Putative Species Research Articles

Deep nasal sinus cavity microbiota dysbiosis in Parkinson\u2019s disease

Olfactory dysfunction is a pre-motor symptom of Parkinson’s disease (PD) that appears years prior to diagnosis and can affect quality of life in PD. Changes in microbiota community in deep nasal cavity near the olfactory bulb may trigger the olfactory bulb-mediated neuroinflammatory cascade and eventual dopamine loss in PD. To determine if the deep nasal cavity microbiota of PD is significantly altered in comparison to healthy controls, we characterized the microbiota of the deep nasal cavity using 16S rRNA gene amplicon sequencing in PD subjects and compared it to that of spousal and non-spousal healthy controls. Correlations between microbial taxa and PD symptom severity were also explored. Olfactory microbial communities of PD individuals were more similar to those of their spousal controls than to non-household controls. In direct comparison of PD and spousal controls and of PD and non-spousal controls, significantly differently abundant taxa were identified, and this included increased relative abundance of putative opportunistic-pathobiont species such as Moraxella catarrhalis. M. catarrhalis was also significantly correlated with more severe motor scores in PD subjects. This proof-of-concept study provides evidence that potential pathobionts are detected in the olfactory bulb and that a subset of changes in the PD microbiota community could be a consequence of unique environmental factors associated with PD living. We hypothesize that an altered deep nasal microbiota, characterized by a putative pro-inflammatory microbial community, could trigger neuroinflammation in PD.

Hidden biodiversity in microarthropods (Acari, Oribatida, Eremaeoidea, Caleremaeus)

A challenge for taxonomists all over the world and across all taxonomic groups is recognizing and delimiting species, and cryptic species are even more challenging. However, an accurate identification is fundamental for all biological studies from ecology to conversation biology. We used a multidisciplinary approach including genetics as well as morphological and ecological data to assess if an easily recognizable, widely distributed and euryoecious mite taxon represents one and the same species. According to phylogenetic (based on mitochondrial and nuclear genes) and species delimitation analyses, five distinct putative species were detected and supported by high genetic distances. These genetic lineages correlate well with ecological data, and each species could be associated to its own (micro)habitat. Subsequently, slight morphological differences were found and provide additional evidence that five different species occur in Central and Southern Europe. The minuteness and the characteristic habitus of Caleremaeus monilipes tempted to neglect potential higher species diversity. This problem might concern several other “well-known” euryoecious microarthropods. Five new species of the genus Caleremaeus are described, namely Caleremaeus mentobellus sp. nov., C. lignophilus sp. nov., C. alpinus sp. nov., C. elevatus sp. nov., and C. hispanicus sp. nov. Additionally, a morphological evaluation of C. monilipes is presented.

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

Primary Amine Catalyzed Activation of Carbonyl Compounds: A Study on Reaction Pathways and Reactive Intermediates by Mass Spectrometry

AbstractThe field of organocatalysis is expanding at a fast pace. Its growth is sustained by major stimuli, such as the effort toward an understanding of the mechanisms of reaction and catalytic processes in general, the elucidation of basic properties leading to stereocontrol and the search for broad applicability and scalability of the synthetic methodology. This paper reports a thorough study based on ESI‐MS spectrometry of amino‐organocatalyzed model reactions under different experimental conditions. Off‐line reaction monitoring of mixtures containing different catalytic systems, by ESI‐MSn showed the presence of several putative intermediate species, either in their protonated or sodiated forms. In addition, enantioselective chromatography of crude reactions provides the stereochemical outcome of asymmetric reactions. The bulk of the data collected offers a clue of the intricate pathways occurring in solution for the studied reactions.

Molecular phylogenetic analysis of the Prostanthera phylicifolia (Lamiaceae) assemblage resolves relationships of the ‘Critically Endangered’ P. gilesii and other putative new species

Prostanthera gilesii is a critically endangered species from the Central Tablelands of New South Wales. A conservation management strategy is currently underway for this species, whose phylogenetic affinities are not known. Morphologically, P. gilesii resembles P. phylicifolia and a population of uncertain identity from Evans Crown Nature Reserve in the Central Tablelands of New South Wales (P. sp. Evans Crown). The taxonomy of P. phylicifolia, however, is unclear. Prostanthera phylicifolia was described from populations in the Victorian Alps and Monaro; however, populations spanning from Victoria to southern Queensland have been variously identified as either P. phylicifolia or P. scutellarioides despite substantial geographic disjunctions and morphological dissimilarity. To examine the relationship between populations identified as P. phylicifolia, P. gilesii and P. sp. Evans Crown, nuclear (external transcribed spacer, ETS) and chloroplast (trnH-psbA intergenic spacer) regions were sequenced and combined with an existing Prostanthera dataset and analysed with maximum-likelihood and Bayesian-inference methods. Prostanthera gilesii and P. sp. Evans Crown were recovered as sister taxa within a clade consisting of populations morphologically similar to the type of P. phylicifolia from the Victorian Alps and Snowy Mountains, Monaro and Southern Tablelands of New South Wales. Populations from northern New South Wales and southern Queensland identified as P. phylicifolia or P. scutellarioides were recovered as an assemblage of unrelated clades. The molecular phylogeny supports P. gilesii and P. phylicifolia as closely related as hypothesised based on morphology and supports P. sp. Evans Crown as a population which requires additional study to assess its taxonomic status.

Biogeography of Long-Jawed Spiders Reveals Multiple Colonization of the Caribbean

Dispersal ability can affect levels of gene flow thereby shaping species distributions and richness patterns. The intermediate dispersal model of biogeography (IDM) predicts that in island systems, species diversity of those lineages with an intermediate dispersal potential is the highest. Here, we tested this prediction on long-jawed spiders (Tetragnatha) of the Caribbean archipelago using phylogenies from a total of 318 individuals delineated into 54 putative species. Our results support a Tetragnatha monophyly (within our sampling) but reject the monophyly of the Caribbean lineages, where we found low endemism yet high diversity. The reconstructed biogeographic history detects a potential early overwater colonization of the Caribbean, refuting an ancient vicariant origin of the Caribbean Tetragnatha as well as the GAARlandia land-bridge scenario. Instead, the results imply multiple colonization events to and from the Caribbean from the mid-Eocene to late-Miocene. Among arachnids, Tetragnatha uniquely comprises both excellently and poorly dispersing species. A direct test of the IDM would require consideration of three categories of dispersers; however, long-jawed spiders do not fit one of these three a priori definitions, but rather represent a more complex combination of attributes. A taxon such as Tetragnatha, one that readily undergoes evolutionary changes in dispersal propensity, can be referred to as a ‘dynamic disperser’.

Integrative taxonomy-based discovery of Dussumieria modakandai sp. nov. from India.

This study is based on integrative taxonomy and reports a new fish species Dussumieria modakandai sp. nov. from India. The new species differs from three valid species within the genus by a combination of characters such as longer maxilla (9.1%-9.9% standard length vs. 8.7% in Dussumieria elopsoides, 6.3%-8.5% in Dussumieria acuta) and one or two rows of small conical teeth on palatine (vs. several rows in D. elopsoides and Dussumieria albulina). It also differs by the absence of longitudinal striae on the posterior side of body scales (vs. presence in D. acuta and D. albulina) and the absence of parasphenoid teeth (vs. presence in D. acuta). The maxilla length of D. modakandai sp. nov. is greater than snout length, which distinguishes it from other congeners. The multivariate analysis of morphometric characters using PCA differentiated the new species from D. elopsoides and D. acuta samples collected in this study. The molecular analysis, based on cytochrome c oxidase I, distinguished the new species from D. acuta, D. albulina and D. elopsoides with a high genetic distance of 13.73%, 12.22% and 12.74%, respectively. The maximum-likelihood phylogenetic tree and automatic barcode gap discovery analysis showed the existence of six putative species in Dussumieria. Even the exhaustive sub-clade formation within species and high intra-species genetic distance in D. acuta (1.59) and D. modakandai (1.95) indicate the possibility of a few more cryptic species. This warrants comprehensive sample collection across the distribution range and integrative taxonomic study of the genus Dussumieria.

The endemic plant species of Mt Kupe, Cameroon with a new Critically Endangered cloud-forest tree species, Vepris zapfackii (Rutaceae)

SummaryWe revise and update the records of strict and near-endemic species of Mt Kupe, Cameroon respectively from 31 strict endemics in 2004, to 25 today, and with near-endemic species 30, unchanged in number but with turnover. The changes result from new collections, discoveries and taxonomic changes in the last 16 years. While 15 of the provisionally named putative endemic species have now been formally published, a further 18 have not. The majority of the 30 near-endemic species (18) are shared with the adjacent Bakossi Mts, far exceeding the numbers shared with the more distant Mt Etinde-Mt Cameroon, Rumpi Hills and Ebo forest areas (sharing three near-endemic species each with Mt Kupe). We test the hypothesis that a further one of the provisionally named putative Mt Kupe species, Vepris sp. 1 from submontane forest near the summit, is indeed new to science. We compare it morphologically with the two other bicarpellate high altitude Cameroon Highland tree species V. montisbambutensis Onana and V. bali Cheek, concluding that it is a new undescribed species here named as Vepris zapfackii. The new species is illustrated and its conservation status assessed as Critically Endangered using the 2012 IUCN standard, due to habitat clearance from agricultural pressures at its sole location which is unprotected. Vepris zapfackii and V. bali appear unique in African trifoliolate species of the genus in having opposite leaves. Vepris zapfackii differs in having hairy petiolules and midribs and petiolules with the blade decurrent distally, narrowing towards a winged-canaliculate base (vs glabrous and petiolule long, terete), and sparsely golden hairy pistillodes and a glabrous calyx (vs densely black hairy pistillodes, and sepals hairy).

Metagenome-assembled genomes and gene catalog from the chicken gut microbiome aid in deciphering antibiotic resistomes

Gut microbial reference genomes and gene catalogs are necessary for understanding the chicken gut microbiome. Here, we assembled 12,339 microbial genomes and constructed a gene catalog consisting of ~16.6 million genes by integrating 799 public chicken gut microbiome samples from ten countries. We found that 893 and 38 metagenome-assembled genomes (MAGs) in our dataset were putative novel species and genera, respectively. In the chicken gut, Lactobacillus aviarius and Lactobacillus crispatus were the most common lactic acid bacteria, and glycoside hydrolases were the most abundant carbohydrate-active enzymes (CAZymes). Antibiotic resistome profiling results indicated that Chinese chicken samples harbored a higher relative abundance but less diversity of antimicrobial resistance genes (ARGs) than European samples. We also proposed the effects of geography and host species on the gut resistome. Our study provides the largest integrated metagenomic dataset from the chicken gut to date and demonstrates its value in exploring chicken gut microbial genes.

Macro- and micro-scale adaptations allow distinct Stylophora pistillata-symbiodiniaceae holobionts to optimize performance across a broad light habitat.

In sessile organisms, phenotypic plasticity represents an important strategy for dealing with environmental variability. Here we test if phenotypic plasticity enables the common coral Stylophora pistillata to occupy a broad niche. We find clear differences in the photo-physiology of four putative species of photosynthetic dinoflagellate symbionts associated with the coral S. pistillata, namely, Cladocopium 'C35a', 'C79', 'C78a' and 'C8a'. Coral phenotypic responses were also tightly linked to symbiont identity. Corals with Cladocopium 'C8a' have more "open" macro-morphology compared to colonies associating with depth-restricted Cladocopium 'C35a' or 'C78a' in the same shallow water habitat. Corals with Cladocopium 'C8a' had 40 to 60% lower symbiont cell densities compared to other holobionts but were more efficient at acclimating over a range of light levels, with clear mechanisms to dissipate excess light energy. This holobiont contains host-based green fluorescent pigments, increased concentrations of symbiont-based mycosporine amino acids, and xanthophyll cycling in high light habitats. Photosynthetic efficiency was also adjusted over the light habitat. In contrast, limited micro-scale responses were observed between three depth-restricted symbionts: Cladocopium 'C79', 'C35a', and 'C78a'. To optimize light levels reaching the photosynthetic unit, these colonies rely on a more closed macro-morphology under high light levels, which reduces incident light levels by up to 43%, and higher symbiont densities . Our results show that distinct macro- and micro-scale adaptations lead to functional differences between four distinct S. pistillata holobionts, allowing them to co-exist by filling specific niches on a small, but environmentally diverse, spatial scale. Key index words: Light, Symbiodiniaceae, coral, pigments, Stylophora pistillata, ITS2, phenotypic plasticity, niche diversification.

Eight in One: Hidden Diversity of the Bagrid Catfish Tachysurus albomarginatus s.l. (Rendhal, 1928) Widespread in Lowlands of South China.

There is increasing evidence that species diversity is underestimated in the current taxonomy of widespread freshwater fishes. The bagrid species T. albomarginatus s.l. is mainly distributed in the lowlands of South China, as currently identified. A total of 40 localities (including the type locality), which covers most of its known range, were sampled. Molecular phylogenetic analyses based on concatenated mtDNA and nuclear genes recover nine highly supported lineages clustering into eight geographic populations. The integration of molecular evidence, morphological data, and geographic distribution demonstrates the delineation of T. albomarginatus s.l. as eight putative species. Four species, namely, T. albomarginatus, T. lani, T. analis, and T. zhangfei sp. nov. and the T. similis complex are taxonomically recognized herein. Moreover, T. zhangfei sp. nov. comprises two genetically distinct lineages with no morphological and geographical difference. This study also reveals aspects of estimation of divergence time, distribution, and ecological adaption within the T. albomarginatus group. The unraveling of the hidden species diversity of this lowland bagrid fish highlights the need for not only the molecular scrutiny of widely distributed species of South China but also the adjustment of current biodiversity conservation strategies to protect the largely overlooked diversity of fishes from low-elevation rapids.

An assessment of the taxonomic validity of three species of marsupial frogs (Anura: Hemiphractidae: Gastrotheca) from the Yungas of Bolivia based on external morphology and cranial osteology.

The genus Gastrotheca (Anura: Hemiphractidae) is a group of marsupial frogs particularly diverse in Andean regions. Several taxonomic studies of this genus have been conducted in the humid cloud forestsor Yungasof the Andean eastern slopes of central Bolivia (departments of Cochabamba and Santa Cruz). Yet, the distinction among three species that occur sympatrically in these forests, G. lauzuricae (proposed as a junior synonym of G. coeruleomaculatus in 2015), G. piperata, and G. splendens, remains unclear since the morphological characters that purportedly support their differentiation are variable and partly shared among them. We have carried out external morphological studies, including multivariate morphometric analyses, to assess how they support the taxonomic status of these three species. We also evaluated characters of the cranial osteology of a sample of six individuals using micro CT-scanning. Principal component and linear discriminant analyses resulted in a great overlap among the putative species. Cranial osteological comparisons did not reveal highly significant differences among them, but suggested that different degrees of hyperossification could be related to the developmental state of individuals. Our results indicate that most morphological and osteological reported differences between the three species likely represent intraspecific variation. Thus, we propose that the three nominal species belong to a single biological entity, for which the name Gastrotheca splendens (Schmidt, 1857) has priority. We also restrict the name Gastrotheca coeruleomaculatus (Werner, 1899) to externally similar congeneric populations from the Yungas forests of department of La Paz, but highlighting the need of a detailed evaluation of their taxonomic identity.

Adding pieces to the puzzle: insights into diversity and distribution patterns of Cumacea (Crustacea: Peracarida) from the deep North Atlantic to the Arctic Ocean.

The Nordic Seas have one of the highest water-mass diversities in the world, yet large knowledge gaps exist in biodiversity structure and biogeographical distribution patterns of the deep macrobenthic fauna. This study focuses on the marine bottom-dwelling peracarid crustacean taxon Cumacea from northern waters, using a combined approach of morphological and molecular techniques to present one of the first insights into genetic variability of this taxon. In total, 947 specimens were assigned to 77 morphologically differing species, representing all seven known families from the North Atlantic. A total of 131 specimens were studied genetically (16S rRNA) and divided into 53 putative species by species delimitation methods (GMYC and ABGD). In most cases, morphological and molecular-genetic delimitation was fully congruent, highlighting the overall success and high quality of both approaches. Differences were due to eight instances resulting in either ecologically driven morphological diversification of species or morphologically cryptic species, uncovering hidden diversity. An interspecific genetic distance of at least 8% was observed with a clear barcoding gap for molecular delimitation of cumacean species. Combining these findings with data from public databases and specimens collected during different international expeditions revealed a change in the composition of taxa from a Northern Atlantic-boreal to an Arctic community. The Greenland-Iceland-Scotland-Ridge (GIS-Ridge) acts as a geographical barrier and/or predominate water masses correspond well with cumacean taxa dominance. A closer investigation on species level revealed occurrences across multiple ecoregions or patchy distributions within defined ecoregions.

MtDNA species-level phylogeny and delimitation support significantly underestimated diversity and endemism in the largest Neotropical cichlid genus (Cichlidae: Crenicichla).

Crenicichla is the largest and most widely distributed genus of Neotropical cichlids. Here, we analyze a mtDNA dataset comprising 681 specimens (including Teleocichla, a putative ingroup of Crenicichla) and 77 out of 105 presently recognized valid species (plus 10 out of 36 nominal synonyms plus over 50 putatively new species) from 129 locations in 31 major river drainages throughout the whole distribution of the genus in South America. Based on these data we make an inventory of diversity and highlight taxa and biogeographic areas worthy of further sampling effort and conservation protection. Using three methods of molecular species delimitation, we find between 126 and 168 species-like clusters, i.e., an average increase of species diversity of 65–121% with a range of increase between species groups. The increase ranges from 0% in the Missioneira and Macrophthama groups, through 25–40% (Lacustris group), 50–87% (Reticulata group, Teleocichla), 68–168% (Saxatilis group), 125–200% (Wallacii group), and 158–241% in the Lugubris group. We found a high degree of congruence between clusters derived from the three used methods of species delimitation. Overall, our results recognize substantially underestimated diversity in Crenicichla including Teleocichla. Most of the newly delimited putative species are from the Amazon-Orinoco-Guiana (AOG) core area (Greater Amazonia) of the Neotropical region, especially from the Brazilian and Guiana shield areas of which the former is under the largest threat and largest degree of environmental degradation of all the Amazon.

Application of the Double-Mutant Cycle Strategy to Protein Aggregation Reveals Transient Interactions in Amyloid-β Oligomers.

Transient oligomeric intermediates in the peptide or protein aggregation pathway are suspected to be the key toxic species in many amyloid diseases, but deciphering their molecular nature has remained a challenge. Here we show that the strategy of "double-mutant cycles", used effectively in probing protein-folding intermediates, can reveal transient interactions during protein aggregation. It does so by comparing the changes in thermodynamic parameters between the wild type, and single and double mutants. We demonstrate the strategy by probing the possible transient salt bridge partner of lysine 28 (K28) in the oligomeric states of amyloid β-40 (Aβ40), the putative toxic species in Alzheimer's disease. In mature fibrils, the binding partner is aspartate 23. This interaction differentiates Aβ40 from the more toxic Aβ42, where K28's binding partner is the C-terminal carboxylate. We selectively acetylated K28 and amidated the C-terminus of Aβ40, creating four distinct variants. Spectroscopic measurements of the kinetics and thermodynamics of aggregation show that K28 and the C-terminus interact transiently in the early phases of the Aβ40 aggregation pathway. Hydrogen-deuterium exchange mass spectrometry (using a simple analysis method that we introduce here that takes into account the isotopic mass distribution) supports this interpretation. It is also supported by cellular toxicity measurements, suggesting possible similarities in the mechanisms of toxicity of Aβ40 oligomers (which are more toxic than Aβ40 fibrils) and Aβ42. Our results show that double-mutant cycles can be a powerful tool for probing transient interactions during protein aggregation.

Multi-Omics Study of Keystone Species in a Cystic Fibrosis Microbiome.

Ecological networking and in vitro studies predict that anaerobic, mucus-degrading bacteria are keystone species in cystic fibrosis (CF) microbiomes. The metabolic byproducts from these bacteria facilitate the colonization and growth of CF pathogens like Pseudomonas aeruginosa. Here, a multi-omics study informed the control of putative anaerobic keystone species during a transition in antibiotic therapy of a CF patient. A quantitative metagenomics approach combining sequence data with epifluorescence microscopy showed that during periods of rapid lung function loss, the patient’s lung microbiome was dominated by the anaerobic, mucus-degrading bacteria belonging to Streptococcus, Veillonella, and Prevotella genera. Untargeted metabolomics and community cultures identified high rates of fermentation in these sputa, with the accumulation of lactic acid, citric acid, and acetic acid. P. aeruginosa utilized these fermentation products for growth, as indicated by quantitative transcriptomics data. Transcription levels of P. aeruginosa genes for the utilization of fermentation products were proportional to the abundance of anaerobic bacteria. Clindamycin therapy targeting Gram-positive anaerobes rapidly suppressed anaerobic bacteria and the accumulation of fermentation products. Clindamycin also lowered the abundance and transcription of P. aeruginosa, even though this patient’s strain was resistant to this antibiotic. The treatment stabilized the patient’s lung function and improved respiratory health for two months, lengthening by a factor of four the between-hospitalization time for this patient. Killing anaerobes indirectly limited the growth of P. aeruginosa by disrupting the cross-feeding of fermentation products. This case study supports the hypothesis that facultative anaerobes operated as keystone species in this CF microbiome. Personalized multi-omics may become a viable approach for routine clinical diagnostics in the future, providing critical information to inform treatment decisions.

Seroepidemiological Study of Spotted Fever Group Rickettsiae and Identification of a Putative New Species, Rickesttsia sp. Da-1, in Gongliao, Northeast Taiwan.

Tick-borne spotted fever group (SFG) rickettsioses were neglected in Taiwan. The study reported a seroepidemiological survey of SFG rickettsiae in residents in Gongliao District, Northeast Taiwan. Blood samples were examined for antibodies against SFG rickettsiae by enzyme-linked immunosorbent assay and immunofluorescence assay. Risk factors were assessed using logistic regression. Ticks parasitizing dogs were collected within a 2 km radius from the houses of seropositive participants, and PCR was performed to detect possible tick-borne pathogens. Of 1108 participants, 75 (6.8%) had antibodies against SFG rickettsiae. Residents were more likely to be seropositive if they were older than 65 years, recruited by Dr. Enjoy’s Clinic, or resided in Jilin village. A total of 184 ticks including 5 species (Rhipicephalus sanguineus, Rhipicephalus haemaphysaloides, Dermacentor auratus, Haemaphysalis hystricis, Haemaphysalis ornithophila) were collected. Rickettsia spp. were detected in 6.5% (12/184) of ticks. Rickettsia sp. TwKM01 was found in 6 R. sanguineus and 4 R. haemaphysaloides; while Rickettsia sp. TwKM03 was identified in 1 R. sanguineus. Moreover, gene-based pairwise analysis indicated identification of a putative new species, Rickettsia sp. Da-1, in D. auratus. These findings provided evidence of SFG rickettsiae infection in ticks and suggested SFG rickettsiae exposure in the residents.

Global gap-analysis of amphipod barcode library.

In the age of global climate change and biodiversity loss there is an urgent need to provide effective and robust tools for diversity monitoring. One of the promising techniques for species identification is the use of DNA barcoding, that in Metazoa utilizes the so called ‘gold-standard’ gene of cytochrome c oxidase (COI). However, the success of this method relies on the existence of trustworthy barcode libraries of the species. The Barcode of Life Data System (BOLD) aims to provide barcodes for all existing organisms, and is complemented by the Barcode Index Number (BIN) system serving as a tool for potential species recognition. Here we provide an analysis of all public COI sequences available in BOLD of the diverse and ubiquitous crustacean order Amphipoda, to identify the barcode library gaps and provide recommendations for future barcoding studies. Our gap analysis of 25,702 records has shown that although 3,835 BINs (indicating putative species) were recognised by BOLD, only 10% of known amphipod species are represented by barcodes. We have identified almost equal contribution of both records (sequences) and BINs associated with freshwater and with marine realms. Three quarters of records have a complete species-level identification provided, while BINs have just 50%. Large disproportions between identification levels of BINs coming from freshwaters and the marine environment were observed, with three quarters of the former possessing a species name, and less than 40% for the latter. Moreover, the majority of BINs are represented by a very low number of sequences rendering them unreliable according to the quality control system. The geographical coverage is poor with vast areas of Africa, South America and the open ocean acting as “white gaps”. Several, of the most species rich and highly abundant families of Amphipoda (e.g., Phoxocephalidae, Ampeliscidae, Caprellidae), have very poor representation in the BOLD barcode library. As a result of our study we recommend stronger effort in identification of already recognised BINs, prioritising the studies of families that are known to be important and abundant components of particular communities, and targeted sampling programs for taxa coming from geographical regions with the least knowledge.

Recent speciation and hybridization in Icelandic deep-sea isopods: An integrative approach using genomics and proteomics.

The crustacean marine isopod species Haploniscusbicuspis (Sars, 1877) shows circum-Icelandic distribution in a wide range of environmental conditions and along well-known geographic barriers, such as the Greenland-Iceland-Faroe (GIF) Ridge. We wanted to explore population genetics, phylogeography and cryptic speciation as well as investigate whether previously described, but unaccepted subspecies have any merit. Using the same set of specimens, we combined mitochondrial COI sequences, thousands of nuclear loci (ddRAD), and proteomic profiles, plus selected morphological characters using confocal laser scanning microscopy (CLSM). Five divergent genetic lineages were identified by COI and ddRAD, two south and three north of the GIF Ridge. Assignment of populations to the three northern lineages varied and detailed analyses revealed hybridization and gene flow between them, suggesting a single northern species with a complex phylogeographic history. No apparent hybridization was observed among lineages south of the GIF Ridge, inferring the existence of two more species. Differences in proteomic profiles between the three putative species were minimal, implying an ongoing or recent speciation process. Population differentiation was high, even among closely associated populations, and higher in mitochondrial COI than nuclear ddRAD loci. Gene flow is apparently male-biased, leading to hybrid zones and instances of complete exchange of the local nuclear genome through immigrating males. This study did not confirm the existence of subspecies defined by male characters, which probably instead refer to different male developmental stages.

Does the transport of larvae throughout the south Atlantic support the genetic and morphometric diversity of the Sally Lightfoot Crabs Grapsus grapsus (Linnaeus, 1758) and Grapsus adscensionis (Osbeck, 1765) (Decapoda: Grapsidae) among the oceanic islands?

Grapsus grapsus and Grapsus adscensionis are supralittoral crabs that are known to inhabit oceanic islands and depend on surface currents to recruit in the rocky shores. The ornamentation of the cephalothorax is very distinct among species, but morphological differences are controversial, and integrative studies with different approaches are needed. This study investigated the genetic variation among the populations of G. grapsus from Saint Peter and Saint Paul Archipelago (SP), Fernando de Noronha (FN), Rocas Atoll (RA) and Trindade Island (TR) in the western Atlantic, and G. adscensionis from the islands of Ascension (AI) and Saint Helena (SH) in the mid-Atlantic. Morphology was assessed by geometric morphometric analyses of the carapace and chelae, and numerical analyses of tubercles in the frontal plate of SP, FN, RA, TR and AI populations. In addition, dispersal of the larvae in the Atlantic Ocean was simulated performing a Lagrangian analysis using HYCOM reanalysis dataset as the ocean surface velocity field. The data obtained for the mitochondrial D-loop gene confirmed the distinctness of the two putative species and demonstrated the connectivity between the populations of G. grapsus from the three equatorial islands. The TR population presented unique haplotypes, as well as AI and SH. The geometric morphometric analyses showed differentiation between the carapace shapes for G. grapsus and G. adscensionis, however, the chelae shape does not allow to distinguish between the species or the population. The morphometric and molecular results were consistent with the pattern of particles dispersion in the Atlantic ocean. The larvae of SP, FN and RA mix after two months of drift, while the larvae of TR, AI, SH circulate only around the respective islands. The results reinforce the validation of the two species and the isolation of populations of G. grapsus in TR and of G. adscensionis in AI and SH. The populations of these islands might be maintained by self-recruitment, through larval behavior associated with the local current system, and therefore should be the target of conservation measures.