Number of ancestral human species: a molecular perspective

A new approach to exploratory data analysis in hominin phylogenetic reconstruction

The phylogenetic relationships between fossil hominin taxa have been a contentious topic for decades. Recent discoveries of new taxa, rather than resolving the issue, have only further confused it. Compounding this problem are the limitations of some of the tools frequently used by paleoanthropologists to analyze these relationships. Most commonly, phylogenetic questions are investigated using analytical methods such as maximum parsimony and Bayesian analysis. While these are useful analytical tools, these tree-building methods can have limitations when investigating taxa that may have complex evolutionary histories. Exploratory data analysis can provide information about patterns in a dataset that are obscured by tree-based methods. These patterns include phylogenetic signal conflict, which is not depicted in tree-based methods. Signal conflict can have a number of sources, including methodological issues with character choice, taxonomic issues, homoplasy, and gene flow between taxa. In this study, an exploratory data analysis of fossil hominin morphological data is conducted using the tree-based analytical method neighbor-joining and the network-based analytical method neighbor-net with the goal of visualizing phylogenetic signal conflict within a hominin morphological data set. The data set is divided into cranial regions, and each cranial region is analyzed individually to investigate which regions of the skull contain the highest levels of signal conflict. Results of this analysis show that conflicting phylogenetic signals are present in the hominin fossil record during the relatively speciose period between 3 and 1 Ma, and they also indicate that levels of signal conflict vary by cranial region. Possible sources of these conflicting signals are then explored. Exploratory data analyses such as this can be a useful tool in generating phylogenetic hypotheses and in refining character choice. This study also highlights the value network-based approaches can bring to the hominin phylogenetic analysis toolkit.

Evolution of Brain Active Gene Promoters in Human Lineage Towards the Increased Plasticity of Gene Regulation

Adaptability to a variety of environmental conditions is a prominent feature of Homo sapiens. We hypothesize that this feature can be explained by evolutionary changes in gene promoters active in the brain prefrontal cortex leading to a more flexible gene regulation network. The genotype-dependent range of gene expression can be broader in humans than in other higher primates. Thus, we searched for specific signatures of evolutionary changes in promoter architectures of multiple hominid genes, including the genes active in human cortical neurons that may indicate an increase of variability of gene expression rather than just changes in the level of expression, such as downregulation or upregulation of the genes. We performed a whole-genome search for genetic-based alterations that may impact gene regulation "flexibility" in a process of hominids evolution, such as (i) CpG dinucleotide content, (ii) predicted nucleosome-DNA dissociation constant, and (iii) predicted affinities for TATA-binding protein (TBP) in gene promoters. We tested all putative promoter regions across the human genome and especially gene promoters in active chromatin state in neurons of prefrontal cortex, the brain region critical for abstract thinking and social and behavioral adaptation. Our data imply that the origin of modern man has been associated with an increase of flexibility of promoter-driven gene regulation in brain. In contrast, after splitting from the ancestral lineages of H. sapiens, the evolution of ape species is characterized by reduced flexibility of gene promoter functioning, underlying reduced variability of the gene expression.

Hypothesis: brain size and skull shape as criteria for a new hominin family tree

Today, gorillas and chimpanzees live in tropical forests, where acid soils do not favor fossilization. It is thus widely believed that there are no fossils of chimpanzees or gorillas. However, four teeth of a 0.5-million-year (Ma)-old chimpanzee were discovered in the rift valley of Kenya (McBrearty and Jablonski, 2005), and a handful of teeth of a 10-Ma-old gorilla-like creature were found in Ethiopia (Suwa et al., 2007), close to the major sites of Homo discoveries. These discoveries indicate that chimpanzees and gorillas once shared their range with early Homo. However, the thousands of hominin fossils discovered in the past century have all been attributed to the Homo line. Thus far, our family tree looks like a bush with many dead-branches. If one admits the possibility that the australopithecines can also be the ancestors of African great apes, one can place Paranthropus on the side of gorilla ancestors and divide the remaining Australopithecus based on the brain size into the two main lines of humans and chimpanzees, thereby resulting in a coherent family tree.

Brains, innovations, tools and cultural transmission in birds, non-human primates, and fossil hominins

Recent work on birds and non-human primates has shown that taxonomic differences in field measures of innovation, tool use and social learning are associated with size of the mammalian cortex and avian mesopallium and nidopallium, as well as ecological traits like colonization success. Here, I review this literature and suggest that many of its findings are relevant to hominin intelligence. In particular, our large brains and increased intelligence may be partly independent of our ape phylogeny and the result of convergent processes similar to those that have molded avian and platyrrhine intelligence. Tool use, innovativeness and cultural transmission might be linked over our past and in our brains as operations of domain-general intelligence. Finally, colonization of new areas may have accompanied increases in both brain size and innovativeness in hominins as they have in other mammals and in birds, potentially accelerating hominin evolution via behavioral drive.

Unexpectedly many extinct hominins

Recent studies indicate that Neanderthal and Denisova hominins may have been separate species, while debate continues on the status of Homo floresiensis. The decade-long debate between "splitters," who recognize over 20 hominin species, and "lumpers," who maintain that all these fossils belong to just a few lineages, illustrates that we do not know how many extinct hominin species to expect. Here, we present probability distributions for the number of speciation events and the number of contemporary species along a branch of a phylogeny. With estimates of hominin speciation and extincton rates, we then show that the expected total number of extinct hominin species is 8, but may be as high as 27. We also show that it is highly unlikely that three very recent species disappeared due to natural, background extinction. This may indicate that human-like remains are too easily considered distinct species. Otherwise, the evidence suggesting that Neanderthal and the Denisova hominin represent distinct species implies a recent wave of extinctions, ostensibly driven by the only survivor, H. sapiens.

Evolution in the Genus Homo

We review the fossil and genetic evidence that relate to evolution in the genus Homo. We focus on the origin of Homo and on the evidence for taxonomic diversity at the beginning of the evolutionary history of Homo and in the last 200,000 years. We set out the arguments for recognizing a second early Homo taxon, Homo rudolfensis, and the arguments for and against including Homo habilis sensu stricto and Homo rudolfensis within Homo. We end by reviewing recent genomic evolution within Homo. The challenge of the upcoming decades is to meld innovations in molecular genetic methods and technology with evidence from the fossil record to generate hypotheses about the developmental bases of the phenotypic and behavioral developments we see within the genus Homo.

Is Homo sapiens polytypic? Human taxonomic diversity and its implications

The term race is a traditional synonym for subspecies, however it is frequently asserted that Homo sapiens is monotypic and that what are termed races are nothing more than biological illusions. In this manuscript a case is made for the hypothesis that H. sapiens is polytypic, and in this way is no different from other species exhibiting similar levels of genetic and morphological diversity. First it is demonstrated that the four major definitions of race/subspecies can be shown to be synonymous within the context of the framework of race as a correlation structure of traits. Next the issue of taxonomic classification is considered where it is demonstrated that H. sapiens possesses high levels morphological diversity, genetic heterozygosity and differentiation (F(ST)) compared to many species that are acknowledged to be polytypic with respect to subspecies. Racial variation is then evaluated in light of the phylogenetic species concept, where it is suggested that the least inclusive monophyletic units exist below the level of species within H. sapiens indicating the existence of a number of potential human phylogenetic species; and the biological species concept, where it is determined that racial variation is too small to represent differentiation at the level of biological species. Finally the implications of this are discussed in the context of anthropology where an accurate picture of the sequence and timing of events during the evolution of human taxa are required for a complete picture of human evolution, and medicine, where a greater appreciation of the role played by human taxonomic differences in disease susceptibility and treatment responsiveness will save lives in the future.

Natural history of Homo erectus

Our view of H. erectus is vastly different today than when Pithecanthropus erectus was described in 1894. Since its synonimization into Homo, views of the species and its distribution have varied from a single, widely dispersed, polytypic species ultimately ancestral to all later Homo, to a derived, regional isolate ultimately marginal to later hominin evolution. A revised chronostratigraphic framework and recent work bearing either directly or indirectly on reconstructions of life-history patterns are reviewed here and, together with a review of the cranial and postcranial anatomy of H. erectus, are used to generate a natural history of the species. Here I argue that H. erectus is a hominin, notable for its increased body size, that originates in the latest Pliocene/earliest Pleistocene of Africa and quickly disperses into Western and Eastern Asia. It is also an increasingly derived hominin with several regional morphs sustained by intermittent isolation, particularly in Southeast Asia. This view differs from several current views, most especially that which recognizes only a single hominin species in the Pleistocene, H. sapiens, and those which would atomize H. erectus into a multiplicity of taxa. Following Jolly ([2001] Yrbk Phys Anthropol 44:177-204), the regional morphs of H. erectus may be productively viewed as geographically replacing allotaxa, rather than as the focus of unresolvable species debates. Such a view allows us to focus on the adaptations and biology of local groups, including questions of biogeographic isolation and local adaptation. A number of issues remain unresolved, including the significance of diversity in size and shape in the early African and Georgian records.

Modern human origins in Australasia: Testing the predictions of competing models

The evolutionary background to the emergence of modern humans remains controversial. Four models have been proposed to explain this process and each has clearly definable and testable predictions about the geographical origins of early Australians and their possible biological interaction with other Pleistocene populations. The present study considers the phenetic affinities of early Australians from Kow Swamp (KS 1 and KS 5) and Keilor to Pleistocene Africans and Asians from calvarial dimensions. The study includes analyses employing log-transformed and size-corrected (Mosimann variables) data. The strongest signals to emerge are as follows: (1) a phenetic pattern in which Australians are most like each other, (2) all three crania possess a mosaic of archaic and modern features, (3) Kow Swamp crania also show strong affinities to archaic remains, (4) Keilor is more modern than KS 1 and KS 5 and (5) Keilor shows affinities to Pleistocene East Asian modern crania (Liujiang and Upper Cave 101) providing evidence for a broad regional morphology. The results refute the predictions of multi-species replacement models for early Australians but are consistent with single-species models. Combined with published evidence from DNA, the present study indicates that the Assimilation model presently offers the best explanation for the origins of Pleistocene Australians.

Odontometric systematic assessment of the Swartkrans SK 15 mandible

This study reports a comparison of molar crown and cusp size and shape in the Swartkrans early Homo mandible SK 15 with relevant Plio-Pleistocene taxa. Univariate and multivariate methods are employed to consider the morphological affinities of this specimen and to assess its taxonomy. The case exists for classifying SK 15 in Homo habilis with 11 features aligning it with this species. The results of multivariate studies are consistent with this hypothesis. Moreover, SK 15 lacks a number of important features that characterise the mandibular molars of Homo sapiens erectus. Considerable evidence for parallelism in the dental morphology of SK 15 and H. habilis with A. robustus is discussed. Fossil evidence for the presence of H. sapiens erectus during the Plio-Pleistocene of South Africa presently seems to be lacking. Archaeological interpretations should take greater account of this gap in the fossil record.

Species resilience in Pleistocene hominids that traveled far and ate widely: An analogy to the wolf-like canids

Morphological and genetic analyses have yet to resolve the question of whether more than one species of Homo existed contemporaneously in the Pleistocene. In an effort to contribute a process-related perspective to hominid phylogenetic reconstruction, this paper uses an analogy to the northern wolf-like canids (the wolves and coyotes) to ask the question, How many Homo species should there be, given their likely behavioral profile(s)? In contrast to earlier comparisons to social carnivores which sought to illuminate specific aspects of hominid behavioral ecology, this paper explores behavioral constraints on the process of speciation itself. The analogy suggests that because Pleistocene Homo probably exhibited high habitat tolerance, they would not have had the opportunity to speciate, especially in Africa. In contrast to an earlier single-species hypothesis based on competitive exclusion between sympatric hominid species, this paper explores constraints on the process of speciation under conditions of temporary allopatry.

Timing and tempo of primate speciation

Published molecular clocks for primates are used to estimate typical divergence times for phylogroups (1.6 Ma), species (3.3 Ma), sister species (2.7 Ma), genera (8.9 Ma) and sister genera (8.6 Ma). Significant median differences exist between major groups (infraorders and superfamilies) for various divergence times. These data are employed to estimate typical maximum duration of speciation. Typical primate values (1.1 Ma) suggest this process to be faster than is characteristic of many vertebrates. However, after considering divergence times for hybridizing congeneric and confamilial primates, this value is likely only to estimate the commencement of prezygotic isolating mechanisms, rather than the completion of reproductive isolation. Thus, speciation typically takes around 1.0 Ma to more than 4.0 Ma to occur, depending on whether prezygotic or post-zygotic isolating mechanisms are emphasized. Typical primate genus age is around 5.3 Ma, but we note differences among major groups. In light of these estimates, the classification of humans and chimpanzees is reconsidered using a molecular yardstick approach. Three taxonomic frameworks may flow from molecular analyses, all of them having major implications for understanding the evolution of humans and chimpanzees.

Haplotype trees and modern human origins

A haplotype is a multisite haploid genotype at two or more polymorphic sites on the same chromosome in a defined DNA region. An evolutionary tree of the haplotypes can be estimated if the DNA region had little to no recombination. Haplotype trees can be used to reconstruct past human gene-flow patterns and historical events, but any single tree captures only a small portion of evolutionary history, and is subject to error. A fuller view of human evolution requires multiple DNA regions, and errors can be minimized by cross-validating inferences across loci. An analysis of 25 DNA regions reveals an out-of-Africa expansion event at 1.9 million years ago. Gene flow with isolation by distance was established between African and Eurasian populations by about 1.5 million years ago, with no detectable interruptions since. A second out-of-Africa expansion occurred about 700,000 years ago, and involved interbreeding with at least some Eurasian populations. A third out-of-Africa event occurred around 100,000 years ago, and was also characterized by interbreeding, with the hypothesis of a total Eurasian replacement strongly rejected (P < 10(-17)). This does not preclude the possibility that some Eurasian populations could have been replaced, and the status of Neanderthals is indecisive. Demographic inferences from haplotype trees have been inconsistent, so few definitive conclusions can be made at this time. Haplotype trees from human parasites offer additional insights into human evolution and raise the possibility of an Asian isolate of humanity, but once again not in a definitive fashion. Haplotype trees can also indicate which genes were subject to positive selection in the lineage leading to modern humans. Genetics provides many insights into human evolution, but those insights need to be integrated with fossil and archaeological data to yield a fuller picture of the origin of modern humans.

Race and the odd history of human paleontology

Although the late 17th century witnessed the recognition of fossils as the remains of extinct organisms-because they could be incorporated into the creation story embodied in the Great Chain of Being-acceptance of human antiquity through the indisputable demonstration of the contemporaneity of human bones, stone tools, and accepted fossils was not forthcoming for nearly 2 centuries thereafter. When it did occur, however, ancient humans were not seen as presenting a pattern of diversity similar to that seen in the fossil records of nonhuman organisms. Instead, human evolution then, as now, has typically been interpreted as being unilinear. This belief can be traced to Huxley (1863), who argued that the Feldhofer Grotto Neanderthal skullcap was merely an extension into the past of morphology seen in the Australian Aborigine, whom he took to represent the primitive end of an extreme range of variation he thought characterized Homo sapiens. During the mid-20th century, Mayr and Dobzhansky (mis)used their clout as founders of the evolutionary synthesis to cement in paleoanthropology the idea that human evolutionary history was characterized by nonspeciation. As such, anything that could be interpreted as potentially representing taxic diversity was relegated to the status of individual variation. Lack of understanding of the history of human paleontology, and the biases that constrained its perspective on human evolution, continue to affect the ways in which most paleoanthropologists pigeonhole human fossils.

Description, new reconstruction, comparative anatomy, and classification of the Sterkfontein Stw 53 cranium, with discussions about the taxonomy of other southern African early Homo remains

Specimen Stw 53 was recovered in 1976 from Member 5 of the Sterkfontein Formation. Since its incomplete initial description and comparison, the partial cranium has figured prominently in discussions about the systematics of early Homo. Despite publication of a preliminary reconstruction in 1985, Stw 53 has yet to be compared comprehensively to other Plio-Pleistocene fossils or assessed systematically. In this paper, we report on a new reconstruction of this specimen and provide a detailed description and comparison of its morphology. Our reconstruction differs in important respects from the earlier one, especially in terms of neurocranial length, breadth, and height. However, given that Stw 53 exhibits extensive damage, these dimensions are most likely prone to much error in reconstruction. In areas of well-preserved bone, Stw 53 shares many cranial features with Homo habilis, and we propose retaining it within this species. We also consider the affinities of dental remains from Sterkfontein Member 5, along with those from Swartkrans and Drimolen previously assigned to Homo. We find evidence for sympatry of H. habilis and Australopithecus robustus and possibly Plio-Pleistocene Homo sapiens sensu lato in Sterkfontein Member 5. At Swartkrans and Drimolen, we find evidence of H. habilis. We also compare the morphologies of Stw 53 and SK 847 and find compelling evidence to assign the latter specimen to H. habilis, as has been proposed.

Hominins are a single lineage: brain and body size variability does not reflect postulated taxonomic diversity of hominins

Fossil hominin taxonomy is still debated, chiefly due to the fragmentary nature of fossils and the use of qualitative (subjective) morphological traits. A quantitative analysis of a complete database of hominin cranial capacities (CC, n = 207) and body weight estimates (Wt, n = 285), covering a period from 5.1 ma (millions of years) to 10 ka (thousands of years) shows no discontinuities through time or geographic latitude. Distributions of residuals of CC and Wt around regressions on date and latitude are continuous and do not differ significantly from normal. Thus, with respect to these characteristics, all hominins appear to be a single gradually evolving lineage.

Hypervariability, suppressed recombination and the genetics of individuality

We define 'genetic individuality' as intraspecies variation that has substantial heritability and involves traits that are sufficiently common that they can be observed in any modest-sized sampling of individuals. We propose that genetic individuality is largely shaped by the combinatory shuffling of a modest number of genes, each of which exists as a family of functionally and structurally diverged alleles. Unequivocal examples of such allele families are found at the O-antigen-biosynthetic locus in Pseudomonas aeruginosa and the human leucocyte antigen locus in humans. We examine characteristic features of these allele families and explore the possibility that genetic loci with similar characteristics can be recognized in a whole-genome scan of human genetic variation.

Problems with the use of cladistic analysis in palaeoanthropology

Cladistic analysis is a popular method for reconstructing evolutionary relationships on the human lineage. However, it has limitations and hidden assumptions that are often not considered by palaeoanthropologists. Some researchers who are opposed to its use regard cladistics as the preferred method for taxonomic "splitters" and claim it has lead to a revitalisation of typology. Typology remains a part of human evolutionary studies, regardless of the acceptance or use of cladistics. The assumption/preference for "splitting" over "lumping" in cladistics (alpha) taxonomy and the general failure to evaluate (post-hoc) such taxonomies have served to reinforce this assertion. Researchers have also adopted a number of practices that are logically untenable or introduce considerable error. The evolutionary trend of human encephalisation, apparently isometric with body size, and concurrent reduction in the gut and masticatory apparatus, suggests continuous cladistic characters are biased by problems of body size. The method suffers a logical weakness, or circularity, leading to bias when characters with multiple states are used. Coding of such characters can only be done using prior criteria, and this is usually done using an existing phylogenetic scheme. Another problem with coding character states is the handling of variation within species. While this form of variation is usually ignored by palaeoanthropologists, when characters are recognised as varying, their treatment as a separate state adds considerable error to cladograms. The genetic proximity of humans, chimpanzees and gorillas has important implications for cladistic analyses. It is argued that chimpanzees and gorillas should be treated as ingroup taxa and an alternative outgroup such as orangutans should be used, or an (hypothetical) ancestral body plan developed. Making chimpanzees and gorillas ingroup taxa would considerably enhance the biological utility of anthropological cladograms. All published human cladograms fail to meet standard quality criteria indicating that none of them may be considered reliable. The continuing uncertainty over the number and composition of fossil human species is the largest single source of error for cladistics and human phylogenetic reconstruction.