Browsing by Author "Bradley, Robert D. (TTU)"
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Item A new species of big-eared climbing rat, genus Ototylomys (Cricetidae: Tylomyinae), from Chiapas, Mexico(2017) Porter, Calvin A.; Beasley, Nia E.; Ordóñez-Garza, Nicté (TTU); Lindsey, Laramie L. (TTU); Rogers, Duke S.; Lewis-Rogers, Nicole; Sites, Jack W.; Bradley, Robert D. (TTU)An allopatric population of big-eared climbing rats (Ototylomys) from the Northern Highlands of Chiapas, Mexico, is described as a new species. The new taxon is part of a unique montane rainforest community that includes several other endemic species in the limited geographic range between the Río Grijalva and the Central Depression of Chiapas. Several cranial, external, and molecular characters distinguish this new species of big-eared climbing rat from its more widely distributed congener, Ototylomys phyllotis. We performed principal component and discriminate function analyses of cranial measurements, and found that specimens of the new species consistently could be distinguished from other Ototylomys with strong statistical support. Compared withexemplars of Ototylomys from elsewhere in their range, the new species possesses a karyotype that differs by 3 additional biarmed chromosome pairs, is fixed or nearly fixed for distinct electromorphs at 12 allozyme loci, and the mean genetic distance exceeds 14%, based on comparisons of the mitochondrial cytochrome b gene between the new species of Ototylomys and representatives of O. phyllotis. The restricted distribution in montane karst rainforest suggests that the species and its habitat may be a matter of conservation concern. Una población alopátrica de rata orejuda trepadora (Ototylomys) de las Tierras Altas del Norte de Chiapas, México se describe como una nueva especie. El nuevo taxón es parte de una comunidad única de bosque lluvioso montano que incluye varias especies endémicas en el área de distribución geográfica limitada entre el Río Grijalva y la Depresión Central de Chiapas. Varios caracteres craneales, externos, y moleculares distinguen la nueva rata orejuda trepadora de su congénere más ampliamente distribuido, Ototylomys phyllotis. Se realizaron análisis de componentes principales y de función discriminante de los caracteres craneales, y se encontró que los especímenes de La Pera fueron consistentemente distinguidos de otros Ototylomys con un fuerte soporte estadístico. En comparación con ejemplares de Ototylomys del rango, la nueva especie posee un cariotipo que difiere por 3 pares adicionales de cromosomas biarmados, está fijo o casi fijo por distintos electromorfos en 12 loci alozímicos. Adicionalmente, la media de la distancia genética comparada del gen mitochondrial citocromo b entre la nueva especie de Ototylomys y representantes de O. phyllotis, excede el 14%. La distribución restringida en el bosque lluvioso montano kárstico sugiere que la especie y su hábitat pueden ser de importancia para la conservación.Item Comparison of genetic variation between rare and common congeners of Dipodomys with estimates of contemporary and historical effective population size(2022) Halsey, Michaela K. (TTU); Stuhler, John D. (TTU); Bayona-Vásquez, Natalia J.; Platt, Roy N.; Goetze, Jim R.; Martin, Robert E.; Matocha, Kenneth G.; Bradley, Robert D. (TTU); Stevens, Richard D. (TTU); Ray, David A. (TTU)Species with low effective population sizes are at greater risk of extinction because of reduced genetic diversity. Such species are more vulnerable to chance events that decrease population sizes (e.g. demographic stochasticity). Dipodomys elator, (Texas kangaroo rat) is a kangaroo rat that is classified as threatened in Texas and field surveys from the past 50 years indicate that the distribution of this species has decreased. This suggests geographic range reductions that could have caused population fluctuations, potentially impacting effective population size. Conversely, the more common and widespread D. ordii (Ord’s kangaroo rat) is thought to exhibit relative geographic and demographic stability. We assessed the genetic variation of D. elator and D. ordii samples using 3RAD, a modified restriction site associated sequencing approach. We hypothesized that D. elator would show lower levels of nucleotide diversity, observed heterozygosity, and effective population size when compared to D. ordii. We were also interested in identifying population structure within contemporary samples of D. elator and detecting genetic variation between temporal samples to understand demographic dynamics. We analyzed up to 61,000 single nucleotide polymorphisms. We found that genetic variability and effective population size in contemporary D. elator populations is lower than that of D. ordii. There is slight, if any, population structure within contemporary D. elator samples, and we found low genetic differentiation between spatial or temporal historical samples. This indicates little change in nuclear genetic diversity over 30 years. Results suggest that genetic diversity of D. elator has remained stable despite reduced population size and/or abundance, which may indicate a metapopulation-like system, whose fluctuations might counteract species extinction.Item Differential Expression in Testis and Liver Transcriptomes from Four Species of Peromyscus (Rodentia: Cricetidae)(2019) Lindsey, Laramie L. (TTU); Platt, Roy N.; Phillips, Caleb D. (TTU); Ray, David A. (TTU); Bradley, Robert D. (TTU)The genus Peromyscus represents a rapidly diverged clade of Cricetid rodents that contains multiple cryptic species and has a propensity for morphologic conservation across its members. The unresolved relationships in previously proposed phylogenies reflect a suspected rapid adaptive radiation. To identify functional groups of genes that may be important in reproductive isolation in a reoccurring fashion across the Peromyscus phylogeny, liver and testis transcriptomes from four species (P. attwateri, P. boylii, P. leucopus, and P. maniculatus) were generated and differential expression (DE) tests were conducted. Taxa were selected to represent members diverged from a common ancestor: P. attwateri + P. boylii (clade A), and P. leucopus + P. maniculatus (clade B). Comparison of clades (A vs. B) suggested that 252 transcripts had significant DE in the liver data set, whereas significant DE was identified for 657 transcripts in the testis data set. Further, 45 genes had DE isoforms in the 657 testis transcripts and most of these functioned in major reproductive roles such as acrosome assembly, spermatogenesis, and cell cycle processes (meiosis). DE transcripts in the liver mapped to more broad gene ontology terms (metabolic processes, catabolic processes, response to chemical, and regulatory processes), and DE transcripts in the testis mapped to gene ontology terms associated with reproductive processes, such as meiosis, sperm motility, acrosome assembly, and sperm-egg fusion. These results suggest that a suite of genes that conduct similar functions in the testes may be responsible for the adaptive radiation events and potential reoccurring speciation of Peromyscus in terms of reproduction through varying expression levels.Item Distinct mtDNA lineages in free-ranging Ammotragus(aoudad) from the United States indicate multiple introductions from northern Africa(2022) Wright, Emily A. (TTU); Wiedmeier, Rachael C. (TTU); Roberts, Emma K. (TTU); Pipkin, David R.; Hernández, Froylán; Bayouth, Joseph P. (TTU); Conway, Warren C. (TTU); Bradley, Robert D. (TTU)Translocation records indicate aoudad (Ammotragus lervia) populations in the United States are a product of multiple human-mediated introductions. Two mitochondrial markers (cytochrome b, cytb; displacement loop, D loop) and one nuclear gene (prion protein gene exon 3, PRNP) were used to determine: (1) genetic variation, (2) if genetic units correspond to taxonomic designations, (3) the number and geographic origin of translocations, and (4) divergence times. Three phylogenetic analyses (Bayesian inference, maximum likelihood, and parsimony) produced similar topologies with two clades (I and II). Clade I contained progeny of individuals resulting from introductions to Texas and Spain, and individuals from Algeria. Individuals in Clade II were progeny of past introductions to the United States and Europe, and northern Algeria. Clade II was subdivided into two subclades (A and B) representing two haplogroups. No genetic variation was detected in the PRNP sequences. Three haplogroups appeared to correspond to the subspecies A. l. lervia and A. l. sahariensis whose native distribution includes northwestern Africa. Network analyses assigned haplogroups to two major groups similar to those depicted in the phylogenetic analyses. Genetic distances ranged from 0.80% to 5.17% and 2.99% to 15.42% for cytb and D loop, respectively; and were higher than normally recovered for caprids, warranting a reexamination of subspecific status. Divergence dates indicated a major split between A. l. lervia and A. l. sahariensis circa 2.38 mya. Together, the high level of genetic divergences among US populations and apparent presence of two subspecies of aoudad in the United States support the hypothesis of multiple introductions from multiple sources.Item Gamete Recognition Gene Divergence Yields a Robust Eutherian Phylogeny across Taxonomic Levels(2023) Roberts, Emma K. (TTU); Wright, Emily A. (TTU); Worsham, Asha E. (TTUHSC); Hardy, Daniel M. (TTUHSC); Bradley, Robert D. (TTU)The extraordinary morphological diversity among extant mammals poses a challenge for studies of speciation, adaptation, molecular evolution, and reproductive isolation. Despite the recent wealth of molecular studies on mammalian phylogenetics, uncertainties remain surrounding both ancestral and more recent divergence events that have proven difficult to resolve. Multi-gene datasets, especially including genes that are highly divergent, often provide increased support for higher-level affinities within Mammalia; however, such analyses require vast amounts of genomic sequence data and at times, intensive, high-performance computational effort. Furthermore, despite the large-scale efforts dedicated to comprehensive, multi-gene phylogenetic analyses using a combination of mitochondrial, nuclear, and other sequences (e.g., tRNA, ultra-conserved elements, and transposable elements), many relationships across Mammalia remain highly controversial. To offer another approach and provide a phylogenetic solution to this longstanding issue, here we present a phylogenetic tool based on a single reproductive molecular marker, zonadhesin (gene: Zan), one of two known mammalian speciation genes, which encodes the rapidly evolving sperm protein zonadhesin that mediates species-specific adhesion to the egg and thereby promotes reproductive isolation among placental mammals (Eutheria). Topological comparison of Zan Maximum Likelihood phylogenies to a nearly complete mammalian supertree confirmed Zan’s striking phylogenetic utility and resolution at both deeper and more terminal nodes in the placental mammalian phylogeny. This single gene marker yielded an equivalent and/or superiorly supported topology in comparison to a supertree generated using DNA sequences from a supermatrix of 31 genes from 5911 species (extinct and extant). Resolution achieved with this new phylogenetic approach provides unique insights into the divergence of both early and recent mammalian radiations. Finally, and perhaps most importantly, the utility of zonadhesin as a singular molecular marker was especially useful in clades where sufficient taxon sampling is impossible to achieve, and where only a subset of members of the mammalian species tree is available. The eutherian relationships presented here provide a foundation for future studies in the reconstruction of mammalian classifications, including reproductive isolation, hybridization, and biodiversification of species.Item Mammal collections of the Western Hemisphere: A survey and directory of collections(2018) Dunnum, Jonathan L.; McLean, Bryan S.; Dowler, Robert C.; Alvarez-Castañeda, Sergio Ticul; Bradley, Jeff E.; Bradley, Robert D. (TTU); Carraway, Leslie N.; Carrera-E, Juan P. (TTU); Conroy, Christopher J.; Coyner, Brandi S.; Demboski, John R.; Dick, Carl W.; Doyle, Kate; Esselstyn, Jacob A.; Gutiérrez, Eliecer; Hanson, John D.; Holahan, Paula M.; Holmes, Thorvald; Iudica, Carlos A.; Leite, Rafael N.; Lee, Thomas E.; Lim, Burton K.; Malaney, Jason L.; McLaren, Suzanne B.; Moncrief, Nancy D.; Olson, Link; Ordóñez-Garza, Nicte (TTU); Phillips, Caleb D. (TTU); Revelez, Marcia A.; Rickart, Eric A.; Rogers, Duke S.; Thompson, Cody W.; Upham, Nathan S.; Velazco, Paul M.As a periodic assessment of the mammal collection resource, the Systematic Collections Committee (SCC) of the American Society of Mammalogists undertakes decadal surveys of the collections held in the Western Hemisphere. The SCC surveyed 429 collections and compiled a directory of 395 active collections containing 5,275,155 catalogued specimens. Over the past decade, 43 collections have been lost or transferred and 38 new or unsurveyed collections were added. Growth in number of total specimens, expansion of genomic resource collections, and substantial gains in digitization and web accessibility were documented, as well as slight shifts in proportional representation of taxonomic groups owing to increasingly balanced geographic representation of collections relative to previous surveys. While we find the overall health of Western Hemisphere collections to be adequate in some areas, gaps in spatial and temporal coverage and clear threats to long-term growth and vitality of these resources have also been identified. Major expansion of the collective mammal collection resource along with a recommitment to appropriate levels of funding will be required to meet the challenges ahead for mammalogists and other users, and to ensure samples are broad and varied enough that unanticipated future needs can be powerfully addressed.Item Morphometric and genetic variation in 8 breeds of Ethiopian camels (Camelus dromedarius)(2018) Legesse, Yoseph W.; Dunn, Christopher D. (TTU); Mauldin, Matthew R.; Ordonez-Garza, Nicte (TTU); Rowden, Gage R. (TTU); Gebre, Yoseph Mekasha; Kurtu, Mohammed Y.; Ali, Seid Mohammed; Whibesilassie, Wondmagegne D.; Ballou, Michael (TTU); Tefera, Melaku; Perry, Gad (TTU); Bradley, Robert D. (TTU)Dromedary camels (Camelus dromedarius) are a domesticated and closely guarded economic staple of indigenous people located throughout Ethiopian territorial states. Seventeen morphometric variables were examined to determine intraspecific variation among 8 pastoralist- designated breeds of camels. Additionally, DNA sequences from mitochondrial cytochrome-b gene and genotyping of 6 nuclear microsatellite loci were examined to assess genetic diversity and phylogenetic relationship of Ethiopian camels. Examination of 525 individuals revealed significant morphometric differentiation in Afar as compared with the remaining 7 breeds. Analysis of cytochrome-b sequences failed to recover monophyletic groups associated with pastoralist-recognized breeds. Analysis of 6 microsatellite loci from 104 individuals depicted no resolution of distinct genetic lineages in accordance to geographical or designated breeds. Overall, separation of 2 ecotypes based on the morphometric data was supported; however, genetic analysis of cytochrome-b and microsatellite data failed to support any unique genetic lineage or statistically significant population structure.Item Prospecting for Zoonotic Pathogens by Using Targeted DNA Enrichment(2023) Enabulele, Egie E.; Clec'h, Winka Le; Roberts, Emma K. (TTU); Thompson, Cody W.; McDonough, Molly M.; Ferguson, Adam W.; Bradley, Robert D. (TTU); Anderson, Timothy J.C.; Platt, Roy N.More than 60 zoonoses are linked to small mammals, including some of the most devastating pathogens in human history. Millions of museum-archived tissues are available to understand natural history of those pathogens. Our goal was to maximize the value of museum collections for pathogen-based research by using targeted sequence capture. We generated a probe panel that includes 39,916 80-bp RNA probes targeting 32 pathogen groups, including bacteria, helminths, fungi, and protozoans. Laboratory-generated, mock-control samples showed that we are capable of enriching targeted loci from pathogen DNA 2,882-6,746-fold. We identified bacterial species in museum-archived samples, including Bartonella, a known human zoonosis. These results showed that probe-based enrichment of pathogens is a highly customizable and efficient method for identifying pathogens from museum-archived tissues.Item Updated distribution of the Texas kangaroo rat (Dipodomys elator) and patterns of rodent species associations from county road surveys in Texas(2023) Stuhler, John D. (TTU); Halsey, Michaela K. (TTU); Goetze, Jim R.; Bradley, Robert D. (TTU); Ray, David A. (TTU); Stevens, Richard D. (TTU)The Texas kangaroo rat (Dipodomys elator) is a rare species of conservation interest at both the state and federal level. Therefore, an updated understanding of distribution and abundance of D. elator is critical for initiating informed decisions about its conservation status and subsequent management strategies. We surveyed more than 850 locations along unpaved county roads across the historical range of this species in north-central Texas to identify sites of D. elator presence and examine patterns of rodent species associations. We determined that D. elator presently occurs in five counties in Texas within its historical range and was the eighth most abundant species of the 14 species that we captured. Moreover, we found that the majority of pairwise species associations, including those involving D. elator, were random and there was no strong evidence that pairs of rodents were aggregating or segregating with respect to each other. We did observe negative associations between D. elator and both Dipodomys ordii (Ord’s kangaroo rat) and Sigmodon hispidus (hispid cotton rat). Nonetheless, these patterns indicate that interspecific interactions do not play a strong role in influencing the distribution of D. elator. However, the restricted and temporally dynamic distribution of this species suggests that a metapopulation perspective should be considered when making future conservation considerations.Item Whole mitochondrial genomes provide increased resolution and indicate paraphyly in deer mice(2017) Sullivan, Kevin A.M. (TTU); Platt, Roy N. (TTU); Bradley, Robert D. (TTU); Ray, David A. (TTU)Background Recent phylogenies of deer mice, genus Peromyscus, have relied heavily on mitochondrial markers. These markers provided resolution at and below the level of species groups, but relationships among species groups and Peromyscus affiliated genera have received little support. Here, we present the mitochondrial genomes of 14 rodents and infer the phylogeny of Peromyscus and related taxa. Results Our analyses support results from previous molecular phylogenies, but also yield support for several previously unsupported nodes throughout the Peromyscus tree. Our results also confirm several instances of paraphyly within the clade and suggest additional taxonomic work will be required to clarify some relationships. Conclusions Our findings greatly enhance our understanding of the evolution of Peromyscus providing support for previously unsupported relationships. However, the results also highlight the need to address paraphyly that may exist in this clade.