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  • 1
    Online Resource
    Online Resource
    Disentangling the effects of geographic peripherality and habitat suitability on neutral and adaptive genetic variation in Swiss stone pine
    Wiley ; 2020
    In:  Molecular Ecology Vol. 29, No. 11 ( 2020-06), p. 1972-1989
    Details
    In: Molecular Ecology, Wiley, Vol. 29, No. 11 ( 2020-06), p. 1972-1989
    Abstract: It is generally accepted that the spatial distribution of neutral genetic diversity within a species’ native range mostly depends on effective population size, demographic history, and geographic position. However, it is unclear how genetic diversity at adaptive loci correlates with geographic peripherality or with habitat suitability within the ecological niche. Using exome‐wide genomic data and distribution maps of the Alpine range, we first tested whether geographic peripherality correlates with four measures of population genetic diversity at 〉  17,000 SNP loci in 24 Alpine populations (480 individuals) of Swiss stone pine ( Pinus cembra ) from Switzerland. To distinguish between neutral and adaptive SNP sets, we used four approaches (two gene diversity estimates, F ST outlier test, and environmental association analysis) that search for signatures of selection. Second, we established ecological niche models for P. cembra in the study range and investigated how habitat suitability correlates with genetic diversity at neutral and adaptive loci. All estimates of neutral genetic diversity decreased with geographic peripherality, but were uncorrelated with habitat suitability. However, heterozygosity ( H e ) at adaptive loci based on Tajima's D declined significantly with increasingly suitable conditions. No other diversity estimates at adaptive loci were correlated with habitat suitability. Our findings suggest that populations at the edge of a species' geographic distribution harbour limited neutral genetic diversity due to demographic properties. Moreover, we argue that populations from suitable habitats went through strong selection processes, are thus well adapted to local conditions, and therefore exhibit reduced genetic diversity at adaptive loci compared to populations at niche margins.
    Type of Medium: Online Resource
    ISSN: 0962-1083 , 1365-294X
    URL: Issue
    URL: Article
    DOI: 10.1111/mec.v29.11
    DOI: 10.1111/mec.15467
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 2020749-9
    detail.hit.zdb_id: 1126687-9
    SSG: 12
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  • 2
    Online Resource
    Online Resource
    A range‐wide postglacial history of Swiss stone pine based on molecular markers and palaeoecological evidence
    Wiley ; 2023
    In:  Journal of Biogeography Vol. 50, No. 6 ( 2023-06), p. 1049-1062
    Details
    In: Journal of Biogeography, Wiley, Vol. 50, No. 6 ( 2023-06), p. 1049-1062
    Abstract: Knowing a species' response to historical climate shifts helps understanding its perspectives under global warming. We infer the hitherto unresolved postglacial history of Pinus cembra. Using independent evidence from genetic structure and demographic inference of extant populations, and from palaeoecological findings, we derive putative refugia and re‐colonisation routes. Location European Alps and Carpathians. Taxa Pinus cembra. Methods We genotyped nuclear and chloroplast microsatellite markers in nearly 3000 individuals from 147 locations across the entire natural range of P. cembra . Spatial genetic structure (Bayesian modelling) and demographic history (approximate Bayesian computation) were combined with palaeobotanical records (pollen, macrofossils) to infer putative refugial areas during the Last Glacial Maximum (LGM) and re‐colonisation of the current range. Results We found distinct spatial genetic structure, despite low genetic differentiation even between the two disjunct mountain ranges. Nuclear markers revealed five genetic clusters aligned East–West across the range, while chloroplast haplotype distribution suggested nine clusters. Spatially congruent separation at both marker types highlighted two main genetic lineages in the East and West of the range. Demographic inference supported early separation of these lineages dating back to a previous interstadial or interglacial c. 210,000 years ago. Differentiation into five biologically meaningful genetic clusters likely established during postglacial re‐colonisation. Main Conclusions Combining genetic and palaeoecological evidence suggests that P. cembra primarily survived the LGM in ‘cold period’ refugia south of the Central European Alps and near the Carpathians, from where it expanded during the Late Glacial into its current Holocene ‘warm period’ refugia. This colonisation history has led to the distinct East–West structure of five genetic clusters. The two main genetic lineages likely derived from ancient divergence during an interglacial or interstadial. The respective contact zone (Brenner line) matches a main biogeographical break in the European Alps also found in herbaceous alpine plant species.
    Type of Medium: Online Resource
    ISSN: 0305-0270 , 1365-2699
    URL: Issue
    URL: Article
    DOI: 10.1111/jbi.v50.6
    DOI: 10.1111/jbi.14586
    Language: English
    Publisher: Wiley
    Publication Date: 2023
    detail.hit.zdb_id: 2020428-0
    detail.hit.zdb_id: 188963-1
    SSG: 12
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  • 3
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    Online Resource
    Using transcriptome sequencing and pooled exome capture to study local adaptation in the giga‐genome of Pinus cembra
    Wiley ; 2019
    In:  Molecular Ecology Resources Vol. 19, No. 2 ( 2019-03), p. 536-551
    Details
    In: Molecular Ecology Resources, Wiley, Vol. 19, No. 2 ( 2019-03), p. 536-551
    Abstract: Despite decreasing sequencing costs, whole‐genome sequencing for population‐based genome scans for selection is still prohibitively expensive for organisms with large genomes. Moreover, the repetitive nature of large genomes often represents a challenge in bioinformatic and downstream analyses. Here, we use in‐depth transcriptome sequencing to design probes for exome capture in Swiss stone pine ( Pinus cembra ), a conifer with an estimated genome size of 29.3 Gbp and no reference genome available. We successfully applied around 55,000 self‐designed probes, targeting 25,000 contigs, to DNA pools of seven populations from the Swiss Alps and identified 〉 160,000 SNPs in around 15,000 contigs. The probes performed equally well in pools of the closely related species Pinus sibirica ; in both species, more than 70% of the targeted contigs were sequenced at a depth ≥40× (number of haplotypes in the pool). However, a thorough analysis of individually sequenced P. cembra samples indicated that a majority of the contigs (63%) represented multi‐copy genes. We therefore removed paralogous contigs based on heterozygote excess and deviation from allele balance. Without putatively paralogous contigs, allele frequencies of population pools represented accurate estimates of individually determined allele frequencies. We show that inferences of neutral and adaptive genetic variation may be biased when not accounting for such multi‐copy genes. Without individual genotype data, it would have been nearly impossible to recognize and deal with the problem of multi‐copy contigs. We advocate to put more emphasis on identifying paralogous loci, which will be facilitated by the establishment of additional high‐quality reference genomes.
    Type of Medium: Online Resource
    ISSN: 1755-098X , 1755-0998
    URL: Issue
    URL: Article
    DOI: 10.1111/men.2019.19.issue-2
    DOI: 10.1111/1755-0998.12986
    Language: English
    Publisher: Wiley
    Publication Date: 2019
    detail.hit.zdb_id: 2406833-0
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    Genomic vulnerability to rapid climate warming in a tree species with a long generation time
    Wiley ; 2021
    In:  Global Change Biology Vol. 27, No. 6 ( 2021-03), p. 1181-1195
    Details
    In: Global Change Biology, Wiley, Vol. 27, No. 6 ( 2021-03), p. 1181-1195
    Abstract: The ongoing increase in global temperature affects biodiversity, especially in mountain regions where climate change is exacerbated. As sessile, long‐lived organisms, trees are especially challenged in terms of adapting to rapid climate change. Here, we show that low rates of allele frequency shifts in Swiss stone pine ( Pinus cembra ) occurring near the treeline result in high genomic vulnerability to future climate warming, presumably due to the species’ long generation time. Using exome sequencing data from adult and juvenile cohorts in the Swiss Alps, we found an average rate of allele frequency shift of 1.23 × 10 −2 /generation (i.e. 40 years) at presumably neutral loci, with similar rates for putatively adaptive loci associated with temperature (0.96 × 10 −2 /generation) and precipitation (0.91 × 10 −2 /generation). These recent shifts were corroborated by forward‐in‐time simulations at neutral and adaptive loci. Additionally, in juvenile trees at the colonisation front we detected alleles putatively beneficial under a future warmer and drier climate. Notably, the observed past rate of allele frequency shift in temperature‐associated loci was decidedly lower than the estimated average rate of 6.29 × 10 −2 /generation needed to match a moderate future climate scenario (RCP4.5). Our findings suggest that species with long generation times may have difficulty keeping up with the rapid climate change occurring in high mountain areas and thus are prone to local extinction in their current main elevation range.
    Type of Medium: Online Resource
    ISSN: 1354-1013 , 1365-2486
    URL: Issue
    URL: Article
    DOI: 10.1111/gcb.v27.6
    DOI: 10.1111/gcb.15469
    Language: English
    Publisher: Wiley
    Publication Date: 2021
    detail.hit.zdb_id: 2020313-5
    SSG: 12
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