Department Fish Ecology and Evolution

array(2 items)
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   libraryUrl => '' (0 chars)

array(20 items)
   0 => Snowflake\Publications\Domain\Model\Publicationprototypepersistent entity (uid=32245, pid=124)
      originalId => protected32245 (integer)
      authors => protected'Frei, D.; Mwaiko, S.; Seehausen, O.; Feulner, P. G.
          D.' (84 chars)
      title => protected'Ecological disturbance reduces genomic diversity across an Alpine whitefish 
         adaptive radiation' (94 chars)
      journal => protected'Evolutionary Applications' (25 chars)
      year => protected2024 (integer)
      volume => protected17 (integer)
      issue => protected'2' (1 chars)
      startpage => protected'e13617 (12 pp.)' (15 chars)
      otherpage => protected'' (0 chars)
      categories => protected'Alpine whitefish; anthropogenic environmental change; genomic diversity decl
         ine' (79 chars)
      description => protected'Genomic diversity is associated with the adaptive potential of a population 
         and thereby impacts the extinction risk of a species during environmental ch
         ange. However, empirical data on genomic diversity of populations before env
         ironmental perturbations are rare and hence our understanding of the impact 
         of perturbation on diversity is often limited. We here assess genomic divers
         ity utilising whole-genome resequencing data from all four species of the La
         ke Constance Alpine whitefish radiation. Our data covers a period of strong 
         but transient anthropogenic environmental change and permits us to track cha
         nges in genomic diversity in all species over time. Genomic diversity became
          strongly reduced during the period of anthropogenic disturbance and has not
          recovered yet. The decrease in genomic diversity varies between 18% and 30%
         , depending on the species. Interspecific allele frequency differences of SN
         Ps located in potentially ecologically relevant genes were homogenized over 
         time. This suggests that in addition to the reduction of genome-wide genetic
          variation, the differentiation that evolved in the process of adaptation to
          alternative ecologies between species might have been lost during the ecolo
         gical disturbance. The erosion of substantial amounts of genomic variation w
         ithin just a few generations in combination with the loss of potentially ada
         ptive genomic differentiation, both of which had evolved over thousands of y
         ears, demonstrates the sensitivity of biodiversity in evolutionary young ada
         ptive radiations towards environmental disturbance. Natural history collecti
         ons, such as the one used for this study, are instrumental in the assessment
          of genomic consequences of anthropogenic environmental change. Historical s
         amples enable us to document biodiversity loss against the shifting baseline
          syndrome and advance our understanding of the need for efficient biodiversi
         ty conservation on a global scale.' (1934 chars)
      serialnumber => protected'1752-4571' (9 chars)
      doi => protected'10.1111/eva.13617' (17 chars)
      uid => protected32245 (integer)
      _localizedUid => protected32245 (integer)modified
      _languageUid => protectedNULL
      _versionedUid => protected32245 (integer)modified
      pid => protected124 (integer)
   1 => Snowflake\Publications\Domain\Model\Publicationprototypepersistent entity (uid=32289, pid=124)
      originalId => protected32289 (integer)
      authors => protected'Haltiner, L.; Spaak, P.; Dennis, S. R.; Feulner, P.
          G. D.' (92 chars)
      title => protected'Population genetic insights into establishment, adaptation, and dispersal of
          the invasive quagga mussel across perialpine lakes' (127 chars)
      journal => protected'Evolutionary Applications' (25 chars)
      year => protected2024 (integer)
      volume => protected17 (integer)
      issue => protected'1' (1 chars)
      startpage => protected'e13620 (16 pp.)' (15 chars)
      otherpage => protected'' (0 chars)
      categories => protected'ddRADseq; dispersal; Dreissena; phenotypic plasticity; population genetics' (74 chars)
      description => protected'Human activities have facilitated the invasion of freshwater ecosystems by v
         arious organisms. Especially, invasive bivalves such as the quagga mussels, 
         <em>Dreissena bugensis</em>, have the potential to alter ecosystem function 
         as they heavily affect the food web. Quagga mussels occur in high abundance,
          have a high filtration rate, quickly spread within and between waterbodies 
         via pelagic larvae, and colonize various substrates. They have invaded vario
         us waterbodies across the Northern Hemisphere. In Central Europe, they have 
         invaded multiple large and deep perialpine lakes with first recordings in La
         ke Geneva in 2015 and 2016 in Lake Constance. In the deep perialpine lakes, 
         quagga mussels quickly colonized the littoral zone but are also abundant dee
         per (&gt;80 m), where they are often thinner and brighter shelled. We anal
         ysed 675 quagga mussels using ddRAD sequencing to gain in-depth insights int
         o the genetic population structure of quagga mussels across Central European
          lakes and across various sites and depth habitats in Lake Constance. We rev
         ealed substantial genetic differentiation amongst quagga mussel populations 
         from three unconnected lakes, and all populations showed high genetic divers
         ity and effective population size. In Lake Constance, we detected no genetic
          differentiation amongst quagga mussels sampled across different sites and d
         epth habitats. We also did not identify any convincing candidate loci eviden
         tial for adaptation along a depth gradient and a transplant experiment showe
         d no indications of local adaptation to living in the deep based on investig
         ating growth and survival. Hence, the shallow-water and the deep-water morph
         otypes seem to be a result of phenotypic plasticity rather than local adapta
         tion to depth. In conclusion, our ddRAD approach revealed insight into the e
         stablishment of genetically distinct quagga mussel populations in three peri
         alpine lakes and suggests that phenotypic plasticity and life history traits
          (broadcast spawner with...' (2138 chars)
      serialnumber => protected'1752-4571' (9 chars)
      doi => protected'10.1111/eva.13620' (17 chars)
      uid => protected32289 (integer)
      _localizedUid => protected32289 (integer)modified
      _languageUid => protectedNULL
      _versionedUid => protected32289 (integer)modified
      pid => protected124 (integer)
   2 => Snowflake\Publications\Domain\Model\Publicationprototypepersistent entity (uid=30693, pid=124)
      originalId => protected30693 (integer)
      authors => protected'Le Pennec,&nbsp;G.; Retel,&nbsp;C.; Kowallik,&nbsp;V.; Becks,&nbsp;L.; Feul
         ner,&nbsp;P.&nbsp;G.&nbsp;D.' (104 chars)
      title => protected'Demographic fluctuations and selection during host–parasite co-evolution i
         nteractively increase genetic diversity' (115 chars)
      journal => protected'Molecular Ecology' (17 chars)
      year => protected2024 (integer)
      volume => protected33 (integer)
      issue => protected'10' (2 chars)
      startpage => protected'e16939 (14 pp.)' (15 chars)
      otherpage => protected'' (0 chars)
      categories => protected'demography; experimental evolution; genetic diversity; host–parasite inter
         actions; selective sweeps' (101 chars)
      description => protected'Host–parasite interactions can cause strong demographic fluctuations accom
         panied by selective sweeps of resistance/infectivity alleles. Both demograph
         ic bottlenecks and frequent sweeps are expected to reduce the amount of segr
         egating genetic variation and therefore might constrain adaptation during co
         -evolution. Recent studies, however, suggest that the interaction of demogra
         phic and selective processes is a key component of co-evolutionary dynamics 
         and may rather positively affect levels of genetic diversity available for a
         daptation. Here, we provide direct experimental testing of this hypothesis b
         y disentangling the effects of demography, selection and their interaction i
         n an experimental host–parasite system. We grew 12 populations of a unicel
         lular, asexually reproducing algae (<em>Chlorella variabilis</em>) that expe
         rienced either growth followed by constant population sizes (three populatio
         ns), demographic fluctuations (three populations), selection induced by expo
         sure to a virus (three populations), or demographic fluctuations together wi
         th virus-induced selection (three populations). After 50 days (~50 generatio
         ns), we conducted whole-genome sequencing of each algal host population. We 
         observed more genetic diversity in populations that jointly experienced sele
         ction and demographic fluctuations than in populations where these processes
          were experimentally separated. In addition, in those three populations that
          jointly experienced selection and demographic fluctuations, experimentally 
         measured diversity exceeds expected values of diversity that account for the
          cultures' population sizes. Our results suggest that eco-evolutionary feedb
         acks can positively affect genetic diversity and provide the necessary empir
         ical measures to guide further improvements of theoretical models of adaptat
         ion during host–parasite co-evolution.' (1864 chars)
      serialnumber => protected'0962-1083' (9 chars)
      doi => protected'10.1111/mec.16939' (17 chars)
      uid => protected30693 (integer)
      _localizedUid => protected30693 (integer)modified
      _languageUid => protectedNULL
      _versionedUid => protected30693 (integer)modified
      pid => protected124 (integer)
   3 => Snowflake\Publications\Domain\Model\Publicationprototypepersistent entity (uid=32573, pid=124)
      originalId => protected32573 (integer)
      authors => protected'Stankowski,&nbsp;S.; Cutter,&nbsp;A.&nbsp;D.; Satokangas,&nbsp;I.; Lerch,&nb
         sp;B.&nbsp;A.; Rolland,&nbsp;J.; Smadja,&nbsp;C.&nbsp;M.; Segami Marzal,&nbs
         p;J.&nbsp;C.; Cooney,&nbsp;C.&nbsp;R.; Feulner,&nbsp;P.&nbsp;G.&nbsp;D.; Bic
         alho Domingos,&nbsp;F.&nbsp;M.&nbsp;C.; North,&nbsp;H.&nbsp;L.; Yamaguchi,&n
         bsp;R.; Butlin,&nbsp;R.&nbsp;K.; Wolf,&nbsp;J.&nbsp;B.&nbsp;W.; Coughlan,&nb
         sp;J.; Heidbreder,&nbsp;P.; Hernández-Gutiérrez,&nbsp;R.; Barnard-Kubow,&n
         bsp;K.&nbsp;B.; Peede,&nbsp;D.; Rancilhac,&nbsp;L.; Salvador,&nbsp;R.&nbsp;B
         .; Thompson,&nbsp;K.&nbsp;A.; Stacy,&nbsp;E.&nbsp;A.; Moyle,&nbsp;L.&nbsp;C.
         ; Garlovsky,&nbsp;M.&nbsp;D.; Maulana,&nbsp;A.; Kantelinen,&nbsp;A.; Cacho,&
         nbsp;N.&nbsp;I.; Schneemann,&nbsp;H.; Domínguez,&nbsp;M.; Dopman,&nbsp;E.&n
         bsp;B.; Lohse,&nbsp;K.; Rometsch,&nbsp;S.&nbsp;J.; Comeault,&nbsp;A.&nbsp;A.
         ; Merrill,&nbsp;R.&nbsp;M.; Scordato,&nbsp;E.&nbsp;S.&nbsp;C.; Singhal,&nbsp
         ;S.; Pärssinen,&nbsp;V.; Lackey,&nbsp;A.&nbsp;C.&nbsp;R.; Kumar,&nbsp;S.; M
         eier,&nbsp;J.&nbsp;I.; Barton,&nbsp;N.; Fraïsse,&nbsp;C.; Ravinet,&nbsp;M.;
          Kulmuni,&nbsp;J.' (1081 chars)
      title => protected'Toward the integration of speciation research' (45 chars)
      journal => protected'Evolutionary Journal of the Linnean Society' (43 chars)
      year => protected2024 (integer)
      volume => protected3 (integer)
      issue => protected'1' (1 chars)
      startpage => protected'1' (1 chars)
      otherpage => protected'24' (2 chars)
      categories => protected'collaboration; diversity; equity and inclusion; scientific practices; synthe
         sis' (79 chars)
      description => protected'Speciation research—the scientific field focused on understanding the orig
         in and diversity of species—has a long and complex history. While relevant
          to one another, the specific goals and activities of speciation researchers
          are highly diverse, and scattered across a collection of different perspect
         ives. Thus, our understanding of speciation will benefit from efforts to bri
         dge scientific findings and the diverse people who do the work. In this pape
         r, we outline two ways of integrating speciation research: (i) scientific in
         tegration, through the bringing together of ideas, data, and approaches; and
          (ii) social integration, by creating ways for a diversity of researchers to
          participate in the scientific process. We then discuss five challenges to 
         integration: (i) the multidisciplinary nature of speciation research, (ii) t
         he complex language of speciation; (iii) a bias toward certain study systems
         ; (iv) the challenges of working across scales; and (v) inconsistent measure
         s and reporting standards. We provide practical steps that individuals and g
         roups can take to help overcome these challenges, and argue that integration
          is a team effort in which we all have a role to play.' (1194 chars)
      serialnumber => protected'2752-938X' (9 chars)
      doi => protected'10.1093/evolinnean/kzae001' (26 chars)
      uid => protected32573 (integer)
      _localizedUid => protected32573 (integer)modified
      _languageUid => protectedNULL
      _versionedUid => protected32573 (integer)modified
      pid => protected124 (integer)
   4 => Snowflake\Publications\Domain\Model\Publicationprototypepersistent entity (uid=26070, pid=124)
      originalId => protected26070 (integer)
      authors => protected'Frei,&nbsp;D.; Reichlin,&nbsp;P.; Seehausen,&nbsp;O.; Feulner,&nbsp;P.&nbsp;
         G.&nbsp;D.' (86 chars)
      title => protected'Introgression from extinct species facilitates adaptation to its vacated nic
         he' (78 chars)
      journal => protected'Molecular Ecology' (17 chars)
      year => protected2023 (integer)
      volume => protected32 (integer)
      issue => protected'4' (1 chars)
      startpage => protected'841' (3 chars)
      otherpage => protected'853' (3 chars)
      categories => protected'adaptive radiation; deep-water adaptation; environmental change; extinction 
         by hybridization; introgression' (107 chars)
      description => protected'Anthropogenic disturbances of ecosystems are causing a loss of biodiversity 
         at an unprecedented rate. Species extinctions often leave ecological niches 
         underutilized, and their colonization by other species may require new adapt
         ation. In Lake Constance, on the borders of Germany, Austria and Switzerland
         , an endemic profundal whitefish species went extinct during a period of ant
         hropogenic eutrophication. In the process of extinction, the deep-water spec
         ies hybridized with three surviving whitefish species of Lake Constance, res
         ulting in introgression of genetic variation that is potentially adaptive in
          deep-water habitats. Here, we sampled a water depth gradient across a known
          spawning ground of one of these surviving species, <em>Coregonus macrophtha
         lmus</em>, and caught spawning individuals at greater depths (down to 90 m
         ) than historically recorded. We sequenced a total of 96 whole genomes, 11-1
         7 for each of six different spawning depth populations (4, 12, 20, 40, 60 an
         d 90 m), to document genomic intraspecific differentiation along a water d
         epth gradient. We identified 52 genomic regions that are potentially under d
         ivergent selection between the deepest (90 m) and all shallower (4-60 m)
          spawning habitats. At 12 (23.1%) of these 52 loci, the allele frequency pat
         tern across historical and contemporary populations suggests that introgress
         ion from the extinct species potentially facilitates ongoing adaptation to d
         eep water. Our results are consistent with the syngameon hypothesis, proposi
         ng that hybridization between members of an adaptive radiation can promote f
         urther niche expansion and diversification. Furthermore, our findings demons
         trate that introgression from extinct into extant species can be a source of
          evolvability, enabling rapid adaptation to environmental change, and may co
         ntribute to the ecological recovery of ecosystem functions after extinctions
         .' (1901 chars)
      serialnumber => protected'0962-1083' (9 chars)
      doi => protected'10.1111/mec.16791' (17 chars)
      uid => protected26070 (integer)
      _localizedUid => protected26070 (integer)modified
      _languageUid => protectedNULL
      _versionedUid => protected26070 (integer)modified
      pid => protected124 (integer)
   5 => Snowflake\Publications\Domain\Model\Publicationprototypepersistent entity (uid=25558, pid=124)
      originalId => protected25558 (integer)
      authors => protected'De-Kayne,&nbsp;R.; Selz,&nbsp;O.&nbsp;M.; Marques,&nbsp;D.&nbsp;A.; Frei,&nb
         sp;D.; Seehausen,&nbsp;O.; Feulner,&nbsp;P.&nbsp;G.&nbsp;D.' (135 chars)
      title => protected'Genomic architecture of adaptive radiation and hybridization in Alpine white
         fish' (80 chars)
      journal => protected'Nature Communications' (21 chars)
      year => protected2022 (integer)
      volume => protected13 (integer)
      issue => protected'1' (1 chars)
      startpage => protected'4479 (13 pp.)' (13 chars)
      otherpage => protected'' (0 chars)
      categories => protected'' (0 chars)
      description => protected'Adaptive radiations represent some of the most remarkable explosions of dive
         rsification across the tree of life. However, the constraints to rapid diver
         sification and how they are sometimes overcome, particularly the relative ro
         les of genetic architecture and hybridization, remain unclear. Here, we addr
         ess these questions in the Alpine whitefish radiation, using a whole-genome 
         dataset that includes multiple individuals of each of the 22 species belongi
         ng to six ecologically distinct ecomorph classes across several lake-systems
         . We reveal that repeated ecological and morphological diversification along
          a common environmental axis is associated with both genome-wide allele freq
         uency shifts and a specific, larger effect, locus, associated with the gene 
         <em>edar</em>. Additionally, we highlight the possible role of introgression
          between species from different lake-systems in facilitating the evolution a
         nd persistence of species with unique trait combinations and ecology. These 
         results highlight the importance of both genome architecture and secondary c
         ontact with hybridization in fuelling adaptive radiation.' (1121 chars)
      serialnumber => protected'' (0 chars)
      doi => protected'10.1038/s41467-022-32181-8' (26 chars)
      uid => protected25558 (integer)
      _localizedUid => protected25558 (integer)modified
      _languageUid => protectedNULL
      _versionedUid => protected25558 (integer)modified
      pid => protected124 (integer)
   6 => Snowflake\Publications\Domain\Model\Publicationprototypepersistent entity (uid=24480, pid=124)
      originalId => protected24480 (integer)
      authors => protected'Frei,&nbsp;D.; De-Kayne,&nbsp;R.; Selz,&nbsp;O.&nbsp;M.; Seehausen,&nbsp;O.;
          Feulner,&nbsp;P.&nbsp;G.&nbsp;D.' (109 chars)
      title => protected'Genomic variation from an extinct species is retained in the extant radiatio
         n following speciation reversal' (107 chars)
      journal => protected'Nature Ecology & Evolution' (26 chars)
      year => protected2022 (integer)
      volume => protected6 (integer)
      issue => protected'' (0 chars)
      startpage => protected'461' (3 chars)
      otherpage => protected'468' (3 chars)
      categories => protected'' (0 chars)
      description => protected'Ecosystem degradation and biodiversity loss are major global challenges. Whe
         n reproductive isolation between species is contingent on the interaction of
          intrinsic lineage traits with features of the environment, environmental ch
         ange can weaken reproductive isolation and result in extinction through hybr
         idization. By this process called speciation reversal, extinct species can l
         eave traces in genomes of extant species through introgressive hybridization
         . Using historical and contemporary samples, we sequenced all four species o
         f an Alpine whitefish radiation before and after anthropogenic lake eutrophi
         cation and the associated loss of one species through speciation reversal. D
         espite the extinction of this taxon, substantial fractions of its genome, in
         cluding regions shaped by positive selection before eutrophication, persist 
         within surviving species as a consequence of introgressive hybridization dur
         ing eutrophication. Given the prevalence of environmental change, studying s
         peciation reversal and its genomic consequences provides fundamental insight
         s into evolutionary processes and informs biodiversity conservation.' (1132 chars)
      serialnumber => protected'' (0 chars)
      doi => protected'10.1038/s41559-022-01665-7' (26 chars)
      uid => protected24480 (integer)
      _localizedUid => protected24480 (integer)modified
      _languageUid => protectedNULL
      _versionedUid => protected24480 (integer)modified
      pid => protected124 (integer)
   7 => Snowflake\Publications\Domain\Model\Publicationprototypepersistent entity (uid=24360, pid=124)
      originalId => protected24360 (integer)
      authors => protected'Retel,&nbsp;C.; Kowallik,&nbsp;V.; Becks,&nbsp;L.; Feulner,&nbsp;P.&nbsp;G.&
         nbsp;D.' (83 chars)
      title => protected'Strong selection and high mutation supply characterize experimental<em> Chlo
         rovirus </em>evolution' (98 chars)
      journal => protected'Virus Evolution' (15 chars)
      year => protected2022 (integer)
      volume => protected8 (integer)
      issue => protected'1' (1 chars)
      startpage => protected'veac003 (14 pp.)' (16 chars)
      otherpage => protected'' (0 chars)
      categories => protected'virus evolution; genomics; repeatable genomic change; predicted phenotypic e
         ffect; Chlorovirus PBCV-1' (101 chars)
      description => protected'Characterizing how viruses evolve expands our understanding of the underlyin
         g fundamental processes, such as mutation, selection and drift. One group of
          viruses whose evolution has not yet been extensively studied are the <em>Ph
         ycodnaviridae</em>, a globally abundant family of aquatic large dsDNA viruse
         s. Here we studied the evolutionary change of <em>Paramecium bursaria</em> c
         hlorella virus 1 (PBCV-1) during experimental coevolution with its algal hos
         t. We used pooled genome sequencing of six independently evolved populations
          to characterize genomic change over five time points. Across six experiment
         al replicates involving either strong or weak demographic fluctuations, we f
         ound single nucleotide polymorphisms (SNPs) at 67 sites. The occurrence of g
         enetic variants was highly repeatable, with just two of the SNPs found in on
         ly a single experimental replicate. Three genes <em>A122/123R, A140/145R</em
         > and <em>A540L</em> showed an excess of variable sites, providing new infor
         mation about potential targets of selection during <em>Chlorella</em>-Chloro
         virus coevolution. Our data indicated that the studied populations were not 
         mutation-limited and experienced strong positive selection. Our investigatio
         n highlighted relevant processes governing the evolution of aquatic large ds
         DNA viruses, which ultimately contributes to a better understanding of the f
         unctioning of natural aquatic ecosystems.' (1409 chars)
      serialnumber => protected'' (0 chars)
      doi => protected'10.1093/ve/veac003' (18 chars)
      uid => protected24360 (integer)
      _localizedUid => protected24360 (integer)modified
      _languageUid => protectedNULL
      _versionedUid => protected24360 (integer)modified
      pid => protected124 (integer)
   8 => Snowflake\Publications\Domain\Model\Publicationprototypepersistent entity (uid=21849, pid=124)
      originalId => protected21849 (integer)
      authors => protected'De‐Kayne,&nbsp;R.; Frei,&nbsp;D.; Greenway,&nbsp;R.; Mendes,&nbsp;S.&nbsp;
         L.; Retel,&nbsp;C.; Feulner,&nbsp;P.&nbsp;G.&nbsp;D.' (128 chars)
      title => protected'Sequencing platform shifts provide opportunities but pose challenges for com
         bining genomic datasets' (99 chars)
      journal => protected'Molecular Ecology Resources' (27 chars)
      year => protected2021 (integer)
      volume => protected21 (integer)
      issue => protected'3' (1 chars)
      startpage => protected'653' (3 chars)
      otherpage => protected'660' (3 chars)
      categories => protected'' (0 chars)
      description => protected'Technological advances in DNA sequencing over the last decade now permit the
          production and curation of large genomic datasets in an increasing number o
         f non‐model species. Additionally, this new data provides the opportunity 
         for combining datasets, resulting in larger studies with a broader taxonomic
          range. Whilst the development of new sequencing platforms has been benefici
         al, resulting in a higher throughput of data at a lower per‐base cost, shi
         fts in sequencing technology can also pose challenges for those wishing to c
         ombine new sequencing data with data sequenced on older platforms. Here, we 
         outline the types of studies where the use of curated data might be benefici
         al, and highlight potential biases that might be introduced by combining dat
         a from different sequencing platforms. As an example of the challenges assoc
         iated with combining data across sequencing platforms, we focus on the impac
         t of the shift in Illumina's base calling technology from a four‐channel t
         o a two‐channel system. We caution that when data is combined from these t
         wo systems, erroneous guanine base calls that result from the two‐channel 
         chemistry can make their way through a bioinformatic pipeline, eventually le
         ading to inaccurate and potentially misleading conclusions. We also suggest 
         solutions for dealing with such potential artifacts, which make samples sequ
         enced on different sequencing platforms appear more differentiated from one 
         another than they really are. Finally, we stress the importance of archiving
          tissue samples and the associated sequences for the continued reproducibili
         ty and reusability of sequencing data in the face of ever‐changing sequenc
         ing platform technology.' (1696 chars)
      serialnumber => protected'1755-098X' (9 chars)
      doi => protected'10.1111/1755-0998.13309' (23 chars)
      uid => protected21849 (integer)
      _localizedUid => protected21849 (integer)modified
      _languageUid => protectedNULL
      _versionedUid => protected21849 (integer)modified
      pid => protected124 (integer)
   9 => Snowflake\Publications\Domain\Model\Publicationprototypepersistent entity (uid=20700, pid=124)
      originalId => protected20700 (integer)
      authors => protected'De-Kayne,&nbsp;R.; Zoller,&nbsp;S.; Feulner,&nbsp;P.&nbsp;G.&nbsp;D.' (68 chars)
      title => protected'<em>A de novo</em> chromosome-level genome assembly of <em>Coregonus sp. "Ba
         lchen"</em>: one representative of the Swiss Alpine whitefish radiation' (147 chars)
      journal => protected'Molecular Ecology Resources' (27 chars)
      year => protected2020 (integer)
      volume => protected20 (integer)
      issue => protected'4' (1 chars)
      startpage => protected'1093' (4 chars)
      otherpage => protected'1109' (4 chars)
      categories => protected'Alpine whitefish; Coregonus; whitefish; Salmonidae; genome assembly' (67 chars)
      description => protected'Salmonids are of particular interest to evolutionary biologists due to their
          incredible diversity of life-history strategies and the speed at which many
          salmonid species have diversified. In Switzerland alone, over 30 species of
          Alpine whitefish from the subfamily Coregoninae have evolved since the last
          glacial maximum, with species exhibiting a diverse range of morphological a
         nd behavioural phenotypes. This, combined with the whole genome duplication 
         which occurred in the ancestor of all salmonids, makes the Alpine whitefish 
         radiation a particularly interesting system in which to study the genetic ba
         sis of adaptation and speciation and the impacts of ploidy changes and subse
         quent rediploidization on genome evolution. Although well curated genome ass
         emblies exist for many species within Salmonidae, genomic resources for the 
         subfamily Coregoninae are lacking. To assemble a whitefish reference genome,
          we carried out PacBio sequencing from one wild-caught <em>Coregonus sp. "Ba
         lchen"</em> from Lake Thun to ~90x coverage. PacBio reads were assembled ind
         ependently using three different assemblers, Falcon, Canu and wtdbg2 and sub
         sequently scaffolded with additional Hi-C data. All three assemblies were hi
         ghly contiguous, had strong synteny to a previously published <em>Coregonus<
         /em> linkage map, and when mapping additional short-read data to each of the
          assemblies, coverage was fairly even across most chromosome-scale scaffolds
         . Here, we present the first <em>de novo</em> genome assembly for the Salmon
         id subfamily Coregoninae. The final 2.2 Gb wtdbg2 assembly included 40 scaff
         olds, an N50 of 51.9 Mb, and was 93.3% complete for BUSCOs. The assembly con
         sisted of ~52% TEs and contained 44,525 genes.' (1718 chars)
      serialnumber => protected'1755-098X' (9 chars)
      doi => protected'10.1111/1755-0998.13187' (23 chars)
      uid => protected20700 (integer)
      _localizedUid => protected20700 (integer)modified
      _languageUid => protectedNULL
      _versionedUid => protected20700 (integer)modified
      pid => protected124 (integer)
   10 => Snowflake\Publications\Domain\Model\Publicationprototypepersistent entity (uid=18184, pid=124)
      originalId => protected18184 (integer)
      authors => protected'Feulner,&nbsp;P.&nbsp;G.&nbsp;D.; Seehausen,&nbsp;O.' (52 chars)
      title => protected'Genomic insights into the vulnerability of sympatric whitefish species flock
         s' (77 chars)
      journal => protected'Molecular Ecology' (17 chars)
      year => protected2019 (integer)
      volume => protected28 (integer)
      issue => protected'' (0 chars)
      startpage => protected'615' (3 chars)
      otherpage => protected'629' (3 chars)
      categories => protected'coregonus spp; ecological speciation; RADseq; speciation reversal' (65 chars)
      description => protected'The erosion of habitat heterogeneity can reduce species diversity directly b
         ut can also lead to the loss of distinctiveness of sympatric species through
          speciation reversal. We know little about changes in genomic differentiatio
         n during the early stages of these processes, which can be mediated by anthr
         opogenic perturbation. Here, we analyse three sympatric whitefish species (<
         em>Coregonus</em> spp) sampled across two neighbouring and connected Swiss p
         re‐alpine lakes, which have been differentially affected by anthropogenic 
         eutrophication. Our data set comprises 16,173 loci genotyped across 138 whit
         efish using restriction‐site associated DNA sequencing (RADseq). Our analy
         sis suggests that in each of the two lakes the population of a different, bu
         t ecologically similar, whitefish species declined following a recent period
          of eutrophication. Genomic signatures consistent with hybridisation are mor
         e pronounced in the more severely impacted lake. Comparisons between sympatr
         ic pairs of whitefish species with contrasting ecology, where one is shallow
          benthic and the other one more profundal pelagic, reveal genomic differenti
         ation that is largely correlated along the genome, while differentiation is 
         uncorrelated between pairs of allopatric provenance with similar ecology. We
          identify four genomic loci that provide evidence of parallel divergent adap
         tation between the shallow benthic species and the two different more profun
         dal species. Functional annotations available for two of those loci are cons
         istent with divergent ecological adaptation. Our genomic analysis indicates 
         the action of divergent natural selection between sympatric whitefish specie
         s in pre‐alpine lakes and reveals the vulnerability of these species to an
         thropogenic alterations of the environment and associated adaptive landscape
         .' (1825 chars)
      serialnumber => protected'0962-1083' (9 chars)
      doi => protected'10.1111/mec.14977' (17 chars)
      uid => protected18184 (integer)
      _localizedUid => protected18184 (integer)modified
      _languageUid => protectedNULL
      _versionedUid => protected18184 (integer)modified
      pid => protected124 (integer)
   11 => Snowflake\Publications\Domain\Model\Publicationprototypepersistent entity (uid=19270, pid=124)
      originalId => protected19270 (integer)
      authors => protected'Retel,&nbsp;C.; Kowallik,&nbsp;V.; Huang,&nbsp;W.; Werner,&nbsp;B.; Künzel,
         &nbsp;S.; Becks,&nbsp;L.; Feulner,&nbsp;P.&nbsp;G.&nbsp;D.' (134 chars)
      title => protected'The feedback between selection and demography shapes genomic diversity durin
         g coevolution' (89 chars)
      journal => protected'Science Advances' (16 chars)
      year => protected2019 (integer)
      volume => protected5 (integer)
      issue => protected'10' (2 chars)
      startpage => protected'eaax0530 (9 pp.)' (16 chars)
      otherpage => protected'' (0 chars)
      categories => protected'' (0 chars)
      description => protected'Species interactions and coevolution are integral to ecological communities,
          but we lack empirical information on when and how these interactions genera
         te and purge genetic diversity. Using genomic time series data from host-vir
         us experiments, we found that coevolution occurs through consecutive selecti
         ve sweeps in both species, with temporal consistency across replicates. Swee
         ps were accompanied by phenotypic change (resistance or infectivity increase
         s) and expansions in population size. In the host, population expansion enab
         led rapid generation of genetic diversity in accordance with neutral process
         es. Viral molecular evolution was, in contrast, confined to few genes, all p
         utative targets of selection. This study demonstrates that molecular evoluti
         on during species interactions is shaped by both eco-evolutionary feedback d
         ynamics and interspecific differences in how genetic diversity is generated 
         and maintained.' (927 chars)
      serialnumber => protected'' (0 chars)
      doi => protected'10.1126/sciadv.aax0530' (22 chars)
      uid => protected19270 (integer)
      _localizedUid => protected19270 (integer)modified
      _languageUid => protectedNULL
      _versionedUid => protected19270 (integer)modified
      pid => protected124 (integer)
   12 => Snowflake\Publications\Domain\Model\Publicationprototypepersistent entity (uid=15607, pid=124)
      originalId => protected15607 (integer)
      authors => protected'Stapley,&nbsp;J.; Feulner,&nbsp;P.&nbsp;G.&nbsp;D.; Johnston,&nbsp;S.&nbsp;E
         .; Santure,&nbsp;A.&nbsp;W.; Smadja,&nbsp;C.&nbsp;M.' (128 chars)
      title => protected'Variation in recombination frequency and distribution across eukaryotes: pat
         terns and processes' (95 chars)
      journal => protected'Philosophical Transactions of the Royal Society B: Biological Sciences' (70 chars)
      year => protected2017 (integer)
      volume => protected372 (integer)
      issue => protected'1736' (4 chars)
      startpage => protected'20160455 (10 pp.)' (17 chars)
      otherpage => protected'' (0 chars)
      categories => protected'crossing over; meiosis; genetic linkage; evolution; adaptation; genomic arch
         itecture' (84 chars)
      description => protected'Recombination, the exchange of DNA between maternal and paternal chromosomes
          during meiosis, is an essential feature of sexual reproduction in nearly al
         l multicellular organisms. While the role of recombination in the evolution 
         of sex has received theoretical and empirical attention, less is known about
          how recombination rate <i>itself</i> evolves and what influence this has on
          evolutionary processes within sexually reproducing organisms. Here, we expl
         ore the patterns of, and processes governing recombination in eukaryotes. We
          summarize patterns of variation, integrating current knowledge with an anal
         ysis of linkage map data in 353 organisms. We then discuss proximate and ult
         imate processes governing recombination rate variation and consider how thes
         e influence evolutionary processes. Genome-wide recombination rates (cM/Mb) 
         can vary more than tenfold across eukaryotes, and there is large variation i
         n the distribution of recombination events across closely related taxa, popu
         lations and individuals. We discuss how variation in rate and distribution r
         elates to genome architecture, genetic and epigenetic mechanisms, sex, envir
         onmental perturbations and variable selective pressures. There has been grea
         t progress in determining the molecular mechanisms governing recombination, 
         and with the continued development of new modelling and empirical approaches
         , there is now also great opportunity to further our understanding of how an
         d why recombination rate varies. <br/> This article is part of the themed is
         sue 'Evolutionary causes and consequences of recombination rate variation in
          sexual organisms'.' (1615 chars)
      serialnumber => protected'0962-8436' (9 chars)
      doi => protected'10.1098/rstb.2016.0455' (22 chars)
      uid => protected15607 (integer)
      _localizedUid => protected15607 (integer)modified
      _languageUid => protectedNULL
      _versionedUid => protected15607 (integer)modified
      pid => protected124 (integer)
   13 => Snowflake\Publications\Domain\Model\Publicationprototypepersistent entity (uid=17867, pid=124)
      originalId => protected17867 (integer)
      authors => protected'De-Kayne,&nbsp;R.; Feulner,&nbsp;P.&nbsp;G.&nbsp;D.' (51 chars)
      title => protected'A European whitefish linkage map and its implications for understanding geno
         me-wide synteny between salmonids following whole genome duplication' (144 chars)
      journal => protected'G3: Genes, Genomes, Genetics' (28 chars)
      year => protected2018 (integer)
      volume => protected8 (integer)
      issue => protected'12' (2 chars)
      startpage => protected'3745' (4 chars)
      otherpage => protected'3755' (4 chars)
      categories => protected'Coregonus; RAD; recombination rate; Salmonidae; sex-specific linkage maps; s
         ynteny' (82 chars)
      description => protected'Genomic datasets continue to increase in number due to the ease of productio
         n for a wider selection of species including non-model organisms. For many o
         f these species, especially those with large or polyploid genomes, highly co
         ntiguous and well-annotated genomes are still rare due to the complexity and
          cost involved in their assembly. As a result, a common starting point for g
         enomic work in non-model species is the production of a linkage map. Dense l
         inkage maps facilitate the analysis of genomic data in a variety of ways, fr
         om broad scale observations regarding genome structure e.g. chromosome numbe
         r and type or sex-related structural differences, to fine scale patterns e.g
         . recombination rate variation and co-localization of differentiated regions
         . Here we present both sex-averaged and sex-specific linkage maps for <em>Co
         regonus sp. "Albock"</em>, a member of the European whitefish lineage (<em>C
         . lavaretus</em> spp. complex), containing 5395 single nucleotide polymorphi
         sm (SNP) loci across 40 linkage groups to facilitate future investigation in
         to the genomic basis of whitefish adaptation and speciation. The map was pro
         duced using restriction-site associated digestion (RAD) sequencing data from
          two wild-caught parents and 156 F1 offspring. We discuss the differences be
         tween our sex-averaged and sex-specific maps and identify genome-wide synten
         y between <em>C. sp. "Albock"</em> and Atlantic Salmon (<em>Salmo salar</em>
         ), which have diverged following the salmonid-specific whole genome duplicat
         ion. Our analysis confirms that many patterns of synteny observed between At
         lantic Salmon and <em>Oncorhynchus and Salvelinus</em> species are also shar
         ed by members of the Coregoninae subfamily. We also show that regions known 
         for their species-specific rediploidization history can pose challenges for 
         synteny identification since these regions have diverged independently in ea
         ch salmonid species following the salmonid-specific whole genome duplication
         . The European whitefish...' (2243 chars)
      serialnumber => protected'' (0 chars)
      doi => protected'10.1534/g3.118.200552' (21 chars)
      uid => protected17867 (integer)
      _localizedUid => protected17867 (integer)modified
      _languageUid => protectedNULL
      _versionedUid => protected17867 (integer)modified
      pid => protected124 (integer)
   14 => Snowflake\Publications\Domain\Model\Publicationprototypepersistent entity (uid=16857, pid=124)
      originalId => protected16857 (integer)
      authors => protected'Frickel,&nbsp;J.; Feulner,&nbsp;P.&nbsp;G.&nbsp;D.; Karakoc,&nbsp;E.; Becks,
         &nbsp;L.' (84 chars)
      title => protected'Population size changes and selection drive patterns of parallel evolution i
         n a host–virus system' (99 chars)
      journal => protected'Nature Communications' (21 chars)
      year => protected2018 (integer)
      volume => protected9 (integer)
      issue => protected'1' (1 chars)
      startpage => protected'1760 (10 pp.)' (13 chars)
      otherpage => protected'' (0 chars)
      categories => protected'' (0 chars)
      description => protected'Predicting the repeatability of evolution remains elusive. Theory and empiri
         cal studies suggest that strong selection and large population sizes increas
         e the probability for parallel evolution at the phenotypic and genotypic lev
         els. However, selection and population sizes are not constant, but rather ch
         ange continuously and directly affect each other even on short time scales. 
         Here, we examine the degree of parallel evolution shaped through ecoevolutio
         nary dynamics in an algal host population coevolving with a virus. We find h
         igh degrees of parallelism at the level of population size changes (ecology)
          and at the phenotypic level between replicated populations. At the genomic 
         level, we find evidence for parallelism, as the same large genomic region wa
         s duplicated in all replicated populations, but also substantial novel seque
         nce divergence between replicates. These patterns of genome evolution can be
          explained by considering population size changes as an important driver of 
         rapid evolution.' (1004 chars)
      serialnumber => protected'' (0 chars)
      doi => protected'10.1038/s41467-018-03990-7' (26 chars)
      uid => protected16857 (integer)
      _localizedUid => protected16857 (integer)modified
      _languageUid => protectedNULL
      _versionedUid => protected16857 (integer)modified
      pid => protected124 (integer)
   15 => Snowflake\Publications\Domain\Model\Publicationprototypepersistent entity (uid=17146, pid=124)
      originalId => protected17146 (integer)
      authors => protected'Feulner,&nbsp;P.&nbsp;G.&nbsp;D.; Schwarzer,&nbsp;J.; Haesler,&nbsp;M.&nbsp;
         P.; Meier,&nbsp;J.&nbsp;I.; Seehausen,&nbsp;O.' (122 chars)
      title => protected'A dense linkage map of Lake Victoria cichlids improved the <em>Pundamilia</e
         m> genome assembly and revealed a major QTL for sex-determination' (141 chars)
      journal => protected'G3: Genes, Genomes, Genetics' (28 chars)
      year => protected2018 (integer)
      volume => protected8 (integer)
      issue => protected'7' (1 chars)
      startpage => protected'2411' (4 chars)
      otherpage => protected'2420' (4 chars)
      categories => protected'genetics of sex; amh; Cichlidae; RAD; recombination rate; sex chromosome evo
         lution; sex determination; synteny; XY system' (121 chars)
      description => protected'Genetic linkage maps are essential for comparative genomics, high quality ge
         nome sequence assembly and fine scale quantitative trait locus (QTL) mapping
         . In the present study we identified and genotyped markers via restriction-s
         ite associated DNA (RAD) sequencing and constructed a genetic linkage map ba
         sed on 1,597 SNP markers of an interspecific F2 cross of two closely related
          Lake Victoria cichlids (<em>Pundamilia pundamilia</em> and <em>P.</em> sp. 
         'red head'). The SNP markers were distributed on 22 linkage groups and the t
         otal map size was 1,594 cM with an average marker distance of 1.01 cM. This 
         high-resolution genetic linkage map was used to anchor the scaffolds of the 
         <em>Pundamilia</em> genome and estimate recombination rates along the genome
         . Via QTL mapping we identified a major QTL for sex in a ∼1.9 Mb region on
          Pun-LG10, which is homologous to <em>Oreochromis niloticus</em> LG 23 (Ore-
         LG23) and includes a well-known vertebrate sex-determination gene (<em>amh</
         em>).' (993 chars)
      serialnumber => protected'' (0 chars)
      doi => protected'10.1534/g3.118.200207' (21 chars)
      uid => protected17146 (integer)
      _localizedUid => protected17146 (integer)modified
      _languageUid => protectedNULL
      _versionedUid => protected17146 (integer)modified
      pid => protected124 (integer)
   16 => Snowflake\Publications\Domain\Model\Publicationprototypepersistent entity (uid=15184, pid=124)
      originalId => protected15184 (integer)
      authors => protected'Feulner,&nbsp;P.&nbsp;G.&nbsp;D.; De-Kayne,&nbsp;R.' (51 chars)
      title => protected'Genome evolution, structural rearrangements and speciation' (58 chars)
      journal => protected'Journal of Evolutionary Biology' (31 chars)
      year => protected2017 (integer)
      volume => protected30 (integer)
      issue => protected'8' (1 chars)
      startpage => protected'1488' (4 chars)
      otherpage => protected'1490' (4 chars)
      categories => protected'' (0 chars)
      description => protected'' (0 chars)
      serialnumber => protected'1010-061X' (9 chars)
      doi => protected'10.1111/jeb.13101' (17 chars)
      uid => protected15184 (integer)
      _localizedUid => protected15184 (integer)modified
      _languageUid => protectedNULL
      _versionedUid => protected15184 (integer)modified
      pid => protected124 (integer)
   17 => Snowflake\Publications\Domain\Model\Publicationprototypepersistent entity (uid=10420, pid=124)
      originalId => protected10420 (integer)
      authors => protected'Huang,&nbsp;Y.; Chain,&nbsp;F.&nbsp;J.&nbsp;J.; Panchal,&nbsp;M.; Eizaguirre
         ,&nbsp;C.; Kalbe,&nbsp;M.; Lenz,&nbsp;T.&nbsp;L.; Samonte,&nbsp;I.&nbsp;E.; 
         Stoll,&nbsp;M.; Bornberg-Bauer,&nbsp;E.; Reusch,&nbsp;T.&nbsp;B.&nbsp;H.; Mi
         linski,&nbsp;M.; Feulner,&nbsp;P.&nbsp;G.&nbsp;D.' (277 chars)
      title => protected'Transcriptome profiling of immune tissues reveals habitat-specific gene expr
         ession between lake and river sticklebacks' (118 chars)
      journal => protected'Molecular Ecology' (17 chars)
      year => protected2016 (integer)
      volume => protected25 (integer)
      issue => protected'4' (1 chars)
      startpage => protected'943' (3 chars)
      otherpage => protected'958' (3 chars)
      categories => protected'habitat-specific gene expression; immune genes; parasites; RNA-Seq; three-sp
         ined strickleback; transcriptomics' (110 chars)
      description => protected'The observation of habitat-specific phenotypes suggests the action of natura
         l selection. The three-spined stickleback (<I>Gasterosteus aculeatus</I>) ha
         s repeatedly colonized and adapted to diverse freshwater habitats across the
          northern hemisphere since the last glaciation, while giving rise to recurri
         ng phenotypes associated with specific habitats. Parapatric lake and river p
         opulations of sticklebacks harbour distinct parasite communities, a factor p
         roposed to contribute to adaptive differentiation between these ecotypes. Ho
         wever, little is known about the transcriptional response to the distinct pa
         rasite pressure of those fish in a natural setting. Here, we sampled wild-ca
         ught sticklebacks across four geographical locations from lake and river hab
         itats differing in their parasite load. We compared gene expression profiles
          between lake and river populations using 77 whole-transcriptome libraries f
         rom two immune-relevant tissues, the head kidney and the spleen. Differentia
         l expression analyses revealed 139 genes with habitat-specific expression pa
         tterns across the sampled population pairs. Among the 139 differentially exp
         ressed genes, eight are annotated with an immune function and 42 have been i
         dentified as differentially expressed in previous experimental studies in wh
         ich fish have been immune challenged. Together, these findings reinforce the
          hypothesis that parasites contribute to adaptation of sticklebacks in lake 
         and river habitats.' (1463 chars)
      serialnumber => protected'0962-1083' (9 chars)
      doi => protected'10.1111/mec.13520' (17 chars)
      uid => protected10420 (integer)
      _localizedUid => protected10420 (integer)modified
      _languageUid => protectedNULL
      _versionedUid => protected10420 (integer)modified
      pid => protected124 (integer)
   18 => Snowflake\Publications\Domain\Model\Publicationprototypepersistent entity (uid=9158, pid=124)
      originalId => protected9158 (integer)
      authors => protected'Feulner,&nbsp;P.&nbsp;G.&nbsp;D.; Chain,&nbsp;F.&nbsp;J.&nbsp;J.; Panchal,&n
         bsp;M.; Huang,&nbsp;Y.; Eizaguirre,&nbsp;C.; Kalbe,&nbsp;M.; Lenz,&nbsp;T.&n
         bsp;L.; Samonte,&nbsp;I.&nbsp;E.; Stoll,&nbsp;M.; Bornberg-Bauer,&nbsp;E.; R
         eusch,&nbsp;T.&nbsp;B.&nbsp;H.; Milinski,&nbsp;M.' (277 chars)
      title => protected'Genomics of divergence along a continuum of parapatric population differenti
         ation' (81 chars)
      journal => protected'PLoS Genetics' (13 chars)
      year => protected2015 (integer)
      volume => protected11 (integer)
      issue => protected'2' (1 chars)
      startpage => protected'1' (1 chars)
      otherpage => protected'18' (2 chars)
      categories => protected'' (0 chars)
      description => protected'The patterns of genomic divergence during ecological speciation are shaped b
         y a combination of evolutionary forces. Processes such as genetic drift, loc
         al reduction of gene flow around genes causing reproductive isolation, hitch
         hiking around selected variants, variation in recombination and mutation rat
         es are all factors that can contribute to the heterogeneity of genomic diver
         gence. On the basis of 60 fully sequenced three-spined stickleback genomes, 
         we explore these different mechanisms explaining the heterogeneity of genomi
         c divergence across five parapatric lake and river population pairs varying 
         in their degree of genetic differentiation. We find that divergent regions o
         f the genome are mostly specific for each population pair, while their size 
         and abundance are not correlated with the extent of genome-wide population d
         ifferentiation. In each pair-wise comparison, an analysis of allele frequenc
         y spectra reveals that 25–55% of the divergent regions are consistent with
          a local restriction of gene flow. Another large proportion of divergent reg
         ions (38–75%) appears to be mainly shaped by hitchhiking effects around po
         sitively selected variants. We provide empirical evidence that alternative m
         echanisms determining the evolution of genomic patterns of divergence are no
         t mutually exclusive, but rather act in concert to shape the genome during p
         opulation differentiation, a first necessary step towards ecological speciat
         ion.' (1448 chars)
      serialnumber => protected'1553-7390' (9 chars)
      doi => protected'10.1371/journal.pgen.1004966' (28 chars)
      uid => protected9158 (integer)
      _localizedUid => protected9158 (integer)modified
      _languageUid => protectedNULL
      _versionedUid => protected9158 (integer)modified
      pid => protected124 (integer)
   19 => Snowflake\Publications\Domain\Model\Publicationprototypepersistent entity (uid=9142, pid=124)
      originalId => protected9142 (integer)
      authors => protected'Chain,&nbsp;F.&nbsp;J.&nbsp;J.; Feulner,&nbsp;P.&nbsp;G.&nbsp;D.; Panchal,&n
         bsp;M.; Eizaguirre,&nbsp;C.; Samonte,&nbsp;I.&nbsp;E.; Kalbe,&nbsp;M.; Lenz,
         &nbsp;T.&nbsp;L.; Stoll,&nbsp;M.; Bornberg-Bauer,&nbsp;E.; Milinski,&nbsp;M.
         ; Reusch,&nbsp;T.&nbsp;B.&nbsp;H.' (261 chars)
      title => protected'Extensive copy-number variation of young genes across stickleback population
         s' (77 chars)
      journal => protected'PLoS Genetics' (13 chars)
      year => protected2014 (integer)
      volume => protected10 (integer)
      issue => protected'12' (2 chars)
      startpage => protected'1' (1 chars)
      otherpage => protected'18' (2 chars)
      categories => protected'' (0 chars)
      description => protected'Duplicate genes emerge as copy-number variations (CNVs) at the population le
         vel, and remain copy-number polymorphic until they are fixed or lost. The su
         ccessful establishment of such structural polymorphisms in the genome plays 
         an important role in evolution by promoting genetic diversity, complexity an
         d innovation. To characterize the early evolutionary stages of duplicate gen
         es and their potential adaptive benefits, we combine comparative genomics wi
         th population genomics analyses to evaluate the distribution and impact of C
         NVs across natural populations of an eco-genomic model, the three-spined sti
         ckleback. With whole genome sequences of 66 individuals from populations inh
         abiting three distinct habitats, we find that CNVs generally occur at low fr
         equencies and are often only found in one of the 11 populations surveyed. A 
         subset of CNVs, however, displays copy-number differentiation between popula
         tions, showing elevated within-population frequencies consistent with local 
         adaptation. By comparing teleost genomes to identify lineage-specific genes 
         and duplications in sticklebacks, we highlight rampant gene content differen
         ces among individuals in which over 30% of young duplicate genes are CNVs. T
         hese CNV genes are evolving rapidly at the molecular level and are enriched 
         with functional categories associated with environmental interactions, depic
         ting the dynamic early copy-number polymorphic stage of genes during populat
         ion differentiation.' (1464 chars)
      serialnumber => protected'1553-7390' (9 chars)
      doi => protected'10.1371/journal.pgen.1004830' (28 chars)
      uid => protected9142 (integer)
      _localizedUid => protected9142 (integer)modified
      _languageUid => protectedNULL
      _versionedUid => protected9142 (integer)modified
      pid => protected124 (integer)