Krzysztof Spalik

A phylogeny of Apiaceae tribe Scandiceae: evidence from nuclear ribosomal DNA internal transcribed spacer sequences.

The evolutionary relationships among members of Apiaceae (Umbelliferae) tribe Scandiceae and representatives of all major lineages of Apioideae (including putatively allied Caucalideae) identified in earlier molecular studies were inferred from nucleotide sequence variation in the internal transcribed spacer regions (ITS1 and ITS2) of nuclear ribosomal DNA. In all, 134 accessions representing 18 genera commonly treated in Scandiceae were analyzed. Phylogenies estimated using maximum parsimony and distance methods were generally similar and suggest that: (1) Scandiceae form a well-supported clade, consisting of the genera Anthriscus, Athamanta (in part), Balansaea, Chaerophyllum, Conopodium, Geocaryum, Kozlovia, Krasnovia, Myrrhis, Myrrhoides, Neoconopodium, Osmorhiza, Scandix, Sphallerocarpus, and Tinguarra; (2) Athamanta is polyphyletic, with A. della-cellae allied with Daucus and A. macedonica placed close to Pimpinella; and (3) Rhabdosciadium and Grammosciadium find affinity with the Aegopodium group of umbellifers, whereas the placement of the monotypic Molopospermum cannot be inferred because of its high sequence divergence. The genus Bubon has been restored with two new combinations, B. macedonicum subsp. albanicum and B. macedonicum subsp. arachnoideum. Scandiceae arise within paraphyletic Caucalideae, the latter comprising two major lineages whose relationships to Scandiceae are not clear. Therefore, a broad treatment of Scandiceae is proposed, with subtribes Scandicinae, Daucinae, and Torilidinae (the latter two representing the Daucus and Torilis subgroups, respectively, of recent molecular systematic investigations).

Tribes and clades within apiaceae subfamily apioideae: The contribution of molecular data

Phylogenetic analyses of chloroplast gene ( rbc L, mat K), intron ( rpl 16, rps 16, rpo C1) and nuclear ribosomal DNA internal transcribed spacer (ITS) sequences and chloroplast DNA restriction sites, with supplementary data from variation in size of the chloroplast genome inverted repeat, have been used to elucidate major clades within Apiaceae ( Umbelliferae ) subfamily Apioideae Drude. This paper summarizes the results of previously published molecular cladistic analyses and presents a provisional classification of the subfamily based on taxonomic congruence among the data sets. Ten tribes ( Aciphylleae M. F. Watson & S. R. Downie, Bupleureae Spreng., Careae Baill., Echinophoreae Benth., Heteromorpheae M. F. Watson & S. R. Downie, Oenantheae Dumort., Pleurospermeae M. F. Watson & S. R. Downie, Pyramidoptereae Boiss., Scandiceae Spreng. and Smyrnieae Spreng.) are erected or confirmed as monophyletic, with Scandiceae comprising subtribes Daucinae Dumort., Scandicinae Tausch and Torilidinae Dumort. Seven additional clades are also recognized but have yet to be treated formally, and at least 23 genera examined to date are of dubious tribal or clade placement. The utility of these different molecular markers for phylogenetic inference in Apioideae is compared based on maximum parsimony analyses of subsets of previously published molecular data sets. Of the six loci sequenced, the ITS region is seen to be evolving most rapidly and rbc L is the most conservative. Intermediate in rate of evolution are mat K and the three chloroplast introns; with rpl 16 and rps 16 evolving slightly faster than mat K or rpo C1. The analysis of restriction sites, however, provided 2–4 times more parsimony informative characters than any single DNA locus sequenced, with estimates of divergence just slightly lower than that of the ITS region. The trees obtained from separate analyses of these reduced data sets are consistent with regard to the major clades inferred and the relationships among them. Similar phylogenies are obtained by combining data or combining trees, representing the supermatrix and supertree approaches to phylogenetic analysis, respectively. The inferred relationship among the tribes and informally recognized major clades within Apioideae is presented.

PHYLOGENETIC POSITION OF KOLIELLA (CHLOROPHYTA) AS INFERRED FROM NUCLEAR AND CHLOROPLAST SMALL SUBUNIT rDNA

The phylogenetic position of Koliella, a chlorophyte characterized by Klebsormidium type cell division, was inferred from analyses of partial 18S rDNA and partial 16S rDNA. Parsimony and distance analyses of separate and combined data sets indicated that the members of Koliella belonged to Trebouxiophyceae, and high decay indices and bootstrap values supported this affinity. However, the genus appeared to be polyphyletic. Koliella spiculiformis, the nomenclatural type of the genus, was allied with Nannochloris eucaryota and the “true” chlorellas (Chlorella vulgaris, C. lobophora, C. sorokiniana, and C. kessleri). The close relatives of Koliella longiseta (≡Raphidonema longiseta) and Koliella sempervirens appeared to be Stichococcus bacillaris and some species traditionally classified in Chlorella that were characterized by the production of secondary carotenoids under nitrogen‐deficient conditions. This clade was also supported by the presence of a relatively phylogenetically stable group I intron (1506) in the 18S rRNA gene. Because of the presence of Klebsormidium type cell division, some authors regarded the members of Koliella as closely related to charophytes. Molecular analyses, however, did not confirm this affinity and suggested that a Klebsormidium type cell division is homoplastic in green plants.

Major clades within Apiaceae subfamily Apioideae as inferred by phylogenetic analysis of nrDNA ITS sequences

Downie, S.R., Spalik, K., Katz-Downie, D.S. & Reduron, J.-P.: Major clades within Apiaceae subfamily Apioideae as inferred by phylogenetic analysis of nrDNA ITS sequences. — Plant Div. Evol. 128: 111–136. 2010. — ISSN 1869-6155. The results of phylogenetic analyses of 1240 nrDNA ITS sequences of Apiaceae subfamily Apioideae, representing 292 genera and 959 species from all major clades of the subfamily except those most basally branching, were compared to a preexisting phylogenetic classification for the group based on several molecular markers and a smaller sampling of taxa. This was done to confirm previously defined tribal and generic limits and to identify additional major clades and genera whose monophyly and relationships can be tested in future studies. All species for which ITS data are available in GenBank plus newly obtained sequences for 53 additional taxa were considered for inclusion in this study and their simultaneous analysis permitted misidentifications and other problematic sequences to be revealed. Analyses of these ITS data, in conjunction with results of recently published molecular studies, identified 41 major clades in Apioideae, of which 21 have already been recognized at the tribal or subtribal rank. No major changes to the preexisting phylogenetic classification of Apioideae are proposed, other than the recognition of additional major clades and the expansion of others to accommodate increased sampling. As noted in previous studies, many genera are not monophyletic; indeed, 18 genera are highly polyphyletic, with their members occurring in 2 to 7 major clades. Each of the 1240 accessions examined can be unambiguously assigned to a particular major clade. Resolution of relationships, as well as the formal recognition of several major clades, must await supporting data, such as that from the cpDNA trnQ(UUG)–5’trnK(UUU) intergenic spacer region. An ITS-based classification of the subfamily is proposed that enables direct and precise references to specific groups and facilitates sampling and hypothesis testing in future systematic studies.

The phylogenetic position of Peucedanum sensu lato and allied genera and their placement in tribe Selineae (Apiaceae, subfamily Apioideae)

ITS sequences of members of Peucedanum and its segregates (Cervaria, Holandrea, Imperatoria, Oreoselinum, Pteroselinum, Thysselinum, Tommasinia, and Xanthoselinum), as well as representatives of other members of the previously identified ‘Angelica’ and ‘Arracacia’ clades, were analysed using distance, maximum likelihood, and maximum parsimony methods in order to establish their phylogenetic relationships. The ‘Angelica’ and ‘Arracacia’ clades comprise a strongly supported monophyletic group that is formally recognised as tribe Selineae. The genus Holandrea, expanded to include Cervaria caucasica and Peucedanum achaicum, is distantly related to the other peucedanoid genera. The remaining segregates are closely related to one another and to Peucedanum sensu stricto. The genera Seseli and Selinum are polyphyletic. Members of the genus Angelica form a single clade that also includes representatives of Selinum and Sphenosciadium. New combinations in Holandrea (H. caucasica, H. achaica) and Angelica (A. capitellata) are proposed, and Selinum pyrenaeum is recognised in Angelica (A. pyrenaea).

The evolutionary history of Sium sensu lato (Apiaceae): dispersal, vicariance, and domestication as inferred from ITS rDNA phylogeny

The biogeographic history of Sium sensu lato (s.l.) (including Sium sensu stricto [s.s.], Afrocarum, and Berula) was inferred using a nuclear rDNA ITS sequence phylogeny and dispersal-vicariance analysis. One hundred accessions were analyzed, including 86 specimens of Sium s.l., representing all taxa throughout their geographical range. The phylogenetic analyses showed that Afrocarum and the African and St. Helena species of Sium were nested within Berula forming the Berula s.l. clade. The remaining species of Sium constituted a weakly supported Sium s.s. clade. The cultivated S. sisarum is closely related to the western Asian S. sisaroideum. The divergence of Sium s.s. from Berula s.l., estimated under the assumption of a molecular clock and using a substitution rate of 0.61% per million years, took place around 10.4 million years ago. Dispersal-vicariance analysis suggested that the biogeographic pattern of this group resulted from simple vicariance and eventual migration to adjacent areas rather than from long-distance dispersal. The ancestral area of Sium s.l. was probably western Palearctic. The dispersal of Berula to North America occurred ca. 3 million years ago, possibly by island hopping. The migration of S. suave to North America took place ca 0.6 million years ago through Beringia.

Influence of the size and density of Carpinus betulus on the spatial distribution and rate of deletion of forest-floor species in thermophilous oak forest

The change in the species richness following a gradual invasion of Carpinus betulus in the patch of oak forest (Potentillo albae-Quercetum) in Białowieża was studied between years 1980 and 1994. Species richness and species deletion were compared to the spatial variation in the density and size of C. betulus individuals. The study showed that, in a microscale, (1) the rate of deletion of heliophilous species was similar to that of shade-tolerant ones and was c. 2 species per 4 m2 per 10 years, (2) species richness was negatively correlated with the density and size of C. betulus saplings recruited to the shrub layer, (3) species deletion was positively correlated with the number of saplings in the shrub layer. The results support the hypothesis that the invasion of C. betulus is a proximate cause of the decline of Potentillo albae-Quercetum, and in a microscale, it has three stages: (a) initial colonisation of the ground layer by the seedlings, (b) recruitment of juveniles to the shrub layer, deterioration of light conditions and rapid deletion of species, and (c) closure of the canopy and deletion of remaining heliophilous species and vulnerable shade-tolerant species. Nomenclature: follows Ehrendorfer (1973) and Matuszkiewicz (1981).

Circumscription of Apiaceae tribe Oenantheae

Previous molecular systematic investigations into the higher-level relationships of Apiaceae subfamily Apioideae have revealed a strongly supported clade recognised as tribe Oenantheae Dumort. These plants may have clusters of fibrous or tuberous-thickened roots, corky-thickened fruits, and other adaptations for existence in wet or aquatic habitats. In some species, the leaves may be finely dissected or linear-septate and much reduced. We have initiated collaborative studies to produce a comprehensive estimate of phylogeny of the tribe, but such investigations are thwarted because information on the composition of the tribe is lacking. Herein, tribe Oenantheae is circumscribed to include the following genera: Afrocarum, Berula, Bifora (pro parte), Cicuta, Cryptotaenia (pro parte), Cynosciadium, Daucosma, Helosciadium, Lilaeopsis, Limnosciadium, Neogoezia, Oenanthe, Oxypolis, Perideridia, Ptilimnium, Sium, and Trepocarpus. Relationships inferred from phylogenetic analyses of nuclear rDNA ITS sequences from 64 accessions representing all 17 genera reveal that four genera are not monophyletic. Bifora and Cryptotaenia have members that fall outside of the tribe; Berula and Sium each comprise two or more lineages within Oenantheae. The St Helena endemics, Sium bracteatum and S. burchellii, ally with African Berula erecta; this clade is sister to the African endemic species Sium repandum and Afrocarum imbricatum, and this entire group is allied closely with north temperate Berula erecta. Nomenclatural changes are in order, but must await further study. Representatives of eight genera native to North America comprise a monophyletic group, and results from relative rate tests suggest that this lineage is evolving much faster than any other major clade recognised within the tribe.

Phylogenetic position of the genus Ferula (Apiaceae) and its placement in tribe Scandiceae as inferred from nrDNA ITS sequence variation

Recent molecular systematic investigations suggested that Ferula, an umbellifer genus of about 170 species, is polyphyletic, with its members placed in the apioid superclade and within tribe Scandiceae. We analyzed ITS sequence variation from 134 accessions of Apiaceae, including 83 accessions (74 species) of Ferula to ascertain the phylogenetic position of the genus within the family. Phylogenetic analyses of these data using maximum parsimony, Bayesian, and neighbor-joining methods support the monophyly of Ferula upon the addition of Dorema and Leutea (as Ferula sensu lato) and its placement in tribe Scandiceae. Ferula sensu is closely allied with other major lineages of Scandiceae, corresponding to subtribes Scandicinae, Daucinae, and Torilidinae. Therefore, we recognize the Ferula clade as subtribe Ferulinae. Another addition to tribe Scandiceae is a clade composed of genera Glaucosciadium and Mozaffariania. The three accessions of Ferula misplaced in the apioid superclade represent a species of Silaum.

Molecular systematics of the trans-pacific alpine genus Oreomyrrhis (apiaceae) : Phylogenetic affinities and biogeographic implications

The alpine ecosystem is the only terrestrial biogeographic unit that is distributed globally. Studying phylogenetics of the plant species in this widespread ecosystem can provide insights into the historical biogeographic processes that have shaped the global biodiversity. The trans-Pacific disjunct alpine genus Oreomyrrhis (Apiaceae) was investigated using nrDNA ITS sequences to test the taxonomic and biogeographic hypotheses. Phylogenetic analyses using maximum parsimony, maximum likelihood, and Bayesian inference revealed that species of Oreomyrrhis form a weakly supported monophyletic clade that is nested within Chaerophyllum sect. Chaerophyllum (subtribe Scandicinae, tribe Scandiceae). The optimal solutions of dispersal-vicariance analysis indicate that the ancestor of Chaerophyllum sect. Chaerophyllum (including Oreomyrrhis) was distributed in Eurasia and subsequently dispersed to North America and southern Pacific Rim. Based on dating using ITS sequence variation, these dispersal events were most likely recent, probably during late Tertiary to Quaternary. The structure of the ITS haplotype network suggests that a rapid range expansion via long-distance dispersal had been crucial in generating the trans-Pacific disjunction of Oreomyrrhis. Furthermore, evolution toward smaller mericarp size and a transition from outcrossing to selfing during Oreomyrrhiss evolution might have increased the chances for long-distance dispersal, facilitating its range expansion and occupation on alpine environments.