Symbiote transmission and maintenance of extra-genomic associations
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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... 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...
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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... 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
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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... 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 ...
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... 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. ...
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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.... 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.
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,... 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...
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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... 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.
Research Interests: Bioinformatics, Evolutionary Biology, Informatics, Genomics, Computational Biology, and 15 moreBiotechnology, Cancer, Biomarkers, Biology, Biomedical informatics, Medicine, Bioscience, Evolutionary Bioinformatics, Microarray, Clinical Medicine, Biological, Genetic modification, Evidence Based, Biochemistry and cell biology, and ENVIRONMENTAL SCIENCE AND MANAGEMENT
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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... 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
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Research Interests: Genetics, Invasive Species, Endangered Species, Multidisciplinary, Natural Selection, and 12 moreMultivariate Analysis, Population viability analysis, Animals, Nucleic acid hybridization, Molecular Phylogenetics and Evolution, Evolutionary Dynamics, Genotype, Urodela, Conservation of Natural Resources, Native Species, Ambystoma, and hybrid vigor
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Research Interests: Genetics, Algorithms, Polymorphism, Conservation Genetics, Gene Flow, and 15 morePopulation Genetics, Great Lakes Region, Molecular Ecology, Biological Sciences, Markov chains, Biological Diversity, Animals, Cluster Analysis, Genome, North America, Genotype, Molecular Marker, Bayes Theorem, Likelihood Functions, and alleles
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The tradition of classifying cases of speciation into discrete geographic categories (allopatric, parapatric and sympatric) fuelled decades of fruitful research and debate. Not surprisingly, as the science has become more sophisticated,... more
The tradition of classifying cases of speciation into discrete geographic categories (allopatric, parapatric and sympatric) fuelled decades of fruitful research and debate. Not surprisingly, as the science has become more sophisticated, this simplistic taxonomy has become increasingly obsolete. Geographic patterns are now reasonably well understood. Sister species are rarely sympatric, implying that sympatric speciation, it its most general sense, is rare. However, sympatric speciation, even in its most restricted population genetic sense, is possible. Several case studies have demonstrated that divergence has occurred in nature without geographic barriers to gene flow. Obviously, different sets of criteria for sympatric speciation will lead to different numbers of qualifying cases. But changing the rules of nomenclature to make 'sympatric speciation' more or less common does not constitute scientific progress. Advances in the study of speciation have come from studies of the processes that constrain or promote divergence, and how they are affected by geography.
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Correlations in behavioural traits across time, situation and ecological context (i.e.... more
Correlations in behavioural traits across time, situation and ecological context (i.e. 'behavioural syndromes' or 'personality') have been documented for a variety of behaviours, and in diverse taxa. Perhaps the most controversial inference from the behavioural syndromes literature is that correlated behaviour may act as an evolutionary constraint and evolutionary change in one's behaviour may necessarily involve shifts in others. We test the two predictions of this hypothesis using comparative data from eighteen populations of the socially polymorphic spider, Anelosimus studiosus (Araneae, Theriidae). First, we ask whether geographically distant populations share a common syndrome. Second, we test whether population differences in behaviour are correlated similarly to within-population trait correlations. Our results reveal that populations separated by as much as 36 degrees latitude shared similar syndromes. Furthermore, population differences in behaviour were correlated in the same manner as within-population trait correlations. That is, population divergence tended to be along the same axes as within-population covariance. Together, these results suggest a lack of evolutionary independence in the syndrome's constituent traits.
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ABSTRACT The Turks Island Boa (Epicrates chrysogaster) is endemic to the Turks and Caicos Islands and is currently known from only 11 islands. The subspecies has likely been extirpated from several islands in its historic range, and all... more
ABSTRACT The Turks Island Boa (Epicrates chrysogaster) is endemic to the Turks and Caicos Islands and is currently known from only 11 islands. The subspecies has likely been extirpated from several islands in its historic range, and all remaining populations are threatened with extirpation owing to habitat loss, introduced feral predators, malicious killing, and vehicle strikes. To assist conservation efforts, we undertook a genetic analysis of 53 individual E.c. chrysogaster, representing five island populations, with the goal of identifying existing population structure and genetic diversity. For each snake sampled, we sequenced one mitochondrial and two nuclear genes, resulting in 1591 bp of sequence, and screened nine microsatellite loci.All individuals were found to be monomorphic at the four microsatellite loci that amplified, and only three individuals were found to vary (by a single nucleotide polymorphism) in either nuclear gene. Nine mitochondrial haplotypes were found, with a maximum sequence divergence of < 1%. Taken together, these data indicate shallow genetic divergence in this subspecies, possibly owing to a lack of historical population structure and small population size when the Turks and Caicos Banks were each single islands during the last glacial maximum. Epicrates chrysogaster appears to represent a single evolutionarily significant unit, a significant finding suggesting that conservation strategies focusing on ecologically intact populations might be more appropriate than alternate strategies involving near-impossible reversal of declining populations on heavily disturbed islands. In addition, reintroduction programs would likely not disrupt any significant historical population structure.
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Cave organisms occupy a special place in evolutionary biology because convergent morphologies of many species demonstrate repeatability in evolution even as they obscure phylogenetic relationships. The origin of specialized cave-dwelling... more
Cave organisms occupy a special place in evolutionary biology because convergent morphologies of many species demonstrate repeatability in evolution even as they obscure phylogenetic relationships. The origin of specialized cave-dwelling species also raises the issue of the relative importance of isolation vs. natural selection in speciation. Two alternative hypotheses describe the origin of subterranean species. The 'climate-relict' model proposes allopatric speciation after populations of cold-adapted species become stranded in caves due to climate change. The 'adaptive-shift' model proposes parapatric speciation driven by divergent selection between subterranean and surface habitats. Our study of the Tennessee cave salamander complex shows that the three nominal forms (Gyrinophilus palleucus palleucus, G. p. necturoides, and G. gulolineatus) arose recently and are genealogically nested within the epigean (surface-dwelling) species, G. porphyriticus. Short bran...
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Flowering dogwood (Cornus florida L.) 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.... more
Flowering dogwood (Cornus florida L.) 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.
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All animals and plants have intimate associations with microbes. Opinion has shifted from viewing microbes primarily as pathogens to the idea that healthy animals and plants carry specialized communities of coevolving microorganisms.... more
All animals and plants have intimate associations with microbes. Opinion has shifted from viewing microbes primarily as pathogens to the idea that healthy animals and plants carry specialized communities of coevolving microorganisms. However, the generality of this proposition is unknown because surveys rarely compare host-associated microbes with samples from relevant microhabitats. Symbiotic communities might be assembled from local environments with little evolutionary specialization. We evaluated the specificity of bacteria associated with salamander skin in comparison with surfaces in their immediate environments using 16S rRNA sequences. Host-associated and free-living samples were significantly different. However, relative abundances were strongly correlated; the most abundant taxa on salamander skin were also most abundant on moist debris on the forest floor. Thus, although bacterial assemblages on salamander skin are statistically differentiated from those on inanimate surfaces, they are not entirely 'distinct'. Candidate salamander specialists were few in number and occurred at low relative abundances. Within some OTUs, differences in allele frequency suggested genetic specialization at finer levels. Although host-associated and free-living assemblages were similar, a range of more or less specialized symbiotes was evident and bacteria on salamander skin were often specific genotypes of OTUs commonly found on other moist surfaces in the environment.
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Research Interests: Evolutionary Biology, Gene Flow, Evolution, Population Dynamics, Chiroptera, and 14 moreFelidae, Rodentia, Mammals, Mitochondrial DNA, Animals, Shrews, Regression Analysis, Comparative method, Sympatric Speciation, Allopatric Speciation, Lagomorpha, Antelopes, Geographic Range, and Monte Carlo Method
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Climatic and geological processes associated with glaciation cycles during the Pleistocene have been implicated in influencing patterns of genetic variation and promoting speciation of temperate flora and fauna. However, determining the... more
Climatic and geological processes associated with glaciation cycles during the Pleistocene have been implicated in influencing patterns of genetic variation and promoting speciation of temperate flora and fauna. However, determining the factors promoting divergence and speciation is often difficult in many groups because of our limited understanding of potential vicariant barriers and connectivity between populations. Pleistocene glacial cycles are thought to have significantly influenced the distribution and diversity of subterranean invertebrates; however, impacts on subterranean aquatic vertebrates are less clear. We employed several hypothesis-driven approaches to assess the impacts of Pleistocene climatic and geological changes on the Northern Cavefish, Amblyopsis spelaea, whose current distribution occurs near the southern extent of glacial advances in North America. Our results show that the modern Ohio River has been a significant barrier to dispersal and is correlated with patterns of genetic divergence. We infer that populations were isolated in two refugia located north and south of the Ohio River during the most recent two glacial cycles with evidence of demographic expansion in the northern isolate. Finally, we conclude that climatic and geological processes have resulted in the formation of cryptic forms and advocate recognition of two distinct phylogenetic lineages currently recognized as A. spelaea.
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Almost 30 years ago, A. C. Wilson and colleagues presented results indicating that hybrid inviability between species evolves 10 times faster in mammals than in birds and frogs. Here I revisit this question for birds and mammals using... more
Almost 30 years ago, A. C. Wilson and colleagues presented results indicating that hybrid inviability between species evolves 10 times faster in mammals than in birds and frogs. Here I revisit this question for birds and mammals using modern molecular data (mitochondrial cytochrome b DNA) and a more phylogenetically appropriate statistical approach. My analyses confirm that diverging mammals lose the ability to form viable hybrids faster than birds. To explain the difference in rates of evolutionary loss of hybridization potential, Wilson and coworkers proposed that mammals have higher rates of regulatory evolution, causing higher probabilities of developmental incompatibilities between mammal species. I briefly discuss this and other potential explanations.