Faculty Bibliography

Rod visual pigment genes have been studied in a wide range of vertebrates including a number of mammalian species. However, no marsupials have yet been examined. To correct this omission, we have studied the rod pigments in two marsupial species, the nocturnal and frugivorous bare-tailed woolly opossum, Caluromys philander, from Central and South America, and the arhythmic and insectivorous fat-tailed dunnart, Sminthopsis crassicaudata, from Australia. Phylogenetic analysis establishes that the cloned opsin sequences are orthologues of rod opsin genes from other vertebrate species. The deduced amino acid sequences show that both possess glutamate at residue 122, a feature of rod opsins, and the corresponding gene follows the typical vertebrate rod opsin pattern of five exons separated by four introns. Compared to other vertebrates, a stretch of five residues near the C-terminus is deleted in the rod opsin of both marsupials and all eutherian mammals. From microspectrophotometric measurements, the pigments in the two species show an 8 nm difference in peak absorbance; the molecular basis for this spectral shift is discussed and two candidate substitutions are identified.

Trichromacy in all Old World primates is dependent on separate X-linked MW and LW opsin genes that are organized into a head-to-tail tandem array flanked on the upstream side by a locus control region (LCR). The 5' regions of these two genes show homology for only the first 236 bp, although within this region, the differences are conserved in humans, chimpanzees, and two species of cercopithecoid monkeys. In contrast, most New World primates have only a single polymorphic X-linked opsin gene; all males are dichromats and trichromacy is achieved only in those females that possess a different form of this gene on each X chromosome. By sequencing the upstream region of this gene in a New World monkey, the marmoset, we have been able to demonstrate the presence of an LCR in an equivalent position to that in Old World primates. Moreover, the marmoset sequence shows extensive homology from the coding region to the LCR with the upstream sequence of the human LW gene, a distance of >3 kb, whereas homology with the human MW gene is again limited to the first 236 bp, indicating that the divergent MW sequence identifies the site of insertion of the duplicated gene. This is further supported by the presence of an incomplete Alu element on the upstream side of this insertion point in the MW gene of both humans and a cercopithecoid monkey, with additional Alu elements present further upstream. Therefore, these Alu elements may have been involved in the initial gene duplication and may also be responsible for the high frequency of gene loss and gene duplication within the opsin gene array. Full trichromacy is present in one species of New World monkey, the howler monkey, in which separate MW and LW genes are again present. In contrast to the separate genes in humans, however, the upstream sequences of the two howler genes show homology with the marmoset for at least 600 bp, which is well beyond the point of divergence of the human MW and LW genes, and each sequence is associated with a different LCR, indicating that the duplication in the howler monkey involved the entire upstream region. [The sequence data described in this paper have been submitted to GenBank under accession nos. AF155218, AF156715, and AF156716.]

In order to test hypotheses about the phylogenetic relationships among living genera of New World monkeys, 1.3 kb of DNA sequence information was collected for two introns of the glucose-6-phosphate dehydrogenase (G6PD) locus, encoded on the X chromosome, for 24 species of New World monkeys. These data were analyzed using a maximum parsimony algorithm. The strict consensus of the three most-parsimonious gene trees that result shows support for the following clades: a pitheciine clade including Callicebus within which Chiropotes and Cacajao are sister taxa, an Alouatta-atelin clade within which Brachyteles is the sister taxon of Lagothrix and which is sister to another clade containing the callitrichines, and a callitrichine/Aotus/Cebus/Saimiri clade. Within the callitrichines, Callimico is the sister taxon of Callithrix. Cebus and Saimiri form a clade. These results are broadly consistent with previously published DNA sequence analyses of platyrrhine phylogeny and provide additional support for groupings provisionally proposed in those earlier studies. Nevertheless, questions remain as to the relative phylogenetic placement of Leontopithecus and Saguinus, the branching order within the Aotus/Cebus/Saimiri/callitrichine clade, and the placement of the pitheciine clade relative to the atelines and the callitrichines.

Here we present a DNA sequence study that incorporates intraspecific variation from all five genera of hominoids (apes and humans). Recently it has been claimed that using single individuals to analyze species' relationships might be misleading if within-species variation is great. Our results indicate that despite high intraspecific variation in mitochondrial cytochrome oxidase subunit II gene sequences of some hominoids, humans and chimpanzees are nonetheless significantly most closely related. We also report the observation that variation within the gorilla species exceeds that between common and pygmy chimpanzee species, a finding with implications for conservation. In contrast, humans are less mitochondrially diverse than lowland gorillas inhabiting western Africa.

Although there is evidence for reduced fertility in Andean and Himalayan populations at higher altitudes, factors other than hypoxia may be primarily responsible. A valuable approach in the investigation of these fertility determinants is the use of salivary steroid assays. However, coca-leaf chewing--a ubiquitous practice among high altitude Andean populations--has negative consequences for the accurate measurement of ovarian steroids. This report evaluates the effects of coca-leaf chewing on assays of salivary progesterone. Study participants include naive and habitual users of coca leaf from La Paz and El Alto, Bolivia. Approximately 300 saliva samples were collected immediately before, during, and after coca-leaf chewing. The series includes samples with and without the alkaloid enhancer typically used by coca-leaf chewers. Coca chewing produces false salivary progesterone values that mimic luteal phase values. On the basis of this study, an appropriate protocol is developed for the collection of salivary samples in coca-leaf chewing populations. These results verify the feasibility of salivary assays, even for very difficult field conditions, and highlight the necessity of establishing suitable collection procedures before full field implementation of saliva sampling.

The aim of this study is to measure human mitochondrial sequence variability in the relatively slowly evolving mitochondrial gene cytochrome oxidase subunit II (COII) and to estimate when the human common ancestral mitochondrial type existed. New COII gene sequences were determined for five humans (Homo sapiens), including some of the most mitochondrially divergent humans known; for two pygmy chimpanzees (Pan paniscus); and for a common chimpanzee (P. troglodytes). COII sequences were analyzed with those from another relatively slowly evolving mitochondrial region (ND4-5). From class 1 (third codon position) sequence data, a relative divergence date for the human mitochondrial ancestor is estimated as 1/27 th of the human-chimpanzee divergence time. If it is assumed that humans and chimpanzees diverged 6 Mya, this places a human mitochondrial ancestor at 222,000 years, significantly different from 1 Myr (the presumed time of an H. erectus emergence from Africa). The mean coalescent time estimated from all 1,580 sites of combined mitochondrial data, when a 6-Mya human-chimpanzee divergence is assumed, is 298,000 years, with 95% confidence interval of 129,000-536,000 years. Neither estimate is compatible with a 1-Myr-old human mitochondrial ancestor. The mitochondrial DNA sequence data from COII and ND4-5 regions therefore do not support this multiregional hypothesis for the emergence of modern humans.