19 Works

Data from: How does ascertainment bias in SNP analyses affect inferences about population history?

Emily Jane McTavish & David M. Hillis
Background: The selection of variable sites for inclusion in genomic analyses can influence results, especially when exemplar populations are used to determine polymorphic sites. We tested the impact of ascertainment bias on the inference of population genetic parameters using empirical and simulated data representing the three major continental groups of cattle: European, African, and Indian. We simulated data under three demographic models. Each simulated data set was subjected to three ascertainment schemes: (I) random selection;...

Data from: Synthesis of phylogeny and taxonomy into a comprehensive tree of life

Cody E. Hinchliff, Stephen A. Smith, James F. Allman, J. Gordon Burleigh, Ruchi Chaudhary, Lyndon M. Coghill, Keith A. Crandall, Jiabin Deng, Bryan T. Drew, Romina Gazis, Karl Gude, David S. Hibbett, Laura A. Katz, , Emily Jane McTavish, Peter E. Midford, Christopher L. Owen, Richard H. Ree, Jonathan A. Rees, Douglas E. Soltis, Tiffani Williams & Karen Ann Cranston
Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips—the Open Tree of Life. Realization of this tree required the assembly...

Data from: Sun skink landscape genomics: assessing how microevolutionary processes shape genetic and phenotypic diversity across a heterogeneous and fragmented landscape

Anthony J. Barley, Patrick J. Monnahan, Robert C. Thomson, L. Lee Grismer & Rafe M. Brown
Incorporating genomic data sets into landscape genetic analyses allows for powerful insights into population genetics, explicitly geographical correlates of selection, and morphological diversification of organisms across the geographical template. Here, we utilize an integrative approach to examine gene flow and detect selection, and we relate these processes to genetic and phenotypic population differentiation across South-East Asia in the common sun skink, Eutropis multifasciata. We quantify the relative effects of geographic and ecological isolation in this...

Data from: Evolution of codfishes (Teleostei: Gadinae) in geographical and ecological space: evidence that physiological limits drove diversification of subarctic fishes

Hannah L. Owens
Aim: To develop a holistic biogeographical history of codfishes in the subfamily Gadinae based on historical relationships, ecological niche, and evolution of physiological tolerances. Two alternative diversification scenarios were tested in two co-distributed, Northern Hemisphere clades: (1) clade ancestors were temperate, and environmental niche has been conserved over evolutionary time, implying that speciation was driven by vicariance associated with ice sheet formation; and (2) clade ancestors were Arctic, and species convergently adapted to temperate environmental...

Data from: Placing cryptic, recently extinct, or hypothesized taxa into an ultrametric phylogeny using continuous character data: A case study with the lizard Anolis roosevelti

Liam J. Revell, D. Luke Mahler, Robert Graham Reynolds & Graham James Slater
In recent years, enormous effort and investment has been put into assembling the tree of life: a phylogenetic history for all species on Earth. Overwhelmingly, this progress toward building an ever increasingly complete phylogeny of living things has been accomplished through sophisticated analysis of molecular data. In the modern genomic age, molecular genetic data have become very easy and inexpensive to obtain for many species. However, some lineages are poorly represented in or absent from...

Data from: Life history traits and phenotypic selection among sunflower crop-wild hybrids and their wild counterpart: implications for crop allele introgression

Matthew A. Kost, Helen M. Alexander, D. Jason Emry & Kristin L. Mercer
Hybridization produces strong evolutionary forces. In hybrid zones, selection can differentially occur on traits and selection intensities may differ among hybrid generations. Understanding these dynamics in crop-wild hybrid zones can clarify crop-like traits likely to introgress into wild populations and the particular hybrid generations through which introgression proceeds. In a field experiment with four crop-wild hybrid Helianthus annuus (sunflower) cross types, we measured growth and life history traits and performed phenotypic selection analysis on early...

Data from: Centromere–associated meiotic drive and female fitness variation in Mimulus

Lila Fishman & John Kennedy Kelly
Female meiotic drive, in which chromosomal variants preferentially segregate to the egg pole during asymmetric female meiosis, is a theoretically pervasive but still mysterious form of selfish evolution. Like other selfish genetic elements, driving chromosomes may be maintained as balanced polymorphisms by pleiotropic or linked fitness costs. A centromere-associated driver (D) with a ∼58:42 female-specific transmission advantage occurs at intermediate frequency (32-40%) in the Iron Mountain population of the yellow monkeyflower, Mimulus guttatus. Previously determined...

Data from: Spatial analysis of anthropogenic landscape disturbance and Buruli ulcer disease in Benin

Lindsay P. Campbell, Andrew O. Finley, Mark Eric Benbow, Jenni Gronseth, Pamela Small, Roch Christian Johnson, Ghislain E. Sopoh, Richard M. Merritt, Heather Williamson & Jiaguo Qi
Background: Land use and land cover (LULC) change is one anthropogenic disturbance linked to infectious disease emergence. Current research has focused largely on wildlife and vector-borne zoonotic diseases, neglecting to investigate landscape disturbance and environmental bacterial infections. One example is Buruli ulcer (BU) disease, a necrotizing skin disease caused by the environmental pathogen Mycobacterium ulcerans (MU). Empirical and anecdotal observations have linked BU incidence to landscape disturbance, but potential relationships have not been quantified as...

Data from: Multilocus phylogenetic analyses of Hispaniolan and Bahamian trunk anoles (distichus species group)

Anthony J. Geneva, Jared Hilton, Sabina Noll & Richard E. Glor
The distichus species group includes six species and 21 subspecies of trunk ecomorph anoles distributed across Hispaniola and its satellite islands as well as the northern Bahamas. Although this group has long served as a model system for studies of reproductive character displacement, adaptation, behavior and speciation, it has never been the subject of a comprehensive phylogenetic analysis. Our goal here is to generate a multilocus phylogenetic dataset (one mitochondrial and seven nuclear loci) and...

Data from: Hybridization and reproductive isolation between diploid Erythronium mesochoreum and its tetraploid congener E. albidum (Liliaceae)

Kathy Roccaforte, Sabrina E. Russo & Diana Pilson
Polyploidy has played an important role in angiosperm diversification, but how polyploidy contributes to reproductive isolation remains poorly understood. Most work has focused on postzygotic reproductive barriers, and the influence of ploidy differences on prezygotic barriers is understudied. To address these gaps, we quantified hybrid occurrence, interspecific self-compatibility differences, and the contributions of multiple pre- and postzygotic barriers to reproductive isolation between diploid Erythronium mesochoreum (Liliaceae) and its tetraploid congener E. albidum. Reproductive isolation between...

Data from: Atlas of Mexican Triatominae (Reduviidae: Hemiptera) and vector transmission of Chagas disease

Janine M. Ramsey, A. Townsend Peterson, Oscar Carmona-Castro, David A. Moo-Llanes, Yoshinori Nakazawa, Butrick Morgan, Ezequiel Tun-Ku, Keynes De La Cruz-Félix, Carlos N. Ibarra-Cerdeña & Morgan Butrick
Chagas disease is one of the most important yet neglected parasitic diseases in Mexico and is transmitted by Triatominae. Nineteen of the 31 Mexican triatomine species have been consistently found to invade human houses and all have been found to be naturally infected with Trypanosoma cruzi. The present paper aims to produce a state-of-knowledge atlas of Mexican triatomines and analyse their geographic associations with T. cruzi, human demographics and landscape modification. Ecological niche models (ENMs)...

Data from: Inferring speciation history in the Andes with reduced-representation sequence data: an example in the bay-backed antpittas (Aves; Grallariidae; Grallaria hypoleuca s. l.)

Benjamin M. Winger, Peter A. Hosner, Gustavo A. Bravo, Andrés M. Cuervo, Natalia Aristizábal, Luis E. Cueto & John M. Bates
In the Andes, humid-forest organisms frequently exhibit pronounced genetic structure and geographic variation in phenotype, often coincident with physical barriers to dispersal. However, phylogenetic relationships of clades have often been difficult to resolve due to short internodes. Consequently, even in taxa with well-defined genetic structure, the temporal and geographic sequences of dispersal and vicariance events that led to this differentiation have remained opaque, hindering efforts to test the association between diversification and earth history and...

Data from: Having a lot of a good thing: multiple important group memberships as a source of self-esteem

Jolanda Jetten, Nyla R. Branscombe, S. Alexander Haslam, Catherine Haslam, Tegan Cruwys, Janelle M. Jones, Lijuan Cui, Genevieve Dingle, James Liu, Sean Murphy, Anh Thai, Zoe Walter & Airong Zhang
Membership in important social groups can promote a positive identity. We propose and test an identity resource model in which personal self-esteem is boosted by membership in additional important social groups. Belonging to multiple important group memberships predicts personal self-esteem in children (Study 1a), older adults (Study 1b), and former residents of a homeless shelter (Study 1c). Study 2 shows that the effects of multiple important group memberships on personal self-esteem are not reducible to...

Data from: Worldwide evidence of a unimodal relationship between productivity and plant species richness

Lauchlan H. Fraser, Jason Pither, Anke Jentsch, Marcelo Sternberg, Martin Zobel, Diana Askarizadeh, Sandor Bartha, Carl Beierkuhnlein, Jonathan A. Bennett, Alex Bittel, Bazartseren Boldgiv, Ilsi I. Boldrini, Edward Bork, Leslie Brown, Marcelo Cabido, James Cahill, Cameron N. Carlyle, Giandiego Campetella, Stefano Chelli, Ofer Cohen, Anna-Maria Csergo, Sandra Diaz, Lucas Enrico, David Ensing, Alessandra Fidelis … & Talita Zupo
The search for predictions of species diversity across environmental gradients has challenged ecologists for decades. The humped-back model (HBM) suggests that plant diversity peaks at intermediate productivity; at low productivity few species can tolerate the environmental stresses, and at high productivity a few highly competitive species dominate. Over time the HBM has become increasingly controversial, and recent studies claim to have refuted it. Here, by using data from coordinated surveys conducted throughout grasslands worldwide and...

Data from: Clonal reproduction shapes evolution in the lizard malaria parasite Plasmodium floridense

Bryan G. Falk, Richard E. Glor & Susan L. Perkins
The preponderant clonal evolution hypothesis (PCE) predicts that frequent clonal reproduction (sex between two clones) in many pathogens capable of sexual recombination results in strong linkage disequilibrium and the presence of discrete genetic subdivisions characterized by occasional gene flow. We expand on the PCE and predict that higher rates of clonal reproduction will result in: (1) morphologically cryptic species that exhibit (2) low within-species variation and (3) recent between-species divergence. We tested these predictions in...

Data from: Isolation by environment in white-breasted nuthatches (Sitta carolinensis) of the Madrean Archipelago sky islands: a landscape genomics approach

Joseph D. Manthey & Robert G. Moyle
Understanding landscape processes driving patterns of population genetic differentiation and diversity has been a long-standing focus of ecology and evolutionary biology. Gene flow may be reduced by historical, ecological or geographic factors, resulting in patterns of isolation by distance (IBD) or isolation by environment (IBE). Although IBE has been found in many natural systems, most studies investigating patterns of IBD and IBE in nature have used anonymous neutral genetic markers, precluding inference of selection mechanisms...

Data from: Phylogeny of the island archipelago frog genus Sanguirana: another endemic Philippine radiation that diversified 'Out-of-Palawan'

Rafe M. Brown, Yong-Chao Su, Brenna Barger, Cameron D. Siler, Marites B. Sanguila, Arvin C. Diesmos & David C. Blackburn
Recent higher-level frog phylogenetic analyses have included a few members of the endemic Philippine frog genus Sanguirana. Although the monophyly of the group has never been disputed, the recent phylogenetically-supported inclusion of the Palawan Wood Frog (Sanguirana sanguinea) in this clade was highly unexpected. In addition, species boundaries and relationships remain unclear and new species continue to be discovered. We estimate the phylogeny for this endemic Philippine genus using two mitochondrial gene regions and six...

Data from: Chromosomal patterns of diversity and differentiation in creepers: a next-gen phylogeographic investigation of Certhia americana

Joseph Manthey, John Klicka & Garth Spellman
With methods for sequencing thousands of loci for many individuals, phylogeographic studies have increased inferential power and the potential for applications to new questions. In songbirds, strong patterns of inter-chromosomal synteny, the published genome of a songbird and the ability to obtain thousands of genetic loci for many individuals permit the investigation of differentiation between and diversity within lineages across chromosomes. Here, we investigate patterns of differentiation and diversity in Certhia americana, a widespread North...

Data from: No silver bullets in correlative ecological niche modeling: insights from testing among many potential algorithms for niche estimation

Huijie Qiao, Jorge Soberón & Andrew Townsend Peterson
The field of ecological niche modeling or species distribution modeling has seen enormous activity and attention in recent years, in light of exciting biological inferences that can be drawn from correlational models of species’ environmental requirements (i.e., ecological niches) and inferences of potential geographic distributions. Among the many methods used in the field, one or two are in practice assumed to be ‘best’ and are used commonly, often without explicit testing. We explore herein implications...

Registration Year

  • 2015

Resource Types

  • Dataset


  • University of Kansas
  • University of Florida
  • Field Museum of Natural History
  • Michigan State University
  • University of Camerino
  • Victoria University of Wellington
  • National Museum
  • University of Montana
  • Islamic Azad University
  • Sao Paulo State University