21 Works

Data from: Quantifying effects of environmental and geographical factors on patterns of genetic differentiation

Cheng-Ruei Lee & Thomas Mitchell-Olds
Elucidating the factors influencing genetic differentiation is an important task in biology, and the relative contribution from natural selection and genetic drift has long been debated. In this study, we used a regression-based approach to simultaneously estimate the quantitative contributions of environmental adaptation and isolation by distance on genetic variation in Boechera stricta, a wild relative of Arabidopsis. Patterns of discrete and continuous genetic differentiation coexist within this species. For the discrete differentiation between two...

Data from: Genetic structure in a dynamic baboon hybrid zone corroborates behavioral observations in a hybrid population

Marie J.E. Charpentier, Michael C. Fontaine, Julien P. Renoult, Thomas Jenkins, Erwan Cherel, Laure Benoit, Nicolas Barthès, Susan C. Alberts & Jenny Tung
Behavior and genetic structure are intimately related: mating patterns and patterns of movement between groups or populations influence the movement of genetic variation across the landscape and from one generation to the next. In hybrid zones, the behavior of the hybridizing taxa can also have an important impact on the incidence and outcome of hybridization events. Hybridization between yellow baboons and anubis baboons has been well-documented in the Amboseli basin of Kenya, where more anubis-like...

Data from: Classification tree methods provide a multifactorial approach to predicting insular body size evolution in rodents

Paul A. P. Durst, V. Louise Roth & V. Louise Roth
Many hypotheses have been proposed to explain size changes in insular mammals, but no single variable suffices to explain the diversity of responses, particularly within Rodentia. Here in a dataset on insular rodents we observe strong consistency in the direction of size change within islands and within species, but (outside of Heteromyidae) little consistency at broader taxonomic scales. Using traits of islands and of species in a classification-tree analysis we find the most important factor...

Data from: Interploidal hybridization and mating patterns in the Sphagnum subsecundum complex

Mariana Ricca, P. Szövényi, Matthew G Johnson, A Jonathan Shaw & Eva M. Temsch
Polyploidization is thought to result in instant sympatric speciation, but several cases of hybrid zones between one of the parental species and its polyploid derivative have been documented. Previous work showed that diploid Sphagnum lescurii is an allopolyploid derived from the haploids S. lescurii (maternal progenitor) and S. subsecundum (paternal progenitor). Here we report the results from analyses of a population where allodiploid and haploid S. lescurii co-occur and produce sporophytes. We tested (1) whether...

Data from: Testing a developmental model in the fossil record: molar proportions in South American ungulates

Laura A. B. Wilson, Richard H. Madden, Richard F. Kay & Marcelo R. Sánchez-Villagra
A developmental model, based upon murine rodents, has been proposed by Kavanagh et al. (2007) to explain lower molar proportions in mammals. We produce a clade-wide macroevolutionary test of the model using the dental evolutionary trends in a unique radiation of extinct mammals endemic to South America (“Meridiungulata”) that comprise a diverse array of molar morphologies. All of the South American ungulate groups examined follow the inhibitory cascade model with the exception of two groups:...

Data from: A microbiotic survey of lichen-associated bacteria reveals a new lineage from the Rhizobiales

Brendan P. Hodkinson & François Lutzoni
This study uses a set of PCR-based methods to examine the putative microbiota associated with lichen thalli. In initial experiments, generalized oligonucleotide-primers for the 16S rRNA gene resulted in amplicon pools populated almost exclusively with fragments derived from lichen photobionts (i.e., Cyanobacteria or chloroplasts of algae). This effectively masked the presence of other lichen-associated prokaryotes. In order to facilitate the study of the lichen microbiota, 16S ribosomal oligonucleotide-primers were developed to target Bacteria, but exclude...

Data from: DOG1 expression is predicted by the seed-maturation environment and contributes to geographic variation in germination in Arabidopsis thaliana.

George C K Chiang, Melanie Bartsch, Deepak Barua, Kazumi Nakabayashi, Marilyne Debieu, Ilkka Kronholm, Maarten Koornneef, Wim J J Soppe, Kathleen Donohue & Juliette De Meaux
Seasonal germination timing of Arabidopsis thaliana strongly influences overall life history expression and is the target of intense natural selection. This seasonal germination timing depends strongly on the interaction between genetics and seasonal environments both before and after seed dispersal. DELAY OF GERMINATION 1 (DOG1) is the first gene that has been identified to be associated with natural variation in primary dormancy in Arabidopsis thaliana. Here, we report inter-accession variation in DOG1 expression and document...

Data from: Loss of sexual recombination and segregation is associated with increased diversification in evening primroses

Marc T. J. Johnson, Richard Gareth FitzJohn, Stacey D. Smith, Mark D. Rausher & Sarah P. Otto
The loss of sexual recombination and segregation in asexual organisms has been portrayed as an irreversible process that commits asexually-reproducing lineages to reduced diversification. We test this hypothesis by estimating rates of speciation, extinction, and transition between sexuality and functional asexuality in the evening primroses. Specifically, we estimate these rates using the recently developed BiSSE (Binary State Speciation and Extinction) phylogenetic comparative method, which employs maximum likelihood and Bayesian techniques. We infer that net diversification...

Data from: Molecular signatures of selection on reproductive character displacement of flower color in Phlox drummondii

Robin Hopkins, Donald A. Levin & Mark D Rausher
Character displacement, which arises when species diverge in sympatry to decrease competition for resources or reproductive interference, has been observed in a wide variety of plants and animals. A classic example of reproductive character displacement, presumed to be caused by reinforcing selection, is flower-color variation in the native Texas wildflower Phlox drummondii. Here we use population genetic analyses to investigate molecular signatures of selection on flower-color variation in this species. First, we quantify patterns of...

Data from: Genetic tradeoffs and conditional neutrality contribute to local adaptation

Jill T. Anderson, Cheng-Ruei Lee, Catherine A. Rushworth, Robert I. Colautti & Thomas Mitchell-Olds
Divergent natural selection promotes local adaptation and can lead to reproductive isolation of populations in contrasting environments; however, the genetic basis of local adaptation remains largely unresolved in natural populations. Local adaptation might result from antagonistic pleiotropy, where alternate alleles are favored in distinct habitats, and polymorphism is maintained by selection. Alternatively, under conditional neutrality some alleles may be favored in one environment but neutral at other locations. Antagonistic pleiotropy maintains genetic variation across the...

Data from: Boechera, a model system for ecological genomics

Catherine A. Rushworth, Bao-Hua Song, Cheng-Ruei Lee & Thomas Mitchell-Olds
The selection and development of a study system for evolutionary and ecological functional genomics (EEFG) depends on a variety of factors. Here we present the genus Boechera as an exemplary system with which to address ecological and evolutionary questions. Our focus on Boechera is based on several characteristics: 1) native populations in undisturbed habitats where current environments reflect historical conditions over several thousand years; 2) functional genomics benefitting from its close relationship to Arabidopsis thaliana;...

Data from: Aging in the natural world: comparative data reveal similar mortality patterns across primates

Anne M. Bronikowski, Jeanne Altmann, Diane K. Brockman, Marina Cords, Linda M. Fedigan, Anne Pusey, Tara Stoinski, William F. Morris, Karen B. Strier & Susan C. Alberts
Human senescence patterns – late onset of mortality increase, slow mortality acceleration, and exceptional longevity – are often described as unique in the animal world. Using an individual-based dataset from longitudinal studies of wild populations of seven primate species, we show that contrary to assumptions of human uniqueness, human senescence falls within the primate continuum of aging, the tendency for males to have shorter lifespans and higher age-specific mortality than females throughout much of adulthood...

Data from: Male-mediated effects on female meiotic recombination

Laurie S Stevison
Recombination rates vary owing to an individual’s genetic composition and/or its environmental condition. Yet, the effects of mating partner on recombination rates have not been considered. Here, I document a previously undescribed male-mediated effect on female recombination rates. After crossing females to males from different genetic backgrounds, I observed a significant difference in proportion of recombinant offspring based on the genetic background of the father (p=0.0292; 3 df; F=3.07). Genetic variation in male ability to...

Data from: Lepidostroma vilgalysii, a new basidiolichen from the New World

Brendan P. Hodkinson, Jessie K. Uehling & Matthew E. Smith
The lichenized basidiomycete Lepidostroma vilgalysii is described from Mexico based on morphological analyses. The species is only the second representative of the family Lepidostromataceae documented from the New World, and is one of the few described lichens with an inverted morphology, with the algae in a layer at the base of the thallus. Molecular sequence data from the nuclear ribosomal LSU locus are used to confirm the placement of the holotype in Lepidostroma and to...

Data from: Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome

Brendan P. Hodkinson, Neil R. Gottel, Christopher W. Schadt & François Lutzoni
Although common knowledge dictates that the lichen thallus is formed solely by a fungus (mycobiont) that develops a symbiotic relationship with an alga and/or cyanobacterium (photobiont), the non-photoautotrophic bacteria found in lichen microbiomes are increasingly regarded as integral components of lichen thalli. For this study, comparative analyses were conducted on lichen-associated bacterial communities to test for effects of photobiont-types (i.e., green algal vs. cyanobacterial), mycobiont-types, and large-scale spatial distances (from tropical to arctic latitudes). Amplicons...

Data from: Concatenation and concordance in the reconstruction of mouse lemur phylogeny: an empirical demonstration of the effect of allele sampling in phylogenetics.

David W. Weisrock, Stacey D. Smith, Lauren M. Chan, Karla Biebouw, Peter M. Kappeler & Anne D. Yoder
The systematics and speciation literature is rich with discussion relating to the potential for gene tree/species tree discordance. Numerous mechanisms have been proposed to generate discordance, including differential selection, long-branch attraction, gene duplication, genetic introgression, and/or incomplete lineage sorting. For speciose clades in which divergence has occurred recently and rapidly, recovering the true species tree can be particularly problematic due to incomplete lineage sorting. Unfortunately, the availability of multi-locus or “phylogenomic” data sets does not...

Data from: Effects of inversions on within- and between-species recombination and divergence

Laurie S. Stevison, Mohamed A. F. Noor & Kenneth B. Hoehn
Chromosomal inversions disrupt recombination in heterozygotes by both reducing crossing over within inverted regions and increasing it elsewhere in the genome. The reduction of recombination in inverted regions facilitates the maintenance of hybridizing species, as outlined by various models of chromosomal speciation. We present a comprehensive comparison of the effects of inversions on recombination rates and on nucleotide divergence. Within an inversion differentiating Drosophila pseudoobscura and D. persimilis, we detected one double-recombinant among 9739 progeny...

Data from: Recently-formed polyploid plants diversify at lower rates

Itay Mayrose, Shing H. Zhan, Carl J. Rothfels, Karen Magnuson-Ford, Michael S. Barker, Loren H. Rieseberg & Sarah P. Otto
Polyploidy, the doubling of genomic content, is a widespread feature, especially among plants, yet its macro-evolutionary impacts are contentious. Traditionally, polyploidy has been considered an evolutionary dead-end, whereas recent genomic studies suggest that polyploidy has been a key driver of macro-evolutionary success. Here we examine the consequences of polyploidy on the time scale of genera across a diverse set of vascular plants, encompassing hundreds of inferred polyploidization events. Likelihood-based analyses indicate that polyploids generally exhibit...

Data from: Extremely long-distance seed dispersal by an overfished Amazonian frugivore

Jill T. Anderson, Tim Nuttle, Joe S. Saldaña Rojas, Thomas H. Pendergast, Alexander S. Flecker, A. S. Flecker, J. T. Anderson, T. H. Pendergast & T. Nuttle
Throughout Amazonia, overfishing has decimated populations of fruit-eating fishes, especially the largebodied characid, Colossoma macropomum. During lengthy annual floods, frugivorous fishes enter vast Amazonian floodplains, consume massive quantities of fallen fruits and egest viable seeds. Many tree and liana species are clearly specialized for icthyochory, and seed dispersal by fish may be crucial for the maintenance of Amazonian wetland forests. Unlike frugivorous mammals and birds, little is known about seed dispersal effectiveness of fishes. Extensive...

Data from: Genetics of hybrid male sterility among strains and species in the Drosophila pseudoobscura species group

Shannon R. McDermott & Mohamed A. F. Noor
Taxa in the early stages of speciation may bear intraspecific allelic variation at loci conferring barrier traits in hybrids such as hybrid sterility. Additionally, hybridization may spread alleles that confer barrier traits to other taxa. Historically, few studies examine within- and between-species variation at loci conferring reproductive isolation. Here, we test for allelic variation within Drosophila persimilis and within the Bogota subspecies of D. pseudoobscura at regions previously shown to contribute to hybrid male sterility....

Data from: Does hybridization drive the transition to asexuality in diploid Boechera?

James Benjamin Beck, Patrick J. Alexander, Loreen Allphin, Ihsan A. Al-Shehbaz, Catherine Rushworth, C. Donovan Bailey & Michael D. Windham
Gametophytic apomixis is a common form of asexual reproduction in plants. Virtually all gametophytic apomicts are polyploids, and some view polyploidy as a prerequisite for the transition to apomixis. However, any causal link between apomixis and polyploidy is complicated by the fact that most apomictic polyploids are allopolyploids, leading some to speculate that hybridization, rather than polyploidy, enables apomixis. Diploid apomixis presents a rare opportunity to isolate the role of hybridization, and a number of...

Registration Year

  • 2011

Resource Types

  • Dataset


  • Duke University
  • The Bronx Defenders
  • University of British Columbia
  • Centre d'Ecologie Fonctionnelle et Evolutive
  • The University of Texas at Austin
  • Columbia University
  • New Mexico State University
  • Princeton University
  • University of Pittsburgh
  • Oak Ridge National Laboratory