221 Works

Abu Dhabi Blue Carbon project

Lisa Schile, J. Boone Kauffman, J. Patrick Megonigal, James Fourqurean & Stephen Crooks
Coastal ecosystems produce and sequester significant amounts of carbon (‘blue carbon’), which has been well documented in humid and semi-humid regions of temperate and tropical climates but less so in arid regions where mangroves, marshes, and seagrasses exist near the limit of their tolerance for extreme temperature and salinity. To better understand these unique systems, we measured whole-ecosystem carbon stocks (above- and belowground biomass and soil) in 58 sites across the United Arab Emirates in...

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...

Supplementary information for integrating sequence capture and restriction-site associated DNA sequencing to resolve recent radiations of Pelagic seabirds

Joan Ferrer-Obiol, Helen F. James, R. Terry Chesser, Vincent Bretagnolle, Jacob González-Solís, Julio Rozas, Marta Riutort & Andreanna J. Welch
The diversification of modern birds has been shaped by a number of radiations. Rapid diversification events make reconstructing the evolutionary relationships among taxa challenging due to the convoluted effects of incomplete lineage sorting (ILS) and introgression. Phylogenomic datasets have the potential to detect patterns of phylogenetic incongruence, and to address their causes. However, the footprints of ILS and introgression on sequence data can vary between different phylogenomic markers at different phylogenetic scales depending on factors...

The filtered VCF file containing SNPs detected from the Vitis bryoniifolia clade using RAD-seq.

Zhi-Yao Ma, Jun Wen, Jing-Pu Tian, Liu-Liu Gui & Xiu-Qun Liu
The grape genus (Vitis L.) is of great agronomic importance and represents an economically valuable resource. Researchers have explored the phylogenetic relationships of subgenus Vitis for decades. However, the evolutionary patterns of many morphological characters of subgenus Vitis have not yet been explored in the context of a robust phylogenetic framework. Within the East Asian clade, V. bryoniifolia and its closely related taxa form the V. bryoniifolia clade, which is taxonomically complex. The phylogenetic relationships...

Data from: Modifications during early plant development promote the evolution of nature’s most complex woods

Joyce G. Chery, Marcelo R. Pace, Pedro Acevedo-Rodriguez, Chelsea D. Specht & Carl J. Rothfels
Secondary growth is the developmental process by which woody plants grow radially. The most complex presentations of secondary growth are found in lianas (woody vines) as a result of their unique demand to maintain stems that can twist without breaking. The complex woody forms in lianas arise as non-circular stem outlines, aberrant tissue configurations, and/or shifts in the relative abundance of secondary tissues. Previous studies demonstrate that abnormal activity of the vascular cambium leads to...

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: Measuring rates of phenotypic evolution and the inseparability of tempo and mode

Gene Hunt
Rates of phenotypic evolution are central to many issues in paleontology, but traditional rate metrics such as darwins or haldanes are seldom used because of their strong dependence on interval length. In this paper, I argue that rates are usefully thought of as model parameters that relate magnitudes of evolutionary divergence to elapsed time. Starting with models of directional evolution, random walks, and stasis, I derive for each a reasonable rate metric. These metrics can...

Data from: Does soil moisture availability explain liana seedling distribution across a tropical rainfall gradient?

Eric Manzané-Pinzön, Guillermo Goldstein & Stefan A. Schnitzer
Liana density tends to increase with decreasing rainfall and increasing seasonality. However, the pattern of liana distribution may be due to differences in soil water retention capacity, not rainfall and seasonality per se. We tested the effect of rainfall and soil substrate with respect to the distribution of liana seedlings in six sites across a rainfall gradient from the wet Atlantic to the dry Pacific in central Panama. Soils were either limestone, with low water-holding...

Data from: Host-associated genomic differentiation in congeneric butterflies: now you see it, now you don’t

Alexander S. Mikheyev, Carolyn S. McBride, Ulrich G. Mueller, Camille Parmesan, Melanie R. Smee, Constanti Stefanescu, Brian Wee & Michael C. Singer
Ecotypic variation among populations may become associated with widespread genomic differentiation, but theory predicts that this should happen only under particular conditions of gene flow, selection and population size. In closely related species, we might expect the strength of host-associated genomic differentiation (HAD) to be correlated with the degree of phenotypic differentiation in host-adaptive traits. Using microsatellite and Amplified Fragment Length Polymorphism (AFLP) markers, and controlling for isolation by distance between populations, we sought HAD...

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: Phylogeny suggests non-directional and isometric evolution of sexual size dimorphism in argiopine spiders

Ren-Chung Cheng & Matjaž Kuntner
Sexual dimorphism describes substantial differences between male and female phenotypes. In spiders, sexual dimorphism research almost exclusively focuses on size, and recent studies have recovered steady evolutionary size increases in females, and independent evolutionary size changes in males. Their discordance is due to negative allometric size patterns caused by different selection pressures on male and female size (converse Rensch's rule). Here, we investigated macroevolutionary patterns of sexual size dimorphism (SSD) in Argiopinae, a global lineage...

Data from: Low plant density enhances gene dispersal in the Amazonian understory herb Heliconia acuminata

Marina Corrêa Côrtes, María Uriarte, Maristerra R. Lemes, Rogério Gribel, W. John Kress, Peter E. Smouse & Emilio M. Bruna
In theory, conservation genetics predicts that forest fragmentation will reduce gene dispersal, but in practice, genetic and ecological processes are also dependent on other population characteristics. We used Bayesian genetic analyses to characterize parentage and propagule dispersal in Heliconia acuminata L. C. Richard (Heliconiaceae), a common Amazonian understory plant that is pollinated and dispersed by birds. We studied these processes in two continuous forest sites and three 1-ha fragments in Brazil's Biological Dynamics of Forest...

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: Testing the link between phenotypic evolution and speciation: an integrated paleontological and phylogenetic analysis

Gene Hunt
1. The punctuated equilibrium model predicts that phenotypic change is concentrated into pulses associated with speciation, with little change otherwise accruing in established lineages. Paleontological tests of this model have generally lacked an adequate phylogenetic and modeling framework, whereas tests relying on extant populations lack direct constraints on the evolutionary dynamics within lineages. 2. The present study extends a modeling approach developed in comparative studies and applies it to a clade with a rich fossil...

Data from: Taxon cycle predictions supported by model-based inference in Indo-Pacific trap-jaw ants (Hymenoptera: Formicidae: Odontomachus)

Pável Matos-Maraví, Nicholas J. Matzke, Fredrick J. Larabee, Ronald M. Clouse, Ward C. Wheeler, Daniela Magdalena Sorger, Andrew V. Suarez & Milan Janda
Non-equilibrium dynamics and non-neutral processes, such as trait-dependent dispersal, are often missing from quantitative island biogeography models despite their potential explanatory value. One of the most influential non-equilibrium models is the taxon cycle, but it has been difficult to test its validity as a general biogeographical framework. Here, we test predictions of the taxon-cycle model using six expected phylogenetic patterns and a time-calibrated phylogeny of Indo-Pacific Odontomachus (Hymenoptera: Formicidae: Ponerinae), one of the ant genera...

Data from: Loss of migratory behavior increases infection risk for a butterfly host

Dara A. Satterfield, John C. Maerz & Sonia Altizer
Long-distance animal migrations have important consequences for infectious disease dynamics. In some cases, migration lowers pathogen transmission by removing infected individuals during strenuous journeys and allowing animals to periodically escape contaminated habitats. Human activities are now causing some migratory animals to travel shorter distances or form sedentary (non-migratory) populations. We focused on North American monarch butterflies and a specialist protozoan parasite to investigate how the loss of migratory behaviours affects pathogen spread and evolution. Each...

Data from: Congruent deep relationships in the grape family (Vitaceae) based on sequences of chloroplast genomes and mitochondrial genes via genome skimming

Ning Zhang, Jun Wen & Elizabeth A. Zimmer
Vitaceae is well-known for having one of the most economically important fruits, i.e., the grape (Vitis vinifera). The deep phylogeny of the grape family was not resolved until a recent phylogenomic analysis of 417 nuclear genes from transcriptome data. However, it has been reported extensively that topologies based on nuclear and organellar genes may be incongruent due to differences in their evolutionary histories. Therefore, it is important to reconstruct a backbone phylogeny of the grape...

Data from: Evolutionary novelty in a butterfly wing pattern through enhancer shuffling

Richard W. R. Wallbank, Simon W. Baxter, Carolina Pardo-Diaz, Joseph J. Hanly, Simon H. Martin, James Mallet, Kanchon K. Dasmahapatra, Camilo Salazar, Mathieu Joron, Nicola Nadeau, W. Owen McMillan & Chris D. Jiggins
An important goal in evolutionary biology is to understand the genetic changes underlying novel morphological structures. We investigated the origins of a complex wing pattern found among Amazonian Heliconius butterflies. Genome sequence data from 142 individuals across 17 species identified narrow regions associated with two distinct red colour pattern elements, dennis and ray. We hypothesise that these modules in non-coding sequence represent distinct cis-regulatory loci that control expression of the transcription factor optix, which in...

Data from: Phylogenetic evidence from freshwater crayfishes that cave adaptation is not an evolutionary dead-end

David Ben Stern, Jesse Breinholt, Carlos Pedraza-Lara, Marilú López-Mejía, Christopher L. Owen, Heather Bracken-Grissom, , Keith A. Crandall & James W. Fetzner
Caves are perceived as isolated, extreme habitats with a set of uniquely specialized biota, which long ago led to the idea that caves are ‘evolutionary dead-ends.’ This suggests that cave-adapted taxa may be doomed for extinction before they can diversify or transition to a more stable state. However, this hypothesis has not been explicitly tested in a phylogenetic framework with multiple independent cave-dwelling groups. Here we use the freshwater crayfish, a group with dozens of...

Data from: Idiosyncratic responses to climate-driven forest fragmentation and marine incursions in reed frogs from Central Africa and the Gulf of Guinea Islands

Rayna C. Bell, Juan L. Parra, Gabriel Badjedjea, Michael F. Barej, David C. Blackburn, Marius Burger, Alan Channing, J. Maximilian Dehling, Eli Greenbaum, Václav Gvoždík, Jos Kielgast, Chifundera Kusamba, Stefan Lötters, Patrick J. McLaughlin, Zoltán T. Nagy, Mark-Oliver Rödel, Daniel M. Portik, Bryan L. Stuart, Jeremy VanDerWal, Ange-Ghislain Zassi Boulou & Kelly R. Zamudio
Organismal traits interact with environmental variation to mediate how species respond to shared landscapes. Thus, differences in traits related to dispersal ability or physiological tolerance may result in phylogeographic discordance among co-distributed taxa, even when they are responding to common barriers. We quantified climatic suitability and stability, and phylogeographic divergence within three reed frog species complexes across the Guineo-Congolian forests and Gulf of Guinea archipelago of Central Africa to investigate how they responded to a...

Data from: Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data

Lily C. Hughes, Guillermo Ortí, Yu Huang, Ying Sun, Carole C. Baldwin, Andrew W. Thompson, Dahiana Arcila, Ricardo Betancur-R, Chenhong Li, Leandro Becker, Nicolás Bellora, Xiaomeng Zhao, Xiaofeng Li, Min Wang, Chao Fang, Bing Xie, Zhuocheng Zhou, Hai Huang, Songlin Chen, Byrappa Venkatesh & Qiong Shi
Our understanding of phylogenetic relationships among bony fishes has been transformed by analysis of a small number of genes, but uncertainty remains around critical nodes. Genome-scale inferences so far have sampled a limited number of taxa and genes. Here we leveraged 144 genomes and 159 transcriptomes to investigate fish evolution with an unparalleled scale of data: >0.5 Mb from 1,105 orthologous exon sequences from 303 species, representing 66 out of 72 ray-finned fish orders. We...

Data from: Trait independence primes convergent trait loss

Molly C. Womack, Tyler S. Fiero & Kim L. Hoke
The repeated, independent evolution of traits (convergent evolution) is often attributed to shared environmental selection pressures. However, developmental dependencies among traits can limit the phenotypic variation available to selection and bias evolutionary outcomes. Here we determine how changes in developmentally correlated traits may impact convergent loss of the tympanic middle ear, a highly labile trait within toads that currently lack adaptive explanation. The middle ear’s lability could reflect evolutionary trade-offs with other skull features under...

Data from: Phylogenomic insights into the evolution of stinging wasps and the origins of ants and bees

Michael G. Branstetter, Bryan N. Danforth, James P. Pitts, Brant C. Faircloth, Philip S. Ward, Matthew L. Buffington, Michael W. Gates, Robert R. Kula & Seán G. Brady
The stinging wasps (Hymenoptera: Aculeata) are an extremely diverse lineage of hymenopteran insects, encompassing over 70,000 described species and a diversity of life history traits, including ectoparasitism, cleptoparasitism, predation, pollen feeding (bees [Anthophila] and Masarinae) and eusociality (social vespid wasps, ants, and some bees) [1]. The most well-studied lineages of Aculeata are the ants, which are ecologically dominant in most terrestrial ecosystems [2], and the bees, the most important lineage of angiosperm-pollinating insects [3]. Establishing...

Data from: Genome sequence and population declines in the critically endangered greater bamboo lemur (Prolemur simus) and implications for conservation

Melissa T. R. Hawkins, Ryan R. Culligan, Cynthia L. Frasier, Rebecca B. Dikow, Ryan Hagenson, Runhua Lei &
Background: The greater bamboo lemur (Prolemur simus) is a member of the Family Lemuridae that is unique in their dependency on bamboo as a primary food source. This Critically Endangered species lives in small forest patches in eastern Madagascar, occupying a fraction of its historical range. Here we sequence the genome of the greater bamboo lemur for the first time, and provide genome resources for future studies of this species that can be applied across...

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