229 Works

Data from: A genomic approach for distinguishing between recent and ancient admixture as applied to cattle

Emily Jane McTavish & David M. Hillis
Genomic data facilitate opportunities to track complex population histories of divergence and gene flow. We developed a metric, scaled block size (SBS), that uses the unrecombined block size of introgressed regions of chromosomes to differentiate between recent and ancient admixture, and applied it to reconstructing admixture in cattle. Cattle are descendants of two independently domesticated lineages, taurine and indicine, that diverged 200,000 or more years ago. Several breeds have hybrid ancestry between these divergent lineages....

Data from: Species delimitation with gene flow: a methodological comparison and population genomics approach to elucidate cryptic species boundaries in Malaysian Torrent Frogs

Kin Onn Chan, Alana M. Alexander, Jesse L. Grismer, Yong-Chao Su, Evan S.H. Quah, Rafe M. Brown, Evan S. H. Quah & L. Lee Grismer
Accurately delimiting species boundaries is a non-trivial undertaking that can have significant effects on downstream inferences. We compared the efficacy of commonly-used species delimitation methods (SDMs) and a population genomics approach based on genome-wide single nucleotide polymorphisms (SNPs) to assess lineage separation in the Malaysian Torrent Frog Complex currently recognized as a single species (Amolops larutensis). First, we used morphological, mitochondrial DNA and genome-wide SNPs to identify putative species boundaries by implementing non-coalescent and coalescent-based...

Data from: Non-clonal coloniality: genetically chimeric colonies through fusion of sexually produced polyps in the hydrozoan Ectopleura larynx

E. Sally Chang, Maria E. Orive & Paulyn Cartwright
Hydrozoans typically develop colonies through asexual budding of polyps. Although colonies of Ectopleura are similar to other hydrozoans in that they consist of multiple polyps physically connected through continuous epithelia and shared gastrovascular cavity, Ectopleura larynx does not asexually bud polyps indeterminately. Instead, after an initial phase of limited budding in a young colony, E. larynx achieves its large colony size through the aggregation and fusion of sexually (non-clonally) produced polyps. The apparent chimerism within...

Data from: Life history traits and phenotypic selection among sunflower crop-wild hybrids and their wild counterpart: implications for crop allele introgression

Matthew A. Kost, Helen M. Alexander, D. Jason Emry & Kristin L. Mercer
Hybridization produces strong evolutionary forces. In hybrid zones, selection can differentially occur on traits and selection intensities may differ among hybrid generations. Understanding these dynamics in crop-wild hybrid zones can clarify crop-like traits likely to introgress into wild populations and the particular hybrid generations through which introgression proceeds. In a field experiment with four crop-wild hybrid Helianthus annuus (sunflower) cross types, we measured growth and life history traits and performed phenotypic selection analysis on early...

Data from: A Bayesian method for the joint estimation of outcrossing rate and inbreeding depression

John K. Kelly, Vanessa A. Koelling & Patrick J. Monnahan
The population outcrossing rate (t) and adult inbreeding coefficient (F) are key parameters in mating system evolution. The magnitude of inbreeding depression as expressed in the field can be estimated given t and F via the method of Ritland (1990). For a given total sample size, the optimal design for the joint estimation of t and F requires sampling large numbers of families (100-400) with fewer offspring (1-4) per family. Unfortunately, the standard inference procedure...

Data from: Placing cryptic, recently extinct, or hypothesized taxa into an ultrametric phylogeny using continuous character data: A case study with the lizard Anolis roosevelti

Liam J. Revell, D. Luke Mahler, Robert Graham Reynolds & Graham James Slater
In recent years, enormous effort and investment has been put into assembling the tree of life: a phylogenetic history for all species on Earth. Overwhelmingly, this progress toward building an ever increasingly complete phylogeny of living things has been accomplished through sophisticated analysis of molecular data. In the modern genomic age, molecular genetic data have become very easy and inexpensive to obtain for many species. However, some lineages are poorly represented in or absent from...

Data from: Greenhouse biogeography: the relationship of geographic range to invasion and extinction in the Cretaceous Western Interior Seaway

Corinne E. Myers, , Bruce S. Lieberman & Richard A. MacKenzie
Significant warming of Earth's climate in the near term seems increasingly likely. If significant enough, this climatic regime could, in the long term, come to resemble previous greenhouse intervals in earth history. Consequently, analysis of the fossil record during periods of extreme warmth may provide important lessons for species biology, including biogeography, in a much warmer world. To explore this issue, we analyzed the biogeographic response of 63 molluscan species to the long-term global warmth...

Data from: Fitness consequences of outcrossing in a social spider with an inbreeding mating system

Reut Berger-Tal, Cristina Tuni, Yael Lubin, Debroah Smith, Trine Bilde & Deborah Smith
Inbreeding mating systems are uncommon because of inbreeding depression. Mating among close relatives can evolve, however, when outcrossing is constrained. Social spiders show obligatory mating among siblings. In combination with a female-biased sex ratio, sib-mating results in small effective populations. In such a system high genetic homozygosity is expected, and drift may cause population divergence. We tested the effect of outcrossing in the social spider Stegodyphus dumicola. Females were mated to sib-males, to a non-nestmate...

Data from: Quantifying morphological change during an evolutionary radiation of Devonian trilobites

Francine R. Abe & Bruce S. Lieberman
The fossil record provides an important source of data on adaptive radiations, and indeed some of the earliest theoretical insights on the nature of these radiations were made by paleontologists. Here we focus on the diverse Devonian Metacryphaeus group calmoniid trilobites, known from the Malvinokaffric Realm; these have been considered a classic example of an adaptive radiation preserved in the fossil record. A geometric morphometric analysis is used in conjunction with phylogenetic and biogeographic patterns...

A morphometric assessment of species boundaries in a widespread anole lizard (Squamata: Dactyloidae)

Tanner Myers, Pietro De Mello & Richard Glor
Cryptic species - genetically distinct species that are morphologically difficult to distinguish - present challenges to systematists. Operationally, cryptic species are very difficult to identify and sole usage of genetic data or morphological data can fail to recognize evolutionarily isolated lineages. We use morphometric data to test species boundaries hypothesized with genetic data in the North Caribbean Bark Anole (Anolis distichus), a suspected species complex. We use univariate and multivariate analyses to test if candidate...

Codes: A new approach to interspecific synchrony in population ecology using tail association

Shyamolina Ghosh, Lawrence W. Sheppard, Philip C. Reid & Daniel C. Reuman
Standard methods for studying the association between two ecologically important variables provide only a small slice of the information content of the association, but statistical approaches are available that provide comprehensive information. In particular, available approaches can reveal tail associations, i.e., accentuated or reduced associations between the more extreme values of variables. We here study the nature and causes of tail associations between phenological or population-density variables of co-located species, and their ecological importance. We...

Quantifying shell outline variability in extant and fossil Laqueus (Brachiopoda: Terebratulida): are outlines good proxies for long-looped brachidial morphology and can they help us characterize species?

Natalia Lopez Carranza & Sandra Carlson
Extant and extinct terebratulide brachiopod species have been defined primarily on the basis of morphology. What is the fidelity of morphological species to biological species? And how can we test this fidelity with fossils? Taxonomically and phylogenetically, the most informative internal feature in the brachiopod suborder Terebratellidina is the geometrically complex long-looped brachidium, which, given their fragile nature, are not commonly preserved in the fossil record. In their absence, it is essential to test other...

Supplementary information for: The effects of geographic range size and abundance on extinction during a time of ‘sluggish’ evolution

Michelle Casey, Erin Saupe & Bruce Lieberman
Geographic range size and abundance are important determinants of extinction risk in fossil and extant taxa. However, the relationship between these variables and extinction risk has not been tested extensively during evolutionarily ‘quiescent’ times of low extinction and speciation in the fossil record. Here we examine the influence of geographic range size and abundance on extinction risk during the late Paleozoic (Mississippian–Permian), a time of ‘sluggish’ evolution when global rates of origination and extinction were...

Functional niche constraints on carnivore assemblages (mammalia: carnivora) in the Americas: What facilitates coexistence through space and time?

Andrés Arias-Alzate, Felber J. Arroyave, Oscar Y. Romero Goyeneche, Rafael Hurtado Heredia, José F. Gonzalez-Maya, Joaquín Arroyo-Cabrales, A. Townsend Peterson & Enrique Martínez-Meyer
Aim: Mammalian carnivores are among the best studied groups in terms of evolutionary history. However, the effects of species interactions in shaping community assemblages remain poorly understood. We hypothesize that indirect interactions via ecological trait filtering play a key role in structuring carnivoran assemblages, mediate coexistence, and thus should show high functional diversity in space and time at continental scales. Location: Americas. Taxon: Mammalian carnivores (Mammalia: Carnivora). Methods: We followed a macroecological perspective via ecological...

Code and resulting candidate gene datasets from Anopheles genome environment association testing

Devon DeRaad
The concept of a fundamental ecological niche is central to questions of geographic distribution, population demography, species conservation, and evolutionary potential. But robust inference of genomic regions associated with evolutionary adaptation to particular environmental conditions remains difficult due to the myriad of potential confounding processes that can generate heterogeneous patterns of variation across the genome. Here, we interrogate the potential role of genome environment association (GEA) testing as an initial step in building an understanding...

Data from: Temporal scale of environmental correlations affects ecological synchrony

Robert A. Desharnais, Daniel C. Reuman, Robert F. Costantino & Joel E. Cohen
Population densities of a species, measured in different locations are often correlated over time, a phenomenon referred to as synchrony. Synchrony results from dispersal of individuals among locations and spatially correlated environmental variation, among other causes. Synchrony is often measured by a correlation coefficient. However, synchrony can vary with timescale. We demonstrate theoretically and experimentally that the timescale-specificity of environmental correlation affects the overall magnitude and timescale-specificity of synchrony, and that these effects are modified...

Data from: Age, state, environment and season dependence of senescence in body mass

Svenja B. Kroeger, Daniel T. Blumstein, Kenneth B. Armitage, Jane M. Reid, Julien G.A. Martin & Julien G. A. Martin
Data file in csv formatBMdata.csvRcode

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
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: Greater host breadth still not associated with increased diversification rate in the Nymphalidae – a response to Janz et al

Christopher Alan Hamm & James Andrew Fordyce
In their technical comment, Janz et al. take issue with our recent study examining the association between host breadth and diversification rates in the brush footed butterflies (Lepidoptera: Nymphalidae) (Hamm and Fordyce 2015). Specifically, they are concerned that we misrepresent their “oscillation hypothesis” (OH) (Janz et al. 2016; Janz and Nylin 2008) and that one of our models was inadequate to test hypotheses regarding host breadth and diversification rate. Given our mutual interests in the...

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: 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
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: MycoDB, a global database of plant response to mycorrhizal fungi

V. Bala Chaudhary, Megan A. Rúa, Anita Antoninka, James D. Bever, Jeffery Cannon, Ashley Craig, Jessica Duchicela, Alicia Frame, Monique Gardes, Catherine Gehring, Michelle Ha, Miranda Hart, Jacob Hopkins, Baoming Ji, Nancy Collins Johnson, Wittaya Kaonongbua, Justine Karst, Roger T. Koide, Louis J. Lamit, James Meadow, Brook G. Milligan, John C. Moore, , Bridget Piculell, Blake Ramsby … & Jason D. Hoeksema
Plants form belowground associations with mycorrhizal fungi in one of the most common symbioses on Earth. However, few large-scale generalizations exist for the structure and function of mycorrhizal symbioses, as the nature of this relationship varies from mutualistic to parasitic and is largely context-dependent. We announce the public release of MycoDB, a database of 4,010 studies (from 438 unique publications) to aid in multi-factor meta-analyses elucidating the ecological and evolutionary context in which mycorrhizal fungi...

Data from: Evidence for repeated acquisition and loss of complex body form characters in an insular clade of Southeast Asian semi-fossorial skinks

Cameron David Siler & Rafe M. Brown
Evolutionary simplification, or loss of complex characters, is a major theme in studies of body form evolution. The apparently infrequent evolutionary reacquisition of complex characters has led to the assertion (Dollo’s Law) that once lost, complex characters may be impossible to re-evolve, at least via the exact same evolutionary process. Here we provide one of the most comprehensive, fine-scale analyses of squamate body-form evolution to date, introducing a new model system of closely related, morphologically...

Data from: Negative plant-phyllosphere feedbacks in native Asteraceae hosts – a novel extension of the plant-soil feedback framework

Briana K. Whitaker, Jonathan T. Bauer, James D. Bever & Keith Clay
Over the past 25 years, the plant-soil feedback (PSF) framework has catalyzed our understanding of how belowground microbiota impact plant fitness and species coexistence. Here, we apply a novel extension of this framework to microbiota associated with aboveground tissues, termed ‘plant-phyllosphere feedback (PPFs)’. In parallel greenhouse experiments, rhizosphere and phyllosphere microbiota of con- and heterospecific hosts from four species were independently manipulated. In a third experiment, we tested the combined effects of soil and phyllosphere...

Data from: Ancient genomes revisit the ancestry of domestic and Przewalski’s horses

Charleen Gaunitz, Antoine Fages, Kristian Hanghøj, Anders Albrechtsen, Naveed Khan, Mikkel Schubert, Andaine Seguin-Orlando, Ivy J. Owens, Sabine Felkel, Olivier Bignon-Lau, Peter De Barros Damgaard, Alissa Mittnik, Azadeh F. Mohaseb, Hossein Davoudi, Saleh Alquraishi, Ahmed H. Alfarhan, Khaled A. S. Al-Rasheid, Eric Crubézy, Norbert Benecke, Sandra Olsen, Dorcas Brown, David Anthony, Ken Massy, Vladimir Pitulko, Aleksei Kasparov … & Ludovic Orlando
The Eneolithic Botai culture of the Central Asian steppes provides the earliest archaeological evidence for horse husbandry, ~5500 years ago, but the exact nature of early horse domestication remains controversial. We generated 42 ancient-horse genomes, including 20 from Botai. Compared to 46 published ancient- and modern-horse genomes, our data indicate that Przewalski’s horses are the feral descendants of horses herded at Botai and not truly wild horses. All domestic horses dated from ~4000 years ago...

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