428 Works

Data from: An expanded plastid phylogeny of Marsilea with emphasis on North American species

W. Mark Whitten, Colette C. Jacono & Nathalie S. Nagalingum
Ferns of the genus Marsilea (water clover) are potentially invasive aquatic and wetland plants. They are difficult to identify to species because of subtle diagnostic characters, the sterile condition of many specimens, and unresolved taxonomic problems. We sequenced four plastid regions (rbcL, rps4, rps4-trnS spacer, and trnL-F spacer) from 223 accessions across ca. 38 species. Our goals were to: 1) attempt to identify problematic Marsilea specimens from the southeastern U.S., and 2) assess species delimitation...

Data from: Life histories and conservation of long-lived reptiles, an illustration with the American Crocodile (Crocodylus acutus)

Venetia Briggs-Gonzalez, Christophe Bonenfant, Mathieu Basille, Michael Cherkiss, Jeff Beauchamp & Frank Mazzotti
1. Successful species conservation is dependent on adequate estimates of population dynamics, but age-specific demographics are generally lacking for long-lived iteroparous species. Accurate demographic information allows estimation of population growth rate, as well as projection of future population sizes and quantitative analyses of fitness trade-offs involved in evolution of life-history strategies. 2. Here, a long-term capture-recapture study was conducted from 1978-2014 on the American crocodile (Crocodylus acutus) in southern Florida. Over the study period, 7,427...

Data from: Estimating field capacity from volumetric soil water content time series using automated processing algorithms

Eban Z. Bean, Ray G. Huffaker & Kati W. Migliaccio
Vadose zone measurements of volumetric soil water content (θ) using soil moisture sensors (SMSs) have become more common due to advances in technology and reduction of costs. Soil moisture sensor data exhibit a characteristic cyclical pattern reflecting water flux dynamics into and out of the observed soil volume. Expert review of SMS datasets to distinguish valid from corrupt or incomplete soil water cycles is arguably the most precise method for determining field capacity (θFC) but...

Data from: Silenced rRNA genes are activated and substitute for partially eliminated active homoelogs in the recently formed allotetraploid, Tragopogon mirus (Asteraceae)

Ales Kovařík, Eva Dobešová, Roman Matyášek, Andrew R. Leitch, Pamela S. Soltis, Douglas E. Soltis & Hana Malinska
To study the relationship between uniparental rDNA (encoding 18S, 5.8S and 26S ribosomal RNA) silencing (nucleolar dominance) and rRNA gene dosage, we studied a recently emerged (within the last 80 years) allotetraploid Tragopogon mirus (2n=24), formed from the diploid progenitors T. dubius (2n=12, D-genome donor) and T. porrifolius (2n=12, P-genome donor). Here, we used molecular, cytogenetic and genomic approaches to analyse rRNA gene activity in two sibling T. mirus plants (33A and 33B) with widely...

Data from: Historical climatic variability and geographical barriers as drivers of community composition in a biodiversity hotspot

Jessica A. Oswald, J. Gordon Burleigh, David W. Steadman, Scott K. Robinson & Andrew W. Kratter
Aim: To evaluate the roles of Quaternary (< 2.6 Ma) climatic stability and geologic barriers (i.e. the Andes Mountains) in shaping the modern community composition and patterns of endemism in Neotropical dry forest bird communities. Location: Marañón Valley and Tumbes, north-western Peru. Methods: We recorded presence and abundance of species in six dry forest bird communities on either side of the Andes Mountains. We used the data to calculate the beta diversity and phylogenetic beta...

Data from: The tale of the shrinking weapon: seasonal changes in nutrition affect weapon size and sexual dimorphism, but not contemporary evolution

Christine W. Miller, Grant C. McDonald, Allen J. Moore, A. J. Moore, C. W. Miller & G. C. McDonald
Sexually selected traits are often highly variable in size within populations due to their close link with the physical condition of individuals. Nutrition has a large impact on physical condition, and thus, any seasonal changes in nutritional quality are predicted to alter the average size of sexually selected traits as well as the degree of sexual dimorphism in populations. However, although traits affected by mate choice are well studied, we have a surprising lack of...

Data from: Geosmithia associated with bark beetles and woodborers in the western USA: taxonomic diversity and vector specificity

Miroslav Kolařík, Steven J. Seybold, Ned Tisserat, Wilhelm De Beer, David M. Rizzo, Jiri Hulcr & Martin Kostovčík
Fungi in the genus Geosmithia (Ascomycota: Hypocreales) are frequent associates of bark beetles and woodborers that colonize hardwood and coniferous trees. One species, Geosmithia morbida, is an economically damaging invasive species. The authors surveyed the Geosmithia species of California and Colorado, USA, to (i) provide baseline data on taxonomy of Geosmithia and beetle vector specificity across the western USA; (ii) investigate the subcortical beetle fauna for alternative vectors of the invasive G. morbida; and (iii)...

Data from: The hindgut-lumen prokaryotic microbiota of the lignocellulose-degrading termite Reticulitermes flavipes and its responses to dietary lignocellulose composition

Drion G. Boucias, Yunpeng Cai, Yijun Sun, Verena-Ulrike Lietze, Ruchira Sen, Rhitoban Raychoudhury & Michael E. Scharf
Reticulitermes flavipes (Isoptera: Rhinotermitidae) is a highly eusocial insect that thrives on recalcitrant lignocellulosic diets through nutritional symbioses with gut-dwelling prokaryotes and eukaryotes. In the R. flavipes hindgut, there are up to 12 eukaryotic protozoan symbionts; the number of prokaryotic symbionts has been estimated in the hundreds. Despite its biological relevance, this diverse community, to date, has been investigated only by culture- and cloning-dependent methods. Moreover, it is unclear how termite gut microbiomes respond to...

Data from: Edge effects on growth and biomass partitioning of an Amazonian understory herb (Heliconia acuminata; Heliconiaceae)

Emilio M. Bruna, Ana Segalin De Andrade & Ana Segalin De Andrade
PREMISE: After deforestation, environmental changes in the remaining forest fragments are often most intense near the forest edge, but few studies have evaluated plant growth or plasticity of plant growth in response to edge effects. METHODS: In a 2-year common garden experiment, we compared biomass allocation and growth of Heliconia acuminata with identical genotypes grown in 50 × 35 m common gardens on a 25-year-old edge and in a forest interior site. KEY RESULTS: Genetically...

Data from: Inhibition of BTK and ITK with ibrutinib is effective in the prevention of chronic graft-versus-host disease in mice

Steven D. Schutt, Jianing Fu, Hung Nguyen, David Bastian, Jessica Heinrichs, Yongxia Wu, Chen Liu, Daniel G. McDonald, Joseph Pidala & Xue-Zhong Yu
Bruton’s Tyrosine Kinase (BTK) and IL-2 Inducible T-cell Kinase (ITK) are enzymes responsible for the phosphorylation and activation of downstream effectors in the B-cell receptor (BCR) signaling and T cell receptor (TCR) signaling pathways, respectively. Ibrutinib is an FDA-approved potent inhibitor of both BTK and ITK that impairs B-cell and T-cell function. CD4 T cells and B cells are essential for the induction of chronic graft-versus-host disease (cGVHD). We evaluated these targets by testing the...

Data from: Rigorous approaches to species delimitation have significant implications for African crocodilian systematics and conservation

Matthew Shirley, Kent Vliet, Amanda Carr, James Austin, J. D. Austin, A. N. Carr, M. H. Shirley & K. A. Vliet
Accurate species delimitation is a central assumption of biology that, in groups such as the Crocodylia, is often hindered by highly conserved morphology and frequent introgression. In Africa, crocodilian systematics has been hampered by complex regional biogeography and confounded taxonomic history. We used rigorous molecular and morphological species delimitation methods to test the hypothesis that the slender-snouted croco- dile (Mecistops cataphractus) is composed of multiple species corresponding to the Congolian and Guinean biogeographic zones. Speciation...

Data from: Data sources for trait databases: comparing the phenomic content of monographs and evolutionary matrices

T. Alex Dechecchi, Paula M. Mabee, David C. Blackburn & T. Alex Dececchi
Databases of organismal traits that aggregate information from one or multiple sources can be leveraged for large-scale analyses in biology. Yet the differences among these data streams and how well they capture trait diversity have never been explored. We present the first analysis of the differences between phenotypes captured in free text of descriptive publications (‘monographs’) and those used in phylogenetic analyses (‘matrices’). We focus our analysis on osteological phenotypes of the limbs of four...

Data from: Phylogenetic signal detection from an ancient rapid radiation: effects of noise reduction, long-branch attraction, and model selection in crown clade Apocynaceae

Shannon C. K. Straub, Michael J. Moore, Pamela S. Soltis, Douglas E. Soltis, Aaron Liston, Tatyana Livshultz & Shannon C.K. Straub
Crown clade Apocynaceae comprise seven primary lineages of lianas, shrubs, and herbs with a diversity of pollen aggregation morphologies including monads, tetrads, and pollinia, making them an ideal group for investigating the evolution and function of pollen packaging. Traditional molecular systematic approaches utilizing small amounts of sequence data have failed to resolve relationships along the spine of the crown clade, a likely ancient rapid radiation. The previous best estimate of the phylogeny was a five-way...

Data from: Opsin repertoire and expression patterns in horseshoe crabs: evidence from the genome of Limulus polyphemus (Arthropoda: Chelicerata)

Barbara-Anne Battelle, Joseph F. Ryan, Karen E. Kempler, Spencer R. Saraf, Catherine E. Marten, Wesley C. Warren, Patrick Minx, Michael J. Montague, Pamela J. Green, Skye A. Schmidt, Lucinda Fulton, Nipam H. Patel, Merideth E. Protas, Richard K. Wilson & Megan L. Porter
Horseshoe crabs are xiphosuran chelicerates, the sister group to arachnids. As such, they are important for understanding the most recent common ancestor of Euchelicerata and the evolution and diversification of Arthropoda. Limulus polyphemus is the most investigated of the four extant species of horseshoe crabs, and the structure and function of its visual system have long been a major focus of studies critical for understanding the evolution of visual systems in arthropods. Likewise, studies of...

Data from: Insights into the genetic basis of blueberry fruit-related traits using diploid and polyploid models in a GWAS context

Luis Felipe V. Ferrão, Juliana Benevenuto, Ivone De Bem Oliveira, Catherine Cellon, James Olmstead, Matias Kirst, , Patricio Munoz & Marcio F. R. Resende
Polyploidization is an ancient and recurrent process in plant evolution, impacting the diversification of natural populations and plant breeding strategies. Polyploidization occurs in many important crops; however, its effects on inheritance of many agronomic traits are still poorly understood compared with diploid species. Higher levels of allelic dosage or more complex interactions between alleles could affect the phenotype expression. Hence, the present study aimed to dissect the genetic basis of fruit-related traits in autotetraploid blueberries...

Data from: Building the avian tree of life using a large-scale, sparse supermatrix

J. Gordon Burleigh, Rebecca T. Kimball & Edward L. Braun
Birds are the most diverse tetrapod class, with about 10,000 extant species that represent a remarkable evolutionary radiation in which most taxa arose during a short period of time. There has been a tremendous increase in the amount of molecular data available from birds, and more than two-thirds of these species have some sequence data available. Here we assembled these available sequence data from birds to estimate a large-scale avian phylogeny. We performed an unconstrained...

Data from: Do thermoregulatory costs limit altitude distributions of Andean forest birds?

Gustavo A. Londono, Mark A. Chappell, Jill E. Jankowski & Scott K. Robinson
Along tropical mountains, species often occupy narrow altitude ranges. Numerous biotic and abiotic factors have been proposed as determinants of altitude occupancy. We measured several aspects of thermal physiology of 215 bird species across a 2·6-km altitude gradient in the Peruvian Andes. We predicted that highland species would show adaptation to the colder high-altitude climate and that energy costs of thermoregulation might limit upslope dispersal of lowland natives. We found reductions in thermal conductance, body...

Data from: Grass invasion and drought interact to alter the diversity and structure of native plant communities

Catherine Fahey, Christine Angelini & S. Luke Flory
Understanding the interactive effects of species invasions and climate change is essential for predicting future shifts in biodiversity. Because multiple stressors can interact in synergistic or antagonistic ways, it is notoriously difficult to anticipate their combined effects on species assemblages. However, some hypotheses predict that plant invasions will become increasingly problematic as climate change improves conditions for invaders or lowers the biotic resistance of native communities. In a four-year field experiment, we quantified the individual...

Data from: Macroevolutionary consequences of profound climate change on niche evolution in marine mollusks over the past three million years

Erin E. Saupe, Jonathan R. Hendricks, Roger W. Portell, Harry J. Dowsett, Alan Haywood, Stephen J. Hunter, Bruce S. Lieberman, B. S. Lieberman, E. E. Saupe, A. Haywood, S. J. Hunter, H. J. Dowsett & R. W. Portell
In order to predict the fate of biodiversity in a rapidly changing world, we must first understand how species adapt to new environmental conditions. The long-term evolutionary dynamics of species' physiological tolerances to differing climatic regimes remain obscure. Here, we unite palaeontological and neontological data to analyse whether species' environmental tolerances remain stable across 3 Myr of profound climatic changes using 10 phylogenetically, ecologically and developmentally diverse mollusc species from the Atlantic and Gulf Coastal...

Data from: Phylogenetic utility of ycf1 in orchids: a plastid gene more variable than matK

Kurt M. Neubig, W. Mark Whitten, Barbara S. Carlsward, Mario A. Blanco, Lorena Endara, Norris H. Williams & Michael Moore
Plastid DNA sequences have been widely used by systematists for reconstructing plant phylogenies. The utility of any DNA region for phylogenetic analysis is determined by ease of amplification and sequencing, confidence of assessment in phylogenetic character alignment, and by variability across broad taxon sampling. Often, a compromise must be made between using relatively highly conserved coding regions or highly variable introns and intergenic spacers. Analyses of a combination of these types of DNA regions yield...

Data from: The unexpected depths of genome-skimming data: a case study examining Goodeniaceae floral symmetry genes

Brent A. Berger, Jiahong Han, Emily B. Sessa, Andrew G. Gardner, Kelly A. Shepherd, Vincent A. Ricigliano, Rachel S. Jabaily & Dianella G. Howarth
Premise of the study: The use of genome skimming allows systematists to quickly generate large data sets, particularly of sequences in high abundance (e.g., plastomes); however, researchers may be overlooking data in low abundance that could be used for phylogenetic or evo-devo studies. Here, we present a bioinformatics approach that explores the low-abundance portion of genome-skimming next-generation sequencing libraries in the fan-flowered Goodeniaceae. Methods: Twenty-four previously constructed Goodeniaceae genome-skimming Illumina libraries were examined for their...

Data from: The mutational decay of male-male and hermaphrodite-hermaphrodite competitive fitness in the androdioecious nematode C. elegans

Shu-Dan Yeh, Ayush Shekhar Saxena, Timothy A. Crombie, Dorian Feistel, Lindsay M. Johnson, Isabel Lam, Jennifer Lam, Sayran Saber & Charles F. Baer
Androdioecious Caenorhabditis have a high frequency of self-compatible hermaphrodites and a low frequency of males. The effects of mutations on male fitness are of interest for two reasons. First, when males are rare, selection on male-specific mutations is less efficient than in hermaphrodites. Second, males may present a larger mutational target than hermaphrodites because of the different ways in which fitness accrues in the two sexes. We report the first estimates of male-specific mutational effects...

Data from: Counteracting effects of a non-native prey on demography of a native predator culminate in positive population growth

Christopher E. Cattau, , Brian E. Reichert, Wiley M. Kitchens & Robert J. Fletcher
Identifying impacts of non-native species on native populations is central to conservation and ecology. While effects of non-native predators on native prey populations have recently received much attention, impacts of introduced prey on native predator populations are less understood. Non-native prey can influence predator behavior and demography through direct and indirect pathways, yet quantitative assessments of the relative impacts of multiple, potentially counteracting, effects on native predator population growth remain scarce. Using ≈20 years of...

Data from: A chromosomal-scale genome assembly of Tectona grandis reveals the importance of tandem gene duplication and enables discovery of genes in natural product biosynthetic pathways

Dongyan Zhao, John P. Hamilton, Wajid Waheed Bhat, Sean R. Johnson, Grant T. Godden, Taliesin J. Kinser, Benoît Boachon, Natalia Dudareva, Douglas E. Soltis, Pamela S. Soltis, Bjoern Hamberger & C. Robin Buell
Background: Teak, a member of the Lamiaceae family, produces one of the most expensive hardwoods in the world. High demand coupled with deforestation have caused a decrease in natural teak forests, and future supplies will be reliant on teak plantations. Hence, selection of teak tree varieties for clonal propagation with superior growth performance is of great importance, and access to high-quality genetic and genomic resources can accelerate the selection process by identifying genes underlying desired...

Data from: Integrating phylogenomic and population genomic patterns in avian lice provides a more complete picture of parasite evolution

Andrew D. Sweet, Bret M. Boyd, Julie M. Allen, Scott M. Villa, Michel P. Valim, Jose L. Rivera-Parra, Robert E. Wilson & Kevin P. Johnson
Parasite diversity accounts for most of the biodiversity on earth, and is shaped by many processes (e.g. cospeciation, host-switching). To identify the effects of the processes that shape parasite diversity, it is ideal to incorporate both deep (phylogenetic) and shallow (population) perspectives. To this end, we developed a novel workflow to obtain phylogenetic and population genetic data from whole genome sequences of body lice parasitizing New World ground-doves. Phylogenies from these data showed consistent, highly...

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