Joel D. Irish

Homo naledi, a new species of the genus Homo from the Dinaledi Chamber, South Africa

Homo naledi is a previously-unknown species of extinct hominin discovered within the Dinaledi Chamber of the Rising Star cave system, Cradle of Humankind, South Africa. This species is characterized by body mass and stature similar to small-bodied human populations but a small endocranial volume similar to australopiths. Cranial morphology of H. naledi is unique, but most similar to early Homo species including Homo erectus, Homo habilis or Homo rudolfensis. While primitive, the dentition is generally small and simple in occlusal morphology. H. naledi has humanlike manipulatory adaptations of the hand and wrist. It also exhibits a humanlike foot and lower limb. These humanlike aspects are contrasted in the postcrania with a more primitive or australopith-like trunk, shoulder, pelvis and proximal femur. Representing at least 15 individuals with most skeletal elements repeated multiple times, this is the largest assemblage of a single species of hominins yet discovered in Africa. DOI: http://dx.doi.org/10.7554/eLife.09560.001

Characteristic high- and low-frequency dental traits in sub-Saharan African populations.

In an earlier investigation (Irish [1993] Biological Affinities of Late Pleistocene Through Modern African Aboriginal Populations: The Dental Evidence [Ann Arbor: University Microfilms]), biological affinities of 32 sub-Saharan and North African dental samples were estimated using comparative analyses of 36 dental morphological traits. Marked dental homogeneity was revealed among samples within each of the two geographic regions, but significant interregional differences were noted. Assuming dental phenetic expression approximates or is an estimate of genetic variation, the present study of 976 sub-Saharan-affiliated Africans indicates they are not closely related to other world groups; they are characterized by numerous morphologically complex crown and root traits. Turner ([1984] Acta Anthropogenetica 8:23-78; [1985] in R Kirk and E Szathmary (eds.): Out of Asia: Peopling the Americas and the Pacific [Canberra: The Journal of Pacific History], pp. 31-78; [1990] Am. J. Phys. Anthropol. 82:295-318; [1992] Persp. Hum. Biol. 2/Archaeol. Oceania 27:120-127; [1992] in T Akaszawa, K Aoki, and T Kimura (eds.): The Evolution and Dispersal of Modern Humans in Asia [Tokyo: Hokusen-Sha Publishing Co-], pp. 415-438) reports that Northeast Asian/New World sinodonts also have complex teeth relative to Europeans, Southeast Asian sundadonts, Australian/Tasmanians, and Melanesians. However, sinodonty is characterized by UI1 winging, UI1 shoveling, UI1 double shoveling, one-rooted UP1, UM1 enamel extension, M3 agenesis, and three-rooted LM1. Sub-Saharan peoples exhibit very low frequencies of these features. It is proposed that the collection of dental traits which best differentiate sub-Saharan Africans from other worldwide samples includes high frequencies of the Bushman Canine, two-rooted UP1, UM1 Carabellis trait, three-rooted UM2, LM2 Y-groove pattern, LM1 cusp 7, LP1 Tomes root, two-rooted LM2, UM3 presence, and very low incidences of UI1 double shoveling and UM1 enamel extension. This suite of diagnostic traits is termed the sub-Saharan African dental complex.

Ancient teeth and modern human origins: An expanded comparison of African Plio-Pleistocene and recent world dental samples

Previous research by the first author revealed that, relative to other modern peoples, sub-Saharan Africans exhibit the highest frequencies of ancestral (or plesiomorphic) dental traits and, thus, appear to be least derived dentally from an ancestral hominin state. This determination, in conjunction with various other lines of dental morphological evidence, was interpreted to be supportive of an African origin for modern humans. The present investigation expands upon this work by using: 1) direct observations of fossil hominin teeth, rather than data gleaned from published sources, 2) a single morphological scoring system (the Arizona State University Dental Anthropology System) with consistent trait breakpoints, and 3) data from larger and more varied modern human comparative samples. As before, a multivariate distance statistic, the mean measure of divergence, was used to assess diachronic phenetic affinities among the Plio-Pleistocene hominins and modern humans. The present study also employed principal components analysis on dental trait frequencies across samples. Both methods yielded similar results, which support the previous findings; that is, of all modern human samples, sub-Saharan Africans again exhibit the closest phenetic similarity to various African Plio-Pleistocene hominins-through their shared prevalence of morphologically complex crown and root traits. The fact that sub-Saharan Africans express these apparently plesiomorphic characters, along with additional information on their affinity to other modern populations, evident intra-population heterogeneity, and a world-wide dental cline emanating from the sub-continent, provides further evidence that is consistent with an African origin model.

The mean measure of divergence: Its utility in model-free and model-bound analyses relative to the Mahalanobis D2 distance for nonmetric traits

The mean measure of divergence (MMD) distance statistic has been used by researchers for nearly 50 years to assess inter‐sample phenetic affinity. Its widespread and often successful use is well documented, especially in the study of cranial and dental nonmetric traits. However, the statistic has accumulated some undesired mathematical baggage through the years from various workers in their attempts to improve or alter its performance. Others may not fully understand how to apply the MMD or interpret its output, whereas some described a number of perceived shortcomings. As a result, the statistic and its sometimes flawed application(s) have taken several well‐aimed hits; a few researchers even argued that it should no longer be utilized or, at least, that its use be reevaluated. The objective of this report is to support the MMD, and in the process: (1) provide a brief history of the statistic, (2) review its attributes and applicability relative to the often‐used Mahalanobis D2 statistic for nonmetric traits, (3) compare results from MMD and D2 model‐free analyses of previously‐recorded sub‐Saharan African dental samples, and (4) investigate its utility for model‐bound analyses. In the latter instance, the ability of the D2 and other squared Euclidean‐based statistics to approximate a genetic relationship matrix and Sewall Wrights fixation index using phenotypic data, and the inability of the MMD to do so, is addressed. Three methods for obtaining such results with nonlinear MMD distances, as well as an assessment of the fit of the isolation‐by‐distance model, are presented. Am. J. Hum. Biol., 2010.

Dental Morphology and the Phylogenetic “Place” of Australopithecus sediba

To characterize further the Australopithecus sediba hypodigm, we describe 22 dental traits in specimens MH1 and MH2. Like other skeletal elements, the teeth present a mosaic of primitive and derived features. The new nonmetric data are then qualitatively and phenetically compared with those in eight other African hominin samples, before cladistic analyses using a gorilla outgroup. There is some distinction, largely driven by contrasting molar traits, from East African australopiths. However, Au. sediba links with Au. africanus to form a South African australopith clade. These species present five apomorphies, including shared expressions of Carabelli’s upper first molar (UM1) and protostylid lower first molar (LM1). Five synapomorphies are also evident between them and monophyletic Homo habilis/rudolfensis + H. erectus. Finally, a South African australopith + Homo clade is supported by four shared derived states, including identical LM1 cusp 7 expression.

A terminal Pleistocene child cremation and residential structure from eastern Beringia.

Cremated remains and a burial site in central Alaska provide information on early humans in North America. The dearth of human remains and residential sites has constrained inquiry into Beringian lifeways at the transition of the late Pleistocene–early Holocene. We report on human skeletal remains and a residential structure from central Alaska dated to ~11,500 calendar years ago. The remains are from a ~3-year-old child who was cremated in a pit within a semisubterranean house. The burial-cremation and house have exceptional integrity and preservation and exhibit similarities and differences to both Siberian Upper Paleolithic and North American Paleoindian features.

Two contemporaneous mitogenomes from terminal Pleistocene burials in eastern Beringia.

Significance Beringia gave rise to the first Western Hemisphere colonists, although the genetic characterization of that source population has remained obscure. We report two mitogenomes from human remains within Beringia, with an age (∼11,500 cal B.P.) that postdates the end of the initial colonization by only a few millennia. The mitochondrial lineages identified (B2, C1b) are rare to absent in modern northern populations, indicating greater genetic diversity in early Beringia than in modern populations of the region. The antiquity and geographic location of these two burials, and the combined genomic and archaeological analyses, provide new perspectives on the link between Asia and the Americas, and the genetic makeup of the first Americans. Pleistocene residential sites with multiple contemporaneous human burials are extremely rare in the Americas. We report mitochondrial genomic variation in the first multiple mitochondrial genomes from a single prehistoric population: two infant burials (USR1 and USR2) from a common interment at the Upward Sun River Site in central Alaska dating to ∼11,500 cal B.P. Using a targeted capture method and next-generation sequencing, we determined that the USR1 infant possessed variants that define mitochondrial lineage C1b, whereas the USR2 genome falls at the root of lineage B2, allowing us to refine younger coalescence age estimates for these two clades. C1b and B2 are rare to absent in modern populations of northern North America. Documentation of these lineages at this location in the Late Pleistocene provides evidence for the extent of mitochondrial diversity in early Beringian populations, which supports the expectations of the Beringian Standstill Model.

Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans

Despite broad agreement that the Americas were initially populated via Beringia, the land bridge that connected far northeast Asia with northwestern North America during the Pleistocene epoch, when and how the peopling of the Americas occurred remains unresolved. Analyses of human remains from Late Pleistocene Alaska are important to resolving the timing and dispersal of these populations. The remains of two infants were recovered at Upward Sun River (USR), and have been dated to around 11.5 thousand years ago (ka). Here, by sequencing the USR1 genome to an average coverage of approximately 17 times, we show that USR1 is most closely related to Native Americans, but falls basal to all previously sequenced contemporary and ancient Native Americans. As such, USR1 represents a distinct Ancient Beringian population. Using demographic modelling, we infer that the Ancient Beringian population and ancestors of other Native Americans descended from a single founding population that initially split from East Asians around 36 ± 1.5 ka, with gene flow persisting until around 25 ± 1.1 ka. Gene flow from ancient north Eurasians into all Native Americans took place 25–20 ka, with Ancient Beringians branching off around 22–18.1 ka. Our findings support a long-term genetic structure in ancestral Native Americans, consistent with the Beringian ‘standstill model’. We show that the basal northern and southern Native American branches, to which all other Native Americans belong, diverged around 17.5–14.6 ka, and that this probably occurred south of the North American ice sheets. We also show that after 11.5 ka, some of the northern Native American populations received gene flow from a Siberian population most closely related to Koryaks, but not Palaeo-Eskimos, Inuits or Kets, and that Native American gene flow into Inuits was through northern and not southern Native American groups. Our findings further suggest that the far-northern North American presence of northern Native Americans is from a back migration that replaced or absorbed the initial founding population of Ancient Beringians.

New insights into Eastern Beringian mortuary behavior: A terminal Pleistocene double infant burial at Upward Sun River

Significance Two interred infants with associated grave goods and a third cremated child represent the earliest known human remains from the North American subarctic, and they provide evidence for novel mortuary behaviors at the end of the last Ice Age. Two bifacial points with decorated foreshafts represent hafted projectiles, confirming earlier conclusions about Paleoindian weapon system form and function. Excellent faunal and other contextual data indicate broad-spectrum foraging behaviors. Here we report on the discovery of two infant burials dating to ∼11,500 calibrated years (cal) B.P. at the Upward Sun River site in central Alaska. The infants were interred in a pit feature with associated organic and lithic grave goods, including the earliest known North American hafted bifaces with decorated antler foreshafts. Skeletal and dental analyses indicate that Individual 1 died shortly after birth and Individual 2 was a late-term fetus, making these the youngest-aged late Pleistocene individuals known for the Americas and the only known prenate, offering, to our knowledge, the first opportunity to explore mortuary treatment of the youngest members of a terminal Pleistocene North American population. This burial was situated ∼40 cm directly below a cremated 3-y-old child previously discovered in association with a central hearth of a residential feature. The burial and cremation are contemporaneous, and differences in body orientation, treatment, and associated grave goods within a single feature and evidence for residential occupation between burial episodes indicate novel mortuary behaviors. The human remains, grave goods, and associated fauna provide rare direct data on organic technology, economy, seasonality of residential occupations, and infant/child mortality of terminal Pleistocene Beringians.

Questions of khoesan continuity: Dental affinities among the indigenous holocene peoples of South Africa

The present report follows up on the findings of previous research, including recent bioarchaeological study of well-dated Khoesan skeletal remains, that posits long term biological continuity among the indigenous peoples of South Africa after the Pleistocene. The Arizona State University Dental Anthropology System was used to record key crown, root, and intraoral osseous nonmetric traits in six early-through-late Holocene samples from the Cape coasts. Based on these data, phenetic affinities and an identification of traits most important in driving intersample variation were determined using principal components analysis and the mean measure of divergence distance statistic. To expand biological affinity comparisons into more recent times, and thus preliminarily assess the dental impact of disproportionate non-Khoesan gene flow into local peoples, dental data from historic Khoekhoe and San were also included. Results from the prehistoric comparisons are supportive of population continuity, though a sample from Matjes River Rockshelter exhibits slight phenetic distance from other early samples. This and some insignificant regional divergence among these coastal samples may be related to environmental and cultural factors that drove low-level reproductive isolation. Finally, a close affinity of historic San to all samples, and a significant difference of Khoekhoe from most early samples is reflective of documented population history following immigration of Bantu-speakers and, later, Europeans into South Africa.