Small changes, big results: evolution of morphological discontinuity in mammals

Comparative morphological and developmental studies, including a recent comparative study of tooth development among the Afrotherian mammals, are indicating the types of genetic mechanisms responsible for the evolution of morphological differences among major mammalian groups

Site specific rates of mitochondrial genomes and the phylogeny of eutheria

BACKGROUND: Traditionally, most studies employing data from whole mitochondrial genomes to diagnose relationships among the major lineages of mammals have attempted to exclude regions that potentially complicate phylogenetic analysis. Components generally excluded are 3(rd )codon positions of protein-encoding genes, the control region, rRNAs, tRNAs, and the ND6 gene (encoded on the opposite strand). We present an approach that includes all the data, with the exception of the control region. This approach is based on a site-specific rate model that accommodates excessive homoplasy and that utilizes secondary structure as a reference for proper alignment of rRNAs and tRNAs. RESULTS: Mitochondrial genomic data for 78 eutherian mammals, 8 metatherians, and 3 monotremes were analyzed with a Bayesian analysis and our site specific rate model. The resultant phylogeny revealed strong support for most nodes and was highly congruent with more recent phylogenies based on nuclear DNA sequences. In addition, many of the conflicting relationships observed by earlier mitochondrial-based analyses were resolved without need for the exclusion of large subsets of the data. CONCLUSION: Rather than exclusion of data to minimize presumed noise associated with non-protein encoding genes in the mitochondrial genome, our results indicate that selection of an appropriate model that accommodates rate heterogeneity across data partitions and proper treatment of RNA genes can result in a mitochondrial genome-based phylogeny of eutherian mammals that is reasonably congruent with recent phylogenies derived from nuclear genes

Multi-locus phylogeny of dolphins in the subfamily Lissodelphininae: character synergy improves phylogenetic resolution

BACKGROUND: Dolphins of the genus Lagenorhynchus are anti-tropically distributed in temperate to cool waters. Phylogenetic analyses of cytochrome b sequences have suggested that the genus is polyphyletic; however, many relationships were poorly resolved. In this study, we present a combined-analysis phylogenetic hypothesis for Lagenorhynchus and members of the subfamily Lissodelphininae, which is derived from two nuclear and two mitochondrial data sets and the addition of 34 individuals representing 9 species. In addition, we characterize with parsimony and Bayesian analyses the phylogenetic utility and interaction of characters with statistical measures, including the utility of highly consistent (non-homoplasious) characters as a conservative measure of phylogenetic robustness. We also explore the effects of removing sources of character conflict on phylogenetic resolution. RESULTS: Overall, our study provides strong support for the monophyly of the subfamily Lissodelphininae and the polyphyly of the genus Lagenorhynchus. In addition, the simultaneous parsimony analysis resolved and/or improved resolution for 12 nodes including: (1) L. albirostris, L. acutus; (2) L. obscurus and L. obliquidens; and (3) L. cruciger and L. australis. In addition, the Bayesian analysis supported the monophyly of the Cephalorhynchus, and resolved ambiguities regarding the relationship of L. australis/L. cruciger to other members of the genus Lagenorhynchus. The frequency of highly consistent characters varied among data partitions, but the rate of evolution was consistent within data partitions. Although the control region was the greatest source of character conflict, removal of this data partition impeded phylogenetic resolution. CONCLUSION: The simultaneous analysis approach produced a more robust phylogenetic hypothesis for Lagenorhynchus than previous studies, thus supporting a phylogenetic approach employing multiple data partitions that vary in overall rate of evolution. Even in cases where there was apparent conflict among characters, our data suggest a synergistic interaction in the simultaneous analysis, and speak against a priori exclusion of data because of potential conflicts, primarily because phylogenetic results can be less robust. For example, the removal of the control region, the putative source of character conflict, produced spurious results with inconsistencies among and within topologies from parsimony and Bayesian analyses

Multi-locus phylogeography of the dusky dolphin (Lagenorhynchus obscurus): passive dispersal via the west-wind drift or response to prey species and climate change?

<p>Abstract</p> <p>Background</p> <p>The dusky dolphin (<it>Lagenorhynchus obscurus</it>) is distributed along temperate, coastal regions of New Zealand, South Africa, Argentina, and Peru where it feeds on schooling anchovy, sardines, and other small fishes and squid tightly associated with temperate ocean sea surface temperatures. Previous studies have suggested that the dusky dolphin dispersed in the Southern Hemisphere eastward from Peru via a linear, temperate dispersal corridor provided by the circumpolar west-wind drift. With new mitochondrial and nuclear DNA sequence data, we propose an alternative phylogeographic history for the dusky dolphin that was structured by paleoceanographic conditions that repeatedly altered the distribution of its temperate prey species during the Plio-Pleistocene.</p> <p>Results</p> <p>In contrast to the west-wind drift hypothesis, phylogenetic analyses support a Pacific/Indian Ocean origin, with a relatively early and continued isolation of Peru from other regions. Dispersal of the dusky dolphin into the Atlantic is correlated with the history of anchovy populations, including multiple migrations from New Zealand to South Africa. Additionally, the cooling of the Eastern Equatorial Pacific led to the divergence of anchovy populations, which in turn explains the north-south equatorial transgression of <it>L. obliquidens </it>and the subsequent divergence of <it>L. obscurus </it>in the Southern Hemisphere.</p> <p>Conclusion</p> <p>Overall, our study fails to support the west-wind drift hypothesis. Instead, our data indicate that changes in primary productivity and related abundance of prey played a key role in shaping the phylogeography of the dusky dolphin, with periods of ocean change coincident with important events in the history of this temperate dolphin species. Moderate, short-term changes in sea surface temperatures and current systems have a powerful effect on anchovy populations; thus, it is not infeasible that repeated fluctuations in anchovy populations continue to play an important role in the history of coastal dolphin populations.</p

Phylogeography of Scaled Quail

Scaled quail (Callipepla squamata) are distributed over much of the Chihuahuan Desert in the United States and south into central Mexico. Four subspecies have been described based on slight variations in coloration and body size, but the distinctiveness of the subspecies is unknown. We conducted a range-wide phylogeographic analysis of scaled quail based on the mitochondrial control region (D-loop). Our objectives were to: (1) ascertain the overall genetic diversity, (2) examine the phylogeographic structure of the scaled quail, and (3) examine the genetic distinctiveness of its 4 subspecies. We obtained D-loop sequences from 190 hunter-harvested wings and 38 museum specimens. Haplotype diversity (Hd 1⁄4 0.386) and nucleotide diversity (p 1⁄4 0.002) were relatively low. We found 16 D- loop haplotypes, 5 of which were shared by 2 or more subspecies. Haplotype A (carried by 178 individuals) was most widespread and occurred in nearly every population. Analysis of molecular variance revealed that most of the genetic variation in scaled quail occurred within populations rather than among subspecies. The low levels of genetic diversity probably reflect a historically restricted distribution within the Chihuahuan Desert, and wide geographic distribution of some haplotypes implies expansion from a single refugium. Our data indicate the scaled quail subspecies probably do not represent historically independent units. Phenotypic-based subspecies should not be used as proxies for management units if preserving genetic diversity and evolutionary potential is a goal of management, unless molecular data demonstrate the subspecies represent genetically distinct entities. Our data support viewing the entire species as a single management unit

Phylogeography of Bobwhites

Bobwhites (Colinus spp.) are a widely distributed genus of New World quails. Four species are recognized with a geographic range spanning the eastern United States to northern South America. The northern bobwhite (C. virginianus) historically occurred throughout much of the eastern United States and eastern Mexico with disjunct populations in Sonora and Cuba. The Yucata ́n bobwhite (C. nigrogularis) occurs in allopatric populations in Nicaragua and Honduras, and on the Yucata ́n Peninsula. The spot-bellied and crested bobwhites (C. leucopogon and C. cristatus) constitute a species complex with the spot-bellied bobwhite distributed from Guatemala to Costa Rica, and the crested bobwhite from Panama to northern Brazil. The 4 species exhibit substantial intraspecific variation, and up to 56 subspecies are recognized among Colinus largely on the basis of geographic distribution and male plumage coloration. However, relationships within and among species have not been studied in detail. We sampled museum study skins and obtained DNA sequences from mitochondrial control region and ND2 genes. We used concatenated sequences of control region and ND2 to investigate relationships among the bobwhite species, and the control region to assess the geographic distribution of genetic variation within each species. Maximum likelihood analysis of bobwhite phylogeny revealed Colinus is composed of two deeply divergent lineages, one clade of northern and Yucata ́n bobwhites and another of spot-bellied and crested bobwhites. The Yucata ́n bobwhite was genetically distinct from the northern bobwhite. The Yucata ́n bobwhite was composed of 2 distinct subclades, one confined to the Yucata ́n Peninsula and another occurring in Nicaragua. The genetic data showed the spot-bellied bobwhite is closely related to the crested bobwhite, but did not reveal clear support for 2 distinct species. The crested bobwhite was composed of 3 distinct lineages: a western clade that occurs in Panama and west of the northern Andes in Venezuela and Colombia, an eastern clade concentrated in Venezuela (east of the Andes), and a clade restricted to northern Brazil. We found 58 control region haplotypes, of which 29 were shared among 2 northern bobwhite subspecies and 5 haplotypes were especially geographically widespread. We found 16 haplotypes in the Yucata ́n bobwhite with 4 restricted to the Yucata ́n Peninsula and shared among the 3 subspecies found there, and 3 other haplotypes restricted to the Nicaraguan subspecies. The spot-bellied bobwhite did not share haplotypes with any of the 3 crested bobwhite subclades. We found little phylogeographic structure within the spot-bellied bobwhite, and 2 of the 5 haplotypes occurred across much of the species’ range and were shared among the 6 subspecies. The crested bobwhite exhibited strong phylogeographic structure and a lack of shared haplotypes among subspecies. The 20 haplotypes of the crested bobwhite were distributed unevenly among its 3 clades: 2 haplotypes in the Brazilian clade, 6 in the eastern clade, and 12 in the western clade. The weak phylogeographic structure and geographically widespread haplotypes of the northern bobwhite suggests large effective population size and gene flow among subspecies. The deep phylogeographic breaks within the Yucata ́n bobwhite and the spot-bellied bobwhite-crested bobwhite complex may be due to changes in the availability of suitable habitat and geological events during the Pleistocene. The lack of geographically distinct groups within the northern bobwhite implies that many subspecies may not provide good management units. Our data support the continued recognition of the Yucata ́n bobwhite as a distinct species. The 2 intraspecific groups identified in the Yucata ́n and the 4 groups within the spot- bellied/crested bobwhite complex may each represent discrete management units. Further assessment of the phylogenetic relationships and the phylogeography of the bobwhite species is warranted to clarify the phylogeny of Colinus

Diet-Morphology Correlations in the Radiation of South American Geophagine Cichlids (Perciformes: Cichlidae: Cichlinae)

Genera within the South American cichlid tribe Geophagini display specialized feeding and reproductive strategies, with some taxa specialized for both substrate-sifting and mouth brooding. Several lineages within the clade also possess an epibranchial lobe (EBL), a unique pharyngeal structure that has been proposed to have a function in feeding and/or mouth brooding. A recently published genus-level phylogeny of Neotropical cichlids was used as the evolutionary framework for investigating the evolution of morphological features presumably correlated with diet and mouth brooding in the tribe Geophagini. We tested for possible associations between the geophagine epibranchial lobe and benthic feeding and mouth brooding. We also addressed whether the EBL may be associated with unique patterns of diversification in certain geophagine clades. Tests of binary character correlations revealed the EBL was significantly associated with mouth brooding. We also tested for a relationship between diet and morphology. We analyzed stomach contents and morphometric variation among 21 species, with data for two additional species obtained from the literature. Principal Components Analysis revealed axes of morphological variation significantly correlated with piscivory and benthivory, and both morphology and diet were significantly associated with phylogeny. These results suggest that the EBL could be an adaptation for either feeding or mouth brooding. The EBL, however, was not associated with species richness or accelerated rates of phyletic diversification

Restocking Northern Bobwhites in East Texas: A Genetic Assessment

Habitat on a 610-ha study area in the Pineywoods Ecological Region of eastern Texas was enhanced for northern bobwhites ( Coli nus virginianus). In February and March 1990, 1991, and 1992, bobwhites from south Texas (C. v. texanus) and disjunct areas of east Texas (C. v. mexicanus) were captured, radio tagged, and relocated to the study area which had a small ( \u3c25 birds) resident population. Blood samples were collected from the birds relocated in 1991. Samples were also collected from birds in the resident population during 1991 and 1992; these birds were assumed to be offspring of the previous years\u27 resident and relocated bobwhites. Restriction site variation of mitochondrial DNA (mtDNA) revealed geographic subdivision between the subspecies but not between resident and east Texas relocated birds. The observed frequency differences of mtDNA haplotypes were used to assess the relative reproductive success of the 2 subspecies. Among the birds examined for mtDNA variation, offspring produced on the study area during 1990 and 1991 were genetically more similar to the east Texas subspecies than to the south Texas subspecies. These results suggest that efforts to restock northern bobwhite should involve either local birds or birds from the same subspecies. Management implications of these findings are discussed

Mammalian mitochondrial DNA evolution: A comparison of the cytochrome b and cytochrome c oxidase II genes

The evolution of two mitochondrial genes, cytochrome b and cytochrome c oxidase subunit II, was examined in several eutherian mammal orders, with special emphasis on the orders Artiodactyla and Rodentia. When analyzed using both maximum parsimony, with either equal or unequal character weighting, and neighbor joining, neither gene performed with a high degree of consistency in terms of the phylogenetic hypotheses supported. The phylogenetic inconsistencies observed for both these genes may be the result of several factors including differences in the rate of nucleotide substitution among particular lineages (especially between orders), base composition bias, transition/transversion bias, differences in codon usage, and different constraints and levels of homoplasy associated with first, second, and third codon positions. We discuss the implications of these findings for the molecular systematics of mammals, especially as they relate to recent hypotheses concerning the polyphyly of the order Rodentia, relationships among the Artiodactyla, and various interordinal relationships.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/48049/1/239_2004_Article_BF00163231.pd

Genetic evidence of Dobrava virus in Apodemus agrarius in Hungary.

Using nested polymerase chain reaction, we sequenced Dobrava virus (DOB) from the rodent Apodemus agrarius in Hungary. The samples we isolated group with DOB samples previously isolated from A. flavicollis. This grouping may indicate host switching