27 Works

Data from: Moving in the Anthropocene: global reductions in terrestrial mammalian movements

Marlee A. Tucker, Katrin Böhning-Gaese, William F. Fagan, John M. Fryxell, Bram Van Moorter, Susan C. Alberts, Abdullahi H. Ali, Andrew M. Allen, Nina Attias, Tal Avgar, Hattie Bartlam-Brooks, Buuveibaatar Bayarbaatar, Jerrold L. Belant, Alessandra Bertassoni, Dean Beyer, Laura Bidner, Floris M. Van Beest, Stephen Blake, Niels Blaum, Chloe Bracis, Danielle Brown, P. J. Nico De Bruyn, Francesca Cagnacci, Justin M. Calabrese, Constança Camilo-Alves … & Thomas Mueller
Animal movement is fundamental for ecosystem functioning and species survival, yet the effects of the anthropogenic footprint on animal movements have not been estimated across species. Using a unique GPS-tracking database of 803 individuals across 57 species, we found that movements of mammals in areas with a comparatively high human footprint were on average one-half to one-third the extent of their movements in areas with a low human footprint. We attribute this reduction to behavioral...

Data from: Beyond thermal limits: comprehensive metrics of performance identify key axes of thermal adaptation in ants

Clint A. Penick, Sarah E. Diamond, Nathan J. Sanders & Robert R. Dunn
How species respond to temperature change depends in large part on their physiology. Physiological traits, such as critical thermal limits (CTmax and CTmin), provide estimates of thermal performance but may not capture the full impacts of temperature on fitness. Rather, thermal performance likely depends on a combination of traits—including thermal limits—that vary among species. Here we examine how thermal limits correlate with the main components that influence fitness in ants. First, we compare how temperature...

Data from: Idiosyncratic responses to climate-driven forest fragmentation and marine incursions in reed frogs from Central Africa and the Gulf of Guinea Islands

Rayna C. Bell, Juan L. Parra, Gabriel Badjedjea, Michael F. Barej, David C. Blackburn, Marius Burger, Alan Channing, J. Maximilian Dehling, Eli Greenbaum, Václav Gvoždík, Jos Kielgast, Chifundera Kusamba, Stefan Lötters, Patrick J. McLaughlin, Zoltán T. Nagy, Mark-Oliver Rödel, Daniel M. Portik, Bryan L. Stuart, Jeremy VanDerWal, Ange-Ghislain Zassi Boulou & Kelly R. Zamudio
Organismal traits interact with environmental variation to mediate how species respond to shared landscapes. Thus, differences in traits related to dispersal ability or physiological tolerance may result in phylogeographic discordance among co-distributed taxa, even when they are responding to common barriers. We quantified climatic suitability and stability, and phylogeographic divergence within three reed frog species complexes across the Guineo-Congolian forests and Gulf of Guinea archipelago of Central Africa to investigate how they responded to a...

Data from: Spatiotemporal variation in completeness of the early cynodont fossil record and its implications for mammalian evolutionary history

Grace Varnham, Philip Mannion & Christian Kammerer
Mammals are the only surviving group of Cynodontia, a synapsid clade that first appears in the fossil record in the late Permian, ~260 million years ago. Here, using three metrics that capture skeletal completeness, we quantify the quality of the early cynodont fossil record in time and space to evaluate the impact of sampling and preservational biases on our understanding of the group’s evolutionary history. There is no consistent global sampling signal for early cynodonts....

Data from: Does hunting or hiking affect wildlife communities in protected areas?

Roland Kays, Arielle W. Parsons, Megan C. Baker, Ellizabeth L. Kalies, Tavis Forrester, Robert Costello, Christopher T. Rota, Joshua J. Millspaugh & William J. McShea
Managed public wild areas have dual mandates to protect biodiversity and provide recreational opportunities for people. These goals could be at odds if recreation, ranging from hiking to legal hunting, disrupts wildlife enough to alter their space use or community structure. We evaluated the effect of managed hunting and recreation on 12 terrestrial wildlife species by employing a large citizen science camera trapping survey at 1947 sites stratified across different levels of human activities in...

Data from: Assessment of coyote-wolf-dog admixture using ancestry-informative diagnostic SNPs

Javier Monzón, Roland Kays & Daniel E. Dykhuizen
The evolutionary importance of hybridization as a source of new adaptive genetic variation is rapidly gaining recognition. Hybridization between coyotes and wolves may have introduced adaptive alleles into the coyote gene pool that facilitated an expansion in their geographic range and dietary niche. Furthermore, hybridization between coyotes and domestic dogs may facilitate adaptation to human-dominated environments. We genotyped 63 ancestry-informative single nucleotide polymorphisms in 427 canids in order to examine the prevalence, spatial distribution, and...

A combined approach of mitochondrial DNA and anchored nuclear phylogenomics sheds light on unrecognized diversity, phylogeny, and historical biogeography of the cascade frogs, genus Amolops (Anura: Ranidae)

Yunhe Wu, Fang Yan, Bryan L. Stuart, Elizabeth Prendini, Chatmongkon Suwannapoom, Hollis A. Dahn, Bao-Lin Zhang, Hong-Xia Cai, Yong-Biao Xu, Ke Jiang, Hong-Man Chen, Alan R. Lemmon, Emily Moriarty Lemmon, Christopher J. Raxworthy, Nikolai L. Orlov, Robert W. Murphy & Jing Che
Amolops is one of the most species-rich genera in Ranidae, with 59 recognized species. This genus currently includes six species groups diagnosed mainly by morphology. Several recent molecular studies indicated that the classification of species groups within Amolops remains controversial, and key nodes in the phylogeny have been inadequately resolved. In addition, the diversity of cascade frogs remains poorly understood, especially for those from incompletely sampled regions. Herein, we investigate the species-level diversity within genus...

A recovery network leads to the natural recolonization of an archipelago and a potential trailing edge refuge

Matthew Smith, Jonathan Gilbert, Erik Olson, Kim Scribner, Timothy Van Deelen, Julie Van Stappen, Bronwyn Williams, James Woodford & Jonathan Pauli
Rapid environmental change is reshaping ecosystems and driving species loss globally. Carnivore populations have declined and retracted rapidly and have been the target of numerous translocation projects. Success, however, is complicated when these efforts occur in novel ecosystems. Identifying refuges, locations that are resistant to environmental change, within a translocation framework should improve population recovery and persistence. American martens (Martes americana) are the most frequently translocated carnivore in North America. As elsewhere, martens were extirpated...

Effects of taphonomic deformation on geometric morphometric analysis of fossils: a case study using the dicynodont Diictodon feliceps (Therapsida, Anomodontia)

Christian Kammerer, Michol Deutsch, Jacqueline Lungmus & Kenneth Angielczyk
Taphonomic deformation, the distortion of fossils as a result of geological processes, poses problems for the use of geometric morphometrics in addressing paleobiological questions. Signal from biological variation, such as ontogenetic trends and sexual dimorphism, may be lost if variation from deformation is too high. Here, we investigate the effects of taphonomic deformation on geometric morphometric analyses of the abundant, well known Permian therapsid Diictodon feliceps. Distorted Diictodon crania can be categorized into seven typical...

Data from: Biologically and diagenetically derived peptide modifications in Moa collagens

Timothy P. Cleland, Elena R. Schroeter & Mary Higby Schweitzer
The modifications that occur on proteins in natural environments over time are not well studied, yet characterizing them is vital to correctly interpret sequence data recovered from fossils. The recently extinct moa (Dinornithidae) is an excellent candidate for investigating the preservation of proteins, their post-translational modifications (PTMs) and diagenetic alterations during degradation. Moa protein extracts were analysed using mass spectrometry, and peptides from collagen I, collagen II and collagen V were identified. We also identified...

Data from: Diversity and evolution of the primate skin microbiome

Sarah E. Council, Amy M. Savage, Julie M. Urban, Megan E. Ehlers, J. H. Pate Skene, Michael L. Platt, Robert R. Dunn & Julie E. Horvath
Skin microbes play a role in human body odour, health and disease. Compared to gut microbes we know comparatively little about the changes in the composition of skin microbes in response to evolutionary changes in hosts, or more recent behavioral and cultural changes in humans. No studies have used sequence-based approaches to consider the skin microbe communities of gorillas and chimpanzees, for example. Comparison of the microbial associates of non-human primates with those of humans...

Data from: Deep genetic structure and ecological divergence in a widespread human commensal toad

Guinevere O. U. Wogan, Bryan L. Stuart, Djoko T. Iskandar & Jimmy A. McGuire
The Asian common toad (Duttaphrynus melanostictus) is a human commensal species that occupies a wide variety of habitats across tropical Southeast Asia. We test the hypothesis that genetic variation in D. melanostictus is weakly associated with geography owing to natural and human-mediated dispersal facilitated by its commensal nature. Phylogenetic and population genetic analyses of mitochondrial and nuclear DNA sequence variation, and predictive species distribution modelling, unexpectedly recovered three distinct evolutionary lineages that differ genetically and...

Data from: Mammal communities are larger and more diverse in moderately developed areas

Arielle Waldstein Parsons, Tavis Forrester, Megan C. Baker-Whatton, William J. McShea, Christopher T. Rota, Stephanie G. Schuttler, Joshua J. Millspaugh & Roland Kays
Developed areas are thought to have low species diversity, low animal abundance, few native predators, and thus low resilience and ecological function. Working with citizen scientist volunteers to survey mammals at 1427 sites across two development gradients (wild-rural-exurban-suburban-urban) and four plot types (large forests, small forest fragments, open areas and residential yards) in the eastern US, we show that developed areas actually had significantly higher or statistically similar mammalian occupancy, relative abundance, richness and diversity...

Data from: Large birds travel farther in homogeneous environments

Marlee A. Tucker, Olga Alexandrou, , Keith L. Bildstein, Katrin Böhning-Gaese, Chloe Bracis, John N. Brzorad, Evan R. Buechley, David Cabot, Justin M. Calabrese, Carlos Carrapato, André Chiaradia, Lisa C. Davenport, Sarah C. Davidson, Mark Desholm, Christopher R. DeSorbo, Robert Domenech, Peter Enggist, William F. Fagan, Nina Farwig, Wolfgang Fiedler, Christen H. Fleming, Alastair Franke, John M. Fryxell, Clara García-Ripollés … & João Paulo Silva
Aim: Animal movement is an important determinant of individual survival, population dynamics, and ecosystem structure and function. Yet it is still unclear how local movements are related to resource availability and the spatial arrangement of resources. Using resident bird species and migratory bird species outside of the migratory period, we examined how the distribution of resources affect the movement patterns of both large terrestrial birds (e.g., raptors, bustards, hornbills) and waterbirds (e.g., cranes, storks, ducks,...

Data from: The evolutionary history of Darwin's finches: speciation, gene flow, and introgression in a fragmented landscape

Heather L. Farrington, Lucinda P. Lawson, Courtney M. Clark & Kenneth Petren
Many classic examples of adaptive radiations take place within fragmented systems such as islands or mountains, but the roles of mosaic landscapes and variable gene flow in facilitating species diversification is poorly understood. Here we combine phylogenetic and landscape genetic approaches to understand diversification in Darwin's finches, a model adaptive radiation. We combined sequence data from 14 nuclear introns, mitochondrial markers, and microsatellite variation from 51 populations of all 15 recognized species. Phylogenetic species-trees recovered...

Data from: Convergence of multiple markers and analysis methods defines the genetic distinctiveness of cryptic pitvipers

, Roger S. Thorpe, Simon Creer, Delphine Lallias, Louise Dawnay, Bryan L. Stuart, Anita Malhotra, &
Using multiple markers and multiple analytical approaches is critical for establishing species boundaries reliably, especially so in the case of cryptic species. Despite development of new and powerful analytical methods, most studies continue to adopt a few, with the choice often being subjective. One such example is routine analysis of Amplified Fragment Length Polymorphism (AFLP) data using population genetic models despite disparity between method assumptions and data properties. The application of newly developed methods for...

An integrative phylogenomic approach illuminates the evolutionary history of Old World tree frogs (Anura: Rhacophoridae)

Jinmin Chen, Elizabeth Prendini, Yun-He Wu, Bao-Lin Zhang, Chatmongkon Suwannapoom, Hong-Man Chen, Jie-Qiong Jin, Emily Moriarty Lemmon, Alan R. Lemmon, Bryan L. Stuart, Christopher J. Raxworthy, Robert W. Murphy, Zhi-Yong Yuan & Jing Che
Rhacophoridae is one of the most speciose and ecologically diverse families of amphibians. Resolution of its evolutionary relationships is key to understanding the accumulation of biodiversity, yet previous hypotheses based on Sanger sequencing exhibit much discordance amongst generic relationships. This conflict precludes the making of sound macroevolutionary conclusions. Herein, we conduct the first phylogenomic study using broad-scale sampling and sequences of 352 nuclear DNA loci obtained using anchored hybrid enrichment targeted sequencing. The robust time-calibrated...

Data from: High genomic diversity and candidate genes under selection associated with range expansion in eastern coyote (Canis latrans) populations

Elizabeth Heppenheimer, Kristin E. Brzeski, Joseph W. Hinton, Brent R. Patterson, Linda Y. Rutledge, Alexandra L. DeCandia, Tyler Wheeldon, Steven R. Fain, Paul A. Hohenlohe, Roland Kays, Bradley N. White, Michael J. Chamberlain & Bridgett M. VonHoldt
Range expansion is a widespread biological process, with well described theoretical expectations for the genomic outcomes accompanying the colonization of novel ranges. However, comparatively few empirical studies address the genome-wide consequences associated with the range expansion process, particularly in recent or on-going expansions. Here, we assess two recent and distinct eastward expansion fronts of a highly mobile carnivore, the coyote (Canis latrans), to investigate patterns of genomic diversity and identify variants that may have been...

Data from: Does the house sparrow Passer domesticus represent a global model species for egg rejection behavior?

Thomas Manna, Caren Cooper, Shane Baylis, Matthew D. Shawkey, Geoffrey I. N. Waterhouse, Tomas Grim & Mark E. Hauber
Conspecific brood parasitism (CP) is a facultative breeding tactic whereby females lay their eggs in the nests of conspecifics. In some species, potential host individuals have evolved the ability to identify and reject foreign eggs from their nest. Previous studies suggest that the ubiquitous House Sparrow Passer domesticus in Spain and South Africa employs both CP and parasitic egg rejection, while a population in China does not. Given the species’ invasive range expansions, the House...

Data from: A phylogeny of the treehopper subfamily Heteronotinae reveals convergent pronotal traits (Hemiptera: Auchenorrhyncha: Membracidae)

Olivia Evangelista, Albino M. Sakakibara, Jason R. Cryan & Julie M. Urban
Even within an insect family famous for its morphological diversity, the treehopper subfamily Heteronotinae is a microcosm of pronotal variation, displaying remarkably dissimilar thoracic ornamentations among its ten included genera. Presented here is a reconstruction of heteronotine relationships based on DNA nucleotide sequence data from five nuclear and two mitochondrial genes from a comprehensive sample of ingroup taxa (including exemplars of all genera except for the monotypic Dysyncritus Fowler, 1895). Concordant phylogenetic estimates support the...

Data from: A jungle in there: bacteria in belly buttons are highly diverse, but predictable

Jiri Hulcr, Andrew M. Latimer, Jessica B. Henley, Nina R. Rountree, Noah Fierer, Andrea Lucky, Margaret D. Lowman & Robert R. Dunn
The belly button is one of the habitats closest to us, and yet it remains relatively unexplored. We analyzed bacteria and arachaea from the belly buttons of humans from two different populations sampled within a nation-wide citizen science project. We examined bacterial and archaeal phylotypes present and their diversity using multiplex pyrosequencing of 16S rDNA libraries. We then tested the oligarchy hypothesis borrowed from tropical macroecology, namely that the frequency of phylotypes in one sample...

Data from: Diversity change during the rise of tetrapods and the impact of the ‘Carboniferous rainforest collapse’

Emma M. Dunne, Roger A. Close, David J. Button, Neil Brocklehurst, Daniel D. Cashmore, Graeme T. Lloyd & Richard J. Butler
The Carboniferous and early Permian were critical intervals in the diversification of early four-limbed vertebrates (tetrapods), yet the major patterns of diversity and biogeography during this time remain unresolved. Previous estimates suggest that global tetrapod diversity rose continuously across this interval and that habitat fragmentation following the ‘Carboniferous rainforest collapse’ (CRC) drove increased endemism among communities. However, previous work failed to adequately account for spatial and temporal biases in sampling. Here, we reassess early tetrapod...

Data from: Mapping the expansion of coyotes (Canis latrans) across North and Central America

James W. Hody & Roland Kays
The geographic distribution of coyotes (Canis latrans) has dramatically expanded since 1900, spreading across much of North America in a period when most other mammal species have been declining. Although this considerable expansion has been well documented at the state/provincial scale, continent-wide descriptions of coyote spread have portrayed conflicting distributions for coyotes prior to the 1900s, with popularly referenced anecdotal accounts showing them restricted to the great plains, and more obscure, but data-rich accounts suggesting...

Data from: Eyes wide shut: the impact of dim-light vision on neural investment in marine teleosts

Teresa L. Iglesias, Alex Dornburg, Dan L. Warren, Peter C. Wainwright, Lars Schmitz & Evan P. Economo
Understanding how organismal design evolves in response to environmental challenges is a central goal of evolutionary biology. In particular, assessing the extent to which environmental requirements drive general design features among distantly related groups is a major research question. The visual system is a critical sensory apparatus that evolves in response to changing light regimes. In vertebrates, the optic tectum is the primary visual processing center of the brain, and yet it is unclear how,...

Data from: A multispecies occupancy model for two or more interacting species

Christopher T. Rota, Marco A. R. Ferreira, Roland W. Kays, Tavis D. Forrester, Elizabeth L. Kalies, William J. McShea, Arielle W. Parsons & Joshua J. Millspaugh
Species occurrence is influenced by environmental conditions and the presence of other species. Current approaches for multispecies occupancy modelling are practically limited to two interacting species and often require the assumption of asymmetric interactions. We propose a multispecies occupancy model that can accommodate two or more interacting species. We generalize the single-species occupancy model to two or more interacting species by assuming the latent occupancy state is a multivariate Bernoulli random variable. We propose modelling...

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