269 Works

Data from: Validating the use of coloration patterns for individual recognition in the worm pipefish using a novel set of microsatellite markers

Nuno M. Monteiro, Rodolfo M. Silva, Mário Cunha, Agostinho Antunes, Adam G. Jones & Maria N. Vieira
In studies of behaviour, ecology and evolution, identification of individual organisms can be an invaluable tool, capable of unravelling otherwise cryptic information regarding group structure, movement patterns, population size and mating strategies. The use of natural markings is arguably the least invasive method for identification. However, to be truly useful natural markings must be sufficiently variable to allow for unique identification, while being stable enough to permit long-term studies. Non-invasive marking techniques are especially important...

Data from: How far is too close? Restricted, sex-biased dispersal in black-capped vireos

Giri Athrey, Richard F. Lance & Paul L. Leberg
Understanding the interplay of dispersal and how it translates into gene flow is key to understanding population processes, and especially so for endangered species occupying fragmented habitats. In migratory songbirds, there is evidence that long-distance movement capabilities are not highly related to observed dispersal. Our objectives were to 1) define the fine-scale spatial genetic structure in the endangered black-capped vireos to shed light on dispersal patterns, and 2) to relate dispersal dynamics to overall population...

Data from: Genetic isolation within the malaria mosquito Anopheles melas

Kevin C. Deitz, Giridhar Athrey, Michael R. Reddy, Hans J. Overgaard, Abrahan Matias, Jawara Musa, Alessandra Della Torre, Vincenzo Petrarca, Joao Pinto, Anthony E. Kiszewski, Pierre Kengne, Carlo Costantini, Adalgisa Caccone, Michel A. Slotman, Musa Jawara & Giri Athrey
Anopheles melas is a brackish water-breeding member of the An. gambiae complex that is distributed along the coast of West Africa and is a major malaria vector within its range. Because little is known about the population structure of this species, we analyzed 15 microsatellite markers and 1,161 bp of mtDNA in 11 An. melas populations collected throughout its range. Compared to its sibling species An. gambiae, An. melas populations have a high level of...

Data from: Maternal size and age shape offspring size in a live-bearing fish, Xiphophorus birchmanni

Holly K. Kindsvater, Gil G. Rosenthal & Suzanne H. Alonzo
Many studies of offspring size focus on differences in maternal investment that arise from ecological factors such as predation or competition. Classic theory predicts that these ecological factors will select for an optimal offspring size, and therefore that variation in a given environment will be minimized. Yet recent evidence suggests maternal traits such as size or age could also drive meaningful variation in offspring size. The generality of this pattern is unclear, as some studies...

Data from: Effects of mating order and male size on embryo survival in a pipefish

Ines Braga Goncalves, Kenyon B. Mobley, Ingrid Ahnesjö, Gry Sagebakken, Adam G. Jones & Charlotta Kvarnemo
In species that provide parental care, individuals should invest adaptively in their offspring in relation to the pre- and post-zygotic care provided by their partners. In the broad-nosed pipefish, Syngnathus typhle L., females transfer large, nutrient-rich eggs into the male brood pouch during mating. The male broods and nourishes the embryos for several weeks before independent juveniles emerge at parturition. Given a choice, females clearly prefer large partners. Yet, females provide protein-richer eggs when the...

Data from: Polyceraty (multi-horns) in Damara sheep maps to ovine chromosome 2

Ockert F. C. Greyvenstein, Coralie M. Reich, Este Van Marle-Koster, David G. Riley & Ben J. Hayes
Polyceraty (presence of multiple horns) is rare in modern day ungulates. Although not found in wild sheep, polyceraty does occur in a small number of domestic sheep breeds covering a wide geographical region. Damara are fat-tailed hair sheep, from the south-western region of Africa, which display polyceraty, with horn number ranging from zero to four. We conducted a genome-wide association study for horn number with 43 Damara genotyped with 606 006 SNP markers. The analysis...

Data from: Limitations of climate data for inferring species boundaries: insights from speckled rattlesnakes

Jesse M. Meik, Jeffrey W. Streicher, A. Michelle Lawing, Oscar Flores-Villela & Matthew K. Fujita
Phenotypes, DNA, and measures of ecological differences are widely used in species delimitation. Although rarely defined in such studies, ecological divergence is almost always approximated using multivariate climatic data associated with sets of specimens (i.e., the “climatic niche”); the justification for this approach is that species-specific climatic envelopes act as surrogates for physiological tolerances. Using identical statistical procedures, we evaluated the usefulness and validity of the climate-as-proxy assumption by comparing performance of genetic (nDNA SNPs...

Data from: Genetic differences in the response to landscape fragmentation by a habitat generalist, the bobcat, and a habitat specialist, the ocelot

Jan E. Janecka, Michael E. Tewes, Imogene A. Davis, Aaron M. Haines, Arturo Caso, Terry L. Blankenship & Rodney L. Honeycutt
The ecology of a species strongly influences genetic variation and population structure. This interaction has important conservation implications because taxa with low dispersal capability and inability to use different habitats are more susceptible to anthropogenic stressors. Ocelots (Leopardus pardalisalbescens) and bobcats (Lynx rufus texensis) are sympatric in Texas and northeastern Mexico; however, their ecology and conservation status are markedly different. We used 10 microsatellite loci and a 397-bp segment of the mitochondrial control region to...

Data from: Identifying signatures of sexual selection using genomewide selection components analysis

Sarah P. Flanagan & Adam G. Jones
Sexual selection must affect the genome for it to have an evolutionary impact, yet signatures of selection remain elusive. Here we use an individual-based model to investigate the utility of genome-wide selection components analysis, which compares allele frequencies of individuals at different life history stages within a single population to detect selection without requiring a priori knowledge of traits under selection. We modeled a diploid, sexually reproducing population and introduced strong mate choice on a...

Data from: Testing for ancient adaptive radiations in Neotropical cichlid fishes

Hernán López-Fernández, Jessica H. Arbour, Kirk O. Winemiller & Rodney L. Honeycutt
Most contemporary studies of adaptive radiation focus on relatively recent and geographically restricted clades. It is less clear whether diversification of ancient clades spanning entire continents is consistent with adaptive radiation. We used novel fossil calibrations to generate a chronogram of Neotropical cichlid fishes and to test whether patterns of lineage and morphological diversification are congruent with hypothesized adaptive radiations in South and Central America. We found that diversification in the Neotropical cichlid clade and...

Data from: The curious case of Hermodice carunculata (Annelida: Amphinomidae): evidence for genetic homogeneity throughout the Atlantic Ocean and adjacent basins

Joseph B. Ahrens, Elizabeth Borda, Rômulo Barroso, Paulo C. Paiva, Alexandra M. Campbell, Alexander Wolf, Maggy M. Nugues, Greg W. Rouse & Anja Schulze
Over the last few decades, advances in molecular techniques have led to the detection of strong geographic population structure and cryptic speciation in many benthic marine taxa, even those with long-lived pelagic larval stages. Polychaete annelids, in particular, generally show a high degree of population divergence, especially in mitochondrial genes. Rarely have molecular studies confirmed the presence of ‘cosmopolitan’ species. The amphinomid polychaete Hermodice carunculata was long considered the sole species within its genus, with...

Data from: Combined analyses of kinship and FST suggest potential drivers of chaotic genetic patchiness in high gene flow populations

Matthew Iacchei, Tal Ben-Horin, Kimberly A. Selkoe, Christopher E. Bird, Francisco J. Garcia-Rodriguez & Robert J. Toonen
We combine kinship estimates with traditional F-statistics to explain contemporary drivers of population genetic differentiation despite high gene flow. We investigate range-wide population genetic structure of the California spiny (or red rock) lobster (Panulirus interruptus) and find slight, but significant global population differentiation in mtDNA (ΦST = 0.006, P = 0.001; Dest_Chao = 0.025) and seven nuclear microsatellites (FST = 0.004, P < 0.001; Dest_Chao = 0.03), despite the species’ 240- to 330-day pelagic larval...

Data from: Gene trees, species trees and Earth history combine to shed light on the evolution of migration in a model avian system

Gary Voelker, Rauri C. K. Bowie & John Klicka
The evolution of migration in birds has fascinated biologists for centuries. In this study, we performed phylogenetic-based analyses of Catharus thrushes, a model genus in the study of avian migration, and their close relatives. For these analyses, we used both mitochondrial and nuclear genes, and the resulting phylogenies were used to trace migratory traits and biogeographic patterns. Our results provide the first robust assessment of relationships within Catharus and relatives and indicate that both mitochondrial...

Data from: More than meets the eye: detecting cryptic microgeographic population structure in a parasite with a complex life cycle

Charles D Criscione, Román Vilas, Esperanza Paniagua & Michael S Blouin
Nonrandom recruitment of parasites among hosts can lead to genetic differentiation among hosts and mating dynamics that promote inbreeding. It has been hypothesized that strictly aquatic parasites with intermediate hosts will behave as panmictic populations among hosts because ample opportunity exists for random mixing of unrelated individuals during transmission to the definitive host. A previous allozyme study on the marine trematode Lecithochirium fusiforme did not support this hypothesis in that there was genetic differentiation among,...

Data from: Evolution in extreme environments: replicated phenotypic differentiation in livebearing fish inhabiting sulfidic springs

Michael Tobler, Maura Palacios, Lauren J Chapman, Igor Mitrofanov, David Bierbach, Martin Plath, Lenin Arias-Rodriguez, Francisco J García De León & Mariana Mateos
We investigated replicated ecological speciation in the livebearing fishes Poecilia mexicana and P. sulphuraria (Poeciliidae), which inhabit freshwater habitats and have also colonized multiple sulfidic springs in southern Mexico. These springs exhibit extreme hypoxia and high concentrations of hydrogen sulfide, which is lethal to most metazoans. We used phylogenetic analyses to test whether springs were independently colonized, performed phenotypic assessments of body and gill morphology variation to identify convergent patterns of trait differentiation, and conducted...

Data from: Constraints on the FST–heterozygosity outlier approach

Sarah P. Flanagan & Adam G. Jones
The FST-heterozygosity outlier approach has been a popular method for identifying loci under balancing and positive selection since Beaumont and Nichols first proposed it in 1996 and recommended its use for studies sampling a large number of independent populations (at least 10). Since then, their program FDIST2 and a user-friendly program optimized for large datasets, LOSITAN, have been used widely in the population genetics literature, often without the requisite number of samples. We observed empirical...

Data from: Relationships between forest cover and fish diversity in the Amazon River floodplain

Caroline C. Arantes, Kirk O. Winemiller, Miguel Petrere, Leandro Castello, Laura L. Hess, Carlos E.C. Freitas & Carlos E. C. Freitas
1.Habitat degradation leads to biodiversity loss and concomitant changes in ecosystem processes. Tropical river floodplains are highly threatened by land cover changes and support high biodiversity and important ecosystems services, but the extent to which changes in floodplain land cover affect fish biodiversity remains unknown. 2.We combined fish and environmental data collected in situ and satellite-mapped landscape features to evaluate how fish species with different ecological strategies and assemblage structures respond to deforestation in floodplains...

Data from: The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing

Alvaro Martinez Barrio, Sangeet Lamichhaney, Guangyi Fan, Nima Rafati, Mats Pettersson, He Zhang, Jacques Dainat, Diana Ekman, Marc Höppner, Patric Jern, Marcel Martin, Björn Nystedt, Xin Liu, Wenbin Chen, Xinming Liang, Chengcheng Shi, Yuanyuan Fu, Kailong Ma, Xiao Zhan, Chungang Feng, Ulla Gustafson, Carl-Johan Rubin, Markus Sällman Almén, Martina Blass, Michele Casini … & Leif Andersson
Ecological adaptation is of major relevance to speciation and sustainable population management, but the underlying genetic factors are typically hard to study in natural populations due to genetic differentiation caused by natural selection being confounded with genetic drift in subdivided populations. Here, we use whole genome population sequencing of Atlantic and Baltic herring to reveal the underlying genetic architecture at an unprecedented detailed resolution for both adaptation to a new niche environment and timing of...

Data from: A bridge between oceans: Overland migration of marine birds in a wind energy corridor

Juliet S. Lamb, David J. Newstead, Lianne M. Koczur, Bart M. Ballard, M. Clay Green, Patrick G.R. Jodice & Patrick G. R. Jodice
Located at the shortest overland route between the Gulf of Mexico and the Pacific Ocean, Mexico's Tehuantepec Isthmus is a globally important migratory corridor for many terrestrial bird species. The Pacific coast of the Isthmus also contains a significant wetland complex that supports large multi-species aggregations of non-breeding waterbirds during the boreal winter. In recent years, extensive wind energy development has occurred in the plains bordering these wetlands, directly along the migratory flyway. Using recent...

Data from: Larval pheromones act as colony-wide regulators of collective foraging behavior in honeybees

Rong Ma, Gabriel Villar, Christina M. Grozinger & Juliana Rangel
When animals move or forage in groups, collective behaviors arise from independent decisions that individuals make based on limited information about the environment. In decentralized systems in which individuals use local cues to decide how to allocate their time amongst multiple tasks, a “global” signal detectable over large distances by all members of the group could have a profound effect on task allocation and coordination. Honey bees provide a unique opportunity to study how information...

Data from: Necrobiome framework for bridging decomposition ecology of autotrophically and heterotrophically derived organic matter

Mark Eric Benbow, Philip S. Barton, Michael D. Ulyshen, James C. Beasley, Travis L. DeVault, Michael S. Strickland, Jeffery K. Tomberlin, Heather R. Jordan & Jennifer L. Pechal
Decomposition contributes to global ecosystem function by contributing to nutrient recycling, energy flow and limiting biomass accumulation. The decomposer organisms influencing this process form diverse, complex, and highly dynamic communities that often specialize on different plant or animal resources. Despite performing the same net role, there is a need to conceptually synthesize information on the structure and function of decomposer communities across the spectrum of dead plant and animal resources. A lack of synthesis has...

Data from: Surveying the spatial distribution of feral sorghum (Sorghum bicolor L.) and its sympatry with johnsongrass (S. halepense) in South Texas

Sara Ohadi, Matthew Littlejohn, Mohsen Mesgaran, William Rooney, Muthu Bagavathiannan & Muthukumar Bagavathiannan
Sorghum (Sorghum bicolor) is an important grain and forage crop grown across the US. In some areas, sorghum can become feral along roadsides and other ruderal areas, as a result of seed spill during harvest or transport. In some of these situations, feral sorghum grows in or near established johnsongrass (S. halepense) populations. Johnsongrass, a wild relative of sorghum and an incredibly noxious weed, is capable of hybridizing with cultivated sorghum. Because commercial hybrid sorghum...

Data from: Natural selection interacts with recombination to shape the evolution of hybrid genomes

Molly Schumer, Chenling Xu, Daniel L Powell, Arun Durvasula, Laurits Skov, Chris Holland, John C Blazier, Sriram Sankararaman, Peter Andolfatto, Gil G Rosenthal & Molly Przeworski
To investigate the consequences of hybridization between species, we studied three replicate hybrid populations that formed naturally between two swordtail fish species, estimating their fine-scale genetic map and inferring ancestry along the genomes of 690 individuals. In all three populations, ancestry from the “minor” parental species is more common in regions of high recombination and where there is linkage to fewer putative targets of selection. The same patterns are apparent in a reanalysis of human...

Data from: Soil carbon response to woody plant encroachment: Importance of spatial heterogeneity and deep soil storage

Yong Zhou, Thomas W. Boutton & X. Ben Wu
1. Recent global trends of increasing woody plant abundance in grass-dominated ecosystems may substantially enhance soil organic carbon (SOC) storage and could represent a strong carbon (C) sink in the terrestrial environment. However, few studies have quantitatively addressed the influence of spatial heterogeneity of vegetation and soil properties on SOC storage at the landscape scale. In addition, most studies assessing SOC response to woody encroachment consider only surface soils, and have not explicitly assessed the...

Data from: The lek mating system of the worm pipefish (Nerophis lumbriciformis): a molecular maternity analysis and test of the phenotype-linked fertility hypothesis

Nuno M. Monteiro, Diana Carneiro, Agostinho Antunes, Nuno Queiroz, Maria N. Vieira & Adam G. Jones
The origin and maintenance of mating preferences continues to be an important and controversial topic in sexual selection research. Leks and lek-like mating systems, where individuals gather in particular spots for the sole purpose of mate choice, are particularly puzzling, because the strong directional selection imposed by mate choice should erode genetic variation among competing individuals and negate any benefit for the choosing sex. Here, we take advantage of the lek-like mating system of the...

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