Genetic relationships and ecological divergence in Salix species and populations in Taiwan

Huang, Chang-Jen; Chang, Chih-Hsiung; Huang, Bing; Chung, Jeng Der; Chen, Jui Hung; Chiang, Yu Chung; Hwang, Shih Ying

doi:10.1007/s11295-015-0862-1

Cited by 22 publications

(30 citation statements)

References 86 publications

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“…According to extant hybridization patterns, isolation of the polyploid willows appears to be strongly influenced by the strength of habitat differentiation. In extant willow species, differentiation along altitudinal gradients appear to be a strong factor preventing hybridization with other species, as discussed by Martini and Paiero (1988), Hörandl et al (2012) and, Gramlich et al (2016) for Central European species, and by Huang et al (2015) on species from Taiwan. These findings support the notion that occupation of a separate niche is important for the establishment of a newly formed polyploid willow lineage.…”

Section: Discussionmentioning

confidence: 92%

Relationships and genome evolution of polyploid Salix species revealed by RAD sequencing data

Wagner

Hörandl

2019

Preprint

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14Despite the general progress in using next generation sequencing techniques for 15 evolutionary research questions, the analysis of polyploid species is still hampered by the lack 16 of suitable analytical tools and the statistical difficulties of dealing with more than two alleles 17 per locus. Polyploidization and especially allopolyploidy leads to new combinations of traits 18 by combining genomes of two or more parental species. This enhances the adaptive potential 19 and often results in speciation. However, multiple origins of polyploids, backcrossing to the 20 parental species and post-origin evolution can strongly influence the genome composition of 21 polyploid species. Here, we used RAD sequencing, which revealed 23,393 loci and 320,010 22 high quality SNPs, to analyze the relationships and origin of seven polyploid species of the 23 diverse genus Salix by utilizing a phylogenomic and a network approach, as well as analyzing 24 the genetic structure and composition of the polyploid genome in comparison to putative 25 parental species. We adapted the SNiPloid pipeline that was originally developed to analyse 26 SNP composition of recently established allotetraploid crop lineages to RAD sequencing data 27 by using concatenated RAD loci as reference. Our results revealed a well-resolved phylogeny 28 of 35 species of Eurasian shrub willows (Salix subg. Chamaetia/Vetrix), including 28 diploid 29 and 7 polyploid species. Polyploidization in willows appears to be predominantly connected 30 to hybridization, i.e. to an allopolyploid origin of species. More ancient allopolyploidization 31 events involving hybridization of more distantly related, ancestral lineages were observed for 32 two hexaploid and one octoploid species. Our data suggested a more recent allopolyploid 33 origin for the included tetraploids within the major subclades and identified putative parental 34 taxa that appear to be plausible in the context of geographical, morphological and ecological 35 patterns. SNiPloid and HyDe analyses disentangled the different genomic signatures resulting 36 from hybrid origin, backcrossing, and secondary post-origin evolution in the polyploid 37 species. All tetraploids showed a considerable post-origin, species-specific proportion of 38 Origin of polyploid Salix species 3 SNPs. The amount of extant hybridization appears to be related to the degree of geographical 39 and ecological isolation of species. Our data demonstrate that high-quality RAD sequencing 40 data are suitable and highly informative for the analysis of the origin and relationships of 41 polyploid species. The combination of the traditional tools RAxML, STRUCTURE, 42 SplitsTree and recently developed programs like SNAPP, HyDe and SNiPloid established a 43 bioinformatic pipeline for unraveling the complexity of polyploid genomes.44

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Section: Discussionmentioning

confidence: 92%

Relationships and genome evolution of polyploid Salix species revealed by RAD sequencing data

Wagner

Hörandl

2019

Preprint

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“…Studies of other temperate and subtropical tree species have also identified a greater proportion of SNPs associated with temperature than with precipitation (Cox, Vanden Broeck, Van Calster, & Mergeay, 2011;De Kort et al, 2014;Gugger et al, 2016;Huang et al, 2015;Jaramillo-Correa et al, 2015). In addition, studies of high-altitude co-occurring species along the TMVB have found a strong and significant historical influence of temperature variables in shaping geographic distribution (Ruiz-Sanchez & Specht, 2014;Velo-Antón et al, 2013).…”

Section: Population Divergence and Eas Of Individual Locimentioning

confidence: 99%

Landscape genomics provides evidence of climate‐associated genetic variation in Mexican populations ofQuercus rugosa

Martins

Gugger

Llanderal‐Mendoza

et al. 2018

Evolutionary Applications

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Local adaptation is a critical evolutionary process that allows plants to grow better in their local compared to non‐native habitat and results in species‐wide geographic patterns of adaptive genetic variation. For forest tree species with a long generation time, this spatial genetic heterogeneity can shape the ability of trees to respond to rapid climate change. Here, we identify genomic variation that may confer local environmental adaptations and then predict the extent of adaptive mismatch under future climate as a tool for forest restoration or management of the widely distributed high‐elevation oak species Quercus rugosa in Mexico. Using genotyping by sequencing, we identified 5,354 single nucleotide polymorphisms (SNPs) genotyped from 103 individuals across 17 sites in the Trans‐Mexican Volcanic Belt, and, after controlling for neutral genetic structure, we detected 74 F ST outlier SNPs and 97 SNPs associated with climate variation. Then, we deployed a nonlinear multivariate model, Gradient Forests, to map turnover in allele frequencies along environmental gradients and predict areas most sensitive to climate change. We found that spatial patterns of genetic variation were most strongly associated with precipitation seasonality and geographic distance. We identified regions of contemporary genetic and climatic similarities and predicted regions where future populations of Q. rugosa might be at risk due to high expected rate of climate change. Our findings provide preliminary details for future management strategies of Q. rugosa in Mexico and also illustrate how a landscape genomic approach can provide a useful tool for conservation and resource management strategies.

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“…However, these two scenarios can be distinguished by an analysis of niche similarity combined with the assessment of the geographic distribution of genetic diversity. Previous analysis of divergence within widely distributed tree species with populations living in different environments has shown that climate can influence genetic and morphological variation (Riordan et al, ; Sork et al, ), what could lead to differentiation through local adaptation or simply because of variation in flowering phenology (Cavender‐Bares & Pahlich, ; Huang et al, ; Sork et al, ).…”

Section: Introductionmentioning

confidence: 99%

Regional patterns of genetic structure and environmental differentiation in willow populations (Salix humboldtiana Willd.) from Central Mexico

Hernández‐Leal

Suárez‐Atilano

González‐Rodríguez

2019

Ecology and Evolution

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Aim To infer the geological and climatic factors that have shaped the genetic diversity and structure of a willow species (Salix humboldtiana) in three basins of Central Mexico. Location Central Mexico. Methods We collected samples from 11 populations across two hydrological basins (Balsas and Lerma) and one population from another basin (Ameca) within the Mexican Central Plateau (MCP). Individuals were analyzed using sequences of two chloroplast DNA (cpDNA) regions and eight nuclear simple sequence repeats (nSSR). Population genetic diversity and structure were determined from these data. To evaluate whether genetic structure was associated with ecological niche differentiation, we determined whether there is niche equivalence, overlap, or divergence between the Balsas and Lerma basins. Also, we evaluated the relative contributions of geographic distribution and climatic variation on population genetic structuring through redundancy analysis (RDA) and partial RDA. Results Both cpDNA and nSSRs data indicated the presence of three highly differentiated genetic groups, mostly geographically congruent with the three main hydrological basins. According to nSSRs, the three genetic groups can be further subdivided into eight subgroups corresponding to different rivers within the main basins. The niche equivalency test showed that the niches of the species in the Balsas and Lerma basins are significantly nonequivalent. The RDA indicated a significant association of genetic variation among populations with climate variables (particularly those related to the precipitation regime), while controlling for geographic distribution. Main conclusions The genetic structure of S. humboldtiana is strongly associated with the historical and current geological configuration of the basins and the rivers within basins. The observed hierarchical genetic differentiation can be due to gene flow limitation resulting from physical barriers to the dispersal of S. humboldtiana, but also to some degree of isolation by environment, as suggested by the significant association between genetic variation among populations and precipitation regime.

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Genetic relationships and ecological divergence in Salix species and populations in Taiwan

Cited by 22 publications

References 86 publications

Relationships and genome evolution of polyploid Salix species revealed by RAD sequencing data

Relationships and genome evolution of polyploid Salix species revealed by RAD sequencing data

Landscape genomics provides evidence of climate‐associated genetic variation in Mexican populations ofQuercus rugosa

Regional patterns of genetic structure and environmental differentiation in willow populations (Salix humboldtiana Willd.) from Central Mexico

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