201 Works

Data from: A gateway for phylogenetic analysis powered by grid computing featuring GARLI 2.0

Adam L. Bazinet, Derrick J. Zwickl & Michael P. Cummings
We introduce molecularevolution.org, a publicly available gateway for high-throughput, maximum likelihood phylogenetic analysis powered by grid computing. The gateway features a garli 2.0 web service that enables a user to quickly and easily submit thousands of maximum likelihood tree searches or bootstrap searches that are executed in parallel on distributed computing resources. The garli web service allows one to easily specify partitioned substitution models using a graphical interface, and it performs sophisticated post-processing of phylogenetic...

Data from: Can RNA-Seq resolve the rapid radiation of advanced moths (Lepidoptera: Apoditrysia)? An exploratory study

Adam L. Bazinet, Michael P. Cummings, Kim T. Mitter & Charles W. Mitter
Recent molecular phylogenetic studies of the insect order Lepidoptera have robustly resolved family-level divergences within most superfamilies, and most divergences among the relatively species-poor early-arising superfamilies. In sharp contrast, relationships among the superfamilies of more advanced moths and butterflies that comprise the mega-diverse clade Apoditrysia (ca. 145,000 spp.) remain mostly poorly supported. This uncertainty, in turn, limits our ability to discern the origins, ages and evolutionary consequences of traits hypothesized to promote the spectacular diversification...

Data from: Prey preference follows phylogeny: evolutionary dietary patterns within the marine gastropod group Cladobranchia (Gastropoda: Heterobranchia: Nudibranchia)

Jessica A. Goodheart, Adam L. Bazinet, Ángel Valdés, Allen G. Collins & Michael P. Cummings
Background: The impact of predator-prey interactions on the evolution of many marine invertebrates is poorly understood. Since barriers to genetic exchange are less obvious in the marine realm than in terrestrial or freshwater systems, non-allopatric divergence may play a fundamental role in the generation of biodiversity. In this context, shifts between major prey types could constitute important factors explaining the biodiversity of marine taxa, particularly in groups with highly specialized diets. However, the scarcity of...

Data from: Ecological genomics meets community-level modeling of biodiversity: mapping the genomic landscape of current and future environmental adaptation

Matthew C. Fitzpatrick & Stephen R. Keller
Local adaptation is a central feature of most species occupying spatially heterogeneous environments, and may factor critically in responses to environmental change. However, most efforts to model the response of species to climate change ignore intraspecific variation due to local adaptation. Here, we present a new perspective on spatial modelling of organism–environment relationships that combines genomic data and community-level modelling to develop scenarios regarding the geographic distribution of genomic variation in response to environmental change....

Data from: Population genetic structure and secondary symbionts in host-associated populations of the pea aphid complex

Julia Ferrari, Joan A West, Sara Via & H. Charles J. Godfray
Polyphagous insect herbivores experience different selection pressures on their various host plant species. How this affects population divergence and speciation may be influenced by the bacterial endosymbionts that many harbor. Here, we study the population structure and symbiont community of the pea aphid (Acyrthosiphon pisum), which feeds on a range of legume species and is known to form genetically differentiated host-adapted populations. Aphids were collected from eight legume genera in England and Germany. Extensive host...

Data from: Parental genetic effects in a cavefish adaptive behavior explain disparity between nuclear and mitochondrial DNA

Masato Yoshizawa, Go Ashida & William R. Jeffery
Epigenetic parental genetic effects are important in many biological processes but their roles in the evolution of adaptive traits and their consequences in naturally evolving populations remain to be addressed. By comparing two divergent blind cave-dwelling cavefish populations with a sighted surface-dwelling population (surface fish) of the teleost Astyanax mexicanus, we report here that convergences in vibration attraction behavior (VAB), the lateral line sensory receptors underlying this behavior, and the feeding benefits of this behavior...

Data from: Combined effects of seed and soil quality drive seedling performance of a late-successional canopy tree in a tropical forest

Jenny Zambrano, Henry F. Howe & Miquel Gonzalez-Meler
Habitat loss and fragmentation affect the structure and functioning of forested ecosystems worldwide, yet we lack an understanding of how species respond to environmental changes. Here, we examined reproductive success and seedling performance of Poulsenia armata (Moraceae) in continuous and fragmented forests of Los Tuxtlas, southern Mexico. We further investigated how maternal habitat and soil conditions manifested in the seedling stage. We determined seed quality and seedling performance by combining isotopic analyses in seed quality...

Data from: Estimating encounter location distributions from animal tracking data

Michael Noonan, Ricardo Martinez-Garcia, Grace H. Davis, Margaret C. Crofoot, Roland Kays, Ben T. Hirsch, Damien Caillaud, Eric Payne, Andrew Sih, David L. Sinn, Orr Spiegel, William F. Fagan, Christen H. Fleming & Justin M. Calabrese
1. Ecologists have long been interested in linking individual behavior with higher-level processes. For motile species, this 'upscaling' is governed by how well any given movement strategy maximizes encounters with positive factors, and minimizes encounters with negative factors. Despite the importance of encounter events for a broad range of ecological processes, encounter theory has not kept pace with developments in animal tracking or movement modeling. Furthermore, existing work has focused primarily on the relationship between...

Diurnal timing of nonmigratory movement by birds: the importance of foraging spatial scales

Julie Mallon, Marlee Tucker, Annalea Beard, , Keith Bildstein, Katrin Böhning-Gaese, John Brzorad, Evan Buechley, Javier Bustamante, Carlos Carrapato, José Castillo-Guerrero, Elizabeth Clingham, Mark Desholm, Christopher DeSorbo, Robert Domenech, Hayley Douglas, Olivier Duriez, Peter Enggist, Nina Farwig, Wolfgang Fiedler, Anna Gagliardo, Clara García-Ripollés, Juan Antonio Gil, Morgan Gilmour, Roi Harel … & Bill Fagan
Timing of activity can reveal an organism’s efforts to optimize foraging either by minimizing energy loss through passive movement or by maximizing energetic gain through foraging. Here, we assess whether signals of either of these strategies are detectable in the timing of activity of daily, local movements by birds. We compare the similarities of timing of movement activity among species using six temporal variables: start of activity relative to sunrise, end of activity relative to...

Multiscale analysis of canopy arthropod diversity in a volcanically fragmented landscape

Elske K. Tielens, Maile N. Neel, Devin R. Leopold, Christian P. Giardina & Daniel S. Gruner
Dataset and code associated with the article "Multiscale analysis of canopy arthropod diversity in a volcanically fragmented landscape" (Tielens et al 2019, Ecosphere). Article abstract: Habitat fragmentation resulting in habitat loss and increased isolation is a dominant driver of global species declines. Habitat isolation and connectivity vary across scales, and understanding how con- nectivity affects biodiversity can be challenging because the relevant scale depends on the taxa involved. A multiscale analysis can provide insight in...

Elevated rates of positive selection drive the evolution of pestiferousness in the Colorado potato beetle ( Leptinotarsa decemlineata, Say)

Zachary Cohen, Kristian Brevik, Yolanda H. Chen, David J. Hawthorne, Benjamin D. Weibel & Sean D. Schoville
In order to understand the evolution of pestiferousness, which we define as the accumulation of traits that contribute to an insect population’s success in an agroecosystem, we tested the importance of known genomic properties associated with rapid adaptation. Within the leaf beetle genus Leptinotarsa, only the Colorado potato beetle (CPB), Leptinotarsa decemlineata Say, and a few populations therein, has risen to pest status on cultivated nightshades, Solanum. Using whole genomes from ten closely related Leptinotarsa...

Late Cretaceous domatia reveals the antiquity of plant–mite mutualisms in flowering plants

S. Augusta Maccracken, Ian Miller & Conrad Labandeira
Mite houses, or acarodomatia, are found on the leaves of over 2,000 living species of flowering plants today. These structures facilitate tri-trophic interactions between the host plant, its fungi or herbivore adversaries, and fungivorous or predaceous mites by providing shelter for the consumers. Previously, the oldest acarodomatia were described on a Cenozoic Era fossil leaf dating to 49 million years in age. Here, we report the first occurrence of Mesozoic Era acarodomatia in the fossil...

Data from - Ecological insights from three decades of animal movement tracking across a changing Arctic

Gil Bohrer, Sarah Davidson, Eliezer Gurarie, Scott LaPoint, Peter Mahoney, Emma Grier, Ophélie Couriot, Allicia Kelly, Bryan Bedrosian, Jerrold Belant, Travis Booms, Bridget Borg, Stan Boutin, Erica Craig, Tracy Davison, Robert Domenech, James Hodson, Kyle Joly, Nicholas Larter, A. David M. Latham, Stephen Lewis, Carol McIntyre, Tricia Miller, Kelsey Russell, Dale Seip … & Judy Williams
We provide here the data used in analysis of 3 test cases, presented in the manuscript "Ecological insights from three decades of animal movement tracking across a changing Arctic". We utilized the new Arctic Animal Movement Archive (AAMA), a growing collection of 201 standardized terrestrial and marine animal tracking studies from 1991–present. The AAMA supports public data discovery, preserves fundamental baseline data for the future, and facilitates efficient, collaborative data analysis. With three AAMA-based case...

Are native and non-native pollinator friendly plants equally valuable for native wild bee communities?

Nicola Seitz, Dennis VanEngelsdorp & Sara D. Leonhardt
Bees rely on floral pollen and nectar for food. Therefore, pollinator friendly plantings are often used to enrich habitats in bee conservation efforts. As part of these plantings, non-native plants may provide valuable floral resources, but their effects on native bee communities have not been assessed in direct comparison with native pollinator friendly plantings. In this study, we performed a common garden experiment by seeding mixes of 20 native and 20 non-native pollinator friendly plant...

Spatial and temporal heterogeneity in pollinator communities maintains within-species floral odour variation

Mark A. Szenteczki, Adrienne Godschalx, Andrea Galmán, Anahí Espíndola, Marc Gibernau, Nadir Alvarez & Sergio Rasmann
Flowering plants emit complex bouquets of volatile organic compounds (VOCs) to mediate interactions with their pollinators. These bouquets are undoubtedly influenced by pollinator-mediated selection, particularly in deceptively-pollinated species that rely on chemical mimicry. However, many uncertainties remain regarding how spatially and temporally heterogeneous pollinators affect the diversity and distribution of floral odour variation. Here, we characterized and compared the floral odours of ten populations of deceptively-pollinated Arum maculatum (Araceae), and inter-annual and decadal variation in...

Genome-wide sequence data show no evidence of hybridization and introgression among pollinator wasps associated with a community of Panamanian strangler figs

Jordan Satler, Allen Herre, Tracy Heath, Carlos Machado, Adalberto Gomez & John Nason
The specificity of pollinator host choice influences opportunities for reproductive isolation in their host plants. Similarly, host plants can influence opportunities for reproductive isolation in their pollinators. For example, in the fig and fig wasp mutualism, offspring of fig pollinator wasps mate inside the inflorescence that the mothers pollinate. Although often host specific, multiple fig pollinator species are sometimes associated with the same fig species, potentially enabling hybridization between wasp species. Here we study the...

Experimental tests of pollinator dependence in Avicennia germinans, the black mangrove

Mayda Nathan
Avicennia germinans (L.) L. (Black Mangrove) is a common, sometimes dominant member of intertidal vegetation in tropical and subtropical regions of the Americas and West Africa. Its flowers are known to be attractive to animals – there are records of a variety of floral visitors – and it is widely believed to be zoophilous, but the degree to which it relies on pollinators for full fruit set is not entirely clear. Molecular methods have revealed...

Mesoscale stereo retrievals from Hunga Tonga-Hunga Ha’apai Eruption of 15 January 2022

James Carr, Akos Horvath, Dong Wu & Mariel Friberg
Stereo methods using GOES-17 and Himawari-8 applied to the Hunga Tonga-Hunga Ha’apai volcanic plume on 15 January 2022 show overshooting tops reaching 50-55 km altitude, a record in the satellite era. Plume height is important to understand dispersal and transport in the stratosphere and climate impacts. Stereo methods, using geostationary satellite pairs, offer the ability to accurately capture the evolution of plume top morphology quasi-continuously over long periods. Manual photogrammetry estimates plume height during the...

Cucurbit[7]uril as a Supramolecular Artificial Enzyme for Diels-Alder Reactions

Aniello Palma, Markus Artelsmair, Guanglu Wu, Xiaoyong Lu, Steven J. Barrow, Najib Uddin, Edina Rosta, Eric Masson & Oren Scherman
Copycat.: Cucurbit[7]uril (CB[7]) is able to catalyse DielsâAlder reactions for substituted and otherwise unreactive N-allyl-2-furfurylamines, thus imitating the role of a DielsâAlderase enzyme. Desp...

Glycoluril‐Derived Molecular Clips are Potent and Selective Receptors for Cationic Dyes in Water

Vladimir Sindelar, Nengfang She, Damien Moncelet, Laura Gilberg, Xiaoyong Lu, Volker Briken & Lyle Isaacs
Abstract Molecular clip 1 remains monomeric in water and engages in host–guest recognition processes with suitable guests. We report the Ka values for 32 1⋅guest complexes measured by 1H NMR, UV/Vi...

Data from: Population genetic structure and secondary symbionts in host-associated populations of the pea aphid complex

Julia Ferrari, Joan A West, Sara Via & H. Charles J. Godfray
Polyphagous insect herbivores experience different selection pressures on their various host plant species. How this affects population divergence and speciation may be influenced by the bacterial endosymbionts that many harbor. Here, we study the population structure and symbiont community of the pea aphid (Acyrthosiphon pisum), which feeds on a range of legume species and is known to form genetically differentiated host-adapted populations. Aphids were collected from eight legume genera in England and Germany. Extensive host...

Data from: Species delimitation in fungal endophyte diversity studies and its implications in ecological and biogeographic inferences

Romina Gazis, Stephen Rehner & Priscila Chaverri
The estimation of species diversity in fungal endophyte communities is based either on species counts or the assignment of operational taxonomic units (OTUs). Consequently, the application of different species recognition criteria affects not only diversity estimates but also the ecological hypotheses that arise from those observations. The main objective of the study was to examine how the choice and number of genetic markers and species delimitation criteria influences biodiversity estimates. Here, we compare approaches to...

Data from: Ecological effects on metabolic scaling amphipod responses to fish predators in freshwater springs

Douglas S. Glazier, Eric M. Butler, Sara A. Lombardi, Travis J. Deptola, Andrew J. Reese & Erin V. Satterthwaite
Metabolic rate is commonly thought to scale with body mass to the 3/4-power as a result of universal body-design constraints. However, recent comparative work has shown that the metabolic scaling slope may vary significantly among species and higher taxa, apparently in response to different lifestyles and ecological conditions, though the precise mechanisms involved are not well understood. To better understand these under-appreciated ecological effects and their causes, it is important to control for extraneous phylogenetic...

Data from: Coevolution of male mating signal and female preference during early lineage divergence of the Hawaiian cricket, Laupala cerasina

Jaime L Grace & Kerry L Shaw
Sexual selection is a powerful evolutionary force shaping mate choice phenotypes, initiating phenotypic shifts resulting in (or reinforcing) population divergence and speciation when such shifts reduce mating probabilities among divergent populations. In the Hawaiian cricket genus Laupala, pulse rate of male calling song, a conspicuous mating signal, differs among species, potentially behaving as a speciation phenotype. Populations of the widespread species L. cerasina show variation in pulse rate. We document the degree of population differentiation...

Data from: Does selfing or outcrossing promote local adaptation?

Joe Hereford
The degree to which plants self-fertilize may impact their potential for genetic adaptation. Given that the mating system influences genetic processes within and among populations, the mating system could limit or promote local adaptation. I conducted a literature survey of published reciprocal transplant experiments in plant populations to quantify the effect of mating system on the magnitude of local adaptation. Mating system had no effect on local adaptation. I detected no effect when species were...

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