Nuclear Protein-coding Genes Research Articles

Geomorphic impacts within Red River Fault and island shifting as witnessed by the phylogeography of the largest water strider

Palaeogeological events and climate oscillations profoundly impact the demographics and distributions of small-range species, increasing the extinction risk. The largest water strider worldwide, Gigantometra gigas (Hemiptera: Gerridae), exhibits restricted distributions in Vietnam and southern China. Herein, we generated three genomic datasets (mitogenomes, 146 nuclear protein-coding genes and single nucleotide polymorphisms) with ecological niche modelling (ENM) to explicitly test whether the present-day distribution of G. gigas actually resulted from geographical and climatic effects. We found that the origin of this largest water strider reached the divergence time of the genus within Gerridae, providing a greater opportunity to explore its response to geographic movements. The right-lateral motion of the Red River Fault facilitated the divergence of two phylogeographic lineages, resulting in the “north–south component” genetic pattern in G. gigas. The Hainan and southeast Vietnam populations of the southern linage were completely separated by the Beibu Gulf but exhibited similar genetic compositions, confirming that Hainan had a continental origin and that Hainan Island joined with the Indo-China Peninsula to promote gene exchange among populations. Additionally, we noticed the low genetic diversity but long demographic history of the northern lineage, which displayed population dynamics opposite to those of other organisms. Integrating the demographic changes and ENM findings revealed that suitable habitat contraction and rapid demographic decline during the Last Glacial Maximum (LGM) triggered the low genetic diversity of the northern lineage. Overall, the demographic history of the largest water strider was mainly shaped by geographical features, and first provided evidence from the phylogeographic perspective of aquatic insects to support the hypothesis of Hainan Island shifting.

Novel molecular resources for single-specimen barcoding of enigmatic crustacean y-larvae.

Despite discovery more than 100years ago and documented global occurrence from shallow waters to the deep sea, the life cycle of the enigmatic crustacean y-larvae isincompletely understood and adult forms remain unknown. To date, only 2 of the 17 formally described species, all based on larval stages, have been investigated using an integrative taxonomic approach. This approach provided descriptions of the morphology of the naupliar and cyprid stages, and made use of exuvial voucher material and DNA barcodes. To improve our knowledge about the evolutionary history and ecological importance of y-larvae, we developed a novel protocol that maximises the amount of morpho-ecological and molecular data that can be harvested from single larval specimens. This includes single-specimen DNA barcoding and daily imaging of y-nauplii reared in culture dishes, mounting of the last naupliar exuviae on a slide as a reference voucher, live imaging of the y-cyprid instar that follows, and fixation, DNA extraction, amplification and sequencing of the y-cyprid specimen. Through development and testing of a suite of new primers for both nuclear and mitochondrial protein-coding and ribosomal genes, we showcase how new sequence data can be used to estimate the phylogeny of Facetotecta. We expect that our novel procedure will help to unravel the complex systematics of y-larvae and show how these fascinating larval forms have evolved. Moreover, we posit that our protocols should work on larval specimens from a diverse array of moulting marine invertebrate taxa.

First Report of Botrytis cinerea Causing Gray Mold on Tea (Camellia sinensis) in China.

Tea (Camellia sinensis (L.) O. Kuntze) is an important economic crop cultivated in China. In March 2019, leaf blight symptoms were observed on tea trees (C. sinensis cv. Fuding-dabaicha) in Enshi City (30º02'66" S, 109º01'56" W), Hubei Province (Fig. 1A). The disease occurred on the senescent flowers and mature leaves. The average disease incidence was approximately 10% of plants in the surveyed 30 ha tea garden. Initial symptoms consisted of brown lesions, which expanded and became covered with gray mold, followed by abscission. To identify the pathogen, 20 symptomatic leaves were collected and 0.5 cm2 diseased leaf pieces were excised and surface sterilized by immersion in 1.5% sodium hypochlorite (NaOCl) for 2 min, and rinsed three times in sterilized distilled water. The leaf pieces were allowed to dry, placed on potato dextrose agar (PDA) plates, and incubated at 20°C under 12h fluorescent light. The fungus formed gray to grayish brown colonies (Fig. 1B) and produced conidia after 1 week. The isolate was purified by single spore isolation. The conidia were one-celled, ellipsoid or ovoid, almost colorless, with a size range of 5.3 to 10.24 × 5.2 to 8.1 μm (n = 50) (Fig. 1C). The sclerotia produced in culture were black, round or irregular in shape and 1.3 to 2.2 × 2.0 to 3.3 mm (average 1.8 × 2.3 mm) in size. Morphological characteristics of these isolates matched the description of Botrytis spp. (Hong et al. 2001). Representative isolate LCHM was selected for molecular identification based on DNA sequencing of the ITS region of rDNA and three nuclear protein-coding genes (G3PDH, HSP60 and RPB2) (Staats et al. 2005). BLAST analysis showed that isolate LCHM (GenBank Acc. Nos. MN448502, MN448500, MN433708 and MN448501 for ITS, G3PDH, HSP60 and RPB2, respectively) shared 99 to 100% identity with B. cinerea (GenBank Acc. Nos. MH316147.1, MG846500.1, MG846504.1 and MG846510.1, respectively), which suggested that isolate LCHM belongs to B. cinerea. This identification was further confirmed by phylogenetic analysis based on combined DNA sequence data of G3PDH, HSP60 and RPB2 (Fig. 2). For the pathogenicity test, needle-wounded, attached leaves on 1-year-old C. sinensis cv. Fuding-dabaicha plants were inoculated with mycelial plugs (6 mm diameter from 2-day-old PDA cultures) or a conidial suspension (20 μL, 1×106 conidia/ml in half strength potato dextrose broth) of isolate LCHM on three plants per treatment (six leaves). The control treatments were also wounded, but only treated with agar plugs or half strength PDB. All inoculated plants and controls were incubated in a growth chamber (20°C, 90 ± 10% RH). Leaves inoculated with mycelial plugs, whether wounded or not, showed brown necrotic lesions around the agar plugs after 2 days (Fig. 1D, E), whereas conidial inoculations of wound sites showed necrotic lesions after 6 days (Fig. 1 F, G). Non-wounded leaves inoculated with conidia and all the control treatments remained symptomless. B. cinerea was reisolated from the inoculated leaves and isolates were morphologically similar to the original cultures. Gray mold of C. sinensis caused by B. cinerea has been recorded in Japan, Turkey, and Brazil (Hamaya 1981, Aziz and Harun 2010, Pereira and Mio, 2020). To our knowledge, this is the first report of gray mold caused by B. cinerea on C. sinensis in China. B. cinerea may cause economic losses of tea, therefore, more surveys in other tea-growing regions should be done to specifically search for this disease.

A new species of the genus Yoldiella (Bivalvia, Protobranchia, Yoldiidae) from Haima Cold Seep, South China Sea, China.

In present study, a previously unidentified but frequently encountered species of deep-sea protobranch, Yoldiellahaimaensis sp. nov., is described new to science from the Haima Cold Seep on the northwestern slope of the South China Sea. A morphological analysis confirmed that this species belongs to a previously undescribed species of the genus Yoldiella A.E. Verrill & K.J. Bush, 1897. It differs morphologically from other known species within the genus in its shell shape, degree of inflation, beaks, and number of hinge teeth. Furthermore, we sequenced three gene segments of Y.haimaensis sp. nov., comprising a nuclear ribosomal gene (18S rRNA), a nuclear protein-coding gene (histone H3), and a mitochondrial gene (cytochrome c oxidase subunit I, COI). Our phylogenetic analysis performed on the superfamily Nuculanoidea and family Yoldiidae indicates that the genus Yoldiella is non-monophyletic, and the widely recognized families within the superfamily Nuculanoidea are also not monophyletic. Our results provide molecular insights into the Protobranchia and highlight the necessity for further samples and data to revise the classification of families and genera within the superfamily using an integrative approach that combines morphological analysis and molecular data.

Meteora sporadica, a protist with incredible cell architecture, is related to Hemimastigophora

"Kingdom-level" branches are being added to the tree of eukaryotes at a rate approaching one per year, with no signs of slowing down.1,2,3,4 Some are completely new discoveries, whereas others are morphologically unusual protists that were previously described but lacked molecular data. For example, Hemimastigophora are predatory protists with two rows of flagella that were known since the 19th century but proved to represent a new deep-branching eukaryote lineage when phylogenomic analyses were conducted.2Meteora sporadica5 is a protist with a unique morphology; cells glide over substrates along a long axis of anterior and posterior projections while a pair of lateral "arms" swing back and forth, a motility system without any obvious parallels. Originally, Meteora was described by light microscopy only, from a short-term enrichment of deep-sea sediment. A small subunit ribosomal RNA (SSU rRNA) sequence was reported recently, but the phylogenetic placement of Meteora remained unresolved.6 Here, we investigated two cultivated Meteora sporadica isolates in detail. Transmission electron microscopy showed that both the anterior-posterior projections and the arms are supported by microtubules originating from a cluster of subnuclear microtubule organizing centers (MTOCs). Neither have a flagellar axoneme-like structure. Sequencing the mitochondrial genome showed this to be among the most gene-rich known, outside jakobids. Remarkably, phylogenomic analyses of 254 nuclear protein-coding genes robustly support a close relationship with Hemimastigophora. Our study suggests that Meteora and Hemimastigophora together represent a morphologically diverse "supergroup" and thus are important for resolving the tree of eukaryote life and early eukaryote evolution.

Gill Structure Linked to Ecological and Species Diversification in a Clade of Caddisflies

Streams represent a special case of directional environmental gradients where ecological opportunity for diversification may be associated with upstream and downstream dispersal into habitats that differ in selective pressures. Temperature, current velocity and variability, sediment erosion dynamics and oxygen saturation are key environmental parameters that change in predictable ways from springs to river mouth. Many aquatic insects occupy specific longitudinal regions along these gradients, indicating a high degree of adaptation to these specific environmental conditions. In caddisflies, the evolution of tracheal gills in larval and pupal stages may be a major driver in oxygen uptake efficiency and ecological diversification. Here we study the evolution of larval gill structure in the Rhyacophila vulgaris species group using phylogenomic methods. Based on anchored hybrid enrichment, we sequenced 97 kbp of data representing 159 independent nuclear protein coding gene regions to infer the phylogeny of the R. vulgaris species group, whose species exhibit both high diversity of gill types and varied longitudinal preferences. We find that the different gill types evolved independently as derived characters in the genus and that gill structure is linked to the longitudinal habitat preference, thereby serving as a possible ecological key innovation in the R. vulgaris group.

Sexual morph of Allophoma tropica and Didymella coffeae-arabicae (Didymellaceae, Pleosporales, Dothidiomycetes), including novel host records from leaf litter in Thailand

ABSTRACT Studying the taxonomy, diversity and host preference of leaf litter inhabiting microfungi contributes towards elucidating hidden taxa, their host affinities and recovering novel life modes dwelling inside forest ecosystems. Leaf litter-inhabiting microfungi also play a crucial role in forest ecosystems through decomposition and nutrient recycling. This study resulted in the introduction of saprobic Didymellaceae microfungi from Doi Tung Forest Reserve, Chiang Rai, northern Thailand. Fungal isolates were characterised based on morphology and molecular phylogeny of the nuclear ribosomal DNA (ITS, LSU) and protein-coding genes (tub2, rpb2). Allophoma tropica and Remotididymella ageratinae are recorded from dead leaves of Nayariophyton zizyphifolium (Malvaceae), and Didymella coffeae-arabicae from Dalbergia cultrata and Afzelia xylocarpa (Fabaceae). This study also reports the sexual morph of Allophoma tropica and Didymella coffeae-arabicae and provides molecular evidence for the first reports of sexual morphs from Thailand.

Systematics and integrative taxonomic revision of the tribe Scopulini Duponchel, 1845 in Iran (Lepidoptera: Geometridae: Sterrhinae).

The Iranian taxa of the tribe Scopulini are taxonomically revised. The systematic positions of the genera Cinglis Guene, 1858, Glossotrophia Prout, 1913, Pseudocinglis Hausmann, 1994 and Scopuloides Hausmann, 1994, with uncertain validity and/or position within the tribe Scopulini Duponchel, 1845 (Lepidoptera: Sterrhinae), are further elucidated by use of one mitochondrial and up to nine protein-coding nuclear gene regions. Available type specimens of the described species and more than 2,600 additional specimens were morphologically investigated. In addition, over 400 genitalia preparations were made and examined together with distribution data and DNA barcodes. As a result of the multi-gene analysis, the genera Cinglis stat. rev. and Scopuloides stat. rev. are re-validated at the genus level. The genus Pseudocinglis syn. nov. is regarded as a junior synonym of the genus Cinglis stat. rev. and Glossotrophia syn. nov. is regarded as a junior synonym of the genus Scopula. Cinglis eurata (Prout, 1913) comb. nov. and Cinglis benigna (Brandt, 1941) comb. nov. are combined with the genus Cinglis. Additionally, Cinglis benigna amseli (Wiltshire, 1967) syn. nov. is regarded as a synonym of C. benigna. Scopula adulteraria (Erschov, 1874) stat. nov. is raised from subspecies to species rank; Scopula iranaria Bytinski-Salz & Brandt, 1937 syn. nov. is synonymized with S. flaccidaria (Zeller, 1852); S. transcaspica taftanica Brandt, 1941 syn. nov. is synonymized with S. transcaspica Prout, 1935; S. diffinaria asiatica (Brandt, 1938) syn. nov. is synonymized with S. diffinaria (Prout, 1913) and Glossotrophia bullata Vojnits, 1986 syn. nov. is synonymized with Scopula sacraria ariana (Ebert, 1965). The female genitalia of Scopula lactarioides Brandt, 1941 are described and illustrated for the first time. In total, the presence of 33 species of Scopulini in Iran is confirmed. Wing patterns, male and female genitalia and diagnostic characters of most Iranian Scopulini species are depicted and their distribution ranges are mapped.

New suggestion of the species group reconstruction of genus Nomada Scopoli, 1770 (Hymenoptera, Apidae) from Korea

Genus Nomada, which includes approximately 800 species, is the largest genus in the subfamily Nomadinae and the sole genus in the tribe Nomadini. Its taxonomic classification is particularly challenging due to high morphological variations, making it one of the most controversial groups in the subfamily. In order to shed light on the complex classification of Nomada species and their tribal position, this study conducted a multi-locus phylogeny using one mitochondrial gene (COI) and five nuclear protein-coding genes (EF1α, Nak, Opsin, Pol Ⅱ, Wingless). The study focused on expanding the knowledge of some East Palearctic species, with the ultimate goal of reviewing species groups of Nomada present in Korea. In this study, we suggest that the ruficornis species group is polyphyletic. Some species should be moved to more appropriate species groups as follows: N. tsunekiana, N. emarginata, and N. flavopicta into the basalis species group; N. aswensis, N. kaguya, and N. taicho into the armata species group.

"Star like" disease of persimmon (Diospyros kaki) fruit caused by Botrytis cinerea in Israel.

During May 2016, a corky textured, "star like" symptom, located at the apex on the far side of the fruit was observed on young persimmon fruitlets (Fig. 1), on several persimmon varieties in plantations located along the Mediterranean Sea coast. The lesions caused cosmetic damage, which disqualified the fruit from marketing and can affect as much as 50% of the fruit in the orchard. Symptoms were correlated with the presence of wilting flower parts (petals and stamens) attached to the fruitlet (Fig. 1). Fruitlets with no flower parts attached did not develop the corky star symptom, while almost all fruitlets with an attached wilted flower parts had symptoms underneath the flower parts. Flower parts and fruitlets displaying the phenomenon were sampled (orchard near the town of Zichron Yaccov) and used for fungi isolation. At least ten fruitlets were surface sterilized by immersion in 1% NaOCl for 1 min. Pieces of the infected tissue were then placed on 0.25% potato dextrose agar (PDA) supplemented with 12 µg/mL tetracycline (Sigma, Rehovot, Israel). In addition, the inner parts of at least ten moldy flowers were placed on 0.25% PDA supplemented with tetracycline and incubated at 25°C for 7 days. Two fungi were isolated from the flower parts and the symptomatic fruitlets: Alternaria sp. and Botrytis sp. Koch postulates were conducted by inoculating 10 µl of conidial suspension of each fungus (105 conidia/ml in H2O, single spore originated), on four wounds, made by puncturing a 2 mm deep hole with 21G sterile syringe needle, on the apex of surface sterilized, small, green fruits. Fruits were placed in sealed 2-liter plastic boxes. Symptoms similar to those found on the fruitlets in the orchards were observed on the fruit inoculated with Botrytis sp. (corky like, but not in the shape of stars) about 14 days post inoculation. Botrytis sp. was re-isolated from the symptomatic fruit to fulfill Koch's postulates. Alternaria and water inoculation did not cause any symptoms. The Botrytis sp. colonies, when grown on PDA, grow initially as white colonies becoming gray to brown after about seven days. Elliptical conidia, 8 to 12 μm long and 6 to 10 μm wide, were observed under light microscope. Isolate Pers-1, incubated at 21°C for 21 days, produced blackish, spherical to irregular microsclerotia, ranging from 0.55 to 4 mm (width and length, respectively). For molecular characterization of the Botrytis sp. isolate, Pers-1, fungal genomic DNA was extracted as previously described by Freeman et al. (2013). The internal transcribed spacer (ITS) sequence region of rDNA was amplified using ITS1/ITS4 primers (White et al. 1990), and sequenced. ITS analysis revealed that it belongs to genus Botrytis (MT573470.1 with 99.80% identity). For further confirmation, nuclear protein-coding genes (RPB2 and BT-1, Malkuset et al. 2006 and Glass et al. 1995) were sequenced and found to have 99.87% and 99.80% identity to Botrytis cinerea Pers. Sequences, deposited in GenBank as accessions OQ286390, OQ587946 and OQ409867, respectively. Botrytis was previously reported to cause persimmon fruit scarring and damage of calyces (Rheinländer et al. 2013) and fruit rot during post-harvest (Barkai-Golan. 2001), yet to the best of our knowledge, this is the first report of B. cinerea causing "star like" corky symptoms on persimmon in Israel.

Multilocus phylogeny and historical biogeography of theCrematogaster inflata-group (Hymenoptera: Formicidae) in South-East Asia

AbstractA recent molecular phylogeny of the genus Crematogaster reclassified some members of the former subgenera Paracrema and Physocrema into the C. inflata-group, now comprised of five species: C. ampullaris, C. inflata, C. modiglianii, C. onusta and C. subcircularis. Here, a molecular analysis of the Crematogaster inflata-group and eight other species of the former subgenus Physocrema (C. aurita, C. difformis, C. mucronata, C. physothorax, C. sewardi, C. tanakai, C. vacca and C. yamanei) is conducted using a total of c. 4 kb of sequence data from six nuclear protein-coding genes and two mitochondrial genes. Monophyly of the C. inflata-group is strongly supported. A revised morphological delineation of the subgroups is proposed, supported by the molecular phylogeny: three morphologically distinct subgroups, the C. difformis-subgroup, the C. vacca-subgroup and the C. inflata-subgroup. Molecular dating and biogeographical analyses indicate that the C. inflata-group originated in the Sundaic region around the Middle Miocene 12 Mya and diversified from the Late Miocene to Pliocene. Ancestral state reconstructions indicate that the C. inflata-group diversified from an ancestor with a swollen propodeum and circular-shaped metapleural gland opening. Biogeographical reconstruction indicates that dispersal to peripheral areas and allopatry due to sea-level changes shaped the evolutionary history of the C. inflata-group.

Appendage-Bearing Sordariomycetes from Dipterocarpus alatus Leaf Litter in Thailand.

Leaf litter is an essential functional aspect of forest ecosystems, acting as a source of organic matter, a protective layer in forest soils, and a nurturing habitat for micro- and macro-organisms. Through their successional occurrence, litter-inhabiting microfungi play a key role in litter decomposition and nutrient recycling. Despite their importance in terrestrial ecosystems and their abundance and diversity, information on the taxonomy, diversity, and host preference of these decomposer taxa is scarce. This study aims to clarify the taxonomy and phylogeny of four saprobic fungal taxa inhabiting Dipterocarpus alatus leaf litter. Leaf litter samples were collected from Doi Inthanon National Park in Chiang Mai, northern Thailand. Fungal isolates were characterized based on morphology and molecular phylogeny of the nuclear ribosomal DNA (ITS, LSU) and protein-coding genes (tub2, tef1-α, rpb2). One novel saprobic species, Ciliochorella dipterocarpi, and two new host records, Pestalotiopsis dracontomelon and Robillarda australiana, are introduced. The newly described taxa are compared with similar species, and comprehensive descriptions, micrographs, and phylogenetic trees are provided.

First phylogenetic analysis of the Nearctic madicolous midges of the genus Androprosopa Mik (Diptera: Thaumaleidae)

Molecular phylogenetic analyses were conducted to infer relationships between the eastern and western Nearctic Androprosopa Mik and amongst the considerably more diverse western Nearctic species. Fresh, molecular-grade material was obtained for all Nearctic Androprosopa species except two Mexican species, An. sonorensis (Arnaud & Boussy) and An. zempoala Sinclair & Huerta, that eluded capture. Molecular sequences from two nuclear protein-coding genes, big zinc finger (BZF) and molybdenum cofactor sulfurase (MCS), were sampled from representatives of several outgroup and ingroup taxa and analyzed phylogenetically using maximum likelihood criteria to confirm identifications of females and immatures using a barcoding approach, test species boundaries among morphologically similar species, and infer relationships among more morphologically disparate groups. Resulting phylogenies suggest the following with significant node (bootstrap) support: (1) the eastern Nearctic Androprosopa species form the sister group to the lineage comprised of all sampled Palearctic thaumaleids, i.e., An. larvata (Mik), An. striata (Okada), and Thaumalea testacea Ruthe; (2) the aforementioned lineage is the sister group to the clade comprised of western Nearctic Androprosopa species; (3) the western Nearctic Androprosopa species form three multispecies lineages, two of which can be further divided into three or more well founded species groups. Our results suggest that Androprosopa as currently defined is paraphyletic. Additionally, we propose several new species groups within the western Nearctic Androprosopa based on molecular and morphological data.

Geographical subdivision of Alviniconcha snail populations in the Indian Ocean hydrothermal vent regions

The hairy snails of the genusAlviniconchaare representative deep-sea hydrothermal vent animals distributed across the Western Pacific and Indian Ocean. Out of six known species in the genusAlviniconcha, only one nominal species ofA. marisindicawas found in the Indian Ocean from the Carlsberg Ridge (CR), Central Indian Ridge (CIR) to the northern part of Southwest Indian Ridge (SWIR) and Southeast Indian Ridge (SEIR). Recently, theAlviniconchasnails were found at three new vent fields, named Onnare, Onbada, and Onnuri, in the northern CIR, which promotes a more comprehensive phylogeographic study of this species. Here, we examined the phylogeography and connectivity of theAlviniconchasnails among seven vent fields representing the CR and CIR based on DNA sequence data of a mitochondrialCOIgene and two protein-coding nuclear genes. Phylogenetic inferences revealed that theAlviniconchasnails of the newly found in the northern CIR and two vent fields of Wocan and Tianxiu in the CR were divergent with the previously identifiedA. marisindicain the southern CIR and mitochondrialCOIdata supported the divergence with at least greater than 3% sequence divergence. Population structure analyses based on the three genetic markers detected a phylogeographic boundary between Onnuri and Solitaire that divides the whole snail populations into northern and southern groups with a low migration rate. The high degree of genetic disconnection around the ‘Onnuri’ boundary suggests that theAlviniconchasnails in the Indian Ocean may undergo allopatric speciation. The border may similarly act as a dispersal barrier to many other vent species co-distributed in the CIR. This study would expand understanding the speciation and connectivity of vent species in the Indian Ocean.

A high-quality reference genome for the fission yeast Schizosaccharomyces osmophilus.

Fission yeasts are an ancient group of fungal species that diverged from each other from tens to hundreds of million years ago. Among them is the preeminent model organism Schizosaccharomyces pombe, which has significantly contributed to our understandings of molecular mechanisms underlying fundamental cellular processes. The availability of the genomes of S. pombe and 3 other fission yeast species S. japonicus, S. octosporus, and S. cryophilus has enabled cross-species comparisons that provide insights into the evolution of genes, pathways, and genomes. Here, we performed genome sequencing on the type strain of the recently identified fission yeast species S. osmophilus and obtained a complete mitochondrial genome and a nuclear genome assembly with gaps only at rRNA gene arrays. A total of 5,098 protein-coding nuclear genes were annotated and orthologs for more than 95% of them were identified. Genome-based phylogenetic analysis showed that S. osmophilus is most closely related to S. octosporus and these 2 species diverged around 16 million years ago. To demonstrate the utility of this S. osmophilus reference genome, we conducted cross-species comparative analyses of centromeres, telomeres, transposons, the mating-type region, Cbp1 family proteins, and mitochondrial genomes. These analyses revealed conservation of repeat arrangements and sequence motifs in centromere cores, identified telomeric sequences composed of 2 types of repeats, delineated relationships among Tf1/sushi group retrotransposons, characterized the evolutionary origins and trajectories of Cbp1 family domesticated transposases, and discovered signs of interspecific transfer of 2 types of mitochondrial selfish elements.

The African endemic species “ Nychiodes” tyttha Prout, 1915 (Lepidoptera, Geometridae, Ennominae) belongs to the genus Aphilopota Warren, 1899

An extensive examination of the external and internal morphological characters of the genus Nychiodes shows that “Nychiodes” tyttha Prout, 1915 is incorrectly placed in this genus. The systematic position of this species was investigated by using a multigene analysis, including one mitochondrial and up to nine protein-coding nuclear gene regions, and morphological characters. These results support a re-classification of this species as Aphilopota tyttha, comb. nov. A re-description supported by illustrations of morphological characters for A. tyttha is provided.

Phylogenetic Relationships of the Strongyloid Nematodes of Australasian Marsupials Based on Mitochondrial Protein Sequences

Australasian marsupials harbour a diverse group of gastrointestinal strongyloid nematodes. These nematodes are currently grouped into two subfamilies, namely the Cloacininae and Phascolostrongylinae. Based on morphological criteria, the Cloacininae and Phascolostrongylinae were defined as monophyletic and placed in the family Cloacinidae, but this has not been supported by molecular data and they are currently placed in the Chabertiidae. Although molecular data (internal transcribed spacers of the nuclear ribosomal RNA genes or mitochondrial protein-coding genes) have been used to verify morphological classifications within the Cloacininae and Phascolostrongylinae, the phylogenetic relationships between the subfamilies have not been rigorously tested. This study determined the phylogenetic relationships of the subfamilies Cloacininae and Phascolostrongylinae using amino acid sequences conceptually translated from the twelve concatenated mitochondrial protein-coding genes. The findings demonstrated that the Cloacininae and Phascolostrongylinae formed a well-supported monophyletic assemblage, consistent with their morphological classification as an independent family, Cloacinidae. Unexpectedly, however, the subfamily Phascolostrongylinae was split into two groups comprising the genera from macropodid hosts (kangaroos and wallabies) and those from vombatid hosts (wombats). Genera of the Cloacininae and Phascolostrongylinae occurring in macropodid hosts were more closely related compared to genera of the Phascolostrongylinae occurring in wombats that formed a sister relationship with the remaining genera from macropods. These findings provide molecular evidence supporting the monophyly of the family Cloacinidae and an alternative hypothesis for the origin of marsupial strongyloid nematodes in vombatid hosts that requires further exploration using molecular approaches and additional samples.

Resolving the deep phylogeny: Implications for early adaptive radiation, cryptic, and present-day ecological diversity of Papuan microhylid frogs

The microhylid frogs of the New Guinea region are the largest and most ecologically diverse subfamily (Asterophryinae) of one of the largest anuran families in the world and can live in communities of up to 20 species. While there has been recent progress in resolving the phylogenetic relationships of Asterophryinae, significant uncertainties remain, impeding further progress in understanding the evolution of microhabitat use, parental care, and life history variation in this group. In particular, the early divergences at the base of the tree remain unclear; as does the monophyly of some genera; and recent studies have discovered that species with wide geographic distribution are instead cryptic species complexes. In this study, we fortified geographic sampling of the largest previous phylogenetic effort by sequencing an additional 62 taxa and increased data quality and quantity by adding new layers of data vetting and by filling in previously incomplete loci to the five gene dataset (2 mitochondrial, 3 nuclear protein-coding genes) to obtain a dataset that is now 99% complete in over 2400 characters for 233 samples (205 taxa) of Asterophryinae and 3 outgroup taxa, and analyzed microhabitat use data for these taxa from field data and data collected from the literature. Importantly, our sampling includes complete community complements at 19 sites as well as representatives at over 80 sites across New Guinea and its offshore islands. We present a highly resolved molecular phylogeny which, for the first time, has over 95% of nodes supported (84% highly supported) whether using Maximum Likelihood or Bayesian Inference, allowing clarification of all genera (whether monophyletic or clearly not), their sister genera relationships, as well as an age estimate for the Asterophryinae at approximately 20MYA. Early generic diversification occurring between 17 and 12 MYA gave rise to a surprising diversity of about 18 genera as well as the 5 putative microhabitat types. Our tree reveals extensive cryptic diversity calling any widespread taxa into doubt, and clearly demonstrates that complex multispecies communities of Asterophryinae are ecologically diverse, are numerous, and of ancient origin across New Guinea. We discuss the implications of our phylogeny for explaining the explosive diversification of Asterophryinae as the result of adaptive radiation, niche conservatism, and non-adaptive radiation.

A preliminary molecular phylogeny of the family Hydroptilidae (Trichoptera): an exploration of combined targeted enrichment data and legacy sequence data.

Hydroptilidae is an extremely diverse family within Trichoptera, containing over 2,600 known species, that displays a wide array of ecological, morphological, and habitat diversity. However, exploration into the evolutionary history of microcaddisflies based on current phylogenetic methods is mostly lacking. The purpose of this study is to provide a proof-of-concept that the use of molecular data, particularly targeted enrichment data, and statistically supported methods of analysis can result in the construction of a stable phylogenetic framework for the microcaddisflies. Here, a preliminary exploration of the hydroptilid phylogeny is presented using a combination of targeted enrichment data for ca. 300 nuclear protein-coding genes and legacy (Sanger-based) sequence data for the mitochondrial COI gene and partial sequence from the 28S rRNA gene.

Phylogenomic resolution of the root of Panpulmonata, a hyperdiverse radiation of gastropods: new insight into the evolution of air breathing.

Transitions to terrestriality have been associated with major animal radiations including land snails and slugs in Stylommatophora (>20 000 described species), the most successful lineage of 'pulmonates' (a non-monophyletic assemblage of air-breathing gastropods). However, phylogenomic studies have failed to robustly resolve relationships among traditional pulmonates and affiliated marine lineages that comprise clade Panpulmonata (Mollusca, Gastropoda), especially two key taxa: Sacoglossa, a group including photosynthetic sea slugs, and Siphonarioidea, intertidal limpet-like snails with a non-contractile pneumostome (narrow opening to a vascularized pallial cavity). To clarify the evolutionary history of the panpulmonate radiation, we performed phylogenomic analyses on datasets of up to 1160 nuclear protein-coding genes for 110 gastropods, including 40 new transcriptomes for Sacoglossa and Siphonarioidea. All 18 analyses recovered Sacoglossa as the sister group to a clade we named Pneumopulmonata, within which Siphonarioidea was sister to the remaining lineages in most analyses. Comparative modelling indicated shifts to marginal habitat (estuarine, mangrove and intertidal zones) preceded and accelerated the evolution of a pneumostome, present in the pneumopulmonate ancestor along with a one-sided plicate gill. These findings highlight key intermediate stages in the evolution of air-breathing snails, supporting the hypothesis that adaptation to marginal zones played an important role in major sea-to-land transitions.