DAMBE6: New Tools for Microbial Genomics, Phylogenetics, and Molecular Evolution

The complete mitochondrial genome of a jujube geometrid, Sucra jujuba (Lepidoptera: Geometridae) and its phylogenetic analysis

Sucra jujuba Chu, 1979 (Lepidoptera: Geometridae) is a major insect pest in jujube plantation. In this study, we have sequenced the complete mitochondrial genome of S. jujuba. The circular genome was 15,557 bp in length and contained 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and one AT-rich region (GenBank accession no. MZ507574). The nucleotide composition was significantly biased (A, T, C, and G were 41.85%, 39.65%, 10.97%, and 7.53%, respectively) with A + T contents of 81.50%. The Bayesian phylogenetic analysis of the concatenated nucleotide sequences of 13 PCGs from 30 species in the subfamily Ennominae and two outgroup species was performed. The results indicated that S. jujuba was closely related to Amraica recursaria in the subfamily Ennominae.

Congruent patterns of cryptic cladogenesis revealed using RADseq and Sanger sequencing in a velvet worm species complex (Onychophora: Peripatopsidae: Peripatopsis sedgwicki)

In the present study, first generation DNA sequencing (mitochondrial cytochrome c oxidase subunit one, COI) and reduced-representative genomic RADseq data were used to understand the patterns and processes of diversification of the velvet worm, Peripatopsis sedgwicki species complex across its distribution range in South Africa. For the RADseq data, three datasets (two primary and one supplementary) were generated corresponding to 1,259-11,468 SNPs, in order to assess the diversity and phylogeography of the species complex. Tree topologies for the two primary datasets were inferred using maximum likelihood and Bayesian inferences methods. Phylogenetic analyses using the COI datasets retrieved four distinct, well-supported clades within the species complex. Five species delimitation methods applied to the COI data (ASAP, bPTP, bGMYC, STACEY and iBPP) all showed support for the distinction of the Fort Fordyce Nature Reserve specimens. In the main P. sedgwicki species complex, the species delimitation methods revealed a variable number of operational taxonomic units and overestimated the number of putative taxa. Divergence time estimates coupled with the geographic exclusivity of species and phylogeographic results suggest recent cladogenesis during the Plio/Pleistocene. The RADseq data were subjected to a principal components analysis and a discriminant analysis of principal components, under a maximum-likelihood framework. The latter results corroborate the four main clades observed using the COI data, however, applying additional filtering revealed additional diversity. The high overall congruence observed between the RADseq data and COI data suggest that first generation sequence data remain a cheap and effective method for evolutionary studies, although RADseq does provide a far greater resolution of contemporary temporo-spatial patterns.

Discovery of Epichloë as novel endophytes of Psathyrostachys lanuginosa in China and their alkaloid profiling

The Epichloë genus represents a significant group of above-ground endophytes extensively researched for their potential applications in agriculture and ecology. Additionally, Epichloë species synthesize bioactive alkaloids, which generally cause health problems in livestock and have detrimental effects on the performance of insect herbivores. Psathyrostachys lanuginosa serves as a valuable forage grass for livestock owing to its high nutritional value and resilience in adverse environmental conditions. Nevertheless, to date, no reports have documented Epichloë as endophytes of P. lanuginosa. In this study, four strains (PF5, PF9, QG2, and QG4) were isolated and identified through morphological, molecular, and phylogenetic analyses as endophytes of P. lanuginosa. Morphological analysis indicated colony characteristics and conidia features consistent with symbiotic Epichloë, with no significant differences observed in growth rates or conidia dimensions among the four strains. Phylogenetic analysis confirmed all strains as E. bromicola. Additionally, alkaloid biosynthetic genes were detected, revealing differences in the potential synthesis of peramine and indole diterpenoid alkaloids among strains from different geographic origins. However, all four E. bromicola strains exhibited similar potential for synthesizing ergot alkaloids, but not loline alkaloids. Overall, this study identified P. lanuginosa as a novel host for E. bromicola and provided insights into the alkaloid profiles of these strains, laying a solid foundation for the scientific and rational utilization of Epichloë resources.

An integrative approach highlights the discrepancy in the genetic, phenotypic, and presumptive taxonomic structure of Phoxinus (Actinopterygii, Leuciscidae, Phoxininae) in Bulgaria

The present drainage network of Bulgaria is the result of a complex Neogene and Quaternary evolution. Karst, which has developed on 23% of the territory, further complicates the hydrological pattern. Fresh waters of Bulgaria drain into the Black Sea and the Aegean Sea basins and can be roughly divided into the Danube (Middle and Lower Danube), non-Danube Black Sea, East Aegean, and West Aegean hydrological regions. Phoxinus, a small leuciscid fish, has a mosaic distribution in all four of these regions, inhabiting small mountainous and semi-mountainous streams. Based on morphology, it was identified as three species, Phoxinus phoxinus in the Danube, Phoxinus strandjae in the non-Danube, and Phoxinus strymonicus in West Aegean region. Later, molecular data revealed Phoxinus csikii and Phoxinus lumaireul in the Middle Danube and P. csikii in the Lower Danube. Phoxinus has been the focus of many studies, showing a high molecular and morphological diversity, which is not entirely consistent with previous morphology-only-based taxonomic concepts. In this study, molecular (a mitochondrial marker and a nuclear marker) and morphological data from both historical and recently sampled collections were analysed to assess the applicability of the integrative approach in Phoxinus. The results showed a significant influence of the complex paleo- and recent hydrology on the currently observed genetic structure of the considered populations and species. Furthermore, the study also demonstrated a strong influence of phenotypic plasticity on the morphological analysis of Phoxinus and the lack of a clear differentiation between P. csikii and P. strandjae. A barcoded specimen was designated as neotype to fix the species named P. strandjae in the current taxonomic concept. Finally, a significant discordance between genetically delimited clades and phenotypic groups did not allow a proper delineation of the species distributed in Bulgaria, demonstrating that more molecular markers are needed for further taxonomic study of the Phoxinus complex.

Phylomitogenomics of two Neotropical species of long-legged crickets Endecous Saussure, 1878 (Orthoptera: Phalangopsidae)

Mitochondrial genomes have provided significant insights into the evolution of several insects. A typical mitogenome contains 37 genes, and variations in gene order can indicate evolutionary relationships between species. In this study, we have assembled the first complete mitogenomes of Endecous chape and E. onthophagus and analyzed the phylogenetic implications for the Gryllidea infraorder. We performed DNA extractions and genome sequencing for both Endecous species. Subsequently, we searched for raw data in the Sequence Read Archive (SRA) in NCBI. Using the SRA data, we assembled the partial mitogenome of Dianemobius nigrofasciatus and annotated the protein-coding genes (PCGs) for nine species. Phylogenomic relationships were reconstructed using Maximum Likelihood (ML) and Bayesian Inference (BI), utilizing the PCGs from 49 Gryllidea species. The mitogenome lengths of E. chape and E. onthophagus are 16,266 bp and 16,023 bp, respectively, while D. nigrofasciatus has a length of 15,359 bp. Our results indicate that species within the infraorder exhibit four types of gene order arrangements that align with their phylogenetic relationships. Both phylogenomic trees displayed strong support, and the ML corroborated with the literature. Gryllidea species have significantly contributed to various fields, and studying their mitogenomes can provide valuable insights into this infraorder evolution.

Differential Selection for Translation Efficiency Shapes Translation Machineries in Bacterial Species

Different bacterial species have dramatically different generation times, from 20-30 min in Escherichia coli to about two weeks in Mycobacterium leprae. The translation machinery in a cell needs to synthesize all proteins for a new cell in each generation. The three subprocesses of translation, i.e., initiation, elongation, and termination, are expected to be under stronger selection pressure to optimize in short-generation bacteria (SGB) such as Vibrio natriegens than in the long-generation Mycobacterium leprae. The initiation efficiency depends on the start codon decoded by the initiation tRNA, the optimal Shine-Dalgarno (SD) decoded by the anti-SD (aSD) sequence on small subunit rRNA, and the secondary structure that may embed the initiation signals and prevent them from being decoded. The elongation efficiency depends on the tRNA pool and codon usage. The termination efficiency in bacteria depends mainly on the nature of the stop codon and the nucleotide immediately downstream of the stop codon. By contrasting SGB with long-generation bacteria (LGB), we predict (1) SGB to have more ribosome RNA operons to produce ribosomes, and more tRNA genes for carrying amino acids to ribosomes, (2) SGB to have a higher percentage of genes using AUG as the start codon and UAA as the stop codon than LGB, (3) SGB to exhibit better codon and anticodon adaptation than LGB, and (4) SGB to have a weaker secondary structure near the translation initiation signals than LGB. These differences between SGB and LGB should be more pronounced in highly expressed genes than the rest of the genes. We present empirical evidence in support of these predictions.

New descriptions of the larval and pupal stages of Orthocladiusnitidoscutellatus and Psectrocladiusnevalis from Xizang, China (Diptera, Chironomidae)

Background

Tibetan Plateau is one of the most typical areas of biodiversity in the world because of its unique environmental and regional units, which breed unique biological communities and concentrate on many unique and rare wild animals and plants. Research on Chironomidae in the Tibetan Plateau is relatively weak. At present, the identification of Chironomidae species mainly depends on male adults, while identification of larvae and pupae is relatively difficult and there is less research on them.

New information

During the investigations of insect diversity in the Tibetan Plateau, larval and pupal stages of Orthocladiusnitidoscutellatus Lundström, 1915 and Psectrocladiusnevalis Akhrorov, 1977 were described and illustrated. Matching and identification of larval and pupal stages were based on DNA barcodes. Neighbour-joining trees were reconstructed, based on known Orthocladius and Psectrocladius COI DNA barcodes, respectively.

A review of Palaemonella (Decapoda: Caridea: Palaemonidae), with clarification of the taxonomic status of Cuapetes americanus, Eupontonia and Vir

The pantropical genus Palaemonella Dana, 1852 (Caridea: Palaemonidae) currently includes 27 species of free-living and symbiotic marine shrimps. The monophyly of Palaemonella with respect to several closely related genera, however, has been questioned by recent analyses. We tested the monophyly of Palaemonella based on multigene phylogenetic analysis and the genus was revealed to be a paraphyletic assemblage by inclusion of species of the genera Eupontonia Bruce, 1971 and Vir Holthuis, 1952, and two genetic lineages of the western Atlantic Cuapetes americanus (Kingsley, 1878). We recognise one of the latter lineages as the previously described Periclimenes rhizophorae Lebour, 1949. Eupontonia and Vir are synonymised with Palaemonella . We also transfer Cuapetes americanus and Periclimenes rhizophorae to Palaemonella . Species previously assigned to Vir were revised; V. colemani Bruce, 2003, V. orientalis (Dana, 1852), V. philippinensis Bruce & Svoboda, 1984 and V. smiti Fransen & Holthuis, 2007 are regarded as valid species of Palaemonella ; Vir longidactylus Marin, 2008 is synonymised with P. smiti ; and the status of V. euphyllius Marin & Anker, 2005 remains unresolved. Palaemonella is currently regarded as a taxon with variable states of two main diagnostic characters, i.e. the plesiomorphic mandibular palp (fully reduced in P. americana ) and the hepatic tooth (fully reduced in former species of Vir and Eupontonia - evidently due to symbiotic modes of life). ZooBank: urn:lsid:zoobank.org:pub:7EEBC655-7EDE-4E46-BCB2-2A3BA16ED7DD.

First Record of Comparative Plastid Genome Analysis and Phylogenetic Relationships among Corylopsis Siebold & Zucc. (Hamamelidaceae)

Corylopsis Siebold & Zucc. (Hamamelidaceae) is widely used as a horticultural plant and comprises approximately 25 species in East Asia. Molecular research is essential to distinguish Corylopsis species, which are morphologically similar. Molecular research has been conducted using a small number of genes but not in Corylopsis. Plastid genomes of Corylopsis species (Corylopsis gotoana, Corylopsis pauciflora, and Corylopsis sinensis) were sequenced using next-generation sequencing techniques. Repeats and nucleotide diversity that could be used as DNA markers were also investigated. A phylogenetic investigation was carried out using 79 protein-coding genes to infer the evolutionary relationships within the genus Corylopsis. By including new plastomes, the overall plastid genome structure of Corylopsis was similar. Simple sequence repeats of 73-106 SSRs were identified in the protein-coding genes of the plastid genomes, and 33-40 long repeat sequences were identified in the plastomes. The Pi value of the rpl33_rps18 region, an intergenic spacer, was the highest. Phylogenetic analysis demonstrated that Corylopsis is a monophyletic group and Loropetalum is closely related to Corylopsis. C. pauciflora, C. gotoana, and C. spicata formed a clade distributed in Japan, whereas C. sinensis, C. glandulifera, and C. velutina formed a clade that was distributed in China.

Isolation, characterization, and circulation sphere of a filovirus in fruit bats

Bats are associated with the circulation of most mammalian filoviruses (FiVs), with pathogenic ones frequently causing deadly hemorrhagic fevers in Africa. Divergent FiVs have been uncovered in Chinese bats, raising concerns about their threat to public health. Here, we describe a long-term surveillance to track bat FiVs at orchards, eventually resulting in the identification and isolation of a FiV, Dehong virus (DEHV), from Rousettus leschenaultii bats. DEHV has a typical filovirus-like morphology with a wide spectrum of cell tropism. Its entry into cells depends on the engagement of Niemann-Pick C1, and its replication is inhibited by remdesivir. DEHV has the largest genome size of filoviruses, with phylogenetic analysis placing it between the genera Dianlovirus and Orthomarburgvirus, suggesting its classification as the prototype of a new genus within the family Filoviridae. The continuous detection of viral RNA in the serological survey, together with the wide host distribution, has revealed that the region covering southern Yunnan, China, and bordering areas is a natural circulation sphere for bat FiVs. These emphasize the need for a better understanding of the pathogenicity and potential risk of FiVs in the region.

Mitogenomic Characterization and Phylogenetic Placement of African Hind, Cephalopholis taeniops: Shedding Light on the Evolution of Groupers (Serranidae: Epinephelinae)

The global exploration of evolutionary trends in groupers, based on mitogenomes, is currently underway. This research extensively investigates the structure of and variations in Cephalopholis species mitogenomes, along with their phylogenetic relationships, focusing specifically on Cephalopholis taeniops from the Eastern Atlantic Ocean. The generated mitogenome spans 16,572 base pairs and exhibits a gene order analogous to that of the ancestral teleost's, featuring 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an AT-rich control region. The mitogenome of C. taeniops displays an AT bias (54.99%), aligning with related species. The majority of PCGs in the mitogenome initiate with the start codon ATG, with the exceptions being COI (GTG) and atp6 (TTG). The relative synonymous codon usage analysis revealed the maximum abundance of leucine, proline, serine, and threonine. The nonsynonymous/synonymous ratios were <1, which indicates a strong negative selection among all PCGs of the Cephalopholis species. In C. taeniops, the prevalent transfer RNAs display conventional cloverleaf secondary structures, except for tRNA-serine (GCT), which lacks a dihydrouracil (DHU) stem. A comparative examination of conserved domains and sequence blocks across various Cephalopholis species indicates noteworthy variations in length and nucleotide diversity. Maximum likelihood, neighbor-joining, and Bayesian phylogenetic analyses, employing the concatenated PCGs and a combination of PCGs + rRNAs, distinctly separate all Cephalopholis species, including C. taeniops. Overall, these findings deepen our understanding of evolutionary relationships among serranid groupers, emphasizing the significance of structural considerations in mitogenomic analyses.

Across the highest mountain on earth: discordant phylogeographic patterns and recent dispersal of Tibetan stone loaches (Triplophysa) in the Himalayas

Phylogeographic congruence among co-distributed taxa is regarded as an inherent inference to vicariance events. Nonetheless, incongruent patterns of contemporary lineage divergence among taxa indicated that species differ in their response to common past events. To investigate the role of past events, ecological traits and lineage diversification time in shaping the contemporary phylogeographic patterns, comparative analyses were conducted for Tibetan stone loaches in the Himalayas using three gene markers and two ecological traits (depth of caudal peduncle in their length and presence/absence of posterior chamber of the air bladder). By a thorough sampling in two flanks of the Himalayas, the authors detected that phylogenetic breaks were spatially discordant and divergences of populations were also temporally asynchronous in co-distributed loaches. Estimated divergence time using fossil-calibrated node dating indicated that the Tibetan stone loaches colonised into the south flank of the Himalayas until the Pleistocene. The demographic expansions were also disconcerted between populations in north and south flanks, or east and west Himalayas. Ongoing gene flows between populations in north and south sides implied that the Himalayas do not strictly impede dispersal of cold-adapted species. The results highlight that the quaternary climatic oscillation, in conjunction with ecological traits and lineage diversification time, shaped contemporary phylogenetic patterns of stone loaches in the Himalayas and provide new insights into the biodiversity and composition of species in the Himalayas and surrounding region.

The Genome of Plasmodium gonderi: Insights into the Evolution of Human Malaria Parasites

Plasmodium species causing malaria in humans are not monophyletic, sharing common ancestors with nonhuman primate parasites. Plasmodium gonderi is one of the few known Plasmodium species infecting African old-world monkeys that are not found in apes. This study reports a de novo assembled P. gonderi genome with complete chromosomes. The P. gonderi genome shares codon usage, syntenic blocks, and other characteristics with the human parasites Plasmodium ovale s.l. and Plasmodium malariae, also of African origin, and the human parasite Plasmodium vivax and species found in nonhuman primates from Southeast Asia. Using phylogenetically aware methods, newly identified syntenic blocks were found enriched with conserved metabolic genes. Regions outside those blocks harbored genes encoding proteins involved in the vertebrate host-Plasmodium relationship undergoing faster evolution. Such genome architecture may have facilitated colonizing vertebrate hosts. Phylogenomic analyses estimated the common ancestor between P. vivax and an African ape parasite P. vivax-like, within the Asian nonhuman primates parasites clade. Time estimates incorporating P. gonderi placed the P. vivax and P. vivax-like common ancestor in the late Pleistocene, a time of active migration of hominids between Africa and Asia. Thus, phylogenomic and time-tree analyses are consistent with an Asian origin for P. vivax and an introduction of P. vivax-like into Africa. Unlike other studies, time estimates for the clade with Plasmodium falciparum, the most lethal human malaria parasite, coincide with their host species radiation, African hominids. Overall, the newly assembled genome presented here has the quality to support comparative genomic investigations in Plasmodium.

A multidisciplinary approach to tackling invasive species: barcoding, morphology, and metataxonomy of the leafhopper Arboridia adanae

The leafhopper genus Arboridia includes several species that feed on Vitis vinifera and cause leaf chlorosis. We report the first alien Arboridia infestation in Italy in 2021 in an Apulian vineyard. To confirm the taxonomic status of the species responsible for crop damage, and reconstruct its demographic history, we barcoded individuals from Apulia together with Arboridia spp. from Crete (Greece), A. adanae from Central Turkey and other specimens of the presumed sister species, A. dalmatina from Dalmatia (Croatia). Molecular phylogenies and barcoding gap analysis identified clades not associated with sampling locations. This result is incongruent with classical specimen assignment and is further supported by morphological analyses, which did not reveal significant differences among the populations. Therefore, we propose A. dalmatina as a junior synonym of A. adanae, which would become the only grapevine-related Arboridia species in the eastern Mediterranean. To further characterise A. adanae evolution, we performed a molecular clock analysis that suggested a radiation during the Pleistocene glaciations. Finally, to assess whether the Apulian individuals carried microorganisms of agricultural relevance, we sequenced their bacterial microbiota using 16S rRNA amplicon sequencing identifying three phytopathogens not generally associated with Arboridia activities as well as Wolbachia in one Apulian haplogroup. We discuss the agricultural implications of this infestation.

Molecular delimitation methods validate morphologically similar species of red snappers (Perciformes: Lutjanidae)

In this study, we tested the taxonomic validation of red snappers species (Southern red snapper Lutjanus purpureus; Silk snapper L. vivanus; Blackfin snapper L. buccanella; and Pacific red snapper L. peru) based on comparative analysis, using four methods for species delimitation. These methods were based on either genetic similarity or phylogenetic trees inferred from two mitochondrial (Cytochrome b and D-loop) and two nuclear (Myostatin and S7 introns) markers. On one hand, the genetic results corroborated the presence of four red snapper species, confirming their taxonomic validation despite their remarkable morphological similarity. On the other hand, few incongruencies in the species delimitation methods were observed according to the phylogenetic reconstruction method (maximum likelihood or Bayesian inference) when using. Based on the phylogenetic results, L. buccanella should represent a more ancient lineage in relation to the clade that encompasses L. purpureus, L. peru and L. vivanus. The single-locus phylogenetic analysis based on Cytb recovered each the red snapper species as a well-supported clade. Overall, this study provided a DNA-based validation of the traditional morphological taxonomy of red snappers.

Comparative analysis of mitogenomes among three species of grasshoppers (Orthoptera: Acridoidea: Gomphocerinae) and their phylogenetic implications

Whole mitochondrial genomes have been widely used in phylogenetic analysis, population genetics and biogeography studies. This study sequenced and characterized three complete mitochondrial genomes (Dasyhippus peipingensis, Myrmeleotettix palpalis, Aeropedellus prominemarginis) and determined their phylogenetic position in Acrididae. The length of the mitochondrial genomes ranged from 15,621-15,629 bp and composed of 13 PCGs, 2 rRNA, 22 tRNA genes and an AT control region. The arrangement and structure of the mitochondrial genomes were similar to those of other invertebrates. Comparative genomics revealed that the three mitochondrial genomes were highly conserved in terms of gene size, structure, and codon usage, all PCGs were purified selections with an ATN start codon and a TAN stop codon. All tRNAs could be folded into the typical clover-leaf structure, except tRNA Ser (AGN) that lacked a dihydrouridine (DHU) arm. Phylogenetic analysis based on 13 PCGs of 34 Acrididae species and seven outgroup species revealed that differences in the shape of antennae within the family Acrididae should be given less weight as a taxonomic character for higher-level classification. Moreover, the divergence time estimates indicates that in Gomphocerinae, the species with clubbed antennae were formed within the nearest 18 Mya, and Pacris xizangensis is more ancient.

Pleistocene Landscape Dynamics Drives Lineage Divergence of a Temperate Freshwater Fish Gobio rivuloides in Coastal Drainages of Northern China

Understanding historical processes underlying lineage distribution patterns is a primary goal of phylogeography. We selected Gobio rivuloides (Cypriniformes: Gobionidae) as a model to improve our knowledge about how intraspecific genetic divergence of freshwater fishes arises in coastal drainages of northern China via statistical analysis using cytochrome b gene. The time-calibrated phylogeny of G. rivuloides showed the divergence of two major lineages (I and II) at ~0.98 Ma (million years ago). Lineage I can be divided into two sub-lineages (I-A and I-B) with a divergence time of ~0.83 Ma. Sub-lineage I-A inhabits the Amur River, and sub-lineage I-B lives in the Luan River and Liao River. Lineage II is distributed in the Yellow River and Hai River, with close genetic relationships between the two drainages, and can be split into two sub-lineages (II-C and II-D) with a divergence time of ~0.60 Ma. Our findings indicate that the splitting of lineages and sub-lineages could be attributed to geographic isolation caused by the formation of the Bohai Sea, river capture, and the episodic hydrologic closing of a paleolake during the late Lower-Middle Pleistocene. It is also the first report we know of displaying a clear phylogeographic break for freshwater fishes across coastal drainages in northern China.

Comparative analysis of the mitochondrial genomes of the family Mactridae (Mollusca: Venerida) and their phylogenetic implications

Taxonomy and phylogenetic relationships within the family Mactridae have remained debatable because of the plasticity of morphological characteristics and the lack of accurate molecular data, thereby resulting in abundant synonyms and taxa rearrangements. Mitochondrial genomes (mitogenomes) have been widely used as powerful tools to reconstruct phylogenies of various groups of mollusks; however, they have not been used for studying the phylogeny of mactrids specifically. In the present study, mitogenomes of seven Mactridae species, namely Mactra chinensis, Mactra cygnus, Mactra quadrangularis, Mactra cumingii, Mactrinula dolabrata, Raeta pulchella, and Raeta sp., were sequenced by Illumina high-throughput sequencing, and a comparative mitochondrial genomic analysis was conducted. The newly sequenced mitogenomes were double-stranded circular molecules, with all functional genes encoded on the heavy strand. All the new mactrid mitogenomes had two rRNA genes (12S and 16S), 13 protein-coding genes (PCGs) (atp6, cox1, cox2, cox3, cytb, nad1, nad2, nad3, nad4, nad4l, nad5, nad6, and atp8), and 22 tRNAs. The mitogenomes showed considerable variation in AT content, GC skew, and AT skew. The results of the phylogenetic analysis confirmed monophyly of the family Mactridae and suggested that genera Mactrinula, Spisula, Rangia, and Mulinia should not be placed under subfamily Mactrinae. Our results supported that potential cryptic species existed in Mactra antiquata. We also proposed subfamily Kymatoxinae should belong to the family Mactridae rather than Anatinellidae and Mactra alta in China should be Mactra cygnus. Additionally, conservation in functional gene arrangement was found in genera Mactra, Raeta, and Lutraria. But gene orders in S. sachalinensis and S. solida were quite different, questioning their congeneric relationship. Our results further suggested that the taxonomy within the family Mactridae requires an integrative revision.

Bradyrhizobium xenonodulans sp. nov. isolated from nodules of Australian Acacia species invasive to South Africa

A genealogical concordance approach was used to delineate strains isolated from Acacia dealbata and Acacia mearnsii root nodules in South Africa. These isolates form part of Bradyrhizobium based on 16S rRNA sequence similarity. Phylogenetic analysis of six housekeeping genes (atpD, dnaK, glnII, gyrB, recA and rpoB) confirmed that these isolates represent a novel species, while pairwise average nucleotide identity (ANIb) calculations with the closest type strains (B. cosmicum 58S1T, B. betae PL7HG1T, B. ganzhouense CCBAU 51670 T, B. cytisi CTAW11T and B. rifense CTAW71T) resulted in values well below 95-96%. We further performed phenotypic tests which revealed that there are high levels of intraspecies variation, while an additional analysis of the nodA and nifD loci indicated that the symbiotic loci of the strains are closely related to those of Bradyrhizobium isolates with an Australian origin. Strain 14ABT (=LMG 31415 T = SARCC-753 T) is designated as the type strain of the novel species for which we propose the name Bradyrhizobium xenonodulans sp. nov.

Two new species of the genus Laena (Coleoptera, Tenebrionidae, Lagriinae) from northern Sichuan in China based on morphological and molecular data

In this study, the Laena species from northern Sichuan Province were reviewed using a combination of molecular and morphological datasets. Three molecular methods for species delimitation were firstly used in the genus Laena to explore species boundaries. The results show that the number of morphospecies and putative species using Automatic Barcode Gap Discovery (ABGD) is consistent. Based on the results, two new species are described and illustrated: Laenamounigouicasp. nov. and Laenadentithoraxasp. nov. New materials and distribution of 10 Laena species are also provided in this study. This work also provides valuable molecular data for species identification and phylogenetic analyses of the genus Laena and subfamily Lagriinae.

Molecular Phylogeny and Evolution of the Tuerkayana (Decapoda: Brachyura: Gecarcinidae) Genus Based on Whole Mitochondrial Genome Sequences

Tuerkayana is of particular interest because it has been separated, in recent years, from Cardisoma and Discoplax but studies of its taxonomic status, especially from a whole mitochondrial genome perspective, have been lacking. In this study, the mitogenomes of four species (Tuerkayana magnum, Tuerkayana rotundum, Tuerkayana hirtipes, and Tuerkayana celeste) of Tuerkayana are sequenced and contrasted with other species in Brachyura for the first time. The phylogenetic tree of Brachyura, which includes 206 crab species (189 species of Brachyuran and 17 Anomura species) with a complete mitogenome, was constructed to evaluate the phylogenetic position of Tuerkayana and Gecarcinidae within Brachyuran, and explore the monophyly of Gecarcinidae. Furthermore, two single gene trees based on cox1 and 16SrRNA separately within interspecies of Gecarcinidae were reconstructed, providing molecular evidence for Tuerkayana and further clarifying the division of genera in Gecarcinidae. Based on the mitogenome dataset of 206 crabs, the branch-site model was utilized to explore selective pressure in individual codons with CodeML. The strong selective pressure shown in nad6 indicates that it may have played a significant role in the evolution of Gecarcinidae.

The Complete Mitochondrial Genome and Phylogenetic Analyses of To Chicken in Vietnam

Indigenous chicken breeds have both cultural significance and economic value since they possess unique genetic characteristics that enable them to adapt to the local environment and contribute to biodiversity, food security, and sustainable agriculture in Vietnam. To (Tò in Vietnamese) chicken, a Vietnamese indigenous chicken breed, is popularly raised in Thai Binh province; however, little known is about the genetic diversity of this breed. In this study, we sequenced the complete mitochondrial genome of To chicken for a better understanding of the diversity and origin of the breed. The results of sequencing showed that the mitochondrial genome of To chicken spans a total length of 16,784 base pairs and comprises one non-coding control region (known as the displacement-loop (D-loop) region), two ribosomal RNA genes, 13 protein-coding genes, and 22 transfer RNA genes. The phylogenetic tree analyses and estimated genetic distances based on 31 complete mitochondrial genome sequences indicated that To chicken has a close genetic distance with the Laotian native chicken breed, Lv'erwu breed in China, and Nicobari black and Kadaknath breeds in India. The result of the current study might be important for conservation, breeding, and further genetic studies of To chicken.

Diversification of the African legless skinks in the subfamily Acontinae (Family Scincidae)

Cladogenic diversification is often explained by referring to climatic oscillations and geomorphic shifts that cause allopatric speciation. In this regard, southern Africa retains a high level of landscape heterogeneity in vegetation, geology, and rainfall patterns. The legless skink subfamily Acontinae occurs broadly across the southern African subcontinent and therefore provides an ideal model group for investigating biogeographic patterns associated with the region. A robust phylogenetic study of the Acontinae with comprehensive coverage and adequate sampling of each taxon has been lacking up until now, resulting in unresolved questions regarding the subfamily's biogeography and evolution. In this study, we used multi-locus genetic markers (three mitochondrial and two nuclear) with comprehensive taxon coverage (all currently recognized Acontinae species) and adequate sampling (multiple specimens for most taxa) of each taxon to infer a phylogeny for the subfamily. The phylogeny retrieved four well-supported clades in Acontias and supported the monophyly of Typhlosaurus. Following the General Lineage Concept (GLC), many long-standing phylogenetic enigmas within Acontias occidentalis and the A. kgalagadi, A. lineatus and A. meleagris species complexes, and within Typhlosaurus were resolved. Our species delimitation analyses suggest the existence of hidden taxa in the A. occidentalis, A. cregoi and A. meleagris species groups, but also suggest that some currently recognized species in the A. lineatus and A. meleagris species groups, and within Typhlosaurus, should be synonymised. We also possibly encountered "ghost introgression" in A. occidentalis. Our inferred species tree revealed a signal of gene flow, which implies possible cross-over in some groups. Fossil evidence calibration dating results showed that the divergence between Typhlosaurus and Acontias was likely influenced by cooling and increasing aridity along the southwest coast in the mid-Oligocene caused by the opening of the Drake Passage. Further cladogenesis observed in Typhlosaurus and Acontias was likely influenced by Miocene cooling, expansion of open habitat, uplifting of the eastern Great Escarpment (GE), and variation in rainfall patterns, together with the effect of the warm Agulhas Current since the early Miocene, the development of the cold Benguela Current since the late Miocene, and their co-effects. The biogeographic pattern of the Acontinae bears close resemblance to that of other herpetofauna (e.g., rain frogs and African vipers) in southern Africa.

Conservation Genetics of the Critically Endangered Southern River Terrapin (Batagur affinis) in Malaysia: Genetic Diversity and Novel Subspecies Distribution Ranges

A population genetics study was carried out on the Southern River terrapin (Batagur affinis) from four places in Peninsular Malaysia: Pasir Gajah, Kemaman (KE), Terengganu; Bukit Pinang (BP), Kedah; Bota Kanan (BK), Perak; and Bukit Paloh, Kuala Berang (KB), Terengganu. The goal of this study is to identify genetic differences in two subspecies of B. affinis in Malaysia. No previous reports were available on the genetic diversity, phylogenetic relationships and matrilineal hereditary structure of these terrapin populations in Malaysia. The sequencing identified 46 single nucleotide polymorphisms that defined six mitochondrial haplotypes in the Southern River terrapins. Tajima’s D test and Fu’s Fs neutrality tests were performed to evaluate the signatures of recent historical demographic events. Based on the tests, the B. affinis edwardmolli was newly subspecies identified in the west coast–northern region of Kedah state. In addition, the B. affinis edwardmolli in Bukit Paloh, Kuala Berang (KB), Terengganu (Population 4), was shown to have a single maternal lineage compared to other populations. Low genetic diversity, but significant genetic differences, were detected among the studied Southern River terrapin populations.

New species, a new combination, and DNA barcodes of Parachironomus Lenz, 1921 (Diptera, Chironomidae)

The genus Parachironomus has a cosmopolitan distribution including 85 valid described species worldwide. Species records and studies of the genus in the Tibetan Plateau are scarce. In this study, the genus Parachironomus from China is revised and two new species, Parachironomus wangi Liu & Lin, sp. nov. and Parachironomus nankaiensis Liu & Lin, sp. nov., are described based on adult morphology and molecular data. Paracladopelma demissum Yan, Wang & Bu is placed in the genus Parachironomus as a new combination. A neighbor-joining tree was reconstructed based on all known ParachironomusCOI DNA barcodes. A key to adult males of the genus Parachironomus from China is also provided.

Diversity and Endemism of Southern African Gekkonids Linked with the Escarpment Has Implications for Conservation Priorities

South Africa is recognised for its high reptile diversity and endemism, specifically among lizards. Phylogenetic diversity, endemism, and richness can have clear implications or raise important questions in a range of fields, and most urgently in conservation. Among squamate reptiles, these indices are very commonly associated with high temperatures and topographic heterogeneity. Indeed, mountainous biogeography has been a critical driver in the radiation of the family Gekkonidae within the subregion. Here, we assess the species richness, diversity, and endemism of Gekkonidae species inhabiting South Africa, Lesotho, and Eswatini, accounting for phylogenetic relationships. We also employ the CANAPE method to identify regions that have neo- and/or paleoendemics. Southern African gekkonids appear to be most diverse and show high levels of endemism in three regions of Southern Africa: the northwestern Richtersveld, the escarpment running west to southeast, and the northeastern escarpment in the Limpopo province. Implications for conservation priorities are discussed.

Conflicts in Mitochondrial Phylogenomics of Branchiopoda, with the First Complete Mitogenome of Laevicaudata (Crustacea: Branchiopoda)

Conflicting phylogenetic signals are pervasive across genomes. The potential impact of such systematic biases may be reduced by phylogenetic approaches accommodating for heterogeneity or by the exclusive use of homoplastic sites in the datasets. Here, we present the complete mitogenome of Lynceus grossipedia as the first representative of the suborder Laevicaudata. We employed a phylogenomic approach on the mitogenomic datasets representing all major branchiopod groups to identify the presence of conflicts and concordance across the phylogeny. We found pervasive phylogenetic conflicts at the base of Diplostraca. The homogeneity of the substitution pattern tests and posterior predictive tests revealed a high degree of compositional heterogeneity among branchiopod mitogenomes at both the nucleotide and amino acid levels, which biased the phylogenetic inference. Our results suggest that Laevicaudata as the basal clade of Phyllopoda was most likely an artifact caused by compositional heterogeneity and conflicting phylogenetic signal. We demonstrated that the exclusive use of homoplastic site methods combining the application of site-heterogeneous models produced correct phylogenetic estimates of the higher-level relationships among branchiopods.

First mitochondrial genome of subfamily Julodinae (Coleoptera, Buprestidae) with its phylogenetic implications

Complete mitochondrial genomes of three species of the family Buprestidae were sequenced, annotated, and analyzed in this study. To explore the mitogenome features of the subfamily Julodinae and verify its phylogenetic position, the complete mitogenome of Julodisvariolaris was sequenced and annotated. The complete mitogenomes of Ptosimachinensis and Chalcophorajaponica were also provided for the phylogenetic analyses within Buprestidae. Compared to the known mitogenomes of Buprestidae species varied from 15,499 bp to 16,771 bp in length, three newly sequenced mitogenomes were medium length (15,759-16,227 bp). These mitogenomes were encoded 37 typical mitochondrial genes. Among the three studied mitogenomes, Leu2 (L2), Ser2 (S2), and Pro (P) were the three most frequently encoded amino acids. Within the Buprestidae, the heterogeneity in sequence divergences of Agrilinae was highest, whereas the sequence homogeneity of Chrysochroinae was highest. Moreover, phylogenetic analyses were performed based on nucleotide matrix (13 PCGs + 2 rRNAs) among the available sequenced species of Buprestidae using Bayesian Inference and Maximum Likelihood methods. The results showed that the Julodinae was closely related to the subfamily Polycestinae. Meanwhile, the genera Melanophila, Dicerca, and Coomaniella were included in Buprestinae, which was inconsistent with the current classification system of Buprestidae. These results could contribute to further studies on genetic diversity and phylogeny of Buprestidae.

Cryptic diversity in Zoraptera: Latinozoros barberi (Gurney, 1938) is a complex of at least three species (Zoraptera: Spiralizoridae)

The order Zoraptera contains relatively few species, but current molecular phylogenetic studies suggest an unexpectedly high level of cryptic diversity in the order with many overlooked species based on morphology alone. Latinozoros Kukalova-Peck & Peck, 1993 represents the only genus of monotypic Latinozorinae (Zoraptera: Spiralizoridae) with only one species described, L. barberi (Gurney, 1938), until now. Although this species has been repeatedly reported from a number of locations in South and Central America, it is likely a complex of unrecognized species. Here, we present a molecular phylogenetic reconstruction revealing three genetically distinct lineages in Latinozoros, and we also present detailed morphological comparisons that prove the species status of Latinozoros cacaoensis sp. nov. from French Guiana and L. gimmeli sp. nov. from the Dominican Republic, Trinidad and Panama. The results indicate that the species previously referred to L. barberi is actually a species complex that includes L. barberi, the new species described here, and perhaps other species.

Comparison of chloroplast genomes and phylogenomics in the Ficus sarmentosa complex (Moraceae)

Due to maternal inheritance and minimal rearrangement, the chloroplast genome is an important genetic resource for evolutionary studies. However, the evolutionary dynamics and phylogenetic performance of chloroplast genomes in closely related species are poorly characterized, particularly in taxonomically complex and species-rich groups. The taxonomically unresolved Ficus sarmentosa species complex (Moraceae) comprises approximately 20 taxa with unclear genetic background. In this study, we explored the evolutionary dynamics, hotspot loci, and phylogenetic performance of thirteen chloroplast genomes (including eleven newly obtained and two downloaded from NCBI) representing the F. sarmentosa complex. Their sequence lengths, IR boundaries, repeat sequences, and codon usage were compared. Both sequence length and IR boundaries were found to be highly conserved. All four categories of long repeat sequences were found across all 13 chloroplast genomes, with palindromic and forward sequences being the most common. The number of simple sequence repeat (SSR) loci varied from 175 (F. dinganensis and F. howii) to 190 (F. polynervis), with the dinucleotide motif appearing the most frequently. Relative synonymous codon usage (RSCU) analysis indicated that codons ending with A/T were prior to those ending with C/T. The majority of coding sequence regions were found to have undergone negative selection with the exception of ten genes (accD, clpP, ndhK, rbcL, rpl20, rpl22, rpl23, rpoC1, rps15, and rps4) which exhibited potential positive selective signatures. Five hypervariable genic regions (rps15, ycf1, rpoA, ndhF, and rpl22) and five hypervariable intergenic regions (trnH-GUG-psbA, rpl32-trnL-UAG, psbZ-trnG-GCC, trnK-UUU-rps16 and ndhF-rpl32) were identified. Overall, phylogenomic analysis based on 123 Ficus chloroplast genomes showed promise for studying the evolutionary relationships in Ficus, despite cyto-nuclear discordance. Furthermore, based on the phylogenetic performance of the F. sarmentosa complex and F. auriculata complex, the chloroplast genome also exhibited a promising phylogenetic resolution in closely related species.

Genomic Characterization of hox Genes in Senegalese Sole (Solea senegalensis, Kaup 1858): Clues to Evolutionary Path in Pleuronectiformes

The Senegalese sole (Solea senegalensis, Kaup 1858), a marine flatfish, belongs to the Pleuronectiformes order. It is a commercially important species for fisheries and aquaculture. However, in aquaculture, several production bottlenecks have still to be resolved, including skeletal deformities and high mortality during the larval and juvenile phase. The study aims to characterize the hox gene clusters in S. senegalensis to understand better the developmental and metamorphosis process in this species. Using a BAC library, the clones that contain hox genes were isolated, sequenced by NGS and used as BAC-FISH probes. Subsequently the hox clusters were studied by sequence analysis, comparative genomics, and cytogenetic and phylogenetic analysis. Cytogenetic analysis demonstrated the localization of four BAC clones on chromosome pairs 4, 12, 13, and 16 of the Senegalese sole cytogenomic map. Comparative and phylogenetic analysis showed a highly conserved organization in each cluster and different phylogenetic clustering in each hox cluster. Analysis of structural and repetitive sequences revealed accumulations of polymorphisms mediated by repetitive elements in the hoxba cluster, mainly retroelements. Therefore, a possible loss of the hoxb7a gene can be established in the Pleuronectiformes lineage. This work allows the organization and regulation of hox clusters to be understood, and is a good base for further studies of expression patterns.

Testing alternative hypotheses on the origin and speciation of Hawaiian katydids

Background

Hawaiian Islands offer a unique and dynamic evolutionary theatre for studying origin and speciation as the islands themselves sequentially formed by erupting undersea volcanos, which would subsequently become dormant and extinct. Such dynamics have not been used to resolve the controversy surrounding the origin and speciation of Hawaiian katydids in the genus Banza, whose ancestor could be from either the Old-World genera Ruspolia and Euconocephalus, or the New World Neoconocephalus. To address this question, we performed a chronophylogeographic analysis of Banza species together with close relatives from the Old and New Worlds.

Results

Based on extensive dated phylogeographic analyses of two mitochondrial genes (COX1 and CYTB), we show that our data are consistent with the interpretation that extant Banza species resulted from two colonization events, both by katydids from the Old World rather than from the New World. The first event was by an ancestral lineage of Euconocephalus about 6 million years ago (mya) after the formation of Nihoa about 7.3 mya, giving rise to B. nihoa. The second colonization event was by a sister lineage of Ruspolia dubia. The dating result suggests that this ancestral lineage first colonized an older island in the Hawaiian–Emperor seamount chain before the emergence of Hawaii Islands, but colonized Kauai after its emergence in 5.8 mya. This second colonization gave rise to the rest of the Banza species in two major lineages, one on the older northwestern islands, and the other on the newer southwestern islands.

Conclusion

Chronophylogeographic analyses with well-sampled taxa proved crucial for resolving phylogeographic controversies on the origin and evolution of species colonizing a new environment.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-02037-2.

One-way ticket to the blue: A large-scale, dated phylogeny revealed asymmetric land-to-water transitions in acariform mites (Acari: Acariformes)

Acariform mites are an ancient and megadiverse lineage that may have experienced a complex pattern of invasions into terrestrial and aquatic habitats. These among-realm transitions may relate to periods of turmoil in Earth's history or be simply results of uneven biodiversity patterns across habitats. Here, we inferred a dated, representative acariform phylogeny (five genes, 9,200 bp aligned, 367 terminals belonging to 150 ingroup plus 15 outgroup families, 23 fossil calibration points) which was used to infer transitions between marine/freshwater/terrestrial habitats. We detected four unambiguous transitions from terrestrial to freshwater habitats (Hydrozetes, Naiadacarus, Fusohericia, Afronothrus, Homocaligus); one from freshwater to marine (Pontarachnidae), and four from marine to brackish or freshwater transitions (all among Halacaridae: Acarothrix; Halacarellus petiti; Copidognathus sp.; clade Limnohalacarus + Soldanellonyx + Porohalacarus + Porolohmannella). One transition to the sea was inferred ambiguously with respect to the ancestor being either terrestrial or freshwater (Hyadesiidae), and another must be most carefully examined by adding potential related taxa (Selenoribatidae + Fortuyniidae). Finally, we inferred a single, remarkable transition from aquatic to terrestrial habitats involving early evolution of the large and ecologically diverse lineage: the ancestor of the Halacaridae + Parasitengona clade was probably freshwater given our dataset, thus making terrestrial Parasitengona secondarily terrestrial. Overall, our results suggested a strong asymmetry in environmental transitions: the majority occurred from terrestrial to aquatic habitats. This asymmetry is probably linked to mites' biological properties and uneven biodiversity patterns across habitats rather than Earth's geological history. Since the land holds more acariform diversity than water habitats, a shift from the former is more likely than from the latter. We inferred the following relationships: alicid endeostigmatid + eriophyoid (Alycidae, (Nanorchestidae, (Nematalycidae, Eriophyoidea))) being sister group to the remaining Acariformes: (proteonematalycid Endeostigmata, alicorhagiid Endeostigmata, Trombidiformes, Oribatida (including Astigmata)). Trombidiform relationships had several novel rearrangements: (i) traditional Eupodina lacked support for the inclusion of Bdelloidea; (ii) Teneriffidae, traditionally placed among Anystina, was consistently recovered in a clade including Heterostigmata in Eleutherengona; (iii) several lineages, such as Adamystidae, Paratydeidae, Caeculidae and Erythracaridae, were recovered in a large clade along other Anystina and Eleutherengona, suggesting single origins of several fundamental character states, such as the reduction of the cheliceral fixed digit and development of the palpal thumb-claw complex.

Phylogenetic Analyses Support the Monophyly of the Genus Lispe Latreille (Diptera: Muscidae) with Insights into Intrageneric Relationships

Lispe Latreille (Diptera: Muscidae) are a widespread group of predatory flies that inhabit semi-aquatic environments. Previous studies on this genus have mainly focused on morphological classification, so molecular data are entirely lacking, and there has been no attempt at a phylogenetic placement of the genus or the resolution of intragenic relationships. To address the phylogenetic placement of Lispe and to fill its gap in the Tree of Life Web Project, 58 Lispe spp. (covering 11 out of 13 acknowledged Lispe species groups) were selected to reconstruct a phylogeny using Maximum likelihood (ML) estimates, Maximum Parsimony (MP) analyses, and Bayesian inference (BI) based on two mitochondrial protein-coding genes (cytochrome c oxidase subunit I (COXI) and cytochrome b gene (CYTB)) and one nuclear gene (a fragment of the carbamoyl phosphate synthetase region of the CAD gene). The phylogenetic analyses indicated that the monophyletic Lispe is the sister group of the monophyletic Limnophora, together forming the tribe Limnophorini under the subfamily Coenosiinae. Three generic categories are proven obsolete: Chaetolispa Malloch, Lispacoenosia Snyder, and Xenolispa Malloch. Within the genus, the validity of 11 species groups is clarified by both molecular and morphological data. This study provides a sound basis for continuing intergeneric and intrageneric research into this fascinating and widespread genus.

MORPHOLOGICAL AND GENETIC CHARACTERIZATION OF DIDELPHONEMA LONGISPICULATA (NEMATODA: SPIRUROIDEA) IN THE BLACK-EARED OPOSSUM DIDELPHIS MARSUPIALIS

Didelphonema longispiculata (Hill, 1939), a gastric nematode parasite of the black-eared opossum, Didelphis marsupialis Linnaeus, 1758, collected from 2 municipalities of Mato Grosso state, Brazil, in the ecotone region of the Amazon and Cerrado biomes was analyzed with integrative taxonomy using light and scanning electron microscopy (SEM) for morphological studies and sequencing of the 18S small subunit ribosomal RNA for phylogenetic inference through maximum likelihood and Bayesian phylogenetic inference. Here details of the helminth surface, oral aperture with octagonal border, pseudo- and inter-labia, amphids, external cephalic papillae, 2 dorsal and ventral internal plates distally indented, and stoma with strongly chitinized wall are presented. Caudal male papillae, spicules, female vulva, anus, and caudal tip were detailed using SEM. Morphological characteristics and phylogenetic data corroborated the taxonomic placement of the genus Didelphonema within the subfamily Ascaropsinae.

Evolution and codon usage bias of mitochondrial and nuclear genomes in Aspergillus section Flavi

The fungal genus Aspergillus contains a diversity of species divided into taxonomic sections of closely related species. Section Flavi contains 33 species, many of industrial, agricultural, or medical relevance. Here, we analyze the mitochondrial genomes (mitogenomes) of 20 Flavi species-including 18 newly assembled mitogenomes-and compare their evolutionary history and codon usage bias patterns to their nuclear counterparts. Codon usage bias refers to variable frequencies of synonymous codons in coding DNA and is shaped by a balance of neutral processes and natural selection. All mitogenomes were circular DNA molecules with highly conserved gene content and order. As expected, genomic content, including GC content, and genome size differed greatly between mitochondrial and nuclear genomes. Phylogenetic analysis based on 14 concatenated mitochondrial genes predicted evolutionary relationships largely consistent with those predicted by a phylogeny constructed from 2,422 nuclear genes. Comparing similarities in interspecies patterns of codon usage bias between mitochondrial and nuclear genomes showed that species grouped differently by patterns of codon usage bias depending on whether analyses were performed using mitochondrial or nuclear relative synonymous usage values. We found that patterns of codon usage bias at gene level are more similar between mitogenomes of different species than the mitogenome and nuclear genome of the same species. Finally, we inferred that, although most genes-both nuclear and mitochondrial-deviated from the neutral expectation for codon usage, mitogenomes were not under translational selection while nuclear genomes were under moderate translational selection. These results contribute to the study of mitochondrial genome evolution in filamentous fungi.

Comparative Mitogenomic Analyses and New Insights into the Phylogeny of Thamnocephalidae (Branchiopoda: Anostraca)

Thamnocephalidae, a family of Anostraca which is widely distributed on all continents of the world except Antarctica, currently consists of six genera and approximately 63 recognized species. The relationships among genera in Thamnocephalidae and the monophyly of Thamnocephalidae, determined using morphological characteristics or gene markers, remain controversial. In order to address the relationships within Thamnocephalidae, we sequenced Branchinella kugenumaensis mitogenomes and conducted a comparative analysis to reveal the divergence across mitogenomes of B. kugenumaensis. Using newly obtained mitogenomes together with available Anostracan genomic sequences, we present the most complete phylogenomic understanding of Anostraca to date. We observed high divergence across mitogenomes of B. kugenumaensis. Meanwhile, phylogenetic analyses based on both amino acids and nucleotides of the protein-coding genes (PCG) provide significant support for a non-monophyletic Thamnocephalidae within Anostraca, with Asian Branchinella more closely related to Streptocephalidae than Australian Branchinella. The phylogenetic relationships within Anostraca were recovered as follows: Branchinectidae + Chirocephalidae as the basal group of Anostraca and halophilic Artemiidae as a sister to the clade Thamnocephalidae + Streptocephalidae. Both Bayesian inference (BI)- and maximum likelihood (ML)-based analyses produced identical topologies.

First molecular phylogeny of the freshwater planarian genus Girardia (Platyhelminthes: Tricladida) unveils hidden taxonomic diversity and initiates resolution of its historical biogeography

The genus Girardia (Platyhelminthes: Tricladida) comprises several species of which some have spread from their original areas of distribution in the Americas to other parts of the globe. Due to great anatomical similarity between species, morphology-based phylogenetic analyses have struggled to resolve the affinities between species and species-groups. This problem is exacerbated by the fact that populations of Girardia may show only asexual reproduction by fissiparity and, thus, do not exhibit a copulatory apparatus, which hampers taxonomic identification of phylogenetic characters. In the present work, this problem has been resolved by constructing a molecular phylogeny of the genus. Although our samples do not include representatives of all known species, they cover a large part of the original distributional range of the genus Girardia. Our phylogenetic results suggest the presence of two main clades, which are genetically and karyologically highly differentiated. North and South American populations of G. tigrina actually constitute two sibling species that are not even closely related. The South American form is here described as a new species. The phylogenetic tree brings to light that Girardia arose on the South American portion of Gondwanaland, from which it, subsequently, dispersed to the Nearctic Region, probably more than once.

Comparative chloroplast genome and phylogenetic analyses of Chinese Polyspora

Polyspora Sweet (Theaceae) are winter ornamental landscape plants native to southern and southeastern Asia, some of which have medicinal value. The chloroplast (cp) genome data of Polyspora are scarce, and the gene evolution and interspecific relationship are still unclear. In this study, we sequenced and annotated Polyspora chrysandra cp genome and combined it with previously published genomes for other Chinese Polyspora species. The results showed that cp genomes of six Chinese Polyspora varied in length between 156,452 bp (P. chrysandra) and 157,066 bp (P. speciosa), but all contained 132 genes, with GC content of 37.3%, and highly similar genes distribution and codon usage. A total of eleven intergenic spacer regions were found having the highest levels of divergence, and eight divergence hotspots were identified as molecular markers for Phylogeography and genetic diversity studies in Polyspora. Gene selection pressure suggested that five genes were subjected to positive selection. Phylogenetic relationships among Polyspora species based on the complete cp genomes were supported strongly, indicating that the cp genomes have the potential to be used as super barcodes for further analysis of the phylogeny of the entire genus. The cp genomes of Chinese Polyspora species will provide valuable information for species identification, molecular breeding and evolutionary analysis of genus Polyspora.

Gene rearrangements in the mitochondrial genome of ten ascaris species and phylogenetic implications for Ascaridoidea and Heterakoidea families

The Ascaridoidea family and Heterakoidea family are the most common and typical representative of large parasites. Although our understanding of these parasites' diversity has expanded by analyses of some mitochondrial genes, there is limited information on these species' evolutionary rates. Here we determined ten complete mitogenome sequences of five subfamilies of Ascaridoidea and one subfamily of Heterakoidea. The phylogenetic tree divided the Ascaridoidea into six monophyletic major clades, and the divergence time of Heterakoidea family and Ascaridoidea family can be placed during the early Carboniferous Period (300-360 Mya). The reconstruction of the ancestral state showed that the gene orders of all species in Ascaridoidea were conserved, and the Heterakoidea had obvious genome rearrangement. The conserved blocks between them were divided into five and the main types are tandem-duplication/random loss (TDRL). These results will help to better understand the gene rearrangements and evolutionary position of ascaris species.

Enhanced Resolution of Evolution and Phylogeny of the Moths Inferred from Nineteen Mitochondrial Genomes

The vast majority (approximately 90%) of Lepidoptera species belong to moths whose phylogeny has been widely discussed and highly controversial. For the further understanding of phylogenetic relationships of moths, nineteen nearly complete mitochondrial genomes (mitogenomes) of moths involved in six major lineages were sequenced and characterized. These mitogenomes ranged from 15,177 bp (Cyclidia fractifasciata) to 15,749 bp (Ophthalmitis albosignaria) in length, comprising of the core 37 mitochondrial genes (13 protein-coding genes (PCGs) + 22 tRNAs + two rRNAs) and an incomplete control region. The order and orientation of genes showed the same pattern and the gene order of trnM-trnI-trnQ showed a typical rearrangement of Lepidoptera compared with the ancestral order of trnI-trnQ-trnM. Among these 13 PCGs, ATP8 exhibited the fastest evolutionary rate, and Drepanidae showed the highest average evolutionary rate among six families involved in 66 species. The phylogenetic analyses based on the dataset of 13 PCGs suggested the relationship of (Notodontidae + (Noctuidae + Erebidae)) + (Geometridae + (Sphingidae + Drepanidae)), which suggested a slightly different pattern from previous studies. Most groups were well defined in the subfamily level except Erebidae, which was not fully consistent across bayesian and maximum likelihood methods. Several formerly unassigned tribes of Geometridae were suggested based on mitogenome sequences despite a not very strong support in partial nodes. The study of mitogenomes of these moths can provide fundamental information of mitogenome architecture, and the phylogenetic position of moths, and contributes to further phylogeographical studies and the biological control of pests.

Comparative Mitogenomics of Two Sympatric Catfishes of Exostoma (Siluriformes: Sisoridae) from the Lower Yarlung Tsangpo River and Its Application for Phylogenetic Consideration

The genus Exostoma is a group of stenotopic and rheophilic glyptosternine catfishes distributed in South and Southeast Asia. So far, comprehensive studies on mitogenomics referring to this genus are very scarce. In this study, we first sequenced and annotated the complete mitochondrial genomes of Exostoma tibetanum and Exostoma tenuicaudatum—two sympatric congeners from the lower Yarlung Tsangpo River, Tibet, China. The mitogenomes of both species contained 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, one light-strand origin of replication, and one control region, with lengths of 16,528 bp and 16,533 bp, respectively. The mitogenome architecture, nucleotide composition, and codon usage of protein-coding genes were almost identical between the two Exostoma species, although some estimated parameters varied. Phylogenetic analysis strongly supported the monophyly of Exostoma in the subfamily Glyptosternae, and Exostoma tibetanum had the closest relationship to Exostoma tenuicaudatum. The divergence time estimation demonstrated that these two species diverged approximately 1.51 Ma during the early Pleistocene, which was speculated to be triggered by the river system changes caused by the uplift of the southeastern Tibetan Plateau. Selection pressure analyses indicated that all protein-coding genes of Exostoma species underwent a strong purifying selection, while minority positive sites from NADH dehydrogenase complex genes were detected. These findings are expected to promote our understanding of the molecular phylogeny of the genus Exostoma and provide valuable mitogenomic resources for the subfamily Glyptosternae

Molecular phylogeny and historical biogeography of marine palaemonid shrimps (Palaemonidae: Palaemonella-Cuapetes group)

Palaemonidae is the most speciose shrimp family within the infraorder Caridea, composed predominately of freshwater species and marine symbiotic species. The subject of this study is a clade of mainly free-living marine taxa representing a basally separated lineage from most of the symbiotic marine palaemonid genera. Phylogenetic and biogeographic relationships were explored by analysing sequence data from two mitochondrial and four nuclear markers. Maximum likelihood and Bayesian analyses, based on sequences from 52 species of 11 genera, provided similar tree topologies revealing the genera Palaemonella, Cuapetes and Eupontonia as non-monophyletic groups. Divergence time and S-DIVA analyses reveals that the focal clade originated during the Late Cretaceous in the Paleotethys region respective to the present Indo-West Pacific area, a minor part of which spread out to the eastern Pacific during the Paleocene, followed by further migration into the Atlantic (before the closure of the Panama Isthmus). The ancestral state reconstruction of host associations revealed eight independent symbiotic lineages originating from free-living ancestors, entering primary symbioses. The first associations with Cnidaria are estimated to have evolved in the Eocene. This study points to the need of taxonomic revisions of the non-monophyletic genera concerned.

Phylogeny and evolution of Cupressaceae: Updates on intergeneric relationships and new insights on ancient intergeneric hybridization

After the merger of the former Taxodiaceae and Cupressaceae s.s., currently the conifer family Cupressaceae (sensu lato) comprises seven subfamilies and 32 genera, most of which are important components of temperate and mountainous forests. With the exception of a recently published genus-level phylogeny of gymnosperms inferred from sequence analysis of 790 orthologs, previous phylogenetic studies of Cupressaceae were based mainly on morphological characters or a few molecular markers, and did not completely resolve the intergeneric relationships. In this study, we reconstructed a robust and well-resolved phylogeny of Cupressaceae represented by all 32 genera, using 1944 genes (Orthogroups) generated from transcriptome sequencing. Reticulate evolution analyses detected a possible ancient hybridization that occurred between ancestors of two subclades of Cupressoideae, including Microbiota-Platycladus-Tetraclinis (MPT) and Juniperus-Cupressus-Hesperocyparis-Callitropsis-Xanthocyparis (JCHCX), although both concatenation and coalescent trees are highly supported. Moreover, divergence time estimation and ancestral area reconstruction indicate that Cupressaceae very likely originated in Asia in the Triassic, and geographic isolation caused by continental separation drove the vicariant evolution of the two subfamilies Cupressoideae and Callitroideae in the northern and southern hemispheres, respectively. Evolutionary analyses of some morphological characters suggest that helically arranged linear-acicular leaves and imbricate bract-scale complexes represent ancestral states, and the shift from linear-acicular leaves to scale-like leaves was associated with the shift from helical to decussate arrangement. Our study sheds new light on phylogeny and evolutionary history of Cupressaceae, and strongly suggests that both dichotomous phylogenetic and reticulate evolution analyses be conducted in phylogenomic studies.

Phylogeographic and phenotypic divergence between two subspecies of Testudo graeca (T. g. buxtoni and T. g. zarudnyi) across their contact zone in Iran

Contact zones are considered as windows into the evolutionary process, allowing identification of factors influencing the evolutionary forces. Here, we combined phylogenetic and morphometric analyses to explore the evolutionary process affecting the taxonomic pattern of two subspecies of Testudo graeca (T. g. buxtoni and T. g. zarudnyi) across their contact zone in Central Iran. Our results showed high levels of phylogeographic and phenotypic variation in the contact zone. Two monophyletic clades including, clade 1 (T. g. zarudnyi) and clade 2 (T. g. buxtoni) were identified. Furthermore, four distinct subclades were found in T. g. buxtoni, across a wide geographic range. Divergence time analysis suggests that the two subspecies diverged from one another after the uplifting of the Zagros Mountains during the early Pliocene. Using neutrality tests and mismatch distribution analysis, we found no evidence of recent population expansion. Morphological associations among geographical populations in the contact zone found more distinctions, with some significant adaptive and non-adaptive morphological variations in these populations. These distinctive morphological populations can be considered as management units (MUs) to conserve the evolutionary potential of this species. Finer scale evolutionary studies are required to address the southern part of the Zagros mountain range, where the overlapping of mitochondrial clades and subclades has occurred. Such information is essential for effective conservation of T. graeca populations, preventing translocation or mixing of individuals without comprehensive genetic and morphological assessment.

Decoding molecular factors shaping human angiotensin converting enzyme 2 receptor usage by spike glycoprotein in lineage B beta-coronaviruses

Acquiring the human ACE2 receptor usage trait enables the coronaviruses to spill over to humans. However, the origin of the ACE2 usage trait in coronaviruses is poorly understood. Using a multi-disciplinary approach combining evolutionary bioinformatics and molecular dynamics simulation, we decode the principal driving force behind human ACE2 receptor recognition in coronaviruses. Genomic content, evolutionary divergence, and codon usage bias analysis reveal that SARS-CoV2 is evolutionarily divergent from other human ACE2-user CoVs, indicating that SARS-CoV2 originates from a different lineage. Sequence analysis shows that all the human ACE2-user CoVs contain two insertions in the receptor-binding motif (RBM) that directly interact with ACE2. However, the insertion sequences in SARS-CoV2 are divergent from other ACE2-user CoVs, implicating their different recombination origins. The potential of mean force calculations reveals that the high binding affinity of SARS-CoV2 RBD to human ACE2 is primarily attributed to its ability to form a higher number of hydrogen bonds than the other ACE2-user CoVs. The adaptive branch-site random effects likelihood method identifies positive selection bias across the ACE2 user CoVs lineages. Recombination and selection forces shape the spike evolution in human ACE2-using beta-CoVs to optimize the interfacial hydrogen bonds between RBD and ACE2. However, these evolutionary forces work within the constraints of nucleotide composition, ensuring optimum codon adaptation of the spike (S) gene within the host cell.

Rhizobium leguminosarum symbiovar viciae strains are natural wheat endophytes that can stimulate root development

Although rhizobia that establish a nitrogen-fixing symbiosis with legumes are also known to promote growth in non-legumes, studies on rhizobial associations with wheat roots are scarce. We searched for Rhizobium leguminosarum symbiovar viciae (Rlv) strains naturally competent to endophytically colonize wheat roots. We isolated 20 strains from surface-sterilized wheat roots, and found a low diversity of Rlv compared to that observed in the Rlv species complex. We tested the ability of a subset of these Rlv for wheat root colonization when co-inoculated with other Rlv. Only a few strains, including those isolated from wheat roots, and one strain isolated from pea nodules, were efficient in colonizing roots in co-inoculation conditions, while all the strains tested in single strain inoculation conditions were found to colonize the surface and interior of roots. Furthermore, Rlv strains isolated from wheat roots were able to stimulate root development and early arbuscular mycorrhizal fungi colonization. These responses were strain and host genotype dependent. Our results suggest that wheat can be an alternative host for Rlv; nevertheless, there is a strong competition between Rlv strains for wheat root colonization. In addition, we showed that Rlv are endophytic wheat root bacteria with potential ability to modify wheat development.