Large-scale diversity reassessment,evolutionary history,and taxonomic revision of the green macroalgae family Udoteaceae (Bryopsidales,Chlorophyta)

Udoteaceae is a morphologically diverse family of the order Bryopsidales. Despite being very widespread geographically, this family is little known as compared with the closely related Halimedaceae or Caulerpaceae. Using the most extensive Udoteaceae collection to date and a multilocus genetic data set (tufA, rbcL, and 18S rDNA), we reassessed the species diversity of the family, as well as the phylogenetic relationships, the diagnostic morphoanatomical characters, and evolutionary history of its genera, toward a proposed taxonomic revision. Our approach included a combination of molecular and morphological criteria, including species delimitation methods, phylogenetic reconstruction, and mapping of trait evolution. We successfully delimited 62 species hypotheses, of which 29 were assigned (existing) species names and 13 represent putative new species. Our results also led us to revise the genera Udotea s.s., Rhipidosiphon s.s., and Chlorodesmis s.s., to validate the genus Rhipidodesmis, and to propose three new genera: Glaukea gen. nov., Ventalia gen. nov., and Udoteopsis gen. nov. We also identified two large species complexes, which we refer to as the “Penicillus–Rhipidosiphon–Rhipocephalus–Udotea complex” and the “Poropsis–Penicillus–Rhipidodesmis complex”. Using a time-calibrated phylogeny, we estimated the origin of the family Udoteaceae at Late Triassic (ca. 216 Ma), whereas most of the genera originated during Paleogene. Our morphological inference results indicated that the thallus of the Udoteaceae ancestor was likely entirely corticated and calcified, composed of a creeping axis with a multisiphonous stipe and a pluristromatic flabellate frond. The frond shape, cortication, and calcification are still symplesiomorphies for most extant Udoteaceae genera and represent useful diagnostic characters.     

Interspecific delimitation and phylogenetic origin of Pugionium(Brassicaceae)

Pugionium(Brassicaceae)is a small genus that occurs in central Asian deserts.The interspecific delimitation and taxonomic treatments of this genus are disputed and its phylogenetic origin remains unknown. In the present study,we examined these issues based on morphological and molecular data obtained for the first time.We used statistical methods to examine inter-and intraspecific morphological variations.The results suggest that only two species,namely P.dolabratum and P.cornutum,can be warranted for all examined populations and specimens,whereas three species(P.calcaratum,P.cristatum,and P.pterocarpum)should be incorporated into P. dolabratum.This delimitation was further supported by the molecular data:all populations of P.dolabratum,P. calcaratum,P.cristatum,and P.pterocarpum shared the same internal transcribed spacer genotype,whereas those from P.cornutum had another type.Phylogenetic analyses of Pugionium and representative genera of Brassicaceae based on ndhF sequences suggest that this genus is sister to the genus Megacarpaea,which,together,comprise a well-supported lineage with Farsetia,Lobularia,Iberis,and Ionopsidium,whereas the two other genera that were previously suggested to be closely related to this genus(Isatis and Bunias)were placed in the other lineages.We further discuss the origin of Pugionium and suggest that it probably originated in central Asia when the climate became drier from the late Miocene.     

Interspecific delimitation and phylogenetic origin of Pugionium (Brassicaceae)

Pugionium (Brassicaceae) is a small genus that occurs in central Asian deserts. The interspecific delimitation and taxonomic treatments of this genus are disputed and its phylogenetic origin remains unknown.In the present study, we examined these issues based on morphological and molecular data obtained for the first time. We used statistical methods to examine inter- and intraspecific morphological variations. The results suggest that only two species, namely P. dolabratum and P cornutum, can be warranted for all examined populations and specimens, whereas three species (P. calcaratum, P. cristatum, and R pterocarpum) should be incorporated into P.dolabratum. This delimitation was further supported by the molecular data: all populations of P. dolabratum, P.calcaratum, P. cristatum, and P. pterocarpum shared the same internal transcribed spacer genotype, whereas those from P. cornutum had another type. Phylogenetic analyses of Pugionium and representative genera of Brassicaceae based on ndhF sequences suggest that this genus is sister to the genus Megacarpaea, which, together, comprise a well-supported lineage with Farsetia, Lobularia, Iberis, and Ionopsidium, whereas the two other genera that were previously suggested to be closely related to this genus (Isatis and Bunias) were placed in the other lineages. We further discuss the origin of Pugionium and suggest that it probably originated in central Asia when the climate became drier from the late Miocene.     

Morphometrics confirm taxonomic deflation in dwarf lemurs (Primates: Cheirogaleidae), as suggested by genetics

Detailed knowledge of the identity and distributions of extant species is essential for unravelling patterns and mechanisms of biodiversity, and it provides indispensable baseline data for conservation efforts. The taxonomy of the primates of Madagascar (Lemuriformes) has experienced drastic revisions in the last decades, with species numbers skyrocketing, especially in the genera Microcebus, Avahi, and Lepilemur. The dwarf lemurs (genus Cheirogaleus) have received less attention in terms of their taxonomy, even though they are closely related and syntopic with these diverse genera. The last revision of the genus was based on morphological data from museum specimens, and accepted seven species: Cheirogaleus medius, Cheirogaleus major, Cheirogaleus crossleyi, Cheirogaleus adipicaudatus, Cheirogaleus sibreei, Cheirogaleus ravus, and Cheirogaleus minusculus, whereas a more recent multilocus molecular study only detected three lineages: C. medius, C. major, and C. crossleyi. The goal of this study was to reassess the currently accepted taxonomy of the genus by examining six external and 32 craniodental characters of 120 museum specimens and 36 new specimens from the field. This study, in conjunction with a complementary molecular study, revealed lower diversity and a lower number of distinct morphs of dwarf lemurs than previously postulated. We conclude that in our sample there are three distinct morphs in the genus Cheirogaleus that correspond to C. medius, C. major, and C. crossleyi. We formally recognize C. adipicaudatus and C. ravus as synonyms of C. medius and C. major, respectively, and consider C. minusculus and C. sibreei to be potential synonyms of C. medius. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010.     

The snake family Psammophiidae (Reptilia: Serpentes): phylogenetics and species delimitation in the African sand snakes (Psammophis Boie, 1825) and allied genera

This study constitutes the first evolutionary investigation of the snake family Psammophiidae--the most widespread, most clearly defined, yet perhaps the taxonomically most problematic of Africa's family-level snake lineages. Little is known of psammophiid evolutionary relationships, and the type genus Psammophis is one of the largest and taxonomically most complex of the African snake genera. Our aims were to reconstruct psammophiid phylogenetic relationships and to improve characterisation of species boundaries in problematic Psammophis species complexes. We used approximately 2500 bases of DNA sequence from the mitochondrial and nuclear genomes, and 114 terminals covering all psammophiid genera and incorporating approximately 75% of recognised species and subspecies. Phylogenetic reconstructions were conducted primarily in a Bayesian framework and we used the Wiens/Penkrot protocol to aid species delimitation. Rhamphiophis is diphyletic, with Rhamphiophis acutus emerging sister to Psammophylax. Consequently we transfer the three subspecies of Rhamphiophis acutus to the genus Psammophylax. The monotypic genus Dipsina is sister to Psammophis. The two species of Dromophis occupy divergent positions deeply nested within Psammophis, and we therefore relegate Dromophis to the synonymy of Psammophis. Our results allow division of the taxonomically problematic Psammophis 'sibilans' species complex into two monophyletic entities, provisionally named the 'phillipsii' and 'subtaeniatus' complexes. Within these two clades we found support for the status of many existing species, but not for a distinction between P.p. phillipsii and P. mossambicus. Additionally, P. cf. phillipsii occidentalis deserves species status as the sister taxon of P. brevirostris.     

Molecular phylogenetics of Sarcolaenaceae (Malvales), Madagascar's largest endemic plant family

With 72 species belonging to ten genera, Sarcolaenaceae are the largest and most diverse of Madagascar's endemic plant families. Comprising shrubs and trees, with members found in nearly all of this island nation's biogeographic regions, they are characterised by the presence of a distinctive extra‐floral involucre that is more or less accrescent, partially or completely covering or enveloping the fruit. We present the first molecular phylogenetic study of Sarcolaenaceae, using broad sampling that encompasses the family's taxonomic and morphological diversity, including 46 species representing all ten genera and sequence data from one nuclear marker (ITS) and three plastid regions (psaA‐ORF170, psbA‐trnH and rbcL), to reconstruct phylogenetic relationships using Bayesian inference and maximum likelihood. Results confirm the monophyly of Sarcolaenaceae and of eight of the ten genera; the monophyly of Rhodolaena remains ambiguous, although the taxa sampled were recovered in two well supported clades that are coherent in terms of morphology and geography. Only a single species of Eremolaena was available for study. The phylogenetic backbone of Sarcolaenaceae is not fully resolved, making it difficult to identify potential morphological synapomorphies or ecological preferences between and within genera. In the family, two monophyletic groups were, however, found [Pentachlaena + Eremolaena + Perrierodendron (Clade A) and Xyloolaena + Leptolaena + Sarcolaena + Mediusella + Xerochlamys (Clade B)] that are consistent with previous results based on morphology. Expanded species sampling and data from additional, more quickly evolving markers will be needed to produce a fully resolved phylogenetic tree for Sarcolaenaceae, which could then serve as a basis for exploring macroevolutionary patterns and processes in this remarkable family and reconstructing its biogeographic history.     

Molecular phylogeny of the subterranean genus Niphargus (Crustacea: Amphipoda) in the Middle East: a comparison with European Niphargids

The subterranean genus Niphargus is one of the most species‐rich genera among freshwater amphipods in the world, distributed in the Western Palearctic. Thus far, taxonomic and phylogenetic research has focused mainly on the European half of the genus range. In this study, 25 populations of Niphargus from Iran, Lebanon and the Crimean Peninsula were investigated. Bayesian inference based on 28S, H3 and COI gene sequences suggests that populations from the area belong to four different clades. Three species from Crimea and one species from Iran are nested at basal nodes, indicating their rather ancient origin. The rest of the species are younger and belong to two separate clades. One Crimean species is a sister‐species to east Romanian species. The second clade includes one species from Lebanon and all but one population from Iran. The origin of this clade corresponds to marine transgression between the Black Sea and Mediterranean approximately 12 Mya. This clade was further investigated taxonomically. Revision of qualitative morphological traits and unilocus species delimitation methods using COI suggest that this clade comprises 12–16 species, of which only three have been described so far. Multilocus coalescence delimitation methods (using fragments of COI, 28S, H3 and ITS) strongly supported 11 of these species. The remaining populations comprise at least two species complexes that require further and more detailed taxonomic research. © 2015 The Linnean Society of London     

Testing the success of palaeontological methods in the delimitation of clam shrimp (Crustacea,Branchiopoda) on extant species

Fossil spinicaudatan taxonomy heavily relies on carapace features (size, shape, ornamentation) and palaeontologists have greatly refined methods to study and describe carapace variability. Whether carapace features alone are sufficient for distinguishing between species of a single genus has remained untested. In our study, we tested common palaeontological methods on 481 individuals of the extant Australian genus Ozestheria that have been previously assigned to ten species based on genetic analysis. All species are morphologically distinct based on geometric morphometrics (p ≤ 0.001), but they occupy overlapping regions in Ozestheria morphospace. Linear discriminant analysis of Fourier shape coefficients reaches a mean model performance of 93.8% correctly classified individuals over all possible 45 pairwise species comparisons. This can be further increased by combining the size and shape datasets. Nine of the ten examined species are clearly sexually dimorphic but male and female morphologies strongly overlap within species with little influence on model performance. Ornamentation is commonly species-diagnostic; seven ornamentation types are distinguished of which six are species-specific while one is shared by four species. A transformation of main ornamental features (e.g. from punctate to smooth) can occur among closely related species suggesting short evolutionary timescales. Our overall results support the taxonomic value of carapace features, which should also receive greater attention in the taxonomy of extant species. The extensive variation in carapace shape and ornamentation is noteworthy and several species would probably have been assigned to different genera or families if these had been fossils, bearing implications for the systematics of fossil Spinicaudata.     

Generic delimitation and biogeography of Maianthemum and Smilacina (Ruscaceae sensu lato): preliminary results based on partial 3′ matK gene and trnK 3′ intron sequences of cpDNA

The controversy over generic delimitation between Maianthemum and Smilacina has been unresolved for almost two centuries. Distributions of the two genera in the Northern Hemisphere also provide an excellent opportunity to further understand the disjunct distribution patterns of the North Temperate Flora. To test the generic delimitation and to investigate biogeographic patterns, we sequenced the partial 3′ matK gene and trnK 3′ intron of chloroplast DNA for 38 accessions, representing three species of Maianthemum, seven species of Smilacina, and four outgroup taxa. Maximum parsimony and neighbor-joining trees showed reciprocal monophyly of the two genera with very weak bootstrap support for each genus. Within each genus, relationships among species were poorly resolved. Despite its low resolution, this study shows that eastern Asian species of Smilacina and Maianthemum are generally more closely related to eastern North American taxa than to western ones. More detailed sampling of Smilacina from different geographic regions, especially from the two centers of diversity (southeastern Asia and Mexico/Central America), and additional sequences from cpDNA, as well as from nuclear DNA, are needed to test the reciprocal monophyly of the two genera and also to understand current distributions of disjunct taxa.     

Phylogenetic classification of Eudorylini (Diptera: Pipunculidae)

Abstract. The phylogenetic relationships of members of Eudorylini (Diptera: Pipunculidae: Pipunculinae) were explored. Two hundred and fifty-seven species of Eudorylini from all biogeographical regions and all known genera were examined. Sixty species were included in an exemplar-based phylogeny for the tribe. Two new genera are described, Clistoabdominalis and Dasydorylas . The identity of Eudorylas Aczél, the type genus for Eudorylini, has been obscure since its inception. The genus is re-diagnosed and a proposal to stabilize the genus and tribal names is discussed. An illustrated key to the genera of Pipunculidae is presented and all Eudorylini genera are diagnosed. Numerous new generic synonyms are proposed. Moriparia nigripennis Kozánek & Kwon is preoccupied by Congomyia nigripennis Hardy when both are transferred to Claraeola , so Cla. koreana Skevington is proposed as a new name for Mo. nigripennis .     

Phylogenetic relationships within the Archiloa genus complex (Proseriata,Monocelididae)

Of the seven genera which we have recognised within the Archiloa genus complex sensu Karling (1966) the cosmopolitan genus Archilina is the most primitive and is characterised only by plesiomorphic characters, and has to be considered paraphyletic. All other species of the Archiloa genus complex are hypothesized to be derived from Archilina-like ancestors through different evolutionary lineages. One lineage led to the genera Archiloa, Inaloa, Archilopsis and Monocelopsis, taxa found in the Atlantic and the Mediterranean. These genera are monophyletic and their relationships are analyzed. The genera Mesoda (Brazil) and Tajikina (Northern Pacific) can be considered as two other separate lineages. Similarly, within what we now consider as the genus Archilina different lineages can be recognized in different regions.     

A phylogenetic analysis of subtribe Pleurothallidinae (Orchidaceae)

A cladistic analysis of subtribe, Pleurothallidinae (Orchidaceae) is based on 45 anatomical/ morphological characters. The ingroup members comprise 24 genera; the large genus Pleurothallis consists of two subgenera and ten species complexes. Three taxa representing subtribes Laeliinae and Arpophyllinae are designated as outgroup. Eight most parsimonious trees were discovered using computer assisted software (length = 230; CI = 0.27). The hypothesis that subtribe Pleurothallidinae has undergone a unilinear reduction in the number of pollinia is not supported by this study. Although the eight-pollinia state as represented by Octomeria apparently is plesiomorphic, the two-pollinia and four-pollinia states arose early in the phylogeny of the subtribe. Both two-and four-pollinia states subsequently reappeared as parallelisms. The six-pollinia state exhibited in Brachionidium is autapomorphic. This cladistic analysis suggests that Pleurothallis is not a natural genus and, perhaps may be divided into several discrete genera.     

A phylogenetic analysis of subtribe Pleurothallidinae (Orchidaceae)

A cladistic analysis of subtribe, Pleurothallidinae (Orchidaceae) is based on 45 anatomical/ morphological characters. The ingroup members comprise 24 genera; the large genus Pkurothallis consists of two subgenera and ten species complexes. Three taxa representing subtribes Laeliinae and ArpophyUinae are designated as outgroup. Eight most parsimonious trees were discovered using computer assisted software (length = 230; CI = 0.27). The hypothesis that subtribe Pleurothallidinae has undergone a unilinear reduction in the number of pollinia is not supported by this study. Although the eight-pollinia state as represented by Octomeria apparently is plesiomorphic, the two-pollinia and four-pollinia states arose early in the phytogeny of the subtribe. Both two-and four-pollinia states subsequently reappeared as parallelisms. The six-pollinia state exhibited in Brachionidium is autapomorphic. This cladistic analysis suggests that Pkurothallis is not a natural genus and, perhaps may be divided into several discrete genera.     

The Genus Artemisia and its Allies: Phylogeny of the Subtribe Artemisiinae (Asteraceae, Anthemideae) Based on Nucleotide Sequences of Nuclear Ribosomal DNA Internal Transcribed Spacers (ITS)

Abstract: Sequences of the internal transcribed spacers (ITS1 and ITS2) of nuclear ribosomal DNA were analysed for 44 Artemisia species (46 populations) representing all the five classical subgenera and the geographical range of the genus, 11 species from 10 genera closely related to Artemisia, and six outgroup species from five other genera of the Anthemideae. The results definitely support the monophyly of the genus Artemisia in its broadest sense (including some taxa segregated as independent genera, like Oligosporus and Seriphidium ). Eight main clades are established in this molecular phylogeny within Artemisia; they agree in part with the classical subdivision of the genus, but they also suggest that some infrageneric groups must be redefined, especially the subgenus Artemisia. The subgenera Tridentatae and Seriphidium are independent from each other. Some of the satellite genera are clearly placed within Artemisia ( Artemisiastrum, Filifolium, Mausolea, Picrothamnus, Sphaeromeria, Turaniphytum ), whereas some others fall outside the large clade formed by this genus (Brachanthemum, Elachanthemum, Hippolytia, Kaschgaria). Our results, correlated to other data such as pollen morphology, allow us to conclude that the subtribe Artemisiinae as currently defined is a very heterogeneous group. Affinities of the largest genus of the subtribe and tribe, Artemisia, and of other genera of the subtribe to some genera from other subtribes of the Anthemideae strongly suggest that subtribe Artemisiinae needs a deep revision and redefinition. Phylogenetic utility of region trnL-F of the plastid DNA in the genus Artemisia and allies was also evaluated: sequences of the trnL-F region in Artemisia do not provide phylogenetic information.     

Genus-specific host range of Phomopsis amaranthicola (Sphaeropsidales), a bioherbicide agent for Amaranthus spp.

Phomopsis amaranthicola, a newly described species discovered in Florida, is under development as a biological control agent for weeds belonging to the genus Amaranthus. Host-range testing was performed on the fungus, using the centrifugal phylogenetic scheme, with Amaranthus hybridus as the focal plant. Forty-five accessions of 21 species in the genus Amaranthus were tested for susceptibility to infection by this fungus. Fifty-six plant species outside the genus Amaranthus were also tested. The latter included crops in which the fungus might be used as a bioherbicide, members of genera that are closely related to Amaranthus, and selections of species that have been reported as hosts of other species of the genera Phomopsis or Diaporthe. Phomopsis amaranthicola did not infect any of the plants from outside the genus Amaranthus but was highly pathogenic to several species in the genus Amaranthus. All Amaranthus species tested were infected to varying degrees by P. amaranthicola; the resulting mortality levels were also variable. Thus, P. amaranthicola appears to be host-specific to the members of the genus Amaranthus. The generic level of specificity of this pathogen renders it not only a safe bioherbicide agent but also one that could be used against several weedy Amaranthus species.     

Species delimitation of the liquorice tribe (Leguminosae: Glycyrrhizeae) based on phylogenomic and machine learning analyses

The liquorice tribe Glycyrrhizeae is a leguminous herbaceous group of plants comprised of the genera Glycyrrhiza and Glycyrrhizopsis. Some Glycyrrhiza taxa contain glycyrrhizin, a pharmacologically significant sweet substance that also has applications in crafting industrial materials. Here, we utilized an expanded taxon sampling of Glycyrrhizeae to reconstruct the phylogenetic relationships in the tribe based on genome skimming data, including whole chloroplast genomes, nuclear ribosomal DNA, and low-copy nuclear DNA. We also launched machine learning analysis (MLA) for one species pair with controversial taxonomic boundary. The integrated results indicated Glycyrrhizopsis should be split from Glycyrrhiza, while the former genus Meristotropis should be treated as part of Glycyrrhiza. Glycyrrhizopsis includes two species, Glycyrrhizopsis asymmetrica and Glycyrrhizopsis flavescens, and we recognize 13 species in Glycyrrhiza: Glycyrrhiza acanthocarpa, Glycyrrhiza astragalina, Glycyrrhiza bucharica, Glycyrrhiza echinata, Glycyrrhiza foetida, Glycyrrhiza glabra, Glycyrrhiza gontscharovii, Glycyrrhiza lepidota, Glycyrrhiza macedonica, Glycyrrhiza pallidiflora, Glycyrrhiza squamulosa, Glycyrrhiza triphylla, and Glycyrrhiza yunnanensis. We propose a broader G. glabra that includes former Glycyrrhiza aspera, G. glabra s.s., Glycyrrhiza inflata, and Glycyrrhiza uralensis, and represents the glycyrrhizin-contained medicinal group. Our ancestral state inferences show the ancestor of Glycyrrhiza lacked glycyrrhizin, and the presence of glycyrrhizin evolved twice within Glycyrrhiza during the last one million years. Our integrative phylogenomics-MLA study not only provides new insights into long-standing taxonomic controversies of Glycyrrhizeae, but also represents a useful approach for future taxonomic studies on other plant taxa.     

Revision of generic limits in Hyptis Jacq. (Labiatae) and its allies

The primarily neotropical sub-tribe Hyptidinae (Labiatae: tribe Ocimeae) consists of six or seven genera of which the largest is the genus Hyptis with over 300 species. Over the last 12 years, work on the group at the Royal Botanic Gardens, Kew, examining macro-morphological and anatomical characters, as well as pollen surface and chromosome number, has indicated that the genus Hyptis is paraphyletic, with a few of the larger-flowered sections apparently being more closely related to the neighbouring genus Eriope than to the smaller-flowered sections of Hyptis . This has been confirmed by preliminary cladistic studies now in progress. In order to provide a working classification for the group, prior to the publication of the more detailed study, two new genera: Hypenia and Hyptidendron are created. A key to genera of South American Hyptidinae is provided, as well as one to distinguish the two new sections of Hyptidendron . Forty-five new combinations are made.