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| Open AccessCandidate genes under selection in song sparrows co-vary with climate and body mass in support of Bergmann’s Rule
Ecogeographic rules link spatial patterns in phenotype and environment, potentially reflecting adaptation. This study identifies nine genes associated with body mass variation in song sparrow populations, supporting Bergmann’s Rule and highlighting the role of natural selection in local adaptation.
- Katherine Carbeck
- , Peter Arcese
- & Jennifer Walsh
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| Open AccessThe parasitic nematode Strongyloides ratti exists predominantly as populations of long-lived asexual lineages
Nematodes are important parasites of people and animals. Here, the authors study the population structure of a nematode parasite of wild rats finding that it consists of mixtures of mainly asexual lineages widely dispersed across the host population.
- Rebecca Cole
- , Nancy Holroyd
- & Mark Viney
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| Open AccessSingle-gene resolution of diversity-driven overyielding in plant genotype mixtures
Biodiversity often increases the functioning and productivity of ecosystems or communities. This work shows that such a positive diversity effect, namely overyielding in mixtures of two divergent Arabidopsis thaliana genotypes, can be genetically mapped and resolved to a single gene.
- Samuel E. Wuest
- , Lukas Schulz
- & Pascal A. Niklaus
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| Open AccessInsights and achievements from the Tara Pacific expedition
The Tara Pacific program and expedition focused on coral reefs across the Pacific Ocean and used a coordinated sampling effort to address questions at multiple scales using a common suite of samples. Here, we highlight some of the Tara Pacific achievements, discussing the benefits of long-duration sea expeditions for investigating a wide array of research questions within a selected ecosystem.
- Serge Planes
- & Denis Allemand
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| Open AccessClimate-induced range shifts drive adaptive response via spatio-temporal sieving of alleles
The interplay of migration and adaptation was key in shaping species’ responses to Quaternary climate change. Illustrating this, Luqman et al. show that adaptive responses in a plant species emerged from climate-induced range shifts due to heterogenous sieving of adaptive alleles across space and time.
- Hirzi Luqman
- , Daniel Wegmann
- & Alex Widmer
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| Open AccessMalaria-driven adaptation of MHC class I in wild bonobo populations
A variant of MHC class I is protective against severe malaria disease and enriched in affected African populations. Here, Wroblewski et al., characterise the consequences of malaria infection in wild bonobo populations showing that the presence of malaria drives a similar evolution in immune genes.
- Emily E. Wroblewski
- , Lisbeth A. Guethlein
- & Peter Parham
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| Open AccessA molecular atlas reveals the tri-sectional spinning mechanism of spider dragline silk
The genetic basis of spider major ampullate (Ma) gland silk production remains unknown. Hu et al. unveil a molecular atlas of this gland for the golden orb-weaving spider combining genome assembly and multiomics, revealing the single-cell spatial architecture of silk production in the Ma gland.
- Wenbo Hu
- , Anqiang Jia
- & Yi Wang
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| Open AccessThe combination of genomic offset and niche modelling provides insights into climate change-driven vulnerability
Species responses to climate change may be challenging to predict. Here, the authors demonstrate the value of combining genomics, niche modelling, and landscape connectivity to estimate population-level vulnerability under future climate scenarios in two bird species.
- Yilin Chen
- , Zhiyong Jiang
- & Yanhua Qu
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| Open AccessGenomic evidence for homoploid hybrid speciation between ancestors of two different genera
Carpinus fangiana exhibits intermediate morphology between C. viminea and Ostrya rehderiana. Here, the authors report that Carpinus sect. Distegocarpus likely originate through homoploid hybrid speciation (HHS) during the early divergence between Carpinus and Ostrya through genomic analyses.
- Zefu Wang
- , Minghui Kang
- & Jianquan Liu
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Article
| Open AccessNorway spruce postglacial recolonization of Fennoscandia
Contrasting theories exist regarding how Norway spruce recolonized Fennoscandia after the last glaciation. Here, the authors provide evidences from sedimentary ancient DNA and modern population genomics to support that Norway spruce was present in southern Fennoscandia shortly after deglaciation and the early Holocene migration from the east.
- Kevin Nota
- , Jonatan Klaminder
- & Laura Parducci
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| Open AccessAlternative splicing in seasonal plasticity and the potential for adaptation to environmental change
Little is known about how alternative splicing and other post-transcriptional molecular mechanisms impact plasticity. Steward et al. use transcriptomic and genomic data from the butterfly Bicyclus anynana, finding that splicing plasticity is likely to experience genetic constraints.
- Rachel A. Steward
- , Maaike A. de Jong
- & Christopher W. Wheat
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| Open AccessExtensive standing genetic variation from a small number of founders enables rapid adaptation in Daphnia
Standing genetic variation allows natural populations to evolve rapidly. Genome sequences of a resurrected Daphnia population show that genetic variation carried by only five founding individuals from the regional genotype pool is enough to fuel rapid evolution in response to strong selection pressures with no evidence of genetic erosion.
- Anurag Chaturvedi
- , Jiarui Zhou
- & Luc De Meester
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| Open AccessAnnual aboveground carbon uptake enhancements from assisted gene flow in boreal black spruce forests are not long-lasting
The long-term effectiveness of assisted gene flow of trees could be jeopardised by rapid climate change. Here the authors analyse a large dataset of relocated black spruce populations in Canada, finding that local adaptation to climate of origin improved NPP responses, but only for up to ~15 years after planting.
- Martin P. Girardin
- , Nathalie Isabel
- & Patrick Lenz
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| Open AccessPyropia yezoensis genome reveals diverse mechanisms of carbon acquisition in the intertidal environment
The nori producing seaweed Pyropia yezoensis has heteromorphic generations that occupy distinct habitats. Here, via genome assembly, transcriptome analysis, and 13 C isotope labeling, the authors show the interplay between inorganic carbon availability and life cycle evolution in the intertidal environment.
- Dongmei Wang
- , Xinzi Yu
- & Yunxiang Mao
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| Open AccessCommunity-level signatures of ecological succession in natural bacterial communities
Metagenome approaches can unravel relationships between environment, community composition, and ecological functions. Here, the authors show that bacterial communities sampled from rainwater pools can be clustered into few classes with distinct functional capacities and genetic repertoires, the assembly of which is likely driven by local conditions.
- Alberto Pascual-García
- & Thomas Bell
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| Open AccessDNA metabarcoding and spatial modelling link diet diversification with distribution homogeneity in European bats
Ecological niche breadth may help explain spatial distribution patterns in animals. In this study on European bats, Alberdi et al. combine DNA metabarcoding and species distribution modelling to show that dietary niche breadth is related to hunting flexibility and broad-scale spatial patterns in species distribution.
- Antton Alberdi
- , Orly Razgour
- & M. Thomas P. Gilbert
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| Open AccessGlobal determinants of freshwater and marine fish genetic diversity
Biogeographic patterns of genetic diversity are poorly documented, especially for fish species. Here the authors show that (mitochondrial) genetic diversity has global spatial organization patterns with different environmental drivers for marine and freshwater fishes, where genetic diversity is only partly congruent with species richness.
- Stéphanie Manel
- , Pierre-Edouard Guerin
- & Loïc Pellissier
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| Open AccessStanding genetic variation fuels rapid adaptation to ocean acidification
Reductions in seawater pH are affecting marine ecosystems globally. Here, the authors describe phenotypic and genetic modifications associated with rapid adaptation to reduced seawater pH in the mussel Mytilus galloprovincialis, and suggest that standing variation within natural populations plays an important role in bolstering species’ adaptive capacity to global change.
- M. C. Bitter
- , L. Kapsenberg
- & C. A. Pfister
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| Open AccessThermal cues drive plasticity of desiccation resistance in montane salamanders with implications for climate change
Climate change will threaten plants and animals across the planet by increasing the risk of desiccation. Here, authors demonstrate that salamanders regulate water loss using temperature-sensitive gene expression related to blood vessel regeneration and skin lipids.
- Eric A. Riddell
- , Emma Y. Roback
- & Michael W. Sears
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| Open AccessEmergence of a floral colour polymorphism by pollinator-mediated overdominance
Examples of overdominance are usually explained by deleterious effects in homozygotes. Here, Kellenberger et al. describe a case of overdominance in the floral color of the Alpine orchid Gymnadenia rhellicani apparently maintained by pollinator preferences without deleterious effects in homozygotes.
- Roman T. Kellenberger
- , Kelsey J. R. P. Byers
- & Philipp M. Schlüter
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| Open AccessGenomic effects of population collapse in a critically endangered ironwood tree Ostrya rehderiana
Here, Liu et al. compare the genomic signatures of two tree species, one of which had undergone population collapse. The declining species had low genetic diversity, but had more strongly purged severely deleterious recessive variations, likely due to inbreeding and perhaps mitigating extinction risk.
- Yongzhi Yang
- , Tao Ma
- & Jianquan Liu
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| Open AccessDemographic histories and genetic diversity across pinnipeds are shaped by human exploitation, ecology and life-history
Historical hunting has caused documented declines in pinnipeds, but the extent to which hunting caused genetic bottlenecks among species was unknown. Here, the authors show evidence of severe bottlenecks in several pinniped species, particularly those that breed on land.
- M. A. Stoffel
- , E. Humble
- & J. I. Hoffman
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| Open AccessA mapping framework of competition–cooperation QTLs that drive community dynamics
Genetic variation from coexisting species influences interspecific interactions in a community. Here, the authors develop a framework for identifying quantitative trait loci (QTLs) underlying community dynamics and validate the tool using data from co-culturing of two bacterial species.
- Libo Jiang
- , Xiaoqing He
- & Rongling Wu
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| Open AccessCold adaptation recorded in tree rings highlights risks associated with climate change and assisted migration
Assisted migration has been proposed to aid trees in altering their ranges under climate change. Here, Montwé et al. use common garden experiments to show that lodgepole pine populations vary in their cold susceptibility, suggesting seed transfer may increase the risk of frost damage.
- David Montwé
- , Miriam Isaac-Renton
- & Heinrich Spiecker
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| Open AccessEvolutionary genetics of immunological supertypes reveals two faces of the Red Queen
Host-parasite coevolution can lead to arms races favouring novel immunogenetic alleles or the maintenance of diversity in a balanced polymorphism. Here, Lighten et al. combine data on MHC diversity across three guppy species and simulations to show that polymorphisms of immunogenetic supertypes may persist even as alleles within supertypes are involved in an arms race.
- Jackie Lighten
- , Alexander S. T. Papadopulos
- & Cock van Oosterhout
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| Open AccessOn the post-glacial spread of human commensal Arabidopsis thaliana
Population structure of the model plantArabidopsis thaliana is shaped by glacial refugia and recent admixture. Here the authors show that genetically distinct groups of A. thalianahave spread east-west across Europe since the most recent ice age, likely as a result of human activity.
- Cheng-Ruei Lee
- , Hannes Svardal
- & Magnus Nordborg
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| Open AccessAbsolute abundance of southern bluefin tuna estimated by close-kin mark-recapture
Accurate determination of population size for highly-mobile marine animals is often prohibitively difficult. Here, Bravingtonet al.estimate the abundance of southern bluefin tuna using a method based on the number of parent-offspring pairs detected genetically in samples from the catch.
- Mark V. Bravington
- , Peter M. Grewe
- & Campbell R. Davies
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| Open AccessFull circumpolar migration ensures evolutionary unity in the Emperor penguin
Delimiting populations is crucial for conserving threatened species. Using genome-wide data from the whole of Antarctica, Cristofari et al.show that Emperor penguins are organised into a single global population that have shared demography since the late Quarternary.
- Robin Cristofari
- , Giorgio Bertorelle
- & Emiliano Trucchi
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| Open AccessGenomics reveals historic and contemporary transmission dynamics of a bacterial disease among wildlife and livestock
The role of wild elk in the spread and persistence of bovine brucellosis in the Great Yellowstone area is unclear. Here, Kamath et al. analyse the genomic sequences of 245 Brucella abortusisolates from elk, bison and cattle, supporting the idea that elk is an important reservoir and source of livestock infections.
- Pauline L. Kamath
- , Jeffrey T. Foster
- & Paul C. Cross
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| Open AccessThe epigenomic landscape of African rainforest hunter-gatherers and farmers
Genetic and environmental factors affect genome-wide patterns of epigenetic variation. Here, the authors show that while current habitat and historical lifestyle impact the methylome of rainforest hunter-gatherers and sedentary farmers, the biological functions affected and the degree of genetic control differ.
- Maud Fagny
- , Etienne Patin
- & Lluis Quintana-Murci
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| Open AccessThe genomics of ecological vicariance in threespine stickleback fish
Threespine stickleback fish are adapted to lake and stream habitats in Central Europe. Here, the authors show colonization of a lake basin by a stream-adapted ancestor, followed by the emergence of a lake-adapted population in the face of gene flow across lake–stream boundaries.
- Marius Roesti
- , Benjamin Kueng
- & Daniel Berner
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| Open AccessNew loci and coding variants confer risk for age-related macular degeneration in East Asians
Age-related macular degeneration (AMD) is a major cause of blindness worldwide. Here, the authors carry out a two-stage genome-wide association study for AMD and identify three new AMD risk loci, highlighting the shared and distinct genetic basis of the disease in East Asians and Europeans.
- Ching-Yu Cheng
- , Kenji Yamashiro
- & Chiea Chuen Khor
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| Open AccessGenomic identification and characterization of the pseudoautosomal region in highly differentiated avian sex chromosomes
The genetic basis of sex chromosome pseudoautosomal regions (PAR) in organisms with female heterogamety is largely unknown. Smeds et al.provide the first molecular characterization of the PAR in birds with differentiated sex chromosomes and show a potential recombination hotspot and no evidence for strong sexual antagonism in this region.
- Linnéa Smeds
- , Takeshi Kawakami
- & Hans Ellegren
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| Open AccessThe Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle
Spirodela, or duckweed, is a basal monocotyledonous plant with both pharmaceutical and commercial value. Here, the authors sequence the genome of Spirodela polyrhiza, suggesting its genome has evolved by neotenous reduction and clonal propagation, and provide a platform for future comparative genomic studies in angiosperms.
- W. Wang
- , G. Haberer
- & J Messing
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Article |
Whole-community DNA barcoding reveals a spatio-temporal continuum of biodiversity at species and genetic levels
A correlation between species and genetic diversity has been suggested. Here Baselga et al.provide evidence of a concordant decrease in beetle community similarity at species and genetic levels with geographic distance, suggesting a macroecological pattern which may follow neutral evolutionary processes.
- Andrés Baselga
- , Tomochika Fujisawa
- & Alfried P. Vogler