270 Works

Double digest RADseq loci using standard Illumina indexes improve deep and shallow phylogenetic resolution of Lophodermium, a widespread fungal endophyte of pine needles

Ryoko Oono & Rodolfo Salas Lizana
The phylogenetic and population genetic structure of symbiotic microorganisms may correlate with important ecological traits that can be difficult to directly measure, such as host preferences or dispersal rates. This study develops and tests a low-cost double digest restriction site-associated DNA sequencing (ddRADseq) protocol to reveal among- and within-species genetic structure for Lophodermium, a genus of fungal endophytes whose evolutionary analyses have been limited by the scarcity of informative markers. The protocol avoids expensive barcoded...

Data from: Tracking climate change in a dispersal-limited species: reduced spatial and genetic connectivity in a montane salamander

Guillermo Velo-Antón, Juan L. Parra, Gabriela Parra-Olea & Kelly R. Zamudio
Tropical montane taxa are often locally adapted to very specific climatic conditions, contributing to their lower dispersal potential across complex landscapes. Climate and landscape features in montane regions affect population genetic structure in predictable ways, yet few empirical studies quantify the effects of both factors in shaping genetic structure of montane-adapted taxa. Here, we considered temporal and spatial variability in climate to explain contemporary genetic differentiation between populations of the montane salamander, Pseudoeurycea leprosa. Specifically,...

Diurnal foraging ant–tree co-occurrence networks are similar between canopy and understorey in a Neotropical rain forest

Reuber Antoniazzi, Jose Garcia-Franco, Milan Janda, Maurice Leponce & Wesley Dáttilo
Discussion of the vertical stratification of organisms in tropical forests has traditionally focused on species distribution. Most studies have shown that, due to differences in abiotic conditions and resource distribution, species can be distributed along the vertical gradient according to their eco-physiological needs. However, the network structure between distinct vertical strata remains little-explored. To fill this gap in knowledge, we used baits to sample ants in the canopy and understorey trees of a Mexican tropical...

Data from: Modifications during early plant development promote the evolution of nature’s most complex woods

Joyce G. Chery, Marcelo R. Pace, Pedro Acevedo-Rodriguez, Chelsea D. Specht & Carl J. Rothfels
Secondary growth is the developmental process by which woody plants grow radially. The most complex presentations of secondary growth are found in lianas (woody vines) as a result of their unique demand to maintain stems that can twist without breaking. The complex woody forms in lianas arise as non-circular stem outlines, aberrant tissue configurations, and/or shifts in the relative abundance of secondary tissues. Previous studies demonstrate that abnormal activity of the vascular cambium leads to...

Geographic variation in the duets of the Rufous-naped Wren (Campylorhynchus rufinucha) complex

J. Roberto Sosa-López, Adolfo G. Navarro-Sigüenza, Wiliam Ku-Peralta & Luis Sandoval
Acoustic signals used in animal communication play a key role in mate attraction, species recognition and territory defense. Variation in acoustic signals may reflect population structure, lack of gene flow, and phylogenetic relationships. In birds, the study of geographic variation in acoustic signals has been useful for elucidating potential factors involved in phenotypic divergence and for establishing species limits. However, most of the studies on geographic variation have focused on calls and solo songs, with...

Data from: Impact of a hurricane on the herpetofaunal assemblages of a successional chronosequence in a tropical dry forest

Ireri Suazo-Ortuño, José Nicolás Urbina-Cardona, Nancy Lara-Uribe, Jorge Marroquín-Páramo, Yunuen Soto-Sandoval, Jorge Rangel-Orozco, Leonel Lopez-Toledo, Julieta Benítez-Malvido & Javier Alvarado-Díaz
Land‐use change is the main cause of deforestation and degradation of tropical forest in Mexico. Frequently, these lands are abandoned leading to a mosaic of natural vegetation in secondary succession. Further degradation of the natural vegetation in these lands could be exacerbated by stochastic catastrophic events such as hurricanes. Information on the impact of human disturbance parallel to natural disturbance has not yet been evaluated for faunal assemblages in tropical dry forests. To evaluate the...

Data from: Towards smarter harvesting from natural palm populations by sparing the individuals that contribute most to population growth or productivity

Merel Jansen, Niels P.R. Anten, Frans Bongers, Miguel Martínez-Ramos, Pieter A. Zuidema & Niels P. R. Anten
1. Natural populations deliver a wide range of products that provide income for millions of people and need to be exploited sustainably. Large heterogeneity in individual performance within these exploited populations has the potential to improve population recovery after exploitation and thus help sustaining yields over time. 2. We explored the potential of using individual heterogeneity to design smarter harvest schemes, by sparing individuals that contribute most to future productivity and population growth, using the...

Data from: Non-equilibrium dynamics and floral trait interactions shape extant angiosperm diversity

Brian C. O'Meara, Stacey D. Smith, W. Scott Armbruster, Lawrence D. Harder, Christopher R. Hardy, Lena C. Hileman, Larry Hufford, Amy Litt, Susana Magallon, Stephen A. Smith, Peter F. Stevens, Charles B. Fenster & Pamela K. Diggle
Why are some traits and trait combinations exceptionally common across the tree of life, whereas others are vanishingly rare? The distribution of trait diversity across a clade at any time depends on the ancestral state of the clade, the rate at which new phenotypes evolve, the differences in speciation and extinction rates across lineages, and whether an equilibrium has been reached. Here we examine the role of transition rates, differential diversification (speciation minus extinction), and...

Data from: High fidelity: extra-pair fertilisations in eight Charadrius plover species are not associated with parental relatedness or social mating system

Kathryn H. Maher, Luke J. Eberhart-Phillips, András Kosztolányi, Natalie Dos Remedios, María Cristina Carmona-Isunza, Medardo Cruz-López, Sama Zefania, James J. H. St Clair, Monif AlRashidi, Michael A. Weston, Martín A. Serrano-Meneses, Oliver Krüger, Joseph I. Hoffmann, Tamás Székely, Terry Burke, Clemens Küpper & Joseph I. Hoffman
Extra-pair paternity is a common reproductive strategy in many bird species. However, it remains unclear why extra-pair paternity occurs and why it varies among species and populations. Plovers (Charadrius spp.) exhibit considerable variation in reproductive behaviour and ecology, making them excellent models to investigate the evolution of social and genetic mating systems. We investigated inter- and intra-specific patterns of extra-pair parentage and evaluated three major hypotheses explaining extra-pair paternity using a comparative approach based on...

Data from: Domestication genomics of the open-pollinated scarlet runner bean (Phaseolus coccineus L.)

Azalea Guerra-García, Marco Suárez-Atilano, Alicia Mastretta-Yanes, Alfonso Delgado-Salinas & Daniel Piñero
The runner bean is a legume species from Mesoamerica closely related to common bean (Phaseolus vulgaris). It is a perennial species, but it is usually cultivated in small-scale agriculture as an annual crop for its dry seeds and edible immature pods. Unlike the common bean, P. coccineus has received little attention from a genetic standpoint. In this work we aim to (1) provide information about the domestication history and domestication events of P. coccineus; (2)...

Data from: Correlates of extinction risk in squamate reptiles: the relative importance of biology, geography, threat and range size

Monika Böhm, Rhiannon Williams, Huw R. Bramhall, Kirsten M. McMillan, Ana D. Davidson, Andrés Garcia, Lucie M. Bland, Jon Bielby & Ben Collen
Aim Evaluating the relative roles of biological traits and environmental factors that predispose species to an elevated risk of extinction is of fundamental importance to macroecology. Identifying species that possess extinction-promoting traits allows targeted conservation action before precipitous declines occur. Such analyses have been carried out for several vertebrate groups, with the notable exception of reptiles. We identify traits correlating with high extinction risk in squamate reptiles, assess whether these differ with geography, taxonomy and...

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: Reorganization of interaction networks modulates the persistence of species in late successional stages

Serguei Saavedra, Simone Cenci, Ek Del-Val, Karina Boege & Rudolf P. Rohr
1.Ecological interaction networks constantly reorganize as interspecific interactions change across successional stages and environmental gradients. This reorganization can also be associated with the extent to which species change their preference for types of niches available in their local sites. Despite the pervasiveness of these interaction changes, previous studies have revealed that network reorganizations have a minimal or insignificant effect on global descriptors of network architecture, such as: connectance, modularity, and nestedness. However, little is known...

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: Soil-mediated filtering organizes tree assemblages in regenerating tropical forests

Bruno Ximenes Pinho, Felipe Pimentel Lopes De Melo, Víctor Arroyo-Rodríguez, Simon Pierce, Madelon Lohbeck & Marcelo Tabarelli
1.Secondary forests are increasingly dominant in human-modified tropical landscapes, but the drivers of forest recovery remain poorly understood. Soil conditions influence plant community composition, and are expected to change over a gradient of succession. However, the role of soil conditions as an environmental filter driving community assembly during forest succession has rarely been explicitly assessed. 2.We evaluated the role of stand basal area and soil conditions on community assembly and its consequences for community functional...

Data from: Complex phylogeographic patterns indicate Central American origin of two widespread Mesoamerican Quercus (Fagaceae) species

Hernando Rodríguez-Correa, Ken Oyama, Mauricio Quesada, Eric J. Fuchs, Maura Quezada, Lilian Ferrufino, Susana Valencia-Ávalos, Alfredo Cascante-Marín & Antonio González-Rodríguez
The northern Neotropical region is characterized by a heterogeneous geological and climatic history. Recent studies have shown contrasting patterns regarding the role of geographic elements as barriers that could have determined phylogeographic structure in various species. Recently, the phylogeography and biogeography of Quercus species have been studied intensively, and the patterns observed so far suggest contrasting evolutionary histories for Neotropical species in comparison with their Holarctic relatives. The goal of this study was to describe...

Data from: Evolutionary changes in plant tolerance against herbivory through a resurrection experiment

Carlos Bustos-Segura, Juan Fornoni & J. Núñez-Farfán
Both theoretical and empirical works have highlighted the difference in the evolutionary implications of host resistance and tolerance against their enemies. However, it has been difficult to show evolutionary changes in host defences in natural populations; thus, evaluating theoretical predictions of simultaneous evolution of defences remains a challenge. We studied the evolutionary changes in traits related to resistance and tolerance against herbivory in a natural plant population using seeds from two collections made in a...

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: Why are flowers sweeter than fruits or buds? Variation in extrafloral nectar secretion throughout the floral ontogeny of a myrmecophile

Nora Villamil
Extrafloral nectar provision during floral ontogeny in ant-plants has not been widely studied. Extrafloral nectar secretion differed between leaves associated with buds, flowers, and fruits, and peaked during anthesis when pollinators were present. This ontogenetic variation may result from mixed selective pressures involving strategies for defense and mutualist management.

Data from: Species limits and phylogenomic relationships of Darwin’s finches remain unresolved: potential consequences of a volatile ecological setting

Robert M. Zink & Hernán Vázquez-Miranda
Island biotas have become paradigms for illustrating many evolutionary processes. The fauna of the Galapagos Islands includes several taxa that have been focal points for evolutionary studies. Perhaps their most famous inhabitants, Darwin’s finches, represent a go-to icon when thinking about how species originate and adapt to the environment. However, unlike other adaptive radiations, past morphological and molecular studies of Darwin’s finches have yielded inconsistent hypotheses of species limits and phylogenetic relationships. Expecting that idiosyncrasies...

Data from: Phylogenetic evidence from freshwater crayfishes that cave adaptation is not an evolutionary dead-end

David Ben Stern, Jesse Breinholt, Carlos Pedraza-Lara, Marilú López-Mejía, Christopher L. Owen, Heather Bracken-Grissom, , Keith A. Crandall & James W. Fetzner
Caves are perceived as isolated, extreme habitats with a set of uniquely specialized biota, which long ago led to the idea that caves are ‘evolutionary dead-ends.’ This suggests that cave-adapted taxa may be doomed for extinction before they can diversify or transition to a more stable state. However, this hypothesis has not been explicitly tested in a phylogenetic framework with multiple independent cave-dwelling groups. Here we use the freshwater crayfish, a group with dozens of...

Data from: Adsorption and corrosion inhibition behavior of new theophylline-triazole based derivatives for steel in acidic medium

Araceli Espinoza-Vázquez, Francisco Javier Rodríguez Gómez, Ivonne Karina Martínez-Cruz, Deyanira Ángeles-Beltrán, Guillermo Enrique Negrón-Silva, Manuel Palomar-Pardavé, Leticia Lomas Romero, Diego Pérez Martínez & Alejandra M. Navarrete-López
The design and synthesis of a series of theophylline derivatives containing 1,2,3-triazole moieties is presented. The corrosion inhibition activities of these new triazole-theophylline compounds were evaluated by studying the corrosion of API 5L X52 steel in 1 M HCl media. The results showed that an increase in the concentration of the theophylline-triazole derivatives also increases the charge transference resistance (Rct) value, enhancing inhibition efficiency and decreasing the corrosion process. The electrochemical impedance spectroscopy under static...

Data from: Bats, primates, and the evolutionary origins and diversification of mammalian gammaherpesviruses

Marina Escalera-Zamudio, Edith Rojas-Anaya, Sergios-Orestis Kolokotronis, Blanca Taboada, Elizabeth Loza-Rubio, Maria L. Méndez-Ojeda, Carlos F. Arias, Nikolaus Osterrieder & Alex D. Greenwood
Gammaherpesviruses (γHVs) are generally considered host specific and to have codiverged with their hosts over millions of years. This tenet is challenged here by broad-scale phylogenetic analysis of two viral genes using the largest sample of mammalian γHVs to date, integrating for the first time bat γHV sequences available from public repositories and newly generated viral sequences from two vampire bat species (Desmodus rotundus and Diphylla ecaudata). Bat and primate viruses frequently represented deep branches...

Data from: Sympatric parallel diversification of major oak clades in the Americas and the origins of Mexican species diversity

Andrew L. Hipp, Paul S. Manos, Antonio Gonzalez-Rodriguez, Marlene Hahn, Matthew Kaproth, John D. McVay, Susana Valencia Avalos & Jeannine Cavender-Bares
Oaks (Quercus, Fagaceae) are the dominant tree genus of North America in species number and biomass, and Mexico is a global center of oak diversity. Understanding the origins of oak diversity is key to understanding biodiversity of northern temperate forests. A phylogenetic study of biogeography, niche evolution and diversification patterns in Quercus was performed using 300 samples, 146 species. Next-generation sequencing data were generated using the restriction-site associated DNA (RAD-seq) method. A time-calibrated maximum likelihood...

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