is a major concern in biology. Many studies have documented the interplay between recombination and selection in modulating the genomic landscape of introgression, but few have considered how associations with phenotype may affect this landscape. Here, we use the European seabass (Dicentrarchus labrax), a key species in marine aquaculture that undergoes natural hybridization, to determine how selection on phenotype modulates the introgression landscape between Atlantic and Mediterranean lineages. We use a high-density single nucleotide polymorphism array to assess individual local ancestry along the genome and improve the mapping of muscle fat content, a polygenic trait that is divergent between lineages. Taking into account variation in recombination rates, we reveal a purging of Atlantic ancestry in the admixed Mediterranean populations. While Atlantic individuals had higher muscle fat content, we observed that genomic regions associated with this trait in Mediterranean populations displayed reduced introgression of Atlantic ancestry. These results emphasize how selection against maladapted alleles shapes the genomic landscape of introgression.

The evolutionary fate of Neanderthal DNA in 30,780 admixed genomes with recent African-like ancestry

Following introgression, Neanderthal DNA was initially purged from non-African genomes, but the evolutionary fate of remaining introgressed DNA has not been explored yet. To fill this gap, we analyzed 30,780 admixed genomes with African-like ancestry from the All of Us research program, in which Neanderthal alleles encountered novel genetic backgrounds during the last 15 generations. Observed amounts of Neanderthal DNA approximately match expectations based on ancestry proportions, suggesting neutral evolution. Nevertheless, we identified genomic regions that have significantly less or more Neanderthal ancestry than expected and are associated with spermatogenesis, innate immunity, and other biological processes. We also identified three novel introgression desert-like regions in recently admixed genomes, whose genetic features are compatible with hybrid incompatibilities and intrinsic negative selection. Overall, we find that much of the remaining Neanderthal DNA in human genomes is not under strong selection, and complex evolutionary dynamics have shaped introgression landscapes in our species.

Recurrent gene flow between Neanderthals and modern humans over the past 200,000 years

Although it is well known that the ancestors of modern humans and Neanderthals admixed, the effects of gene flow on the Neanderthal genome are not well understood. We develop methods to estimate the amount of human-introgressed sequences in Neanderthals and apply it to whole-genome sequence data from 2000 modern humans and three Neanderthals. We estimate that Neanderthals have 2.5 to 3.7% human ancestry, and we leverage human-introgressed sequences in Neanderthals to revise estimates of Neanderthal ancestry in modern humans, show that Neanderthal population sizes were significantly smaller than previously estimated, and identify two distinct waves of modern human gene flow into Neanderthals. Our data provide insights into the genetic legacy of recurrent gene flow between modern humans and Neanderthals.

Facilitated introgression from domestic goat into Alpine ibex at immune loci

Hybridization can result in the transfer of adaptive genetic material from one species to another, known as adaptive introgression. Bottlenecked (and hence genetically depleted) species are expected to be particularly receptive to adaptive introgression, since introgression can introduce new or previously lost adaptive genetic variation. The Alpine ibex (Capra ibex), which recently recovered from near extinction, is known to hybridize with the domestic goat (Capra aegagrus hircus), and signals of introgression previously found at the major histocompatibility complex were suggested to potentially be adaptive. Here, we combine two ancient whole genomes of Alpine ibex with 29 modern Alpine ibex genomes and 31 genomes representing six related Capra species to investigate the genome-wide patterns of introgression and confirm the potential relevance of immune loci. We identified low rates of admixture in modern Alpine ibex through various F statistics and screening for putative introgressed tracts. Further results based on demographic modelling were consistent with introgression to have occurred during the last 300 years, coinciding with the known species bottleneck, and that in each generation, 1-2 out of 100 Alpine ibex had a domestic goat parent. The putatively introgressed haplotypes were enriched at immune-related genes, where the adaptive value of alternative alleles may give individuals with otherwise depleted genetic diversity a selective advantage. While interbreeding with domestic species is a prevalent issue in species conservation, in this specific case, it resulted in putative adaptive introgression. Our findings highlight the complex interplay between hybridization, adaptive evolution, and the potential risks and benefits associated with anthropogenic influences on wild species.

Functional characterization of archaic-specific variants in mitonuclear genes: insights from comparative analysis in S. cerevisiae

Neanderthal and Denisovan hybridisation with modern humans has generated a non-random genomic distribution of introgressed regions, the result of drift and selection dynamics. Cross-species genomic incompatibility and more efficient removal of slightly deleterious archaic variants have been proposed as selection-based processes involved in the post-hybridisation purge of archaic introgressed regions. Both scenarios require the presence of functionally different alleles across Homo species onto which selection operated differently according to which populations hosted them, but only a few of these variants have been pinpointed so far. In order to identify functionally divergent archaic variants removed in humans, we focused on mitonuclear genes, which are underrepresented in the genomic landscape of archaic humans. We searched for non-synonymous, fixed, archaic-derived variants present in mitonuclear genes, rare or absent in human populations. We then compared the functional impact of archaic and human variants in the model organism Saccharomyces cerevisiae. Notably, a variant within the mitochondrial tyrosyl-tRNA synthetase 2 (YARS2) gene exhibited a significant decrease in respiratory activity and a substantial reduction of Cox2 levels, a proxy for mitochondrial protein biosynthesis, coupled with the accumulation of the YARS2 protein precursor and a lower amount of mature enzyme. Our work suggests that this variant is associated with mitochondrial functionality impairment, thus contributing to the purging of archaic introgression in YARS2. While different molecular mechanisms may have impacted other mitonuclear genes, our approach can be extended to the functional screening of mitonuclear genetic variants present across species and populations.

G-quadruplex propensity in H. neanderthalensis, H. sapiens and Denisovans mitochondrial genomes

Current methods of processing archaeological samples combined with advances in sequencing methods lead to disclosure of a large part of H. neanderthalensis and Denisovans genetic information. It is hardly surprising that the genome variability between modern humans, Denisovans and H. neanderthalensis is relatively limited. Genomic studies may provide insight on the metabolism of extinct human species or lineages. Detailed analysis of G-quadruplex sequences in H. neanderthalensis and Denisovans mitochondrial DNA showed us interesting features. Relatively similar patterns in mitochondrial DNA are found compared to modern humans, with one notable exception for H. neanderthalensis. An interesting difference between H. neanderthalensis and H. sapiens corresponds to a motif found in the D-loop region of mtDNA, which is responsible for mitochondrial DNA replication. This area is directly responsible for the number of mitochondria and consequently for the efficient energy metabolism of cell. H. neanderthalensis harbor a long uninterrupted run of guanines in this region, which may cause problems for replication, in contrast with H. sapiens, for which this run is generally shorter and interrupted. One may propose that the predominant H. sapiens motif provided a selective advantage for modern humans regarding mtDNA replication and function.

Uncovering the genetic architecture and evolutionary roots of androgenetic alopecia in African men

Androgenetic alopecia is a highly heritable trait. However, much of our understanding about the genetics of male pattern baldness comes from individuals of European descent. Here, we examined a novel dataset comprising 2,136 men from Ghana, Nigeria, Senegal, and South Africa that were genotyped using a custom array. We first tested how genetic predictions of baldness generalize from Europe to Africa, finding that polygenic scores from European GWAS yielded AUC statistics that ranged from 0.513 to 0.546, indicating that genetic predictions of baldness in African populations performed notably worse than in European populations. Subsequently, we conducted the first African GWAS of androgenetic alopecia, focusing on self-reported baldness patterns at age 45. After correcting for present age, population structure, and study site, we identified 266 moderately significant associations, 51 of which were independent (p-value < 10-5, r2 < 0.2). Most baldness associations were autosomal, and the X chromosomes does not appear to have a large impact on baldness in African men. Finally, we examined the evolutionary causes of continental differences in genetic architecture. Although Neanderthal alleles have previously been associated with skin and hair phenotypes, we did not find evidence that European-ascertained baldness hits were enriched for signatures of ancient introgression. Most loci that are associated with androgenetic alopecia are evolving neutrally. However, multiple baldness-associated SNPs near the EDA2R and AR genes have large allele frequency differences between continents. Collectively, our findings illustrate how evolutionary history contributes to the limited portability of genetic predictions across ancestries.

A Neanderthal/Denisovan GLI3 variant contributes to anatomical variations in mice

Changes in genomic structures underlie phenotypic diversification in organisms. Amino acid-changing mutations affect pleiotropic functions of proteins, although little is known about how mutated proteins are adapted in existing developmental programs. Here we investigate the biological effects of a variant of the GLI3 transcription factor (GLI3R1537C) carried in Neanderthals and Denisovans, which are extinct hominins close to modern humans. R1537C does not compromise protein stability or GLI3 activator-dependent transcriptional activities. In contrast, R1537C affects the regulation of downstream target genes associated with developmental processes. Furthermore, genome-edited mice carrying the Neanderthal/Denisovan GLI3 mutation exhibited various alterations in skeletal morphology. Our data suggest that an extinct hominin-type GLI3 contributes to species-specific anatomical variations, which were tolerated by relaxed constraint in developmental programs during human evolution.

Neanderthal introgression in SCN9A impacts mechanical pain sensitivity

The Nav1.7 voltage-gated sodium channel plays a key role in nociception. Three functional variants in the SCN9A gene (encoding M932L, V991L, and D1908G in Nav1.7), have recently been identified as stemming from Neanderthal introgression and to associate with pain symptomatology in UK BioBank data. In 1000 genomes data, these variants are absent in Europeans but common in Latin Americans. Analysing high-density genotype data from 7594 Latin Americans, we characterized Neanderthal introgression in SCN9A. We find that tracts of introgression occur on a Native American genomic background, have an average length of ~123 kb and overlap the M932L, V991L, and D1908G coding positions. Furthermore, we measured experimentally six pain thresholds in 1623 healthy Colombians. We found that Neanderthal ancestry in SCN9A is significantly associated with a lower mechanical pain threshold after sensitization with mustard oil and evidence of additivity of effects across Nav1.7 variants. Our findings support the reported association of Neanderthal Nav1.7 variants with clinical pain, define a specific sensory modality affected by archaic introgression in SCN9A and are consistent with independent effects of the Neanderthal variants on Nav1.7 function.

Exploring the Neandertal legacy of pancreatic ductal adenocarcinoma risk in Eurasians

BACKGROUND

The genomes of present-day non-Africans are composed of 1-3% of Neandertal-derived DNA as a consequence of admixture events between Neandertals and anatomically modern humans about 50-60 thousand years ago. Neandertal-introgressed single nucleotide polymorphisms (aSNPs) have been associated with modern human disease-related traits, which are risk factors for pancreatic ductal adenocarcinoma (PDAC), such as obesity, type 2 diabetes, and inflammation. In this study, we aimed at investigating the role of aSNPs in PDAC in three Eurasian populations.

RESULTS

The high-coverage Vindija Neandertal genome was used to select aSNPs in non-African populations from 1000 Genomes project phase 3 data. Then, the association between aSNPs and PDAC risk was tested independently in Europeans and East Asians, using existing GWAS data on more than 200 000 individuals. We did not find any significant associations between aSNPs and PDAC in samples of European descent, whereas, in East Asians, we observed that the Chr10p12.1-rs117585753-T allele (MAF = 10%) increased the risk to develop PDAC (OR = 1.35, 95%CI 1.19-1.54, P = 3.59 × 10-6), with a P-value close to a threshold that takes into account multiple testing.

CONCLUSIONS

Our results show only a minimal contribution of Neandertal SNPs to PDAC risk.

Automatic landmarking identifies new loci associated with face morphology and implicates Neanderthal introgression in human nasal shape

We report a genome-wide association study of facial features in >6000 Latin Americans based on automatic landmarking of 2D portraits and testing for association with inter-landmark distances. We detected significant associations (P-value <5 × 10-8) at 42 genome regions, nine of which have been previously reported. In follow-up analyses, 26 of the 33 novel regions replicate in East Asians, Europeans, or Africans, and one mouse homologous region influences craniofacial morphology in mice. The novel region in 1q32.3 shows introgression from Neanderthals and we find that the introgressed tract increases nasal height (consistent with the differentiation between Neanderthals and modern humans). Novel regions include candidate genes and genome regulatory elements previously implicated in craniofacial development, and show preferential transcription in cranial neural crest cells. The automated approach used here should simplify the collection of large study samples from across the world, facilitating a cosmopolitan characterization of the genetics of facial features.

Human evolution: When admixture met selection

Admixture has been a major force during human evolution. Two new studies using ancient DNA now show how two key admixture events in the evolutionary history of Europeans altered their adaptive trajectories and facilitated rapid evolution.

Review: The different adaptive trajectories in Neanderthals and Homo sapiens and their implications for contemporary human physiological variation

Neanderthals are our one of our closest evolutionary cousins, but while they evolved in Eurasia, we (anatomically modern humans, AMH) originated in Africa. This contrasting evolutionary history has led to morphological and genetic distinctions between our species. Neanderthals are characterised by a relatively stocky build, high body mass, proportionally wide bodies and shorter limbs, a bell-shaped ribcage with a wide pelvis, and a long, low cranial vault compared with AMH. Classic readings of Neanderthal morphology link many of these traits to cold climate adaptations, however these interpretations have been questioned and alternative hypotheses including behavioural factors, dietary adaptations, locomotor specialisations, evolutionary history and neutral evolutionary processes have been invoked. Compared with AMH, Neanderthals may have been adapted for strength and power rather than endurance and may have consumed a diet high in animal products. However, reviewing these hypotheses highlights a number of limitations in our understanding of contemporary human physiology and metabolism, including the relationship between climate and morphology in AMH and Neanderthals, physiological limits on protein consumption, and the relationship between gut morphology and diet. As various relevant factors are clearly linked (e.g. diet, behaviour, metabolism, morphology, activity), ultimately a more integrated approach may be needed to fully understand Neanderthal biology. Variation among contemporary AMHs may offer, with caveats, a useful model for understanding the evolution of both Neanderthal and modern human characteristics, which in turn may further deepen our understanding of variability within and between contemporary humans. Neanderthals; Anatomically modern humans; morphology; climate adaptation; power adaptations; metabolism; diet; physiology; endurance running.

Introgression from extinct species facilitates adaptation to its vacated niche

Anthropogenic disturbances of ecosystems are causing a loss of biodiversity at an unprecedented rate. Species extinctions often leave ecological niches underutilized, and their colonization by other species may require new adaptation. In Lake Constance, on the borders of Germany, Austria and Switzerland, an endemic profundal whitefish species went extinct during a period of anthropogenic eutrophication. In the process of extinction, the deep-water species hybridized with three surviving whitefish species of Lake Constance, resulting in introgression of genetic variation that is potentially adaptive in deep-water habitats. Here, we sampled a water depth gradient across a known spawning ground of one of these surviving species, Coregonus macrophthalmus, and caught spawning individuals at greater depths (down to 90 m) than historically recorded. We sequenced a total of 96 whole genomes, 11-17 for each of six different spawning depth populations (4, 12, 20, 40, 60 and 90 m), to document genomic intraspecific differentiation along a water depth gradient. We identified 52 genomic regions that are potentially under divergent selection between the deepest (90 m) and all shallower (4-60 m) spawning habitats. At 12 (23.1%) of these 52 loci, the allele frequency pattern across historical and contemporary populations suggests that introgression from the extinct species potentially facilitates ongoing adaptation to deep water. Our results are consistent with the syngameon hypothesis, proposing that hybridization between members of an adaptive radiation can promote further niche expansion and diversification. Furthermore, our findings demonstrate that introgression from extinct into extant species can be a source of evolvability, enabling rapid adaptation to environmental change, and may contribute to the ecological recovery of ecosystem functions after extinctions.