141 Works

Low oxygen levels as a trigger for enhancement of respiratory metabolism in Saccharomyces cerevisiae [Datasets]

Eija Rintala, Mervi Toivari, Juha-Pekka Pitkänen, Marilyn G Wiebe, Laura Ruohonen & Merja Penttilä
Data from the manuscript: Rintala E, Toivari M, Pitkänen JP, Wiebe MG, Ruohonen L, Penttilä M. Low oxygen levels as a trigger for enhancement of respiratory metabolism in Saccharomyces cerevisiae. BMC Genomics. 2009;10:461. Published 2009 Oct 5. doi:10.1186/1471-2164-10-461

The sources of variation for individual prey-to-predator size ratios

Jorge Henriques, Mariángeles Lacava, Celeste Guzman, Maria Pilar Gavín-Centol, Dolores Ruiz-Lupión, Eva De Mas, Sara Magalhães & Jordi Moya-Laraño
The relative body size at which predators are willing to attack prey, a key trait for predator-prey interactions, is usually considered invariant. However, this ratio can vary widely among individuals or populations. Identifying the range and origin of such variation is key to understanding the strength and constraints on selection in both predators and prey. Still, these sources of variation remain largely unknown. We filled this gap by measuring the genetic, maternal and environmental variation...

Ant taxonomic and functional beta-diversity

Clara Frasconi Wendt, Ana Ceia-Hasse, Alice Nunes, Robin Verble, Giacomo Santini, Mário Boieiro & Cristina Branquinho
The decomposition of beta-diversity (β-diversity) into its replacement (βrepl) and richness (βrich) components in combination with a taxonomic and functional approach, may help to identify processes driving community composition along environmental gradients. We aimed to understand which abiotic and spatial variables influence ant β-diversity and identify which processes may drive ant β-diversity patterns in Mediterranean drylands by measuring the percentage of variation in ant taxonomic and functional β-diversity explained by local environmental, regional climatic and...

Social learning by mate-choice copying increases dispersal and reduces local adaptation

Manuel Sapage, Susana A. M. Varela & Hanna Kokko
1. In heterogeneous environments, dispersal may be hampered not only by direct costs, but also because immigrants may be locally maladapted. While maladaptation affects both sexes, this cost may be modulated in females if they express mate preferences that are either adaptive or maladaptive in the new local population. 2. Dispersal costs under local adaptation may be mitigated if it is possible to switch to expressing traits of locally adapted residents. In a sexual selection...

Stable leaders pave the way for cooperation under time-dependent exploration rates

Flávio L. Pinheiro, Jorge M. Pacheco & Francisco C. Santos
The exploration of different behaviors is part of the adaptation repertoire of individuals to new environments. Here, we explore how the evolution of cooperative behavior is affected by the interplay between exploration dynamics and social learning, in particular when individuals engage on the Prisoner's Dilemma along the edges of a social network. We show that when the population undergoes a transition from strong to weak exploration rates a decline in the overall levels of cooperation...

The genetic ancestry of American Creole cattle inferred from uniparental and autosomal genetic markers

Oscar Cortes Gardyn, Catarina Ginja, Luis Telo De Gama, Amparo Martínez, Inmaculada Martín Burriel & Juan Vicente Delgado
Cattle imported from the Iberian Peninsula spread throughout America in the early years of discovery and colonization to originate Creole breeds, which adapted to a wide diversity of environments and later received infuences from other origins, including zebu cattle in more recent years. We analyzed uniparental genetic markers and autosomal microsatellites in DNA samples from 114 cattle breeds distributed worldwide, including 40 Creole breeds representing the whole American continent, and samples from the Iberian Peninsula,...

Major inconsistencies of inferred population genetic structure estimated in a large set of domestic horse breeds using microsatellites

Stephan Funk, Jose Luis Vega-Pla, Cristina Luis, Gus Cothran & Rytis Juras
STRUCTURE remains the most applied tool aimed at recovering the true, but unknown, population structure from observed microsatellite data or other genetic markers. About 30% of STRUCTURE-based studies could not be reproduced (Gilbert et al., 2012). Here we use a large set of data from 2323 horses from 93 domestic breeds plus the Przewalski horse, typed at 15 microsatellite markers, to evaluate how program settings, in particular the so far insufficiently evaluated number of replicates,...

Food talk: 40-Hz fin whale calls are associated with prey biomass

Miriam Romagosa, Sergi Pérez-Jorge, Irma Cascão, Helena Mouriño, Patrick Lehodey, Andreia Pereira, Tiago A. Marques, Luís Matias & Mónica A. Silva
Animals use varied acoustic signals that play critical roles in their lives. Understanding the function of these signals may inform about key life-history processes relevant for conservation. In the case of fin whales (Balaenoptera physalus), that produce different call types associated with different behaviours, several hypotheses have emerged regarding call function, but the topic still remains in its infancy. Here, we investigate the potential function of two fin whale vocalizations, the song-forming 20-Hz call and...

Data from: Genomic data and multi-species demographic modelling uncover past hybridization between currently allopatric freshwater species

Sofia L. Mendes, Miguel P. Machado, Maria M. Coelho & Vitor C. Sousa
Evidence for ancient interspecific gene flow through hybridization has been reported in many animal and plant taxa based on genetic markers. The study of genomic patterns of closely related species with allopatric distributions allows the assessment of the relative importance of vicariant isolating events and past gene flow. Here, we investigated the role of gene flow in the evolutionary history of four closely related freshwater fish species with currently allopatric distributions in western Iberian rivers...

Bat phylogenetic responses to regenerating Amazonian forests

Fábio Z. Farneda, Ricardo Rocha, Sabhrina Gita Aninta, Adrià López-Baucells, Erica M. Sampaio, Jorge M. Palmeirim, Paulo E. D. Bobrowiec, Cristian S. Dambros & Christoph F. J. Meyer
1. Throughout the tropics, regenerating secondary forests occupy vast areas previously cleared for agriculture and cattle ranching. However, despite the importance of regenerating forests in mitigating the pervasive negative consequences of forest loss and fragmentation on forest-associated biodiversity, longitudinal studies on species’ phylogenetic responses to matrix regeneration are rare. 2. We surveyed bats in continuous primary forest, primary forest fragments and in the regenerating secondary forest matrix of a whole-ecosystem Amazonian fragmentation experiment, ~15 and...

Data from: Community-level responses of African carnivores to prescribed burning

Laura Gigliotti, Goncalo Curveira-Santos, Rob Slotow, Craig Sholto-Douglas, Lourens Swanepoel & David Jachowski
Fires are common in many ecosystems worldwide, and are frequently used as a management tool. Although the responses of herbivores to fire have been well-studied, the responses of carnivores to fire remain unclear. In particular, post-fire habitat changes, and the associated changes in prey availability, might affect the coexistence or competition of carnivore species within the larger carnivore community, but few studies have focused on how fires influence multiple carnivore species simultaneously. Using South African...

Data from: Anthropogenic disturbance of tropical forests threatens pollination services to açaí palm in the Amazon river delta

Alistair John Campbell, Luísa Gigante Carvalheiro, Marcia Motta Maués, Rodolfo Jaffé, Tereza Cristina Giannini, Madson Antonio Benjamin Freitas, Beatriz Woiski Texeira Coelho & Cristiano Menezes
The açaí palm Euterpe oleracea Mart. in the Amazon river delta has seen rapid expansion to meet increased demand for its fruit. This has been achieved by transforming lowland forest habitats (floodplains) into simplified agroforests and intensive plantation in upland areas. As açaí palm makes an important contribution to the economy and food security of local communities, identifying management approaches that support biodiversity and ecosystem processes that underpin fruit production on açaí farms is essential....

Data from: Genetic footprints of Iberian cattle in America 500 years after the arrival of Columbus

Amparo M. Martínez, Luis T. Gama, Javier Cañón, Catarina Ginja, Juan V. Delgado, Susana Dunner, Vincenzo Landi, Inmaculada Martín-Burriel, M. Cecilia T. Penedo, Clementina Rodellar, Jose Luis Vega-Pla, Atzel Acosta, Luz Ángela Álvarez, Esperanza Camacho, Óscar Cortés, José Ribamar Marques, Óscar Roberto Martínez, Rubén Darío Martínez, Lilia Melucci, Guillermo Martínez-Velázquez, Jose Ernesto Muñoz, Alicia Postiglioni, Jorge Quiroz, Philip Sponenberg, Odalys Uffo … & Ruben D. Martínez
BACKGROUND: American Creole cattle presumably descend from animals imported from the Iberian Peninsula during the period of colonization and settlement, through different migration routes, and may have also suffered the influence of cattle directly imported from Africa. The introduction of European cattle, which began in the 18th century, and later of Zebu from India, has threatened the survival of Creole populations, some of which have nearly disappeared or were admixed with exotic breeds. Assessment of...

Data from: Temperature niche shift observed in a Lepidoptera population under allochronic divergence

Helena Santos, Maria Rosa Paiva, Catarina Tavares, Carole Kerdelhué & Manuela Branco
A process of adaptive divergence for tolerance to high temperatures was identified by using a rare model-system, consisting of two sympatric populations of a Lepidoptera (Thaumetopoea pityocampa) with different life-cycle timings, a "mutant" population with summer larval development, Leiria SP, and the founder natural population, having winter larval development, Leiria WP. A third, allopatric population (Bordeaux WP) was also studied. First and second instar larvae were experimentally exposed to daily-cycles of heat treatment reaching maximum...

Data from: Evolution of Drosophila resistance against different pathogens and infection routes entails no detectable maintenance costs

Vitor G. Faria, Nelson E. Martins, Tânia Paulo, Luís Teixeira, Élio Sucena & Sara Magalhães
Pathogens exert a strong selective pressure on hosts, entailing host adaptation to infection. This adaptation often affects negatively other fitness-related traits. Such trade-offs may underlie the maintenance of genetic diversity for pathogen resistance. Trade-offs can be tested with experimental evolution of host populations adapting to parasites, using two approaches: (1) measuring changes in immunocompetence in relaxed-selection lines and (2) comparing life-history traits of evolved and control lines in pathogen-free environments. Here, we used both approaches...

Data from: Genome-wide SNP data unveils the globalization of domesticated pigs

Bin Yang, Leilei Cui, Miguel Perez-Enciso, Aleksei Traspov, Richard P. M. A. Crooijmans, Natalia Zinovieva, Lawrence B. Schook, Alan Archibald, Kesinee Gatphayak, Christophe Knorr, Alex Triantafyllidis, Panoraia Alexandri, Gono Semiadi, Olivier Hanotte, Deodália Dias, Peter Dovč, Pekka Uimari, Laura Iacolina, Massimo Scandura, Martien A. M. Groenen, Lusheng Huang & Hendrik-Jan Megens
Background: Pigs were domesticated independently in Eastern and Western Eurasia early during the agricultural revolution, and have since been transported and traded across the globe. Here, we present a worldwide survey on 60K genome-wide single nucleotide polymorphism (SNP) data for 2093 pigs, including 1839 domestic pigs representing 122 local and commercial breeds, 215 wild boars, and 39 out-group suids, from Asia, Europe, America, Oceania and Africa. The aim of this study was to infer global...

Data from: Revisiting the measurement of anomie

Ali Teymoori, Jolanda Jetten, Brock Bastian, Amarina Ariyanto, Frédérique Autin, Nadia Ayub, Constantina Badea, Tomasz Besta, Fabrizio Butera, Rui Costa-Lopes, Lijuan Cui, Carole Fantini, Gillian Finchilesc, Lowell Gaertner, Mario Gollwitzer, Ángel Gómez, Roberto González, Ying Yi Hong, Dorthe Høj Jensen, Minoru Karasawa, Thomas Kessler, Olivier Klein, Marcus Lima, Tuuli Anna Mähönen, Laura Megevand … & Gillian Finchilescu
Sociologists coined the term "anomie" to describe societies that are characterized by disintegration and deregulation. Extending beyond conceptualizations of anomie that conflate the measurements of anomie as 'a state of society' and as a 'state of mind', we disentangle these conceptualizations and develop an analysis and measure of this phenomenon focusing on anomie as a perception of the 'state of society'. We propose that anomie encompasses two dimensions: a perceived breakdown in social fabric (i.e.,...

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: \"Discovery and characterization of 80 SNPs and 1,624 SSRs in the transcriptome of Atlantic mackerel (Scomber scombrus, L)\" in Genomic Resources Notes Accepted 1 June 2015 to 31 July 2015

Iratxe Montes, Jorge Langa, César Vilas, Sarah J. Helyar, Paula Álvarez, Darrell Conklin & Andone Estonba
This paper reports on SNP discovery in the Atlantic mackerel transcriptome, using next generation sequencing technologies and applying developed methodology already proven successful for the European anchovy. A total of 9,966 high quality transcriptome contigs were assembled, from which 951 putative SNPs were discovered. In all, 479 putative SNPs and 1,624 simple sequence repeats (SSRs) suitable for genotyping were identified. A subset of 96 was selected for genotyping; from these, 80 SNPs were considered polymorphic...

Data from: Riparian plant guilds become simpler and most likely fewer following flow regulation

María D. Bejarano, Christer Nilsson & Francisca C. Aguiar
1. River regulation affects riparian systems worldwide and conservation and restoration efforts are essential to retain biodiversity, and the functioning and services of riverine ecosystems. Effects of regulation on plant species richness have been widely addressed, but the filtering effect of regulation on guilds has received less attention. 2. We used a functional trait approach to identify adaptive plant strategies through regulation-tolerant traits and predict shifts of riparian vegetation communities in response to regulation. We...

Data from: Evolution of mir-92a underlies natural morphological variation in Drosophila melanogaster

Saad Arif, Sophie Murat, Isabel Almudi, Maria D. S. Nunes, Diane Bortolamiol-Becet, Naomi S. McGregor, James M. S. Currie, Harri Hughes, Matthew Ronshaugen, Élio Sucena, Eric C. Lai, Christian Schlötterer & Alistair P. McGregor
eworoRL514BC_QTLPhenotype and genotype data for QTL mapping between strains e, wo, ro and RAL514.eworoRL514BC.xlsstsse_ORER_QTL_mapMap information for QTL mapping between strains st, ss, e and oregon R.ssste_ORER_QTL_crossCross information for QTL mapping between strains st, ss, e and oregon R.

Data from: Long term on-farm participatory maize breeding by stratified mass selection retains molecular diversity while improving agronomic performance

Mara Lisa Alves, Maria Belo, Bruna Carbas, Cláudia Brites, Manuel Paulo, Pedro Mendes-Moreira, Carla Brites, Maria Do Rosário Bronze, Zlatko Šatović & Maria Carlota Vaz Patto
Modern maize breeding programs gave rise to genetically uniform varieties that can affect maize's capacity to cope with increasing climate unpredictability. Maize populations, genetically more heterogeneous, can evolve and better adapt to a broader range of edaphic-climatic conditions. These populations usually suffer from low yields; it is therefore desirable to improve their agronomic performance while maintaining their valuable diversity levels. With this objective, a long-term participatory breeding/on-farm conservation program was established in Portugal. In this...

Data from: Keeping your options open: maintenance of thermal plasticity during adaptation to a stable environment

Inês Fragata, Miguel Lopes-Cunha, Margarida Bárbaro, Bárbara Kellen, Margarida Lima, Gonçalo Faria, Sofia G. Seabra, Mauro Santos, Pedro Simões & Margarida Maria Matos
Phenotypic plasticity may allow species to cope with environmental variation. The study of thermal plasticity and its evolution helps understanding how populations respond to variation in temperature. In the context of climate change, it is essential to realize the impact of historical differences in the ability of populations to exhibit a plastic response to thermal variation and how it evolves during colonization of new environments. We have analyzed the real-time evolution of thermal reaction norms...

Utilizing field collected insects for next generation sequencing: effects of sampling, storage, and DNA extraction methods

Kimberly Ballare, Nathaniel Pope, Antonio Castilla, Sarah Cusser, Richard Metz & Shalene Jha
DNA sequencing technologies continue to advance the biological sciences, expanding opportunities for genomic studies of non-model organisms for basic and applied questions. Despite these opportunities, many next-generation sequencing protocols have been developed assuming a substantial quantity of high molecular weight DNA (>100 ng), which can be difficult to obtain for many study systems. In particular, the ability to sequence field-collected specimens that exhibit varying levels of DNA degradation remains largely unexplored. In this study we...

Explaining illness with evil: Pathogen prevalence fosters moral vitalism

Brock Bastian, Christin-Melanie Vauclair, Steve Loughnan, Paul Bain, Ashwini Ashokkumar, Maja Becker, Michal Bilewicz, Emma Collier-Baker, Carla Crespo, Paul W. Eastwick, Ronald Fischer, Malte Friese, Ángel Gómez, Valeschka M. Guerra, Jose Luis Castellanos Guevara, Katja Hanke, Nic Hooper, Li-Li Huang, Shi Junqi, Minoru Karasawa, Peter Kuppens, Siri Leknes, Müjde Peker, Cesar Pelay, Afoditi Pina … & William B. Swann
Pathogens represent a significant threat to human health leading to the emergence of strategies designed to help manage their negative impact. We examined how spiritual beliefs developed to explain and predict the devastating effects of pathogens and spread of infectious disease. Analysis of existing data in Studies 1 and 2 suggests that moral vitalism (beliefs about spiritual forces of evil) is higher in geographical regions characterized by historical higher levels of pathogens. Furthermore, drawing on...

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