Elevated diversity in loci linked to facial morphology is consistent with the hypothesis that individual facial recognition is important across hominoids.

Objectives: The ability to use visual signals to identify individuals is an important feature of primate social groups, including humans. Sheehan and Nachman (2014) showed that loci linked to facial morphology had elevated levels of diversity and interpreted this as evidence that the human face is under frequency-dependent selection to enhance individual recognition (Nature Communications 5). In our study, we tested whether this pattern is found in non-human ape species, to help understand whether individual recognition might also play a role in species other than humans.

Hominoid intraspecific cranial variation mirrors neutral genetic diversity.

Natural selection, developmental constraint, and plasticity have all been invoked as explanations for intraspecific cranial variation in humans and apes. However, global patterns of human cranial variation are congruent with patterns of genetic variation, demonstrating that population history has influenced cranial variation in humans. Here we show that this finding is not unique to but is also broadly evident across extant ape species.

Elite swimmers do not exhibit a body mass index trade-off across a wide range of event distances.

There is a trade-off reflected in the contrasting phenotypes of elite long-distance runners, who are typically leaner, and elite sprinters, who are usually more heavily muscled. It is unclear, however, whether and how swimmers' bodies vary across event distances from the 50 m swim, which is about a 20-30 s event, to the 10 000 m marathon swim, which is about a 2 h event. We examined data from the 2012 Olympics to test whether swimmers' phenotypes differed across event distances.

Strong links between genomic and anatomical diversity in both mammalian olfactory chemosensory systems.

Mammalian olfaction comprises two chemosensory systems: the odorant-detecting main olfactory system (MOS) and the pheromone-detecting vomeronasal system (VNS). Mammals are diverse in their anatomical and genomic emphases on olfactory chemosensation, including the loss or reduction of these systems in some orders. Despite qualitative evidence linking the genomic evolution of the olfactory systems to specific functions and phenotypes, little work has quantitatively tested whether the genomic aspects of the mammalian olfactory chemosensory systems are correlated to anatomical diversity.

Molecular phylogenetic analysis of the Papionina using concatenation and species tree methods.

The Papionina is a geographically widespread subtribe of African cercopithecid monkeys whose evolutionary history is of particular interest to anthropologists. The phylogenetic relationships among arboreal mangabeys (Lophocebus), baboons (Papio), and geladas (Theropithecus) remain unresolved. Molecular phylogenetic analyses have revealed marked gene tree incongruence for these taxa, and several recent concatenated phylogenetic analyses of multilocus datasets have supported different phylogenetic hypotheses.

Evidence for a convergent slowdown in primate molecular rates and its implications for the timing of early primate evolution.

A long-standing problem in primate evolution is the discord between paleontological and molecular clock estimates for the time of crown primate origins: the earliest crown primate fossils are ~56 million y (Ma) old, whereas molecular estimates for the haplorhine-strepsirrhine split are often deep in the Late Cretaceous. One explanation for this phenomenon is that crown primates existed in the Cretaceous but that their fossil remains have not yet been found. Here we provide strong evidence that this discordance is better-explained by a convergent molecular rate slowdown in early primate evolution.

The SLC4A1 gene is under differential selective pressure in primates infected by Plasmodium falciparum and related parasites.

Malaria is a disease caused by Plasmodium parasites and is responsible for high mortality in humans. This disease is caused by four different species of Plasmodium though the main source of mortality is Plasmodium falciparum. Humans have a number of genetic adaptations that act to combat Plasmodium.

Dating primate divergences through an integrated analysis of palaeontological and molecular data.

Estimation of divergence times is usually done using either the fossil record or sequence data from modern species. We provide an integrated analysis of palaeontological and molecular data to give estimates of primate divergence times that utilize both sources of information. The number of preserved primate species discovered in the fossil record, along with their geological age distribution, is combined with the number of extant primate species to provide initial estimates of the primate and anthropoid divergence times.

Fossil and molecular evidence constrain scenarios for the early evolutionary and biogeographic history of hystricognathous rodents.

The early evolutionary and paleobiogeographic history of the diverse rodent clade Hystricognathi, which contains Hystricidae (Old World porcupines), Caviomorpha (the endemic South American rodents), and African Phiomorpha (cane rats, dassie rats, and blesmols) is of great interest to students of mammalian evolution, but remains poorly understood because of a poor early fossil record. Here we describe the oldest well-dated hystricognathous rodents from an earliest late Eocene (approximately 37 Ma) fossil locality in the Fayum Depression of northern Egypt. These taxa exhibit a combination of primitive and derived features, the former shared with Asian "baluchimyine" rodents, and the latter shared with Oligocene phiomorphs and caviomorphs.

Mitochondrial COII Introgression into the Nuclear Genome of Gorilla gorilla.

Numts are nonfunctional mitochondrial sequences that have translocated into nuclear DNA, where they evolve independently from the original mitochondrial DNA (mtDNA) sequence. Numts can be unintentionally amplified in addition to authentic mtDNA, complicating both the analysis and interpretation of mtDNA-based studies. Amplification of numts creates particular issues for studies on the noncoding, hypervariable 1 mtDNA region of gorillas.

Phylogenetic analysis of the promoter region of the CD40L gene in primates and other mammals.

CD40L is a type II membrane protein comprised of 261 amino acids. CD40L plays a crucial role in the immune system where it is primarily expressed on activated T cells and triggers immunoglobulin class switching. The genetic disease X-linked hypergammaglobulinemia (HIGM1, XHIGM or XHIM) is caused by mutations in the CD40L gene.

Primate molecular divergence dates.

With genomic data, alignments can be assembled that greatly increase the number of informative sites for analysis of molecular divergence dates. Here, we present an estimate of the molecular divergence dates for all of the major primate groups. These date estimates are based on a Bayesian analysis of approximately 59.

Population history, biogeography, and taxonomy of orangutans (Genus: Pongo) based on a population genetic meta-analysis of multiple loci.

This paper examines orangutan population history and evolution through a meta-analysis of seven loci collected from both Sumatran and Bornean orangutans. Within orangutans, most loci show that the Sumatran population is about twice as diverse as the Bornean population. Orangutans are more diverse than African apes and humans.

The phylogenetic and evolutionary history of a novel alpha-globin-type gene in orangutans (Pongo pygmaeus).

The alpha-globin genes are implicated in human resistance to malaria, a disease caused by Plasmodium parasites. This study is the first to analyze DNA sequences from a novel alpha-globin-type gene in orangutans, a species affected by Plasmodium. Phylogenetic methods show that the gene is a duplication of an alpha-globin gene and is located 5' of alpha-2 globin.

The population genetics of the alpha-2 globin locus of orangutans (Pongo pygmaeus).

In this study, the molecular population genetics of the orangutan's alpha-2 globin (HBA2) gene were investigated in order to test for the action of natural selection. Haplotypes from 28 orangutan chromosomes were collected from a 1.46-kilobase region of the alpha-2 globin locus.

Genomic data support the hominoid slowdown and an Early Oligocene estimate for the hominoid-cercopithecoid divergence.

Several lines of indirect evidence suggest that hominoids (apes and humans) and cercopithecoids (Old World monkeys) diverged around 23-25 Mya. Importantly, although this range of dates has been used as both an initial assumption and as a confirmation of results in many molecular-clock analyses, it has not been critically assessed on its own merits. In this article we test the robusticity of the 23- to 25-Mya estimate with approximately 150,000 base pairs of orthologous DNA sequence data from two cercopithecoids and two hominoids by using quartet analysis.

Genetic sex identification in orangutans.

To date, no established protocol for genetic sex identification in orangutans (Pongo pygmaeus) exists. In nearly all apes (gibbons, gorillas, chimpanzees, and humans), genetic sex identification is possible using the amelogenin gene because copies located on X and Y chromosomes have different sizes. Here we report that orangutan sex identification can be resolved through multiplex polymerase chain reaction (PCR) of the Y-linked SRY locus and the amelogenin locus.

New World monkey phylogeny based on X-linked G6PD DNA sequences.

The Platyrrhini, or New World monkeys, are an infraorder of Primates comprised of 16 genera. Molecular phylogenetic analyses have consistently sorted these genera into three groups: the Pitheciidae (e.g.