44 Works

Data from: Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis

Arlin Stoltzfus, Brian O'Meara, Jamie Whitacre, Ross Mounce, Emily L. Gillespie, Sudhir Kumar, Dan F. Rosauer & Rutger A. Vos
BACKGROUND: Recently, various evolution-related journals adopted policies to encourage or require archiving of phylogenetic trees and associated data. Such attention to practices that promote data sharing reflects rapidly improving information technology, and rapidly expanding potential to use this technology to aggregate and link data from previously published research. Nevertheless, little is known about current practices, or best practices, for publishing phylogenetic trees and associated data in a way that promotes re-use. RESULTS: Here we summarize...

Ants of the State of Pará, Brazil: a historical and comprehensive dataset of a key biodiversity hotspot in the Amazon Basin

Emília Zoppas De Albuquerque, Lívia Pires Do Prado, Joudellys Andrade-Silva, Emely Laira Silva De Siqueira, Kelly Liane Da Silva Sampaio, Diego Alves, Carlos Roberto F. Brandão, Paloma L. Andrade, Rodrigo Machado Feitosa, Elmo Borges De Azevedo Koch, Jacques Hubert Charles Delabie, Itanna Fernandes, Fabrício Beggiato Baccaro, Jorge Luiz Pereira Souza, Rony Peterson Almeida & Rogério R. Silva
The state of Pará in northern Brazil is located entirely within the Amazon Basin and harbors a great diversity of landscape and vegetation types that support high levels of biodiversity. Here, we provide a comprehensive inventory of ant species and their distribution in Pará. This regional list is based on an extensive review of species records from published and unpublished sources covering a period of 134 years (1886–2020) and includes the five most representative ant...

Data from: Diversification of Hawaiian Cyrtandra (Gesneriaceae) under the influence of incomplete lineage sorting and hybridization

Joseph A Kleinkopf, Wade R Roberts, Warren L Wagner & Eric H Roalson
Cyrtandra (Gesneriaceae) is a genus of flowering plants with over 800 species distributed throughout Southeast Asia and the Pacific Islands. On the Hawaiian Islands, 60 named species and over 89 putative hybrids exist, most of which are identified on the basis of morphology. Despite many previous studies on the Hawaiian Cyrtandra lineage, questions regarding the reconciliation of morphology and genetics remain, many of which can be attributed to the relatively young age and evidence of...

Data from: Multi-proxy evidence highlights a complex evolutionary legacy of maize in South America

Logan Kistler, S. Yoshi Maezumi, Jonas Gregorio De Souza, Natalia A. S. Przelomska, Flaviane Malaquias Costa, Oliver Smith, Hope Loiselle, Jazmín Ramos-Madrigal, Nathan Wales, Eduardo Rivail Ribeiro, Ryan R. Morrison, Claudia Grimaldo, Andre P. Prous, Bernardo Arriaza, M. Thomas P. Gilbert, Fabio De Oliveira Freitas & Robin G. Allaby
Domesticated maize evolved from wild teosinte under human influences in Mexico beginning around 9,000 BP, traversed Central America by ~7,500 BP, and spread into South America by ~6,500 BP. Landrace and archaeological maize genomes from South America suggest that the ancestral population to South American maize was brought out of the domestication center in Mexico and became isolated from the wild teosinte gene pool before traits of domesticated maize were fixed. Deeply structured lineages then...

Data from: Deep COI sequencing of standardized benthic samples unveils overlooked diversity of Jordanian coral reefs in the Northern Red Sea

Mamoon M. D. Al-Rshaidat, Allison Snider, Sydney Rosebraugh, Amanda M. Devine, Thomas D. Devine, Laetitia Plaisance, Nancy Knowlton, Matthieu Leray & Mamoon M.D. Al-Rshaidat
High-Throughput Sequencing (HTS) of DNA barcodes (metabarcoding), particularly when combined with standardized sampling protocols, is one of the most promising approaches for censusing overlooked cryptic invertebrate communities. We present biodiversity estimates based on sequencing of the cytochrome c oxidase subunit 1 (COI) gene for coral reefs of the Gulf of Aqaba, a semi-enclosed system in the Northern Red Sea. Samples were obtained from standardized sampling devices [Autonomous Reef Monitoring Structures (ARMS)] deployed for 18 months....

Data from: Binary-state speciation and extinction method is conditionally robust to realistic violations of its assumptions

Andrew G. Simpson, Peter J. Wagner, Scott L. Wing & Charles B. Fenster
Background: Phylogenetic comparative methods allow us to test evolutionary hypotheses without the benefit of an extensive fossil record. These methods, however, make simplifying assumptions, among them that clades are always increasing or stable in diversity, an assumption we know to be false. This study simulates hypothetical clades to test whether the Binary State Speciation and Extinction (BiSSE) method can be used to correctly detect relative differences in diversification rate between ancestral and derived character states...

Data from: Arthropod diversity in a tropical forest

Yves Basset, Lukas Cizek, Philippe Cuénoud, Raphael K. Didham, François Guilhaumon, Olivier Missa, Vojtech Novotny, Frode Ødegaard, Tomas Roslin, Jürgen Schmidl, Alexey K. Tishechkin, Neville N. Winchester, David W. Roubik, Henri-Pierre Aberlenc, Johannes Bail, Héctor Barrios, Jon R. Bridle, Gabriela Castaño-Meneses, Bruno Corbara, Gianfranco Curletti, Wesley Duarte Da Rocha, Domir De Bakker, Jacques H. C. Delabie, Alain Dejean, Laura L. Fagan … & Maurice Leponce
Most eukaryotic organisms are arthropods. Yet, their diversity in rich terrestrial ecosystems is still unknown. Here we produce tangible estimates of the total species richness of arthropods in a tropical rainforest. Using a comprehensive range of structured protocols, we sampled the phylogenetic breadth of arthropod taxa from the soil to the forest canopy in the San Lorenzo forest, Panama. We collected 6,144 arthropod species from 0.48 ha and extrapolated total species richness to larger areas...

Data from: Divergence estimates and early evolutionary history of Figitidae (Hymenoptera: Cynipoidea)

Matthew L. Buffington, Seán G. Brady, Shelah I. Morita & Simon Van Noort
matrix08REDUCEDBayes04The combined molecular and morphological dataset analyzed using MrBayes.cynipoid_dating_all_calibrationsThe molecular dataset analyzed using BEAST.

Data from: A molecular phylogeny of Staphyleaceae: implications for generic delimitation and classical biogeographic disjunctions in the family

AJ Harris, Ping-Ting Chen, Xin-Wei Xu, Xue Yang, Jun Wen & Jian-Qiang Zhang
Staphyleaceae traditionally comprises three genera of temperate and tropical trees and shrubs: Euscaphis Siebold & Zucc., Staphylea L., and Tuprinia Vent. These genera are clearly supported by morphology, but a recent classification based on four chloroplast genes and nuclear ITS treats Staphylea, Euscaphis, and New World Turpinia in Staphylea s.l. and Old World Turpinia in Dalrympelea Roxb. In this study, our objectives were to (1) resolve the phylogenetic relationships within Staphyleaceae using two nuclear and...

Data from: Response of deep-sea biodiversity to abrupt deglacial and Holocene climate changes in the North Atlantic Ocean

Moriaki Yasuhara, Hisayo Okahashi, Thomas M. Cronin, Tine L. Rasmussen & Gene Hunt
Aim: Little is known about how marine biodiversity responds to oceanographic and climatic changes over the decadal to centennial time-scales which are most relevant for predicted climate changes due to greenhouse gas forcing. This paper aims to reveal decadal–centennial scale deep-sea biodiversity dynamics for the last 20,000 years and then explore potential environmental drivers. Location: The North Atlantic Ocean. Methods: We investigated deep-sea benthic microfossil records to reveal biodiversity dynamics and subsequently applied comprehensive ecological...

Data from: Varyingly hungry caterpillars: predictive models and foliar chemistry suggest how to eat a rainforest

Simon T. Segar, Martin Volf, Brus Isua, Mentap Sisol, Conor M. Redmond, Margaret E. Rosati, Bradley Gewa, Kenneth Molem, Chris Dahl, Jeremy D. Holloway, Yves Basset, Scott E. Miller, George D. Weiblen, Juha-Pekka Salminen & Vojtech Novotny
A long-term goal in evolutionary ecology is to explain the incredible diversity of insect herbivores and patterns of plant host use in speciose groups like tropical Lepidoptera. Here we used standardised food-web data, multigene phylogenies of both trophic levels and plant chemistry data to model interactions between Lepidoptera larvae (caterpillars) from two lineages (Geometridae and Pyraloidea) and plants in species-rich lowland rainforest in New Guinea. Model parameters were used to make and test blind predictions...

Data from: Pollinator-mediated selection in a specialized hummingbird-Heliconia system in the eastern Caribbean

Ethan J. Temeles, Yoon J. Rah, Jonathan Andicoechea, Katerina L. Byanova, Geoffrey S. J. Giller, Shaylon B. Stolk & W. J. Kress
Phenotypic matches between plants and their pollinators often are interpreted as examples of reciprocal selection and adaptation. For the two co-occurring plant species, Heliconia bihai and H. caribaea in the Eastern Caribbean, we evaluated for five populations over two years the strength and direction of natural selection on corolla length and number of bracts per inflorescence. These plant traits correspond closely to the bill lengths and body masses of their primary pollinators, female or male...

Data from: Patterns and controlling factors of species diversity in the Arctic Ocean

Moriaki Yasuhara, Gene Hunt, Gert Van Dijken, Kevin R. Arrigo, Thomas M. Cronin & Jutta E. Wollenburg
AIM: The Arctic Ocean is one of the last near-pristine regions on Earth and although human activities are expected to impact on Arctic ecosystems, we know very little about baseline patterns of Arctic Ocean biodiversity. This paper aims to describe Arctic Ocean-wide patterns of benthic biodiversity and to explore factors related to the large-scale species diversity patterns. LOCATION: Arctic Ocean. METHODS: We used large ostracode and foraminiferal datasets to describe the biodiversity patterns and apply...

Data from: Evolutionary and dispersal history of Eurasian wild mice Mus musculus clarified by more extensive geographic sampling of mitochondrial DNA

Hitoshi Suzuki, Mitsuo Nunome, Ghota Kinotshita, K. P. Aplin, Peter Vogel, Alexey P. Kryukov, Mei-Lei Jin, Sang-Hoon Han, Ibnu Maryanto, Kimiyuki Tsuchiya, Hidetoshi Ikeda, T. Shiroishi, Hiromichi Yonekawa & Kazuo Moriwaki
We examined sequence variation of mitochondrial DNA control region and cytochrome b gene of the house mouse (Mus musculus sensu lato) drawn from ca. 200 localities, with 290 new samples drawn primarily from previously unsampled portions of their Eurasian distribution and with the objective of further clarifying evolutionary episodes of this species before and after the onset of human-mediated long-distance dispersals. Phylogenetic analysis of the expanded data detected five equally distinct clades, with geographic ranges...

Data from: Molecular detection of trophic links in a complex insect host-parasitoid food web

Jan Hrcek, Scott E Miller, Donald L J Quicke & M. Alex Smith
Previously, host-parasitoid links have been unveiled almost exclusively by time-intensive rearing, while molecular methods were used only in simple agricultural host-parasitoid systems in the form of species specific primers. Here we present a general method for molecular detection of these links applied to a complex caterpillar-parasitoid food web from tropical rainforest of Papua New Guinea. We DNA barcoded hosts, parasitoids and their tissue remnants and matched the sequences to our extensive library of local species....

Data from: Diversity dynamics of Phanerozoic terrestrial tetrapods at the local-community scale

Roger A. Close, Roger B. J. Benson, John Alroy, Anna K. Behrensmeyer, Juan Benito, Matthew T. Carrano, Terri J. Cleary, Emma M. Dunne, Philip D. Mannion, Mark D. Uhen & Richard J. Butler
The fossil record provides one of the strongest tests of the hypothesis that diversity within local communities is constrained over geological timescales. Constraints to diversity are particularly controversial in modern terrestrial ecosystems, yet long-term patterns are poorly understood. Here we document patterns of local richness in Phanerozoic terrestrial tetrapods using a global data set comprising 145,332 taxon occurrences from 27,531 collections. We show that the local richness of non-flying terrestrial tetrapods has risen asymptotically since...

Data from: Monadelpha (Euphorbiaceae, Plukenetieae), a new genus of Tragiinae from the Amazon rainforest of Venezuela and Brazil

Lynn J. Gillespie, Warren M. Cardinal-McTeague & Kenneth J. Wurdack
Monadelpha L.J.Gillespie & Card.-McTeag., gen. nov., is described as a new member of Euphorbiaceae tribe Plukenetieae subtribe Tragiinae, to accommodate Tragia guayanensis, a species known from western Amazonas, Venezuela and, newly reported here, from Amazonas, Brazil. The genus is unique in the subtribe for having 5-colpate pollen and staminate flowers with filaments entirely connate into an elongate, cylindrical staminal column terminated by a tight cluster of anthers. Phylogenetic analyses based on nuclear rDNA ITS and...

Ediacara growing pains: Modular addition and development in Dickinsonia costata

Scott Evans, James G. Gehling, Douglas Erwin & Mary Droser
Constraining patterns of growth using directly observable and quantifiable characteristics can reveal a wealth of information regarding the biology of the Ediacara Biota – the oldest macroscopic, complex community forming organisms in the fossil record. However, these rely on individuals captured at an instant in time at various growth stages, and so different interpretations can be derived from the same material. Here we leverage newly discovered and well-preserved Dickinsonia costata Sprigg 1947 from South Australia,...

Data from: A phylogenetic, biogeographic, and taxonomic study of all extant species of Anolis (Squamata; Iguanidae)

Steven Poe, Adrian Nieto-Montes De Oca, Omar Torres-Carvajal, Kevin De Queiroz, Julian A. Velasco, Brad Truett, Levi N. Gray, Mason J. Ryan, Gunther Kohler, Fernando Ayala-Varela & Ian Latella
Anolis lizards (anoles) are textbook study organisms in evolution and ecology. Although several topics in evolutionary biology have been elucidated by the study of anoles, progress in some areas has been hampered by limited phylogenetic information on this group. Here we present a phylogenetic analysis of all 379 extant species of Anolis, with new phylogenetic data for 139 species including new DNA data for 101 species. We use the resulting estimates as a basis for...

Data from: Evolutionary history of endemic Sulawesi squirrels constructed from UCEs and mitogenomes sequenced from museum specimens

Melissa T. R. Hawkins, Jennifer A. Leonard, Kristofer M. Helgen, Molly M. McDonough, Larry L. Rockwood & Jesus E. Maldonado
Background: The Indonesian island of Sulawesi has a complex geological history. It is composed of several landmasses that have arrived at a near modern configuration only in the past few million years. It is the largest island in the biodiversity hotspot of Wallacea—an area demarcated by the biogeographic breaks between Wallace’s and Lydekker’s lines. The mammal fauna of Sulawesi is transitional between Asian and Australian faunas. Sulawesi’s three genera of squirrels, all endemic (subfamily Nannosciurinae:...

Data from: How temporal patterns in rainfall determine the geomorphology and carbon fluxes of tropical peatlands

Alexander R. Cobb, Alison M. Hoyt, Laure Gandois, Jangarun Eri, René Dommain, Kamariah Abu Salim, Fuu Ming Kai, Nur Salihah Haji Su'ut & Charles F. Harvey
Tropical peatlands now emit hundreds of megatons of carbon dioxide per year because of human disruption of the feedbacks that link peat accumulation and groundwater hydrology. However, no quantitative theory has existed for how patterns of carbon storage and release accompanying growth and subsidence of tropical peatlands are affected by climate and disturbance. Using comprehensive data from a pristine peatland in Brunei Darussalam, we show how rainfall and groundwater flow determine a shape parameter (the...

Data from: Population divergence and gene flow in an endangered and highly mobile seabird

Andreanna J. Welch, Robert C. Fleischer, Helen F. James, Anne E. Wiley, Peggy H. Ostrom, Josh Adams, Fern Duvall, Nick Holmes, Jay Penniman, Keith A. Swindle & Darcy Hu
Seabirds are highly vagile and can disperse up to thousands of kilometers, therefore it can be difficult to identify the factors that promote isolation between populations. The endemic Hawaiian petrel (Pterodroma sandwichensis) is one such species. Today it is endangered, and known to breed only on the islands of Hawaii, Maui, Lanai, and Kauai. Historical records indicate that a large population formerly bred on Molokai as well, but this population has recently been extirpated. Given...

Data from: The rise of army ants and their relatives: diversification of specialized predatory doryline ants

Sean G. Brady, Brian L. Fisher, Ted R. Schultz & Philip S. Ward
Background Army ants are dominant invertebrate predators in tropical and subtropical terrestrial ecosystems. Their close relatives within the dorylomorph group of ants are also highly specialized predators, although much less is known about their biology. We analyzed molecular data generated from 11 nuclear genes to infer a phylogeny for the major dorylomorph lineages, and incorporated fossil evidence to infer divergence times under a relaxed molecular clock. Results Because our results indicate that one subfamily and...

Data from: Evolution of stenophagy in spiders (Araneae): evidence based on the comparative analysis of spider diets

Stano Pekár, Jonathan A. Coddington & Todd A. Blackledge
Stenophagy (narrow diet breadth) represents an extreme of trophic specialization in carnivores, but little is known about the forces driving its evolution. We used spiders, the most diversified group of terrestrial predators, to investigate whether stenophagy 1) promoted diversification, 2) was phylogenetically conserved and evolutionarily derived state, and 3) was determined either by geographical distribution and foraging guild. We utilized published data on the prey of almost 600 species. Six categories of stenophagy were found:...

Data from: 346 target gene sequences from Vitaceae for Hyb-Seq

Jun Wen
The Vitaceae (the grape family) consists of 16 genera and ca. 950 species. It is best known for the economically important fruit crop -- the grape Vitis vinifera. The deep phylogenetic relationships and character evolution of the grape family have attracted the attention of researchers in recent years. We herein reconstruct the phylogenomic relationships within Vitaceae using nuclear and plastid genes based on the Hyb-Seq approach and test the newly proposed classification system of the...

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