121 Works

A tale of four bears: Environmental signal on the phylogeographical patterns within the extant Ursus species

Ella Vázquez-Domínguez, Carlos Luna‐Aranguré & Jorge Soberón
Aim: Assessing the relevance of niche evolution in the diversification patterns and geographical distribution of species driven by climate remains a challenge. We apply an integrative approach to evaluate the role of the environment on the phylogeography of bear species, incorporating fossil data to characterize the changes in the ecological niche through time. We evaluate our approach with the four extant species of bears within Ursus, the best represented taxon in the fossil record of...

Parachute geckos free fall into synonymy: Gekko phylogeny, and a new subgeneric classification, inferred from thousands of ultraconserved elements

Perry Wood, Xianguang Guo, Scott Travers, Yong-Chao Su, Karen Olson, Aaron Bauer, Lee Grismer, Cameron Siler, Robert Moyle, Michael Andersen & Rafe Brown
Recent phylogenetic studies of gekkonid lizards have revealed unexpected, widespread paraphyly and polyphyly among genera, unclear generic boundaries, and a tendency towards the nesting of taxa exhibiting specialized, apomorphic morphologies within geographically widespread “generalist” clades. This is especially true in Australasia, where monophyly of Gekko proper has been questioned with respect to phenotypically ornate flap-legged geckos of the genus Luperosaurus, the Philippine false geckos of the genus Pseudogekko, and even the elaborately “derived” parachute geckos...

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...

Assessing seasonal demographic covariation to understand environmental-change impacts on a hibernating mammal

Maria Paniw, Dylan Childs, Kenneth Armitage, Daniel Blumstein, Julien Martin, Madan Oli & Arpat Ozgul
Natural populations are exposed to seasonal variation in environmental factors that simultaneously affect several demographic rates (survival, development, reproduction). The resulting covariation in these rates determines population dynamics, but accounting for its numerous biotic and abiotic drivers is a significant challenge. Here, we use a factor-analytic approach to capture partially unobserved drivers of seasonal population dynamics. We use 40 years of individual-based demography from yellow-bellied marmots (Marmota flaviventer) to fit and project population models that...

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...

Diversity in lac Operon Regulation among Diverse Escherichia coli Isolates Depends on the Broader Genetic Background but Is Not Explained by Genetic Relatedness

Tim Cooper, Kelly Phillips, Scott Widmann, Jennifer Nguyen, Christian Ray, Gabor Balazsi & Huei-Yi Lai
Transcription of bacterial genes is controlled by the coordinated action of cis- and trans-acting regulators. The activity and mode of action of these regulators can reflect different requirements for gene products in different environments. A well-studied example is the regulatory function that integrates the environmental availability of glucose and lactose to control the Escherichia coli lac operon. Most studies of lac operon regulation have focused on a few closely related strains. To determine the range...

Extensive paraphyly in the typical owl family (Strigidae)

Jessie F Salter, Carl H Oliveros, Peter A Hosner, Joseph D Manthey, Mark B Robbins, Robert G Moyle, Robb T Brumfield & Brant C Faircloth
The typical owl family (Strigidae) comprises 194 species in 28 genera, 14 of which are monotypic. Relationships within and among genera in the typical owls have been challenging to discern because mitochondrial data have produced equivocal results and because many monotypic genera have been omitted from previous molecular analyses. Here, we collected and analyzed DNA sequences of ultraconserved elements (UCEs) from 43 species of typical owls to produce concatenated and multispecies coalescent-based phylogenetic hypotheses for...

Data from: Helianthus maximiliani and species fine-scale spatial pattern affect diversity interactions in reconstructed tallgrass prairies

Thomas McKenna, Jack McDonnell, Kathryn Yurkonis & Caroline Brophy
1. Biodiversity and Ecosystem Function analyses aim to explain how individual species and their interactions affect ecosystem function. With this study we asked in what ways do species interact, are these interactions affected by species planting pattern, and are initial (planted) proportions or previous year (realized) proportions a better reference point for characterizing grassland diversity effects? 2. We addressed these questions with experimental communities compiled from a pool of 16 tallgrass prairie species. We planted...

Data from: Quantifying cryptic function loss during community disassembly

Akira Terui, Jacques Finlay, Amy Hansen & Jessica Kozarek
1. Emerging theory suggests that the ecosystem-level consequences of anthropogenic pressures depend on how species will be disassembled from ecological communities (i.e., the disassembly rule). Species loss, however, is not the sole ecological cause of ecosystem function loss: behaviors underpinning ecosystem function can also be disrupted by anthropogenic pressures without detectable declines of component species (“cryptic function loss”). 2. Here, we introduce a novel framework that integrates behavioral responses into community disassembly metrics. We applied...

Data from: The Teleost Anatomy Ontology: anatomical representation for the genomics age

Wasila M. Dahdul, John G. Lundberg, Peter E. Midford, James P. Balhoff, Hilmar Lapp, Todd J. Vision, Melissa A. Haendel, Monte Westerfield & Paula M. Mabee
The rich knowledge of morphological variation among organisms reported in the systematic literature has remained in free-text format, impractical for use in large-scale synthetic phylogenetic work. This noncomputable format has also precluded linkage to the large knowledgebase of genomic, genetic, developmental, and phenotype data in model organism databases. We have undertaken an effort to prototype a curated, ontology-based evolutionary morphology database that maps to these genetic databases (http://kb.phenoscape.org) to facilitate investigation into the mechanistic basis...

Data from: Anolis sex chromosomes are derived from a single ancestral pair

Tony Gamble, Anthony J. Geneva, Richard E. Glor & David Zarkower
To explain the frequency and distribution of heteromorphic sex chromosomes in the lizard genus Anolis we compared the relative roles of sex chromosome conservation vs. turnover of sex determining mechanisms. We used model based comparative methods to reconstruct karyotype evolution and the presence of heteromorphic sex chromosomes onto a newly generated Anolis phylogeny. We found that heteromorphic sex chromosomes evolved multiple times in the genus. Fluorescent in situ hybridization (FISH) of repetitive DNA showed variable...

Data from: Phylogeny and biogeography of the core babblers (Aves: Timaliidae)

Robert G. Moyle, Michael J. Andersen, Carl H. Oliveros, Frank Steinheimer & Sushma Reddy
The avian family Timaliidae is a species rich and morphologically diverse component of African and Asian tropical forests. The morphological diversity within the family has attracted interest from ecologists and evolutionary biologists, but systematists have long suspected that this diversity might also mislead taxonomy, and recent molecular phylogenetic work has supported this hypothesis. We produced and analyzed a dataset of six genes and almost 300 individuals to assess the evolutionary history of the family. Although...

Data from: Spatial analysis of anthropogenic landscape disturbance and Buruli ulcer disease in Benin

Lindsay P. Campbell, Andrew O. Finley, Mark Eric Benbow, Jenni Gronseth, Pamela Small, Roch Christian Johnson, Ghislain E. Sopoh, Richard M. Merritt, Heather Williamson, Jiaguo Qi & M. Eric Benbow
Background: Land use and land cover (LULC) change is one anthropogenic disturbance linked to infectious disease emergence. Current research has focused largely on wildlife and vector-borne zoonotic diseases, neglecting to investigate landscape disturbance and environmental bacterial infections. One example is Buruli ulcer (BU) disease, a necrotizing skin disease caused by the environmental pathogen Mycobacterium ulcerans (MU). Empirical and anecdotal observations have linked BU incidence to landscape disturbance, but potential relationships have not been quantified as...

Data from: Mutations in different pigmentation genes are associated with parallel melanism in island flycatchers

J. Albert C. Uy, Elizabeth A. Cooper, Stephen Cutie, Moira R. Concannon, Jelmer W. Poelstra, Robert G. Moyle & Christopher E. Filardi
The independent evolution of similar traits across multiple taxa provides some of the most compelling evidence of natural selection. Little is known, however, about the genetic basis of these convergent or parallel traits: are they mediated by identical or different mutations in the same genes, or unique mutations in different genes? Using a combination of candidate gene and reduced representation genomic sequencing approaches, we explore the genetic basis of and the evolutionary processes that mediate...

Data from: Phylogenomic analyses support traditional relationships within Cnidaria

Felipe Zapata, Freya E. Goetz, Stephen A. Smith, Mark Howison, Stefan Siebert, Samuel H. Church, Steven M. Sanders, Cheryl Lewis Ames, Catherine S. McFadden, Scott C. France, Marymegan Daly, Allen G. Collins, Steven H. D. Haddock, Casey W. Dunn & Paulyn Cartwright
Cnidaria, the sister group to Bilateria, is the most diverse group of animals in terms of morphology, lifecycles, ecology, and development. How this diversity originated and evolved is not well understood because phylogenetic relationships among major cnidarian lineages are unclear, and recent studies present contrasting phylogenetic hypotheses. Here, we use transcriptome data from 15 newly-sequenced species in combination with 26 publicly available genomes and transcriptomes to assess phylogenetic relationships among major cnidarian lineages. Phylogenetic analyses...

Data from: Atlas of Mexican Triatominae (Reduviidae: Hemiptera) and vector transmission of Chagas disease

Janine M. Ramsey, A. Townsend Peterson, Oscar Carmona-Castro, David A. Moo-Llanes, Yoshinori Nakazawa, Butrick Morgan, Ezequiel Tun-Ku, Keynes De La Cruz-Félix, Carlos N. Ibarra-Cerdeña & Morgan Butrick
Chagas disease is one of the most important yet neglected parasitic diseases in Mexico and is transmitted by Triatominae. Nineteen of the 31 Mexican triatomine species have been consistently found to invade human houses and all have been found to be naturally infected with Trypanosoma cruzi. The present paper aims to produce a state-of-knowledge atlas of Mexican triatomines and analyse their geographic associations with T. cruzi, human demographics and landscape modification. Ecological niche models (ENMs)...

Data from: Evolution of codfishes (Teleostei: Gadinae) in geographical and ecological space: evidence that physiological limits drove diversification of subarctic fishes

Hannah L. Owens
Aim: To develop a holistic biogeographical history of codfishes in the subfamily Gadinae based on historical relationships, ecological niche, and evolution of physiological tolerances. Two alternative diversification scenarios were tested in two co-distributed, Northern Hemisphere clades: (1) clade ancestors were temperate, and environmental niche has been conserved over evolutionary time, implying that speciation was driven by vicariance associated with ice sheet formation; and (2) clade ancestors were Arctic, and species convergently adapted to temperate environmental...

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: Fitness of crop-wild hybrid sunflowers under competitive conditions: implications for crop-to-wild introgression

Kristin L. Mercer, D. Jason Emry, Allison A. Snow, Matthew A. Kost, Brian A. Pace & Helen M. Alexander
Understanding the likelihood and extent of introgression of novel alleles in hybrid zones requires comparison of lifetime fitness of parents and hybrid progeny. However, fitness differences among cross types can vary depending on biotic conditions, thereby influencing introgression patterns. Based on past work, we predicted that increased competition would enhance introgression between cultivated and wild sunflower (Helianthus annuus) by reducing fitness advantages of wild plants. To test this prediction, we established a factorial field experiment...

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, Cureton II, James C, 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: Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution

Richard E. Broughton, Ricardo Betancur-R., Chenhong Li, Gloria Arratia & Guillermo Orti
Over half of all vertebrates are “fishes”, which exhibit enormous diversity in morphology, physiology, behavior, reproductive biology, and ecology. Investigation of fundamental areas of vertebrate biology depend critically on a robust phylogeny of fishes, yet evolutionary relationships among the major actinopterygian and sarcopterygian lineages have not been conclusively resolved. Although a consensus phylogeny of teleosts has been emerging recently, it has been based on analyses of various subsets of actinopterygian taxa, but not on a...

Data from: Multilocus phylogeny and Bayesian estimates of species boundaries reveal hidden evolutionary relationships and cryptic diversity in Southeast Asian monitor lizards

Luke J. Welton, Cameron D. Siler, Jamie R. Oaks, Arvin C. Diesmos, Rafe M. Brown, L. J. Welton, J. R. Oaks, R. M. Brown, C. D. Siler & A. C. Diesmos
Recent conceptual, technological, and methodological advances in phylogenetics have enabled increasingly robust statistical species delimitation in studies of biodiversity. As the variety of evidence purporting species diversity has increased, so too have the kinds of tools and inferential power of methods for delimiting species. Here we showcase an organismal system for a data-rich, comparative molecular approach to evaluating strategies of species delimitation among monitor lizards of the genus Varanus. The water monitors (Varanus salvator Complex),...

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, M. Latvis, E. V. Mavrodiev, P. S. Soltis, J. G. Burleigh, B. C. O'Meara, M. E. Mort & D. E. Soltis
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: Mapping QTL contributing to variation in posterior lobe morphology between strains of Drosophila melanogaster

Jennifer L. Hackett, Xiaofei Wang, Brittny R. Smith, Stuart Macdonald & Stuart J. Macdonald
Closely-related, and otherwise morphologically similar insect species frequently show striking divergence in the shape and/or size of male genital structures, a phenomenon thought to be driven by sexual selection. Comparative interspecific studies can help elucidate the evolutionary forces acting on genital structures to drive this rapid differentiation. However, genetic dissection of sexual trait divergence between species is frequently hampered by the difficulty generating interspecific recombinants. Intraspecific variation can be leveraged to investigate the genetics of...

Data from: A fast-evolving X-linked duplicate of importin-α2 is overexpressed in sex-ratio drive in Drosophila neotestacea

Kathleen E. Pieper, Robert L. Unckless & Kelly A. Dyer
Selfish genetic elements that manipulate gametogenesis to achieve a transmission advantage are known as meiotic drivers. Sex-ratio X-chromosomes (SR) are meiotic drivers that prevent the maturation of Y-bearing sperm in male carriers to result in the production of mainly female progeny. The spread of an SR chromosome can affect host genetic diversity and genome evolution, and can even cause host extinction if it reaches sufficiently high prevalence. Meiotic drivers have evolved independently many times, though...

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