Putative Species Research Articles

A chromosome-scale Mytilus edulis genome assembly for aquaculture, marine ecology, and evolution.

The smooth-shelled blue mussel, Mytilus edulis is part of the Mytilus species complex, encompassing at least three putative species: M. edulis, Mytilus galloprovincialis, and Mytilus trossulus. These three species occur on both sides of the Atlantic and hybridize in nature, and both M. edulis and M. galloprovincialis are important aquaculture species. They are also invasive species in many parts of the world. Here, we present a chromosome-level assembly of M. edulis. We used a combination of PacBio sequencing and Dovetail's Omni-C technology to generate an assembly with 14 long scaffolds containing 94% of the predicted length of the M. edulis genome (1.6 out of 1.7 Gb). Assembly statistics were as follows: total length = 1.65 Gb, N50 = 116 Mb, L50 = 7, and L90 = 13. BUSCO analysis showed 92.55% eukaryote BUSCOs identified. AB-Initio annotation using RNA-seq from mantle, gills, muscle, and foot predicted 47,128 genes. These gene models were combined with IsoSeq validation resulting in 45,379 full CDS protein sequences and 129,708 isoforms. Using GBS and shotgun sequencing, we also sequenced several eastern Canadian populations of Mytilus to characterize single-nucleotide as well as structural variance. This high-quality genome for M. edulis provides a platform to develop tools that can be used in breeding, molecular ecology and evolution to address questions of both commercial and environmental perspectives.

Diversity of Rhizophydiales (Chytridiomycota) in Thailand: unveiling the hidden gems of the Kingdom

Chytrids, often overshadowed by their other fungal counterparts, take center stage as we unravel the mysteries surrounding new species within Rhizophydiales and explore their unique characteristics. In the broader spectrum of chytrids, their significance lies not only in their roles as decomposers but also as key players in nutrient cycling within aquatic ecosystems as parasites and saprobes. Baited soil and aquatic samples collected from various provinces of Thailand, yielded new species of the Rhizophydiales (Chytridiomycota), some of which expanded previously single species genera. Our investigation incorporated a combination of morphological and phylogenetic approaches, enabling us to identify these isolates as distinct taxa. The novel isolates possess distinguishing features, such as variations in size and shape of the sporangium and zoospores, that somewhat differentiate them from described taxa. To confirm the novelty of the species, we employed robust phylogenetic analyses using maximum likelihood and bayesian methods. The results provided strong support for the presence of eight distinct lineages within the Rhizophydiales, representing our newly discovered species. Furthermore, we employed Poisson Tree Processes to infer putative species boundaries and supplement evidence for the establishment of our new Rhizophydiales species. By meticulously exploring their morphological characteristics and genetic makeup, we expand the known catalogue of fungal diversity by describing Alphamyces thailandicus, Angulomyces ubonensis, Gorgonomyces aquaticus, G. chiangraiensis, G. limnicus, Pateramyces pingflumenensis, Terramyces aquatica, and T. flumenensis and also provide valuable insights into the intricacies of this order. This newfound knowledge not only enriches our understanding of Rhizophydiales but also contributes significantly to the broader field of mycology, addressing a critical gap in the documentation of fungal species. The identification and characterization of these eight novel species mark a noteworthy stride towards a more comprehensive comprehension of fungal ecosystems and their vital role.

An integrative framework for dark taxa biodiversity assessment at scale: A case study using Megaselia (Diptera, Phoridae)

Abstract Species extinctions increase at a global scale; therefore, rapid inventorying of our planet's biodiversity is becoming more and more important. As insects represent the highest portion of the fauna and play key ecological roles, it is a pressing need to investigate their biodiversity and accelerate species discovery, especially for understudied insect groups, also known as “dark taxa.” Phoridae (Diptera) are a great example of a “dark taxon,” in particular the genus Megaselia Rondani. The use of integrative methodologies is the best approach to face up to the task of describing hyperdiverse and dark taxa, as morphology alone can be imprecise and slow, and molecular methods alone are often insufficient and lead to errors. Here, we used the Large‐Scale Integrative Taxonomy (LIT) approach to sort 9000 Megaselia into 277 putative species based on DNA barcodes. Each cluster passed through an evaluation of the predictors for incongruence indices between clusters and morphology (maximum p‐distance, stability index), and a subset of specimens were morphologically examined. We provided species estimates with Chao1, and our results suggest a 15% increase in species richness on our dataset. As this estimate was mostly based on samples from southern Germany, the species count will likely increase with expanded geographic sampling. This is a step forward in the study of this taxon, despite the fact that the German insect fauna is one of the best known in Europe and boasts more than one hundred years of study on phorids.

Genetic characterization of the first Deltacoronavirus from wild birds around Qinghai Lake.

Deltacoronavirus, widely distributed among pigs and wild birds, pose a significant risk of cross-species transmission, including potential human epidemics. Metagenomic analysis of bird samples from Qinghai Lake, China in 2021 reported the presence of Deltacoronavirus. A specific gene fragment of Deltacoronavirus was detected in fecal samples from wild birds at a positive rate of 5.94% (6/101). Next-generation sequencing (NGS) identified a novel Deltacoronavirus strain, which was closely related to isolates from the United Arab Emirates (2018), China (2022), and Poland (2023). Subsequently the strain was named A/black-headed gull/Qinghai/2021(BHG-QH-2021) upon confirmation of the Cytochrome b gene of black-headed gull in the sample. All available genome sequences of avian Deltacoronavirus, including the newly identified BHG-QH-2021 and 5 representative strains of porcine Deltacoronavirus (PDCoV), were classified according to ICTV criteria. In contrast to Coronavirus HKU15, which infects both mammals and birds and shows the possibility of cross-species transmission from bird to mammal host, our analysis revealed that BHG-QH-2021 is classified as Putative species 4. Putative species 4 has been reported to infect 5 species of birds but not mammals, suggesting that cross-species transmission of Putative species 4 is more prevalent among birds. Recombination analysis traced BHG-QH-2021 origin to dut148cor1 and MW01_1o strains, with MW01_1o contributing the S gene. Surprisingly, SwissModle prediction showed that the optimal template for receptor-binding domain (RBD) of BHG-QH-2021 is derived from the human coronavirus 229E, a member of the Alphacoronavirus, rather than the anticipated RBD structure of PDCoV of Deltacoronavirus. Further molecular docking analysis revealed that substituting the loop 1-2 segments of HCoV-229E significantly enhanced the binding capability of BHG-QH-2021 with human Aminopeptidase N (hAPN), surpassing its native receptor-binding domain (RBD). Most importantly, this finding was further confirmed by co-immunoprecipitation experiment that loop 1-2 segments of HCoV-229E enable BHG-QH-2021 RBD binding to hAPN, indicating that the loop 1-2 segment of the RBD in Putative species 4 is a probable key determinant for the virus ability to spill over into humans. Our results summarize the phylogenetic relationships among known Deltacoronavirus, reveal an independent putative avian Deltacoronavirus species with inter-continental and inter-species transmission potential, and underscore the importance of continuous surveillance of wildlife Deltacoronavirus.

Highly diverse RNA viruses and phage sequences concealed within birds.

The diversity of birds in most parts of the world is very high, and thus, they may carry different types of highly differentiated and unknown viruses. Thanks to advanced sequencing technologies, studies on the diversity of bird-associated viruses have increased over the past few years. In this study, a large-scale viral metagenomics survey was performed on cloacal swabs of 2,990 birds from nine provinces of the Chinese mainland. To detect undescribed RNA viruses in birds, more than 1,800 sequences sharing relatively low (<60%) amino acid sequence identity with the best match in the GenBank database were screened. Potentially novel viruses related to vertebrates have been identified, and several potential recombination signals were found. Additionally, hundreds of RNA viral sequences related to plants, fungi, and insects were detected, including previously unknown viruses. Furthermore, we investigated the novelty, functionality, and classification of the phages examined in this study. These viruses occupied topological positions on the evolutionary trees to a certain extent and might form novel putative families, genera, or species, thus providing information to fill the phylogenetic gaps of related viruses. These findings provided new insights into bird-associated viruses, but the interactions among these viruses remain unknown and require further investigation.IMPORTANCEStudying the diversity of RNA viruses in birds and mammals is crucial due to their potential impact on human health and the global ecosystem. Many RNA viruses, such as influenza and coronaviruses, have been shown to cross the species barrier and cause zoonotic diseases. In this metagenomics study involving 2,990 birds from at least 82 species, we identified over 1,800 RNA sequences with distant relationships to known viruses, some of which are rare in birds. The study highlights the scope and diversity of RNA viruses in birds, providing data to predict disease risks and monitor potential viral threats to wildlife, livestock, and human health. This information can aid in the development of strategies for disease prevention and control.

Occurrence, distribution and threats to mobulid rays in Brazil: A review and updated database

Abstract Mobulid rays are medium‐ to large‐sized pelagic‐dwelling planktivorous elasmobranchs that are circumglobally distributed. Brazil has a high diversity of Mobula species, with five of the nine globally valid species and one additional putative new species. Brazil represents a substantial knowledge gap concerning the ecology, distribution and threats to mobulid rays. In global distribution analyses, several species have been underrepresented along the Brazilian coast. The dataset is composed of information from peer‐reviewed and grey literature, as well as data from scientific expeditions, citizen science collaboration, social media and local news. We found 6,450 records of manta and devil rays along the Brazilian coast, including Mobula tarapacana, Mobula mobular, Mobula thurstoni, Mobula hypostoma, Mobula birostris and the putative new species (Mobula cf. birostris). Our results revealed alarmingly high captures, such as 4.5 tons of M. hypostoma in a single fishery cruise and 809 individuals of Mobula spp. from a single fleet during one year in the Southeastern region. These findings evidence the fisheries' threats to mobulid species in Brazil and highlight previously unnoted species records, such as the occurrence of M. hypostoma on the entire Brazilian continental shelf, including estuaries and M. tarapacana in coastal regions. Integrative information on the occurrence, distribution, and threats to mobulid rays on local and global scales is crucial to supporting strategies for their effective management and conservation.

Geminiviridae and Alphasatellitidae Diversity Revealed by Metagenomic Analysis of Susceptible and Tolerant Tomato Cultivars across Distinct Brazilian Biomes.

The diversity of Geminiviridae and Alphasatellitidae species in tomatoes was assessed via high-throughput sequencing of 154 symptomatic foliar samples collected from 2002 to 2017 across seven Brazilian biomes. The first pool (BP1) comprised 73 samples from the North (13), Northeast (36), and South (24) regions. Sixteen begomoviruses and one Topilevirus were detected in BP1. Four begomovirus-like contigs were identified as putative novel species (NS). NS#1 was reported in the semi-arid (Northeast) region and NS#2 and NS#4 in mild subtropical climates (South region), whereas NS#3 was detected in the warm and humid (North) region. The second pool (BP2) comprised 81 samples from Southeast (39) and Central-West (42) regions. Fourteen viruses and subviral agents were detected in BP2, including two topileviruses, a putative novel begomovirus (NS#5), and two alphasatellites occurring in continental highland areas. The five putative novel begomoviruses displayed strict endemic distributions. Conversely, tomato mottle leaf curl virus (a monopartite species) displayed the most widespread distribution occurring across the seven sampled biomes. The overall diversity and frequency of mixed infections were higher in susceptible (16 viruses + alphasatellites) in comparison to tolerant (carrying the Ty-1 or Ty-3 introgressions) samples, which displayed 9 viruses. This complex panorama reinforces the notion that the tomato-associated Geminiviridae diversity is yet underestimated in Neotropical regions.

Diversity and Abundance of Non-Geniculate Coralline Algae (NGCA) in Different Reef Conditions and Depth Zones

Non-g eniculate coralline red algae (NGCA) provide habitats for many epiphytic fauna and flora, and are considered reef engineers. The identification of NGCA is challenging due to cryptic speciation and their phenotypic plasticity that can be mediated by environmental conditions. Using DNA sequence data (psbA gene), a systematic examination was undertaken of the diversity and abundance of NGCA from two different reef conditions (fair and poor reef) and depth zones (shallow and deep zone) of a subtidal reef in the Gulf of Thailand at Koh Taen, Surat Thani Province, Thailand. Phylogentic analysis revealed 11 putative species: Chamberlainium sp., Dawsoniolithon sp., Hydrolithon boergesenii, Lithophyllum sp.1, Lithophyllum sp.2, Neogoniolithon sp.1, Neogoniolithon sp.2, Parvicellularium sp., Sporolithon ptychoides, Sporolithon sp.1 and Sporolithon sp.2. Specimens attributed to a newly recorded genus Parvicellularium, showed its highest abundance in the deep zone, while specimens attributed to Lithophyllum and Sporolithon were dominant in the shallow zone. The abundance of all NGCA genera showed no significant differences among reef conditions. Here, we present an updated overview of the diversity and abundance of NGCA in Thai waters.

Molecular differentiation analysis of ten putative species of Fannia (Diptera: Fanniidae) collected in carrion-baited traps from Colombia.

The genus Fannia is the most representative of the Fannidae family of true flies with worldwide distribution. Some species are attracted to decomposing materials and live vertebrate animals, which makes them important in forensics, medical and veterinary fields. However, identifying Fannia species can be difficult due to the high similarity in the external morphology of females and limited descriptions and morphological keys. Herein, molecular markers could provide a complementary tool for species identification. However, molecular identification has still limited application since databases contain few data for neotropical species of Fannia. This study assessed the potential of two molecular markers, the COI-3' region and internal transcribed spacer 2 (ITS2), to differentiate 10 putative species of the genus Fannia from Colombia using distance-based and tree-based approaches. The partial ITS2 and/or COI-3' regions allowed molecular diagnosis of six species, while pairs of species Fannia colazorrensis + F. dodgei and F. laclara + F. aburrae are conflicting. Although these results might suggest that conflicting pair species are conspecific, consistent morphological differences between males do not support this hypothesis. The lack of differentiation at the nuclear and mitochondrial molecular markers for the conflicting species may be due to incomplete evolutionary lineage separation, hybridization, or introgression events. In addition, sexual selection on male morphological traits before species-specific differences in molecular markers emerge may partially explain the results. Our study provides a valuable dataset to identify and confirm some Fannia species molecularly. Further, they could be used to associate females and immature stages with their conspecifics as a baseline to deep into their biology, ecology, distribution and potential applications in forensic and medico-veterinary entomology.

DNA barcoding reveals cryptic species in the sea slater Ligia italica (Crustacea, Isopoda) from Tunisia

Barcoding studies have provided significant insights into phylogenetic relationships among species belonging to the genus Ligia (Crustacea, Isopoda). Herein the diversity of the Italian sea slater Ligia italica from Tunisia is studied for the first time. Samples were collected from 18 localities in Tunisia, and the analysis included previously published sequences from Italy and Greece available in GenBank. Bayesian and Maximum Likelihood phylogenetic analyses were carried out using a fragment of the mitochondrial COI gene. Putative cryptic species were explored using the ‘barcode gap’ approach in the software ASAP. A genetic landscape shape analysis was carried out using the program Alleles in Space. The analyses revealed highly divergent and well-supported clades of L. italica dispersed across Tunisia (Clades A1 and A2), Greece (Clade B) and Italy (Clades C1 and C2). High genetic dissimilarity among clades suggested that L. italica constitute a cryptic species complex. Divergence among different L. italica lineages (Clades A, B and C) occurred around 7–4.5 Ma. The detected high genetic distances among clades did not result from atypical mitochondrial DNAs or intracellular infection by Wolbachia bacteria. The complex history of the Mediterranean Sea appears to have played a significant role in shaping the phylogeographic pattern of Ligia italica. Additional morphological and molecular studies are needed to confirm the existence of cryptic species in Ligia italica in Mediterranean.

Associations of plant-based foods, red and processed meat, and dairy with gut microbiome in Finnish adults

PurposePopulation-based studies on the associations of plant-based foods, red meat or dairy with gut microbiome are scarce. We examined whether the consumption of plant-based foods (vegetables, potatoes, fruits, cereals), red and processed meat (RPM) or dairy (fermented milk, cheese, other dairy products) are related to gut microbiome in Finnish adults.MethodsWe utilized data from the National FINRISK/FINDIET 2002 Study (n = 1273, aged 25–64 years, 55% women). Diet was assessed with 48-hour dietary recalls. Gut microbiome was analyzed using shallow shotgun sequencing. We applied multivariate analyses with linear models and permutational ANOVAs adjusted for relevant confounders.ResultsFruit consumption was positively (beta = 0.03, SE = 0.01, P = 0.04), while a dairy subgroup including milk, cream and ice-creams was inversely associated (beta=-0.03, SE 0.01, P = 0.02) with intra-individual gut microbiome diversity (alpha-diversity). Plant-based foods (R2 = 0.001, P = 0.03) and dairy (R2 = 0.002, P = 0.01) but not RPM (R2 = 0.001, P = 0.38) contributed to the compositional differences in gut microbiome (beta-diversity). Plant-based foods were associated with several butyrate producers/cellulolytic species including Roseburia hominis. RPM associations included an inverse association with R. hominis. Dairy was positively associated with several lactic producing/probiotic species including Lactobacillus delbrueckii and potentially opportunistic pathogens including Citrobacter freundii. Dairy, fermented milk, vegetables, and cereals were associated with specific microbial functions.ConclusionOur results suggest a potential association between plant-based foods and dairy or their subgroups with microbial diversity measures. Furthermore, our findings indicated that all the food groups were associated with distinct overall microbial community compositions. Plant-based food consumption particularly was associated with a larger number of putative beneficial species.

Deep genetic divergence among bluefish (Pomatomus saltatrix) of the Southwestern Atlantic

AbstractNeglected cryptic diversity can lead to the permanent loss of locally adapted alleles, which can reduce resilience to rapid environmental change. It can also result in overestimation of fisheries stock sizes that can result from treating different species as if they belonged to one. Bluefish (Pomatomus saltatrix) is considered a circumtropical and subtropical species and an important fishery resource all over the world. Differences in ecologically relevant traits are observed among isolated populations. Also, in the Southwestern Atlantic, molecular data suggest multiple populations, but these are treated as a single fish stock by regulatory agencies due to a lack of definitive information. We used whole mitogenome sequences, nuclear (rho) and mitochondrial (coxI and cytb) genes, as well as microsatellites to investigate historical and current genetic population structure and parameters of bluefish in the Western Atlantic. A total of 263 samples were collected along the Brazilian coast and in the USA (New Jersey, Northwest Atlantic). Data revealed the existence of two evolutionarily significant units (ESU) of bluefish along the South American coast, later confirmed by whole mitogenome sequencing of both haplogroups. These two ESUs have a mostly parapatric distribution, with some areas of overlap, which vary along the year. We also conducted seasonal sampling in Brazil to investigate migration patterns. ESUs occur mostly north and south of parallel 23° 40′ S, with an overlap area that varied seasonally. The level of differentiation between those two ESUs in the SW Atlantic, even in sympatry, is as high as that found between them and those from the NW Atlantic and Europe. Parapatric distribution and restricted gene flow suggest the existence of ecological barriers and local adaptation. The splitting of an ancient population from the Southwestern Atlantic into two putative species is important to understand bluefish evolutionary diversification and has implications for fishery regulatory measures in Brazil.

Molecular Detection and Characterization of Hemotropic Mycoplasma in Assamese Macaques (Macaca assamensis) of Northern Thailand.

Hemotropic mycoplasmas, also known as hemoplasmas, are parasitic bacteria that infect red blood cells, potentially leading to varying degrees of anemia across numerous mammalian species, including nonhuman primates. The present study aims to investigate the prevalence of hemoplasma infection and identify the species involved among free-ranging Assamese macaques (Macaca assamensis) inhabiting northern Thailand. A total of 133 blood samples were collected from Assamese macaques in Chiang Rai province, Thailand, and subjected to screening for hemoplasma infection utilizing nested PCR amplification targeting the 16S rRNA gene. Positive samples were subsequently analyzed through nucleotide sequencing and phylogenetic analysis for putative species identification. Current study results revealed that 17.3% (23/133; 95% CI 11.29-24.81) of Assamese macaques tested positive for hemoplasma infection using the nested PCR assay. Partial 16S rRNA sequences derived from hemoplasma isolates in Assamese macaques exhibited 99% homology, forming a cluster within the same phylogenetic clade as "Candidatus Mycoplasma haematomacacae," previously identified in long-tailed macaques, rhesus macaques, and Japanese macaques. These findings suggest the presence of "Ca. M. haematomacacae" not only in long-tailed macaques and rhesus macaques but also in Assamese macaques in Thailand. To our knowledge, this marks the first molecular detection of "Ca. M. haematomacacae" in Assamese macaques in Thailand. These results hold significance as they enhance our understanding of hemoplasma infection distribution among macaque populations in Thailand.

Detection of Anaplasma and Ehrlichia bacteria in humans, wildlife, and ticks in the Amazon rainforest

Tick-borne bacteria of the genera Ehrlichia and Anaplasma cause several emerging human infectious diseases worldwide. In this study, we conduct an extensive survey for Ehrlichia and Anaplasma infections in the rainforests of the Amazon biome of French Guiana. Through molecular genetics and metagenomics reconstruction, we observe a high indigenous biodiversity of infections circulating among humans, wildlife, and ticks inhabiting these ecosystems. Molecular typing identifies these infections as highly endemic, with a majority of new strains and putative species specific to French Guiana. They are detected in unusual rainforest wild animals, suggesting they have distinctive sylvatic transmission cycles. They also present potential health hazards, as revealed by the detection of Candidatus Anaplasma sparouinense in human red blood cells and that of a new close relative of the human pathogen Ehrlichia ewingii, Candidatus Ehrlichia cajennense, in the tick species that most frequently bite humans in South America. The genome assembly of three new putative species obtained from human, sloth, and tick metagenomes further reveals the presence of major homologs of Ehrlichia and Anaplasma virulence factors. These observations converge to classify health hazards associated with Ehrlichia and Anaplasma infections in the Amazon biome as distinct from those in the Northern Hemisphere.

Culicoides Midge Abundance across Years: Modeling Inter-Annual Variation for an Avian Feeder and a Candidate Vector of Hemorrhagic Diseases in Farmed Wildlife

(1) Background: Epizootic hemorrhagic disease virus (EHDV) and bluetongue virus (BTV) are orbiviruses that cause hemorrhagic disease (HD) with significant economic and population health impacts on domestic livestock and wildlife. In the United States, white-tailed deer (Odocoileus virginianus) are particularly susceptible to these viruses and are a frequent blood meal host for various species of Culicoides biting midges (Diptera: Ceratopogonidae) that transmit orbiviruses. The species of Culicoides that transmit EHDV and BTV vary between regions, and larval habitats can differ widely between vector species. Understanding how midges are distributed across landscapes can inform HD virus transmission risk on a local scale, allowing for improved animal management plans to avoid suspected high-risk areas or target these areas for insecticide control. (2) Methods: We used occupancy modeling to estimate the abundance of gravid (egg-laden) and parous (most likely to transmit the virus) females of two putative vector species, C. stellifer and C. venustus, and one species, C. haematopotus, that was not considered a putative vector. We developed a universal model to determine habitat preferences, then mapped a predicted weekly midge abundance during the HD transmission seasons in 2015 (July–October) and 2016 (May–October) in Florida. (3) Results: We found differences in habitat preferences and spatial distribution between the parous and gravid states for C. haematopotus and C. stellifer. Gravid midges preferred areas close to water on the border of well and poorly drained soil. They also preferred mixed bottomland hardwood habitats, whereas parous midges appeared less selective of habitat. (4) Conclusions: If C. stellifer is confirmed as an EHDV vector in this region, the distinct spatial and abundance patterns between species and physiological states suggest that the HD risk is non-random across the study area.

Biodiversity of Trichoderma species of healthy and Fusarium wilt-infected banana rhizosphere soils in Tenerife (Canary Islands, Spain).

Banana (Musa acuminata) is the most important crop in the Canary Islands (38.9% of the total cultivated area). The main pathogen affecting this crop is the soil fungal Fusarium oxysporum f. sp. cubense subtropical race 4 (Foc-STR4), for which there is no effective control method under field conditions. Therefore, the use of native biological control agents may be an effective and sustainable alternative. This study aims to: (i) investigate the diversity and distribution of Trichoderma species in the rhizosphere of different banana agroecosystems affected by Foc-STR4 in Tenerife (the island with the greatest bioclimatic diversity and cultivated area), (ii) develop and preserve a culture collection of native Trichoderma species, and (iii) evaluate the influence of soil chemical properties on the Trichoderma community. A total of 131 Trichoderma isolates were obtained from 84 soil samples collected from 14 farms located in different agroecosystems on the northern (cooler and wetter) and southern (warmer and drier) slopes of Tenerife. Ten Trichoderma species, including T. afroharzianum, T. asperellum, T. atrobrunneum, T. gamsii, T. guizhouense, T. hamatum, T. harzianum, T. hirsutum, T. longibrachiatum, and T. virens, and two putative novel species, named T. aff. harzianum and T. aff. hortense, were identified based on the tef1-α sequences. Trichoderma virens (35.89% relative abundance) and T. aff. harzianum (27.48%) were the most abundant and dominant species on both slopes, while other species were observed only on one slope (north or south). Biodiversity indices (Margalef, Shannon, Simpson, and Pielou) showed that species diversity and evenness were highest in the healthy soils of the northern slope. The Spearman analysis showed significant correlations between Trichoderma species and soil chemistry parameters (mainly with phosphorus and soil pH). To the best of our knowledge, six species are reported for the first time in the Canary Islands (T. afroharzianum, T. asperellum, T. atrobrunneum, T. guizhouense, T. hamatum, T. hirsutum) and in the rhizosphere of banana soils (T. afroharzianum, T. atrobrunneum, T. gamsii, T. guizhouense, T. hirsutum, T. virens). This study provides essential information on the diversity/distribution of native Trichoderma species for the benefit of future applications in the control of Foc-STR4.

Revisiting the phylogeny and taxonomy of the genus Sidera (Hymenochaetales, Basidiomycota) with particular emphasis on S.vulgaris.

The genus Sidera (Hymenochaetales, Basidiomycota) comprises white-rot, mono- or dimitic fungi with poroid or hydnoid hymenophore. It has a worldwide distribution albeit with fewer species present in the Southern Hemisphere. Although recent studies revealed the existence of several new Sidera species, there are still taxonomic inconsistencies and obscure phylogenetic relationships amongst certain taxa of the genus. In this work, a large number of Sidera collections were used to obtain an updated phylogeny, based on ITS and 28S rDNA sequences by including new material from Mediterranean Europe. The monophyly of the genus was strongly supported and all species with poroid hymenophore formed a highly-supported lineage with two major subclades. In total, 23 putative species were recognised. Amongst those, five are considered to possibly represent entities new to science, but further work is required since they are represented by single specimens or environmental sequences. Examined collections originally named S.lenis from southern Europe were grouped within S.vulgaris. Similarly, several collections under various names were hereby identified as S.vulgaris, including those of the recently described species S.tibetica. Furthermore, a critical discussion (based on morphoanatomical findings) is made on the key features that could be used to distinguish S.lenis from S.vulgaris.

Checklist of Water mites in Mexico. Historical background and DNA barcoding perspectives

Water mites are the most ubiquitous, abundant, diverse, and ecologically important group of arachnids in all freshwater environments. In Mexico, despite being a megadiverse country, only 271 species have been recorded so far since 1873. This is probably due to the scarcity of taxonomists in the country or the inherent complex morphology of this group, which challenges its systematics and its integration into other research studies. Molecular identification has been highly useful for practical applications of these organisms, while taxonomic identification work continues. Until now, a species checklist and reference information about water mites diversity and distribution in Mexico is lacking. In this work, we compiled species described or recorded in Mexico and provided preliminary data for a COI barcode library of the water mites in the country. This checklist includes 271 species from 25 families and 61 genera. In addition, the COI barcode library is supplied in a public dataset from the BOLD database (boldsystems.org); it contains 794 sequences corresponding to 103 BINs or putative species, of which only five of them have been identified to the species. We predict that the discovery of hidden diversity of mites will continue and improve after the use of integrative taxonomy tools. Also, their value as indicators of water quality will be re-evaluated, helping in the conservation of freshwater environments and the evaluation of the global warming impact.

Cryptic diversity within two widespread diadromous freshwater fishes (Teleostei: Galaxiidae).

Identification of taxonomically cryptic species is essential for the effective conservation of biodiversity. Freshwater-limited organisms tend to be genetically isolated by drainage boundaries, and thus may be expected to show substantial cryptic phylogenetic and taxonomic diversity. By comparison, populations of diadromous taxa, that migrate between freshwater and marine environments, are expected to show less genetic differentiation. Here we test for cryptic diversity in Australasian populations (both diadromous and non-diadromous) of two widespread Southern Hemisphere fish species, Galaxias brevipinnis and Galaxias maculatus. Both mtDNA and nuclear markers reveal putative cryptic species within these taxa. The substantial diversity detected within G. brevipinnis may be explained by its strong climbing ability which allows it to form isolated inland populations. In island populations, G. brevipinnis similarly show deeper genetic divergence than those of G. maculatus, which may be explained by the greater abundance of G. maculatus larvae in the sea allowing more ongoing dispersal. Our study highlights that even widespread, 'high-dispersal' species can harbour substantial cryptic diversity and therefore warrant increased taxonomic and conservation attention.

Polyploidy and hybridization in the Mediterranean: unravelling the evolutionary history of Centaurium (Gentianaceae).

Polyploidy is considered one of the main mechanisms of plant evolution and speciation. In the Mediterranean Basin, polyploidy has contributed to making this region a biodiversity hotspot, along with its geological and climatic history and other ecological and biogeographical factors. The Mediterranean genus Centaurium (Gentianaceae) comprises ~25 species, of which 60 % are polyploids, including tetraploids and hexaploids. To date, the evolutionary history of centauries has been studied using Sanger sequencing phylogenies, which have been insufficient to fully understand the phylogenetic relationships in this lineage. The goal of this study is to gain a better understanding of the evolutionary history of Centaurium by exploring the mechanisms that have driven its diversification, specifically hybridization and polyploidy. We aim to identify the parentage of hybrid species, at the species or clade level, as well as assessing whether morphological traits are associated with particular ploidy levels. We sequenced RADseq markers from 42 samples of 28 Centaurium taxa, and performed phylogenomic analyses using maximum likelihood, summary coalescent SVDquartets and Neighbor-Net approaches. To identify hybrid taxa, we used PhyloNetworks and the fastSTRUCTURE algorithm. To infer the putative parental species of the allopolyploids, we employed genomic analyses (SNIPloid). The association between different traits and particular ploidy levels was explored with non-metric multidimensional scaling. Our phylogenetic analyses confirmed the long-suspected occurrence of recurrent hybridization. The allopolyploid origin of the tetraploid C. serpentinicola and the hexaploids C. mairei, C. malzacianum and C. centaurioides was also confirmed, unlike that of C. discolor. We inferred additional signatures of hybridization events within the genus and identified morphological traits differentially distributed in different ploidy levels. This study highlights the important role that hybridization has played in the evolution of a Mediterranean genus such as Centaurium, leading to a polyploid complex, which facilitated its diversification and may exemplify that of other Mediterranean groups.