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Genetic adaptation as a biological buffer against climate change:Potential and limitations

Integrative Zoology 2018年第4期13卷 372-391页

作者： Luc De MEESTER Robby STOKS Kristien I.BRANS Laboratory of Aquatic ecology Evolution and ConservationLeuvenBelgium evolutionary stress ecology and ecotoxicology LeuvenBelgium

Climate change profoundly impacts ecosystems and their biota,resulting in range shifts,novel interactions,food web alterations,changed intensities of host–parasite interactions,and *** increasing number of studies have documented evolutionary changes in traits such as phenology and thermal *** this opinion paper,we argue that,while evolutionary responses have the potential to provide a buffer against extinctions or range shifts,a number of constraints and complexities blur this simple ***,there are limits to evolutionary potential both in terms of genetic variation and demographic effects,and these limits differ strongly among taxa and ***,there can be costs associated with genetic adaptation,such as a reduced evolutionary potential towards other(human-induced)environmental stressors or direct fitness costs due to ***,the differential capacity of taxa to genetically respond to climate change results in novel interactions because different organism groups respond to a different degree with local compared to regional(dispersal and range shift)*** complexities result in additional changes in the selection pressures on *** conclude that evolution can provide an initial buffer against climate change for some taxa and populations but does not guarantee their *** does not necessarily result in reduced extinction risks across the range of taxa in a region or ***,considering evolution is crucial,as it is likely to strongly change how biota will respond to climate change and will impact which taxa will be the winners or losers at the local,metacommunity and regional scales.

关键词： climate change evolutionary rescue evolutionary constraints evolving metacommunities extinction risk range shifts

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Angiosperm phylogeny inferred from sequences of four mitochondrial genes

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Journal of Systematics and Evolution 2010年第6期48卷 391-425页

作者： Tory A.HENDRY Joseph W.BROWN Geordan T.HUDSON Department of ecology and evolutionary Biology University of Michigan

An angiosperm phylogeny was reconstructed in a maximum likelihood analysis of sequences of four mitochondrial genes,atp1,matR,nad5,and rps3,from 380 species that represent 376 genera and 296 families of seed *** is largely congruent with the phylogeny of angiosperms reconstructed from chloroplast genes atpB,matK,and rbcL,and nuclear 18S *** basalmost lineage consists of Amborella and Nymphaeales(including Hydatellaceae).Austrobaileyales follow this clade and are sister to the mesangiosperms,which include Chloranthaceae,Ceratophyllum,magnoliids,monocots,and *** the exception of Chloranthaceae being sister to Ceratophyllum,relationships among these five lineages are not well *** eudicots,Ranunculales,Sabiales,Proteales,Trochodendrales,Buxales,Gunnerales,Saxifragales,Vitales,Berberidopsidales,and Dilleniales form a basal grade of lines that diverged before the diversification of rosids and *** rosids,the COM(Celastrales-Oxalidales-Malpighiales) clade is sister to malvids(or rosid II),instead of to the nitrogen-fixing clade as found in all previous large-scale molecular analyses of *** and Caryophyllales are members of an expanded asterid *** study shows that the mitochondrial genes are informative markers for resolving relationships among genera,families,or higher rank taxa across *** low substitution rates and low homoplasy levels of the mitochondrial genes relative to the chloroplast genes,as found in this study,make them particularly useful for reconstructing ancient phylogenetic relationships.A mitochondrial gene-based angiosperm phylogeny provides an independent and essential reference for comparison with hypotheses of angiosperm phylogeny based on chloroplast genes,nuclear genes,and non-molecular data to reconstruct the underlying organismal phylogeny.

关键词： angiosperm homoplasy mitochondrial gene molecular evolutionary rate phylogeny rosids.

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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

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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

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Large males have a mating advantage in a species of darter with smaller,allopaternal males Etheostoma olmstedi

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Current Zoology 2010年第1期56卷 1-5页

作者： Kelly A.STIVER Suzanne H.ALONZO Department of ecology and evolutionary Biology Yale University

Theory suggests that males that are larger than their competitors may have increased mating success, due to both greater competitive ability and increased attractiveness to females. We examined how male mating suceess varies with male size in the tessellated darter Etheostoma olmstedi. Previous work has shown that large males tend to move around and breed in vacant breeding sites, and consequently provide less care for their eggs, while smaller individuals can be allopaternal, caring for the eggs of other males as well as for their own. We studied female egg deposition in a natural breeding population using artificial breeding sites and in the laboratory, where female choice of spawning site was restricted to two breeding sites tended by two males of different sizes. In both the field and the laboratory, nests tended by larger males were more likely to receive new eggs. Additionally, the mean size of males associated with a nest was positively correlated with both the maximum coverage of eggs at the nest and the number of times new eggs were deposited. We discuss how the increased mating success of larger males, despite their decreased parental care, may help explain aUopaternal care in this species [Current Zoology 56 （1）： 1-5, 2010].

关键词： Alloparental care Male competition Paternal care Sexual selection Mate choice Tessellated darter

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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

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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

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Redox physiology in animal function:The struggle of living in an oxidant environment

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Current Zoology 2010年第6期56卷 687-702页

作者： David COSTANTINI Division of ecology and evolutionary Biology Faculty of Biomedical and Life SciencesUniversity of Glasgow

A strong focus of ecological research for several decades has been to understand the factors underlying the variation in animal life-histories. In recent times, ecological studies have begun to show that oxidative stress may represent another important modulator of competitive trade-offs among fitness traits or of positively integrated patterns of traits. Therefore, incorporating mechanisms underlying oxidative physiology into evolutionary ecology has the potential to help understand variation in life-history strategies. In this review, I provide a general overview of oxidative stress physiology, and subsequently focus on topics that have been neglected in previous ecological reviews on oxidative stress. Specifically, I introduce and discuss the adaptations that animals have evolved to cope with oxidative stress; the environmental stressors that can generate changes in oxidative balance; the role of reactive species in transduction of environmental stimuli and cell signaling; and the range of hormetic responses to oxidative stress [Current Zoology 56 （6）： 687-702, 2010].

关键词： Antioxidants Free radicals Life-history Oxidative stress stress response Vertebrates

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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

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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

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