Studies of molecular evolutionary rates have yielded a wide range of rate estimates for various genes and taxa. Recent studies based on population-level and pedigree data have produced remarkably high estimates of mutation rate, which strongly contrast with substitution rates inferred in phylogenetic (species-level) studies. Using Bayesian analysis with a relaxed-clock model, we estimated rates for three groups of mitochondrial data: avian protein-coding genes, primate protein-coding genes, and primate d-loop sequences. In all three cases, we found a measurable transition between the high, short-term (<1–2 Myr) mutation rate and the low, long-term substitution rate. The relationship between the age of the calibration and the rate of change can be described by a vertically translated exponential decay curve, which may be used for correcting molecular date estimates. The phylogenetic substitution rates in mitochondria are approximately 0.5% per million years for avian protein-coding sequences and 1.5% per million years for primate protein-coding and d-loop sequences. Further analyses showed that purifying selection offers the most convincing explanation for the observed relationship between the estimated rate and the depth of the calibration. We rule out the possibility that it is a spurious result arising from sequence errors, and find it unlikely that the apparent decline in rates over time is caused by mutational saturation. Using a rate curve estimated from the d-loop data, several dates for last common ancestors were calculated: modern humans and Neandertals (354 ka; 222–705 ka), Neandertals (108 ka; 70–156 ka), and modern humans (76 ka; 47–110 ka). If the rate curve for a particular taxonomic group can be accurately estimated, it can be a useful tool for correcting divergence date estimates by taking the rate decay into account. Our results show that it is invalid to extrapolate molecular rates of change across different evolutionary timescales, which has important consequences for studies of populations, domestication, conservation genetics, and human evolution.

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Time Dependency of Molecular Rate Estimates and Systematic Overestimation of Recent Divergence Times

The role of fossils in dating the tree of life has been misunderstood. Fossils can provide good "minimum" age estimates for branches in the tree, but "maximum" constraints on those ages are poorer. Current debates about which are the "best" fossil dates for calibration move to consideration of the most appropriate constraints on the ages of tree nodes. Because fossil-based dates are constraints, and because molecular evolution is not perfectly clock-like, analysts should use more rather than fewer dates, but there has to be a balance between many genes and few dates versus many dates and few genes. We provide "hard" minimum and "soft" maximum age constraints for 30 divergences among key genome model organisms; these should contribute to better understanding of the dating of the animal tree of life.

/pdf/paleontological-evidence-to-date-the-tree-of-life-5dhwbwgnyr.pdf

Paleontological Evidence to Date the Tree of Life

The search for the earliest fossil evidence of the human lineage has been concentrated in East Africa. Here we report the discovery of six hominid specimens from Chad, central Africa, 2,500 km from the East African Rift Valley. The fossils include a nearly complete cranium and fragmentary lower jaws. The associated fauna suggest the fossils are between 6 and 7 million years old. The fossils display a unique mosaic of primitive and derived characters, and constitute a new genus and species of hominid. The distance from the Rift Valley, and the great antiquity of the fossils, suggest that the earliest members of the hominid clade were more widely distributed than has been thought, and that the divergence between the human and chimpanzee lineages was earlier than indicated by most molecular studies. From their initial description in 1925 1 until 1995, hominids from the Pliocene (5.3‐1.6 million years, Myr) and late Upper Miocene (,7.5‐5.3 Myr) were known only from southern and eastern Africa. This distribution led some authors to postulate an East African origin for the hominid clade (where the term ‘hominid’ refers to any member of that group more closely related to extant humans than to

A new hominid from the Upper Miocene of Chad, Central Africa

Currently, it is widely accepted that only one hominin genus, Homo, was present in Pleistocene Asia, represented by two species, Homo erectus and Homo sapiens. Both species are characterized by greater brain size, increased body height and smaller teeth relative to Pliocene Australopithecus in Africa. Here we report the discovery, from the Late Pleistocene of Flores, Indonesia, of an adult hominin with stature and endocranial volume approximating 1 m and 380 cm3, respectively--equal to the smallest-known australopithecines. The combination of primitive and derived features assigns this hominin to a new species, Homo floresiensis. The most likely explanation for its existence on Flores is long-term isolation, with subsequent endemic dwarfing, of an ancestral H. erectus population. Importantly, H. floresiensis shows that the genus Homo is morphologically more varied and flexible in its adaptive responses than previously thought.

https://www.cogsci.ucsd.edu/~sereno/107B/readings/09.08-FloresHomininDebate.pdf

A new small bodied hominin from the Late Pleistocene of Flores, Indonesia

Gorillas are humans' closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human-chimpanzee and human-chimpanzee-gorilla speciation events at approximately 6 and 10 million years ago. In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution.

/pdf/insights-into-hominid-evolution-from-the-gorilla-genome-15sk1bbvu1.pdf

Insights into hominid evolution from the gorilla genome sequence

Preface Acknowledgements 1. Introduction to the primate fossil record Walter Carl Hartwig 2. The origin of primates David Tab Rasmussen Part I. The Earliest Primates and the Fossil Record of Prosimians: 3. The earliest fossil primates and the evolution of prosimians Herbert H. Covert 4. Adapiformes: phylogeny and adaptation Daniel L. Gebo 5. Tarsiiformes: evolutionary history and adaptation Gregg F. Gunnell and Kenneth D. Rose 6. Fossil lorisoids Erica Phillips and Alan C. Walker 7. Quaternary fossil lemurs Laurie R. Godfrey and William L. Jungers Part II. The Origin and Diversification of Anthropoid Primates: 8. The origin and diversification of anthropoid primates - introduction Marian Dagosto 9. Basal anthropoids K. Christopher Beard 10. Platyrrhine paleontology and systematics: the paradigm shifts Alfred L. Rosenberger 11. Early platyrrhines of southern South America John G. Fleagle and Marcelo F. Tejedor 12. Miocene platyrrhines of the northern neotropics Walter Carl Hartwig and D. Jeffrey Meldrum 13. Extinct Quaternary platyrrhines of the Greater Antilles and Brazil Ross D. E. MacPhee and Ines Horovitz Part III. The Fossil Record of the Early Catarrhines and Old World Monkeys: 14. Early catarrhines of the African Eocene and Oligocene David Tab Rasmussen 15. The Pliopithecoidea David Begun 16. The Victoriapithecidae, Cercopithecoidea Brenda Benefit and Monte L. McCrossin 17. Fossil Old World monkeys: the Late Neogene radiation Nina G. Jablonski Part IV. The Fossil Record of Hominoid Primates: 18. Perspectives on the Miocene Hominoidea David R. Pilbeam 19. Late Oligocene to Middle Miocene catarrhines from Afro-Arabia Terry Harrison 20. European hominoids David Begun 21. The hominoid radiation in Asia Jay Kelley 22. Middle and Late Miocene African hominoids Steven C. Ward and Dana Duren Part V. The Fossil Record of Human Ancestry: 23. Introduction to the fossil record of human ancestry Henry M. McHenry 24. Earliest hominids Tim D. White 25. Early genus Homo Holly Dunsworth and Alan C. Walker 26. Migrations, radiations and continuity: patterns in the evolution of Middle and Late Pleistocene humans Fred Smith References cited Index.

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The Primate Fossil Record

A nearly complete skeleton of a robust-bodied New World monkey that resembles living spider monkeys was recovered from undisturbed Pleistocene deposits in the Brazilian state of Bahia. The skeleton displays the highly specialized postcranial pattern typical of spider and woolly spider monkeys and shares cranial similarities to the spider monkey exclusively. It is generically distinct on the basis of its robustness (>20 kg) and on the shape of its braincase. This new genus indicates that New World monkeys nearly twice the size of those living today were part of the mammalian biomass of southern Amazonia in the late Pleistocene. The discovery of this specimen expands the known adaptive diversity of New World monkeys and demonstrates that they underwent body size expansion in the terminal Pleistocene, as did many other types of mammals.

https://www.pnas.org/content/pnas/93/13/6405.full.pdf

A new extinct primate among the Pleistocene megafauna of Bahia, Brazil.

A COMPLETE skeleton of a large-bodied New World monkey has been found in Pleistocene cave deposits in the Brazilian state of Bahia. It demonstrates an unprecedented combination of body size, locomotor and cranial morphology. Skeletal features indicate an animal of approximately 25 kg, more than twice the mass of any living South American monkey. We refer the specimen to Protopithecus brasiliensis Lund, 1838, a large Pleistocene primate originally represented by only a proximal femur and distal humerus1–4. The skeleton resembles species of two distinct New World monkey lineages. The cranium is modified for an enlarged vocal sac typical of living howler monkeys5–7, and the postcranium includes suspensory and brachiating components of locomotion as seen in living spider and woolly spider monkeys8. This skeleton confirms that adaptive diversity in neotropical primates was greater in the recent past, and that current interpretations of how their distinctive adaptations evolved should be revised.

A complete skeleton of the giant South American primate Protopithecus

Life's solution: Inevitable humans in a lonely universe

Gestation length, neonatal and maternal body weight, and neonatal and adult brain weight data were collected for New World monkeys in an attempt to establish typical patterns of perinatal life history. This study attempts to illuminate the most accurate values from the available data, which suggest that gestation length and prenatal growth rate are broadly conserved in relation to maternal size in New World monkeys. Exceptions to the patterns evident in the data point to derivations in life history strategies. In particular, this study suggests that the extended gestation length of callitrichines is a function of minimum viable neonate size and not exclusively energy minimization associated with simultaneous lactation. Cebus is shown to undergo more postnatal brain growth relative to other New World monkeys, but not as much as previously believed. Alouatta is shown to be relatively small brained at birth as well as in adulthood. Saimiri is shown to present the most unusual package of perinatal life history traits, in which precocial neonates are gestated for a relatively long time and at a slightly faster growth rate than is typical for New World monkeys. © 1996 Wiley-Liss, Inc.

Walter Carl Hartwig

Papers

The Primate Fossil Record

A new extinct primate among the Pleistocene megafauna of Bahia, Brazil.

A complete skeleton of the giant South American primate Protopithecus

Life's solution: Inevitable humans in a lonely universe

Perinatal life history traits in New World monkeys