17 Works

Data from: Improving Illumina assemblies with Hi-C and long reads: an example with the North African dromedary

Jean P. Elbers, Mark F. Rogers, Polina L. Perelman, Anastasia A. Proskuryakova, Natalia A. Serdyukova, Warren E. Johnson, Petr Horin, Jukka Corander, David Murphy & Pamela A. Burger
Researchers have assembled thousands of eukaryotic genomes using Illumina reads, but traditional mate-pair libraries cannot span all repetitive elements, resulting in highly fragmented assemblies. However, both chromosome conformation capture techniques, such as Hi-C and Dovetail Genomics Chicago libraries and long-read sequencing, such as Pacific Biosciences and Oxford Nanopore, help span and resolve repetitive regions and therefore improve genome assemblies. One important livestock species of arid regions that does not have a high-quality contiguous reference genome...

Data from: Genomic, ecological, and morphological approaches to investigating species limits: a case study in modern taxonomy from Tropical Eastern Pacific surgeonfishes

William B. Ludt, Moises A. Bernal, Erica Kenworthy, Eva Salas & Prosanta Chakrabarty
A wide variety of species are distinguished by slight color variations. However, molecular analyses have repeatedly demonstrated that coloration does not always correspond to distinct evolutionary histories between closely related groups, suggesting that this trait is labile and can be misleading for species identification. In the present study, we analyze the evolutionary history of sister species of Prionurus surgeonfishes in the Tropical Eastern Pacific (TEP), which are distinguished by the presence or absence of dark...

Data from: An empirical assessment of a single family-wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae

Katy E Jones, Tomáš Fér, Roswitha E Schmickl, Rebecca B Dikow, Vicki A Funk, Sonia Herrando-Moraira, Norbert Kilian, Carolina M Siniscalchi, Alfonso Susanna, Marek Slovák, Ramhari Thapa, Linda E Watson & Jennifer R Mandel
Premise of the study: Hybrid capture with high-throughput sequencing (Hyb-Seq) is a powerful tool for evolutionary studies. The applicability of an Asteraceae family-specific Hyb-Seq method and the outcomes of different phylogenetic analyses are assessed. Methods: Hyb-Seq data from 112 Asteraceae samples were organized into groups at different taxonomic levels (tribe, genus, and species). For each group, datasets of non-paralogous loci were built and proportions of parsimony informative characters estimated. The impacts of the analyzing alternative...

Data from: Functional richness shows spatial scale dependency in Pheidole ant assemblages from Neotropical savannas

Karen Neves, Mario Moura, Jonas Maravalhas, Renata Pacheco, Marcio Pie, Ted Schultz & Heraldo Vasconcelos
There is a growing recognition that spatial scale is important for understanding ecological processes shaping community membership, but empirical evidence on this topic is still scarce. Ecological processes such as environmental filtering can decrease functional differences among species and promote functional clustering of species assemblages, whereas interspecific competition can do the opposite. These different ecological processes are expected to take place at different spatial scales, with competition being more likely at finer scales and environmental...

Data from: Marine latitudinal diversity gradients, niche conservatism, and out of the tropics and Arctic: climatic sensitivity of small organisms

Wing Tung Ruby Chiu, Moriaki Yasuhara, Thomas Cronin, Gene Hunt, Laura Gemery & Chih-Lin Wei
Aim The latitudinal diversity gradient (LDG) is a consequence of evolutionary and ecological mechanisms acting over long history, and thus is best investigated with organisms that have rich fossil records. However, combined neontological-paleontological investigations are mostly limited to large, shelled invertebrates, which keeps our mechanistic understanding of LDGs in its infancy. This paper aims to describe the modern meiobenthic ostracod LDG and to explore the possible controlling factors and the evolutionary mechanisms of this large-scale...

Data from: An update and reassessment of fern and lycophyte diversity data in the Japanese Archipelago

Atsushi Ebihara & Joel H. Nitta
The fern and lycophyte flora of Japan comprising 721 native taxa (including subspecies and varieties) plus 371 interspecific hybrids was reassessed using a nearly comprehensively sampled distribution map at 10 km resolution vouchered by 216,687 specimens, up-to-date cytotaxonomic information covering 74% of the taxa, and an rbcL sequence dataset covering 97.9% of the taxa. Spatial distribution of species richness and phylogenetic diversity was visualized. Apomixis was observed in 11.0% of the native taxa whose reproductive...

Data from: The role of glycine betaine in range expansions; protecting mangroves against extreme freeze events

Matthew A. Hayes, Audrey C. Shor, Amber Jesse, Christopher Miller, John Paul Kennedy & Ilka Feller
1. Due to a warming climate, mangrove populations within the Gulf of Mexico and along the Florida Atlantic coastline are expanding their range poleward. As mangroves expand their range limit, leading edge individuals are more likely to experience an increased incidence of freeze events. However, we still lack a clear understanding of the mechanisms used by mangroves to survive freezing conditions. 2. Here, we conducted common garden experiments at different locations experiencing variable winter freeze...

Data from: Phylogenomic incongruence, hypothesis testing, and taxonomic sampling: the monophyly of characiform fishes

Ricardo Betancur-R., Dahiana Arcila, Richard P. Vari, Lily C. Hughes, Claudio Oliveira, Mark H. Sabaj & Guillermo Ortí
Phylogenomic studies using genome‐wide datasets are quickly becoming the state of the art for systematics and comparative studies, but in many cases, they result in strongly supported incongruent results. The extent to which this conflict is real depends on different sources of error potentially affecting big datasets (assembly, stochastic, and systematic error). Here, we apply a recently developed methodology (GGI or gene genealogy interrogation) and data curation to new and published datasets with more than...

Data from: The niches of nuthatches affect their lineage evolution differently across latitude

Yu-Chi Chen, Masoud Nazarizadeh, Fu‐Min Lei, Xiao‐Jun Yang, Cheng‐Te Yao, Feng Dong, Lu Dong, Fa‐Sheng Zou, Sergei V. Drovetski, Yang Liu, Chun-Cheng Huang, Chih-Ming Hung, Fu-Min Lei, Yu‐Chi Chen, Chun‐Cheng Huang & Chih‐Ming Hung
Ecological niche evolution can promote or hinder the differentiation of taxa and determine their distribution. Niche‐mediated evolution may differ among climatic regimes, and thus species that occur across a wide latitudinal range offer a chance to test these heterogeneous evolutionary processes. In this study, we examine (1) how many lineages have evolved across the continent‐wide range of the Eurasian nuthatch (Sitta europaea), (2) whether the lineages’ niches are significantly divergent or conserved, and (3) how...

Data from: A phylum-wide survey reveals multiple independent gains of head regeneration in Nemertea

Eduardo Zattara, Fernando Fernández-Álvarez, Terra Hiebert, Alexa Bely & Jon Norenburg
Animals vary widely in their ability to regenerate, suggesting that regenerative ability has a rich evolutionary history. However, our understanding of this history remains limited because regenerative ability has only been evaluated in a tiny fraction of species. Available comparative regeneration studies have identified losses of regenerative ability, yet clear documentation of gains is lacking. We assessed ability to regenerate heads and tails either through our own experiments or from literature reports for 35 species...

Data from: StomataCounter: a neural network for automatic stomata identification and counting

Karl C. Fetter, Sven Eberhardt, Rich S. Barclay, Scott Wing & Stephen R. Keller
Stomata regulate important physiological processes in plants and are often phenotyped by researchers in diverse fields of plant biology. Currently, there are no user friendly, fully-automated methods to perform the task of identifying and counting stomata, and stomata density is generally estimated by manually counting stomata. We introduce StomataCounter, an automated stomata counting system using a deep convolutional neural network to identify stomata in a variety of different microscopic images. We use a human-in-the-loop approach...

Data from: Exploring rainforest diversification using demographic model testing in the African foam-nest treefrog (Chiromantis rufescens)

Adam Leache, Daniel Portik, Danielle Rivera, Mark-Oliver Rodel, Johannes Penner, Václav Gvoždík, Eli Greenbaum, Gregory Jongsma, Caleb Ofori-Boateng, Marius Burger, Edem Eniang, Rayna Bell & Matthew Fujita
Aim: Species with wide distributions spanning the African Guinean and Congolian rainforests are often composed of genetically distinct populations or cryptic species with geographic distributions that mirror the locations of the remaining forest habitats. We used phylogeographic inference and demographic model testing to evaluate diversification models in a widespread rainforest species, the African Foam-nest Treefrog (Chiromantis rufescens). Location: Guinean and Congolian rainforests, West and Central Africa. Taxon: Chiromantis rufescens. Methods: We collected mitochondrial DNA (mtDNA)...

Characterization of zinc carboxylates on an oil paint test panel [dataset]

Joshua Taillon, Christine P. Romano, Thomas Lam, G. Asher Newsome, Nicole C. Little & Jia-sun Tsang
This dataset contains X-ray EDS (energy dispersive spectroscopy), FTIR (Fourier transform infrared spectroscopy), and DART-MS (Direct analysis in real time mass spectrometry) data and analysis files thatcan be used to reproduce the results from the paper:Christine P. Romano, Thomas Lam, G. Asher Newsome, Joshua A. Taillon, Nicole C. Little, and Jia-sun Tsang. "Characterization of zinc carboxylates on an oil paint test panel," Studies in Conservation, (2019). [in press]For a detailed description of the files contained...

Data from: Earth history and the passerine superradiation

Carl H. Oliveros, Daniel J. Field, Daniel T. Ksepka, F. Keith Barker, Alexandre Aleixo, Michael J. Andersen, Per Alström, Brett W. Benz, Edward L. Braun, Michael J. Braun, Gustavo A. Bravo, Robb T. Brumfield, R. Terry Chesser, Santiago Claramunt, Joel Cracraft, Andrés M. Cuervo, Elizabeth P. Derryberry, Travis C. Glenn, Michael G. Harvey, Peter A. Hosner, Leo Joseph, Rebecca T. Kimball, Andrew L. Mack, Colin M. Miskelly, A. Townsend Peterson … & Brant C. Faircloth
Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyperdiverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships...

Data from: Phylogenomic resolution of the cetacean tree of life using target sequence capture

Michael McGowen, Georgia Tsagkogeorga, Sandra Álvarez-Carretero, Mario Dos Reis, Monika Struebig, Rob Deaville, Paul Jepson, Simon Jarman, Andrea Polanowski, Phillip Morin & Stephen Rossiter
The evolution of the cetaceans, from their early transition to an aquatic lifestyle to their subsequent diversification, has been the subject of numerous studies. However, while the higher-level relationships among cetacean families have been largely settled, several aspects of the systematics within these groups remain unresolved. Problematic clades include the oceanic dolphins (37 spp.), which have experienced a recent rapid radiation, and the beaked whales (22 spp.), which have not been investigated in detail using...

Data from: Marking mosquitoes in their natural larval sites using 2H-enriched water: a promising approach for tracking over extended temporal and spatial scales

Roy Faiman, Adama Dao, Alpha Yaro, Moussa Diallo, Samake Djibril, Zana L. Sonogo, Yossi Ousmane, Margerie Sullivan, Laura Veru, Benjamin Krajacich, Asha Krishna, Joy Matthews, Christine France, Gabriel Hamer, Keith Hobson & Tovi Lehmann
1. Background. Tracking mosquitoes using current methods of mark-release-recapture are limited to small spatial and temporal scales exposing major gaps in understanding long-range movements and extended survival. Novel approaches to track mosquitoes may yield fresh insights into their biology which improves intervention activities to reduce disease transmission. Stable isotope enrichment of natural mosquito breeding sites allows large-scale marking of wild mosquitoes absent human handling. Mosquito larvae that develop in 2H-enriched water are expected to be...

Data from: The evolution of microendemism in a reef fish (Hypoplectrus maya)

Benjamin M. Moran, Kosmas Hench, Robin S. Waples, Marc P. Höppner, Carole C. Baldwin, W. Owen McMillan & Oscar Puebla
Marine species tend to have extensive distributions, which are commonly attributed to the dispersal potential provided by planktonic larvae and the rarity of absolute barriers to dispersal in the ocean. Under this paradigm, the occurrence of marine microendemism without geographic isolation in species with planktonic larvae poses a dilemma. The recently described Maya hamlet (Hypoplectrus maya, Serranidae) is exactly such a case, being endemic to a 50-km segment of the Mesoamerican Barrier Reef System (MBRS)....

Registration Year

  • 2019
    17

Resource Types

  • Dataset
    17

Affiliations

  • Smithsonian Institution
    17
  • Zoological Society of London
    2
  • University of Kansas
    1
  • University of Bath
    1
  • Sun Yat-sen University
    1
  • University of Washington
    1
  • Department of Plant Biology
    1
  • University of Georgia
    1
  • Royal Ontario Museum
    1
  • Museu Paraense Emílio Goeldi
    1