Comprehensive Phylogenetic Tree Research Articles

Molecular Study of Eimeria species in Quail birds (Coturnix coturnix japonica) in Thi-Qar Province, Southern Iraq

Fecal samples were collected from 330 quail birds from different areas of Thi-Qar province, Iraq. Allsamples were examined by traditional laboratory methods. Four species of Eimeria were diagnosed inquail (Eimeria bateri, Eimeria uzura, Eimeria tsunodai and Eimeria fluminensis), with a total infectionwas 64.54% (213 out of 330). DNA was extracted from 100 positive samples confirm the small subunitrRNA (18s) gene by Polymerase chain reaction using a general primer for Eimeria species, Sevengenotypes were according to the identify of DNA sequences of Eimeria species in Japanese quail, theaccession codes to NCBI-Genbank. using A comprehensive phylogenetic tree was generated in thepresent study, this details were being analyzed. This was the first molecular study in Iraq for Eimeriain common quail.

Identifying a Novel Bile Salt Hydrolase from the Keystone Gut Bacterium Christensenella minuta.

Christensenella minuta are human gut dwelling bacteria that have been proposed as key members of the gut microbiome, regulating energy balance and adiposity of their host. We formerly identified that a novel strain of C. minuta (strain DSM33407) boosted microbiota diversity and stimulated deconjugation of the primary bile acid taurocholic acid in human samples. However, there is no description of a bile salt hydrolase (BSH) protein carried in the genome of C. minuta. Here, we identified and cloned a protein from C. minuta’s genome that carries a potent BSH activity, which preferentially deconjugates glycine-conjugated bile acids. We then retrieved 14,319 putative BSH sequences from the NCBI database and filtered them using the UHGP database to collect a total of 6701 sequences that were used to build the most comprehensive phylogenetic tree of BSH-related enzymes identified in the human microbiome so far. This phylogenetic tree revealed that C. minuta’s BSH amino acid sequence clusters away from others with a threshold of 70% identity. This is therefore the first description of C. minuta’s BSH protein, which may be involved in its unique role within the human gut microbial ecosystem.

Chloroplast genome analysis of Angiosperms and phylogenetic relationships among Lamiaceae members with particular reference to teak (Tectona grandis L.f)

Availability of comprehensive phylogenetic tree for flowering plants which includes many of the economically important crops and trees is one of the essential requirements of plant biologists for diverse applications. It is the first study on the use of chloroplast genome of 3265 Angiosperm taxa to identify evolutionary relationships among the plant species. Sixty genes from chloroplast genome was concatenated and utilized to generate the phylogenetic tree. Overall the phylogeny was in correspondence with Angiosperm Phylogeny Group (APG) IV classification with very few taxa occupying incongruous position either due to ambiguous taxonomy or incorrect identification. Simple sequence repeats (SSRs) were identified from almost all the taxa indicating the possibility of their use in various genetic analyses. Large proportion (95.6%) of A/T mononucleotide was recorded while the di, tri, tetra, penta and hexanucleotide amounted to less than 5%. Ambiguity of the taxonomic status of Tectona grandis L.f was assessed by comparing the chloroplast genome with closely related Lamiaceae members through nucleotide diversity and contraction/expansion of inverted repeat regions. Although the gene content was highly conserved, structural changes in the genome was evident. Phylogenetic analysis suggested that Tectona could qualify for a subfamily Tectonoideae. Nucleotide diversity in intergenic and genic sequences revealed prominent hyper-variable regions such as, rps16-trnQ, atpH-atpI, psc4-psbJ, ndhF, rpl32 and ycf1 which have high potential in DNA barcoding applications.

NEW CHROMOSOME COUNTS OF ASIAN COSTACEAE AND INITIAL INSIGHTS INTO THE GENOME EVOLUTION OF THE FAMILY

Chromosome counts were obtained from six species of Costaceae from Asia. Our count of 2n = 18 for Cheilocostus speciosus confirms previous counts, and the other five counts have been made for the first time (Cheilocostus borneensis, Cheilocostus globosus, Cheilocostus sopuensis, Costus muluensis and Paracostus sp.). These chromosome counts reveal two somatic numbers, 2n = 18 and 2n = 36, of which the former is a new diploid number for the genus Paracostus. A comprehensive review of existing counts was conducted through literature and database searches. Mapping of these on a published comprehensive phylogenetic tree suggests that the diploid count of 2n = 18 is probably ancestral in the Costaceae, with repeated parallel evolution of tetraploidy and one case of octoploidy. The existence of triploid counts in several lineages harbouring polyploids suggests that diploids and tetraploids may exist in close proximity, and that crosses or meioticirregularities may lead to triploid genotypes occurring frequently.

The Mutation Profile of SARS-CoV-2 Is Primarily Shaped by the Host Antiviral Defense.

Understanding SARS-CoV-2 evolution is a fundamental effort in coping with the COVID-19 pandemic. The virus genomes have been broadly evolving due to the high number of infected hosts world-wide. Mutagenesis and selection are two inter-dependent mechanisms of virus diversification. However, which mechanisms contribute to the mutation profiles of SARS-CoV-2 remain under-explored. Here, we delineate the contribution of mutagenesis and selection to the genome diversity of SARS-CoV-2 isolates. We generated a comprehensive phylogenetic tree with representative genomes. Instead of counting mutations relative to the reference genome, we identified each mutation event at the nodes of the phylogenetic tree. With this approach, we obtained the mutation events that are independent of each other and generated the mutation profile of SARS-CoV-2 genomes. The results suggest that the heterogeneous mutation patterns are mainly reflections of host (i) antiviral mechanisms that are achieved through APOBEC, ADAR, and ZAP proteins, and (ii) probable adaptation against reactive oxygen species.

Issues in cyanobacterial taxonomy: comprehensive case study of unbranched, false branched and true branched heterocytous cyanobacteria.

The order Nostocales is represented by morphologically diverse forms with respect to the branching patterns and polarity of the filaments. With growing understanding of taxonomy and systematics, members of the order Nostocales have also undergone multiple taxonomic revisions. The last decade has seen a surge in the description of new genera and families within the order Nostocales. In this study, we discuss the taxonomic status of all the newly described and reclassified taxa of some of the prominent morphological forms within the order Nostocales by constructing comprehensive phylogenetic trees. Further, we propose certain strategies that would contribute to resolving the taxonomic complexities arising due to inadequate taxon sampling.

A whole-genome worldwide molecular epidemiology approach for contagious caprine pleuropneumonia

Contagious caprine pleuropneumonia is an infectious and contagious disease affecting goats and wildlife ruminants, mostly in Africa and Asia. It is caused by a mycoplasma, Mycoplasma capricolum susbp. capripneumoniae, which is very fastidious. This may be the reason why there are few reports of its isolation and characterization. This study describes the development of a whole genome typing strategy based on sequencing reads assemblies on a reference genome (Abomsa, GenBank accession LM995445) and extraction of informative single nucleotide polymorphism. FASTA sequences inferred from the variant calling files were used to establish a comprehensive phylogenetic tree based on 2880 SNPs. This tree included a total of 34 strains originating from all the regions where CCPP has been detected, as well as strains isolated from wildlife. A recent isolate from West-Niger was positioned closely to another 1995 East-Niger isolate, an indication that CCPP may be extending westward in Africa. Six 2013 Tanzanian isolates had identical sequences in spite of diverse geographical origins. This could be explained by the clonal expansion of a virulent strain at that time in East Africa. Although all strains isolated from wildlife in the Middle East were in the same phylogenetic group, this may not sign an adaptation to new hosts. The most probable explanation for wildlife contamination remains the contact with goats. This strategy will easily accommodate new data in the near future and should become a gold-standard high-resolution typing procedure for the surveillance of contagious caprine pleuropneumonia.

The complete mitochondrial genome of the medicinal fish, Cyprinion semiplotum: Insight into its structural features and phylogenetic implications

Assamese kingfish (Cyprinion semiplotum) belonging to the subfamily Barbinae is an important food as well as aquarium fish having identified pharmacological benefits. The species has a complex taxonomic history and its phylogenetic position remains uncertain. Molecular data employed in earlier phylogenetic studies was inadequate for its phylogenetic placement. Therefore, we characterized 16,671 bp long complete mitogenome of C. semiplotum using next-generation sequencing. The mitogenome encodes the typical set of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and two non-coding regions. Its gene organization, distribution pattern, nucleotide composition, tRNA secondary structure and codon usage was similar to other Cyprinid mitogenomes. However, a distinctive 90 bp insertion was found in 3′ periphery of the AT-rich control region. This can be a tool for identification of the species at the population level. Further, we reconstructed the most comprehensive phylogenetic trees of Cyprinidae based on complete mitogenome. In the resulting phylogenetic trees, C. semiplotum clustered tightly with other Barbinae species and exhibited a sister relationship with the species of the genera Aulopye, Barbus, Luciobarbus and Capoeta. The results presented herein will support future investigations on molecular taxonomy, population genetics, evolution and molecular phylogeny of C. semiplotum and its relatives.

Key novelties in the evolution of the aquatic colonial phylum Bryozoa: evidence from soft body morphology.

ABSTRACTMolecular techniques are currently the leading tools for reconstructing phylogenetic relationships, but our understanding of ancestral, plesiomorphic and apomorphic characters requires the study of the morphology of extant forms for testing these phylogenies and for reconstructing character evolution. This review highlights the potential of soft body morphology for inferring the evolution and phylogeny of the lophotrochozoan phylum Bryozoa. This colonial taxon comprises aquatic coelomate filter‐feeders that dominate many benthic communities, both marine and freshwater. Despite having a similar bauplan, bryozoans are morphologically highly diverse and are represented by three major taxa: Phylactolaemata, Stenolaemata and Gymnolaemata. Recent molecular studies resulted in a comprehensive phylogenetic tree with the Phylactolaemata sister to the remaining two taxa, and Stenolaemata (Cyclostomata) sister to Gymnolaemata. We plotted data of soft tissue morphology onto this phylogeny in order to gain further insights into the origin of morphological novelties and character evolution in the phylum. All three larger clades have morphological apomorphies assignable to the latest molecular phylogeny. Stenolaemata (Cyclostomata) and Gymnolaemata were united as monophyletic Myolaemata because of the apomorphic myoepithelial and triradiate pharynx. One of the main evolutionary changes in bryozoans is a change from a body wall with two well‐developed muscular layers and numerous retractor muscles in Phylactolaemata to a body wall with few specialized muscles and few retractors in the remaining bryozoans. Such a shift probably pre‐dated a body wall calcification that evolved independently at least twice in Bryozoa and resulted in the evolution of various hydrostatic mechanisms for polypide protrusion. In Cyclostomata, body wall calcification was accompanied by a unique detachment of the peritoneum from the epidermis to form the hydrostatic membraneous sac. The digestive tract of the Myolaemata differs from the phylactolaemate condition by a distinct ciliated pylorus not present in phylactolaemates. All bryozoans have a mesodermal funiculus, which is duplicated in Gymnolaemata. A colonial system of integration (CSI) of additional, sometimes branching, funicular cords connecting neighbouring zooids via pores with pore‐cell complexes evolved at least twice in Gymnolaemata. The nervous system in all bryozoans is subepithelial and concentrated at the lophophoral base and the tentacles. Tentacular nerves emerge intertentacularly in Phylactolaemata whereas they partially emanate directly from the cerebral ganglion or the circum‐oral nerve ring in myolaemates. Overall, morphological evidence shows that ancestral forms were small, colonial coelomates with a muscular body wall and a U‐shaped gut with ciliary tentacle crown, and were capable of asexual budding. Coloniality resulted in many novelties including the origin of zooidal polymorphism, an apomorphic landmark trait of the Myolaemata.

Complete mitochondrial genome of Ophichthus brevicaudatus reveals novel gene order and phylogenetic relationships of Anguilliformes

Generally, a teleostean group possesses only one type or a set of similar mitochondrial gene arrangement. However, two types of gene arrangement have been identified in the mitochondrial genomes (mitogenomes) of Anguilliformes. Here, a newly sequenced mitogenome of Ophichthus brevicaudatus (Anguilliformes; Ophichthidae) was presented. The total length of the O. brevicaudatus mitogenome was 17,773 bp, and it contained 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNA (tRNA) genes, and two identical control regions (CRs). The gene order differed from that of the typical vertebrate mitogenomes. The genes ND6 and the conjoint trnE were translocated to the location between trnT and trnP, and one of the duplicated CR was translocated to the upstream of the ND6. The duplication-random loss model was adopted to explain the gene rearrangement events in this mitogenome. The most comprehensive phylogenetic trees of Anguilliformes based on complete mitogenome was constructed. The non-monophyly of Congridae was well supported, whereas the non-monophyly of Derichthyidae and Chlopsidae was not supported. These results provide insight into gene arrangement features of anguilliform mitogenomes and lay the foundation for further phylogenetic studies on Anguilliformes.

Testing the higher-level phylogenetic classification of Digenea (Platyhelminthes, Trematoda) based on nuclear rDNA sequences before entering the age of the 'next-generation' Tree of Life.

Digenea Carus, 1863 represent a highly diverse group of parasitic platyhelminths that infect all major vertebrate groups as definitive hosts. Morphology is the cornerstone of digenean systematics, but molecular markers have been instrumental in searching for a stable classification system of the subclass and in establishing more accurate species limits. The first comprehensive molecular phylogenetic tree of Digenea published in 2003 used two nuclear rRNA genes (ssrDNA = 18S rDNA and lsrDNA = 28S rDNA) and was based on 163 taxa representing 77 nominal families, resulting in a widely accepted phylogenetic classification. The genetic library for the 28S rRNA gene has increased steadily over the last 15 years because this marker possesses a strong phylogenetic signal to resolve sister-group relationships among species and to infer phylogenetic relationships at higher levels of the taxonomic hierarchy. Here, we have updated the database of 18S and 28S rRNA genes until December 2017, we have added newly generated 28S rDNA sequences and we have reassessed phylogenetic relationships to test the current higher-level classification of digeneans (at the subordinal and subfamilial levels). The new dataset consisted of 1077 digenean taxa allocated to 106 nominal families for 28S and 419 taxa in 98 families for 18S. Overall, the results were consistent with previous higher-level classification schemes, and most superfamilies and suborders were recovered as monophyletic assemblages. With the advancement of next-generation sequencing (NGS) technologies, new phylogenetic hypotheses from complete mitochondrial genomes have been proposed, although their power to resolve deep levels of trees remains controversial. Since data from NGS methods are replacing other widely used markers for phylogenetic analyses, it is timely to reassess the phylogenetic relationships of digeneans with conventional nuclear rRNA genes, and to use the new analysis to test the performance of genomic information gathered from NGS, e.g. mitogenomes, to infer higher-level relationships of this group of parasitic platyhelminths.

Identification and characterization of novel homeodomain leucine zipper (HD-Zip) transcription factors associated with heat tolerance in perennial ryegrass

The homeodomain leucine zipper (HD-Zip) family transcription factors play roles in regulating plant development and responses to abiotic stress; however, how HD-Zip genes are associated with plant heat tolerance is unclear. The objectives of this study were to characterize HD-Zip I genes in perennial ryegrass (Lolium perenne), analyze the expression pattern under different abiotic stresses and identify novel HD-Zip I members associated with genetic variations in heat tolerance. A total of 13 HD-Zip I genes were identified in the transcriptome of perennial ryegrass. A comprehensive phylogenetic tree of HD-Zip I proteins in perennial ryegrass, Arabidopsis and rice was constructed. Motif analysis between LpHD-Zip I and OsHD-Zip I by MEME was characterized. LpHD-Zip I had close evolutionary relationship to OsHD-Zip I, and HD-Zip I may be subject to functional differentiation between monocotyledons and dicotyledons. qPCR analysis of 13 HD-Zip I genes showed these genes expressed at different levels in roots and leaves. These genes also showed various expression levels under different abiotic stresses (cold, heat, salt and osmotic). Physiological responses of heat-sensitive lines (321681 and 418714) and heat-tolerant lines (231565 and 275660) of perennial ryegrass to heat stress were evaluated. Differential expression levels of four genes (LpHOX6, -8, -21 and -24) were detected between heat-sensitive and heat-tolerant lines. LpHOX6, -8 and -24 expression levels were negatively associated with heat tolerance while LpHOX21 was positively associated with heat tolerance of perennial ryegrass. This is the first study demonstrating the association of four members of the HD-Zip I family (LpHOX6, -8, -21, and -24) with genetic variations in heat tolerance.

Insights into the historical assembly of global dryland floras: the diversification of Zygophyllaceae

BackgroundDrylands cover nearly 41% of Earth’s land surface and face a high risk of degradation worldwide. However, the actual timeframe during which dryland floras rose on a global scale remains unknown. Zygophyllaceae, an important characteristic component of dryland floras worldwide, offers an ideal model group to investigate the diversification of dryland floras. Here, we used an integration of the phylogenetic, molecular dating, biogeographic, and diversification methods to investigate the timing and patterns of lineage accumulation for Zygophyllaceae overall and regionally. We then incorporated the data from other dominant components of dryland floras in different continents to investigate the historical construction of dryland floras on a global scale.ResultsWe provide the most comprehensive phylogenetic tree for Zygophyllaceae so far based on four plastid and nuclear markers. Detailed analyses indicate that Zygophyllaceae colonized Africa, Asia, Australia, and the New World at different periods, sometimes multiple times, but Zygophyllaceae lineages in the four regions all experienced a rapid accumulation beginning at the mid-late Miocene (~ 15–10 Ma). Other eleven essential elements of dryland floras become differentiated at the same time.ConclusionsOur results suggest that the rise of global dryland floras is near-synchronous and began at the mid-late Miocene, possibly resulting from the mid-Miocene global cooling and regional orogenetic and climate changes. The mid-late Miocene is an essential period for the assembly and evolution of global dryland floras.

Robust demarcation of fourteen different species groups within the genus Streptococcus based on genome-based phylogenies and molecular signatures

The genus Streptococcus comprises many important pathogens that impact human and animal health. Despite their widespread relevance, accurate classification and methods to reliably distinguish its members remain inadequate. Hence, we conducted comprehensive phylogenomics and comparative genomic analyses on 70 genome-sequenced members of this genus to delineate their interrelationships. Comprehensive phylogenetic trees were constructed based on multiple datasets of proteins, including 737 core proteins for the genus Streptococcus, 87 proteins conserved within the phylum Firmicutes, GyrA-GyrB, and RpoB-RpoC sequences. Based on the core proteins for Streptococcus species, genetic relatedness based on average amino acid identity was also determined. In parallel, comparative genomic analyses on protein sequences from this genus have identified 134 highly specific molecular markers in the form of conserved signature indels (CSIs) that are specifically shared by either the entire genus or its distinct clades/subclades. Based on the results from these multiple lines of investigations, a reliable picture of the overall evolutionary relationships within the genus Streptococcus has emerged. At the highest level, members of this genus form 2 main clades termed the “Mitis-Suis” and “Pyogenes-Equinus-Mutans” clades. Among these 2 major clades, 14 distinct subclades have been identified which include 4 previously identified species groups (viz. Pyogenes, Mutans, Salivarius and Equinus (or Bovis)); the Mitis clade, which is comprised of the Anginosus subclade and three novel subclades (viz. Pneumoniae, Gordonii and Parasanguinis), and six novel subclades termed the Suis, Sobrinus, Halotolerans, Porci, Entericus and Orisratti subclades. Members of the aforementioned subclades are reliably distinguished on the basis of their distinct branching in phylogenetic trees and multiple identified CSIs that are specifically shared by them. The molecular markers described here serve to dermarcate and clarify the interrelationships among different species groups of streptococci, and provide important means for developing novel diagnostic tests and functional studies on these bacteria which should enhance our understanding of them.

Swimbladder Evolution of Longfin Herrings (Pristigasteridae, Teleostei).

Sébastien Lavoué, Sahat Ratmuangkhwang, Hsuan-Ching Ho, Wei-Jen Chen, and Mohd Nor Siti Azizah (2018) Longfin herrings form a monophyletic, circumtropically distributed family of mostly marine teleost fishes, the Pristigasteridae (Clupeoidei), that includes 38 species classified into nine genera and three main lineages (the Pelloninae, Pristigasterinae, and the genus Ilisha). The external morphology and osteology of the Pristigasteridae provide only a few, sometimes conflicting, informative characters which makes it difficult to reconstruct their phylogeny, but their swimbladder (a visceral gas-filled chamber that has several important functions in the Teleostei) appears to be highly specialized and variable among species. In particular, the swimbladder of most Indo-West Pacific pristigasterid species exhibits one or paired post-coelomic extensions, whereas New World species do not. The presence of these extensions conflicts with the current systematic classification, as they are only found in subsets of different taxa. To examine this conflict, the most comprehensive molecular phylogenetic tree of the Pristigasteridae to date was built using six molecular markers and 21 species. This tree deeply disagreed with the current classification in that it indicated that the subfamilies Pelloninae and Pristigasterinae are not monophyletic and neither are the genera Ilisha, Pellona, and Opisthopterus. Using this tree to infer the evolution of the post-coelomic extensions, it was found that their absence is the ancestral condition in the Pristigasteridae. Indo-West Pacific species with post-coelomic extensions evolved later and form a monophyletic group, inside which species with only one extension form a monophyletic group. The consequences of our findings on the evolution and classification of Pristigasteridae are discussed. We suggest that only species of Pristigasteridae having one or paired post-coelomic extensions should be included in the genus Ilisha.

Evolution of floral traits and impact of reproductive mode on diversification in the phlox family (Polemoniaceae)

Pollinator-mediated selection is a major driver of evolution in flowering plants, contributing to the vast diversity of floral features. Despite long-standing interest in floral variation and the evolution of pollination syndromes in Polemoniaceae, the evolution of floral traits and known pollinators has not been investigated in an explicit phylogenetic context. Here we explore macroevolutionary patterns of both pollinator specificity and three floral traits long considered important determinants of pollinator attraction across the most comprehensive species-level phylogenetic tree yet produced for the family. The presence of floral chlorophyll is reconstructed as the ancestral character state of the family, even though the presence of floral anthocyanins is the most prevalent floral pigment in extant taxa. Mean corolla length and width of the opening of the floral tube are correlated, and both appear to vary with pollinator type. The evolution of pollination systems appears labile, with multiple gains and losses of selfing and conflicting implications for patterns of diversification. Explicit testing of diversification models rejects the hypothesis that selfing is an evolutionary dead-end. This study begins to disentangle the individual components that comprise pollination syndromes and lays the foundation for future work on the genetic mechanisms that control each trait.

Molecular phylogeny of the genus Fissidens (Fissidentaceae, Bryophyta) and a refinement of the infrageneric classification

The genus Fissidens (ca. 440 spp.) is one of the phylogenetically poorly studied groups of mosses (Bryophyta). While various classifications of this genus have been proposed, no attempt at a classification of the genus based on combined molecular and morphological evidence has been made. Here, we present for the first time a comprehensive phylogenetic tree consisting of 50 representatives of Fissidens, reconstructed using sequence data from chloroplast rbcL and rps4 genes. Ancestral state reconstructions provide three clear apomorphies within Fissidens: peristome teeth, limbidium and chromosome number. Based on the phylogeny and morphological reassessment, we recognize three subgenera, Pachyfissidens, Neoamblyothallia, and Fissidens. Subgenus Neoamblyothallia consists of two sections: Neoamblyothallia and Crispidium. Subgenus Fissidens consists of five sections: Fissidens, Polypodiopsis, Aloma, Areofissidens, and Semilimbidium. High diversity of the most derived sect. Semilimbidium in the tropics suggests that the evolutionary history of the genus is through adaptation and diversification in tropical regions.

Tetrapods on the EDGE: Overcoming data limitations to identify phylogenetic conservation priorities.

The scale of the ongoing biodiversity crisis requires both effective conservation prioritisation and urgent action. As extinction is non-random across the tree of life, it is important to prioritise threatened species which represent large amounts of evolutionary history. The EDGE metric prioritises species based on their Evolutionary Distinctiveness (ED), which measures the relative contribution of a species to the total evolutionary history of their taxonomic group, and Global Endangerment (GE), or extinction risk. EDGE prioritisations rely on adequate phylogenetic and extinction risk data to generate meaningful priorities for conservation. However, comprehensive phylogenetic trees of large taxonomic groups are extremely rare and, even when available, become quickly out-of-date due to the rapid rate of species descriptions and taxonomic revisions. Thus, it is important that conservationists can use the available data to incorporate evolutionary history into conservation prioritisation. We compared published and new methods to estimate missing ED scores for species absent from a phylogenetic tree whilst simultaneously correcting the ED scores of their close taxonomic relatives. We found that following artificial removal of species from a phylogenetic tree, the new method provided the closest estimates of their “true” ED score, differing from the true ED score by an average of less than 1%, compared to the 31% and 38% difference of the previous methods. The previous methods also substantially under- and over-estimated scores as more species were artificially removed from a phylogenetic tree. We therefore used the new method to estimate ED scores for all tetrapods. From these scores we updated EDGE prioritisation rankings for all tetrapod species with IUCN Red List assessments, including the first EDGE prioritisation for reptiles. Further, we identified criteria to identify robust priority species in an effort to further inform conservation action whilst limiting uncertainty and anticipating future phylogenetic advances.

First insights into the phylogeny of deep-sea glass sponges (Hexactinellida) from polymetallic nodule fields in the Clarion-Clipperton Fracture Zone (CCFZ), northeastern Pacific

Glass sponges represent a dominant group of megabenthic deep-sea fauna and play a key role in benthic deep-sea ecosystems. Especially in the Clarion-Clipperton Fracture Zone (CCFZ), a potential deep-sea mining area, they grow on polymetallic nodules or on the surrounding sediment. We investigate hexactinellids from the CCFZ to understand the ecological aspects of deep-sea mining and support the development of future pre-mining risk assessments and monitoring actions. Therefore, this study is published as part of a series of studies, all focusing on deep-sea glass sponges from the CCFZ. Resolving genetic relationships between species is still a fundamental as well as challenging task. Especially understudied groups mostly lack resolution. Combining results derived from taxonomic and phylogenetic data gives deeper insights into glass sponge relationships. Here, we present (1) a set of new primers for sequencing mitochondrial 16S rDNA as well as nuclear 18S and 28S rDNA of glass sponges, (2) first DNA sequencing data for 6 hexactinellid genera and 19 species, as well as (3) the most comprehensive phylogenetic tree of hexactinellid sponges to date including data available from previous studies.

Rolling into the deep of the land planarian genus Choeradoplana (Tricladida, Continenticola, Geoplanidae) taxonomy

The land planarian genus Choeradoplana (Plathelminthes, Tricladida) is currently integrated by 13 species. In previous works, morphological variation in its type species, Choeradoplana iheringi, was reported, but no attempt to test whether it is just a single species has been made yet. In order to disentangle the taxonomy of this species and further members of the genus, we sampled new specimens and combined morphological and molecular data and also have evaluated the performance of diverse methods of molecular species delimitation. Our data point to the presence of two cryptic species named C. iheringi, plus two new species, all hidden under the same general appearance. An in-depth morphological study of the specimens allowed detection of diagnostic morphological traits in each species, for which we also propose a molecular diagnosis. This integrative taxonomic study demonstrates once again the usefulness of molecular tools to weigh minor morphological characteristics and thus reveal the existence of species that would otherwise remain cryptic. However, under certain parameters, the molecular methods may over-split species with a high genetic structure, maybe pointing to incipient speciation. This makes critical the use of these methods combined with a comprehensive morphological approach. We also present a comprehensive phylogenetic tree including most Choeradoplana species. The tree, well supported, allows making some preliminary inferences on the evolution of the group and its historical biogeography.