Background: Among the various biochemical markers, fatty acids or lipid profiles represent a chemically relatively inert class of compounds that is easy to isolate from biological material. Fatty acid (FA) profiles are considered as chemotaxonomic markers to define groups of various taxonomic ranks in flowering plants, trees and other embryophytes. Results: The fatty acid profiles of 2076 microalgal strains from the culture collection of algae of Göttingen University (SAG) were determined in the stationary phase. Overall 76 different fatty acids and 10 other lipophilic substances were identified and quantified. The obtained FA profiles were added into a database providing information about fatty acid composition. Using this database we tested whether FA profiles are suitable as chemotaxonomic markers. FA distribution patterns were found to reflect phylogenetic relationships at the level of phyla and classes. In contrast, at lower taxonomic levels, e.g. between closely related species and even among multiple isolates of the same species, FA contents may be rather variable. Conclusion: FA distribution patterns are suitable chemotaxonomic markers to define taxa of higher rank in algae. However, due to their extensive variation at the species level it is difficult to make predictions about the FA profile in a novel isolate.

Although species are central units for biological research, recent findings in genomics are raising awareness that what we call species can be ill-founded entities due to solely morphology-based, regional species descriptions. This particularly applies to groups characterized by intricate evolutionary processes such as hybridization, polyploidy, or asexuality. Here, challenges of current integrative taxonomy (genetics/genomics + morphology + ecology, etc.) become apparent: different favored species concepts, lack of universal characters/markers, missing appropriate analytical tools for intricate evolutionary processes, and highly subjective ranking and fusion of datasets. Now, integrative taxonomy combined with artificial intelligence under a unified species concept can enable automated feature learning and data integration, and thus reduce subjectivity in species delimitation. This approach will likely accelerate revising and unraveling eukaryotic biodiversity.

Chlorella and Stichococcus are morphologically simple airborne microalgae, omnipresent in terrestrial and aquatic habitats. The minute cell size and resistance against environmental stress facilitate their long-distance dispersal. However, the actual distribution of Chlorella - and Stichococcus -like species has so far been inferred only from ambiguous morphology-based evidence. Here we contribute a phylogenetic analysis of an expanded SSU and ITS2 rDNA sequence dataset representing Chlorella - and Stichococcus -like species from terrestrial habitats of polar, temperate and tropical regions. We aim to uncover biogeographical patterns at low taxonomic levels. We found that psychrotolerant strains of Chlorella and Stichococcus are closely related with strains originating from the temperate zone. Species closely related to Chlorella vulgaris and Muriella terrestris , and recovered from extreme terrestrial environments of polar regions and hot deserts, are particularly widespread. Stichococcus strains from the temperate zone, with their closest relatives in the tropics, differ from strains with the closest relatives being from the polar regions. Our data suggest that terrestrial Chlorella and Stichococcus might be capable of intercontinental dispersal, however, their actual distributions exhibit biogeographic patterns.

Summary: Speciation via hybridization and polyploidization is a major evolutionary force in plant evolution but is still poorly understood for neopolyploid groups. Challenges are attributed to high heterozygosity, low genetic divergence, and missing information on progenitors, ploidy, and reproduction. We study the large Eurasian Ranunculus auricomus species complex and use a comprehensive workflow integrating reduced‐representation sequencing (RRS) genomic data to unravel reticulate evolution, genome diversity and composition of polyploids. We rely on 97 312 restriction site‐associated DNA sequencing (RAD‐Seq) loci, 576 targeted nuclear genes (48 phased), and 71 plastid regions derived from 78 polyploid apomictic taxa and four diploid and one tetraploid putative sexual progenitor species. We applied (phylo)genomic structure, network, and single nucleotide polymorphism (SNP)‐origin analyses. Results consistently showed only 3–5 supported and geographically structured polyploid genetic groups, each containing extant sexual and one unknown progenitor species. Combined analyses demonstrated predominantly allopolyploid origins, each involving 2–3 different diploid sexual progenitor species. Young allotetraploids were characterized by subgenome dominance and nonhybrid SNPs, suggesting substantial post‐origin but little lineage‐specific evolution. The biodiversity of neopolyploid complexes can result from multiple hybrid origins involving different progenitors and substantial post‐origin evolution (e.g. homoeologous exchanges, hybrid segregation, gene flow). Reduced‐representation sequencing genomic data including multi‐approach information is efficient to delimit shallow reticulate relationships.

The time frame and geographical patterns of diversification processes in European temperate‐montane herbs are still not well understood. We used the sexual species of the Ranunculus auricomus complex as a model system to understand how vicariance versus dispersal processes in the context of Pleistocene climatic fluctuations have triggered speciation in temperate‐montane plant species. We used target enrichment sequence data from about 600 nuclear genes and coalescent‐based species tree inference methods to resolve phylogenetic relationships among the sexual taxa of the complex. We estimated absolute divergence times and, using ancestral range reconstruction, we tested if speciation was enhanced by vicariance or by dispersal processes. Phylogenetic relationships among taxa were fully resolved with some incongruence in the position of the tetraploid R. marsicus. Speciation events took place in a very short time at the end of the Mid‐Pleistocene Transition (830–580 thousand years ago [ka]). A second wave of intraspecific geographical differentiation occurred at the end of the Riss glaciation or during the Eemian interglacial between 200 and 100 ka. Ancestral range reconstruction suggests a widespread European ancestor of the R. auricomus complex. Vicariance has triggered allopatric speciation in temperate‐montane plant species during the climatic deterioration that occurred during the last phase of the Mid‐Pleistocene Transition. Vegetation restructuring from forest into tundra could have confined these forest species into isolated glacial macro‐ and microrefugia. During subsequent warming periods, range expansions of these species could have been hampered by apomictic derivatives and by other congeneric competitors in the same habitat.

Species are the basic units of biodiversity and evolution. Nowadays, they are widely considered as ancestor‐descendant lineages. Their definition remains a persistent challenge for taxonomists due to lineage evolutionary role and circumscription, i.e., persistence in time and space, ecological niche, or a shared phenotype. Recognizing and delimiting species is particularly methodically challenging in fast‐evolving, evolutionary young species complexes often characterized by low genetic divergence, hybrid origin, introgression, and incomplete lineage sorting. Ranunculus auricomus is a large Eurasian apomictic polyploid complex that probably has arisen from the hybridization of a few sexual progenitor species. However, even delimitation of and relationships among diploid sexual progenitors are unclear, ranging from 2 to 12 species. Here, we present an innovative workflow combining phylogenomic methods based on 86,782 parameter‐optimized RADseq loci and target enrichment of 663 nuclear genes accompanied by geometric morphometrics to delimit sexual species in this evolutionary young complex (<1 Mya). For the first time, we revealed a fully resolved and well‐supported maximum likelihood tree phylogeny congruent to neighbor‐net network and STRUCTURE results based on RADseq data. In a few clades, we found evidence of discordant patterns indicated by quartet sampling, and reticulation events in the neighbor‐net network probably caused by introgression and incomplete lineage sorting. Together with coalescent‐based species delimitation approaches based on target enrichment data, we found five main genetic lineages, with an allopatric distribution in central and southern Europe. A concatenated geometric morphometric dataset including data from basal and stem leaves, as well as receptacles, revealed the same five main clusters. We accept those five morphologically differentiated, geographically isolated, genetic main lineages as species: R. cassubicifolius s.l. (incl. R. carpaticola), R. envalirensis s.l. (incl. R. cebennensis), R. flabellifolius, R. marsicus, and R. notabilis s.l. (incl. R. austroslovenicus, R. calapius, R. mediocompositus, R. peracris, and R. subcarniolicus). Our comprehensive workflow combing phylogenomic methods supported by geometric morphometrics proved to be successful in delimiting closely related sexual taxa and applying an evolutionary species concept. This workflow is also applicable to other evolutionarily young complexes.