Caro-Beth Stewart

Asian Primate Classification

In the foreseeable future there is little likelihood of achieving consensus on the number of Asian primate genera and species, and their subspecific composition. There is a more realistic hope of reaching agreement on the number of recognizable subspecies. The latter objective is more urgent because in order to reliably assess generic and specific numbers, it is essential that effective conservation measures are implemented for as many subspecies as possible. This cannot be comprehensively accomplished until their validity is assessed and they are satisfactorily established and defined. The Asian primate classification that we present is the outcome of electronic communication among the co-authors after a workshop, which was especially convened to attempt to determine the number of recognizable primate subspecies and to identify potentially recognizable subspecies. The generic and specific arrangement is a compromise that does not necessarily reflect the individual views of the co-authors: 183 subspecies in 77 species in 16 genera. The 31 subspecies allotted a low credibility rating are almost balanced by the 22 scientifically unnamed populations that may warrant subspecific status.

Primate evolution – in and out of Africa

Abstract A synthetic analysis of molecular, fossil and biogeographical data gives a remarkably consistent scenario for the evolution of the catarrhine primates – the hominoids and Old World monkeys. This analysis supports the African location of the common ancestor of the Old World monkeys, and suggests that the Asian colobine monkeys and macaques dispersed out of Africa into Eurasia within the past ten million years. More interestingly and controversially, this analysis further suggests that the lineage leading to the living hominoids dispersed out of Africa about twenty million years ago, and that the common ancestor of the living African apes, including humans, migrated back into Africa from Eurasia within about the past ten million years.

Successive radiations, not stasis, in the South American primate fauna

The earliest Neotropical primate fossils complete enough for taxonomic assessment, Dolichocebus, Tremacebus, and Chilecebus, date to approximately 20 Ma. These have been interpreted as either closely related to extant forms or as extinct stem lineages. The former hypothesis of morphological stasis requires most living platyrrhine genera to have diverged before 20 Ma. To test this hypothesis, we collected new complete mitochondrial genomes from Aotus lemurinus, Saimiri sciureus, Saguinus oedipus, Ateles belzebuth, and Callicebus donacophilus. We combined these with published sequences from Cebus albifrons and other primates to infer the mitochondrial phylogeny. We found support for a cebid/atelid clade to the exclusion of the pitheciids. Then, using Bayesian methods and well-supported fossil calibration constraints, we estimated that the platyrrhine most recent common ancestor (MRCA) dates to 19.5 Ma, with all major lineages diverging by 14.3 Ma. Next, we estimated catarrhine divergence dates on the basis of platyrrhine divergence scenarios and found that only a platyrrhine MRCA less than 21 Ma is concordant with the catarrhine fossil record. Finally, we calculated that 33% more change in the rate of evolution is required for platyrrhine divergences consistent with the morphologic stasis hypothesis than for a more recent radiation. We conclude that Dolichocebus, Tremacebus, and Chilecebus are likely too old to be crown platyrrhines, suggesting they were part of an extinct early radiation. We note that the crown platyrrhine radiation was concomitant with the radiation of 2 South American xenarthran lineages and follows a global temperature peak and tectonic activity in the Andes.

Evidence from Cameroon reveals differences in the genetic structure and histories of chimpanzee populations

The history of the genus Pan is a topic of enduring interest. Chimpanzees (Pan troglodytes) are often divided into subspecies, but the population structure and genetic history of chimpanzees across Africa remain unclear. Some population genetics studies have led to speculation that, until recently, this species constituted a single population with ongoing gene flow across its range, which resulted in a continuous gradient of allele frequencies. Chimpanzees, designated here as P. t. ellioti, occupy the Gulf of Guinea region that spans southern Nigeria and western Cameroon at the center of the distribution of this species. Remarkably, few studies have included individuals from this region, hindering the examination of chimpanzee population structure across Africa. Here, we analyzed microsatellite genotypes of 94 chimpanzees, including 32 designated as P. t. ellioti. We find that chimpanzees fall into three major populations: (i) Upper Guinea in western Africa (P. t. verus); (ii) the Gulf of Guinea region (P. t. ellioti); and (iii) equatorial Africa (P. t. troglodytes and P. t. schweinfurthii). Importantly, the Gulf of Guinea population is significantly different genetically from the others, sharing a last common ancestor with the populations in Upper Guinea ~0.46 million years ago (mya) and equatorial Africa ~0.32 mya. Equatorial chimpanzees are subdivided into up to three populations occupying southern Cameroon, central Africa, and eastern Africa, which may have constituted a single population until ~0.10–0.11 mya. Finally, occasional hybridization may be occurring between the Gulf of Guinea and southern Cameroon populations.

Episodic Evolution in the Stomach Lysozymes of Ruminants

SummaryBy sequencing lysozymesc from deer and pig stomachs and comparing them to the known amino acid sequences of other lysozymesc, it was possible to examine the rate of sequence change during and after the period in which this enzyme acquired a new function. Evolutionary tree analysis suggests that the rate went up while lysozyme was being recruited to function as a digestive enzyme in the stomach of early ruminants. Later, presumably after lysozyme was well adapted for functioning in the new environment, which contains acid, pepsin, and fermentation products, the rate of amino acid replacement became subnormal.

Molecular phylogeny and biogeography of langurs and leaf monkeys of South Asia (Primates: Colobinae)

The two recently proposed taxonomies of the langurs and leaf monkeys (Subfamily Colobinae) provide different implications to our understanding of the evolution of Nilgiri and purple-faced langurs. Groves (2001) [Groves, C.P., 2001. Primate Taxonomy. Smithsonian Institute Press, Washington], placed Nilgiri and purple-faced langurs in the genus Trachypithecus, thereby suggesting disjunct distribution of the genus Trachypithecus. [Brandon-Jones, D., Eudey, A.A., Geissmann, T., Groves, C.P., Melnick, D.J., Morales, J.C., Shekelle, M., Stewart, C.-B., 2003. Asian primate classification. Int. J. Primatol. 25, 97-162] placed these langurs in the genus Semnopithecus, which suggests convergence of morphological characters in Nilgiri and purple-faced langurs with Trachypithecus. To test these scenarios, we sequenced and analyzed the mitochondrial cytochrome b gene and two nuclear DNA-encoded genes, lysozyme and protamine P1, from a variety of colobine species. All three markers support the clustering of Nilgiri and purple-faced langurs with Hanuman langur (Semnopithecus), while leaf monkeys of Southeast Asian (Trachypithecus) form a distinct clade. The phylogenetic position of capped and golden leaf monkeys is still unresolved. It is likely that this species group might have evolved due to past hybridization between Semnopithecus and Trachypithecus clades.

A quick, direct method that can differentiate expressed mitochondrial genes from their nuclear pseudogenes

Direct sequencing of mitochondrial DNA (mtDNA) following amplification using the polymerase chain reaction (PCR) has found widespread use in population genetic and phylogenetic research over the past few years. Recently, nuclear copies of mitochondrial genes have been reported in diverse eukaryotic species, often confounding such research (reviewed in [2,3]). Under certain circumstances, nuclear pseudogenes can be amplified more efficiently than the intended mtDNA target, even when using as template mtDNA that has been purified by gradient centrifugation. If the transfer of the gene copy to the nucleus happened recently, it can be difficult-if not impossible-to identify the legitimate mitochondrial sequence. Here, we present a simple method that can identify expressed mitochondrial genes, using the cytochrome b gene of the particularly problematical proboscis monkey as an example. Because mtDNA is transcribed and processed into polyadenylated mRNAs reverse transcription coupled to PCR can be used to amplify the expressed mitochondrial version. This method produced an unambiguous sequence for the proboscis monkey mitochondrial cytochrome b gene; in contrast, traditional DNA-based PCR methods produced ambiguous sequence, because many nuclear pseudogenes were present. Phylogenetic analysis of the cytochrome b gene suggests that the proboscis monkey groups with the Asian langurs, rather than forming a sister taxon to all Asian and African colobines as was previously suggested. Reverse transcriptase-coupled PCR should be applicable to many other cases of nuclear transfer of mtDNA, including those involving ribosomal genes.

Comprehensive Analysis of Two Alu Yd Subfamilies

Alu elements have inserted in the human genome throughout primate evolution. A small number of Alu insertions have occurred after the divergence of humans from nonhuman primates and therefore should not be present in nonhuman primate genomes. Most of these recently integrated Alu elements are contained with a series of discrete Alu subfamilies that are related to each other based upon diagnostic nucleotide substitutions. We have extracted members of the Alu Yd subfamily that are derivatives of the Alu Y subfamily that share a common 12-bp deletion that defines the Yd lineage from the draft sequence of the human genome. Analysis of the Yd Alu elements resulted in the recovery of two new Alu subfamilies, Yd3 and Yd6, which contain a total of 295 members (198 Yd3 and 97 Yd6). DNA sequence analysis of each of the Alu Yd subfamilies yielded age estimates of 8.02 and 1.20 million years old for the Alu Yd3 and Yd6 subfamilies, respectively. Two hundred Alu Yd3 and Yd6 loci were screened using polymerase chain reaction (PCR) assays to determine their phylogenetic origin and associated levels of human genomic diversity. The Alu Yd3 subfamily appears to have started amplifying relatively early in primate evolution and continued propagating albeit at a low level as many of its members are found in a variety of hominoid (humans, greater and lesser ape) genomes. Only two of the elements are polymorphic in the human genome and absent from the genomes of nonhuman primates. By contrast all of the members of the Alu Yd6 subfamily are restricted to the human genome, with 12% of the elements representing insertion polymorphisms in human populations. A single Alu Yd6 locus contained an independent parallel forward insertion of a paralogous Alu Sq sequence in the owl monkey. These Alu subfamilies are a source of genomic fossil relics for the study of primate phylogenetics and human population genetics.

Xenopus laevis peripherin (XIF3) is expressed in radial glia and proliferating neural epithelial cells as well as in neurons

Neuronal intermediate filament (nIF) proteins form the most abundant component of the axonal cytoskeleton. Thus, understanding their function and the regulation of their expression is essential for comprehending how axonal structure is regulated. Although most vertebrate nIF proteins are classified as type IV intermediate filament (IF) proteins, additional nIF proteins exist in frogs (Xenopus laevis), cyprinid fishes, and mammals (called XIF3, plasticin, and peripherin, respectively) that are classified as type III. Expression of a type III nIF protein is correlated strongly with the earliest phases of axonal outgrowth in fishes but less so in mammals. To understand better how the correlation between type III nIF protein expression and early phases of axonal outgrowth has changed during evolution, the authors examined XIF3 expression in Xenopus laevis. In Xenopus, the association between XIF3 expression and early axonal outgrowth was especially strong. For example, during early axonal development, XIF3 expression preceded and was more abundant and widespread than that of any of the type IV nIF proteins. As axons matured, neuronal expression of XIF3 gradually became more restricted while that of type IV nIF proteins increased. These results support the idea that type III nIF proteins play a special role during early phases of axonal outgrowth. In addition to finding XIF3 in neurons, the authors also unexpectedly found it in regions of the central nervous system that contain proliferating cells and radial glia. As a framework for interpreting variations in nIF expression in different vertebrate species, the authors built phylogenetic trees to clarify relationships among vertebrate nIF proteins. These trees supported the classification of XIF3, plasticin, and peripherin as orthologs (products of the same genetic locus, evolving separately only since the species lineages diverged). Thus, XIF3, plasticin, and peripherin probably should be referred to as Xenopus, fish, and mammalian peripherin, respectively. This finding argues that differences in expression of these three proteins in frogs, fishes, and mammals are the result of regulatory changes to the peripherin ancestral gene along each lineage. The expression of a peripherin ortholog in Xenopus glia may represent either an adaptation that arose since the divergence of Xenopus from mammals or, alternatively, a feature retained from an ancestral IF protein that was expressed originally both in neurons and in glia. J. Comp. Neurol. 423:512–531, 2000.

Evolution of the mammalian lysozyme gene family

BackgroundLysozyme c (chicken-type lysozyme) has an important role in host defense, and has been extensively studied as a model in molecular biology, enzymology, protein chemistry, and crystallography. Traditionally, lysozyme c has been considered to be part of a small family that includes genes for two other proteins, lactalbumin, which is found only in mammals, and calcium-binding lysozyme, which is found in only a few species of birds and mammals. More recently, additional testes-expressed members of this family have been identified in human and mouse, suggesting that the mammalian lysozyme gene family is larger than previously known.ResultsHere we characterize the extent and diversity of the lysozyme gene family in the genomes of phylogenetically diverse mammals, and show that this family contains at least eight different genes that likely duplicated prior to the diversification of extant mammals. These duplicated genes have largely been maintained, both in intron-exon structure and in genomic context, throughout mammalian evolution.ConclusionsThe mammalian lysozyme gene family is much larger than previously appreciated and consists of at least eight distinct genes scattered around the genome. Since the lysozyme c and lactalbumin proteins have acquired very different functions during evolution, it is likely that many of the other members of the lysozyme-like family will also have diverse and unexpected biological properties.