33 Works

Near-complete sequence of a novel reovirus genome identified from Callinectes sapidus

Mingli Zhao, Emily FLowers & Eric J. Schott
The Atlantic blue crab, Callinectes sapidus, is an estuarine keystone species that functions as both predator and prey in food webs and supports a multi-million dollar fishery along the western Atlantic coast from the US mid-Atlantic to southern Brazil. Throughout their range, blue crabs are host to viral, bacterial, fungal, protozoan, and metazoan pathogens. Reoviruses are non-enveloped icosahedral viruses with genomes comprised of 9 to 12 segments of linear double-stranded RNA (dsRNA). They have been...

Data from: Tracking dragons: stable isotopes reveal the annual cycle of a long-distance migratory insect

Michael T. Hallworth, Peter P. Marra, Kent P. McFarland, Sara Zahendra & Colin E. Studds
Insect migration is globally ubiquitous and can involve continental-scale movements and complex life-histories. Apart from select species of migratory moths and butterflies, little is known about the structure of the annual cycle for migratory insects. Using stable-hydrogen isotope analysis of 852 wing samples from eight countries spanning 140 years, combined with 21 years of citizen science data, we determined the full annual cycle of a large migratory dragonfly, the common green darner (Anax junius). We...

Data from: Connectivity increases trophic subsidies in fragmented landscapes

Christine L. Hawn, John D. Herrmann, Sean R. Griffin & Nick M. Haddad
Landscape corridors mitigate the negative effects of habitat fragmentation by increasing dispersal. Corridors also increase biodiversity in connected habitat fragments, suggestive of metacommunity dynamics. What is unknown in this case is the mechanisms through which metacommunity dynamics act. Working in a large-scale fragmentation experiment, we tested the effect of corridors on the movement of prey species and subsequent effects on predator nutrition (which we call trophic subsidies). We enriched plants of central patches with 15N,...

Data from: The large-scale drivers of population declines in a long-distance migratory shorebird

Nicholas J. Murray, Peter P. Marra, Richard A. Fuller, Robert S. Clemens, Kiran Dhanjal-Adams, Ken B. Gosbell, Chris J. Hassell, Takuya Iwamura, David Melville, Clive D. T. Minton, Adrian C. Riegen, Danny I. Rogers, Eric J. Woehler & Colin E. Studds
Migratory species can travel tens of thousands of kilometers each year, spending different parts of their annual cycle in geographically distinct locations. Understanding the drivers of population change is vital for conserving migratory species, yet the challenge of collecting data over entire geographic ranges has hindered attempts to identify the processes leading to observed population changes. Here, we use remotely sensed environmental data and count data to investigate the factors driving variability in abundance in...

Data from: Aligner optimization increases accuracy and decreases compute times in multi-species sequence data

Kelly M. Robinson, Aziah S. Hawkins, Ivette Santana-Cruz, Ricky S. Adkins, Amol C. Shetty, Sushma Nagaraj, Lisa Sadzewicz, Luke J. Tallon, David A. Rasko, Claire M. Fraser, Anup Mahurkar, Joana C. Silva & Julie C. Dunning Hotopp
As sequencing technologies have evolved, the tools to analyze these sequences have made similar advances. However, for multi-species samples, we observed important and adverse differences in alignment specificity and computation time for bwa- mem (Burrows–Wheeler aligner-maximum exact matches) relative to bwa-aln. Therefore, we sought to optimize bwa-mem for alignment of data from multi-species samples in order to reduce alignment time and increase the specificity of alignments. In the multi-species cases examined, there was one majority...

Data from: Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data

Kelly M. Robinson, Jonathan Crabtree, John S. A. Mattick, Kathleen E. Anderson & Julie C. Dunning Hotopp
Background: A variety of bacteria are known to influence carcinogenesis. Therefore, we sought to investigate if publicly available whole genome and whole transcriptome sequencing data generated by large public cancer genome efforts, like The Cancer Genome Atlas (TCGA), could be used to identify bacteria associated with cancer. The Burrows-Wheeler aligner (BWA) was used to align a subset of Illumina paired-end sequencing data from TCGA to the human reference genome and all complete bacterial genomes in...

Data from: Divergence in calls but not songs in the orchard oriole complex: Icterus spurius and I. fuertesi

Rachel J. Sturge, Kevin E. Omland, J. Jordan Price & Bernard Lohr
Birdsong has important functions in attracting and competing for mates, and song characteristics are thought to diverge rapidly during the process of speciation. In contrast, other avian vocalizations that may have non-reproductive functions, such as calls, are thought to be more evolutionarily conserved and may diverge more slowly among taxa. This study examines differences in both male song and an acoustically simpler vocalization, the ‘jeet’ call, between two closely related taxa, Icterus spurius and I....

Influence of Climate and Human Preferences on Patterns of Taxonomic and Functional Biodiversity of Recreational Parks

Peter Ibsen, Dorothy Borowy, Mia Rochford, Christopher Swan & G Darrel Jenerette
Recreational urban parks support diverse assemblages of plants that contribute ecosystem services to billions of individuals in cities throughout the world. Drivers of ecosystem services in parks are complex, as climate and human preferences interact with multiple species of vegetation types. Yet, informal observations suggest that recreational parks are built consistently to a specific typology. Here we ask: what are the patterns of ecosystem services and vegetation biodiversity in cities of varying climate in the...

Data from: Female song is widespread and ancestral in songbirds

Karan J. Odom, Michelle L. Hall, Katharina Riebel, Kevin E. Omland & Naomi E. Langmore
Bird song has historically been considered an almost exclusively male trait, an observation fundamental to the formulation of Darwin’s theory of sexual selection. Like other male ornaments, song is used by male songbirds to attract females and compete with rivals. Thus, bird song has become a textbook example of the power of sexual selection to lead to extreme neurological and behavioural sex differences. Here we present an extensive survey and ancestral state reconstruction of female...

Data from: Preference for conspecifics evolves earlier in males than females in a sexually dimorphic radiation of fishes

Tamra C. Mendelson, Jennifer M. Gumm, Michael D. Martin & Patrick J. Ciccotto
Speciation by sexual selection is generally modeled as the co-evolution of female preferences and elaborate male ornaments leading to behavioral (sexual) reproductive isolation. One prediction of these models is that female preference for conspecific males should evolve earlier than male preference for conspecific females in sexually dimorphic species with male ornaments. We tested that prediction in darters, a diverse group of freshwater fishes with sexually dimorphic ornamentation. Focusing on the earliest stages of divergence, we...

Data from: Defense traits of larval Drosophila melanogaster exhibit genetically based tradeoffs against different species of parasitoids

Jeff Leips, Theresa K. Hodges, Kate L. Laskoski, Giuseppe L. Squadrito & Maria De Luca
Populations of Drosophila melanogaster face significant mortality risks from parasitoid wasps that use species-specific strategies to locate and survive in hosts. We tested the hypothesis that parasitoids with different strategies select for alternative host defense characteristics and in doing so contribute to the maintenance of fitness variation and produce trade-offs among traits. We characterized defense traits of Drosophila when exposed to parasitoids with different host searching behaviors (Aphaereta sp. and Leptopilina boulardi). We used host...

Data from: Trends and determinants of gastric bacterial colonization of preterm neonates in a NICU setting

Ketki S. Patel, Kavitha Konduru, Alok K. Patra, Dinesh S. Chandel, Pinaki Panigrahi & Ketki Patel
Background: Newborn gastrointestinal (GI) tract is considered sterile but rapidly acquires a diverse microbiota from its intimate environment. Early acquisition of a bacterial species in the upper GI tract may play a role in establishing the colonic microbiota. There is paucity of molecular data on the upper GI tract microbiota in preterm neonates. Methods: Gastric aspirates from 22 neonates with an average gestational age 27.7 weeks (±2.8), weighing 973.2 grams (±297.9) admitted to a neonatal...

Data from: Suburban watershed nitrogen retention: estimating the effectiveness of stormwater management structures

Benjamin J. Koch, Catherine M. Febria, Roger M. Cooke, Jacob D. Hosen, Matthew E. Baker, Abigail R. Colson, Solange Filoso, Katharine Hayhoe, J. V. Loperfido, Anne M. K. Stoner & Margaret A. Palmer
Excess nitrogen (N) is a primary driver of freshwater and coastal eutrophication globally, and urban stormwater is a rapidly growing source of N pollution. Stormwater best management practices (BMPs) are used widely to remove excess N from runoff in urban and suburban areas, and are expected to perform under a wide variety of environmental conditions. Yet the capacity of BMPs to retain excess N varies; and both the variation and the drivers thereof are largely...

Data from: Evolutionary history of chemosensory-related gene families across the Arthropoda

Seong-Il Eyun, Ho Young Soh, Marijan Posavi, James B. Munro, Daniel S. T. Hughes, Shwetha C. Murali, Jiaxin Qu, Shannon Dugan, Sandra L. Lee, Hsu Chao, Huyen Dinh, Yi Han, HarshaVardhan Doddapaneni, Kim C. Worley, Donna M. Muzny, Eun-Ok Park, Joana C. Silva, Richard A. Gibbs, Stephen Richards & Carol Eunmi Lee
Chemosensory-related gene (CRG) families have been studied extensively in insects, but their evolutionary history across the Arthropoda had remained relatively unexplored. Here, we address current hypotheses and prior conclusions on CRG family evolution using a more comprehensive data set. In particular, odorant receptors were hypothesized to have proliferated during terrestrial colonization by insects (hexapods), but their association with other pancrustacean clades and with independent terrestrial colonizations in other arthropod subphyla have been unclear. We also...

Data from: Ancestral ecological regime shapes reaction to food limitation in the Least Killifish, Heterandria formosa

Anja Felmy, Jeff Leips & Joseph Travis
Populations with different densities often show genetically-based differences in life histories. The divergent life histories could be driven by several agents of selection, one of which is variation in per-capita food levels. Its relationship with population density is complex, as it depends on overall food availability, individual metabolic demand, and food-independent factors potentially affecting density, such as predation intensity. Here we present a case study of two populations of a small live-bearing freshwater fish, one...

Data from: The ephemerality of secondary forests in southern Costa Rica

J. Leighton Reid, Matthew E. Fagan, James Lucas, Joshua Slaughter & Rakan A. Zahawi
Secondary forests are increasingly recognized for conserving biodiversity and mitigating global climate change, but these and other desired outcomes can only be achieved after decades of regeneration, and secondary forests are frequently recleared before they recover to predisturbance conditions. We used a time series of aerial photographs (1947-2014) to evaluate multidecadal persistence of secondary forests across a 320 sq. km landscape in southern Costa Rica. Secondary forests had relatively short lifespans, with 50% recleared within...

Sampling data, colony runfiles, VCFs, and Rscripts for: genomic determination of reproductive mode in facultatively parthenogenetic Opiliones

Mercedes Burns, Nobuo Tsurusaki & Tyler Brown
Sexual reproduction may pose myriad short-term costs to females. Despite these costs, sexual reproduction is near ubiquitous. Facultative parthenogenesis is theorized to mitigate some of the costs of sex, as individuals can participate in occasional sex to limit costs while obtaining many benefits. However, most theoretical models assume sexual reproduction is fixed following mating, with no possibility of clutches of mixed reproductive ontogeny. Therefore, we asked: if coercive males are present at high frequency in...

Data from: Brood ball-mediated transmission of microbiome members in the dung beetle, Onthophagus taurus (Coleoptera: Scarabaeidae)

Anne M. Estes, David J. Hearn, Emilie C. Snell-Rood, Michele Feindler, Karla Feeser, Tselotie Abebe, Julie C. Dunning Hotopp & Armin P. Moczek
Insects feeding on plant sap, blood, and other nutritionally incomplete diets are typically associated with mutualistic bacteria that supplement missing nutrients. Herbivorous mammal dung contains more than 86% cellulose and lacks amino acids essential for insect development and reproduction. Yet one of the most ecologically necessary and evolutionarily successful groups of beetles, the dung beetles (Scarabaeinae) feeds primarily, or exclusively, on dung. These associations suggest that dung beetles may benefit from mutualistic bacteria that provide...

Data from: Genome sequencing and comparative analysis of three Chlamydia pecorum strains associated with different pathogenic outcomes

Michelle Sait, Morag Livingstone, Ewan M. Clark, Nick Wheelhouse, Lucy Spalding, Bryan Markey, Simone Magnino, F. Alex Lainson, Garry S. A. Myers & David Longbottom
Background: Chlamydia pecorum is the causative agent of a number of acute diseases, but most often causes persistent, subclinical infection in ruminants, swine and birds. In this study, the genome sequences of three C. pecorum strains isolated from the faeces of a sheep with inapparent enteric infection (strain W73), from the synovial fluid of a sheep with polyarthritis (strain P787) and from a cervical swab taken from a cow with metritis (strain PV3056/3) were determined...

Data from: Genomic basis of life history evolution in Drosophila melanogaster

Silvia C. Remolina, Peter L. Chang, Jeff Leips, Sergey V. Nuzhdin & Kimberly A. Hughes
Natural diversity in aging and other life history patterns is a hallmark of organismal variation. Related species, populations, and individuals within populations show genetically based variation in life span and other aspects of age-related performance. Population differences are especially informative because these differences can be large relative to within-population variation and because they occur in organisms with otherwise similar genomes. We used experimental evolution to produce populations divergent for life span and late-age fertility and...

Data from: Cracking the case: seed traits and phylogeny predict time to germination in prairie restoration species

Rebecca S. Barak, Taran M. Lichtenberger, Alyssa Wellman-Houde, Andrea T. Kramer & Daniel J. Larkin
1. Traits are important for understanding how plant communities assemble and function, providing a common currency for studying ecological processes across species, locations, and habitat types. However, most studies relating species traits to community assembly rely upon vegetative traits of mature plants. Seed traits, which are understudied relative to whole-plant traits, are key to understanding assembly of plant communities. This is particularly true in restored communities, which are typically started from seed, making germination a...

Data from: A randomized synbiotic trial to prevent sepsis among infants in rural India

Pinaki Panigrahi, Sailajanandan Parida, Nimai C. Nanda, Radhanath Satpathy, Lingaraj Pradhan, Dinesh S. Chandel, Lorena Baccaglini, Arijit Mohapatra, Subhranshu S. Mohapatra, Pravas R. Misra, Rama Chaudhry, Hegang H. Chen, Judith A. Johnson, J. Glenn Morris, Nigel Paneth & Ira H. Gewolb
Sepsis in early infancy results in one million annual deaths worldwide, most of them in developing countries. No efficient means of prevention is currently available. Here we report on a randomized, double-blind, placebo-controlled trial of an oral synbiotic preparation (Lactobacillus plantarum plus fructooligosaccharide) in rural Indian newborns. We enrolled 4,556 infants that were at least 2,000 g at birth, at least 35 weeks of gestation, and with no signs of sepsis or other morbidity, and...

Data from: The accumulation of reproductive isolation in early stages of divergence supports a role for sexual selection

Michael D. Martin & Tamra C. Mendelson
Models of speciation by sexual selection propose that male-female coevolution leads to the rapid evolution of behavioral reproductive isolation. Here, we compare the strength of behavioral isolation to ecological isolation, gametic incompatibility, and hybrid inviability in a group of dichromatic stream fishes. In addition, we examine whether any of these individual barriers, or a combined measure of total isolation, is predicted by body shape differences, male color differences, environmental differences, or genetic distance. Behavioral isolation...

Data from: Random interbreeding between cryptic lineages of the Common Raven: evidence for speciation in reverse

William C Webb, John M Marzluff & Kevin E Omland
DNA sequence studies frequently reveal evidence of cryptic lineages in morphologically uniform species, many of which turn out to be evolutionarily distinct species. The Common Raven (Corvus corax) includes two deeply divergent mtDNA lineages: one lineage seems restricted to western North America and the other is Holarctic in distribution. These deep clades hint of the possibility of cryptic species in the western United States. We tested this hypothesis in a population consisting of an equal...

Data from: Evolution of carotenoid pigmentation in caciques and meadowlarks (Icteridae): repeated gains of red plumage coloration by carotenoid C4-oxygenation

Nicholas R. Friedman, Kevin J. McGraw & Kevin E. Omland
Many animals use carotenoid pigments to produce yellow, orange, and red coloration. In birds, at least 10 carotenoid compounds have been documented in red feathers; most of these are produced through metabolic modification of dietary precursor compounds. However, it is poorly understood how lineages have evolved the biochemical mechanisms for producing red coloration. We used high-performance liquid chromatography to identify the carotenoid compounds present in feathers from 15 species across two clades of blackbirds (the...

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