Rodney L. Honeycutt

Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification.

Molecular phylogenetic analysis, calibrated with fossils, resolves the time frame of the mammalian radiation. Previous analyses of relations, divergence times, and diversification patterns among extant mammalian families have relied on supertree methods and local molecular clocks. We constructed a molecular supermatrix for mammalian families and analyzed these data with likelihood-based methods and relaxed molecular clocks. Phylogenetic analyses resulted in a robust phylogeny with better resolution than phylogenies from supertree methods. Relaxed clock analyses support the long-fuse model of diversification and highlight the importance of including multiple fossil calibrations that are spread across the tree. Molecular time trees and diversification analyses suggest important roles for the Cretaceous Terrestrial Revolution and Cretaceous-Paleogene (KPg) mass extinction in opening up ecospace that promoted interordinal and intraordinal diversification, respectively. By contrast, diversification analyses provide no support for the hypothesis concerning the delayed rise of present-day mammals during the Eocene Period.

Higher-level systematics of rodents and divergence time estimates based on two congruent nuclear genes

Phylogenetic analysis of over 4600 aligned nucleotide sequences from two nuclear genes, growth hormone receptor and BRCA1, provided congruent phylogenies depicting relationships among the major lineages of rodents. Separate and combined analyses resulted in five major conclusions: (1) strong support for a monophyletic Myodonta (containing the superfamilies Muroidea + Dipodoidea), with subfamily Gerbillinae being more closely related to Murinae than is Sigmodontinae; (2) a sister-group relationship between the family Castoridae and the superfamily Geomyoidea; (3) monophyly of Ctenohystrica (containing the suborders Sciuravida and Hystricognatha); (4) a near polytomy among Myodonta (suborder Myomorpha), Pedetes (family Pedetidae, suborder Anomaluromorpha), Castoridae (suborder Sciuromorpha) + Geomyoidea (suborder Myomorpha), and Ctenohystrica; and (5) basal position of a monophyletic group containing Graphiurus (family Gliridae, suborder Myomorpha) + two members of the Sciuromorpha (Sciuridae + Aplodontidae). Divergence dates among rodents and primates were also estimated using the combined data. Applying a global molecular clock and a primate calibration point, divergence dates among rodents exceeded fossil-based dates but were generally compatible with other molecule-based dates estimated under similar conditions. However, when a relaxed molecular clock was applied, estimated divergence dates were highly compatible with the fossil record.

Discovery of tetraploidy in a mammal

Polyploidy, or having more than a pair of each type of chromosome, is considered to be unlikely in mammals because it would disrupt the mechanism of dosage compensation that normally inactivates one X chromosome in females. Also, any imbalance in chromosome number should affect the normal developmental processes and therefore constitute an evolutionary end, as in triploid humans.

Evolution of the Primate Cytochrome c Oxidase Subunit II Gene

We examined the nucleotide and amino acid sequence variation of the cytochrome c oxidase subunit II (COII) gene from 25 primates (4 hominoids, 8 Old World monkeys, 2 New World monkeys, 2 tarsiers, 7 lemuriforms, 2 lorisiforms). Marginal support was found for three phylogenetic conclusions: (1) sister-group relationship between tarsiers and a monkey/ape clade, (2) placement of the aye-aye (Daubentonia) sister to all other strepsirhine primates, and (3) rejection of a sister-group relationship of dwarf lemurs (i.e., Cheirogaleus) with lorisiform primates. Stronger support was found for a sister-group relationship between the ring-tail lemur (Lemur catta) and the gentle lemurs (Hapalemur). In congruence with previous studies on COII, we found that the monkeys and apes have undergone a nearly two-fold increase in the rate of amino acid replacement relative to other primates. Although functionally important amino acids are generally conserved among all primates, the acceleration in amino acid replacements in higher primates is associated with increased variation in the amino terminal end of the protein. Additionally, the replacement of two carboxyl-bearing residues (glutamate and aspartate) at positions 114 and 115 may provide a partial explanation for the poor enzyme kinetics in cross-reactions between the cytochromes c and cytochrome c oxidases of higher primates and other mammals.

Systematics of mustelid-like carnivores

The phylogenetic relationships of the skunks to the Mustelidae and other caniform carnivores were examined using mitochondrial-DNA (mtDNA) sequence data from portions of the 12S and 16S ribosomal RNA (rRNA) genes. Data were combined with partial sequences of the cytochrome b gene and morphological data obtained from the literature, and used in a total-evidence analysis. The Mustelidae represented a paraphyletic group, with the skunks ( Conepatus, Mephitis , and Spilogale ) and the Oriental stink badger ( Mydaus ) forming a monophyletic clade separate from a clade containing the rest of the Mustelidae and the monophyletic Procyonidae. Within the Mustelidae, minus the skunks and stink badger, only one currently recognized subfamily, the Lutrinae, represented a monophyletic group. The families Phocidae, Otariidae, and Odobenidae formed a monophyletic group that was the sister group to the clade composed of the skunks, procyonids, and mustelids. The families Ursidae and Canidae occurred at the base of the Caniformia clade. It is proposed that the skunks be elevated to the level of family and be referred to as the Mephitidae. The family Mephitidae includes the genera Mephitis (striped and hooded skunks), Conepatus (hog-nosed skunks), Spilogale (spotted skunks), and Mydaus (Oriental stink badgers).

Site specific rates of mitochondrial genomes and the phylogeny of eutheria

BackgroundTraditionally, 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 3rd 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.ResultsMitochondrial 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.ConclusionRather 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.

Are naked and common mole-rats eusocial and if so, why?

Abstract Eusociality in mammals is defined in the present paper by the following criteria: reproductive altruism (which involves reproductive division of labor and cooperative alloparental brood care), overlap of adult generations, and permanent (lifelong) philopatry. We argue that additional criteria such as the existence of castes, colony size, reproductive skew, and social cohesion are not pertinent to the definition of eusociality in mammals. According to our definition of mammalian eusociality, several rodent species of the African family Bathyergidae can be considered eusocial, including the naked mole-rat (Heterocephalus glaber), Damaraland mole-rat (Cryptomys damarensis), and several additional, if not all, species in the genus Cryptomys. Furthermore, some species of social voles (like Microtus ochrogaster) may also fulfill criteria of mammalian eusociality. Understanding the evolution of eusociality in mole-rats requires answers to two primary questions: (1) What are the preconditions for the development of their eusocial systems? (2) Why do offspring remain in the natal group rather than dispersing and reproducing? Eusociality in mammals is by definition a special case of monogamy (more specifically: monogyny one female breeding), involving prolonged pair bonding for more than one breeding period. We argue that eusociality in mole-rats evolved from a monogamous mating system where cooperative brood care was already established. A tendency for group living is considered to be an ancestral (plesiomorph) trait among African bathyergid mole-rats, linking them to other hystricognath rodents. A solitary lifestyle seen in some genera, such as Bathyergus, Georychus, and Heliophobius, is assumed to be a derived trait that arose independently in different lineages of bathyergids, possibly as a consequence of selective constraints associated with the subterranean environment. In proximate terms, in eusocial mole-rats either puberty is assumed to be developmentally delayed so that under natural conditions most animals die before dispersal is triggered (e.g., in the case of Heterocephalus) or dispersal is induced only by an incidental encounter with an unfamiliar, yet adequate sexual partner (e.g., in the case of Cryptomys). Ultimately, a combination of strategies involving either dispersal and/or philopatry can be beneficial, especially in a highly unpredictable environment. If genetic relatedness among siblings is high (e.g., a coefficient of relatedness of 0.5 or more), then philopatry would not invoke an appreciable loss of fitness, especially if the cost of dispersing is higher than staying within the natal group. High genetic relatedness is more likely in a monogamous mating system or a highly inbred population. In this paper, we argue that the preconditions for eusociality in bathyergid mole-rats were a monogamous mating system and high genetic relatedness among individuals. We argue against the aridity food-distribution hypothesis (AFDH) that suggests a causal relationship between cooperative foraging for patchily distributed resources and the origin of eusociality. The AFDH may explain group size dynamics of social mole-rats as a function of the distribution and availability of resources but it is inadequate to explain the formation of eusocial societies of mole-rats, especially with respect to providing preconditions conducive for the emergence of eusociality.

HISTORICAL BIOGEOGRAPHY AND CONTEMPORARY PATTERNS OF MITOCHONDRIAL DNA VARIATION IN WHITE-TAILED DEER FROM THE SOUTHEASTERN UNITED STATES

Mitochondrial DNA (mtDNA) was used to characterize patterns of geographic variation among white‐tailed deer (Odocoileus virginianus) populations in the southeastern United States. Fifteen restriction enzymes were employed to survey and map 99 restriction sites in 142 deer from 18 localities in five southeastern states. Phylogenetic analysis revealed three primary groups of haplotypes: (1) southern Florida and the Florida Keys, (2) the remainder of peninsular Florida northward to South Carolina, and (3) the Florida panhandle westward to Mississippi. Geographical heterogeneity in haplotype frequencies suggests that stochastic lineage sorting or isolation by distance are not important determinates of mtDNA differentiation among deer populations. The pattern of mtDNA variation in white‐tailed deer is concordant spatially with those observed in unrelated taxa suggesting the common influence of historical biogeographic events. The data (1) support previous hypotheses that relate contemporary patterns of intraspecific phylogeography in northern Florida to the physiogeographic history of the region; and (2) suggest that genetic differentiation in southern Florida may be attributable to episodes of Pleistocene dispersal. Despite potentially high vagility and human intervention, ecological and demographic characteristics of deer have effectively preserved the historical pattern of intraspecific mtDNA differentiation.

Molecular systematics of the South American caviomorph rodents: relationships among species and genera in the family Octodontidae

Nucleotide sequences from mitochondrial (12S rRNA) and nuclear (growth hormone receptor) genes were used to investigate phylogenetic relationships among South American hystricognath rodents of the superfamily Octodontoidea, with special emphasis on the family Octodontidae. Relationships among most taxa were well resolved by a combined analysis of both genes, and the molecular phylogeny was used to address several long-standing phylogenetic problems. The family Abrocomidae was the most basal lineage within the superfamily Octodontoidea, sensu stricto, and the family Ctenomyidae was sister to the family Octodontidae, followed by a monophyletic group containing the families Myocastoridae and Echimyidae. A basic dichotomy was observed within the family Octodontidae. The Argentine desert specialists, Tympanoctomys and Octomys, grouped separate from Octodontomys, which was sister to a clade containing a monophyletic Octodon and a clade represented by species of Aconaemys and Spalacopus. Aconaemys was paraphyletic relative to Spalacopus. The phylogeny was used as an interpretive framework for an examination of variation in several non-molecular characters. The primitive diploid number for most of the octodontoids was determined to be between 46 and 56, and the primitive genome size 8.2 pg. Members of the Octodontidae appeared to be derived from an ancestral stock occupying lower elevations in scrub habitat. Furthermore, estimates of divergence time from the molecular data provided a temporal perspective for changes in plant communities, which demonstrated turnover and diversification in response to climatic and geologic events occurring in the Miocene through the Pleistocene.

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.