93 Works

Data from: Phylogenomics reveals the evolutionary timing and pattern of butterflies and moths

Akito Y. Kawahara, David Plotkin, Marianne Espeland, Karen Meusemann, Emmanuel F. A. Toussaint, Alexander Donath, France Gimnich, Paul B. Frandsen, Andreas Zwick, Mario Dos Reis, Jesse R. Barber, Ralph S. Peters, Shanlin Liu, Xin Zhou, Christoph Mayer, Lars Podsiadlowski, Caroline Storer, Jayne E. Yack, Bernhard Misof & Jesse W. Breinholt
Butterflies and moths (Lepidoptera) are one of the major super-radiations of insects, comprising nearly 160,000 described extant species. As herbivores, pollinators, and prey, Lepidoptera play a fundamental role in almost every terrestrial ecosystem. Lepidoptera are also indicators of environmental change and serve as model organisms for research on mimicry and genetics. They have been central to the development of co-evolutionary hypotheses, such as butterflies with flowering plants, and moths' evolutionary arms race with echolocating bats....

Evolutionary history of Neotropical savannas geographically concentrates species, phylogenetic and functional diversity of lizards

Jessica Fenker, Fabricius M. C. B. Domingos, Leonardo G. Tedeschi, Dan F. Rosauer, Fernanda P. Werneck, Guarino R. Colli, Roger M. D. Ledo, Emanuel M. Fonseca, Adrian A. Garda, Derek Tucker, , Maria F. Breitman, Flavia Soares, Lilian G. Giugliano & Craig Moritz
Supporting information (scripts) to compute diversity and endemism indices copied and available by Dan Rosauer (https ://github.com/DanRosauer/phylospatial). Aim: Understanding where and why species diversity is geographically concentrated remains a challenge in biogeography and macroevolution. This is true for the Cerrado, the most biodiverse tropical savanna in the world, which has experienced profound biodiversity loss. Previous studies have focused on a single metric (species composition), neglecting the fact that ‘species’ within the biome are often composed...

Large losses of ammonium-nitrogen from a rice ecosystem under elevated CO2

Lei Cheng, Chenchao Xu, Kaihang Zhang, Wanying Zhu, Jing Xiao, Chen Zhu, Naifang Zhang, Fangjian Yu, Shuyao Li, Chunwu Zhu, Qichao Tu, Xin Chen, Jianguo Zhu, Shuijin Hu, Roger T Koide & Mary K Firestone
Inputs of nitrogen into terrestrial ecosystems, mainly via the use of ammonium-based fertilizers in agroecosystems, are enormous, but its fate under elevated atmospheric carbon dioxide (CO2) is not well understood. We have taken advantage of a 15-year free air CO2 enrichment study to investigate the influence of elevated CO2 on the transformation of ammonium-nitrogen in a rice ecosystem in which ammonium is usually assumed to be stable under anaerobic conditions. We demonstrate that elevated CO2...

Data from: Higher-level phylogeny and reclassification of Lampyridae (Coleoptera: Elateroidea)

Gavin Martin, Kathrin Stanger-Hall, Marc Branham, Luiz Da Silveira, Sarah Lower, David Hall, Xue-Yan Li, Alan Lemmon, Emily Lemmon & Seth Bybee
Fireflies (Lampyridae) are a diverse family of beetles which exhibit an array of morphologies including varying antennal and photic organ morphologies. Due in part to their morphological diversity, the classification within the Lampyridae has long been in flux. Here we use an anchored hybrid enrichment approach to reconstruct the most extensive molecular phylogeny of Lampyridae to date (436 loci and 98 taxa) and to evaluate firefly higher-level classification. We propose several classification changes supported by...

Data from: Differences in patterns of reproductive allocation between the sexes in Nicrophorus orbicollis

Ashlee N. Smith, J. Curtis Creighton & Mark C. Belk
Organisms are selected to maximize lifetime reproductive success by balancing the costs of current reproduction with costs to future survival and fecundity. Males and females typically face different reproductive costs, which makes comparisons of their reproductive strategies difficult. Burying beetles provide a unique system that allows us to compare the costs of reproduction between the sexes because males and females are capable of raising offspring together or alone and carcass preparation and offspring care represent...

Data from: Divergent natural selection promotes immigrant inviability at early and late stages of evolutionary divergence

Jerald B. Johnson & Spencer J. Ingley
Natural selection's role in speciation has been of fundamental importance since Darwin first outlined his theory. Recently, work has focused on understanding how selection drives trait divergence, and subsequently reproductive isolation. ‘Immigrant inviability’, a barrier that arises from selection against immigrants in their non-native environment, appears to be of particular importance. Although immigrant inviability is likely ubiquitous, we know relatively little about how selection acts on traits to drive immigrant inviability, and how important immigrant...

Data from: Opsins have evolved under the permanent heterozygote model: insights from phylotranscriptomics of Odonata

Anton Suvorov, Nicholas O. Jensen, Camilla R. Sharkey, M. Stanley Fujimoto, Paul Bodily, Haley M. Cahill Wightman, T. Heath Ogden, Mark J. Clement & Seth M. Bybee
Gene duplication plays a central role in adaptation to novel environments by providing new genetic material for functional divergence and evolution of biological complexity. Several evolutionary models have been proposed for gene duplication to explain how new gene copies are preserved by natural selection, but these models have rarely been tested using empirical data. Opsin proteins, when combined with a chromophore, form a photopigment that is responsible for the absorption of light, the first step...

Data from: A temporal banding approach for consistent taxonomic ranking above the species level

Ekaphan Kraichak, Ana Crespo, Pradeep K. Divakar, Steven D. Leavitt & H. Thorsten Lumbsch
Comparable taxonomic ranks within clades can facilitate more consistent classifications and objective comparisons among taxa. Here we use a temporal approach to identify taxonomic ranks. This is an extension of the temporal banding approach including a Temporal Error Score that finds an objective cut-off for each taxonomic rank using information for the current classification. We illustrate this method using a data set of the lichenized fungal family Parmeliaceae. To assess its performance, we simulated the...

Data from: Anchored phylogenomics of burrowing mayflies (Ephemeroptera) and the evolution of tusks

Dustin B. Miller, Stephanie Bartlett, Michel Sartori, Jesse W. Breinholt & T. Heath Ogden
This study investigated the phylogenetic relationships among seven burrowing mayfly families. Genetic data from four ribosomal DNA genes (12S, 16S, 18S, and 28S) generated with sanger sequencing, 448 protein coding loci generated using a novel hybrid enrichment probe set and available RNAseq and genome assembly for 19 ingroup taxa and 4 outgroup taxa. Maximum Likelihood, and Bayesian analyses were carried out to estimate phylogenetic relationships. The results indicated that Potamanthidae, Euthyplociidae, Behningiidae, and Palingeniidae were...

Data from: Invertebrate community response to fire and rodent activity in the Mojave and Great Basin Deserts

Joshua D. Day, Jackson H. Birrell, Tyson J. Terry, Amy Clark, Phil Allen & Samuel B. St. Clair
Recent increases in the frequency and size of desert wildfires bring into question the impacts of fire on desert invertebrate communities. Furthermore, consumer communities can strongly impact invertebrates through predation and top‐down effects on plant community assembly. We experimentally applied burn and rodent exclusion treatments in a full factorial design at sites in both the Mojave and Great Basin deserts to examine the impact that fire and rodent consumers have on invertebrate communities. Pitfall traps...

Data from: Sexual dimorphism, phenotypic integration, and the evolution of head structure in casque-headed lizards

Gregory W. Taylor, Juan C. Santos, Benjamin J. Perrault, Mariana Morando, Carlos Roberto Vásquez Almazán, & Jack W. Sites
Sexes can differ in features associated with differential reproduction, which can be used during courtship or aggressive encounters. Some traits tend to evolve independently between sexes and emerge as sexually dimorphic within the organismal phenotype. We characterize such a relationship by estimating the phenotypic integration of the head morphology and modularity of the crest in the casque-headed lizards (Corytophanidae). In this clade, some species show extreme sexual dimorphism (e.g., head crests in the genus Basiliscus)...

Data from: A cure for the blues: opsin duplication and subfunctionalization for short-wavelength sensitivity in jewel beetles (Coleoptera: Buprestidae)

Nathan P. Lord, Rebecca L. Plimpton, Camilla R. Sharkey, Anton Suvorov, Jonathan P. Lelito, Barry M. Willardson & Seth M. Bybee
Background: Arthropods have received much attention as a model for studying opsin evolution in invertebrates. Yet, relatively few studies have investigated the diversity of opsin proteins that underlie spectral sensitivity of the visual pigments within the diverse beetles (Insecta: Coleoptera). Previous work has demonstrated that beetles appear to lack the short-wavelength-sensitive (SWS) opsin class that typically confers sensitivity to the “blue” region of the light spectrum. However, this is contrary to established physiological data in...

Data from: Phylogeography and species delimitation in convict cichlids (Cichlidae: Amatitlania): implications for taxonomy and Plio–Pleistocene evolutionary history in Central America

Justin C. Bagley, Wilfredo A. Matamoros, Caleb D. McMahan, Michael Tobler, Prosanta Chakrabarty & Jerald B. Johnson
We investigate phylogeographic patterns and delimit species boundaries within Amatitlania, a genus of Central American cichlid fishes. Phylogenetic analyses of mitochondrial DNA sequences from 318 individuals spanning the geographical ranges of all three currently recognized Amatitlania species strongly supported one major clade, with a relatively diverged subclade corresponding to A. kanna samples from eastern Costa Rica and Panama. Gene trees and networks revealed marked incongruences between phylogeographic structure and morpho-species taxonomy as a result of...

Data from: Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species

John J. Wiens, Carl R. Hutter, Daniel G. Mulcahy, Brice P. Noonan, Ted M. Townsend, , Tod W. Reeder & J. W. Sites
Squamate reptiles (lizards and snakes) are one of the most diverse groups of terrestrial vertebrates. Recent molecular analyses have suggested a very different squamate phylogeny relative to morphological hypotheses, but many aspects remain uncertain from molecular data. Here, we analyse higher-level squamate phylogeny with a molecular dataset of unprecedented size, including 161 squamate species for up to 44 nuclear genes each (33,717 base pairs), using both concatenated and species-tree methods for the first time. Our...

Data from: Size doesn't matter, sex does: a test for boldness in sister species of Brachyrhaphis fishes

Spencer J. Ingley, Jeremy Rehm & Jerald B. Johnson
The effect of divergent natural selection on the evolution of behavioral traits has long been a focus of behavioral ecologists. Predation, due to its ubiquity in nature and strength as a selective agent, has been considered an important environmental driver of behavior. Predation is often confounded with other environmental factors that could also play a role in behavioral evolution. For example, environments that contain predators are often more ecologically complex and “risky” (i.e., exposed and...

Data from: Biogeography of the livebearing fish Poecilia gillii in Costa Rica: are phylogeographic breaks congruent with fish community boundaries?

Jared Lee & Jerald Johnson
One of the original goals of phylogeography was to use genetic data to identify historical events that might contribute to breaks among communities. In this study, we examine the phylogeography of a common livebearing fish (Poecilia gillii) from Costa Rica. Our goal was to determine if phylogeographic breaks in this species were congruent with previously-defined boundaries among four fish community provinces. We hypothesized that if abiotic factors influence both community boundaries and genetic structuring in...

Data from: Accuracy and precision of species trees: effects of locus, individual, and base-pair sampling on inference of species trees of the Liolaemus darwinii group (Squamata, Liolaemidae)

Arley Camargo, Luciano J. Avila, Mariana Morando, Jack W. Sites & Jack W. Sites
Molecular phylogenetics has entered a new era in which species trees are estimated from a collection of gene trees using methods that accommodate their heterogeneity and discordance with the species tree. Empirical evaluation of species trees is necessary to assess the performance (i.e., accuracy and precision) of these methods with real data, which consist of gene genealogies likely shaped by different historical and demographic processes. We analyzed 20 loci for 16 species of the South...

Data from: Lizards on ice: evidence for multiple refugia in Liolaemus pictus (Liolaemidae) during the Last Glacial Maximum in the southern Andean beech forests

Iván Vera-Escalona, Guillermo D’Elía, Nicolás Gouin, Frank M. Fontanella, Carla Muñoz-Mendoza, , Pedro F. Victoriano, Guillermo D'Elía & Jack W. Sites
Historical climate changes and orogenesis are two important factors that have shaped intraspecific biodiversity patterns worldwide. Although southern South America has experienced such complex events, there is a paucity of studies examining the effects on intraspecific diversification in this part of the world. Liolaemus pictus is the southernmost distributed lizard in the Chilean temperate forest, whose genetic structure has likely been influenced by Pleistocene glaciations. We conducted a phylogeographic study of L. pictus in Chile...

Data from: Phylogeny and biogeography of rainbowfishes (Melanotaeniidae) from Australia and New Guinea

Peter J. Unmack, Gerald R. Allen & Jerald B. Johnson
The family Melanotaeniidae (rainbowfishes) represents the largest monophyletic group of freshwater fishes found in Australia and New Guinea. The family consists of seven genera and a total of 81 species, which are broadly distributed throughout the region. We conducted a phylogenetic analysis of Melanotaeniidae based on nearly complete taxonomic sampling of all species. We sequenced seven protein coding mitochondrial genes and the first two introns of the nuclear S7 gene, for a total of 6827...

Data from: Dragons in our midst: phyloforensics of illegally traded Southeast Asian monitor lizards

Welton J. Luke, Cameron D. Siler, Charles W. Linkem, Arvin C. Diesmos, Mae L. Diesmos, Emerson Sy, Rafe M. Brown & Luke J. Welton
We provide a phylogenetic and population genetic evaluation of the illegal pet and bush meat trade of monitor lizards in the Philippines. We use a molecular dataset assembled from vouchered samples with known localities throughout the country, as a reference for statistical phylogenetic, population genetic, and DNA barcoding analyses of genetic material obtained during a three year survey of the Manila pet trade. Our results provide the first genetic evaluation of a major Southeast Asian...

Data from: How lizards survived blizzards: phylogeography of the Liolaemus lineomaculatus group (Liolaemidae) reveals multiple breaks and refugia in southern Patagonia, and their concordance with other co-distributed taxa

Maria Breitman, Luciano Avila, Jack Sites, Mariana Morando & Jack W. Sites
Patagonia was shaped by a complex geological history, including the Miocene uplift of the Andes, followed by volcanism, marine introgressions, and extreme climatic oscillations during Pleistocene glaciation–deglaciation cycles. The distributional patterns and phylogenetic relationships of southern patagonian animals and plants were affected in different ways, and those imprints are reflected in the seven phylogeographic breaks and eight refugia that have been previously proposed. In this study we estimated time-calibrated phylogenetic/phylogeographic patterns in lizards of the...

Data from: Deep sequencing of amplicons reveals widespread intraspecific hybridization and multiple origins of polyploidy in big sagebrush (Artemisia tridentata)

Bryce A. Richardson, Justin T. Page, Prabin Bajgain, Stewart C. Sanderson & Joshua A. Udall
PREMISE OF THE STUDY: Hybridization has played an important role in the evolution and ecological adaptation in diploid and polyploid plants. Artemisia tridentata (Asteraceae) tetraploids are extremely widespread and of great ecological importance. These tetraploids are often taxonomically identified as A. tridentata ssp. wyomingensis, or as autotetraploids of diploid subspecies tridentata and vaseyana. Few details are available as to how these tetraploids are formed or how they are related to diploid subspecies. METHODS: We used...

Data from: Limitations of species delimitation based on phylogenetic analyses: a case study in the (Hypogymnia hypotrypa) group (Parmeliaceae, Ascomycota)

Xinli Wei, Bruce McCune, H. Thorsten Lumbsch, Hui Li, Steven Leavitt, Yoshikazu Yamamoto, Svetlana Tchabanenko & Jiangchun Wei
Delimiting species boundaries among closely related lineages often requires a range of independent data sets and analytical approaches. Similar to other organismal groups, robust species circumscriptions in fungi are increasingly investigated within an empirical framework. Here we attempt to delimit species boundaries in a closely related clade of lichen-forming fungi endemic to Asia, the Hypogymnia hypotrypa group (Parmeliaceae). In the current classification, the Hypogymnia hypotrypa group includes two species: H. hypotrypa and H. flavida, which...

Data from: Use of auto-germ to model germination timing in the Sagebrush-steppe

William C. Richardson, Dallin R. Whitaker, Kyler P. Sant, Nicholas S. Barney, Ryan S. Call, Bruce A. Roundy, Zachary T. Aanderud & Matthew D. Madsen
Germination timing has a strong influence on direct seeding efforts, and therefore is a closely tracked demographic stage in a wide variety of wildland and agricultural settings. Predictive seed germination models, based on soil moisture and temperature data in the seed zone are an efficient method of estimating germination timing. We utilized Visual Basic for Applications (VBA) to create Auto-Germ, which is an Excel workbook that allows a user to estimate field germination timing based...

Morphometric Response of Galaxias maculatus (Jenyns) to Lake Colonization in Chile

Margaret Mercer, Peter C. Searle, Roberto Cifuentes, Evelyn Habit & Mark C. Belk
Body and head shape in fish responds to environmental factors such as water flow rate, food sources, and niche availability. However, the way in which fish respond to these environmental factors varies. In Central Chile, multiple river and lake systems along the coast provide an ideal study site to investigate these types of shape changes. We use geometric morphometrics to characterize shape differences in Galaxias maculatus (Jenyns) between river and lake populations. Lake fish converge...

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