20 Works

Data from: Inferring responses to climate dynamics from historical demography in neotropical forest lizards

Ivan Prates, Alexander T. Xue, Jason L. Brown, Diego F. Alvarado-Serrano, Miguel T. Rodrigues, Michael J. Hickerson & Ana C. Carnaval
We apply a comparative framework to test for concerted demographic changes in response to climate shifts in the neotropical lowland forests, learning from the past to inform projections of the future. Using reduced genomic (SNP) data from three lizard species codistributed in Amazonia and the Atlantic Forest (Anolis punctatus, Anolis ortonii, and Polychrus marmoratus), we first reconstruct former population history and test for assemblage-level responses to cycles of moisture transport recently implicated in changes of...

Data from: Temporal regularity increases with repertoire complexity in the Australian pied butcherbird’s song

Eathan Janney, Hollis Taylor, Constance Scharff, David Rothenberg, Lucas C. Parra & Ofer Tchernichovski
Music maintains a characteristic balance between repetition and novelty. Here, we report a similar balance in singing performances of free-living Australian pied butcherbirds. Their songs include many phrase types. The more phrase types in a bird's repertoire, the more diverse the singing performance can be. However, without sufficient temporal organization, avian listeners may find diverse singing performances difficult to perceive and memorize. We tested for a correlation between the complexity of song repertoire and the...

Data from: Sustained high levels of neuregulin-1 in the longest-lived rodents; a key determinant of rodent longevity

Yael H. Edrey, Diana Casper, Dorothee Huchon, James Mele, Jonathan A. Gelfond, Deborah M. Kristan, Eviatar Nevo & Rochelle Buffenstein
Naked mole-rats (Heterocephalus glaber), the longest-lived rodents, live 7-10 times longer than similarly–sized mice and exhibit normal activities for ∼75% of their lives. Little is known about the mechanisms that allow them to delay the aging process and live so long. Neuregulin-1 (NRG-1) signaling is critical for normal brain function during both development and adulthood. We hypothesized that long-lived species will maintain higher levels of NRG-1 and that this contributes to their sustained brain function...

Biotic predictors with phenological information improve range estimates for migrating monarch butterflies in Mexico

Jamie M. Kass, Robert P. Anderson, Alejandro Espinosa-Lucas, Verónica Juárez-Jaimes, Esteban Martínez-Salas, Francisco Botello, Gloria Tavera, José Juan Flores-Martínez & Víctor Sánchez-Cordero
Although long-standing theory suggests that biotic variables are only relevant at local scales for explaining the patterns of species’ distributions, recent studies have demonstrated improvements to species distribution models (SDMs) by incorporating predictor variables informed by biotic interactions. However, some key methodological questions remain, such as which kinds of interactions are permitted to include in these models, how to incorporate the effects of multiple interacting species, and how to account for interactions that may have...

Junco hyemalis Bone Microstructure

Leeann Louis, Rauri Bowie & Robert Dudley
Migration is the primary strategy that temperate birds use to avoid overwintering under harsh conditions. As a consequence, migratory birds have evolved specific morphological features in their wings and skeleton. However, in addition to varying in overall shape and size, bone can also change at the microstructural level by, for example, increasing its thickness. Such changes are critical to preventing fracture and damage under repeated loading (fatigue), yet it is not known whether migratory behaviour...

Evolutionary tradeoffs between male secondary sexual traits revealed by a phylogeny of the hyperdiverse tribe Eumaeini (Lepidoptera: Lycaenidae)

Wendy A. Valencia-Montoya, Tiago B. Quental, João Filipe R. Tonini, Gerard Talavera, James D. Crall, Gerardo Lamas, Robert C. Busby, Ana Paula S. Carvalho, Ana B. Morais, Nicolás Oliveira Mega, Helena Piccoli Romanowski, Marjorie A. Liénard, Shayla Salzman, Melissa R. L. Whitaker, Akito Y. Kawahara, David J. Lohman, Robert K. Robbins & Naomi E. Pierce
Male butterflies in the hyperdiverse tribe Eumaeini possess an unusually complex and diverse repertoire of secondary sexual characteristics involved in pheromone production and dissemination. Maintaining multiple sexually selected traits is likely to be metabolically costly, potentially resulting in trade-offs in the evolution of male signals. However, a phylogenetic framework to test hypotheses regarding the evolution and maintenance of male sexual traits in Eumaeini has been lacking. Here, we infer a comprehensive, time-calibrated phylogeny from 379...

Data from: A comprehensive and dated phylogenomic analysis of butterflies

Marianne Espeland, Jesse W. Breinholt, Keith R. Willmott, Andrew D. Warren, Roger Vila, Emmanuel F. A. Toussaint, Sarah C. Maunsell, Kwaku Aduse-Poku, Gerard Talavera, Rodney Eastwood, Marta A. Jarzyna, Robert Guralnick, David J. Lohman, Naomi E. Pierce, Akito Y. Kawahara, Jesse Breinholt & Emmanuel F.A. Toussaint
Butterflies (Papilionoidea), with over 18,000 described species [1], have captivated naturalists and scientists for centuries. They play a central role in the study of speciation, community ecology, biogeography, climate change, and plant-insect interactions and include many model organisms and pest species [2, 3]. However, a robust higher-level phylogenetic framework is lacking. To fill this gap, we inferred a dated phylogeny by analyzing the first phylogenomic dataset, including 352 loci (> 150,000 bp) from 207 species...

Data from: ABC inference of multi-population divergence with admixture from unphased population genomic data

John D. Robinson, Lynsey Bunnefeld, Jack Hearn, Graham N. Stone & Michael J. Hickerson
Rapidly developing sequencing technologies and declining costs have made it possible to collect genome-scale data from population-level samples in non-model systems. Inferential tools for historical demography given these datasets are, at present, underdeveloped. In particular, approximate Bayesian computation (ABC) has yet to be widely embraced by researchers generating these data. Here, we demonstrate the promise of ABC for analysis of the large datasets that are now attainable from non-model taxa through current genomic sequencing technologies....

Data from: Model misspecification confounds the estimation of rates and exaggerates their time dependency

Brent Emerson, Diego Alvarado-Serrano, Michael Hickerson, Brent C. Emerson & Michael J. Hickerson
While welcoming the comment of Ho et al. (2015), we find little that undermines the strength of our criticism, and it would appear they have misunderstood our central argument. Here we respond with the purpose of reiterating that we are (i) generally critical of much of the evidence presented in support of the time-dependent molecular rate (TDMR) hypothesis and (ii) specifically critical of estimates of μ derived from tip-dated sequences that exaggerate the importance of...

Data from: Dispersal out of Wallacea spurs diversification of Pteropus flying foxes, the world’s largest bats (Mammalia: Chiroptera)

Susan M. Tsang, Sigit Wiantoro, Maria Josefa Veluz, Norimasa Sugita, Y-Lan Nguyen, Nancy B. Simmons & David J. Lohman
Aim: Islands provide opportunities for isolation and speciation. Many landmasses in the Indo-Australian Archipelago (IAA) are oceanic islands, and founder-event speciation is expected to be the predominant form of speciation of volant taxa on these islands. We studied the biogeographic history of flying foxes, a group with many endemic species and a predilection for islands, to test this hypothesis and infer the biogeographic origin of the group. Location: Australasia, Indo-Australian Archipelago, Madagascar, Pacific Islands Taxon:...

Data from: Paleotemperatures and recurrent habitat shifts drive diversification of treefrogs across distinct biodiversity hotspots in sub-Amazonian South America

Mariana Vasconcellos
Aim: We investigate the biogeographic history and diversification in a treefrog lineage distributed in contrasting (open and forested) ecoregions of South America, including three biodiversity hotspots. We evaluate the role of dispersal and whether other factors such as diversity-dependence or paleotemperatures could explain the diversification pattern for this group. Especially focusing on the savanna endemics, we illuminate on processes governing the species assembly and evolution of the Cerrado savanna. Location: South American ecoregions south of...

Saproxylic fly diversity in a Costa Rican forest mosaic

Lance Jones & Amy Berkov
This paper presents the first assessment of the diversity of tropical saproxylic Diptera, done on the Osa Peninsula of Costa Rica. Forty-one trees representing nine species and six plant families were sampled in a rearing experiment. In total, 272 individuals attributable to 18 families of Diptera were reared. Low abundance and species richness of flies was observed overall. A majority of taxa were in saprophagous and mycophagous larval feeding guilds, followed by predators. Host associations,...

Exploring scenarios of climate-induced extremes on the food, energy, water nexus (C-FEWS) and the role of engineered and natural infrastructure

Seth Tuler & Charles Vörösmarty

Data from: A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents

Matthieu Leray, Joy Y. Yang, Christopher P. Meyer, Suzanne C. Mills, Natalia Agudelo, Ranwez Vincent, Joel T. Boehm & Ryuji J. Machida
Introduction: The PCR-based analysis of homologous genes has become one of the most powerful approaches for species detection and identification, particularly with the recent availability of Next Generation Sequencing platforms (NGS) making it possible to identify species composition from a broad range of environmental samples. Identifying species from these samples relies on the ability to match sequences with reference barcodes for taxonomic identification. Unfortunately, most studies of environmental samples have targeted ribosomal markers, despite the...

­­Evolution of floral morphology and symmetry in the Miconieae (Melastomataceae): multiple generalization trends within a specialized family

Maria Gavrutenko, Marcelo Reginato, Ricardo Kriebel, Antoine M. Nicolas & Fabián A. Michelangeli
Premise of the Research:Analyses of evolution of floral morphology and symmetry broaden our understanding of the drivers of angiosperm diversification. Integrated within a flower, labile floral characters produce different phenotypes that promote variable interactions with pollinators. Thus, investigation of floral evolution may help infer potential historic transitions in pollinator modes and ecological pressures that generated present diversity. This study aims to explore morphological evolution of flowers in Miconieae, a species-rich Neotropical tribe within the Melastomataceae....

Data from: Recommendations for using msBayes to incorporate uncertainty in selecting an ABC model prior: a response to Oaks et al.

Michael James Hickerson, Graham N. Stone, Konrad Lohse, Terrence C. Demos, Xiaoou Xie, Cedric Landerer & Naoki Takebayashi
Prior specification is an essential component of parameter estimation and model comparison in Approximate Bayesian computation (ABC). Oaks et al. present a simulation-based power analysis of msBayes and conclude that msBayes has low power to detect genuinely random divergence times across taxa, and suggest the cause is Lindley's paradox. Although the predictions are similar, we show that their findings are more fundamentally explained by insufficient prior sampling that arises with poorly chosen wide priors that...

Data from: Bayesian hierarchical models suggest oldest known plant-visiting bat was omnivorous

Laurel R. Yohe, Paúl M. Velazco, Danny Rojas, Beth E. Gerstner, Nancy B. Simmons & Liliana M. Dávalos
The earliest record of plant visiting in bats dates to the Middle Miocene of La Venta, the world's most diverse tropical palaeocommunity. Palynephyllum antimaster is known from molars that indicate nectarivory. Skull length, an important indicator of key traits such as body size, bite force and trophic specialization, remains unknown. We developed Bayesian models to infer skull length based on dental measurements. These models account for variation within and between species, variation between clades, and...

Data from: Prediction of phylogeographic endemism in an environmentally complex biome.

Ana Carolina Carnaval, Eric Waltari, Miguel T. Rodrigues, Dan Rosauer, Jeremy VanDerWal, Roberta Damasceno, Ivan Prates, Maria Strangas, Zoe Spanos, Danielle Rivera, Marcio R. Pie, Carina R. Firkowski, Marcos R. Bornschein, Luiz F. Ribeiro & Craig Moritz
Phylogeographic endemism, the degree to which the history of recently evolved lineages is spatially restricted, reflects fundamental evolutionary processes such as cryptic divergence, adaptation and biological responses to environmental heterogeneity. Attempts to explain the extraordinary diversity of the tropics, which often includes deep phylogeographic structure, frequently invoke interactions of climate variability across space, time and topography. To evaluate historical versus contemporary drivers of phylogeographic endemism in a tropical system, we analyse the effects of current...

Data from: Global terrestrial Human Footprint maps for 1993 and 2009

Oscar Venter, Eric W. Sanderson, Ainhoa Magrach, James R. Allan, Jutta Beher, Kendall R. Jones, Hugh P. Possingham, William F. Laurance, Peter Wood, Balázs M. Fekete, Marc A. Levy & James E.M. Watson
Remotely-sensed and bottom-up survey information were compiled on eight variables measuring the direct and indirect human pressures on the environment globally in 1993 and 2009. This represents not only the most current information of its type, but also the first temporally-consistent set of Human Footprint maps. Data on human pressures were acquired or developed for: 1) built environments, 2) population density, 3) electric infrastructure, 4) crop lands, 5) pasture lands, 6) roads, 7) railways, and...

Data from: Anchored phylogenomics illuminates the skipper butterfly tree of life

Emmanuel F.A. Toussaint, Jesse W. Breinholt, Chandra Earl, Andrew D. Warren, Andrew V.Z. Brower, Masaya Yago, Kelly M. Dexter, Marianne Espeland, Naomi E. Pierce, David J. Lohman & Akito Y. Kawahara
Butterflies (Papilionoidea) are perhaps the most charismatic insect lineage, yet phylogenetic relationships among them remain incompletely studied and controversial. We sequenced nearly 400 loci using Anchored Hybrid Enrichment and sampled all tribes and more than 120 genera of skippers (Hesperiidae), one of the most species-rich and poorly studied butterfly families. Maximum-likelihood, parsimony and coalescent multi-species methods all converged on a novel, robust phylogenetic hypothesis for skippers. Different optimality criteria and methodologies recovered almost identical phylogenetic...

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