46 Works

Data from: Safari science: assessing the reliability of citizen science data for wildlife surveys

Cara Steger, Bilal Butt & Mevin B. Hooten
1. Protected areas are the cornerstone of global conservation, yet financial support for basic monitoring infrastructure is lacking in 60% of them. Citizen science holds potential to address these shortcomings in wildlife monitoring, particularly for resource-limited conservation initiatives in developing countries - if we can account for the reliability of data produced by volunteer citizen scientists (VCS) . 2. This study tests the reliability of VCS data vs. data produced by trained ecologists, presenting a...

Data from: Group augmentation, collective action, and territorial boundary patrols by male chimpanzees

Kevin E. Langergraber, David P. Watts, Linda Vigilant & John C. Mitani
How can collective action evolve when individuals benefit from cooperation regardless of whether they pay its participation costs? According to one influential perspective, collective action problems are common, especially when groups are large, but may be solved when individuals who have more to gain from the collective good or can produce it at low costs provide it to others as a byproduct. Several results from a 20-y study of one of the most striking examples...

Data from: Anthropogenic N deposition increases soil C storage by reducing the relative abundance of lignolytic fungi

Elizabeth M. Entwistle, Donald R. Zak & William A. Argiroff
Atmospheric nitrogen (N) deposition has increased dramatically since preindustrial times and continues to increase across many regions of the Earth. In temperate forests, this agent of global change has increased soil carbon (C) storage, but the mechanisms underlying this response are not understood. One long-standing hypothesis proposed to explain the accumulation of soil C proposes that higher inorganic N availability may suppress both the activity and abundance of fungi which decay lignin and other polyphenols...

Data from: The past sure is tense: on interpreting phylogenetic divergence time estimates

Joseph W. Brown & Stephen A. Smith
Divergence time estimation — the calibration of a phylogeny to geological time — is an integral first step in modelling the tempo of biological evolution (traits and lineages). However, despite increasingly sophisticated methods to infer divergence times from molecular genetic sequences, the estimated age of many nodes across the tree of life contrast significantly and consistently with timeframes conveyed by the fossil record. This is perhaps best exemplified by crown angiosperms, where molecular clock (Triassic)...

Data from: Genomic analysis of a cardinalfish with larval homing potential reveals genetic admixture in the Okinawa Islands

Alison L. Gould & Paul V. Dunlap
Discrepancies between potential and observed dispersal distances of reef fish indicate the need for a better understanding of the influence of larval behaviour on recruitment and dispersal. Population genetic studies can provide insight on the degree to which populations are connected, and the development of restriction site-associated sequencing (RAD-Seq) methods has made such studies of nonmodel organisms more accessible. We applied double-digest RAD-Seq methods to test for population differentiation in the coral reef-dwelling cardinalfish, Siphamia...

Data from: Squamate Conserved Loci (SqCL): a unified set of conserved loci for phylogenomics and population genetics of squamate reptiles

Sonal Singhal, Maggie Grundler, Guarino Colli & Daniel L. Rabosky
The identification of conserved loci across genomes, along with advances in target capture methods and high-throughput sequencing, has helped spur a phylogenomics revolution by enabling researchers to gather large numbers of homologous loci across clades of interest with minimal upfront investment in locus design. Target capture for vertebrate animals is currently dominated by two approaches – anchored hybrid enrichment (AHE) and ultraconserved elements (UCE) – and both approaches have proven useful for addressing questions in...

Data from: Consequences of divergence and introgression for speciation in Andean cloud forest birds

Benjamin M. Winger
Divergence with gene flow is well documented and reveals the influence of ecological adaptation on speciation. Yet it remains intuitive that gene exchange inhibits speciation in many scenarios, particularly among ecologically similar populations. The influence of gene flow on the divergence of populations facing similar selection pressures has received less empirical attention than scenarios where differentiation is coupled with local environmental adaptation. I used a paired study design to test the influence of genomic divergence...

Data from: Heritable variation in colour patterns mediating individual recognition

Michael J. Sheehan, Juanita Choo & Elizabeth A. Tibbetts
Understanding the developmental and evolutionary processes that generate and maintain variation in natural populations remains a major challenge for modern biology. Populations of Polistes fuscatus paper wasps have highly variable colour patterns that mediate individual recognition. Previous experimental and comparative studies have provided evidence that colour pattern diversity is the result of selection for individuals to advertise their identity. Distinctive identity-signalling phenotypes facilitate recognition, which reduces aggression between familiar individuals in P. fuscatus wasps. Selection...

Data from: Ecological interactions and coexistence are predicted by gene expression similarity in freshwater green algae

Anita Narwani, Bastian Bentlage, Markos A. Alexandrou, Keith J. Fritschie, Charles Delwiche, Todd H. Oakley & Bradley J. Cardinale
Phenotypic variation controls the species interactions which determine whether or not species coexist. Long-standing hypotheses in ecology and evolution posit that phenotypic differentiation enables coexistence by increasing the size of niche differentiation. This hypothesis has only been tested using macroscopic traits to date, but niche differentiation, particularly of microscopic organisms, also occurs at the molecular and metabolic level. We examined how phenotypic variation that arises at the level of gene expression over evolutionary time affects...

Data from: Rapid evolution rescues hosts from competition and disease but—despite a dilution effect—increases the density of infected hosts

Alexander T. Strauss, Jessica L. Hite, Marta S. Shocket, Carla E. Cáceres, Meghan A. Duffy & Spencer R. Hall
Virulent parasites can depress the densities of their hosts. Taxa that reduce disease via dilution effects might alleviate this burden. However, ‘diluter’ taxa can also depress host densities through competition for shared resources. The combination of disease and interspecific competition could even drive hosts extinct. Then again, genetically variable host populations can evolve in response to both competitors and parasites. Can rapid evolution rescue host density from the harm caused by these ecological enemies? How...

Data from: Infectious disease dynamics inferred from genetic data via sequential Monte Carlo

R. A. Smith, E. L. Ionides, A. A. King, R.A. Smith & E.L. Ionides
Genetic sequences from pathogens can provide information about infectious disease dynamics that may supplement or replace information from other epidemiological observations. Most currently available methods first estimate phylogenetic trees from sequence data, then estimate a transmission model conditional on these phylogenies. Outside limited classes of models, existing methods are unable to enforce logical consistency between the model of transmission and that underlying the phylogenetic reconstruction. Such conflicts in assumptions can lead to bias in the...

Data from: Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high-Andean diversification (Asteraceae: Astereae: Diplostephium)

Oscar M. Vargas, Edgardo M. Ortiz & Beryl B. Simpson
High-throughput sequencing is helping biologists to overcome the difficulties of inferring the phylogenies of recently diverged taxa. The present study analyzes the phylogenetic signal of genomic regions with different inheritance patterns using genome skimming and ddRAD-seq in a species-rich Andean genus (Diplostephium) and its allies. We analyzed the complete nuclear ribosomal cistron, the complete chloroplast genome, a partial mitochondrial genome, and a nuclear-ddRAD matrix separately with phylogenetic methods. We applied several approaches to understand the...

Data from: Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events

Ya Yang, Michael J. Moore, Samuel F. Brockington, Jessica Mikenas, Julia Olivieri, Joseph F. Walker & Stephen A. Smith
• Studies of the macroevolutionary legacy of polyploidy are limited by an incomplete sampling of these events across the tree of life. To better locate and understand these events, we need comprehensive taxonomic sampling as well as homology inference methods that accurately reconstruct the frequency and location of gene duplications. • We assembled a dataset of transcriptomes and genomes from 169 species in Caryophyllales, of which 43 were newly generated for this study, representing one...

Data from: Lizards in pinstripes: morphological and genomic evidence for two new species of scincid lizards within Ctenotus piankai Storr and C. duricola Storr (Reptilia: Scincidae) in the Australian arid zone

Daniel L Rabosky, Paul Doughty & Huateng Huang
The scincid lizard genus Ctenotus is one of the most species-rich genera of squamate reptiles, but few molecular phylogenetic studies have been undertaken on the group. Here we assess molecular and morphological variation within C. piankai and C. duricola, an arid-adapted pair of nominate species characterized by a pattern of thin pale longitudinal lines on a dark background that occur primarily in the western deserts and Pilbara region of Australia. We sequenced mitochondrial DNA and...

Data from: Disparity, diversity, and duplications in the Caryophyllales

Stephen A. Smith, Joseph W. Brown, Ya Yang, Riva Bruenn, Chloe P. Drummond, Samuel F. Brockington, Joseph F. Walker, Noah Last, Norman A. Douglas & Michael J. Moore
The role played by whole genome duplication (WGD) in plant evolution is actively debated. WGDs have been associated with advantages such as superior colonization, various adaptations, and increased effective population size. However, the lack of a comprehensive mapping of WGDs within a major plant clade has led to uncertainty regarding the potential association of WGDs and higher diversification rates. Using seven chloroplast and nuclear ribosomal genes, we constructed a phylogeny of 5036 species of Caryophyllales,...

Data from: Inferring the geographic origin of a range expansion: latitudinal and longitudinal coordinates inferred from genomic data in an ABC framework with the program X-ORIGIN

Qixin He, Joyce R. Prado & Laura Lacey Knowles
Climatic or environmental change is not only driving distributional shifts in species today, but it has also caused distributions to expand and contract in the past. Inferences about the geographic locations of past populations, especially regions that served as refugia (i.e., source populations) and migratory routes are a challenging endeavor. Refugial areas may be evidenced from fossil records or regions of temporal stability inferred from ecological niche models. Genomic data offer an alternative and broadly...

Data from: Floral resource availability from groundcover promotes bee abundance in coffee agroecosystems

Kaleigh Fisher, David J. Gonthier, Katherine K. Ennis & Ivette Perfecto
Patterns of bee abundance and diversity across different spatial scales have received thorough research consideration. However, the impact of short and long term temporal resource availability on biodiversity has been less explored. This is highly relevant in tropical agricultural systems for pollinators, as many foraging periods of pollinators extend beyond flowering of any single crop species. In this study, we sought to understand how bee communities in tropical agroecosystems changed between seasons, and if short...

Data from: Bringing ecology blogging into the scientific fold: measuring reach and impact of science community blogs

Manu E. Saunders, Meghan A. Duffy, Stephen B. Heard, Margaret Kosmala, Simon R. Leather, Terrence P. McGlynn, Jeff Ollerton & Amy L. Parachnowitsch
The popularity of science blogging has increased in recent years, but the number of academic scientists who maintain regular blogs is limited. The role and impact of science communication blogs aimed at general audiences is often discussed, but the value of science community blogs aimed at the academic community has largely been overlooked. Here, we focus on our own experiences as bloggers to argue that science community blogs are valuable to the academic community. We...

Data from: Quantifying the similarity between genes and geography across Alaska's alpine small mammals

L. Lacey Knowles, Rob Massatti, Qixin He, Link E. Olson & Hayley C. Lanier
Aim: Quantitatively evaluate the similarity of genomic variation and geography in five different alpine small mammals in Alaska, and use this quantitative assessment of concordance as a framework for refining hypotheses about the processes structuring population genetic variation in either a species-specific or shared manner. Location: Alaska and adjacent north-western Canada. Methods: For each taxon we generated 3500–7500 single-nucleotide polymorphisms and applied a Procrustes analysis to find an optimal transformation that maximizes the similarity between...

Data from: Distributional shifts – not geographic isolation – as a probable driver of montane species divergence

L. Lacey Knowles, Robert Massatti & Rob Massatti
As biodiversity hotspots, montane regions have been a focus of research to understand the divergence process. Like their oceanic counterparts, the diversity of the “sky islands” might be ascribed to geographic isolation of mountaintops. However, because the sky islands, and especially those in northern latitudes, are subject to extreme climatic events such as the glacial cycles that drove both altitudinal and geographical shifts in species’ distributions, the dynamic colonization process is also a possible factor...

Data from: Making it last: storage time and temperature have differential impacts on metabolite profiles of airway samples from cystic fibrosis patients

Stephen Wandro, Lisa Carmody, Tara Gallagher, John J. LiPuma & Katrine Whiteson
Metabolites of human or microbial origin have the potential to be important biomarkers of disease state in cystic fibrosis (CF). Clinical sample collection and storage conditions may impact metabolite abundances with clinical relevance. We measured the change in metabolite composition based on untargeted gas chromatography mass spectrometry (GC-MS) when CF sputum samples were stored at either 4°C, -20°C, or -80°C with one or two freeze-thaw cycles. Daily time points were taken for one week and...

Data from: Is BAMM flawed? Theoretical and practical concerns in the analysis of multi-rate diversification models

Daniel L. Rabosky, Jonathan S. Mitchell & Jonathan Chang
BAMM (Bayesian Analysis of Macroevolutionary Mixtures) is a statistical framework that uses reversible jump MCMC to infer complex macroevolutionary dynamics of diversification and phenotypic evolution on phylogenetic trees. A recent article by Moore and coauthors (MEA) reported a number of theoretical and practical concerns with BAMM. Major claims from MEA are that (1) BAMM's likelihood function is incorrect, because it does not account for unobserved rate shifts; (2) the posterior distribution on the number of...

Data from: Reconstructing Asian faunal introductions to eastern Africa from multi-proxy biomolecular and archaeological datasets

Mary E. Prendergast, Michael Buckley, Alison Crowther, Heidi Eager, Laurent Frantz, Ophélie Lebrasseur, Rainer Hutterer, Ardern Hulme-Beaman, Wim Van Neer, Katerina Douka, Margaret-Ashley Veall, Eréndira M. Quintana Morales, Verena J. Schuenemann, Ella Reiter, Richard Allen, Evangelos A. Dimopoulos, Richard M. Helm, Ceri Shipton, Ogeto Mwebi, Christiane Denys, Mark C. Horton, Stephanie Wynne-Jones, Jeffrey Fleisher, Chantal Radimilahy, Henry Wright … & Mark Horton
Human-mediated biological exchange has had global social and ecological impacts. In sub-Saharan Africa, several domestic and commensal animals were introduced from Asia in the pre-modern period; however, the timing and nature of these introductions remain contentious. One model supports introduction to the eastern African coast after the mid-first millennium CE, while another posits introduction dating back to 3000 BCE. These distinct scenarios have implications for understanding the emergence of long-distance maritime connectivity, and the ecological...

Data from: FiSSE: A simple non-parametric test for the effects of a binary character on lineage diversification rates

Daniel L. Rabosky & Emma E. Goldberg
It is widely assumed that phenotypic traits can influence rates of speciation and extinction, and several statistical approaches have been used to test for correlations between character states and lineage diversification. Recent work suggests that model-based tests of state-dependent speciation and extinction are sensitive to model inadequacy and phylogenetic pseudoreplication. We describe a simple non-parametric statistical test ("FiSSE") to assess the effects of a binary character on lineage diversification rates. The method involves computing a...

Data from: Wide but not impermeable: Testing the riverine barrier hypothesis for an Amazonian plant species

Alison G. Nazareno, Christopher W. Dick & Lucia G. Lohmann
Wallace's riverine barrier hypothesis postulates that large rivers, such as the Amazon and its tributaries, reduce or prevent gene flow between populations on opposite banks, leading to allopatry and areas of species endemism occupying interfluvial regions. Several studies have shown that two major tributaries, Rio Branco and Rio Negro, are important barriers to gene flow for birds, amphibians and primates. No botanical studies have considered the potential role of the Rio Branco as a barrier,...

Registration Year

  • 2017
    46

Resource Types

  • Dataset
    46

Affiliations

  • University of Michigan-Ann Arbor
    46
  • University of Cambridge
    3
  • University of Minnesota
    3
  • University of California, Berkeley
    3
  • University of Sao Paulo
    3
  • Oberlin College
    3
  • University of California System
    2
  • University of Georgia
    2
  • University of Chicago
    2
  • Yale University
    2