Magnus Popp

Rare arctic‐alpine plants of the European Alps have different immigration histories: the snow bed species Minuartia biflora and Ranunculus pygmaeus

Minuartia biflora and Ranunculus pygmaeus are circumarctic plants with a few isolated occurrences in the European Alps. We analysed amplified fragment length polymorphism (AFLP) and chloroplast DNA sequence data to unravel the history of their immigration into the Alps and to provide data on their circumpolar phylogeography. In spite of the similar ecological requirements of the two species, they exhibit strikingly different immigration histories into the Alps. In M. biflora, the Alpine populations are most probably derived from source populations located between the Alpine and Scandinavian ice sheets, in accordance with the traditional biogeographic hypothesis. In contrast, the Alpine populations of R. pygmaeus cluster with those from the Tatra Mountains and the Taymyr region in northern Siberia, indicating that the distant Taymyr area served as source for the Alpine populations. Both species showed different levels of genetic diversity in formerly glaciated areas. In contrast to the considerable AFLP diversity observed in M. biflora, R. pygmaeus was virtually nonvariable over vast areas, with a single phenotype dominating all over the Alps and another, distantly related one dominating the North Atlantic area from Greenland over Svalbard to Scandinavia. The same pattern was observed in chloroplast DNA sequence data. Thus, postglacial colonization of R. pygmaeus was accompanied by extreme founder events.

Origin and Evolution of a Circumpolar Polyploid Species Complex in Silene (Caryophyllaceae) Inferred from Low Copy Nuclear RNA Polymerase Introns, rDNA, and Chloroplast DNA

Abstract Phylogenetic analyses of two chloroplast and five putatively unlinked nuclear DNA regions were used to explore the evolutionary relationships of a circumpolar arctic polyploid species complex in Silene. Gene phylogenies inferred from introns in the low copy nuclear genes RPA2, RPB2, RPD2a, and RPD2b, and ITS1 and ITS2 from the nuclear ribosomal DNA region, indicate two consecutive polyploidization events. The first involved the diploid arctic/subarctic S. uralensis lineage as the cytoplasmic donor, as indicated by chloroplast rps16 and psbE-petL sequences, and highly unexpected from a morphological perspective, the diploid Siberian/northeast Asian S. ajanensis lineage as pollen donor. The hybridization and polyploidization resulted in the tetraploid S. involucrata lineage. A second hybridization and polyploidization with the S. ajanensis lineage as pollen donor, and the tetraploid S. involucrata lineage as cytoplasmic donor, resulted in the hexaploid lineages of S. sorensenis and S. ostenfeldii. In general, two paralogous sequences were identified from the tetraploids and three paralogues from the hexaploids in the low copy nuclear genes. Interlocus concerted evolution appears to have homogenized the ITS regions, because only the sequences corresponding to the paternal lineage were recovered in the polyploids. The power, and neccessity, of using several potentially unlinked regions is revealed by the fact that the gene phylogenies had small deviations from the general pattern explained by alloploidy. These deviations are better explained as gene duplication and/or lineage sorting events, or simply lack of information.

Nuclear vs. plastid data: complex Pleistocene history of a circumpolar key species

To fully understand the contemporary genetic structure of plants, both nuclear and plastid markers are needed. Three chloroplast DNA (cpDNA) lineages, which probably diverged before the major Pleistocene glaciations, have been identified in the circumpolar/circumboreal Vaccinium uliginosum. Here we investigate its nuclear DNA variation using nuclear ribosomal internal transcribed spacer (ITS) sequences, DNA ploidy level measurements and amplified fragment length polymorphisms (AFLPs). We also extend the cpDNA dataset. Two ITS lineages, corresponding to diploids and tetraploids, respectively, were identified. However, both main sequence types apparently occurred in most individual plants but showed ploidy‐biased homogenization and possibly reflect paralogy predating the origin of V. uliginosum. The ploidy levels were largely consistent with the cpDNA lineages, suggesting that the initial cpDNA divergence followed early polyploidizations. Five main AFLP groups were identified, consistent with recent glacial refugia in Beringia, western Siberia, the southern European mountains and areas south/east of the Scandinavian and Laurentide ice sheets. Except from the southern European mountains, there has been extensive expansion from all refugia, resulting in several contact zones. Surprisingly, the presumably older ploidy and cpDNA patterns were partly inconsistent with the main AFLP groups and more consistent with AFLP subgroups. A likely major driver causing the inconsistencies is recent nuclear gene flow via unreduced pollen from diploids to tetraploids. This may prevent cytoplasmic introgression and result in overlayed patterns formed by processes dominating at different time scales. The data also suggest more recent polyploidizations, as well as several chloroplast capture events, further complicating this scenario. This study highlights the importance of combining different marker systems to unravel intraspecific histories.

Glacial survival may matter after all: nunatak signatures in the rare European populations of two west‐arctic species

Biogeographers claimed for more than a century that arctic plants survived glaciations in ice‐free refugia within the limits of the North European ice sheets. Molecular studies have, however, provided overwhelming support for postglacial immigration into northern Europe, even from the west across the Atlantic. For the first time we can here present molecular evidence strongly favouring in situ glacial persistence of two species, the rare arctic‐alpine pioneer species Sagina caespitosa and Arenaria humifusa. Both belong to the ‘west‐arctic element’ of amphi‐Atlantic disjuncts, having their few and only European occurrences well within the limits of the last glaciation. Sequencing of non‐coding regions of chloroplast DNA revealed only limited variation. However, two very distinct and partly diverse genetic groups, one East and one West Atlantic, were detected in each species based on amplified fragment length polymorphisms (AFLPs), excluding postglacial dispersal from North America as explanation for their European occurrences. Patterns of genetic diversity and distinctiveness indicate that glacial populations existed in East Greenland and/or Svalbard (A. humifusa) and in southern Scandinavia (S. caespitosa). Despite their presumed lack of long‐distance dispersal adaptations, intermixed populations in several regions indicate postglacial contact zones. Both species are declining in Nordic countries, probably due to climate change‐induced habitat loss. Little or no current connectivity between their highly fragmented and partly distinct populations call for conservation of several populations in each geographic region.

A single Mid-Pleistocene long-distance dispersal by a bird can explain the extreme bipolar disjunction in crowberries (Empetrum)

The proposed age of the striking biogeographic disjunction between the Arctic and southernmost South America varies from more than 65 million to a few thousand years, but no estimates based on explicit models and molecular data are available. Here we address the origin of bipolarity in crowberries (Empetrum), which are heath-forming dwarf shrubs with animal-dispersed fruits. We apply a fossil-calibrated relaxed molecular clock to model sequence evolution in two nuclear low-copy and two plastid DNA regions from 41 individual plants (420 clones for the nuclear regions) representing the entire geographic distribution of crowberries. The plastid region matK and four fossil calibration points were used to infer the ages of the crowberry stem and crown groups. All analyses resolved three major crowberry clades (A–C). Clade A contained sequences from the eastern Canadian pink-fruited crowberry (E. eamesii) as sister to clades B and C, which both contained sequences from the black-fruited northern hemisphere crowberry (E. nigrum). Clade B also contained a subclade with all sequences from the red-fruited southern hemisphere crowberry, which is often referred to as a distinct species, E. rubrum. Its closest relatives were consistently identified as black-fruited plants from northwestern North America. The median time to the most recent common ancestor for northern and southern hemisphere crowberries was estimated to 0.56–0.93 Ma, and 0.26–0.59 Ma for the southern plants only. We conclude that a single dispersal by a bird from northwestern North America to southernmost South America, taking place in the Mid-Pleistocene, is sufficient to explain the disjunction in crowberries.

Origin and evolution of North American polyploid Silene (Caryophyllaceae)

Nuclear DNA sequences from introns of the low-copy nuclear gene family encoding the second largest subunit of RNA polymerases and the ribosomal internal transcribed spacer (ITS) regions, combined with the psbE-petL spacer and the rps16 intron from the chloroplast genome were used to infer origins and phylogenetic relationships of North American polyploid Silene species and their closest relatives. Although the vast majority of North American Silene species are polyploid, which contrasts to the diploid condition dominating in other parts of the world, the phylogenetic analyses rejected a single origin of the North American polyploids. One lineage consists of tetraploid Silene menziesii and its diploid allies. A second lineage, Physolychnis s.l., consists of Arctic, European, Asian, and South American taxa in addition to the majority of the North American polyploids. The hexaploid S. hookeri is derived from an allopolyploidization between these two lineages. The tetraploid S. nivea does not belong to any of these lineages, but is closely related to the European diploid S. baccifera. The poor resolution within Physolychnis s.l. may be attributed to rapid radiation, recombination among homoeologues, homoplasy, or any combination of these factors. No extant diploid donors could be identified in Physolychnis s.l.

Evolution of a RNA polymerase gene family in silene (Caryophyllaceae)-incomplete concerted evolution and topological congruence among paralogues

Four low-copy nuclear DNA intron regions from the second largest subunits of the RNA polymerase gene family (RPA2, RPB2, RPD2a, and RPD2b), the internal transcribed spacers (ITSs) from the nuclear ribosomal regions, and the rps16 intron from the chloroplast were sequenced and used in a phylogenetic analysis of 29 species from the tribe Sileneae (Caryophyllaceae). We used a low stringency nested polymerase chain reaction (PCR) approach to overcome the difficulties of constructing specific primers for amplification of the low copy nuclear DNA regions. Maximum parsimony analyses resulted in largely congruent phylogenetic trees for all regions. We tested overall model congruence in a likelihood context using the software PLATO and found that ITSs, RPA2, and RPB2 deviated from the maximum likelihood model for the combined data. The topology parameter was then isolated and topological congruence assessed by nonparametric bootstrapping. No strong topological incongruence was found. The analysis of the combined data sets resolves previously poorly known major relationships within Sileneae. Two paralogues of RPD2 were found, and several independent losses and incomplete concerted evolution were inferred. The among-site rate variation was significantly lower in the RNA polymerase introns than in the rps16 intron and ITSs, a property that is attractive in phylogenetic analyses.

Use of ancient sedimentary DNA as a novel conservation tool for high-altitude tropical biodiversity.

Conservation of biodiversity may in the future increasingly depend upon the availability of scientific information to set suitable restoration targets. In traditional paleoecology, sediment-based pollen provides a means to define preanthropogenic impact conditions, but problems in establishing the exact provenance and ecologically meaningful levels of taxonomic resolution of the evidence are limiting. We explored the extent to which the use of sedimentary ancient DNA (sedaDNA) may complement pollen data in reconstructing past alpine environments in the tropics. We constructed a record of afro-alpine plants retrieved from DNA preserved in sediment cores from 2 volcanic crater sites in the Albertine Rift, eastern Africa. The record extended well beyond the onset of substantial anthropogenic effects on tropical mountains. To ensure high-quality taxonomic inference from the sedaDNA sequences, we built an extensive DNA reference library covering the majority of the afro-alpine flora, by sequencing DNA from taxonomically verified specimens. Comparisons with pollen records from the same sediment cores showed that plant diversity recovered with sedaDNA improved vegetation reconstructions based on pollen records by revealing both additional taxa and providing increased taxonomic resolution. Furthermore, combining the 2 measures assisted in distinguishing vegetation change at different geographic scales; sedaDNA almost exclusively reflects local vegetation, whereas pollen can potentially originate from a wide area that in highlands in particular can span several ecozones. Our results suggest that sedaDNA may provide information on restoration targets and the nature and magnitude of human-induced environmental changes, including in high conservation priority, biodiversity hotspots, where understanding of preanthropogenic impact (or reference) conditions is highly limited.

The origin and number of introductions of the Hawaiian endemic Silene species (Caryophyllaceae)

The Hawaiian endemic Silene are a small group of woody or semiwoody representatives from a large, predominantly herbaceous, species-rich genus. We here investigated the origin and number of introductions of the endemic Hawaiian Silene based on phylogenetic relationships inferred from DNA sequences from both the plastid (the rps16 intron) and the nuclear (ribosomal internal transcribed sequences, ITS, and intron 23 of the RPB2 gene) genomes. Silene antirrhina, a widespread weedy American annual, is strongly supported as sister to a monophyletic group consisting of the Hawaiian Silene, indicating a single colonization event. There are no obvious morphological similarities between S. antirrhina and any of the species of Hawaiian Silene. Our results suggest an American origin for the Hawaiian endemics because that would require only a single trans-ocean dispersal. Two of the Hawaiian endemics (S. struthioloides and S. hawaiiensis) that form a subclade in the analyses have evolved woodiness after introduction to the Hawaiian Islands. Our results contribute to other recent results based on molecular phylogenetics that emphasize the American continent as a source area for the Hawaiian flora and support a striking morphological radiation and evolution of woodiness from a single introduction to the archipelago.

The evolutionary history of Afrocanarian blue tits inferred from genomewide SNPs

A common challenge in phylogenetic reconstruction is to find enough suitable genomic markers to reliably trace splitting events with short internodes. Here, we present phylogenetic analyses based on genomewide single‐nucleotide polymorphisms (SNPs) of an enigmatic avian radiation, the subspecies complex of Afrocanarian blue tits (Cyanistes teneriffae). The two sister species, the Eurasian blue tit (Cyanistes caeruleus) and the azure tit (Cyanistes cyanus), constituted the out‐group. We generated a large data set of SNPs for analysis of population structure and phylogeny. We also adapted our protocol to utilize degraded DNA from old museum skins from Libya. We found strong population structuring that largely confirmed subspecies monophyly and constructed a coalescent‐based phylogeny with full support at all major nodes. The results are consistent with a recent hypothesis that La Palma and Libya are relic populations of an ancient Afrocanarian blue tit, although a small data set for Libya could not resolve its position relative to La Palma. The birds on the eastern islands of Fuerteventura and Lanzarote are similar to those in Morocco. Together they constitute the sister group to the clade containing the other Canary Islands (except La Palma), in which El Hierro is sister to the three central islands. Hence, extant Canary Islands populations seem to originate from multiple independent colonization events. We also found population divergences in a key reproductive trait, viz. sperm length, which may constitute reproductive barriers between certain populations. We recommend a taxonomic revision of this polytypic species, where several subspecies should qualify for species rank.