Well-supported Monophyletic Group Research Articles

Phylogenomics corroborates morphology: New discussions on the systematics of Trichostomatia (Ciliophora, Litostomatea)

The subclass Trichostomatia (Ciliophora, Litostomatea) constitutes a well-supported monophyletic group, which includes ciliates exclusively found as symbionts of vertebrates, primarily herbivorous mammals. Recent molecular analyses reinforce the subclass monophyly, though almost all orders, suborders, families, and genera are found to be non-monophyletic. Here, we reconstructed the evolutionary history of the subclass Trichostomatia using a phylogenomic approach and discussed some systematic inconsistencies. We propose a new Ophryoscolecidae genus, Dagostonium, to include Diplodinium polygonale. Monoposthium cynodontum is transferred to the genus Cycloposthium.

In the Dawn of an Early Invasion: No Genetic Diversity of Angiostrongylus cantonensis in Ecuador?

The nematode Angiostrongylus cantonensis has been reported worldwide. However, some basic questions remain unanswered about A. cantonensis in Ecuador: (1) Was the invasion of A. cantonensis in Ecuador unique, or did it occur in different waves? (2) Was this invasion as recent as historical records suggest? (3) Did this invasion come from other regions of South America or elsewhere? To address these issues, we assessed the genetic diversity of MT-CO1 gene sequences from isolates obtained in 11 of Ecuador's 24 provinces. Our Bayesian inference phylogenetic tree recovered A. cantonensis as a well-supported monophyletic group. All 11 sequences from Ecuador were identical and identified as AC17a. The haplotype AC17a, found in Ecuador and the USA, formed a cluster with AC17b (USA), AC13 (Thailand), and AC12a-b (Cambodia). Notably, all the samples obtained in Ecuadorian provinces' different geographic and climatic regions had no genetic difference. Despite the lack of genetic information on A. cantonensis in Latin America, except in Brazil, our finding differs from previous studies by its absence of gene diversity in Ecuador. We concluded that the invasion of A. cantonensis in Ecuador may have occurred: (1) as a one-time event, (2) recently, and (3) from Asia via the USA. Further research should include samples from countries neighboring Ecuador to delve deeper into this.

Genetic structural variation in mitochondrial genomes of four species of Gomphidae and their phylogenetic implications

The Gomphids are the most diverse and important group in the (sub)tropics. Currently, research on Gomphids is mainly focused on fieldwork and morphological classification, however, the molecular-based study is still insufficient. Here, complete mitogenomes of Nihonogomphus semanticus (15,368 bp), Nihonogomphus lieftincki (15,342 bp), Asiagomphus septimus (15,334 bp), and Davidius fruhstorferi (15,682 bp) were obtained by high-throughput sequencing. Of the 37 genes conserved in order and orientation, 9 protein-coding genes (PCGs) and 14 tRNA genes were encoded by heavy strand, while the rest were encoded by light strand. The secondary structures of the protein encoded by 13 PCGs showed a general trend of proportion: α helix > random coil > extended strand > β turn. The trnS1 gene lacked a dihydrouridine arm and was thus reduced to a loop. The 3D structures of the protein encoded by 13 PCGs showed moderate to high levels of consistency among species. Phylogenetic analysis showed that Gomphids were well-supported monophyletic group, both BI and ML tree showed clear phylogenetic relationships in known Gomphidae: ((((D. lunatus + D. fruhstorferi) + A. septimus) + ((N. semanticus + N. lieftincki) + Ophiogomphus cecilia)) + Ictinogomphus sp MT 2014). Our study provides insight into the gene or their protein structure features of the family Gomphidae mitogenomes and lays the foundation for further phylogenetic studies.

Phylogenetic analysis of the critically endangered Karpathos water frog (Anura, Amphibia): conservation insights from complete mitochondrial genome sequencing

Abstract The Karpathos water frog (Pelophylax cerigensis) is classified as Critically Endangered according to the IUCN Red List and its distribution is restricted on the island of Karpathos, South Aegean Sea. Utilizing a next generation sequencing approach, we obtained whole mitochondrial genomes of P. cerigensis to determine the species phylogenetic position within the genus Pelophylax and to clarify the phylogenetic relationship between the species’ population on Karpathos Island and the population of P. cf. bedriagae from the neighboring Rhodes Island. High-throughput sequencing generated mean ± SD = 227 945 ± 18 306 reads averaged per sample. High quality reads were assembled resulting in the complete mitogenome of P. cerigensis of a total size of 17 922 bp. Mitogenome organization was similar to other Pelophylax species, comprising of 13 Protein Coding Genes (PCGs), 22 tRNAs, two rRNAs and one Control Region. Overall mean genetic distance for the 13 PCGs, within the Ranidae family, ranged from 8.01% (COIII) to 11.6% (ATP8), while ratios of synonymous and non-synonymous substitutions were <1 in all the 13 PCGs, indicating purifying selection. Maximum Likelihood and Bayesian Inference analyses based on the concatenated sequences of 13 PCGs and two rRNAs (12S and 16S), showed that individuals from Karpathos and Rhodes form a well-supported monophyletic group with low genetic distance between them (p-distance = 0.1%). Hence, the Rhodes populations seem to belong to P. cerigensis and not to P. bedriagae as formerly thought, highlighting the need for revision of P. cerigensis current conservation status as well as further examination of the P. bedriagae species group.

Disclisioproctaedmondsii (Butler, 1882) comb. nov. (Lepidoptera, Geometridae, Larentiinae).

The generic assignment of the geometrid moth Xanthorhoeedmondsii (Butler, 1882) (Lepidoptera, Geometridae, Larentiinae), originally described under Hypochroma Guenée, [1858], a junior homonym of Hypochroma Herrich-Schäffer, [1855] (Geometridae, Ennominae), is assessed using genitalia morphology and analysis of mitochondrial DNA sequences. Morphological characters revealed closeness to the type species of Disclisioprocta Wallengren, 1861 (Larentiinae). In agreement with morphology, the molecular analysis clustered X.edmondsii with species of Disclisioprocta in a well-supported monophyletic group distantly related to members of Xanthorhoe Hübner, [1825]. Accordingly, Disclisioproctaedmondsii (Butler, 1882) comb. nov. is proposed.

Stilbocrea banihashemiana sp. nov. a New Fungal Pathogen Causing Stem Cankers and Twig Dieback of Fruit Trees.

Stem cankers and twig dieback were the most serious disease of fig (Ficus carica) and loquat (Eriobotrya japonica) noticed in a survey of fruit tree orchards in the Fars Province, Iran. Isolates of Bionectriaceae were consistently recovered from symptomatic fig and loquat trees. Phylogenetic analyses of multiple nuclear loci, internal transcribed spacer regions (ITS) of rDNA, RNA polymerase II subunit 2 (rpb2), and translation elongation factor 1-α (tef1), combined with morphological observations, revealed that isolates could be referred to a still unknown taxon, which was formally described as Stilbocrea banihashemiana sp. nov. Phylogenetically, isolates from fig and loquat trees clustered in a well-supported monophyletic group within the Stilbocrea clade of Bionectriaceae, closely related to S. walteri. Stilbocrea banihashemiana sp. nov. was characterized by the lack of stilbella-like asexual structure in both natural substrates and pure cultures and produced two morphologically distinct types of conidia, globose and cylindrical, formed on short and long simple phialides. In pathogenicity tests, S. banihashemiana sp. nov. induced stem cankers in both fig and loquat, wood discoloration in fig and twig dieback in loquat. Pathogenicity tests also showed that the potential host range of this novel pathogen includes other economically relevant horticultural trees.

The complete mitochondrial genome of a marine triclad Miroplana shenzhensis (Platyhelminthes, Tricladida, Maricola)

The complete mitochondrial genome (mitogenome) of Miroplana shenzhensis Yu & Wang, 2013 is reported in the present study, representing the second mitogenome recorded in the suborder Maricola. The circular mitogenome is 14,344 bp in length, containing 12 protein-coding genes, 2 ribosomal RNAs and 22 transfer RNAs. Comparative analysis on mitochondrial gene order reveals a rearrangement in the suborder Maricola, indicating that mitochondrial gene order is conserved only in Continenticola, and is divergent across Tricladida. Phylogenetic analysis shows M. shenzhensis is clustered with an another marine triclad, forming a well-supported monophyletic group of Maricloan.

Two New Species of the Lycophyte Genus Selaginella (Selaginellaceae) from China, with Notes on the Phylogenetic Positions of Related Species

Abstract— Two new species of lycophytes, Selaginella obovata and S. zhangii, were discovered in southeastern Yunnan, China. Selaginella obovata is characterized by the prostrate habit and relatively small size of plant, obovate median leaves, and short, dorsiventral strobili, and is not apparently similar to any known species. Phylogenetic analyses of plastid sequences (rbcL, atpI, psbA) indicated that S. obovata is closely allied to S. bisulcata, which is also supported by spore morphology, and that these two taxa together with S. pennata constitute a well-supported monophyletic group. Selaginella zhangii is comparable to S. rolandi-principis in their broad stems and shape and arrangement of vegetative leaves; but the former differs from the latter in its prostrate habit and dorsiventral strobili. The results of phylogenetic analyses indicated that S. zhangii is allied to S. heterostachys in the S. heterostachys‐S. ciliaris clade, while S. rolandi-principis is distantly placed in the S. doederleinii‐S. involvens clade. Finally, we provide comprehensive descriptions, photographs of living plants, line drawings, and scanning electron micrographs of spores to facilitate their recognition.

Characterization, Comparison of Four New Mitogenomes of Centrotinae (Hemiptera: Membracidae) and Phylogenetic Implications Supports New Synonymy.

To explore the phylogenetic relationships of the subfamily Centrotinae from the mitochondrial genome data, four complete mitogenomes (Anchon lineatus, Anchon yunnanensis, Gargara genistae and Tricentrus longivalvulatus) were sequenced and analyzed. All the newly sequenced mitogenomes contain 37 genes. Among the 13 protein-coding genes (PCGs) of the Centrotinae mitogenomes, a sliding window analysis and the ratio of Ka/Ks suggest that atp8 is a relatively fast evolving gene, while cox1 is the slowest. All PCGs start with ATN, except for nad5 (start with TTG), and stop with TAA or the incomplete stop codon T, except for nad2 and cytb (terminate with TAG). All tRNAs can fold into the typical cloverleaf secondary structure, except for trnS1, which lacks the dihydrouridine (DHU) arm. The BI and ML phylogenetic analyses of concatenated alignments of 13 mitochondrial PCGs among the major lineages produce a well-resolved framework. Phylogenetic analyses show that Membracoidea, Smiliinae and Centrotinae, together with tribes Centrotypini and Leptobelini are recovered as well-supported monophyletic groups. The tribe Gargarini (sensu Wallace et al.) and its monophyly are supported.

An integrative study of Pannaria hookeri (Ascomycota lichenized) from Argentina and the update of the taxon circumscription based on specimens from the Northern and Southern Hemispheres

Pannaria hookeri (Borrer ex Sm.) Nyl. is reported as a bipolar cyanolichen that occurs in more than twenty countries in both Hemispheres. In the Northern Hemisphere, a minor variation is attributed to the species, whereas larger morphological and chemical variations have been reported in specimens from the Southern Hemisphere. Six P. hookeri DNA sequences are available in GenBank, and only one (from Australia) is associated with a published morphological description. In this study, we performed a preliminary phylogenetic analysis including seven nuITS and mtSSU sequences from eight specimens collected in south Argentina. In addition, we provide an update of the taxon circumscription based on 50 specimens from 13 countries. Here, the molecular analyses revealed a well-supported monophyletic group formed by the P. hookeri sequences from Argentina, Australia, Norway and USA (Alaska). Regarding the morphological and anatomical characteristics, the Southern Hemisphere specimens did not present the historical reported variations, resulting in the proposition of a concise species description that accomplishes most of P. hookeri known geographical distribution.

The Complete Mitochondrial Genomes of Four Species in the Subfamily Limenitidinae (Lepidoptera, Nymphalidae) and a Phylogenetic Analysis.

Simple SummaryAs it is currently delineated, the subfamily Limenitidinae (Lepidoptera: Nymphalidae) is comprised of 50 genera with approximately 1100 species. The classification of this subfamily has always been unstable. There are tribes and genera whose status is doubtful. Their phylogenetic relationships are far from being clarified and the monophyly of some of them is under question. To provide further insight into the relationships among included tribes, four newly-completed mitochondrial genomes of Limenitidinae (Neptis thisbe, Athyma zeroca, and Aldania raddei) have been sequenced and analyzed. Results indicate that the gene orientation and arrangement are similar to typical mitogenomes in Lepidoptera. The inferred phylogenetic analysis shows that tribe levels are well-supported monophyletic groups. Taken together, this work will provide a well-resolved framework for future study of this subfamily.The complete mitogenomes of four species, Neptis thisbe, Neptis obscurior, Athyma zeroca, and Aldania raddei, were sequenced with sizes ranging from 15,172 bp (N. obscurior) to 16,348 bp (Al. raddei). All four mitogenomes display similar nucleotide content and codon usage of protein-coding genes (PCGs). Typical cloverleaf secondary structures are identified in 21 tRNA genes, while trnS1 (AGN) lacks the dihydrouridine (DHC) arm. The gene orientation and arrangement of the four mitogenomes are similar to that of other typical mitogenomes of Lepidoptera. The Ka/Ks ratio of 13 PCGs among 58 Limenitidinae species reveals that cox1 had the slowest evolutionary rate, while atp8 and nad6 exhibited a higher evolutionary rate. The phylogenetic analysis reveals that tribe-levels are well-supported monophyletic groups. Additionally, Maximum Likelihood analysis recovered the relationship (Parthenini + ((Chalingini + (Cymothoini + Neptini)) + (Adoliadini + Limenitidini))). However, a Bayesian analysis based on the same dataset recovered the relationship (Parthenini + (Adoliadini + ((Cymothoini + Neptini) + (Chalingini + Limenitidini)))). These results will offer valuable data for the future study of the phylogenetic relationships for Limenitidinae.

Two new species in the fern genus Lomariopsis (Lomariopsidaceae) from East Asia.

Two East Asian Lomariopsis (Lomariopsidaceae, Polypodiales) species, Lomariopsismoorei and Lomariopsislongini, which were previously misidentified as L.spectabilis, are here described as new species based on evidence from morphological characters and a molecular phylogeny. The two species differ from the three other described species in East Asia by their venation, pinna shapes, and perine morphology. A phylogeny based on a combined dataset of three chloroplast regions (rbcL+ rps4-trnS + trnL-L-F) showed that L.moorei and L.longini each formed a well-supported monophyletic group which was distantly related to both L.spectabilis and the other morphologically similar East Asian species, L.boninensis.

Discordance of genetic diversification between deep‐ and shallow‐water species of Kobeltocochlea Lindholm, 1909 (Caenogastropoda: Truncatelloidea: Benedictiidae) endemic to Lake Baikal with the description of a new species, review of the genus, and notes on its origin

We describe a new species, Kobeltocochlea tamarae Sitnikova, Teterina & Maximova sp. nov., from Lake Baikal discovered in the Saint Petersburg methane seep at a depth of approximately 1400 m. The uncorrected genetic distance was 4.26% of the COI gene between this new species and K. falsipumyla collected from the Academic Ridge at depths between 157 and 163 m. The two shallow-water species, K. martensiana and K. olchonensis, differed in substrate preference and geographic habitats, with a genetic distance of 0.97% for COI. Phylogenetic analysis of mitochondrial (COI, 16S) and nuclear (ITSI, 28S) sequences indicated that Kobeltocochlea was paraphyletic with respect to other benedictiid genera Benedictia and Yaroslawiella, formed well-supported monophyletic groups. We revealed the discordance of morphological and genetic data within Kobeltocochlea and other benedictiids, which reflected their complicated history. The current knowledge of benedictiids does not allow for significant changes in the taxonomy of the Benedictiidae, except for synonymizing K. lindholmiana with K. olchonensis and Pseudobenedictia with Benedictia that were also investigated. We speculate that three main lineages of benedictiids originated from three populations of a single ancient species approximately 3.2 Ma. The speciation of deep-water species was probably driven independently by bathymetric isolation in the cold methane seeps of different geomorphological structures. The diversification of the third lineage consisting of littoral (including K. martensiana/K. olchonensis), deep-water, and eurybathic benedictiids may be explained by rapid adaptive radiation to intralacustrine environments.

Integrative taxonomy of West African Magelona (Annelida: Magelonidae): species with thoracic pigmentation

Abstract Benthic samples collected during several cruises from shelf areas along the West African coast from Morocco to Angola, have highlighted a huge diversity of magelonid species (over 20 species), many of which are undescribed. The majority of samples were taken as part of two large-scale projects in the region: the Canary Current Large Marine Ecosystem project (CCLME) and the Guinea Current Large Marine Ecosystem project (GCLME). Six magelonid species bearing posterior thoracic pigmentation have been highlighted, Magelona alleni and five species new to science: Magelona fasciata sp. nov., Magelona guineensis sp. nov., Magelona mackiei sp. nov., Magelona nanseni sp. nov. and Magelona picta sp. nov. West African magelonids and comparative material from the UK and Norway have been investigated using COI, 16S and 28S markers. An integrated taxonomic approach is used to delineate species of Magelona carrying posterior thoracic pigmentation. These species from West African waters constitute a well-supported monophyletic group, with the species M. alleni being sister to the new species herein described. Our 41 COI DNA-barcode-sequences had between species distances from 9.3 to 26.8% and were allocated to ten different BINs in Boldsystems.org.

Supplementary morphological data and molecular analyses of Eimeria labbeana (Labbé, 1896) Pinto, 1928 (Chromista: Miozoa: Eimeriidae) from columbiform birds in Portugal.

Columbiformes have a worldwide distribution, of which 166 species occur in Eurasia. They have been reported parasitized by coccidians recurrently in recent years; however, Eimeria labbeana (Labbé, 1896) Pinto, 1928, which is first Eimeria sp. from Columbiformes described in the late nineteenth century, is not taxonomically identified by its oocysts since the 1930s. In this context, the current study aimed to supplement the morphology of E. labbeana from Eurasian collared doves Streptopelia decaocto Frivaldszky, 1838 and from a common woodpigeon Columba palumbus Linnaeus, 1758 in Portugal, providing a preliminary genotypic characterization. Three of the four columbiforms were positive for oocysts identified as E. labbeana, which were morphologically revised as having micropyles, in addition to other minor adjustments. Oocysts from S. decaocto and C. palumbus were morphologically identical and equivalent in all morphometric aspects, besides having genotypic similarity of 99.5%. Phylogenetic analysis based on the mitochondrial cytochrome c oxidase subunit 1 gene resulted in a large clade with Eimeria spp. and Isospora spp. from different vertebrates and low similarity between Eimeria spp. from Columbiformes, whereas the phylogenetic analysis based on the small subunit ribosomal RNA gene resulted in well-supported monophyletic groups, including one with the coccidians of columbiform birds.

Morphological phylogenetic analyses and taxonomic revision of the Panorpa davidi group (Mecoptera: Panorpidae)

Abstract The Chinese Panorpa species without anal horn are normally assigned to the Panorpa davidi group. Here, we taxonomically revise the P. davidi group, which currently includes 17 known species and four new species: P. gaokaii sp. nov., P. huayuani sp. nov., P. uncinata sp. nov. and P. yaoluopingensis sp. nov. Panorpa shanyangensis Chou & Wang, 1981 and P. sexspinosa zhongnanensis Chou & Ran, 1981 are treated as junior synonyms of P. sexspinosa Cheng, 1949. We describe for the first time the male of P. stigmosa Zhou, 2006, and the females of P. curva Carpenter, 1938, P. davidi Navás, 1908, P. difficilis Carpenter, 1938, P. fructa Cheng, 1949, and P. jinchuana Hua, Sun & Li, 2001. A key to species of the group is provided. Phylogenetic analyses of maximum parsimony and maximum likelihood based on 79 morphological characters show that the newly defined P. davidi group is a well-supported monophyletic group and is sister to the genus Cerapanorpa Gao, Ma & Hua, 2016.

Morphological phylogenetic analyses and taxonomic revision of the Panorpa davidi group (Mecoptera: Panorpidae)

Abstract The Chinese Panorpa species without anal horn are normally assigned to the Panorpa davidi group. Here, we taxonomically revise the P. davidi group, which currently includes 17 known species and four new species: P. gaokaii sp. nov., P. huayuani sp. nov., P. uncinata sp. nov. and P. yaoluopingensis sp. nov. Panorpa shanyangensis Chou & Wang, 1981 and P. sexspinosa zhongnanensis Chou & Ran, 1981 are treated as junior synonyms of P. sexspinosa Cheng, 1949. We describe for the first time the male of P. stigmosa Zhou, 2006, and the females of P. curva Carpenter, 1938, P. davidi Navás, 1908, P. difficilis Carpenter, 1938, P. fructa Cheng, 1949, and P. jinchuana Hua, Sun & Li, 2001. A key to species of the group is provided. Phylogenetic analyses of maximum parsimony and maximum likelihood based on 79 morphological characters show that the newly defined P. davidi group is a well-supported monophyletic group and is sister to the genus Cerapanorpa Gao, Ma & Hua, 2016.

Diversity and emendation of the genus Planktoniella (Bacillariophyceae), with descriptions of P.tubulata sp. nov. and P.trifurcata sp. nov.

For the first time, LSU and SSU sequences were obtained from four species of the marine planktonic diatom Planktoniella. Samples were collected and cultured from Chinese coastal waters, and morphological observations were made using light and scanning electron microscopy. Combined morphological and DNA sequence data revealed two new species herein described as Planktoniella tubulata and Planktoniella trifurcata. Planktoniella tubulata is characterized by the prominent external tubes of two rimoportulae and the long external tubes of the marginal fultoportulae. The latter are organized regularly in a ring, externally on the mantle, and protrude parallel to the valvar plane. Planktoniella trifurcata is unique in having mucilaginous extensions that usually expand into three lobes, and external extensions of the marginal fultoportulae being either tubes or spines. In the phylogenetic analyses inferred from SSU and LSU sequences, the four analyzed Planktoniella taxa formed a well-supported monophyletic group. A suite of three characters, mucilage membranes or wings, two marginal rimoportulae, and mantle ribs are diagnostic for Planktoniella. Based on these detailed ultrastructural observations, the description of Planktoniella is emended.

Evaluating the monophyly of Mammillaria series Supertextae (Cactaceae).

Mammillaria (Cactaceae) taxonomy has been historically problematic due to the morphological variability and sympatry of the species. This has led to several proposals for infrageneric classification, including subgeneric, section and series categories. Mammillaria ser. Supertextae is one of 15 series and is made up of a variable set of species that are mainly distributed in southern Mexico and Central America. However, the phylogenetic relationships within M. ser. Supertextae and its relationship to other Mammillaria taxa are far from fully understood. Here we attempt to elucidate these relationships using complete terminal sampling and newly obtained chloroplast marker sequences and comparing them to Mammillaria species sequences from GenBank. Our phylogenetic analyses showed that M. ser. Supertextae comprises a well-supported monophyletic group that diverged approximately 2.1 Mya and has M. ser. Polyacanthae as its sister group; however, relationships within M. ser. Supertextae remain unresolved. The topology obtained within M. ser. Supertextae must also be interpreted under the distribution shared by these taxa, but it is difficult to differentiate ancestral polymorphisms from possible introgression, given the short time elapsed and the markers used. Our results show that the infrageneric units of M. haageana and M. albilanata can be considered independent evolutionary units. We also suggest that the relationship between M. haageana and M. albilanata is convoluted because their distribution overlaps (mainly towards southern Mexico), with genetic differences that possibly indicate they represent more than two taxonomic entities. One possible explanation is that there could still be gene flow between these taxa, and we might be witnessing an ongoing speciation process.

THE VIOLETS OF THE BRAZILIAN SAVANNA: A REVISION OF THE POMBALIA LANATA COMPLEX (VIOLACEAE), WITH DESCRIPTIONS OF TWO NEW SPECIES

Pombalia Vand. (Violaceae) is represented in the Cerrado by a well-supported monophyletic group of species known as the Pombalia lanata complex, characterised by some unique vegetative and reproductive features within the genus. This group includes six species – Pombalia cristalina, P. insignis, P. lanata, P. poaya, P. strigoides and P. velutina – the first two of which are new to science. Pombalia lanata shows the widest geographical distribution throughout the Central Brazilian Plateau and the Espinhaço Range in Minas Gerais state, with a disjunction in Misiones Province, Argentina. Because most species in this group are narrow endemics, we evaluated the conservation status of all taxa. An identification key for the species, descriptions, illustrations, maps of geographical distribution and nomenclatural notes are also provided.