Elvira Hoerandl - Academia.edu (original) (raw)

Papers by Elvira Hoerandl

Complex genome evolution of young polyploid complexes is poorly understood. Besides challenges ca... more Complex genome evolution of young polyploid complexes is poorly understood. Besides challenges caused by hybridization, polyploidization, and incomplete lineage sorting, bioinformatic analyses are often exacerbated by missing information on progenitors, ploidy, and reproduction modes. By using a comprehensive, self-developed bioinformatic pipeline integrating phylogenetic, structure, network, and SNP-origin analyses, we for the first time unraveled polyploid phylogenetic relationships and genome evolution within the large Eurasian Ranunculus auricomus species complex comprising more than 840 taxa. Our results rely on 97,312 genomic RAD-Seq loci, target enrichment of 576 nuclear genes (48 phased), and 71 plastid regions (Hyb-Seq; OMICS-data) derived from the 75 most widespread polyploid apomictic taxa and four di- and one tetraploid potential sexual progenitor species. Phylogenetic tree and structure analyses consistently showed 3–5 supported polyploid groups, each containing sexual ...

Genome evolution in asexual organisms is theoretically expected to be shaped by various factors: ... more Genome evolution in asexual organisms is theoretically expected to be shaped by various factors: first, hybrid origin and polyploidy confer a genomic constitution of highly heterozygous genotypes with multiple copies of genes; second, asexuality confers a lack of recombination and genetic variation in populations, which reduces the efficiency of selection to purge deleterious mutations, hence, deleterious mutations would accumulate (Muller’s ratchet) and lead to early extinction of such asexual lineages; third, allelic sequence divergence is expected to result in rapid differentiation of lineages (Meselson effect). Here we review genomic studies using next-generation sequencing (NGS) technologies on two asexual plant systems, Boechera (Brassicaceae) and Ranunculus (Ranunculaceae). In Boechera, population genetic data suggest high levels of heterozygosity resulting from multiple hybrid origins and from allelic sequence divergence over a longer evolutionary time frame. RNA-Seq in tran...

The Hengduan Mountains (HDM) in South West China are an important hotspot of plant diversity and ... more The Hengduan Mountains (HDM) in South West China are an important hotspot of plant diversity and endemism and considered to be a secondary diversification center for the woody plant genus Salix (Salicaceae). This study aimed to reconstruct the spatio-temporal evolution of the Salix Chamaetia-Vetrix clade in the HDM and to test for the occurrence of a radiation. We inferred phylogenetic relationships based on more than 34,000 RAD loci of 27 species. Phylogenetic analyses recovered a well-resolved tree topology with two major clades, the Eurasian and the HDM clade and a divergence time of c. 23.9 Ma. The HDM clade comprises two subclades. The species of the HDM clade originated in north HDM and adjacent areas and then dispersed into the south HDM, westwards to the Himalayas and eastwards to the Qinling Mountains. Niche modelling analyses revealed that during the last glacial maximum, range contractions were observed in the northern areas, while southward expansions resulted in range o...

ABSTRACTThe time frame and geographical patterns of diversification processes in European tempera... more ABSTRACTThe time frame and geographical patterns of diversification processes in European temperate-montane herbs are still not well understood. We used the sexual species of the Ranunculus auricomus complex as a model system to understand how vicariance vs. dispersal processes in the context of Pleistocene climatic fluctuations have triggered speciation in temperate-montane plant species. We employed Target Enrichment sequence data from about 600 nuclear genes and coalescent-based species tree inference methods to resolve phylogenetic relationships among the sexual taxa of the complex. We estimated absolute divergence times and, using ancestral range reconstruction, we tested if speciation was rather enhanced by vicariance or dispersal processes.Phylogenetic relationships among taxa were fully resolved. Incongruence among species trees mainly concerned the intraspecific relationships in R. notabilis s.l., R. cassubicifolius s.l., and the position of the tetraploid R. marsicus. Spec...

Species are the basic units of biodiversity and evolution. Nowadays, they are widely considered a... more Species are the basic units of biodiversity and evolution. Nowadays, they are widely considered as ancestor-descendant lineages. Their definition remains a persistent challenge for taxonomists due to lineage evolutionary role and circumscription, i.e., persistence in time and space, ecological niche or a shared phenotype of a lineage. Recognizing and delimiting species is particularly methodically challenging in fast-evolving, evolutionary young species complexes often characterized by low genetic divergence, hybrid origin, introgression and incomplete lineage sorting (ILS). Ranunculus auricomus is a large Eurasian apomictic polyploid complex that probably has arisen from the hybridization of a few sexual progenitor species. However, even delimitation and relationships of diploid sexual progenitors have been unclearly ranging from two to twelve species. Here, we present an innovative workflow combining phylogenomic methods based on 86,782 parameter-optimized RADseq loci and target e...

Plant Systematics and Evolution, 2017

The New phytologist, Jan 28, 2015

Biological invasions can be associated with shifts of the species' climatic niches but the in... more Biological invasions can be associated with shifts of the species' climatic niches but the incidence of such shifts is under debate. The reproductive system might be a key factor controlling such shifts because it influences a species' evolutionary flexibility. However, the link between reproductive systems and niche dynamics in plant invasions has been little studied so far. We compiled global occurrence data sets of 13 congeneric sexual and apomictic species pairs, and used principal components analysis (PCA) and kernel smoothers to compare changes in climatic niche optima, breadths and unfilling/expansion between native and alien ranges. Niche change metrics were compared between sexual and apomictic species. All 26 species showed changes in niche optima and/or breadth and 14 species significantly expanded their climatic niches. However, we found no effect of the reproductive system on niche dynamics. Instead, species with narrower native niches showed higher rates of nic...

Evolutionary Biology: Biodiversification from Genotype to Phenotype, 2015

Apomixis , the asexual reproduction via seed, often occurs in huge plant polyploid complexes with... more Apomixis , the asexual reproduction via seed, often occurs in huge plant polyploid complexes with large geographical distributions. However, the long-term evolutionary fate of asexuals traditionally was regarded as doomed by extinction. A seven-step evolutionary model is presented to explain the role of sex → apomixis shifts on geographical cytotype distributions, and the potential consequences of reversals apomixis → sex on plant diversity. Accordingly, apomictic polyploid genotypes act as facilitators for range expansions of asexual taxa in agamic complexes by functioning as pioneer explorers of new niches . High intragenomic (allelic) diversity and epigenetic variability may help for rapid adaptation. Therefore, they could rapidly expand the distribution areas of their progenitor sexual populations by occupying new ecological niches and geographical areas. Hence, apomixis would result in divergent patterns of geographic distribution between sexual and asexuals, a pattern described as “geographical parthenogenesis,” in which apomicts occupy extensive geographical areas and higher latitudinal zones while sexual relatives are restricted to small refugees. Later on, reversals to complete sexuality would allow for the establishment of new sexual populations in different habitats without the long-term disadvantages of asexuality. The new sexual recombinants will be genetically isolated from the original sexual populations and consequently predisposed to a divergent evolution, and potentially enabled to evolve into new sexual species. The present model stresses a previously unidentified evolutionary significance of the geographical parthenogenesis as a motor for plant diversification .

Plant Biosystems

Apomixis, the asexual reproduction via seed, has long been regarded a blind alley of evolution. T... more Apomixis, the asexual reproduction via seed, has long been regarded a blind alley of evolution. This hypothesis was based on the assumption that apomixis is an irreversible, phylogenetically derived trait that would rapidly lead to extinction of the respective lineages. However, recent updates of the taxonomic distribution of apomixis in angiosperms suggest an alternative evolutionary scenario. Apomixis is taxonomically scattered and occurs both in early and late branching lineages, with several reversals from apomixis to obligate sex along phylogeny. Genetic control of apomixis is based on altered expression patterns of the same genes that control sexual development; epigenetic changes following polyploidization and/or hybridization may trigger shifts from sexuality to apomixis. Mendelian inheritance confirms the facultative nature and possible reversibility of apomixis to sexual reproduction. Apomixis, therefore, could represent a transition period in the evolution of polyploid co...

Molecular Ecology, 2013

Asexual lineages are thought to be prone to extinction because of deleterious mutation accumulati... more Asexual lineages are thought to be prone to extinction because of deleterious mutation accumulation (Muller's ratchet). Here, we analyse genomic effects of hybridity, polyploidy and allelic divergence in apomictic plants, and identify loci under divergent selection among sexual/apomictic lineages. RNAseq was used to sequence the flower-specific transcriptomes of five genotypes of the Ranunculus auricomus complex, representing three sexual and two apomictic reproductive biotypes. The five sequence libraries were pooled and de novo assembly performed, and the resultant assembly was used as a backbone for a subsequent alignment of each separate library. High-quality single-nucleotide (SNP) and insertion-deletion (indel) polymorphisms were mined from each library. Annotated genes for which open reading frames (ORF) could be determined were analysed for signatures of divergent versus stabilizing selection. A comparison between all genotypes supports the hypothesis of Pleistocene hybrid origin of both apomictic genotypes from R. carpaticola and R. cassubicifolius, with subsequent allelic divergence of apomictic lineages (Meselson effect). Pairwise comparisons of nonsynonymous (dN) to synonymous (dS) substitution rate ratios between apomictic and sexual genotypes for 1231 genes demonstrated similar distributions for all comparisons, although 324 genes demonstrated outlier (i.e. elevated) dN/dS ratios. Gene ontology analyses of these outliers revealed significant enrichment of genes associated with reproduction including meiosis and gametogenesis, following predictions of divergent selection between sexual and apomictic reproduction, although no significant signal of genome-wide mutation accumulation could be identified. The results suggest that gene function should be considered in order to understand effects of mutation accumulation in asexual lineages.

Sex determination systems in plants can involve either female or male heterogamety (ZW or XY, res... more Sex determination systems in plants can involve either female or male heterogamety (ZW or XY, respectively). Here we used Illumina short reads, Oxford Nanopore Technologies (ONT) long reads, and Hi-C reads to assemble the first chromosome-scale genome of a female willow tree (Salix dunnii), and to predict genes using transcriptome sequences and available databases. The final genome sequence of 328 Mb in total was assembled in 29 contigs, and includes 31,501 genes. We inferred a male heterogametic sex determining factor on chromosome 7, suggesting that, unlike the female heterogamety of most species in the genus Salix, male heterogamety evolved in the subgenus Salix. The S. dunnii X-linked region occupies about 3.21 Mb of chromosome 7, and is probably in a pericentromeric region. Our data suggest that this region is enriched for transposable element insertions, and about one third of its 124 protein-coding genes were gained via duplications from other genome regions. We detect purify...

AoB PLANTS, Jan 4, 2016

Apomictic plants expand their geographical distributions more to higher elevations compared to th... more Apomictic plants expand their geographical distributions more to higher elevations compared to their sexual progenitors. It was so far unclear whether this tendency is related to mode of reproduction itself or represents a side effect of polyploidy. Apomixis is advantageous for range expansions as no mating partners and pollinators are needed (Baker's rule). Polyploidy is thought to infer fitness advantages and a higher vigor that would enable plants to adjust better to more extreme climatic conditions. However, little is known about actual performance of plants at higher elevations. We analyzed 81 populations of Ranunculus kuepferi from the whole distribution area in the European Alps to quantify apomictic versus sexual seed formation via flow cytometric seed screening. Seed set and vegetative growth were measured as fitness parameters. All parameters were correlated to geographical distribution, elevation, temperature, and precipitation. Flow cytometric seed screening revealed...

Journal of Biogeography, 2015

Critical Reviews in Plant Sciences, 2014

The reconstruction of reticulate evolutionary histories in plants is still a major methodological... more The reconstruction of reticulate evolutionary histories in plants is still a major methodological challenge. Sequences of the ITS nrDNA are a popular marker to analyze hybrid relationships, but variation of this multicopy spacer region is affected by concerted evolution, high intraindividual polymorphism, and shifts in mode of reproduction. The relevance of changes in secondary structure is still under dispute. We aim to shed light on the extent of polymorphism within and between sexual species and their putative natural as well as synthetic hybrid derivatives in the Ranunculus auricomus complex to test morphology-based hypotheses of hybrid origin and parentage of taxa. We employed direct sequencing of ITS nrDNA from 68 individuals representing three sexuals, their synthetic hybrids and one sympatric natural apomict, as well as cloning of ITS copies in four representative individuals, RNA secondary structure analysis, and landmark geometric morphometric analysis on leaves. Phylogene...

Genome evolution in asexual organisms is theoretically expected to be shaped by various factors: ... more Genome evolution in asexual organisms is theoretically expected to be shaped by various factors: first, hybrid origin and polyploidy confer a genomic constitution of highly heterozygous genotypes with multiple copies of genes; second, asexuality confers a lack of recombination and genetic variation in populations, which reduces the efficiency of selection to purge deleterious mutations, hence, deleterious mutations would accumulate (Muller's ratchet) and lead to early extinction of such asexual lineages; third, allelic sequence divergence is expected to result in rapid differentiation of lineages (Meselson effect). Here we review genomic studies using next-generation sequencing (NGS) technologies on two asexual plant systems, Boechera (Brassicaceae) and Ranunculus (Ranunculaceae). In Boechera, population genetic data suggest high levels of heterozygosity resulting from multiple hybrid origins and from allelic sequence divergence over a longer evolutionary time frame. RNA-Seq in transcripts of flowering buds in Ranunculus confirmed hybrid origin and showed allelic sequence divergence within a short time frame (ca. 70,000 years). However, dN/dS ratios did not support a genome-wide accumulation of mutations in asexuals compared to sexuals, but divergence in a limited number of genes related to development. We hypothesize that facultative sexuality reduces mutation accumulation of apomictic lineages and thus could escape its long-term deleterious effects. Both facultative sexuality and allelic divergence may facilitate acquisition of new gene functions and biological diversification. Transcriptome studies suggest global differences in gene expression between sexual and apomictic development. Finally we review constraints and potentials when studying asexual non-model organisms via NGS methods.

P. Pontarotti (ed.), Evolutionary Biology: Biodiversification from Genotype to Phenotype, 2015

Apomixis, the asexual reproduction via seed, often occurs in huge plant polyploid complexes with ... more Apomixis, the asexual reproduction via seed, often occurs in huge plant polyploid complexes with large geographical distributions. However, the long-term evolutionary fate of asexuals traditionally was regarded as doomed by extinction. A seven-step evolutionary model is presented to explain the role of sex → apomixis shifts on geographical cytotype distributions, and the potential consequences of reversals apomixis → sex on plant diversity. Accordingly, apomictic polyploid genotypes act as facilitators for range expansions of asexual taxa in agamic complexes by functioning as pioneer explorers of new niches. High intragenomic (allelic) diversity and epigenetic variability may help for rapid adaptation. Therefore, they could rapidly expand the distribution areas of their progenitor sexual populations by occupying new ecological niches and geographical areas. Hence, apomixis would result in divergent patterns of geographic distribution between sexual and asexuals, a pattern described as “geographical parthenogenesis,” in which apomicts occupy extensive geographical areas and higher latitudinal zones while sexual relatives are restricted to small refugees. Later on, reversals to complete sexuality would allow for the establishment of new sexual populations in different habitats without the long-term disadvantages of asexuality. The new sexual recombinants will be genetically isolated from the original sexual populations and consequently predisposed to a divergent evolution, and potentially enabled to evolve into new sexual species. The present model stresses a previously unidentified evolutionary significance of the geographical parthenogenesis as a motor for plant diversification.

… -An International Journal Dealing with all …, Jan 1, 2012

Complex genome evolution of young polyploid complexes is poorly understood. Besides challenges ca... more Complex genome evolution of young polyploid complexes is poorly understood. Besides challenges caused by hybridization, polyploidization, and incomplete lineage sorting, bioinformatic analyses are often exacerbated by missing information on progenitors, ploidy, and reproduction modes. By using a comprehensive, self-developed bioinformatic pipeline integrating phylogenetic, structure, network, and SNP-origin analyses, we for the first time unraveled polyploid phylogenetic relationships and genome evolution within the large Eurasian Ranunculus auricomus species complex comprising more than 840 taxa. Our results rely on 97,312 genomic RAD-Seq loci, target enrichment of 576 nuclear genes (48 phased), and 71 plastid regions (Hyb-Seq; OMICS-data) derived from the 75 most widespread polyploid apomictic taxa and four di- and one tetraploid potential sexual progenitor species. Phylogenetic tree and structure analyses consistently showed 3–5 supported polyploid groups, each containing sexual ...

Genome evolution in asexual organisms is theoretically expected to be shaped by various factors: ... more Genome evolution in asexual organisms is theoretically expected to be shaped by various factors: first, hybrid origin and polyploidy confer a genomic constitution of highly heterozygous genotypes with multiple copies of genes; second, asexuality confers a lack of recombination and genetic variation in populations, which reduces the efficiency of selection to purge deleterious mutations, hence, deleterious mutations would accumulate (Muller’s ratchet) and lead to early extinction of such asexual lineages; third, allelic sequence divergence is expected to result in rapid differentiation of lineages (Meselson effect). Here we review genomic studies using next-generation sequencing (NGS) technologies on two asexual plant systems, Boechera (Brassicaceae) and Ranunculus (Ranunculaceae). In Boechera, population genetic data suggest high levels of heterozygosity resulting from multiple hybrid origins and from allelic sequence divergence over a longer evolutionary time frame. RNA-Seq in tran...

The Hengduan Mountains (HDM) in South West China are an important hotspot of plant diversity and ... more The Hengduan Mountains (HDM) in South West China are an important hotspot of plant diversity and endemism and considered to be a secondary diversification center for the woody plant genus Salix (Salicaceae). This study aimed to reconstruct the spatio-temporal evolution of the Salix Chamaetia-Vetrix clade in the HDM and to test for the occurrence of a radiation. We inferred phylogenetic relationships based on more than 34,000 RAD loci of 27 species. Phylogenetic analyses recovered a well-resolved tree topology with two major clades, the Eurasian and the HDM clade and a divergence time of c. 23.9 Ma. The HDM clade comprises two subclades. The species of the HDM clade originated in north HDM and adjacent areas and then dispersed into the south HDM, westwards to the Himalayas and eastwards to the Qinling Mountains. Niche modelling analyses revealed that during the last glacial maximum, range contractions were observed in the northern areas, while southward expansions resulted in range o...

ABSTRACTThe time frame and geographical patterns of diversification processes in European tempera... more ABSTRACTThe time frame and geographical patterns of diversification processes in European temperate-montane herbs are still not well understood. We used the sexual species of the Ranunculus auricomus complex as a model system to understand how vicariance vs. dispersal processes in the context of Pleistocene climatic fluctuations have triggered speciation in temperate-montane plant species. We employed Target Enrichment sequence data from about 600 nuclear genes and coalescent-based species tree inference methods to resolve phylogenetic relationships among the sexual taxa of the complex. We estimated absolute divergence times and, using ancestral range reconstruction, we tested if speciation was rather enhanced by vicariance or dispersal processes.Phylogenetic relationships among taxa were fully resolved. Incongruence among species trees mainly concerned the intraspecific relationships in R. notabilis s.l., R. cassubicifolius s.l., and the position of the tetraploid R. marsicus. Spec...

Species are the basic units of biodiversity and evolution. Nowadays, they are widely considered a... more Species are the basic units of biodiversity and evolution. Nowadays, they are widely considered as ancestor-descendant lineages. Their definition remains a persistent challenge for taxonomists due to lineage evolutionary role and circumscription, i.e., persistence in time and space, ecological niche or a shared phenotype of a lineage. Recognizing and delimiting species is particularly methodically challenging in fast-evolving, evolutionary young species complexes often characterized by low genetic divergence, hybrid origin, introgression and incomplete lineage sorting (ILS). Ranunculus auricomus is a large Eurasian apomictic polyploid complex that probably has arisen from the hybridization of a few sexual progenitor species. However, even delimitation and relationships of diploid sexual progenitors have been unclearly ranging from two to twelve species. Here, we present an innovative workflow combining phylogenomic methods based on 86,782 parameter-optimized RADseq loci and target e...

Plant Systematics and Evolution, 2017

The New phytologist, Jan 28, 2015

Biological invasions can be associated with shifts of the species' climatic niches but the in... more Biological invasions can be associated with shifts of the species' climatic niches but the incidence of such shifts is under debate. The reproductive system might be a key factor controlling such shifts because it influences a species' evolutionary flexibility. However, the link between reproductive systems and niche dynamics in plant invasions has been little studied so far. We compiled global occurrence data sets of 13 congeneric sexual and apomictic species pairs, and used principal components analysis (PCA) and kernel smoothers to compare changes in climatic niche optima, breadths and unfilling/expansion between native and alien ranges. Niche change metrics were compared between sexual and apomictic species. All 26 species showed changes in niche optima and/or breadth and 14 species significantly expanded their climatic niches. However, we found no effect of the reproductive system on niche dynamics. Instead, species with narrower native niches showed higher rates of nic...

Evolutionary Biology: Biodiversification from Genotype to Phenotype, 2015

Apomixis , the asexual reproduction via seed, often occurs in huge plant polyploid complexes with... more Apomixis , the asexual reproduction via seed, often occurs in huge plant polyploid complexes with large geographical distributions. However, the long-term evolutionary fate of asexuals traditionally was regarded as doomed by extinction. A seven-step evolutionary model is presented to explain the role of sex → apomixis shifts on geographical cytotype distributions, and the potential consequences of reversals apomixis → sex on plant diversity. Accordingly, apomictic polyploid genotypes act as facilitators for range expansions of asexual taxa in agamic complexes by functioning as pioneer explorers of new niches . High intragenomic (allelic) diversity and epigenetic variability may help for rapid adaptation. Therefore, they could rapidly expand the distribution areas of their progenitor sexual populations by occupying new ecological niches and geographical areas. Hence, apomixis would result in divergent patterns of geographic distribution between sexual and asexuals, a pattern described as “geographical parthenogenesis,” in which apomicts occupy extensive geographical areas and higher latitudinal zones while sexual relatives are restricted to small refugees. Later on, reversals to complete sexuality would allow for the establishment of new sexual populations in different habitats without the long-term disadvantages of asexuality. The new sexual recombinants will be genetically isolated from the original sexual populations and consequently predisposed to a divergent evolution, and potentially enabled to evolve into new sexual species. The present model stresses a previously unidentified evolutionary significance of the geographical parthenogenesis as a motor for plant diversification .

Plant Biosystems

Apomixis, the asexual reproduction via seed, has long been regarded a blind alley of evolution. T... more Apomixis, the asexual reproduction via seed, has long been regarded a blind alley of evolution. This hypothesis was based on the assumption that apomixis is an irreversible, phylogenetically derived trait that would rapidly lead to extinction of the respective lineages. However, recent updates of the taxonomic distribution of apomixis in angiosperms suggest an alternative evolutionary scenario. Apomixis is taxonomically scattered and occurs both in early and late branching lineages, with several reversals from apomixis to obligate sex along phylogeny. Genetic control of apomixis is based on altered expression patterns of the same genes that control sexual development; epigenetic changes following polyploidization and/or hybridization may trigger shifts from sexuality to apomixis. Mendelian inheritance confirms the facultative nature and possible reversibility of apomixis to sexual reproduction. Apomixis, therefore, could represent a transition period in the evolution of polyploid co...

Molecular Ecology, 2013

Asexual lineages are thought to be prone to extinction because of deleterious mutation accumulati... more Asexual lineages are thought to be prone to extinction because of deleterious mutation accumulation (Muller's ratchet). Here, we analyse genomic effects of hybridity, polyploidy and allelic divergence in apomictic plants, and identify loci under divergent selection among sexual/apomictic lineages. RNAseq was used to sequence the flower-specific transcriptomes of five genotypes of the Ranunculus auricomus complex, representing three sexual and two apomictic reproductive biotypes. The five sequence libraries were pooled and de novo assembly performed, and the resultant assembly was used as a backbone for a subsequent alignment of each separate library. High-quality single-nucleotide (SNP) and insertion-deletion (indel) polymorphisms were mined from each library. Annotated genes for which open reading frames (ORF) could be determined were analysed for signatures of divergent versus stabilizing selection. A comparison between all genotypes supports the hypothesis of Pleistocene hybrid origin of both apomictic genotypes from R. carpaticola and R. cassubicifolius, with subsequent allelic divergence of apomictic lineages (Meselson effect). Pairwise comparisons of nonsynonymous (dN) to synonymous (dS) substitution rate ratios between apomictic and sexual genotypes for 1231 genes demonstrated similar distributions for all comparisons, although 324 genes demonstrated outlier (i.e. elevated) dN/dS ratios. Gene ontology analyses of these outliers revealed significant enrichment of genes associated with reproduction including meiosis and gametogenesis, following predictions of divergent selection between sexual and apomictic reproduction, although no significant signal of genome-wide mutation accumulation could be identified. The results suggest that gene function should be considered in order to understand effects of mutation accumulation in asexual lineages.

Sex determination systems in plants can involve either female or male heterogamety (ZW or XY, res... more Sex determination systems in plants can involve either female or male heterogamety (ZW or XY, respectively). Here we used Illumina short reads, Oxford Nanopore Technologies (ONT) long reads, and Hi-C reads to assemble the first chromosome-scale genome of a female willow tree (Salix dunnii), and to predict genes using transcriptome sequences and available databases. The final genome sequence of 328 Mb in total was assembled in 29 contigs, and includes 31,501 genes. We inferred a male heterogametic sex determining factor on chromosome 7, suggesting that, unlike the female heterogamety of most species in the genus Salix, male heterogamety evolved in the subgenus Salix. The S. dunnii X-linked region occupies about 3.21 Mb of chromosome 7, and is probably in a pericentromeric region. Our data suggest that this region is enriched for transposable element insertions, and about one third of its 124 protein-coding genes were gained via duplications from other genome regions. We detect purify...

AoB PLANTS, Jan 4, 2016

Apomictic plants expand their geographical distributions more to higher elevations compared to th... more Apomictic plants expand their geographical distributions more to higher elevations compared to their sexual progenitors. It was so far unclear whether this tendency is related to mode of reproduction itself or represents a side effect of polyploidy. Apomixis is advantageous for range expansions as no mating partners and pollinators are needed (Baker's rule). Polyploidy is thought to infer fitness advantages and a higher vigor that would enable plants to adjust better to more extreme climatic conditions. However, little is known about actual performance of plants at higher elevations. We analyzed 81 populations of Ranunculus kuepferi from the whole distribution area in the European Alps to quantify apomictic versus sexual seed formation via flow cytometric seed screening. Seed set and vegetative growth were measured as fitness parameters. All parameters were correlated to geographical distribution, elevation, temperature, and precipitation. Flow cytometric seed screening revealed...

Journal of Biogeography, 2015

Critical Reviews in Plant Sciences, 2014

The reconstruction of reticulate evolutionary histories in plants is still a major methodological... more The reconstruction of reticulate evolutionary histories in plants is still a major methodological challenge. Sequences of the ITS nrDNA are a popular marker to analyze hybrid relationships, but variation of this multicopy spacer region is affected by concerted evolution, high intraindividual polymorphism, and shifts in mode of reproduction. The relevance of changes in secondary structure is still under dispute. We aim to shed light on the extent of polymorphism within and between sexual species and their putative natural as well as synthetic hybrid derivatives in the Ranunculus auricomus complex to test morphology-based hypotheses of hybrid origin and parentage of taxa. We employed direct sequencing of ITS nrDNA from 68 individuals representing three sexuals, their synthetic hybrids and one sympatric natural apomict, as well as cloning of ITS copies in four representative individuals, RNA secondary structure analysis, and landmark geometric morphometric analysis on leaves. Phylogene...

Genome evolution in asexual organisms is theoretically expected to be shaped by various factors: ... more Genome evolution in asexual organisms is theoretically expected to be shaped by various factors: first, hybrid origin and polyploidy confer a genomic constitution of highly heterozygous genotypes with multiple copies of genes; second, asexuality confers a lack of recombination and genetic variation in populations, which reduces the efficiency of selection to purge deleterious mutations, hence, deleterious mutations would accumulate (Muller's ratchet) and lead to early extinction of such asexual lineages; third, allelic sequence divergence is expected to result in rapid differentiation of lineages (Meselson effect). Here we review genomic studies using next-generation sequencing (NGS) technologies on two asexual plant systems, Boechera (Brassicaceae) and Ranunculus (Ranunculaceae). In Boechera, population genetic data suggest high levels of heterozygosity resulting from multiple hybrid origins and from allelic sequence divergence over a longer evolutionary time frame. RNA-Seq in transcripts of flowering buds in Ranunculus confirmed hybrid origin and showed allelic sequence divergence within a short time frame (ca. 70,000 years). However, dN/dS ratios did not support a genome-wide accumulation of mutations in asexuals compared to sexuals, but divergence in a limited number of genes related to development. We hypothesize that facultative sexuality reduces mutation accumulation of apomictic lineages and thus could escape its long-term deleterious effects. Both facultative sexuality and allelic divergence may facilitate acquisition of new gene functions and biological diversification. Transcriptome studies suggest global differences in gene expression between sexual and apomictic development. Finally we review constraints and potentials when studying asexual non-model organisms via NGS methods.

P. Pontarotti (ed.), Evolutionary Biology: Biodiversification from Genotype to Phenotype, 2015

Apomixis, the asexual reproduction via seed, often occurs in huge plant polyploid complexes with ... more Apomixis, the asexual reproduction via seed, often occurs in huge plant polyploid complexes with large geographical distributions. However, the long-term evolutionary fate of asexuals traditionally was regarded as doomed by extinction. A seven-step evolutionary model is presented to explain the role of sex → apomixis shifts on geographical cytotype distributions, and the potential consequences of reversals apomixis → sex on plant diversity. Accordingly, apomictic polyploid genotypes act as facilitators for range expansions of asexual taxa in agamic complexes by functioning as pioneer explorers of new niches. High intragenomic (allelic) diversity and epigenetic variability may help for rapid adaptation. Therefore, they could rapidly expand the distribution areas of their progenitor sexual populations by occupying new ecological niches and geographical areas. Hence, apomixis would result in divergent patterns of geographic distribution between sexual and asexuals, a pattern described as “geographical parthenogenesis,” in which apomicts occupy extensive geographical areas and higher latitudinal zones while sexual relatives are restricted to small refugees. Later on, reversals to complete sexuality would allow for the establishment of new sexual populations in different habitats without the long-term disadvantages of asexuality. The new sexual recombinants will be genetically isolated from the original sexual populations and consequently predisposed to a divergent evolution, and potentially enabled to evolve into new sexual species. The present model stresses a previously unidentified evolutionary significance of the geographical parthenogenesis as a motor for plant diversification.

… -An International Journal Dealing with all …, Jan 1, 2012