16 Works

Data from: Diabolical survival in Death Valley: recent pupfish colonization, gene flow, and genetic assimilation in the smallest species range on earth

Christopher Martin, Jacob Crawford, Bruce Turner, Lee Simons, Jacob E. Crawford & Christopher H. Martin
One of the most endangered vertebrates, the Devils Hole pupfish Cyprinodon diabolis, survives in a nearly impossible environment: a narrow subterranean fissure in the hottest desert on earth, Death Valley. This species became a conservation icon after a landmark 1976 U.S. Supreme Court case affirming federal groundwater rights to its unique habitat. However, one outstanding question about this species remains unresolved: how long has diabolis persisted in this hellish environment? We used next-generation sequencing of...

Data from: Unravelling the life history of Amazonian fishes through otolith microchemistry

Theodore W. Hermann, Donald J. Stewart, Karin E. Limburg & Leandro Castello
Amazonian fishes employ diverse migratory strategies, but the details of these behaviours remain poorly studied despite numerous environmental threats and heavy commercial exploitation of many species. Otolith microchemistry offers a practical, cost-effective means of studying fish life history in such a system. This study employed a multi-method, multi-elemental approach to elucidate the migrations of five Amazonian fishes: two ‘sedentary’ species (Arapaima sp. and Plagioscion squamosissimus), one ‘floodplain migrant’ (Prochilodus nigricans) and two long-distance migratory catfishes...

Data from: Genome reduction uncovers a large dispensable genome and adaptive role for copy number variation in asexually propagated Solanum tuberosum

Michael A. Hardigan, Emily Crisovan, John P. Hamilton, Jeongwoon Kim, Parker Laimbeer, Courtney P. Leisner, Norma C. Manrique-Carpintero, Linsey Newton, Gina M. Pham, Brieanne Vaillancourt, Xueming Yang, Zixian Zeng, David S. Douches, Jiming Jiang, Richard E. Veilleux & C. Robin Buell
Clonally reproducing plants have the potential to bear a significantly greater mutational load than sexually reproducing species. To investigate this possibility, we examined the breadth of genome-wide structural variation in a panel of monoploid/doubled monoploid clones generated from native populations of diploid potato (Solanum tuberosum), a highly heterozygous asexually propagated plant. As rare instances of purely homozygous clones, they provided an ideal set for determining the degree of structural variation tolerated by this species, and...

Ancient and modern colonization of North America by hemlock woolly adelgid, Adelges tsugae (Hemiptera: Adelgidae), an invasive insect from East Asia

Nathan P. Havill, Shigehiko Shiyake, Ashley Lamb Galloway, Robert G. Foottit, Guoyue Yu, Annnie Paradis, Joseph Elkinton, Michael E. Montgomery, Masakazu Sano, Adalgisa Caccone & Annie Paradis
Hemlock woolly adelgid, Adelges tsugae, is an invasive pest of hemlock trees (Tsuga) in eastern North America. We used 14 microsatellites and mitochondrial COI sequences to assess its worldwide genetic structure and reconstruct its colonization history. The resulting information about its life cycle, biogeography and host specialization could help predict invasion by insect herbivores. We identified eight endemic lineages of hemlock adelgids in central China, western China, Ulleung Island (South Korea), western North America, and...

Data from: Using camera trapping and hierarchical occupancy modelling to evaluate the spatial ecology of an African mammal community

Lindsey N. Rich, David A. W. Miller, Hugh S. Robinson, J. Weldon McNutt & Marcella J. Kelly
Emerging conservation paradigms have shifted from single to multi-species approaches focused on sustaining biodiversity. Multi-species hierarchical occupancy modelling provides a method for assessing biodiversity while accounting for multiple sources of uncertainty. We analysed camera trapping data with multi-species models using a Bayesian approach to estimate the distributions of a terrestrial mammal community in northern Botswana and evaluate community, group, and species-specific responses to human disturbance and environmental variables. Groupings were based on two life-history traits:...

Data from: Effect of acute stressor on reproductive behavior differs between urban and rural birds

Mikus Abolins-Abols, Sydney F. Hope & Ellen D. Ketterson
The life-history trade-off between self-maintenance and reproduction posits that investment in one function decreases investment in the other. Manipulating the costs and benefits of functions involved in a trade-off may alter this interaction. Here we ask whether investment in self-maintenance during a stress response alters territorial behavior in wild Dark-eyed Juncos and whether rural and urban birds, which are known to differ in the magnitude of the stress response (greater in rural), also differ in...

Data from: Phylogenomics reveals three sources of adaptive variation during a rapid radiation

James B. Pease, David C. Haak, Matthew W. Hahn & Leonie C. Moyle
Speciation events often occur in rapid bursts of diversification, but the ecological and genetic factors that promote these radiations are still much debated. Using whole transcriptomes from all 13 species in the ecologically and reproductively diverse wild tomato clade (Solanum sect. Lycopersicon), we infer the species phylogeny and patterns of genetic diversity in this group. Despite widespread phylogenetic discordance due to the sorting of ancestral variation, we date the origin of this radiation to approximately...

Data from: Convergent local adaptation to climate in distantly related conifers

Sam Yeaman, Kathryn A. Hodgins, Katie E. Lotterhos, Haktan Suren, Simon Nadeau, Kristin A. Nurkowski, Pia Smets, Tongli Wang, Laura K. Gray, Katharina J. Liepe, Andreas Hamann, Jason A. Holliday, Michael C. Whitlock, Loren H. Rieseberg & Sally N. Aitken
When confronted with an adaptive challenge, such as extreme temperature, closely related species frequently evolve similar phenotypes using the same genes. Although such repeated evolution is thought to be less likely in highly polygenic traits and distantly related species, this has not been tested at the genome scale. We performed a population genomic study of convergent local adaptation among two distantly related species, lodgepole pine and interior spruce. We identified a suite of 47 genes,...

Data from: Patterns and limitations of urban human mobility resilience under the influence of multiple types of natural disaster

Qi Wang & John E. Taylor
Natural disasters pose serious threats to large urban areas, therefore understanding and predicting human movements is critical for evaluating a population’s vulnerability and resilience and developing plans for disaster evacuation, response and relief. However, only limited research has been conducted into the effect of natural disasters on human mobility. This study examines how natural disasters influence human mobility patterns in urban populations using individuals’ movement data collected from Twitter. We selected fifteen destructive cases across...

Data from: Context-dependent outcomes in a reproductive mutualism between two freshwater fish species

Brandon K. Peoples & Emmanuel A. Frimpong
1. The development of encompassing general models of ecology is precluded by underrepresentation of certain taxa and systems. Models predicting context-dependent outcomes of biotic interactions have been tested using plants and bacteria, but their applicability to higher taxa is largely unknown. 2. We examined context dependency in a reproductive mutualism between two stream fish species: mound nest-building bluehead chub Nocomis leptocephalus and mountain redbelly dace Chrosomus oreas, which often uses N. leptocephalus nests for spawning....

Data from: Conservation priorities of Iberoamerican pig breeds and their ancestors based on microsatellite information

Oscar Cortés, A. M. Martinez, J. Cañon, N. Sevane, L. T. Gama, C. Ginja, V. Landi, P. Zaragoza, N. Carolino, A. Vicente, P. Sponenberg & J. V. Delgado
Criollo pig breeds are descendants from pigs brought to the American continent starting with Columbus second trip in 1493. Pigs currently play a key role in social economy and community cultural identity in Latin America. The aim of this study was to establish conservation priorities among a comprehensive group of Criollo pig breeds based on a set of 24 microsatellite markers and using different criteria. Spain and Portugal pig breeds, wild boar populations of different...

Data from: Joint effects of habitat, zooplankton, host stage structure and diversity on amphibian chytrid

Jessica L. Hite, Jaime Bosch, Saioa Fernández-Beaskoetxea, Daniel Medina & Spencer R. Hall
Why does the severity of parasite infection differ dramatically across habitats? This question remains challenging to answer because multiple correlated pathways drive disease. Here, we examined habitat–disease links through direct effects on parasites and indirect effects on parasite predators (zooplankton), host diversity and key life stages of hosts. We used a case study of amphibian hosts and the chytrid fungus, Batrachochytrium dendrobatidis, in a set of permanent and ephemeral alpine ponds. A field experiment showed...

Data from: A new species of Illacme Cook & Loomis, 1928 from Sequoia National Park, California, with a world catalog of the Siphonorhinidae (Diplopoda, Siphonophorida)

Paul E. Marek, Jean K. Krejca & William A. Shear
Members of the family Siphonorhinidae Cook, 1895 are thread-like eyeless millipedes that possess an astounding number of legs, including one individual with 750. Due to their cryptic lifestyle, rarity in natural history collections, and sporadic study over the last century, the family has an unclear phylogenetic placement, and intrafamilial relationships remain unknown. Here we report the discovery of a second species of Illacme, a millipede genus notable for possessing the greatest number of legs of...

Data from: The rules for symbiont community assembly change along a mutualism-parasitism continuum

James Skelton, Sam Doak, Meredith Leonard, Robert P. Creed & Bryan L. Brown
Symbiont community assembly is driven by host-symbiont and symbiont-symbiont interactions.The effects that symbionts exert on their hosts are often context-dependent and existing theoretical frameworks of symbiont community assembly do not consider the implications of variable outcomes to assembly processes. We hypothesized that symbiont-symbiont interactions become increasingly important along a parasitism/mutualism continuum because; a) negative outcomes favor host resistance which in turn reduces symbiont colonization and subsequently reduce symbiont-symbiont interactions, whereas b) positive host outcomes favor...

Data from: Infection reduces anti-predator behaviors in house finches

James S. Adelman, Corinne Mayer & Dana M. Hawley
Infectious diseases can cause host mortality through direct or indirect mechanisms, including altered behavior. Diminished anti-predator behavior is among the most-studied causes of indirect mortality during infection, particularly for systems in which a parasite's life-cycle requires transmission from prey to predator. Significantly less work has examined whether directly-transmitted parasites and pathogens also reduce anti-predator behaviors. Here we test whether the directly-transmitted bacterial pathogen, Mycoplasma gallisepticum (MG), reduces responses to predation-related stimuli in house finches Haemorhous...

Data from: A multispecies occupancy model for two or more interacting species

Christopher T. Rota, Marco A. R. Ferreira, Roland W. Kays, Tavis D. Forrester, Elizabeth L. Kalies, William J. McShea, Arielle W. Parsons & Joshua J. Millspaugh
Species occurrence is influenced by environmental conditions and the presence of other species. Current approaches for multispecies occupancy modelling are practically limited to two interacting species and often require the assumption of asymmetric interactions. We propose a multispecies occupancy model that can accommodate two or more interacting species. We generalize the single-species occupancy model to two or more interacting species by assuming the latent occupancy state is a multivariate Bernoulli random variable. We propose modelling...

Registration Year

  • 2016
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Resource Types

  • Dataset
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Affiliations

  • Virginia Tech
    16
  • Indiana University Bloomington
    3
  • University of Massachusetts Amherst
    1
  • University of Montana
    1
  • The University of Texas at Austin
    1
  • Osaka Museum of Natural History
    1
  • SUNY College of Environmental Science and Forestry
    1
  • West Virginia University
    1
  • University of Zaragoza
    1
  • University of North Carolina
    1