The evolution of substrate differentiation in Minuartia series Laricifoliae (Caryophyllaceae) in the European Alps: In situ origin or repeated colonization?

Relationships within Mcneillia Indicate a Complex Evolutionary History and Reveal a New Species of Minuartiella (Caryophyllaceae, Alsinoideae)

The genus Mcneillia has been recently segregated from Minuartia L. based on molecular results, also supported by morphology. However, to date, a comprehensive study on the phylogenetic relationships within this genus is lacking. In this paper, we provide a multigene phylogeny of all the species and subspecies of Mcneillia employing two nuclear and six chloroplast markers. We documented extensive gene flow between taxa, sometimes separated at specific rank. In addition, Mcneillia as currently circumscribed, is not monophyletic. In fact, Mcneillia graminifolia subsp. brachypetala, strictly endemic to Greece, truly belongs to Minuartiella, a genus otherwise limited to South-West Asia. Moreover, even after removal of this taxon, our results do not support the monophyly of the taxa included in M. graminifolia s.l., the most variable and widespread species of the genus. Further controversial subspecies of Mcneillia graminifolia, i.e., subsp. hungarica and subsp. rosanoi, are shown to deserve taxonomic recognition as separate species, whereas Mc. moraldoi is not distinct at specific rank. In addition, Mc. saxifraga subsp. tmolea is here regarded as a further distinct species. A consistent taxonomic treatment is therefore proposed with six new combinations and nomenclatural notes, providing the necessary typifications.

Tempo and drivers of plant diversification in the European mountain system

There is still limited consensus on the evolutionary history of species-rich temperate alpine floras due to a lack of comparable and high-quality phylogenetic data covering multiple plant lineages. Here we reconstructed when and how European alpine plant lineages diversified, i.e., the tempo and drivers of speciation events. We performed full-plastome phylogenomics and used multi-clade comparative models applied to six representative angiosperm lineages that have diversified in European mountains (212 sampled species, 251 ingroup species total). Diversification rates remained surprisingly steady for most clades, even during the Pleistocene, with speciation events being mostly driven by geographic divergence and bedrock shifts. Interestingly, we inferred asymmetrical historical migration rates from siliceous to calcareous bedrocks, and from higher to lower elevations, likely due to repeated shrinkage and expansion of high elevation habitats during the Pleistocene. This may have buffered climate-related extinctions, but prevented speciation along elevation gradients as often documented for tropical alpine floras.

Here, the authors use full-plastome phylogenomics and multiclade comparative models to reconstruct the tempo and drivers of six European Alpine angiosperm lineages before and during the Pleistocene. They find that geographic divergence and bedrock shifts drive speciation events, while diversification rates remained steady.

Cytogenetic, Morphometric, and Ecological Characterization of Festuca indigesta Boiss. in the Southeast of Spain

Festuca indigesta subsp. indigesta (Poaceae) is endemic to the southeast of Spain, and until recently, it was considered that its range of distribution was restricted to the siliceous core of Sierra Nevada. However, it has been recently extended in the territory to others calcareous mountains. This study investigates the cytogenetic variability throughout the geographic range of this taxon, the possible edaphic preferences of each cytotype, and the morphological variation of cytotypes. Genome sizes and ploidy levels were estimated using flow cytometry and chromosome count. Soil samples were collected to test the nature of the substrate, i.e., pH, and calcium and magnesium contents. Finally, morphological characters were measured in herbarium specimens. This study provides the first genome size data for the species. Hidden cytogenetic diversity was detected in the taxon, comprising hexaploid (2n = 6x = 42), octoploid (2n = 8x = 56) and dodecaploid (2n = 12x = 84) individuals. No relationship between substrate nature and cytotype was observed. Morphological differences were detected for the size of floral parts and stomata among cytotypes, but these were blurred if the entire morphological variation range was considered. Our results suggest that each mountain range could act as a reservoir of morphologically cryptic genetic diversity regarding this taxon.

Discovery of cryptic plant diversity on the rooftops of the Alps

High elevation temperate mountains have long been considered species poor owing to high extinction or low speciation rates during the Pleistocene. We performed a phylogenetic and population genomic investigation of an emblematic high-elevation plant clade (Androsace sect. Aretia, 31 currently recognized species), based on plant surveys conducted during alpinism expeditions. We inferred that this clade originated in the Miocene and continued diversifying through Pleistocene glaciations, and discovered three novel species of Androsace dwelling on different bedrock types on the rooftops of the Alps. This highlights that temperate high mountains have been cradles of plant diversity even during the Pleistocene, with in-situ speciation driven by the combined action of geography and geology. Our findings have an unexpected historical relevance: H.-B. de Saussure likely observed one of these species during his 1788 expedition to the Mont Blanc and we describe it here, over two hundred years after its first sighting.

Range and niche expansion through multiple interspecific hybridization: a genotyping by sequencing analysis of Cherleria (Caryophyllaceae)

BACKGROUND

Cherleria (Caryophyllaceae) is a circumboreal genus that also occurs in the high mountains of the northern hemisphere. In this study, we focus on a clade that diversified in the European High Mountains, which was identified using nuclear ribosomal (nrDNA) sequence data in a previous study. With the nrDNA data, all but one species was monophyletic, with little sequence variation within most species. Here, we use genotyping by sequencing (GBS) data to determine whether the nrDNA data showed the full picture of the evolution in the genomes of these species.

RESULTS

The overall relationships found with the GBS data were congruent with those from the nrDNA study. Most of the species were still monophyletic and many of the same subclades were recovered, including a clade of three narrow endemic species from Greece and a clade of largely calcifuge species. The GBS data provided additional resolution within the two species with the best sampling, C. langii and C. laricifolia, with structure that was congruent with geography. In addition, the GBS data showed significant hybridization between several species, including species whose ranges did not currently overlap.

CONCLUSIONS

The hybridization led us to hypothesize that lineages came in contact on the Balkan Peninsula after they diverged, even when those lineages are no longer present on the Balkan Peninsula. Hybridization may also have helped lineages expand their niches to colonize new substrates and different areas. Not only do genome-wide data provide increased phylogenetic resolution of difficult nodes, they also give evidence for a more complex evolutionary history than what can be depicted by a simple, branching phylogeny.

Occurrence of apomictic conspecifics and ecological preferences rather than colonization history govern the geographic distribution of sexual Potentilla puberula

The geographic distribution of sexual-apomictic taxa (i.e., comprising individuals usually reproducing either sexually or asexually via seeds) is traditionally thought to be driven by their ecological preferences and colonization histories. Where sexuals and apomicts get into contact with each other, competitive and reproductive interactions can interfere with these factors, an aspect which hitherto received little attention in biogeographic studies. We disentangled and quantified the relative effects of the three factors on the distribution of tetraploid sexuals in Potentilla puberula in a latitudinal transect through the Eastern European Alps, in which they are codistributed with penta-, hepta-, and octoploid apomictic conspecifics. Effects were explored by means of binomial generalized linear regression models combining a single with a multiple predictor approach. Postglacial colonization history was inferred from population genetic variation (AFLPs and cpDNA) and quantified using a cost distance metric. The study was based on 235 populations, which were purely sexual, purely apomictic, or of mixed reproductive mode. The occurrence of apomicts explained most of the variation in the distribution of sexuals (31%). Specifically, the presence of sexual tetraploids was negatively related to the presence of each of the three apomictic cytotypes. Effects of ecological preferences were substantial too (7% and 12% of the total variation explained by ecological preferences alone, or jointly with apomicts' occurrence, respectively). In contrast, colonization history had negligible effects on the occurrence of sexuals. Taken together, our results highlight the potentially high impact of reproductive interactions on the geographic distribution of sexual and apomictic conspecifics and that resultant mutual exclusion interrelates to ecological differentiation, a situation potentially promoting their local coexistence.

Peripatric speciation in an endemic Macaronesian plant after recent divergence from a widespread relative

The Macaronesian Scrophularia lowei is hypothesized to have arisen from the widespread S. arguta on the basis of several phylogenetic studies of the genus, but sampling has been limited. Although these two annual species are morphologically distinct, the origin of S. lowei is unclear because genetic studies focused on this Macaronesian species are lacking. We studied 5 S. lowei and 25 S. arguta populations to determine the relationship of both species and to infer the geographical origin of S. lowei. The timing of S. lowei divergence and differentiation was inferred by dating analysis of the ITS region. A phylogenetic analysis of two nuclear (ITS and ETS) and two chloroplast (psbJ–petA and psbA–trnH) DNA regions was performed to study the relationship between the two species, and genetic differentiation was analysed by AMOVA. Haplotype network construction and Bayesian phylogeographic analysis were conducted using chloroplast DNA regions and a spatial clustering analysis was carried out on a combined dataset of all studied regions. Our results indicate that both species constitute a well-supported clade that diverged in the Miocene and differentiated in the Late Miocene-Pleistocene. Although S. lowei constitutes a well-supported clade according to nDNA, cpDNA revealed a close relationship between S. lowei and western Canarian S. arguta, a finding supported by the spatial clustering analysis. Both species have strong population structure, with most genetic variability explained by inter-population differences. Our study therefore supports a recent peripatric speciation of S. lowei—a taxon that differs morphologically and genetically at the nDNA level from its closest relative, S. arguta, but not according to cpDNA, from the closest Macaronesian populations of that species. In addition, a recent dispersal of S. arguta to Madeira from Canary Islands or Selvagens Islands and a rapid morphological differentiation after the colonization to generate S. lowei is the most likely hypothesis to explain the origin of the last taxon.

Simultaneous speciation in the European high mountain flowering plant genus Facchinia (Minuartia s.l., Caryophyllaceae) revealed by genotyping-by-sequencing

Understanding the relative importance of different mechanisms of speciation in a given lineage requires fully resolved interspecific relationships. Using Facchinia, a genus of seven species centred in the European Alps, we explore whether the polytomy found by Sanger sequencing analyses of standard nuclear (ITS) and plastid markers (trnQ-rps16) is a hard or soft polytomy by substantially increasing the amount of DNA sequence data, generated by genotyping-by-sequencing. In comparison to 142 phylogenetically informative sites in the Sanger sequences the GBS sequences yielded 3363 phylogenetically informative sites after exclusion of apparently oversaturated SNPs. Maximum parsimony, maximum likelihood, NeighborNet, SVDquartets and Astral-II analyses all resulted in phylogenetic trees (and networks) in which interspecific relationships were largely unresolved. After excluding incomplete lineage sorting, hybridisation and oversaturation of characters as possible causes for lack of phylogenetic resolution, we conclude that the polytomy obtained most likely represents a hard polytomy. We hypothesize that diversification of Facchinia is best interpreted as the result of multiple simultaneous vicariance in response to climatic changes during the Early Quaternary.

Scrophularia arguta, a widespread annual plant in the Canary Islands: a single recent colonization event or a more complex phylogeographic pattern?

Many studies have addressed evolution and phylogeography of plant taxa in oceanic islands, but have primarily focused on endemics because of the assumption that in widespread taxa the absence of morphological differentiation between island and mainland populations is due to recent colonization. In this paper, we studied the phylogeography of Scrophularia arguta, a widespread annual species, in an attempt to determine the number and spatiotemporal origins of dispersal events to Canary Islands. Four different regions, ITS and ETS from nDNA and psbA-trnH and psbJ-petA from cpDNA, were used to date divergence events within S. arguta lineages and determine the phylogenetic relationships among populations. A haplotype network was obtained to elucidate the phylogenetic relationships among haplotypes. Our results support an ancient origin of S. arguta (Miocene) with expansion and genetic differentiation in the Pliocene coinciding with the aridification of northern Africa and the formation of the Mediterranean climate. Indeed, results indicate for Canary Islands three different events of colonization, including two ancient events that probably happened in the Pliocene and have originated the genetically most divergent populations into this species and, interestingly, a recent third event of colonization of Gran Canaria from mainland instead from the closest islands (Tenerife or Fuerteventura). In spite of the great genetic divergence among populations, it has not implied any morphological variation. Our work highlights the importance of nonendemic species to the genetic richness and conservation of island flora and the significance of the island populations of widespread taxa in the global biodiversity.