Anthropological Genetics: Inferring the History of Our Species Through the Analysis of DNA

The genetic material, deoxyribonucleic acid (DNA), contains information about the evolutionary history of life. Both the relationships amongst organisms and the times of their divergence can be inferred from DNA sequences. Anthropological geneticists use DNA sequences to infer the evolutionary history of humans and their primate relatives. We review the basic methodology used to infer these relationships. We then review the anthropological genetic evidence for modern human origins. We conclude that modern humans evolved recently in Africa and then left to colonize the rest of the world within the last 50,000 years, largely replacing the other human groups that they encountered. Modern humans likely exchanged genes with Neanderthals prior to or early during their expansion out of Africa.     

Phylogenomics,molecular evolution,and estimated ages of lineages from the deep phylogeny of Poaceae

The deeply diverging subfamilies of grasses: Anomochlooideae, Pharoideae, and Puelioideae, today inhabit tropical forest floors as sparsely distributed depauperate lineages. The BEP/PACMAD grasses, which make up the majority of the family, are the result of a more recent radiation. Species in the deeply diverging subfamilies were here investigated to better understand molecular evolutionary processes and ages of divergence. Complete chloroplast genomes (plastomes) of Pharus latifolius L., P. lappulaceus Aubl., and Puelia olyriformis (Franch.) Clayton were determined. Four plastome loci from seven species of the deep subfamilies were also sequenced. Phylogenetic and mutation analyses and divergence estimations were conducted on all sequences together with homologous sequences from other Poaceae. Mutation analyses surveyed insertion/deletion mutations across the plastomes, clarified a trend in the molecular evolution of the rpoC2 locus, and indicated unique pseudogenizations in the plastomes of Pharus and Puelia. Phylogenetic analyses largely confirmed earlier multi-gene phylogenies. Phylogenomic and divergence analyses produced estimated origins of the crown nodes of Anomochlooideae at 65–104 Ma, Pharoideae at 44–71 Ma, and Puelioideae at 62–96 Ma. The upper ends of our estimated ranges are in general agreement with previous estimates. However, the lower ends of our ranges are considerably older than previous estimates, reflecting the influence of the less commonly used oldest fossil calibration point. The deeply diverging subfamilies exhibited the accumulation of numerous substitution and indel mutations consistent with a long evolutionary history that predated the radiation of the BEP/PACMAD grasses. We hypothesize that relatively rapid warming and drying in Africa at 55–56.5 Ma may have acted as selective forces stimulating adaptive radiations of grasses from the African tropical forests into diverse habitats.     

The Evolutionary History of the Australopiths

The australopiths are a group of early hominins (humans and their close extinct relatives) that lived in Africa between approximately 4.1 and 1.4 million years ago. Formerly known as the australopithecines, they are not a “natural” group, in that they do not represent all of the descendants of a single common ancestor (i.e., they are not a “clade”). Rather, they are grouped together informally because nearly all share a similar adaptive grade (i.e., they have similar adaptations). In particular, they are bipedal apes that, to a greater or lesser extent, exhibit enlarged molar and premolar teeth (postcanine megadontia) and other associated modifications to their feeding apparatuses. Dietary adaptations clearly played an important role in shaping their evolutionary history. They also are distinguished by their lack of derived features typically associated with the genus Homo, such as a large brain, a broad complement of adaptations for manual dexterity, and advanced tool use. However, Homo is almost certainly descended from an australopith ancestor, so at least one or some australopiths belong directly to the human lineage. Regardless, australopiths had a rich evolutionary history deserving of study independent of questions about our direct ancestry. They were diverse, geographically widespread, and anatomically derived, they lived through periods of pronounced climate change, and their story dominates the narrative of human evolution for millions of years.     

Reconstructing cranial evolution in an extinct hominin

Homo erectus is the first hominin species with a truly cosmopolitan distribution and resembles recent humans in its broad spatial distribution. The microevolutionary events associated with dispersal and local adaptation may have produced similar population structure in both species. Understanding the evolutionary population dynamics of H. erectus has larger implications for the emergence of later Homo lineages in the Middle Pleistocene. Quantitative genetics models provide a means of interrogating aspects of long-standing H. erectus population history narratives. For the current study, cranial fossils were sorted into six major palaeodemes from sites across Africa and Asia spanning 1.8–0.1 Ma. Three-dimensional shape data from the occipital and frontal bones were used to compare intraspecific variation and test evolutionary hypotheses. Results indicate that H. erectus had higher individual and group variation than Homo sapiens, probably reflecting different levels of genetic diversity and population history in these spatially disperse species. This study also revealed distinct evolutionary histories for frontal and occipital bone shape in H. erectus, with a larger role for natural selection in the former. One scenario consistent with these findings is climate-driven facial adaptation in H. erectus, which is reflected in the frontal bone through integration with the orbits.     

Ancient mitochondrial genomes from Chinese cave hyenas provide insights into the evolutionary history of the genus Crocuta

Cave hyenas (genus Crocuta) are extinct bone-cracking carnivores from the family Hyaenidae and are generally split into two taxa that correspond to a European/Eurasian and an (East) Asian lineage. They are close relatives of the extant African spotted hyenas, the only extant member of the genus Crocuta. Cave hyenas inhabited a wide range across Eurasia during the Pleistocene, but became extinct at the end of the Late Pleistocene. Using genetic and genomic datasets, previous studies have proposed different scenarios about the evolutionary history of Crocuta. However, causes of the extinction of cave hyenas are widely speculative and samples from China are severely understudied. In this study, we assembled near-complete mitochondrial genomes from two cave hyenas from northeastern China dating to 20 240 and 20 253 calBP, representing the youngest directly dated fossils of Crocuta in Asia. Phylogenetic analyses suggest a monophyletic clade of these two samples within a deeply diverging mitochondrial haplogroup of Crocuta. Bayesian analyses suggest that the split of this Asian cave hyena mitochondrial lineage from their European and African relatives occurred approximately 1.85 Ma (95% CI 1.62–2.09 Ma), which is broadly concordant with the earliest Eurasian Crocuta fossil dating to approximately 2 Ma. Comparisons of mean genetic distance indicate that cave hyenas harboured higher genetic diversity than extant spotted hyenas, brown hyenas and aardwolves, but this is probably at least partially due to the fact that their mitochondrial lineages do not represent a monophyletic group, although this is also true for extant spotted hyenas. Moreover, the joint female effective population size of Crocuta (both cave hyenas and extant spotted hyenas) has sustained two declines during the Late Pleistocene. Combining this mitochondrial phylogeny, previous nuclear findings and fossil records, we discuss the possible relationship of fossil Crocuta in China and the extinction of cave hyenas.     

The fossil vertebrate locality Kossom Bougoudi,Djurab desert,Chad: A window in the distribution of the carnivoran faunas at the Mio–Pliocene boundary in Africa

The fossil vertebrate bearing locality Kossom Bougoudi (KB) is situated in the Djurab desert (Chad, Africa), 600 km north-east of N’djamena. It has yielded about 1250 specimens with many mammalian remains, principally artiodactyls. Its geologic age has been estimated to be about 5 Ma by biochronologic estimation and about 5.3 Ma by radiometric studies on cosmogenic nuclides of beryllium (authigenic ¹⁰B/⁹B). The carnivoran fauna contains few specimens which belong to five different families. All the taxa were unknown in central Africa. A large lutrine is close to Sivaonyx but different from known species of the genus. Another large lutrine is similar by its size to a species described from the Middle Pliocene of Uganda. An edentulous mandible of a small machairodont cat resembles a small species of Dinofelis, while a distal humerus indicates the presence of a larger member of the same genus. A hunting hyaenid is also much like the European species. An unidentified canid reaches the size of the recent Canis aureus and an isolated calcaneum matches that of the large extant viverrid. This small fauna allows a first look at the guild of the carnivorans at the Latest Miocene–Pliocene boundary in Central Africa and is a milestone between North African, East African and South African carnivore faunas.     

New observations on the Late Miocene–Early Pliocene Lutrinae (Mustelidae: Carnivora,Mammalia) from the Middle Awash,Afar Rift,Ethiopia

New observations on the Late Miocene and Earliest Pliocene mustelids from the Middle Awash of Ethiopia are presented. The Middle Awash study area samples the last six million years of African vertebrate evolutionary history. Its Latest Miocene (Asa Koma Member of the Adu-Asa Formation, 5.54–5.77 Ma) and Earliest Pliocene (Kuseralee and Gawto Members of the Sagantole Formation, 5.2 and 4.85 Ma, respectively) deposits sample a number of large and small carnivore taxa among which mustelids are numerically abundant. Among the known Late Miocene and Early Pliocene mustelid genera, the Middle Awash Late Miocene documents the earliest Mellivora in eastern Africa and its likely first appearance in Africa, a new species of Plesiogulo, and a species of Vishnuonyx. The latter possibly represents the last appearance of this genus in Africa. Torolutra ougandensis is known from both the Late Miocene and Early Pliocene deposits of the Middle Awash. The genus Sivaonyx is represented by at least two species: S. ekecaman and S. aff. S. soriae. Most of the lutrine genera documented in the Middle Awash Late Miocene/Early Pliocene are also documented in contemporaneous sites of eastern Africa. The new observations presented here show that mustelids were more diverse in the Middle Awash Late Miocene and Early Pliocene than previously documented.     

Paleogenomics of archaic hominins

In order to understand the genetic basis for the evolutionary success of modern humans, it is necessary to compare their genetic makeup to that of closely related species. Unfortunately, our closest living relatives, the chimpanzees, are evolutionarily quite distant. With the advent of ancient DNA study and more recently paleogenomics - the study of the genomes of ancient organisms - it has become possible to compare human genomes to those of much more closely related groups. Our closest known relatives are the Neanderthals, which evolved and lived in Europe and Western Asia, from about 600,000 years ago until their disappearance around 30,000 years ago following the expansion of anatomically modern humans into their range. The closely related Denisovans are only known by virtue of their DNA, which has been extracted from bone fragments dating around 30,000 to 50,000 years ago found in a single Siberian cave. Analyses of Neanderthal and Denisovan nuclear and mitochondrial genomes have revealed surprising insights into these archaic humans as well as our own species. The genomes provide a preliminary catalogue of derived amino acids that are specific to all extant modern humans, thus offering insights into the functional differences between the three lineages. In addition, the genomes provide evidence of gene flow between the three lineages after anatomically modern humans left Africa, drastically changing our view of human evolution.     

Variation in enamel thickness within the genus Homo

Recent humans and their fossil relatives are classified as having thick molar enamel, one of very few dental traits that distinguish hominins from living African apes. However, little is known about enamel thickness in the earliest members of the genus Homo, and recent studies of later Homo report considerable intra- and inter-specific variation. In order to assess taxonomic, geographic, and temporal trends in enamel thickness, we applied micro-computed tomographic imaging to 150 fossil Homo teeth spanning two million years. Early Homo postcanine teeth from Africa and Asia show highly variable average and relative enamel thickness (AET and RET) values. Three molars from South Africa exceed Homo AET and RET ranges, resembling the hyper thick Paranthropus condition. Most later Homo groups (archaic European and north African Homo, and fossil and recent Homo sapiens) possess absolutely and relatively thick enamel across the entire dentition. In contrast, Neanderthals show relatively thin enamel in their incisors, canines, premolars, and molars, although incisor AET values are similar to H. sapiens. Comparisons of recent and fossil H. sapiens reveal that dental size reduction has led to a disproportionate decrease in coronal dentine compared with enamel (although both are reduced), leading to relatively thicker enamel in recent humans. General characterizations of hominins as having ‘thick enamel’ thus oversimplify a surprisingly variable craniodental trait with limited taxonomic utility within a genus. Moreover, estimates of dental attrition rates employed in paleodemographic reconstruction may be biased when this variation is not considered. Additional research is necessary to reconstruct hominin dietary ecology since thick enamel is not a prerequisite for hard-object feeding, and it is present in most later Homo species despite advances in technology and food processing.     

Nepotistic cooperation in non-human primate groups

Darwin was struck by the many similarities between humans and other primates and believed that these similarities were the product of common ancestry. He would be even more impressed by the similarities if he had known what we have learned about primates over the last 50 years. Genetic kinship has emerged as the primary organizing force in the evolution of primate social organization and the patterning of social behaviour in non-human primate groups. There are pronounced nepotistic biases across the primate order, from tiny grey mouse lemurs (Microcebus murinus) that forage alone at night but cluster with relatives to sleep during the day, to cooperatively breeding marmosets that rely on closely related helpers to rear their young, rhesus macaque (Macaca mulatta) females who acquire their mother''s rank and form strict matrilineal dominance hierarchies, male howler monkeys that help their sons maintain access to groups of females and male chimpanzees (Pan troglodytes) that form lasting relationships with their brothers. As more evidence of nepotism has accumulated, important questions about the evolutionary processes underlying these kin biases have been raised. Although kin selection predicts that altruism will be biased in favour of relatives, it is difficult to assess whether primates actually conform to predictions derived from Hamilton''s rule: br > c. In addition, other mechanisms, including contingent reciprocity and mutualism, could contribute to the nepotistic biases observed in non-human primate groups. There are good reasons to suspect that these processes may complement the effects of kin selection and amplify the extent of nepotistic biases in behaviour.     

The Date of Interbreeding between Neandertals and Modern Humans

Comparisons of DNA sequences between Neandertals and present-day humans have shown that Neandertals share more genetic variants with non-Africans than with Africans. This could be due to interbreeding between Neandertals and modern humans when the two groups met subsequent to the emergence of modern humans outside Africa. However, it could also be due to population structure that antedates the origin of Neandertal ancestors in Africa. We measure the extent of linkage disequilibrium (LD) in the genomes of present-day Europeans and find that the last gene flow from Neandertals (or their relatives) into Europeans likely occurred 37,000–86,000 years before the present (BP), and most likely 47,000–65,000 years ago. This supports the recent interbreeding hypothesis and suggests that interbreeding may have occurred when modern humans carrying Upper Paleolithic technologies encountered Neandertals as they expanded out of Africa.     

The Leporid Datum: a late Miocene biotic marker

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Age of the Association between Helicobacter pylori and Man

When modern humans left Africa ca. 60,000 years ago (60 kya), they were already infected with Helicobacter pylori, and these bacteria have subsequently diversified in parallel with their human hosts. But how long were humans infected by H. pylori prior to the out-of-Africa event? Did this co-evolution predate the emergence of modern humans, spanning the species divide? To answer these questions, we investigated the diversity of H. pylori in Africa, where both humans and H. pylori originated. Three distinct H. pylori populations are native to Africa: hpNEAfrica in Afro-Asiatic and Nilo-Saharan speakers, hpAfrica1 in Niger-Congo speakers and hpAfrica2 in South Africa. Rather than representing a sustained co-evolution over millions of years, we find that the coalescent for all H. pylori plus its closest relative H. acinonychis dates to 88–116 kya. At that time the phylogeny split into two primary super-lineages, one of which is associated with the former hunter-gatherers in southern Africa known as the San. H. acinonychis, which infects large felines, resulted from a later host jump from the San, 43–56 kya. These dating estimates, together with striking phylogenetic and quantitative human-bacterial similarities show that H. pylori is approximately as old as are anatomically modern humans. They also suggest that H. pylori may have been acquired via a single host jump from an unknown, non-human host. We also find evidence for a second Out of Africa migration in the last 52,000 years, because hpEurope is a hybrid population between hpAsia2 and hpNEAfrica, the latter of which arose in northeast Africa 36–52 kya, after the Out of Africa migrations around 60 kya.     

Population genetics of malaria resistance in humans

The high mortality and widespread impact of malaria have resulted in this disease being the strongest evolutionary selective force in recent human history, and genes that confer resistance to malaria provide some of the best-known case studies of strong positive selection in modern humans. I begin by reviewing JBS Haldane''s initial contribution to the potential of malaria genetic resistance in humans. Further, I discuss the population genetics aspects of many of the variants, including globin, G6PD deficiency, Duffy, ovalocytosis, ABO and human leukocyte antigen variants. Many of the variants conferring resistance to malaria are ‘loss-of-function'' mutants and appear to be recent polymorphisms from the last 5000–10 000 years or less. I discuss estimation of selection coefficients from case–control data and make predictions about the change for S, C and G6PD-deficiency variants. In addition, I consider the predicted joint changes when the two β-globin alleles S and C are both variable in the same population and when there is a variation for α-thalassemia and S, two unlinked, but epistatic variants. As more becomes known about genes conferring genetic resistance to malaria in humans, population genetics approaches can contribute both to investigating past selection and predicting the consequences in future generations for these variants.     

Cross-Species Pathogen Transmission and Disease Emergence in Primates

Many of the most virulent emerging infectious diseases in humans, e.g., AIDS and Ebola, are zoonotic, having shifted from wildlife populations. Critical questions for predicting disease emergence are: (1) what determines when and where a disease will first cross from one species to another, and (2) which factors facilitate emergence after a successful host shift. In wild primates, infectious diseases most often are shared between species that are closely related and inhabit the same geographic region. Therefore, humans may be most vulnerable to diseases from the great apes, which include chimpanzees and gorillas, because these species represent our closest relatives. Geographic overlap may provide the opportunity for cross-species transmission, but successful infection and establishment will be determined by the biology of both the host and pathogen. We extrapolate the evolutionary relationship between pathogen sharing and divergence time between primate species to generate “hotspot” maps, highlighting regions where the risk of disease transfer between wild primates and from wild primates to humans is greatest. We find that central Africa and Amazonia are hotspots for cross-species transmission events between wild primates, due to a high diversity of closely related primate species. Hotspots of host shifts to humans will be most likely in the forests of central and west Africa, where humans come into frequent contact with their wild primate relatives. These areas also are likely to sustain a novel epidemic due to their rapidly growing human populations, close proximity to apes, and population centers with high density and contact rates among individuals.     

Fossil evidence for key innovations in the evolution of insect diversity

Explaining the taxonomic richness of the insects, comprising over half of all described species, is a major challenge in evolutionary biology. Previously, several evolutionary novelties (key innovations) have been posited to contribute to that richness, including the insect bauplan, wings, wing folding and complete metamorphosis, but evidence over their relative importance and modes of action is sparse and equivocal. Here, a new dataset on the first and last occurrences of fossil hexapod (insects and close relatives) families is used to show that basal families of winged insects (Palaeoptera, e.g. dragonflies) show higher origination and extinction rates in the fossil record than basal wingless groups (Apterygota, e.g. silverfish). Origination and extinction rates were maintained at levels similar to Palaeoptera in the more derived Polyneoptera (e.g. cockroaches) and Paraneoptera (e.g. true bugs), but extinction rates subsequently reduced in the very rich group of insects with complete metamorphosis (Holometabola, e.g. beetles). Holometabola show evidence of a recent slow-down in their high net diversification rate, whereas other winged taxa continue to diversify at constant but low rates. These data suggest that wings and complete metamorphosis have had the most effect on family-level insect macroevolution, and point to specific mechanisms by which they have influenced insect diversity through time.     

First Early Hominin from Central Africa (Ishango,Democratic Republic of Congo)

Despite uncontested evidence for fossils belonging to the early hominin genus Australopithecus in East Africa from at least 4.2 million years ago (Ma), and from Chad by 3.5 Ma, thus far there has been no convincing evidence of Australopithecus, Paranthropus or early Homo from the western (Albertine) branch of the Rift Valley. Here we report the discovery of an isolated upper molar (#Ish25) from the Western Rift Valley site of Ishango in Central Africa in a derived context, overlying beds dated to between ca. 2.6 to 2.0 Ma. We used µCT imaging to compare its external and internal macro-morphology to upper molars of australopiths, and fossil and recent Homo. We show that the size and shape of the enamel-dentine junction (EDJ) surface discriminate between Plio-Pleistocene and post-Lower Pleistocene hominins, and that the Ishango molar clusters with australopiths and early Homo from East and southern Africa. A reassessment of the archaeological context of the specimen is consistent with the morphological evidence and suggest that early hominins were occupying this region by at least 2 Ma.