89 Works

Data from: Blue whale population structure along the eastern South Pacific Ocean: evidence of more than one population

Juan P. Torres-Florez, Rodrigo Hucke-Gaete, Rick LeDuc, Aimee Lang, Barbara Taylor, Lida E. Pimper, Luis Bedriñana-Romano, Howard C. Rosenbaum & Christian C. Figueroa
Blue whales (Balaenoptera musculus) were among the most intensively exploited species of whales in the world. As a consequence of this intense exploitation, blue whale sightings off the coast of Chile were uncommon by the end of the 20th century. In 2004, a feeding and nursing ground was reported in southern Chile (SCh). With the aim to investigate the genetic identity and relationship of these Chilean blue whales to those in other Southern Hemisphere areas,...

Data from: Genetic signals of artificial and natural dispersal linked to colonization of South America by non-native Chinook salmon (Oncorhynchus tshawytscha)

Daniel Gomez-Uchida, Diego Cañas-Rojas, Carla M. Riva-Rossi, Javier E. Ciancio, Miguel A. Pascual, Billy Ernst, Eduardo Aedo, Selim S. Musleh, Francisca Valenzuela-Aguayo, Thomas P. Quinn, James E. Seeb & Lisa W. Seeb
Genetics data have provided unprecedented insights into evolutionary aspects of colonization by non-native populations. Yet, our understanding of how artificial (human-mediated) and natural dispersal pathways of non-native individuals influence genetic metrics, evolution of genetic structure, and admixture remains elusive. We capitalize on the widespread colonization of Chinook salmon Oncorhynchus tshawytscha in South America, mediated by both dispersal pathways, to address these issues using data from a panel of polymorphic SNPs. First, genetic diversity and the...

Data from: Energy expenditure and body size are targets of natural selection across a wide geographic range, in a terrestrial invertebrate

José Luis Bartheld, Juan Diego Gaitán-Espitia, Paulina Artacho, Cristian Salgado-Luarte, Ernesto Gianoli & Roberto F. Nespolo
One of the central questions in evolutionary ecology is how different functional capacities impact fitness, and how it varies across populations. For instance, do phenotypic attributes influence fitness similarly across geographic gradients? Which traits (physiological, morphological, life history) are most likely to be targets of natural selection? Do particular combinations of traits maximize fitness? In a semi-natural experiment, we analyzed introduced populations of an invasive species, the garden snail (Cornu aspersum) in Chile, which show...

Data from: Genetic variation in blue whales in the eastern Pacific: implication for taxonomy and use of common wintering grounds

Richard G. LeDuc, F.I. Archer, Aimee R. Lang, Karen K. Martien, Brittany Hancock-Hanser, Juan P. Torres-Florez, Rodrigo Hucke-Gaete, Howard C. Rosenbaum, Koen Van Waerebeek, Robert L. Brownell, Barbara L. Taylor & F. I. Archer
Many aspects of blue whale biology are poorly understood. Some of the gaps in our knowledge, such as those regarding their basic taxonomy and seasonal movements, directly affect our ability to monitor and manage blue whale populations. As a step towards filling in some of these gaps, microsatellite and mtDNA sequence analyses were conducted on blue whale samples from the Southern Hemisphere, the eastern tropical Pacific (ETP), and the northeast Pacific. The results indicate that...

Data from: Larval dispersal and fishing pressure influence recruitment in a coral reef fishery

Richard J. Hamilton, Diego Lozano-Cortés, Michael Bode, Glenn Almany, Hugo B. Harrison, John Pita, Pablo Saenz-Agudelo, Colin Gereniu, Nate Peterson, Howard Choat, Peter A. Waldie & Michael L. Berumen
Understanding larval connectivity patterns in exploited fishes is a fundamental prerequisite for developing effective management strategies and assessing the vulnerability of a fishery to recruitment overfishing and localised extinction. To date however, researchers have not considered how regional variations in fishing pressure also influence recruitment. We used genetic parentage analyses and modelling to infer the dispersal patterns of bumphead parrotfish (Bolbometopon muricatum) larvae in the Kia fishing grounds, Isabel Province, Solomon Islands. We then extrapolated...

Supplementary material: Ultraconserved elements improve the resolution of difficult nodes within the rapid radiation of neotropical sigmodontine rodents (Cricetidae: Sigmodontinae)

Andrés Parada, Guillermo D'Elía & John Hanson
Sigmodontine rodents (Cricetidae, Sigmodontinae) represent the second largest muroid subfamily and the most species-rich group of New World mammals, encompassing above 410 living species and ca. 87 genera. Even with advances on the clarification of sigmodontine phylogenetic relationships that have been made recently, the phylogenetic relationships among the 11 main group of genera (i.e., tribes) remain poorly resolved, in particular among those forming the large clade Oryzomyalia. This pattern has been interpreted as consequence of...

Stability of rocky intertidal communities in response to species removal varies across spatial scales

Nelson Valdivia, Daniela Lopez, Eliseo Fica, Alexis Catalán, Moisés Aguilera, Marjorie Araya, Claudia Betancourtt, Katherine Burgos-Andrade, Thais Carvajal-Baldeon, Valentina Escares, Simon Gartenstein, Mariana Grossmann, Bárbara Gutiérrez, Jonne Kotta, Diego Morales-Torres, Bárbara Riedemann-Saldivia, Sara Rodríguez, Catalina Velasco-Charpentier, Vicente Villalobos & Bernardo Broitman
Improving our understanding of stability across spatial scales is crucial in the current scenario of biodiversity loss. Still, most empirical studies of stability target small scales. Here we experimentally removed the local space-dominant species (macroalgae, barnacles, or mussels) at eight sites spanning more than 1000 km of coastline in north- and south-central Chile, and quantified the relationship between area (the number of aggregated sites) and stability in aggregate community variables (total cover) and taxonomic composition....

Data from: An association between differential expression and genetic divergence in the Patagonian olive mouse (Abrothrix olivacea)

Facundo M. Giorello, Matias Feijoo, Guillermo D'Elía, Daniel E. Naya, Lourdes Valdez, Juan C. Opazo & Enrique P. Lessa
Recent molecular studies have found striking differences between desert-adapted species and model mammals regarding water conservation. In particular, aquaporin 4, a classical gene involved in water regulation of model species, is absent or not expressed in the kidneys of desert-adapted species. To further understand the molecular response to water availability we studied the Patagonian olive mouse Abrothrix olivacea, a species with an unusually broad ecological tolerance that exhibits a great urine concentration capability. The species...

Data from: Conflicting evolutionary patterns due to mitochondrial introgression and multilocus phylogeography of the Patagonian freshwater crab Aegla neuquensis

Brian R. Barber, Jiawu Xu, Marcos Pérez-Losada, Carlos G. Jara & Keith A. Crandall
BACKGROUND: Multiple loci and population genetic methods were employed to study the phylogeographic history of the Patagonian freshwater crab Aegla neuquensis (Aeglidae: Decopoda). This taxon occurs in two large river systems in the Patagonian Steppe, from the foothills of the Andes Mountains east to the Atlantic Ocean. METHODOLOGY/PRINCIPAL FINDINGS: A nuclear phylogeny and multilocus nested clade phylogeographic analysis detected a fragmentation event between the Negro and Chico-Chubut river systems. This event occurred approximately 137 thousand...

Data from: Differences in endophyte communities of introduced trees depend on the phylogenetic relatedness of the receiving forest

Michael J. Gundale, Juan P. Almeida, Håkan Wallander, David A. Wardle, Paul Kardol, Marie-Charlotte Nilsson Hegethorn, Alex Fajardo, Anibal Pauchard, Duane A. Peltzer, Seppo Ruotsalainen, Bill Mason, Nicholas Rosenstock & Marie-Charlotte Nilsson
Plant species sometimes perform extraordinarily well when introduced to new environments, through achieving higher growth rates, individual biomasses or higher densities in their receiving communities compared to their native range communities. One hypothesis proposed to explain enhanced performance in species’ new environments is that their soil microbial communities may be different and provide greater benefit than microbial communities encountered in species’ native environments. However, detailed descriptions of soil biota associated with species in both their...

Data from: Widespread hybridization and bidirectional introgression in sympatric species of coral reef fish

Hugo B. Harrison, Michael L. Berumen, Pablo Saenz-Agudelo, Eva Salas, David H. Williamson & Geoffrey P. Jones
Coral reefs are highly diverse ecosystems, where numerous closely related species often coexist. How new species arise and are maintained in these high geneflow environments have been long-standing conundrums. Hybridization and patterns of introgression between sympatric species provide a unique insight into the mechanisms of speciation and the maintenance of species boundaries. In this study, we investigate the extent of hybridization between two closely related species of coral reef fish: the common coral trout (Plectropomus...

Data from: Local persistence of Mann’s soft-haired mouse Abrothrix manni (Rodentia, Sigmodontinae) during Quaternary glaciations in southern Chile

Lourdes Valdez & Guillermo D'Elía
Quaternary climatic oscillations have impacted Patagonian sigmodontine fauna, leaving traceable genetic footprints. In southern Chile, changes in the landscape included transitions to different vegetation formations as well as the extension of ice sheets. In this study, we focus on the Valdivian forest endemic and recently described sigmodontine species Abrothrix manni. We aim to assess the genetic structure of this species, testing for the existence of intraspecific lineages, and inferring the recent demographic history of the...

Data from: Using a butterflyfish genome as a general tool for RAD-Seq studies in specialized reef fish

Joseph D. DiBattista, Pablo Saenz-Agudelo, Marek J. Piatek, Xin Wang, Manuel Aranda & Michael L. Berumen
Data from a large-scale restriction site associated DNA (RAD-Seq) study of nine butterflyfish species in the Red Sea and Arabian Sea provided a means to test the utility of a recently published draft genome (Chaetodon austriacus) and assess apparent bias in this method of isolating nuclear loci. We here processed double-digest restriction-site (ddRAD) associated DNA sequencing data to identify single nucleotide polymorphism (SNP) markers and their associated function with and without our reference genome to...

Data from: Exploring seascape genetics and kinship in the reef sponge Stylissa carteri in the Red Sea

Emily C. Giles, Pablo Saenz-Agudelo, Nigel E. Hussey, Timothy Ravasi & Michael L. Berumen
A main goal of population geneticists is to study patterns of gene flow to gain a better understanding of the population structure in a given organism. To date most efforts have been focused on studying gene flow at either broad scales to identify barriers to gene flow and isolation by distance or at fine spatial scales in order to gain inferences regarding reproduction and local dispersal. Few studies have measured connectivity at multiple spatial scales...

Evaluating aspects of biodiversity loss, and associated indicators, for application to the assessment of the impacts of agricultural commodity trade

Amy Molotoks, América Paz Durán, Jonathan Green & Christopher David West
This output has been funded in whole or part by the UK Research and Innovation’s Global Challenges Research Fund under the Trade, Development and the Environment Hub project (project number ES/S008160/1).

A practical approach to measuring the biodiversity impacts of land conversion

América P. Durán, Jonathan M. H. Green, Christopher D. West, Piero Visconti, Neil Burgess, Malika Virah-Sawmy & Andrew Balmford
1. Further progress in reducing biodiversity loss relies on the improved quantification of the connections between drivers of habitat loss and subsequent biodiversity impacts. To this end, biodiversity impact metrics should be able to report linked trends in specific human activities and changes in biodiversity state, accounting for both the ecology of different species, and the cumulative effects of historical habitat losses. These characteristics are not currently captured within a single metric. 2. Here we...

Why bears hibernate? Redefining the scaling energetics of hibernation

Roberto Nespolo
Hibernation is a natural state of suspended animation that many mammals experience and has been interpreted as an adaptive strategy for saving energy. However, the actual amount of savings that hibernation represents, and particularly its dependence on body mass (the “scaling”) has not been calculated properly. Here we estimated the scaling of daily energy expenditure of hibernation (DEEH), covering a range of five orders of magnitude in mass. We found that DEEH scales isometrically with...

Data from: Heat tolerance in Drosophila subobscura along a latitudinal gradient: contrasting patterns between plastic and genetic responses

Luis E. Castañeda, Enrico L. Rezende & Mauro Santos
Susceptibility to global warming relies on how thermal tolerances respond to increasing temperatures through plasticity or evolution. Climatic adaptation can be assessed examining the geographic variation in thermal-related traits. We studied latitudinal patterns in heat tolerance in Drosophila subobscura reared at two temperatures. We used four static stressful temperatures to estimate the thermal death time curves (TDT), and two ramping assays with fast and slow heating rates. TDT curves allow estimating the critical thermal maximum...

Data from: Does sex-biased dispersal account for the lack of geographic and host-associated differentiation in introduced populations of an aphid parasitoid?

Francisca Zepeda-Paulo, Blas Lavandero, Frédérique Mahéo, Emilie Dion, Yannick Outreman, Jean-Christophe Simon & Christian C. Figueroa
Host recognition and use in female parasitoids strongly relies on host fidelity, a plastic behavior which can significantly restrict the host preferences of parasitoids, thus reducing the gene flow between parasitoid populations attacking different insect hosts. However, the effect of migrant males on the genetic differentiation of populations has been frequently ignored in parasitoids, despite its known impact on gene flow between populations. Hence, we studied the extent of gene flow mediated by female and...

Data from: ClonEstiMate, a Bayesian method for quantifying rates of clonality of populations genotyped at two-time steps

Ronan Becheler, Jean-Pierre Masson, Sophie Arnaud-Haond, Fabien Halkett, Stéphanie Mariette, Marie-Laure Guillemin, Myriam Valero, Christophe Destombe & Solenn Stoeckel
Partial clonality is commonly used in Eukaryotes and has large consequences for their evolution and ecology. Assessing accurately the relative importance of clonal versus sexual reproduction matters for studying and managing such species. Here, we proposed a Bayesian approach, ClonEstiMate, to infer rates of clonality c from populations sampled twice over a short time interval, ideally one generation time. The method relies on the likelihood of the transitions between genotype frequencies of ancestral and descendent...

Monitoring vertebrate biodiversity of a protected coastal wetland using eDNA metabarcoding

Pablo Saenz-Agudelo, Erwan Delrieu-Trottin, Joseph D. DiBattista, Diego Martinez, Sarai Morales-Gonzáles, Felipe Pontigo, Paula Ramirez, Andrea Silva, Mauricio Soto & Cristian Correa
Monitoring plans using environmental DNA have the potential to offer a standardized and cost-efficient method to survey biodiversity in aquatic ecosystems. Among these ecosystems, coastal wetlands are key elements that serve as transition zones between marine and freshwater ecosystems and are today the target of many conservation and restoration efforts. In this sense, eDNA monitoring could provide a rapid and efficient tool for studying and generating baseline biodiversity information to guide coastal wetland management programs....

Exploring the genetic consequences of clonality in haplodiplontic taxa

Stacy Krueger-Hadfield, Marie-Laure Guillemin, Christophe Destombe, Myriam Valero & Solenn Stoeckel
Partially clonality is an incredibly common reproductive mode found across all the major eukaryotic lineages. Yet, population genetic theory is based on exclusive sexuality or exclusive asexuality and partial clonality is often ignored. This is particularly true in haplodiplontic eukaryotes, including algae, ferns, mosses, and fungi, where somatic development occurs in both the haploid and diploid stages. Haplodiplontic life cycles are predicted to be correlated with asexuality, but tests of this prediction are rare. Moreover,...

Data from: Introduced beaver improve growth of non–native trout in Tierra del Fuego, South America

Ivan Arismendi, Brooke Penaluna & Carlos Jara
Species introductions threaten ecosystem function worldwide and interactions among introduced species may amplify their impacts. Effects of multiple invasions are still poorly studied and often the mechanisms underlying potential interactions among invaders are unknown. Despite being a remote and well–conserved area, the southern portion of South America has been greatly impacted by invasions of both the American Beaver (Castor canadensis) and Brown Trout (Salmo trutta fario). Here, we compared growth, condition, diet, and stable isotopes...

Didimosphenia geminata: sequences and morphology data set

Leyla Cardenas
Microalgae and their invasiveness are recurrent themes in aquatic environments and many invasions by microalgae are linked to eutrophication. However the diatom Didymosphenia geminata has gained notoriety in forming thick mucilaginous mats in pristine, rocky-bottomed rivers with no obvious connection to elevated levels of nutrients. This species is native to freshwaters of the circumboreal region of the Northern Hemisphere and blooms in the Southern Hemisphere have been attributed to recent introductions of the species to...

Data from: Travel with your kin ship! Insights from genetic sibship among settlers of a coral damselfish

Vanessa Robitzch, Pablo Saenz-Agudelo & Michael L. Berumen
Coral reef fish larvae are tiny, exceedingly numerous, and hard to track. They are also highly capable, equipped with swimming and sensory abilities that may influence their dispersal trajectories. Despite the importance of larval input to the dynamics of a population, we remain reliant on indirect insights to the processes influencing larval behavior and transport. Here, we used genetic data (300 independent single nucleotide polymorphisms) derived from a light trap sample of a single recruitment...

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