Papers by Rodney Honeycutt
Mitochondrial DNA Variation and the Phylogeny of African Mole Rats (Rodentia: Bathyergidae)
Systematic zoology, Sep 1, 1987
Page 1. Syst. Zool., 36(3):280-292, 1987 MITOCHONDRIAL DNA VARIATION AND THE PHYLOGENY OF AFRICAN... more Page 1. Syst. Zool., 36(3):280-292, 1987 MITOCHONDRIAL DNA VARIATION AND THE PHYLOGENY OF AFRICAN MOLE RATS (RODENTIA: BATHYERGIDAE) RODNEY L. HONEYCUTT,1 SCOTT V. EDWARDS,1-3 KlMBERLYN ...
Whole Genome Amplification for Sequencing and Applications in Conservation Genetics
Journal of Wildlife Management, Jun 1, 2007
ABSTRACT We describe a method for rapidly amplifying whole genomes via a Phi29 DNA polymerase-med... more ABSTRACT We describe a method for rapidly amplifying whole genomes via a Phi29 DNA polymerase-mediated strand displacement reaction (SDR). Genomic amplification products derived from the SDR reaction resulted in high quantities of DNA suitable for polymerase chain reaction (PCR) amplification and sequencing of mitochondrial genomes. Control region sequences of DNA derived directly from PCR amplicons of extracted DNA were identical to those derived from PCR amplification of SDR genomic DNA. Effective SDR amplification and subsequent sequencing was successful across tissues sources ranging in age from 1 year to 19 years. Strand replacement reaction genomic amplification offers a means of obtaining large quantities of DNA from small amounts of tissue.
Evolution, Jul 1, 1987
Restriction-enzyme analysis of mitochondrial DNA and protein electrophoresis were used to documen... more Restriction-enzyme analysis of mitochondrial DNA and protein electrophoresis were used to document patterns of gene flow across a hybrid zone between chromosomal races of Peromyscus leucopus. Chromosomal markers (three inversions) are such that individuals can be classified as potential F, 's, backcrosses, or parental types. Allozymic characterization ofthe hybrid zone is congruent with the chromosomal data (Stangl, 1986) and indicates an assymetrical distribution of markers, with the northeastern markers being distributed at a higher frequency into southwestern populations. Restriction patterns ofmtDNA suggest that the two cytotypes may have had different evolutionary histories, and the distribution of haplotypes is concordant with other genetic markers used to identify the hybrid zone. Concordant changes in chromosomes, allozymes, and mtDNA suggest that the most viable hypothesis for the origin ofthe zone is secondary contact. A unique aspect of this study is that the same individuals were used for protein electrophoresis, mtDNA analysis, and chromosomal analysis. Thus, patterns ofgenetic variation can be interpreted free of any historical bias associated with samples collected at different times.
Molecular Biology and Evolution, 1992
The evolution of the Old World monkey tribe Papionini, composed of macaques, baboons, mandrills, ... more The evolution of the Old World monkey tribe Papionini, composed of macaques, baboons, mandrills, drills, and mangabeys, was examined using mitochondrial DNA (mtDNA) sequence data on the cytochrome ox&se subunit II gene. When analyzed cladisticahy, these data support a baboon clade of savannah (Pupio) plus gelada (Theropithecus) baboons, as well as a clade containing drill (Mandrillus) plus mangabey (Cercocebus) genera. This result stands in opposition to most morphological phylogenies, which break up the baboon clade by placing Papio and Mandrillus as sister taxa and Theropithecus as a more distantly related lineage. Analyses of CO11 gene sequences also suggest that the papionin ancestral stock divided into two lineages, one leading to macaques and the other to the purely African genera. From a molecular evolutionary perspective, the papionin CO11 gene sequences reveal a pattern of amino acid replacements concentrated in the regions spanning the mitochondrial membrane.
2. Systematics and Evolution of the Family Bathyergidae
Proceedings of the National Academy of Sciences of the United States of America, Feb 15, 1991
Resolution of the African hominoid trichotomy by use of a mitochondrial gene sequence (hominoid p... more Resolution of the African hominoid trichotomy by use of a mitochondrial gene sequence (hominoid phylogeny/mitochondrial DNA/cytochrome oxidase subunit H gene/molecular anthropology)
Microsatellite DNA variation in Spalacopus cyanus, a social subterranean rodent endemic to Chile (Rodentia: Octodontidae)
Lynx, 2023
We used five polymorphic microsatellite loci to examine patterns of genetic variation within and ... more We used five polymorphic microsatellite loci to examine patterns of genetic variation within and among colonies of coruros (Spalacopus cyanus) at three localities in central Chile. Detailed comparisons of genetic variation at two locations, Los Maitenes in the northern portion of the species’ range and El Alamo in the south, displayed very different patterns of variation. Overall variation (alleles per locus and heterozygosity) within and among colonies at Los Maitenes was several times higher than observed at El Alamo, with the latter showing patterns of variation more consistent with a social species of subterranean rodent. Comparisons among Los Maitenes, El Alamo, and Los Vilos, another northern population, revealed a distinct genetic subdivision between northern and southern localities, indicating little evidence of genetic exchange between these two regions. We discuss these patterns of variation in relation to previous genetic research on Spalacopus and other subterranean rodents.
Annals of Carnegie Museum, Nov 7, 1986
Taxonomic and distributional comments are given for six species in three families of bats from Ke... more Taxonomic and distributional comments are given for six species in three families of bats from Kenya. Two species {Hipposideros camerunensis and Tadarida russata) are reported from Kenya for the first time.
The Influence of Topography and Vegetation on the Distribution of Small Mammals in Southwestern Utah
Southwestern Naturalist, Aug 21, 1981
... Although reported to be widely distributed in southwestern Utah (Hardy, 1945; Durrant, 1952),... more ... Although reported to be widely distributed in southwestern Utah (Hardy, 1945; Durrant, 1952), the two species of Perognathus were found at only two sites in the creosote bush community. ... 5( Peromyscus mani&amp;amp;amp;amp;amp;amp;#x27;culatus 2(2.2) 1 (0. 9) 5(3.9) 17(6.8) 12(1.4) 9(3.4) ...
Journal of Mammalogy, Sep 14, 2012
Knowledge of population boundaries and long-distance movements is important for wildlife conserva... more Knowledge of population boundaries and long-distance movements is important for wildlife conservation. We used genetic tools to investigate genetic diversity, population structure, and movements of mountain lions (Puma concolor) in Texas. We amplified 11 microsatellite loci for 245 individuals collected during 1985-2010 from Texas and New Mexico. Bayesian clustering and values of F ST suggested a partitioning of mountain lions into 3 genetically differentiated groups, New Mexico, western Texas, and southern Texas. New Mexico and western Texas exhibited moderate levels of genetic diversity (expected heterozygosity [H E ] ¼ 0.61 and 0.58, respectively), whereas diversity in southern Texas was lower (H E ¼ 0.47). Southern Texas displayed elevated genetic structure when compared to western Texas and New Mexico (F ST ¼ 0.102-0.148), whereas the comparison between New Mexico and western Texas revealed less subdivision (F ST ¼ 0.056). We documented long-distance movement among regions, and New Mexico and western Texas were sources for putative dispersers we sampled outside known populations. Differences in genetic structure and diversity between southern and western Texas support the designation of separate management units. Southern Texas appears isolated and further investigation is needed to determine the current population status. Mountain lion populations in New Mexico and western Texas may be important for future recolonization into portions of the southern United States.
Microsatellite Variation in Two Populations of Mountain Lions (Puma concolor) in Texas
Southwestern Naturalist, Jun 1, 2000
... Queller et al., 1993; Paetkau and Stro-beck, 1994; Garcia-Moreno et al., 1996; Lade et al., 1... more ... Queller et al., 1993; Paetkau and Stro-beck, 1994; Garcia-Moreno et al., 1996; Lade et al., 1996; Garcia de Leon et al ... a weighted analysis of variance (Weir and Cockerham, 1984), and the analogous Rhots which includes a correlation in allele sizes (Micha-lakis and Excoffier ...
Southwestern Naturalist, Sep 1, 2011
We used non-invasive genetic techniques to investigate the number and distribution of cougars (Pu... more We used non-invasive genetic techniques to investigate the number and distribution of cougars (Puma concolor) inhabiting Guadalupe Mountains National Park, Texas. During 8 years, $31 resident and transient cougars were identified genetically and $15 individuals used the park in 2002. Based on estimates of size of home ranges of males and females, the park should support 4-6 resident adults. Genetic data suggest a high number of transients and, perhaps, an unstable population that may be the result of intense hunting pressure outside protected areas. Analysis of genetic diversity indicates restricted gene flow between the park and other populations in western Texas.
Evolution, Jul 1, 1987
Restriction-enzyme analysis of mitochondrial DNA and protein electrophoresis were used to documen... more Restriction-enzyme analysis of mitochondrial DNA and protein electrophoresis were used to document patterns of gene flow across a hybrid zone between chromosomal races of Peromyscus leucopus. Chromosomal markers (three inversions) are such that individuals can be classified as potential F, 's, backcrosses, or parental types. Allozymic characterization ofthe hybrid zone is congruent with the chromosomal data (Stangl, 1986) and indicates an assymetrical distribution of markers, with the northeastern markers being distributed at a higher frequency into southwestern populations. Restriction patterns ofmtDNA suggest that the two cytotypes may have had different evolutionary histories, and the distribution of haplotypes is concordant with other genetic markers used to identify the hybrid zone. Concordant changes in chromosomes, allozymes, and mtDNA suggest that the most viable hypothesis for the origin ofthe zone is secondary contact. A unique aspect of this study is that the same individuals were used for protein electrophoresis, mtDNA analysis, and chromosomal analysis. Thus, patterns ofgenetic variation can be interpreted free of any historical bias associated with samples collected at different times.
Molecular Ecology, Jun 1, 1993
The details of mitochondrial DNA (mtDNA) phylogenetic structure of the northern grasshopper mouse... more The details of mitochondrial DNA (mtDNA) phylogenetic structure of the northern grasshopper mouse Onychomys leucogaster were examined using populations from a postulated area of endemism that includes three arid regions (Colorado Plateaus, Interior Plains, and Wyoming Basins) in western North America. Fifteen tetra-and heptanucleotide restriction enzymes were used to assay restriction-site variation in a 2150-bp PCRamplified fragment of mtDNA representing the ND2 and part of the COI gene regions. A total of 18 mtDNA haplotypes were detected. Although overall genetic divergence among these haplotypes was low (average = 1.1 %), phylogeographic structuring was apparent. Notably, a clear phylogenetic split separated one group of haplotypes restricted to the Wyoming Basins from all others. This phylogenetic split was further corroborated by examination of nucleotide sequence variation from a 270-bp stretch of the mtDNA cytochrome b gene. Overall geographic and phylogenetic patterns suggest a complex history of geographic structuring and subsequent mixing of populations of grasshopper mice throughout the late Pleistocene. These patterns of variation are evaluated relative to alternative hypotheses about biotic responses to Quaternary climatic oscillations in western North American arid regions.
Behavioral Ecology and Sociobiology, Apr 20, 2000
Eusociality in mammals is defined in the present paper by the following criteria: reproductive al... more Eusociality in mammals is defined in the present paper by the following criteria: reproductive altruism (which involves reproductive division of labor and cooperative alloparental brood care), overlap of adult generations, and permanent (lifelong) philopatry. We argue that additional criteria such as the existence of castes, colony size, reproductive skew, and social cohesion are not pertinent to the definition of eusociality in mammals. According to our definition of mammalian eusociality, several rodent species of the African family Bathyergidae can be considered eusocial, including the naked mole-rat (Heterocephalus glaber), Damaraland mole-rat (Cryptomys damarensis), and several additional, if not all, species in the genus Cryptomys. Furthermore, some species of social voles (like Microtus ochrogaster) may also fulfill criteria of mammalian eusociality. Understanding the evolution of eusociality in mole-rats requires answers to two primary questions: (1) What are the preconditions for the development of their eusocial systems? (2) Why do offspring remain in the natal group rather than dispersing and reproducing? Eusociality in mammals is by definition a special case of monogamy (more specifically: monogyny one female breeding), involving prolonged pair bonding for more than one breeding period. We argue that eusociality in mole-rats evolved from a monogamous mating system where cooperative brood care was already established. A tendency for group living is considered to be an ancestral (plesiomorph) trait among African bathyergid mole-rats, linking them to other hystricognath rodents. A solitary lifestyle seen in
Microsatellites from the South American Coruro, Spalacopus cyanus
Molecular Ecology, Sep 1, 2000
Skip to Main Content. There will be a release of Wiley Online Library scheduled for Saturday 27th... more Skip to Main Content. There will be a release of Wiley Online Library scheduled for Saturday 27th November 2010. Access to the website will be disrupted as follows: New York 0630 EDT to 0830 EDT; London 1130 GMT to 1330 GMT; Singapore 1730 SGT to 1930 SGT. ...
Zenodo (CERN European Organization for Nuclear Research), Oct 11, 2019
An overview is provided herein of advancements in the species composition and phylogenetics of th... more An overview is provided herein of advancements in the species composition and phylogenetics of the Peromyscus maniculatus species group since Carleton's 1989 review of the genus. These advancements primarily are the result of studies of chromosomal chondrial genome. Evidence is summarized supporting the conclusion that variation in b gene as well as previously published and new sequences of the mitochondrial ND3/ND4/ND4L genes, the number of species in the P. maniculatus group is increased to nine (P.
National Quail Symposium Proceedings, 2000
Molecular Biology and Evolution, 1992
The evolution of the Old World monkey tribe Papionini, composed of macaques, baboons, mandrills, ... more The evolution of the Old World monkey tribe Papionini, composed of macaques, baboons, mandrills, drills, and mangabeys, was examined using mitochondrial DNA (mtDNA) sequence data on the cytochrome ox&se subunit II gene. When analyzed cladisticahy, these data support a baboon clade of savannah (Pupio) plus gelada (Theropithecus) baboons, as well as a clade containing drill (Mandrillus) plus mangabey (Cercocebus) genera. This result stands in opposition to most morphological phylogenies, which break up the baboon clade by placing Papio and Mandrillus as sister taxa and Theropithecus as a more distantly related lineage. Analyses of CO11 gene sequences also suggest that the papionin ancestral stock divided into two lineages, one leading to macaques and the other to the purely African genera. From a molecular evolutionary perspective, the papionin CO11 gene sequences reveal a pattern of amino acid replacements concentrated in the regions spanning the mitochondrial membrane.
Journal of Mammalogy, 2018
For polytypic mammal species, biogeographic barriers including rivers have often been used to del... more For polytypic mammal species, biogeographic barriers including rivers have often been used to delineate taxonomic units under the assumption that barriers have structured their distribution. We tested the importance of major riverine systems as biogeographic barriers in fox squirrels (Sciurus niger) across the state of Florida, where 4 currently recognized subspecies are delineated at major rivers. We also explored whether phylogeographic structure may be limited to ecologically divergent subspecies, specifically between S. n. avicennia and S. n. shermani. Using a multilocus approach to examine diversity, we found that restricted gene flow was only present between S. n. avicennia, located south of the Caloosahatchee River in south Florida, and the rest of S. niger, which is widespread across the state. Mitochondrial DNA revealed that 2 divergent groups of haplotypes are present and widespread across Florida, thus supporting the hypothesis that fox squirrels persisted in multiple refugia during the Pleistocene, and that S. n. avicennia diverged ecologically from other populations of fox squirrels relatively recently. This was supported by isolation with migration models that indicated matrilineal isolation since the onset of divergence between S. n. avicennia and S. n. shermani, which corresponds to the onset of ecological divergence in south Florida during the early Holocene. Isolation by distance at 8 microsatellite loci from the western panhandle to the southern end of the peninsula was significant only when S. n. avicennia was included; however, this was due to the hierarchical genetic patterns identified between S. n. avicennia and the other subspecies as determined by Bayesian clustering, and not due to spatially restricted dispersal. We postulate that the demographic isolation of S. n. avicennia is the result of adaptation to the unique ecological conditions of south Florida.
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Papers by Rodney Honeycutt