Robert Bradley

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Jayjit Majumdar

University of Kalyani

Bert Vaux

University of Cambridge

Josiah Townsend

Indiana University of Pennsylvania

Philipp Wolfgang Stockhammer

Ludwig-Maximilians-Universität München

Jose Ruben Guzman-Gutierrez

Universidad Humanista de las Americas

Kalevi Kull

University of Tartu

Thomas Holtz

University of Maryland

Antonio Saez Romero

Universidad de Sevilla

Freddy Bravo

Universidade Estadual de Feira de Sanana

Lena Geise

UERJ - Universidade do Estado do Rio de Janeiro / Rio de Janeiro State University

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Papers by Robert Bradley

Geographic Distribution and Genetic Diversity of Whitewater Arroyo Virus in the Southwestern United States

Emerging Infectious Diseases, Jun 1, 2001

The virus family Arenaviridae comprises two serocomplexes. The lymphocytic choriomeningitis-Lassa... more

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Bioinformatics : a multidisciplinary approach for the life sciences

Occasional papers

I pleistocene 1999 mammals hunting fishing rabies lyme disease emerging viruses hantavirus herbic... more I pleistocene 1999 mammals hunting fishing rabies lyme disease emerging viruses hantavirus herbicides cattle craps wetlands endangered species migratory birds elevation geology biological data water (patients birth defects Bioinformatics: A Multidisciplinary Approach for the Life Sciences .et cetera

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Ancient hybridization and subsequent mitochondrial capture in ground squirrels (genus Ictidomys)

The sister species Ictidomys parvidens and I. tridecemlineatus exhibit hybridization in southeast... more The sister species Ictidomys parvidens and I. tridecemlineatus exhibit hybridization in southeastern New Mexico and western Texas. Presumably, hybridization was due to secondary contact as a result of recent anthropogenic changes to the landscape. However, recent phylogenetic studies of Spermophilus, which previously included Ictidomys, indicated the possibility of widespread introgression due to paraphyly of haploytypes in the mitochondrial cytochrome-b (Cytb) gene. Samples of Ictidomys were obtained from 38 populations (N = 211) in the presumed zone of sympatry, as well as samples from 58 populations (N = 208) throughout the distribution of both sister species. DNA sequences from the Cytb gene (N = 419) and the Y-linked structural maintenance of chromosomes (SmcY) gene (N = 129) were used to determine the origin of paraphyly among Cytb haplotypes. In addition, divergence date estimates were calculated to determine the association between hybridization and climate oscillations. Ana...

Noteworthy karyotypes of rodents from Durango, Mexico /

Herein, vve report karyotypes for 10 species of rodents. Among these are karyotypes that to our k... more

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Mammal records from Briscoe, Dickens, Hall, and Motley counties, Texas

Occasional papers, 2009

In 2008, fieldwork was conducted that resulted in the identification of 18 new mammal records fro... more In 2008, fieldwork was conducted that resulted in the identification of 18 new mammal records from three counties (Dickens, Hall, and Motley) in northwest Texas. An additional 13 county records collected from 1956-2005 (including from Briscoe County) were identified after an examination of specimens housed in the Natural Science Research Laboratory of the Museum of Texas Tech University. Collecting efforts such as these provide important natural history data that can be used in future assessments of the mammalian diversity within Texas.

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A century of mammal research: changes in research paradigms and emphases

Journal of Mammalogy, 2018

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Evolutionary Modeling and Prediction of Non-Coding RNAs in Drosophila

PLoS ONE, 2009

We performed benchmarks of phylogenetic grammar-based ncRNA gene prediction, experimenting with e... more We performed benchmarks of phylogenetic grammar-based ncRNA gene prediction, experimenting with eight different models of structural evolution and two different programs for genome alignment. We evaluated our models using alignments of twelve Drosophila genomes. We find that ncRNA prediction performance can vary greatly between different gene predictors and subfamilies of ncRNA gene. Our estimates for false positive rates are based on simulations which preserve local islands of conservation; using these simulations, we predict a higher rate of false positives than previous computational ncRNA screens have reported. Using one of the tested prediction grammars, we provide an updated set of ncRNA predictions for D. melanogaster and compare them to previously-published predictions and experimental data. Many of our predictions show correlations with protein-coding genes. We found significant depletion of intergenic predictions near the 39 end of coding regions and furthermore depletion of predictions in the first intron of protein-coding genes. Some of our predictions are colocated with larger putative unannotated genes: for example, 17 of our predictions showing homology to the RFAM family snoR28 appear in a tandem array on the X chromosome; the 4.5 Kbp spanned by the predicted tandem array is contained within a FlyBase-annotated cDNA.

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Evolutionary Triplet Models of Structured RNA

PLoS Computational Biology, 2009

The reconstruction and synthesis of ancestral RNAs is a feasible goal for paleogenetics. This wil... more The reconstruction and synthesis of ancestral RNAs is a feasible goal for paleogenetics. This will require new bioinformatics methods, including a robust statistical framework for reconstructing histories of substitutions, indels and structural changes. We describe a ''transducer composition'' algorithm for extending pairwise probabilistic models of RNA structural evolution to models of multiple sequences related by a phylogenetic tree. This algorithm draws on formal models of computational linguistics as well as the 1985 protosequence algorithm of David Sankoff. The output of the composition algorithm is a multiple-sequence stochastic context-free grammar. We describe dynamic programming algorithms, which are robust to null cycles and empty bifurcations, for parsing this grammar. Example applications include structural alignment of non-coding RNAs, propagation of structural information from an experimentally-characterized sequence to its homologs, and inference of the ancestral structure of a set of diverged RNAs. We implemented the above algorithms for a simple model of pairwise RNA structural evolution; in particular, the algorithms for maximum likelihood (ML) alignment of three known RNA structures and a known phylogeny and inference of the common ancestral structure. We compared this ML algorithm to a variety of related, but simpler, techniques, including ML alignment algorithms for simpler models that omitted various aspects of the full model and also a posterior-decoding alignment algorithm for one of the simpler models. In our tests, incorporation of basepair structure was the most important factor for accurate alignment inference; appropriate use of posterior-decoding was next; and fine details of the model were least important. Posterior-decoding heuristics can be substantially faster than exact phylogenetic inference, so this motivates the use of sum-over-pairs heuristics where possible (and approximate sum-over-pairs). For more exact probabilistic inference, we discuss the use of transducer composition for ML (or MCMC) inference on phylogenies, including possible ways to make the core operations tractable.

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Fast Statistical Alignment

PLoS Computational Biology, 2009

should build and run smoothly on most *NIX machines, including Mac OS X and popular distributions... more should build and run smoothly on most *NIX machines, including Mac OS X and popular distributions of Linux. The program is compiled by navigating to the FSA root directory and typing the standard configure, make, make install. Use the configure script to specify installation options, etc. In order to align long DNA sequences, FSA requires that MUMmer [1] be installed. It is recommend that exonerate [2] is installed as well. If you wish to run FSA in parallelized mode, you must have a PostgreSQL [3] database available and a computer cluster managed by Condor [4].

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Transducers: an emerging probabilistic framework for modeling indels on trees

Bioinformatics, 2007

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The northern rock mouse : peromyscus nasutus (mammalia: rodentia), from the Davis Mountains, Texas /

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Obituary: Robert James Baker (1942–2018)

Journal of Mammalogy, Jul 20, 2018

On 30 March 2018, the science of mammalogy and the American Society of Mammalogists lost one of t... more On 30 March 2018, the science of mammalogy and the American Society of Mammalogists lost one of the most influential figures of the last half-century. Robert James Baker died quietly at his home in Lubbock, Texas (Fig. 1). He was born on 8 April 1942 to James Simeon Baker and Laura Cooper in Warren, Arkansas. His father was killed during World War II and his mother remarried, resulting in his growing up with six halfsiblings. According to Robert's autobiography in Going afield (330-number refers to specific publication in "Bibliography"), he spent a good deal of his youth with his grandparents on a 100-acre farm in the West Gulf Coastal Plain of southeastern Arkansas. He identified his maternal grandmother, "Grandma Rosie," as his best friend and his greatest influence during these years. His marriage to Jean Joyner on 19 August 1961 ended in divorce in 1975, but the marriage resulted in a daughter, April Baker-Padilla, and two grandchildren, Jason Baker and Faith Padilla. Robert was married to his wife of 39 years, Laura Kyle (M.D.), on 28 May 1978 in Lubbock. Their son, Robert Kyle Baker, preceded his father in death, which was a tragedy from which neither Robert nor Laura ever completely recovered. Robert was always more than willing to admit to his "type A" personality and he seemed to try to live daily by his motto "anything worth doing is worth overdoing." He must have always been a human dynamo, but with the diagnosis of type 1 diabetes while in the field in Alamos, Sonora, in the summer of 1966, he went into hyperdrive. He did not reduce his life goals, but instead decided that they would need to be accomplished in much less time. At the time of his diagnosis, diabetes typically was responsible for shortening life expectancy by one-third and could cause loss of eyesight, amputation of limbs, kidney failure, heart disease, and loss of nerve function. Robert stated in his autobiography, "Diabetes has been such a constant and obnoxious companion that it has often been a major statement of who I am" (330). Robert seemed to have a clock ticking at the back of his mind and everything needed to be moving at top speed. Anytime a colleague or student needed to repeat an experiment, his question would be: "Why is there always time to do it over but never enough to do it right the first time?" Anyone who accompanied Robert into the field could expect at least two things-Robert would do more work than you no matter how hard you worked and Robert would have a low blood sugar crisis at some point. The insulin control of diabetes, particularly in the early years using insulin from pigs, was imperfect at best. Colleagues and students who went to the field with Robert soon learned to pack a couple of extra cans of Coca-Cola, a bag of caramel candies, and Snickers bars, or to be prepared for a highspeed drive (always by Robert) to the nearest Allsup's or some local grog shop dispensing soft drinks. However, ultimately Robert won the race with diabetes, living longer than predicted and accomplishing most of his life goals. Age and accumulating health issues finally slowed the engine shortly after his retirement from Texas Tech University. Laura was constantly at his side until the end, giving loving and professional care. Robert began his collegiate education at Ouachita Baptist University in 1959 on an academic scholarship. He described his experience there as "nearly ending my college education" (330). Fortunately, he transferred to University of Arkansas at Monticello (then Arkansas A&M College) where he graduated in 1963. While at the university he was mentored by two professors

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Mammalogy at Texas Tech University : a historical perspective /

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Origin of a novel allele in a mammalian hybrid zone

Proceedings of the National Academy of Sciences, 1993

The occurrence of rare or novel alleles has been documented in at least 23 different hybrid zones... more The occurrence of rare or novel alleles has been documented in at least 23 different hybrid zones spanning vertebrate and invertebrate taxa. As most novel alleles either occur at high frequencies in hybrid populations or are exclusively restricted to hybrids, it has seemed probable that hybridization has a role in their origin; however, the molecular nature of these novel alleles and the mechanisms responsible for their origin remain obscure. We examined the complete coding sequences of six alleles of alcohol dehydrogenase in a mammalian hybrid zone between two species of pocket gophers (Geomys). One of these sequences encodes a novel electromorph that had been identified in earlier allozyme studies; this novel allele differs from one of the parental alleles by a single base substitution. This substitution generates an amino acid replacement that affects the net charge of the translated protein. This resultant charge change is congruent with the observed allozyme mobility patterns. ...

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Molecular Systematics Ofdipodomys Elator(Rodentia: Heteromyidae) and Its Phylogeographic Implications

Journal of Mammalogy, 2000

Previous systematic studies, using morphometric, allozymic, and cytogenetic data, have produced c... more Previous systematic studies, using morphometric, allozymic, and cytogenetic data, have produced conflicting results as to the relationship of Dipodomys elator to other species of kangaroo rats. In this study, phylogenetic relationships of D. elator and other closely related taxa (D. merriami, D. phillipsii, D. ordii, D. spectabilis, and D. nelsoni) were examined using nucleotide-sequence data (1,143 bp) from the mitochondrial cytochrome-b gene. With 1 exception, all parsimony and neighbor-joining analyses (regardless of differential weighting scheme or method of calculating genetic distances) indicated that D. elator is most closely related to D. phillipsii. As a result, it is recommended that D. elator and D. phillipsii be included within the phillipsii species group.

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Mitochondrial Dna Sequence Data Indicate Evidence For Multiple Species Within Peromyscus Maniculatus

Zenodo (CERN European Organization for Nuclear Research), Oct 10, 2019

Peromyscus maniculatus is one of the most commonly encountered and intensively studied small mamm... more Peromyscus maniculatus is one of the most commonly encountered and intensively studied small mammal species in North America. Because of a broad geographic distribution (Canada to central Mexico), relatively large amounts of morphometric and genetic variation, and a voluminous taxonomic history, the taxonomic delimitations of this taxon have been difficult to discern. Herein, a comprehensive phylogenetic study was conducted to assess patterns of genetic variation throughout the range of P. maniculatus to resolve the taxonomy and ascertain the distribution of phylogroups. DNA sequences from the mitochondrial cytochrome-b gene were included from 681 individuals, representing 28 of the 68 recognized subspecies formally assigned to P. maniculatus, as well as all members assigned to the P. maniculatus species group, to assess genetic variation across a broad geographic context. Parsimony, Bayesian, and maximum likelihood analyses were conducted to determine phylogenetic relationships; further, genetic distances and divergence dates were approximated to assist in determining the time of origin for phylogroups. Results of these analyses reveal the presence of eight major phylogenetic groups. With one exception, each lineage appears to represent a unique phylogenetic group that corresponds to a distinct geographic region. Results are in agreement with other studies suggesting that P. maniculatus (sensu lato) contained multiple phylogroups. Recognition of phylogroups followed by the application of the principals of taxonomic priority indicate that: 1) samples from western Nevada, southern California, and Baja California should be referred to as Peromyscus gambelii; 2) samples from the southwestern Yukon should be referred to as P. sp.; 3) samples from southeastern Alaska and southcentral Yukon southward along coastal British Columbia to southwestern Washington should be referred to as P. keeni; 4) samples from central and western North America should be referred to as Peromyscus sonoriensis; 5) samples from eastern Canada and the eastern United States should be referred to as P. maniculatus; 6) samples from extreme southwestern New Mexico and central Mexico should be referred to as Peromyscus labecula; and 7) Peromyscus sejugis from Isla Santa Cruz, Baja del Sur, Mexico, should be tentatively retained as a valid species name. These seven species along with Peromyscus melanotis and Peromyscus polionotus comprise the P. maniculatus species group.

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Two new species of<i>Peromyscus</i>(Cricetidae: Neotominae) from the Transverse Volcanic Belt of Mexico

Journal of Mammalogy, Dec 28, 2021

Specimens of the Peromyscus boylii species group distributed in the western and northeastern mont... more Specimens of the Peromyscus boylii species group distributed in the western and northeastern montane regions of Michoacán, México, historically have been assigned to P. levipes. Previous studies indicated that these specimens possessed mitochondrial DNA haplotypes that were distinct from both P. levipes and P. kilpatricki, a recently named species in the P. boylii species group from northeastern Michoacán and western Morelos. Herein karyotypic, DNA sequence, and morphological data were analyzed from those populations to evaluate their taxonomic affinity. Karyotypic data indicated that individuals from western Michoacán (Dos Aguas and Aguililla) and from a newly discovered population in northeastern Michoacán (Zinapécuaro) were chromosomally similar to P. carletoni (FN = 68) but distinct from other taxa assigned to the P. boylii species group. Analyses of cranial characteristics indicated that, relative to other species in the P. boylii species group, two morphologically distinct groups were present that corresponded to the Dos Aguas/Aguililla and Zinapécuaro populations, respectively. The latter population, although represented by a small sample size (n = 5 specimens), appeared to exhibit some trenchant morphological distinctions compared with other cryptic species in the P. boylii group. Phylogenetic analyses (parsimony, Bayesian, and likelihood) of DNA sequences obtained from the mitochondrial cytochrome-b gene indicated that although the individuals from Dos Aguas/Aguililla and Zinapécuaro formed a sister group relationship, they formed monophyletic clades that differed genetically (2.54%)—a level approaching that seen between other sister species of Peromyscus. Further, the Dos Aguas/Aguililla and Zinapécuaro clade was more closely aligned with a clade containing representatives of P. carletoni and P. levipes instead of with those from closer geographic proximities (P. kilpatricki) located in eastern Michoacán. Together, these results indicated that these two populations seemingly represent two undescribed species in the P. boylii species group for which we propose the names Peromyscus greenbaumi for populations in western Michoacán (circa Dos Aguas and Aguililla) and Peromyscus ensinki for populations in northeastern Michoacán (circa Zinapécuaro).Los especímenes del grupo de especies de Peromyscus boylii distribuidos en las regiones montañosas occidentales y el noreste de Michoacán, México, históricamente fueron asignados a P. levipes. Sin embargo, estudios previos han indicado que estos especímenes poseen haplotipos de ADN mitocondrial que son distintos de P. levipes y P. kilpatricki, una especie recientemente nombrada en el grupo de especies P. boylii del noreste de Michoacán y el oeste de Morelos. Los datos cariotípicos indicaron que los individuos del oeste de Michoacán (Dos Aguas y Aguililla) y de una población recién descubierta en el noreste de Michoacán (Zinapécuaro) eran cromosómicamente similares a P. carletoni (FN = 68), pero distintos de otros taxones asignados al grupo de especies P. boylii. Los análisis de las características craneales indicaron que en relación con otras especies del grupo de especies P. boylii, dos grupos morfológicamente distintos estaban presentes, y que correspondían a las poblaciones de Dos Aguas/Aguililla y Zinapécuaro, respectivamente. Aunque representada por un tamaño de muestra pequeño (n = 5 especímenes), esta última población pareció exhibir algunas diferencias morfológicas en comparación con las otras especies crípticas en el grupo P. boylii. Los análisis filogenéticos (parsimonia, inferencia bayesiana y verosimilitud) de secuencias de ADN obtenidas del gen mitocondrial citocromo-b, indicaron que, aunque los individuos de Dos Aguas/Aguililla y Zinapécuaro tienen una relación de grupo hermano, estos forman clados monofiléticos que difieren genéticamente (2.54%), nivel que se acerca al observado entre otras especies hermanas de Peromyscus. Además, el clado de Dos Aguas/Aguililla y Zinapécuaro está más estrechamente alineado con un clado que contenía representantes de P. carletoni y P. levipes en lugar de aquellos de proximidades geográficas más cercanas (P. kilpatricki) ubicados en el este de Michoacán. Estos resultados indicaron que estas dos poblaciones aparentemente representan dos especies no descritas en el grupo de especies P. boylii para las cuales proponemos los nombres Peromyscus greenbaumi para poblaciones en el oeste de Michoacán (hacia Dos Aguas y Aguililla) y Peromyscus ensinki para poblaciones en el noreste de Michoacán (circa Zinapécuaro).

Prospecting for Zoonotic Pathogens by Using Targeted DNA Enrichment

Emerging Infectious Diseases, Aug 1, 2023

Prospecting for zoonotic pathogens using targeted DNA enrichment

bioRxiv (Cold Spring Harbor Laboratory), Dec 8, 2022

There are over 60 zoonoses linked to small mammals, including some of the most devastating pathog... more There are over 60 zoonoses linked to small mammals, including some of the most devastating pathogens in human history. Meanwhile, millions of museum-archived tissues are available to understand natural history of these pathogens. Our goal is to maximize the value of museum collections for pathogen-based research using targeted sequence capture. To this end, we have generated a probe panel that includes 39,916, 80bp RNA probes targeting 32 pathogen groups, including bacteria, helminths, fungi, and protozoans. Lab generated, mock control samples show that we are capable of enriching targeted loci from pathogen DNA 2,882 to 6,746-fold. Further, we were able to identify bacterial species in museum-archived samples, including Bartonella, a known human zoonosis. These results show that probe-based enrichment of pathogens is a highly customizable and efficient method for identifying pathogens from museum-archived tissues.

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A Non-invasive, Biomarker Assay for Detecting Chronic Wasting Disease Pathology in White-tailed Deer

ABSTRACTWe describe a blood test that exploits differences in the abundance of diagnostic miRNA b... more ABSTRACTWe describe a blood test that exploits differences in the abundance of diagnostic miRNA biomarkers associated with prion infections in cervids. Using sera from 93 pen-raised white-tailed deer euthanized after unintentional exposure to Chronic Wasting Disease (CWD), quantification of candidate reference and diagnostic miRNAs revealed sensitivity of the q-RT-PCR method to interference from sample degradation, requiring exclusion of 60 specimens that exhibited excessive hemolysis or yielded poor amplification of reference or diagnostic miRNAs. Subsequent quantification of three potentially diagnostic and two control miRNAs in the 33 remaining, minimally degraded sera established diagnostic criteria congruent (100% sensitivity, 92.3% specificity, 93.9% accuracy) with results from standard CWD diagnosis by microscopic detection of immunoreactivity in obex and/or medial retropharyngeal lymph nodes (conducted by the National Veterinary Services Laboratory, NVSL, Ames, IA). Overall,...

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Geographic Distribution and Genetic Diversity of Whitewater Arroyo Virus in the Southwestern United States

Emerging Infectious Diseases, Jun 1, 2001

The virus family Arenaviridae comprises two serocomplexes. The lymphocytic choriomeningitis-Lassa... more

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Bioinformatics : a multidisciplinary approach for the life sciences

Occasional papers

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Ancient hybridization and subsequent mitochondrial capture in ground squirrels (genus Ictidomys)