We present the data from the Insect Biome Atlas project (IBA), characterizing the terrestrial arthropod faunas of Sweden and Madagascar. Over 12 months, Malaise trap samples were collected weekly (biweekly or monthly in the winter, when feasible) at 203 locations within 100 sites in Sweden and weekly at 50 locations within 33 sites in Madagascar; this was complemented by soil and litter samples from each site. The field samples comprise 4,749 Malaise trap, 192 soil and 192 litter samples from Sweden and 2,566 Malaise trap and 190 litter samples from Madagascar. Samples were processed using mild lysis or homogenization, followed by DNA metabarcoding of CO1 (418 bp). The data comprise 698,378 non-chimeric sequence variants from Sweden and 687,866 from Madagascar, representing 33,989 (33,046 Arthropoda) and 77,599 (77,380 Arthropoda) operational taxonomic units, respectively. These are the most comprehensive data presented on these faunas so far, allowing unique analyses of the size, composition, spatial turnover and seasonal dynamics of the sampled communities. They also provide an invaluable baseline against which to gauge future changes.

Classification of Potentilla L. has varied considerably through time. Some authors have collapsed all of the Potentilleae tribe into a single genus, while others have divided it into more than 20 genera. All those classifications, except for the one that collapsed them all, have rendered the genus Potentilla polyphyletic. We discuss Potentilla from a phylogenetic perspective in order to achieve a reasonable classification in which Potentilla is based on a clade (monophyly). Other criteria are taken into account, namely: history, phylogenetic stability, gene flow, information content and ease of identification. All previously described genera in Potentillinae are briefly discussed and assigned to major clades. In order to do this, it was necessary to designate types for: Fraga Lapeyr., Trichothalamus Spreng., and Dactylophyllum Spenn. We discuss seven scenarios, representing the effects of classifying Potentilla at the seven major clades in Potentillinae, and conclude that the most supported and least disruptive is to classify Potentilla as the clade comprising all of Potentillinae excluding the Anserina clade.

The process of polyploidization (genome duplication) is a common mechanism in plant speciation. Autopolyploidy arises within one species, and allopolyploidy arises after hybridization. Ploidy levels in the genus Potentilla in the rose family (Rosaceae) range from 2x to 16x, but taxonomists have disagreed on which species should be included in the genus. In previous phylogenetic analyses, a few major subclades were identified and informally named Alba, Anserina, Argentea, Fragarioides, Ivesioid and Reptans, but their relationships to one another differed depending on what type of DNA (chloroplast or nuclear ribosomal) was studied. In addition, some species were found in different subclades in the trees. The fact that chloroplast or nuclear ribosomal DNA may be uniparentally inherited and that most of the species are polyploid led to an interpretation of an evolutionary history that involves hybridization and polyploidization in Potentilla. Better suited for the study of polyploids are low-copy nuclear (LCN) DNA markers, which are present in each subgenome and inherited from both the maternal and the paternal parent. LCN markers were in this thesis used for three different purposes in Potentilla: 1), to infer the relationships of the major subclades in the genus (Paper I); 2), to trace the putative hybrid origins of a number of North American polyploid species in the ‘Rivales group’ (Papers II and III); and 3), to assess the generic delimitation of Potentilla (Paper IV). 

A fully resolved and supported tree showing the major subclades in Potentilla was obtained after excluding the Fragarioides species. Two of the clades, the Ivesioid and Reptans clades, showed signs of being of autopolyploid origin. In contrast, five of the six species in the Rivales group occurring in North America were inferred to be allopolyploids with ancestral lineages in the Argentea and Ivesioid clades. Four lines of evidence (ploidy level, distribution of extant species, relationships seen in the gene trees, and a set of network analyses) indicated that precursors to three of the Rivales species have taken part in hybridizations that eventually formed a common ancestor for the high-ploidy Rivales species P. intermedia and P. norvegica. Parts of this population dispersed to Eurasia, while the rest remained in North America. Both lineages went through at least one more hybridization each and formed P. intermedia in Eurasia and P. norvegica in North America. Since many floras state that P. norvegica is of European origin, this will have implications for its assessment as native or introduced on both continents. The gene trees inferred in Papers I, II and III showed a network of gene flow between the Alba, Argentea, Fragarioides, Ivesioid and Reptans clades. Thus, the generic delimitation of Potentilla was set to include these clades, and excluding the Anserina clade. With this delimitation only six species, out of the ca 400 in the whole genus, had to be recombined to get new Potentilla names. 

The LCN markers revealed relationships that could not have been found by chloroplast or nuclear ribosomal markers. This points to the importance of continuing using LCN markers when investigating the evolutionary history of polyploids. Additional markers are, however, needed to resolve some relationships, especially the putatively diploid Fragarioides species destabilizing the backbone phylogeny, and some species in the Rivales group of which we could not find all putative ancestral lineages. The High-Throughput Sequencing technique Target Capture could potentially generate enough data to solve these problems. Software programs that analyze reticulate evolution still struggle with species of high ploidy levels, and a good deal of manual preparation of analyses and interpretation of the results are still needed. In addition, a discussion is needed concerning criteria for species delimitation of allopolyploids. If the ancestral lineages are distantly related, this could have implications at even higher taxonomical levels, such as genera and families.

Background: Most cinquefoils (Potentilla L., Rosaceae) are polyploids, ranging from tetraploid (4x) to dodecaploid (12x), diploids being a rare exception. Previous studies based on ribosomal and chloroplast data indicated that Norwegian cinquefoil (P. norvegica L.) has genetic material from two separate clades within Potentilla; the Argentea and the Ivesioid clades-A nd thus a possible history of hybridization and polyploidization (allopolyploidy). In order to trace the putative allopolyploid origin of the species, sequence data from low-copy, biparentally inherited, nuclear markers were used. Specimens covering the circumpolar distribution of P. norvegica and its two subspecies were included, along with the morphologically similar P. intermedia. Potentilla species of low ploidy level known to belong to other relevant clades were also included.

Results: Gene trees based on three low-copy nuclear markers, obtained by Bayesian Inference and Maximum Likelihood analyses, showed slightly different topologies. This is likely due to genomic reorganizations following genome duplication, but the gene trees were not in conflict with a species tree of presumably diploid taxa obtained by Multispecies Coalescent analysis. The results show that both P. norvegica and P. intermedia are allopolyploids with a shared evolutionary history involving at least four parental lineages, three from the Argentea clade and one from the Ivesioid clade.

Conclusions: This is the first time that reticulate evolution has been proven in the genus Potentilla, and shows the importance of continuing working with low-copy markers in order to properly resolve its evolutionary history. Several hybridization events between the Argentea and Ivesioid clades may have given rise to the species of Wolf's grex Rivales. To better estimate when and where these hybridizations occurred, other Argentea, Ivesioid and Rivales species should be included in future studies.

The genus Potentilla (Rosaceae) has been subjected to several phylogenetic studies, but resolving its evolutionary history has proven challenging. Previous analyses recovered six, informally named, groups: the Argentea, Ivesioid, Fragarioides, Reptans, Alba and Anserina clades, but the relationships among some of these clades differ between data sets. The Reptans clade, which includes the type species of Potentilla, has been noticed to shift position between plastid and nuclear ribosomal data sets. We studied this incongruence by analysing four low-copy nuclear markers, in addition to chloroplast and nuclear ribosomal data, with a set of Bayesian phylogenetic and Multispecies Coalescent (MSC) analyses. A selective taxon removal strategy demonstrated that the included representatives from the Fragarioides clade, P. dickinsii and P. fragarioides, were the main sources of the instability seen in the trees. The Fragarioides species showed different relationships in each gene tree, and were only supported as a monophyletic group in a single marker when the Reptans clade was excluded from the analysis. The incongruences could not be explained by allopolyploidy, but rather by homoploid hybridization, incomplete lineage sorting or taxon sampling effects. When P. dickinsii and P. fragarioides were removed from the data set, a fully resolved, supported backbone phylogeny of Potentilla was obtained in the MSC analysis. Additionally, indications of autopolyploid origins of the Reptans and Ivesioid clades were discovered in the low-copy gene trees.

Background and aims - The species of the 'Briza complex' (Pooideae, Poaceae) are distributed in South America and Eurasia. They are relatively well-studied morphologically and have a complex taxonomic history, but only a few phylogenetic studies have been conducted using molecular data. Monophyly of the complex, which is based on presence of 'brizoid' spikelets, has not been questioned and sampling strategies in previous studies have prevented assessments thereof.

Methods - We investigate phylogeny and node ages in the Briza complex and test monophyly of the group using nuclear and chloroplast data. Extensive sampling from the Briza complex and putatively related species in the subfamily Pooideae is employed.

Key results - Despite morphological similarity among species, the Briza complex is polyphyletic. Members were found in three different Glades, showing the South American species, the Eurasian species and Briza humilis to be distinct groups. The South American and the Eurasian clades originated about 11 and 13 million years ago, respectively. Briza humilis diverged from Phleum (or a related genus) about 10 million years ago, whereas its crown clade is from the Pliocene-Pleistocene border. The almost simultaneous origins of these clades in the mid-Miocene coincide with temporal estimates of major diversification in grasses and formation of grassland habitats.

Conclusions - Based on our results, we support the names Chascolytrum for the South American Glade and Briza for the Eurasian clade. For the Briza humilis clade, we propose the name Brizochloa. The parallel evolution of (seemingly) similar 'brizoid' spikelets in the Pooideae is surprising; however, studies have shown that floral morphology can alter dramatically by one-step mutations, causing evolutionarily distantly related species to have similar appearance. Our findings may hopefully inspire new morphological investigations of the species of the former Briza complex, as well as other poorly studied and potentially polyphyletic genera, such as Deschampsia and Echinopogon.