459 Works

Data from: Species-specific responses to island connectivity cycles: refined models for testing phylogeographic concordance across a Mediterranean Pleistocene Aggregate Island complex

Anna Papadopoulou & L. Lacey Knowles
The contribution of Pleistocene sea level changes to diversification patterns in archipelagos around the world, and specifically whether the repeated cycles of island connectivity and isolation acted as a ‘species pump’ is debated. The debate has been perpetuated in part because of the type of evidence used to evaluate the species-pump hypothesis. Specifically, existing tests of the ‘Pleistocene Aggregate Island Complex’ (PAIC) model of diversification interpret the lack of concordant divergence times among multiple codistributed...

Data from: Synopsis and taxonomic revision of three genera in the snake tribe Sonorini

Christian L. Cox, Alison R. Davis Rabosky, Iris A. Holmes, Jacobo Reyes-Velasco, Corey E. Roelke, Eric N. Smith, Oscar Flores-Villel, Jimmy A. McGuire & Jonathan A. Campbell
Delimiting species is a crucial goal of integrative biology, and yet can be misled by homoplasy and high levels of morphological variation. The snake tribe Sonorini contains three genera that have long confounded taxonomists: Chilomeniscus, Chionactis and Sonora. Dynamic colour evolution in this group, including rampant geographic variation in colour and colour polymorphism, has led to a chaotic taxonomy. We used mitochondrial and high-throughput nuclear data (ddRADseq) and complete taxonomic sampling of each genus to...

Data from: Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants

Stephen A. Smith, Ya Yang, Joseph W. Brown & Michael J. Moore
Background: The use of transcriptomic and genomic datasets for phylogenetic reconstruction has become increasingly common as researchers attempt to resolve recalcitrant nodes with increasing amounts of data. The large size and complexity of these datasets introduce significant phylogenetic noise and conflict into subsequent analyses. The sources of conflict may include hybridization, incomplete lineage sorting, or horizontal gene transfer, and may vary across the phylogeny. For phylogenetic analysis, this noise and conflict has been accommodated in...

Data from: A robust semi-parametric test for detecting trait-dependent diversification

Daniel L. Rabosky & Huateng Huang
Rates of species diversification vary widely across the tree of life and there is considerable interest in identifying organismal traits that correlate with rates of speciation and extinction. However, it has been challenging to develop methodological frameworks for testing hypotheses about trait-dependent diversification that are robust to phylogenetic pseudoreplication and to directionally biased rates of character change. We describe a semi-parametric test for trait-dependent diversification that explicitly requires replicated associations between character states and diversification...

Data from: Human birth seasonality: latitudinal gradient and interplay with childhood disease dynamics

M. Martinez-Bakker, K. M. Bakker, A. A. King & P. Rohani
More than a century of ecological studies have demonstrated the importance of demography in shaping spatial and temporal variation in population dynamics. Surprisingly, the impact of seasonal recruitment on infectious disease systems has received much less attention. Here, we present data encompassing 78 years of monthly natality in the USA, and reveal pronounced seasonality in birth rates, with geographical and temporal variation in both the peak birth timing and amplitude. The timing of annual birth...

Data from: BAMM at the court of false equivalency: a response to Meyer and Wiens

Daniel L. Rabosky
The software program BAMM has been widely used to study rates of speciation, extinction, and phenotypic evolution on phylogenetic trees. The program implements a model-based clustering algorithm to identify clades that share common macroevolutionary rate dynamics and to estimate parameters. A recent simulation study by Meyer and Wiens (M&W) claimed that (i) a simple inference framework ("MS") performs much better than BAMM, and (ii) evolutionary rates inferred with BAMM are poorly correlated with true rates....

Data from: Differential changes in bone strength of two inbred mouse strains following administration of a sclerostin-neutralizing antibody during growth

Noah J. Mathis, Emily N. Adaniya, Lauren M. Smith, Alexander G. Robling, Karl J. Jepsen & Stephen H. Schlecht
Administration of sclerostin-neutralizing antibody (Scl-Ab) treatment has been shown to elicit an anabolic bone response in growing and adult mice. Prior work characterized the response of individual mouse strains but did not establish whether the impact of Scl-Ab on whole bone strength would vary across different inbred mouse strains. Herein, we tested the hypothesis that two inbred mouse strains (A/J and C57BL/6J (B6)) will show different whole bone strength outcomes following sclerostin-neutralizing antibody (Scl-Ab) treatment...

Data from: Nocturnal flight-calling behaviour predicts vulnerability to artificial light in migratory birds

Benjamin M. Winger, Brian C. Weeks, Andrew Farnsworth, Andrew W. Jones, Mary Hennen & David E. Willard
Understanding interactions between biota and the built environment is increasingly important as human modification of the landscape expands in extent and intensity. For migratory birds, collisions with lighted structures are a major cause of mortality, but the mechanisms behind these collisions are poorly understood. Using 40 years of collision records of passerine birds, we investigated the importance of species’ behavioral ecologies in predicting rates of building collisions during nocturnal migration through Chicago, IL and Cleveland,...

Data from: Automatic detection of key innovations, rate shifts, and diversity-dependence on phylogenetic trees

Daniel L. Rabosky
A number of methods have been developed to infer differential rates of species diversification through time and among clades using time-calibrated phylogenetic trees. However, we lack a general framework that can delineate and quantify heterogeneous mixtures of dynamic processes within single phylogenies. I developed a method that can identify arbitrary numbers of time-varying diversification processes on phylogenies without specifying their locations in advance. The method uses reversible-jump Markov Chain Monte Carlo to move between model...

Data from: The implications of stratigraphic compatibility for character integration among fossil taxa

Peter J. Wagner & George F. Estabrook
Two characters are stratigraphically compatible if some phylogenies indicate that their combinations (state-pairs) evolved without homoplasy and in an order consistent with the fossil record. Simulations assuming independent character change indicate that we expect approximately 95% of compatible character pairs to also be stratigraphically compatible over a wide range of sampling regimes and general evolutionary models. However, two general models of rate heterogeneity elevate expected stratigraphic incompatibility: “early burst” models, where rates of change are...

Data from: Sex difference in prevalence of depression after stroke

Liming Dong, Brisa N. Sanchez, Lesli E. Skolarus, Eric Stulberg, Lewis B. Morgenstern & Lynda D. Lisabeth
Objective: This study investigated the sex difference in prevalence of depression at 90 days after first-ever stroke. Methods: Patients with first-ever stroke (n = 786) were identified from the population-based Brain Attack Surveillance in Corpus Christi project (2011–2016). Poststroke depressive symptoms were assessed by the 8-itemPatient Health Questionnaire, and prestroke depression status (history and medication use) was self-reported. Logistic regression was used to examine the association between sex and depression after stroke, and effect modification...

A Paleocene (Danian) marine osteoglossid (Teleostei, Osteoglossomorpha) from the Nuussuaq Basin of Greenland, with a brief review of Palaeogene marine bonytongue fishes

Alessio Capobianco, Ethan Foreman & Matt Friedman
The early Palaeogene represents a key interval in the evolution of modern marine fish faunas. Together with the first appearances of many familiar fish lineages characteristic of contemporary marine environments, early Palaeogene marine deposits worldwide feature the occurrence of osteoglossid bonytongues. Their presence in marine rocks is surprising, as these fishes are strictly associated with freshwater environments in modern settings and other parts of the fossil record. Despite its possible relevance to faunal recovery after...

Data from: Phylogeny, ancestors, and anagenesis in the hominin fossil record

Caroline Parins-Fukuchi, Elliot Greiner, Laura M. MacLatchy & Daniel C. Fisher
Probabilistic approaches to phylogenetic inference have recently gained traction in paleontological studies. Because they directly model processes of evolutionary change, probabilistic methods facilitate a deeper assessment of variability in evolutionary patterns by weighing evidence for competing models. Although phylogenetic methods used in paleontological studies have generally assumed that evolution proceeds by splitting cladogenesis, extensions to previous models help explore the potential for morphological and temporal data to provide differential support for contrasting modes of evolutionary...

Data from: Genomic tests of the species-pump hypothesis: recent island connectivity cycles drive population divergence but not speciation in Caribbean crickets across the Virgin Islands

Anna Papadopoulou & L. Lacey Knowles
Harnessing the power of genomic scans, we test the debated ‘species pump’ hypothesis that implicates repeated cycles of island connectivity and isolation as drivers of divergence. This question has gone understudied given the limited resolution of past molecular markers for studying such dynamic phenomena. With an average of 32000 SNPs from the genome of 136 individuals from ten populations of a Caribbean flightless ground cricket species (Amphiacusta sanctaecrucis) and a complementary set of statistical approaches,...

Data from: Heterochrony in chimpanzee and bonobo spatial memory development

Alexandra G. Rosati
Objectives: The emergence of human-unique cognitive abilities has been linked to our species' extended juvenile period. Comparisons of cognitive development across species can provide new insights into the evolutionary mechanisms shaping cognition. This study examined the development of different components of spatial memory, cognitive mechanisms that support complex foraging, by comparing two species with similar life history that vary in wild ecology: bonobos (Pan paniscus) and chimpanzees (Pan troglodytes). Materials and methods: Spatial memory development...

Data from: Flexible gaze-following in rhesus monkeys

Rosemary Bettle & Alexandra G. Rosati
Humans are characterized by complex social cognitive abilities that emerge early in development. Comparative studies of nonhuman primates can illuminate the evolutionary history of these social capacities. We examined the cognitive skills that rhesus monkeys (Macaca mulatta) use to follow gaze, a foundational skill in human social development. While rhesus monkeys can make inferences about others’ gaze when competing, it is unclear how they think about gaze information in other contexts. In study 1, monkeys...

Data from: Crop pests and predators exhibit inconsistent responses to surrounding landscape composition

Daniel S. Karp, Rebecca Chaplin-Kramer, Timothy D. Meehan, Emily A. Martin, Fabrice DeClerck, Heather Grab, Claudio Gratton, Lauren Hunt, Ashley E. Larsen, Alejandra Martínez-Salinas, Megan E. O’Rourke, Adrien Rusch, Katja Poveda, Mattias Jonsson, Jay A. Rosenheim, Nancy A. Schellhorn, Teja Tscharntke, Stephen D. Wratten, Wei Zhang, Aaron L. Iverson, Lynn S. Adler, Matthias Albrecht, Audrey Alignier, Gina M. Angelella, Muhammad Zubair Anjum … & Yi Zou
The idea that noncrop habitat enhances pest control and represents a win–win opportunity to conserve biodiversity and bolster yields has emerged as an agroecological paradigm. However, while noncrop habitat in landscapes surrounding farms sometimes benefits pest predators, natural enemy responses remain heterogeneous across studies and effects on pests are inconclusive. The observed heterogeneity in species responses to noncrop habitat may be biological in origin or could result from variation in how habitat and biocontrol are...

Data from: The relative contribution of natural landscapes and human-mediated factors on the connectivity of a noxious invasive weed

Diego F. Alvarado-Serrano, Megan L. Van Etten, Shu-Mei Chang & Regina S. Baucom
Examining how the landscape may influence gene flow is at the forefront of understanding population differentiation and adaptation. Such understanding is crucial in light of ongoing environmental changes and the elevated risk of ecosystems alteration. In particular, knowledge of how humans may influence population structure is imperative to allow for informed decisions in management and conservation as well as to gain a better understanding of anthropogenic impacts on the interplay between gene flow, genetic drift...

Data from: Habitat corridors facilitate genetic resilience irrespective of species dispersal abilities or population sizes

Mark R. Christie & L. Lacey Knowles
Corridors are frequently proposed to connect patches of habitat that have become isolated due to human-mediated alterations to the landscape. While it is understood that corridors can facilitate dispersal between patches, it remains unknown whether corridors can mitigate the negative genetic effects for entire communities modified by habitat fragmentation. These negative genetic effects, which include reduced genetic diversity, limit the potential for populations to respond to selective agents such as disease epidemics and global climate...

Data from: Evolutionary bursts in Euphorbia (Euphorbiaceae) are linked with photosynthetic pathway

James W. Horn, Zhenxiang Xi, Ricarda Riina, Jess A. Peirson, Ya Yang, Brian L. Dorsey, Paul E. Berry, Charles C. Davis & Kenneth J. Wurdack
The mid-Cenozoic decline of atmospheric CO2 levels that promoted global climate change was critical to shaping contemporary arid ecosystems. Within angiosperms, two CO2-concentrating mechanisms (CCMs)—CAM and C4—evolved from the C3 photosynthetic pathway, enabling more efficient whole-plant function in such environments. Many angiosperm clades with CCMs are thought to have diversified rapidly due to Miocene aridification, but links between this climate change, CCM evolution, and increased net diversification rates (r) remain to be further understood. Euphorbia...

Public health and economic benefits of spotted hyenas (Crocuta crocuta) in a peri-urban system

Chinmay Sonawane, Gidey Yirga & Neil Carter
Species that depend on anthropogenic waste for food can remove pathogens that pose health risks to humans and livestock, thereby saving lives and money. Quantifying these benefits is rare, yet can lead to innovative conservation solutions. To assess these benefits, we examined the feeding ecology and population size of peri-urban spotted hyenas (Crocuta crocuta) in Mekelle, Ethiopia. We integrated these field data into a disease transmission model to predict: a) the number of anthrax and...

Dataset from: Predation as an explanation for a latitudinal gradient in arm number among featherstars

James Saulsbury & Tomasz Baumiller
Aim: The role of biotic interactions in generating broad patterns in organismal phenotypes is a central question in macroecology. We investigate global patterns in feeding morphology among featherstars, a globally widespread group of suspension-feeding echinoderms whose evolutionary history has been demonstrably shaped by predators. Location: World's oceans. Major taxon studied: Crinoidea. Methods: We tested for global patterns in the featherstar suspension feeding apparatus, a filter made up of five to 200 arms which is the...

Data from: Body temperature, heart rate, and activity patterns of two boreal homeotherms in winter: homeostasis, allostasis, and ecological coexistence

Allyson Menzies, Emily Studd, Yasmine Majchrzak, Michael Peers, Stan Boutin, Ben Dantzer, Jeffrey Lane, Andrew McAdam & Murray Humphries
Organisms survive environmental variation by combining homeostatic regulation of critical states with allostatic variation of other traits, and species differences in these responses can contribute to coexistence in temporally-variable environments. In this paper, we simultaneously record variation in three functional traits – body temperature (Tb), heart rate, and activity - in relation to three forms of environmental variation – air temperature (Ta), photoperiod, and experimentally-manipulated resource levels – in free-ranging snowshoe hares and North American...

Lack of phenological shift leads to increased camouflage mismatch in mountain hares

Marketa Zimova
Understanding whether organisms will be able to adapt to human-induced stressors currently endangering their existence is an urgent priority. Globally, multiple species moult from a dark summer to white winter coat to maintain camouflage against snowy landscapes. Decreasing snow cover duration due to climate change is increasing mismatch in seasonal camouflage. To directly test for adaptive responses to recent changes in snow cover, we repeated historical (1950s) field studies of moult phenology in mountain hares...

The oldest Devonian circumpolar ray-finned fish?

Rodrigo Figueroa, Luiz Carlos Weinschütz & Matthew Friedman
Actinopterygians (ray-finned fishes) are the most diverse group of living fishes, but have a sparse early fossil record restricted to low palaeolatitudes. Here we report a new actinopterygian from the Paraná Basin of Brazil, an area that occupied a circumpolar position in the Palaeozoic. Available geological evidence supports a Middle Devonian or older age for this taxon, which shares features of the mandibular symphysis with the latest Devonian Tegeolepis. A phylogenetic analysis resolves these two...

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