Putative Taxa Research Articles

Genetic Diversity and Structure of Physaria on the Kaibab Plateau: Implications for Conservation.

Assessing patterns of genetic diversity within and among closely related congeners is important for evaluating the conservation status of rare plant taxa. We used nuclear microsatellite genotyping to examine the genetic relatedness among three Physaria taxa on the Kaibab Plateau in northern Arizona. Over 100 species of Physaria are recognized, and are widely distributed in Western North America. On the Kaibab Plateau several taxa occur, including Physaria arizonica and two subspecies of P. kingii, P. kingii subsp. latifolia and P. kingii subsp. kaibabensis. The latter subspecies, the Kaibab bladderpod, is rare and endemic to the Kaibab Plateau and is a potential candidate to be listed under the Endangered Species Act. Morphological characters, primarily flower color, have been used to distinguish P. kingii subsp. kaibabensis from other subspecies. Here we aim to assess its genetic diversity and differentiation as compared to congeners on and around the Kaibab Plateau. We genotyped DNA obtained from leaf samples from 463 individuals collected from 26 sites representing the three putative taxa (12 P. kingii subsp. kaibabensis, 8 P. kingii subsp. latifolia, and 6 P. arizonica). Our results showed that all samples initially identified as P. kingii subsp. latifolia and P. kingii subsp. kaibabensis on the Kaibab Plateau form a single genetic cluster that is well-differentiated from P. kingii subsp. latifolia sampled from sites off the plateau or P. arizonica on or off the plateau. For P. kingii on the plateau, our findings do not support the previous subspecies designations based on morphological characters. While additional studies of P. kingii will further resolve taxonomic uncertainties within this species, our findings indicate that the Kaibab Plateau population is genetically diverse and genetically distinct, and federal protection is justified in light of the threats faced on the Kaibab Plateau and its limited range.

Population genomic evidence of a putative ‘far-west’ African cryptic taxon in the Anopheles gambiae complex

The two main Afrotropical malaria vectors - Anopheles coluzzii and An. gambiae – are genetically distinct and reproductively isolated across West Africa. However, populations at the western extreme of their range are assigned as “intermediate” between the two species by whole genome sequence (WGS) data, and as hybrid forms by conventional molecular diagnostics. By exploiting WGS data from 1190 specimens collected across west Africa via the Anopheles gambiae 1000 Genomes network, we identified a putative taxon in the far-west (provisionally named Bissau molecular form), which did not arise by admixture but rather may have originated at the same time as the split between An. coluzzii and An. gambiae. Intriguingly, this taxon lacks insecticide resistance mechanisms commonly observed in the two main species. These findings lead to a change of perspective on malaria vector species in the far-west region with potential for epidemiological implications, and a new challenge for genetic-based mosquito control approaches.

Identifiability of speciation times under the multispecies coalescent

The advent of rapid and inexpensive sequencing technologies has necessitated the development of computationally efficient methods for analyzing sequence data for many genes simultaneously in a phylogenetic framework. The coalescent process is the most commonly used model for linking the underlying genealogies of individual genes with the global species-level phylogeny, but inference under the coalescent model is computationally daunting in the typical inference frameworks (e.g., the likelihood and Bayesian frameworks) due to the dimensionality of the space of both gene trees and species trees. Here we consider estimation of the branch lengths in fixed species trees with three or four taxa, and show that these branch lengths are identifiable. We also show that for three and four taxa simple estimators for the branch lengths can be derived based on observed site pattern frequencies. Properties of these estimators, such as their asymptotic variances and large-sample distributions, are examined, and performance of the estimators is assessed using simulation. Finally, we use these estimators to develop a hypothesis test that can be used to delimit species under the coalescent model for three or four putative taxa.

Ten new species and notes on the genus Psoralea L. (Psoraleeae, Fabaceae) from South Africa

Background and aims – Following detailed phylogenetic and biogeographic studies of the tribe Psoraleeae, the genus Psoralea L. was shown to have been derived out of Otholobium C.H.Stirt. As Psoralea has nomenclatural priority, Otholobium has been subsumed into Psoralea, whereby two broad subgeneric groups are aligned with the previous descriptions of the separate genera, but some problems of placement of a few species remain unresolved. Work is ongoing to study and describe the nearly 20 undescribed species that will have to be considered before sectional groups can be established. In this paper we describe ten new species, including several putative taxa already recognized in regional floras, based on historic specimens and more recent field collections. Material and methods – Standard practices of herbarium and field taxonomy have been applied to study herbarium material available at B, BLFU, BM, BOL, BR, E, GRA, J, JRAU, K, KEI, L, LE, LINN, M, MO, NBG, NH, NU, NY, OXF, P, PRA, PRC, PRE, PRU, S, SAM, SCHG, SRGH, TCD, Z, ZT, and US. Additional material was provided from fieldwork by the authors and collaborators. Key results – Ten new species of Psoralea from southern Africa are described: Psoralea crista C.H.Stirt. & Muasya, P. fulva C.H.Stirt. & Muasya, P. luteovirens C.H.Stirt. & Muasya, P. nubicola C.H.Stirt. & Muasya, P. oreopola C.H.Stirt., P. pallescens C.H.Stirt. & Muasya, P. papillosa C.H.Stirt. & Muasya, P. prompta C.H.Stirt. & Muasya, P. schutteae C.H.Stirt. & Muasya, and P. vlokii C.H.Stirt. & Muasya. Conclusion – The newly described species, all restricted to South Africa, increases the number of Psoralea species to 129. These species arise from expanded fieldwork into previously under-collected areas, as well as from better refinement in species delimitations in the leafless ‘aphylla’ and pinnately-leaved species complexes.

Campylobacter devanensis sp. nov., Campylobacter porcelli sp. nov., and Campylobacter vicugnae sp. nov., three novel Campylobacter lanienae-like species recovered from swine, small ruminants, and camelids.

In a previous study characterizing Campylobacter strains deficient in selenium metabolism, 50 strains were found to be similar to, but distinct from, the selenonegative species Campylobacter lanienae. Initial characterization based on multilocus sequence typing and the phylogeny of a set of 20 core genes determined that these strains form three putative taxa within the selenonegative cluster. A polyphasic study was undertaken here to further clarify their taxonomic position within the genus. The 50 selenonegative strains underwent phylogenetic analyses based on the sequences of the 16S rRNA gene and an expanded set of 330 core genes. Standard phenotypic testing was also performed. All strains were microaerobic and anaerobic, Gram-negative, spiral or curved cells with some displaying coccoid morphologies. Strains were motile, oxidase, catalase, and alkaline phosphatase positive, urease negative, and reduced nitrate. Strains within each clade had unique phenotypic profiles that distinguished them from other members of the genus. Core genome phylogeny clearly placed the 50 strains into three clades. Pairwise average nucleotide identity and digital DNA-DNA hybridization values were all below the recommended cut-offs for species delineation with respect to C. lanienae and other related Campylobacter species. The data presented here clearly show that these strains represent three novel species within the genus, for which the names Campylobacter devanensis sp. nov. (type strain RM3662T=LMG 33097T=NCTC 15074T), Campylobacter porcelli sp. nov. (type strain RM6137T=LMG 33098T=CCUG 77054T=NCTC 15075T) and Campylobacter vicugnae sp. nov. (type strain RM12175T=LMG 33099T=CCUG 77055T=NCTC 15076T) are proposed.

Temperature growth profiles for five fungi isolated from a teaching laboratory in West Virginia.

Every year, fungal infections kill approximately 1.5 million people worldwide. About 90% of these invasive infections are caused by fungi from only four genera. High human body temperature serves as a growth barrier that prevents many fungal species from infecting human hosts. This study assessed the growth of five environmental fungal isolates at temperatures ranging from ambient room temperature to 39°C, above average human body temperature of 37°C. These five isolates were captured from the indoor air of a teaching laboratory at Shepherd University and identified to putative taxon through sequence of the nuclear ribosomal internal transcribed spacer (ITS) region in a previous study. All five fungal isolates grew well at ambient temperature, but did not grow well at 38°C. Specific patterns of growth between room temperature and 38°C were different for each isolate. This research was supported by a NASA-WVSGC Undergraduate Research Fellowship (ER) and a NASA-WVSGC Research Enhancement Award (LSR).

Clarifying genetic and taxonomic relationships among Pistacia taxa (Anacardiaceae) in Croatia

In the eastern Adriatic flora the genus Pistacia L. (Anacardiaceae) is represented with P. lentiscus L., P. terebinthus L., their hybrid P. × saportae Burnat and the cultivated P. vera L. In addition, an endemic putative taxon from Mt. Biokovo was described in 1985 as P. calcivora Radić. Our aim was to resolve relationships between the four putative indigenous taxa of this genus in Croatia (P. lentiscus, P. terebinthus, P. × saportae and P. calcivora) based on genetic (AFLP) and morphological data. Specifically, we aimed to determine the presence of the hybrid taxon P. × saportae and to validate the controversial taxonomic status of P. calcivora at the molecular and morphological levels. Our combined results indicate the presence of two well separated groups of populations. The first group included all individuals of P. terebinthus and the individuals initially assigned to the potential taxon P. calcivora based on leaf morphology, suggesting that there is no support for the described taxon P. calcivora and that it should be considered as a synonym for P. terebinthus. The second group corresponded to P. lentiscus and included the majority of the presumed hybrid individuals of P. × saportae. However, four hybrid individuals were confirmed at the molecular level and were placed between the two parental taxa in the phylogenetic tree, confirming the presence of P. × saportae in Croatia. Although confirmed P. × saportae individuals were genetically closer to P. lentiscus, they were morphologically more similar to P. terebinthus, hindering their correct identification in the field.

High diversity of Bacidia (Ramalinaceae, Lecanorales) species in the Caucasus as revealed by molecular and morphological analyses

AbstractDuring a study of the incompletely known lichen flora of the Caucasus, we analyzed 237 specimens of corticolous Bacidia s. str. collected in the Northern and Southern Caucasus, including Armenia, Azerbaijan, Georgia, and Russia. Of these, 54 specimens belonging to 11 species of Bacidia s. str. were selected for molecular studies, representing the observed morphological variability of the genus. We obtained 142 sequences from three RNA-coding genes (nrITS, nrLSU, and mtSSU) and two protein-coding genes (RPB1 and RPB2). The single and concatenated datasets were complemented with Bacidia s. str. sequences from GenBank and subjected to Bayesian inference and two maximum likelihood analyses (RAxML and IQ-TREE). The resulting trees yielded highly concordant topologies of the groups and corresponded with previous results, supporting two main clades correlating with apothecia pigmentation. Our analyses are the first to reveal the presence of Bacidia heterochroa in the Caucasus. An exceptionally high degree of morphological plasticity was found in the Rubella and Suffusa groups. As a result of morphological examination and phylogenetic results, B. caucasica (Suffusa group) was described as new to science. Furthermore, two putative taxa in the Rubella group, Bacidia inconspicua ined. and B. maritima ined., were introduced. This study furthers our understanding and documentation of the understudied lichen flora of the Caucasus, bringing the total number of Bacidia species for the region to 13.

The Importance of Contact Zones for Distinguishing Interspecific from Intraspecific Geographic Variation.

With limited sampling, geographic variation within a single species can be difficult to distinguish from interspecific variation, confounding our ability to draw accurate species boundaries. We argue that thorough sampling and analysis of contact zones between putative taxa can determine if assortative mating or selection against hybrids exists (supporting the presence of two distinct species), or alternatively if mating is random among genotypes and admixture among adjacent populations is gradual and continuous (supporting geographic variation within a single species). Here, we test two alternative hypotheses for two pairs of named taxa at contact zones within the American milksnake (Lampropeltis triangulum) complex. A prior morphological analysis found areas of gradual intergradation among named taxa, and concluded that the taxa represented geographical races of a single polytypic species. In contrast, a subsequent analysis of gene sequence data, but with limited sampling near the contact zones, hypothesized distinct boundaries between species at the contact zones. At the contact zone between proposed species L. triangulum and Lampropeltis gentilis, we examined a $\sim$700 km-wide transect across the states of Kansas and Missouri, with thorough sampling and reduced-representation genomic-level sequencing, to test the two opposing taxonomic hypotheses. Our transect analyses included examinations of population structure, fixed differences, cline-fitting, and an admixture index analysis. These analyses all supported a gradual and continuous geographic cline across a broad intergrade zone between two geographic forms of L. triangulum, thus providing strong support for a single species in this region (and no support for the recognition of L. gentilis as a distinct species). At a second contact zone between proposed species L. triangulum and Lampropeltis elapsoides (but variously treated as species or subspecies by different researchers) in Kentucky and Tennessee, we re-evaluated morphological data. In this case, the contact zone analysis indicated sympatry and reproductive isolation of the two taxa, and thus strongly supported L. triangulum and L. elapsoides as distinct species. We conclude that detailed studies of contact zones, based on either genetic or morphological data, are essential for distinguishing intraspecific from interspecific variation in the case of widely and continuously distributed taxa. [Contact zones; speciation; species concepts; species delimitation; taxonomy.].

World Heritage lizard: population genetics and species status of the range-restricted Hamelin skink, Ctenotus zastictus

The Shark Bay World Heritage region in western Australia is home to a number of species of substantial conservation concern. Among these is a small scincid lizard, Ctenotus zastictus, which represents one of the most geographically-restricted vertebrates on the Australian mainland. The long-term persistence of Ctenotus zastictus is threatened due to the small size of its range, isolation from suitable habitat patches elsewhere, and potential impacts from climate change and mining. Accordingly, conservation efforts in Australia have targeted C. zastictus as the focus of protection. But this attention might be unwarranted – the species might not be evolutionarily unique. Previous genetic assessments have suggested limited differentiation between C. zastictus and its putative sister taxon, and the taxonomic status of C. zastictus has never been formally evaluated. Here, we use population genomic, phylogenetic, and ecoclimatic analyses to characterize the species status of C. zastictus in context of its closely-related congeners. In doing so, we explore the practical and conceptual challenges of revising species boundaries in threatened species, many of which are also rare and range-restricted. We demonstrate that C. zastictus is a coherent evolutionary unit that has been isolated from its putative sister species for at least two million years. Based on these results, we recommend that C. zastictus should retain its taxonomic status.

Appropriate Irrigation and Fertilization Regime Restrain Indigenous Soil Key Ammonia-Oxidizing Archaeal and Bacterial Consortia to Mitigate Greenhouse Gas Emissions

Harnessing an ammonia-oxidizing microbiome has become an increasingly attractive form of management for mitigating greenhouse gas emissions in rice paddies; however, the relationship between greenhouse gas emissions and ammonia-oxidizing microbiomes, using a nitrogen application and irrigation regime, has not been well investigated. To decipher which of (and how) the specific mmonia-oxidizing bacterial species drive the greenhouse gas CH4 and N2O emissions, a field experiment with varying nitrogen application and irrigation regimes was initiated to investigate the succession of key bacterial consortia associated with GHG emissions. The results showed that water-saving irrigation (AWD) significantly increased NO3-N and NH4+-N concentrations, compared with conventional irrigation (FDF), whereas (total nitrogen) TN was little higher in FDF (1.38 g kg−1) compared with the AWD (1.36 g kg−1). During the rice-growing season, CH4 emissions ascended speedily, and emissions peaked at maximum values of 3.32 and 4.41 ug mg−2 h−1 on day 5 in FDF and AWD irrigation regimes, respectively, and then they rapidly decreased during the midseason period, maintaining a relatively low emission rate until the rice was harvested. The patterns of N2O emission fluxes had the same tendencies with N fertilization. Putative key taxa, such as Flavobacterium, Massilia, Arenimonas, Novosphingobium, Pseudomonas, exhibited significant positive relationships with higher GHG emissions, suggesting that they make particularly obvious contributions to N2O emissions. These putative taxa should be considered when designing a high nitrogen application and irrigation strategy. As such, the nitrogen application of N180, and the irrigation regimes of water-saving irrigation, are recommended methods for N conservation and the mitigation of greenhouse gas emissions in rice paddies.

Taxonomic revision of the southern hemisphere pygmy forget-me-not group (Myosotis; Boraginaceae) based on morphological, population genetic and climate-edaphic niche modelling data

A taxonomic revision of the southern hemisphere pygmy forget-me-not group (Myosotis L.; Boraginaceae) is presented here. Climate-edaphic niches are modelled and compared for five species in the pygmy group, namely, M. antarctica Hook.f., M. brevis de Lange & Barkla, M. drucei (L.B.Moore) de Lange & Barkla, M. pygmaea Colenso and M. glauca (G.Simpson & J.S.Thomson) de Lange & Barkla, and one unnamed putative taxon, M. “Volcanic Plateau”. In this case, niche-modelling data mostly do not aid species delimitation, but morphological and genetic data provide evidence for recognising the following three species within the group: M. brevis and M. glauca (both endemic to New Zealand), and an enlarged M. antarctica (native to New Zealand, Campbell Island and Chile). Myosotis antarctica is here circumscribed to include M. antarctica sens. strict., M. drucei and M. pygmaea. The following two allopatric subspecies of M. antarctica are recognised on the basis of minor morphological differences: subsp. antarctica (formerly M. antarctica from Campbell Island and Chile, M. drucei and M. “Volcanic Plateau”) and subsp. traillii Kirk (formerly known by New Zealand botanists as M. pygmaea Colenso, an illegitimate name). For all three species, which are considered Threatened or At Risk, most of their genetic variation is partitioned between rather than within populations, meaning that conserving as many populations as possible should be the priority to minimise risk of extinction.

Phylogenetic analysis of the Neotropical Albitarsis Complex based on mitogenome data

BackgroundSome of the most important malaria vectors in South America belong to the Albitarsis Complex (Culicidae; Anophelinae; Anopheles). Understanding the origin, nature, and geographical distribution of species diversity in this important complex has important implications for vector incrimination, control, and management, and for modelling future responses to climate change, deforestation, and human population expansion. This study attempts to further explore species diversity and evolutionary history in the Albitarsis Complex by undertaking a characterization and phylogenetic analysis of the mitogenome of all 10 putative taxa in the Albitarsis Complex.MethodsMitogenome assembly and annotation allowed for feature comparison among Albitarsis Complex and Anopheles species. Selection analysis was conducted across all 13 protein-coding genes. Maximum likelihood and Bayesian inference methods were used to construct gene and species trees, respectively. Bayesian methods were also used to jointly estimate species delimitation and species trees.ResultsGene composition and order were conserved across species within the complex. Unique signatures of positive selection were detected in two species—Anopheles janconnae and An. albitarsis G—which may have played a role in the recent and rapid diversification of the complex. The COI gene phylogeny does not fully recover the mitogenome phylogeny, and a multispecies coalescent-based phylogeny shows that considerable uncertainty exists through much of the mitogenome species tree. The origin of divergence in the complex dates to the Pliocene/Pleistocene boundary, and divergence within the distinct northern South American clade is estimated at approximately 1 million years ago. Neither the phylogenetic trees nor the delimitation approach rejected the 10-species hypothesis, although the analyses could not exclude the possibility that four putative species with scant a priori support (An. albitarsis G, An. albitarsis H, An. albitarsis I, and An. albitarsis J), represent population-level, rather than species-level, splits.ConclusionThe lack of resolution in much of the species tree and the limitations of the delimitation analysis warrant future studies on the complex using genome-wide data and the inclusion of additional specimens, particularly from two putative species, An. albitarsis I and An. albitarsis J.Graphical

Molecular phylogeny and species delimitation of the freshwater prawn Macrobrachium pilimanus species group, with descriptions of three new species from Thailand.

Specific status and species boundaries of several freshwater prawns in the Macrobrachium pilimanus species group remain ambiguous, despite the taxonomic re-description of type materials and additional specimens collected to expand the boundaries of some species. In this study, the “pilimanus” species group of Macrobrachium sensu Johnson (1958) was studied using specimens collected from montane streams of Thailand. Molecular phylogenetic analyses based on sequences of three molecular markers (COI, 16S and 18S rRNA) were performed. The phylogenetic results agreed with morphological identifications, and indicated the presence of at least nine putative taxa. Of these, six morphospecies were recognised as M. malayanum, M. forcipatum, M. dienbienphuense, M. hirsutimanus, M. eriocheirum, and M. sirindhorn. Furthermore, three morphologically and genetically distinct linages were detected, and are described herein as M. naiyanetri Siriwut sp. nov., M. palmopilosum Siriwut sp. nov. and M. puberimanus Siriwut sp. nov. The taxonomic comparison indicated wide morphological variation in several species and suggested additional diagnostic characters that are suitable for use in species diagnoses, such as the shape and orientation of fingers, the rostrum form, and the presence or absence of velvet pubescence hairs and tuberculated spinulation on each telopodite of the second pereiopods. The “pilimanus” species group was portrayed as non-monophyletic in both ML and BI analyses. The genetic structure of different geographical populations in Thailand was detected in some widespread species. The species delimitation based on the four delimitation methods (BIN, ABGD, PTP and GMYC) suggested high genetic diversity of the “pilimanus” species group and placed the candidate members much higher than in previous designations based on traditional morphology. This finding suggests that further investigation of morphological and genetic diversity of Southeast Asian freshwater prawns in the genus Macrobrachium is still required to provide a comprehensive species list to guide efforts in conservation and resource management.

GC–MS ‘chemophenetics’ on Australian pink-flowered Phebalium (Rutaceae) using herbarium leaf material demonstrates phenetic agreement with putative new species

Abstract The aromatic pink-flowered Phebalium complex is comprised by P. nottii Maiden & Betche, P. speciosum I. Telford and the very similar but mostly white-flowered P. woombye (F.M.Bailey) Domin. Phebalium nottii, as currently circumscribed, includes several geographically disjunct populations that have been segregated at the N.C.W. Beadle Herbarium as putatively distinct species, several of high conservation value. To study volatiles sustainably, large-scale hydrodistillation was aborted and only single leaves were removed from herbarium vouchers, extracted into solvent and analysed by GC–MS. Unlike other species of Phebalium, volatiles in pink-flowered Phebalium are mostly dominated by spathulenol and bicyclogermacrene. Multivariate analysis of the chemistry of volatiles clearly demonstrated good agreement between chemotypes and putative taxa in central Queensland populations. Southern taxa, and the true P. nottii sensu stricto from northern Queensland, express high levels of volatile coumarins. Thus, morphological relationships are mostly reflected in morphometric clusters. As with other members of Phebalium, most taxa can be distinguished on chemistry alone, using only GC–MS analysis of herbarium material. These results corroborate several new species and reveal relationships within the heterogeneous species aggregate of P. nottii.

DNA barcode library for European Gelechiidae (Lepidoptera) suggests greatly underestimated species diversity.

For the first time, a nearly complete barcode library for European Gelechiidae is provided. DNA barcode sequences (COI gene – cytochrome c oxidase 1) from 751 out of 865 nominal species, belonging to 105 genera, were successfully recovered. A total of 741 species represented by specimens with sequences ≥ 500bp and an additional ten species represented by specimens with shorter sequences were used to produce 53 NJ trees. Intraspecific barcode divergence averaged only 0.54% whereas distance to the Nearest-Neighbour species averaged 5.58%. Of these, 710 species possessed unique DNA barcodes, but 31 species could not be reliably discriminated because of barcode sharing or partial barcode overlap. Species discrimination based on the Barcode Index System (BIN) was successful for 668 out of 723 species which clustered from minimum one to maximum 22 unique BINs. Fifty-five species shared a BIN with up to four species and identification from DNA barcode data is uncertain. Finally, 65 clusters with a unique BIN remained unidentified to species level. These putative taxa, as well as 114 nominal species with more than one BIN, suggest the presence of considerable cryptic diversity, cases which should be examined in future revisionary studies.

Comparative genome characterization of the periodontal pathogen Tannerella forsythia

BackgroundTannerella forsythia is a bacterial pathogen implicated in periodontal disease. Numerous virulence-associated T. forsythia genes have been described, however, it is necessary to expand the knowledge on T. forsythia’s genome structure and genetic repertoire to further elucidate its role within pathogenesis. Tannerella sp. BU063, a putative periodontal health-associated sister taxon and closest known relative to T. forsythia is available for comparative analyses. In the past, strain confusion involving the T. forsythia reference type strain ATCC 43037 led to discrepancies between results obtained from in silico analyses and wet-lab experimentation.ResultsWe generated a substantially improved genome assembly of T. forsythia ATCC 43037 covering 99% of the genome in three sequences. Using annotated genomes of ten Tannerella strains we established a soft core genome encompassing 2108 genes, based on orthologs present in > = 80% of the strains analysed. We used a set of known and hypothetical virulence factors for comparisons in pathogenic strains and the putative periodontal health-associated isolate Tannerella sp. BU063 to identify candidate genes promoting T. forsythia’s pathogenesis. Searching for pathogenicity islands we detected 38 candidate regions in the T. forsythia genome. Only four of these regions corresponded to previously described pathogenicity islands. While the general protein O-glycosylation gene cluster of T. forsythia ATCC 43037 has been described previously, genes required for the initiation of glycan synthesis are yet to be discovered. We found six putative glycosylation loci which were only partially conserved in other bacteria. Lastly, we performed a comparative analysis of translational bias in T. forsythia and Tannerella sp. BU063 and detected highly biased genes.ConclusionsWe provide resources and important information on the genomes of Tannerella strains. Comparative analyses enabled us to assess the suitability of T. forsythia virulence factors as therapeutic targets and to suggest novel putative virulence factors. Further, we report on gene loci that should be addressed in the context of elucidating T. forsythia’s protein O-glycosylation pathway. In summary, our work paves the way for further molecular dissection of T. forsythia biology in general and virulence of this species in particular.

Species delimitation and systematics of the green pythons (Morelia viridis complex) of melanesia and Australia

Molecular data sets and the increasing use of integrative systematics is revealing cryptic diversity in a range of taxa – particularly in remote and poorly sampled landscapes like the island of New Guinea. Green pythons (Morelia viridis complex) are one of the most conspicuous elements of this island’s fauna, with large numbers taken from the wild to supply international demand for exotic pets. We test hypotheses about species boundaries in green pythons from across New Guinea and Australia with mitochondrial genomes, 389 nuclear exons, and comprehensive assessment of morphological variation. Strong genetic structuring of green python populations and species delimitation methods confirm the presence of two species, broadly occurring north and south of New Guinea’s central mountains. Our data also support three subspecies within the northern species. Subtle but consistent morphological divergence among the putative taxa is concordant with patterns of molecular divergence. Our extensive sampling identifies several zones of hitherto unknown biogeographical significance on the island of New Guinea. We revise the taxonomy of the group, discuss the relevance of our findings in the context of Papuan biogeography and the implications of our systematic changes for the conservation management of these taxa.

Taxonomy and diversity of a little-known diatom genus Simonsenia (Bacillariaceae) in the marine littoral: novel taxa from the Yellow Sea and the Gulf of Mexico

Background and aims – The diatom genus Simonsenia has been considered for some time a minor taxon, limited in its distribution to fresh and slightly brackish waters. Recently, knowledge of its diversity and geographic distribution has been enhanced with new species described from brackish-marine waters of the southern Iberian Peninsula and from inland freshwaters of South China, and here we report novel Simonsenia from fully marine waters.
 Methods – New isolates of Simonsenia species were obtained from marine waters, the littoral zone of the Korean Yellow Sea coast and the Gulf of Mexico in Corpus Christi (Texas), and documented in LM, SEM and with DNA sequence data (plastid-encoded rbcL and psbC). Phylogenetic trees of raphid diatoms were constructed to assess the relationships of the new species and of the genus as a whole.
 Key results and conclusions – Two novel species of Simonsenia (S. eileencoxiae and S. paucistriata) are described and a further putative taxon is characterized morphologically. The molecular phylogeny of the new Simonsenia species and previously sequenced species supports both the monophyly of the genus and its place within the Bacillariaceae. The Simonsenia clade clusters with clades composed of Cylindrotheca, Denticula and some Nitzschia spp. (including N. amphibia, N. frustulum, N. inconspicua). Hence Simonsenia is firmly positioned within the Bacillariaceae by molecular phylogenies, confirming its position within this group based on the possession of a canal raphe and its ultrastructure, and rejecting its classification within the Surirellaceae. Morphological data from the new Simonsenia species is typical for the genus, with a “simonsenioid” canal raphe type supported over the valve face with fenestral braces, alar canals connecting the canal raphe with the cell lumen, and the presence of fenestrae between the alar canals externally. Our results indicate unequivocally that the biogeography and the biodiversity of Simonsenia remain highly underestimated.

Description of new chiactine-bearing sponges provides insights into the higher classification of Calcaronea (Porifera: Calcarea).

A recent phylogenetic study revealed a close relationship between chiactine-bearing (family Achramorphidae, order Leucosolenida) and pugiole-bearing (order Baerida) calcaronean sponges as well as new putative taxa within Achramorphidae. In this study, we present a revision of chiactine-bearing sponges based on morphological re-examination of type material and recently collected specimens, in addition to new molecular data for the ribosomal 18S and C-region of the 28S. We provide re-descriptions for all known chiactine-bearing species, and further describe two new species from the Antarctic (Achramorpha antarctica sp. nov. and Megapogon schiaparellii sp. nov.) and two new species and a new genus from the Nordic Seas (Achramorpha ingolfi sp. nov. and Sarsinella karasikensis gen. nov. sp. nov.). The new phylogenetic reconstruction based on ribosomal 18S and C-region of the 28S confirms previous findings about the close relationship of some members of Baerida and the family Achramorphidae of the order Leucosolenida. However, new material and the addition of molecular data from the type species of both taxa would be required to formally propose changes at (sub-)ordinal levels within the classification of Calcaronean sponges.