63 Works

Data from: Open-ocean fish reveal an omnidirectional solution to camouflage in polarized environments

Parrish C. Brady, Alexander A. Gilerson, George W. Kattawar, James M. Sullivan, Michael S. Twardowski, Heidi M. Dierssen, Meng Gao, Kort Travis, Robert I. Etheredge, Alberto Tonizzo, Amir Ibrahim, Carlos Carrizo, Yalong Gu, Brandon J. Russell, Kathryn Mislinski, Shulei Zhao & Molly E. Cummings
Despite appearing featureless to our eyes, the open ocean is a highly variable environment for polarization-sensitive viewers. Dynamic visual backgrounds coupled with predator encounters from all possible directions make this habitat one of the most challenging for camouflage. We tested open-ocean crypsis in nature by collecting more than 1500 videopolarimetry measurements from live fish from distinct habitats under a variety of viewing conditions. Open-ocean fish species exhibited camouflage that was superior to that of both...

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: 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...

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...

A new genus of treeshrew and other micromammals from the middle Miocene hominoid locality of Ramnagar, Udhampur District, Jammu & Kashmir, India

Ramesh Sehgal, Abhishek Singh, Christopher Gilbert, Biren Patel, Christopher Campisano, Keegan Selig, Rajeev Patnaik & Ningthoujam Premjit Singh
The fossil record of treeshrews, hedgehogs, and other micromammals from the Lower Siwaliks of India is sparse. Here, we report on a new genus and species of fossil treeshrew, specimens of the hedgehog Galerix, and other micromammals from the middle Miocene (Lower Siwalik) deposits surrounding Ramnagar (Udhampur District, Jammu & Kashmir), at a fossil locality known as Dehari. The treeshrew from Dehari (Sivatupaia ramnagarensis gen. nov. et sp. nov.) currently represents the oldest record of...

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: Lineage diversification in a widespread species: roles for niche divergence and conservatism in the Common Kingsnake, Lampropeltis getula

Robert Alexander Pyron & Frank T Burbrink
Niche conservatism and niche divergence are both important ecological mechanisms associated with promoting allopatric speciation across geographic barriers. However, the potential for variable responses in widely distributed organisms has not been fully investigated. For allopatric sister lineages, three patterns for the interaction of ecological niche preference and geographic barriers are possible: i) niche conservatism at a physical barrier, ii) niche divergence at a physical barrier, and iii) niche divergence in the absence of a physical...

Genomic analysis of the only blind cichlid reveals extensive inactivation in eye and pigment formation genes

S. Elizabeth Alter
Trait loss represents an intriguing evolutionary problem, particularly when it occurs across independent lineages. Fishes in light-poor environments often evolve “troglomorphic” traits, including reduction or loss of both pigment and eyes. Here we investigate the genomic basis of trait loss in a blind and depigmented African cichlid, Lamprologus lethops, and explore evolutionary forces (selection and drift) that may have contributed to these losses. This species, the only known blind cichlid, is endemic to the lower...

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: 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: Using three-dimensional geometric morphometric and dental topographic analyses to infer the systematics and paleoecology of fossil treeshrews (Mammalia, Scandentia)

Keegan Selig, Eric Sargis, Stephen Chester & Mary Silcox
Treeshrews are small, Indomalayan mammals closely related to primates. Previously, three-dimensional geometric morphometric analyses were used to assess patterns of treeshrew lower second molar morphology, which showed that the position of molar landmarks covaries with intraordinal systematics. Another analysis used dental topographic metrics to test patterns of functional dental morphology and found that molar curvature, complexity, and relief were an effective means for examining patterns of variation in treeshrew dietary ecology. Here, we build on...

The geometry of resource constraint: an empirical study of the golden snub-nosed monkey

Rong Hou, Colin Chapman, Jessica Rothman, He Zhang, Kang Huang, Songtao Guo, Baoguo Li & David Raubenheimer
1. Apposite conceptualization and measurement of resource variation is critical for understanding many issues in ecology, including ecological niches, persistence and distribution of populations, the structure of communities, and population resilience to perturbations. 2. We apply the nutritional geometry framework to conceptualise and quantify the responses of a temperate-living primate, the golden snub-nosed monkey (Rhinopithecus roxellana) to variation in resource quality and quantity and in nutrient requirements associated with seasonal environments. 3. We present a...

Data from: Universal target-enrichment baits for anthozoan (Cnidaria) phylogenomics: new approaches to long-standing problems

Andrea M. Quattrini, Brant C. Faircloth, Luisa F. Dueñas, Thomas C.L. Bridge, Mercer R. Brügler, Ivan F. Calixto-Botía, Danielle M. DeLeo, Sylvain Foret, Santiago Herrera, Simon M.Y. Lee, David J. Miller, Carlos Prada, Gandhi Rádis-Baptista, Catalina Ramírez-Portilla, Juan A. Sánchez, Estefania Rodriguez, Catherine S. McFadden, Tom C. L. Bridge & Simon M. Y. Lee
Anthozoans (e.g., corals, anemones) are an ecologically important and diverse group of marine metazoans that occur from shallow to deep waters worldwide. However, our understanding of the evolutionary relationships among the ~7500 species within this class is hindered by the lack of phylogenetically informative markers that can be reliably sequenced across a diversity of taxa. We designed and tested 16,308 RNA baits to capture 720 Ultraconserved Element loci and 1,071 exon loci. Library preparation and...

Data from: Lecanora caperatica (Lecanoraceae, lichenized ascomycetes) a new sorediate species widespread in eastern North America

Olivia A. Asher & James C. Lendemer
Lecanora caperatica is described based on collections from throughout temperate eastern North America. It is a crustose sorediate species in the L. subfusca group which has pulcaris-type apothecia, and produces atranorin and caperatic acid often with accessory roccellic/angardianic acid. The species is chemically similar to the European L. mugosphagneti which differs in ecology, thallus morphology and in having albella-type apothecia. The generic placement of L. caperatica, and its affinity to the L. subfusca group, are...

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: Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes

Thomas J. Near, Alex Dornburg, Ron I. Eytan, Benjamin P. Keck, W. Leo Smith, Kristen L. Kuhn, Jon A. Moore, Samantha A. Price, Frank T. Burbrink, Matt Friedman & Peter C. Wainwright
Spiny-rayed fishes, or acanthomorphs, comprise nearly one-third of all living vertebrates. Despite their dominant role in aquatic ecosystems, the evolutionary history and tempo of acanthomorph diversification is poorly understood. We investigate the pattern of lineage diversification in acanthomorphs by using a well-resolved time-calibrated phylogeny inferred from a nuclear gene supermatrix that includes 520 acanthomorph species and 37 fossil age constraints. This phylogeny provides resolution for what has been classically referred to as the “bush at...

Data from: Considering gene flow when using coalescent methods to delimit lineages of North American pitvipers of the genus Agkistrodon

Frank T. Burbrink & Timothy J. Guiher
Examining species diversity and mechanisms of speciation using coalescent models provides a framework for how regional diversity is accrued, even in well-studied areas such as the Nearctic. It is likely, that gene flow among closely-related species with adjacent distributions may be common. However, the absence of gene flow is a primary assumption of many phylogeographical methods that produce species trees and delimit species using Bayesian or likelihood functions in a coalescent framework. In the present...

Data from: Out of the Orient: Post-Tethyan transoceanic and trans-Arabian routes fostered the spread of Baorini skippers in the Afrotropics

Emmanuel F.A. Toussaint, Roger Vila, Masaya Yago, Hideyuki Chiba, Andrew D. Warren, Kwaku Aduse-Poku, Caroline Storer, Kelly M. Dexter, Kiyoshi Maruyama, David J. Lohman & Akito Y. Kawahara
The origin of taxa presenting a disjunct distribution between Africa and Asia has puzzled biogeographers for more than a century. This biogeographic pattern has been hypothesized to be the result of transoceanic long‐distance dispersal, Oligocene dispersal through forested corridors, Miocene dispersal through the Arabian Peninsula or passive dispersal on the rifting Indian plate. However, it has often been difficult to pinpoint the mechanisms at play. We investigate biotic exchange between the Afrotropics and the Oriental...

Data from: Transcriptome resources for the white-footed mouse (Peromyscus leucopus): new genomic tools for investigating ecologically divergent urban and rural populations

Stephen E. Harris, Rachel J. O'Neill & Jason Munshi-South
Genomic resources are important and attainable for examining evolutionary change in divergent natural populations of non-model species. We utilized two Next Generation Sequencing (NGS) platforms, 454 and SOLiD 5500XL, to assemble low coverage transcriptomes of the white-footed mouse (Peromyscus leucopus), a widespread and abundant native rodent in eastern North America. We sequenced liver mRNA transcripts from multiple individuals collected from urban populations in New York City and rural populations in undisturbed protected areas nearby and...

Data from: A new family of dissimilarity metrics for discrete character matrices that include inapplicable characters and its importance for disparity studies

Melanie J. Hopkins, Katherine St. John & Katherine St John
The use of discrete character data for disparity analyses has become more popular, partially due to the recognition that character data describe variation at large taxonomic scales, as well as the increasing availability of both character matrices co-opted from phylogenetic analysis and software tools. As taxonomic scope increases, the need to describe variation leads to some characters that may describe traits not found across all the taxa. In such situations, it is common practice to...

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