184 Works

Data from: Isolation by environment in white-breasted nuthatches (Sitta carolinensis) of the Madrean Archipelago sky islands: a landscape genomics approach

Joseph D. Manthey & Robert G. Moyle
Understanding landscape processes driving patterns of population genetic differentiation and diversity has been a long-standing focus of ecology and evolutionary biology. Gene flow may be reduced by historical, ecological or geographic factors, resulting in patterns of isolation by distance (IBD) or isolation by environment (IBE). Although IBE has been found in many natural systems, most studies investigating patterns of IBD and IBE in nature have used anonymous neutral genetic markers, precluding inference of selection mechanisms...

Data from: Phylogeny of the island archipelago frog genus Sanguirana: another endemic Philippine radiation that diversified 'Out-of-Palawan'

Rafe M. Brown, Yong-Chao Su, Brenna Barger, Cameron D. Siler, Marites B. Sanguila, Arvin C. Diesmos & David C. Blackburn
Recent higher-level frog phylogenetic analyses have included a few members of the endemic Philippine frog genus Sanguirana. Although the monophyly of the group has never been disputed, the recent phylogenetically-supported inclusion of the Palawan Wood Frog (Sanguirana sanguinea) in this clade was highly unexpected. In addition, species boundaries and relationships remain unclear and new species continue to be discovered. We estimate the phylogeny for this endemic Philippine genus using two mitochondrial gene regions and six...

Data from: Chromosomal patterns of diversity and differentiation in creepers: a next-gen phylogeographic investigation of Certhia americana

Joseph Manthey, John Klicka & Garth Spellman
With methods for sequencing thousands of loci for many individuals, phylogeographic studies have increased inferential power and the potential for applications to new questions. In songbirds, strong patterns of inter-chromosomal synteny, the published genome of a songbird and the ability to obtain thousands of genetic loci for many individuals permit the investigation of differentiation between and diversity within lineages across chromosomes. Here, we investigate patterns of differentiation and diversity in Certhia americana, a widespread North...

Data from: No silver bullets in correlative ecological niche modeling: insights from testing among many potential algorithms for niche estimation

Huijie Qiao, Jorge Soberón & Andrew Townsend Peterson
The field of ecological niche modeling or species distribution modeling has seen enormous activity and attention in recent years, in light of exciting biological inferences that can be drawn from correlational models of species’ environmental requirements (i.e., ecological niches) and inferences of potential geographic distributions. Among the many methods used in the field, one or two are in practice assumed to be ‘best’ and are used commonly, often without explicit testing. We explore herein implications...

Data from: Using data from related species to overcome spatial sampling bias and associated limitations in ecological niche modeling

Huijie Qiao, Andrew Townsend Peterson, Liqiang Ji & Junhua Hu
1. Ecological niche modeling (ENM) is used widely to aid in conservation planning and management, often focusing on rare species characterized by the biased observations associated with restricted geographic ranges, habitat specialization, small population size, and limited natural history information. Generating reliable ENMs for such species is a challenge, however, owing to issues that arise from spatial sampling bias, such as model inaccuracy and overfitting. Here, using virtual scenarios, we assess the utility of integrating...

Data from: Phenology differences between native and novel exotic-dominated grasslands rival the effects of climate change

Brian J. Wilsey, Leanne M. Martin & Andrew D. Kaul
1. Novel ecosystems can differ from the native systems they replaced. We used phenology measures to compare ecosystem functioning between novel exotic-dominated and native-dominated grasslands in the central US. 2. Phenology, or timing of biological events, is affected by climate and land use changes. We assessed how phenology shifts are being altered by exotic species dominance by comparing remotely sensed Normalized Difference Vegetation Index (NDVI) within growing seasons at exotic- and native-dominated sites along a...

Data from: Did true frogs ‘dispersify’?

Kin Onn Chan & Rafe M. Brown
The interplay between range expansion and concomitant diversification is of fundamental interest to evolutionary biologists, particularly when linked to intercontinental dispersal and/or large scale extinctions. The evolutionary history of true frogs has been characterized by circumglobal range expansion. As a lineage that survived the Eocene–Oligocene extinction event (EOEE), the group provides an ideal system to test the prediction that range expansion triggers increased net diversification. We constructed the most densely sampled, time-calibrated phylogeny to date...

Data from: Monarch butterfly population decline in North America: identifying the threatening processes

Wayne E. Thogmartin, Ruscena Wiederholt, Karen Oberhauser, Ryan G. Drum, Jay E. Diffendorfer, Sonia Altizer, Orley R. Taylor, John Pleasants, Darius Semmens, Brice Semmens, Richard Erickson, Kaitlin Libby & Laura Lopez-Hoffman
The monarch butterfly (Danaus plexippus) population in North America has sharply declined over the last two decades. Despite rising concern over the monarch butterfly's status, no comprehensive study of the factors driving this decline has been conducted. Using partial least-squares regressions and time-series analysis, we investigated climatic and habitat-related factors influencing monarch population size from 1993 to 2014. Potential threats included climatic factors, habitat loss (milkweed and overwinter forest), disease and agricultural insecticide use (neonicotinoids)....

Data from: Drivers of vegetative dormancy across herbaceous perennial plant species

Richard P. Shefferson, Tiiu Kull, Michael J. Hutchings, Marc-André Selosse, Hans Jacquemyn, Kimberly M. Kellett, Eric S. Menges, Richard B. Primack, Juha Tuomi, Kirsi Alahuhta, Sonja Hurskainen, Helen M. Alexander, Derek S. Anderson, Rein Brys, Emilia Brzosko, Slavomir Dostálik, Katharine Gregg, Zdeněk Ipser, Anne Jäkäläniemi, Jana Jersáková, W. Dean Kettle, Melissa K. McCormick, Ana Mendoza, Michael T. Miller, Asbjørn Moen … & Dennis F. Whigham
Vegetative dormancy, that is the temporary absence of aboveground growth for ≥ 1 year, is paradoxical, because plants cannot photosynthesise or flower during dormant periods. We test ecological and evolutionary hypotheses for its widespread persistence. We show that dormancy has evolved numerous times. Most species displaying dormancy exhibit life‐history costs of sprouting, and of dormancy. Short‐lived and mycoheterotrophic species have higher proportions of dormant plants than long‐lived species and species with other nutritional modes. Foliage...

Data from: What influences the worldwide genetic structure of sperm whales (Physeter macrocephalus)?

Alana Alexander, Debbie Steel, Kendra Hoekzema, Sarah L. Mesnick, Daniel Engelhaupt, Iain Kerr, Roger Payne & Charles Scott Baker
The interplay of natural selection and genetic drift, influenced by geographic isolation, mating systems and population size, determines patterns of genetic diversity within species. The sperm whale provides an interesting example of a long-lived species with few geographic barriers to dispersal. Worldwide mtDNA diversity is relatively low, but highly structured among geographic regions and social groups, attributed to female philopatry. However, it is unclear whether this female philopatry is due to geographic regions or social...

Data from: On population abundance and niche structure

Luis Osorio-Olvera, Jorge Soberon & Manuel Falconi
Recent published evidence indicates a negative correlation between density of populations and the distance of their environments to a suitably defined ‘niche centroid’. This empirical observation lacks theoretical grounds. We provide a theoretical underpinning for the empirical relationship between population density and position in niche space, and use this framework to understand the circumstances under which the relationship will fail. We propose a metapopulation model for the area of distribution, as a system of ordinary...

Data from: Genomic data reveals potential for hybridization, introgression, and incomplete lineage sorting to confound phylogenetic relationships in an adaptive radiation of narrow-mouth frogs

Alana Mary Alexander, Yong-Chao Su, Carl Hirang Oliveros, Karen Veronica Olson, Scott Louis Travers & Rafe M. Brown
The microhylid frog genus Kaloula is an adaptive radiation spanning the edge of the Asian mainland and multiple adjacent island archipelagos, with much of the clade's diversity associated with an endemic Philippine radiation. Relationships among clades from the Philippines, however, remain unresolved. With ultraconserved element (UCE) and mitogenomic data, we identified highly-supported differences in topology and areas of poor resolution, for each marker set. Using the UCE data, we then identified possible instances of contemporary...

Data from: Dissection of signaling modalities and courtship timing reveals a novel signal in Drosophila saltans courtship

Kaila Colyott, Cynthia Odu & Jennifer M. Gleason
Courtship signalling, necessary for the recognition of potential mates, is often complex, using many modalities with multiple components. Drosophila courtship comprises chemical, tactile, visual and acoustic stimuli. Ablation of single sensory channels, either signal production or reception, can determine the roles of individual modalities in overall reproductive success. Adding measures of courtship timing, particularly courtship latency, the time for the male to initiate courtship, and courtship duration, the time from courtship initiation until the female...

Data from: Herbivory enhances the diversity of primary producers in pond ecosystems

Mathew A. Leibold, Spencer R. Hall, Val H. Smith & David A. Lytle
Diversity of primary producer is often surprisingly high, despite few limiting factors such as nutrients and light to facilitate species coexistence. In theory, the presence of herbivores could increase the diversity of primary producers, resolving this “paradox of the plankton”. Little experimental evidence supports this natural enemies hypothesis, but previous tests suffer from several deficiencies. Previous experiments often did not allow for multigeneration effects; utilized low diversity assemblages of herbivores; and limited opportunities for new...

Data from: Relative importance of competition and plant-soil feedback, their synergy, context dependency and implications for coexistence

Ylva Lekberg, James D. Bever, Rebecca A. Bunn, Ray M. Callaway, Miranda M. Hart, Stephanie N. Kivlin, John Klironomos, Beau G. Larkin, John L. Maron, Kurt O. Reinhart, Michael Remke, Wim H. Van Der Putten & Ragan M. Callaway
Plants interact simultaneously with each other and with soil biota, yet the relative importance of competition versus plant soil feedback (PSF) on plant performance is poorly understood. Using a meta-analysis of 38 published studies and 150 plant species, we show that effects of interspecific competition (either growing plants with a competitor or singly, or comparing inter- vs. intraspecific competition) and PSF (comparing home vs. away soil, live vs. sterile soil, or control vs. fungicide-treated soil)...

Data from: Fitness of crop-wild hybrid sunflowers under competitive conditions: implications for crop-to-wild introgression

Kristin L. Mercer, D. Jason Emry, Allison A. Snow, Matthew A. Kost, Brian A. Pace & Helen M. Alexander
Understanding the likelihood and extent of introgression of novel alleles in hybrid zones requires comparison of lifetime fitness of parents and hybrid progeny. However, fitness differences among cross types can vary depending on biotic conditions, thereby influencing introgression patterns. Based on past work, we predicted that increased competition would enhance introgression between cultivated and wild sunflower (Helianthus annuus) by reducing fitness advantages of wild plants. To test this prediction, we established a factorial field experiment...

Data from: Multilocus phylogeny and a new classification for Southeast Asian and Melanesian forest frogs (family Ceratobatrachidae)

Rafe M. Brown, Cameron D. Siler, Stephen J. Richards, Arvin C. Diesmos & David C. Cannatella
We present a near comprehensive, densely sampled, multilocus phylogenetic estimate of species relationships within the anuran family Ceratobatrachidae, a morphologically and ecologically diverse group of frogs from the island archipelagos of Southeast Asia and the South-West Pacific. Ceratobatrachid frogs consist of three clades: a small clade of enigmatic, primarily high-elevation, semi-aquatic Sundaland species currently assigned to Ingerana (for which we erect a new genus), which is the sister taxon of two large, monophyletic radiations, each...

Data from: Lineage space and the propensity of bacterial cells to undergo growth transitions

Arnab Bandyopadhyay, Huijing Wang & J. Christian J. Ray
The molecular makeup of the offspring of a dividing cell gradually becomes phenotypically decorrelated from the parent cell by noise and regulatory mechanisms that amplify phenotypic heterogeneity. Such regulatory mechanisms form networks that contain thresholds between phenotypes. Populations of cells can be poised near the threshold so that a subset of the population probabilistically undergoes the phenotypic transition. We sought to characterize the diversity of bacterial populations around a growth-modulating threshold via analysis of the...

Data from: Novel traits, flower symmetry, and transcriptional autoregulation: new hypotheses from bioinformatic and experimental data

Aniket Sengupta & Lena C. Hileman
A common feature in developmental networks is the autoregulation of transcription factors which, in turn, positively or negatively regulate additional genes critical for developmental patterning. When a transcription factor regulates its own expression by binding to cis-regulatory sites in its gene, the regulation is direct transcriptional autoregulation (DTA). Indirect transcriptional autoregulation (ITA) involves regulation by proteins expressed downstream of the target transcription factor. We review evidence for a hypothesized role of DTA in the evolution...

Data from: Non-random latitudinal gradients in range size and niche breadth predicted by spatial patterns of climate

Erin E. Saupe, Corinne E. Myers, A. Townsend Peterson, Jorge Soberón, Joy Singarayer, Paul Valdes & Huijie Qiao
Aim. Tropical species are thought to experience and be adapted to narrow ranges of abiotic conditions. This idea has been invoked to explain a broad array of biological phenomena, including the latitudinal diversity gradient and differential rates of speciation and extinction. However, debate continues regarding the broad-scale applicability of this pattern and potential processes responsible. Here, we use a simulation approach to test two propositions: (1) strong geographic patterns of variation in realized niche breadth...

Data from: Dispersal to or from an African biodiversity hotspot?

David C Blackburn & John Measey
Biodiversity hotspots are centers of endemism and thus contain many range-restricted species. In addition, within these hotspots are often widespread species that might have originated within a hotspot before dispersing to neighboring or distant regions. We test this hypothesis through a phylogeographic analysis of a miniature leaf litter frog, Arthroleptis xenodactyloides, that has a large distribution throughout the Eastern Arc, a biodiversity hotspot, and other regions in East Africa. Maximum likelihood and Bayesian estimates of...

Data from: A new squeaker frog (Arthroleptidae: Arthroleptis) from the Cameroon Volcanic Line with redescriptions of Arthroleptis adolfifriederici Nieden, 1911 \"1910\" and A. variabilis Matschie, 1893

David C. Blackburn, Legrand N Gonwouo, Raffael Ernst & Mark-Oliver Rödel
We describe a new species of squeaker frog (Arthroleptis) from Mt. Manengouba in southwestern Cameroon. The new species is distinguished from other Cameroonian Arthroleptis by moderately larger body size; a darkened throat and posterior thigh, both with many white spots; and, in females, a fourth finger longer than the first and second fingers. This species corresponds to a Cameroonian taxon previously identified as Arthroleptis adolfifriederici but which has been long recognized as distinct. Multivariate morphometric...

Data from: Phylogeny and biogeography of the core babblers (Aves: Timaliidae)

Robert G. Moyle, Michael J. Andersen, Carl H. Oliveros, Frank Steinheimer & Sushma Reddy
The avian family Timaliidae is a species rich and morphologically diverse component of African and Asian tropical forests. The morphological diversity within the family has attracted interest from ecologists and evolutionary biologists, but systematists have long suspected that this diversity might also mislead taxonomy, and recent molecular phylogenetic work has supported this hypothesis. We produced and analyzed a dataset of six genes and almost 300 individuals to assess the evolutionary history of the family. Although...

Data from: Evidence for climate-driven diversification? A caution for interpreting ABC inferences of simultaneous historical events

Jamie R. Oaks, Jeet Sukumaran, Jacob A. Esselstyn, Charles W. Linkem, Cameron David Siler, Mark T. Holder & Rafe M. Brown
Approximate Bayesian computation (ABC) is rapidly gaining popularity in population genetics. One example, msBayes, infers the distribution of divergence times among pairs of taxa, allowing phylogeographers to test hypotheses about historical causes of diversification in co-distributed groups of organisms. Using msBayes, we infer the distribution of divergence times among 22 pairs of populations of vertebrates distributed across the Philippine Archipelago. Our objective was to test whether sea-level oscillations during the Pleistocene caused diversification across the...

Data from: Brazilian marsupial frogs are diphyletic (Anura: Hemiphractidae: Gastrotheca)

David C. Blackburn & William E. Duellman
Molecular phylogenetic analyses based on expanded taxonomic and geographic sampling support the monophyly of the marsupial frog genera (family Hemiphractidae), resolve six geographically circumscribed lineages within Gastrotheca, and, for the first time, reveal that two divergent lineages of Gastrotheca inhabit the Atlantic Coastal Forests of Brazil. Within Gastrotheca, the earliest diverging clade is confined to northeastern Brazil, whereas the three subsequent diverging lineages are restricted to northern Venezuela (G. walkeri), southeastern Brazil, and northwestern South...

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