John C. Hafner

BASAL CLADES AND MOLECULAR SYSTEMATICS OF HETEROMYID RODENTS

Abstract The New World rodent family Heteromyidae shows a marvelous array of ecomorphological types, from bipedal, arid-adapted forms to scansorial, tropical-adapted forms. Although recent studies have resolved most of the phylogenetic relationships among heteromyids at the shallower taxonomic levels, fundamental questions at the deeper taxonomic levels remain unresolved. This study relies on DNA sequence information from 3 relatively slowly evolving mitochondrial genes, cytochrome c oxidase subunit I, 12S, and 16S, to examine basal patterns of phylogenesis in the Heteromyidae. Because slowly evolving mitochondrial genes evolve and coalesce more rapidly than most nuclear genes, they may be superior to nuclear genes for resolving short, basal branches. Our molecular data (2,381 base pairs for the 3-gene data set) affirm the monophyly of the family and resolve the major basal clades in the family. Alternative phylogenetic hypotheses of subfamilial relationships are examined statistically and the Perognathinae and Heteromyinae are found to represent sister clades relative to the Dipodomyinae. The 3 traditional subfamilial groupings are supported; the controversial placement of Microdipodops as a sister clade to Dipodomys in the Dipodomyinae is affirmed, Perognathus and Chaetodipus are distinct sister clades within the Perognathinae, and species of Liomys and Heteromys form the resolved clade Heteromyinae. However, Liomys is found to be paraphyletic relative to Heteromys and, given that this finding corroborates earlier studies, we present a formal taxonomy of Heteromys wherein we place Liomys in synonymy. Semiparametric and parametric methods are used to estimate divergence times from our molecular data and a chronogram of the Heteromyidae, calibrated by the oldest known fossils of Dipodomys and Perognathus, is presented. Our time estimates reveal subfamilial differentiation in the early Miocene (22.3–21.8 million years ago) and pose testable times of divergence for the basal heteromyid nodes. With the basal heteromyid clades resolved and cladogenic events positioned in a time framework, we review the major geological and paleoecological events of the Oligocene and Miocene associated with the early historical biogeography of the family.

HYBRID ZONES IN THOMOMYS BOTTAE POCKET GOPHERS: GENETIC, PHENETIC, AND ECOLOGIC CONCORDANCE PATTERNS

In a recent summary of geographic variability of both chromosomal and genic systems in Thomomys bottae pocket gophers, Patton and Yang (1977) presented data depicting extensive degrees of interpopulation genetic divergence. In several instances, adjacent or near adjacent pairs of populations were seen to differ by lOIS fixed chromosomal rearrangements and to share less than 80% in overall allelic similarity in structural genes as measured by starch gel electrophoresis. Despite the enormity of observed interpopulation divergence (in many cases greater than that found between species of other mammals), available data suggested that these geographic segments retained the ability to interbreed. Evidence for this conclusion came from studies by other workers suggesting intergradation between several of the differentiated units based on the morphological intermediacy of some specimens. In no study, however, had the gross morphological indications of intergradation been fully supported by genetic analyses. The purpose of the present report is to provide a concomitant comparison of intergradation from a genetic, morphologic, and ecologic perspective between two of the most strongly differentiated, geographically adjacent units of T. bottae that were recognized by Patton and Yang (1977). Pocket gophers of the conifer forest zones of the White and Sacramento mountains of south central New Mexico, described as T. b . ruidosae by Hall (1932), are characterized by moderate size, dark coloration, and a karyotype composed of nearly all biarmed autosomes (2n = 76). This form meets T. b. actuosus Kelson Revised December 16, 1978

Macrogeographic Patterns of Genetic Differentiation in the Pocket Gopher Thomomys Umbrinus

Electromorphic and chromosomal variation is analyzed in 26 populations of Tho- momys umbrinus sampled from throughout the range of the species. Interpopulation levels of genic differentiation are extreme, generally exceeding values measured between conspecific populations of most animals or plants. Two principal groups of T. umbrinus are recognized based on chromosomal evidence, one with 2n = 76 chromosomes and the other with 2n = 78. Further, the 2n = 78 group (but not the 2n = 76 group) is bisected into geographic subgroups with respect to chromosome morphology and heterochromatin position. The kind and degree of chromosomal differentiation observed suggests that the three groups may be reproductively incompatible. Allozymic evidence corroborates the above groupings, and an analysis of patterns of allele sharing suggests the absence of gene flow among the groups. A cladistic analysis of electro- morphic data indicates that the two 2n = 78 groups may be independently derived from the 2n = 76 lineage. The combined evidence supports the hypothesis that T. umbrinus is actually a composite of at least three biological species and confirms the observation that speciation in the genus Thomomys is unrelated to the level of genic differentiation between populations. (Evolu- tionary genetics; geographic variation; evolutionary concordance; pocket gophers; cladistic anal- ysis; paraphyly; speciation.)

Isolation and characterization of 17 polymorphic microsatellite loci in the kangaroo mouse, genus Microdipodops (Rodentia: Heteromyidae)

We isolated and characterized 17 microsatellite loci from kangaroo mice, Microdipodops megacephalus and M. pallidus. Loci were screened in 24 individuals from 21 general localities across their distributional range in the Great Basin Desert. In total, the number of alleles per locus ranged from 4 to 16, observed heterozygosity ranged from 0.333 to 1, and the probability of identity values ranged from 0.013 to 1. These loci provide new tools for examining the biogeographic history and population dynamics of Microdipodops in the context of molecular ecology.

Do nocturnal rodents in the Great Basin Desert avoid moonlight

Abstract Rodents make foraging decisions by balancing demands to acquire energy and mates with the need to avoid predators. To identify variations in the risk of predation, nocturnal rodents may use moonlight as a cue of risk. Moonlight avoidance behaviors have been observed in many nocturnal rodent species and are widely generalized to small mammals. However, most prior studies have been limited to 1 species or 1 study site, or occurred in modified habitats. We evaluated desert rodent activity patterns in natural habitats from 1999 to 2006 at 62 study sites across the Great Basin Desert of western North America. Rodent activity was examined by livetrapping in open habitats, using the presence of the sand-obligate kangaroo mouse (Microdipodops) as a habitat indicator. Activity patterns were assessed on 69 nights with clear skies and compared to corresponding moonlight values (moon phase and brightness) to evaluate the frequency of moonlight avoidance. Analyses of total activity of all species in the rodent assemblage relative to moonlight showed a distinct nonrandom (triangular-shaped) pattern but no significant correlations. However, individual genera of desert rodents responded differently to moonlight. Only kangaroo rats (Dipodomys) displayed significant moonlight avoidance patterns; they were maximally active at significantly different moonlight levels and avoided bright moonlight to a greater extent than co-occurring rodents. Moonlight seemed to limit the activity of kangaroo rats most strongly on bright nights during waxing moon phases and summer seasons, but not significantly during the spring or fall seasons, or during waning moons. Rather than avoiding moonlight, the activity of deer mice (Peromyscus), pocket mice (Perognathus), and kangaroo mice may be governed by changes in competition with kangaroo rats. Differences in the body size, locomotion, and space use of kangaroo rats relative to other rodents may explain why different moonlight responses were detected, especially if these traits alter how rodents perceive risk from bright moonlight. These findings indicate that moonlight avoidance may be a specialized trait of kangaroo rats rather than a general behavior of nocturnal desert rodents in the Great Basin.

Heterochrony in Rodents

The mammalian order Rodentia is by far the largest order of mammals (approximately 1700 species), and rodents show ranges in body size, body plan, and ecological diversity that far exceed those seen in any other group of mammals, including bats and cetaceans. Living rodents inhabit all continents except Antarctica, and they are found in nearly every terrestrial habitat throughout their geographic range. Rodents usually play integral roles in the terrestrial ecosystems they inhabit, and they are often the most abundant and diverse of all vertebrates in a terrestrial community.

GENETIC INTERACTIONS AT A CONTACT ZONE OF URODERMA BILOBATUM (CHIROPTERA: PHYLLOSTOMIDAE)

Studies of genetic interactions between taxa in zones of hybridization can provide evolutionary biologists with an important empirical basis for exploring the nature of speciation. Importantly, such contact-zone studies allow critical assessment of the types of genetic changes (e.g., chromosomal rearrangements or protein dissimilarity) that may be instrumental in effecting reproductive isolation. Hence, it is crucial that underlying empiricism in such studies, as well as any proffered interpretations, be critically evaluated and reassessed. The patterns of chromosomal and protein variation in a contact zone of the tentmaking bat, Uroderma bilobatum, were summarized recently in two stimulating companion papers (Baker, 1981; Greenbaum, 1981). This contact zone involves two karyotypically defined taxa, U. b. davisi (44 chromosomes) and U. b. convexum (38 chromosomes), that hybridize about the Golfo de Fonseca, Honduras on the Pacific versant of Middle America. Baker (1981) and Greenbaum (1981) conclude that this contact zone is unique for its great width, introgressive hybridization does not occur between these subspecies, the pattern of chromosomal variation is maintained by selection, and that the hybrid zone is a result of primary contact and speciation should ensue. These interpretations and conclusions are provocative and I am reluctant to accept their explanations of the genetic characteristics of the hybrid zone. Accordingly, here I evaluate their hypotheses and present an alternative interpretation of the genetic interactions observed at this interesting contact zone. METHODS

Phylogeography of the pallid kangaroo mouse, Microdipodops pallidus: a sand‐obligate endemic of the Great Basin, western North America

Aim Kangaroo mice, genus Microdipodops Merriam, are endemic to the Great Basin and include two species: M. pallidus Merriam and M. megacephalus Merriam. The pallid kangaroo mouse, M. pallidus, is a sand-obligate desert rodent. Our principal intent is to identify its current geographical distribution and to formulate a phylogeographical hypothesis for this taxon. In addition, we test for orientation patterns in haplotype sharing for evidence of past episodes of movement and gene flow. Location The Great Basin Desert region of western North America, especially the sandy habitats of the Lahontan Trough and those in south-central Nevada. Methods Mitochondrial DNA sequence data from portions of three genes (16S ribosomal RNA, cytochrome b, and transfer RNA for glutamic acid) were obtained from 98 individuals of M. pallidus representing 27 general localities sampled throughout its geographical range. Molecular sequence data were analysed using neighbour-joining, maximum-parsimony, maximum-likelihood and Bayesian methods of phylogenetic inference. Directional analysis of phylogeographical patterns, a novel method, was used to examine angular measurements of haplotype sharing between pairs of localities to detect and quantify historical events pertaining to movement patterns and gene flow. Results Collecting activities showed that M. pallidus is a rather rare rodent (mean trapping success was 2.88%), and its distribution has changed little from that determined three-quarters of a century ago. Two principal phylogroups, distributed as eastern and western moieties, are evident from the phylogenetic analyses (mean sequence divergence for cytochrome b is c. 8%). The western clade shows little phylogenetic structure and seems to represent a large polytomy. In the eastern clade, however, three subgroups are recognized. Nine of the 42 unique composite haplotypes are present at two or more localities and are used for the orientation analyses. Axial data from haplotype sharing between pairwise localities show significant, non-random angular patterns: a north-west to south-east orientation in the western clade, and a north-east to south-west directional pattern in the eastern clade. Main conclusions The geographical range of M. pallidus seems to be remarkably stable in historical times and does not show a northward (or elevationally upward) movement trend, as has been reported for some other kinds of organism in response to global climate change. The eastern and western clades are likely to represent morphologically cryptic species. Estimated times of divergence of the principal clades of M. pallidus (4.38 Ma) and between M. pallidus and M. megacephalus (8.1 Ma; data from a related study) indicate that kangaroo mice diverged much earlier than thought previously. The phylogeographical patterns described here may serve as a model for other sand-obligate members of the Great Basin Desert biota.

Phylogeography of the dark kangaroo mouse, Microdipodops megacephalus: cryptic lineages and dispersal routes in North America's Great Basin.

Aim The rodent genus Microdipodops (kangaroo mice) includes two sand-obligate endemics of the Great Basin Desert: M. megacephalus and M. pallidus. The dark kangaroo mouse, M. megacephalus, is distributed throughout the Great Basin and our principal aims were to formulate phylogenetic hypotheses for this taxon and make phylogeographical comparisons with its congener. Location The Great Basin Desert of western North America. Methods DNA sequence data from three mitochondrial genes were examined from 186 individuals of M. megacephalus, representing 47 general localities. Phylogenetic inference was used to analyse the sequence data. Directional analysis of phylogeographical patterns was used to examine haplotype sharing patterns and recover routes of gene exchange. Haplotype–area curves were constructed to evaluate the relationship between genetic variation and distributional island size for M. megacephalus and M. pallidus. Results Microdipodops megacephalus is a rare desert rodent (trapping success was 2.67%). Temporal comparison of trapping data shows that kangaroo mice are becoming less abundant in the study area. The distribution has changed slightly since the 1930s but many northern populations now appear to be small, fragmented, or locally extinct. Four principal phylogroups (the Idaho isolate and the western, central and eastern clades) are evident; mean sequence divergence between phylogroups for cytochrome b is c. 8%. Data from haplotype sharing show two trends: a north–south trend and a web-shaped trend. Analyses of haplotype–area curves reveal significant positive relationships. Main conclusions The four phylogroups of M. megacephalus appear to represent morphologically cryptic species; in comparison, a companion study revealed two cryptic lineages in M. pallidus. Estimated divergence times of the principal clades of M. megacephalus (c. 2–4 Ma) indicate that these kangaroo mice were Pleistocene invaders into the Great Basin coincident with the formation of sandy habitats. The north–south and web patterns from directional analyses reveal past routes of gene flow and provide evidence for source–sink population regulation. The web pattern was not seen in the companion study of M. pallidus. Significant haplotype–area curves indicate that the distributional islands are now in approximate genetic equilibrium. The patterns described here are potentially useful to conservation biologists and wildlife managers and may serve as a model for other sand-obligate organisms of the Great Basin.

Production of digestive enzymes along the gut of the giant keyhole limpet Megathura crenulata (Mollusca: Vetigastropoda)

The esophagus and intestine form the longest regions of the digestive tract in the giant keyhole limpet and are lined by epithelial cells sharing a common morphology and releasing materials into the gut lumen by apocrine secretion. The purpose of this study was to determine if these morphologically similar regions release similar digestive enzymes and compare their contributions to digestive enzymes released from other regions of the gut. Principal component analysis of enzymes detected by the API ZYM system for 19 enzymes plus EnzChek assays for protease, α-amylase, lipase, cellulase, and lysozyme identify four distinct regions of the gut: 1) crystalline style and style sac, 2) digestive gland, 3) salivary glands, and 4) esophagus and intestine. Heterogeneity in enzymatic activity was observed in regions of the gut with similar cell morphology (middle and posterior esophagus and intestine) as well as regions with different cell morphology (salivary glands, digestive gland and crystalline style). Enzyme activity in each of these regions is compared to other gastropods, in particular the abalone. Although much of the length of the digestive tract is lined by a morphologically similar epithelium, different regions of the alimentary tract produce a different suite of enzymes which may contribute to the digestive process. These data will help enhance our limited understanding of the digestive physiology of Megathura crenulata and lead to improvement of its culture for clinical research.