184 Works

Data from: Two-phase increase in the maximum size of life over 3.5 billion years reflects biological innovation and environmental opportunity

Jonathan L. Payne, Alison G. Boyer, James H. Brown, Seth Finnegan, Michal Kowaleski, , S. Kathleen Lyons, Craig R. McClain, Daniel W. McShea, Phillip M. Novack-Gottshall, Felisa A. Smith, Jennifer A. Stempien, Steve C. Wang, M. Kowalewski & R. A. Krause
NOTE: See also http://bodysize.nescent.org. ABSTRACT: The maximum size of organisms has increased enormously since the initial appearance of life >3.5 billion years ago (Gya), but the pattern and timing of this size increase is poorly known. Consequently, controls underlying the size spectrum of the global biota have been difficult to evaluate. Our period-level compilation of the largest known fossil organisms demonstrates that maximum size increased by 16 orders of magnitude since life first appeared in...

Data from: Metabolic rate associates with, but does not generate covariation between, behaviours in western stutter-trilling crickets, Gryllus integer

Indrikis A. Krams, Petri T. Niemelä, Giedrius Trakimas, Ronalds Krams, Gordon M. Burghardt, Tatjana Krama, Aare Kuusik, Marika Mand, Markus J. Rantala, Raivo Mand, Jukka Kekäläinen, Ilkka Sirkka, Severi Luoto, Raine Kortet & Indrikis Krams
The causes and consequences of among-individual variation and covariation in behaviours are of substantial interest to behavioural ecology, but the proximate mechanisms underpinning this (co)variation are still unclear. Previous research suggests metabolic rate as a potential proximate mechanism to explain behavioural covariation. We measured the resting metabolic rate (RMR), boldness and exploration in western stutter-trilling crickets, Gryllus integer, selected differentially for short and fast development over two generations. After applying mixed-effects models to reveal the...

Data from: Length, body depth, and gape relationships and inference on piscivory among North American centrarchids

Anthony V. Fernando, Kyler B. Hecke & Michael A. Eggleton
Species of Centrarchidae are major components of inland fisheries in much of North America. Thus, information gained from the assessment of interspecies interactions and/or quantifying predator-prey relationships is a useful tool for fisheries managers. Using preserved fish specimens (n = 717) from 20 species of centrarchids, we made measurements of total length (TL), standard length (SL), horizontal gape, and body depth for each individual. We fitted mathematical models that included horizontal gape and body depth...

Data from: Efficacy of visual surveys for white-nose syndrome at bat hibernacula

Amanda F. Janicki, Winifred F. Frick, A. Marm Kilpatrick, Katy L. Parise, Jeffrey T. Foster & Gary F. McCracken
White-Nose Syndrome (WNS) is an epizootic disease in hibernating bats caused by the fungus Pseudogymnoascus destructans. Surveillance for P. destructans at bat hibernacula consists primarily of visual surveys of bats, collection of potentially infected bats, and submission of these bats for laboratory testing. Cryptic infections (bats that are infected but display no visual signs of fungus) could lead to the mischaracterization of the infection status of a site and the inadvertent spread of P. destructans....

Data from: Evidence for repeated loss of selective constraint in rhodopsin of amblyopsid cavefishes (Teleostei: Amblyopsidae)

Matthew Lance Niemiller, Benjamin Minault Fitzpatrick, Premal Shah, Lars Schmitz & Thomas J. Near
The genetic mechanisms underlying regressive evolution—the degeneration or loss of a derived trait—are largely unknown, particularly for complex structures such as eyes in cave organisms. In several eyeless animals, the visual photoreceptor rhodopsin appeared to retain functional amino-acid sequences. Hypotheses to explain apparent maintenance of function include weak selection for retention of light-sensing abilities and its pleiotropic roles in circadian rhythms and thermotaxis. In contrast, we show that there has been repeated loss of functional...

Data from: Genetic analyses reveal cryptic diversity in the native North American fire ants (Hymenoptera: Formicidae: Solenopsis)

Pablo Chialvo, Dietrich A. Gotzek, D. DeWayne Shoemaker, Kenneth G. Ross & DEWAYNE SHOEMAKER
The native North American fire ants (Solenopsis) comprise a difficult group taxonomically that has undergone multiple revisions in the past century yet remains in a state of taxonomic uncertainty. In this study, we utilized a large set of microsatellite markers to conduct the first robust genetic analysis of the nominal species. Our approach used a variety of methods to test operational criteria commonly employed in species delimitation, including genotypic clustering, reproductive isolation/cohesion, and monophyly. We...

Data from: Two additional species of Gymnopus (Eugarics, Basidiomycotina)

Ronald Petersen, Karen Hughes, Ronald H. Petersen & Karen W. Hughes
For more than a decade, a combination of molecular phylogenetic analyses and morphological characterization have led to a renovation of the Omphalotaceae, especially of Gymnopus sensu lato. Numerous new genera have been proposed, but Gymnopus sensu stricto has also seen an accretion of species and species complexes. In this manuscript, two species are added to Gymnopus sensu stricto within Section Androsacei.

Data from: Replicated divergence in cichlid radiations mirrors a major vertebrate innovation

Matthew D. McGee, Brant C. Faircloth, Samuel R. Borstein, Jimmy Zheng, Christopher Darrin Hulsey, Peter C. Wainwright & Michael E. Alfaro
Decoupling of the upper jaw bones—jaw kinesis—is a distinctive feature of the ray-finned fishes, but it is not clear how the innovation is related to the extraordinary diversity of feeding behaviours and feeding ecology in this group. We address this issue in a lineage of ray-finned fishes that is well known for its ecological and functional diversity—African rift lake cichlids. We sequenced ultraconserved elements to generate a phylogenomic tree of the Lake Tanganyika and Lake...

Data from: Hybridization between two gartersnake species (Thamnophis) of conservation concern: A threat or an important natural interaction?

John S. Placyk, Benjamin M. Fitzpatrick, Gary S. Casper, Randall L. Small, R. Graham Reynolds, Daniel W. A. Noble, Ronald J. Brooks & Gordon M. Burghardt
Distinguishing between hybrid zones formed by secondary contact versus parapatric divergence-with-gene-flow is an important challenge for understanding the interplay of geographic isolation and local adaptation in the origin of species. Similarly, distinguishing between natural hybrid zones and those that formed as a consequence of recent human activities has important conservation implications. Recent work has demonstrated the existence of a narrow hybrid zone between the plains gartersnake (Thamnophis radix) and Butler’s gartersnake (T. butleri) in the...

Data from: Fish functional traits correlated with environmental variables in a temperate biodiversity hotspot

Benjamin P. Keck, Zachary H. Marion, Derek J. Martin, Jason C. Kaufman, Carol P. Harden, John S. Schwartz & Richard J. Strange
The global biodiversity crisis has invigorated the search for generalized patterns in most disciplines within the natural sciences. Studies based on organismal functional traits attempt to broaden implications of results by identifying the response of functional traits, instead of taxonomic units, to environmental variables. Determining the functional trait responses enables more direct comparisons with, or predictions for, communities of different taxonomic composition. The North American freshwater fish fauna is both diverse and increasingly imperiled through...

Data from: Diffusion tensor imaging of dolphin brains reveals direct auditory pathway to temporal lobe

Gregory S. Berns, Peter F. Cook, Sean Foxley, Saad Jbabdi, Karla L. Miller & Lori Marino
The brains of odontocetes (toothed whales) look grossly different from their terrestrial relatives. Because of their adaptation to the aquatic environment and their reliance on echolocation, the odontocetes' auditory system is both unique and crucial to their survival. Yet, scant data exist about the functional organization of the cetacean auditory system. A predominant hypothesis is that the primary auditory cortex lies in the suprasylvian gyrus along the vertex of the hemispheres, with this position induced...

Data from: Phenological mismatch with trees reduces wildflower carbon budgets

J. Mason Heberling, Caitlin McDonough MacKenzie, Jason D. Fridley, Susan Kalisz & Richard B. Primack
Interacting species can respond differently to climate change, causing unexpected consequences. Many understory wildflowers in deciduous forests leaf out and flower in the spring when light availability is highest before overstory canopy closure. Therefore, different phenological responses by understory and overstory species to increased spring temperature could have significant ecological implications. Pairing contemporary data with historical observations initiated by Henry David Thoreau (1850s), we found that overstory tree leaf out is more responsive to increased...

Data from: Data sharing by scientists: practices and perceptions

Carol Tenopir, Suzie Allard, Kimberly Douglass, Arsev Umur Aydinoglu, Lei Wu, Eleanor Read, Maribeth Manoff & Mike Frame
Background: Scientific research in the 21st century is more data intensive and collaborative than in the past. It is important to study the data practices of researchers –data accessibility, discovery, re-use, preservation and, particularly, data sharing. Data sharing is a valuable part of the scientific method allowing for verification of results and extending research from prior results. Methodology/Principal Findings: A total of 1329 scientists participated in this survey exploring current data sharing practices and perceptions...

Data from: Into and out of the tropics: global diversification patterns in a hyper-diverse clade of ectomycorrhizal fungi

Brian P. Looney, Martin Ryberg, Felix Hampe, Marisol Sánchez-García & P. Brandon Matheny
Ectomycorrhizal (ECM) fungi, symbiotic mutualists of many dominant tree and shrub species, exhibit a biogeographic pattern counter to the established latitudinal diversity gradient of most macroflora and fauna. However, an evolutionary basis for this pattern has not been explicitly tested in a diverse lineage. In this study, we reconstructed a mega-phylogeny of a cosmopolitan and hyper-diverse genus of ECM fungi, Russula, sampling from annotated collections and utilizing publically available sequences deposited in GenBank. Metadata from...

Data from: Comparative limb bone loading in the humerus and femur of the tiger salamander: testing the ‘mixed-chain’ hypothesis for skeletal safety factors

Sandy M. Kawano, D. Ross Economy, Marian S. Kennedy, Delphine Dean & Richard W. Blob
Locomotion imposes some of the highest loads upon the skeleton, and diverse bone designs have evolved to withstand these demands. Excessive loads can fatally injure organisms; however, bones have a margin of extra protection, called a ‘safety factor’ (SF), to accommodate loads that are higher than normal. The extent to which SFs might vary amongst an animal's limb bones is unclear. If the limbs are likened to a chain composed of bones as ‘links’, then...

Data from: Feeding ecology underlies the evolution of cichlid jaw mobility

Christopher M. Martinez, Matthew David McGee, Samuel Robert Borstein & Peter C. Wainwright
The fish feeding apparatus is among the most diverse functional systems in vertebrates. While morphological and mechanical variation of feeding systems are well studied, we know far less about the diversity of the motions that they produce. We explored patterns of feeding movements in African cichlids from Lakes Malawi and Tanganyika, asking whether the degree of kinesis is associated with dietary habits of species. We used geometric morphometrics to measure feeding kinesis as trajectories of...

Data from: Micromphale sect. Perforantia (Agaricales, Basidiomycetes); expansion and phylogenetic placement

Ronald H. Petersen & Karen W. Hughes
DNA sequences show that the traditional genus Micromphale appears to be polyphyletic. Nuclear ribosomal LSU and ITS DNA sequences place Micromphale sect. Perforantia Singer (typus sect. M. perforans) within Gymnopus, comprising a clade sister to a mixture of traditional Gymnopus taxa including G. fusipes (typus generis) plus traditional Marasmius sect. Androsacei. This study enlarges sect. Perforantia and shows that sect. Perforantia is a clade separate from those including Micromphale sect. Micromphale and sect. Rhizomorphigena. A...

Protected area, easement, and rental contract data reveal five communities of land protection in the United States

Heather Bird Jackson, Kailin Kroetz, James Sanchirico, Alexandra Thompson & Paul Armsworth
Land protection efforts represent large societal investments and are critical to biodiversity conservation. Land protection involves a complex mosaic of areas managed by multiple organizations, using a variety of mechanisms to achieve different levels of protection. We develop an approach to synthesize, describe, and map this land protection diversity over large spatial scales. We use cluster analysis to find distinct “communities” of land protection based on the organizations involved, the strictness of land protection, and...

Data for: Phylogenomic analyses reveal non-monophyly of the antbird genera Herpsilochmus and Sakesphorus (Thamnophilidae), with description of a new genus for Herpsilochmus sellowi

Gustavo Bravo, Bret Whitney, Ricardo Belmonte-Lopes, Marcos Bornschein, Natalia Aristizabal, Renata Beco, Jaqueline Battilana, Luciano Naka, Alexandre Aleixo, Marcio Pie, Luis Silveira, Elizabeth Derryberry & Robb Brumfield
The family Thamnophilidae is a species-rich Neotropical radiation of passerine birds. Current classification of its 235 species is mostly based on morphological similarities, but recent studies integrating comprehensive phenotypic and phylogenetic data have redefined taxonomic limits of several taxa. Here, we assess generic relationships of Herpsilochmus, Sakesphorus, Thamnophilus, Biatas, and Dysithamnus using DNA sequences from the mitochondrion, nuclear exons, and ultraconserved elements (UCEs), with further attention to interspecific relationships within Herpsilochmus. We show that Herpsilochmus...

Do selfing species have greater niche breadth? Support from ecological niche modeling

Alannie-Grace Gabrielle Grant
We explore the relationship between plant mating system (selfing or outcrossing) and niche breadth to gain new insights into processes that drive species distributions. Using a comparative approach with highly selfing versus highly outcrossing sister species, we test the extent to which: (1) species pairs have evolved significant niche divergence and less niche overlap, (2) selfers have wider niche breadths than outcrossers or vice versa, and (3) niches of selfers and outcrossers are defined by...

Valenzuela phylogenomic dataset from: Illumina whole genome sequencing indicates ploidy level differences within the Valenzuela flavidus (Psocodea: Psocomorpha: Caeciliusidae) species complex

Robert De Moya
This contains data for the manuscript: "Illumina Whole Genome Sequencing indicates Ploidy Level Differences within the Valenzuela flavidus (Psocodea: Psocomorpha: Caeciliusidae) Species Complex". Valenzuela flavidus is a species of bark louse which is known to have asexual parthenogenetic populations in Europe but is believed to have sexual and asexual populations in North America as well. Historically, Valenzuela aurantiacus was the species epithet recognized for North American members until reports of asexual reproduction surfaced in certain...

Methodological advances for hypothesis‐driven ethnobiology

Orou G. Gaoue, Jacob Moutouama, Michael Coe, Matthew Bond, Elizabeth Green, Nadejda Sero, Bezeng Simmy & Kowiyou Yessoufou
Ethnobiology as a discipline has evolved recently to increasingly embrace theory-inspired and hypothesis driven approaches to study why and how local people choose plants and animals they interact with and use for their livelihood. However, testing complex hypotheses or a network of ethnobiological hypotheses is challenging, particularly for datasets with non-independent observations due to species phylogenetic relatedness or socio-relational links between participants. Further, to fully account for the dynamics of local ecological knowledge, it is...

Evolution and development at the origin of a phylum

Bradley Deline, Jeffery Thompson, Nicholas Smith, Samuel Zamora, Imran Rahman, Sarah Sheffield, William Ausich, Thomas Kammer & Colin Sumrall
Quantifying morphological evolution is key to determining the patterns and processes underlying the origin of phyla. We constructed a hierarchical morphological character matrix to characterize the radiation and establishment of echinoderm body plans during the early Paleozoic. This showed that subphylum-level clades diverged gradually through the Cambrian, and the distinctiveness of the resulting body plans was amplified by the extinction of transitional forms and obscured by convergent evolution during the Ordovician. Higher-order characters that define...

Recent hybrids recapitulate ancient hybrid outcomes

Zachariah Gompert, Samridhi Chaturvedi, Lauren Lucas, C. Alex Buerkle, James Fordyce, Matthew Forister & Chris Nice
Genomic outcomes of hybridization depend on selection and recombination in hybrids. Whether these processes have similar effects on hybrid genome composition in contemporary hybrid zones versus ancient hybrid lineages is unknown. Here we show that patterns of introgression in a contemporary hybrid zone in Lycaeides butterflies predict patterns of ancestry in geographically adjacent, older hybrid populations. We find a particularly striking lack of ancestry from one of the hybridizing taxa, Lycaeides melissa, on the Z...

Data from: Habitat suitability and connectivity modeling reveal priority areas for Indiana bat (Myotis sodalis) conservation in a complex habitat mosaic

Ashleigh Cable, Joy O'Keefe, Jill Deppe, Tara Hohoff, Steven Taylor & Mark Davis
Context Conservation for the Indiana bat (Myotis sodalis), a federally endangered species in the United States of America, is typically focused on local maternity sites; however, the species is a regional migrant, interacting with the environment at multiple spatial scales. Hierarchical levels of management may be necessary, but we have limited knowledge of landscape-level ecology, distribution, and connectivity of suitable areas in complex landscapes. Objectives We sought to 1) identify factors influencing M. sodalis maternity...

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