240 Works

Hierarchical multi-grain models improve descriptions of species’ environmental associations, distribution, and abundance

Katherine Mertes, Marta Jarzyna & Walter Jetz
The characterization of species’ environmental niches and spatial distribution predictions based on them are now central to much of ecology and conservation, but implicitly requires decisions about the appropriate spatial scale (i.e. grain) of analysis. Ecological theory and empirical evidence suggest that range-resident species respond to their environment at two characteristic, hierarchical spatial grains: (i) response grain, the (relatively fine) grain at which an individual uses environmental resources, and (ii) occupancy grain, the (relatively coarse)...

Data from: DNA barcoding gap: reliable species identification over morphological and geographical scales

Klemen Čandek & Matjaž Kuntner
The philosophical basis, and utility of DNA barcoding has been a subject of numerous debates. While most literature embraces it, some studies continue to question its use in dipterans, butterflies, and marine gastropods. Here, we explore the utility of DNA barcoding in identifying spider species that vary in taxonomic affiliation, morphological diagnosibility and geographic distribution. Our first test searched for a “barcoding gap” by comparing intra- and interspecific means, medians and overlap in more than...

Data from: Biomechanical and leaf-climate relationships: a comparison of ferns and seed plants

Daniel J. Peppe, Casee R. Lemons, Dana L. Royer, Scott L. Wing, Ian J. Wright, Christopher H. Lusk & Chazelle H. Rhoden
Premise of the study: Relationships of leaf size and shape (physiognomy) with climate have been well characterized for woody non-monocotyledonous angiosperms (dicots), allowing the development of models for estimating paleoclimate from fossil leaves. More recently, petiole width of seed plants has been shown to scale closely with leaf mass. By measuring petiole width and leaf area in fossils, leaf mass per area (MA) can be estimated and an approximate leaf life span inferred. However, little...

Data from: Testing reticulate evolution of four Vitis species from East Asia using restriction‐site associated DNA sequencing

Zhi-Yao Ma, Jun Wen, Jing-Pu Tian, Abbas Jamal, Longqing Chen, Xiu-Qun Liu & Long-Qing Chen
Reticulate evolution is an important driving force of angiosperm evolution. It has been proposed as an important evolutionary process in Vitis subgenus Vitis. Events of natural hybridization and introgression of several taxa native to North America have been hypothesized and discussed. However, there is no convincing evidence of reticulate evolution reported for closely related Vitis taxa from East Asia. We aim to explore natural hybridization and introgression among four closely related Vitis taxa from East...

Data from: Rediscovery of the enigmatic fungus-farming ant \"Mycetosoritis\" asper Mayr (Hymenoptera: Formicidae): Implications for taxonomy, phylogeny, and the evolution of agriculture in ants

Jeffrey Sosa-Calvo, Ana Ješovnik, Heraldo L. Vasconcelos, , Ted R. Schultz & Mauricio Bacci
We report the rediscovery of the exceedingly rarely collected and enigmatic fungus-farming ant species Mycetosoritis asper. Since the description of the type specimen in 1887, only four additional specimens are known to have been added to the world's insect collections. Its biology is entirely unknown and its phylogenetic position within the fungus-farming ants has remained puzzling due to its aberrant morphology. In 2014 we excavated and collected twenty-one colonies of M. asper in the Floresta...

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: Delimiting shades of gray: phylogeography of the Northern Fulmar, Fulmarus glacialis

Kevin C. R. Kerr & Carla J. Dove
The Northern Fulmar (Fulmarus glacialis) is a common tube-nosed seabird with a disjunct Holarctic range. Taxonomic divisions within the Northern Fulmar have historically been muddled by geographical variation notably including highly polymorphic plumage. Recent molecular analyses (i.e., DNA barcoding) have suggested that genetic divergence between Atlantic and Pacific populations could be on par with those typically observed between species. We employ a multigene phylogenetic analysis to better explore the level of genetic divergence between these...

Data from: Repeated invasions into the twilight zone: evolutionary origins of a novel assemblage of fishes from deep Caribbean reefs

Luke Tornabene, James Van Tassell, D. Ross Robertson & Carole C. Baldwin
Mesophotic and deeper reefs of the tropics are poorly known and underexplored ecosystems worldwide. Collectively referred to as the ‘twilight zone’, depths below ~30–50 m are home to many species of reef fishes that are absent from shallower depths, including many undescribed and endemic species. We currently lack even a basic understanding of the diversity and evolutionary origins of fishes on tropical mesophotic reefs. Recent submersible collections in the Caribbean have provided new specimens that...

Data from: Simple versus complex models of trait evolution and stasis as a response to environmental change

Gene Hunt, Melanie J. Hopkins & Scott Lidgard
Previous analyses of evolutionary patterns, or modes, in fossil lineages have focused overwhelmingly on three simple models: stasis, random walks, and directional evolution. Here we use likelihood methods to fit an expanded set of evolutionary models to a large compilation of ancestor–descendant series of populations from the fossil record. In addition to the standard three models, we assess more complex models with punctuations and shifts from one evolutionary mode to another. As in previous studies,...

Data from: Two pulses of morphological diversification in Pacific pelagic fishes following the Cretaceous–Palaeogene mass extinction

Elizabeth Sibert, Matthew Friedman, Pincelli Hull, Gene Hunt, Richard Norris & Matt Friedman
Molecular phylogenies suggest some major radiations of open-ocean fish clades occurred roughly coincident with the K/Pg boundary, however the timing and nature of this diversification is poorly constrained. Here we investigate evolutionary patterns in ray-finned fishes across the Cretaceous-Palaeogene (K/Pg) Mass Extinction 66 million years ago (Ma), using microfossils (isolated teeth) preserved in a South Pacific sediment core spanning 72-43 Ma. Our record does not show significant turnover of fish tooth morphotypes at the K/Pg...

Data from: First circumglobal assessment of Southern Hemisphere humpback whale mitochondrial genetic variation and implications for management

Howard C. Rosenbaum, Francine Kershaw, Martin Mendez, Cristina Pomilla, Matthew S. Leslie, Ken P. Findlay, Peter B. Best, Timothy Collins, Michel Vely, Marcia H. Engel, Robert Baldwin, Gianna Minton, Michael Meyer, Lillian Florez-Gonzalez, M. Michael Poole, Nan Hauser, Claire Garrigue, Muriel Brasseur, John Bannister, Megan Anderson, Carlos Olavarria & C. Scott Baker
The description of genetic population structure over a species’ geographic range can provide insights into its evolutionary history and also support effective management efforts. Assessments for globally distributed species are rare, however, requiring significant international coordination and collaboration. The global distribution of demographically discrete populations for the humpback whale Megaptera novaeangliae is not fully known, hampering the definition of appropriate management units. Here, we present the first circumglobal assessment of mitochondrial genetic population structure across...

Data from: Does morphological variation buffer against extinction? A test using veneroid bivalves from the Plio-Pleistocene of Florida

Sarah E. Kolbe, Rowan Lockwood & Gene Hunt
Although morphological variation is known to influence the evolutionary fates of species, the relationship between morphological variation and survivorship in the face of extinction-inducing perturbations is poorly understood. Here, we investigate this relationship for veneroid bivalves in association with the Plio-Pleistocene extinction in Florida. Fourteen pairs of related species were selected for analysis, with each pair including one species that survived the Plio-Pleistocene extinction and another that became extinct during the interval. Morphological landmark data...

Data from: Atmospheric rivers and the mass mortality of wild oysters: insight into an extreme future?

Brian S. Cheng, Andrew L. Chang, Anna Deck & Matthew C. Ferner
Climate change is predicted to increase the frequency and severity of extreme events. However, the biological consequences of extremes remain poorly resolved owing to their unpredictable nature and difficulty in quantifying their mechanisms and impacts. One key feature delivering precipitation extremes is an atmospheric river (AR), a long and narrow filament of enhanced water vapour transport. Despite recent attention, the biological impacts of ARs remain undocumented. Here, we use biological data coupled with remotely sensed...

Data from: Prioritizing tiger conservation through landscape genetics and habitat linkages

Bibek Yumnam, Yadvendradev V. Jhala, Qamar Qureshi, Jesus E. Maldonado, Rajesh Gopal, Swati Saini, Y. Srinivas & Robert C. Fleischer
Even with global support for tiger (Panthera tigris) conservation their survival is threatened by poaching, habitat loss and isolation. Currently about 3,000 wild tigers persist in small fragmented populations within seven percent of their historic range. Identifying and securing habitat linkages that connect source populations for maintaining landscape-level gene flow is an important long-term conservation strategy for endangered carnivores. However, habitat corridors that link regional tiger populations are often lost to development projects due to...

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: The roles of ecology, behavior and effective population size in the evolution of a community

Chih-Ming Hung, Sergei V. Drovetski & Robert M. Zink
Organismal traits such as ecological specialization and migratory behavior may affect colonization potential, population persistence, and degree of isolation, factors that determine the composition and genetic structure of communities. However, studies focusing on community assembly rarely consider these factors jointly. We sequenced 16 nuclear and one mitochondrial genes from Caucasian and European populations of 30 forest-dwelling avian species that represent diverse ecological (specialist-generalist) and behavioral (migratory-resident) backgrounds. We tested the effects of organismal traits on...

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: Paleotropical diversification dominates the evolution of the hyperdiverse ant tribe Crematogastrini (Hymenoptera: Formicidae)

Bonnie B. Blaimer, Philip S. Ward, Ted R. Schultz, Brian L. Fisher & Seán G. Brady
Levels of diversity vary strikingly among different phylogenetic lineages of ants. Rapid radiations in early ant evolution have often proven difficult to resolve with traditional Sanger-sequencing data sets of modest size. We provide a phylogenomic perspective on the evolution of the hyperdiverse ant tribe Crematogastrini by analyzing sequence data for nearly 1800 ultraconserved element (UCE) loci from 153 species comprising 56 genera. We reconstruct a next-to-complete genus-level phylogeny using concatenated maximum-likelihood and species-tree approaches, estimate...

Data from: Herbarium specimens reveal a historical shift in phylogeographic structure of common ragweed during native range disturbance

Michael D. Martin, Elizabeth A. Zimmer, Morten T. Olsen, Andrew D. Foote, M. Thomas P. Gilbert & Grace S. Brush
Invasive plants provide ample opportunity to study evolutionary shifts that occur after introduction to novel environments. However, although genetic characters pre-dating introduction can be important determinants of later success, large-scale investigations of historical genetic structure have not been feasible. Common ragweed (Ambrosia artemisiifolia L.) is an invasive weed native to North America that is known for its allergenic pollen. Palynological records from sediment cores indicate that this species was uncommon before European colonization of North...

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: 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: Maintenance of genetic diversity in an introduced island population of Guanacos after seven decades and two severe demographic bottlenecks: implications for camelid conservation

Benito A. González, Pablo Orozco-TerWengel, Rainer Von Borries, Warren E. Johnson, William L. Franklin & Juan C. Marín
Fifteen Guanacos were introduced to Staats Island in Falklands/Malvinas archipelago from Patagonia in the 1930s. After introduction, the Guanaco population increased to almost 400 animals that retained a footprint of the founding effect and bottleneck reflected in the genetic status of this isolated population. The goals of this study were to (i) make a genetic assessment of this island population through comparisons with mainland populations and simulation, and (ii) assess the likely source population of...

Data from: Phylogenomic analyses of the Photinia complex support the recognition of a new genus Phippsiomeles and the resurrection of a redefined Stranvaesia in Maleae (Rosaceae)

Bin-Bin Liu, De-Yuan Hong, Shi-Liang Zhou, Chao Xu, Wen-Pan Dong, Gabriel Johnson & Jun Wen
Photinia and its morphologically similar allies in Maleae (Rosaceae) consist of five currently recognized genera: Aronia, Heteromeles, Photinia, Pourthiaea, and Stranvaesia, and 68 species, distributed in Asia and North & Central America. Despite previous efforts to clarify relationships in this group, the generic delimitations have remained uncertain. Our goals were to reconstruct a robust phylogeny of Photinia and its close allies to test the monophyly of the currently recognized genera, especially Photinia and Stranvaesia, and...

Data from: Paleoenvironmental and paleobiogeographical implications of a Middle Pleistocene mollusc assemblage from the marine terraces of Baía das Pipas, southwest Angola

Jocelyn A. Sessa, Pedro M. Callapez, Pedro A. Dinis & Austin J. W. Hendy
Quaternary raised marine terraces containing the remains of diverse, shallow water marine invertebrate faunas are widespread across coastal Angola. These deposits and faunas have not been studied in the same detail as contemporaneous features in northwest and southernmost Africa. We analyzed the fossil assemblages and sedimentology of two closely spaced Middle Pleistocene marine terrace deposits in Baía das Pipas, southwest Angola. This revealed 46 gastropod and 29 bivalve species, along with scleractinian corals, encrusting bryozoans,...

Data from: Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species

John J. Wiens, Carl R. Hutter, Daniel G. Mulcahy, Brice P. Noonan, Ted M. Townsend, , Tod W. Reeder & J. W. Sites
Squamate reptiles (lizards and snakes) are one of the most diverse groups of terrestrial vertebrates. Recent molecular analyses have suggested a very different squamate phylogeny relative to morphological hypotheses, but many aspects remain uncertain from molecular data. Here, we analyse higher-level squamate phylogeny with a molecular dataset of unprecedented size, including 161 squamate species for up to 44 nuclear genes each (33,717 base pairs), using both concatenated and species-tree methods for the first time. Our...

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