Taming the Red Bastards: Hybridisation and species delimitation in the Rhodanthemum arundanum-group (Compositae, Anthemideae)

Obtainment and confirmation of intergeneric hybrids between marguerite (Argyranthemum frutescens (L.) Sch.Bip.) and two Rhodanthemum species (R. hosmariense (Ball) B. H. Wilcox, K. Bremer & Humphries and R. catananche (Ball) B. H. Wilcox, K. Bremer & Humphries)

Argyranthemum frutescens (L.) Sch.Bip. and Rhodanthemum gayanum (Coss. & Durieu) B. H. Wilcox, K. Bremer & Humphries are capable of hybridization. To expand flower color variation in this intergeneric hybrid group, we performed crosses using A. frutescens as the seed parent and R. hosmariense (Ball) B. H. Wilcox, K. Bremer & Humphries, R. catananche (Ball) B. H. Wilcox, K. Bremer & Humphries as the pollen parent. One plantlet was obtained from each cross between the white to pale pink-flowered A. frutescens and white-flowered R. hosmariense, and from a cross between the pink-flowered A. frutescens and cream to pale yellow-flowered R. catananche, via ovule culture. The cross with R. hosmariense produced an individual with white to pale pink ray florets, and the cross with R. catananche produced an individual with red ray florets. The flower and leaf shape of the progenies was intermediate between the parents, and other morphological traits were also characterized in the same manner. Morphological observations and a cleaved amplified polymorphic sequence marker-based determination, using the internal transcribed spacer region as a target for amplification and the restriction enzyme Afl II, revealed that both individuals are hybrids between A. frutescens and R. hosmariense, R. catananche. To the best of our knowledge, this is the first study to report that crossbreeding between A. frutescens (seed parent) and R. hosmariense, R. catananche (pollen parent) is possible. Moreover, further development of Argyranthemum breeding, especially that of a series of hybrid cultivars with different flower colors, is expected.

Geometric Morphometric Versus Genomic Patterns in a Large Polyploid Plant Species Complex

Plant species complexes represent a particularly interesting example of taxonomically complex groups (TCGs), linking hybridization, apomixis, and polyploidy with complex morphological patterns. In such TCGs, mosaic-like character combinations and conflicts of morphological data with molecular phylogenies present a major problem for species classification. Here, we used the large polyploid apomictic European Ranunculus auricomus complex to study relationships among five diploid sexual progenitor species and 75 polyploid apomictic derivate taxa, based on geometric morphometrics using 11,690 landmarked objects (basal and stem leaves, receptacles), genomic data (97,312 RAD-Seq loci, 48 phased target enrichment genes, 71 plastid regions) from 220 populations. We showed that (1) observed genomic clusters correspond to morphological groupings based on basal leaves and concatenated traits, and morphological groups were best resolved with RAD-Seq data; (2) described apomictic taxa usually overlap within trait morphospace except for those taxa at the space edges; (3) apomictic phenotypes are highly influenced by parental subgenome composition and to a lesser extent by climatic factors; and (4) allopolyploid apomictic taxa, compared to their sexual progenitor, resemble a mosaic of ecological and morphological intermediate to transgressive biotypes. The joint evaluation of phylogenomic, phenotypic, reproductive, and ecological data supports a revision of purely descriptive, subjective traditional morphological classifications.

Picks in the Fabric of a Polyploidy Complex: Integrative Species Delimitation in the Tetraploid Leucanthemum Mill. (Compositae, Anthemideae) Representatives

Based on the results of a preceding species-delimitation analysis for the diploid representatives of the genus Leucanthemum (Compositae, Anthemideae), the present study aims at the elaboration of a specific and subspecific taxonomic treatment of the tetraploid members of the genus. Following an integrative taxonomic approach, species-level decisions on eight predefined morphotaxon hypotheses were based on genetic/genealogical, morphological, ecological, and geographical differentiation patterns. ddRADseq fingerprinting and SNP-based clustering revealed genetic integrity for six of the eight morphotaxa, with no clear differentiation patterns observed between the widespread L. ircutianum subsp. ircutianum and the N Spanish (Cordillera Cantábrica) L. cantabricum and the S French L. delarbrei subsp. delabrei (northern Massif Central) and L. meridionale (western Massif Central). The inclusion of differentiation patterns in morphological (leaf dissection and shape), ecological (climatological and edaphic niches), and geographical respects (pair-wise tests of sympatry vs. allopatry) together with the application of a procedural protocol for species-rank decisions (the 'Wettstein tesseract') led to the proposal of an acknowledgement of the eight predefined morphotaxon hypotheses as six species (two of them with two subspecies). Nomenclatural consequences following from these results are drawn and lead to the following new combinations: Leucanthemum delarbrei subsp. meridionale (Legrand) Oberpr., T.Ott & Vogt, comb. nov. and Leucanthemum ruscinonense (Jeanb. & Timb.-Lagr.) Oberpr., T.Ott & Vogt, comb. et stat. nov.

The Warps and Wefts of a Polyploidy Complex: Integrative Species Delimitation of the Diploid Leucanthemum (Compositae, Anthemideae) Representatives

Species delimitation—owing to the paramount role of the species rank in evolutionary, ecological, and nature conservation studies—is an essential contribution of taxonomy to biodiversity research. In an ‘integrative taxonomy’ approach to species delimitation on the diploid level, we searched for evolutionary significant units (the warps and wefts) that gave rise to the polyploid complex of European ox-eye daisies (Leucanthemum; Compositae-Anthemideae). Species discovery and validation methods based on genetic, ecological, geographical, and morphometric datasets were applied to test the currently accepted diploid morpho-species, i.e., morphologically delimited species, in Leucanthemum. Novel approaches were taken in the analyses of RADseq data (consensus clustering), morphometrics of reconstructed leaf silhouettes from digitized herbarium specimens, and quantification of species-distribution overlaps. We show that 17 of the 20 Leucanthemum morpho-species are supported by genetic evidence. The taxonomic rank of the remaining three morpho-species was resolved by combining genealogic, ecologic, geographic, and morphologic data in the framework of von Wettstein’s morpho-geographical species concept. We herewith provide a methodological pipeline for the species delimitation in an ‘integrative taxonomy’ fashion using sources of evidence from genealogical, morphological, ecological, and geographical data in the philosophy of De Queiroz’s “Unified Species Concept”.

Long-read genotyping with SLANG (Simple Long-read loci Assembly of Nanopore data for Genotyping)

PREMISE

Most phylogenomic library preparation methods and bioinformatic analysis tools in restriction site-associated DNA sequencing (RADseq)/genotyping-by-sequencing (GBS) studies are designed for use with Illumina data. The lack of alternative bioinformatic pipelines hinders the exploration of long-read multi-locus data from other sequencing platforms. The Simple Long-read loci Assembly of Nanopore data for Genotyping (SLANG) pipeline enables locus assembly, orthology estimation, and single-nucleotide polymorphism (SNP) calling using Nanopore-sequenced multi-locus data.

METHODS AND RESULTS

Two test libraries (Leucanthemum spp., Senecio spp.; Compositae) were prepared using an amplified fragment length polymorphism (AFLP)-based method to reduce genome complexity, then Nanopore-sequenced, and analyzed with SLANG. We identified 704 and 448 orthologous loci with 12,368 and 10,048 SNPs, respectively. The constructed phylogenetic networks were identical to a GBS network produced using Leucanthemum Illumina data and were consistent with Senecio species circumscriptions based on morphology.

CONCLUSIONS

SLANG identifies orthologous loci and extracts SNPs from long-read multi-locus Nanopore data for phylogenetic inference, population genetics, or phylogeographical studies. Combined with an AFLP-based library preparation, SLANG provides an easily scalable, cost-effective, and affordable alternative to Illumina-based RADseq/GBS procedures.

How challenging RADseq data turned out to favor coalescent-based species tree inference. A case study in Aichryson (Crassulaceae)

Analysing multiple genomic regions while incorporating detection and qualification of discordance among regions has become standard for understanding phylogenetic relationships. In plants, which usually have comparatively large genomes, this is feasible by the combination of reduced-representation library (RRL) methods and high-throughput sequencing enabling the cost effective acquisition of genomic data for thousands of loci from hundreds of samples. One popular RRL method is RADseq. A major disadvantage of established RADseq approaches is the rather short fragment and sequencing range, leading to loci of little individual phylogenetic information. This issue hampers the application of coalescent-based species tree inference. The modified RADseq protocol presented here targets ca. 5,000 loci of 300-600nt length, sequenced with the latest short-read-sequencing (SRS) technology, has the potential to overcome this drawback. To illustrate the advantages of this approach we use the study group Aichryson Webb & Berthelott (Crassulaceae), a plant genus that diversified on the Canary Islands. The data analysis approach used here aims at a careful quality control of the long loci dataset. It involves an informed selection of thresholds for accurate clustering, a thorough exploration of locus properties, such as locus length, coverage and variability, to identify potential biased data and a comparative phylogenetic inference of filtered datasets, accompanied by an evaluation of resulting BS support, gene and site concordance factor values, to improve overall resolution of the resulting phylogenetic trees. The final dataset contains variable loci with an average length of 373nt and facilitates species tree estimation using a coalescent-based summary approach. Additional improvements brought by the approach are critically discussed.

The natural hybridization between species Ligularia nelumbifolia and Cremanthodium stenoglossum (Senecioneae, Asteraceae) suggests underdeveloped reproductive isolation and ambiguous intergeneric boundary

Natural hybridization is frequent in plants and is considered an important factor facilitating speciation. The natural intergeneric hybridization between Ligularia and Cremanthodium was previously confirmed using a couple of DNA markers. However, the mechanism of this intergeneric hybridization and the role of reproductive isolation in the process of hybridization remain unclear. Here we used double-digest restriction site-associated DNA sequencing (ddRAD-seq) to further quantify the occurrence of hybridization, the genetic structure of the hybrid population and the role of reproductive isolation between Ligularia nelumbifolia and Cremanthodium stenoglossum. The results based on the ddRAD-seq SNP data sets indicated that hybridization between L. nelumbifolia and C. stenoglossum was restricted to F₁s, and no gene introgression was identified between these two species. STRUCTURE analysis and maximum likelihood (ML) tree results showed a slightly larger genetic contribution of L. nelumbifolia to putative hybrid F₁s. We deduced that the reproductive isolation between these two parent species is not well-developed but still strong enough to maintain the genetic integrity of the species, and that their F₁s are sterile or with low fertility. Given the poorly resolved phylogenetic relationship between Ligularia and Cremanthodium, the occurrence of natural hybridization between L. nelumbifolia and C. stenoglossum may provide new insights into the re-circumscription and re-delimitation of these two genera.

Gene flow creates a mirage of cryptic species in a Southeast Asian spotted stream frog complex

Most new cryptic species are described using conventional tree- and distance-based species delimitation methods (SDMs), which rely on phylogenetic arrangements and measures of genetic divergence. However, although numerous factors such as population structure and gene flow are known to confound phylogenetic inference and species delimitation, the influence of these processes is not frequently evaluated. Using large numbers of exons, introns, and ultraconserved elements obtained using the FrogCap sequence-capture protocol, we compared conventional SDMs with more robust genomic analyses that assess population structure and gene flow to characterize species boundaries in a Southeast Asian frog complex (Pulchrana picturata). Our results showed that gene flow and introgression can produce phylogenetic patterns and levels of divergence that resemble distinct species (up to 10% divergence in mitochondrial DNA). Hybrid populations were inferred as independent (singleton) clades that were highly divergent from adjacent populations (7%-10%) and unusually similar (<3%) to allopatric populations. Such anomalous patterns are not uncommon in Southeast Asian amphibians, which brings into question whether the high levels of cryptic diversity observed in other amphibian groups reflect distinct cryptic species-or, instead, highly admixed and structured metapopulation lineages. Our results also provide an alternative explanation to the conundrum of divergent (sometimes nonsister) sympatric lineages-a pattern that has been celebrated as indicative of true cryptic speciation. Based on these findings, we recommend that species delimitation of continuously distributed "cryptic" groups should not rely solely on conventional SDMs, but should necessarily examine population structure and gene flow to avoid taxonomic inflation.