20 Works

Data from: Untangling the evolutionary history of a highly polymorphic species: introgressive hybridization and high genetic structure in the desert cichlid fish Herichthys minckleyi

Isabel S. Magalhaes, Claudia Patricia Ornelas-García, Mariana Leal-Cardin, Tania Ramírez & Marta Barluenga
Understanding the origin of biodiversity requires knowledge on the evolutionary processes that drive divergence and speciation, as well as on the processes constraining it. Intraspecific polymorphisms can provide insight into the mechanisms that generate and maintain phenotypic, behavioural and life history diversification, and can help us understand not only the processes that lead to speciation but also the processes that prevent local fixation of morphs. The ‘desert cichlid’ Herichtys minckleyi is a highly polymorphic species...

Data from: Phylogenomic resolution of scorpions reveals multilevel discordance with morphological phylogenetic signal

Prashant P. Sharma, Rosa Fernández, Lauren A. Esposito, Edmundo González-Santillán, Lionel Monod, E. Gonzalez-Santillan & R. Fernandez
Scorpions represent an iconic lineage of arthropods, historically renowned for their unique bauplan, ancient fossil record and venom potency. Yet, higher level relationships of scorpions, based exclusively on morphology, remain virtually untested, and no multilocus molecular phylogeny has been deployed heretofore towards assessing the basal tree topology. We applied a phylogenomic assessment to resolve scorpion phylogeny, for the first time, to our knowledge, sampling extensive molecular sequence data from all superfamilies and examining basal relationships...

Data from: Limitations of climate data for inferring species boundaries: insights from speckled rattlesnakes

Jesse M. Meik, Jeffrey W. Streicher, A. Michelle Lawing, Oscar Flores-Villela & Matthew K. Fujita
Phenotypes, DNA, and measures of ecological differences are widely used in species delimitation. Although rarely defined in such studies, ecological divergence is almost always approximated using multivariate climatic data associated with sets of specimens (i.e., the “climatic niche”); the justification for this approach is that species-specific climatic envelopes act as surrogates for physiological tolerances. Using identical statistical procedures, we evaluated the usefulness and validity of the climate-as-proxy assumption by comparing performance of genetic (nDNA SNPs...

Data from: Genomic variation in recently collected maize landraces from Mexico

María Clara Arteaga, Alejandra Moreno-Letelier, Alicia Mastretta-Yanes, Alejandra Vázquez-Lobo, Alejandra Breña-Ochoa, Andrés Moreno-Estrada, Luis E. Eguiarte & Daniel Piñero
The present dataset comprises 36,931 SNPs genotyped in 46 maize landraces native to Mexico as well as the teosinte subspecies Zea maiz ssp. Parviglumis and ssp. Mexicana. These landraces were collected directly from farmers mostly between 2006 and 2010. We accompany these data with a short description of the variation within each landrace, as well as maps, principal component analyses and neighbor joining trees showing the distribution of the genetic diversity relative to landrace, geographical...

Data from: The evolution of bat nucleic acid sensing Toll-like receptors

Marina Escalera-Zamudio, Lisandra M. Zepeda-Mendoza, Elizabeth Loza-Rubio, Edith Rojas-Anaya, Maria L. Méndez-Ojeda, Carlos F. Arias & Alex D. Greenwood
We characterized the nucleic acid sensing Toll-like receptors (TLR) of a New World bat species, the common vampire bat (Desmodus rotundus), and through a comparative molecular evolutionary approach searched for general adaptation patterns among the nucleic acid sensing TLRs of eight different bats species belonging to three families (Pteropodidae, Vespertilionidae and Phyllostomidae). We found that the bat TLRs are evolving slowly and mostly under purifying selection and that the divergence pattern of such receptors is...

Data from: Microbial invasion of the Caribbean by an Indo-Pacific coral zooxanthella

D. Tye Pettay, Drew C. Wham, Robin T. Smith, Roberto Iglesias-Prieto & Todd C. LaJeunesse
Human-induced environmental changes have ushered in the rapid decline of coral reef ecosystems, particularly by disrupting the symbioses between reef-building corals and their photosymbionts. However, escalating stressful conditions enable some symbionts to thrive as opportunists. We present evidence that a stress-tolerant “zooxanthella” from the Indo-Pacific Ocean, Symbiodinium trenchii, has rapidly spread to coral communities across the Greater Caribbean. In marked contrast to populations from the Indo-Pacific, Atlantic populations of S. trenchii contained exceptionally low genetic...

Data from: Deepwater Horizon oil spill impacts on sea turtles could span the Atlantic

Nathan F. Putman, F. Alberto Abreu-Grobois, Iñaky Iturbe-Darkistade, Emily M. Putman, Paul M. Richards & Philippe Verley
We investigated the extent that the 2010 Deepwater Horizon oil spill potentially affected oceanic-stage sea turtles from populations across the Atlantic. Within an ocean-circulation model, particles were backtracked from the Gulf of Mexico spill site to determine the probability of young turtles arriving in this area from major nesting beaches. The abundance of turtles in the vicinity of the oil spill was derived by forward-tracking particles from focal beaches and integrating population size, oceanic-stage duration...

Data from: Phylogeny and biogeography of the American live oaks (Quercus subsection Virentes): a genomic and population genetics approach

Jeannine Cavender-Bares, Antonio González-Rodríguez, Deren A. R. Eaton, Andrew A. L. Hipp, Anne Beulke & Paul S. Manos
The nature and timing of evolution of niche differentiation among closely related species remains an important question in ecology and evolution. The American live oak clade, Virentes, which spans the unglaciated temperate and tropical regions of North America and Mesoamerica, provides an instructive system in which to examine speciation and niche evolution. We generated a fossil-calibrated phylogeny of Virentes using RADseq data to estimate divergence times and used nuclear microsatellites, chloroplast sequences and an intron...

Data from: Genetic structure in village dogs reveals a Central Asian domestication origin

Laura M. Shannon, Ryan H. Boyko, Marta Castelhano, Elizabeth Corey, Jessica J. Hayward, Corin McLean, Michelle E. White, Mounir Abi Said, Baddley A. Anita, Nono Bondjengo Ikombe, Jorge Calero, Ana Galov, Marius Hedimbi, Bulu Imam, Rajashree Khalap, Douglas Lally, Andrew Masta, Kyle C. Oliveira, Lucía Pérez, Julia Randall, Nguyen Minh Tam, Francisco J. Trujillo-Cornejo, Carlos Valeriano, Nathan B. Sutter, Rory J. Todhunter … & Adam R. Boyko
Dogs were the first domesticated species, originating at least 15,000 y ago from Eurasian gray wolves. Dogs today consist primarily of two specialized groups—a diverse set of nearly 400 pure breeds and a far more populous group of free-ranging animals adapted to a human commensal lifestyle (village dogs). Village dogs are more genetically diverse and geographically widespread than purebred dogs making them vital for unraveling dog population history. Using a semicustom 185,805-marker genotyping array, we...

Data from: Chronic anthropogenic disturbance drives the biological impoverishment of the Brazilian Caatinga vegetation

Elâine Maria S. Ribeiro, Víctor Arroyo-Rodríguez, Bráulio A. Santos, Marcelo Tabarelli & Inara R. Leal
1. In addition to acute transformations of ecosystems caused by deforestation, old-growth forests worldwide are being increasingly altered by low-intensity but chronic human disturbance. Overgrazing and the continuous extraction of forest products are important drivers of chronic disturbance, which can lead to the gradual local extinction of species and the alteration of vegetation structure. 2. We tested this hypothesis in the Brazilian Caatinga vegetation, one of the most species-rich and populated semi-arid regions of the...

Data from: Evolving from static to dynamic signals: evolutionary compensation between two communicative signals

Emilia P. Martins, Alison G. Ossip-Klein, J. Jaime Zúñiga-Vega, Cuauhcihuatl Vital García, Stephanie M. Campos & Diana K. Hews
Signals that convey related information may impose selection on each other, creating evolutionary links between different components of the communicative repertoire. Here, we ask about the consequences of the evolutionary loss of one signal (a colour patch) on another (a motion display) in Sceloporus lizards. We present data on male lizards of four species: two pairs of sister taxa representing two independent evolutionary losses of the static colour patch (S. cozumelae and S. parvus; S....

Data from: Functional coupling constrains craniofacial diversification in Lake Tanganyika cichlids

Masahito Tsuboi, Alejandro Gonzalez-Voyer & Niclas Kolm
Functional coupling, where a single morphological trait performs multiple functions, is a universal feature of organismal design. Theory suggests that functional coupling may constrain the rate of phenotypic evolution, yet empirical tests of this hypothesis are rare. In fish, the evolutionary transition from guarding the eggs on a sandy/rocky substrate (i.e. substrate guarding) to mouthbrooding introduces a novel function to the craniofacial system and offers an ideal opportunity to test the functional coupling hypothesis. Using...

Data from: Estimating the temporal and spatial extent of gene flow among sympatric lizard populations (genus Sceloporus) in the southern Mexican highlands

Jared A. Grummer, Martha L. Calderón-Espinosa, Adrián Nieto-Montes De Oca, Eric N. Smith, Fausto R. Méndez De La Cruz & Adam D. Leaché
Interspecific gene flow is pervasive throughout the tree of life. Although detecting gene flow between populations has been facilitated by new analytical approaches, determining the timing and geography of hybridization has remained difficult, particularly for historical gene flow. A geographically explicit phylogenetic approach is needed to determine the overlap of ancestral populations. In this study, we performed population genetic analyses, species delimitation, simulations and a recently developed approach of species tree diffusion to infer the...

Data from: Maize diversity associated to social origin and environmental variation in southern Mexico

Quetzalcoatl Orozco-Ramirez, Jeffrey Ross-Ibarra, Amalio Santacruz-Varela & Stephen Brush
While prevailing theories of crop evolution suggest that crop diversity and cultural diversity should be linked, empirical evidence for such a link remains inconclusive. In particular, few studies have investigated such patterns on a local scale. Here, we address this issue by examining the determinants of maize diversity in a local region of high cultural and biological richness in Southern Mexico. We collected maize samples from villages at low and middle elevations in two adjacent...

Data from: Patterns and predictors of β-diversity in the fragmented Brazilian Atlantic forest: a multiscale analysis of forest specialist and generalist birds

José Carlos Morante-Filho, Victor Arroyo-Rodríguez & Deborah Faria
1. Biodiversity maintenance in human-altered landscapes (HALs) depends on the species turnover among localities, but the patterns and determinants of β-diversity in HALs are poorly known. In fact, declines, increases, and neutral shifts in β-diversity have all been documented, depending on the landscape, ecological group and spatial scale of analysis. 2. We shed some light on this controversy by assessing the patterns and predictors of bird β-diversity across multiple spatial scales considering forest specialist and...

Data from: Fish faunal provinces of the conterminous United States of America reflect historical geography and familial composition

Wilfredo A. Matamoros, Christopher W. Hoagstrom, Jacob F. Schaefer & Brian R. Kreiser
Although the conterminous USA has a long history of ichthyological exploration, the description of biogeographical provinces has been ad hoc. In this study we quantitatively determined fish faunal provinces and interpreted them in the context of the geological history of North America. We also evaluated influences of major river basin occupancy and contemporary environmental factors on provincial patterns. Our data set comprised 794 native fishes, which we used to generate a presence and absence matrix...

Data from: Environmental gradients and the evolution of successional habitat specialization: a test case with 14 Neotropical forest sites

Susan G. Letcher, Jesse R. Lasky, Robin L. Chazdon, Natalia Norden, S. Joseph Wright, Jorge A. Meave, Eduardo A. Pérez-García, Rodrigo Muñoz, Eunice Romero-Pérez, Ana Andrade, José Luis Andrade, Patricia Balvanera, Justin M. Becknell, Tony V. Bentos, Radika Bhaskar, Frans Bongers, Vanessa Boukili, Pedro H. S. Brancalion, Ricardo G. César, Deborah A. Clark, David B. Clark, Dylan Craven, Alexander DeFrancesco, Juan M. Dupuy, Bryan Finegan … & G. Bruce Williamson
1. Successional gradients are ubiquitous in nature, yet few studies have systematically examined the evolutionary origins of taxa that specialize at different successional stages. Here we quantify successional habitat specialization in Neotropical forest trees and evaluate its evolutionary lability along a precipitation gradient. Theoretically, successional habitat specialization should be more evolutionarily conserved in wet forests than in dry forests due to more extreme microenvironmental differentiation between early and late successional stages in wet forest. 2....

Data from: Molecular and iridescent feather reflectance data reveal recent genetic diversification and phenotypic differentiation in a cloud forest hummingbird

Juan Fransisco Ornelas, Clementina González, Blanca E. Hernández-Baños, Jaime García-Moreno & Juan Francisco Ornelas
The present day distribution and spatial genetic diversity of Mesoamerican biota reflects a long history of responses to habitat change. The hummingbird Lampornis amethystinus is distributed in northern Mesoamerica, with geographically disjunct populations. Based on sampling across the species range using mitochondrial DNA (mtDNA) sequences and nuclear microsatellites jointly analysed with phenotypic and climatic data, we (1) test whether the fragmented distribution is correlated with main evolutionary lineages, (2) assess body size and plumage color...

Data from: Dietary overlap and seasonality in three species of mormoopid bats from a tropical dry forest

Valeria B. Salinas-Ramos, Luis Gerardo Herrera Montalvo, Virginia León-Regagnon, Aitor Arrizabalaga-Escudero & Elizabeth L. Clare
Competing hypotheses explaining species’ use of resources have been advanced. Resource limitations in habitat and/or food are factors that affect assemblages of species. These limitations could drive the evolution of morphological and/or behavioural specialization, permitting the coexistence of closely related species through resource partitioning and niche differentiation. Alternatively, when resources are unlimited, fluctuations in resources availability will cause concomitant shifts in resource use regardless of species identity. Here, we used next-generation sequencing to test these...

Data from: Speciation genomics and a role for the Z chromosome in the early stages of divergence between Mexican ducks and mallards

Philip Lavretsky, Jeffrey M. DaCosta, Blanca E. Hernández-Baños, , Michael D. Sorenson, Jeffrey L. Peters & Andrew Engilis
Speciation is a continuous and dynamic process, and studying organisms during the early stages of this process can aid in identifying speciation mechanisms. The mallard (Anas platyrhynchos) and Mexican duck (A. [p.] diazi) are two recently diverged taxa with a history of hybridization and controversial taxonomy. To understand their evolutionary history, we conducted genomic scans to characterize patterns of genetic diversity and divergence across the mitochondrial DNA (mtDNA) control region, 3523 autosomal loci and 172...

Registration Year

  • 2015

Resource Types

  • Dataset


  • National Autonomous University of Mexico
  • Stanford University
  • University of Minnesota
  • The University of Texas at Arlington
  • Texas A&M University
  • Yale University
  • University of the Basque Country
  • Museo de Historia Natural Noel Kempff Mercado
  • University of Washington