28 Works

Data from: Related plant species respond similarly to chronic anthropogenic disturbance: implications for conservation decision-making

Alejandra Martínez-Blancas, Horacio Paz, Gerardo A. Salazar & Carlos Martorell
1. Many developing countries harbor inordinate numbers of species that face little-understood, gradual changes in their environment, such as chronic anthropogenic disturbance (CAD, a high frequency but low intensity form of disturbance). These countries also lack the resources to study each species, so conservation practices have had to be generalized assuming that complete taxonomic groups (e.g., cacti or cetaceans) may be managed in the same way. This could be justified if closely related species respond...

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: 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: 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: Phylogenetic systematics of subtribe Spiranthinae (Orchidaceae: Orchidoideae: Cranichideae) based on nuclear and plastid DNA sequences of a nearly complete generic sample

Gerardo A. Salazar, Joao A.N. Batista, Lidia I. Cabrera, Cassio Van Den Berg, W. Mark Whitten, Eric C. Smidt, Cristiano R. Buzatto, Rodrigo B. Singer, Gunter Gerlach, Rolando Jimenez-Machorro, Jose A. Radins, Irma S. Insaurralde, Leonardo R.S. Guimaraes, Fabio De Barros, Francisco Tobar, Jose L. Linares, Ernesto Mujica, Robert L. Dressler, Mario A. Blanco, Eric Hagsater & Mark W. Chase
Subtribe Spiranthinae is the most species-rich lineage of terrestrial Neotropical orchids, encompassing > 500 species and 40 genera. We conducted maximum parsimony and maximum likelihood phylogenetic analyses of DNA sequence data of plastid matK-trnK and trnL-trnF and nuclear ribosomal ITS sequences for 36 genera and 182 species of Spiranthinae plus appropriate outgroups. The results strongly support monophyly of Spiranthinae (minus Discyphus, Discyphinae and Galeottiella, Galeottiellinae) and five major lineages, namely monospecific Cotylolabium (sister to the...

Data from: Macroecology of birds potentially susceptible to the West Nile Virus

María J. Tolsá, Gabriel E. García-Peña, Oscar Rico-Chavez, Benjamin Roche & Gerardo Suzán
Zoonotic diseases transmitted by wildlife affect biological conservation, public and animal health, and the economy. Current research efforts are aimed at finding wildlife pathogens at a given location. However, a meta-analytical approach may reveal emerging macroecological patterns in the host-pathogen relationship at different temporal and spatial scales. West Nile Virus (WNV) is a pathogen with worldwide detrimental impacts on bird populations. To understand macroecological patterns driving WNV infection, we aimed to recognise unknown competent reservoirs...

Data from: Inferring introgression using RADseq and DFOIL: power and pitfalls revealed in a case study of spiny lizards (Sceloporus)

Shea M. Lambert, Jeffrey W. Streicher, M. Caitlin Fisher-Reid, Fausto R. Mendez De La Cruz, Norberto Martínez‐Méndez, Uri Omar García Vázquez, Adrián Nieto Montes De Oca & John J. Wiens
Introgression is now commonly reported in studies across the Tree of Life, aided by recent advancements in data collection and analysis. Nevertheless, researchers working with non‐model species lacking reference genomes may be stymied by a mismatch between available resources and methodological demands. In this study, we demonstrate a fast and simple approach for inferring introgression using RADseq data, and apply it to a case study involving spiny lizards (Sceloporus) from northeastern México. First, we find...

Data from: Carotenoid-based skin ornaments reflect foraging propensity in a seabird, Sula leucogaster

Nathan P. Michael, Roxana Torres, Andreanna J. Welch, Josh Adams, Mario Erandi Bonillas-Monge, Jonathan Felis, Laura Lopez-Marquez, Alejandro Martínez-Flores & Anne E. Wiley
Carotenoid-based ornaments are common signaling features in animals. It has long been proposed that such ornaments communicate information about foraging abilities to potential mates. However, evidence linking foraging with ornamentation is largely missing from unmanipulated, free-ranging populations. To investigate this relationship, we studied the brown booby (Sula leucogaster brewsteri), a seabird with a carotenoid-based gular skin ornament. 13C values from both feathers and blood plasma were negatively correlated with male gular color, indicating birds that...

Data from: Contrasting patterns of population history and seed-mediated gene flow in two endemic Costa Rican oak species

Hernando Rodríguez-Correa, Ken Oyama, Mauricio Quesada, Eric J. Fuchs & Antonio González-Rodríguez
Lower Central America is an important area to study recent population history and diversification of Neotropical species due to its complex and dynamic geology and climate. Phylogeographic studies in this region are few in comparison with other regions and even less for tree species. The aim of the present study was to characterize the phylogeographic structure in two partially co-distributed endemic oak species (Quercus costaricensis and Q. bumelioides) of the Costa Rican mountains using chloroplast...

Data from: Phylogeography of a widespread lizard complex reflects patterns of both geographic and ecological isolation

Levi N. Gray, Anthony J. Barley, Steven Poe, Robert C. Thomson, Adrián Nieto-Montes De Oca & Ian J. Wang
A primary challenge for modern phylogeography is understanding how ecology and geography, both contemporary and historical, shape the spatial distribution and evolutionary histories of species. Phylogeographic patterns are the result of many factors, including geology, climate, habitat, colonization history, and lineage-specific constraints. Assessing the relative influences of these factors is difficult because few species, regions, and environments are sampled in enough detail to compare competing hypotheses rigorously and because a particular phylogeographic pattern can potentially...

Data from: Legume abundance along successional and rainfall gradients in neotropical forests

Maga Gei, Danaë M. A. Rozendaal, Lourens Poorter, Frans Bongers, Janet I. Sprent, Mira D. Garner, T. Mitchell Aide, José Luis Andrade, Patricia Balvanera, Justin M. Becknell, Pedro H.S. Brancalion, George A. L. Cabral, Ricardo Gomes César, Robin L. Chazdon, Rebecca J. Cole, Gabriel Dalla Colletta, Ben De Jong, Julie S. Denslow, Daisy H. Dent, Saara J. DeWalt, Juan Manuel Dupuy, Sandra M. Durán, Mário Marcos Do Espírito Santo, G. Wilson Fernandes, Yule Roberta Ferreira Nunes … & Jennifer S. Powers
The nutrient demands of regrowing tropical forests are partly satisfied by nitrogen (N)-fixing legume trees, but our understanding of the abundance of those species is biased towards wet tropical regions. Here we show how the abundance of Leguminosae is affected by both recovery from disturbance and large-scale rainfall gradients through a synthesis of forest-inventory plots from a network of 42 Neotropical forest chronosequences. During the first three decades of natural forest regeneration, legume basal area...

Data from: Thirty clues to the exceptional diversification of flowering plants

Susana Magallón, Luna L. Sánchez-Reyes & Sandra L. Gómez-Acevedo
Background and Aims: As angiosperms became one of the megadiverse groups of macroscopic eukaryotes, they forged modern ecosystems and promoted the evolution of extant terrestrial biota. Unequal distribution of species among lineages suggests that diversification, the process which ultimately determines species-richness, acted differentially through angiosperm evolution. Methods: We investigate how angiosperms became megadiverse by identifying the phylogenetic and temporal placement of exceptional radiations, by combining the most densely fossil-calibrated molecular clock phylogeny with a Bayesian...

Data from: Landscape genomics provides evidence of climate-associated genetic variation in Mexican populations of Quercus rugosa Nee

Karina Martins, Paul Gugger, Jesus Llanderal-Mendoza, Antonio González-Rodríguez, Sorel T. Fitz-Gibbon, Jian-Li Zhao, Hernando Rodríguez-Correa, Ken Oyama, Victoria L. Sork & Paul F. Gugger
Local adaptation is a critical evolutionary process that allows plants to grow better in their local compared to nonnative habitat and results in species-wide geographic patterns of adaptive genetic variation. For forest tree species with a long generation time, this spatial genetic heterogeneity can shape the ability of trees to respond to rapid climate change. Here, we identify genomic variation that may confer local environmental adaptations and then predict the extent of adaptive mismatch under...

Data from: Quantifying uncertainty due to fission-fusion dynamics as a component of social complexity

Gabriel Ramos-Fernandez, Andrew J. King, Jacinta C. Beehner, Thore J. Bergman, Margaret C. Crofoot, Anthony Di Fiore, Julia Lehmann, Colleen M. Schaffner, Noah Snyder-Mackler, Klaus Zuberbühler, Filippo Aureli & Denis Boyer
Groups of animals (including humans) may show flexible grouping patterns, in which temporary aggregations or subgroups come together and split, changing composition over short temporal scales, i.e. fission and fusion). A high degree of fission-fusion dynamics may constrain the regulation of social relationships, introducing uncertainty in interactions between group members. Here we use Shannon's entropy to quantify the predictability of subgroup composition for three species known to differ in the way their subgroups come together...

Data from: Effect of distance to edge and edge interaction on seedling regeneration and biotic damage in tropical rainforest fragments: a long‐term experiment

Julieta Benítez-Malvido, Amparo Lazaro & Isolde D. K. Ferraz
In forest fragments, edge effects can influence forest regeneration, but little is known about how edge effects influence seedling performance and the interaction between seedlings and their natural enemies over time. In central Amazonia, we recorded survival and growth (in height and leaf number) and damage by insect herbivores and leaf‐fungal pathogens of Chrysophyllum pomiferum (Sapotaceae) seedlings that were exposed to different numbers of edges and to different distances from the forest edge. Grown seedlings...

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: 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: 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: Biodiversity in species, traits and structure determines carbon stocks and uptake in tropical forests

Masha T. Van Der Sande, Lourens Poorter, Lammert Kooistra, Patricia Balvanera, Kirsten Thonicke, Jill Thompson, Eric J. M. M. Arets, Nashieli Garcia Alaniz, Laurence Jones, Francisco Mora, Tuyeni H. Mwampamba, Terry Parr & Marielos Peña-Claros
Impacts of climate change require that society urgently develops ways to reduce amounts of carbon in the atmosphere. Tropical forests present an important opportunity, as they take up and store large amounts of carbon. It is often suggested that forests with high biodiversity have large stocks and high rates of carbon uptake. Evidence is, however, scattered across geographic areas and scales, and it remains unclear whether biodiversity is just a co‐benefit or also a requirement...

Data from: Body mass as a supertrait linked to abundance and behavioural dominance in hummingbirds: a phylogenetic approach

Rafael Bribiesca, Leonel Herrera-Alsina, Eduardo Ruiz-Sanchez, Luis A. Sánchez-González & Jorge E. Schondube
Body mass has been considered one of the most critical organismal traits, and its role in many ecological processes has been widely studied. In hummingbirds body mass has been linked to ecological features like foraging performance, metabolic rates, and cost of flying, among others. We used an evolutionary approach to test if body mass is a good predictor of two of the main ecological features of hummingbirds: their abundances and behavioural dominance. To determine whether...

Data from: Contemporaneous radiations of fungi and plants linked to symbiosis

François Lutzoni, Michael D. Nowak, Michael E. Alfaro, Valérie Reeb, Jolanta Miadlikowska, Michael Krug, A. Elizabeth Arnold, Louise A. Lewis, David L. Swofford, David Hibbett, Khidir Hilu, Timothy Y. James, Dietmar Quandt & Susana Magallón
Interactions between fungi and plants, including parasitism, mutualism, and saprotrophy, have been invoked as key to their respective macroevolutionary success. Here we evaluate the origins of plant-fungal symbioses and saprotrophy using a time-calibrated phylogenetic framework that reveals linked and drastic shifts in diversification rates of each kingdom. Fungal colonization of land was associated with at least two origins of terrestrial green algae and preceded embryophytes (as evidenced by losses of fungal flagellum, ca. 720 Ma),...

Data from: Genomewide genotyping of a novel Mexican Chile Pepper collection illuminates the history of landrace differentiation after Capsicum annuum L. domestication

Nathan Taitano, Vivian Bernau, Lev Jardón-Barbolla, Brian Leckie, Michael Mazourek, Kristin Mercer, Leah McHale, Andrew Michel, David Baumler, Michael Kantar, Esther Van Der Knapp & Esther Van Der Knaap
Studies of genetic diversity among phenotypically distinct crop landraces improve our understanding of fruit evolution and genome structure under domestication. Chile peppers (Capsicum spp. L.) are economically valuable and culturally important species, and extensive phenotypic variation among landraces exists in southern Mexico, a center of C. annuum diversity. We collected 103 chile pepper seed accessions from 22 named landraces across 27 locations in southern Mexico. We genotyped these accessions with genotyping-by-sequencing (GBS), yielding 32,623 filtered...

Data from: Mycorrhizal symbiosis increases the benefits of plant facilitative interactions

Alicia Montesinos Navarro, Alfonso Valiente-Banuet & Miguel Verdu
The diversity of pathways through which mycorrhizal fungi alter plant coexistence hinders the understanding of their effects on plant-plant interactions. The outcome of plant facilitative interactions can be indirectly affected by mycorrhizal symbiosis, ultimately shaping biodiversity patterns. We tested whether mycorrhizal symbiosis enhances plant facilitative interactions and whether its effect is consistent across different methodological approaches and biological scenarios. We conducted a meta-analysis of 215 cases (involving 21 nurse and 29 facilitated species), in which...

Registration Year

  • 2018
    28

Resource Types

  • Dataset
    28

Affiliations

  • National Autonomous University of Mexico
    28
  • University of Michigan-Ann Arbor
    3
  • University of Minnesota
    3
  • University of California System
    2
  • Universidade Federal de Minas Gerais
    2
  • University of Hawaii at Manoa
    2
  • University of Connecticut
    2
  • University of Arizona
    2
  • University of Maryland, College Park
    2
  • Instituto Politécnico Nacional
    2