Rodney L Honeycutt

Rodney L Honeycutt
Pepperdine University · Division of Natural Science

Ph.D. in Biology

About

510
Publications
51,890
Reads
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12,303
Citations
Additional affiliations
August 2011 - August 2018
Pepperdine University
Position
  • Head of Faculty
August 2006 - present
Pepperdine University
Position
  • Professor
May 2006 - present
Pepperdine University
Position
  • Professor
Description
  • I teach undergraduate courses in animal biology, ecology, genetics, natural history of the vertebrates, and environmental policy and politics. Currently, I am chairperson of the division.
Education
September 1983 - September 1984
University of Michigan
Field of study
  • Molecular Biology
May 1981 - September 1983
Australian National University
Field of study
  • Population Biology
January 1978 - May 1981
Texas Tech University
Field of study
  • Biology

Publications

Publications (510)
Article
Full-text available
Aim: Comprehensive, global information on species' occurrences is an essential biodiversity variable and central to a range of applications in ecology, evolution, biogeography and conservation. Expert range maps often represent a species' only available distributional information and play an increasing role in conservation assessments and macroeco...
Article
Full-text available
Editorial on the Research Topic DNA Barcodes: Controversies, Mechanisms, and Future Applications Biodiversity provides ecosystem services and direct and indirect benefits to society. Unfortunately, human activities are now accelerating the extinction rate of biodiversity at an alarming rate, and in many cases, species will disappear before their di...
Article
Full-text available
Fencing wildlife populations can aid wildlife management goals, but potential benefits may not always outweigh costs of confinement. Population isolation can erode genetic diversity and lead to the accumulation of inbreeding, reducing viability and limiting adaptive potential. We used microsatellite and mitochondrial DNA data collected from 640 whi...
Article
Full-text available
The emergence of several zoonotically-driven pandemics and near-pandemics (MERS, SARS, H1N1, Ebola, COVID-19, among others) over the last 20 years has placed an increasing emphasis on the importance of symbiotypes and the role of natural history collections, as virologic and human health studies are incorporating symbiotypes and host specimens as p...
Article
Full-text available
Climate change-induced extinctions are estimated to eliminate one in six known species by the end of the century. One major factor that will contribute to these extinctions is extreme climatic events. Here, we show the ecological impacts of recent record warm air temperatures and simultaneous peak drought conditions in California. From 2008–2016, t...
Article
Full-text available
Urbanization is increasing throughout the world, transforming natural habitats. Coyotes (Canis latrans) are found in highly urban, suburban, rural and undeveloped mountainous habitats, making them an exemplary model organism to investigate the effects of urbanization on animals. We hypothesized that coyotes in natural habitats are more genetically...
Article
Full-text available
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 a...
Article
Full-text available
Objective: The ruffed grouse, Bonasa umbellus, is broadly distributed across North America and displays considerable taxonomic diversity. Except for a genetic study of some western populations of ruffed grouse, nothing is known about genetic variation in other regions of Canada and the United States. Our objective is to examine patterns of mitocho...
Article
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 re...
Research
Full-text available
DNA Barcodes: Controversies, Mechanisms and Future Applications Invitation to submit manuscripts Oct 2018 - July 2019 Frontiers in Ecology and Evolution > Research Topics Editors: David S. Thaler and Rodney L. Honeycutt https://www.frontiersin.org/research-topics/8789/dna-barcodes-controversies-mechanisms-and-future-applications#overview
Article
The deer mouse species group centers around Peromyscus maniculatus and contains four peripherally distributed species. In order to address phylogenetic, taxonomic, and biogeographic questions concerning the westernmost deer mice, we analyzed mitochondrial sequence variation for 174 specimens from California to Washington and compared these to relev...
Article
The deer mouse species group centers around Peromyscus maniculatus and contains four peripherally distributed species. In order to address phylogenetic, taxonomic, and biogeographic questions concerning the westernmost deer mice, we analyzed mitochondrial sequence variation for 174 specimens from California to Washington and compared these to relev...
Article
We introduce a mathematical model for studying the population dynamics under drought of the California newt (Taricha torosa), a species of special concern in the state of California. Since 2012, California has experienced a record-setting drought, and multiple studies predict drought conditions currently underway will persist and even increase in s...
Article
Full-text available
The ecology of a species strongly influences genetic variation and population structure. This interaction has important conservation implications because taxa with low dispersal capability and inability to use different habitats are more susceptible to anthropogenic stressors. Ocelots (Leopardus pardalis albescens) and bobcats (Lynx rufus texensis)...
Article
The bobwhites (Colinus) consist of 3 grassland-associated, allopatric species of New World quails (family Odontophoridae): the northern bobwhite (C. virginianus), distributed from the eastern United States to Guatemala; the black-throated bobwhite (C. nigrogularis), which occurs in scattered localities in the Yucatán Peninsula, Nicaragua, and Hondu...
Article
Reproduction is timed so that parturition coincides with optimal conditions for offspring survival, with strong fitness implications in northern regions. However, in the southern United States the breeding season of white-tailed deer (Odocoileus virginianus) is relatively heterogeneous over short distances. To test the hypothesis that genetic diffe...
Article
The role of genetic relatedness in the evolution of eusociality has been the topic of much debate, especially when contrasting eusocial insects with vertebrates displaying reproductive altruism. The naked mole-rat, Heterocephalus glaber, was the first described eusocial mammal. Although this discovery was based on an ecological constraints model of...
Article
For millennia house mice and humans have been cohabitants, yet unlike man’s best friend, the mouse has been an unwelcome guest in the human domain. Despite the house mouse’s reputation as both beggar and thief, its current role as a model organism for the study of human disease has exalted this particular taxon, Mus musculus, above the approximatel...
Article
Twelve novel microsatellite markers were developed for the naked mole-rat, Heterocephalus glaber, a species characterized by a social structure analogous to that seen in eusocial insects. All but one locus (Hglab01) were found to be polymorphic across the 33 samples screened, with the number of alleles ranging from one to seven (average 3.58). Aver...
Article
We used mitochondrial DNA to study the population structure and genetic diversity of the northern bobwhite (Colinus virginianus) west of the Mississippi River. We observed a lack of phylogeographic structure, high haplotype diversity, and low nucleotide diversity for northern bobwhites in this part of their geographic range. Despite the discordance...
Article
We used sequences from the mitochondrial control region to examine the phylogeography and historical demography of the Scaled Quail and to determine whether the geographic distributions of mtDNA genealogy were concordant with the distribution of the subspecies. Overall, the Scaled Quail exhibited lower haplotype and nucleotide diversity than other...
Article
Full-text available
We conducted a phylogeographic study of the Gambel's Quail (Callipepla gambelii) using sequences of the mitochondrial control region and NADH dehydrogenase subunit 2 (ND2) obtained from 167 specimens including hunter–harvested wings and museum study skins. The Gambel's Quail exhibited strong phylogeographic structure, large genetic gaps, and relati...
Article
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Understanding of relationships between morphology and ecological performance can help to reveal how natural selection drives biological diversification. We investigate relationships between feeding behavior, foraging performance and morphology within a diverse group of teleost fishes, and examine the extent to which associations can be explained by...
Article
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Ocelots (Leopardus pardalis) in the United States currently exhibit low levels of genetic diversity. One hypothesis for this observation is that habitat fragmentation, resulting from human induced changes in the landscape during the 20(th) century, created island populations with highly reduced gene flow and increased genetic drift and inbreeding....
Article
Aquatic amphibians are known to be vulnerable to a myriad of invasive predators. Invasive crayfish are thought to have eliminated native populations of amphibians in some streams in the semi-arid Santa Monica Mountains of southern California. Despite their toxic skin secretions that defend them from native predators, newts are vulnerable to crayfis...
Article
Thesis (Ph. D.)--Texas Tech University, 1981. Includes bibliographical references (p. 84-89). Photocopy.
Article
Most contemporary studies of adaptive radiation focus on relatively recent and geographically restricted clades. It is less clear whether diversification of ancient clades spanning entire continents is consistent with adaptive radiation. We used novel fossil calibrations to generate a chronogram of Neotropical cichlid fishes and to test whether pat...
Article
Most contemporary studies of adaptive radiation focus on relatively recent and geographically restricted clades. It is less clear whether diversification of ancient clades spanning entire continents is consistent with adaptive radiation. We used novel fossil calibrations to generate a chronogram of Neotropical cichlid fishes and to test whether pat...
Chapter
The diversity of terrestrial mammals in South America is the result of both isolation and continental interchanges, preceded and followed by extinction and speciation (Simpson 1980; Marshall 1988). Mammalian biodiversity in South America can be partitioned into three major phases, beginning in the Paleocene (65.5–55.8 million years ago – Ma) with x...
Data
Full-text available
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. B...
Article
Full-text available
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. B...
Article
Full-text available
Genera within the South American cichlid tribe Geophagini display specialized feeding and reproductive strategies, with some taxa specialized for both substrate-sifting and mouth brooding. Several lineages within the clade also possess an epibranchial lobe (EBL), a unique pharyngeal structure that has been proposed to have a function in feeding and...
Data
Species scores in a Principal Components Analysis and Procrustes Superimposition of 7 diet categories and 10 morphometric variables associated with feeding without phylogenetic correction. See text for explanation of the methods and Table 3 for rotation matrix and Procrustes rotation matrices for diet and morphology eigenvector values. (DOC)
Data
Species scores in a Principal Components Analysis of 7 diet categories and 10 morphometric variables associated with feeding with phylogenetic correction. Results are not given in the main text because correlations between diet and morphology disappear after phylogenetic correction. See text for details. (DOC)
Data
PCA Eigenvectors and individual scores for a dataset of 10 morphological variables for 207 individuals in 21 genera and 55 species of South American cichlids, including 15 geophagine genera. See text and Figure 2 for details. Institutional abbreviations are as follows: ANSP - Academy of Natural Sciences of Philadelphia, USA; FMNH: Field Museum of N...
Data
Datafile. Raw genus-level morphometric data used in Principal Components Analyses to evaluate morphological differentiation at the genus level as illustrated in Figure 2 of the main paper. (XLS)
Data
Description of morphometric measurements taken in this study. The fist list includes the intial 23 variables measured in the comparative study of morphology and diet correlations. The second list shows the measures used in the comparison of intrageneric versus intergeneric morphometric variation illustrated in Fig. 2. (DOC)
Data
Dataset. Nexus file containing the 23-taxa pruned tree with branch lengths. (NEX)
Data
Dataset. Nexus file containing the topologies of the 166 taxon phylogeny from [16], the 350 and 635 taxon trees used in this paper and the binary matrices representing presence/absence of the Epibranchial lobe and mouthbrooding in each taxon for all trees. (NEX)
Data
Dataset. Excel file containing the raw mean values of the original 23 morphometric variables used in the diet-morphology correlation analyses. Diet data as used in the analyses are given in Table 1 of the main manuscript. (XLS)
Article
Full-text available
• Premise of the study: Microsatellite (simple sequence repeat [SSR]) markers were developed for Ceanothus megacarpus, a chaparral species endemic to coastal southern California, to investigate potential processes (e.g., fragmentation, genetic drift, and interspecific hybridization) responsible for the genetic structure within and among populations...
Article
Full-text available
The ocelot Leopardus pardalis has become a conservation priority in the US as a result of severe population decline and loss of habitat during the 20th century. Only two small populations remain in this country. Their short‐term viability is threatened by the disappearance of dense thornshrub communities, human‐caused mortality and demographic stoc...
Article
Full-text available
Previous analyses of relations, divergence times, and diversification patterns among extant mammalian families have relied on supertree methods and local molecular clocks. We constructed a molecular supermatrix for mammalian families and analyzed these data with likelihood-based methods and relaxed molecular clocks. Phylogenetic analyses resulted i...
Article
Full-text available
Food webs of streams draining tropical rain forests on Costa Rica's Pacific and Caribbean coasts were examined in the 1980s via dietary analyses, and the same streams were surveyed again in 2004 to compare trophic structure based on analysis of stable isotope ratios of fish, macro-invertebrate and plant tissues. Estimates of species’ trophic positi...
Article
Full-text available
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, t...
Article
In cattle (Bos taurus), there is evidence of more than 50 alleles of BoLA-DQB (bovine lymphocyte antigen DQB) that are distributed across at least five DQB loci, making this region one of the most complex in the BoLA gene family. In this study, DQB alleles were analysed for the water buffalo (Bubalus bubalis), another economically important bovine...
Article
Ecosystem processes and biological community structure are expected to change in a relatively predictable manner along fluvial gradients within river basins. Such predictions are heavily based on temperate rivers, and food web variation along fluvial gradients in Mesoamerican rivers has received limited attention. In this study, we analyzed carbon...
Chapter
This chapter adds detail to the current picture of dusky dolphin sociality by investigating the sex and relatedness of interacting individuals across different habitats and different behavioral contexts. The same features that make dusky dolphins such a challenging system for addressing social behavior questions (e.g., marine habitat, large group s...
Conference Paper
Background/Question/Methods Chaparral vegetation of southern California is regularly subjected to freezing, as temperatures can drop well below 0 C in cold valleys as well as at high elevations. Previous experiments established that Ceanothus species in the Santa Monica Mountains exhibit a broad range in cold tolerance, with lethal temperature fo...
Article
Full-text available
The increased battery of molecular markers, derived from comparative genomics, is aiding our understanding of the genetics of domestication. The recent BMC Biology article pertaining to the evolution of small size in dogs is an example of how such methods can be used to study the origin and diversification of the domestic dog. We are still challeng...
Article
Neotropical cichlid fishes comprise approximately 60 genera and at least 600 species, but despite this diversity, their phylogeny is only partially understood, which limits taxonomic, ecological and evolutionary research. We report the largest molecular phylogeny of Neotropical cichlids produced to date, combining data from three mitochondrial and...
Chapter
Full-text available
During the eighteenth, nineteenth, and early twentieth centuries, scientific inventories of biodiversity flourished as naturalists participated in expeditions throughout different geographic regions of the world (Köhler et al. 2005). These expeditions and the various journals produced by many prominent naturalists provided materials for extensive s...
Article
Aim: In order to resolve disputed biogeographical histories of biota with Gondwanan continental distributions, and to assess the null hypothesis of vicariance, it is imperative that a robust geological time-frame be established. As an example, the sudden and coincident appearance of hystricognath rodents (Rodentia: Hystricognathi) on both the Afric...
Article
ABSTRACT We used nucleotide sequence data from a mitochondrial DNA fragment to characterize variation within the endangered Lower Keys marsh rabbit (Sylvilagus palustris hefneri). We observed 5 unique mitochondrial haplotypes across different sampling sites in the Lower Florida Keys, USA. Based on the frequency of these haplotypes at different geog...
Article
Full-text available
In west-central Texas, USA, abatement efforts for the gray fox (Urocyon cinereoargenteus) rabies epizootic illustrate the difficulties inherent in large-scale management of wildlife disease. The rabies epizootic has been managed through a cooperative oral rabies vaccination program (ORV) since 1996. Millions of edible baits containing a rabies vacc...
Article
Full-text available
Although the type specimen of California Grunion (Leuresthes tenuis) was described from a local fish market In 1860, this coastal marine fish was not seen in San Francisco again until 2001, when California Grunion were taken during trawl surveys in San Francisco Bay. In 2005, spawning California Grunion were confirmed on a sandy beach In San Franci...
Article
Full-text available
We used genetic-based paternity assignments from 3 diverse populations of white-tailed deer (Odocoileus virginianus) to evaluate the long-held assumption that male reproductive success in this species is highly skewed toward a small number of mature, dominant individuals. The study populations represented a range of adult sex ratios and male age st...
Conference Paper
Background/Question/Methods The Humboldt Lily (Lilium humboldtii) is a rare riparian plant endemic to California, and listed on the California Native Plant Society's Inventory of Rare and Endangered Plants. These plants are subject to human impact in a variety of ways, including urbanization, horticultural collection, deer browsing, and other thre...
Article
Despite the widely recognized incidence of homoplasy characterizing this region, the hypervariable region I (HVRI) of the mitochondrial control region is one of the most frequently used genetic markers for population genetic and phylogeographic studies. We present an evolutionary analysis of HVRI and cytochrome b sequences from a range-wide survey...
Article
Management strategies that incorporate the social behavior of wildlife may be more efficient in achieving population objectives. Our current knowledge of white-tailed deer (Odocoileus virginianus) social behaviors may not be adequate for application to management. Using captive white-tailed deer, we investigated the long-held assumption that relati...
Article
Aim In order to resolve disputed biogeographical histories of biota with Gondwanan continental distributions, and to assess the null hypothesis of vicariance, it is imperative that a robust geological time-frame be established. As an example, the sudden and coincident appearance of hystricognath rodents (Rodentia: Hystricognathi) on both the Africa...