180 Works

Phylogeographic and phenotypic outcomes of brown anole colonization across the Caribbean provide insight into the beginning stages of an adaptive radiation

Jason J. Kolbe, Richard E. Glor, Marta López‐Darias, C. Verónica Gómez Pourroy, Alexis S. Harrison, Kevin De Queiroz, Liam J. Revell, Jonathan B. Losos & Robert Graham Reynolds
Some of the most important insights into the ecological and evolutionary processes of diversification and speciation have come from studies of island adaptive radiations, yet relatively little research has examined how these radiations initiate. We suggest that Anolis sagrei is a candidate for understanding the origins of the Caribbean Anolis adaptive radiation and how a colonizing anole species begins to undergo allopatric diversification, phenotypic divergence and, potentially, speciation. We undertook a genomic and morphological analysis...

Severe inbreeding depression is predicted by the “rare allele load” in Mimulus guttatus

Keely E. Brown & John K. Kelly
Most flowering plants are hermaphroditic and experience strong pressures to evolve self‐pollination (automatic selection, reproductive assurance). Inbreeding depression (ID) can oppose selection for selfing, but it remains unclear if ID is typically strong enough to maintain outcrossing. To measure the full cost of sustained inbreeding on fitness, and its genomic basis, we planted highly homozygous, fully genome‐sequenced inbred lines of yellow monkeyflower (Mimulus guttatus) in the field next to outbred plants from crosses between the...

Self-organising cicada choruses respond to the local sound and light environment

Lawrence Sheppard, Brandon Mechtley, Jonathan Walter & Daniel Reuman
1. Periodical cicadas exhibit an extraordinary capacity for self-organising spatially synchronous breeding behavior. The regular emergence of periodical cicada broods across the US is a phenomenon of longstanding public and scientific interest, as the cicadas of each brood emerge in huge numbers and briefly dominate their ecosystem. During the emergence, the 17-year periodical cicada species Magicicada cassini is found to form synchronised choruses, and we investigated their chorusing behavior from the standpoint of spatial synchrony....

Dissecting the genetic basis of variation in Drosophila sleep using a multiparental QTL mapping resource

Stuart Macdonald & Brittny R. Smith
There is considerable variation in sleep duration, timing and quality in human populations, and sleep dysregulation has been implicated as a risk factor for a range of health problems. Human sleep traits are known to be regulated by genetic factors, but also by an array of environmental and social factors. These uncontrolled, non-genetic effects complicate powerful identification of the loci contributing to sleep directly in humans. The model system, Drosophila melanogaster, exhibits a behavior that...

Data from: The tree of life and a new classification of bony fishes

Ricardo Betancur-R., Adela Roa-Varon, Nancy I. Holcroft, W. Calvin Borden, Terry Grande, Kent Carpenter, Millicent Sanciangco, Chenhong Li, Dahiana Arcila, Jesus A Ballesteros, Guillermo Ortí, J. Andrés López, Matthew A. Campbell, Edward O. Wiley, Gloria Arratia, Guoqing Lu, Stuart Willis, Richard E. Broughton, , Feifei Zhang & Daniel J. Hough
The tree of life of fishes is in a state of flux because we still lack a comprehensive phylogeny that includes all major groups. The situation is most critical for a large clade of spiny-finned fishes, traditionally referred to as percomorphs, whose uncertain relationships have plagued ichthyologists for over a century. Most of what we know about the higher-level relationships among fish lineages has been based on morphology, but rapid influx of molecular studies is...

Data from: Phylogenetic relationships and character evolution analysis of Saxifragales using a supermatrix approach

Douglas E. Soltis, Mark E. Mort, Maribeth Latvis, Evgeny V. Mavrodiev, Brian C. O'Meara, Pamela S. Soltis, J. Gordon Burleigh & Rafael Rubio De Casas
Premise of the study: We sought novel evolutionary insights for the highly diverse Saxifragales by constructing a large phylogenetic tree encompassing 36.8% of the species-level biodiversity. Methods: We built a phylogenetic tree for 909 species of Saxifragales and used this hypothesis to examine character evolution for: annual or perennial habit, woody or herbaceous habit, ovary position, petal number, carpel number, and stamen: petal ratio. We employed likelihood approaches to investigate the effect of habit and...

Data from: Patterns of host plant utilization and diversification in the brush-footed butterflies

Christopher A. Hamm & James A. Fordyce
Herbivorous insects represent one of the most successful animal radiations known. They occupy a wide range of niches, feed on a great variety of plants, and are species rich; yet the factors that influence their diversification are poorly understood. Host breadth is often cited as a major factor influencing diversification, and, according to the Oscillation Hypothesis, shifts from generalist to specialist feeding states increase the diversification rate for a clade. We explored the relationship between...

Data from: A total evidence approach to understanding phylogenetic relationships and ecological diversity in Selaginella subg. Tetragonostachys

Nils Arrigo, James Therrien, Cajsa Lisa Anderson, Michael D. Windham, Christopher H. Haufler & Michael S. Barker
Premise of the Study: Several members of Selaginella are renowned for their ability to survive extreme drought and “resurrect” when conditions improve. Many of these belong to subgenus Tetragonostachys, a group of ∼45 species primarily found in North and Central America, with substantial diversity in the Sonoran and Chihuahuan Deserts. We evaluated the monophyly and the age of subgenus Tetragonostachys and assess how drought tolerance contributed to the evolution of this clade. Methods: Our study...

Data from: Molecular systematics of the Philippine forest skinks (Squamata: Scincidae: Sphenomorphus): testing morphological hypotheses of interspecific relationships

Charles W. Linkem, Arvin C. Diesmos & Rafe M. Brown
Skinks of the genus Sphenomorphus are the most diverse clade of squamates in the Philippine Archipelago. Morphological examination of these species has defined six phenotypic groups that are commonly used in characterizations of taxonomic hypotheses. We used a molecular phylogeny based on four mitochondrial and two nuclear genes to assess the group's biogeographical history in the archipelago and examine the phylogenetic validity of the currently recognized Philippine species groups. We re-examined traditional characters used to...

Data from: Mycorrhizal feedbacks generate positive frequency dependence accelerating grassland succession

Liz Koziol & James D. Bever
1. Plant mutualists including arbuscular mycorrhizal (AM) fungi have been postulated as being important drivers of plant community diversity and succession. Late successional plants have been shown to be more responsive to AM fungi and more sensitive to AM fungal species identity, which could generate positive feedback and potentially accelerate succession. 2. We test the effect of AM fungi on plant diversity and on frequency dependence predicted by positive plant‐AM fungi feedback across a successional...

Data from: Tectonic collision and uplift of Wallacea triggered the global songbird radiation

Robert G. Moyle, Carl H. Oliveros, Michael J. Andersen, Peter A. Hosner, Brett W. Benz, Joseph D. Manthey, Scott L. Travers, Rafe M. Brown & Brant C. Faircloth
Songbirds (oscine passerines) are the most species rich and cosmopolitan bird group, comprising almost half of global avian species diversity. Because of their diversity and ubiquity, songbirds are used extensively in studies of evolutionary ecology, diversification, and ethology. Songbirds originated in Australia, but the evolutionary trajectory from a single species in an isolated continent to worldwide proliferation is poorly understood. Prior research suggested songbird diversification scenarios that are largely uncoupled from Earth history, including extensive...

Data from: Conservation genetics of Australasian sailfin lizards: flagship species threatened by coastal development and insufficient protected area coverage

Cameron D. Siler, Andrés Lira-Noriega & Rafe M. Brown
Despite rampant coastal development throughout Southeast Asia and the Pacific, studies of conservation genetics and ecology of vulnerable, coastal species are rare. Large bodied vertebrates with highly specialized habitat requirements may be at particular risk of extinction due to habitat degradation and fragmentation, especially if these habitats are naturally patchily distributed, marginal, or otherwise geographically limited, or associated in space with high human population densities or heavy anthropogenic disturbance. Particularly telling examples of these conservation...

Data from: Multilocus phylogeny reveals unexpected diversification patterns in Asian Wolf Snakes (genus Lycodon)

Cameron Siler, Rafe M. Brown, Carl H. Oliveros, Anssi Santanen & Cameron D. Siler
The diverse group of Asian Wolf Snakes of the genus Lycodon represents one of many poorly understood radiations of advanced snakes in the superfamily Colubroidea. Outside of three species having previously been represented in higher-level phylogenetic analyses, nothing is known of the relationships among species in this unique, moderately diverse, group. The genus occurs widely from central to southeast Asia, with a variety of range sizes from widespread forms to those that are endmic to...

Data from: Loci contributing to boric acid toxicity in two reference populations of Drosophila melanogaster

Michael A. Najarro, Jennifer L. Hackett & Stuart J. Macdonald
Populations maintain considerable segregating variation in the response to toxic, xenobiotic compounds. To identify variants associated with resistance to boric acid, a commonly-used household insecticide with a poorly understood mechanism of action, we assayed thousands of individuals from hundreds of strains. Using the Drosophila Synthetic Population Resource (DSPR), a multi-parental population (MPP) of inbred genotypes, we mapped six QTL to short genomic regions containing few protein-coding genes (3–188), allowing us to identify plausible candidate genes...

Data from: SNP-skimming: a fast approach to map loci generating quantitative variation in natural populations

Carrie A. Wessinger, John K. Kelly, Peng Jiang, Mark D. Rausher, Lena C. Hileman & Carolyn A. Wessinger
Genome-wide association mapping (GWAS) is a method to estimate the contribution of segregating genetic loci to trait variation. A major challenge for applying GWAS to non-model species has been generating dense genome-wide markers that satisfy the key requirement that marker data is error-free. Here we present an approach to map loci within natural populations using inexpensive shallow genome sequencing. This 'SNP skimming' approach involves two steps: an initial genome-wide scan to identify putative targets followed...

Data from: Synthesis of phylogeny and taxonomy into a comprehensive tree of life

Cody E. Hinchliff, Stephen A. Smith, James F. Allman, J. Gordon Burleigh, Ruchi Chaudhary, Lyndon M. Coghill, Keith A. Crandall, Jiabin Deng, Bryan T. Drew, Romina Gazis, Karl Gude, David S. Hibbett, Laura A. Katz, , Emily Jane McTavish, Peter E. Midford, Christopher L. Owen, Richard H. Ree, Jonathan A. Rees, Douglas E. Soltis, Tiffani Williams & Karen Ann Cranston
Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips—the Open Tree of Life. Realization of this tree required the assembly...

Data from: How does ascertainment bias in SNP analyses affect inferences about population history?

Emily Jane McTavish & David M. Hillis
Background: The selection of variable sites for inclusion in genomic analyses can influence results, especially when exemplar populations are used to determine polymorphic sites. We tested the impact of ascertainment bias on the inference of population genetic parameters using empirical and simulated data representing the three major continental groups of cattle: European, African, and Indian. We simulated data under three demographic models. Each simulated data set was subjected to three ascertainment schemes: (I) random selection;...

Data from: Sympatric, temporally isolated populations of the pine white butterfly Neophasia menapia, are morphologically and genetically differentiated

Katherine L. Bell, Christopher A. Hamm, Arthur M. Shapiro & Chris C. Nice
Temporal isolation remains an understudied, and potentially under-appreciated, mechanism of reproductive isolation. Phenological differences have been discovered in populations of the pine white butterfly (Neophasia menapia), a typically univoltine species found throughout western North America. At two locations in the Coast Range of California there are two periods of adult emergence per year, one in early summer (July) and one in late summer/autumn (September/October). Differences in flight time are accompanied by differences in wing shape...

Data from: Sun skink landscape genomics: assessing how microevolutionary processes shape genetic and phenotypic diversity across a heterogeneous and fragmented landscape

Anthony J. Barley, Patrick J. Monnahan, Robert C. Thomson, L. Lee Grismer & Rafe M. Brown
Incorporating genomic data sets into landscape genetic analyses allows for powerful insights into population genetics, explicitly geographical correlates of selection, and morphological diversification of organisms across the geographical template. Here, we utilize an integrative approach to examine gene flow and detect selection, and we relate these processes to genetic and phenotypic population differentiation across South-East Asia in the common sun skink, Eutropis multifasciata. We quantify the relative effects of geographic and ecological isolation in this...

Data from: Synchrony is more than its top-down and climatic parts: interacting Moran effects on phytoplankton in British seas

Lawrence William Sheppard, Emma J. Defriez, Philip Christopher Reid & Daniel C. Reuman
Large-scale spatial synchrony is ubiquitous in ecology. We examined 56 years of data representing chlorophyll density in 26 areas in British seas monitored by the Continuous Plankton Recorder survey. We used wavelet methods to disaggregate synchronous fluctuations by timescale and determine that drivers of synchrony include both biotic and abiotic variables. We tested these drivers for statistical significance by comparison with spatially synchronous surrogate data. We generated timescale-specific models, accounting for 61% of long-timescale (>...

Data from: Speciation in Western Scrub-Jays, Haldane’s rule, and genetic clines in secondary contact

Fiona C. Gowen, James M. Maley, Carla Cicero, A. Townsend Peterson, Brant C. Faircloth, T. Caleb Warr & John E. McCormack
Background: Haldane’s Rule, the tendency for the heterogametic sex to show reduced fertility in hybrid crosses, can obscure the signal of gene flow in mtDNA between species where females are heterogametic. Therefore, it is important when studying speciation and species limits in female-heterogametic species like birds to assess the signature of gene flow in the nuclear genome as well. We studied introgression of microsatellites and mtDNA across a secondary contact zone between coastal and interior...

Data from: Non-equilibrium dynamics and floral trait interactions shape extant angiosperm diversity

Brian C. O'Meara, Stacey D. Smith, W. Scott Armbruster, Lawrence D. Harder, Christopher R. Hardy, Lena C. Hileman, Larry Hufford, Amy Litt, Susana Magallon, Stephen A. Smith, Peter F. Stevens, Charles B. Fenster & Pamela K. Diggle
Why are some traits and trait combinations exceptionally common across the tree of life, whereas others are vanishingly rare? The distribution of trait diversity across a clade at any time depends on the ancestral state of the clade, the rate at which new phenotypes evolve, the differences in speciation and extinction rates across lineages, and whether an equilibrium has been reached. Here we examine the role of transition rates, differential diversification (speciation minus extinction), and...

Data from: The missing link in grassland restoration: arbuscular mycorrhizal fungi inoculation increases plant diversity and accelerates succession

Liz Koziol & James D. Bever
Because soil microbial communities are often altered by anthropogenic disturbance, successful plant community restoration may require the restoration of beneficial soil microbes, such as arbuscular mycorrhizal (AM) fungi. Recent evidence suggests that later successional grassland species are more strongly affected by AM fungi relative to early successional plants and that late successional plants consistently benefit from some AM fungi but not other AM fungal species. Many of these late successional species are also often missing...

Data from: From success to persistence: Identifying an evolutionary regime shift in the diverse Paleozoic aquatic arthropod group Eurypterida, driven by the Devonian biotic crisis

James C. Lamsdell & Paul A. Selden
Mass extinctions have altered the trajectory of evolution a number of times over the Phanerozoic. During these periods of biotic upheaval a different selective regime appears to operate, although it is still unclear whether consistent survivorship rules apply across different extinction events. We compare variations in diversity and disparity across the evolutionary history of a major Paleozoic arthropod group, the Eurypterida. Using these data, we explore the group's transition from a successful, dynamic clade to...

Data from: Conservation genetics of the Philippine tarsier: cryptic genetic variation restructures conservation priorities for an island archipelago primate

Rafe M. Brown, Jennifer A. Weghorst, Karen V. Olson, Mariano R. M. Duya, Anthony J. Barley, Melizar V. Duya, Myron Shekelle, Irene Neri-Arboleda, Jacob A. Esselstyn, Nathaniel J. Dominy, Perry S. Ong, Gillian L. Moritz, Adrian Luczon, Mae Lowe L. Diesmos, Arvin C. Diesmos & Cameron D. Siler
Establishment of conservation priorities for primates is a particular concern in the island archipelagos of Southeast Asia, where rates of habitat destruction are among the highest in the world. Conservation programs require knowledge of taxonomic diversity to ensure success. The Philippine tarsier is a flagship species that promotes environmental awareness and a thriving ecotourism economy in the Philippines. However, assessment of its conservation status has been impeded by taxonomic uncertainty, a paucity of field studies,...

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