46 Works

Data from: Suitability of Laurentian Great Lakes for invasive species based on global species distribution models and local habitat

Andrew M. Kramer, Gust Annis, Marion E. Wittmann, William L. Chadderton, Edward S. Rutherford, David M. Lodge, Lacey Mason, Dmitry Beletsky, Catherine Riseng & John M. Drake
Efficient management and prevention of species invasions requires accurate prediction of where species of concern can arrive and persist. Species distribution models provide one way to identify potentially suitable habitat by developing the relationship between climate variables and species occurrence data. However, these models when applied to freshwater invasions are complicated by two factors. The first is that the range expansions that typically occur as part of the invasion process violate standard species distribution model...

Data from: Not all weeds are created equal: a database approach uncovers differences in the sexual system of native and introduced weeds

Megan L. Van Etten, Jeffrey K. Conner, Shu-Mei Chang & Regina S. Baucom
Weedy species provide excellent opportunities to examine the process of successful colonization of novel environments. Despite the influence of the sexual system on a variety of processes from reproduction to genetic structure, how the sexual system of species influences weediness has received only limited consideration. We examined the hypothesis that weedy plants have an increased likelihood of being self-compatible compared with nonweedy plants; this hypothesis is derived from Baker's law, which states that species that...

Data from: History cleans up messes: the impact of time in driving divergence and introgression in a tropical suture zone

Sonal Singhal & Ke Bi
Contact zones provide an excellent arena in which to address questions about how genomic divergence evolves during lineage divergence. They allow us to both infer patterns of genomic divergence in allopatric populations isolated from introgression and to characterize patterns of introgression after lineages meet. Thusly motivated, we analyze genome-wide introgression data from four contact zones in three genera of lizards endemic to the Australian Wet Tropics. These contact zones all formed between morphologically cryptic lineage-pairs...

Data from: Widespread paleopolyploidy, gene tree conflict, and recalcitrant relationships among the carnivorous Caryophyllales

Joseph F. Walker, Ya Yang, Moore J. Michael, Jessica Mikenas, Alfonso Timoneda, Samuel Frasier Brockington, Stephen Andrew Smith & Michael J. Moore
PREMISE OF STUDY: The carnivorous members of the large, hyperdiverse Caryophyllales (e.g., Venus flytrap, sundews, and Nepenthes pitcher plants) represent perhaps the oldest and most diverse lineage of carnivorous plants. However, despite numerous studies seeking to elucidate their evolutionary relationships, the early-diverging relationships remain unresolved. METHODS: To explore the utility of phylogenomic data sets for resolving relationships among the carnivorous Caryophyllales, we sequenced 10 transcriptomes, including all the carnivorous genera except those in the rare...

Data from: Genetic diversity is largely unpredictable but scales with museum occurrences in a species-rich clade of Australian lizards

Sonal Singhal, Huateng Huang, Pascal O. Title, Stephen C. Donnellan, Iris Holmes & Daniel L. Rabosky
Genetic diversity is a fundamental characteristic of species and is affected by many factors, including mutation rate, population size, life history and demography. To better understand the processes that influence levels of genetic diversity across taxa, we collected genome-wide restriction-associated DNA data from more than 500 individuals spanning 76 nominal species of Australian scincid lizards in the genus Ctenotus. To avoid potential biases associated with variation in taxonomic practice across the group, we used coalescent-based...

Data from: A nutrient mediates intraspecific competition between rodent malaria parasites in vivo

Nina Wale, Derek G. Sim & Andrew F. Read
Hosts are often infected with multiple strains of a single parasite species. Within-host competition between parasite strains can be intense and has implications for the evolution of traits that impact patient health, such as drug resistance and virulence. Yet the mechanistic basis of within-host competition is poorly understood. Here, we demonstrate that a parasite nutrient, para-aminobenzoic acid (pABA), mediates competition between a drug resistant and drug susceptible strain of the malaria parasite, Plasmodium chabaudi. We...

Data from: Experimental small-scale flower patches increase species density but not abundance of small urban bees

Maria-Carolina M. Simao, Jill Matthijs & Ivette Perfecto
1. Large flower plantings are often used to combat negative effects of habitat loss on pollinators, but whether these floral additions are effective at smaller scales remains unclear, particularly in urban settings. 2. To test the effectiveness of small-scale floral additions on enhancing urban bee populations, as well as their impact from one year to the next, different quantities of potted sweet alyssum (Lobularia maritima) flowers were placed across sites in Ann Arbor, Michigan for...

Data from: Spinosity, regeneration, and targeting among Paleozoic crinoids and their predators

Valerie J.P. Syverson, Carlton E. Brett, Forest J. Gahn & Tomasz K. Baumiller
Evolving interactions between predators and prey constitute one of the major adaptive influences on marine animals during the Paleozoic. Crinoids and fish constitute a predator-prey system that may date back to at least the Silurian, as suggested by patterns of crinoid regeneration and spinosity in concert with changes in the predatory fauna. Here we present data on the frequency of breakage and regeneration in the spines of the Middle Devonian camerate Gennaeocrinus and Late Paleozoic...

Data from: Structure of FlgK reveals the divergence of the bacterial hook-filament junction of Campylobacter

Paula V. Bulieris, Nausad H. Shaikh, Peter L. Freddolino & Fadel A. Samatey
Evolution of a nano-machine consisting of multiple parts, each with a specific function, is a complex process. A change in one part should eventually result in changes in other parts, if the overall function is to be conserved. In bacterial flagella, the filament and the hook have distinct functions and their respective proteins, FliC and FlgE, have different three-dimensional structures. The filament functions as a helical propeller and the hook as a flexible universal joint....

Data from: Divergence of thermal physiological traits in terrestrial breeding frogs along a tropical elevational gradient

Rudolf Von May, Alessandro Catenazzi, Ammon Corl, Roy Santa-Cruz, Ana Carolina Carnaval & Craig Moritz
Critical thermal limits are thought to be correlated with the elevational distribution of species living in tropical montane regions, but with upper limits being relatively invariant compared to lower limits. To test this hypothesis, we examined the variation of thermal physiological traits in a group of terrestrial breeding frogs (Craugastoridae) distributed along a tropical elevational gradient. We measured the critical thermal maximum (CTmax; n = 22 species) and critical thermal minimum (CTmin; n = 14...

Data from: Stream nitrogen concentration, but not plant N-fixing capacity, modulates litter diversity effects on decomposition

Alan M. Tonin, Luz Boyero, Silvia Monroy, Ana Basaguren, Javier Perez, Richard G. Pearson, Bradley J. Cardinale, & Jesus Pozo
1. We are facing major biodiversity loss and there is evidence that such loss can alter ecosystem functioning. However, the effects of plant diversity on decomposition – a key component of the global carbon cycle – are still unclear. A recent study suggested that a plant trait – their nitrogen (N)-fixing capacity – could mediate effects of litter diversity on decomposition by means of a microbial transfer of N from N-fixers to non-fixers. 2. We...

Data from: Minimum sample sizes for population genomics: an empirical study from an Amazonian plant species

Alison G. Nazareno, Jordan B. Bemmels, Christopher W. Dick & Lúcia G. Lohmann
High throughput DNA sequencing facilitates the analysis of large portions of the genome in non-model organisms, ensuring high accuracy of population genetic parameters. However, empirical studies evaluating the appropriate sample size for these kinds of studies are still scarce. In this study, we use double digest restriction associated DNA sequencing (ddRADseq) to recover thousands of single nucleotide polymorphisms (SNPs) for two physically isolated populations of Amphirrhox longifolia (Violaceae), a non-model plant species for which no...

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: 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: 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: 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: 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: 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: 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: 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: 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: 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...

Registration Year

  • 2017

Resource Types

  • Dataset


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