Bayesian phylogenetic estimation of fossil ages

Recent advances have allowed for both morphological fossil evidence and molecular sequences to be integrated into a single combined inference of divergence dates under the rule of Bayesian probability. In particular, the fossilized birth–death tree prior and the Lewis-Mk model of discrete morphological evolution allow for the estimation of both divergence times and phylogenetic relationships between fossil and extant taxa. We exploit this statistical framework to investigate the internal consistency of these models by producing phylogenetic estimates of the age of each fossil in turn, within two rich and well-characterized datasets of fossil and extant species (penguins and canids). We find that the estimation accuracy of fossil ages is generally high with credible intervals seldom excluding the true age and median relative error in the two datasets of 5.7% and 13.2%, respectively. The median relative standard error (RSD) was 9.2% and 7.2%, respectively, suggesting good precision, although with some outliers. In fact, in the two datasets we analyse, the phylogenetic estimate of fossil age is on average less than 2 Myr from the mid-point age of the geological strata from which it was excavated. The high level of internal consistency found in our analyses suggests that the Bayesian statistical model employed is an adequate fit for both the geological and morphological data, and provides evidence from real data that the framework used can accurately model the evolution of discrete morphological traits coded from fossil and extant taxa. We anticipate that this approach will have diverse applications beyond divergence time dating, including dating fossils that are temporally unconstrained, testing of the ‘morphological clock'', and for uncovering potential model misspecification and/or data errors when controversial phylogenetic hypotheses are obtained based on combined divergence dating analyses.This article is part of the themed issue ‘Dating species divergences using rocks and clocks’.     

Orang-like manual adaptations in the fossil hominoid Hispanopithecus laietanus: first steps towards great ape suspensory behaviours

Morphological and biometrical analyses of the partial hand IPS18800 of the fossil great ape Hispanopithecus laietanus (=Dryopithecus laietanus), from the Late Miocene (about 9.5Ma) of Can Llobateres (Catalonia, Spain), reveal many similarities with extant orang-utans (Pongo). These similarities are interpreted as adaptations to below-branch suspensory behaviours, including arm-swinging and clambering/postural feeding on slender arboreal supports, due to an orang-like double-locking mechanism. This is confirmed by the long and highly curved phalanges of Hispanopithecus. The short and stout metacarpals with dorsally constricted heads, together with the dorsally extended articular facets on proximal phalanges, indicate the persistence of significant degrees of palmigrady. A powerful grasping capability is indicated by the great development of basal phalangeal tubercles, the marked insertions for the flexors on phalangeal shafts and the large pits for the collateral ligaments. The morphology of the Hispanopithecus long bones of the hand indicates a unique positional repertoire, combining orthogrady with suspensory behaviours and palmigrade quadrupedalism. The retention of powerful grasping and palmigrady suggests that the last common ancestor of hominids might have been more primitive than what can be inferred on the basis of extant taxa, suggesting that pronograde behaviours are compatible with an orthograde bodyplan suitable for climbing and suspension.     

New material of Qatrania from Egypt with comments on the phylogenetic position of the parapithecidae (primates,Anthropoidea)

New material of the early anthropoid primate Qatrania wingi and a new species of that genus are described. Several features of the dental anatomy show that Qatrania, while quite primitive relative to other anthropoids in many ways, is most likely a parapithecid primate. The new material suggests that several dental features previously thought to ally parapithecids with the catarrhine primates were actually evolved in parallel in catarrhines and some parapithecids. Furthermore, all nonparapithecid anthropoids (including platyrrhines and catarrhines) share a suite of derived dental and postcranial features not found in parapithecids. Therefore, parapithecid origins may predate the platyrrhine/catarrhine split.     

Problems of body-weight estimation in fossil primates

Body-weight estimates of fossil primates are commonly used to infer many important aspects of primate paleobiology, including diet, ecology, and relative encephalization. It is important to examine carefully the methodologies and problems associated with such estimates and the degree to which one can have confidence in them. New regression equations for predicting body weight in fossil primates are given which provide body-weight estimates for most nonhominid primate species in the fossil record. The consequences of using different subgroups (evolutionary “grades”) of primate species to estimate fossil-primate body weights are explored and the implications of these results for interpreting the primate fossil record are discussed. All species (fossil and extant) were separated into the following “grades”: prosimian grade, monkey grade, ape grade, anthropoid grade, and all-primates grade. Regression equations relating lower molar size to body weight for each of these grades were then calculated. In addition, a female-anthropoid grade regression was also calculated for predicting body weight infernales of extinct, sexually dimorphic anthropoid species. These equations were then used to generate the fossil-primate body weights. In many instances, the predicted fossil-primate body weights differ substantially from previous estimates.     

Molecular clocks do not support the Cambrian explosion

The fossil record has long supported the view that most animal phyla originated during a brief period approximately 520 MYA known as the Cambrian explosion. However, molecular data analyses over the past 3 decades have found deeper divergences among animals (approximately 800 to 1,200 MYA), with and without the assumption of a global molecular clock. Recently, two studies have instead reported time estimates apparently consistent with the fossil record. Here, we demonstrate that methodological problems in these studies cast doubt on the accuracy and interpretations of the results obtained. In the study by Peterson et al., young time estimates were obtained because fossil calibrations were used as maximum limits rather than as minimum limits, and not because invertebrate calibrations were used. In the study by Aris-Brosou and Yang, young time estimates were obtained because of problems with rate models and other methods specific to the study, and not because Bayesian methods were used. This also led to many anomalous findings in their study, including a primate-rodent divergence at 320 MYA. With these results aside, molecular clocks continue to support a long period of animal evolution before the Cambrian explosion of fossils.     

First direct dating of a presumed Pleistocene hominid from China: AMS radiocarbon age of a femur from the Ordos Plateau

Human remains from the Xarusgol Valley, Ordos Plateau, northwestern China, have been considered to date to the Late Pleistocene. In order to ascertain their true age, direct AMS (14)C dating of a femur collected in the early 1920s was conducted. The results demonstrate that the femur is very young, with one sample of 'post-bomb' age and the other sample c. 200 years old. This first direct dating of a Chinese fossil hominid underscores the need to apply the same methodology to other Chinese modern human fossils currently believed to be of Pleistocene age.     

Intellectual activity during formation of quantitative concepts in the lower and higher monkeys

Results of study of formation of quantitative concepts in the lower and higher monkey are presented. Various authors used different methods of study of this issue. It has been established that not only the higher primates, such as chimpanzees and orangutans, but also the lower ones—macaques, capuchins, squirrel monkeys—have the “mathematical capabilities.” The detailed study of formation of quantitative concepts in primates of different levels of phylogenesis allows disclosing mechanisms of formation of this function in human.     

Development of Lake Kortowskie in relation to the climatic changes in three Holocene periods

Paleolimnological studies which included analyses of diatoms, plant pigments and physico-chemical characteristics of the bottom sediments have been used to describe the evolution of Lake Kortowskie in three Holocene periods. Characteristic stages of lake development have been distinguished in the Atlantic, Subboreal and Subatlantic periods, these stages differed with respect to the level of production, water level, impact of allochthonic factors and variety of taxonomic composition of the diatoms. It has been shown that Lake Kortowskie was most productive in the Atlantic and the Subatlantic period. On the other hand, the Subboreal period was characterized by a considerable drop of production, most probably caused by strong erosion and worsening climatic conditions. It has been suggested that lake fertility in Atlantic period was probably due to climatic optimum, whereas in the youngest, Subatlantic period the increase of productivity resulted more from internal features of the lake, viz. its age, the time - related increase in the pool of nutrients. The great variety of diatom remains, which increases towards the surface of the sediment profile, confirms the suggestion of generally favourable conditions for lake development as well as its increasing fertility.     

Intra- and interspecific variation of the CCR5 gene in higher primates

We have evaluated the molecular evolution of the chemokine receptor CCR5 in primates. The chemokine receptor CCR5 serves as a major co-receptor for human immunodeficiency virus/simian immunodeficiency virus (HIV/SIV) infection. Knowledge of evolution of the CCR5 molecule and selection on the CCR5 gene may shed light on its functional role. The comparison of differences between intraspecific polymorphisms and interspecific fixed substitutions provides useful information regarding modes of selection during the course of evolution. There is marked polymorphism in the CCR5 gene sequence within different primate species, whereas sequence divergence between different species is small. By using contingency tests, we compared synonymous (SS) and nonsynonymous (NS) CCR5 mutations occurring within and between a broad range of primates. Our results demonstrate that CCR5 evolution did not follow expectations of strict neutrality at the level of the whole gene. The proportion of NS to SS at the intraspecific level was significantly higher than that observed at the interspecific level. These results suggest that most CCR5 NS polymorphisms are slightly deleterious. However, at domains more closely correlated with its known biological functions, there was no obvious evidence to support deviation from neutrality.     

Phylogenetic relationships of the Cretaceous frog Beelzebufo from Madagascar and the placement of fossil constraints based on temporal and phylogenetic evidence

The placement of fossil calibrations is ideally based on the phylogenetic analysis of extinct taxa. Another source of information is the temporal variance for a given clade implied by a particular constraint when combined with other, well-supported calibrations. For example, the frog Beelzebufo ampinga from the Cretaceous of Madagascar has been hypothesized to be a crown-group member of the New World subfamily Ceratophryinae, which would support a Late Cretaceous connection with South America. However, phylogenetic analyses and molecular divergence time estimates based on other fossils do not support this placement. We derive a metric, Δt, to quantify temporal divergence among chronograms and find that errors resulting from mis-specified calibrations are localized when additional nodes throughout the tree are properly calibrated. The use of temporal information from molecular data can further assist in testing phylogenetic hypotheses regarding the placement of extinct taxa.     

Fossil Humankind and Other Anthropoid Primates of China

More than 70 sites have yielded human fossils in China. They are attributed to Homo sapiens erectus and Homo sapiens sapiens. The earliest one is possibly about 1.7 Ma. A series of common morphological features, including shovel-shaped incisors and flatness of the face, characterize them. There is a morphological mosaic between H. s. erectus and H. s. sapiens in China. The existence of common features and the morphological mosaic suggest continuity of human evolution in China. That there are a few features which are more commonly seen in the Neanderthal lineage, occurring in a few Chinese fossil skulls, probably suggests gene flow between China and the West. Based on them, in 1998 I proposed an hypothesis—continuity with hybridization—for human evolution in China. The hypothesis is supported by paleolithic archeology, and it supports the multiregional evolution hypothesis of modern human origins. The anatomically modern humans of East Asia originated most probably in China. Although some nonhuman anthropoid primates of China—Gigantopithecus, Sivapithecus, Ramapithecus and Lufengpithecus—have been suggested as the direct ancestors of human beings, the discovery of more specimens and further studies do not support these suggestions. Therefore, it is most probable that the transition between apes and humans did not occur in China.     

昆虫拟态的历史发展

昆虫的拟态理论是由英国自然学家Bates于1862年提出的,Fisher称其为达尔文后自然选择最重要的依据之一.大量的科学研究表明,昆虫的拟态行为最晚出现在石炭纪,自那时起昆虫与捕食者、昆虫与植物之间开始出现了共同的演变和进化.拟态的模仿方式一般包括颜色、花纹以及形态,但是也可以单指行为方面,且拟态大部分情况下可能模仿的是一个动物群体或者只是另外一种动物身上的一部分.拟态包括多种定义,不同的定义之间用小同的标准来区分拟态现象和非拟态现象,如贝茨氏拟态、缪勒氏拟态、侵略性拟态和瓦曼氏拟态等.本文从其中广义拟态的角度,对当前不同类群昆虫化石中拟态现象的研究进展进行了简要总结.     

The impact of fossils and taxon sampling on ancient molecular dating analyses

The number and complexity of molecular dating studies has increased over the past decade. Along with a broadening acceptance of their utility has come significant controversy over the methods and models that are appropriate, as well as the accuracy of the estimates yielded by molecular clock analyses. Radically different age estimates have been published for the same divergences from analyses of different datasets with different fossil constraints obtained with different methods, and the underlying explanation for these differences is often unclear. Here we utilize two previously published datasets to examine the effect of fossil calibrations and taxon sampling on the age estimates for two deep eukaryote divergences in an attempt to discern the relative impact of these factors. Penalized likelihood, non-parametric rate smoothing, and Bayesian methods were utilized to generate age estimates for the origin of the Metazoa from a 7-gene dataset and for the divergence of Eukaryotes from a 129-gene dataset. From these analyses, it is clear that the fossil calibrations chosen and the method for applying constraints to these nodes have a large impact on age estimates, while the degree of taxon sampling within a dataset is less important in terms of the resulting age estimates. Concerns and recommendations for addressing these two factors when initiating a dating analysis are discussed.