Phylogenetic Distinctiveness Research Articles

High functional vulnerability across the world’s deep-sea hydrothermal vent communities

At the nearly pristine hydrothermal vents of the deep sea, highly endemic animals depend upon bacteria nourished by hydrothermal fluids that emerge as outflows from the seafloor. These animals are remarkable in tolerating extreme conditions, including high heat, toxic reduced sulfide, and low oxygen. Here, we test whether the extreme vent environment has selected for functionally similar species across the world's deep ocean, despite well-established global geographic patterns of high phylogenetic distinctness. High functional redundancy in species pools within regions suggests that the extreme environments select for species with specific traits. Yet, some regions emerge as functional hotspots where species pools with distinct functional trait compositions may represent geological idiosyncrasies of the habitats. Moreover, many species are functionally unique, an outcome of low species richness in a system where the species pool is small at all scales. Given the high proportion of functionally unique species, simulated species extinctions indicate that species losses would rapidly translate to the elimination of functionally irreplaceable species and could tip vent systems to functional collapse. Ocean changes and human-induced threats are expected to significantly impact many vent species as human activities expand in the remote deep sea. The opportunity exists now to take precautionary actions to limit the rates of extinction now ubiquitous in more accessible areas of Earth.

Characterization of switchgrass (Panicum virgatum L.) PvKSL1 as a levopimaradiene/abietadiene-type diterpene synthase.

The diverse class of plant diterpenoid metabolites serves important functions in mediating growth, chemical defence, and ecological adaptation. In major monocot crops, such as maize (Zea mays), rice (Oryza sativa), and barley (Hordeum vulgare), diterpenoids function as core components of biotic and abiotic stress resilience. Switchgrass (Panicum virgatum) is a perennial grass valued as a stress-resilient biofuel model crop. Previously we identified an unusually large diterpene synthase family that produces both common and species-specific diterpenoids, several of which accumulate in response to abiotic stress. Here, we report discovery and functional characterization of a previously unrecognized monofunctional class I diterpene synthase (PvKSL1) via in vivo co-expression assays with different copalyl pyrophosphate (CPP) isomers, structural and mutagenesis studies, as well as genomic and transcriptomic analyses. In particular, PvKSL1 converts ent-CPP into ent-abietadiene, ent-palustradiene, ent-levopimaradiene, and ent-neoabietadiene via a 13-hydroxy-8(14)-ent-abietene intermediate. Notably, although featuring a distinct ent-stereochemistry, this product profile is near-identical to bifunctional (+)-levopimaradiene/abietadiene synthases occurring in conifer trees. PvKSL1 has three of four active site residues previously shown to control (+)-levopimaradiene/abietadiene synthase catalytic specificity. However, mutagenesis studies suggest a distinct catalytic mechanism in PvKSL1. Genome localization of PvKSL1 distant from other diterpene synthases, and its phylogenetic distinctiveness from known abietane-forming diterpene synthases, support an independent evolution of PvKSL1 activity. Albeit at low levels, PvKSL1 gene expression predominantly in roots suggests a role of diterpenoid formation in belowground tissue. Together, these findings expand the known chemical and functional space of diterpenoid metabolism in monocot crops.

Methylobacterium amylolyticum sp. nov. and Methylobacterium ligniniphilum sp. nov., isolated from soil.

Two pink-pigmented bacteria, designated strains NEAU-140T and NEAU-KT, were isolated from field soil collected from Linyi, Shandong Province, PR China. Both isolates were aerobic, Gram-stain-negative, rod-shaped, and facultatively methylotrophic. 16S rRNA gene sequences analysis showed that these two strains belong to the genus Methylobacterium. Strain NEAU-140T exhibited high 16S rRNA gene sequence similarities to Methylobacterium radiotolerans NBRC 15690T (97.43 %) and Methylobacterium phyllostachyos NBRC 105206T (97.36 %). Strain NEAU-KT exhibited high 16S rRNA gene sequence similarities to M. phyllostachyos NBRC 105206T (99.00 %) and Methylobacterium longum DSM 23933T (98.72 %). A phylogenetic tree based on 16S rRNA gene sequences showed that strain NEAU-140T formed a clade with Methylobacterium aerolatum (95.94 %), Methylobacterium persicinum (95.66 %) and Methylobacterium komagatae (96.87 %), and strain NEAU-KT formed a cluster with M. phyllostachyos and M. longum. The predominant fatty acid in both strains was C18 : 1 ω7c. Both strains contained ubiquinone Q-10 as the only respiratory quinone. The polar lipid profiles of both strains contained diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylcholine. Whole-genome phylogeny showed that strains NEAU-140T and NEAU-KT formed a phyletic line with M. aerolatum, M. persicinum, Methylobacterium radiotolerans, Methylobacterium fujisawaense, Methylobacterium oryzae, Methylobacterium tardum, M. longum and M. phyllostachyos. The orthologous average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain NEAU-140T and its closely related strains were lower than 82.62 and 25.90 %, respectively. The ANI and dDDH values between strain NEAU-KT and its closely related strains were lower than 86.29 and 31.7 %, respectively. The genomic DNA G+C contents were 71.63 mol% for strain NEAU-140T and 69.08 mol% for strain NEAU-KT. On the basis of their phenotypic and phylogenetic distinctiveness and the results of dDDH and ANI hybridization, these two isolates represent two novel species within the genus Methylobacterium, for which the names Methylobacterium amylolyticum sp. nov. (type strain NEAU-140T=MCCC 1K08801T=DSM 110568T) and Methylobacterium ligniniphilum sp. nov. (type strain NEAU-KT=MCCC 1K08800T=DSM 110567T) are proposed.

Undibacterium cyanobacteriorum sp. nov., an auxin-producing bacterium isolated from fresh water during cyanobacterial bloom period.

A novel Gram-negative, white-pigmented, and auxin-producing strain, 20NA77.5T, was isolated from fresh water during cyanobacterial bloom period. Pairwise comparison of the 16S rRNA gene sequences showed that strain 20NA77.5T belonged to the genus Undibacterium and exhibited the highest sequence similarity to the type strains of Undibacterium danionis (98.00%), Undibacterium baiyunense (97.93%), Undibacterium macrobrachii (97.92%), and Undibacterium fentianense (97.71%). The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain 20NA77.5T and its related type strains were below 79.93 and 23.80%, respectively. The predominant fatty acids (> 10% of the total fatty acids) were C16:0 and summed feature 3 (C16:1ω7c and/or C16:1ω6c). The genomic DNA G + C content of strain 20NA77.5T was found to be 48.61%. Based on the phylogenetic distinctness, chemotaxonomic features, and phenotypic features, strain 20NA77.5T is considered to represent a novel species of the genus Undibacterium, for which the name Undibacterium cyanobacteriorum sp. nov is proposed. The type strain is 20NA77.5T (= KCTC 8005T = LMG 33136T).

Combining extinction probability and functional or phylogenetic distinctiveness to define conservation priorities

Given the current accelerating extinction rates, an increasing number of species-based conservation strategies have emerged because of the public interest in helping save particular species by funding rescue actions. Although public interest has focused mainly on well-studied, charismatic species, conservation scientists have developed tools to help prioritize species conservation from a more objective perspective, preserving ecosystem functioning and human well-being for future generations. For that purpose, species-centered biodiversity indicators that account not only for the extinction risk of a species but also for its evolutionary and/or functional distinctiveness have been developed. A species is considered irreplaceable and distinctive if it is isolated on the phylogenetic tree and/or if it has distinct traits, especially functional traits that determine the species' effects on ecosystems. The quantitative values representing extinction risk and distinctiveness of species have often been multiplied to define a quantitative conservation priority score. However, there is a plethora of ways to combine several conservation criteria into a single quantitative priority score, and the product of this multiplication is one such possibility. Each possible way of combining extinction risk and distinctiveness provides a different point of view on which of these should prevail to set conservation priorities. We set up an axiomatic framework on how a species' distinctiveness could be combined with its extinction risk via a tool used to define conservation priorities. By doing so, we show that further work is still needed to better communicate biodiversity indicators to the public and ensure an informed choice of indicators.

Use of rpoB gene phylogenetic marker-based distinction of abiotic stress tolerant and plant-growth promoting Bacillus paralicheniformis isolates from their closely related Bacillus licheniformis

Use of rpoB gene phylogenetic marker-based distinction of abiotic stress tolerant and plant-growth promoting Bacillus paralicheniformis isolates from their closely related Bacillus licheniformis

Global patterns and determinants of multiple facets of plant diversity

AbstractAimCombining different biodiversity dimensions can reveal new diversity patterns disclosing the relative roles of historical, environmental and anthropogenic factors in shaping global seed plant diversity.LocationGlobal.Time periodPresent.Major taxa studiedVascular plants.MethodsWe collated a database encompassing taxonomic (249,000 species), functional and phylogenetic information (34,694 species) of seed plants across different regions of the world. Species richness in each region was weighted accounting for their phylogenetic and functional distinctiveness, obtaining a new metric—μ‐diversity—which was modelled to disentangle the relative roles of historical factors such as climate variability since the Last Glacial Maximum (LGM), environmental features (e.g. actual evapotranspiration—AET) and anthropogenic factors (past and current).ResultsHigher μ‐diversity was observed in Papuasia, South East Asia, Australia and Central America, whereas the lowest values were primarily located in the Northern Hemisphere. Climate variability and AET were the most important determinants of μ‐diversity and individual diversity facets, whereas the importance of past human impacts (i.e. the onset of pastoralism) equated or exceeded those of the present ones.Main conclusionsOur integrative approach proved more sensitive in describing species diversity patterns. Few areas on Earth host high and unique proportions of multiple diversity facets and individual diversity facets contribute differently to μ‐diversity across continents. Historical climate stability and water‐energy dynamics strongly affect species diversity, but we also observed that past land‐use legacy may have influenced current plant diversity, which is under intense anthropogenic pressure, especially in Asia as well as in Central and South America.

Xanthomonas chitinilytica sp. nov., a novel chitinolytic bacterium isolated from a microbial fermentation bed material.

A Gram-stain-negative bacterium, H13-6T, was isolated from a microbial fermentation bed material collected from a pig farm located in Yan'an, Shaanxi, China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain H13-6T was affiliated with the genus Xanthomonas and showed highest similarity to strain Xanthomonas maliensis M97T (98.38%), Xanthomonas prunicola CFBP 8353T (98.26%) and Xanthomonas oryzae ATCC 35933T (98.11%). The pairwise ortho Average Nucleotide Identity values and the digital DNA-DNA hybridization values between strain H13-6T and the other Xanthomonas species were all below their respective cut-offs. Two genes encoding for chitinase were found and the strain showed a strong chitin-degrading activity. The major fatty acids were Iso-C15:0 (55.9%), Antesio-C15:0 (7.4%) and Iso-C11:0 (5.5%) and the major polar lipids were diphosphatidylglycerol, phosphatidyglycerol and phosphatidylethanolamine. Based on the phenotypic properties and phylogenetic distinctiveness, Xanthomonas chitinilytica was proposed as a novel species of the genus Xanthomonas, with strain H13-6T (= CGMCC 1.61317T = NBRC 115641T) as type strain.

More cryptic diversity among spiny lizards of the Sceloporus torquatus complex discovered through a multilocus approach

Abstract A phylogenetic reassessment of the Sceloporus torquatus species complex is presented using a multilocus approach. Topological conflicts related to a clade belonging to disjunct southern populations of S. madrensis are resolved, confirming the identity of such populations as distinct from the nominal populations of S. madrensis located 175 kilometres to the north. We describe this southern clade as a new species distributed in the Sierra Madre Oriental based on its phylogenetic distinctiveness and a combination of morphological characters and measurements, increasing the number of recognised species in the S. torquatus complex to seven.

First molecular evidence of lichen-inhabiting Acrospermum and new insights into the evolution of lifestyles of Acrospermales (Dothideomycetes)

ABSTRACT Acrospermales represent one of the least studied lineages of Dothideomycetes and are characterized by diverse ecological strategies, including saprotrophic, epiphytic, fungicolous, lichenicolous, and bryophilous lifestyles. The order is composed of two teleomorphic genera, Acrospermum and Oomyces, and five anamorphic genera of unclear relationships. The objectives of the study were to establish the phylogenetic position of Acrospermum species collected from lichens in the tropical forest of Bolivia and to infer the evolution of the lichenicolous lifestyle in Acrospermales. Our results reveal that the examined specimens from Bolivia represent a new species, A. bolivianum, which is well characterized by its phylogenetic distinctness, morphological characteristics, and host selection. The new species is the first lichenicolous member of Acrospermum and forms a well-supported clade sister to the bryophilous Acrospermum adeanum. The evolution of lifestyles, concluded by phylogenetic analyses and ancestral state reconstructions, indicated that the saprotrophic lifestyle is ancestral to Acrospermales. This corresponds to their close relationship to other saprotrophic lineages of Dothideomycetes and indicates that the wide spectrum of nutritional strategies, currently observed in Acrospermales, may be a result of more recent shifts in their ecology. Our results also suggest that the lichenicolous lifestyle in Acrospermales appeared independently at least two times. Lichenicolous species are represented in our data set by Acrospermum bolivianum and Gonatophragmium physciae, which evolved from lichenicolous and plant-parasite ancestors, respectively. The genus Oomyces, represented by O. carneoalbus, was included for the first time in the phylogenetic analysis and showed a sister relationship to the remaining taxa of Acrospermales.

Geographical isolation as reproductive barrier in phylogenetically related Aquilegia species (Ranunculaceae)

Knowing the determinants of biodiversity is crucial to understanding the differentiation of living organisms. Several gene-flow limiting processes can drive divergence, including adaptive ecological differentiation or geographical isolation both constituting environmental-dependent reproductive barriers. Furthermore, the strength of these processes may be associated to the degree to which ecological niches are conserved and shared by phylogenetically related species. Here, we aim to disentangle these two alternatives reproductive barriers by evaluating the degree of ecological niche similarity among phylogenetically related species. We performed ecological niche modelling (ENM) on four species belonging to a recently diversified genus (Aquilegia, Ranunculaceae) occurring in montane environments of the Alpine and Apennine chains (southern Europe). Results show that niche differentiation among species is related to phylogenetic distinctiveness. Nevertheless, niche similarity tests indicated that the conditions selected by the species are more similar than expected from the null models, even though they are sparsely available in the respective ecological spaces, suggesting that the observed pattern may result from phylogenetic niche conservatism. These results, highlight that paleogeographic events in south-European mountains may have driven divergence by isolation in Aquilegia while partially retaining the possibly ancestral characters of the niches.

Low‐cost management interventions and their impact on multilevel trade‐offs in agricultural grasslands

Abstract Cost‐effective strategies to increase biodiversity are a fundamental requirement to reconcile conservation and food production in agricultural landscapes. Key for the implementation of such strategies is an accurate quantification of both their benefits and potential associated trade‐offs. We therefore assessed, in a commercially managed grassland, biodiversity responses to two low‐cost management interventions and their mediating effects on ecosystem services. In a 6‐year experiment, we showed that a one‐time seed bank activation treatment had strong initial impacts on biodiversity, increasing plant richness in year 1 by 61%. Long‐term effects, which were also driven by the second management intervention, the propagation of the keystone species yellow rattle, were weaker but nonetheless substantial. These positive biodiversity responses improved ecosystem multifunctionality through additive positive effects of richness, evenness and phylogenetic distinctiveness on nectar production and structural habitat complexity. In contrast, hay biomass production was negatively affected by both management interventions, resulting in a multilevel trade‐off between biomass production competing with biodiversity conservation and the provisioning of other ecosystem services. Synthesis and applications. In this study, we demonstrate that the maximisation of either biodiversity or biomass production requires largely different land management practices. The evaluation of this trade‐off, however, is strongly dependent on its social, economic and ecological context and requires clearly defined land management priorities for both food production and biodiversity conservation.

Evolutionary history shapes grassland productivity through opposing effects on complementarity and selection.

Phylogenetic diversity (PD), the evolutionary history of the organisms comprising a community, is increasingly recognized as an important driver of ecosystem function. However, biodiversity-ecosystem function experiments have rarely included PD as an a priori treatment. Thus, PD's effects in existing experiments are often confounded by covarying differences in species richness and functional trait diversity (FD). Here we report an experimental demonstration of strong PD effects on grassland primary productivity that are independent of FD, which was separately manipulated, and species richness, which was planted uniformly high to mimic diverse natural grasslands. Partitioning diversity effects demonstrated that higher PD increased complementarity (niche partitioning and/or facilitation) but lowered selection effects (probability of sampling highly productive species). Specifically, for every 5% increase in PD, complementarity increased by 26% on average (±8% SE), while selection effects decreased more modestly (8 ± 16%). PD also shaped productivity through clade-level effects on functional traits, that is, trait values associated with particular plant families. This clade effect was most pronounced in the Asteraceae (sunflower family), which, in tallgrass prairies, generally comprises tall, high-biomass species with low phylogenetic distinctiveness. FD also reduced selection effects but did not alter complementarity. Our results show that PD, independent of richness and FD, mediates ecosystem function through contrasting effects on complementarity and selection. This adds to growing evidence that consideration of phylogenetic dimensions of biodiversity can advance ecological understanding and inform conservation and restoration.

Phylogenetic analyses of Candidatus Branchiomonas cysticola refine the taxonomic classification of Betaproteobacteria associated with epitheliocystis in fish

Candidatus Branchiomonas cysticola is recognized as the most prevalent bacterial agent causing epitheliocystis in Atlantic salmon (Salmo salar). Based on its partial 16S rRNA sequence, the bacterium has previously been found to be a member of Burkholderiales in the class Betaproteobacteria. Multilocus Sequence Analysis (MLSA) of the bacterium and 60 type strains of Betaproteobacteria using newly identified housekeeping genes (dnaK, rpoC, and fusA) and ribosomal subunit sequences (16S and 23S), instead supported the bacterium’s affiliation to Nitrosomodales. Taxonomic rank normalization by Relative Evolutionary Divergence (RED) showed the phylogenetic distinction between Cand. B. cysticola and its closest related type strain to be at the family level. A novel bacterial family named Branchiomonaceae has thus been proposed to include a monophyletic clade of Betaproteobacteria exclusively associated with epitheliocystis in fish.

Microbulbifer zhoushanensis sp. nov., Microbulbifer sediminum sp. nov. and Microbulbifer guangxiensis sp. nov., three marine bacteria isolated from a tidal flat.

Three strains, TT30T, TT37T and L3T, were isolated from tidal flat samples. Cells were Gram-stain-negative, non-motile and rod shaped. Cells of strains TT30T and TT37T were able to grow in a medium containing 1.0-15.0 % (w/v) NaCl (optimum, 3.0 and 4.0 %, respectively), and cells of strain L3T was able to grow in a medium containing 1.0-10.0 % (w/v) NaCl (optimum, 1.0 %). Growth of the three strains was observed at pH 6.0-10.0 and at 10-40 °C. Strains TT30T, TT37T and L3T showed the highest similarity to Microbulbifer hydrolyticus DSM 11525T (97.7 %), M. yueqingensis CGMCC 1.10658T (98.0 %) and M. elongatus DSM 6810T (97.9 %), respectively. Results of phylogenetic analyses indicated that the three isolates represented two distinct lineages within the genus Microbulbifer. The DNA G+C contents of strains TT30T, TT37T and L3T were 61.3, 60.9 and 60.2%, respectively. The average nucleotide identity and in silico DNA-DNA hybridization values among strains TT30T, TT37T and L3T and the reference strains were 84.4-87.4 and 19.6-28.9 %, respectively. Differential phenotypic properties, chemotaxonomic differences, phylogenetic distinctiveness, together with the genomic data, demonstrated that strains TT30T, TT37 T and L3T represent novel species of the genus Microbulbifer, which are named Microbulbifer zhoushanensis sp. nov. (TT30T=KCTC 92167T=MCCC 1K07276T), Microbulbifer sediminum sp. nov. (TT37T=KCTC 92168T=MCCC 1K07277T) and Microbulbifer guangxiensis sp. nov. (L3T=KCTC 92165T=MCCC 1K07278T).

Roseobacter insulae sp. nov. and Loktanella gaetbuli sp. nov., isolated from tidal flats in the Yellow Sea in Korea.

Two bacterial strains (designated as YSTF-M11T and TSTF-M6T) were isolated from tidal flat sediments of the Yellow Sea, Republic of Korea, and taxonomically characterized. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain YSTF-M11T clusters with the type strains of Roseobacter species and strain TSTF-M6T clusters with the type strains of Loktanella salsilacus, Loktanella fryxellensis and Loktanella atrilutea. Strains YSTF-M11T and TSTF-M6T exhibited 16S rRNA gene sequence similarity values of 97.5-98.9 % and 94.1-97.2 % to the type strains of four Roseobacter species and to the type strains of four Loktanella species, respectively. An UBCG tree based on genomic sequences and a tree based on AAI showed that strains YSTF-M11T and TSTF-M6T form a cluster with the type strains of Roseobacter species and with the type strains of L. salsilacus, L. fryxellensis and L. atrilutea, respectively. The ANI and dDDH values between genomic sequences of strain YSTF-M11T and the type strains of four Roseobacter species and between those of strain TSTF-M6T and the type strains of the three Loktanella species were in ranges of 74.0-75.9 and 18.2-19.7 % and 74.7-75.5 and 18.8-19.3 %, respectively. The DNA G+C contents of strains YSTF-M11T and TSTF-M6T were 60.3 and 61.9 % based on their genomic sequences. Both strains contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c as the major fatty acid. Strains YSTF-M11T and TSTF-M6T were separated from recognized Roseobacter species and L. salsilacus, L. fryxellensis and L. atrilutea, respectively, by their phenotypic properties together with the phylogenetic and genetic distinctiveness. Based on data presented in this study, strains YSTF-M11T (=KACC 21642T =NBRC 115155T) and TSTF-M6T (=KACC 21643T =NBRC 115154T) are considered to represent novel species of the genera Roseobacter and Loktanella, respectively, for which the names Roseobacter insulae sp. nov. and Loktanella gaetbuli sp. nov. are proposed.

A multivariate analysis of phenotypic traits of strains of Fusarium graminearum and F. meridionale supports structure by species

AbstractFusarium head blight (FHB) of wheat and Gibberella ear and stalk rot (GER and GSR) of maize are diseases of worldwide importance. Several phylogenetic species belonging to the Fusarium graminearum species complex (FGSC) cause FHB and GER/GSR in Brazil, but the dominant species varies depending on host. Fusarium graminearum is the most frequent cause of FHB, while F. meridionale is more often associated with GER/GSR. These two species are distinguished based on fixed sequence variations at a few genetic loci; however, relevance of these differences to reproduction, pathogenicity and toxigenicity has not been fully explored. A range of phenotypic traits were evaluated for a group of strains of F. graminearum and F. meridionale from wheat and maize. These included radial growth on agar plates, sexual and asexual reproduction, fungicide sensitivity, toxigenicity and pathogenicity on wheat and maize. Although intraspecies variation was observed for most traits, a multivariate analysis showed the strains were strongly structured by species, regardless of host origin. Increased sexual or asexual reproduction, deoxynivalenol production and aggressiveness on wheat heads were most important for distinguishing strains of F. graminearum, while faster mycelial growth in culture, nivalenol production and reduced colonization on detached maize silks were most important for distinguishing strains of F. meridionale. Thus, the phylogenetic distinction between F. graminearum and F. meridionale is supported by phenotypic differences that are relevant for pathogenicity (aggressiveness and mycotoxin production on wheat heads and maize silks, mycelial growth and sexual and asexual reproduction) and disease management (tebuconazole sensitivity).

Decoupling body shape and mass distribution in birds and their dinosaurian ancestors

It is accepted that non-avian theropod dinosaurs, with their long muscular tails and small forelimbs, had a centre-of-mass close to the hip, while extant birds, with their reduced tails and enlarged wings have their mass centred more cranially. Transition between these states is considered crucial to two key innovations in the avian locomotor system: crouched bipedalism and powered flight. Here we use image-based models to challenge this dichotomy. Rather than a phylogenetic distinction between ‘dinosaurian’ and ‘avian’ conditions, we find terrestrial versus volant taxa occupy distinct regions of centre-of-mass morphospace consistent with the disparate demands of terrestrial bipedalism and flight. We track this decoupled evolution of body shape and mass distribution through bird evolution, including the origin of centre-of-mass positions more advantageous for flight and major reversions coincident with terrestriality. We recover modularity in the evolution of limb proportions and centre-of-mass that suggests fully crouched bipedalism evolved after powered flight.

Enterovibrio paralichthyis sp. nov., isolated from the gut of an olive flounder Paralichthys olivaceus.

A Gram-stain-negative, facultatively anaerobic, flagellated and coccoid, ovoid or rod-shaped bacterial strain, NIFS-20-8T, was isolated from the intestine of an olive flounder (Paralichthys olivaceus) from the East Sea, Republic of Korea. The neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strain NIFS-20-8T fell within the clade comprising the type strains of Enterovibrio species. Strain NIFS-20-8T exhibited 16S rRNA gene sequence similarities of 97.2 and 97.1 % to the type strains of Enterovibrio nigricans and Enterovibrio norvegicus, respectively, and of 96.6-97.0 % to the type strains of the other Enterovibrio species. The average nucleotide identity and digital DNA-DNA hybridization values between the genomic sequence of strain NIFS-20-8T and those of the type strains of four Enterovibrio species were 73.8-75.0 and 19.8-21.1 %, respectively. The DNA G+C content of strain NIFS-20-8T from genomic sequence data was 50.55 mol%. Strain NIFS-20-8T contained Q-8 as the predominant ubiquinone and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0 and C18 : 1 ω7c as the major fatty acids. The major polar lipids detected in stain NIFS-20-8T were phosphatidylethanolamine and phosphatidylglycerol. Distinguishing phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain NIFS-20-8T is separated from recognized Enterovibrio species. On the basis of the data presented here, strain NIFS-20-8T is considered to represent a novel species of the genus Enterovibrio, for which the name Enterovibrio paralichthyis sp. nov. is proposed. The type strain is NIFS-20-8T (= KCTC 82873T=NBRC 115237T).

The phylogeny of California, and how it informs setting multispecies conservation priorities.

Incorporating measures of taxonomic diversity into research and management plans has long been a tenet of conservation science. Increasingly, active conservation programs are turning toward multispecies landscape and regional conservation actions, and away from single species approaches. This is both a reflection of changing trends in conservation science and advances in foundational technologies, including genomics and geospatial science. Multispecies approaches may provide more fundamental insights into evolutionary processes and equip managers with a more holistic understanding of the landscapes under their jurisdiction. Central to this approach are data generation and analyses which embrace and reflect a broad range of taxonomic diversity. Here, we examine the family-level phylogenetic breadth of the California Conservation Genomics Project (CCGP) based on family-level phylogenetic diversity (PD), family-level phylogenetic distinctness, and family richness. We place this in the context of the diversity present in California and compare it to the 35-plus years of genetic research compiled in the CaliPopGen Database. We found that the family-level PD in the CCGP reflected that of California very well, slightly overrepresenting chordates and underrepresenting arthropods, and that 42% of CCGP PD represented new contributions to genetic data for the state. In one focused effort, the CCGP was able to achieve roughly half the family-level PD studied over the last several decades. To maximize studied PD, future work should focus on arthropods, a conclusion that likely reflects the overall lack of attention to this hyperdiverse clade.