24 Works

Data from: Differential drivers of benthic foraminiferal and molluscan community composition from a multivariate record of Early Miocene environmental change

Christina L. Belanger & Marites Villarosa Garcia
Climate changes are multivariate in nature, and disentangling the proximal drivers of biotic responses to paleoclimate events requires time series of multiple environmental proxies. We reconstruct a multivariate time series of local environmental change for the early Miocene Newport Member of the Astoria Formation (20.26–18 Ma), using proxies for temperature (δ18O), productivity (δ13C), organic carbon flux (Δδ13C), oxygenation (δ15N), and sedimentary grain size (% mud). Our data suggest increases in productivity and declines in oxygenation...

Data from: A nutrient-driven tRNA modification alters translational fidelity and genome-wide protein coding across an animal genus

John M. Zaborske, Vanessa L. Bauer-DuMont, Edward W. J. Wallace, Tao Pan, Charles F. Aquadro, David Allan Drummond & Vanessa L. Bauer DuMont
Natural selection favors efficient expression of encoded proteins, but the causes, mechanisms, and fitness consequences of evolved coding changes remain an area of aggressive inquiry. We report a large-scale reversal in the relative translational accuracy of codons across 12 fly species in the Drosophila/Sophophora genus. Because the reversal involves pairs of codons that are read by the same genomically encoded tRNAs, we hypothesize, and show by direct measurement, that a tRNA anticodon modification from guanosine...

Data from: Variable post-zygotic isolation in Drosophila melanogaster/D. simulans hybrids

Daniel R. Matute, Jackie Gavin-Smyth & Geoffrey Liu
The study of hybrid inviability reveals cryptic divergence between the genetic interactions that maintain stable phenotypes in the pure species. We characterized the effects of natural variation on the penetrance of hybrid inviability phenotypes in crosses between Drosophila melanogaster and two species of the D. simulans subcomplex, D. simulans and D. sechellia. Using a panel of wild-caught lines, we studied the levels of genetic variance present in D. simulans and D. sechellia affecting prezygotic and...

Data from: Heritable variation in host tolerance and resistance inferred from a wild host– parasite system

Elise Mazé-Guilmo, Géraldine Loot, David James Páez, Thierry Lefèvre, Simon Blanchet, T. Lefevre, D. J. Paez & E. Maze-Guilmo
Hosts have evolved two distinct defence strategies against parasites: resistance (which prevents infection or limit parasite growth) and tolerance (which alleviates the fitness consequences of infection). However, heritable variation in resistance and tolerance and the genetic correlation between these two traits have rarely been characterized in wild host populations. Here, we estimate these parameters for both traits in Leuciscus burdigalensis, a freshwater fish parasitized by Tracheliastes polycolpus. We used a genetic database to construct a...

Data from: Discovery of a relict lineage and monotypic family of passerine birds

Per Alström, Daniel M. Hooper, Yang Liu, Urban Olsson, Dhananjai Mohan, Magnus Gelang, Hung Le Manh, Jian Zhao, Fumin Lei, Trevor D. Price & P. Alstrom
Analysis of one of the most comprehensive datasets to date of the largest passerine bird clade, Passerida, identified 10 primary well-supported lineages corresponding to Sylvioidea, Muscicapoidea, Certhioidea, Passeroidea, the ‘bombycillids’ (here proposed to be recognized as Bombycilloidea), Paridae/Remizidae (proposed to be recognized as Paroidea), Stenostiridae, Hyliotidae, Regulidae (proposed to be recognized as Reguloidea) and spotted wren-babbler Spelaeornis formosus. The latter was found on a single branch in a strongly supported clade with Muscicapoidea, Certhioidea and...

Data from: Serial founder effects and genetic differentiation during worldwide range expansion of monarch butterflies

Amanda A. Pierce, Myron P. Zalucki, Marie Bangura, Milan Udawatta, Marcus R. Kronforst, Sonia Altizer, Juan Fernández Haeger & Jacobus C. De Roode
Range expansions can result in founder effects, increasing genetic differentiation between expanding populations and reducing genetic diversity along the expansion front. However, few studies have addressed these effects in long-distance migratory species, for which high dispersal ability might counter the effects of genetic drift. Monarchs (Danaus plexippus) are best known for undertaking a long-distance annual migration in North America, but have also dispersed around the world to form populations that do not migrate or travel...

Data from: Phylogeography of Heliconius cydno and its closest relatives: disentangling their origin and diversification

Carlos F. Arias, Camilo Salazar, Claudia Rosales, Marcus R. Kronforst, Mauricio Linares, Eldredge Bermingham & W. Owen McMillan
The origins of phenotypic variation within mimetic Heliconius butterflies have long fascinated biologists and naturalists. However, the evolutionary processes that have generated this extraordinary diversity remain puzzling. Here we examine intraspecific variation across Heliconius cydno diversification and compare this variation to that within the closely related H. melpomene and H. timareta radiations. Our data, which consist of both mtDNA and genome scan from nearly 2250 AFLP loci, reveal a complex history of differentiation and admixture...

Data from: Hybridization occurs between Drosophila simulans and D. sechellia in the Seychelles archipelago

Daniel R. Matute & Julien F. Ayroles
Drosophila simulans and D. sechellia are sister species that serve as a model to study the evolution of reproductive isolation. While D. simulans is a human commensal that has spread all over the world, D. sechellia is restricted to the Seychelles archipelago and is found to breed exclusively on the toxic fruit of Morinda citrifolia. We surveyed the relative frequency of males from these two species in a variety of substrates found on five islands...

Data from: A framework phylogeny of the American oak clade based on sequenced RAD data

Andrew L. Hipp, Deren A. R. Eaton, Jeannine Cavender-Bares, Elisabeth Fitzek, Rick Nipper & Paul S. Manos
Previous phylogenetic studies in oaks (Quercus, Fagaceae) have failed to resolve the backbone topology of the genus with strong support. Here, we utilize next-generation sequencing of restriction-site associated DNA (RAD-Seq) to resolve a framework phylogeny of a predominantly American clade of oaks whose crown age is estimated at 23–33 million years old. Using a recently developed analytical pipeline for RAD-Seq phylogenetics, we created a concatenated matrix of 1.40 E06 aligned nucleotides, constituting 27,727 sequence clusters....

Data from: Mediation analysis demonstrates that trans-eQTLs are often explained by cis-mediation: a genome-wide analysis among 1,800 South Asians

Brandon L. Pierce, Lin Tong, Lin S. Chen, Ronald Rahaman, Maria Argos, Farzana Jasmine, Shantanu Roy, Rachelle Paul-Brutus, Harm-Jan Westra, Lude Franke, Tonu Esko, Rakibuz Zaman, Tariqul Islam, Mahfuzar Rahman, John A. Baron, Muhammad G. Kibriya & Habibul Ahsan
A large fraction of human genes are regulated by genetic variation near the transcribed sequence (cis-eQTL, expression quantitative trait locus), and many cis-eQTLs have implications for human disease. Less is known regarding the effects of genetic variation on expression of distant genes (trans-eQTLs) and their biological mechanisms. In this work, we use genome-wide data on SNPs and array-based expression measures from mononuclear cells obtained from a population-based cohort of 1,799 Bangladeshi individuals to characterize cis-...

Data from: Adaptive, convergent origins of the pygmy phenotype in African rainforest hunter-gatherers

George H. Perry, Matthieu Foll, Jean-Christophe Grenier, Etienne Patin, Yohann Nédélec, Alain Pacis, Maxime Barakatt, Simon Gravel, Xiang Zhou, Sam L. Nsobya, Laurent Excoffier, Lluis Quintana-Murci, Nathaniel J. Dominy & Luis B. Barreiro
The evolutionary history of the human pygmy phenotype (small body size), a characteristic of African and Southeast Asian rainforest hunter-gatherers, is largely unknown. Here we use a genome-wide admixture mapping analysis to identify 16 genomic regions that are significantly associated with the pygmy phenotype in the Batwa, a rainforest hunter-gatherer population from Uganda (east central Africa). The identified genomic regions have multiple attributes that provide supporting evidence of genuine association with the pygmy phenotype, including...

Data from: Genome-wide association study of Arabidopsis thaliana leaf microbial community

Matthew W. Horton, Natacha Bodenhausen, Kathleen Beilsmith, Dazhe Meng, Brian D. Muegge, Sathish Subramanian, M. Madlen Vetter, Bjarni J. Vilhjálmsson, Magnus Nordborg, Jeffrey I. Gordon & Joy Bergelson
Identifying the factors that influence the outcome of host–microbial interactions is critical to protecting biodiversity, minimizing agricultural losses and improving human health. A few genes that determine symbiosis or resistance to infectious disease have been identified in model species, but a comprehensive examination of how a host genotype influences the structure of its microbial community is lacking. Here we report the results of a field experiment with the model plant Arabidopsis thaliana to identify the...

Data from: Nonlinear thermal gradients shape broad-scale patterns in geographic range size and can reverse Rapoport’s rule

Adam Tomasovych, David Jablonski, Sarah K. Berke, Andrew Z. Krug & James W. Valentine
Aim: Species living at latitudes that have greater annual temperature variations are expected to achieve broader geographic ranges than species living at latitudes that have smaller annual temperature variations, generating a positive relationship between range size and latitude (Rapoport's rule). However, this prediction fails to take into account the greater latitudinal extent of tropical temperatures relative to those at higher latitudes. Here we model the contributions of the broader latitudinal extent of equal-temperature habitats at...

Data from: Prevalence and beta diversity in avian malaria communities: host species is a better predictor than geography

Elizabeth S. C. Scordato & Melissa R. Kardish
1. Patterns of diversity and turnover in macroorganism communities can often be predicted from differences in habitat, phylogenetic relationships among species, and the geographic scale of comparisons. In this study, we asked if these factors also predict diversity and turnover in parasite communities. 2. We studied communities of avian malaria in two sympatric, ecologically similar, congeneric host species at three different sites. We asked if parasite prevalence and community structure varied with host population, host...

Data from: Genomic divergence in a ring species complex

Miguel Alcaide, Elizabeth S. C. Scordato, Trevor D. Price & Darren E. Irwin
Ring species provide particularly clear demonstrations of how one species can gradually evolve into two, but are rare in nature. In the greenish warbler (Phylloscopus trochiloides) species complex, a ring of populations wraps around Tibet. Two reproductively isolated forms co-exist in central Siberia, with a gradient of genetic and phenotypic characteristics through the southern chain of populations connecting them. Previous genetic evidence has proven inconclusive, however, regarding whether species divergence took place in the face...

Data from: Gene flow between nascent species: geographic, genotypic and phenotypic differentiation within and between Aquilegia formosa and A. pubescens.

Christos Noutsos, Justin O. Borevitz & Scott A. Hodges
Speciation can be described as a reduction, and the eventual cessation, in the ability to interbreed. Thus, determining how gene flow differs within and between nascent species can illuminate the relative stage the taxa have attained in the speciation process. Aquilegia formosa and A. pubescens are fully intercompatible yet occur in different habitats and have flowers specialized for pollination by hummingbirds and hawkmoths respectively. Using 79 SNP loci we genotyped nearly 1,000 individuals from populations...

Data from: Memory and fitness optimization of bacteria under fluctuating environments

Guillaume Lambert & Edo Kussell
Bacteria prudently regulate their metabolic phenotypes by sensing the availability of specific nutrients, expressing the required genes for their metabolism, and repressing them after specific metabolites are depleted. It is unclear, however, how genetic networks maintain and transmit phenotypic states between generations under rapidly fluctuating environments. By subjecting bacteria to fluctuating carbon sources (glucose and lactose) using microfluidics, we discover two types of non-genetic memory in Escherichia coli and analyze their benefits. First, phenotypic memory...

Data from: The evolution of morphological integration in the ruminant skull

Annat Haber
Patterns of morphological integration have the potential to influence evolutionary trajectories. However, this influence depends on the stability of the integration pattern relative to the rate of evolutionary change. Studying the evolution of integration over large phylogenetic scales is complicated by its multivariate nature and the need to have both large sample sizes and a comprehensive taxon coverage. As a result, the question of how integration evolves over long time scales is still poorly understood....

Data from: Microsatellite analyses across three diverse vertebrate transcriptomes (Acipenser fulvescens, Ambystoma tigrinum, and Dipodomys spectabilis)

Jacqueline M. Doyle, Gregor Siegmund, Joseph D. Ruhl, Soo Hyung Eo, Matthew C. Hale, Nicholas J. Marra, Peter M. Waser & J. Andrew DeWoody
Historically, many population genetics studies have utilized microsatellite markers sampled at random from the genome and presumed to be selectively neutral. Recent studies, however, have shown that microsatellites can occur in transcribed regions, where they are more likely to be under selection. In this study, we mined microsatellites from transcriptomes generated by 454-pyrosequencing for three vertebrate species: lake sturgeon (Acipenser fulvescens), tiger salamander (Ambystoma tigrinum), and kangaroo rat (Dipodomys spectabilis). We evaluated (i) the occurrence...

Data from: Population genomic variation reveals roles of history, adaptation, and ploidy in switchgrass

Paul P. Grabowski, Geoffrey P. Morris, Michael D. Casler & Justin O. Borevitz
Geographic patterns of genetic variation are shaped by multiple evolutionary processes, including genetic drift, migration, and natural selection. Switchgrass (Panicum virgatum L.) has strong genetic and adaptive differentiation despite life history characteristics that promote high levels of gene flow and can homogenize intraspecific differences, such as wind-pollination and self-incompatibility. To better understand how historical and contemporary factors shape variation in switchgrass, we use genotyping-by-sequencing to characterize switchgrass from across its range at 98,042 SNPs. Population...

Data from: Assessing the effect of time-scaling methods on phylogeny-based analyses in the fossil record

David W. Bapst
Phylogeny-based approaches can be used to infer diversification dynamics and the rate and pattern of trait change. Applying these analyses to fossil data often requires time-scaling a cladogram of morphotaxon relationships. Although several time-scaling methods have been developed for this purpose, the incomplete sampling of the fossil record can distort the apparent timing of branching. It is unclear how well different time-scaling methods reconstruct the true temporal relationships or how any such inaccuracy could affect...

Data from: Mate preference for a phenotypically plastic trait is learned, and may facilitate preference-phenotype matching

Erica L. Westerman, Napon Chirathivat, Elizabeth Schyling & Antónia Monteiro
Fixed, genetically determined, mate preferences for species whose adult phenotype varies with rearing environment may be maladaptive, as the phenotype that is most fit in the parental environment may be absent in the offspring environment. Mate preference in species with polyphenisms (environmentally dependent alternative phenotypes) should therefore either not focus on polyphenic traits, be polyphenic themselves, or learned each generation. Here we test these alternative hypotheses by first describing a female-limited seasonal polyphenism in a...

Data from: Fine mapping of dominant X-linked incompatibility alleles in Drosophila hybrids

Daniel R. Matute & Jackie Gavin-Smyth
Sex chromosomes have a large effect on reproductive isolation and play an important role in hybrid inviability. In Drosophila hybrids, X-linked genes have pronounced deleterious effects on fitness in male hybrids, which have only one X chromosome. Several studies have succeeded at locating and identifying recessive X-linked alleles involved in hybrid inviability. Nonetheless, the density of dominant X-linked alleles involved in interspecific hybrid viability remains largely unknown. In this report, we study the effects of...

Data from: The magnitude of behavioral isolation is affected by characteristics of the mating community

Daniel R. Matute
Gene exchange between species occurs in areas of secondary contact, where two species have the opportunity to hybridize. If heterospecific males are more common than conspecific males, females will experience more encounters with males of other species. These encounters might increase the likelihood of heterospecific matings, and lead to the production of hybrid progeny. I studied the mating behavior of two pairs of sibling species endemic to Africa: Drosophila yakuba/D. santomea and D. simulans/D. sechellia....

Registration Year

  • 2014

Resource Types

  • Dataset


  • University of Chicago
  • University of North Carolina
  • Australian National University
  • McGill University
  • Emory University
  • Swiss Institute of Bioinformatics
  • Sun Yat-sen University
  • South Dakota School of Mines and Technology
  • The University of Texas at Austin
  • Duke University