Calvin A. Porter

Mammalian Evolution and the Interphotoreceptor Retinoid Binding Protein (IRBP) Gene: Convincing Evidence for Several Superordinal Clades

Phylogenetic relationships of 25 mammalian species representing 17 of the 18 eutherian orders were examined using DNA sequences from a 1.2-kb region of the 5′ end of exon 1 of the single-copy nuclear gene known as interphotoreceptor retinoid binding protein (IRBP). A wide variety of methods of analysis of the DNA sequence, and of the translated products, all supported a five-order clade consisting of elephant shrew (Macroscelidea)/aardvark (Tubulidentata)/and the paenungulates (hyracoids, sirenians, and elephants), with bootstrap support in all cases of 100%. The Paenungulata was also strongly supported by these IRBP data. In the majority of analyses this monophyletic five-order grouping was the first branch off the tree after the Edentata. These results are highly congruent with two other recent sources of molecular data. Another superordinal grouping, with similar 100% bootstrap support in all of the same wide-ranging types of analyses, was Artiodactyla/Cetacea. Other superordinal affinities, suggested by the analyses, but with less convincing support, included a Perissodactyla/Artiodactyla/Cetacea clade, an Insectivora/Chiroptera clade, and Glires (an association of rodents and lagomorphs).

Phylogeny and Evolution of Selected Primates as Determined by Sequences of the ε-Globin Locus and 5′ Flanking Regions

We studied phylogenetic relationships of 39 primate species using sequences of the ε-globin gene. For 13 species, we also included flanking sequences 5′ of this locus. Parsimony analyses support the association of tarsiers with the anthropoids. Our analysis of New World monkeys supports the model in which the callitrichines form a clade with Aotus, Cebus, and Saimiri, with Cebus and Saimiri being sister taxa. However, analysis of the 5′ flanking sequences did not support grouping the atelines with Callicebus and the pitheciins. Our data support the classification of platyrrhines into three families, Cebidae (consisting of Cebus, Saimiri, Aotus, and the callitrichines; Atelidae—the atelines; and Pitheciidae—Callicebus and the pithiciins. The strepsirhines form well-defined lemuroid and lorisoid clades, with the cheirogaleids (dwarf and mouse lemurs) and Daubentonia (aye-aye) in the lemuroids, and the aye-aye being the most anciently derived. These results support the hypothesis that nonhuman primates of Madagascar descended from a single lineage. Local molecular clock calculations indicate that the divergence of lemuroid and lorisoid lineages, and the earliest diversification of lemuroids, occurred during the Eocene. The divergence of major lorisoid lineages was probably considerably more recent, possibly near the Miocene–Oligocene boundary. Within hominoids some estimated dates differ somewhat from those found with more extensive noncoding sequences in the β-globin cluster.

Two related G protein-coupled receptors: The distribution of GPR7 in rat brain and the absence of GPR8 in rodents

GPR7 and GPR8, orphan G protein-coupled receptor (GPCR) genes, expressed in the brain and periphery share highest sequence identity to each other and significant similarity with opioid and somatostatin receptors. To further our knowledge of GPR7s physiological function, we performed in situ hybridization analyses of rat brain to reveal specific patterns of expression in the brain. GPR7 mRNA was found to be discretely localized in areas of the amygdala, hippocampus, hypothalamus and cortex. We previously reported that GPR7 was highly conserved in both human and rodent orthologs while GPR8 was not found in the rodent [9]. We speculated that GPR8 originated after the divergence of the human and rodent. Using primers designed from human GPR8, we isolated lemur GPR8 and subsequently aligned human, monkey, and lemur GPR8 orthologs to design primers recognizing highly conserved regions of GPR8. Using these primers, orthologs of GPR7 and GPR8 were isolated by the PCR from rabbit, tree shrew, and flying lemur, as well as GPR7 in the rat. Subsequent analysis of the clones obtained demonstrated that both GPR7 and GPR8 sequences were highly conserved amongst the species studied, but a rodent GPR8 was not isolated. The absence of a GPR8 gene in the rodent suggests that GPR8 originated from gene duplication of GPR7 after the rodent line diverged from the rabbit, tree shrew, flying lemur, lemur, monkey and human lines. In addition, the taxonomic distribution of GPR8 is consistent with molecular studies grouping rabbits with primates, tree shrews and flying lemurs rather than with rodents.

Evidence on primate phylogeny from epsilon-globin gene sequences and flanking regions.

Phylogenetic relationships among various primate groups were examined based on sequences of ε-globin genes. ε-globin genes were sequenced from five species of strepsirhine primates. These sequences were aligned and compared with other known primate ε-globin sequences, including data from two additional strepsirhine species, one species of tarsier, 19 species of New World monkeys (representing all extant genera), and five species of catarrhines. In addition, a 2-kb segment upstream of the ε-globin gene was sequenced in two of the five strepsirhines examined. This upstream sequence was aligned with five other species of primates for which data are available in this segment. Domestic rabbit and goat were used as outgroups. This analysis supports the monophyly of order Primates but does not support the traditional prosimian grouping of tarsiers, lorisoids, and lemuroids; rather it supports the sister grouping of tarsiers and anthropoids into Haplorhini and the sister grouping of lorisoids and lemuroids into Strepsirhini. The mouse lemur (Microcebus murinus) and dwarf lemur (Cheirogaleus medius) appear to be most closely related to each other, forming a clade with the lemuroids, and are probably not closely related to the lorisoids, as suggested by some morphological studies. Analysis of the ε-globin data supports the hypothesis that the aye-aye (Daubentonia madagascariensis) shares a sister-group relationship with other Malagasy strepsirhines (all being classified as lemuroids). Relationships among ceboids agree with findings from a previous ε-globin study in which fewer outgroup taxa were employed. Rates of molecular evolution were higher in lorisoids than in lemuroids.

Normal disjunction in Robertsonian heterozygotes from a highly polymorphic lizard population

A single population of the iguanid lizard, Sceloporus grammicus, was found to have fission polymorphisms in three of four metacentric macrochromosome pairs. This variation resulted in eight different karyotypes in a sample of 24 lizards. Of these 24 lizards, 7 were single heterozygotes, 11 were double heterozygotes, and 1 was a triple heterozygote. Meiotic analyses of males heterozygous for different combinations of fissions indicated completely normal disjunction and production of chromosomally balanced gametes. The polymorphisms in this population did not appear to deviate strongly from Hardy-Weinberg equilibrium. There was no evidence of selection against chromosomal heterozygotes in this population.

Population Cytogenetics and Evolution of the Sceloporus grammicus Complex (Iguanidae) in Central Mexico

Chromosomal phenotypes were scored from 786 individuals of the Sceloporus gram- micus complex collected from 55 localities in central Mexico, bringing the total to 1383 individuals from 93 localities. Variable chromosomal pairs were coded as Mendelian genotypes and statistically summarized by several clustering and population-genetic algorithms. UPGMA dendrograms were used to group all samples from pairwise genetic distance or similarity matrices, and consistently identified seven discrete groups. These findings confirm and extend results of an earlier population cytogenetics study and provide data necessary to complete distributional maps for some cytotypes. The fine resolution collecting and mapping efforts revealed several additional zones of parapatric hybridization between different cytotypes and brings the total number of hybrid zones identified from chromosomal markers to seven. Several other populations are highly polymorphic for chro- mosomal rearrangements and occur at or near the edges of ranges of particular cytotypes; this suggests that they may represent additional hybrid zones. These populations also contain high frequencies of apparent fusion rearrangements, which are very rare or absent elsewhere, and we suggest that these mutations may be manifestations of the dysgenic effects of hybridization. Population-genetic structures were estimated for all cytotypes on the basis of the distributions and frequencies of chromosomal rearrangements. A hierarchical F statistics analysis showed that most of the overall chromosomal variation could be partitioned into the within-cytotype component (67%) relative to that between cytotypes (33%). Inbreeding coefficients show that most samples do not deviate significantly from random-mating proportions, and in the few cases where they do, the direction is always toward heterozygote excess. Some cytotypes show significant between-sample heterogeneity in chromosomal rearrangement frequencies, and spatial autocorrelation analyses produced correlograms suggesting an isolation-by-distance structure for some cytotypes, and a random pattern in others in which drift was probably the overriding force. Patterns of chromosomal variation and inferred population structure are discussed with respect to implications for several hypotheses of chromosomal evolution and speciation.

Systematics of Vampyressa and Related Genera of Phyllostomid Bats as Determined by Cytochrome-b Sequences

Abstract The phyllostomid bat genus Vampyressa often has been allied with Uroderma, Chiroderma, Platyrrhinus, Vampyrodes, and Mesophylla. However, the relationships among the genera have proven difficult to resolve, and a number of studies have suggested that Vampyressa is not monophyletic. Mesophylla includes a single species, which some taxonomists have placed in Vampyressa and others in the more distantly related genus Ectophylla. Our analysis of sequence data from the cytochrome-b gene (Cytb) gives strong support for Mesophylla being closely related to Vampyressa, rather than Ectophylla. Examination of the Cytb data indicates that Vampyressa pusilla and Mesophylla are members of a lineage distinct from V. bidens and V. brocki. Therefore, we recognize the genus Vampyriscus for V. brocki and V. bidens. Brazilian specimens of V. pusilla are strongly divergent from specimens from elsewhere in Latin America. The degree of genetic distance indicates species-level divergence between these taxa, and supports the recent recognition of Vampyressa thyone for the northern populations.

c-Myc Gene Sequences and the Phylogeny of Bats and Other Eutherian Mammals

The complete protein-coding sequences of the c-myc proto-oncogene were determined for five species of four new orders of eutherian (placental) mammals. These newly obtained sequences were aligned to each other and to other available orthologs for the phylogenetic estimation of eutherian interordinal relationships. Several measures of sequence difference and base composition were first calculated to assess the major evolutionary properties of the three codon positions and two protein-coding exons of the gene. On the basis of these calculations, different parsimony, distance, and maximum likelihood approaches were adopted, with the most sophisticated involving the separate, then combined, likelihood analyses of the third codon positions of exon 2 versus all other sites. These phylogenetic approaches provided clear support for the grouping of Chiroptera (bats) with Artiodactyla (ruminants, camels, and pigs) and Carnivora (cats, dogs, and their allies), an interordinal arrangement that receives strong corroboration from other lines of evidence including complete mitochondrial DNA sequences. In contrast, these analyses failed to provide strong to reasonable support for any other interordinal group. This study concludes with specific recommendations about sampling and other strategies for maximizing the phylogenetic contributions of the c-myc gene to the continued resolution of the eutherian ordinal tree.

Evolution and Phylogenetic Significance of Ribosomal Gene Location in Chromosomes of Squamate Reptiles

Using in situ hybridization with a biotin-labeled probe, we determined the chromosomal location of ribosomal genes in 56 species of squamate reptiles, including representatives of nine major taxa. Where possible, these data were examined in a phylogenetic context, and in several cases they provided phylogenetically useful shared derived character states. The ribosomal genes in Sceloporus variabilis are found on a single pair of microchromosomes, which seems to be primitive for the phrynosomatids. In the remainder of species of Sceloporus we examined, the ribosomal genes are found on the long arm of pair 2. We also found that Holbrookia, Cophosaurus, and Callisaurus share a derived condition not found in Uma. Two species of the viperid genus Agkistrodon share a condition that may be derived relative to other pit vipers. A third species of Agkistrodon differs from all other reptiles we examined in that ribosomal genes are located on the sex chromosomes. Location of rDNA also provides systematic information in several other clades of squamates.

SYSTEMATICS OF ROUND-EARED BATS (TONATIA AND LOPHOSTOMA) BASED ON NUCLEAR AND MITOCHONDRIAL DNA SEQUENCES

Abstract We examined the systematics of round-eared bats (Tonatia and Lophostoma) using sequence data from the nuclear recombination activator gene-2 (Rag2) gene and the mitochondrial valine transfer RNA, 12S ribosomal RNA (rRNA), and 16S rRNA. Some analyses of the mitochondrial and combined data sets indicate that round-eared bats may be paraphyletic relative to the genera Phyllostomus, Phylloderma, and Mimon. Both nuclear and mitochondrial data sets indicate substantial genetic divergence between Tonatia and Lophostoma, and neither data set unambiguously demonstrates monophyly of round-eared bats. However, our analyses cannot exclude the possibility that round-eared bats form a monophyletic lineage that separated anciently into Tonatia and Lophostoma. Within the Tonatia lineage, T. bidens and T. saurophila are sister taxa but are divergent for both nuclear and mitochondrial sequences. Nuclear data suggest that L. silvicolum may be paraphyletic, as currently recognized, because L. evotis appears within this clade.