查看更多>>摘要：Cities and urban environments can do peculiar things to biodiversity that shares them with us。 How cities affect their invited and uninvited inhabitants has become an increasingly important question。 More than half of the world's population dwells in urban areas， and these environments will keep expanding considerably。 Understanding how this relatively recent， rapid， and pervasive form of landscape modification influences the ecology and evolution of organisms that cannot escape， or may benefit from it， is an emerging field of biology。 Although we are aware of how some birds， mammals or plants respond to urban environments， less is known about insects and invertebrates in general。 In this issue of Molecular Ecology， Blumenfeld et al。 (2022) bring new remarkable insights into how a common ant species adjusts to urban settings across the United States by changing its social structure and behaviour。 Using a large‐scale molecular， chemical and behavioural dataset， they document how the odorous house ant Tapinoma sessile differs in its colony organisation and dispersal strategy between rural and urban habitats。 In each of the study regions and continent‐wide， rural and urban colonies are genetically and chemically differentiated， suggesting that urban settings act as potent agents of selection and isolation。 The novelty and importance of this study are that it documents multiple independent transitions toward the same social organisation and the apparent effect of habitat on the life history of a eusocial insect species。
Stephany Virrueta HerreraKevin P. JohnsonAndrew D. SweetEeva Ylinen...
14页
查看更多>>摘要：Abstract Host‐specialist parasites of endangered large vertebrates are in many cases more endangered than their hosts。 In particular， low host population densities and reduced among‐host transmission rates are expected to lead to inbreeding within parasite infrapopulations living on single host individuals。 Furthermore， spatial population structures of directly‐transmitted parasites should be concordant with those of their hosts。 Using population genomic approaches， we investigated inbreeding and population structure in a host‐specialist seal louse (Echinophthirius horridus) infesting the Saimaa ringed seal (Phoca hispida saimensis)， which is endemic to Lake Saimaa in Finland， and is one of the most endangered pinnipeds in the world。 We conducted genome resequencing of pairs of lice collected from 18 individual Saimaa ringed seals throughout the Lake Saimaa complex。 Our analyses showed high genetic similarity and inbreeding between lice inhabiting the same individual seal host， indicating low among‐host transmission rates。 Across the lake， genetic differentiation among individual lice was correlated with their geographic distance， and assignment analyses revealed a marked break in the genetic variation of the lice in the middle of the lake， indicating substantial population structure。 These findings indicate that movements of Saimaa ringed seals across the main breeding areas of the fragmented Lake Saimaa complex may in fact be more restricted than suggested by previous population‐genetic analyses of the seals themselves。
Alexandra M. SparksSusan E. JohnstonIan HandelJill G. Pilkington...
15页
查看更多>>摘要：Abstract Vitamin D has a well‐established role in skeletal health and is increasingly linked to chronic disease and mortality in humans and companion animals。 Despite the clear significance of vitamin D for health and obvious implications for fitness under natural conditions， no longitudinal study has tested whether the circulating concentration of vitamin D is under natural selection in the wild。 Here， we show that concentrations of dietary‐derived vitamin D2 and endogenously produced vitamin D3?metabolites are heritable and largely polygenic in a wild population of Soay sheep (Ovis aries)。 Vitamin D2?status was positively associated with female adult survival， and vitamin D3?status predicted female fecundity in particular， good environment years when sheep density and competition for resources was low。 Our study provides evidence that vitamin D status has the potential to respond to selection， and also provides new insights into how vitamin D metabolism is associated with fitness in the wild。
Lionel N. Di SantoSean HobanThomas L. ParchmanJessica W. Wright...
18页
查看更多>>摘要：Abstract Understanding the contribution of neutral and adaptive evolutionary processes to population differentiation is often necessary for better informed management and conservation of rare species。 In this study， we focused on Pinus torreyana Parry (Torrey pine)， one of the world's rarest pines， endemic to one island and one mainland population in California。 Small population size， low genetic diversity， and susceptibility to abiotic and biotic stresses suggest Torrey pine may benefit from interpopulation genetic rescue to preserve the species' evolutionary potential。 We leveraged reduced representation sequencing to tease apart the respective contributions of stochastic and deterministic evolutionary processes to population differentiation。 We applied these data to model spatial and temporal demographic changes in effective population sizes and genetic connectivity， to identify loci possibly under selection， and evaluate genetic rescue as a potential conservation strategy。 Overall， we observed exceedingly low standing variation within both Torrey pine populations， reflecting consistently low effective population sizes across time， and limited genetic differentiation， suggesting maintenance of gene flow between populations following divergence。 However， genome scans identified more than 2000 candidate SNPs potentially under divergent selection。 Combined with previous observations indicating population phenotypic differentiation， this indicates natural selection has probably contributed to the evolution of population genetic differences。 Thus， while reduced genetic diversity， small effective population size， and genetic connectivity between populations suggest genetic rescue could mitigate the adverse effects of rarity， evidence for adaptive differentiation suggests genetic mixing could disrupt adaptation。 Further work evaluating the fitness consequences of inter‐population admixture is necessary to empirically evaluate the trade‐offs associated with genetic rescue in Torrey pine。
Alexander M. SandercockJared W. WestbrookQian ZhangHayley A. Johnson...
16页
查看更多>>摘要：Abstract American chestnut (Castanea dentata) was once the most economically and ecologically important hardwood species in the eastern United States。 In the first half of the 20th century， an exotic fungal pathogen—Cryphonectria parasitica—decimated the species， killing billions of chestnut trees。 Two approaches to developing blight‐resistant American chestnut populations show promise， but both will require introduction of adaptive genomic diversity from wild germplasm to produce diverse， locally adapted restoration populations。 Here we characterize population structure， demographic history， and genomic diversity in a range‐wide sample of 384 wild American chestnuts to inform conservation and breeding with blight‐resistant varieties。 Population structure analyses suggest that the chestnut range can be roughly divided into northeast， central， and southwest populations。 Within‐population genomic diversity estimates revealed a clinal pattern with the highest diversity in the southwest， which likely reflects bottleneck events associated with Quaternary glaciation。 Finally， we identified genomic regions under positive selection within each population， which suggests that defence against fungal pathogens is a common target of selection across all populations。 Taken together， these results show that American chestnut underwent a postglacial expansion from the southern portion of its range leading to three extant genetic populations。 These populations will serve as management units for breeding adaptive genetic variation into the blight‐resistant tree populations for targeted reintroduction efforts。
Fran?ois‐étienne SylvainEric NormandeauAleicia HollandAdalberto Luis Val...
16页
查看更多>>摘要：Abstract Associations between host genotype and host‐associated microbiomes have been shown in a variety of animal clades， but studies on teleosts mostly show weak associations。 Our study aimed to explore these relationships in four sympatric Serrasalmidae (i。e。， piranha) teleosts from an Amazonian lake， using data sets from the hosts genomes (single nucleotide polymorphisms from genotyping by sequencing)， skin and gut microbiomes (16S rRNA gene metataxonomics) and diets (COI metabarcoding) from the same fish individuals。 First， we investigated whether there were significant covariations of microbiome and fish genotypes at the inter‐ and intraspecific levels。 We also assessed the extent of covariation between Serrasalmidae diet and microbiome， to isolate genotypic from dietary effects on community structure。 We observed a significant covariation of skin microbiomes and host genotypes at interspecific (R2?=?24。4%) and intraspecific (R2?=?6。2%) levels， whereas gut microbiomes correlated poorly with host genotypes。 Serrasalmidae diet composition was significantly correlated to fish genotype only at the interspecific level (R2?=?5。4%)， but did not covary with gut microbiome composition (Mantel R?=??。04)。 Second， we investigated whether the study of interspecific differentiation could benefit from considering host‐associated microbial communities in addition to host genotypes。 By using a nonmetric multidimensional scaling (NMDS) ordination‐based approach， we observed that ordinations from skin‐ and gut species‐specific bacterial biomarkers identified through a random forest algorithm could significantly increase the average interspecific differentiation detected through host genotype data alone。 Although future studies encompassing additional species and environments are needed， our results suggest Serrasalmidae microbiomes could constitute an insightful trait to be considered when studying the interspecific differences between members of this clade。
查看更多>>摘要：Abstract Phenotypic plasticity， the ability of a given genotype to produce alternative phenotypes in response to its environment of development， is an important mechanism for coping with variable environments。 While the mechanisms underlying phenotypic plasticity are diverse， their relative contributions need to be investigated quantitatively to better understand the evolvability of plasticity across biological levels。 This requires relating plastic responses of the epigenome， transcriptome， and organismal phenotype， and investigating how they vary with the genotype。 Here we carried out this approach for responses to osmotic stress in Dunaliella salina， a green microalga that is a model organism for salinity tolerance。 We compared two strains that show markedly different demographic responses to osmotic stress， and showed that these phenotypic responses involve strain‐ and environment‐specific variation in gene expression levels， but a relative low—albeit significant—effect of strain × environment interaction。 We also found an important genotype effect on the genome‐wide methylation pattern， but little contribution from environmental conditions to the latter。 However， we did detect a significant marginal effect of epigenetic variation on gene expression， beyond the influence of genetic differences on epigenetic state， and we showed that hypomethylated regions are correlated with higher gene expression。 Our results indicate that epigenetic mechanisms are either not involved in the rapid plastic response to environmental change in this species， or involve only few changes in trans that are sufficient to trigger concerted changes in the expression of many genes， and phenotypic responses by multiple traits。
Matthew K. BrachmannKevin ParsonsSkúli SkúlasonOscar Gaggiotti...
19页
查看更多>>摘要：Abstract Sympatric adaptive phenotypic divergence should be underlain by genomic differentiation between subpopulations。 When divergence drives similar patterns of phenotypic and ecological variation within species we expect evolution to draw on common allelic variation。 We investigated divergence histories and genomic signatures of adaptive divergence between benthic and pelagic morphs of Icelandic Arctic charr。 Divergence histories for each of four populations were reconstructed using coalescent modelling and 14，187 single nucleotide polymorphisms。 Sympatric divergence with continuous gene flow was supported in two populations while allopatric divergence with secondary contact was supported in one population; we could not differentiate between demographic models in the fourth population。 We detected parallel patterns of phenotypic divergence along benthic‐pelagic evolutionary trajectories among populations。 Patterns of genomic differentiation between benthic and pelagic morphs were characterized by outlier loci in many narrow peaks of differentiation throughout the genome， which may reflect the eroding effects of gene flow on nearby neutral loci。 We then used genome‐wide association analyses to relate both phenotypic (body shape and size) and ecological (carbon and nitrogen stable isotopes) variation to patterns of genomic differentiation。 Many peaks of genomic differentiation were associated with phenotypic and ecological variation in the three highly divergent populations， suggesting a genomic basis for adaptive divergence。 We detected little evidence for a parallel genomic basis of differentiation as most regions and outlier loci were not shared among populations。 Our results show that adaptive divergence can have varied genomic consequences in populations with relatively recent common origins， similar divergence histories， and parallel phenotypic divergence。
Jason A. ToyKristy J. KroekerCheryl A. LoganYuichiro Takeshita...
19页
查看更多>>摘要：Abstract Acidification‐induced changes in neurological function have been documented in several tropical marine fishes。 Here， we investigate whether similar patterns of neurological impacts are observed in a temperate Pacific fish that naturally experiences regular and often large shifts in environmental pH/pCO2。 In two laboratory experiments， we tested the effect of acidification， as well as pH/pCO2 variability， on gene expression in the brain tissue of a common temperate kelp forest/estuarine fish， Embiotoca jacksoni。 Experiment 1 employed static pH treatments (target pH?=?7。85/7。30)， while Experiment 2 incorporated two variable treatments that oscillated around corresponding static treatments with the same mean (target pH?=?7。85/7。70) in an eight‐day cycle (amplitude?±?0。15)。 We found that patterns of global gene expression differed across pH level treatments。 Additionally， we identified differential expression of specific genes and enrichment of specific gene sets (GSEA) in comparisons of static pH treatments and in comparisons of static and variable pH treatments of the same mean pH。 Importantly， we found that pH/pCO2 variability decreased the number of differentially expressed genes detected between high and low pH treatments， and that interindividual variability in gene expression was greater in variable treatments than static treatments。 These results provide important confirmation of neurological impacts of acidification in a temperate fish species and， critically， that natural environmental variability may mediate the impacts of ocean acidification。
Marco L. CalderiniPauliina SalmiCyril RigaudElina Peltomaa...
13页
查看更多>>摘要：Abstract Light availability is the main regulator of primary production， shaping photosynthetic communities and their production of ecologically important biomolecules。 In freshwater ecosystems， increasing dissolved organic carbon (DOC) concentrations， commonly known as browning， leads to lower light availability and the proliferation of mixotrophic phytoplankton。 Here， a mixotrophic algal species (Cryptomonas sp。) was grown under five increasing DOC concentrations to uncover the plastic responses behind the success of mixotrophs in browning environments and their effect in the availability of nutritionally important biomolecules。 In addition to the browning treatments， phototrophic， heterotrophic and mixotrophic growth conditions were used as controls。 Despite reduced light availability， browning did not impair algal growth compared to phototrophic conditions。 Comparative transcriptomics showed that genes related to photosynthesis were down‐regulated， whereas phagotrophy gene categories (phagosome， lysosome and endocytosis) were up‐regulated along the browning gradient。 Stable isotope analysis of phospholipid fractions validated these results， highlighting that the studied mixotroph increases its reliance on heterotrophic processes with browning。 Metabolic pathway reconstruction using transcriptomic data suggests that organic carbon is acquired through phagotrophy and used to provide energy in conjunction with photosynthesis。 Although metabolic responses to browning were observed， essential fatty acid content was similar between treatments while sterol content was slightly higher upon browning。 Together， our results provide a mechanistic model of how a mixotrophic alga responds to browning and how such responses affect the availability of nutritionally essential biomolecules for higher trophic levels。
NSTL
Wiley