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Aim: Whether widespread gene flow among primates is emblematic of their initial radiation or resulted from secondary contactremains a long‐standing question. We address this question on 'sinica' group macaques, highlighting the origin of the white‐cheeked macaque (Macaca leucogenys). Location: Eastern Himalayan highlands of Arunachal Pradesh, India. Taxon: Macaca leucogenys Li, Zhao, Fan, 2015b (Cercopithecidae). Methods: Mitochondrial genomes and Y‐chromosomal TSPY gene sequences of WCM were obtained from two distant populations through low‐depth genome sequencing. Phylogenetic analyses were conducted along with sequences of other available species within the genus Macaca. Results: We observed the presence of a single maternal lineage but two parental lineages. Interestingly, one paternal lineage of the white‐cheeked macaque clustered with a common lineage of M. assamensis and M. munzala. The other paternal lineage clustered with the sequences of the white‐cheeked macaque from the type locality in Southeastern Tibet. Main Conclusions: The result indicates a possible historic male‐mediated introgression in the white‐cheeked macaque, which is also present in the two other species belonging to the 'sinica' group. Therefore, extensive gene flow in 'sinica' group macaques possibly came from one or more introgression events in the past that also played a role in the origin and evolution of these macaque species. [ABSTRACT FROM AUTHOR]

A new genus and species, Castrila latens, native to the south‐eastern Iberian Peninsula, is described here for the first time and compared with its closest relatives. The plant is characterized by being annual, glabrous, having reduplicate leaves in whorls of (5)6–7, inflorescences capitate and involucrate, corolla shortly hypocrateriform and white, with yellowish doliiform tube, stamens included, and ovary and mericarps densely papillose. An endemic plant, it grows on the calcareous mountains of the Sierra Seca, Sierra de Castril, and Sierra de la Cabrilla, between 1800 and 2100 m of elevation, in the Granada and Jaén provinces (eastern Andalusia, Spain). For this genus and species, a description, an illustration, a distribution map, the chromosome number, the assessment of the conservation status, an estimate of the breeding system, and the situation in the Rubieae phylogenetic tree are provided. [ABSTRACT FROM AUTHOR]

AbstractThe 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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The willistoni group of Drosophila is subdivided into the alagitans, bocainensis, and willistoni subgroups, and has been an important model for studying evolutionary processes in the Neotropics for decades. Phylogenetic studies place the bocainensis subgroup as a grade in relation to the monophyletic willistoni subgroup, although these included molecular or morphological data for up to 4 species of the 12 species included in the first subgroup. Here, we characterized the first nucleotide sequences for three mitochondrial and five nuclear genes of Drosophila bocainensis Pavan & da Cunha, 1947 and employed these for addressing the paraphyly of this subgroup under a coalescent approach. Our results still recovered this paraphyletic relationship, placing D. bocainensis, Drosophila capricorni Dobzhansky & Pavan, 1943 and Drosophila sucinea Patterson & Mainland, 1944 in a basal clade, which diverged around 6.81 million years ago. The relationship of Drosophila nebulosa Sturtevant, 1916 and Drosophila fumipennis Duda, 1925 as a sister clade to the willistoni subgroup was recovered. The possible causes of such paraphyly are discussed. [ABSTRACT FROM AUTHOR]

Understanding of the evolutionary history of two closely related canid sister taxa, the geographically restricted, arid-adapted Rüppell's fox (Vulpes rueppellii) and the widespread generalist red fox (Vulpes vulpes), has been hampered by limited sampling in the biogeographically complex region of North Africa and the Middle East. We sequenced mitochondrial DNA (mtDNA) cytochrome b and D-loop fragments from 116 samples for both species and combined these data with previously published sequences, resulting in 459 haplotypes. Obtained phylogenies showed high support for most branches, including for a newly described 'Palearctic clade' that includes North African and Asian individuals from both species. All V. rueppellii individuals fell within the Palearctic clade, forming two previously undescribed subclades that were intermingled with, but not shared with V. vulpes. Our robust placement of V. rueppellii within V. vulpes renders the latter paraphyletic. We propose three scenarios that could explain these observations: (1) rapid, recent speciation of V. rueppellii from V. vulpes , (2) incomplete lineage sorting, or (3) ancient divergence followed by introgression and secondary mtDNA similarity. The third scenario is in best agreement with evidence from the fossil record, and morphometric and ecological distinctiveness between the two taxa, and therefore seems most likely. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Abstract 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.

The family Alaudidae, larks, comprises 93–100 species (depending on taxonomy) that are widely distributed across Africa and Eurasia, with single species extending their ranges to North and northernmost South America and Australia. A decade-old molecular phylogeny, comprising ∼80% of the species, revealed multiple cases of parallel evolution and large variation in rates of morphological evolution, which had misled taxonomists into creating many non-monophyletic genera. Here, we reconstruct the phylogeny of the larks, using a dataset covering one mitochondrial and 16 nuclear loci and comprising all except one of the currently recognised species as well as several recently proposed new species (in total 133 taxa; not all loci available for all species). We provide additional support using genome-wide markers to infer a genus-level phylogeny based on near-complete generic sampling (in total 51 samples of 44 taxa across 40 species). Our results confirm the previous findings of rampant morphological convergence and divergence, and reveal new cases of paraphyletic genera. We propose a new subfamily classification, and also that the genus Mirafra is divided into four genera to produce a more balanced generic classification of the Alaudidae. Our study supports recently proposed species splits as well as some recent lumps, while also questioning some of the latter. This comprehensive phylogeny will form an important basis for future studies, such as comparative studies of lark natural history, ecology, evolution and conservation.

The results of studying the variability of sequences of the ITS rDNA region for 17 species of the genus Spiraea (Magnoliópsida: Rosaceae) occurring within the Russian part of the ranges and in adjacent territories are presented. The results demonstrate the presence of single-nucleotide substitutions (transitions and transversions) and deletions/insertions, including those specific at the level of subgenera, sections, cycles, and series. The variability in the ITS1 intergenic spacer is higher than in ITS2. The high importance of ITS as a molecular marker in the resolution of phylogenetic relationships in the genus Spiraea is emphasized. Closely related Spiraea species usually differ in ITS sequences, but the polymorphic section Chamaedryon has the greatest difficulties in identifying taxa. Phylogenetic analysis carried out in various ways (ML, MP, and BI) confirms the monophyletic origin of the genus Spiraea and the ancient sections Spiraea and Calospira. A hypothesis is formulated about the paraphyletic nature of the section Chamaedryon, which more evolutionarily young, diverse, and richest in the number of species. It is assumed that the paraphyly of the Chamaedryon section is associated with divergence of traits and subsequent isolation of species along with multiple migrations under the influence of contrasting environmental conditions. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Past studies of Sophora sect. Edwardsia using traditional phylogenetic and population genetic markers have been unable to produce a resolved species phylogeny of this recent radiation of shrubs and trees. Here we examined the relationships within and between the New Zealand species of Sophora sect. Edwardsia using next-generation sequencing. We generated genome-wide SNP data with double-digest restriction site-associated DNA sequencing (ddRADseq). Sophora prostrata was resolved as sister to the remaining species in all analyses. Relationships between the remaining taxa exhibited a high level of conflict with many of the genetic clusters reflecting geography rather than species boundaries. This result contrasts with a previous study, which was able to differentiate most species using genotype data from nine microsatellite loci. Overall our ddRADseq results indicate a high level of interspecific hybridisation and introgression within the group, which blurs the taxonomic boundaries throughout the distributional ranges of most species. Hybridisation and introgression among regional metapopulations comprising closely related species may increase the adaptive potential to respond to changing local conditions, and at the same time selection acts to maintain their genetic identity in the face of ongoing gene flow. [ABSTRACT FROM AUTHOR]

Stenochiinae is a subfamily of Tenebrionidae with a mainly pantropical distribution, but with a few species distributed at higher latitudes. In general, Stenochiinae has been little studied, and the taxonomic effort been insufficient to understand all its diversity. Recently, a new taxon of Stenochiinae from Central Chile with remarkable morphological characters was collected. Based on phylogenetic analyses of concatenated 28S, 18S, 16S and COI genes and on morphological analyses, a new genus and two species of Stenochiinae are described from Central Chile. Our results suggest that Nestorinus gen. nov. (with the species Nestorinus roitmani sp. nov. and Nestorinus yanettae sp. nov.) has a basal position in Stenochiinae, related to Homocyrtus. The set of morphological characters shared between Stenochiini and Cnodalonini plus their phylogenetic position make it difficult to classify them at tribal level. [ABSTRACT FROM AUTHOR]

Zygomycete fungi were classified as a single phylum, Zygomycota, based on sexual reproduction by zygospores, frequent asexual reproduction by sporangia, absence of multicellular sporocarps, and production of coenocytic hyphae, all with some exceptions. Molecular phylogenies based on one or a few genes did not support the monophyly of the phylum, however, and the phylum was subsequently abandoned. Here we present phylogenetic analyses of a genome-scale data set for 46 taxa, including 25 zygomycetes and 192 proteins, and we demonstrate that zygomycetes comprise two major clades that form a paraphyletic grade. A formal phylogenetic classification is proposed herein and includes two phyla, six subphyla, four classes and 16 orders. On the basis of these results, the phyla Mucoromycota and Zoopagomycota are circumscribed. Zoopagomycota comprises Entomophtoromycotina, Kickxellomycotina and Zoopagomycotina; it constitutes the earliest diverging lineage of zygomycetes and contains species that are primarily parasites and pathogens of small animals (e.g. amoeba, insects, etc.) and other fungi, i.e. mycoparasites. Mucoromycota comprises Glomeromycotina, Mortierellomycotina, and Mucoromycotina and is sister to Dikarya. It is the more derived clade of zygomycetes and mainly consists of mycorrhizal fungi, root endophytes, and decomposers of plant material. Evolution of trophic modes, morphology, and analysis of genome-scale data are discussed.

The study considers the phylogenetic affinities and taxonomical placement of the previously unknown hepatic from Hengduan Mts. in Yunnan Province of China. This area is known to house a vast assemblage of peculiar and taxonomically secluded taxa of hepatics, serving as kind of storehouse of missing links in the evolution. The newly recorded taxon combines lophozioid appearance with prominent tooth in the antical side of the leaf—the feature previously observed in Cephaloziineae very rarely and in bracts only. Molecular phylogenetic reconstruction, inferred from the nuclear ITS region and the chloroplast rps4 gene, trnL-F region and trnG-intron resolved Konstantinovia gen. nov. as the closest relative of highly phylogenetically isolated monospecific genus Obtusifolium. Their joint clade is sister to the Anastrophyllaceae clade in the tree inferred from combined ITS and trnL sequences, while topology inferred from combined trnG and rps4 sequences fails to resolve its affinity within the Scapaniaceae s.l. clade. Therefore, the new family Obtusifoliaceae is introduced to accommodate these genera, and the familial classification of Cephaloziineae is discussed. [ABSTRACT FROM AUTHOR]

The plastid and mitochondrial genomes of Vavilovia formosa (Stev.) Fed. were assembled on the base of the data of high-throughput sequencing of DNA isolated from a sample from North Osetia, Russia, using Illumina and PacBio platforms. The long PacBio reads were sufficient for reliable assembling organellar genomes while the short Illumina reads obtained from total DNA were unacceptable for this purpose because of substantial contamination by nuclear sequences. The organellar genomes were circular DNA molecules; the genome of mitochondria was represented by two circular chromosomes. A phylogenetic analysis on the basis of plastid genomes available in public databases was performed for some representatives of the tribes Fabeae, Trifolieae and Cicereae. As was expected, the V. formosa branch proved to be sister to the Pisum branch, and the tribe Fabeae was monophyletic. The position of Trifolium L. appeared sensitive to the phylogeny reconstruction method, either clustering with Fabeae or with the genera Medicago L., Trigonella L. and Melilotus Mill., but the internodes between successive divergences were short in all cases, suggesting that the radiation of Trifolium, other Trifolieae and Fabeae was fast, occurring within a small time interval as compared to further evolution of these lineages. The data on the relatedness of the plastid genomes of Trifolium and Fabeae correlate with the similarity of N2-fixing symbionts in these legumes represented by Rhizobium leguminosarum biovars trifolii and viciae, while the symbionts of Medicago, Melilotus and Trigonella belong to the Sinorhizobium meliloti and S. medicae species, which are distant from Rhizobium.

Despite a considerable amount of research, the systematics of the ranid genus Huia have remained unresolved, mostly owing to insufficient sampling and morphological similarities. As currently circumscribed, Huia consists of five species, but multiple studies have consistently demonstrated that it is not a monophyletic genus. However, no study has approached the problem with adequate data and provided a systematically sound solution, leaving the genus to languish in a classification that is phylogenetically incoherent. We generated the most comprehensive sampling of Huia to date, based on extensive fieldwork in Java and Sumatra. Using an integrative taxonomy framework, we analysed four mitochondrial and two nuclear markers and, in conjunction with tadpole morphology, investigated the phylogenetics of Huia and its congeners. Corroborating previous studies, Huia is recovered as a paraphyletic group. Huia cavitympanum emerges as the sister taxon to Meristogenys. The remaining members of Huia form a monophyletic group, sister to the H. cavitympanum + Meristogenys clade. Our extensive geographical sampling in Sumatra and Java reveals multiple highly divergent lineages that potentially represent undescribed species. Using our expanded molecular and morphological dataset, we resolve the paraphyly of Huia by restricting the genus to its type species and propose a new genus to accommodate the strongly supported clade of Sumatran and Javan populations previously belonging to Huia. [ABSTRACT FROM AUTHOR]

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, Microphysogobio elongatus (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. [ABSTRACT FROM AUTHOR]

A spreadsheet dealing with standard deviations allows statistical examination of continuous variables associated with paraphyly in systematics, with examples in the Pottiaceae (Bryophyta). Outlier values in taxonomic representation of distribution with the structure of (w-)x-y(-z) of continuous variables can be empirically supported. The use of the geometric mean and intuitional estimation is reexamined. Published reports of the distance between maximally distant exemplars of individual paraphyletic species in molecular cladograms in several studies were reevaluated as metadata. Levels of standard deviations were assigned with the Running Sigmas spreadsheet. A spike in width of exemplars of a paraphyletic species of a moss in the family Pottiaceae, Exobryum asperifolium, was identified as an outlier. Techniques of macroevolutionary systematics, however, assured that no different evolutionary processes were involved that may have supported an explanation of taxonomic crypsis. Instead it was found that metadata heterogeneity was the problem in that the paraphyly width of 14 molecular cladogram nodes which is evolutionarily acceptable as a clear-cut progenitordescendant lineage with no reversals. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The analytic orientation of this paper is intended as a replacement for the antiquated but still prevalent phylogenetic inferential models and techniques of the late 20th century that are focused entirely on shared descent. Serial descent, that is, progenitor to descendant, may occur at the species or infraspecies level. In molecular systematics, species level paraphyly occurs when two examples of the same species are separated on a cladogram by a second species. This implies linear macroevolution of the second species from the first. Molecular cladograms often show cladistic structure (branching) among examples of the same species. If well-supported, such indicates a potential for evolution. A range of infraspecific and intraspecific cladistic structure in species of Pottiaceae (Bryophyta) was demonstrated in previously published molecular cladograms and data sets of other authors. This includes well-supported cladistic structure of molecular strains, and well-supported paraphyly involving other species. Large numbers of base pair changes among strains are considered here evidence of evolvability and increasing age of a species. Infraspecific strains are apparently lost in older species through speciation and extinction. Cluster analysis using DNA metadata of Oxystegus species matched published molecular cladograms to a large extent. The fact that apparent molecular strains are present in both nonparaphyletic and paraphyletic species, about half the species studied, shore up the theory that internal racial differentiation at the molecular level leads to or signals serial descent of multiple extant morphotaxa. It is because much infraspecific molecular cladistic structure exists that newly speciated taxa are already strongly cladistically dichotomized. Thus, the ultimate source of molecular paraphyly is internal to each species, and does not imply polyphyly by convergent species or cryptic taxa. Molecular systematics cannot effectively model progenitor-descendant radiation. Species with many strains are potential sources of future biological diversity. Recognition of differential evolvability may allow facilitation of complex, interactive, diverse ecosystems successfully tracking climate change.

Sulawesi is the largest, most topographically complex island in the Wallacean biogeographic zone, and it has a rich fauna of endemic small mammals, dominated by rodents of the family Muridae. Among murids, the Bunomys division is the most species‐rich radiation on Sulawesi. In total, the division contains 11 genera and 32 species, five and 20 of which are endemic to Sulawesi. We combined a five‐locus phylogeny and linear cranial morphology to better understand the taxonomy and local scales of endemism within the Bunomys division on Sulawesi. Phylogenetic analyses of mitochondrial and nuclear DNA placed B. fratrorum among other genera and inferred Paruromys as sister to the type species of Taeromys (T. celebensis). We resolve these issues by resurrecting Frateromys, a genus under which B. fratrorum was once placed, and returning Paruromys dominator to Taeromys. Within three species, F. fratrorum, T. callitrichus, and T. taerae, we recovered Pleistocene age divergences between populations sampled across the northern peninsula of Sulawesi; divergence between western and eastern populations of F. fratrorum may reflect the existence of two species. [ABSTRACT FROM AUTHOR]

Zethus is the largest genus in Vespidae with over 270 species. It is currently divided into four subgenera: Z. (Zethus), Z. (Zethoides), Z. (Zethusculus) and Z. (Madecazethus). While the last three are restricted to certain biogeographic areas, the first is spread through western and eastern hemispheres. Studies have shown possible phylogenetic incongruence regarding this current division and even raised the possibility of paraphyly in the genus. To evaluate this classification, morphological pasimony analyses under implied weights was carried out, examining external morphology and male genitalia. Analyses showed paraphyly of the genus under various "k" values and paraphyly of two subgenera. Ischnocoelia and Ctenochilus are lowered to subgenera of Zethus. Zethus (Madecazethus) is no longer restricted to Malagasy species and now includes those of the African continent as well. Zethus (Zethastrum) subg. nov. is defined for Oriental representatives. Z. (Zethus) is subdivided into three subgenera: Z. (Zethus), Z. (Didymogastra) and Z. (Wettsteinia). Zethus (Zethusculus) and Z. (Zethoides) are monophyletic and hold their status as subgenera. Three species-groups are Incertae sedis: Z. albopictus, Z. pallidus and Z. spinosus. [ABSTRACT FROM AUTHOR]

The genus Phyllanthus is paraphyletic as currently circumscribed, with the genera Breynia, Glochidion and Synostemon nested within it. A phylogeny based on nuclear (ITS, PHYC) and chloroplast (matK, accD‐psaI, trnS‐trnG) markers is presented, including 18/18 subgenera and 53/70 sections. Differences in habit, branching type, floral and fruit characters are discussed, and we find indications for shifts in pollination and dispersal strategies possibly underlying the convergent evolution of these characters in multiple clades. Several taxonomic issues were found in the subgeneric classification of Phyllanthus that will require new transfers and rank changes. Phyllanthus subg. Anesonemoides, subg. Conami, subg. Emblica, subg. Gomphidium, subg. Kirganelia and subg. Phyllanthus are polyphyletic, and several sections appear to be paraphyletic (e.g., P. sect. Anisonema, sect. Emblicastrum, sect. Pseudoactephila, sect. Swartziani, and sect. Xylophylla); P. subg. Phyllanthodendron is furthermore paraphyletic with the genus Glochidion nested within. To create a classification of tribe Phyllantheae that comprises exclusively monophyletic taxa, it is necessary to treat several clades at the same taxonomic rank as the genera Breynia, Glochidion and Synostemon. Since combining all genera would lead to one giant heterogeneous genus that is difficult to define, we recommend dividing Phyllanthus into several monophyletic genera, which have previously been recognized and often possess diagnostic (combinations of) morphological characters. This new classification is forthcoming. [ABSTRACT FROM AUTHOR]

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.

Gilliesieae are a South American tribe of Amaryllidaceae characterized by high floral diversity. Given different taxonomic interpretations and proposals for generic and specific relationships, a representative phylogenetic analysis is required to clarify the systematics of this group. The present study provides a framework for understanding phylogenetic relationships and contributing to the development of an appropriate taxonomic treatment of Gilliesieae. Molecular analyses, based on nuclear (ITS) and plastid DNA sequences (trnL-F and rbcL), resolve with strong support the monophyly of the tribe and the differentiation of two major clades. Clade I comprises the genera Gilliesia, Gethyum and Solaria and Clade II includes Miersia and Speea. These well-supported clades are mostly congruent with vegetative and karyotype characters rather than, e.g. floral symmetry. At the generic level, all molecular analyses reveal the paraphyly of Gilliesia and Miersia. Gethyum was found to be paraphyletic, resulting in the confirmation of Ancrumia as a distinct genus. Several instances of incongruent phylogenetic signals were found among data sets. The calibrated tree suggests a recent diversification of the tribe (Pliocene–Pleistocene), a contemporary process of speciation in which instances of hybridization and incomplete lineage sorting could explain patterns of paraphyly and incongruence of floral morphology. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The tyrant‐flycatchers (Tyrannidae) are the largest family of birds in the New World. Although their phylogenetic relationships have been deeply studied based on phenotypic and genetic characters, several systematic uncertainties still exist. In particular, the affinities within the South American genus Ramphotrigon and its close relationship with the Mexican‐endemic Deltarhynchus flammulatus remain unresolved. Here we performed a taxonomic assessment of this intriguing relationship including, for the first time, representatives of all three Ramphotrigon species and the monotypic Deltarhynchus. We carried out phylogenetic analyses based on three mitochondrial markers and one autosomal nuclear intron, and complemented the genetic evidence with the study of morphological and plumage coloration differentiation, in order to provide a more in‐depth reassessment of the Ramphotrigon–Deltarhynchus relationship in general and the genus Ramphotrigon in particular. Genetic data showed that Ramphotrigon is paraphyletic as currently defined, with R. fuscicauda and R. ruficauda being more closely related to D. flammulatus than to R. megacephalum. This paraphyletic relationship was recovered with maximum support based on mitochondrial and nuclear markers. Ramphotrigon megacephalum evidenced a deep genetic divergence from its two congeners and D. flammulatus, comparable to that between the first one and other tyrannids. Ramphotrigon megacephalum was also significantly different from D. flammulatus, R. fuscicauda and R. ruficauda in external morphology and plumage coloration. On the other hand, D. flammulatus, R. fuscicauda and R. ruficauda showed almost no differences in the morphological variables analyzed. In this context, we believe that a taxonomic reorganization of this group is necessary. One possibility would be to transfer D. flammulatus to the genus Ramphotrigon and to assign R. megacephalum to a new genus with at least two species. Lastly, we propose a biogeographic model for the evolutionary history of Ramphotrigon and Deltarhynchus in South and Middle America over the past 12 million years. [ABSTRACT FROM AUTHOR]

An analysis of public DNA barcoding data confirms that the extraction of Arboricaria Bosmans, 2000 from the genus Micaria Westring, 1851 would require the division of Micaria into at least five (and probably more) individual genera, to restore the monophyly of Micaria sensu stricto. Such an excessive splitting of a homogenous and well-defined genus would be neither desirable nor practical, and consequently Arboricaria should be considered a subjective junior synonym of Micaria, as suggested earlier (syn. conf.).

Abstract Background Mitochondrial markers are widely used as a first approach in determining evolutionary relationships among vertebrate taxa at different hierarchical scales. Cytochrome b and cytochrome oxidase I are among the most common markers; they are particularly useful in phylogeography and species delineation studies. Simulation and empirical studies show that increasing the taxon sampling has a clear and strong effect on the accuracy of the inferred trees and therefore on hypothesized phylogenetic relationships (and eventually in new taxonomic rearrangements); this should be considered in the design of studies. The lizard genus Liolaemus is widely distributed in southern South America and includes more than 250 described species. The number of taxa and the distribution of Liolaemus species/populations makes them a good model for testing different hypotheses in systematics. Methods We studied two Liolaemus species, Liolaemus nigroviridis and L. monticola as focal species to evaluate their monophyly and the influence of adding new samples from related taxa in the resulting phylogenies. We performed phylogenetic analyses (maximum likelihood and Bayesian inference) using 141 sequences of the mitochondrial DNA Cytochrome b (cyt-b) of 11 Liolaemus species. Results Our study show that using intensive taxon sampling for phylogenetic reconstructions, two species (L. uniformis and L. nitidus) are placed within the clades of the two focal species (L. nigroviridis and L. monticola, respectively). Conclusions Our study confirms the importance of taxon sampling to infer more accurate phylogenetic relationships, particularly to reveal hidden polyphyly or paraphyly, which may have a strong impact on taxonomic proposals and/or inferring cryptic diversity.

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.

The complete mitochondrial genome (15,573 bp) of an understudied sheep parasite Melophagus ovinus was sequenced and characterized. Its organization and characteristics, including the size, structure, gene order, start/stop codon usage and gene overlaps, are largely typical for Diptera. It exhibits very high A + T bias (81%). Posterior probability values in the inferred phylogenetic dendrogram were very high, but Oestroidea and Muscoidea superfamilies were both paraphyletic. The sequence was nested within the Oestridae clade, thus also rendering the family paraphyletic. A larger number of Hippoboscoidea mitogenomes will have to be available to achieve a better phylogenetic resolution.

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Background and Aims The terrestrial orchid genus Epipactis has become a model system for the study of speciation via transitions from allogamy to autogamy, but close phylogenetic relationships have proven difficult to resolve through Sanger sequencing. Methods We analysed with restriction site-associated sequencing (RAD-seq) 108 plants representing 29 named taxa that together span the genus, focusing on section Epipactis. Our filtered matrix of 12 543 single nucleotide polymorphisms was used to generate an unrooted network and a rooted, well-supported likelihood tree. We further inferred genetic structure through a co-ancestry heat map and admixture analysis, and estimated inbreeding coefficients per sample. Key Results The 27 named taxa of the ingroup were resolved as 11 genuine, geographically widespread species: four dominantly allogamous and seven dominantly autogamous. A single comparatively allogamous species, E. helleborine , is the direct ancestor of most of the remaining species, though one of the derived autogams has generated one further autogamous species. An assessment of shared ancestry suggested only sporadic hybridization between the re-circumscribed species. Taxa with the greatest inclination towards autogamy show less, if any, admixture, whereas the gene pools of more allogamous species contain a mixture alleles found in the autogams. Conclusions This clade is presently undergoing an evolutionary radiation driven by a wide spectrum of genotypic, phenotypic and environmental factors. Epipactis helleborine has also frequently generated many local variants showing inclinations toward autogamy (and occasionally cleistogamy), best viewed as incipient speciation from within the genetic background provided by E. helleborine , which thus becomes an example of a convincingly paraphyletic species. Autogams are often as widespread and ecologically successful as allogams. [ABSTRACT FROM AUTHOR]

Classification is the most important approach to cataloging biological diversity. It serves as a principal means of communication between scientific disciplines, as well as between scientists on one hand and lawmakers and the public on the other. Up to the present, classification of plants, fungi, and animals follows the fundamental principles laid out more than 250 years ago by Linnaeus, with less changes in the formalistic approach although with somewhat diverging rules for plants and fungi on one hand and animals on the other. Linnean classifications obey two fundamental rules, the binomial as basic format for species names, including a genus-level name and a specific epithet, and rank-based higher classifications, with the main ranks encompassing genus, family, order, class, phylum (division), and kingdom. Given that molecular phylogenies have reshaped our understanding of natural relationships between organisms, and following the cladistic principle of monophyly which defines groups but not ranks, it has been repeatedly argued that rank assignments are artificial and subjective, with the suggestion to either abandon rank-based classifications altogether or apply more objective criteria to determine ranks. The most fundamental of such approaches has been the correlation of rank with geological (evolutionary) age, first established by Hennig in the middle of the past century and around the turn of the millenium formalized as "temporal banding," based on the advent of the molecular clock. While initially the temporal banding approach received less attention, in the past ten years several major studies mostly in vertebrates (birds, mammals) and fungi (chiefly lichenized lineages) have proposed novel classifications based on a strict temporal banding approach, partly with highly disruptive results. In this paper, the temporal banding approach is critically revised, pointing out strengths and flaws, and "best practice" recommendations are given how to employ this technique properly and with care to improve existing classifications while avoiding unnecessary disruptions. A main conclusion is that taxa recognized at the same rank do not have to be comparable in age, diversity, or disparity, or any other single criterion, but their ranking should follow integrative principles that best reflect their individual evolutionary history. In a critical appraisal of changes to the classification of Lecanoromycetes (lichenized Fungi) proposed based on temporal banding, the following amendments are accepted: Ostropales split into Graphidales, Gyalectales, Ostropales s.str., and Thelenellales; Arctomiales, Hymeneliales, and Trapeliales subsumed under Baeomycetales; Letrouitiaceae subsumed under Brigantiaeaceae; Lobariaceae and Nephromataceae subsumed under Peltigeraceae; Miltideaceae subsumed under Agyriaceae, and Protoparmeloideae and Austromelanelixia as new subfamily and genus within Parmeliaceae. The following changes are not accepted: Rhizocarpales split into Rhizocarpales s.str. and Sporastatiales (no information gain); Sarrameanales split into Sarrameanales s.str. and Schaereriales (no information gain); Carbonicolaceae subsumed under Lecanoraceae (topological conflict); Graphidaceae split into Diploschistaceae, Fissurinaceae, Graphidaceae s.str., Thelotremataceae (no information gain, topological conflict); Ochrolechiaceae split into Ochrolechiaceae s.str., Varicellariaceae, and Variolariaceae (no information gain, nomenclaturally incorrect); Porinaceae replaced by Trichotheliaceae (nomenclaturally incorrect); Ramalinaceae split into Biatoraceae and Ramalinaceae s.str. (no information gain, topological conflict); Stereocaulaceae subsumed under Cladoniaceae (nomenclaturally incorrect); Thrombiaceae subsumed under Protothelenellaceae (topological conflict); and all proposed genus level synonymies in Parmeliaceae. New fungal taxa: The new order Odontotrematales Lücking ordo nov. is established for the family Odontotremataceae s.str., based on topological grounds. [ABSTRACT FROM AUTHOR]

Plague is a zoonotic infection whose pathogenic agent has caused hundreds of million human deaths. A broad range of hosts and vectors, along with the geographical dispersion of natural plague foci characterized by different ecological conditions, contribute to the formation of the polytypic Y. pestis species, the result of selection of the genetic variants specific for certain natural foci. Through the efforts of a world consortium of scientists, a global coordinated phylogram of the SNP types of the plague pathogen has been developed. However, debates on the intraspecies Y. pestis taxonomy still continue on the vast Russian expanses. The work of a taxonomist has many specific, individual features, formed on the basis of individual experience. It is important in this kind of work to follow an old rule which requires that borders should be placed where they have been put by nature, and should not be put where nature has not put them. With that in mind, we suggest here the rational variant of the plague pathogen nomenclature constructed in accordance with the rules set out in the International Code of Bacterial Nomenclature and Evolutionary Taxonomy. [ABSTRACT FROM AUTHOR]

Freshwater biota especially molluscs are more vulnerable because even the slightest change in the quality of their habitat possibly leads to their mortality. In addition, their importance is felt that particularly molluscs contribute toward carbon sequestering from the environment as atmospheric carbon gets deposited as carbonates in their shell which constitute 10% of their body mass. Hence, the molecular phylogenetic relationships of two families inhabiting freshwater streams viz., Ampullariidae and Viviparidae considering the genera dwelling in Indian subcontinent namely Pila globosa and Bellamya bengalensis using the partial nucleotide sequence of mitochondrial COI gene were of considerable importance in building conservational strategies. The phylogenetic analysis of ampullariid and viviparid species inferred that these two chosen families were paraphyletic and rooted on the genera of Cyclophoroidea and possibly with Saulea vitrea as the connecting link. [ABSTRACT FROM AUTHOR]

A dataset including novel and publicly available mtDNA COI sequences of 14 Mediterranean combtooth blenny species belonging to nine genera was assembled in order to provide a reference dataset for DNA barcoding studies. Some inconsistencies in the current taxonomy of some genera were observed. In particular, the monophyly of the genera Parablennius and Salaria is not supported by the present dataset and the absence of reciprocal monophyly between the morphospecies Salaria basilisca and S. pavo questions their status and stresses the need of a revision of the genus Salaria. [ABSTRACT FROM AUTHOR]

Abstract We critically re-analyzed the 18S rRNA gene phylogeny of the ciliate class Colpodea where four main lineages have been recognized: (1) Bursariomorphida including bryometopids, (2) Platyophryida including sorogenids, (3) Cyrtolophosidida, and (4) Colpodida including bryophryids and grossglockneriids. The Platyophryida branched off first and the Cyrtolophosidida and Colpodida were classified as sister groups. On basis of multiple statistical tests, we unraveled three problematic issues in colpodean phylogenies: the positions of the Bursariomorphida and Platyophryida are unstable and depend on alignment masking; a sister relationship of the Platyophryida and Cyrtolophosidida cannot be excluded by any statistical tree topology test; and clustering of bryophryids and grossglockneriids outside the Colpodida are also statistically valid possibilities. Natural classification of the highly diverse order Colpodida remains puzzling, possibly due to the lack of a phylogenetic signal and morphostasis of the oral ciliature in several Colpoda -like lineages. According to the "Ur- Colpoda " hypothesis, Colpoda represents the stem lineage from which both Colpoda -like and morphologically more derived taxa might have branched off. This evolutionary concept preserves not only information on morphology, ecology, and evolutionary processes of colpodid ciliates, but also aids practicability because the connection to the traditional literature is optimally maintained. [ABSTRACT FROM AUTHOR]

Monomorium Mayr is a speciose, cosmopolitan genus of myrmicine ants that has had a challenging systematic history, comprising numerous lineages whose relationships are problematic. This study employed an extensive sampling of mostly Australian taxa, along with exemplars of other genera of Solenopsidini, to examine relationships among the continent's Monomorium fauna. Sequences from elongation factor 1α F2, wingless and cytochrome oxidase subunit 1 (COI) were analysed using Bayesian and maximum likelihood methods. The resultant phylogeny resolved Australian Monomorium into two major clades separated by exemplars from other genera; one comprised predominantly species with 11-segmented antennae (corresponding to Monomorium s. str. in a recent study of Myrmicinae) along with three Paleotropical species. The second clade included Australian species with 12-segmented antennae, two New Zealand species and two from New Caledonia. Two Australian cryptobiotic species were resolved as sister to Clade 2. COI analysis indicated that some species (M. fieldi Forel, M. leave Mayr and M. leae Forel) possibly represent cryptic species complexes. The New Zealand M. antipodum Forel was recovered as a valid species, and is closely related to an eastern Australian population. We resurrect the genus Chelaner Emery for species in the second clade (with 12-segmented antennae) and outline morphological characters to separate Chelaner from Monomorium s. str. Fifty-three species of Chelaner are treated as either stat. nov. or stat. rev. Monomorium is cosmopolitan and speciose genus of ants and a significant component of the ant fauna in Australia. This study provides the first multigene phylogenetic analysis for the Australian species, tests the monophyly of the Australian species groups and explores the genetic diversity of some species that exhibit high levels of morphological variation. We resurrect the genus Chelaner to encompass a diverse lineage of species with 12-segmented antennae and highlight a number of species with high COI diversity emphasising the need for a comprehensive species level revision of both Monomorium and C helaner in Australia. [ABSTRACT FROM AUTHOR]

Members of the class Armophorea occur in microaerophilic and anaerobic habitats, including the digestive tract of invertebrates and vertebrates. Phylogenetic kinships of metopid and clevelandellid armophoreans conflict with traditional morphology‐based classifications. To reconcile their relationships and understand their morphological evolution and diversification, we utilized the molecular clock theory as well as information contained in the estimated time trees and morphology of extant taxa. The radiation of the last common ancestor of metopids and clevelandellids very likely occurred during the Paleozoic and crown diversification of the endosymbiotic clevelandellids dates back to the Mesozoic. According to diversification analyses, endosymbiotic clevelandellids have higher net diversification rates than predominantly free‐living metopids. Their cladogenic success was very likely associated with sharply isolated ecological niches constituted by their hosts. Conflicts between traditional classifications and molecular phylogenies of metopids and clevelandellids very likely come from processes, leading to further diversification without extinction of ancestral lineages as well as from morphological plesiomorphies incorrectly classified as apomorphies. Our study thus suggests that diversification processes and reconstruction of ancestral morphologies improve the understanding of paraphyly which occurs in groups of organisms with an apparently long evolutionary history and when speciation prevails over extinction. [ABSTRACT FROM AUTHOR]

On the basis of COI-5P, cox2-3 spacer, RuBisCo spacer, and rbcL sequences, Eucheuma was resolved as a paraphyletic genus in the Solieriaceae. Specimens of E. isiforme from the Yucatan Peninsula and Florida form an independent lineage in the family that was also different from E. denticulatum, the generitype. To accommodate this species, we described Eucheumatopsis as a new genus that differs from Eucheuma both molecularly and geographically. Because the four molecular markers used and morphological characters did not support the independence of Eucheuma isiforme var. denudatum from E. isiforme var. isiforme, we have proposed to no longer recognize var. denudatum as a separate variety. [ABSTRACT FROM AUTHOR]