118 Works

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

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: Parallel Miocene dispersal events explain the cosmopolitan distribution of the Hypogymnioid lichens

Pradeep K. Divakar, Xin-Li Wei, Bruce McCune, Paloma Cubas, Carlos D. Boluda, Steven G. Leavitt, H. Ana Crespo, Svetlana Tchabanenko & H. Thorsten Lumbsch
Aim: Contemporary species’ distributions are shaped by both geography and historical events, such as extinction, diversification in specific areas and long-distance dispersals. In the most diverse family of lichen-forming fungi, Parmeliaceae, the Hypogymnioid clade, is an example of an evolutionary lineage comprised of species occurring in temperate to subpolar regions in both hemispheres. Here, we elucidate the timing of diversification events and the impact of historical events on the species distribution in this lineage. Location:...

Data from: Forest Giants on Different Evolutionary Branches: Ecomorphological Convergence in Helicopter Damselflies

Emmanuel F. A. Toussaint, Seth M. Bybee, Robert J. Erickson & Fabien L. Condamine
The convergent evolution of analogous features is an evolutionary process occurring independently across the tree of life. From the evolution of echolocation, prehensile tail, viviparity or winged flight, environmental factors often drive this astonishing phenomenon. However, convergent evolution is not always conspicuous or easily identified. Giant damselflies count among the largest flying insects on Earth, and have astonishing ecologies including orb-web spider plucking and oviposition in phytotelmata. One species occurs in the Afrotropics and 18...

Data from: Genome-wide sensitivity analysis of the microsymbiont Sinorhizobium meliloti to symbiotically important, defensin-like host peptides

Markus F. F. Arnold, Mohammed Shabab, Jon Penterman, Kevin L. Boehme, Joel S. Griffitts & Graham C. Walker
The model legume species Medicago truncatula expresses more than 700 nodule-specific cysteine-rich (NCR) signaling peptides that mediate the differentiation of Sinorhizobium meliloti bacteria into nitrogen-fixing bacteroids. NCR peptides are essential for a successful symbiosis in legume plants of the inverted-repeat-lacking clade (IRLC) and show similarity to mammalian defensins. In addition to signaling functions, many NCR peptides exhibit antimicrobial activity in vitro and in vivo. Bacterial resistance to these antimicrobial activities is likely to be important...

Data from: The role of continental shelf width in determining freshwater phylogeographic patterns in southeastern Australian pygmy perches (Teleostei: Percichthyidae)

Peter J. Unmack, Michael P. Hammer, Mark Adams, Jerald B. Johnson & Thomas E. Dowling
Biogeographic patterns displayed by obligate freshwater organisms are intimately related to the nature and extent of connectivity between suitable habitats. Two of the more significant barriers to freshwater connections are seawater and major drainage divides. South-eastern Australia provides a contrast between these barriers as it has discrete areas that are likely influenced to a greater or lesser extent by each barrier type. We use continental shelf width as a proxy for the potential degree of...

Data from: Negative effects of an exotic grass invasion on small-mammal communities

Eric D. Freeman, Tiffanny R. Sharp, Randy T. Larsen, Robert N. Knight, Steven J. Slater & Brock R. McMillan
Exotic invasive species can directly and indirectly influence natural ecological communities. Cheatgrass (Bromus tectorum) is non-native to the western United States and has invaded large areas of the Great Basin. Changes to the structure and composition of plant communities invaded by cheatgrass likely have effects at higher trophic levels. As a keystone guild in North American deserts, granivorous small mammals drive and maintain plant diversity. Our objective was to assess potential effects of invasion by...

Data from: Archipelago-wide survey of Philippine forest dragons (Agamidae: Gonocephalus): multilocus phylogeny uncovers unprecedented levels of genetic diversity in a biodiversity hotspot

Luke J. Welton, Cameron D. Siler, L. L. Grismer, Arvin C. Diesmos, Jack W. Sites & Rafe M. Brown
We utilize robust geographical genetic sampling, a multilocus dataset, and coalescent-based species delimitation statistics to provide the first phylogenetic inferences of relationships of Philippine Gonocephalus, combined with estimates of putative species diversity in this virtually unknown island radiation. Our results reveal startling levels of undocumented diversity, genetically partitioned at a number of geographic levels across the archipelago. In this paper we present the first survey of genetic lineage diversity, coupled with an archipelago-wide elucidation of...

Data from: Taxonomic resolution is a determinant of biodiversity effects in arbuscular mycorrhizal fungal communities

Haishui Yang, Qian Zhang, Roger T. Koide, Jason D. Hoeksema, Jianjun Tang, Xinmin Bian, Shuijin Hu & Xin Chen
Arbuscular mycorrhizal fungi (AMF) are key regulators of ecosystem processes, yet how their biodiversity works in ecosystems remains poorly understood. We documented the extent to which taxonomic resolution influenced the effect of biodiversity of AMF taxa on plant performance (growth, nutrient uptake and stress tolerance) in a meta-analysis of 902 articles. We found that the effect of biodiversity of AMF taxa depended on taxonomic resolution. Plant performance was positively promoted by AMF family richness, while...

Data from: Integrative taxonomy and preliminary assessment of species limits in the Liolaemus walkeri complex (Squamata, Liolaemidae) with descriptions of three new species from Peru

César Aguilar, , Juan C. Cusi, Alfredo Guzmán, Frank Huari, Mikael Lundberg, Emma Mortensen, César Ramírez, Daniel Robles, Juana Suárez, Andres Ticona, Víctor J. Vargas, Pablo J. Venegas, , Perry Wood & Jack Sites
Species delimitation studies based on integrative taxonomic approaches have received considerable attention in the last few years, and have provided the strongest hypotheses of species boundaries. We used three lines of evidence (molecular, morphological, and niche envelopes) to test for species boundaries in Peruvian populations of the Liolaemus walkeri complex. Our results show that different lines of evidence and analyses are congruent in different combinations, for unambiguous delimitation of three lineages that were “hidden” within...

Integrative biodiversity inventories: characterizing lichen-forming fungal diversity in Glen Canyon National Recreation Area using DNA barcoding and vouchered specimens

Steven Leavitt
The Colorado River and its tributaries on the Colorado Plateau are home to unique desert river ecosystems and changing environmental conditions. Within this region, the Glen Canyon National Recreation Area (GCNRA) is comprised of rugged, high desert terrain and is managed by the United States National Parks Service as both a recreational and conservation area. Despite the ecological and economic importance of GCNRA, significant components of the ecological communities therein remain poorly characterized, including lichens....

Data from: Detecting hybridization by likelihood calculation of gene tree extra lineages given explicit models

Melisa Olave, Luciano J. Avila, , Mariana Morando & Jack W. Sites
Explanations for gene tree discordance with respect to a species tree are commonly attributed to deep coalescence (also known as incomplete lineage sorting [ILS]), as well as different evolutionary processes such as hybridization, horizontal gene transfer and gene duplication. Among these, deep coalescence is usually quantified as the number of extra lineages and has been studied as the principal source of discordance among gene trees, while the other processes that could contribute to gene tree...

Data from: A multigene molecular assessment of cryptic biodiversity in the iconic freshwater blackfishes (Teleostei: Percichthyidae: Gadopsis) of south-eastern Australia

Michael P. Hammer, Peter J. Unmack, Mark Adams, Tarmo A. Raadik & Jerald B. Johnson
Freshwater biodiversity is under ever increasing threat from human activities, and its conservation and management require a sound knowledge of species-level taxonomy. Cryptic biodiversity is a common feature for aquatic systems, particularly in Australia, where recent genetic assessments suggest that the actual number of freshwater fish species may be considerably higher than currently listed. The freshwater blackfishes (genus Gadopsis) are an iconic group in south-eastern Australia and, in combination with their broad, naturally divided distribution...

Data from: Phylogeography of the catfish Hatcheria macraei reveals a negligible role of drainage divides in structuring populations

Peter J. Unmack, Juan P. Barriga, Miguel A. Battini, Evelyn M. Habit & Jerald B. Johnson
Southern South America provides a set of unusual geographic features that make it particularly interesting for studying phylogeography. The Andes Mountains run along a north-to-south axis and act as a barrier to gene flow for much of the biota of this region, with southern portions experiencing extensive historic glaciation. Geological data reveal a series of drainage reversals, shifting from Pacific Ocean outlets to Atlantic Ocean outlets due to glacier formation that dammed and reversed rivers....

Data from: Investigating the effects of Pleistocene events on genetic divergence within Richardsonius balteatus, a widely distributed western North American minnow

Derek D. Houston, Dennis K. Shiozawa, Brian Tilston Smith & Brett R. Riddle
Background: Biogeographers seek to understand the influences of global climate shifts and geologic changes to the landscape on the ecology and evolution of organisms. Across both longer and shorter timeframes, the western North American landscape has experienced dynamic transformations related to various geologic processes and climatic oscillations, including events as recently as the Last Glacial Maximum (LGM; ~20 Ka) that have impacted the evolution of the North American biota. Redside shiner is a cyprinid species...

Data from: Marine-freshwater transitions are associated with the evolution of dietary diversification in terapontid grunters (Teleostei: Terapontidae)

Aaron M. Davis, Peter J. Unmack, Bradley J. Pusey, Richard G. Pearson & Jerry B. Johnson
The ecological opportunities associated with transitions across the marine-freshwater interface are regarded as an important catalyst of diversification in a range of aquatic taxa. Here, we examined the role of these major habitat transitions and trophic diversification in a radiation of Australasian fishes using a new molecular phylogeny incorporating 37 Terapontidae species. A combined mitochondrial and nuclear gene analysis yielded a well supported tree with most nodes resolved. Ancestral terapontids appear to have been euryhaline...

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