Species Circumscription Research Articles

A Taxonomic Revision ofPassiflorasect.Xerogona(Passifloraceae) Using Principal Component Analysis

In subgenus Decaloba (DC.) Rchb. of Passiflora L., the section Xerogona (Raf.) Killip (Passifloraceae) is a group of herbaceous vines found in subtropical and tropical regions of the Americas. Primarily distributed in Central America, with a few also found in the West Indies and South America, the species of Passiflora sect. Xerogona are recognized by their unusual dehiscent capsular fruit, the absence of bracts and laminar nectaries, and their transversely grooved seeds. Passiflora tenella Killip is the only species included in Passiflora sect. Xerogona with a fruit that does not appear to be a capsule, but the shape of the leaves and the absence of floral bracts and laminar nectaries suggest affiliation with this section. Fifteen species, including two subspecies, are recognized within Passiflora sect. Xerogona. Passiflora cobanensis Killip is distinguished as two subspecies, P. cobanensis subsp. cobanensis and P. cobanensis subsp. brevipes (Killip) T. Boza, with the latter subspecies transferred from P. brevipes Killip. From previous species circumscriptions, this section contains two problematic species complexes for P. capsularis L. and P. rubra L. The morphological variation between and within these two species complexes was examined in this study, using Principal Component Analysis and correlation matrices of morphological characters, and this variation was studied throughout their distributional ranges. Passiflora capsularis is recognized as a single variable species. Two species are recognized within the P. rubra complex, based primarily on floral characters, as P. cisnana Harms and P. rubra. Passiflora cisnana is lectotypified.

Combining complete chloroplast genome sequences with target loci data and morphology to resolve species limits in Triplostegia (Caprifoliaceae)

Species represent the most basic unit of taxonomy. As such, species delimitation represents a crucial issue for biodiversity conservation. Taxonomic practices were revolutionized in the last three decades due to the increasing availability of molecular phylogenetic data. The genus Triplostegia (Caprifoliaceae) traditionally consists of two species, T. glandulifera and T. grandiflora, distinguishable mainly based on quantitative morphological features. In this study, we sequenced nine chloroplast loci (i.e., accD, psbK-psbI, rbcL-accD, rpoB-trnC, rps16-trnQ, trnE-trnT, trnF-ndhJ, trnH-psbA, trnS-trnG) and one nuclear locus (ITS) of 16 individuals of Triplostegia representing the entire distribution range of both species recognized. Furthermore, we also obtained whole chloroplast sequences for 11 of the 16 individuals for which silica gel-dried leaves were available. Our phylogenetic analyses integrating chloroplast genome sequences and multiple loci data revealed that Triplostegia includes four main clades that largely match geography. Neither T. grandiflora nor T. glandulifera was recovered as monophyletic and no diagnosable differences in leaf, flower, and pollen traits were detected between the two species, indicating the need for a revised species circumscription within Triplostegia. Our study highlights the importance of combining data from different sources while defining species limits.

First insights on the biogeographical history of Phlegmariurus (Lycopodiaceae), with a focus on Madagascar

We explored the biogeographical history of a group of spore-bearing plants focusing on Phlegmariurus (Lycopodiaceae), a genus of lycophytes comprising ca. 250 species. Given its wide distribution in the Southern Hemisphere, Phlegmariurus provides a good model to address questions about the biogeographical processes underlying southern distributions, notably in Madagascar and surrounding islands, also called the Western Indian Ocean (WIO). Our aims were (i) to discuss the systematics of the Malagasy species in the light of molecular phylogenetic results, (ii) to provide the first dating analysis focused on Phlegmariurus and (iii) to understand the relative role of vicariance, dispersal and diversification in the origin of the Malagasy Phlegmariurus species.The phylogenetic relationships were inferred based on three plastid DNA regions (rbcL, trnH-psbA and trnL+trnL-trnF) and on a dataset comprising 93 species, including 16 Malagasy species (80% of the total Malagasy diversity for the genus). Our results highlighted the need to combine Malagasy Huperzia species in Phlegmariurus, as well as the polyphyly of widely distributed species: Phlegmariurus phlegmaria, P. squarrosus and P. verticillatus with the Malagasy species not belonging with the types of P. phlegmaria or P. squarrosus. This led us to propose new circumscriptions of Phlegmariurus species, especially in the WIO.Our dating analysis, relying on fossil calibrations, showed that Phlegmariurus would have originated in the Late Cretaceous and diversified in the Early Eocene. The biogeographical analysis highlighted uncertainties about the biogeographical origins of Phlegmariurus: the genus would have started to diversify in an ancestral range covering at least the Neotropics and Australasia. Hypotheses on the biogeographical history of Phlegmariurus were discussed, especially the roles of long distance dispersal, migration via Antarctica and via the Boreotropics. Six long distance dispersal events over the last 40 Ma would explain the Malagasy species diversity of Phlegmariurus, in combination with an important in situ diversification starting in the Miocene.

The tempo and mode of the taxonomic correction process: How taxonomists have corrected and recorrected North American bird species over the last 127 years.

While studies of taxonomy usually focus on species description, there is also a taxonomic correction process that retests and updates existing species circumscriptions on the basis of new evidence. These corrections may themselves be subsequently retested and recorrected. We studied this correction process by using the Check-List of North and Middle American Birds, a well-known taxonomic checklist that spans 130 years. We identified 142 lumps and 95 splits across sixty-three versions of the Check-List and found that while lumping rates have markedly decreased since the 1970s, splitting rates are accelerating. We found that 74% of North American bird species recognized today have never been corrected (i.e., lumped or split) over the period of the checklist, while 16% have been corrected exactly once and 10% have been corrected twice or more. Since North American bird species are known to have been extensively lumped in the first half of the 20th century with the advent of the biological species concept, we determined whether most splits seen today were the result of those lumps being recorrected. We found that 5% of lumps and 23% of splits fully reverted previous corrections, while a further 3% of lumps and 13% of splits are partial reversions. These results show a taxonomic correction process with moderate levels of recorrection, particularly of previous lumps. However, 81% of corrections do not revert any previous corrections, suggesting that the majority result in novel circumscriptions not previously recognized by the Check-List. We could find no order or family with a significantly higher rate of correction than any other, but twenty-two genera as currently recognized by the AOU do have significantly higher rates than others. Given the currently accelerating rate of splitting, prediction of the end-point of the taxonomic recorrection process is difficult, and many entirely new taxonomic concepts are still being, and likely will continue to be, proposed and further tested.

Bradyrhizobium algeriense sp. nov., a novel species isolated from effective nodules of Retama sphaerocarpa from Northeastern Algeria

We have characterized genetic, phenotypic and symbiotic properties of bacterial strains previously isolated from nitrogen-fixing nodules of Retama sphaerocarpa from Northern Algeria. Phylogenetic analyses of 16S rRNA genes and three concatenated housekeeping genes, recA, atpD and glnII, placed them in a new divergent group that is proposed to form a new Bradyrhizobium species, Bradyrhizobium algeriense sp. nov. (type strain RST89T, LMG 27618 and CECT 8363). Based on these phylogenetic markers and on genomic identity data derived from draft genomic sequences, Bradyrhizobium valentinum LmjM3T, Bradyrhizobium lablabi CCBAU 23086T, Bradyrhizobium retamae Ro19T, and Bradyrhizobium jicamae PAC68T are the closest relatives of B. algeriense RST89T, with sequence identities of 92–94% and Average Nucleotide Identities (ANIm) under 90%, well below the 95–96% species circumscription threshold. Likewise, a comparison of whole-cell proteomic patterns, estimated by Matrix-Assisted Laser Desorption/Ionization-Time-of-Flight (MALDI-TOF) mass spectrometric analysis, yielded almost identical spectra between B. algeriense strains but significant differences with B. valentinum, Bradyrhizobium paxllaeri, Bradyrhizobium icense, B. lablabi, B. jicamae and B. retamae. A phylogenetic tree based on symbiotic gene nodC revealed that the B. algeriense sequences cluster with sequences from the Bradyrhizobium symbiovar retamae, previously defined with B. retamae strains isolated from Retama monosperma. B. algeriense strains were able to establish effective symbioses with Retama raetam, Lupinus micranthus, Lupinus albus and Genista numidica, but not with Lupinus angustifolius or Glycine max.

Evolution and systematics of polyploid Nigritella (Orchidaceae)

Members of the orchid genus Nigritella are widespread in European mountains, but species circumscriptions and evolutionary patterns in the genus are subjects to conflicting opinions. We analyzed a representative material of Nigritella for differentiation at nuclear and plastid marker loci. In agreement with predictions from embryological studies, diploid members of Nigritella are sexual and mostly out‐crossing, whereas triploid, tetraploid and pentaploid members are apomicts. The diploid taxa were poorly differentiated in the investigated molecular markers, except for the western N. gabasiana, which was separated in plastid haplotypes. Polyploid Nigritella aggregate into three groups and within each of these groups apomictic polyploids have given rise to new species. Within the N. nigra group, the tetraploid N. nigra subsp. austriaca is somewhat differentiated from the triploid subsp. nigra at nuclear as well as plastid loci. Fusion of an unreduced egg cell from subsp. nigra with a haploid microgamete from Gymnadenia conopsea gave rise to Gymnigritella runei. Within the N. widderi group, N. archiducis‐joannis is poorly separated from N. widderi in molecular markers, and the pentaploid N. buschmanniae has evolved by fusion of an unreduced egg cell from N. widderi with a haploid microgamete from a diploid Nigritella. Within the N. miniata group, N. stiriaca is somewhat differentiated from N. miniata at nuclear loci, but no other segregates of N. miniata are supported at species level. Polyploid Nigritella species accumulate genetic diversity by somatic mutations. In the widespread N. nigra subsp. austriaca and N. miniata this diversity is correlated to geography. Although some polyploids may be of recent origins, each polyploid contain genetic markers no longer encountered in diploid members of the genus. According to plastid marker data, Nigritella and Gymnadenia may constitute monophyletic sister genera.

The lytic Myoviridae of Enterobacteriaceae form tight recombining assemblages separated by discontinuities in genome average nucleotide identity and lateral gene flow.

In Bacteria, a working consensus of species circumscription may have been reached and one of the most prominent criteria is high average nucleotide identity (ANI). ANI in effect groups strains that may recombine more or less frequently, depending on their biology, as opposed to rare interspecies gene transfer. For bacteriophages, which show various lifestyles, the nature of the fundamental natural unit, if it exists in a biological sense, is not well understood and defined. The approaches based on dot-plots are useful to group similar bacteriophages, yet are not quantitative and use arbitrarily set cut-offs. Here, we focus on lytic Myoviridae and test the ANI metric for group delineation. We show that ANI-based groups are in agreement with the International Committee on Taxonomy of Viruses (ICTV) classification and already established dot-plot groups, which are occasionally further refined owing to higher resolution of ANI analysis. Furthermore, these groups are separated among themselves by clear ANI discontinuities. Their members readily exchange core genes with each other while they do not with bacteriophages of other ANI groups, not even with the most similar. Thus, ANI-delineated groups may represent the natural units in lytic Myoviridae evolution with features that resemble those encountered in bacterial species.

Are shoots of diagnostic value in Central European bladderworts (Utricularia L., Lentibulariaceae)?

In central Europe, seven native species of Utricularia occur, mainly distinguished by flower features. They can be subdivided in three aggregates according to shoot morphology: (1) Utricularia intermedia aggr., also comprising Utricularia ochroleuca and Utricularia stygia, (2) Utricularia vulgaris aggr., also comprising Utricularia australis and (3) Utricularia minor aggr., also comprising Utricularia bremii. We tested some shoot features as identification tools and investigated quadrifid digestive glands in all the studied species, using geometric morphometrics. For U. intermedia aggr., in most cases, the tooth number per ultimate leaf segment may be diagnostic. The three species of this aggregate overlap in terms of gland shape, but averaging measurements by traps and individuals, a decrease of overlapping among species was found. The shape and the centroid size of quadrifid glands in U. minor aggr. is unsuitable for discriminating species. Concerning U. vulgaris aggr., U. vulgaris bears a higher ratio of setula length to tooth length than U. australis (which is more toothed). This feature may help to distinguish species, but conflicting results were found in one studied population. The relevance of quadrifid gland features as identification tool and the puzzling systematic circumscriptions of the target species are discussed.

Morphological convergences in Ameles Burmeister and PseudoyersiniaKirby: Taxonomic implications of wing reduction and flight predisposition in some West-Mediterranean Amelini (Insecta: Mantodea).

Species in the genus Ameles Burmeister and Pseudoyersinia Kirby (Amelini) are traditionally defined as small-sized, ground-dwelling mantids whose males are distinct for being, respectively, macropterous and brachypterous. However, comparative morphological studies across Amelini confirmed the existence of short-winged males in Ameles, suggesting that this traditional diagnostic concept does not apply to all species. Our analyses of several species from West Mediterranean localities (Canary Islands, Spain, Italy, and Morocco) resulted in the relocation of Pseudoyersinia andreae Galvagni, 1976 to Ameles as Ameles andreae (Galvagni, 1976) (n. comb.) with Ameles insularis Agabiti, Ippolito Lombardo, 2010 as its new synonym (n. syn.), the clarification of the taxonomic identity of A. gracilis (Brullé, 1838) and A. maroccana Uvarov, 1931, including diagnoses of their males, and the description of Ameles spallanzania obscura (n. ssp.) (from Spain). We also take the opportunity to describe Pseudoyersinia maroccana (n. sp.) (from Morocco) based on museum specimens separating it from Ameles maroccana Uvarov, 1931. We also found that wing length is positively correlated to ocelli size. We discuss this trend from an ecological, evolutionary, and biogeographic perspectives to both facilitate species circumscription and justify the taxonomic modifications herein introduced.

Geometric morphometric methods achieve type specimen assignment in the cryptic Plagiochila arbuscula complex (Plagiochilaceae: Jungermanniopsida) with the minimum of morphological evidence

Relating type specimens to morphologically cryptic species is particularly vexing. When type specimens are small, fragmentary and sterile, resolution can seem intractable. In this study of the cryptic Plagiochila arbuscula complex, morphological evidence was reconsidered using geometric morphometric methods to gain insight into patterns of variation and differences in leaf shape between four phylogenetic lineages. The study had two aims: to achieve morphological circumscription of species and to attribute challenging type specimens to species. Considerable overlap in leaf shape among the four lineages was observed, but so were high levels of within-individual partitioning of leaf shape variation. Leaf shape exhibited a significant relationship with leaf size, and size was correlated with shoot order. The greatest leaf shape differences among species were manifest in leaves from primary shoots. In linear discriminant analysis, the highest cross-validation success rates for single leaves was achieved using primary shoot leaf shape and so for nine challenging type specimens, the shape of primary shoot leaves was used to assign them to species. Twelve of 15 sampled type leaves were attributed to a single species with high probability, in agreement with subjective assessment. In the Plagiochila arbuscula complex historical type specimens can be related to groups circumscribed by integrated molecular and morphological evidence using the minimum of morphological evidence: the shape of single leaves.

Phylogeographic and phylogenetic analysis for Tripterygium species delimitation.

Tripterygium wilfordii (Celastraceae) is a traditional Chinese medicine; and the dried root and rhizome constitute the main officinal parts. Tripterygium wilfordii has been identified as a potential candidate for the treatment of systemic lupus erythematosus, rheumatoid arthritis, nephritis, asthma, leprosy, and cancer. The phylogenetic relationships within the Tripterygium genus are ambiguous; thus, our aim is to clarify the relationships within this genus using phylogeographic and phylogenetic analyses. Here, we first sequenced three plastid DNA regions (i.e., psbA‐trnH, rpl32‐trnL, and trnL‐trnF) and found that Tripterygium hypoglaucum and T. wilfordii were clustered together based on the strength of the topology in the phylogenetic analysis: T. hypoglaucum is polyphyletic, and T. wilfordii is paraphyletic. A spatial analysis of molecular variance showed that the best group value is 4, and the groups were almost consistent with the topology of in the phylogenetic analysis. The Mantel analyses of Tripterygium using IBD web showed statistically significant relationships between genetic and geographical distance distributions (r = .3479, p < .0001). The molecular dating using Fossil calibration indicated that the divergence in Tripterygium was approximately 8.13 Ma. Furthermore, we also analyzed four DNA regions (i.e., ITS2, psbA‐trnH, matK, and rbcL) that were obtained from the NCBI nucleotide database; these results showed that T. wilfordii and T. hypoglaucum clustered together, while Tripterygium regelii represented a separate cluster. Tripterygium hypoglaucum and T. wilfordii were never distinct lineages, and the species circumscriptions are artificial. We propose that T. wilfordii and T. hypoglaucum are conspecific, while T. regelii likely constitutes a separate species.

New insights in Russula subsect. Rubrinae: phylogeny and the quest for synapomorphic characters

Russula is one of the most speciose genera of mushroom-forming fungi, but phylogenetic relationships among species and subgeneric groupings are poorly understood. Our multi-locus phylogenetic reconstruction places R. firmula, R. rubra, R. rutila and R. veternosa in a well-supported Rubrinae clade, belonging to the Integrae clade of the Crown clade of the genus Russula. Traditional morphology-based classifications placed these four species in two different subsections based on the presence or absence of incrustations on pileocystidia. The Integrae clade also contains R. integra and related species that are traditionally placed in other groups based on their mild taste. Ancestral state reconstruction suggests that the common ancestor of the Crown clade and the Integrae clade probably did not have any incrustations in the pileipellis, had a mild taste, yellow spore print and were associated with angiosperms. All four species of the Rubrinae clade are defined by a darker yellow or ochre spore print, acrid taste and incrustations on pileocystidia. This last character contradicts the former splitting of the group because incrustations were apparently overlooked in R. firmula and R. veternosa. Incrustation type is now highlighted as being important for the delimitation of species and groups within the Crown clade. Pink or red staining of the incrustations in sulphovanillin is present in all species of the Rubrinae clade and a majority of the analysed species of the Integrae clade. The delimitation of the Rubrinae clade and its species circumscriptions are summarised here in a new diagnostic key.

Molecular diversity and biogeography of Philippine foliose Bangiales (Rhodophyta)

Species circumscription based on phenotypes has frequently masked the actual species diversity in foliose Bangiales. Application of DNA sequence differences in this group has removed dependence on the utility of morphological characters traditionally considered for species discrimination. This study currently represents an extensive analysis of phylogeny and species discrimination of foliose Bangiales across most of their distributional range in the northern Philippines, particularly in Luzon Strait. Molecular assessment based on plastid rbcL and two mitochondrial loci, COI-5P, and cox2–3 spacer, suggested four major groups diagnostic of species lineage. As supported by the results from the four molecular species delimitation methods: PTP, bPTP, ABGD, and SPN, the confirmed Philippine foliose Bangiales species included Pyropia acanthophora, Py. tanegashimensis, and two cryptic taxa from Batanes Islands. The number of species detected in this study suggested that the true species composition of Philippine foliose Bangiales might be considerably lower than what was previously thought. It is possible however that a greater sampling effort in complete seasonal range of collections will reveal more species and extent of their actual distributions. Although the influence of northeast monsoon significantly affects the growth of foliose Bangiales in the Philippines, its role in shaping their present-day distribution remains unclear. Our molecular datasets however suggested that their current biogeographic distribution might reflect past vicariant events and is therefore more complex than have been previously regarded.

Phylogeny, taxonomy and biogeography of Neotropical Quiinoideae (Ochnaceae s.l.)

AbstractAmazonia arguably harbours the highest plant species diversity of all wet tropical regions on earth. There is increasing evidence that this enormous diversity is the product of a rather long and complex process and not of a single cause. Here, we investigated divergence times and diversification dynamics in the Neotropical Quiinoideae (Malpighiales: Ochnaceae s.l.) to explore different evolutionary hypotheses for the accumulation of high species diversity. Additionally, we reappraised the phylogenetic relationships and species circumscriptions using sequences of six plastid and nuclear DNA regions and the most comprehensive taxon sampling of the subfamily to date. Molecular dating indicated that Quiinoideae originated during the late Cretaceous, whereas crown group taxa started to diverge at the Eocene‐Oligocene boundary. The lack of rate shifts in this subfamily supports the “museum” model of diversification. The rather constant species accumulation also suggests that the Pleistocene glacial cycles did not play an important role for the diversification of Quiinoideae. While ancestral area reconstruction was inconclusive, the post‐Miocene divergence times of the west Amazonian species provided some evidence that these areas might not have been available for colonization until the demise of the Lake Pebas and Acre wetlands. New infrageneric groups were inferred, and some species were found to be non‐monophyletic, requiring taxonomic reassessment and demonstrating the need for including multiple individuals per species in species‐level phylogenies.

Bradyrhizobium mercantei sp. nov., a nitrogen-fixing symbiont isolated from nodules of Deguelia costata (syn. Lonchocarpus costatus).

Some bacteria collectively known as rhizobia can establish symbiotic relationships and the N2-fixation process with several legumes used as green manure, in pastures and for wood production. Symbionts belonging to the genus Bradyrhizobium are predominant in the tropics, and an increasing number of studies report high genetic diversity within the genus. We performed a polyphasic study with two strains belonging to the genus Bradyrhizobium- SEMIA 6399T and SEMIA 6404-isolated from root nodules of Deguelia costata (syn. Lonchocarpus costatus), an important legume native to eastern Brazil. In general, sequences of the 16S rRNA gene were highly conserved in members of the genus Bradyrhizobium, and the two strains were positioned in the Bradyrhizobiumelkanii superclade, sharing 100 % nucleotide identity with Bradyrhizobiumembrapense, Bradyrhizobiumerythrophlei and Bradyrhizobiumviridifuturi. However, multilocus sequence analysis with four housekeeping genes (dnaK, glnII, gyrB and recA) confirmed that the two strains belong to a distinct clade, sharing from 87.7 to 96.1 % nucleotide identity with related species of the genus Bradyrhizobium, being most closely related to B. viridifuturi. Average nucleotide identity of genome sequences between SEMIA 6399T and related species was lower than 92 %, below the threshold of species circumscription. nifH phylogeny clustered the SEMIA strains in a clade separated from other species of the genus Bradyrhizobium, and the nodD phylogeny revealed that SEMIA 6399T presents a more divergent sequence. Other phenotypic and genotypic traits were determined for the new group, and our data support the description of the SEMIA strains as representatives of Bradyrhizobium mercantei sp. nov.; SEMIA 6399T (=CNPSo 1165T=BR 6010T=U675T=LMG 30031T) was chosen as the type strain.

Regional Genetic Structure in the Aquatic Macrophyte Ruppia cirrhosa Suggests Dispersal by Waterbirds

The evolutionary history of the genus Ruppia has been shaped by hybridization, polyploidisation and vicariance that have resulted in a problematic taxonomy. Recent studies provided insight into species circumscription, organelle take-over by hybridization, and revealed the importance of verifying species identification to avoid distorting effects of mixing different species, when estimating population connectivity. In the present study, we use microsatellite markers to determine population diversity and connectivity patterns in Ruppia cirrhosa including two spatial scales: (1) from the Atlantic Iberian coastline in Portugal to the Siculo–Tunisian Strait in Sicily and (2) within the Iberian Peninsula comprising the Atlantic–Mediterranean transition. The higher diversity in the Mediterranean Sea suggests that populations have had longer persistence there, suggesting a possible origin and/or refugial area for the species. The high genotypic diversities highlight the importance of sexual reproduction for survival and maintenance of populations. Results revealed a regional population structure matching a continent–island model, with strong genetic isolation and low gene flow between populations. This population structure could be maintained by waterbirds, acting as occasional dispersal vectors. This information elucidates ecological strategies of brackish plant species in coastal lagoons, suggesting mechanisms used by this species to colonize new isolated habitats and dominate brackish aquatic macrophyte systems, yet maintaining strong genetic structure suggestive of very low dispersal.

Plastid phylogenomics and adaptive evolution of Gaultheria series Trichophyllae (Ericaceae), a clade from sky islands of the Himalaya-Hengduan Mountains

Gaultheria series Trichophyllae Airy Shaw is an angiosperm clade of high-alpine shrublets endemic to the Himalaya-Hengduan Mountains and characterized by recent species divergence and convergent character evolution that has until recently caused much confusion in species circumscription. Although multiple DNA sequence regions have been employed previously, phylogenetic relationships among species in the group have remained largely unresolved. Here we examined the effectiveness of the plastid genome for improving phylogenetic resolution within the G. series Trichophyllae clade. Plastid genomes of 31 samples representing all 19 recognized species of the series and three outgroup species were sequenced with Illumina Sequencing technology. Maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) phylogenetic analyses were performed with various datasets, i.e., that from the whole plastid genome, coding regions, noncoding regions, large single-copy region (LSC) and inverted-repeat region a (IRa). The partitioned whole plastid genome with inverted-repeat region b (IRb) excluded was also analyzed with ML and BI. Tree topologies based on the whole plastid genome, noncoding regions, and LSC region datasets across all analyses, and that based on the partitioned dataset with ML and BI analyses, are identical and generally strongly supported. Gaultheria series Trichophyllae form a clade with three species and one variety that is sister to a clade of the remaining 16 species; the latter comprises seven main subclades. Interspecific relationships within the series are strongly supported except for those based on the coding-region and IRa-region datasets. Eight divergence hotspot regions, each possessing >5% percent variable sites, were screened across the whole plastid genome of the 28 individuals sampled in the series. Results of morphological character evolution reconstruction diagnose several clades, and a hypothesis of adaptive evolution for plant habit is postulated.

A new Cynoglossum species, and transfers to Hackelia in eastern Australian Boraginaceae

Recent molecular evidence supports the transfer of two Australian endemic species, Austrocynoglossum latifolium (R.Br.) R.R.Mill and Cynoglossum suaveolens R.Br., to the genus Hackelia Opiz as H. latifolia (R.R.Mill) Dimon &amp; M.A.M.Renner, comb. nov., and H. suaveolens (R.Br.) Dimon &amp; M.A.M.Renner, comb. nov. Hackelia latifolia comprises two morphological entities that, although sharing the procumbent-prostrate habit and production of elongated internodes and frondose bracts in the inflorescence, differ in a range of qualitative and quantitative micro-morphological characters. Hackelia latifolia has few, widely spaced, thorn-like trichomes on stems, a glabrous abaxial lamina surface, and mericarps with free glochids densely and evenly distributed over the outer surface, and a rectangular cicatrix at the mericarp apex, which is beaked. The other entity has many densely packed cellular trichomes on the stems, trichomes on the abaxial leaf lamina, and mericarps with a wing formed by basally connate glochids, and a triangular cicatrix located centrally on the inner mericarp surface. For the latter, we propose the new species Cynoglossum torvum Dimon &amp; M.A.M.Renner, and by implication suggest that H. latifolia is polyphyletic as previously circumscribed. Whereas H. latifolia s.s. is widespread along the south-eastern coast of Australia from Tasmania to south-eastern Queensland, Cynoglossum torvum is restricted to the tablelands of north-eastern New South Wales and south-eastern Queensland. We compare C. torvum with the other Australian Cynoglossum L. species, C. australe R.Br., confirm previous observations of variation in mericarp morphology, and suggest that further investigation to resolve species circumscription is required given this variation.

Species delimitation and phylogeography of the Pectenia species-complex: A misunderstood case of species-pairs in lichenized fungi, where reproduction mode does not delimit lineages

The main goal of this work was to study species boundaries in the genus Pectenia and elucidate the biogeographic history of the four currently accepted species. To accomplish this, we included 92 specimens across the range of Pectenia in Europe and northern Africa. We used three nuclear loci and assessed species circumscription using two Bayesian coalescent-based methods and the Bayes Factor approach. We reviewed the value of reproductive mode and other morphological features as predictors of monophyletic groups. Our results suggest that the production of asexual propagules and sexual structures are not characterizing monophyletic groups. The genus includes two morphologically well-characterized main lineages, where one lineage is composed by two sub-lineages that are with a case of cryptic speciation explained by a biogeographic pattern. We suggest treating the two lineages as two species, which are characterized by lobe structure: Pectenia plumbea and P. atlantica. Both of these species include samples with asexual propagules and apothecia, and thus do not correspond to any of the earlier morphologically defined species. The results of the biogeographic analysis indicate that the Mediterranean basin is the most likely ancestral distribution area of P. plumbea, whereas P. atlantica probably originated in Macaronesia.

Limitations of Species Delimitation Based on Phylogenetic Analyses: A Case Study in the Hypogymnia hypotrypa Group (Parmeliaceae, Ascomycota).

Delimiting species boundaries among closely related lineages often requires a range of independent data sets and analytical approaches. Similar to other organismal groups, robust species circumscriptions in fungi are increasingly investigated within an empirical framework. Here we attempt to delimit species boundaries in a closely related clade of lichen-forming fungi endemic to Asia, the Hypogymnia hypotrypa group (Parmeliaceae). In the current classification, the Hypogymnia hypotrypa group includes two species: H. hypotrypa and H. flavida, which are separated based on distinctive reproductive modes, the former producing soredia but absent in the latter. We reexamined the relationship between these two species using phenotypic characters and molecular sequence data (ITS, GPD, and MCM7 sequences) to address species boundaries in this group. In addition to morphological investigations, we used Bayesian clustering to identify potential genetic groups in the H. hypotrypa/H. flavida clade. We also used a variety of empirical, sequence-based species delimitation approaches, including: the “Automatic Barcode Gap Discovery” (ABGD), the Poisson tree process model (PTP), the General Mixed Yule Coalescent (GMYC), and the multispecies coalescent approach BPP. Different species delimitation scenarios were compared using Bayes factors delimitation analysis, in addition to comparisons of pairwise genetic distances, pairwise fixation indices (FST). The majority of the species delimitation analyses implemented in this study failed to support H. hypotrypa and H. flavida as distinct lineages, as did the Bayesian clustering analysis. However, strong support for the evolutionary independence of H. hypotrypa and H. flavida was inferred using BPP and further supported by Bayes factor delimitation. In spite of rigorous morphological comparisons and a wide range of sequence-based approaches to delimit species, species boundaries in the H. hypotrypa group remain uncertain. This study reveals the potential limitations of relying on distinct reproductive strategies as diagnostic taxonomic characters for Hypogymnia and also the challenges of using popular sequence-based species delimitation methods in groups with recent diversification histories.