Benjamin Fitzpatrick | University of Tennessee Knoxville (original) (raw)

Papers by Benjamin Fitzpatrick

Symbiote transmission and maintenance of extra-genomic associations

Journal of Wildlife Diseases

Ecology, 2018

Recently there have been major theoretical advances in the quantification and partitioning of div... more Recently there have been major theoretical advances in the quantification and partitioning of diversity within and among communities, regions, and ecosystems. However, applying those advances to real data remains a challenge. Ecologists often end up describing their samples rather than estimating the diversity components of an underlying study system, and existing approaches do not easily provide statistical frameworks for testing ecological questions. Here we offer one avenue to do all of the above using a hierarchical Bayesian approach. We estimate posterior distributions of the underlying "true" relative abundances of each species within each unit sampled. These posterior estimates of relative abundance can then be used with existing formulae to estimate and partition diversity. The result is a posterior distribution of diversity metrics describing our knowledge (or beliefs) about the study system. This approach intuitively leads to statistical inferences addressing bio...

Ecology

Beta diversity is an important metric in ecology quantifying differentiation or disparity in comp... more Beta diversity is an important metric in ecology quantifying differentiation or disparity in composition among communities, ecosystems, or phenotypes. To compare systems with different sizes (N, number of units within a system), beta diversity is often converted to related indices such as turnover or local/regional differentiation. Here we use simulations to demonstrate that these naive measures of dissimilarity depend on sample size and design. We show that when N is the number of sampled units (e.g., quadrats) rather than the "true" number of communities in the system (if such exists), these differentiation measures are biased estimators. We propose using average pairwise dissimilarity as an intuitive solution. That is, instead of attempting to estimate an N-community measure, we advocate estimating the expected dissimilarity between any random pair of communities (or sampling units)-especially when the "true" N is unknown or undefined. Fortunately, measures of pairwise dissimilarity or overlap have been used in ecology for decades, and their properties are well known. Using the same simulations, we show that average pairwise metrics give consistent and unbiased estimates regardless of the number of survey units sampled. We advocate pairwise dissimilarity as a general standardization to ensure commensurability of different study systems.

Geographic variation in external morphology of one subspecies of Red-tailed Hawk (Buteo jamaicens... more Geographic variation in external morphology of one subspecies of Red-tailed Hawk (Buteo jamaicensis calurus) in western North America was analyzed by comparing measurements of 249 museum specimens from seven ecoregions. Male and female Red-tailed Hawks showed substantial regional vari- ation within the geographic range of this single subspecies. We used exploratory and confirmatory data analysis to investigate relationships between morphological

Evolution, 2002

Evolution of reproductive isolation as a byproduct of genetic divergence in isolated populations ... more Evolution of reproductive isolation as a byproduct of genetic divergence in isolated populations is the dominant (albeit not exclusive) mode of speciation in sexual animals. But little is known about the factors linking speciation to general divergence. Several authors have argued that allopatric speciation should proceed more rapidly if isolated populations also experience divergent selection. Reproductive isolation between allopatric populations is not subject to direct selection; it can accumulate only by random drift or as a fortuitous byproduct of selection on other traits. Here I present a novel analysis of published data, demonstrating that pre-and postmating isolation of Drosophila species are more tightly correlated with allozyme divergence than with silent DNA divergence. Inasmuch as proteins are more subject to the action of natural selection than are silent DNA polymorphisms, this result provides broad support for a model of selection-mediated allopatric speciation.

Biological Invasions, 2013

Many studies aimed at reconstructing the invasion history of a species rely, in part, on inferenc... more Many studies aimed at reconstructing the invasion history of a species rely, in part, on inferences based on patterns of genetic variation. These inferences warrant careful interpretation, however. In particular, given the time scale of most invasions, the typical demography of invasive species in their invaded range, and the available molecular tools, the underlying assumptions of population genetic models will often be violated. Given this fact, we examined the potential of population genetic data for reconstructing the history of serial introductions of the small Indian mongoose, Herpestes auropunctatus. We used simulations to test the power of existing microsatellite data for testing the credibility of historical introduction records. Although our results are generally consistent with most historical records for H. auropunctatus, the existing data have low power to reject alternative historical hypotheses. Simulations of a wide range of founder population sizes show broadly overlapping results, making rather different historical scenarios of introductions difficult to rule out with typical datasets. We advocate caution in the use of molecular population genetics to infer the history of invasive species, and we suggest extensive simulations as a tool to evaluate, in advance, this approach for addressing important research questions.

Understanding the factors that contribute to reproductive isolation is essential to understanding... more Understanding the factors that contribute to reproductive isolation is essential to understanding the process of speciation. Populations can undergo reproductive isolation when experiencing divergent selection after introduction to a novel environment. In this study, we looked for evidence of the evolution of premating isolation in the host generalist grain pest, red flour beetle (Coleoptera: Tribolium castaneum) after adaptation to a novel environment. Through mate and habitat preference assays, we support the preference-performance hypothesis that females will preferentially lay eggs on hosts that increase offspring performance. We found evidence that T. castaneum may have evolved host specialization as well as incomplete behavioral premating isolation based on female habitat preference.

The origin of novelty is a critical subject for evolutionary biologists. Early geneticists specul... more The origin of novelty is a critical subject for evolutionary biologists. Early geneticists speculated about the sudden appearance of new species via special macromutations, epitomized by Goldschmidt's infamous ''hopeful monster''. Although these ideas were easily dismissed by the insights of the Modern Synthesis, a lingering fascination with the possibility of sudden, dramatic change has persisted. Recent work on hybridization and gene exchange suggests an underappreciated mechanism for the sudden appearance of evolutionary novelty that is entirely consistent with the principles of modern population genetics. Genetic recombination in hybrids can produce transgressive phenotypes, ''monstrous'' phenotypes beyond the range of parental populations. Transgressive phenotypes can be products of epistatic interactions or additive effects of multiple recombined loci. We compare several epistatic and additive models of transgressive segregation in hybrids and find that they are special cases of a general, classic quantitative genetic model. The Dobzhansky-Muller model predicts ''hopeless'' monsters, sterile and inviable transgressive phenotypes. The Bateson model predicts ''hopeful'' monsters with fitness greater than either parental population. The complementation model predicts both. Transgressive segregation after hybridization can rapidly produce novel phenotypes by recombining multiple loci simultaneously. Admixed populations will also produce many similar recombinant phenotypes at the same time, increasing the probability that recombinant ''hopeful monsters'' will establish true-breeding evolutionary lineages. Recombination is not the only (or even most common) process generating evolutionary novelty, but might be the most credible mechanism for sudden appearance of new forms.

Current Zoology, 2015

Most biologists recognize the “species phenomenon” as a real pattern in nature: Biodiversity is c... more Most biologists recognize the “species phenomenon” as a real pattern in nature: Biodiversity is characterized by discontinuities between recognizable groups classified as species. Many conservation laws focus on preventing species extinction. However, species are not fixed. Discontinuities evolve gradually and sometimes disappear. Exactly how to define particular species is not always obvious. Hybridization between taxonomic species reminds us that species classification is not a perfect representation of nature. Classification is a model that is very useful, but not adequate in all cases. Conservationists often confront questions about how to apply species-based laws when hybridization confounds classification. Development of sophisticated techniques and nuanced interpretation of data in the basic study of species and speciation has exposed the need for deeper education in genetics and evolution for applied conservationists and decision makers. Here we offer a brief perspective on ...

... BMC Evolutionary Biology BioMed Central (2004). Download: http://www.biomedcentral. com/conte... more ... BMC Evolutionary Biology BioMed Central (2004). Download: http://www.biomedcentral. com/content/pdf/1471-2148 CACHED: Download as a PDF. by Alex Mira , Ravindra Pushker , Boris A Legault , David Moreira. Add To MetaCart. ...

The American Naturalist, 2015

Most components of an organism's phenotype can be viewed as the expression of multiple traits. Ma... more Most components of an organism's phenotype can be viewed as the expression of multiple traits. Many of these traits operate as complexes, where multiple subsidiary parts function and evolve together. As trait complexity increases, so does the challenge of describing complexity in intuitive, biologically meaningful ways. Traditional multivariate analyses ignore the phenomenon of individual complexity and provide relatively abstract representations of variation among individuals. We suggest adopting well-known diversity indices from community ecology to describe phenotypic complexity as the diversity of distinct subsidiary components of a trait. Using a hierarchical framework, we illustrate how total trait diversity can be partitioned into within-individual complexity (a diversity) and between-individual components (b diversity). This approach complements traditional multivariate analyses. The key innovations are (i) addition of individual complexity within the same framework as between-individual variation and (ii) a group-wise partitioning approach that complements traditional level-wise partitioning of diversity. The complexity-as-diversity approach has potential application in many fields, including physiological ecology, ecological and community genomics, and transcriptomics. We demonstrate the utility of this complexity-as-diversity approach with examples from chemical and microbial ecology. The examples illustrate biologically significant differences in complexity and diversity that standard analyses would not reveal.

Flowering dogwood (Cornus florida) populations recently have experienced severe declines caused b... more Flowering dogwood (Cornus florida) populations recently have experienced severe declines caused by dogwood anthracnose. Mortality has ranged from 48 to 98%, raising the concern that genetic diversity has been reduced significantly. Microsatellite data were used to evaluate the level and distribution of genetic variation throughout much of the native range of the tree. Genetic variation in areas affected by anthracnose was as high as or higher than areas without die-offs. We found evidence of four widespread, spatially contiguous genetic clusters. However, there was little relationship between geographic distance and genetic difference. These observations suggest that high dispersal rates and large effective population sizes have so far prevented rapid loss of genetic diversity. The effects of anthracnose on demography and community structure are likely to be far more consequential than short-term genetic effects.

International Journal of Ecology, 2012

Phenotypic plasticity was once seen primarily as a constraint on adaptive evolution or merely a n... more Phenotypic plasticity was once seen primarily as a constraint on adaptive evolution or merely a nuisance by geneticists. However, some biologists promote plasticity as a source of novelty and a factor in evolution on par with mutation, drift, gene flow, and selection. These claims are controversial and largely untested, but progress has been made on more modest questions about effects of plasticity on local adaptation (the first component of ecological speciation). Adaptive phenotypic plasticity can be a buffer against divergent selection. It can also facilitate colonization of new niches and rapid divergent evolution. The influence of non-adaptive plasticity has been underappreciated. Non-adaptive plasticity, too can interact with selection to promote or inhibit genetic differentiation. Finally, phenotypic plasticity of reproductive characters might directly influence evolution of reproductive isolation (the second component of ecological speciation). Plasticity can cause assortati...

Frontiers in Microbiology, 2014

Symbiotes can be transmitted from parents to offspring or horizontally from unrelated hosts or th... more Symbiotes can be transmitted from parents to offspring or horizontally from unrelated hosts or the environment. A key question is whether symbiote transmission is similar enough to Mendelian gene transmission to generate and maintain coevolutionary associations between host and symbiote genes. Recent papers come to opposite conclusions, with some suggesting that any horizontal transmission eliminates genetic association. These studies are hard to compare owing to arbitrary differences in modeling approach, parameter values, and assumptions about selection. I show that associations between host and symbiote genes (extra-genomic associations) can be described by the same dynamic model as conventional linkage disequilibria between genes in the same genome. Thus, covariance between host and symbiote genomes depends on population history, geographic structure, selection, and co-transmission rate, just as covariance between genes within a genome. The conclusion that horizontal transmission rapidly erodes extra-genomic associations is equivalent to the conclusion that recombination rapidly erodes associations between genes within a genome. The conclusion is correct in the absence of population structure or selection. However, population structure can maintain spatial associations between host and symbiote traits, and non-additive selection (interspecific epistasis) can generate covariances between host and symbiote genotypes. These results can also be applied to cultural or other non-genetic traits. This work contributes to a growing consensus that genomic, symbiotic, and gene-culture evolution can be analyzed under a common theoretical framework. In terms of coevolutionary potential, symbiotes can be viewed as lying on a continuum between the intimacy of genes and the indifference of casually co-occurring species.

Ecology and Evolution, 2013

Understanding factors regulating hybrid fitness and gene exchange is a major research challenge f... more Understanding factors regulating hybrid fitness and gene exchange is a major research challenge for evolutionary biology. Genomic cline analysis has been used to evaluate alternative patterns of introgression, but only two models have been used widely and the approach has generally lacked a hypothesis testing framework for distinguishing effects of selection and drift. I propose two alternative cline models, implement multivariate outlier detection to identify markers associated with hybrid fitness, and simulate hybrid zone dynamics to evaluate the signatures of different modes of selection. Analysis of simulated data shows that previous approaches are prone to false positives (multinomial regression) or relatively insensitive to outlier loci affected by selection (Barton's concordance). The new, theory-based logit-logistic cline model is generally best at detecting loci affecting hybrid fitness. Although some generalizations can be made about different modes of selection, there is no one-to-one correspondence between pattern and process. These new methods will enhance our ability to extract important information about the genetics of reproductive isolation and hybrid fitness. However, much remains to be done to relate statistical patterns to particular evolutionary processes. The methods described here are implemented in a freely available package "HIest" for the R statistical software (CRAN; http://cran.r-project.org/).

Evolutionary bioinformatics online, 2014

Patterns of diversification rate variation detected in phylogenetic hypotheses are frequently use... more Patterns of diversification rate variation detected in phylogenetic hypotheses are frequently used to infer historical, ecological, and evolutionary processes. The parametric rate comparison (PRC) is a method for detecting rate variation in trees that models branch lengths as random variables drawn from familiar statistical distributions. iteRates is a library of functions for the R statistical computing environment for implementing PRC on phylogenetic trees. Here, we describe some of the functions in iteRates for subtree identification, tree manipulation, applying the PRC and K-clades PRC analyses, and conducting a whole-tree randomization test.

Journal of Experimental Zoology, 2003

The ability of an individual to escape predators is an important component of fitness. Several ad... more The ability of an individual to escape predators is an important component of fitness. Several adaptive explanations of body shape variation in amphibians hypothesize relationships between swimming performance and morphology, but these ideas have rarely been tested. Here we investigate bivariate and multivariate relationships between natural variation in morphology and performance. We used high-speed video to examine fast-starts associated with escape responses in small tiger salamander larvae (Ambystoma tigrinum). Our results indicate that performance is influenced by interactions among aspects of morphology, physiology, and behavior. Relationships between morphometric variables and velocity could be detected with multivariate, but not bivariate statistical analyses. In particular, relationships between morphology and velocity depend on tail beat frequency (potentially a measure of effort or vigor). Relationships between morphology and acceleration were detected with bivariate analyses, but multivariate analysis suggests that acceleration performance, too, depends on interactions between morphology and tail beat frequency. We found a positive relationship between tail area and propulsive performance, which supports adaptive interpretations of variation in larval tail shape within and between amphibian species.