Inferring human neutral genetic variation from craniodental phenotypes.

There is a growing consensus that global patterns of modern human cranial and dental variation are shaped largely by neutral evolutionary processes, suggesting that craniodental features can be used as reliable proxies for inferring population structure and history in bioarchaeological, forensic, and paleoanthropological contexts. However, there is disagreement on whether certain types of data preserve a neutral signature to a greater degree than others. Here, we address this unresolved question and systematically test the relative neutrality of four standard metric and nonmetric craniodental data types employing an extensive computational genotype-phenotype comparison across modern populations from around the world. Our computation draws on the largest existing data sets currently available, while accounting for geographically structured environmental variation, population sampling uncertainty, disparate numbers of phenotypic variables, and stochastic variation inherent to a neutral model of evolution. Our results reveal that the four data types differentially capture neutral genomic variation, with highest signals preserved in dental nonmetric and cranial metric data, followed by cranial nonmetric and dental metric data. Importantly, we demonstrate that combining all four data types together maximizes the neutral genetic signal compared with using them separately, even with a limited number of phenotypic variables. We hypothesize that this reflects a lower level of genetic integration through pleiotropy between, compared to within, the four data types, effectively forming four different modules associated with relatively independent sets of loci. Therefore, we recommend that future craniodental investigations adopt holistic combined data approaches, allowing for more robust inferences about underlying neutral genetic variation.

Evolution of Homo in the Middle and Late Pleistocene.

The Middle and Late Pleistocene is arguably the most interesting period in human evolution. This broad period witnessed the evolution of our own lineage, as well as that of our sister taxon, the Neanderthals, and related Denisovans. It is exceptionally rich in both fossil and archaeological remains, and uniquely benefits from insights gained through molecular approaches, such as paleogenetics and paleoproteomics, that are currently not widely applicable in earlier contexts. This wealth of information paints a highly complex picture, often described as 'the Muddle in the Middle,' defying the common adage that 'more evidence is needed' to resolve it. Here we review competing phylogenetic scenarios and the historical and theoretical developments that shaped our approaches to the fossil record, as well as some of the many remaining open questions associated with this period. We propose that advancing our understanding of this critical time requires more than the addition of data and will necessitate a major shift in our conceptual and theoretical framework.

Patterns of recent natural selection on genetic loci associated with sexually differentiated human body size and shape phenotypes.

Levels of sex differences for human body size and shape phenotypes are hypothesized to have adaptively reduced following the agricultural transition as part of an evolutionary response to relatively more equal divisions of labor and new technology adoption. In this study, we tested this hypothesis by studying genetic variants associated with five sexually differentiated human phenotypes: height, body mass, hip circumference, body fat percentage, and waist circumference. We first analyzed genome-wide association (GWAS) results for UK Biobank individuals (~194,000 females and ~167,000 males) to identify a total of 114,199 single nucleotide polymorphisms (SNPs) significantly associated with at least one of the studied phenotypes in females, males, or both sexes (P<5x10-8). From these loci we then identified 3,016 SNPs (2.6%) with significant differences in the strength of association between the female- and male-specific GWAS results at a low false-discovery rate (FDR<0.001). Genes with known roles in sexual differentiation are significantly enriched for co-localization with one or more of these SNPs versus SNPs associated with the phenotypes generally but not with sex differences (2.73-fold enrichment; permutation test; P = 0.0041). We also confirmed that the identified variants are disproportionately associated with greater phenotype effect sizes in the sex with the stronger association value. We then used the singleton density score statistic, which quantifies recent (within the last ~3,000 years; post-agriculture adoption in Britain) changes in the frequencies of alleles underlying polygenic traits, to identify a signature of recent positive selection on alleles associated with greater body fat percentage in females (permutation test; P = 0.0038; FDR = 0.0380), directionally opposite to that predicted by the sex differences reduction hypothesis. Otherwise, we found no evidence of positive selection for sex difference-associated alleles for any other trait. Overall, our results challenge the longstanding hypothesis that sex differences adaptively decreased following subsistence transitions from hunting and gathering to agriculture.

Biocultural evidence of precise manual activities in an Early Holocene individual of the high-altitude Peruvian Andes.

OBJECTIVES: Cuncaicha, a rockshelter site in the southern Peruvian Andes, has yielded archaeological evidence for human occupation at high elevation (4,480 masl) during the Terminal Pleistocene (12,500-11,200 cal BP), Early Holocene (9,500-9,000 cal BP), and later periods. One of the excavated human burials (Feature 15-06), corresponding to a middle-aged female dated to ~8,500 cal BP, exhibits skeletal osteoarthritic lesions previously proposed to reflect habitual loading and specialized crafting labor. Three small tools found in association with this burial are hypothesized to be associated with precise manual dexterity. MATERIALS AND METHODS: Here, we tested this functional hypothesis through the application of a novel multivariate methodology for the three-dimensional analysis of muscle attachment surfaces (entheses). This original approach has been recently validated on both lifelong-documented anthropological samples as well as experimental studies in nonhuman laboratory samples. Additionally, we analyzed the three-dimensional entheseal shape and resulting moment arms for muscle opponens pollicis. RESULTS: Results show that Cuncaicha individual 15-06 shows a distinctive entheseal pattern associated with habitual precision grasping via thumb-index finger coordination, which is shared exclusively with documented long-term precision workers from recent historical collections. The separate geometric morphometric analysis revealed that the individual's opponens pollicis enthesis presents a highly projecting morphology, which was found to strongly correlate with long joint moment arms (a fundamental component of force-producing capacity), closely resembling the form of Paleolithic hunter-gatherers from diverse geo-chronological contexts of Eurasia and North Africa. DISCUSSION: Overall, our findings provide the first biocultural evidence to confirm that the lifestyle of some of the earliest Andean inhabitants relied on habitual and forceful precision grasping tasks.

Frontal bone virtual reconstruction and geometric morphometric analysis of the mid-Pleistocene hominin KNM-OG 45500 (Olorgesailie, Kenya).

KNM-OG 45500 is a hominin fossil composed of parts of a frontal bone, left temporal bone, and cranial vault pieces. Since its discovery along the Olorgesailie Formation (Kenya) in 2003, it has been associated with the Homo erectus hypodigm. The specimen, derived from a geological context dated to ca. 900 Ka BP, has been described as a very small individual of probable female sex. However, despite its status as an important hominin specimen, it has not been used in a quantitative comparative framework because of its fragmentary condition. Here, we undertake a virtual reconstruction of the better-preserved fragment, the frontal bone. We additionally apply geometric morphometric analyses, using a geographically diverse fossil and modern human sample, in order to investigate the morphological affinities of KNM-OG 45500. Our results show that the frontal shape of KNM-OG 45500 exhibits similarities with Early Pleistocene fossils from Eurasia and Africa that are assigned to H. erectus sensu lato (s.l.). Its size, on the other hand, is notably smaller than most other Homo erectus fossils and modern humans and similar to the specimens from Dmanisi (Georgia) and to Homo naledi. Taken together, our analyses of the frontal bone suggest a taxonomic attribution of KNM-OG 45500 to H. erectus s.l. and extend even further the range of size variability associated with this taxon around 900 Ka BP.

A virtual assessment of the suprainiac depressions on the Eyasi I (Tanzania) and Aduma ADU-VP-1/3 (Ethiopia) Pleistocene hominin crania.

Despite a steady increase in our understanding of the phenotypic variation of Pleistocene Homo, debate continues over phylogenetically informative features. One such trait is the suprainiac fossa, a depression on the occipital bone above inion that is commonly considered an autapomorphy of the Neanderthal lineage. Challenging this convention, depressions in the suprainiac region have also been described for two Pleistocene hominin crania from sub-Saharan Africa: Eyasi I (Tanzania) and ADU-VP-1/3 (Ethiopia). Here, we use a combined quantitative and qualitative approach, using µCT imaging, to investigate the occipital depressions on these specimens. The results show that neither the external nor the internal morphologies of these depressions bear any resemblance to the Neanderthal condition. A principal component analysis based on multiple thickness measurements along the occipital squama demonstrates that the relative thickness values for the internal structures in Eyasi I and ADU-VP-1/3 are within the range of Homo sapiens. Thus, our results support the autapomorphic status of the Neanderthal suprainiac fossa and highlight the need to use nuanced approaches and multiple lines of evidence.

Testing the utility of dental morphological trait combinations for inferring human neutral genetic variation.

Researchers commonly rely on human dental morphological features in order to reconstruct genetic affinities among past individuals and populations, particularly since teeth are often the best preserved part of a human skeleton. Tooth form is considered to be highly heritable and selectively neutral and, therefore, to be an excellent proxy for DNA when none is available. However, until today, it remains poorly understood whether certain dental traits or trait combinations preserve neutral genomic signatures to a greater degree than others. Here, we address this long-standing research gap by systematically testing the utility of 27 common dental traits and >134 million possible trait combinations in reflecting neutral genomic variation in a worldwide sample of modern human populations. Our analyses reveal that not all traits are equally well-suited for reconstructing population affinities. Whereas some traits largely reflect neutral variation and therefore evolved primarily as a result of genetic drift, others can be linked to nonstochastic processes such as natural selection or hominin admixture. We also demonstrate that reconstructions of population affinity based on many traits are not necessarily more reliable than those based on only a few traits. Importantly, we find a set of highly diagnostic trait combinations that preserve neutral genetic signals best (up to [Formula: see text] r = 0.580; 95% r range = 0.293 to 0.758; P = 0.001). We propose that these trait combinations should be prioritized in future research, as they allow for more accurate inferences about past human population dynamics when using dental morphology as a proxy for DNA.

Reconstructing the Deep Population History of Central and South America.

We report genome-wide ancient DNA from 49 individuals forming four parallel time transects in Belize, Brazil, the Central Andes, and the Southern Cone, each dating to at least ∼9,000 years ago. The common ancestral population radiated rapidly from just one of the two early branches that contributed to Native Americans today. We document two previously unappreciated streams of gene flow between North and South America. One affected the Central Andes by ∼4,200 years ago, while the other explains an affinity between the oldest North American genome associated with the Clovis culture and the oldest Central and South Americans from Chile, Brazil, and Belize. However, this was not the primary source for later South Americans, as the other ancient individuals derive from lineages without specific affinity to the Clovis-associated genome, suggesting a population replacement that began at least 9,000 years ago and was followed by substantial population continuity in multiple regions.

Reconstructing human population history from dental phenotypes.

Dental phenotypic data are often used to reconstruct biological relatedness among past human groups. Teeth are an important data source because they are generally well preserved in the archaeological and fossil record, even when associated skeletal and DNA preservation is poor. Furthermore, tooth form is considered to be highly heritable and selectively neutral; thus, teeth are assumed to be an excellent proxy for neutral genetic data when none are available. However, to our knowledge, no study to date has systematically tested the assumption of genetic neutrality of dental morphological features on a global scale. Therefore, for the first time, this study quantifies the correlation of biological affinities between worldwide modern human populations, derived independently from dental phenotypes and neutral genetic markers. We show that population relationship measures based on dental morphology are significantly correlated with those based on neutral genetic data (on average r = 0.574, p < 0.001). This relatively strong correlation validates tooth form as a proxy for neutral genomic markers. Nonetheless, we suggest caution in reconstructions of population affinities based on dental data alone because only part of the dental morphological variation among populations can be explained in terms of neutral genetic differences.

Genomic validation of the differential preservation of population history in modern human cranial anatomy.

OBJECTIVES: In modern humans, the significant correlation between neutral genetic loci and cranial anatomy suggests that the cranium preserves a population history signature. However, there is disagreement on whether certain parts of the cranium preserve this signature to a greater degree than other parts. It is also unclear how different quantitative measures of phenotype affect the association of genetic variation and anatomy. Here, we revisit these matters by testing the correlation of genetic distances and various phenotypic distances for ten modern human populations. MATERIALS AND METHODS: Geometric morphometric shape data from the crania of adult individuals (n = 224) are used to calculate phenotypic PST , Procrustes, and Mahalanobis distances. We calculate their correlation to neutral genetic distances, FST , derived from single nucleotide polymorphisms (SNPs). We subset the cranial data into landmark configurations that include the neurocranium, the face, and the temporal bone in order to evaluate whether these cranial regions are differentially correlated to neutral genetic variation. RESULTS: Our results show that PST , Mahalanobis, and Procrustes distances are correlated with FST distances to varying degrees. They indicate that overall cranial shape is significantly correlated with neutral genetic variation. Of the component parts examined, PST distances for both the temporal bone and the face have a stronger association with FST distances than the neurocranium. When controlling for population divergence time, only the whole cranium and the temporal bone have a statistically significant association with FST distances. DISCUSSION: Our results confirm that the cranium, as a whole, and the temporal bone can be used to reconstruct modern human population history.

Tracking modern human population history from linguistic and cranial phenotype.

Languages and genes arguably follow parallel evolutionary trajectories, descending from a common source and subsequently differentiating. However, although common ancestry is established within language families, it remains controversial whether language preserves a deep historical signal. To address this question, we evaluate the association between linguistic and geographic distances across 265 language families, as well as between linguistic, geographic, and cranial distances among eleven populations from Africa, Asia, and Australia. We take advantage of differential population history signals reflected by human cranial anatomy, where temporal bone shape reliably tracks deep population history and neutral genetic changes, while facial shape is more strongly associated with recent environmental effects. We show that linguistic distances are strongly geographically patterned, even within widely dispersed groups. However, they are correlated predominantly with facial, rather than temporal bone, morphology, suggesting that variation in vocabulary likely tracks relatively recent events and possibly population contact.

Inner ear morphology of the cioclovina early modern European calvaria from Romania.

OBJECTIVES: The morphology of the human bony labyrinth is thought to preserve a strong phylogenetic signal and to be minimally, if at all, affected by postnatal processes. The form of the semicircular canals is considered a derived feature of Neanderthals and different from the modern human anatomy. Among other hominins, European Middle Pleistocene humans have been found to be most similar to Neanderthals. Early modern humans have been proposed to show a pattern that is distinct, but most similar to that of Holocene people. Here we examine the inner ear structures of the Cioclovina calvaria, one of the earliest reliably dated and relatively complete modern human crania from Europe, in the context of recent and fossil human variation. MATERIALS AND METHODS: Bony labyrinths were virtually extracted from CT scans of recent Europeans and Cioclovina. Using univariate and multivariate methods, measurements of the semicircular canals were compared with published measurements of other fossil specimens. RESULTS: Our results show that Cioclovina's inner ear morphology falls within the range of modern variation, with affinities to both Late Pleistocene modern humans and recent Europeans. Using discriminant functions, the sex of the Cioclovina specimen is estimated as male. DISCUSSION: Results agree with previous work showing that Cioclovina exhibits fully modern cranial morphology.

Testing modern human out-of-Africa dispersal models and implications for modern human origins.

The modern human expansion process out of Africa has important implications for understanding the genetic and phenotypic structure of extant populations. While intensely debated, the primary hypotheses focus on either a single dispersal or multiple dispersals out of the continent. Here, we use the human fossil record from Africa and the Levant, as well as an exceptionally large dataset of Holocene human crania sampled from Asia, to model ancestor-descendant relationships along hypothetical dispersal routes. We test the spatial and temporal predictions of competing out-of-Africa models by assessing the correlation of geographical distances between populations and measures of population differentiation derived from quantitative cranial phenotype data. Our results support a model in which extant Australo-Melanesians are descendants of an initial dispersal out of Africa by early anatomically modern humans, while all other populations are descendants of a later migration wave. Our results have implications for understanding the complexity of modern human origins and diversity.

Genomic and cranial phenotype data support multiple modern human dispersals from Africa and a southern route into Asia.

Despite broad consensus on Africa as the main place of origin for anatomically modern humans, their dispersal pattern out of the continent continues to be intensely debated. In extant human populations, the observation of decreasing genetic and phenotypic diversity at increasing distances from sub-Saharan Africa has been interpreted as evidence for a single dispersal, accompanied by a series of founder effects. In such a scenario, modern human genetic and phenotypic variation was primarily generated through successive population bottlenecks and drift during a rapid worldwide expansion out of Africa in the Late Pleistocene. However, recent genetic studies, as well as accumulating archaeological and paleoanthropological evidence, challenge this parsimonious model. They suggest instead a "southern route" dispersal into Asia as early as the late Middle Pleistocene, followed by a separate dispersal into northern Eurasia. Here we test these competing out-of-Africa scenarios by modeling hypothetical geographical migration routes and assessing their correlation with neutral population differentiation, as measured by genetic polymorphisms and cranial shape variables of modern human populations from Africa and Asia. We show that both lines of evidence support a multiple-dispersals model in which Australo-Melanesian populations are relatively isolated descendants of an early dispersal, whereas other Asian populations are descended from, or highly admixed with, members of a subsequent migration event.