282 Works

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: Arthropod distribution in a tropical rainforest: tackling a four dimensional puzzle

Yves Basset, Lukas Cizek, Philippe Cuénoud, Raphael K. Didham, Vojtech Novotny, Frode Ødegaard, Tomas Roslin, Alexey K. Tishechkin, Jürgen Schmidl, Neville N. Winchester, David W. Roubik, Henri-Pierre Aberlenc, Johannes Bail, Héctor Barrios, Jonathan R. Bridle, Gabriela Castaño-Meneses, Bruno Corbara, Gianfranco Curletti, Wesley Duarte Da Rocha, Domir De Bakker, Jacques H.C. Delabie, Alain Dejean, Laura L. Fagan, Andreas Floren, Roger L. Kitching … & Jacques H. C. Delabie
Quantifying the spatio-temporal distribution of arthropods in tropical rainforests represents a first step towards scrutinizing the global distribution of biodiversity on Earth. To date most studies have focused on narrow taxonomic groups or lack a design that allows partitioning of the components of diversity. Here, we consider an exceptionally large dataset (113,952 individuals representing 5,858 species), obtained from the San Lorenzo forest in Panama, where the phylogenetic breadth of arthropod taxa was surveyed using 14...

Data from: From cacti to carnivores: improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales

Joseph Frederic Walker, Ya Yang, Tao Feng, Alfonso Timoneda, Jessica Mikenas, Vera Hutchison, Caroline Edwards, Ning Wang, Sonia Ahluwalia, Julia Olivieri, Nathanael Walker-Hale, Lucas C. Majure, Raúl Puente, Gudrun Kadereit, Maximillian Lauterbach, Urs Eggli, Hilda Flores-Olvera, Helga Ochoterena, Samuel F. Brockington, Michael J. Moore & Stephen A. Smith
Premise of the Study— The Caryophyllales contains ~12,500 species and is known for its cosmopolitan distribution, convergence of trait evolution, and extreme adaptations. Some relationships within the Caryophyllales, like those of many large plant clades, remain unclear and phylogenetic studies often recover alternative hypotheses. We explore the utility of broad and dense transcriptome sampling across the order for resolving evolutionary relationships in Caryophyllales. Methods— We generated 84 transcriptomes and combined these with 224 publicly available...

Data from: UV photoreceptors and UV-yellow wing pigments in Heliconius butterflies allow a color signal to serve both mimicry and intraspecific communication

Seth M. Bybee, Furong Yuan, Monica D. Ramstetter, Jorge Llorente-Bousquets, Robert D. Reed, Daniel Osorio & Adriana D. Briscoe
Mimetic wing coloration evolves in butterflies in the context of predator confusion. Unless butterfly eyes have adaptations for discriminating mimetic color variation, mimicry also carries a risk of confusion for the butterflies themselves. Heliconius butterfly eyes, which express recently duplicated UV opsins, have such an adaptation. To examine bird and butterfly color vision as sources of selection on butterfly coloration we studied yellow wing pigmentation in the tribe Heliconiini. We confirmed using reflectance and mass...

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: Molecular proxies for climate maladaptation in a long-lived tree (Pinus pinaster Aiton, Pinaceae)

Juan Pablo Jaramilo-Correa, Isabel Rodríguez-Quilón, Delphine Grivet, Camille Lepoittevin, Federico Sebastiani, Myriam Heuertz, Pauline H. Garnier-Géré, Ricardo Alía, Christophe Plomion, Giovanni G. Vendramin, Santiago C. González-Martínez, J.-P. Jaramillo-Correa, S. C. Gonzalez-Martinez & P. H. Garnier-Gere
Understanding adaptive genetic responses to climate change is a main challenge for preserving biological diversity. Successful predictive models for climate-driven range shifts of species depend on the integration of information on adaptation, including that derived from genomic studies. Long-lived forest trees can experience substantial environmental change across generations, which results in a much more prominent adaptation lag than in annual species. Here, we show that candidate-gene SNPs (Single Nucleotide Polymorphisms) can be used as predictors...

Data from: A new platychelyid turtle (Pan-Pleurodira) from the Late Jurassic (Kimmeridgian) of Oaxaca, México

Oliver Ariel López-Conde, Juliana Sterli, Jesús Alvarado-Ortega & María Luisa Chavarría-Arellano
Until recently, the record of Mesozoic turtles in Mexico has been restricted to the Cretaceous. New discoveries in the Sabinal Formation (Tlaxiaco, Oaxaca) have extended the record into the Kimmeridgian (Late Jurassic). The Sabinal Formation is part of the Tlaxiaco Basin, which was a depocenter of continental and marine sediments dominated by transgressive-regressive marine conditions during the Jurassic–Cretaceous. The new turtle described here consists of an almost complete carapace associated with a plastron. Based on...

Data from: Competition and facilitation determine dwarf mistletoe infection dynamics

Mónica E. Queijeiro-Bolaños, Edgar Javier González, Carlos Martorell & Zenón Cano-Santana
1. Interspecific interactions have a fundamental role in plant population dynamics, as they may set the conditions for species coexistence. Parasitic plants, like dwarf mistletoes, offer the opportunity to study competition for resources that are different from those consumed by most plants, allowing for a better understanding of the interaction. 2. We explored how interspecific interactions between two dwarf mistletoe species (Arceuthobium), co-infecting the same host species (even sharing the same individual tree of Pinus...

Data from: The evolution of floral signals in relation to range overlap in a clade of California Jewelflowers (Streptanthus s.l.)

Marjorie G. Weber, N. Ivalu Cacho, Martin J. Q. Phan, Caprice Disbrow, Santiago R. Ramirez & Sharon Y. Strauss
Because of their function as reproductive signals in plants, floral traits experience distinct selective pressures related to their role in speciation, reinforcement, and prolonged coexistence with close relatives. However, few studies have investigated whether population-level processes translate into detectable signatures at the macroevolutionary scale. Here, we ask whether patterns of floral trait evolution and range overlap across a clade of California Jewelflowers reflect processes hypothesized to shape floral signal differentiation at the population level. We...

Data from: Relating species richness to the structure of continuous landscapes: alternative methodological approaches

J. Alberto Gallardo-Cruz, J. Luis Hernández-Stefanoni, Dietmar Moser, Angelina Martínez-Yrízar, Sergi Llobet & Jorge A. Meave
Numerous studies have focused on the relationship between landscape structure and plant diversity based on the patch-mosaic landscape paradigm, by deriving structural data from classified images. Since the use of discrete classes poses limitations for predicting biodiversity patterns in complex, low human-impacted ecosystems, two alternative methods have been used to analyze changes of landscape attributes in a continuum: moving-window metrics and surface metrics (image texture). Here we compare these two approaches for predicting richness of...

Data from: The impact of reconstruction methods, phylogenetic uncertainty and branch lengths on inference of chromosome number evolution in American daisies (Melampodium, Asteraceae)

Jamie McCann, Gerald M. Schneeweiss, Tod F. Stuessy, Jose L. Villaseñor & Hanna Weiss-Schneeweiss
Chromosome number change (polyploidy and dysploidy) plays an important role in plant diversification and speciation. Investigating chromosome number evolution commonly entails ancestral state reconstruction performed within a phylogenetic framework, which is, however, prone to uncertainty, whose effects on evolutionary inferences are insufficiently understood. Using the chromosomally diverse plant genus Melampodium (Asteraceae) as model group, we assess the impact of reconstruction method (maximum parsimony, maximum likelihood, Bayesian methods), branch length model (phylograms versus chronograms) and phylogenetic...

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: Do freshwater ecoregions and continental shelf width predict patterns of historical gene flow in the freshwater fish Poecilia butleri?

J. Jaime Zúñiga-Vega, Spencer J. Ingley, Peter J. Unmack & Jerald B. Johnson
We examined historical patterns of gene flow in the freshwater fish Poecilia butleri in western Mexico. We tested the hypothesis that the boundaries between four freshwater ecological communities (ecoregions) might have limited the movement of P. butleri because changes in species compositions might restrict establishment between adjacent ecoregions, even in situations where a physical barrier is absent. Hence, we predicted that boundaries between ecoregions should correspond to phylogeographical breaks in P. butleri. We also tested...

Data from: Changing drivers of species dominance during tropical forest succession

Madelon Lohbeck, Lourens Poorter, Miguel Martínez-Ramos, Jorge Rodriguez-Velázquez, Michiel Van Breugel & Frans Bongers
1. Deterministic theories predict that local communities assemble from a regional species pool based on niche differences, thus by plant functional adaptations. We tested whether functional traits can also explain patterns in species dominance among the suite of co-occurring species. 2. We predicted that along a gradient of secondary succession the main driver of species dominance changes from environmental filtering in the relatively harsh (dry and hot) early successional conditions, towards increased competitive interactions and...

Data from: Morphological convergence in a Mexican garter snake associated with the ingestion of a novel prey

Javier Manjarrez, Constantino Macías Garcia & Hugh Drummond
Morphological convergence is expected when organisms which differ in phenotype experience similar functional demands, which lead to similar associations between resource utilization and performance. To consume prey with hard exoskeletons, snakes require either specialized head morphology, or to deal with them when they are vulnerable, e.g. during molting. Such attributes may in turn reduce the efficiency with which they prey on soft-bodied, slippery animals such as fish. Snakes which consume a range of prey may...

Data from: Pathogeography: leveraging the biogeography of human infectious diseases for global health management

Kris A. Murray, Jesús Olivero, Benjamin Roche, Sonia Tiedt & Jean-François Guégan
Biogeography is an implicit and fundamental component of almost every dimension of modern biology, from natural selection and speciation to invasive species and biodiversity management. However, biogeography has rarely been integrated into human or veterinary medicine nor routinely leveraged for global health management. Here we review the theory and application of biogeography to the research and management of human infectious diseases, an integration we refer to as ‘pathogeography’. Pathogeography represents a promising framework for understanding...

Data from: Range‐wide population genetic structure of the Caribbean marine angiosperm Thalassia testudinum

Kor-Jent Van Dijk, Eric Bricker, Brigitta Ine Van Tussenbroek & Michelle Waycott
Many marine species have widespread geographic ranges derived from their evolutionary and ecological history particularly their modes of dispersal. Seagrass (marine angiosperm) species have ranges that are unusually widespread, which is not unexpected following recent reviews of reproductive strategies demonstrating the potential for long distance dispersal combined with longevity through clonality. An exemplar of these dual biological features is turtlegrass (Thalassia testudinum) which is an ecologically important species throughout the tropical Atlantic region. Turtlegrass has...

Data from: Identifying management actions to increase foraging opportunities for shorebirds at semi-intensive shrimp farms

Juan G. Navedo, Guillermo Fernández, Nelson Valdivia, Mark C. Drever & Jose A. Masero
The expansion of aquaculture has resulted in widespread habitat conversion throughout the world. Identifying beneficial management measures may dramatically reduce negative impacts of aquaculture for migratory birds. We studied how densities of foraging shorebirds varied at ponds within a semi-intensive shrimp aquaculture farm on the north-western coast of Mexico, as related to timing of harvest and tidal cycles. Further, we estimated the total daily available area for each shorebird species throughout two entire harvesting seasons...

Data for: Using spatial patterns of seeds and saplings to assess the prevalence of heterospecific replacements among cloud forest canopy tree species

Nancy R. Mejía-Domínguez, Jorge A. Meave, Carlos Díaz-Ávalos & Lorena Gómez-Aparicio
Questions: To gain insights into the role of species-by-species replacements in cloud forest community structuring, we asked: (1) What are the effects of the spatial distribution of standing individuals on the seed rain, soil seed bank, and sapling density and survival in this cloud forest? and (2) What is the prevalence of conspecific vs. heterospecific replacements in the regeneration of this forest? Location: Santo Tomás Teipan, Oaxaca State, southern Mexico. Methods: In a 1-ha cloud...

Elucidating gene expression adaptation of phylogenetically divergent coral holobionts under heat stress

Viridiana Avila-Magaña, Bishoy Kamel, Michael DeSalvo, Kelly Gómez-Campo, Susana Enríquez, Hiroaki Kitano, Rori Rohlfs, Roberto Iglesias-Prieto & Mónica Medina
As coral reefs struggle to survive under climate change, it is crucial to know whether they have the capacity to withstand changing conditions, particularly increasing seawater temperatures. Thermal tolerance requires the integrative response of the different components of the coral holobiont (coral host, algal photosymbiont, and associated microbiome). Here, using a controlled thermal stress experiment across three divergent Caribbean coral species, we attempt to dissect holobiont member metatranscriptome responses from coral taxa with different sensitivities...

Saguaro recruitment data obtained by inverse-growth modelling

Eugenio Larios, Ricardo Efren Felix-Burruel, Edgar J. Gonzalez & Alberto Burquez
Each year, an individual mature large saguaro cactus produces about one million seeds in attractive juicy fruits that lure seed predators and seed dispersers in a three-month feast. From the million seeds produced, however, only a few will persist into mature saguaros. A century of research on saguaro population dynamics has led to the conclusion that saguaro recruitment is an episodic event that depends on the convergence of suitable conditions for survival during the critical...

Colorful traits in female birds relate to individual condition, reproductive performance, and male mate preferences: A meta-analytic approach dataset

America Hernandez, Rene Beamonte-Barrientos, Margarita Martinez-Gomez & Bibiana Montoya
Colorful traits in females are suggested to have evolved and be maintained by sexual selection. Although several studies have evaluated this idea, support is still equivocal. Evidence has been compiled in reviews, and a handful of quantitative synthesis have explored evidence of the link between condition and specific color traits in males and females. However, understanding the potential function of females’ colorful traits in sexual communication has not been the primary focus of any of...

SSP: An R package to estimate sampling effort in studies of ecological communities

Edlin Guerra-Castro, Juan Carlos Cajas, Nuno Simoes, Juan Jose Cruz-Motta & Maite Mascaro
SSP (simulation-based sampling protocol) is an R package that uses simulations of ecological data and dissimilarity-based multivariate standard error (MultSE) as an estimator of precision to evaluate the adequacy of different sampling efforts for studies that will test hypothesis using permutational multivariate analysis of variance. The procedure consists in simulating several extensive data matrixes that mimic some of the relevant ecological features of the community of interest using a pilot data set. For each simulated...

Data from: Low-copy nuclear genes reveal new evidence of incongruence in relationships within Malvaceae s.l.

Rebeca Hernández-Gutiérrez, Carolina Granados Mendoza & Susana Magallón
The family Malvaceae s. l. is a clade that comprises nine subfamilies. Phylogenetic relationships among them are not completely resolved and are inconsistent among studies, probably due to low phylogenetic informativeness of conventional molecular markers. In the present study, we provide new phylogenetic information for Malvaceae s.l. derived from newly-designed group-specific nuclear markers. By mining transcriptome data from the One Thousand Plant Project (1KP) and publicly available genome information from cotton, cacao, and Arabidopsis, we...

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