Robert D. Bradley

A TEST OF THE GENETIC SPECIES CONCEPT: CYTOCHROME- b SEQUENCES AND MAMMALS

Abstract Levels of sequence variation in mitochondrial cytochrome-b gene were examined to ascertain if this molecule can provide a reference point in making decisions concerning species-level distinctions. DNA-sequence data from 4 genera of rodents (Neotoma, Reithrodontomys, Peromyscus, and Sigmodon) and 7 genera of bats (Artibeus, Carollia, Chiroderma, Dermanura, Glossophaga, Rhinophylla, and Uroderma), including recognized sister species, were examined to develop hypotheses for evaluating levels of sequence variation. Several patterns associated with DNA-sequence variation emerged from this study. Specifically, genetic distance values <2% were indicative of intraspecific variation; values between 2 and 11% had a high probability of being indicative of conspecific populations or valid species and merit additional study concerning specific status; and values >11% were indicative of specific recognition. It appears that genetic distance values may be useful for determination of species boundaries under the framework of the Genetic Species Concept.

SPECIATION IN MAMMALS AND THE GENETIC SPECIES CONCEPT

Abstract We define a genetic species as a group of genetically compatible interbreeding natural populations that is genetically isolated from other such groups. This focus on genetic isolation rather than reproductive isolation distinguishes the Genetic Species Concept from the Biological Species Concept. Recognition of species that are genetically isolated (but not reproductively isolated) results in an enhanced understanding of biodiversity and the nature of speciation as well as speciation-based issues and evolution of mammals. We review criteria and methods for recognizing species of mammals and explore a theoretical scenario, the Bateson–Dobzhansky–Muller (BDM) model, for understanding and predicting genetic diversity and speciation in mammals. If the BDM model is operating in mammals, then genetically defined phylogroups would be predicted to occur within species defined by morphology, and phylogroups experiencing stabilizing selection will evolve genetic isolation without concomitant morphological diversification. Such species will be undetectable using classical skin and skull morphology (Morphological Species Concept). Using cytochrome-b data from sister species of mammals recognized by classical morphological studies, we estimated the number of phylogroups that exist within mammalian species and hypothesize that there will be >2,000 currently unrecognized species of mammals. Such an underestimation significantly affects conclusions on the nature of speciation in mammals, barriers associated with evolution of genetic isolation, estimates of biodiversity, design of conservation initiatives, zoonoses, and so on. A paradigm shift relative to this and other speciation-based issues will be needed. Data that will be effective in detecting these “morphologically cryptic genetic species” are genetic, especially DNA-sequence data. Application of the Genetic Species Concept uses genetic data from mitochondrial and nuclear genomes to identify species and species boundaries, the extent to which the integrity of the gene pool is protected, nature of hybridization (if present), and introgression. Genetic data are unique in understanding species because the use of genetic data 1) can quantify genetic divergence from different aspects of the genome (mitochondrial and nuclear genes, protein coding genes, regulatory genes, mobile DNA, microsatellites, chromosomal rearrangements, heterochromatin, etc.); 2) can provide divergence values that increase with time, providing an estimate of time since divergence; 3) can provide a population genetics perspective; 4) is less subject to convergence and parallelism relative to other sets of characters; 5) can identify monophyly, sister taxa, and presence or absence of introgression; and 6) can accurately identify hybrid individuals (kinship and source of hybrid individuals, F1s, backcrosses, direction of hybridization, and in concert with other data identify which hybrids are sterile or fertile). The proposed definition of the Genetic Species Concept is more compatible with a description of biodiversity of mammals than is “reproductively isolated species.” Genetic profiles of mammalian species will result in a genetic description of species and mammalian diversity, and such studies are being accelerated by technological advances that reduce cost and increase speed and efficiency of generating genetic data. We propose that this genetic revolution remain museum- and voucher specimen–based and that new names are based on a holotype (including associated tissues) deposited in an accredited museum.

CRYPTIC SPECIES IN SIGMODON HISPIDUS: EVIDENCE FROM DNA SEQUENCES

Abstract Phylogenetic relationships among 8 subspecies of Sigmodon hispidus from North, Central, and South America were examined using DNA-sequence data from the mitochondrial cytochrome-b gene. The magnitude of DNA-sequence variation detected among these subspecies, in some cases, exceeded levels of interspecific variation observed among currently recognized species of Sigmodon. These data suggest that S. hispidus is paraphyletic and that a minimum of 3 species exist within the currently recognized taxon. Consequently, the taxonomy should be revised to recognize the following samples as distinct species: those from the United States and north-central Mexico, those from southern Mexico, and those from Central and South America.

Toward a Molecular Phylogeny for Peromyscus: Evidence from Mitochondrial Cytochrome-b Sequences

Abstract One hundred DNA sequences from the mitochondrial cytochrome-b gene of 44 species of deer mice (Peromyscus (sensu stricto), 1 of Habromys, 1 of Isthmomys, 2 of Megadontomys, and the monotypic genera Neotomodon, Osgoodomys, and Podomys were used to develop a molecular phylogeny for Peromyscus. Phylogenetic analyses (maximum parsimony, maximum likelihood, and Bayesian inference) were conducted to evaluate alternative hypotheses concerning taxonomic arrangements (sensu stricto versus sensu lato) of the genus. In all analyses, monophyletic clades were obtained that corresponded to species groups proposed by previous authors; however, relationships among species groups generally were poorly resolved. The concept of the genus Peromyscus based on molecular data differed significantly from the most current taxonomic arrangement. Maximum-likelihood and Bayesian trees depicted strong support for a clade placing Habromys, Megadontomys, Neotomodon, Osgoodomys, and Podomys within Peromyscus. If Habromys, Megadontomys, Neotomodon, Osgoodomys, and Podomys are regarded as genera, then several species groups within Peromyscus (sensu stricto) should be elevated to generic rank. Isthmomys was associated with the genus Reithrodontomys; in turn this clade was sister to Baiomys, indicating a distant relationship of Isthmomys to Peromyscus. A formal taxonomic revision awaits synthesis of additional sequence data from nuclear markers together with inclusion of available allozymic and karyotypic data.

RIBOSOMAL-DNA, MITOCHONDRIAL-DNA, CHROMOSOMAL, AND ALLOZYMIC STUDIES ON A CONTACT ZONE IN THE POCKET GOPHER, GEOMYS

We studied 75 individuals of the Plains pocket gopher, Geomys bursarius, from eastern New Mexico, where the subspecies major and knoxjonesi hybridize. Each individual was examined for chromosome number, ribosomal DNA, mitochondrial DNA, and three protein systems for which reference parental populations were fixed for alternative alleles. Twenty individuals were indistinguishable from parental major, 14 individuals were indistinguishable from parental knoxjonesi, and 41 individuals had genotypes composed of combinations of character states that distinguish the two parental types. The parental types appear to represent discrete genetic entities that have restricted introgression across a narrow hybrid zone (width approximately 3 km, using the 20/80 criterion). Parental types overlap in geographic distribution near the center of the zone, and changes in mitochondrial DNA and the five nuclear markers are concordant across the zone. It is probable that there is premating isolation between knoxjonesi males and major females. The frequencies of individuals with certain genotypic combinations within our sample imply differential reproductive success of certain genotypes. We propose that F1s and highly heterozygous males are sterile and that hybrid females are less fertile than parental females. These postmating factors, along with premating isolation for one of the reciprocal crosses, probably account for the restriction of gene flow across the contact zone. The structure of the zone can be explained by the “dynamic equilibrium” model.

MOLECULAR PHYLOGENETICS OF THE NEOTOMA ALBIGULA SPECIES GROUP: FURTHER EVIDENCE OF A PARAPHYLETIC ASSEMBLAGE

Abstract Phylogenetic relationships among 8 subspecies of Neotoma albigula and sister species from the United States and Mexico were examined using DNA sequence data from the mitochondrial DNA cytochrome-b gene. Parsimony, likelihood, and neighbor-joining analyses revealed a strong dichotomy between populations of N. albigula from Texas and eastern Mexico (eastern form) and those from New Mexico, Arizona, and northwestern Mexico (western form). These analyses indicate presence of 2 cryptic species within this taxon that are paraphyletic under current taxonomy. A sister-group relationship was found between N. albigula from Texas and eastern Mexico and N. micropus, whereas populations of N. albigula from New Mexico, Arizona, and northwestern Mexico formed a sister-group relationship with N. floridana. That latter group in turn formed a sister-taxon relationship to the Texas–eastern Mexico N. albigula and N. micropus clade. The Rio Grande and Rio Conchos seem to have been the major barriers restricting gene flow between ancestral populations of a N. floridana–like woodrat. Populations of N. floridana were further isolated geographically by reduction of suitable habitat brought about by changing climatic patterns that allowed formation of xeric plant communities soon after the end of the Late Wisconsin.

Molecular systematics of the genus Neotoma

DNA sequences from the mitochondrial DNA cytochrome-b gene were used to infer the systematic relationships of 13 species of wood rats (genus Neotoma). Parsimony, likelihood, and neighbor-joining analyses produced similar topologies in most cases and produced six systematic conclusions. First, results of previous studies were supported in the recognition of N. floridana magister as distinct species (N. magister). Second, evidence was provided for the recognition of cryptic species within N. albigula (N. albigula and N. leucodon) and N. mexicana (N. mexicana, N. isthmica, and N. picta). Third, the subgenus Neotoma is composed of four species groups (floridana, lepida, mexicana, and micropus). Fourth, support was provided for placement of N. stephensi within the lepida species group. Fifth, support was provided for the recognition of Hodomys as a separate genus, sister to Xenomys. Sixth, support for the elevation of the subgenus Teonoma to generic status is discussed.

MOLECULAR SYSTEMATICS OF THE GENUS SIGMODON (RODENTIA: MURIDAE): EVIDENCE FROM THE MITOCHONDRIAL CYTOCHROME-b GENE

Abstract Phylogenetic relationships of 11 species of cotton rats (Genus Sigmodon) were assessed using nucleotide variation in the mitochondrial cytochrome-b gene. Results of the phylogenetic analyses do not support the conventional composition of the Sigmodon hispidus and S. fulviventer species groups. Instead, 3 species groups are recognized: hispidus (S. alleni, S. arizonae, S. hirsutus, S. hispidus, S. mascotensis, S. ochrognathus, and S. toltecus), fulviventer (S. leucotis, S. fulviventer, and S. peruanus), and alstoni (S. alstoni). Sequence divergence values ranged from 8.7% to 21.2%, indicating that divergence events within the genus occurred approximately 2.5–5.6 × 106 years ago. Taxa comprising the alstoni and fulviventer groups appear to have evolved early, whereas members of the hispidus group evolved more recently. Molecular data reflect an early origin (7 × 106 years ago) and support the hypothesis that cotton rats may occupy a basal position among South American sigmodontines.

Reduced Number of Ribosomal Sites in Bats: Evidence for a Mechanism to Contain Genome Size

To better understand the organization of the genome of bats, we examined by in situ hybridization, the number of ribosomal DNA sites in 50 species of bats representing both suborders, 7 families, and 38 genera. Number of sites ranged from one to four pairs (average, 1.76) in bats, whereas the number of sites in 40 species of rodents ranged from two to ten pairs (average, 4.19). The possible relationship of a reduced number of sites to a smaller amount of DNA in the genome of bats is explored. We find little evidence to support the hypothesis that bats are retaining a fixed primitive condition of a low number of sites and we conclude that the most probable explanation is that bats, like other groups of mammals, have mechanisms that tend to increase the number of sites. However, the balance between mechanisms that increase and those that reduce the number of sites is more strongly in favor of reduction of sites than is characteristic of other mammals such as rodents.

Operational criteria for genetically defined species: analysis of the diversification of the small fruit-eating bats, Dermanura (Phyllostomidae: Stenodermatinae)

Species diversity and species limits of the small fruit-eating bats, genus Dermanura (Phyllostomidae: Stenodermatinae) were examined. Estimates of species diversity based on classical morphological criteria (current taxonomy) were compared to diversity estimates based on monophyly and cytochrome-b sequence divergence. The most recent taxonomic list included nine species, whereas the genetic based list contained 11: anderseni, azteca, bogotensis, cinerea, glauca, gnoma, phaeotis, rava, rosenbergi, tolteca, and watsoni, of which three (bogotensis Andersen, rava Miller, and rosenbergi Thomas) have been considered synonyms of cinerea, glauca, phaeotis, and tolteca by previous authors. In addition, we consider incomitata to be a synonym of watsoni. Phylogenetic analyses of mtDNA sequences resolved the interrelationships among taxa and prompted us to re-evaluate some morphological characters that support the distinction of all the recognized taxa, therefore providing a robust estimate of species status. A phylogenetic tree revealed a geographic component to the diversification of Dermanura, including a historical connection between western Andean and Middle American biota. In South America, no species has been recorded from both sides of the Andes Mountains, and at least one clade (glauca, gnoma, and bogotensis) is restricted to the eastern versant of the Andes. Using genetic data (monophyly and genetic distance) to identify species we were able to produce testable genealogical and biogeographic hypotheses to facilitate further studies.