23 Works

Data from: Genome-wide evidence reveals that African and Eurasian Golden Jackals are distinct species

Klaus-Peter Koepfli, John Pollinger, Raquel Godinho, Jacqueline Robinson, Amanda Lea, Sarah Hendricks, Rena M. Schweizer, Olaf Thalmann, Pedro Silva, Zhenxin Fan, Andrey A. Yurchenko, Pavel Dobrynin, Alexey Makunin, James A. Cahill, Beth Shapiro, Francisco Álvares, José C. Brito, Eli Geffen, Jennifer A. Leonard, Kristofer M. Helgen, Warren E. Johnson, Stephen J. O'Brien, Blaire Van Valkenburgh & Robert K. Wayne
The golden jackal of Africa (Canis aureus) has long been considered a conspecific of jackals distributed throughout Eurasia, with the nearest source populations in the Middle East. However, two recent reports found that mitochondrial haplotypes of some African golden jackals aligned more closely to gray wolves (Canis lupus), which is surprising given the absence of gray wolves in Africa and the phenotypic divergence between the two species. Moreover, these results imply the existence of a...

Data from: DNA metabarcoding illuminates dietary niche partitioning by African large herbivores

Tyler R. Kartzinel, Patricia A. Chen, Tyler C. Coverdale, David L. Erickson, W. John Kress, Maria L. Kuzmina, Daniel I. Rubenstein, Wei Wang & Robert M. Pringle
Niche partitioning facilitates species coexistence in a world of limited resources, thereby enriching biodiversity. For decades, biologists have sought to understand how diverse assemblages of large mammalian herbivores (LMH) partition food resources. Several complementary mechanisms have been identified, including differential consumption of grasses versus nongrasses and spatiotemporal stratification in use of different parts of the same plant. However, the extent to which LMH partition food-plant species is largely unknown because comprehensive species-level identification is prohibitively...

Data from: Chloroplast phylogenomics resolves key relationships in ferns

Jin-Mei Lu, Ning Zhang, Jun Wen, De-Zhu Li & Xin-Yu Du
Studies on chloroplast genomes of ferns and lycophytes are relatively few in comparison with those on seed plants. Although a basic phylogenetic framework of extant ferns is available, relationships among a few key nodes remain unresolved or poorly supported. The primary objective of this study is to explore the phylogenetic utility of large chloroplast gene data in resolving difficult deep nodes in ferns. We sequenced the chloroplast genomes from Cyrtomium devexiscapulae (eupolypod I) and Woodwardia...

Data from: In-solution hybridization for mammalian mitogenome enrichment: pros, cons and challenges associated with multiplexing degraded DNA

Melissa T. R. Hawkins, Courtney A. Hofman, Taylor Callicrate, Molly M. McDonough, Mirian T. N. Tsuchiya, Eliécer E. Gutierrez, Kristofer M. Helgen & Jesús E. Maldonado
Here, we present a set of RNA-based probes for whole mitochondrial genome in-solution enrichment, targeting a diversity of mammalian mitogenomes. This probes set was designed from seven mammalian orders and tested to determine the utility for enriching degraded DNA. We generated 63 mitogenomes representing five orders and 22 genera of mammals that yielded varying coverage ranging from 0 to >5400X. Based on a threshold of 70% mitogenome recovery and at least 10× average coverage, 32...

Data from: Near-stasis in the long-term diversification of Mesozoic tetrapods

Roger B. J. Benson, Richard J. Butler, John Alroy, Philip D. Mannion, Matthew T. Carrano & Graeme T. Lloyd
How did evolution generate the extraordinary diversity of vertebrates on land? Zero species are known prior to ~380 million years ago, and more than 30,000 are present today. An expansionist model suggests this was achieved by large and unbounded increases, leading to substantially greater diversity in the present than at any time in the geological past. This model contrasts starkly with empirical support for constrained diversification in marine animals, suggesting different macroevolutionary processes on land...

Data from: Metabarcoding dietary analysis of coral dwelling predatory fish demonstrates the minor contribution of coral mutualists to their highly partitioned, generalist diet

Matthieu Leray, Christopher P. Meyer & Suzanne C. Mills
Understanding the role of predators in food webs can be challenging in highly diverse predator/prey systems composed of small cryptic species. DNA based dietary analysis can supplement predator removal experiments and provide high resolution for prey identification. Here we use a metabarcoding approach to provide initial insights into the diet and functional role of coral-dwelling predatory fish feeding on small invertebrates. Fish were collected in Moorea (French Polynesia) where the BIOCODE project has generated DNA...

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: 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: Using phylogenomics to resolve mega-families: an example from Compositae

Jennifer R. Mandel, Rebecca B. Dikow & Vicki A. Funk
Next-generation sequencing and phylogenomics hold great promise for elucidating complex relationships among large plant families. Here we performed targeted capture of low copy sequences followed by next-generation sequencing on the Illumina platform in the large and diverse angiosperm family Compositae (Asteraceae). The family is monophyletic based on morphology and molecular data, yet many areas of the phylogeny have unresolved polytomies and interpreting phylogenetic patterns has been historically difficult. In order to outline a method and...

Data from: Placing cryptic, recently extinct, or hypothesized taxa into an ultrametric phylogeny using continuous character data: A case study with the lizard Anolis roosevelti

Liam J. Revell, D. Luke Mahler, Robert Graham Reynolds & Graham James Slater
In recent years, enormous effort and investment has been put into assembling the tree of life: a phylogenetic history for all species on Earth. Overwhelmingly, this progress toward building an ever increasingly complete phylogeny of living things has been accomplished through sophisticated analysis of molecular data. In the modern genomic age, molecular genetic data have become very easy and inexpensive to obtain for many species. However, some lineages are poorly represented in or absent from...

Data from: Taxonomy of deep-sea trachyleberidid, thaerocytherid, and hemicytherid genera (Ostracoda)

Moriaki Yasuhara, Gene Hunt, Hisayo Okahashi, Somone Brandão & Simone N. Brandao
We conducted a comprehensive systematic revision of deep-sea Trachyleberididae, Thaerocytheridae, and Hemicytheridae (Ostracoda, Crustacea) covering almost all Cenozoic genera using high-resolution scanning electron microscopy. Trachyleberididae, our main focus, is one of the most diverse and abundant ostracod families, but its genus-level taxonomy is still confusing. Approximately 700 specimens from 177 species from 47 genera were examined. The studied samples range in age from the Cretaceous to the present day and cover all major oceans in...

Data from: Multilocus phylogeography of a widespread savanna-woodland adapted rodent reveals the influence of Pleistocene geomorphology and climate change in Africa’s Zambezi region

Molly M. McDonough, Radim Šumbera, Vladimír Mazoch, Adam W. Ferguson, Caleb D. Phillips & Josef Bryja
Understanding historical influences of climate and physiographic barriers in shaping patterns of biodiversity remains limited for many regions of the world. For mammals of continental Africa, phylogeographic studies, particularly for West African lineages, implicate both geographic barriers and climate oscillations in shaping small mammal diversity. In contrast, studies for southern African species have revealed conflicting phylogenetic patterns for how mammalian lineages respond to both climate change and geologic events such as river formation, especially during...

Data from: Large wildlife removal drives immune defense increases in rodents

Hillary S. Young, Rodolfo Dirzo, Kristofer M. Helgen, Douglas J. McCauley, Charles L. Nunn, Paul Snyder, Kari E. Veblen, Serena Zhao & Vanessa O. Ezenwa
Anthropogenic disturbances involving land use change, climate disruption, pollution, and invasive species have been shown to impact immune function of wild animals. These immune changes have direct impacts on the fitness of impacted animals and, also, potentially indirect effects on other species and on ecological processes, notably involving the spread of infectious disease. Here, we investigate whether the selective loss of large wildlife can also drive changes in immune function of other consumer species. Using...

Data from: Phylogenetic uncertainty revisited: implications for ecological analyses

Thiago Fernando Rangel, Robert K. Colwell, Gary R. Graves, Karolina Fučíková, Carsten Rahbek & José Alexandre F. Diniz-Filho
Ecologists and biogeographers usually rely on a single phylogenetic tree to study evolutionary processes that affect macroecological patterns. This approach ignores the fact that each phylogenetic tree is a hypothesis about the evolutionary history of a clade, and cannot be directly observed in nature. Also, trees often leave out many extant species, or include missing species as polytomies because of a lack of information on the relationship among taxa. Still, researchers usually do not quantify...

Data from: Range and niche shifts in response to past climate change in the desert horned lizard (Phrynosoma platyrhinos)

Tereza Jezkova, Jef Jaeger, Viktoria Oláh-Hemmings, K. Bruce Jones, Rafael A. Lara-Resendiz, Daniel G. Mulcahy, Brett R. Riddle & Jef R. Jaeger
During climate change, species are often assumed to shift their geographic distributions (geographic ranges) in order to track environmental conditions – niches – to which they are adapted. Recent work, however, suggests that the niches do not always remain conserved during climate change but shift instead, allowing populations to persist in place or expand into new areas. We assessed the extent of range and niche shifts in response to the warming climate after the Last...

Data from: Integrated analyses resolve conflicts over squamate reptile phylogeny and reveal unexpected placements for fossil taxa

Tod W. Reeder, Ted M. Townsend, Daniel G. Mulcahy, Brice P. Noonan, Perry L. Wood, , John J. Wiens & Jack W. Sites
Squamate reptiles (lizards and snakes) are a pivotal group whose relationships have become increasingly controversial. Squamates include >9000 species, making them the second largest group of terrestrial vertebrates. They are important medicinally and as model systems for ecological and evolutionary research. However, studies of squamate biology are hindered by uncertainty over their relationships, and some consider squamate phylogeny unresolved, given recent conflicts between molecular and morphological results. To resolve these conflicts, we expand existing morphological...

Data from: Trophic convergence drives morphological convergence in marine tetrapods

Neil P. Kelley & Ryosuke Motani
Marine tetrapod clades (e.g. seals, whales) independently adapted to marine life through the Mesozoic and Caenozoic, and provide iconic examples of convergent evolution. Apparent morphological convergence is often explained as the result of adaptation to similar ecological niches. However, quantitative tests of this hypothesis are uncommon. We use dietary data to classify the feeding ecology of extant marine tetrapods and identify patterns in skull and tooth morphology that discriminate trophic groups across clades. Mapping these...

Data from: DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity

Matthieu Leray & Nancy Knowlton
Documenting the diversity of marine life is challenging because many species are cryptic, small, and rare, and belong to poorly known groups. New sequencing technologies, especially when combined with standardized sampling, promise to make comprehensive biodiversity assessments and monitoring feasible on a large scale. We used this approach to characterize patterns of diversity on oyster reefs across a range of geographic scales comprising a temperate location [Virginia (VA)] and a subtropical location [Florida (FL)]. Eukaryotic...

Data from: Mandible-powered escape jumps in trap-jaw ants increase survival rates during predator-prey encounters

Fredrick J. Larabee & Andrew V. Suarez
Animals use a variety of escape mechanisms to increase the probability of surviving predatory attacks. Antipredator defenses can be elaborate, making their evolutionary origin unclear. Trap-jaw ants are known for their rapid and powerful predatory mandible strikes, and some species have been observed to direct those strikes at the substrate, thereby launching themselves into the air away from a potential threat. This potential escape mechanism has never been examined in a natural context. We studied...

Data from: DNA barcodes from century-old type specimens using next generation sequencing

Sean W. J. Prosser, Jeremy R. DeWaard, Scott E. Miller & Paul D. N. Hebert
Type specimens have high scientific importance because they provide the only certain connection between the application of a Linnean name and a physical specimen. Many other individuals may have been identified as a particular species, but their linkage to the taxon concept is inferential. Because type specimens are often more than a century old and have experienced conditions unfavorable for DNA preservation, success in sequence recovery has been uncertain. The present study addresses this challenge...

Data from: Molecular phylogeny of the horse flies: a framework for renewing tabanid taxonomy

Shelah I. Morita, Keith M. Bayless, David K. Yeates & Brian M. Wiegmann
Horse flies, family Tabanidae, are the most diverse family-level clade of bloodsucking insects, but their phylogeny has never been thoroughly explored using molecular data. Most adult female Tabanidae feed on nectar and on the blood of various mammals. Traditional horse fly classification tends towards large heterogeneous taxa, which impede much-needed taxonomic work. To guide renewed efforts in the systematics of horse flies and their relatives, we assembled a dataset of 110 exemplar species using nucleotide...

Data from: Bacterial symbiont sharing in Megalomyrmex social parasites and their fungus-growing ant hosts

Joanito Liberti, Panagiotis Sapountzis, Lars H. Hansen, Søren J. Sørensen, Rachelle M. M. Adams & Jacobus J. Boomsma
Bacterial symbionts are important fitness determinants of insects. Some hosts have independently acquired taxonomically related microbes to meet similar challenges, but whether distantly related hosts that live in tight symbiosis can maintain similar microbial communities has not been investigated. Varying degrees of nest sharing between Megalomyrmex social parasites (Solenopsidini) and their fungus-growing ant hosts (Attini) from the genera Cyphomyrmex, Trachymyrmex and Sericomyrmex allowed us to address this question, as both ant lineages rely on the...

Data from: The evolutionary history of ferns inferred from 25 low-copy nuclear genes

Carl J. Rothfels, Fay-Wei Li, Erin M. Sigel, Layne Huiet, Anders Larsson, Dylan O. Burge, Markus Ruhsam, Michael Deyholos, Douglas E. Soltis, , Shane W. Shaw, Lisa Pokorny, Tao Chen, Claude DePamphilis, Lisa DeGironimo, Li Chen, Xiaofeng Wei, Xiao Sun, Petra Korall, Dennis W. Stevenson, Sean W. Graham, Gane Ka-Shu Wong, Kathleen M. Pryer, C. Neal Stewart, Gane K-S. Wong … & Claude De Pamphilis
Premise of the study: Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of comparison necessary for studying the evolution of the fern sister group, seed plants. Molecular phylogenetic investigations have revolutionized our understanding of fern phylogeny, however, to date, these studies have relied almost exclusively on plastid data. Methods: Here we take a curated phylogenomics approach to infer the...

Registration Year

  • 2015

Resource Types

  • Dataset


  • Smithsonian Institution
  • Duke University
  • University of Copenhagen
  • University of Arizona
  • Harvard University
  • University of Kansas
  • Universidade Federal de Goiás
  • National Museum
  • University of Adelaide
  • The Bronx Defenders