Duke S. Rogers

Comparative Phylogeography of Mesoamerican Highland Rodents: Concerted versus Independent Response to Past Climatic Fluctuations

The phylogeography of Sumichrast’s harvest mouse (Reithrodontomys sumichrasti) was examined through maximum‐likelihood and parsimony analyses of 1,130 bp of mitochondrial Cytochrome b sequence data from 43 individuals. The phylogeography of this Middle American highland forest‐dwelling species was compared to that previously published for the codistributed Aztec deer mouse complex (Peromyscus aztecus/Peromyscus hylocetes complex) in order to test competing hypotheses of concerted versus independent responses of codistributed forms to past climatic fluctuations. Qualitatively, there were strong similarities in the phylogeographic patterns of the two groups, yet there were also areas of incongruence. Likelihood‐ratio tests (Kishino‐Hasegawa‐Templeton and parametric bootstrap tests) indicated that this incongruence is significant and cannot be attributed simply to uncertainty in phylogenetic estimation, thereby falsifying the concerted‐response hypothesis. Conversely, tree‐reconciliation analysis of the area relationships inferred for each group separately indicated that there has been a significant history of covicariance between the two groups, falsifying the independent‐response hypothesis. It appears that codistributed taxa in the geologically complex highlands of Mesoamerica share more common biogeographical history than can be accounted for by the independent‐response hypothesis yet have not responded to past climatic fluctuations in the lock‐step fashion predicted by the concerted‐response hypothesis.

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.

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.

In the Wake of Invasion: Tracing the Historical Biogeography of the South American Cricetid Radiation (Rodentia, Sigmodontinae)

The Great American Biotic Interchange (GABI) was greatly influenced by the completion of the Isthmus of Panama and impacted the composition of modern faunal assemblages in the Americas. However, the contribution of preceding events has been comparatively less explored, even though early immigrants in the fossil records are evidence for waif dispersals. The cricetid rodents of the subfamily Sigmodontinae are a classic example of a species-rich South American radiation resulting from an early episode of North American invasion. Here, we provide a temporal and spatial framework to address key aspects of the historical biogeography and diversification of this diverse mammal group by using mitochondrial and nuclear DNA datasets coupled with methods of divergence time estimation, ancestral area reconstruction and comparative phylogenetics. Relaxed-clock time estimates indicate that divergence of the Sigmodontinae began in the middle–late Miocene (ca. 12–9 Ma). Dispersal-vicariance analyses point to the arrival of a single lineage of northern invaders with a widespread ancestral distribution and imply that the initial differentiation between Central and South America gave rise to the most basal groups within the subfamily. These two major clades diversified in the late Miocene followed by the radiation of main tribes until the early Pliocene. Within the Oryzomyalia, tribes diverged initially in eastern South America whereas multiple dispersals into the Andes promoted further diversification of the majority of modern genera. A comparatively uniform background tempo of diversification explains the species richness of sigmodontines across most nodes, except for two akodontine genera with recent increases in diversification rates. The bridging of the Central American seaway and episodes of low sea levels likely facilitated the invasion of South America long before the onset of the post-Isthmian phase of the GABI.

Phylogeography of Peromyscus furvus (Rodentia; muridae) based on cytochrome b sequence data.

We conducted phylogenetic analyses of cytochrome b sequence data to assess genetic variation within and among the three allopatric segments of the distribution of Peromyscus furvus from the Sierra Madre Oriental in eastern Mexico. We identified 24 unique haplotypes among the 54 individuals examined and genetic distances ranged up to 0.078 substitutions per site. Populations from the central portion of the range formed a monophyletic unit, whereas samples from the southern distributional unit were polyphyletic. Furthermore, the southernmost population sampled may represent a distinct species. This high degree of genetic differentiation among populations, currently recognized as conspecific, mirrors the result of other genetic studies of highland rodents in Mesoamerica. Together these studies indicate that the region, already considered hyperdiverse on the basis of species diversity and endemism, may contain considerably greater diversity than is currently appreciated.

ROOSTING AFFINITIES OF TOWNSEND'S BIG-EARED BAT (CORYNORHINUS TOWNSENDII) IN NORTHERN UTAH

Abstract We surveyed abandoned mines, caves, and bridges to identify habitat preferences of day-roosting Townsends big-eared bat (Corynorhinus townsendii) in northern Utah. Of 820 sites surveyed (676 mines, 39 caves, and 105 bridges), 196 (23.9%) were occupied by C. townsendii. Caves were the most frequently used type of roost (84.6%), 21.2% of abandoned mines were used as day roosts, and no bridges were used. Bats occupied mines and caves at lower available elevations (1,350–2,440 m), which were associated with sagebrush–grass steppe, juniper woodlands, and mountain brush vegetation. In general, roosts with single low (<1.5 m height) entrances were more likely to be occupied than those with multiple or tall entrances. Day roosts typically were subject to little disturbance by humans. Aspect and width of entrance, stability and complexity of interior, presence of multiple entrances, length of tunnel, amount of internal air flow, presence of multiple levels, and presence of internal water were not associated significantly with occupancy; however, maternity colonies tended to be located in large complex sites with multiple openings.

Genic Evolution, Historical Biogeography, and Systematic Relationships Among Spiny Pocket Mice (Subfamily Heteromyinae)

Protein variation at 30 presumptive gene loci was examined among 36 populations comprising all species of spiny pocket mice (subfamily Heteromyinae). The bulk of between-sample genic variation involved fixed allelic differences. A distance-Wagner tree divided the heteromyines into two groups, one formed by Heteromys gaumeri and the other composed of all remaining taxa. Within this latter group, species of Heteromys comprising the anomalus species group were genically most similar to members of the genus Liomys . A consensus distance-Wagner tree constructed by use of the jackknifing approach yielded eight unresolved lineages of heteromyines. Genic data support the monophyly of heteromyines relative to other heteromyid rodents, but do not support monophyly of Heteromys and Liomys . Allozyme data were mostly concordant with karyotypic data, but failed to support recent taxonomies based on morphological characters regarding interspecific relationships among species of Heteromys . Genic and karyotypic data indicate that H. desmarestianus is divisible into two moieties in southern Mexico, H. goldmani is not differentiated from geographically adjacent populations of H. desmarestianus , and H. oresterus is not closely allied with H. nelsoni . Based on allozyme data, H. anomalus and H. australis are not closely related. Affinities among species of Liomys derived from allozyme data were in agreement with those based on morphological and chromosomal information, but indicate that L. pictus , as currently constituted, is paraphyletic. The amount of genic divergence within Heteromys from South America most likely precludes the generally accepted view of a recent invasion of South America by these mice.

PATTERNS OF HABITAT USE BY BATS ALONG A RIPARIAN CORRIDOR IN NORTHERN UTAH

Abstract We examined patterns of habitat use within a community of bats along the Provo River in Heber Valley, Utah. The landscape was divided into 5 habitat categories: riparian forest, wetland, agricultural field, edge, and a habitat restoration site. We used Anabat II bat detectors to record the number of echolocation calls per night within each habitat type as an index of bat activity. Echolocation calls were classified into foraging guilds based on acoustic traits, and we analyzed activity by entire community and by the 4 guilds related to habitat type and environmental variables. Activity was not significantly related to moon phase, average temperature, or day of the season. Activity by the entire bat community was significantly higher in riparian forest and edge habitats compared to other habitat types. Activity of the “high” Myotis guild was significantly greater in the riparian forest, edge habitats, and in the restored habitat site. Similarly, activity by the “low” Myotis guild was significantly higher in riparian forest and edge habitats. In contrast to the Myotis guilds, activity of molossids was significantly higher in agricultural fields compared to other habitats. Activity by the “low” Eptesicus guild did not vary significantly among habitats.

Revisiting Amazonian phylogeography: insights into diversification hypotheses and novel perspectives

The Amazon Basin harbors one of the richest biotas on Earth, such that a number of diversification hypotheses have been formulated to explain patterns of Amazonian biodiversity and biogeography. For nearly two decades, phylogeographic approaches have been applied to better understand the underlying causes of genetic differentiation and geographic structure among Amazonian organisms. Although this research program has made progress in elucidating several aspects of species diversification in the region, recent methodological and theoretical developments in the discipline of phylogeography will provide new perspectives through more robust hypothesis testing. Herein, we outline central aspects of Amazonian geology and landscape evolution as well as climate and vegetation dynamics through the Neogene and Quaternary to contextualize the historical settings considered by major hypotheses of diversification. We address each of these hypotheses by reviewing key phylogeographic papers and by expanding their respective predictions. We also propose future directions for devising and testing hypotheses. Specifically, combining the exploratory power of phylogeography with the statistical rigor of coalescent methods will greatly expand analytical inferences on the evolutionary history of Amazonian biota. Incorporation of non-genetic data from Earth science disciplines into the phylogeographic approach is key to a better understanding of the influence of climatic and geophysical events on patterns of Amazonian biodiversity and biogeography. In addition, achieving such an integrative enterprise must involve overcoming issues such as limited geographic and taxonomic sampling. These future challenges likely will be accomplished by a combination of extensive collaborative research and incentives for conducting basic inventories.

Evolutionary implications of allozymic variation in tropical Peromyscus of the Mexicanus species group

To evaluate phylogenetic relationships within the Peromyscus mexicanus species group, we examined allozymic variation at 28 presumptive genetic loci for nine members of the group ( P. guatemalensis, P. gymnotis, P. megalops, P. melanocarpus, P. mexicanus, P. nudipes, P. ochraventer, P. yucatanicus , and P. zarhynchus ), representatives of four other species groups within the subgenus Peromyscus ( boylii, leucopus, maniculatus , and truei species groups), and two outgroups to the subgenus Peromyscus ( Podomys floridanus and Megadontomys thomasi ). Phenetic analysis of genetic distances generally was concordant with cladistic analyses of discrete character states. Among the nine species usually included within the mexicanus group, six ( P. guatemalensis, P. gymnotis, P. mexicanus, P. nudipes, P. yucatanicus , and P. zarhynchus ) were genically similar, and relationships among these taxa generally were undefined in the cladistic analysis. Within this group, a population of P. mexicanus shared two derived allelic character states with P. gymnotis and as currently defined, P. mexicanus appears paraphyletic. P. megalops, P. melanocarpus , and P. ochraventer were neither associated closely with other species in the subgenus Peromyscus nor with each other, phenetically or cladistically. Based on these data, the mexicanus species group, as currently defined, is composite. Our data agree with the removal of P. megalops, P. melanocarpus , and P. ochraventer from the mexicanus group, but not with the assignment of P. megalops and P. melanocarpus to a single species group.