Integrating Sequence Capture and Restriction Site-Associated DNA Sequencing to resolve Recent Radiations of Pelagic Seabirds

The diversification of modern birds has been shaped by a number of radiations. Rapid diversification events make reconstructing the evolutionary relationships among taxa challenging due to the convoluted effects of incomplete lineage sorting (ILS) and introgression. Phylogenomic datasets have the potential to detect patterns of phylogenetic incongruence, and to address their causes. However, the footprints of ILS and introgression on sequence data can vary between different phylogenomic markers at different phylogenetic scales depending on factors such as their evolutionary rates or their selection pressures. We show that combining phylogenomic markers that evolve at different rates, such as paired-end double-digest restriction site-associated DNA (PE-ddRAD) and ultraconserved elements (UCEs), allows a comprehensive exploration of the causes of phylogenetic discordance associated with short internodes at different timescales. We used thousands of UCE and PE-ddRAD markers to produce the first well-resolved phylogeny of shearwaters, a group of medium-sized pelagic seabirds that are among the most phylogenetically controversial and endangered bird groups. We found that phylogenomic conflict was mainly derived from high levels of ILS due to rapid speciation events. We also documented a case of introgression, despite the high philopatry of shearwaters to their breeding sites, which typically limits gene flow. We integrated state-of-the-art concatenated and coalescent-based approaches to expand on previous comparisons of UCE and RAD-Seq datasets for phylogenetics, divergence time estimation and inference of introgression, and we propose a strategy to optimise RAD-Seq data for phylogenetic analyses. Our results highlight the usefulness of combining phylogenomic markers evolving at different rates to understand the causes of phylogenetic discordance at different timescales

Investigation of one-stage meta-analysis methods for joint longitudinal and time-to-event data through simulation and real data application

Background: Joint modeling of longitudinal and time‐to‐event data is often advantageous over separate longitudinal or time‐to‐event analyses as it can account for study dropout, error in longitudinally measured covariates, and correlation between longitudinal and time‐to‐event outcomes. The current literature on joint modeling focuses mainly on the analysis of single studies with a lack of methods available for the meta‐analysis of joint data from multiple studies. Methods: We investigate a variety of one‐stage methods for the meta‐analysis of joint longitudinal and time‐to‐event outcome data. These methods are applied to the INDANA dataset to investigate longitudinally measured systolic blood pressure, with each of time to death, time to myocardial infarction, and time to stroke. Results are compared to separate longitudinal or time‐to‐event meta‐analyses. A simulation study is conducted to contrast separate versus joint analyses over a range of scenarios. Results: The performance of the examined one‐stage joint meta‐analytic models varied. Models that accounted for between study heterogeneity performed better than models that ignored it. Of the examined methods to account for between study heterogeneity, under the examined association structure, fixed effect approaches appeared preferable, whereas methods involving a baseline hazard stratified by study were least time intensive. Conclusions: One‐stage joint meta‐analytic models that accounted for between study heterogeneity using a mix of fixed effects or a stratified baseline hazard were reliable; however, models examined that included study level random effects in the association structure were less reliable

Predictive systems models can help elucidate bee declines driven by multiple combined stressors

Published onlineThis is the author accepted manuscript. The final version is available from Springer Verlag via the DOI in this record.Bee declines are driven by multiple combined stresses, making it exceedingly difficult to identify experimentally the most critical threats to bees and their pollination services. We highlight here the too often ignored potential of mechanistic models in identifying critical stress combinations. Advanced bee models are now available as open access tools and offer an unprecedented opportunity for bee biologists to explore bee resilience tipping points in a variety of environmental contexts. We provide general guidelines on how to run bee models to help detect a priori critical stress combinations to be targeted in the field. This so-called funnel analysis should be performed in tight conjunction with the recent development of large-scale field monitoring programs for bee health surveillance.This work was supported by the European Community program (797/2004) for French beekeeping coordinated by the French Ministry of Agriculture (RISQAPI project). JLO, MAB, and PK were funded by grants from the Biotechnology and Biological Sciences Research Council, UK [BB/J014915/1; BB/K014463/1]. We thank Axel Decourtye and Jean-François Odoux for useful discussions on honeybee colony modeling and field monitoring design, as well as two anonymous reviewers for constructive comments on the manuscript

Genetic analysis of a major international collection of cultivated apple varieties reveals previously unknown historic heteroploid and inbred relationships

Domesticated apple (Malus x domestica Borkh.) is a major global crop and the genetic diversity held within the pool of cultivated varieties is important for the development of future cultivars. The aim of this study was to investigate the diversity held within the domesticated form, through the analysis of a major international germplasm collection of cultivated varieties, the UK National Fruit Collection, consisting of over 2,000 selections of named cultivars and seedling varieties. We utilised Diversity Array Technology (DArT) markers to assess the genetic diversity within the collection. Clustering attempts, using the software STRUCTURE revealed that the accessions formed a complex and historically admixed group for which clear clustering was challenging. Comparison of accessions using the Jaccard similarity coefficient allowed us to identify clonal and duplicate material as well as revealing pairs and groups that appeared more closely related than a standard parent-offspring or full-sibling relations. From further investigation, we were able to propose a number of new pedigrees, which revealed that some historically important cultivars were more closely related than previously documented and that some of them were partially inbred. We were also able to elucidate a number of parent-offspring relationships that had resulted in a number of important polyploid cultivars. This included reuniting polyploid cultivars that in some cases dated as far back as the 18th century, with diploid parents that potentially date back as far as the 13th century

Olfactory Sex Recognition Investigated in Antarctic Prions

Chemical signals can yield information about an animal such as its identity, social status or sex. Such signals have rarely been considered in birds, but recent results have shown that chemical signals are actually used by different bird species to find food and to recognize their home and nest. This is particularly true in petrels whose olfactory anatomy is among the most developed in birds. Recently, we have demonstrated that Antarctic prions, Pachyptila desolata, are also able to recognize and follow the odour of their partner in a Y-maze

Spatial interactions in agent-based modeling

Agent Based Modeling (ABM) has become a widespread approach to model complex interactions. In this chapter after briefly summarizing some features of ABM the different approaches in modeling spatial interactions are discussed. It is stressed that agents can interact either indirectly through a shared environment and/or directly with each other. In such an approach, higher-order variables such as commodity prices, population dynamics or even institutions, are not exogenously specified but instead are seen as the results of interactions. It is highlighted in the chapter that the understanding of patterns emerging from such spatial interaction between agents is a key problem as much as their description through analytical or simulation means. The chapter reviews different approaches for modeling agents' behavior, taking into account either explicit spatial (lattice based) structures or networks. Some emphasis is placed on recent ABM as applied to the description of the dynamics of the geographical distribution of economic activities, - out of equilibrium. The Eurace@Unibi Model, an agent-based macroeconomic model with spatial structure, is used to illustrate the potential of such an approach for spatial policy analysis.Comment: 26 pages, 5 figures, 105 references; a chapter prepared for the book "Complexity and Geographical Economics - Topics and Tools", P. Commendatore, S.S. Kayam and I. Kubin, Eds. (Springer, in press, 2014

Can current farmland landscapes feed declining steppe birds? Evaluating arthropod abundance for the endangered little bustard (Tetrax tetrax) in cereal farmland during the chick-rearing period: Variations between habitats and localities

Agriculture intensification threatens farmland bird populations because, among other reasons, it reduces the availability of food resources required to rear their offspring. In our study, we sampled and analyzed total arthropod abundance, biomass and richness, and orthopteran and coleopteran abundance and biomass in different agricultural habitats (alfalfa fields, stubble fields, grazed fields, and field margins) across 4 study localities with different levels of agriculture abandonment–intensification, comparing between areas used and not used by one of the most threatened farmland birds in Europe, the little bustard (Tetrax tetrax), during the chick-rearing season. Field margins were the taxonomically richest habitat, while alfalfa fields presented significantly higher total arthropod abundance and biomass than other habitats. All arthropod variables were the highest in the localities with clear conservation-focused agrarian management, and the lowest in the most intensive one. Areas used by little bustards had higher orthopteran and coleopteran abundance and biomass than nonused areas, except for coleopteran biomass in grazed fields. These results highlight the relevance of these arthropods for the species, the importance of dry alfalfa fields as food reservoirs in this critical time of year, the food scarcity in sites where agrarian management disregards farmland bird conservation, and the role of stubbles as providers of food resources during the chick-rearing season in areas used by the species. The adequate management of alfalfa fields and stubbles to provide those key resources seems crucial to improve little bustard breeding success.We thank the International Fund for Houbara Conservation (IFHC) and Fundación Patrimonio Natural (FPN) de Castilla y León in the persons of Cédric Ferlat (IFHC), David Cubero (Dirección General de Medio Natural, Junta de CyL), and Francisco Jiménez (FPN) for their financial, administrative, and logistic support. This paper also contributes to project S2018/EMT-4338 REMEDINAL TE-CM from Comunidad de Madrid. We are also thankful to the officers responsible for the Reserve of Villafáfila, Mariano Rodíguez y Jesús Palacios. Little bustard spring survey data were kindly provided by SEO-BirdLife.Peer reviewe

Evolution of Parallel Spindles Like genes in plants and highlight of unique domain architecture#

<p>Abstract</p> <p>Background</p> <p>Polyploidy has long been recognized as playing an important role in plant evolution. In flowering plants, the major route of polyploidization is suggested to be sexual through gametes with somatic chromosome number (2<it>n</it>). <it>Parallel Spindle1 </it>gene in <it>Arabidopsis thaliana </it>(<it>AtPS1</it>) was recently demonstrated to control spindle orientation in the 2nd division of meiosis and, when mutated, to induce 2<it>n </it>pollen. Interestingly, <it>AtPS1 </it>encodes a protein with a FHA domain and PINc domain putatively involved in RNA decay (i.e. Nonsense Mediated mRNA Decay). In potato, 2<it>n </it>pollen depending on parallel spindles was described long time ago but the responsible gene has never been isolated. The knowledge derived from <it>AtPS1 </it>as well as the availability of genome sequences makes it possible to isolate potato <it>PSLike </it>(<it>PSL</it>) and to highlight the evolution of <it>PSL </it>family in plants.</p> <p>Results</p> <p>Our work leading to the first characterization of <it>PSLs </it>in potato showed a greater <it>PSL </it>complexity in this species respect to <it>Arabidopsis thaliana</it>. Indeed, a genomic <it>PSL </it>locus and seven cDNAs affected by alternative splicing have been cloned. In addition, the occurrence of at least two other <it>PSL </it>loci in potato was suggested by the sequence comparison of alternatively spliced transcripts.</p> <p>Phylogenetic analysis on 20 <it>Viridaeplantae </it>showed the wide distribution of <it>PSLs </it>throughout the species and the occurrence of multiple copies only in potato and soybean.</p> <p>The analysis of PSL^FHAand PSL^PINcdomains evidenced that, in terms of secondary structure, a major degree of variability occurred in PINc domain respect to FHA. In terms of specific active sites, both domains showed diversification among plant species that could be related to a functional diversification among <it>PSL </it>genes. In addition, some specific active sites were strongly conserved among plants as supported by sequence alignment and by evidence of negative selection evaluated as difference between non-synonymous and synonymous mutations.</p> <p>Conclusions</p> <p>In this study, we highlight the existence of PSLs throughout <it>Viridaeplantae</it>, from mosses to higher plants. We provide evidence that <it>PSLs </it>occur mostly as singleton in the analyzed genomes except in soybean and potato both characterized by a recent whole genome duplication event. In potato, we suggest the candidate <it>PSL </it>gene having a role in 2<it>n </it>pollen that should be deeply investigated.</p> <p>We provide useful insight into evolutionary conservation of FHA and PINc domains throughout plant PSLs which suggest a fundamental role of these domains for PSL function.</p