Multispecies Coalescent Analyses Research Articles

DNA sequence data, multispecies coalescent and morphometrics shed new light on the systematics of Iberian islamiinae springsnails (Caenogastropoda: Hydrobiidae)

ABSTRACT Multilocus phylogenies have shown that soft-part anatomy alone is insufficient for the systematics of valvatiform- and trochiform-shelled springsnails of the subfamily Islamiinae (family Hydrobiidae) due to morphological similarities between taxa that are not closely related. However, a solid knowledge of their systematics and species boundaries is crucial to conserve this highly imperilled group. Here, we inferred molecular phylogenies based on two mitochondrial and two nuclear gene fragments from representatives of three morphological species of the Iberian genus Iberhoratia and performed multispecies coalescent and shell variation analyses (geometric morphometrics) to reevaluate their taxonomic status. The resulting phylogenetic analyses, which included homologous sequences of 15 other valvatiform-shelled hydrobiid species endemic to the Iberian Peninsula, depicted the topotypical specimens of I. aurorae and I. gatoa elisai distantly related to one another and the type species I. morenoi. Considering their high genetic divergence and morphological differences from other hydrobiid taxa, we have placed the former two species in the new genera Beatrix n. gen. and Actenidia n. gen. The multispecies coalescent delimitation method DELINEATE, a novel approach to the taxonomy of the Hydrobiidae, and shell morphometric data suggested two species within the ‘I. gatoa elisai’ clade. Based on morphological and molecular evidence, we recognized this clade as Actenidia, a new genus comprising the species A. elisai n. gen., n. comb. and A. baetica n. gen., n. sp. Our results underscore the importance of using multiple lines of evidence to delimitate species of Islamiinae and interpret their systematics. We also discuss the implications of our findings for conserving I. gatoa.

Human adaptation and diversification in the Microsporum canis complex.

The Microsporum canis complex consists of one zoophilic species, M. canis, and two anthropophilic species, M. audouinii and M. ferrugineum. These species are the most widespread zoonotic pathogens causing dermatophytosis in cats and humans worldwide. To clarify the evolutionary relationship between the three species and explore the potential host shift process, this study used phylogenetic analysis, population structure analysis, multispecies coalescent analyses, determination of MAT idiomorph distribution, sexual crosses, and macromorphology and physicochemical features to address the above questions. The complex of Microsporum canis, M. audouinii and M. ferrugineum comprises 12 genotypes. MAT1-1 was present only in M. canis, while the anthropophilic entities contained MAT1-2. The pseudocleistothecia were yielded by the mating behaviour of M. canis and M. audouinii. Growth rates and lipase, keratinolysis and urea hydrolytic capacities of zoophilic M. canis isolates were all higher than those of anthropophilic strains; DNase activity of M. ferrugineum exceeded that of M. canis. The optimum growth temperature was 28°C, but 22°C favoured the development of macroconidia. Molecular data, physicochemical properties and phenotypes suggest the adaptation of zoophilic M. canis to anthropophilic M. ferrugineum, with M. audouinii in an intermediate position.

Integrative taxonomy in a rapid speciation group associated with mating system transition: A case study in the Primula cicutariifolia complex

Accurate species delimitation is the key to biodiversity conservation and is fundamental to most branches of biology. However, species delimitation remains challenging in those evolutionary radiations associated with mating system transition from outcrossing to self-fertilization, which have frequently occurred in angiosperms and are usually accompanied by rapid speciation. Here, using the Primula cicutariifolia complex as a case, we integrated molecular, morphological and reproductive isolation evidence to test and verify whether its outcrossing (distylous) and selfing (homostylous) populations have developed into independent evolutionary lineages. Phylogenetic trees based on whole plastomes and SNPs of the nuclear genome both indicated that the distylous and homostylous populations grouped into two different clades. Multispecies coalescent, gene flow and genetic structure analyses all supported such two clades as two different genetic entities. In morphology, as expected changes in selfing syndrome, homostylous populations have significantly fewer umbel layers and smaller flower and leaf sizes compared to distylous populations, and the variation range of some floral traits, such as corolla diameter and umbel layers, show obvious discontinuity. Furthermore, hand-pollinated hybridization between the two clades produced almost no seeds, indicating that well post-pollination reproductive isolation has been established between them. Therefore, the distylous and homostylous populations in this studied complex are two independent evolutionary lineages, and thus these distylous populations should be treated as a distinct species, here named Primula qiandaoensis W. Zhang & J.W. Shao sp. nov.. Our empirical study of the P. cicutariifolia complex highlights the importance of applying multiple lines of evidence, in particular genomic data, to delimit species in pervasive evolutionary plant radiations associated with mating system transition.

Target Capture Methods Offer Insight into the Evolution of Rapidly Diverged Taxa and Resolve Allopolyploid Homeologs in the Fern Genus Polypodium s.s.

Abstract— Like many fern lineages comprising reticulate species complexes, Polypodium s.s. (Polypodiacaeae) has a history shaped by rapid diversification, hybridization, and polyploidy that poses substantial challenges for phylogenetic inference with plastid and single-locus nuclear markers. Using target capture probes for 408 nuclear loci developed by the GoFlag project and a custom bioinformatic pipeline, SORTER, we constructed multi-locus nuclear datasets for diploid temperate and Mesoamerican species of Polypodium and five allotetraploid species belonging to the well-studied Polypodium vulgare complex. SORTER employs a clustering approach to separate putatively paralogous copies of targeted loci into orthologous matrices and haplotype phasing to infer allopolyploid haplotypes across loci, resulting in datasets amenable to both concatenated maximum likelihood and multi-species coalescent phylogenetic analyses. By comparing phylogenies derived from maximum likelihood and multi-species coalescent analyses of unphased and phased datasets, as well as evaluating discordance among gene trees and species trees, we recover support for incomplete lineage sorting within Polypodium s.s., novel relationships among diploid taxa of the Polypodium vulgare complex and its Mesoamerican sister clade, and the placement of several Polypodium species within other genera. Additionally, we were able to infer well-supported phylogenies that identified the hypothesized progenitors of the allotetraploid species, indicating that SORTER is an effective and accurate tool for reconstructing homeolog haplotypes of allopolyploids in fern taxa and other non-model organisms from target capture data.

Range-wide whole-genome resequencing of the brown bear reveals drivers of intraspecies divergence

Population-genomic studies can shed new light on the effect of past demographic processes on contemporary population structure. We reassessed phylogeographical patterns of a classic model species of postglacial recolonisation, the brown bear (Ursus arctos), using a range-wide resequencing dataset of 128 nuclear genomes. In sharp contrast to the erratic geographical distribution of mtDNA and Y-chromosomal haplotypes, autosomal and X-chromosomal multi-locus datasets indicate that brown bear population structure is largely explained by recent population connectivity. Multispecies coalescent based analyses reveal cases where mtDNA haplotype sharing between distant populations, such as between Iberian and southern Scandinavian bears, likely results from incomplete lineage sorting, not from ancestral population structure (i.e., postglacial recolonisation). However, we also argue, using forward-in-time simulations, that gene flow and recombination can rapidly erase genomic evidence of former population structure (such as an ancestral population in Beringia), while this signal is retained by Y-chromosomal and mtDNA, albeit likely distorted. We further suggest that if gene flow is male-mediated, the information loss proceeds faster in autosomes than in X chromosomes. Our findings emphasise that contemporary autosomal genetic structure may reflect recent population dynamics rather than postglacial recolonisation routes, which could contribute to mtDNA and Y-chromosomal discordances.

Traditional taxonomy underestimates the number of species of Bokermannohyla (Amphibia: Anura: Hylidae) diverging in the mountains of southeastern Brazil since the Miocene

Despite the huge difference in land coverage between mountains and lowlands, most species are indeed found in mountains and foothills. The causes of this pattern have challenged biogeographers and evolutionary biologists. The Espinhaço and Mantiqueira Ranges are large mountain ranges from eastern Brazil that are global biodiversity hotspots located between the Brazilian Atlantic Forest (AF) and the Cerrado. However, Espinhaço and Mantiqueira species diversity may still be underestimated, either due taxonomic complexity or morphological cryptic species complexes. Two hylid frogs, Bokermannohyla nanuzae and Bokermannohyla feioi, are endemic, respectively, distributed in these two mountain ranges. These species were recently synonymized based on traditional taxonomy. We used data from the mitochondrial DNA (mtDNA) gene 16S and two nuclear genes to undertake phylogenetic and network, distance-based, and multispecies coalescent analyses on B. nanuzae, B. feioi, and an extensive outgroup dataset. We tested the monophyly of B. nanuzae, as well as the presence of candidate new species. Based on 16S phylogenetic analysis, We recovered B. nanuzae as paraphyletic, with B. sagarana nested within it. We recovered two main groups, with the geographic distribution generally corresponding to the Cerrado and AF boundaries. Probably due to ancestral polymorphism, both nuclear haplotype genealogies failed to distinguish B. nanuzae from the former B. feioi and/or from B. sagarana. The time-calibrated mtDNA tree revealed that B. martinsi, B. sagarana, and B. nanuzae have diverged during the Late Miocene, subsequently splitting into the remaining species/lineages during the Plio-Pleistocene. Taken together, our distance-based barcode and nuclear Bayesian analyses identified the former B. feioi, referred to as the AF group, as a distinct evolutionary lineage from B. nanuzae (Cerrado group). We provide the first insights into how different evolutionary lineages speciated in the highlands of southeastern Brazil and revalidated B. feioi for the AF group.

Phylotranscriptomics reveal the spatio-temporal distribution and morphological evolution of Macrozamia, an Australian endemic genus of Cycadales.

Cycads are regarded as an ancient lineage of living seed plants, and hold important clues to understand the early evolutionary trends of seed plants. The molecular phylogeny and spatio-temporal diversification of one of the species-rich genera of cycads, Macrozamia, have not been well reconstructed. We analysed a transcriptome dataset of 4740 single-copy nuclear genes (SCGs) of 39 Macrozamia species and two outgroup taxa. Based on concatenated (maximum parsimony, maximum likelihood) and multispecies coalescent analyses, we first establish a well-resolved phylogenetic tree of Macrozamia. To identify cyto-nuclear incongruence, the plastid protein coding genes (PCGs) from transcriptome data are extracted using the software HybPiper. Furthermore, we explore the biogeographical history of the genus and shed light on the pattern of floristic exchange between three distinct areas of Australia. Six key diagnostic characters are traced on the phylogenetic framework using two comparative methods, and infra-generic classification is investigated. The tree topologies of concatenated and multi-species coalescent analyses of SCGs are mostly congruent with a few conflicting nodes, while those from plastid PCGs show poorly supported relationships. The genus contains three major clades that correspond to their distinct distributional areas in Australia. The crown group of Macrozamia is estimated to around 11.80 Ma, with a major expansion in the last 5-6 Myr. Six morphological characters show homoplasy, and the traditional phenetic sectional division of the genus is inconsistent with this current phylogeny. This first detailed phylogenetic investigation of Macrozamia demonstrates promising prospects of SCGs in resolving phylogenetic relationships within cycads. Our study suggests that Macrozamia, once widely distributed in Australia, underwent major extinctions because of fluctuating climatic conditions such as cooling and mesic biome disappearance in the past. The current close placement of morphologically distinct species in the phylogenetic tree may be related to neotenic events that occurred in the genus.

Molecular insights on the conflicting generic boundaries in the Carduncellus‐Carthamus complex (Compositae)

AbstractThe Carthamus‐Carduncellus complex is formed by approximately 50 taxa that are widely distributed throughout the Mediterranean basin and western Asia. The generic delineation of this complex has always been controversial. Currently, there are three widely diverging taxonomical proposals, suggesting that the complex is formed by (1) a single genus, Carthamus; (2) two genera, Carduncellus and Carthamus; and (3) four genera, Carduncellus, Carthamus, Femeniasia, and Phonus. The generic classification has varied depending on the importance assigned to some morphological characters, i.e., the morphology/structure of pappus, achenes, and involucral bracts. All these generic changes have complicated the nomenclature of the complex, leading to species wandering between four different genera. To objectively assess the taxonomic delimitation of this complex, we carried out phylogenetic analyses using nuclear (external and internal transcribed spacers of rDNA) and plastid (ndhF, trnH, rpl32, trnT) data, as well as multispecies coalescent model analyses on near‐complete sampling. Phylogenetic reconstructions resolved two monophyletic groups, Carthamus s.str. and Carduncellus s.l. Within the latter, some groups could be differentiated, such as the monophyletic genus Phonus and the monospecific Femeniasia. Our multispecies coalescent analyses strongly support a classification based on four genera in the complex Carthamus‐Carduncellus. In contrast, classifications based on only one or two genera lack relevant support. However, the absence of synapomorphic morphological characters that define the Carduncellus lineage (Carduncellus, Phonus, Femeniasia), and the possible hybridization in the ancestral lineages detected by incongruences between plastid and nuclear markers make it difficult to define clear generic boundaries. We propose maintaining the hypothesis of four genera, which was the first classification supported by molecular evidence, pending a broader study (both molecular and morphological) to reach a more definitive delineation and avoid more unfounded generic changes.

Multilocus Data Analysis Reveal the Diversity of Cryptic Species in the Tillandsia ionantha (Bromeliaceae: Tillansiodeae) Complex.

Independent evolutionary lineages or species that lack phenotypic variation as an operative criterion for their delimitation are known as cryptic species. However, these have been delimited using other data sources and analysis. The aims of this study are: (1) to evaluate the divergence of the populations of the T. ionantha complex; and (2) to delimit the species using multilocus data, phylogenetic analysis and the coalescent model. Phylogenetic analyses, genetic diversity and population structure, and isolation by distance analysis were performed. A multispecies coalescent analysis to delimit the species was conducted. Phylogenetic analysis showed that T. ionantha is polyphyletic composed of eight evolutionary lineages. Haplotype distribution and genetic differentiation analysis detected strong population structure and high values of genetic differentiation among populations. The positive correlation between genetic differences with geographic distance indicate that the populations are evolving under the model of isolation by distance. The coalescent multispecies analysis performed with starBEAST supports the recognition of eight lineages as different species. Only three out of the eight species have morphological characters good enough to recognize them as different species, while five of them are cryptic species. Tillandsia scaposa and T. vanhyningii are corroborated as independent lineages, and T. ionantha var. stricta changed status to the species level.

Highly Resolved Papilionoid Legume Phylogeny Based on Plastid Phylogenomics.

Comprising 501 genera and around 14,000 species, Papilionoideae is not only the largest subfamily of Fabaceae (Leguminosae; legumes), but also one of the most extraordinarily diverse clades among angiosperms. Papilionoids are a major source of food and forage, are ecologically successful in all major biomes, and display dramatic variation in both floral architecture and plastid genome (plastome) structure. Plastid DNA-based phylogenetic analyses have greatly improved our understanding of relationships among the major groups of Papilionoideae, yet the backbone of the subfamily phylogeny remains unresolved. In this study, we sequenced and assembled 39 new plastomes that are covering key genera representing the morphological diversity in the subfamily. From 244 total taxa, we produced eight datasets for maximum likelihood (ML) analyses based on entire plastomes and/or concatenated sequences of 77 protein-coding sequences (CDS) and two datasets for multispecies coalescent (MSC) analyses based on individual gene trees. We additionally produced a combined nucleotide dataset comprising CDS plus matK gene sequences only, in which most papilionoid genera were sampled. A ML tree based on the entire plastome maximally supported all of the deep and most recent divergences of papilionoids (223 out of 236 nodes). The Swartzieae, ADA (Angylocalyceae, Dipterygeae, and Amburaneae), Cladrastis, Andira, and Exostyleae clades formed a grade to the remainder of the Papilionoideae, concordant with nine ML and two MSC trees. Phylogenetic relationships among the remaining five papilionoid lineages (Vataireoid, Dermatophyllum, Genistoid s.l., Dalbergioid s.l., and Baphieae + Non-Protein Amino Acid Accumulating or NPAAA clade) remained uncertain, because of insufficient support and/or conflicting relationships among trees. Our study fully resolved most of the deep nodes of Papilionoideae, however, some relationships require further exploration. More genome-scale data and rigorous analyses are needed to disentangle phylogenetic relationships among the five remaining lineages.

Transcriptomic data reveals nuclear-mitochondrial discordance in Gomphocerinae grasshoppers (Insecta: Orthoptera: Acrididae)

The phylogeny of many groups of Orthoptera remains poorly understood. Previous phylogenetic studies largely restricted to few mitochondrial markers found many species in the grasshopper subfamily Gomphocerinae to be para- or polyphyletic, presumably because of incomplete lineage sorting and ongoing hybridization between putatively young lineages. Resolving the phylogeny of the Chorthippus biguttulus species complex is important because many morphologically cryptic species occupy overlapping ranges across Eurasia and serve important ecological functions. We investigated whether multispecies coalescent analysis of 540 genes generated by transcriptome sequencing could resolve the phylogeny of the C. biguttulus complex and related Gomphocerinae species. Our divergence time estimates confirm that Gomphocerinae is a very young radiation, with an age estimated at 1.38 (2.35–0.77) mya for the C. biguttulus complex. Our estimated topology based on complete mitogenomes recovered some species as para- or polyphyletic. In contrast, the multispecies coalescent based on nuclear genes retrieved all species as monophyletic clusters, corroborating most taxonomic hypotheses. Our results underline the importance of using nuclear multispecies coalescent methods for studying young radiations and highlight the need of further taxonomic revision in Gomphocerinae grasshoppers.

Genome-Scale Data Reveal Deep Lineage Divergence and a Complex Demographic History in the Texas Horned Lizard (Phrynosoma cornutum) throughout the Southwestern and Central United States.

The southwestern and central United States serve as an ideal region to test alternative hypotheses regarding biotic diversification. Genomic data can now be combined with sophisticated computational models to quantify the impacts of paleoclimate change, geographic features, and habitat heterogeneity on spatial patterns of genetic diversity. In this study, we combine thousands of genotyping-by-sequencing (GBS) loci with mtDNA sequences (ND1) from the Texas horned lizard (Phrynosoma cornutum) to quantify relative support for different catalysts of diversification. Phylogenetic and clustering analyses of the GBS data indicate support for at least three primary populations. The spatial distribution of populations appears concordant with habitat type, with desert populations in AZ and NM showing the largest genetic divergence from the remaining populations. The mtDNA data also support a divergent desert population, but other relationships differ and suggest mtDNA introgression. Genotype–environment association with bioclimatic variables supports divergence along precipitation gradients more than along temperature gradients. Demographic analyses support a complex history, with introgression and gene flow playing an important role during diversification. Bayesian multispecies coalescent analyses with introgression (MSci) analyses also suggest that gene flow occurred between populations. Paleo-species distribution models support two southern refugia that geographically correspond to contemporary lineages. We find that divergence times are underestimated and population sizes are overestimated when introgression occurred and is ignored in coalescent analyses, and furthermore, inference of ancient introgression events and demographic history is sensitive to inclusion of a single recently admixed sample. Our analyses cannot refute the riverine barrier or glacial refugia hypotheses. Results also suggest that populations are continuing to diverge along habitat gradients. Finally, the strong evidence of admixture, gene flow, and mtDNA introgression among populations suggests that P. cornutum should be considered a single widespread species under the General Lineage Species Concept.

Comparative analyses of Mikania (Asteraceae: Eupatorieae) plastomes and impact of data partitioning and inference methods on phylogenetic relationships

We assembled new plastomes of 19 species of Mikania and of Ageratina fastigiata, Litothamnus nitidus, and Stevia collina, all belonging to tribe Eupatorieae (Asteraceae). We analyzed the structure and content of the assembled plastomes and used the newly generated sequences to infer phylogenetic relationships and study the effects of different data partitions and inference methods on the topologies. Most phylogenetic studies with plastomes ignore that processes like recombination and biparental inheritance can occur in this organelle, using the whole genome as a single locus. Our study sought to compare this approach with multispecies coalescent methods that assume that different parts of the genome evolve at different rates. We found that the overall gene content, structure, and orientation are very conserved in all plastomes of the studied species. As observed in other Asteraceae, the 22 plastomes assembled here contain two nested inversions in the LSC region. The plastomes show similar length and the same gene content. The two most variable regions within Mikania are rpl32-ndhF and rpl16-rps3, while the three genes with the highest percentage of variable sites are ycf1, rpoA, and psbT. We generated six phylogenetic trees using concatenated maximum likelihood and multispecies coalescent methods and three data partitions: coding and non-coding sequences and both combined. All trees strongly support that the sampled Mikania species form a monophyletic group, which is further subdivided into three clades. The internal relationships within each clade are sensitive to the data partitioning and inference methods employed. The trees resulting from concatenated analysis are more similar among each other than to the correspondent tree generated with the same data partition but a different method. The multispecies coalescent analysis indicate a high level of incongruence between species and gene trees. The lack of resolution and congruence among trees can be explained by the sparse sampling (~ 0.45% of the currently accepted species) and by the low number of informative characters present in the sequences. Our study sheds light into the impact of data partitioning and methods over phylogenetic resolution and brings relevant information for the study of Mikania diversity and evolution, as well as for the Asteraceae family as a whole.

Introgression and Species Delimitation in the Longear Sunfish Lepomis megalotis (Teleostei: Percomorpha: Centrarchidae).

Introgression and hybridization are major impediments to genomic-based species delimitation because many implementations of the multispecies coalescent framework assume no gene flow among species. The sunfish genus Lepomis, one of the world's most popular groups of freshwater sport fish, has a complicated taxonomic history. The results of ddRAD phylogenomic analyses do not provide support for the current taxonomy that recognizes two species, Lepomis megalotis and Lepomis peltastes, in the L. megalotis complex. Instead, evidence from phylogenomics and phenotype warrants recognizing six relatively ancient evolutionary lineages in the complex. The introgressed and hybridizing populations in the L. megalotis complex are localized and appear to be the result of secondary contact or rare hybridization events between nonsister species. Segregating admixed populations from our multispecies coalescent analyses identifies six species with moderate to high genealogical divergence, whereas including admixed populations drives all but one lineage below the species threshold of genealogical divergence. Segregation of admixed individuals also helps reveal phenotypic distinctiveness among the six species in morphological traits used by ichthyologists to discover and delimit species over the last two centuries. Our protocols allow for the identification and accommodation of hybridization and introgression in species delimitation. Genomic-based species delimitation validated with multiple lines of evidence provides a path towards the discovery of new biodiversity and resolving long-standing taxonomic problems.[ddRAD; genealogical divergence index; hybridization; integrative species delimitation; phylogeny; secondary contact; systematics; taxonomy.].

Ancient incomplete lineage sorting of Hyles and Rhodafra (Lepidoptera: Sphingidae)

The hawkmoth genus Rhodafra comprises two African species with unclear relationships, as their wing patterns are markedly different, with one species closely resembling species of a related genus, Hyles. The present paper aims to investigate the monophyly and phylogenetic position of Rhodafra in relation to Hyles and other genera of the subtribe Choerocampina (Sphingidae: Macroglossinae: Macroglossini) using mitochondrial and nuclear sequence data from more species and individuals than have hitherto been studied. As no fresh tissue of Rhodafra was available, ancient-DNA methodology was applied. All data corroborate the genus as monophyletic and that a similar wing pattern is not a good indicator of close phylogenetic relationship in this group of moths. Phylogenetic trees based on mitochondrial data agree in placing Rhodafra within Hyles. In contrast, analysis of nuclear EF1alpha sequences produces a topology in which Rhodafra is placed as the sister clade to Hyles. Although multispecies coalescent analyses suggest a polytomy between Rhodafra, Hyles lineata and the remaining Hyles, total evidence analyses corroborate Rhodafra as sister to Hyles. This relationship is interpreted as the favoured topology. For a more robust result, the question should be re-examined using genomic approaches.

Detecting destabilizing species in the phylogenetic backbone of Potentilla (Rosaceae) using low-copy nuclear markers.

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.

Complex patterns of reticulate evolution in opportunistic weeds (Potentilla L., Rosaceae), as revealed by low-copy nuclear markers

BackgroundMost 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 – and 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.ResultsGene 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.ConclusionsThis 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.

PHYLOGENETIC RELATIONSHIPS OF THE TRIBE NEOSPARTONEAE (VERBENACEAE) BASED ON MOLECULAR DATA

Neospartoneae are a small tribe in Verbenaceae, native to temperate South America and comprising seven species in three genera: Diostea, Lampayo, and Neosparton. Diostea and Neosparton share an ephedroid habit and the presence of a staminode. Diostea and Lampayo share a schizocarpous fruit and bilobed stigma. Previous chloroplast DNA phylogenetic studies first identified Neospartoneae as a clade. However, evolutionary relationships within Neospartoneae remain unclear. In this study, nine loci from both chloroplast and nuclear genomes were used to reconstruct phylogeny with almost complete taxon sampling. Maximum likelihood and Bayesian analyses were conducted using single-locus and concatenated datasets to generate gene trees. A species tree was reconstructed by Bayesian multispecies coalescent analyses. The generic relationships are well resolved and confirm the monophyly of the Neospartoneae and each genus. The topologies show that Neosparton is sister to a clade comprised of Diostea and Lampayo. This study presents a first species-level phylogeny of Neospartoneae and provides insight into morphological character evolution of this tribe. The presence of a staminode shared by Diostea and Neosparton, and dry schizocarpous fruits shared by Diostea and Lampayo, are inferred to be plesiomorphic traits in Neospartoneae and not indicative of close relationship. The ephedroid habit and curved corolla tubes shared by Diostea and Neosparton may have evolved in the common ancestor of Neospartoneae and subsequently reversed in the ancestor of Lampayo, or have evolved in parallel in the two genera.

The Helvella corium species aggregate in Nordic countries - phylogeny and species delimitation.

Mycologists have always been curious about the elaborate morphotypes and shapes of species of the genus Helvella. The small, black, cupulate Helvella specimens have mostly been assigned to Helvella corium, a broadly defined morpho-species. Recent phylogenetic analyses, however, have revealed an aggregate of species hidden under this name. We performed a multispecies coalescent analysis to re-assess species limits and evolutionary relationships of the Helvella corium species aggregate in the Nordic countries. To achieve this, we used morphology and phylogenetic evidence from five loci - heat shock protein 90 (hsp), translation elongation factor 1-alpha (tef), RNA polymerase II (rpb2), and the 5.8S and large subunit (LSU) of the nuclear ribosomal DNA. All specimens under the name Helvella corium in the larger university fungaria of Norway, Sweden and Denmark were examined and barcoded, using partial hsp and/or rpb2 as the preferential secondary barcodes in Helvella. Additional fresh specimens were collected in three years (2015-2018) to obtain in vivo morphological data to aid in species discrimination. The H. corium species aggregate consists of seven phylogenetically distinct species, nested in three divergent lineages, i.e. H. corium, H. alpina and H. pseudoalpina sp. nov. in the /alpina-corium lineage, H. alpestris, H. macrosperma and H. nannfeldtii in the /alpestris-nannfeldtii lineage, and H. alpicola as a weakly supported sister to the /alpestris-nannfeldtii lineage. Among the seven species, the ribosomal loci expressed substantial variation in evolutionary rates, suggesting care in the use of these regions alone in delimitation of Helvella species. Altogether, 469 out of 496 available fungarium specimens were successfully barcoded.

Deep Instability in the Phylogenetic Backbone of Heteroptera is Only Partly Overcome by Transcriptome-Based Phylogenomics

Abstract Heteroptera is a diverse suborder of insects that includes many plant pests, human disease vectors, and nuisance pests, but also beneficial insects. Previous analyses have supported recognition of seven monophyletic infraorders. A clade comprising Leptopodomorpha, Pentatomomorpha, and Cimicomorpha is also well-accepted, but relationships among the early-diverging lineages, including the aquatic infraorders (Nepomorpha and Gerromorpha), have remained poorly resolved and controversial. Phylogenomic analyses of 2,159 gene alignments derived from Illumina sequencing of transcriptomes were employed to explore the stability of relationships among major heteropteran lineages. These analyses included maximum likelihood analyses of amino acid and nucleotide sequences, as well as multi-species coalescent analysis and quartet sampling. All analyses favored a sister position of the Nepomorpha to the remaining Heteroptera. The placement of the Nepomorpha and other ambiguously supported nodes, including some within the Pentatomomorpha were explored with quartet sampling. Results of quartet sampling revealed only a slight majority of quartets supported the placement of the Nepomorpha, and some varying alternate topologies were supported within the Pentatomomorpha. These results highlight the instability of deep nodes that divide aquatic and other early-diverging lineages within the Heteroptera, suggesting that some relationships remain difficult to resolve even with large amounts of data. In addition, despite the large amount of transcriptome data analyzed, quartet sampling revealed considerable underlying conflict for some nodes, even where bootstrap support is high, emphasizing the importance of considering multiple clade support values when analyzing phylogenomic datasets.