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Part I
HUMAN PHYLOGENETIC HISTORY AND THE PALEONTOLOGICAL RECORD

Precious few nonhuman fossils in humanity’s recent “family tree” were known to science in the mid-1800s, but, interestingly, Darwin once briefly held in his hands one of these treasures: a Neandertal skull that had been excavated from Gibraltar in 1848. As additional hominid fossils of various geological ages gradually were unearthed in the ensuing decades (e.g., in Java, Africa, and Europe), anthropologists grappled with naming and classifying such remains and interpreting their proper places in prehuman evolutionary history. Such paleontological finds can be of two general types: fossilized body parts such as leg bones, the pelvic girdle, or the cranium (giving glimpses into humanity’s anatomical heritage), and nonbiotic physical artifacts such as stone tools or cave paintings that can offer important clues about humanity’s cultural heritage. A different but complementary approach to studying human origins has entailed evolutionary reconstructions based on morphological, molecular-genetic, or other features of modern Homo sapiens compared to those of other extant primates. In these reconstructions, phylogeneticists take advantage of the voluminous biological information currently on display in living organisms to deduce the evolutionary ages and properties of the ancestors that humans shared with various other primates, thereby in effect delving backward through time, indirectly.

In Chapter 1, Bernard Wood describes some of the special challenges that have confronted anthropologists wishing to reconstruct human evolution based on morphological evidence (both from fossils and extant primates). One fundamental limitation has been the relative paucity of



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Part I HUMAN PHYLOGENETIC HISTORY AND THE PALEONTOLOGICAL RECORD P recious few nonhuman fossils in humanity’s recent “family tree” were known to science in the mid-1800s, but, interestingly, Darwin once briefly held in his hands one of these treasures: a neander- tal skull that had been excavated from Gibraltar in 1848. As additional hominid fossils of various geological ages gradually were unearthed in the ensuing decades (e.g., in Java, Africa, and europe), anthropologists grappled with naming and classifying such remains and interpreting their proper places in prehuman evolutionary history. such paleontologi- cal finds can be of two general types: fossilized body parts such as leg bones, the pelvic girdle, or the cranium (giving glimpses into humanity’s anatomical heritage), and nonbiotic physical artifacts such as stone tools or cave paintings that can offer important clues about humanity’s cultural heritage. A different but complementary approach to studying human origins has entailed evolutionary reconstructions based on morphological, molecular-genetic, or other features of modern Homo sapiens compared to those of other extant primates. in these reconstructions, phylogeneticists take advantage of the voluminous biological information currently on dis- play in living organisms to deduce the evolutionary ages and properties of the ancestors that humans shared with various other primates, thereby in effect delving backward through time, indirectly. in Chapter 1, Bernard Wood describes some of the special challenges that have confronted anthropologists wishing to reconstruct human evo- lution based on morphological evidence (both from fossils and extant primates). one fundamental limitation has been the relative paucity of 

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 / Part I fossilized hominin material, but additional complications have come from shifting taxonomic paradigms and nomenclatural practices within the systematics community itself, as well as from continuing debates about phylogenetic methods and species concepts, especially as they apply to fossil material. The net result has been an oft-confusing proliferation of species names and taxonomic realignments for putative human ancestors. To help simplify this imbroglio, Wood compiles, describes, and provides geological dates for all named fossil taxa in the human clade, ranging from anatomically modern Homo sapiens back to various archaic hominins and “possible hominins” that lived several million years ago, and many taxa temporally in between. Wood also addresses several looming opportuni- ties for the field of comparative primate morphology, such as the use of new imaging technologies that should help to clarify (by permitting more detailed levels of examination) when similar anatomical traits in differ- ent taxa register genuine homology (shared ancestry) versus homoplasy (evolutionary convergence from separate ancestors). in Chapter 2, Juan luis Arsuaga reviews the history of scientific debate, beginning in Darwin’s era, about the precise phylogenetic inter- relationships among modern humans and the various great apes of Africa and Asia. Another longstanding debate in anthropology is whether two or more species of more recent human ancestry ever inhabited the planet at the same time (which might seem unlikely based on general ecologi - cal considerations for competitive, large-brained primates). Traditionally, fossil-based assessments of this question relied heavily on rather meager population-level data from craniodental anatomy, but more comprehen- sive morphotypic descriptions are now becoming possible as the avail- able number of known postcranial hominin fossils has swelled as well. Arsuaga reviews these recent fossil-based discoveries about anatomical variation within and among particular proto-human populations dating to more than 0.5 mya, and he concludes that the data are consistent with the more-or-less contemporaneous presence of either different species (depending on one’s definition of species) or, perhaps, morphologically distinct populations within a single species that seems to have been much more polytypic in anatomy than are modern humans. increasingly in recent years, the field of physical anthropology has shifted much of its attention from morphology-based appraisals of human evolution to historical reconstructions based on molecular-genetic and genomics data. in Chapter 3, Morris Goodman and Kirsten sterner review the history of molecular approaches in refining our understanding of pri- mate phylogeny, for example, in revealing the branching orders of lineages that led to extant great apes and humans. They then argue that a modern “phylogenomic approach” can go well beyond phylogeny reconstruc- tion per se by helping to identify Darwinian (positively selected) genetic

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Human Phylogenetic History and the Paleontological Record /  changes (in expression profiles as well as protein-coding sequences) that might mechanistically underlie the evolution of such distinctive human features as expanded cognitive ability, sociality, and language. The authors illustrate this phylogenomic approach by recent work that implicates particular loci in the adaptive evolution of high levels of aerobic energy metabolism that a large mammalian brain necessitates. in Chapter 4, Angela hancock and several other authors associated with the laboratory of Anna Di rienzo extend this general phylogenomic perspective to analyze genome-wide scans of snPs (single-nucleotide polymorphisms) in numerous human populations representing distinct ecoregions on planet earth, or that differ in fundamental subsistence mode with respect to diet. in principle, genetic variation among geographic populations might register adaptive differences promoted by environmen- tal selection, or historical population-demographic effects that are mostly independent of the ecological selective regime per se. hancock and her coauthors attempt to distinguish these two classes of historical causation by searching for consistent distributions of snPs vis-à-vis human diet and ecoregion, after applying analytical methods designed to control for gene-environment associations that might be due to historical population demography. The authors conclude that strong signals of natural selec - tion related to diet and climate exist for snPs at particular genes that are centrally involved in carbohydrate utilization and energy metabolism. The authors also compare their phylogenomic approach and findings to those of previous genome-wide association studies in humans. Africa is humanity’s evolutionary cradle, and its contemporary popu - lations retain extraordinary genetic and linguistic diversity that offers anthropologists a wellspring of biological and cultural information about human history on that continent over the past 200 millennia. For example, with respect to languages, researchers recognize more than 2,000 ethno- linguistic groups that can be classified into four major African language families; and with respect to genetic lineages, mitochondrial (mt) DnA (which is inherited maternally) and the y chromosome (which is transmit- ted paternally) both display higher genealogical diversity and evolution - ary depth in Africa than in many other regions of the planet combined (as might be expected under a model of African ancestry for all modern humans). in Chapter 5, laura scheinfeldt, sameer soi, and sarah Tishkoff address the demographic history of human populations in Africa by com - piling and comparing scientific information from archaeology (including cultural artifacts), comparative linguistics, and molecular genetics. Their synthesis reveals various signatures of past population movements on the continent, sometimes registered in particular genetic markers (either neu - tral or under selection), sometimes registered in cultural practices (such as agriculture and pastoralism), sometimes relatable to geophysical changes

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 / Part I in the environment, and sometimes reflected to varied degrees in the cur- rent spatial distributions of languages. The net result is a fascinating but complex picture of African human demographic history, presented in a broad framework that can be further tested as additional archaeological, linguistic, and genetic analyses (especially from autosomal loci) eventually are incorporated into the synthesis.