186 Works

Data from: The comparative biogeography of Philippine geckos challenges predictions from a paradigm of climate-driven vicariant diversification across an island archipelago

Jamie R Oaks, Cameron D. Siler & Rafe M. Brown
A primary goal of biogeography is to understand how large-scale environmental processes, like climate change, affect diversification. One often-invoked but seldom tested process is the so-called ''species-pump'' model, in which repeated bouts of co-speciation is driven by oscillating climate-induced habitat connectivity cycles. For example, over the past three million years, the landscape of the Philippine Islands has repeatedly coalesced and fragmented due to sea-level changes associated with the glacial cycles. This repeated climate-driven vicariance has...

Data from: Frequent fire slows microbial decomposition of newly deposited fine fuels in a pyrophilic ecosystem

Jacob Hopkins
Frequent fires maintain nearly 50% of terrestrial ecosystems, and drive ecosystem changes that govern future fires. Since fires are dependent on available plant or fine fuels, ecosystem processes that alter fine fuel loads like microbial decomposition are particularly important and could modify future fires. We hypothesized that variation in short-term fire history would influence fuel dynamics in such ecosystems. We predicted that frequent fires within a short-time period would slow microbial decomposition of new fine...

A test of island biogeographic theory applied to estimates of gene flow in a Fijian bird is largely consistent with neutral expectations

Ethan Gyllenhaal, Xena Mapel, Alivereti Naikatini, Robert Moyle & Michael Andersen
Islands were key to the development of allopatric speciation theory because they are a natural laboratory of repeated barriers to gene flow caused by open water gaps. Despite their proclivity for promoting divergence, little empirical work has quantified the extent of gene flow among island populations. Following classic island biogeographic theory, two metrics of interest are relative island size and distance. Fiji presents an ideal system for studying these dynamics, with four main islands that...

Gene flow creates a mirage of cryptic species in a Southeast Asian spotted stream frog complex

Kin Onn Chan, Carl Hutter, Perry Lee Wood, Lee Grismer, Indraneil Das & Rafe Brown
Most new cryptic species are described using conventional tree- and distance-based species delimitation methods (SDMs), which rely on phylogenetic arrangements and measures of genetic divergence. However, although numerous factors such as population structure and gene flow are known to confound phylogenetic and species delimitation inferences, the influence of these processes on species estimation is not frequently evaluated. Using large amounts of exons, introns, and ultraconserved elements obtained using the FrogCap sequence-capture protocol, we compared conventional...

Data from: Cumulative reproductive costs on current reproduction in a wild polytocous mammal

Svenja B. Kroeger, Daniel T. Blumstein, Kenneth B. Armitage, Jane M. Reid, Julien G.A. Martin & Julien G. A. Martin
The cumulative cost of reproduction hypothesis predicts that reproductive costs accumulate over an individual’s reproductive lifespan. While short-term costs have been extensively explored, the prevalence of cumulative long-term costs and the circumstances under which such costs occur alongside or instead of short-term costs, are far from clear. Indeed, few studies have simultaneously tested for both short-term and cumulative long-term reproductive costs in natural populations. Even in mammals, comparatively little is known about cumulative effects of...

Data from: Origin and macroevolution of micro-moths on sunken Hawaiian islands

Chris A. Johns, Emmanuel F.A. Toussaint, Jesse W. Breinholt, Akito Y. Kawahara & Emmanuel F. A. Toussaint
The origins and evolution of Hawaiian biodiversity are a matter of controversy, and the mechanisms of lineage diversification for many organisms on this remote archipelago remain unclear. Here we focus on the poorly-known endemic leaf-mining moth genus Philodoria (Lepidoptera, Gracillariidae), whose species feed on a diversity of Hawaiian plant lineages, many of which are critically endangered. We use anchored hybrid enrichment to assemble the first phylogenomic dataset (507 loci) for any Hawaiian animal taxon. To...

The names don’t matter but the numbers do: searching for stability in Carboniferous brachiopod paleocommunities from the North American Midcontinent

Luke Strotz & Bruce Lieberman
A key question in paleoecology and macroevolution is whether assemblages of species (paleocommunities) are persistent entities that endure over millions of years. Whilst community turnover in the face of abiotic change is the presumed norm, paleocommunities have been shown to persist for long time periods and regardless of environmental disruption. It remains an open question however, as to what processes allow for this. We investigate these questions by analyzing the Carboniferous brachiopod paleocommunities from the...

Phylogeny and biogeography of some Cretaceous spatangoid echinoids with special emphasis on taxa from the Western Interior Seaway

Bruce Lieberman & Steven Byrum
Members of the echinoid order Spatangoida, a highly diverse and abundant marine invertebrate clade, were important denizens of the Cretaceous Western Interior Seaway (WIS), an epicontinental seaway that divided North America in two during an interval of greenhouse conditions between roughly 100 and 65 million years ago. A phylogenetic analysis of spatangoids was conducted using a character matrix of 32 characters from 21 species. Species that occur in the WIS were considered comprehensively, and species...

Data from: Natural selection and the genetic basis of osmoregulation in Heteromyid rodents as revealed by RNA-seq

Nicholas J. Marra, Andrea Romero & J. Andrew DeWoody
One adaptation of ecological and evolutionary interest is the extraordinary ability of desert rodents to retain water during waste production. Much is known regarding the unique kidney physiology of kangaroo rats (Dipodomys spp.) and their ability to retain water during waste production, yet the genetic basis of these physiological adaptations is relatively unknown. Herein, we utilized RNA-seq data to conduct a comparative study to identify osmoregulatory genes expressed in Heteromyid rodents. We sequenced kidney tissue...

Data from: Almost a spider: a 305-million-year-old fossil arachnid and spider origins

Russell J. Garwood, Jason A. Dunlop, Paul A. Selden, Alan R. T. Spencer, Robert C. Atwood, Nghia T. Vo & Michael Drakopoulos
Spiders are an important animal group, with a long history. Details of their origins remain limited, with little knowledge of their stem group, and no insights into the sequence of character acquisition during spider evolution. We describe a new fossil arachnid, Idmonarachne brasieri gen. et sp. nov. from the late Carboniferous (Stephanian, ca. 305–299 Ma) of Montceau-les-Mines, France. It is three-dimensionally preserved within a siderite concretion, allowing both laboratory- and synchrotron-based phase-contrast computed tomography (CT)...

Data from: Multiplexed shotgun genotyping resolves species relationships within the North American genus Penstemon

Carolyn A. Wessinger, Craig C. Freeman, Mark E. Mort, Mark D. Rausher & Lena C. Hileman
Premise of the study: Evolutionary radiations provide opportunities to examine large-scale patterns in diversification and character evolution, yet are often recalcitrant to phylogenetic resolution due to rapid speciation events. The plant genus Penstemon has been difficult to resolve using Sanger sequence-based markers, leading to the hypothesis that it represents a recent North American radiation. The present study demonstrates the utility of multiplexed shotgun genotyping (MSG), a style of Restriction site-associated DNA sequencing (RADseq), to infer...

Data from: Hybridization and reproductive isolation between diploid Erythronium mesochoreum and its tetraploid congener E. albidum (Liliaceae)

Kathy Roccaforte, Sabrina E. Russo & Diana Pilson
Polyploidy has played an important role in angiosperm diversification, but how polyploidy contributes to reproductive isolation remains poorly understood. Most work has focused on postzygotic reproductive barriers, and the influence of ploidy differences on prezygotic barriers is understudied. To address these gaps, we quantified hybrid occurrence, interspecific self-compatibility differences, and the contributions of multiple pre- and postzygotic barriers to reproductive isolation between diploid Erythronium mesochoreum (Liliaceae) and its tetraploid congener E. albidum. Reproductive isolation between...

Data from: Seed fates in crop-wild hybrid sunflowers: crop allele and maternal effects

Brian A. Pace, Helen M. Alexander, Jason D. Emry & Kristin L. Mercer
Domestication has resulted in selection upon seed traits found in wild populations, yet crop-wild hybrids retain some aspects of both parental phenotypes. Seed fates of germination, dormancy, and mortality can influence the success of crop allele introgression in crop-wild hybrid zones, especially if crop alleles or crop-imparted seed coverings result in out-of-season germination. We performed a seed burial experiment using crop, wild, and diverse hybrid sunflower (Helianthus annuus) cross types to test how a cross...

Data from: Evolutionary history shapes patterns of mutualistic benefit in Acacia-rhizobial interactions

Luke Barrett, Peter Zee, James D. Bever, Joseph T. Miller, Peter Thrall, Luke G. Barrett & Peter H. Thrall
The ecological and evolutionary factors that drive the emergence and maintenance of variation in mutualistic benefit (i.e. the benefits provided by one partner to another) in mutualistic symbioses are not well understood. In this study we evaluated the role that host and symbiont phylogeny might play in determining patterns of mutualistic benefit (host response) for interactions among nine species of Acacia and 31 strains of nitrogen-fixing rhizobial bacteria. Using phylogenetic comparative methods we compared patterns...

Data from: The geography of spatial synchrony

Jonathan A. Walter, Lawrence W. Sheppard, Thomas L. Anderson, Jude H. Kastens, Ottar N. Bjornstad, Andrew M. Liebhold & Daniel C. Reuman
Spatial synchrony, defined as correlated temporal fluctuations among populations, is a fundamental feature of population dynamics, but many aspects of synchrony remain poorly understood. Few studies have examined detailed geographical patterns of synchrony; instead most focus on how synchrony declines with increasing linear distance between locations, making the simplifying assumption that distance decay is isotropic. By synthesising and extending prior work, we show how geography of synchrony, a term which we use to refer to...

Data from: Experimental test of phytoplankton competition for nutrients and light in poorly mixed water columns

Jarad P. Mellard, Kohei Yoshiyama, Christopher A. Klausmeier & Elena Litchman
A recent theory of the vertical distribution of phytoplankton considers how interacting niche construction processes such as resource depletion, behavior, and population dynamics contribute to spatial heterogeneity in the aquatic environment. In poorly mixed water columns with opposing resource gradients of nutrients and light, theory predicts that a species should aggregate at a single depth. This depth of aggregation, or biomass maximum, should change through time due to depletion of available resources. In addition, the...

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: Rapid evolution caused by pollinator loss in Mimulus guttatus

Sarah A Bodbyl Roels & John Kennedy Kelly
Anthropogenic perturbations including habitat loss and emerging disease are changing pollinator communities and generating novel selection pressures on plant populations. Disruption of plant-pollinator relationships is predicted to cause plant mating system evolution, although this process has not been directly observed. This study demonstrates the immediate evolutionary effects of pollinator loss within experimental populations of a predominately outcrossing wildflower. Initially equivalent populations evolved for five generations within two pollination treatments: abundant bumblebee pollinators vs. no pollinators....

Data from: Did geckos ride the Palawan raft to the Philippines?

Cameron D. Siler, Jamie R. Oaks, Luke J. Welton, Charles W. Linkem, John C. Swab, Arvin C. Diesmos & Rafe M. Brown
AIM: We examine the genetic diversity within the lizard genus Gekko in the Philippine islands to understand the role of geography and geological history in shaping species diversity in this group. We test multiple biogeographical hypotheses of species relationships, including the recently proposed Palawan Ark hypothesis. LOCATION: Southeast Asia and the Philippines. METHODS: Samples of all island endemic and widespread Philippine Gekko species were collected and sequenced for one mitochondrial gene (NADH dehydrogenase subunit 2)...

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: Using geography to infer the importance of dispersal for the synchrony of freshwater plankton

Thomas L. Anderson, Jonathan A. Walter, Todd D. Levine, Susan P. Hendricks, Karla L. Johnston, David S. White & Daniel C. Reuman
Spatial synchrony in population dynamics is a ubiquitous ecological phenomenon that can result from predator-prey interactions, synchronized environmental variation (Moran effects), or dispersal. Of these, dispersal historically has been the least well studied in natural systems, partly because of the difficulty in quantifying dispersal in situ. We hypothesized that dispersal routes of plankton were based on the major and consistent water current movements in Kentucky Lake, a large reservoir in western Kentucky, USA. Then, using...

Data from: Reconstructing ecological niche evolution when niches are incompletely characterized

Erin E. Saupe, Narayani Barve, Hannah L. Owens, Jacob C. Cooper, Peter A. Hosner & A. Townsend Peterson
Evolutionary dynamics of abiotic ecological niches across phylogenetic history can shed light on large-scale biogeographic patterns, macroevolutionary rate shifts, and the relative ability of lineages to respond to global change. An unresolved question is how best to represent and reconstruct evolution of these complex traits at coarse spatial scales through time. Studies have approached this question by integrating phylogenetic comparative methods with niche estimates inferred from correlative and other models. However, methods for estimating niches...

Data from: Hurdiid radiodontans from the middle Cambrian (Series 3) of Utah

Stephen Pates, Allison C. Daley & Bruce S. Lieberman
Radiodontan body elements, some belonging to Peytoia and Hurdia and some unassigned, have been reported from the Langston Formation (Spence Shale Member), Wheeler Formation, and Marjum Formation of the middle Cambrian (Series 3) of Utah. These identifications are reassessed in light of recent work on the morphology of the radiodontan Hurdia. New specimens of Hurdia are identified from the Spence Shale, representing mouthparts (oral cones), cephalic carapace H-elements, frontal appendages, and a single isolated swimming...

The role of evolutionary time, diversification rates and dispersal in determining the global diversity of a large radiation of passerine birds

Tianlong Cai, Shimiao Shao, Jonathan Kennedy, Per Alström, Robert Moyle, Yanhua Qu, Fumin Lei & Jon Fjeldså
Aim: Variation in species diversity among different geographic areas may result from differences in speciation and extinction rates, immigration and time for diversification. An area with high species diversity may be the result of a high net diversification rate, multiple immigration events from adjacent regions,anda long time available for the accumulation of species (know as the “time-for-speciation effect”). Here, we examine the relative importance of the three aforementionedprocesses in shaping the geographic diversity patterns of...

Real-Time Nowcasting of Nominal GDP Under Structural Breaks

William A. Barnett, Marcelle Chauvet & Danilo Leiva-Leon
This paper provides a framework for the early assessment of current U.S. nominal GDP growth, which has been considered a potential new monetary policy target. The nowcasts are computed using the exact amount of information that policy-makers have available at the time predictions are made. However, real-time information arrives at different frequencies and asynchronously, which poses challenges of mixed frequencies, missing data and ragged edges. This paper proposes a multivariate state-space model that not only...

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