150 Works

Data from: Phylogenomic delineation of Physcomitrium (Bryophyta: Funariaceae) based on targeted sequencing of nuclear exons and their flanking regions rejects the retention of Physcomitrella, Physcomitridium and Aphanorrhegma

Rafael Medina, Matthew G. Johnson, Yang Liu, Norman J. Wickett, A. Jonathan Shaw & Bernard Goffinet
Selection on spore dispersal mechanisms in mosses is thought to shape the transformation of the sporophyte. The majority of extant mosses develop a sporangium that dehisces through the loss of an operculum, and regulates spore release through the movement of articulate teeth, the peristome, lining the capsule mouth. Such complexity was acquired by the Mesozoic Era, but was lost in some groups during subsequent diversification events, challenging the resolution of the affinities for taxa with...

Trends and Transitions in 150 years of The American Naturalist

Daniel Bolnick, Vassiliki Smocovitis, Christopher Moore & Patricia Morse
The American Naturalist recently passed its sesquicentennial. Throughout this long history, it regularly encountered moments of introspection and debate over its goals, mission, identity and audience. Here, we chronicle the history of those debates and transitions at critical moments. The Naturalist began as a popular magazine for amateur naturalists in the late 1860’s. In the late 1870’s it transitioned to an increasingly academic journal for professional scientists, from all branches of the natural sciences. By...

Supporting data from: The distribution of leaf form among indigenous woody angiosperms in New Zealand

Tammo Reichgelt & William Lee
New Zealand’s woody indigenous eudicot flora comprises a variety of leaf shapes and features and occupies environments extending from subtropical to cold temperate climates. We used a dataset of over 300,000 occurrences of 557 indigenous woody eudicot species to investigate patterns and trends in the occurrence of six leaf features (leaf pubescence, leaf margin teeth, leaf size, leaf apex and base shape, and leaf length to width ratio) along critical climate gradients. Major climate variables...

Avian point-counts from Rhode Island and Connecticut used to test species distribution models

Valerie Steen, Morgan Tingley, Peter Paton & Chris Elphick
Spatial-biases are a common feature of presence-absence data from citizen scientists. Spatial thinning can mitigate errors in species distribution models (SDMs) that use these data. When detections or non-detections are rare, however, SDMs may suffer from class imbalance or low sample size of the minority (i.e. rarer) class. Poor predictions can result, the severity of which may vary by modeling technique. To explore the consequences of spatial bias and class imbalance in presence-absence data, we...

The amount of RNA editing sites in liverwort organellar genes is correlated with GC content and nuclear PPR protein diversity

Shanshan Dong, Chaoxian Zhao, Shouzhou Zhang, Hong Wu, Weixue Mu, Tong Wei, Na Li, Tao Wan, Huan Liu, Jie Cui, Ruiliang Zhu, Bernard Goffinet & Yang Liu
RNA editing occurs in the organellar mRNAs of all land plants but the marchantioid liverworts, making liverworts a perfect group for studying the evolution of RNA editing. Here we profiled the RNA editing of 42 exemplars spanning the ordinal phylogenetic diversity of liverworts, and screened for the nuclear-encoded PPR proteins in the transcriptome assemblies of these taxa. We identified 7,428 RNA editing sites in 128 organellar genes from 31 non-marchantioid liverwort species, and characterized 25,059...

Resource diversity promotes among-individual diet variation, but not genomic diversity, in lake stickleback

Daniel Bolnick & Kimberly Ballare
Many generalist species consist of specialized individuals that use different resources. This within-population niche variation can stabilize population and community dynamics. Consequently, ecologists wish to identify environmental settings that promote such variation. Theory predicts that environments with greater resource diversity favor ecological diversity (via disruptive selection or plasticity). Alternatively, niche variation might be a side-effect of neutral genomic diversity in larger populations. We tested these alternatives in a metapopulation of threespine stickleback. Stickleback consume benthic...

Data from: Mitochondrial phylogenomics of early land plants: mitigating the effects of saturation, compositional heterogeneity, and codon-usage bias

Yang Liu, Cymon J. Cox, Wei Wang & Bernard Goffinet
Phylogenetic analyses using concatenation of genomic-scale data have been seen as the panacea to resolving the incongruences among inferences from few or single genes. However, phylogenomics may also suffer from systematic errors, due to the, perhaps cumulative, effects of saturation, among-taxa compositional (GC content) heterogeneity, or codon-usage bias plaguing the individual nucleotide loci that are concatenated. Here we provide an example of how these factors affect the inferences of the phylogeny of early land plants...

Data from: Ancient horizontal gene transfer and the last common ancestors

Gregory P. Fournier, Cheryl P. Andam & Johann Peter Gogarten
Background: The genomic history of prokaryotic organismal lineages is marked by extensive non-vertical inheritance of genes, with horizontal gene transfer (HGT) between many groups of organisms at all taxonomic levels. These HGT events have played an essential role in the origin and distribution of biological innovations. Analyses of ancient gene families show that HGT existed in the distant past, even at the time of the organismal last universal common ancestor (LUCA). Most gene transfers originated...

Data from: Environmental gradients and the evolution of successional habitat specialization: a test case with 14 Neotropical forest sites

Susan G. Letcher, Jesse R. Lasky, Robin L. Chazdon, Natalia Norden, S. Joseph Wright, Jorge A. Meave, Eduardo A. Pérez-García, Rodrigo Muñoz, Eunice Romero-Pérez, Ana Andrade, José Luis Andrade, Patricia Balvanera, Justin M. Becknell, Tony V. Bentos, Radika Bhaskar, Frans Bongers, Vanessa Boukili, Pedro H. S. Brancalion, Ricardo G. César, Deborah A. Clark, David B. Clark, Dylan Craven, Alexander DeFrancesco, Juan M. Dupuy, Bryan Finegan … & G. Bruce Williamson
1. Successional gradients are ubiquitous in nature, yet few studies have systematically examined the evolutionary origins of taxa that specialize at different successional stages. Here we quantify successional habitat specialization in Neotropical forest trees and evaluate its evolutionary lability along a precipitation gradient. Theoretically, successional habitat specialization should be more evolutionarily conserved in wet forests than in dry forests due to more extreme microenvironmental differentiation between early and late successional stages in wet forest. 2....

Data from: Determining the advantages, costs, and trade-offs of a novel sodium channel mutation in the copepod Acartia hudsonica to paralytic shellfish toxins (PST)

Michael B. Finiguerra, David E. Avery, Hans G. Dam & Michael Finiguerra
The marine copepod Acartia hudsonica was shown to be adapted to dinoflagellate prey, Alexandrium fundyense, which produce paralytic shellfish toxins (PST). Adaptation to PSTs in other organisms is caused by a mutation in the sodium channel. Recently, a mutation in the sodium channel in A. hudsonica was found. In this study, we rigorously tested for advantages, costs, and trade-offs associated with the mutant isoform of A. hudsonica under toxic and non-toxic conditions. We combined fitness...

Data from: Population of origin and environment interact to determine oomycete infections in spotted salamander populations

Mark C. Urban, Louise A. Lewis, Karolina Fučíková & Alexis Cordone
Spatial variation in disease risk in wild populations can depend both on environmental and genetic factors. Understanding the various contributions of each factor requires experimental manipulation of both the environment and genetic composition of populations under natural field conditions. We first examined natural patterns of oomycete composition and infection in the eggs of 13 populations of the spotted salamander Ambystoma maculatum. We then performed a fully factorial field transplant of the eggs of six populations...

Data from: An integrated occupancy and space-use model to predict abundance of imperfectly detected, territorial vertebrates

Morgan W. Tingley, Robert L. Wilkerson, Christine A. Howell & Rodney B. Siegel
It is often highly desirable to know not only where species are likely to occur (i.e., occupancy) but also how many individuals are supported by a given habitat (i.e., density). For many animals, occupancy and density may be determined by distinct ecological processes. Here we develop a novel abundance model as the product of landscape-scale occupancy probability and habitat-scale density given occupancy. One can conceptualize our model as fully packing a landscape with home ranges...

Data from: Geographic body size variation in the periodical cicadas Magicicada: implications for life cycle divergence and local adaptation

Takuya Koyama, Hiromu Ito, Satoshi Kakishima, Jin Yoshimura, John R. Cooley, Chris Simon & Teiji Sota
Seven species in three species groups (Decim, Cassini and Decula) of periodical cicadas (Magicicada) occupy a wide latitudinal range in the eastern United States. To clarify how adult body size, a key trait affecting fitness, varies geographically with climate conditions and life cycle, we analysed the relationships of population mean head width to geographic variables (latitude, longitude, altitude), habitat annual mean temperature (AMT), life cycle and species differences. Within species, body size was larger in...

Data from: Long-term balancing selection on chromosomal variants associated with crypsis in a stick insect

Dorothea Lindtke, Kay Lucek, Victor Soria-Carrasco, Romain Villoutreix, Timothy E. Farkas, Rüdiger Riesch, Stuart R. Dennis, Zach Gompert & Patrik Nosil
How polymorphisms are maintained within populations over long periods of time remains debated, because genetic drift and various forms of selection are expected to reduce variation. Here, we study the genetic architecture and maintenance of phenotypic morphs that confer crypsis in Timema cristinae stick insects, combining phenotypic information and genotyping-by-sequencing data from 1360 samples across 21 populations. We find two highly divergent chromosomal variants that span megabases of sequence and are associated with color polymorphism....

Data from: Evolution of woody life form on tropical mountains in the tribe Spermacoceae (Rubiaceae)

Suman Neupane, Paul O. Lewis, Steven Dessein, Hunter Lee Shanks, Sushil Paudyal, Frederic Lens & Hunter Shanks
Spermacoceae are mainly an herbaceous group in the Rubiaceae. However, a few lineages are woody, and are found in a diverse range of habitat types. Three of the largest woody lineages (Arcytophyllum, Hedyotis, and Kadua) are characterized by their distribution in the moist tropical mountains, and have disjunct distribution patterns with respect to their closest relatives. In this study, we explore the cases of derived woodiness in these three lineages and their diversification dynamics in...

Data from: The first Cenozoic spinicaudatans from North America

Alycia L. Stigall, Roy E. Plotnick & Lisa E. Park Bousch
A new spinicaudatan species, Estherites? jocelynae new species, is described from more than fiftyspecimens collected from the Medicine Lodge Formation (early Oligocene) of the Beaverhead Basin in southwestern Montana, USA. This is the first spinicaudatan species reported from Cenozoic strata of North America and is the second-youngest fossil clam shrimp described globally. The new species extends the range of the superfamily Estheriteoidea into the Paleogene. Carapaces of E.? jocelynae n. sp. are preserved as a...

Data from: Cross-scale occupancy dynamics of a post-fire specialist in response to variation across a fire regime

Morgan W. Tingley, Andrew N. Stillman, Robert L. Wilkerson, Christine A. Howell, Sarah C. Sawyer & Rodney B. Siegel
1. Fire creates challenges and opportunities for wildlife through rapid destruction, modification, and creation of habitat. Fire has spatially variable effects on landscapes, however, and for species that benefit from the ephemeral resource patches created by fire, it is critical to understand characteristics of fires that promote post-fire colonization and persistence, and the spatial scales on which they operate. 2. Using a model post-fire specialist, the black-backed woodpecker (Picoides arcticus), we examined how colonization and...

Data from: Avoidance, tolerance, and resistance to ectoparasites in nestling and adult tree swallows

Joely G. DeSimone, Ethan D. Clotfelter, Elizabeth C. Black & Sarah A. Knutie
We examined avoidance, tolerance, and resistance strategies of nestling and adult tree swallows Tachycineta bicolor in response to ectoparasitic blowflies Protocalliphora sialia. Tree swallows avoided settling in north-facing nest boxes early in the breeding season. These boxes were more likely to be parasitized later in the season, suggesting that box selection may facilitate blowfly avoidance. After experimentally manipulating blowfly intensity, we found that nestlings were generally tolerant of parasitism. Parasites significantly reduced nestling blood hemoglobin...

Data from: Assessing combinability of phylogenomic data using Bayes Factors

Suman Neupane, Karolina Fučíková, Louise A Lewis, Lynn Kuo, Ming-Hui Chen & Paul Lewis
With the rapid reduction in sequencing costs of high-throughput genomic data, it has become commonplace to use hundreds of genes to infer phylogeny of any study system. While sampling a large number of genes has given us a tremendous opportunity to uncover previously unknown relationships and improve phylogenetic resolution, it also presents us with new challenges when the phylogenetic signal is confused by differences in the evolutionary histories of sampled genes. Given the incorporation of...

Strategies in herbivory by mammals revisited: The role of liver metabolism in a juniper specialist ( Neotoma stephensi ) and a generalist ( Neotoma albigula )

Teri Orr, Smiljka Kitanovic, Katharina Schramm, Michele Skopec, Ross Wilderman, James Halpert, Denise Dearing, Teri J. Orr, Katharina M. Schramm, Michele M. Skopec, P. Ross Wilderman, James R. Halpert, M. Denise Dearing & M. Denise Dearing
Although herbivory is widespread among mammals, few species have adopted a strategy of dietary specialization. Feeding on a single plant species often exposes herbivores to high doses of similar plant secondary metabolites (PSMs), which may exceed the animal’s detoxification capacities. Therefore, theory predicts that specialists will have unique detoxification mechanisms to process high levels of dietary toxins. To evaluate this hypothesis, we compared liver metabolism of a juniper specialist, Neotoma stephensi (diet >85% juniper), to...

Data from: Portable heaters for microhabitat heating experiments

Christina Baer, Diego Dierick & Carlos Garcia-Robledo
1. Global warming will likely cause more ecological change by altering how species interact with each other than by directly affecting individual species. Field heating experiments are essential to test how warming will change species interactions. However, such experiments pose many logistical challenges, including heater construction and accuracy and accessing necessary infrastructure. 2. To facilitate these experiments, we developed portable active heaters suitable for heating microhabitats and sites of species interactions. We validated heater performance...

Data from: Contemporaneous radiations of fungi and plants linked to symbiosis

François Lutzoni, Michael D. Nowak, Michael E. Alfaro, Valérie Reeb, Jolanta Miadlikowska, Michael Krug, A. Elizabeth Arnold, Louise A. Lewis, David L. Swofford, David Hibbett, Khidir Hilu, Timothy Y. James, Dietmar Quandt & Susana Magallón
Interactions between fungi and plants, including parasitism, mutualism, and saprotrophy, have been invoked as key to their respective macroevolutionary success. Here we evaluate the origins of plant-fungal symbioses and saprotrophy using a time-calibrated phylogenetic framework that reveals linked and drastic shifts in diversification rates of each kingdom. Fungal colonization of land was associated with at least two origins of terrestrial green algae and preceded embryophytes (as evidenced by losses of fungal flagellum, ca. 720 Ma),...

Displaced and Invisible: Ukrainian Refugee Crisis Coverage in the US, UK, Ukrainian, and Russian Newspapers

Nataliya Roman, Anna Young & Stephynie Perkins

Multi-species occupancy models as robust estimators of community richness

Morgan W. Tingley, Christopher Nadeau & Manette Sandor
1. Understanding patterns of diversity is central to ecology and conservation, yet estimates of diversity are often biased by imperfect detection. In recent years, multi-species occupancy models (MSOM) have been developed as a statistical tool to account for species-specific heterogeneity in detection while estimating true measures of diversity. Although the power of these models has been tested in various ways, their ability to estimate gamma diversity – or true community size, N – is a...

Data from: Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood

Yufeng Wu
Incomplete lineage sorting can cause incongruence between the phylogenetic history of genes (the gene tree) and that of the species (the species tree), which can complicate the inference of phylogenies. In this paper, I present a new coalescent-based algorithm for species tree inference with maximum likelihood. I first describe an improved method for computing the probability of a gene tree topology given a species tree, which is much faster than an existing algorithm by Degnan...

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