A Combinatorial View on Speciation and Adaptive Radiation

Trends in Ecology & Evolution, Journal Year: 2019, Volume and Issue: 34(6), P. 531 - 544

Published: March 15, 2019

Language: Английский

---

The role of gene flow in rapid and repeated evolution of cave‐related traits in Mexican tetra, Astyanax mexicanus

Molecular Ecology, Journal Year: 2018, Volume and Issue: 27(22), P. 4397 - 4416

Published: Sept. 25, 2018

Abstract Understanding the molecular basis of repeatedly evolved phenotypes can yield key insights into evolutionary process. Quantifying gene flow between populations is especially important in interpreting mechanisms repeated phenotypic evolution, and genomic analyses have revealed that admixture occurs more frequently diverging lineages than previously thought. In this study, we resequenced 47 whole genomes Mexican tetra from three cave populations, two surface outgroup samples. We confirmed are polyphyletic Astyanax mexicanus present our data set. The likely diverged much recently previous mitochondrial estimates 5–7 mya. Divergence their phylogenetically closest population occurred ~161 191 k generations ago. favoured demographic model for most pairs accounts divergence with secondary contact heterogeneous across genome, rigorously identified among all sampled. Therefore, evolution cave‐related traits rapidly thought, trogolomorphic maintained despite populations. recency these estimated events suggests selection may drive cave‐derived traits, as opposed to disuse drift. Finally, show a phenotype QTL enriched regions low caves, suggesting be transferred caves via flow. Our study shows must considered studies independent, trait evolution.

Language: Английский

---

Selection-driven trait loss in independently evolved cavefish populations

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: May 3, 2023

Abstract Laboratory studies have demonstrated that a single phenotype can be produced by many different genotypes; however, in natural systems, it is frequently found phenotypic convergence due to parallel genetic changes. This suggests substantial role for constraint and determinism evolution indicates certain mutations are more likely contribute evolution. Here we use whole genome resequencing the Mexican tetra, Astyanax mexicanus , investigate how selection has shaped repeated of both trait loss enhancement across independent cavefish lineages. We show on standing variation de novo substantially adaptation. Our findings provide empirical support hypothesis genes with larger mutational targets substrate indicate features cave environment may impact rate at which occur.

Language: Английский

---

Dispersal Reduction: Causes, Genomic Mechanisms, and Evolutionary Consequences

Trends in Ecology & Evolution, Journal Year: 2020, Volume and Issue: 35(6), P. 512 - 522

Published: Feb. 22, 2020

Language: Английский

---

Genetic load has potential in large populations but is realized in small inbred populations

Evolutionary Applications, Journal Year: 2021, Volume and Issue: 14(6), P. 1540 - 1557

Published: March 8, 2021

Abstract Populations with higher genetic diversity and larger effective sizes have greater evolutionary capacity (i.e., adaptive potential) to respond ecological stressors. We are interested in how the variation captured protein‐coding genes fluctuates relative overall genomic whether smaller populations suffer costs due their load of deleterious mutations compared populations. analyzed individual whole‐genome sequences ( N = 74) from three different Montezuma quail Cyrtonyx montezumae ), a small ground‐dwelling bird that is sustainably harvested some portions its range but conservation concern elsewhere. Our historical demographic results indicate United States exhibit low levels large part long‐term declines population over nearly million years. The more isolated Texas significantly inbred than Arizona intermediate‐sized New Mexico we surveyed. gene pool has proportion strongly variants segregating pool. demonstrate even populations, highly effectively purged and/or lost drift. However, find realized elevated because inbreeding coupled frequency slightly manifested homozygotes. Overall, our study illustrates genomics can be used proactively assess both neutral functional aspects contemporary framework while simultaneously considering deeper histories.

Language: Английский

---

A Darwinian Laboratory of Multiple Contact Zones

Trends in Ecology & Evolution, Journal Year: 2020, Volume and Issue: 35(11), P. 1021 - 1036

Published: Sept. 8, 2020

Barriers to gene flow are best studied where divergent populations in contact, and studies of single-taxon hybrid zones have generated important knowledge about the nature reproductive barriers.Marine environments, earlier considered host unstructured species due high connectivity, offer multispecies contact structured by simple physical gradients (e.g., salinity) ideal for comparative divergence speciation.Overlapping possibilities comparison barriers among various taxa, life histories, demographic backgrounds test role species-specific traits formation function barriers.Combining genome scans modelling, barrier regions can be located origin traced. With genetic maps, inversions that affect recombination rate (and hence flow) identified. between result (hybrid) zones. Locations multiple overlap used asking: what mechanisms maintain barriers; is variation involved; do differences history barriers? In a review 23 marine species' over postglacial salinity gradient, many showed steep clines supported selection and/or temporal or spatial segregation. Contacts were primary secondary shaped ancestral sometimes involving inversions. The dispersal potential seemed less shaping clines. Studies will increase our understanding speciation, but we need address taxonomic bias focus more on postzygotic isolation. Contact (see Glossary) laboratories taxa [1.Barton N.H. Hewitt G.M. Analysis zones.Annu. Rev. Ecol. Syst. 1985; 16: 113-148Crossref Scopus (2048) Google Scholar, 2.Hewitt Hybrid zones, natural evolutionary studies.Trends Evol. 1988; 3: 158-167Abstract Full Text PDF PubMed (612) 3.Abbot R.J. et al.Genomics hybridization its consequences.Mol. 2016; 25: 2325-2332Crossref (112) Scholar]. Genome-wide sequencing maps powered identification candidates loci investigations genomic landscape speciation [4.Wolf J.B.W. Ellegren H. Making sense islands differentiation light speciation.Nat. Genet. 2017; 18: 87-100Crossref (212) Divergence usually evolve either situ as different regimes acting side (primary contact) after already accumulated drift [5.Bierne N. al.The coupling hypothesis: why may fail map local adaptation genes.Mol. 2011; 20: 2044-2072Crossref (364) 6.Bierne geography introgression patchy environment thorn ecological speciation.Curr. Zool. 2013; 59: 72-86Crossref (97) 7.Ravinet M. al.Interpreting speciation: road finding flow.J. Biol. 30: 1450-1477Crossref (225) 8.Rougemont Q. Bernatchez L. Atlantic salmon (Salmo salar) across distribution range reconstructed from approximate Bayesian computations.Evolution. 2018; 72: 1261-1277Crossref (41) Scholar] (Box 1). both types central evolution maintenance Scholar,7.Ravinet Scholar,9.Faria R. al.Evolving inversions.Trends 2019; 34: 239-248Abstract (81) For example, roles selection, assortative mating (whether spatial, temporal, behavioural isolation), isolation caused intrinsic incompatibilities extrinsic against hybrids?Box 1Primary Secondary ContactA zone originates one two ways: (i) formed diverged during period prior contact; whereas (ii) when population expands an environmental transition under flow. Genomic patterns resulting hybridisation initially very [7.Ravinet Scholar], such difference haplotype structure. produce pattern characterised successively smaller 'pieces' original background haplotypes with increasing distance [87.Leitwein al.Using information conservation genomics.Trends 35: 245-258Abstract (35) This because repeated backcrossing breaks apart large introgressed pieces material (Figure I, 'young' contact). Primary contrast, emerge common occur sharing origin. (green brown loci/alleles Figure I) likely play key role: ancient adaptive remain while polymorphisms segregate selection. Over time, new (dark blue red I), mutations outside establish contribute barriers. form wherever isolated happen meet. However, neutral selected at first move until they become trapped density trough shift Scholar,5.Bierne shifts. Positions might sometime establishment modelling using nonadmixed can, however, help resolve their Also, components origin; instance, if standing evolved periods [85.Van Belleghem S.M. al.Evolution time frames: singular event fuel contemporary parallel evolution.PLoS 14e1007796Crossref (44) A single generate details involved give indication quantitative importance. Moreover, single-species cannot inform us invariable within life-history traits, traits). contacts same external conditions, allow assessments general importance origin, variation, architectures formation. They also enable investigate how dispersal, generation biology gene-flow barriers, prezygotic mechanisms. Multispecies (sometimes referred 'suture zones') present terrestrial [10.Hewitt Some consequences ice ages, speciation.Biol. J. Linn. Soc. 1996; 58: 247-276Crossref Scholar,11.Swenson N.G. Howard D.J. Clustering phylogeographic North America.Am. Nat. 2005; 166: 581-591Crossref (312) Scholar,12.Johannesson K. André C. Life margin - diversity loss peripheral ecosystem, Baltic Sea.Mol. 2006; 15: 2013-2029Crossref (289) 13.Patarnello T. al.Pillars Hercules: Atlantic–Mediterranean phylogeographical break?.Mol. 2007; 4426-4444Crossref (424) 14.DiBattista J.D. al.When biogeographical provinces collide: reef fishes crossroads Arabian Sea.J. Biogeogr. 2015; 42: 1601-1614Crossref (52) 15.Ding S. al.Characterization region inshore fish, Bostrychus sinensis, East China Sea.Heredity. 120: 51-62Crossref (10) 16.Stanley al.A climate-associated cryptic cline northwest Atlantic.Sci. Adv. 4eaaq0929Crossref (50) 17.El Ayari hidden major biogeographic boundary: wide mosaic divide reveals complex interaction mussels.Heredity. 122: 770-784Crossref (17) environments. Compiling recent data entrance Sea, here highlight questions approach address, support increased speciation. Sea (North-East Atlantic) brackish gradient steepest part Danish Straits 1, Key Figure). Importantly, low imposes strong physiological stress most organisms so this impacts heavily area. After 8000 years ago opening freshwater lake into Atlantic, was subsequently colonised subset living Sea. few these established along entire majority only outer [18.Ojaveer al.Status biodiversity Sea.PLoS One. 2010; 5e12467Crossref (207) Many show plasticity phenotypic [19.Kautsky al.Genotypic Mytilus edulis evaluated through reciprocal transplantations. 1. Growth morphology.Mar. Prog. Ser. 1990; 203-210Crossref 20.Wood H.L. al.Physiological presence isopod Idotea baltica (Pallas) Res. 2014; 85: 255-262Crossref (9) 21.Renborg E. al.Variable tolerance ascidian larvae primarily plastic response parental environment.Evol. 28: 561-572Crossref (21) 22.Johansson D. al.Reciprocal transplants plasticity-first scenario colonisation hyposaline basin macro alga.BMC 1714Crossref (11) Scholar]; addition, early had shown examples [23.Sick Haemoglobin polymorphism fishes.Nature. 1961; 192: 894-896Crossref (93) Scholar,24.Christiansen F.B. Frydenberg O. Geographical four Zoarces viviparus evidence selection.Genetics. 1974; 77: 765-770PubMed We scanned published describing Sea–Baltic retrieved useful species. These represent (15 five invertebrates, macroalgae, microalga) histories (Table exception, recently invaded bay barnacle (Balanus improvisus) [25.Wrange A.L. story hitchhiker: invasive Balanus (Amphibalanus) improvisus Darwin 1854.PLoS 11e0147082Crossref (16) all zone. species, separation population, European flounder (Platichthys spp.) there additional subdivision inside populations. Original descriptions indicated 16 22 roughly overlapped 1), fitting enough (14 species) shows coincides although some slightly shifted towards lower salinities 2). 12 available allowed formal analysis supports stepped segmented ten clam [Limecola (Macoma) balthica] tends linear rather than 1).Table 1Species Available Genetic Data Transect Samples Covering TransitionSpeciesCommon nameDispersal potentiala'High' denotes several week-long pelagic highly mobile adults giving 'Low' short larval (or zygote/spore) stage sessile adults.Genetic databFigure number SNPs not specified.FST zoneOutlier distributionSelection agencyFitted modelcThe change analysed each taxon separately three models, which then compared Akaike criterion (AIC): model, model [84], regression relationships (R package 'segmented' [105]), compatible distance, respectively.Type zoneInferred fromBarrier strength; mechanismdSuggested experimentally confirmed followed '?'. Note other mechanisms, yet investigated, add barriers.RefsGadus morhuaAtlantic codHigh1.2 million0.040Three inversionsSalinity, temperatureToo dataSecondaryPhylogenyStrong; separate spawning times, adaptation[42.Berg P.R. al.Adaptation promotes cod (Gadus morhua L.).Genome 7: 1644-1663Crossref (111) 43.Fairweather al.Range-wide synthesis Transatlantic vicariance cod.Ecol. 8: 12140-12152Crossref (4) 44.Weist P. al.Assessing SNP-markers study mixing cod.PLoS 14e0218127Crossref 45.Nissling A. Westin Salinity requirements successful Belt stock interactions Sea.Mar. 1997; 152: 261-271Crossref (108) 46.Barth J.M.I. al.Genome architecture enables despite connectivity.Mol. 26: 4452-4466Crossref (75) 47.Barth al.Disentangling structural behavioral sea 1394-1411Crossref (37) 48.Kirubakaran T.G. al.Two adjacent migratory stationary ecotypes cod.Mol. 2130-2143Crossref (109) Scholar,69.Andersen al.Haemoglobin oxygen binding properties populations.Proc. Sci. 2009; 276: 833-841Crossref (71) Scholar]Clupea harengusAtlantic herringHigh6 million0.030Haplotype blocks, inversionSalinity, temperatureStepped clinePrimaryDemographyWeak; adaptation?[38.Martinez Barrio basis herring revealed sequencing.Elife. 5e12081Crossref (99) Scholar,56.Pettersson M.E. chromosome-level assembly – detection supergene signals selection.Genome 29: 1919-1928Crossref (38) Scholar,90.Berg F. al.Genetic factors effect growth, vertebrae otolith shape (Clupea harengus).PLoS 13e0190995Crossref (30) Scholar]Platichthys flesusEuropean flounderHigh54720.005Few scatteredSalinity, temperatureSegmented clineSecondaryDemographyWeak; adaptation?[39.Le Moan al.Beyond evolution: colonize gradient.bioRxiv. (Published online June 6, 2019. https://doi.org/10.1101/662569)Google Scholar,73.Hemmer-Hansen al.Adaptive environment: Hsc70 flesus L.).Heredity. 99: 592-600Crossref (130) Scholar]P. flesus/Platichthys solemdaliBaltic flounderLow20510.025SalinityToo dataSecondaryDemographyStrong; habitats, adaptation[51.Momigliano al.Extraordinarily rapid fish.Proc. Natl. Acad. U. 114: 6074-6079Crossref (64) Scholar,52.Momigliano al.Platichthys solemdali sp. nov. (Actinopterygii, Pleuronectiformes): Sea.Front. Mar. 5: 225Crossref (22) Scholar]Scophthalmus maximusTurbotHigh33480.012Many scatteredSalinityStepped clinePrimaryDemographyModerate; unknown[31.Momigliano al.Biases process speciation.bioRxiv. 2020; 5, 2020. https://doi.org/10.1101/2020.06.03.128298)Google Scholar]Pleuronectus platessaEuropean plaiceHigh66850.013Two inversionsSalinityToo dataPrimaryDemographyWeak; unknown[39.Le Scholar]Limanda limandaCommon dabHigh34680.008ClusteredSalinityStepped Scholar]Solea soleaCommon soleHigh37140.003Very fewToo dataPrimaryDemographyVery weak; unknown[40.Diopere al.Seascape genetics flatfish levels flow.ICES 75: 675-689Crossref (32) Scholar,41.Le al.Fine scale structure linked sole (Solea solea), fish capacity.bioRxiv. https://doi.org/10.1101/662619)Google Scholar]Ammodytes tobianusSmall sandeelHigh40390.041Salinity, clineStrong; times?[91.Christensen al.Sandeel (Ammodytes marinus) transport individual-based hydrodynamic egg model.Can. Fish. Aquat. 2008; 65: 1498-1511Crossref Scholar,92.Fietz al.Mind gut: insights gut microbial composition keystone species.Microbiome. 682Crossref Scholar]Hyperoplus lanceolatusGreater sandeelHigh43280.039Salinity, times?[92.Fietz Scholar,93.Lynam C.P. al.Spatial trends abundance sandeels Sea: 1950–2005.ICES 70: 540-553Crossref (18) Scholar]Symphodus melopsCorkwing wrasseLow50 1300.120Only spurious outliersStepped clineSecondaryDemographyStrong; trough[49.Mattingsdal al.Demographic history, adaptation, has strongly differentiated corkwing wrasse Northern Europe.Mol. 160-171Crossref Scholar]Labrus bergyltaBallan wrasseLow820.027Stepped clineModerate; trough[50.Seljestad G.W. cleaner break: geographic groups sympatric phenotypes ballan (Labrus bergylta).Ecol. 10: 6120-6135Crossref (6) Scholar]Pomatoschistus minutusSandgobyLow22 1900.020DistributedSalinity, turbidityToo dataSecondaryDemographyModerate; adaptation[94.Larmuseau M.H.D. al.To see seas: rhodopsin sand goby (Pomatoschistus minutus).Mol. 4227-4239Crossref (47) Scholar,95.Leder E.H. al.Postglacial locally adapted gradient.J. 23, https://doi.org/10.1111/jeb.13668)Crossref Scholar]Gasterosterus aculeatusThree-spined sticklebackLow30 0000.015Enriched regionsSalinity, dataPrimaryDemographyModerate; adaptation[67.DeFaveri Merilä Local three-spined stickleback?.J. 27: 290-302Crossref Scholar,96.Guo B. al.Population sticklebacks.BMC 1319Crossref (83) Scholar]Salmo salarAtlantic salmonHigh50340.132Too areas[8.Rougemont Scholar,97.Nilsson al.Matrilinear phylogeography salar L.) Europe colonization area.Mol. 2001; 89-102Crossref (128) Scholar]Ciona intestinalisVase tunicateLow16530.180SalinityVertical (no test)SecondaryDemographyStrong; partly adaptation[53.Dybern B.I. Ciona intestinalis (L.) f. typica special reference waters around southern Scandinavia.Ophelia. 1967; 4: 207-226Crossref (40) Scholar,55.Hudson al.Secondary admixture genotypes amphiatlantic epibenthic invertebrate.Evol. Appl. 13: 600-612Crossref (12) Scholar]Idotea baltica'Isopod'Low33 7740.024SalinityLinear clineWeak; unknown[98.De Wit crustacean herbivore highlights considerations management.Evol. 974-990Crossref (8) Scholar]Balanus improvisusBay barnacleHighmtDNA, microsatellites0.011No outliersNo clineNo barriers[25.Wrange Scholar,99.Wrange al.

Language: Английский

---

Selective sweeps on novel and introgressed variation shape mimicry loci in a butterfly adaptive radiation

PLoS Biology, Journal Year: 2020, Volume and Issue: 18(2), P. e3000597 - e3000597

Published: Feb. 6, 2020

Natural selection leaves distinct signatures in the genome that can reveal targets and history of adaptive evolution. By analysing high-coverage sequence data from 4 major colour pattern loci sampled nearly 600 individuals 53 populations, we show pervasive on wing patterns Heliconius radiation. The strongest correspond to with greatest phenotypic effects, consistent visual by predators, are found geographically restricted distributions. These recent sweeps similar between co-mimics indicate turn-over events despite strong stabilising selection. Using simulations, compare sweep expected under classic hard those resulting introgression, an important aspect mimicry evolution butterflies. Simulated recipient populations a 'volcano' peaks increased genetic diversity around selected target, characteristic introgressed variation some populations. Our genomic surprisingly dynamic co-evolution this

Language: Английский

---

Locally Adaptive Inversions Modulate Genetic Variation at Different Geographic Scales in a Seaweed Fly

Molecular Biology and Evolution, Journal Year: 2021, Volume and Issue: 38(9), P. 3953 - 3971

Published: May 5, 2021

Across a species range, multiple sources of environmental heterogeneity, at both small and large scales, create complex landscapes selection, which may challenge adaptation, particularly when gene flow is high. One key to multidimensional adaptation reside in the heterogeneity recombination along genome. Structural variants, like chromosomal inversions, reduce recombination, increasing linkage disequilibrium among loci potentially massive scale. In this study, we examined how inversions shape genetic variation across range ask their contribution face varies geographic scales. We sampled seaweed fly Coelopa frigida bioclimatic gradient stretching 10° latitude, salinity gradient, heterogeneous, patchy habitats. generated chromosome-level genome assembly analyze 1,446 low-coverage whole genomes collected those gradients. found several nonrecombining genomic regions, including putative inversions. contrast collinear low-recombining regions differentiated populations more strongly, either an ecogeographic cline or fine-grained These were associated with factors adaptive phenotypes, albeit contrasting patterns. Altogether, our results highlight importance shaping local

Language: Английский

---

Genetic variation for adaptive traits is associated with polymorphic inversions inLittorina saxatilis

Evolution Letters, Journal Year: 2021, Volume and Issue: 5(3), P. 196 - 213

Published: May 9, 2021

Abstract Chromosomal inversions have long been recognized for their role in local adaptation. By suppressing recombination heterozygous individuals, they can maintain coadapted gene complexes and protect them from homogenizing effects of flow. However, to fully understand importance adaptation we need know influence on phenotypes under divergent selection. For this, the marine snail Littorina saxatilis provides an ideal study system. Divergent ecotypes adapted wave action crab predation occur close proximity intertidal shores with flow between them. Here, used F2 individuals obtained crosses test associations genomic regions traits distinguishing Crab-/Wave-adapted including size, shape, shell thickness, behavior. We show that most these are influenced by two previously detected inversion ecotypes. thus gain a better understanding one important underlying mechanism responsible rapid repeated formation ecotypes: selection acting inversions. also found some contributed more than trait suggesting may contain several loci involved adaptation, consistent hypothesis suppression within facilitates differentiation presence

Language: Английский

---

Coleoptera genome and transcriptome sequences reveal numerous differences in neuropeptide signaling between species

PeerJ, Journal Year: 2019, Volume and Issue: 7, P. e7144 - e7144

Published: June 17, 2019

Insect neuropeptides are interesting for the potential their receptors hold as plausible targets a novel generation of pesticides. Neuropeptide genes have been identified in number different species belonging to variety insects. Results suggest significant neuropeptide variation between orders, but much less is known neuropeptidome variability within an insect order. I therefore compared neuropeptidomes Coleoptera.Publicly available genome sequences, transcriptomes and original sequence data form short read archives were analyzed presence or absence coding well some seventeen beetle species.Significant differences exist Coleoptera here, while many that previously characterized from Tribolium castaneum appear very similar all species, not others lacking one more species. On other hand, leucokinin, which was presumed be universally absent Coleoptera, still present non-Polyphaga beetles.The composition same order may large exists orders.

Language: Английский

---