Sister Relationship Research Articles

Complete Mitochondrial Genome of Malenka flexura (Plecoptera: Nemouridae) and Phylogenetic Analysis.

The genus-level relationships within the subfamily Amphinemurinae have been controversial, although attempts have been made based on morphology and limited molecular data. With the establishment of two new genera, the phylogenetic relationships within Amphinemurinae should be re-examined. In this study, the complete mitochondrial genome (mitogenome) of Malenka flexura of the genus Malenka was firstly sequenced and analyzed. The phylogeny of Amphinemurinae was also reconstructed using 13 proteincoding genes (PCGs) from previously published stoneflies. This mitogenome was 15,744 bp long and encoded the typical 37 genes, as well as a putative control region. The gene arrangement of M. flexura mitogenome is identical with the putative ancestral mitogenome in Drosophila yakuba. Most PCGs used standard ATN as start codons and TAA/TAG as termination codons. All tRNA genes exhibited the typical cloverleaf secondary structure, except for tRNASer(AGN), whose dihydrouridine (DHU) arm was lacking. Some structural elements in the control region were founded, such as tandem repeat regions, stemloop structures, polyN stretch and microsatellite structure, etc. Phylogenetic analyses of sequenced Amphinemurinae mitogenomes unsupported the sister relationship of Amphinemura and Malenka. Finally, the phylogenetic analyses inferred a relationship within Amphinemurinae: Amphinemura + (Malenka + (Protonemura + (Indonemoura + (Sphaeronemoura + Mesonemoura)))).

Complete Chloroplast Genomes Provide Insights Into Evolution and Phylogeny of Campylotropis (Fabaceae).

The genus Campylotropis Bunge (Desmodieae, Papilionoideae) comprises about 37 species distributed in temperate and tropical Asia. Despite the great potential in soil conservation, horticulture, and medicine usage, little is known about the evolutionary history and phylogenetic relationships of Campylotropis due to insufficient genetic resources. Here, we sequenced and assembled 21 complete chloroplast genomes of Campylotropis species. In combination with the previously published chloroplast genomes of C. macrocarpa and closely related species, we conducted comparative genomics and phylogenomic analysis on these data. Comparative analysis of the genome size, structure, expansion and contraction of inverted repeat (IR) boundaries, number of genes, GC content, and pattern of simple sequence repeats (SSRs) revealed high similarities among the Campylotropis chloroplast genomes. The activities of long sequence repeats contributed to the variation in genome size and gene content in Campylotropis chloroplast genomes. The Campylotropis chloroplast genomes showed moderate sequence variation, and 13 highly variable regions were identified for species identification and further phylogenetic studies. We also reported one more case of matK pseudogene in the legume family. The phylogenetic analysis confirmed the monophyly of Campylotropis and the sister relationship between Lespedeza and Kummerowia, the latter two genera were then sister to Campylotropis. The intrageneric relationships of Campylotropis based on genomic scale data were firstly reported in this study. The two positively selected genes (atpF and rps19) and eight fast-evolving genes identified in this study may help us to understand the adaptation of Campylotropis species. Overall, this study enhances our understanding of the chloroplast genome evolution and phylogenetic relationships of Campylotropis.

The curious case of Charles Darwin’s frog, Rana charlesdarwini Das, 1998: Phylogenetic position and generic placement, with taxonomic insights on other minervaryan frogs (Dicroglossidae: Minervarya) in the Andaman and Nicobar Archipelago

Since the description of Charles Darwin’s frog asRana charlesdarwiniin 1998, its generic placement has been a taxonomic enigma. Subsequent studies first transferred this species to the dicroglossid genusLimnonectes, and then considered it as a ceratobatrachid of the genusIngerana, which has since been moved to the family Dicroglossidae. However, recent works have doubted this generic placement and also suggested the possibility of its sister relationship with the genusLiurana, within Ceratobatrachidae. Nonetheless, there have been no detailed investigations to ascertain the generic placement of this taxon by confirming its phylogenetic position or using integrative taxonomic approaches. Here, we provide the first molecular assessment ofIngerana charlesdarwinibased on mitochondrial and nuclear DNA and reveal that it is nested in the dicroglossid genusMinervarya. A member of theMinervarya andamanensisspecies group,Minervarya charlesdarwinicomb. nov.is sister taxon toM. andamanensisand shows relatively shallow genetic distances (2.8–3.6%) in the 16S gene. Both species are widely distributed, occur sympatrically, and exhibit high morphological variations, leading to long-standing confusions with other dicroglossid frogs reported from the region. Our combined morphological and molecular studies on dicroglossid frogs sampled across the known ranges of these species suggest that reports ofLimnonectes doriae(Boulenger, 1887) andL. hascheanus(Stoliczka, 1870) from the Andamans are misidentifications of the former two, pointing to the absence of genusLimnonectesfrom the Andaman Islands. Our study also reveals the novel record ofMinervarya agricolafrom the Andamans, a species that appears to have been confused withFejervarya limnocharisandMinervarya keralensisin the literature and misidentified museum specimens, and is found to be widely distributed across these islands. We further find another congener from the Nicobar group of Islands,M. nicobariensis, to be closely related toM. charlesdarwini. Similar to the case of Andaman dicroglossids, our work emphasises on the need for further studies to ascertain the taxonomic identities and generic placement ofMinervaryaandLimnonectesspecies reported from the Nicobars.

The Morphology, Ultrastructure and Molecular Phylogeny of a New Soil-Dwelling Kinetoplastid Avlakibodo gracilis gen. et sp. nov. (Neobodonida; Kinetoplastea)

Kinetoplastids represent a stockpile of undiscovered protist diversity. Free-living members of this group have been studied less intensively compared to their important parasitic relatives. We have isolated a new soil-dwelling bacteriotrophic kinetoplastid, which is described here as a new genus and new species, Avlakibodo gracilis gen. et sp. nov. Phylogenetic analysis of 18S rRNA genes showed highly supported sister relationship of this protist with the clade uniting Neobodo borokensis, Neobodo curvifilus, Neobodo saliens, Actuariola framvarensis, some Neobodo designis isolates and several environmental sequences, with high statistical support. We have reconstructed the organization of the microtubular cytoskeleton of A. gracilis and determined the origins of the main bands of microtubules. Characteristic ultrastructural features include cytostome associated microtubules (FAS), cytopharynx associated additional microtubules (CMT), microtubular prism (nemadesm) and three microtubular roots (R1, R2 and R3).

Characterization of the complete mitochondrial genome of Cerogria popularis Borchmann, 1936 (Coleoptera: Tenebrionidae)

In this study, we sequenced the complete mitochondrial genome (mitogenome) of Cerogria popularis Borchmann, 1936 based on the Illumina platform. The circular DNA molecule is 16,175 bp in size, including the 37 typical animal mitochondrial genes and a non-coding control region. All 37 genes are arranged in the same order as the previously reported most mitogenomes of Tenebrionidae. All PCGs initiate with standard start codon ATN (ATA/T/G/C) except cox1 with the special start codon AAT. Most PCGs terminate with TAA/G, whereas cox1, atp6, nad5, and nad4 end with its incomplete form T-. All the 22 tRNAs have the typical clover-leaf structure except for trnS1. The rrnL and rrnS genes are 1,250 and 737 bp in length, with an AT content of 82.6 and 84.5%, respectively. The phylogenetic tree supports the monophyly of the included tenebrionid subfamilies represented by more than one species. Furthermore, the sister relationship between Lagriinae and other tenebrionid subfamilies is recovered.

Complete chloroplast genome of the medicinal herb Veronicastrum axillare (Sieb. et Zucc.) Yamazaki and the phylogenetic relationship analysis within the tribe Veroniceae

Veronicastrum axillare (Sieb. et Zucc.) Yamazaki is a traditional medical plant with versatile biological activities. Here, we reported the complete chloroplast genome sequence of V. axillare with a total length of 152,691 bp, containing two IR regions of 25,765 bp each, an LSC region of 83,559 bp, and an SSC region of 17,602 bp. The genome encodes 131 genes, including 85 protein-coding genes, 37 tRNAs, eight rRNAs, and one pseudogene (ycf1). The overall GC content is 38.3%, with the highest content of 43.31% in IR region. Comparative analysis revealed 4 potential hotspots among V. axillare and other Veroniceae plants, providing potential markers for population investigations in the tribe Veroniceae. A total of 56 simple sequence repeats were identified in V. axillare. Phylogenetic analysis indicated a sister relationship between V. axillare and V. sibiricum, suggesting a close genetic relationship between the two Veronicastrum species. Our results provide basic genetic resources for investigating the evolutionary status of V. axillare within the tribe Veroniceae.

Plastid phylogenomics shed light on intergeneric relationships and spatiotemporal evolutionary history of Melocanninae (Poaceae: Bambusoideae)

AbstractMelocanninae is sister to other subtribes of Paleotropical woody bamboos with some 90 species mainly concentrated in Asia. However, phylogenetic relationships within the subtribe are poorly known. Here, we filled the gaps in complete plastome data of Melocanninae, reconstructed the phylogeny of Melocanninae, and further estimated divergence time and ancestral distribution range. Our results showed that the two major genera, Cephalostachyum Munro and Schizostachyum Nees, were paraphyletic. Species of Cephalostachyum were resolved in two successive basal clades, whereas Annamocalamus H. N. Nguyen, N. H. Xia, & V. T. Tran was embedded in the Schizostachyum clade. Different plastid regions provided inconsistent signals for the relationship of Melocanna and Pseudostachyum. Conservative loci supported a successive divergence rather than sister relationship between them and the difference may be caused by long‐branch attraction. We infer that Melocanninae originated in the East Himalaya to northern Myanmar in the early Miocene. Three routes were revealed in forming its present biogeographic pattern: in situ diversification on the Asian mainland, dispersing southwest to Sri Lanka and to the Western Ghats in South India, and spreading southeast to Malesia and Oceania by way of the Indo‐China Peninsula. The rapid uplift of the Tibetan Plateau and the intensification of Asian monsoons since the Miocene and the sea level fall events since the Late Miocene might be potential driving forces for diversification of Melocanninae and, particularly the latter event, for the species radiation of Schizostachyum.

Two new species in Capillidium (Ancylistaceae, Entomophthorales) from China, with a proposal for a new combination.

A taxonomic revision of Conidiobolus s.l. (Ancylistaceae, Entomophthorales) delimited all members that form capilliconidia into the genus Capillidium. In this study, we report two new species of Capillidium that were isolated in China. Capillidiummacrocapilliconidium sp. nov. is characterised by large capilliconidia. Capillidiumjiangsuense sp. nov. is differentiated by large capilliconidia and long, slender secondary conidiophores. Phylogenetic analyses were performed using sequences from the nuclear large subunit of rDNA (nucLSU), the mitochondrial small subunit of rDNA (mtSSU) and elongation-factor-like (EFL). The analyses revealed sister relationships between Ca.macrocapilliconidium sp. nov. and Ca.globuliferus / Ca.pumilum and between Ca.jiangsuense sp. nov. and Ca.denaeosporum. Additionally, a new combination of Ca.rugosum (Drechsler) B. Huang & Y. Nie comb. nov. is proposed herein. An identification key is provided for the ten accepted Capillidium species.

Genomes, repeatomes and interphase chromosome organization in the meadowfoam family (Limnanthaceae, Brassicales)

SUMMARYThe meadowfoam family (Limnanthaceae) is one of the smallest and genomically underexplored families of the Brassicales. The Limnanthaceae harbor about seven species in the genus Limnanthes (meadowfoam) and Floerkea proserpinacoides (false mermaidweed), all native to North America. Because all Limnanthes and Floerkea species have only five chromosome pairs, i.e., a chromosome number rare in Brassicales and shared with Arabidopsis thaliana (Arabidopsis), we examined the Limnanthaceae genomes as a potential model system. Using low‐coverage whole‐genome sequencing data, we reexamined phylogenetic relationships and characterized the repeatomes of Limnanthaceae genomes. Phylogenies based on complete chloroplast and 35S rDNA sequences corroborated the sister relationship between Floerkea and Limnanthes and two major clades in the latter genus. The genome size of Limnanthaceae species ranges from 1.5 to 2.1 Gb, apparently due to the large increase in DNA repeats, which constitute 60–70% of their genomes. Repeatomes are dominated by long terminal repeat retrotransposons, while tandem repeats represent only less than 0.5% of the genomes. The average chromosome size in Limnanthaceae species (340–420 Mb) is more than 10 times larger than in Arabidopsis (32 Mb). A three‐dimensional fluorescence in situ hybridization analysis demonstrated that the five chromosome pairs in interphase nuclei of Limnanthes species adopt the Rabl‐like configuration.

Mitogenomics and phylogenetics of twelve species of African Saturniidae (Lepidoptera).

African Saturniidae (Lepidoptera) include numerous species consumed at the caterpillar stage throughout the continent, and their importance to local communities as a source of nutrition and seasonal income cannot be overestimated. However, baseline genetic data with utility for the characterization of their diversity, phylogeography and phylogenetic relationships have remained scarce compared to their Asian counterparts. To bridge this gap, we sequenced the mitochondrial genomes of 12 species found in southern Africa for comparative mitogenomics and phylogenetic reconstruction of the family, including the first representatives of the tribes Eochroini and Micragonini. Mitochondrial gene content and organization were conserved across all Saturniidae included in the analyses. The phylogenetic positions of the 12 species were assessed in the context of publicly available mitogenomes using Bayesian inference and maximum likelihood (ML) methods. The monophyly of the tribes Saturniini, Attacini, Bunaeini and Micragonini, the sister relationship between Saturniini and Attacini, and the placement of Eochroa trimenii and Rhodinia fugax in the tribes Eochroini and Attacini, respectively, were strongly supported. These results contribute to significantly expanding genetic data available for African Saturniidae and allow for the development of new mitochondrial markers in future studies.

A new species of medicinal leech in the genus Hirudo Linnaeus, 1758 (Hirudiniformes, Hirudinidae) from Tianjin City, China.

Medicinal leeches in the genus Hirudo have been utilized for therapeutic procedures for thousands of years. To date, six known species of Hirudo are widely distributed in different regions of the Eurasian continent. In this study, a new medicinal leech species Hirudotianjinensis Liu, sp. nov. is described based upon specimens collected from Tianjin City, China. The new species can be distinguished from its congeners by a combination of characters: blackish green dorsum with five continuous yellow longitudinal stripes; six sensillae on dorsal annulus a2 of segments VIII–XXV; greyish green ventrum with irregular bilateral dark brown spots; dorsum and abdomen separated by a pair of pale yellow stripes; front half atrium wrapped by white prostate; apparent albumen gland; epididymis massive in relation to ejaculatory bulb. The phylogenetic tree based upon COI implies a sister relationship to H.nipponia Whitman, 1886. A key to the known species is provided.

Two complete mitochondrial genomes in Scolopendra and a comparative analysis of tRNA rearrangements in centipedes.

Centipedes are one of the oldest terrestrial arthropods belonging to the sub phylum Myriapoda. With the expansion of our understanding of the application of the two centipedes Scolopendra morsitans and Scolopendra hainanum, belonging to the order Scolopendromorpha, an exhaustive classification was required. Although consensus has been reached on the phylogeny of Chilopoda based on morphological traits, recent analyses based on molecular data exhibited differences in results. The mitochondrial genome sequences of S. morsitans and S. hainanum were obtained by next-generation sequencing. S. morsitans contains 13 PCGs, two rRNAs, 11 tRNAs, and one CR. whereas S. hainanum contains 12 PCGs, of which ATP8 remains unpredicted, two rRNAs, 14 tRNAs, and one CR. An obvious tRNA rearrangement was found in the genus Scolopendra. S. morsitans exhibited a loss of trnW, trnC, trnI, trnK, trnD, trnA, trnN, trnQ, trnF, trnT, trnS, trnL, and trnV, and a repeat of trnR and trnL. S. hainanum exhibited a loss of trnQ, trnC, trnW, trnI, trnD, trnQ, trnP, and trnV. Phylogenetic analyses of centipedes based on 12 PCGs supported the sister relationship between the orders Geophilomorpha and Lithobiomorpha and a close relationship between Scolopendra dehaani and S. hainanum. The new mitogenomes determined in this study provide new genomic resources for gene rearrangements and contribute to the understanding of the evolution of gene rearrangement in Chilopoda.

Phylogenetic position of Newhousia (Dictyotales, Phaeophyceae) and the description of N. sumayensis sp. nov. from Guam

ABSTRACT The calcified encrusting brown algal genus Newhousia is reported from three new archipelagos in the Pacific: (1) Society Islands, French Polynesia; (2) Guam, Mariana Islands; and (3) Vanuatu. Newhousia presents a simple morphology consisting of small, rounded, two-layered calcified blades with limited interspecific variability in morphological features. Consequently, resolving cryptic diversity in Newhousia requires molecular phylogenetics. Bayesian and maximum likelihood phylogenetic trees, based on the concatenated cox1, cox3, psbA, rbcL and 18S rDNA sequences, supported a sister relationship of Newhousia with Lobophora/Zonaria clade. Analyses revealed five distinct evolutionary lineages within Newhousia. Genetic variation between the lineage from Guam and the two hitherto known Newhousia species, N. imbricata from Hawaii and N. yagha from Papua New Guinea, warrant the description of one new species, N. sumayensis sp. nov. The other two lineages, from the Society Islands and Vanuatu, were identified as geographically distinct populations of N. imbricata with limited genetic variation, rather than independent species. In the Society Islands, N. imbricata is common between depths of 10 m and 20 m as unattached spherical structures, or attached to hard substrate. In Guam, N. sumayensis sp. nov. grows abundantly in sciophilous habitats at depths of 10–21 m. We provide the first documentation of spores for this genus and of structures resembling plurilocular antheridia. Increased sampling throughout the Indo-Pacific region is required to further elucidate the distribution range and patterns of species richness in Newhousia.

The closest lineage of Archaeplastida is revealed by phylogenomics analyses that include Microheliella maris.

By clarifying the phylogenetic positions of 'orphan' protists (unicellular micro-eukaryotes with no affinity to extant lineages), we may uncover the novel affiliation between two (or more) major lineages in eukaryotes. Microheliella maris was an orphan protist, which failed to be placed within the previously described lineages by pioneering phylogenetic analyses. In this study, we analysed a 319-gene alignment and demonstrated that M. maris represents a basal lineage of one of the major eukaryotic lineages, Cryptista. We here propose a new clade name 'Pancryptista' for Cryptista plus M. maris. The 319-gene analyses also indicated that M. maris is a key taxon to recover the monophyly of Archaeplastida and the sister relationship between Archaeplastida and Pancryptista, which is collectively called 'CAM clade' here. Significantly, Cryptophyceae tend to be attracted to Rhodophyta depending on the taxon sampling (ex., in the absence of M. maris and Rhodelphidia) and the particular phylogenetic 'signal' most likely hindered the stable recovery of the monophyly of Archaeplastida in previous studies.

First complete mitochondrial genome from the genus Coptodryas (Coleoptera: Curculionidae: Scolytinae) and its phylogenetic implications

The complete mitochondrial genome (mitogenome) of Coptodryas elegans was determined, which represents the first sequenced mitogenome from Coptodryas. This mitogenome is 15,959 bp in size and comprises 36 typical coding genes and a control region, the tRNAIle was not detected in this mitogenome, as observed in other species of Curculionidae. The monophyly of the family Scolytinae and the sister relationship between C. elegans and Cyclorhipidion bodoanus is supported by maximum likelihood analysis derived from the protein-coding gene sequences.

Morphology, genetic characterization and molecular phylogeny of the poorly known nematode parasite Cissophyllus leytensis Tubangui & Villaamil, 1933 (Nematoda: Ascaridida) from the Philippine sailfin lizard Hydrosaurus pustulatus (Eschscholtz, 1829) (Reptilia: Squamata)

BackgroundThe genus Cissophyllus (Cosmocercoidea: Kathlaniidae) is a rare group of nematodes parasitic in turtles and lizards. To date, only four species have been reported in Asia and North America. However, most of them are inadequately described. The species Cissophyllus leytensis has never been reported since it was originally described by Tubangui and Villaamil in 1933 from the Philippine sailfin lizard Hydrosaurus pustulatus (Eschscholtz, 1829) (Reptilia: Squamata). Furthermore, the systematic status of Cissophyllus/Cissophyllinae in the family Kathlaniidae of the superfamily Cosmocercoidea remains under debate.MethodsThe detailed morphology of C. leytensis was studied using light microscopy (LM) and, for the first time, scanning electron microscopy (SEM), based on newly collected specimens from the type host H. pustulatus. Six different genetic markers, including nuclear sequences [small ribosomal subunit (18S), internal transcribed spacer (ITS) and large ribosomal subunit (28S)], plus mitochondrial genes [cytochrome c oxidase subunit 1 (cox1), cytochrome c oxidase subunit 2 (cox2) and 12S small subunit ribosomal RNA gene] of C. leytensis were sequenced. Additionally, in order to test the validity of the subfamily Cissophyllinae and clarify the phylogenetic relationships of Cissophyllus and the other genera in the family Kathlaniidae, phylogenetic analyses based on 18S + 28S and ITS sequence data were performed using maximum likelihood (ML) and Bayesian inference (BI) analyses, respectively.ResultsOur observations using LM and SEM revealed some previously unreported morphological features, necessitating the redescription of this poorly known species. The presence of remarkable morphological variation in the isthmus and the position of excretory pore among different individuals was found. Molecular analysis showed no intraspecific nucleotide divergence detected in the 18S, ITS, 28S, cox2 and 12S regions among different individuals of C. leytensis, but a low level of intraspecific genetic variation was found in the cox1 (0.52%). Our phylogenetic results showed the representatives of the Cosmocercoidea divided into four large clades (Cosmocerca + Aplectana + Cosmocercoides representing the family Cosmocercidae, Cruzia representing the subfamily Cruzinae of Kathlaniidae, Falcaustra + Cissophyllus + Megalobatrachonema representing the subfamily Kathlaniinae of Kathlaniidae, and Orientatractis + Rondonia representing the family Atractidae). The genus Cissophyllus clustered together with the genus Megalobatrachonema in both the ML and BI trees using ITS sequence data, but displayed a sister relationship to the genus Falcaustra in the ML tree and to the genera Falcaustra + Megalobatrachonema in the BI tree using 18S + 28S sequence data.ConclusionsMolecular phylogenetic results further confirmed that the family Kathlaniidae is not a monophyletic group. The subfamily Cruziinae should be moved from the hitherto-defined family Kathlaniidae and elevated as a separate family Cruziidae. The present phylogenetic results also negated the validity of the subfamily Cissophyllinae and supported the genus Cissophyllus assigned in the subfamily Kathlaniinae. Molecular analysis indicated that the morphological variation in the isthmus and position of excretory pore among different individuals should be considered as intraspecific variation. Moreover, some characters important for the specific diagnosis of C. leytensis are reported for the first time: the number of acuminate denticles (lamellae) on each lip, the chitinized pharynx with three flabellate pharyngeal plates, the presence of single medioventral precloacal papilla and the detailed morphology of caudal papillae. The present study is only the second record of C. leytensis.Graphical

Morphology and molecular phylogeny of Pauciconfibuloides amazonica gen. n. sp. n. (Platyhelminthes, Monogenoidea) parasitizing the Amazonian croaker Plagioscion squamosissimus.

An integrative study was performed to understand the phylogenetic relationships of an undescribed, freshwater species of microcotylid parasitizing Plagioscion squamosissimus from the Amazon River Basin. Based on morphological and molecular analysis (18S rDNA and partial 28S rDNA genes), a new genus is proposed to accommodate this new species, Pauciconfibuloides amazonica gen. n. sp. n. The new genus is closely related to Protastomicrocotylinae and Pauciconfibula by sharing the vagina, male copulatory organ, and genital atrium all unarmed. However, Pauciconfibuloides gen. n. can be distinguished from those taxa by the prostatic system and position of the vaginal pore. Molecular phylogenetic inference suggests a sister relationship with species of Polylabris (Prostatomicrocotylinae), but to date, there are no available 18S or 28S rDNA sequences of Pauciconfibula to be compared. This is the first report of a microcotylid parasitizing a freshwater sciaenid from South America.

Stasis and diversity in living fossils: Species delimitation and evolution of lingulid brachiopods

The Lingulidae are often considered living fossils, because they have shown little morphological change since the Paleozoic. Limited morphological variation has also made the taxonomic study of living lingulids challenging. We investigated species diversity and phylogenetic relationships of extant lingulids and show that they are substantially more diverse than realized, demonstrating that morphological stasis was commonly accompanied by speciation. Species delimitation based on cytochrome c oxidase subunit I (COI) gene sequences from 194 specimens sampled from East Asia, Australia, Oceania, and the Americas suggested 14–22 species in the lingulids (9–17 species in Lingula and 4–5 species in Glottidia), in contrast to the 11–12 species currently recognized globally in the family. Four-gene phylogenetic analyses supported the sister relationship between Lingula and Glottidia. Within Lingula, L. adamsi, which possesses large, brownish shells, was recovered as sister to all remaining Lingula species, which have more or less greenish shells. Within the greenish Lingula clade, the ‘L. anatina’ complex was sister to the clade that includes the ‘L. reevei’ complex. The ‘L. anatina’ complex was further separated into two major clades with partly separate ranges centered on (i) temperate East Asia, and (ii) the tropical west-central Pacific. Within Glottidia, Pacific species were nested within Atlantic species. Time-calibrated phylogenetic analyses suggested that Lingula likely originated in the early Cretaceous contrary to a previously proposed hypothesis advocating a Cenozoic origin. The separation of Lingula and Glottidia appears to date from the Mesozoic, not from the Carboniferous, contrary to a previous hypothesis. Overall, our results uncovered substantial cryptic diversity in lingulids, which will form the basis for conservation and further taxonomic revision.

Hymenotorrendiella clelandii (Leotiomycetes, Helotiales, Helotiaceae) and related species from Australia and New Zealand

ABSTRACT Fungi in the class Leotiomycetes are ecologically diverse, including mycorrhizas, endophytes of roots and leaves, plant pathogens, aquatic and aero-aquatic hyphomycetes, mammalian pathogens, and saprobes. Hymenotorrendiella species are often assumed to be saprobic, their fruiting bodies developing on fallen leaves and dead wood but, in many cases, these putative saprobes are found on only a single host. For the leaf-inhabiting species this host specialisation has been shown to be driven by an endophytic phase to the life cycle, the initial infection of the host being on living leaves. Host specialisation has resulted in high levels of species diversity but within Hymenotorrendiella most of these species remain unnamed. In this paper four species of Hymenotorrendiella are accepted from Eucalyptus in Australia — the leaf-inhabiting H. communis, as well as three wood-inhabiting species, H. clelandii, and two species described here as new, H. spooneri and H. brevis. The leaf-inhabiting H. communis has an endophytic phase to its life cycle, fruiting on dead leaves but with infection initiated while the leaves are still alive and appears to have been moved around the world along with its Eucalyptus host. The biology of the wood-inhabiting species is unknown although H. clelandii occurs also in New Zealand on introduced Eucalyptus. Also described here are two other wood-inhabiting species from New Zealand that are closely related to H. clelandii – H. coriariae from Coriaria arborea, and H. pruinosa from Leptospermum and Kunzea. H. spooneri as accepted here appears to comprise a phylogenetically diverse complex of several closely related sister populations. These populations differ somewhat morphologically, but each is represented by only one specimen, making it impossible at present to assess the possible taxonomic significance of those morphological differences.

Comparing Likelihood Ratios to Understand Genome-Wide Variation in Phylogenetic Support.

Genomic data have only sometimes brought resolution to the tree of life. Large phylogenomic studies can reach conflicting conclusions about important relationships, with mutually exclusive hypotheses receiving strong support. Reconciling such differences requires a detailed understanding of how phylogenetic signal varies among data sets. Two complementary strategies for better understanding phylogenomic conflicts are to examine support on a locus-by-locus basis and use support values that capture a larger range of variation in phylogenetic information, such as likelihood ratios. Likelihood ratios can be calculated using either maximum or marginal likelihoods. Despite being conceptually similar, differences in how these ratios are calculated and interpreted have not been closely examined in phylogenomics. Here, we compare the behavior of maximum and marginal likelihood ratios when evaluating alternate resolutions of recalcitrant relationships among major squamate lineages. We find that these ratios are broadly correlated between loci, but the correlation is driven by extreme values. As a consequence, the proportion of loci that support a hypothesis can change depending on which ratio is used and whether smaller values are discarded. In addition, maximum likelihood ratios frequently exhibit identical support for alternate hypotheses, making conflict resolution a challenge. We find surprising support for a sister relationship between snakes and iguanians across four different phylogenomic data sets in contrast to previous empirical studies. [Bayes factors; likelihood ratios; marginal likelihood; maximum likelihood; phylogenomics; squamates.].