Showing papers by "Museum of Texas Tech University published in 2015"

What Is Peromyscus? Evidence from Nuclear and Mitochondrial DNA Sequences Suggests the Need for a New Classification

Abstract: The evolutionary relationships between Peromyscus, Habromys, Isthmomys, Megadontomys, Neotomodon, Osgoodomys, and Podomys are poorly understood. In order to further explore the evolutionary boundaries of Peromyscus and compare potential taxonomic solutions for this diverse group and its relatives, we conducted phylogenetic analyses of DNA sequence data from alcohol dehydrogenase (Adh1-I2), beta fibrinogen (Fgb-I7), interphotoreceptor retinoid-binding protein (Rbp3), and cytochrome-b (Cytb). Phylogenetic analyses of mitochondrial and nuclear genes produced similar topologies although levels of nodal support varied. The best-supported topology was obtained by combining nuclear and mitochondrial sequences. No monophyletic Peromyscus clade was supported. Instead, support was found for a clade containing Habromys, Megadontomys, Neotomodon, Osgoodomys, Podomys, and Peromyscus suggesting paraphyly of Peromyscus and confirming previous observations. Our analyses indicated an early divergence of Isthmomys from Peromyscus (approximately 8 million years ago), whereas most other peromyscine taxa emerged within the last 6 million years. To recover a monophyletic taxonomy from Peromyscus and affiliated lineages, we detail 3 taxonomic options in which Habromys, Megadontomys, Neotomodon, Osgoodomys, and Podomys are retained as genera, subsumed as subgenera, or subsumed as species groups within Peromyscus. Each option presents distinct taxonomic challenges, and the appropriate taxonomy must reflect the substantial levels of morphological divergence that characterize this group while maintaining the monophyletic relationships obtained from genetic data.

Dimensionality of community structure: phylogenetic, morphological and functional perspectives along biodiversity and environmental gradients

Abstract: Biodiversity is a complex and multidimensional concept that characterizes variation of life on Earth. Nonetheless, most studies have examined only a few, if not just one, dimension in isolation. Herein we conduct analyses that explicitly incorporate correlations among multiple dimensions of biodiversity by characterizing morphological, phylogenetic, and functional structure of bat communities from Atlantic Forest of South America and examine degree of redundancy among these sets of descriptors. Second, we examine dimensionality (i.e. number of orthogonal dimensions) of community structure by quantitatively determining if these different sets of descriptors correspond to unique dimensions. We assess if dimensionality measured from empirical communities differs from that based on communities randomly assembled from a regional species pool. Finally, we examine whether different indices of community structure respond differently to environmental gradients spanning Atlantic Forest. We find that Atlantic Forest bat communities are highly variable in terms of morphological, phylogenetic, and functional structure. Different sets of community structure indices exhibited substantive correlations. Accordingly, dimensionality was lower than the set of six different descriptors or even the three different biological dimensions represented. Nonetheless, observed dimensionality was greater than that expected from a null model of assembly. Only abundance-based indices of phylogenetic structure exhibited significant environmental gradients. Temperature seasonality was the strongest predictor of phylogenetic structure, with overdispersed communities characterizing more seasonal environments and underdispersed communities occurring in areas of lower variation in temperature. Dimensionality of community structure is low with phylogenetic structure exhibiting the strongest patterns, probably because phylogeny reflects many different ecological aspects of the phenotype that are not restricted to just one index of structure. Temperature seasonality is an important determinant of phylogenetic structure of bat communities in Atlantic Forest. This research helps us to better understand the factors underlying the distribution of biodiversity, which is increasingly important for endangered ecoregions such as Atlantic Forest.

Targeted Capture of Phylogenetically Informative Ves SINE Insertions in Genus Myotis

Abstract: Identification of retrotransposon insertions in nonmodel taxa can be technically challenging and costly. This has inhibited progress in understanding retrotransposon insertion dynamics outside of a few well-studied species. To address this problem, we have extended a retrotransposon-based capture and sequence method (ME-Scan [mobile element scanning]) to identify insertions belonging to the Ves family of short interspersed elements (SINEs) across seven species of the bat genus Myotis. We identified between 120,000 and 143,000 SINE insertions in six taxa lacking a draft genome by comparing to the M. lucifugus reference genome. On average, each Ves insertion was sequenced to 129.6 × coverage. When mapped back to the M. lucifugus reference genome, all insertions were confidently assigned within a 10-bp window. Polymorphic Ves insertions were identified in each taxon based on their mapped locations. Using cross-species comparisons and the identified insertion positions, a presence–absence matrix was created for approximately 796,000 insertions. Dollo parsimony analysis of more than 85,000 phylogenetically informative insertions recovered strongly supported, monophyletic clades that correspond with the biogeography of each taxa. This phylogeny is similar to previously published mitochondrial phylogenies, with the exception of the placement of M. vivesi. These results support the utility of our variation on ME-Scan to identify polymorphic retrotransposon insertions in taxa without a reference genome and for large-scale retrotransposon-based phylogenetics.

Patterns of Secondary Sexual Size Dimorphism in New World Myotis and a Test of Rensch's Rule

Abstract: For bats, when secondary sexual dimorphism is significant, females typically are larger than males. Moreover, in mammals, variation in the degree of sexual dimorphism often follows an allometric relationship whereby differences vary with body size (Rensch's rule). We examined sexual dimorphism across the New World clade of Myotis regarding species-specific and clade-wide patterns of body, cranium, and wing size, Rensch's rule and degree to which such morphological variation is related to phylogeny. Size differences were common with significant cases of both male-biased and female-biased sexual dimorphism. In more than half the cases, females were larger than males. Variation in degree of dimorphism exhibited an allometric pattern. Nonetheless, slope of the relationship between size and degree of dimorphism was no different from unity (i.e., isometry), failing to support Rensch's rule. There was a strong and significant relationship between phylogeny and morphological variation but not between phylogeny an...

New World proboscidean extinctions: comparisons between North and South America

Abstract: In South America, generally accepted dates place humans in coastal Chile and Patagonia ca. 13,000 BP and sites no older than ca. 11,000 BP are common in other areas. Gomphotheres become extinct in the late Pleistocene, probably after humans arrived and as climate changed. However, bone dates suggest that in many regions of South America, especially the Pampean region of Argentina and Uruguay (ca. 21,000 to 18,000 BP), gomphotheres already were gone when the first humans arrived. Although gomphothere remains are present at Monte Verde and other sites, they do not appear to have been important for human subsistence. In North America, human presence also is accepted around 11,500 BP. Gomphotheres range throughout much of Mexico into the US Southwest. Very few places are known with dated Quaternary gomphotheres, and most of them are considered paleontological localities rather than archeological sites. A small number of reliable associations between Clovis artifacts and proboscideans correspond to Mammuthus and Mammut remains. Controversial human evidence has been proposed for Valsequillo (Puebla, Mexico), where gomphotheres coexisted with mammoth and mastodons. Recent findings in northern Sonora, on more secure grounds, point to a human–gomphothere relationship around 11,000 BP. No human–gomphothere association is documented in the USA. Gomphotheres apparently survive until the end of the Pleistocene, but certainly those survivors were unique relict populations. Gomphothere extinction is driven more by climate and ecosystem changes than through human interactions.

Taphonomic analysis of the Folsom bonebed at Lake Theo, Texas

Abstract: The Lake Theo site is one of a handful of excavated Folsom-aged bonebeds on the Southern Plains. Despite the importance of this site, only limited research has been conducted on the collection. Thi...

Secretory Gene Recruitments in Vampire Bat Salivary Adaptation and Potential Convergences With Sanguivorous Leeches

Abstract: Regulatory evolution is thought to be fundamental to adaptive evolution. However, the identification of specific regulatory changes responsible for adaptation are sparse. Bats of the family Phyllostomidae, owing to their unparalleled rate of ecological and morphological evolution, represent an ideal system to identify regulatory evolution of adaptive significance. Among ecological niche leaps observed in this family, the most dramatic is the evolution of obligate sanguivory by vampire bats, which due to their highly derived phenotype, the sporadic phylogenetic occurrence of blood-feeding, and the adaptive potential of salivary glands, has enabled the development of hypotheses about adaptive molecular phenotypes. Using comparative transcriptomics of vampire bat, outgroup insectivorous bats, and sanguivorous leeches we identify genes that have been convergently recruited as secretory products of salivary glands of vampire bats and leeches. Comparisons of vampire bat to lineages maintaining the primitive chiropteran condition of insectivory indicated gene recruitment of alternative splice variants, and 5’ exon evolution, as the mechanisms producing secretory expression in vampire bats, but not in the insectivorous bats Macrotus and Myotis. Biochemical functions of hypothesized recruited genes explain adaptive benefits to sanguivory by modulating host hemostasis and neural signaling. It is difficult to identify how complex phenotypic change and rapid ecological transition, such as that observed in vampire bats, evolved over a short evolutionary timescale. Results indicate that regulatory evolution controlling tissue-specific splicing patterns has been important to successful adaptation of this lineage. Future studies that leverage emerging long sequence-read technologies, increased sample sizes, and expression and sequence comparisons across other sanguivore lineages will further elucidate roles of alternative splicing and gene recruitment in the remarkable evolution of sanguivory.

The First Record of the Jumping Mouse Zapus from the Southern High Plains

Abstract: Macy Locality 100, located on the Southern High Plains in West Texas, has produced a diverse faunal assemblage associated with radiocarbon-dated late Pleistocene alluvial deposits. Cheek teeth representing the jumping mouse Zapus (Rodentia, Zapodidae) provide the first record of jumping mice from the region. They are identified as Zapus hudsonius based on the occlusal pattern. A mesic form, its retreat from the region, is a result of environmental changes at the end of the Pleistocene.

A Mammalian Species New to the Fauna of Louisiana

Abstract: The known distribution of Baiomys taylori taylori is limited to Texas, Oklahoma, New Mexico, and Mexico. Baiomys t. taylori is reported for the first time from Louisiana, from the northwestern portion of the state.