Data_Sheet_1_How to Tackle Phylogenetic Discordance in Recent and Rapidly Radiating Groups? Developing a Workflow Using Loricaria (Asteraceae) as an Example.pdf

A major challenge in phylogenetics and -genomics is to resolve young rapidly radiating groups. The fast succession of species increases the probability of incomplete lineage sorting (ILS), and different topologies of the gene trees are expected, leading to gene tree discordance, i.e., not all gene trees represent the species tree. Phylogenetic discordance is common in phylogenomic datasets, and apart from ILS, additional sources include hybridization, whole-genome duplication, and methodological artifacts. Despite a high degree of gene tree discordance, species trees are often well supported and the sources of discordance are not further addressed in phylogenomic studies, which can eventually lead to incorrect phylogenetic hypotheses, especially in rapidly radiating groups. We chose the high-Andean Asteraceae genus Loricaria to shed light on the potential sources of phylogenetic discordance and generated a phylogenetic hypothesis. By accounting for paralogy during gene tree inference, we generated a species tree based on hundreds of nuclear loci, using Hyb-Seq, and a plastome phylogeny obtained from off-target reads during target enrichment. We observed a high degree of gene tree discordance, which we found implausible at first sight, because the genus did not show evidence of hybridization in previous studies. We used various phylogenomic analyses (trees and networks) as well as the D-statistics to test for ILS and hybridization, which we developed into a workflow on how to tackle phylogenetic discordance in recent radiations. We found strong evidence for ILS and hybridization within the genus Loricaria. Low genetic differentiation was evident between species located in different Andean cordilleras, which could be indicative of substantial introgression between populations, promoted during Pleistocene glaciations, when alpine habitats shifted creating opportunities for secondary contact and hybridization.</p

(a) Regional genetic differentiation and (b) genetic differentiation according to taxonomy, based on AFLP and chloroplast DNA sequence data (<i>trn</i>L/F suprahaplotypes).

<p>Sample size (<i>n</i>), Nei's gene diversity (<i>H_E</i>), proportion of variable markers (FP), and nucleotide diversity (<i>π</i>) with standard deviation are provided. For <i>trn</i>L/F suprahaplotypes effective genetic diversity according to Gregorius (<i>V_a</i>) is additionally displayed. The following seven geographic regions were considered: (1) Balkan Peninsula (Balk), (2) Carpathians (Carp), (3) unglaciated Eastern and Southeastern Alps (UnglaESEAlps), (4) glaciated Eastern Alps (GlaEAlps), (5) glaciated Western Alps (GlaWAlps), (6) unglaciated Central Europe (UnglaCentrEur), and (7) glaciated northern Europe (GlaNEur). <i>Arabidopsis arenosa</i> var. <i>intermedia</i> is integrated within <i>A. arenosa</i> subsp. <i>arenosa</i>. <i>Arabidopsis nitida</i> was omitted from the analyses, as it was represented by one (AFLPs) and three (<i>trn</i>L/F suprahaplotypes) accession(s) only.</p

Taxonomy, ploidal level, and geographic distribution of the various taxa of the <i>Arabidopsis arenosa</i> species complex (for details refer to the text).

<p>Several taxa are awaiting taxonomic recognition (indicated with nom. prov.).</p

Principal Component Analysis of AFLP data from the <i>Arabidopsis arenosa</i> species complex.

<p>Each symbol represents an individual. A: Visualization according to geographic regions. The following seven geographic regions were considered: (1) Balkan Peninsula (Balk), (2) Carpathians (Carp), (3) unglaciated Eastern and Southeastern Alps (UnglaESEAlps), (4) glaciated Eastern Alps (GlaEAlps), (5) glaciated Western Alps (GlaWAlps), (6) unglaciated Central Europe (UnglaCentrEur), and (7) glaciated northern Europe (GlaNEur). These regions are illustrated in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042691#pone-0042691-g001" target="_blank">Figure 1</a>. B: Visualization according to taxonomy. <i>Arabidopsis arenosa</i> var. <i>intermedia</i> is marked with an asterisk. C: Visualization according to ploidal level. Data lacking ploidal level estimates are marked in grey.</p

Distribution of accessions from the <i>Arabidopsis arenosa</i> species complex investigated.

<p>Maximal glaciation and mountain glaciers of the LGM are drawn according to Ehlers and Gibbard <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042691#pone.0042691-Ehlers1" target="_blank">[32]</a>. The borders of the seven geographic regions are indicated (see also <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042691#pone.0042691.s001" target="_blank">Table S1</a>, where the affiliation of each accession to one of these regions is listed). A: Visualization according to taxonomy. Seven entities are distinguished: <i>A. arenosa</i> subsp. <i>arenosa</i>, <i>A. arenosa</i> subsp. <i>borbasii</i>, <i>A. carpatica</i>, <i>A. neglecta</i>, <i>A. nitida</i>, and <i>A. petrogena</i>, following Měsíček <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042691#pone.0042691-Msek1" target="_blank">[14]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042691#pone.0042691-Msek2" target="_blank">[18]</a> and Kolník <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042691#pone.0042691-Kolnk1" target="_blank">[19]</a>, and <i>Arabidopsis arenosa</i> var. <i>intermedia</i> from the Alps. B: Visualization according to ploidal level (diploids and tetraploids). Ploidal level estimates were only available for a subset of accessions. C: Visualization according to chloroplast DNA suprahaplotypes.</p

Chloroplast DNA <i>trn</i>L/F suprahaplotype networks of the <i>Arabidopsis arenosa</i> species complex.

<p>The sizes of the circles indicate the relative frequency of a suprahaplotype. Geographic regions, taxonomic entities, and cytotypes are indicated with the same colours as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042691#pone-0042691-g002" target="_blank">Figure 2</a>. A: Visualization according to geographic regions. B: Visualization according to taxonomy. <i>Arabidopsis arenosa</i> var. <i>intermedia</i> is marked with an asterisk. C: Visualization according to ploidal level.</p

A novel allele of ASY3 is associated with greater meiotic stability in autotetraploid Arabidopsis lyrata

In this study we performed a genotype-phenotype association analysis of meiotic stability in 10 autotetraploid Arabidopsis lyrata and A. lyrata/A. arenosa hybrid populations collected from the Wachau region and East Austrian Forealps. The aim was to determine the effect of eight meiosis genes under extreme selection upon adaptation to whole genome duplication. Individual plants were genotyped by high-throughput sequencing of the eight meiosis genes (ASY1, ASY3, PDS5b, PRD3, REC8, SMC3, ZYP1a/b) implicated in synaptonemal complex formation and phenotyped by assessing meiotic metaphase I chromosome configurations. Our results reveal that meiotic stability varied greatly (20–100%) between individual tetraploid plants and associated with segregation of a novel ASYNAPSIS3 (ASY3) allele derived from A. lyrata. The ASY3 allele that associates with meiotic stability possesses a putative in-frame tandem duplication (TD) of a serine-rich region upstream of the coiled-coil domain that appears to have arisen at sites of DNA microhomology. The frequency of multivalents observed in plants homozygous for the ASY3 TD haplotype was significantly lower than in plants heterozygous for ASY3 TD/ND (non-duplicated) haplotypes. The chiasma distribution was significantly altered in the stable plants compared to the unstable plants with a shift from proximal and interstitial to predominantly distal locations. The number of HEI10 foci at pachytene that mark class I crossovers was significantly reduced in a plant homozygous for ASY3 TD compared to a plant heterozygous for ASY3 ND/TD. Fifty-eight alleles of the 8 meiosis genes were identified from the 10 populations analysed, demonstrating dynamic population variability at these loci. Widespread chimerism between alleles originating from A. lyrata/A. arenosa and diploid/tetraploids indicates that this group of rapidly evolving genes may provide precise adaptive control over meiotic recombination in the tetraploids, the very process that gave rise to them