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Insect Science 2021年第2期28卷 555-565页

作者： Tyler T.Kelly Elizabeth Elle evolutionary and behavioural ecology Research Group Department of Biological SciencesSimon Fraser UniversityBurnabyCanada

Bee dietary preferences,or the floral resources that they consistently collect,likely impact where a species can *** this reason it is likely that bee dietary preferences are dependent upon the composition of the plant *** this study,we evaluated floral visits and pollen loads of the mining bee,Andrena angustitarsata Viereck,across a 630 km north-south range to understand dietary preferences along a floral resource *** research,in a more geographically limited area,suggested this species was an eclectic oligolege on predominantly Apiaceae and in part *** the present study we found the species predominately visited and collected pollen from Apiaceae and Rosaceae,but visited 12 flower families and collected pollen from 32,distinguishing them as generalist *** frequency of Apiaceae pollen on the bees and the species-level specialization index(a measure of visit specialization)were higher in regions with higher Apiaceae *** addition Apiaceae and Rosaceae were the only plant families significantly preferred for pollen collection,regardless of floral *** conclude that across our study region *** has a generalist dietary breadth,but also has dietary preference for Apiaceae and *** study indicates that while bees may overall make generalist foraging decisions they may still prefer and likely benefit from selecting fewer flower taxa.

关键词： andrenidae dietary breadth ecoregions oak-savanna pollen specialization

Multispecies hybridization in birds

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Avian Research 2019年第3期10卷 239-249页

作者： Jente Ottenburghs Resource ecology Group Wageningen University department of ecology and genetics Evolutionary Biology Centre Uppsala University

Hybridization is not always limited to two species;often multiple species are interbreeding. In birds, there are numerous examples of species that hybridize with multiple other species. The advent of genomic data provides the oppotunity to investigate the ecological and evolutionary consequences of multispecies hybridization. The interactions between several hybridizing species can be depicted as a network in which the interacting species are connected by edges. Such hybrid networks can be used to identify ‘hub-species’ that interbreed with multiple other species. Avian examples of such ‘hub-species’ are Common Pheasant (Phasianus colchicus), Mallard (Anas platyrhynchos) and European Herring Gull (Larus argentatus). These networks might lead to the formulation of hypotheses, such as which connections are most likely conducive to interspecific gene flow (i.e. introgression). Hybridization does not necessarily result in introgression. Numerous statistical tests are available to infer interspecific gene flow from genetic data and the majority of these tests can be applied in a multispecies setting. Specifically, model-based approaches and phylogenetic networks are promising in the detection and characterization of multispecies introgression. It remains to be determined how common multispecies introgression in birds is and how often this process fuels adaptive changes. Moreover, the impact of multispecies hybridization on the build-up of reproductive isolation and the architecture of genomic landscapes remains elusive. For example, introgression between certain species might contribute to increased divergence and reproductive isolation between those species and other related species. In the end, a multispecies perspective on hybridization in combination with network approaches will lead to important insights into the history of life on this planet.

关键词： Adaptation Admixture Genomics Introgression Network analysis Phylogenetics Speciation

Origination and evolution of orphan genes and de novo genes in the genome of Caenorhabditis elegans

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Science China(Life Sciences) 2019年第4期62卷 579-593页

作者： Wenyu Zhang Yuanxiao Gao Manyuan Long Bairong Shen Institutes for Systems genetics West China Hospital Sichuan University department of ecology and Evolution the University of Chicago department of evolutionary genetics Max-Planck Institute for Evolutionary Biology department of evolutionary Theory Max-Planck Institute for Evolutionary Biology Committee on genetics the University of Chicago

Orphan genes that lack detectable homologues in other lineages could contribute to a variety of biological functions. However,their origination and function mechanisms remain largely unknown. Herein, through a comprehensive and systematic computational pipeline, we identified 893 orphan genes in the lineage of C. elegans, of which only a low fraction(0.9%) were derived from transposon elements. Six new protein-coding genes that de novo originated from non-coding DNA sequences in the genome of C. elegans were also identified. The authenticity and functionality of these orphan genes and de novo genes are supported by three lines of evidences, consisting of transcriptional data, and in silico proteomic data, and the fixation status data in wild populations. Orphan genes and de novo genes exhibited simple gene structures, such as, short in protein length, of fewer exons,and are frequently X-linked. RNA-seq data analysis showed these orphan genes are enriched with expression in embryo development and gonad, and their potential function in early development was further supported by gene ontology enrichment analysis results. Meanwhile, de novo genes were found to be with significant expression in gonad, and functional enrichment analysis of the co-expression genes of these de novo genes suggested they may be functionally involved in signaling transduction pathway and metabolism process. Our results presented the first systematic evidence on the evolution of orphan genes and de novo origin of genes in nematodes and their impacts on the functional and phenotypic evolution, and thus could shed new light on our appreciation of the importance of these new genes.

关键词： Caenorhabditis elegans,orphan genes de novo genes

The measurement of sexual selection on females and males

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Current Zoology 2013年第4期59卷 558-563页

作者： Karoline FRITZSCHE Isobel BOOKSMYTHE Animal ecology Department of Ecology and Genetics Evolutionary Biology Centre Uppsala University Norbyvagen 18D SE - 752 36 Uppsala Sweden

As in any field of research, the study of sexual selection is subject to ongoing debate over definitions and interpreta- tions of the fundamental concepts involved. These arguments generally promote progress, as they highlight areas where current explanations are incomplete. Here we briefly review two ongoing discussions in the sexual selection literature. First, the definition of sexual selection has received renewed interest in light of increasing research effort into when and how it operates in females. Second, how best to measure sexual selection is an ongoing subject of debate; in practice, recognition that the appropriate measures depend on the focus of the specific study, and that multiple measures should be employed wherever possible, seems to provide the most informative approach. The wide scope of recent empirical work in these and related areas, with the application of new techniques and approaches, reflects that the field of sexual selection is being constantly expanded and enriched

关键词： Sexual selection Mating system Mating success Reproductive success Postcopulatory sexual selection Sex roles

Geographic variation in sexual selection and implications for speciation in the Barn Swallow

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Chinese Birds 2015年第1期5卷 30-42页

作者： Elizabeth SC Scordato Rebecca J Safran department of ecology and evolutionary Biology The University of Colorado

Barn Swallows(Hirundo rustica), a group of passerine birds comprised of six closely related subspecies, are well known throughout their nearly worldwide distribution, in part because of their close association with human settlements.A tractable species for both individual-based and population-level studies, Barn Swallows are a prominent model system in evolutionary, ecological, and behavioral research. Here we review work on sexual selection and population divergence in this species complex, focusing on comparative studies among populations and *** summarize variation in the targets of mate choice and in the information conveyed by sexually selected traits, and conclude that the benefits advertised by different traits may vary geographically. Finally, we consider the role of sexual selection as a driver of population divergence in this widespread and phenotypically variable species complex.

关键词： Barn Swallow Geographic variation Natural selection Sexual selection Speciation Tail streamers Ventral color

The role of male contest competition over mates in speciation

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Current Zoology 2012年第3期58卷 493-509页

作者： Anna QVARNSTROM Niclas VALLIN Andreas RUDH Animal ecology/department of ecology and genetics Evolutionary Biology Centre Uppsala University Norbyv~gen 18DSE-752 36 Uppsala Sweden

Research on the role of sexual selection in the speciation process largely focuses on the diversifying role of mate choice. In particular, much attention has been drawn to the fact that population divergence in mate choice and in the male traits subject to choice directly can lead to assortative mating. However, male contest competition over mates also constitutes an important mechanism of sexual selection. We review recent empirical studies and argue that sexual selection through male contest competition can affect speciation in ways other than mate choice. For example, biases in aggression towards similar competitors can lead to disruptive and negative frequency-dependent selection on the traits used in contest competition in a similar way as competition for other types of limited resources. Moreover, male contest abilities often trade-off against other abilities such as parasite resistance, protection against predators and general stress tolerance. Populations experiencing different ecological condi- tions should therefore quickly diverge non-randomly in a number of traits including male contest abilities. In resource based breeding systems, a feedback loop between competitive ability and habitat use may lead to further population divergence. We discuss how population divergence in traits used in male contest competition can lead to the build up of reproductive isolation through a number of different pathways. Our main conclusion is that the role of male contest competition in speciation remains largely scientifically unexplored [Current Zoology 58 （3）： 493-509, 2012].

关键词： Male-male competition Sexual selection Speciation Resource based breeding systems Contest competition Population divergence Reproductive isolation

gFACs:Gene Filtering,Analysis,and Conversion to Unify Genome Annotations Across Alignment and Gene Prediction Frameworks

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Genomics, Proteomics & Bioinformatics 2019年第3期17卷 305-310页

作者： Madison Caballero Jill Wegrzyn department of ecology and evolutionary Biology University of Connecticut

Published genomes frequently contain erroneous gene models that represent issues associated with identification of open reading frames,start sites,splice sites,and related structural *** source of these inconsistencies is often traced back to integration across text file formats designed to describe long read alignments and predicted gene *** addition,the majority of gene prediction frameworks do not provide robust downstream filtering to remove problematic gene annotations,nor do they represent these annotations in a format consistent with current file *** frameworks also lack consideration for functional attributes,such as the presence or absence of protein domains that can be used for gene model *** provide oversight to the increasing number of published genome annotations,we present a software package,the Gene Filtering,Analysis,and Conversion(gFACs),to filter,analyze,and convert predicted gene models and *** software operates across a wide range of alignment,analysis,and gene prediction files with a flexible framework for defining gene models with reliable structural and functional *** supports common downstream applications,including genome browsers,and generates extensive details on the filtering process,including distributions that can be visualized to further assess the proposed gene *** is freely available and implemented in Perl with support from BioPerl libraries at https://***/PlantGenomicsLab/gFACs.

关键词： Genome annotation Bioinformatics Protein annotation Gene prediction Alignment

Characterization and evolutionary dynamics of complex regions in eukaryotic genomes

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Science China(Life Sciences) 2019年第4期62卷 467-488页

作者： José Ranz Bryan Clifton department of ecology and evolutionary Biology University of California Irvine

Complex regions in eukaryotic genomes are typically characterized by duplications of chromosomal stretches that often include one or more genes repeated in a tandem array or in relatively close proximity. Nevertheless, the repetitive nature of these regions,together with the often high sequence identity among repeats, have made complex regions particularly recalcitrant to proper molecular characterization, often being misassembled or completely absent in genome assemblies. This limitation has prevented accurate functional and evolutionary analyses of these regions. This is becoming increasingly relevant as evidence continues to support a central role for complex genomic regions in explaining human disease, developmental innovations, and ecological adaptations across phyla. With the advent of long-read sequencing technologies and suitable assemblers, the development of algorithms that can accommodate sample heterozygosity, and the adoption of a pangenomic-like view of these regions, accurate reconstructions of complex regions are now within reach. These reconstructions will finally allow for accurate functional and evolutionary studies of complex genomic regions, underlying the generation of genotype-phenotype maps of unprecedented resolution.

关键词： complex genomic regions sequencing technologies genome assembly structural variation tandem gene duplicates,evolutionary novelty

Natural rubber and the Russian dandelion genome

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National Science Review 2018年第1期5卷 88-89页

作者： Brandon S.Gaut department of ecology and evolutionary Biology University of California

The world needs *** is crucial for the tires on the cars,trucks and airplanes that propel modern *** is equally important for daily tasks:latex gloves in the lab,balloons in angioplasty and wetsuits that warm a cold dip in the *** can be made synthetically from petroleum derivatives,but synthetic rubber is not as strong as rubber isolated from *** principal plant source for natural rubber

关键词： Natural rubber and the Russian dandelion genome

Global climate change is confounding species conservation strategies

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Integrative Zoology 2012年第2期7卷 158-164页

作者： Harold KOOPOWITZ Bradford A.HAWKINS department of ecology and evolutionary Biology University of CaliforniaIrvineCaliforniaUSA

Most organisms face similar problems with respect to their conservation in the face of global climate ***,we examine probable effects of climate change on the hyperdiverse plant family *** the 20th century,the major concerns for orchid conservation revolved around unsustainable harvest for the orchid trade and,more importantly,land conversion from natural ecosystems to those unable to support wild orchid pop*** conversion included logging,fire regimes and forest conversions to agricultural ***though those forms of degradation continue,an additional suite of threats has emerged,fueled by global climate *** climate change involves more than responses of orchid populations to increases in ambient *** temperature induces secondary effects that can be more significant than simple changes in *** these new threats are extended and prolonged fire seasons,rising sea levels,increases in cyclonic storms,seasonal climate shifts,changes in orthographic wind dew point and increased *** long-term outlook for orchid biodiversity in the wild is dismal,as it is for many animal groups,and we need to start rethinking strategies for conservation in a rapidly changing world.

关键词： biodiversity climate change conservation biology ex situ conservation orchids