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 distinction between Sagina apetala and S. micropetala (Caryophyllaceae: Sagineae), their phylogenetic relationships, and a note on the coastal origin of some widespread ruderals

The distinction of the annual Sagina apetala and S. micropetala (= S. apetala subsp. erecta, S. filicaulis) is based mainly on the position of sepals in fruit and shape and colour of the sepals, but identification of the two species is difficult. A molecular phylogeny of material identified as S. apetala and S. micropetala as well as other species of the genus using two nuclear and two plastid markers showed that there exist two lineages that are sister to each other and can be unambiguously distinguished molecularly. Although many of the morphological characters used in the literature proved useful in distinguishing these two lineages, sepal indumentum is the most reliable character to discriminate between them in Germany. Whereas S. micropetala usually has glabrous sepals, the sepals of S. apetala usually are glandular-pubescent. The chromosome number of 2n = 12 for S. micropetala, here determined for the first time, is identical to that of S. apetala, supporting the close relationship between the two species. Sagina apetala and S. micropetala are sister to S. maritima, an annual species from European coasts, which may imply a coastal origin of the two species. A brief review of the possible origin of other European ruderals from coastal relatives is provided

Spergularia media C. Presl 1826

<i>Spergularia media</i> (L.) C. Presl (1826: 161) ≡ <i>Arenaria media</i> Linnaeus (1762: 606). <p>Lectotype (designated by Rossbach 1940: 121): Herb. Linn. No. 585.23 [LINN!, image of the lectotype available at https://linnean-online. org/6132/].</p> <p> = <i>Spergularia nobreana</i> Sampaio (1906: 23) ≡ <i>Spergularia media</i> (race) <i>nobreana</i> (Samp.) Sampaio (1908: 24), <i>syn. nov</i>.</p> <p> <b>Lectotype (designated here)</b>: Portugal, <i>Odemira, Moinho d’Além</i> ”, 31 August 1905, <i>Sampaio 4913</i> [PO72112! (Fig. 1); isolectotypes: PO72110!, PO72111!].</p> <p> <b>Etymology:</b> —The epithet <i>nobreana</i> was dedicated by Sampaio (1906) to Augusto Nobre (1865–1946), Portuguese zoologist and professor at the University of Porto.</p> <p> <b>Other specimens:</b> — PORTUGAL. <i>Portimão,</i> 1913, <i>Sampaio</i> 4912 (PO!).</p>Published as part of <i>Iamonico, Duilio & Dillenberger, Markus S., 2023, On the identity of the name Spergularia nobreana (Caryophyllaceae), pp. 254-258 in Phytotaxa 598 (3)</i> on page 256, DOI: 10.11646/phytotaxa.598.3.7, <a href="http://zenodo.org/record/7970016">http://zenodo.org/record/7970016</a&gt

A conspectus of Tephroseris (Asteraceae: Senecioneae) in Europe outside Russia and notes on the decline of the genus

Tephroseris is generally considered a difficult genus. Based on the examination of extensive herbarium material and considering the existing literature, we recognize seven species in Europe outside Russia. These are T. palustris, T. integrifolia with subsp. integrifolia, subsp. aurantiaca, subsp. capitata, subsp. maritima, subsp. serpentini and subsp. “tundricola”, T. balbisiana, T. crispa, T. helenitis, T. longifolia and T. papposa. Phylogenetic analysis of ITS and ETS sequences showed that these species fall into three lineages. These are: (1) T. palustris, clearly related to Arctic species of the genus; (2) T. integrifolia; and (3) the remaining species. Molecular dating of the T. integrifolia lineage resulted in a crown group age of 1.76 (0.85–2.87) million years. Possible reasons for taxonomic difficulties in the genus in Europe outside Russia may include its young phylogenetic age and extensive migration and genetic admixture in the Quaternary. The decline of the genus in Europe outside Russia is documented and discussed. We consider it possible that its decline is related to rising global temperatures

Phylogeny of Saxifraga section Saxifraga subsection Arachnoideae (Saxifragaceae) and the origin of low elevation shade-dwelling species

Saxifraga section Saxifraga subsection Arachnoideae is a lineage of 12 species distributed mainly in the European Alps. It is unusual in terms of ecological diversification by containing both high elevation species from exposed alpine habitats and low elevation species from shady habitats such as overhanging rocks and cave entrances. Our aims are to explore which of these habitat types is ancestral, and to identify the possible drivers of this remarkable ecological diversification. Using a Hybseq DNA‐sequencing approach and a complete species sample we reconstructed and dated the phylogeny of subsection Arachnoideae. Using Landolt indicator values, this phylogenetic tree was used for the reconstruction of the evolution of temperature, light and soil pH requirements in this lineage. Diversification of subsection Arachnoideae started in the late Pliocene and continued through the Pleistocene. Both diversification among and within clades was largely allopatric, and species from shady habitats with low light requirements are distributed in well‐known refugia. We hypothesize that low light requirements evolved when species persisting in cold‐stage refugia were forced into marginal habitats by more competitive warm‐stage vegetation. While we do not claim that such competition resulted in speciation, it very likely resulted in adaptive evolution

Colonization of the Southern Hemisphere by Sagina and Colobanthus (Caryophyllaceae)

Colobanthus (23 species) and Sagina (30–33 species) together are sister to Facchinia. Whereas Facchinia is distributed in western Eurasia, Colobanthus is almost exclusively distributed in the Southern Hemisphere, and Sagina is distributed in both hemispheres with the highest species diversity in western Eurasia. We examined: 1. Whether Sagina and Colobanthus are monophyletic sister genera, 2. Where the two genera originated and how many times dispersal between hemispheres occurred, and 3. Which colonization routes between hemispheres were taken. We reconstructed the phylogeny of Colobanthus and Sagina using nuclear ribosomal internal transcribed spacer (ITS) and two plastid spacers (cpDNA) of altogether 158 ingroup samples of 45 species, and performed molecular dating and ancestral area reconstructions. Sagina and Colobanthus were confrmed as monophyletic sister genera. Biogeographical reconstructions based on ITS and cpDNA showed that Sagina reached the Southern Hemisphere in Australasia or in Africa. For Colobanthus, patterns were less clear and less well-supported: ITS showed Australasia as the region of entry, but cpDNA implied that the Southern Hemisphere may have been entered in America. The extant distributions and the biogeographical histories of Colobanthus and Sagina show both similarities and dissimilarities. This illustrates that biogeographical histories, even of closely related and ecologically very similar lineages, can be highly idiosyncratic

Cherleria_cpDNA_Matrix

The Cherleria-wide alignment from the chloroplast trnQ-rps16 and psbD-trnT regions, used to produce the tree in Fig. 3. The names correspond to those in Voucher_Table.txt. DNA numbers follow the names

Cherleria_cpDNA_Gaps

The coded indels from the Cherleria-wide alignment from the chloroplast trnQ-rps16 and psbD-trnT regions, used to produce the tree in Fig. 3. The names correspond to those in Voucher_Table.txt. DNA numbers follow the names

Caryophyllaceae_matK-ConT_Fig_2

The consensus tree from the BEAST analysis of matK data, shown in Fig. 2 and Online Resource 2. The names correspond to those in Voucher_Table.txt. For our sequences, DNA numbers follow the names, while for sequences downloaded from GenBank, GB follows the names

Cherleria_cpDNA+Indels_ConT_Fig_3

The consensus tree from the BEAST analysis of the trnQ-rps16 and psbD-trnT data, shown in Fig. 3. The names correspond to those in Voucher_Table.txt. DNA numbers follow the names