Large carrion and burying beetles evolved from Staphylinidae (Coleoptera, Staphylinidae, Silphinae): a review of the evidence.

Large carrion beetles (Silphidae) are the focus of ongoing behavioral ecology, forensic, ecological, conservation, evolutionary, systematic, and other research, and were recently reclassified as a subfamily of Staphylinidae. Twenty-three analyses in 21 publications spanning the years 1927-2023 that are relevant to the question of the evolutionary origin and taxonomic classification of Silphidae are reviewed. Most of these analyses (20) found Silphidae nested inside Staphylinidae (an average of 4.38 branches deep), two found Silphidae in an ambiguous position, and one found Silphidae outside Staphylinidae, as sister to Hydrophilidae. There is strong evidence supporting the hypothesis that large carrion beetles evolved from within Staphylinidae and good justification for their classification as the subfamily Silphinae of the megadiverse, and apparently now monophyletic, Staphylinidae. Considerable uncertainty remains regarding the interrelationships and monophyly of many staphylinid subfamilies. Nonetheless, the subfamily Tachyporinae was found to be the sister of Silphinae in more analyses (7) than any other subfamily.

Mitogenomic analysis of Rüppell's fox (Vulpes rueppellii) confirms phylogenetic placement within the Palaearctic clade shared with its sister species, the red fox (Vulpes vulpes).

The Rüppell's fox (Vulpes rueppellii) inhabits desert regions across North Africa, the Arabian Peninsula and southwestern Asia. Its phylogenetic relationship with other fox species, especially within the phylogeographic context of its sister species, V. vulpes, remain unclear. We here report the sequencing and de-novo assembly of the first annotated mitogenome of V. rueppellii, analysed with data from other foxes (tribe Vulpini, subfamily Caninae). We used four bioinformatic approaches to reconstruct the V. rueppellii mitogenome, obtaining identical sequences except for the incompletely assembled tandem-repeat region within the D-loop. The mitogenome displayed an identical organization, number and length of genes as V. vulpes. We found high support for clustering of both known subclades of V. rueppellii within the Palearctic clade of V. vulpes, rendering the latter species paraphyletic, consistent with previous analyses of shorter mtDNA fragments. More work is needed for a full understanding of the evolutionary drivers and consequences of hybridization in foxes.

Mitochondrial phylogenomics provides conclusive evidence that the family Ancyrocephalidae is deeply paraphyletic.

BACKGROUND: Unresolved taxonomic classification and paraphyly pervade the flatworm class Monogenea: the class itself may be paraphyletic and split into Polyopisthocotylea and Monopisthocotylea; there are some indications that the monopisthocotylean order Dactylogyridea may also be paraphyletic; single-gene markers and some morphological traits indicate that the family Ancyrocephalidae is paraphyletic and intertwined with the family Dactylogyridae. METHODS: To attempt to study the relationships of Ancyrocephalidae and Monopisthocotylea using a phylogenetic marker with high resolution, we sequenced mitochondrial genomes of two fish ectoparasites from the family Dactylogyridae: Dactylogyrus simplex and Dactylogyrus tuba. We conducted phylogenetic analyses using three datasets and three methods. Datasets were ITS1 (nuclear) and nucleotide and amino acid sequences of almost complete mitogenomes of almost all available Monopisthocotylea mitogenomes. Methods were maximum likelihood (IQ-TREE), Bayesian inference (MrBayes) and CAT-GTR (PhyloBayes). RESULTS: Both mitogenomes exhibited the ancestral gene order for Neodermata, and both were compact, with few and small intergenic regions and many and large overlaps. Gene sequences were remarkably divergent for nominally congeneric species, with only trnI exhibiting an identity value > 80%. Both mitogenomes had exceptionally low A + T base content and AT skews. We found evidence of pervasive compositional heterogeneity in the dataset and indications that base composition biases cause phylogenetic artefacts. All six mitogenomic analyses produced unique topologies, but all nine analyses produced topologies that rendered Ancyrocephalidae deeply paraphyletic. Mitogenomic data consistently resolved the order Capsalidea as nested within the Dactylogyridea. CONCLUSIONS: The analyses indicate that taxonomic revisions are needed for multiple Polyopisthocotylea lineages, from genera to orders. In combination with previous findings, these results offer conclusive evidence that Ancyrocephalidae is a paraphyletic taxon. The most parsimonious solution to resolve this is to create a catch-all Dactylogyridae sensu lato clade comprising the current Ancyrocephalidae, Ancylodiscoididae, Pseudodactylogyridae and Dactylogyridae families, but the revision needs to be confirmed by another marker with a sufficient resolution.

The phylogeny and evolutionary ecology of hoverflies (Diptera: Syrphidae) inferred from mitochondrial genomes.

Hoverflies (Diptera: Syrphidae) are a diverse group of pollinators and a major research focus in ecology, but their phylogenetic relationships remain incompletely known. Using a genome skimming approach we generated mitochondrial genomes for 91 species, capturing a wide taxonomic diversity of the family. To reduce the required amount of input DNA and overall cost of the library construction, sequencing and assembly was conducted on mixtures of specimens, which raises the problem of chimera formation of mitogenomes. We present a novel chimera detection test based on gene tree incongruence, but identified only a single mitogenome of chimeric origin. Together with existing data for a final set of 127 taxa, phylogenetic analysis on nucleotide and amino acid sequences using Maximum Likelihood and Bayesian Inference revealed a basal split of Microdontinae from all other syrphids. The remainder consists of several deep clades assigned to the subfamily Eristalinae in the current classification, including a clade comprising the subfamily Syrphinae (plus Pipizinae). These findings call for a re-definition of subfamilies, but basal nodes had insufficient support to fully justify such action. Molecular-clock dating placed the origin of the Syrphidae crown group in the mid-Cretaceous while the Eristalinae-Syrphinae clade likely originated near the K/Pg boundary. Transformation of larval life history characters on the tree suggests that Syrphidae initially had sap feeding larvae, which diversified greatly in diet and habitat association during the Eocene and Oligocene, coinciding with the diversification of angiosperms and the evolution of various insect groups used as larval host, prey, or mimicry models. Mitogenomes proved to be a powerful phylogenetic marker for studies of Syrphidae at subfamily and tribe levels, allowing dense taxon sampling that provided insight into the great ecological diversity and rapid evolution of larval life history traits of the hoverflies.

RESOLVING THE PARAPHYLETIC TURTLE BLOOD FLUKES: REVISION OF SPIRORCHIIDAE STUNKARD, 1921 AND PROPOSAL OF CARETTACOLIDAE YAMAGUTI, 1958, HAPALOTREMATIDAE (STUNKARD, 1921) POCHE, 1926, BARACKTREMATIDAE N. FAM., PLATTIDAE N. FAM., AND ATAMATAMIDAE N. FAM.

Turtle blood flukes ("spirorchiids") comprise a paraphyletic assemblage including the monophyletic Schistosomatidae Stiles and Hassall, 1898 as a crown group. We herein morphologically diagnose the natural groups of turtle blood flukes and propose family names for them. Spirorchiidae Stunkard, 1921 (Spirorchis MacCallum, 1919 [type]; Spirhapalum Ejsmont, 1927; Plasmiorchis Mehra, 1934; MonticelliusMehra, 1939; VasotremaStunkard, 1928; provisionally UterotremaPlatt and Pichelin, 1994) has a ventral sucker (lost in Spirorchis), an esophageal gland surrounding the entire esophagus, lateral esophageal diverticula (plicate organ and medial esophageal diverticulum present or absent), a glandular mass at the esophagus base, paired ceca surrounded by vitelline follicles for their entire length, a non-filamented, ovoid egg, and typically a Manter's organ. Baracktrematidae n. fam. (Baracktrema Roberts, Platt, and Bullard, 2016 [type]; Unicaecum Stunkard, 1925; NeospirorchisPrice, 1934) has no ventral sucker, a single cecum or cyclocoel, a coiled or looped testis extending into the anterior body half, a convoluted post-cecal and post-gonadal uterus, a uterine pouch, no metraterm, no Manter's organ, and non-filamented eggs. Plattidae n. fam. (Platt Roberts and Bullard, 2018 [type]; Hapalorhynchus Stunkard, 1922; Coeuritrema Mehra, 1933; Enterohaematotrema Mehra, 1940; CardiotremaDwivedi, 1967; Ruavermis Dutton and Bullard, 2020) has the anatomical sequence of a ventral sucker, external seminal vesicle, cirrus sac, anterior testis, ovary, transverse vitelline duct, and posterior testis (except Enterohaematotrema) plus a pars prostatica, dorsal genital pore, globular excretory vesicle, and no Manter's organ. Carettacolidae Yamaguti, 1958 (CarettacolaManter and Larson, 1950 [type]) has a spinose oral sucker, a spinose and contractile ventral sucker (transverse cavity present), numerous testes distributing in a post-ovarian, inter-cecal column, and an ovary and transverse vitelline duct that are pre-testicular. Hapalotrematidae (Stunkard, 1921) Poche, 1926 (Hapalotrema Loos, 1899 [type]; AmphiorchisPrice, 1934; LearediusPrice, 1934; Cheloneotrema Simha and Chattopadhyaya, 1980; NeocaballerotremaSimha, 1977; Satyanarayanotrema Simha and Chattopadhyaya, 1980; Shobanotrema Simha and Chattopadhyaya, 1980) has the anatomical sequence of a ventral sucker, anterior testis(es), external seminal vesicle and cirrus sac, ovary, and posterior testis(es). Atamatamidae n. fam. (Atamatam Bullard and Roberts, 2019 [type]; Paratamatam Bullard and Roberts, 2019; Pitiutrema Dutton and Bullard, 2019) has an oral sucker with anteroventral spines, vasa efferentia connecting to a pre-ovarian external seminal vesicle, a cirrus sac directed postero-laterad and having an internal seminal vesicle and glandular luminal wall, and a dendritic ovary flanked by the external seminal vesicle and oviducal seminal receptacle. A 28S phylogenetic analysis failed to reject the monophyly of these families.

Characterization of the complete mitochondrial genome of the fluke of turdus, Plagiorchis elegans, and phylogenetic implications.

Plagiorchis elegans (Trematoda: Digenea) is mainly parasitic in the intestines of vertebrate animals, including humans, causing irreversible pathological damage and herd-spherical influences. However, little information is available about its molecular epidemiology, population genetics, and phylogeny. In the present study, we sequenced, assembled, and annotated the complete mitochondrial (mt) genome of P. elegans. Combining with the available mitochondrial data of subclass Digenea, phylogenetic analysis was performed based on Bayesian inference (BI). These results showed that the complete length of P. elegans is 13,862 bp, including 12 protein-coding genes (PCGs), 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), and one non-coding region (NCR). There was an obvious A + T content from 61.0% to 71.3% and the values of the Ka/Ks ratio ranged from 0.119 (cox1) to 1.053 (nad6). In the BI analysis, different from previous studies, phylogenetic analysis showed genus Glypthelmins was paraphyletic rather than monophyletic and had a closer relationship with Plagiorchis and Orientocreadium. Additionally, the BI tree also presented that the genus Echinostoma was monophyletic. Our results provided molecular data in the family Plagiorchiidae proposing new insight within Xiphidiata and Echinostomata.

Phytophthora: an ancient, historic, biologically and structurally cohesive and evolutionarily successful generic concept in need of preservation.

The considerable economic and social impact of the oomycete genus Phytophthora is well known. In response to evidence that all downy mildews (DMs) reside phylogenetically within Phytophthora, rendering Phytophthora paraphyletic, a proposal has been made to split the genus into multiple new genera. We have reviewed the status of the genus and its relationship to the DMs. Despite a substantial increase in the number of described species and improvements in molecular phylogeny the Phytophthora clade structure has remained stable since first demonstrated in 2000. Currently some 200 species are distributed across twelve major clades in a relatively tight monophyletic cluster. In our assessment of 196 species for twenty morphological and behavioural criteria the clades show good biological cohesion. Saprotrophy, necrotrophy and hemi-biotrophy of woody and non-woody roots, stems and foliage occurs across the clades. Phylogenetically less related clades often show strong phenotypic and behavioural similarities and no one clade or group of clades shows the synapomorphies that might justify a unique generic status. We propose the clades arose from the migration and worldwide radiation ~ 140 Mya (million years ago) of an ancestral Gondwanan Phytophthora population, resulting in geographic isolation and clade divergence through drift on the diverging continents combined with adaptation to local hosts, climatic zones and habitats. The extraordinary flexibility of the genus may account for its global 'success'. The 20 genera of the obligately biotrophic, angiosperm-foliage specialised DMs evolved from Phytophthora at least twice via convergent evolution, making the DMs as a group polyphyletic and Phytophthora paraphyletic in cladistic terms. The long phylogenetic branches of the DMs indicate this occurred rather rapidly, via paraphyletic evolutionary 'jumps'. Such paraphyly is common in successful organisms. The proposal to divide Phytophthora appears more a device to address the issue of the convergent evolution of the DMs than the structure of Phytophthora per se. We consider it non-Darwinian, putting the emphasis on the emergent groups (the DMs) rather than the progenitor (Phytophthora) and ignoring the evolutionary processes that gave rise to the divergence. Further, the generic concept currently applied to the DMs is narrower than that between some closely related Phytophthora species. Considering the biological and structural cohesion of Phytophthora, its historic and social impacts and its importance in scientific communication and biosecurity protocol, we recommend that the current broad generic concept is retained by the scientific community.

A snapshot of progenitor-derivative speciation in Iberodes (Boraginaceae).

Traditional classification of speciation modes has focused on physical barriers to gene flow. Allopatric speciation with complete reproductive isolation is viewed as the most common mechanism of speciation. Parapatry and sympatry, by contrast, entail speciation in the face of ongoing gene flow, making them more difficult to detect. The genus Iberodes (Boraginaceae, NW Europe) comprises five species with contrasting morphological traits, habitats and species distributions. Based on the predominance of narrow and geographically distant endemic species, we hypothesized that geographical barriers were responsible for most speciation events in Iberodes. We undertook an integrative study including: (i) phylogenomics through restriction-site-associated DNA sequencing (RAD-seq), (ii) genetic structure analyses, (iii) demographic modelling, (iv) morphometrics, and (v) climatic niche modelling and niche overlap analysis. The results revealed a history of recurrent progenitor-derivative speciation manifested by a paraphyletic pattern of nested species differentiation. Budding speciation mediated by ecological differentiation is suggested for the coastal lineage, deriving from the inland widespread Iberodes linifolia during the Late Pliocene. Meanwhile, geographical isolation followed by niche shifts are suggested for the more recent differentiation of the coastland taxa. Our work provides a model for distinguishing speciation via ecological differentiation of peripheral, narrowly endemic I. kuzinskyanae and I. littoralis from a widespread extant ancestor, I. linifolia. Ultimately, our results illustrate a case of Pliocene speciation in the probable absence of geographical barriers and get away from the traditional cladistic perspective of speciation as producing two species from an extinct ancestor, thus reminding us that phylogenetic trees tell only part of the story.

The complete mitochondrial genome of Microphysogobioelongatus (Teleostei, Cyprinidae) and its phylogenetic implications.

Mitochondria are important organelles with independent genetic material of eukaryotic organisms. In this study, we sequenced and analyzed the complete mitogenome of a small cyprinid fish, Microphysogobioelongatus (Yao & Yang, 1977). The mitogenome of M.elongatus is a typical circular molecule of 16,612 bp in length containing 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a 930 bp control region. The base composition of the M.elongatus mitogenome is 30.8% A, 26.1% T, 16.7% G, and 26.4% C. All PCGs used the standard ATG start codon with the exception of COI. Six PCGs terminate with complete stop codons, whereas seven PCGs (ND2, COII, ATPase 6, COIII, ND3, ND4, and Cyt b) terminate with incomplete (T or TA) stop codons. All tRNA genes exhibited typical cloverleaf secondary structures with the exception of tRNASer(AGY), for which the dihydrouridine arm forms a simple loop. The phylogenetic analysis divided the subfamily Gobioninae in three clades with relatively robust support, and that Microphysogobio is not a monophyletic group. The complete mitogenome of M.elongatus provides a valuable resource for future studies about molecular phylogeny and/or population genetics of Microphysogobio.

Nomenclatural revision of Delphiniumsubg.Consolida (DC.) Huth (Ranunculaceae).

Recent molecular phylogenetic studies have indicated that Aconitella is embedded in Consolida, which in turn is embedded in Delphinium. We choose not to split the genus Delphinium (c. 300 species), as it is horticulturally and pharmaceutically important, by conserving a broad Delphinium by transferring the names from Consolida and Aconitella to Delphinium s.lat., and more precisely in the resurrected D.subg.Consolida. Including 58 species of Aconitella and Consolida within Delphinium causes fewer nomenclatural overall changes than do alternative schemes because most of the species of Aconitella and Consolida were once named under the name Delphinium. We present here the list of synonyms for the species once named under Consolida or Aconitella and gather the information relative to the types of these names. Two new combinations are provided, and 21 lectotypes are designated here.

UCE Phylogenomics, detection of a putative hybrid population, and one older mitogenomic node age of Batrachuperus salamanders.

The prevalence of incomplete lineage sorting complicates the examination of hybridization and species-level paraphyly with gene trees of a small number of loci. In Asian mountain salamanders of the genus Batrachuperus, possible hybridization and species paraphyly had been identified by utilizing mitochondrial genealogy and fixed allozyme differences. Here we sampled 2909 UCEs in 44 local populations from all six Batrachuperus species, inferred gene and species trees, compared them with mitochondrial and allozyme results, and examined the potential hybridization and species paraphyly. The clustering pattern of single-locus trees, increased proportion of heterozygous SNPs, allele frequency-based migration edge estimation, and intrapopulation long branches (as expected from an increase of genetic lineage and nucleotide diversity) support that an eastern B. karlschmidti population has experienced admixture with B. tibetanus. On the 2909-UCE concatenated and species trees, lower nodal supports were observed when similar proportions of loci agreed with alternative topologies, i.e., a reciprocal monophyly between a Pengxian lineage and the remainder of B. pinchonii (0.379) or a paraphyly of the latter with respect to Pengxian (0.362). The UCE phylogenomics agreed with the relatively recent groupings in the allozyme dendrogram. Despite incomplete lineage sorting, the mitochondrial trees were similar to the UCE trees for deeper relationships of the genus. However, one significant branch-length level discordance was identified. The branch between the common ancestor of B. daochengensis and B. yenyuanensis and common ancestor of the genus was approximately three times shorter on the mitochondrial tree than on the UCE tree, suggesting that the split of the mitochondrial lineages was likely a few million years earlier than the split of species. This finding supports considering possible ancestral polymorphism when interpreting different divergence dates estimated from mitochondrial and genome-wide data.

On nanoparticles, paraphyly, inventions, yeasts and diarrhea.

Citations do not always guarantee that a paper aroused interest in the citing author(s).

The published complete mitochondrial genome of the milk shark (Rhizoprionodon acutus) is a misidentified Pacific spadenose shark (Scoliodon macrorhynchos) (Chondrichthyes: Carcharhiniformes).

The recently published mitogenome of milk shark Rhizoprionodon acutus (MN602076/NC_046016) was fully resolved in an unexpected phylogenetic position in the original mitogenome announcement, which rendered the genus Scoliodon paraphyletic. Here, we show that this mitogenome is actually that of a misidentified Pacific spadenose shark (Scoliodon macrorhynchos). The error is documented to avoid the perpetuation of erroneous sequence information in the literature.

Catching speciation in the act-act 2: Metschnikowia lacustris sp. nov., a sister species to Metschnikowia dekortorum.

The isolation of a single yeast strain in the clade containing Metschnikowia dekortorum, in the Amazon biome of Brazil, incited us to re-examine the species boundaries within the clade. The strain (UFMG-CM-Y6306) was difficult to position relative to neighbouring species using standard barcode sequences (ITS-D1/D2 rRNA gene region). Mating took place freely with α strains of M. bowlesiae, M. dekortorum, and M. similis, but two-spored asci, indicative of a fertile meiotic progeny, were formed abundantly only with certain strains of M. dekortorum. Accordingly, we examined mating success among every phylotype in the clade and constructed a phylogeny based on a concatenation of 100 of the largest orthologous genes annotated in draft genomes. The analyses confirmed membership of the Amazonian isolate in M. dekortorum, but also indicated that the species should be subdivided into two. As a result, we retain three original members of M. dekortorum in the species, together with the new isolate, and reassign six isolates recovered from Mesoamerican lacustrine habitats to Metschnikowia lacustris sp. nov. The type is UWOPS 12-619.2T (isotype CBS 16250T). MycoBank: MB 833751.

The Complete Mitochondrial Genome of the Caecal Fluke of Poultry, Postharmostomum commutatum, as the First Representative from the Superfamily Brachylaimoidea.

Postharmostomum commutatum (Platyhelminthes: Brachylaimoidea), a parasite of the caeca of poultry, has been frequently reported from many countries and regions, including China. However, the molecular epidemiology, population genetics and phylogenetics of this parasite are poorly understood. In the present study, we determined and characterized the complete mitochondrial (mt) genome of P. commutatum, as the first representative from the superfamily Brachylaimoidea. The mt genome of P. commutatum is a circular DNA molecule of 13,799 bp in size and encodes the complete set of 36 genes (12 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes) as well as a typical control region. The mt genome of P. commutatum presents a clear bias in nucleotide composition with a negative AT-skew on average (-0.306) and a positive GC-skew on average (0.466). Phylogenetic analyses showed that P. commutatum (superfamily Brachylaimoidea) and other ten members of the order Diplostomida were recovered as sister groups of the order Plagiorchiida, indicating that the order Diplostomida is paraphyletic. This is the first mt genome of any member of the superfamily Brachylaimoidea and should represent a rich source of genetic markers for molecular epidemiological, population genetic and phylogenetic studies of parasitic flukes of socio-economic importance in poultry.

A new species of Caecilia (Gymnophiona, Caeciliidae) from the Magdalena valley region of Colombia.

A new species of the genus Caecilia (Caeciliidae) from the western foothills of the Serranía de los Yariguíes in Colombia is described. Caecilia pulchraserrana sp. nov. is similar to C. degenerata and C. corpulenta but differs from these species in having fewer primary annular grooves and a shorter body length. With this new species, the currently recognized species in the genus are increased to 35. Mitochondrial DNA sequences, including newly sequenced terminals representing two additional, previously unanalyzed species, corroborate the phylogenetic position of the new species within Caecilia and the monophyly of the genus. This analysis also included newly sequenced terminals of Epicrionops aff. parkeri (Rhinatrematidae) and trans-Andean Microcaecilia nicefori (Siphonopidae). Evidence was found for the non-monophyly of the family Siphonopidae and the siphonopid genera Microcaecilia and Siphonops. The implications of these results for caecilian systematics are discussed and the status of the trans-Andean populations of Caecilia degenerata is commented upon.

Re-evaluation of the Wehrle's salamander (Plethodon wehrlei Fowler and Dunn) species group (Caudata: Plethodontidae) using genomic data, with the description of a new species.

Woodland salamanders of the genus Plethodon are characterized by strong ecological and morphological conservatism. One assemblage, the Wehrle's salamander (Plethodon wehrlei Fowler Dunn) species group, is distributed from New York to Tennessee, USA, and includes several morphological variants, four of which are sufficiently distinct to have been recognized as species in the past. For many years after two of these species were placed in synonymy, only P. wehrlei and P. punctatus Highton were recognized. A recent phylogeographic study using mitochondrial DNA and nuclear DNA uncovered considerable genetic diversity within the group and conservatively resurrected one of the previously synonymized forms (P. dixi Pope Fowler). However, their analysis could not resolve all relationships among remaining populations of P. wehrlei, leaving the taxon paraphyletic. We re-evaluated the evolutionary history of this group using genomic data, recovered strong support for at least five distinct clades, and corroborated previously reported relationships. We also collected morphological data and demonstrated morphological distinctiveness for four of the five clades that we herein recognize as species. We resurrect the synonymized name P. jacksoni Newman to represent the southern clades of P. wehrlei in southwestern Virginia and North Carolina exclusive of P. dixi. In addition, we describe a yellow-spotted form of P. wehrlei endemic to the Cumberland Plateau as a new species. Although our proposed changes rectify the paraphyly of P. wehrlei, our sampling was not sufficient to resolve potential taxonomic issues remaining within the species herein recognized as P. jacksoni.

Mitochondrial Genomes of Two Thaparocleidus Species (Platyhelminthes: Monogenea) Reveal the First rRNA Gene Rearrangement among the Neodermata.

Phylogenetic framework for the closely related Ancylodiscoidinae and Ancyrocephalinae subfamilies remains contentious. As this issue was never studied using a large molecular marker, we sequenced the first two Ancylodiscoidinae mitogenomes: Thaparocleidus asoti and Thaparocleidus varicus. Both mitogenomes had two non-coding regions (NCRs) that contained a number of repetitive hairpin-forming elements (RHE). Due to these, the mitogenome of T. asoti (16,074 bp) is the longest among the Monogenea; especially large is its major NCR, with 3500 bp, approximately 1500 bp of which could not be sequenced (thus, the total mitogenome size is ≈ 17,600 bp). Although RHEs have been identified in other monopisthocotyleans, they appear to be independently derived in different taxa. The presence of RHEs may have contributed to the high gene order rearrangement rate observed in the two mitogenomes, including the first report of a transposition of rRNA genes within the Neodermata. Phylogenetic analyses using mitogenomic dataset produced Dactylogyrinae embedded within the Ancyrocephalinae (paraphyly), whereas Ancylodiscoidinae formed a sister-group with them. This was also supported by the gene order analysis. 28S rDNA dataset produced polyphyletic Dactylogyridae and Ancyrocephalinae. The phylogeny of the two subfamilies shall have to be further evaluated with more data.

Diagnosis of mitogenome for robust phylogeny: A case of Cypriniformes fish group.

Phylogenetic tree using mitochondrial genes and nuclear genes have long been used for augmenting biological classification and understanding evolutionary processes in different lineage of life. But a basic question still exists for finding the most suitable gene for constructing robust phylogenetic tree. Much of the controversy appears due to monophyletic, paraphyletic and polyphyletic clade making deviations from original taxonomy. In the present study we report the first complete mitochondrial genome (mitogenome) of queen loach, generated through next-generation sequencing methods. The assembled mitogenome is a 16,492 bp circular DNA, comprising of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. Further in this study we also investigated the suitability of different mitochondrial region for phylogenetic analysis in Cyprinidae and loach group. For this genetic tree were constructed on COI, COII, COIII, 16S rRNA, 12S rRNA, Cyt b, ATPase 6, D-loop, ND1, ND2, ND3, ND4, ND5, and ND6 along with complete mitogenome. The complete mitogenome based phylogenetic tree got inclusive support from available classical taxonomy for these groups. On individual gene basis Cyt b, 12S rRNA, ND2 and ND3 also produced perfect clade at family and subfamily level. For rest of the genes polyphyly were observed for the fishes belonging to same family or subfamily which makes their use questionable for phylogenetic tree construction.