81 Works

Data from: Assessing species boundaries and the phylogenetic position of the rare Szechwan Ratsnake, Euprepiophis perlacea (Serpentes: Colubridae), using coalescent-based methods

Xin Chen, Ke Jiang, Peng Guo, Song Huang, Dingqi Rao, Li Ding, Hirohiko Takeuchi, Jing Che, Yaping Zhang, Edward A. Myers, Frank T. Burbrink & Ya-Ping Zhang
Delimiting species and clarifying phylogenetic relationships are the main goals of systematics. For species with questionable taxonomic status, species delimitation approaches using multi-species coalescent models with multiple loci are recommended if morphological data are unavailable or unhelpful. Moreover, these methods will also reduce subjectivity based on genetic distance or requirement of monophyletic genetic lineages. We determine the validity and phylogenetic position of a rare and long controversial species of Chinese reptile, the Szechwan ratsnake (Euprepiophis...

Data from: The lichens and allied fungi of Mount Mitchell State Park, North Carolina: a first checklist with comprehensive keys and comparison to historical data

James C. Lendemer, Carly R. Anderson Stewart, Betty Besa, Jim Goldsmith, Haley Griffith, Jordan R. Hoffman, Betsy Kraus, Paula LaPoint, Lin Li, Zachary Muscavitch, Joel Schultz, Rebecca Schultz & Jessica L. Allen
A total of 171 species of lichens and allied fungi are reported from the spruce-fir forests of Mount Mitchell State Park, in the Black Mountains of North Carolina, based on both historical and modern records. Comparison of the modern baseline with the historical macrolichen baseline generated in the 1970s revealed potential losses of high-elevation southern Appalachian endemics (2 species), cyanolichens (5 species), species typical of exposed rock outcrops (1 species), and widespread species typical of...

Data from: Quantifying the human impacts on Papua New Guinea reef fish communities across space and time

Joshua A. Drew, Ruth A. Hufbauer & Kathryn L. Amatangelo
Describing the drivers of species loss and of community change are important goals in both conservation and ecology. However, it is difficult to determine whether exploited species decline due to direct effects of harvesting or due to other environmental perturbations brought about by proximity to human populations. Here we quantify differences in species richness of coral reef fish communities along a human population gradient in Papua New Guinea to understand the relative impacts of fishing...

Data from: Multilocus phylogeographic assessment of the California Mountain Kingsnake (Lampropeltis zonata) suggests alternative patterns of diversification for the California Floristic Province

Edward A. Myers, Javier A. Rodríguez-Robles, Dale F. DeNardo, Richard E. Staub, Alyssa Stropoli, Sara Ruane & Frank T. Burbrink
Phylogeographic inference can determine the timing of population divergence, historical demographic processes, patterns of migration, and when extended to multiple species, the history of communities. Single locus analyses can mislead interpretations of the evolutionary history of taxa and comparative analyses. It is therefore important to revisit previous single-locus phylogeographic studies, particularly those that have been used to propose general patterns for regional biotas and the processes responsible for generating inferred patterns. Here we employ a...

Data from: The utility of normalized difference vegetation index for predicting African buffalo forage quality

Sadie J. Ryan, Paul C. Cross, John Winnie, Craig Hay, Justin Bowers & Wayne M. Getz
Many studies of mammalian herbivores have employed remotely sensed vegetation greenness, in the form of Normalized Difference Vegetation Index (NDVI) as a proxy for forage quality. The assumption that reflected greenness represents forage quality often goes untested, and limited data exist on the relationships between remotely sensed and traditional forage nutrient indicators. We provide the first study connecting NDVI and forage nutrient indicators within a free-ranging African herbivore ecosystem. We examined the relationships between fecal...

Data from: Differential effect of selection against LINE retrotransposons among vertebrates inferred from whole-genome data and demographic modeling

Alexander T Xue, Robert P. Ruggiero, Michael J. Hickerson & Stéphane Boissinot
Variation in LINE composition is one of the major determinants for the substantial size and structural differences among vertebrate genomes. In particular, the larger genomes of mammals are characterized by hundreds of thousands of copies from a single LINE clade, L1, whereas nonmammalian vertebrates possess a much greater diversity of LINEs, yet with orders of magnitude less in copy number. It has been proposed that such variation in copy number among vertebrates is due to...

Data from: Scale-dependent home range optimality for a solitary omnivore

Mariela Gantchoff, Guiming Wang, Dean Beyer & Jerrold Belant
Spatial and temporal heterogeneity are fundamental mechanisms structuring home ranges. Under optimality, an individual should structure their space use economically to maximize fitness. We evaluated support for three hypotheses related to range optimality in American black bears (Ursus americanus), predicting (1) range location on a landscape will correspond with high vegetation productivity, (2) increasing forest fragmentation will result in larger ranges, and (3) increasing proportion of forest and/or mean vegetation productivity will result in smaller...

Data from: Pleistocene climatic changes drive diversification across a tropical savanna

Sally Potter, Alexander T. Xue, Jason G. Bragg, Dan F. Rosauer, Emily J. Roycroft & Craig Moritz
Spatial responses of species to past climate change depend on both intrinsic traits (climatic niche breadth, dispersal rates) and the scale of climatic fluctuations across the landscape. New capabilities in generating and analysing population genomic data, along with spatial modelling, have unleashed our capacity to infer how past climate changes have shaped populations, and by extension, complex communities. Combining these approaches, we uncover lineage diversity across four co-distributed lizards from the Australian Monsoonal Tropics and...

Data from: Guidelines and considerations for designing field experiments simulating precipitation extremes in forest ecosystems

Heidi Asbjornsen, John L. Campbell, Katie A. Jennings, Matthew A. Vadeboncoeur, Cameron McIntire, Pamela H. Templer, Richard P. Phillips, Taryn L. Bauerle, Michael C. Dietze, Serita D. Frey, Peter M. Groffman, Rosella Guerrieri, Paul J. Hanson, Eric P. Kelsey, Alan K. Knapp, Nathan G. McDowell, Patrick Meir, Kimberly A. Novick, Scott V. Ollinger, Will T. Pockman, Paul G. Schaberg, Stan D. Wullschleger, Melinda D. Smith & Lindsey E. Rustad
1. Context. Precipitation regimes are changing in response to climate change, yet understanding of how forest ecosystems respond to extreme droughts and pluvials remains incomplete. As future precipitation extremes will likely fall outside the range of historical variability, precipitation manipulation experiments (PMEs) are critical to advancing knowledge about potential ecosystem responses. However, few PMEs have been conducted in forests compared to short-statured ecosystems, and forest PMEs have unique design requirements and constraints. Moreover, past forest...

Data from: Toward the genetic origins of a potentially non-native population of threespine stickleback (Gasterosteus aculeatus) in Alberta

Andrew M. Rezansoff, Erika Crispo, Christopher Blair, Edward Cruz, Jun Kitano, Steven M. Vamosi & Sean M. Rogers
Disentangling the origin of putatively introduced/invasive species is of increasing priority in conservation biology. The presence of a previously undocumented species may be due to an undetected recent population or range expansion associated with environmental change, or due to an introduction by humans. We used molecular tools to address the origin of a population of threespine stickleback (Gasterosteus aculeatus) first identified in central Alberta, Canada in 1980 from a single lake. We characterized this inland,...

Data from: Quantifying the importance of geographic replication and representativeness when estimating demographic rates, using a coastal species as a case study

Christopher R. Field, Katharine J. Ruskin, Bri Benvenuti, Alyssa C. Borowske, Jonathan B. Cohen, Laura Garey, Thomas P. Hodgman, Rebecca A. Kern, Erin King, Alison R. Kocek, Adrienne I. Kovach, Kathleen M. O'Brien, Brian J. Olsen, Nancy Pau, Samuel G. Roberts, Emma Shelly, W. Gregory Shriver, Jennifer Walsh, Chris S. Elphick & Rebecca A. Longenecker
Demographic rates are rarely estimated over an entire species range, limiting empirical tests of ecological patterns and theories, and raising questions about the representativeness of studies that use data from a small part of a range. The uncertainty that results from using demographic rates from just a few sites is especially pervasive in population projections, which are critical for a wide range of questions in ecology and conservation. We developed a simple simulation to quantify...

Data from: Population genomics through time provides insights into the consequences of decline and rapid demographic recovery through head-starting in a Galapagos giant tortoise

Evelyn L. Jensen, Danielle L. Edwards, Ryan C. Garrick, Joshua M. Miller, James P. Gibbs, Linda J. Cayot, Washington Tapia, Aldalgisa Caccone, Michael A. Russello & Adalgisa Caccone
Population genetic theory related to the consequences of rapid population decline is well-developed, but there are very few empirical studies where sampling was conducted before and after a known bottleneck event. Such knowledge is of particular importance for species restoration, given links between genetic diversity and the probability of long-term persistence. To directly evaluate the relationship between current genetic diversity and past demographic events, we collected genome-wide single nucleotide polymorphism data from pre-bottleneck historical (c.1906)...

Data from: Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan area

Stephen E. Harris, Jason Munshi-South, Craig Obergfell, Rachel O'Neill & Rachel O’Neill
Urbanization is a major cause of ecological degradation around the world, and human settlement in large cities is accelerating. New York City (NYC) is one of the oldest and most urbanized cities in North America, but still maintains 20% vegetation cover and substantial populations of some native wildlife. The white-footed mouse, Peromyscus leucopus, is a common resident of NYC’s forest fragments and an emerging model system for examining the evolutionary consequences of urbanization. In this...

Data from: Ungulate distributions in a rangeland with competitors, predators, and pastoralists

Paul Schuette, Scott Creel & Dave Christianson
African rangelands support diverse ungulate communities whose member species exhibit unique combinations of body morphology and behaviour that have evolved over millions of years to limit the effects of competition and predation on fitness, and more recently, to cope with people and livestock. The mechanisms by which native ungulates cope with the combined effects of competition, predation and human disturbance are poorly understood. Addressing this knowledge gap will help guide management and conservation plans for...

Data from: Robust inference on large-scale species habitat use with interview data: the status of jaguars outside protected areas in Central America

Lisanne S. Petracca, Jacqueline L. Frair, Jonathan B. Cohen, Ana Patricia Calderón, Javier Carazo-Salazar, Franklin Castañeda, Daniel Corrales-Gutiérrez, Rebecca J. Foster, Bart Harmsen, Sandra Hernández-Potosme, Luis Herrera, Melva Olmos, Sandy Pereira, Hugh S. Robinson, Nathaniel Robinson, Roberto Salom-Pérez, Yahaira Urbina, Kathy A. Zeller & Howard Quigley
Evaluating range-wide habitat use by a target species requires information on species occurrence over broad geographic regions, a process made difficult by species rarity, large spatiotemporal sampling domains, and imperfect detection. We address these challenges in an assessment of habitat use for jaguars (Panthera onca) outside protected areas in Central America. Occurrence records were acquired within 12 putative corridors using interviews with knowledgeable corridor residents. We developed a Bayesian hierarchical occupancy model to gain robust...

Rapid evolution by sexual selection in a wild, invasive mammal

M. Aaron Owen & David Lahti
Sexual selection theory provides a framework for investigating the evolution of traits involved in attracting and competing for mates. We show that ecological factors can strongly influence the adaptive value of these traits, and changes to these factors can lead to rapid evolutionary change. We compared sexually selected traits in the small Indian mongoose (Urva auropunctata) between their sparsely-populated native range and four tropical islands to which they were introduced within the last 150 years...

Hidden in the DNA: insights on how multiple historical processes and natural history traits shaped patterns of cryptic diversity in an Amazon leaf-litter lizard Loxopholis osvaldoi (Squamata: Gymnophthalmidae).

Sergio Marques De Souza, Katia Machado Pellegrino, Tuliana Oliveira Brunes, Ana Carnaval, Roberta Pacheco Damasceno, Manoela Lima De Oliveira Borges, Carlos Candia Gallardo & Miguel Rodrigues
Aim: To investigate cryptic diversity and diversification timing in the putatively low-dispersal Amazonian leaf-litter lizard Loxopholis osvaldoi, and to ask how geography (rivers, isolation by distance, IBD), ecological drivers (isolation by environment, IBE) and historical factors (climatic refugia) explain intraspecific genetic variation. Location: Central Amazonia, Brazil. Taxon: Squamata; Gymnophthalmidae; Loxopholis osvaldoi. Methods: We sequenced two mitochondrial and two nuclear markers in 157 individuals. Phylogeographic structure and the occurrence of independent evolving lineages where explored through...

SNP analyses reveal a diverse pool of potential colonists to earthquake‐uplifted coastlines

Johnette Peters, Jonathan Waters, Ludovic Dutoit & Ceridwen Fraser
In species that form dense populations, major disturbance events are expected to increase the chance of establishment for immigrant lineages. Real-time tests of the impact of disturbance on patterns of genetic structure are, however, scarce. Central to testing these concepts is determining the pool of potential immigrants dispersing into a disturbed area. In 2016, a 7.8 magnitude earthquake occurred on the South Island of New Zealand. Affecting approximately 100 km of coastline, this quake caused...

Data from: A description of nesting behaviors, including factors impacting nest site selection, in black-and-white ruffed lemurs (Varecia variegata)

Andrea L. Baden
Nest site selection is at once fundamental to reproduction and a poorly understood component of many organisms’ reproductive investment. This study investigates the nesting behaviors of black-and-white ruffed lemurs, Varecia variegata, a litter-bearing primate from the southeastern rainforests of Madagascar. Using a combination of behavioral, geospatial, and demographic data, I test the hypotheses that environmental and social cues influence nest site selection, and that these decisions ultimately impact maternal reproductive success. Gestating females built multiple...

Data from: Speciation with gene flow in whiptail lizards from a Neotropical xeric biome

Eliana F. Oliveira, Marcelo Gehara, Vinícius A. São Pedro, Xin Chen, Edward A. Myers, Frank T. Burbrink, Daniel O. Mesquita, Adrian A. Garda, Guarino R. Colli, Miguel T. Rodrigues, Federico J. Arias, Hussam Zaher, Rodrigo M. L. Santos & Gabriel C. Costa
Two main hypotheses have been proposed to explain the diversification of the Caatinga biota. The riverine barrier hypothesis (RBH) claims that the São Francisco River (SFR) is a major biogeographic barrier to gene flow. The Pleistocene climatic fluctuation hypothesis (PCH) states that gene flow, geographic genetic structure, and demographic signatures on endemic Caatinga taxa were influenced by Quaternary climate fluctuation cycles. Herein we analyze genetic diversity and structure, phylogeographic history, and diversification of a widespread...

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: A taxonomic revision of the North American species of Lepraria s.l. that produce divaricatic acid, with notes on the type species of the genus L. incana.

James C. Lendemer
The divaricatic acid-producing populations of Lepraria in North America north of Mexico are revised using traditional morphological characters, chemistry, ecology, biogeography, and ITS1, 5.8S, and ITS2 sequence data. Three taxa are accepted: L. cryophila, L. hodkinsoniana sp. nov., and L. pacifica sp. nov. Both Lepraria crassissima and L. incana are excluded from the study area. Non-cryptic, semi-cryptic, and fully-cryptic species concepts in Lepraria are discussed with a special emphasis on the practical integration of molecular...

Data from: Pathogen richness and abundance predict patterns of adaptive MHC variation in insular amphibians

Supen Wang, Conghui Liu, Anthony B. Wilson, Na Zhao, Xianping Li, Wei Zhu, Xu Gao, Xuan Liu & Yiming Li
The identification of the factors responsible for genetic variation and differentiation at adaptive loci can provide important insights into the evolutionary process, and is crucial for the effective management of threatened species. We studied the impact of environmental viral richness and abundance on functional diversity and differentiation of the MHC class Ia locus in populations of the black-spotted pond frog (Pelophylax nigromaculatus), an IUCN-listed species, on 24 land-bridge islands of the Zhoushan Archipelago and 3...

Data from: Rate of evolutionary change in cranial morphology of the marsupial genus Monodelphis is constrained by the availability of additive genetic variation

Arthur Porto, Harley Sebastião, Silvia Eliza Pavan, John L. VandeBerg, Gabriel Marroig & James M. Cheverud
We tested the hypothesis that the rate of marsupial cranial evolution is dependent on the distribution of genetic variation in multivariate space. To do so, we carried out a genetic analysis of cranial morphological variation in laboratory strains of Monodelphis domestica and used estimates of genetic covariation to analyze the morphological diversification of the Monodelphis brevicaudata species group. We found that within-species genetic variation is concentrated in only a few axes of the morphospace and...

Data from: Tree-growth is more sensitive than species distributions to recent changes in climate and acidic deposition in the northeastern United States

Jay W. Wason, Martin Dovciak, Colin M. Beier & John J. Battles
Tree-growth responses to environmental change could provide early detection of shifts in forest composition and help facilitate ecosystem management and conservation. We studied forest tree responses to recent trends in climate and acidic deposition using analyses of tree rings and long-term climate, deposition and forest plot data along an elevational climatic gradient in the northeastern United States. We analyzed how (a) individual growth of dominant species (Picea rubens, Abies balsamea), and (b) spatial distributions of...

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  • Queens College, CUNY
  • City University of New York
  • State University of New York
  • American Museum of Natural History
  • Yale University
  • Australian National University
  • University of Sao Paulo
  • Columbia University
  • City College of New York
  • George Washington University