Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago.

The bacteria Yersinia pestis is the etiological agent of plague and has caused human pandemics with millions of deaths in historic times. How and when it originated remains contentious. Here, we report the oldest direct evidence of Yersinia pestis identified by ancient DNA in human teeth from Asia and Europe dating from 2,800 to 5,000 years ago. By sequencing the genomes, we find that these ancient plague strains are basal to all known Yersinia pestis. We find the origins of the Yersinia pestis lineage to be at least two times older than previous estimates. We also identify a temporal sequence of genetic changes that lead to increased virulence and the emergence of the bubonic plague. Our results show that plague infection was endemic in the human populations of Eurasia at least 3,000 years before any historical recordings of pandemics.

Bilateral lunotriquetral coalition: a dynamic four-dimensional computed tomography technical case report.

Lunotriquetral coalitions are the most common form of carpal coalition wherein the cartilage between the lunate and triquetrum ossification centers failed to undergo apoptosis. This technical case report examines the arthrokinematics of bilateral lunotriquetral coalitions with dissimilar Minnaar types in one participant with one asymptomatic wrist and one wrist with suspected distal radioulnar joint injury. Static and dynamic (four-dimensional) CT images during pronosupination were captured using a photon-counting detector CT scanner. Interosseous proximity distributions were calculated between the lunotriquetral coalition and adjacent bones in both wrists to quantify arthrokinematics. Interosseous proximity distributions at joints adjacent to the lunotriquetral coalition demonstrate differences in median and minimum interosseous proximities between the asymptomatic and injured wrists during resisted pronosupination. Altered kinematics from lunotriquetral coalitions may be a source of ulnar-sided wrist pain and discomfort, limiting the functional range of motion. This case report highlights potential alterations to wrist arthrokinematics in the setting of lunotriquetral coalitions and possible associations with ulnar-sided wrist pain, highlighting anatomy to examine in radiographic follow-up. Furthermore, this case report demonstrates the technical feasibility of four-dimensional CT using photon-counting detector technology in assessing arthrokinematics in the setting of variant wrist anatomy.

Patterns of variation in canal and root number in human post-canine teeth.

Descriptive morphology of tooth roots traditionally focuses on number of canals and roots. However, how or if canal and root number are related is poorly understood. While it is often assumed that canal number is concomitant with root number and morphology, in practice canal number and morphology do not always covary with external root features. To investigate the relationship between canal and root number, fully developed, adult post-canine teeth were examined and quantified from computerized tomography scans from a global sample of 945 modern humans. We tested the hypotheses that root and canal number do not follow a 1:1 ratio, that canal to root ratios differ between teeth, and that canal to root ratios differ across major human geographical groups. Results indicate that not only is root number dependent on canal number, but that this relationship becomes more variable as canal number increases, varies between individual teeth and by major geographical group, and changes as these groups increase in geographical distance from Sub-Saharan Africa. These results show that the ratio of canal number to root number is an important indicator of variation in dental phenotypes.

A process-based approach to hominin taxonomy provides new perspectives on hominin speciation.

A longstanding debate in hominin taxonomy is that between "lumpers" and "splitters." We argue that both approaches assume an unrealistically static model of speciation. Speciation is an extended process, of which fossils provide a record. Fossils should be interpreted in a more dynamic framework than is the norm. We introduce the process-based approach (PBA), in which we suggest that "splitters" recognize and name units at an earlier stage of speciation than "lumpers" do. The "determinants" of speciation can control the rate at which population isolates form, or the rate at which these complete the speciation process, or both. Embedded in the PBA, differences between existing lumped and split taxonomies are a heuristic tool to study these processes. We apply the PBA to show that not all hominin populations reached later stages of the speciation process and that populations have a disproportionate likelihood of doing so from ∼3.1 to ∼1.5 Ma. We outline and discuss resulting new research questions.

Terrestrial habitats decouple the relationship between species and subspecies diversification in mammals.

Darwin proposed that lineages with higher diversification rates should evidence this capacity at both the species and subspecies level. This should be the case if subspecific boundaries are evolutionary faultlines along which speciation is generally more likely to occur. This pattern has been described for birds, but remains poorly understood in mammals. To investigate the relationship between species richness (SR) and subspecies richness (SSR), we calculated the strength of the correlation between the two across all mammals. Mammalian taxonomic richness correlates positively, but only very weakly, between the species and subspecies level, deviating from the pattern found in birds. However, when mammals are separated by environmental substrate, the relationship between generic SR and average SSR in non-terrestrial taxa is stronger than that reported for birds (Kendall's tau = 0.31, p < 0.001). By contrast, the correlation in terrestrial taxa alone weakens compared to that for all mammals (Kendall's tau = 0.11, p < 0.001). A significant interaction between environmental substrate and SR in phylogenetic regressions confirms a role for terrestrial habitats in disrupting otherwise linked dynamics of diversification across the taxonomic hierarchy. Further, models including species range size as a predictor show that range size affects SSR more in terrestrial taxa. Taken together, these results suggest that the dynamics of diversification of terrestrial mammals are more affected by physical barriers or ecological heterogeneity within ranges than those of non-terrestrial mammals, at two evolutionary levels. We discuss the implication of these results for the equivalence of avian and mammalian subspecies, their potential role in speciation and the broader question of the relationship between microevolution and macroevolution.

Who were the Nataruk people? Mandibular morphology among late Pleistocene and early Holocene fisher-forager populations of West Turkana (Kenya).

Africa is the birthplace of the species Homo sapiens, and Africans today are genetically more diverse than other populations of the world. However, the processes that underpinned the evolution of African populations remain largely obscure. Only a handful of late Pleistocene African fossils (∼50-12 Ka) are known, while the more numerous sites with human fossils of early Holocene age are patchily distributed. In particular, late Pleistocene and early Holocene human diversity in Eastern Africa remains little studied, precluding any analysis of the potential factors that shaped human diversity in the region, and more broadly throughout the continent. These periods include the Last Glacial Maximum (LGM), a moment of extreme aridity in Africa that caused the fragmentation of population ranges and localised extinctions, as well as the 'African Humid Period', a moment of abrupt climate change and enhanced connectivity throughout Africa. East Africa, with its range of environments, may have acted as a refugium during the LGM, and may have played a critical biogeographic role during the heterogene`ous environmental recovery that followed. This environmental context raises a number of questions about the relationships among early Holocene African populations, and about the role played by East Africa in shaping late hunter-gatherer biological diversity. Here, we describe eight mandibles from Nataruk, an early Holocene site (∼10 Ka) in West Turkana, offering the opportunity of exploring population diversity in Africa at the height of the 'African Humid Period'. We use 3D geometric morphometric techniques to analyze the phenotypic variation of a large mandibular sample. Our results show that (i) the Nataruk mandibles are most similar to other African hunter-fisher-gatherer populations, especially to the fossils from Lothagam, another West Turkana locality, and to other early Holocene fossils from the Central Rift Valley (Kenya); and (ii) a phylogenetic connection may have existed between these Eastern African populations and some Nile Valley and Maghrebian groups, who lived at a time when a Green Sahara may have allowed substantial contact, and potential gene flow, across a vast expanse of Northern and Eastern Africa.

A multivariate ecogeographic analysis of macaque craniodental variation.

OBJECTIVES: To infer the ecogeographic conditions that underlie the evolutionary diversification of macaques, we investigated the within- and between-species relationships of craniodental dimensions, geography, and environment in extant macaque species. We studied evolutionary processes by contrasting macroevolutionary patterns, phylogeny, and within-species associations. MATERIALS AND METHODS: Sixty-three linear measurements of the permanent dentition and skull along with data about climate, ecology (environment), and spatial geography were collected for 711 specimens of 12 macaque species and analyzed by a multivariate approach. Phylogenetic two-block partial least squares was used to identify patterns of covariance between craniodental and environmental variation. Phylogenetic reduced rank regression was employed to analyze spatial clines in morphological variation. RESULTS: Between-species associations consisted of two distinct multivariate patterns. The first represents overall craniodental size and is negatively associated with temperature and habitat, but positively with latitude. The second pattern shows an antero-posterior tooth size contrast related to diet, rainfall, and habitat productivity. After controlling for phylogeny, however, the latter dimension was diminished. Within-species analyses neither revealed significant association between morphology, environment, and geography, nor evidence of isolation by distance. DISCUSSION: We found evidence for environmental adaptation in macaque body and craniodental size, primarily driven by selection for thermoregulation. This pattern cannot be explained by the within-species pattern, indicating an evolved genetic basis for the between-species relationship. The dietary signal in relative tooth size, by contrast, can largely be explained by phylogeny. This cautions against adaptive interpretations of phenotype-environment associations when phylogeny is not explicitly modelled.

Ghosts of extinct apes: genomic insights into African hominid evolution.

We are accustomed to regular announcements of new hominin fossils. There are now some 6000 hominin fossils, and up to 31 species. However, where are the announcements of African ape fossils? The answer is that there are almost none. Our knowledge of African ape evolution is based entirely on genomic analyses, which show that extant diversity is very young. This contrasts with the extensive and deep diversity of hominins known from fossils. Does this difference point to low and late diversification of ape lineages, or high rates of extinction? The comparative evolutionary dynamics of African hominids are central to interpreting living ape adaptations, as well as understanding the patterns of hominin evolution and the nature of the last common ancestor.

Diversity-dependent speciation and extinction in hominins.

The search for drivers of hominin speciation and extinction has tended to focus on the impact of climate change. Far less attention has been paid to the role of interspecific competition. However, research across vertebrates more broadly has shown that both processes are often correlated with species diversity, suggesting an important role for interspecific competition. Here we ask whether hominin speciation and extinction conform to the expected patterns of negative and positive diversity dependence, respectively. We estimate speciation and extinction rates from fossil occurrence data with preservation variability priors in a validated Bayesian framework and test whether these rates are correlated with species diversity. We supplement these analyses with calculations of speciation rate across a phylogeny, again testing whether these are correlated with diversity. Our results are consistent with clade-wide diversity limits that governed speciation in hominins overall but that were not quite reached by the Australopithecus and Paranthropus subclade before its extinction. Extinction was not correlated with species diversity within the Australopithecus and Paranthropus subclade or within hominins overall; this is concordant with climate playing a greater part in hominin extinction than speciation. By contrast, Homo is characterized by positively diversity-dependent speciation and negatively diversity-dependent extinction-both exceedingly rare patterns across all forms of life. The genus Homo expands the set of reported associations between diversity and macroevolution in vertebrates, underscoring that the relationship between diversity and macroevolution is complex. These results indicate an important, previously underappreciated and comparatively unusual role of biotic interactions in Homo macroevolution, and speciation in particular. The unusual and unexpected patterns of diversity dependence in Homo speciation and extinction may be a consequence of repeated Homo range expansions driven by interspecific competition and made possible by recurrent innovations in ecological strategies. Exploring how hominin macroevolution fits into the general vertebrate macroevolutionary landscape has the potential to offer new perspectives on longstanding questions in vertebrate evolution and shed new light on evolutionary processes within our own lineage.

Shibboleth: An agent-based model of signalling mimicry.

Mimicry is an essential strategy for exploiting competitors in competitive co-evolutionary relationships. Protection against mimicry may, furthermore, be a driving force in human linguistic diversity: the potential harm caused by failing to detect mimicked group-identity signals may select for high sensitivity to mimicry of honest group members. Here we describe the results of five agent-based models that simulate multi-generational interactions between two groups of individuals: original members of a group with an honest identity signal, and members of an outsider group who mimic that signal, aiming to pass as members of the in-group. The models correspond to the Biblical story of Shibboleth, where a tribe in conflict with another determines tribe affiliation by asking individuals to pronounce the word, 'Shibboleth.' In the story, failure to reproduce the word phonetically resulted in death. Here, we run five different versions of a 'Shibboleth' model: a first, simple version, which evaluates whether a composite variable of mimicry quality and detection quality is a superior predictor to the model's outcome than is cost of detection. The models thereafter evaluate variations on the simple model, incorporating group-level behaviours such as altruistic punishment. Our results suggest that group members' sensitivity to mimicry of the Shibboleth-signal is a better predictor of whether any signal of group identity goes into fixation in the overall population than is the cost of mimicry detection. Thus, the likelihood of being detected as a mimic may be more important than the costs imposed on mimics who are detected. This suggests that theoretical models in biology should place greater emphasis on the likelihood of detection, which does not explicitly entail costs, rather than on the costs to individuals who are detected. From a language learning perspective, the results suggest that admission to group membership through linguistic signals is powered by the ability to imitate and evade detection as an outsider by existing group members.

The discovery of an in situ Neanderthal remain in the Bawa Yawan Rockshelter, West-Central Zagros Mountains, Kermanshah.

Neanderthal extinction has been a matter of debate for many years. New discoveries, better chronologies and genomic evidence have done much to clarify some of the issues. This evidence suggests that Neanderthals became extinct around 40,000-37,000 years before present (BP), after a period of coexistence with Homo sapiens of several millennia, involving biological and cultural interactions between the two groups. However, the bulk of this evidence relates to Western Eurasia, and recent work in Central Asia and Siberia has shown that there is considerable local variation. Southwestern Asia, despite having a number of significant Neanderthal remains, has not played a major part in the debate over extinction. Here we report a Neanderthal deciduous canine from the site of Bawa Yawan in the West-Central Zagros Mountains of Iran. The tooth is associated with Zagros Mousterian lithics, and its context is preliminary dated to between ~43,600 and ~41,500 years ago.

Developmental plasticity and human health.

Many plants and animals are capable of developing in a variety of ways, forming characteristics that are well adapted to the environments in which they are likely to live. In adverse circumstances, for example, small size and slow metabolism can facilitate survival, whereas larger size and more rapid metabolism have advantages for reproductive success when resources are more abundant. Often these characteristics are induced in early life or are even set by cues to which their parents or grandparents were exposed. Individuals developmentally adapted to one environment may, however, be at risk when exposed to another when they are older. The biological evidence may be relevant to the understanding of human development and susceptibility to disease. As the nutritional state of many human mothers has improved around the world, the characteristics of their offspring--such as body size and metabolism--have also changed. Responsiveness to their mothers' condition before birth may generally prepare individuals so that they are best suited to the environment forecast by cues available in early life. Paradoxically, however, rapid improvements in nutrition and other environmental conditions may have damaging effects on the health of those people whose parents and grandparents lived in impoverished conditions. A fuller understanding of patterns of human plasticity in response to early nutrition and other environmental factors will have implications for the administration of public health.

Language as a marker of ethnic identity among the Yucatec Maya.

Most human variation is structured around symbolically marked cultural ('ethnic') groups that require common codes of communication. Consequently, many have hypothesised that using others' linguistic competences as markers of their descent is part of an evolved human psychology. However, there is also evidence that the use of language as ethnic markers is not universally applied, but context specific. We explore the tension between these views by studying responses to bilingualism among 121 adults living in Mayan communities undergoing rapid socioeconomic changes involving increased contact with Spanish-speaking towns. We show that, although competences in Mayan were strongly tied to perceiving others as having a Mayan ethnic identity, ethnolinguistic category membership was not seen as stable through life, vertically transmitted, nor regarded as incompatible with competences in Spanish. Moreover, we find variation in how people reasoned about ethnolinguistic identities depending on their own linguistic repertoires. Our work suggests that, while there may be an evolved predisposition to use language as a signal of group identity, our developmental plasticity allows us to respond adaptively to social information around us, leading to psychological and behavioural variation within and across populations. How people reason about others based on their linguistic profiles will affect the payoffs of acquiring different languages and ultimately the long-term sustainability of linguistic diversity.

Phylogeography of mtDNA haplogroup R7 in the Indian peninsula.

BACKGROUND: Human genetic diversity observed in Indian subcontinent is second only to that of Africa. This implies an early settlement and demographic growth soon after the first 'Out-of-Africa' dispersal of anatomically modern humans in Late Pleistocene. In contrast to this perspective, linguistic diversity in India has been thought to derive from more recent population movements and episodes of contact. With the exception of Dravidian, which origin and relatedness to other language phyla is obscure, all the language families in India can be linked to language families spoken in different regions of Eurasia. Mitochondrial DNA and Y chromosome evidence has supported largely local evolution of the genetic lineages of the majority of Dravidian and Indo-European speaking populations, but there is no consensus yet on the question of whether the Munda (Austro-Asiatic) speaking populations originated in India or derive from a relatively recent migration from further East. RESULTS: Here, we report the analysis of 35 novel complete mtDNA sequences from India which refine the structure of Indian-specific varieties of haplogroup R. Detailed analysis of haplogroup R7, coupled with a survey of approximately 12,000 mtDNAs from caste and tribal groups over the entire Indian subcontinent, reveals that one of its more recently derived branches (R7a1), is particularly frequent among Munda-speaking tribal groups. This branch is nested within diverse R7 lineages found among Dravidian and Indo-European speakers of India. We have inferred from this that a subset of Munda-speaking groups have acquired R7 relatively recently. Furthermore, we find that the distribution of R7a1 within the Munda-speakers is largely restricted to one of the sub-branches (Kherwari) of northern Munda languages. This evidence does not support the hypothesis that the Austro-Asiatic speakers are the primary source of the R7 variation. Statistical analyses suggest a significant correlation between genetic variation and geography, rather than between genes and languages. CONCLUSION: Our high-resolution phylogeographic study, involving diverse linguistic groups in India, suggests that the high frequency of mtDNA haplogroup R7 among Munda speaking populations of India can be explained best by gene flow from linguistically different populations of Indian subcontinent. The conclusion is based on the observation that among Indo-Europeans, and particularly in Dravidians, the haplogroup is, despite its lower frequency, phylogenetically more divergent, while among the Munda speakers only one sub-clade of R7, i.e. R7a1, can be observed. It is noteworthy that though R7 is autochthonous to India, and arises from the root of hg R, its distribution and phylogeography in India is not uniform. This suggests the more ancient establishment of an autochthonous matrilineal genetic structure, and that isolation in the Pleistocene, lineage loss through drift, and endogamy of prehistoric and historic groups have greatly inhibited genetic homogenization and geographical uniformity.

The influence of leg-to-body ratio, arm-to-body ratio and intra-limb ratio on male human attractiveness.

Human mate choice is influenced by limb proportions. Previous work has focused on leg-to-body ratio (LBR) as a determinant of male attractiveness and found a preference for limbs that are close to, or slightly above, the average. We investigated the influence of two other key aspects of limb morphology: arm-to-body ratio (ABR) and intra-limb ratio (IR). In three studies of heterosexual women from the USA, we tested the attractiveness of male physiques that varied in LBR, ABR and IR, using figures that ranged from -3 to +3 standard deviations from the population mean. We replicated previous work by finding that the optimally attractive LBR is approximately 0.5 standard deviations above the baseline. We also found a weak effect of IR, with evidence of a weak preference for the baseline proportions. In contrast, there was no effect of ABR on attractiveness, and no interactions between the effects of LBR, ABR and IR. Our results indicate that ABR is not an important determinant of human mate choice for this population, and that IR may exert some influence but that this is much smaller than the effects of LBR. We discuss possible reasons for these results, including the limited variability in upper limb proportions and the potentially weak fitness-signal provided by this aspect of morphology.

Mosaic evolution and the pattern of transitions in the hominin lineage.

Humans are uniquely unique, in terms of the extreme differences between them and other living organisms, and the impact they are having on the biosphere. The evolution of humans can be seen, as has been proposed, as one of the major transitions in evolution, on a par with the origins of multicellular organisms or the eukaryotic cell (Maynard Smith & Szathmáry 1997 Major transitions in evolution). Major transitions require the evolution of greater complexity and the emergence of new evolutionary levels or processes. Does human evolution meet these conditions? I explore the diversity of evidence on the nature of transitions in human evolution. Four levels of transition are proposed-baseline, novel taxa, novel adaptive zones and major transitions-and the pattern of human evolution considered in the light of these. The primary conclusions are that changes in human evolution occur continuously and cumulatively; that novel taxa and the appearance of new adaptations are not clustered very tightly in particular periods, although there are three broad transitional phases (Pliocene, Plio-Pleistocene and later Quaternary). Each phase is distinctive, with the first based on ranging and energetics, the second on technology and niche expansion, and the third on cognition and cultural processes. I discuss whether this constitutes a 'major transition' in the context of the evolutionary processes more broadly; the role of behaviour in evolution; and the opportunity provided by the rich genetic, phenotypic (fossil morphology) and behavioural (archaeological) record to examine in detail major transitions and the microevolutionary patterns underlying macroevolutionary change. It is suggested that the evolution of the hominin lineage is consistent with a mosaic pattern of change.This article is part of the themed issue 'Major transitions in human evolution'.

Major transitions in human evolution.

Evolutionary problems are often considered in terms of 'origins', and research in human evolution seen as a search for human origins. However, evolution, including human evolution, is a process of transitions from one state to another, and so questions are best put in terms of understanding the nature of those transitions. This paper discusses how the contributions to the themed issue 'Major transitions in human evolution' throw light on the pattern of change in hominin evolution. Four questions are addressed: (1) Is there a major divide between early (australopithecine) and later (Homo) evolution? (2) Does the pattern of change fit a model of short transformations, or gradual evolution? (3) Why is the role of Africa so prominent? (4) How are different aspects of adaptation-genes, phenotypes and behaviour-integrated across the transitions? The importance of developing technologies and approaches and the enduring role of fieldwork are emphasized.This article is part of the themed issue 'Major transitions in human evolution'.

Lithic landscapes: early human impact from stone tool production on the central Saharan environment.

Humans have had a major impact on the environment. This has been particularly intense in the last millennium but has been noticeable since the development of food production and the associated higher population densities in the last 10,000 years. The use of fire and over-exploitation of large mammals has also been recognized as having an effect on the world's ecology, going back perhaps 100,000 years or more. Here we report on an earlier anthropogenic environmental change. The use of stone tools, which dates back over 2.5 million years, and the subsequent evolution of a technologically-dependent lineage required the exploitation of very large quantities of rock. However, measures of the impact of hominin stone exploitation are rare and inherently difficult. The Messak Settafet, a sandstone massif in the Central Sahara (Libya), is littered with Pleistocene stone tools on an unprecedented scale and is, in effect, a man-made landscape. Surveys showed that parts of the Messak Settafet have as much as 75 lithics per square metre and that this fractured debris is a dominant element of the environment. The type of stone tools--Acheulean and Middle Stone Age--indicates that extensive stone tool manufacture occurred over the last half million years or more. The lithic-strewn pavement created by this ancient stone tool manufacture possibly represents the earliest human environmental impact at a landscape scale and is an example of anthropogenic change. The nature of the lithics and inferred age may suggest that hominins other than modern humans were capable of unintentionally modifying their environment. The scale of debris also indicates the significance of stone as a critical resource for hominins and so provides insights into a novel evolutionary ecology.