DAMBE: software package for data analysis in molecular biology and evolution

Molecular characterization and epidemiological insights into serotypes of foot-and-mouth disease virus in Pakistan

Foot-and-mouth disease virus (FMDV) causes a highly infectious transboundary disease in cloven-hoofed animals. However, there is limited information on comparative genomic and evolutionary analysis of FMDV strains reported in Pakistan. In the current study, we investigated a few disease outbreaks in Pakistan and determined the complete genome sequences of three isolates belonging to different serotypes: O, A, and Asia-1. Comparative genomic analysis showed a close relationship between the FMDV strains from this study and those reported in neighboring Asian countries. Phylogenetic analysis based on the complete genome and VP1 gene sequences revealed that serotype O clustered within the Pak-98 lineage, serotype A within genotype I, and serotype Asia-1 within group 5, grouping with strains from Pakistan, India, and China. Potential negatively selected sites were identified in the region encoding the structural proteins VP4, VP3, VP2, and VP1, with the most episodic diversifying section observed in the VP1 and VP3 regions. Substantial variation was observed in polymorphic and monomorphic sites, with the highest diversity observed in the VP1 protein of serotype O viruses. No evidence of recombination events was found in the FMDV strains from this study. Our findings indicate the cocirculation of multiple serotypes and sublineages of FMDV in Pakistan, underscoring the potential for the emergence of new variants. This study adds to the existing knowledge on the genetic variation and evolutionary dynamics of FMDV serotypes in Pakistan, providing valuable insights for the development of effective vaccines and improved disease control strategies.

New species of Plesioaxymyia Sinclair (Diptera, Axymyiidae) from the Palaearctic Region, including an updated molecular phylogeny of the family

The family Axymyiidae includes four extant genera and nine species known from the Holarctic and Oriental regions, with only one species Mesaxymyiakerteszi (Duda, 1930) occurring in Europe. The genus Plesioaxymyia Sinclair, 2013 was first discovered in Alaska in 1962, but officially described only many years later. Up to now, the genus included one species Plesioaxymyiavespertina Sinclair, 2013, known from two female specimens from western North America. During the study of the Diptera fauna in Paanajarvi National Park (Northwest Russia), one female specimen of Plesioaxymyia, was found. It differs from the Nearctic P.vespertina by details of its female terminalia and is recognized as a new species, herein described as Plesioaxymyiaimprevista sp. nov. The biology and geographic distribution of Plesioaxymyia is briefly discussed. The phylogenetic position of the genus, along with the family Axymyiidae is analyzed in the light of new molecular data, including sequences of three mitochondrial (ribosomal 12S and 16S and protein-encoding COI) and three nuclear genes (ribosomal 18S and 28S, protein-encoding CAD) for 72 terminal taxa. Axymyiidae is recovered as a monophyletic group with closest relatives in the infraorder Culicomorpha and Plesioaxymyiaimprevista sp. nov. representing the sister taxon to all the other species of Axymyiidae included in the analysis.

Coral-associated Symbiodiniaceae exhibit host specificity but lack phylosymbiosis, with Cladocopium and Durusdinium showing different cophylogenetic patterns

Altering the composition of the Symbiodiniaceae community to adapt to anomalous sea water warming represents a potential survival mechanism for scleractinian corals. However, the processes of Symbiodiniaceae assembly and long-standing evolution of coral-Symbiodiniaceae interactions remain unclear. Here, we utilized ITS2 (internal transcribed spacer 2) amplicon sequencing and the SymPortal framework to investigate the diversity and specificity of Symbiodiniaceae across 39 scleractinian coral species. Furthermore, we tested phylosymbiosis and cophylogeny between coral hosts and their Symbiodiniaceae. In our study, environmental samples exhibited the highest Symbiodiniaceae diversity. Cladocopium and Durusdinium dominated the Symbiodiniaceae communities, with significant β-diversity differences among coral species. Additionally, host specificity was widespread in Symbiodiniaceae, especially Durusdinium spp., yet lacked a phylosymbiotic pattern. Moreover, Cladocopium spp. showed cophylogenetic congruence with their hosts, while there was no evidence for Durusdinium spp. Furthermore, host switching was the predominant evolutionary event, implying its contribution to Cladocopium diversification. These findings suggest that Symbiodiniaceae assembly does not recapitulate host phylogeny, and host specificity alone does not drive phylosymbiosis or cophylogeny. As environmental reservoirs, free-living Symbiodiniaceae may influence symbiotic communities. Additionally, Durusdinium-coral associations lack cophylogenetic signals, indicating more flexible partnerships than Cladocopium. Overall, our results enhance understanding of Symbiodiniaceae assembly and coral-Symbiodiniaceae evolutionary interactions.

Historical biogeography and plastome evolution of Commelinaceae Mirb. (Commelinales) corroborate the East Gondwanan origins

BACKGROUND

Commelinaceae are a Pantropical monocot family comprising ca. 36 genera and 810 species. Due to the high morphological variation and limited sampling, the relationships within the family remain unclear. Previous studies, which relied on limited genetic loci or low-resolution sequencing, have not fully resolved these relationships. Additionally, there is a need to investigate the historical biogeography of Commelinaceae using genomic data. To address these issues, we assembled twelve Commelinaceae plastomes and inferred their biogeographical pathways using both newly generated and previously published data.

RESULTS

Our results indicate that all members of the subfamily Commelinoideae have shortened accD and rpoA genes, which do not affect functionality. In contrast, members of the subf. Cartonematoideae possess intact forms of both genes. Phylogenetic analyses based on 79 plastid protein-coding genes provide much-needed insight into the placement of some key genera that had previously remained unplaced or were erroneously placed elsewhere within the family. Of these, our results support the monophyly of the subtribe Streptoliriinae, the non-monophyly of the subtr. Coleotrypinae, and the need to recognise a broader circumscription of Aneilema R.Br. (including Rhopalephora Hassk.). Our biogeographic analysis shows that the ancestor of Commelinaceae originated in the Australian region around 104.8 million years ago (Mya), thus revealing an East Gondwanan origin. We also found that four major dispersal events have shaped the intercontinental diversification of this family: (1) from the Australian to the Ethiopian region ca. 81.4 Mya; (2) from the Ethiopian to the Oriental + Palearctic region ca. 50.4 Mya; (3) from the Oriental + Palearctic to the Neotropical region ca. 50.4 Mya; and (4) from the Neotropical to the Ethiopian region ca. 32.3 Mya.

CONCLUSIONS

We identified genetic events, such as inversions and IR expansion, which shed light on the genomic evolution of Commelinaceae. Our findings support taxonomic updates, and future work will integrate comprehensive phylogenomic and morphological datasets to deepen our understanding of morphological evolution and biogeographic history within Commelinaceae, establishing a robust foundation for systematic revisions in the family.

Morpho-Molecular Discordance and Cryptic Diversity in Jumping Bristletails: A Mitogenomic Analysis of Pedetontus silvestrii (Insecta: Archaeognatha: Machilidae)

Archaeognatha (bristletails) represent an evolutionarily significant but understudied insect group. Notably, the morphological identification method proposed by Mendes for Archaeognatha has certain limitations, which may lead to the underestimation or misidentification of some cryptic species. To address this issue, we employed an integrated strategy that combines morphological and molecular identification methods. Therefore, this study aimed to (1) identify cryptic diversity within Pedetontus silvestrii using mitogenomic data; (2) clarify phylogenetic relationships among Archaeognatha lineages; and (3) estimate divergence times for key taxonomic splits. We analyzed mitochondrial genomes from six P. silvestrii populations (Liaoning, Jilin, and Hebei Provinces) alongside 14 published Archaeognatha genomes. Key findings include the following: (1) Integrative analyses of genetic distances, phylogenetic reconstruction, bPTP-based molecular species delimitation, and divergence time estimation collectively revealed four evolutionarily distinct lineages within P. silvestrii. (2) Machilidae and Machilinae were non-monophyletic, whereas Petrobiellinae showed close affinity to Meinertellidae. (3) Archaeognatha originated ~301.19 Mya (Late Carboniferous); the Machilinae-Petrobiinae split occurred approximately 153.99 Mya (Jurassic). This study underscores the critical importance of mitogenomic analysis in elucidating cryptic biodiversity, while emphasizing the necessity of integrating morphological identification with molecular characterization for comprehensive species delineation in future taxonomic investigations.

Porcine circovirus type 2 (PCV2) in Brazil in the past 55 years (1967-2022): evolutionary rates and patterns

Porcine circovirus type 2 (PCV2) is a common virus that infects pigs. It exhibits marked genetic variability, which is affected by factors such as vaccination and commercial trade. In this study, a retrospective analysis of PCV2 was performed based on molecular characterization, Bayesian inference, and haplotype networks in tissue samples obtained from Brazilian pig herds from 1967 to 2018. A nested PCR targeting a 225-nucleotide fragment of the PCV2 capsid gene was performed, followed by bidirectional sequencing. Out of 178 samples tested, 39 (21.9%) were positive for PCV2. Phylogenetic analysis showed that strains from this study collected before the introduction of a PCV2 vaccine clustered with genotype 2d reference strains. The mean substitution rate was 1.54 × 10-3 substitutions per site per year (s/s/y). The haplotype diversity of PCV2 was 0.98, which shows a high mutation rate compatible with the topology found in the haplotype network. Our study shows that most of the Brazilian isolates, including those obtained before the introduction of the PCV2 vaccine, were similar to PCV2d reference strains, suggesting that this genotype was already circulating before the introduction of the vaccine in Brazil. One of the PCV2 sequences was from an isolate from 1967, making it the oldest sequenced isolate from the Americas, and the second oldest worldwide. Phylogenetic analysis and haplotype network analysis indicated a high degree of diversity of PCV2 as well as a high rate of evolution. These results increase our knowledge about the genetic diversity, evolution, and dispersal patterns of PCV2 in Brazil.

An attempt of DNA barcodes based geographical origin authentication of the Chinese caterpillar fungus, Ophiocordycepssinensis

Ophiocordycepssinensis is one of the best-known traditional Chinese medicines with distribution confined to the Tibetan Plateau and its surrounding regions. Harvesting the fungus contributes greatly to the livelihood of local communities. The quality and price varies amongst different production regions, usually resulting in an intentional mix-up of its production locality during trading processes, which leads to a demand of developing a reliable way that can trace the geographical origin of this fungus. In the present study, a DNA barcoding-based method applying two universal DNA barcodes for identifying fungal and insect, respectively i.e. the nuclear ribosomal internal transcribed spacer (ITS) and the mitochondrial cytochrome oxidase I (COI), was evaluated and used for geographical origin authentication of O.sinensis. A total of 24 ITS and 78 COI haplotypes were recognised from 215 individuals collected from 75 different geographic localities (county level). Ninety-nine haplotypes were defined using the combination of ITS and COI, discriminating the 75 investigated production counties into 99 distinct regions. A "core" production region was recognised which covers areas of Nagqu and Qamdo in Xizang, Yushu and Guoluo in Qinghai, Gannan (Maqu and Xiahe) in Gansu and certain regions in Nyingch (Bomi and Zayü) and Lhasa (Damxung) in Xizang and Garzê (Sêrxü) in Sichuan Province. Haplotype analyses using the combined barcodes of ITS and COI showed an excellent performance in the geographical origin authentication of O.sinensis and the definition of "core" and "non-core" production region.

Comparative Analysis of the Mitochondrial Genomes of Three Species of Elmidae (Coleoptera: Dryopoidea)

The mitochondrial genomes of three species of Elmidae were sequenced. The sizes were 16,309 bp (C. jaechi), 16,291 bp (G. longiusculus), and 15,480 bp (S. punctulata). Each genome includes 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a control region (CR). All three mitogenomes show AT bias. Except for trnS1, lacking the dihydrouridine (DHU) arm, all tRNA genes had a typical cloverleaf structure. The codon usage preferences of the three species showed high similarity. The arrangement of the genes in the three mitogenomes was consistent among them but differed from that in the typical mitogenomes of Coleoptera. The Ka/Ks ratio indicated that COX1 and nad4L had a lower evolutionary rate, being relatively conserved genes among 13 PCGs. The phylogenetic analysis revealed that Elmidae belongs to the superfamily Dryopoidea within the suborder Polyphaga and is monophyletic. The results preliminarily indicate that the taxonomic groups at the subfamily, tribe, and genus levels within Elmidae are ambiguous, and further revisions may be required in the future.

A "Dock-Work" Orange: A Dual-Receptor Biochemical Theory on the Deterrence Induced by Citrusy Aroma on Elephant Traffic Central to a Conservation Effort

Conservation of elephants requires physical, chemical, and biological approaches to ensure the protection of these gargantuan pachyderms. One such approach is using orange plants (as biofencing) for the repellence of elephants, which precludes catastrophic events related to the encroachment of elephants into human habitats. Elephants have sensitive olfactory discrimination of plant volatile compounds for foraging and other behavior using G-protein-coupled receptors (GPCRs). However, 2 such receptors are the A2A and A2B receptors mediating olfaction elicited by a host of ligands, including limonene, the main volatile compound in citrus plants, which is hypothesized to be the chief repelling agent. Bioinformatics at the protein and mRNA levels (BLAST/Multiple Sequence Alignments) were employed to explore the multiple expression products of A2B receptors, namely full-length and truncated proteins produced by isoform mRNAs translated from multiple methionines, while the comparison of the limonene-binding pockets of human and elephant A2B receptors and prediction servers [Netphos 3.1; Protter] was used to focus, respectively, on the contacts limonene binding entails and the post-translational modifications that are involved in cell signaling. Finally, the link between limonene and antifeedant activity was explored by considering limonene content on trees that are preferentially foraged or avoided as part of the feeding behavior by elephants. The African bush elephant (Loxodonta africana) possesses a full-length A2A receptor but unlike most mammals, expresses a highly truncated A2B receptor isoform possessing only transmembrane helices 5, 6, and 7. Truncation may lead to higher traffic and expression of the A2B receptor in olfactory interfaces/pathways and aid stronger activation. In addition, all residues in the putative limonene-binding cleft are perfectly conserved between the human and African bush elephant A2B receptors, both full length and truncated. Shallow activation sites require micromolar affinity and fewer side-chain interactions, which is speculated to be the case for the truncated A2B receptor. An N-terminal extremity N-glycosylation motif is indicative of membrane localization of the truncated A2B receptor following accurate folding. A combination of truncation, indels, substitutions, and transcript isoforms are the attributed roles in the evolution of the L. africana A2B receptor, out of which limonene receptivity may be the key. It is also inferred how limonene may act as a dietary repellent/antifeedant to a generalist herbivore, with the documented limonene content being absent in some dietary favorites including the iconic Sclerocarya birrea.

Genetic Characterization and Zoonotic Potential of Leptospira interrogans Identified in Small Non-Flying Mammals from Southeastern Atlantic Forest, Brazil

Leptospirosis is a zoonotic disease of global public health importance caused by bacteria of the genus Leptospira. Small non-flying mammals are important reservoirs of the pathogen. The Brazilian Atlantic Forest is a biodiversity hotspot located in a densely populated area and subject to intense degradation. Although documented through serosurveys and the detection of leptospiral DNA in wild small mammals, no study has performed a genetic characterization of the bacteria in the region. The present study aimed to evaluate the genetic diversity of pathogenic leptospires identified in small non-flying mammals in the Southeast Atlantic Forest and to perform intraspecific genetic inferences with other hosts. The studied area included five different conservation units. Molecular diagnosis was performed based on the lipl32 gene. The SLST typing method was applied based on the secY gene. In total, 56% of samples were lipL32-PCR-positive and identified as L. interrogans, with a high genetic identity among them, distributed in four main haplogroups. The largest haplogroup also included reference sequences from humans, dogs, and urban rats, all belonging to the Icterohaemorrhagiae serogroup. Our results reinforce the role of small mammals as important carriers of L. interrogans and highlight the Atlantic Forest as a significant environment for the circulation and dissemination of spirochetes with zoonotic potential.

Diaporthe betae sp. nov., a new species associating with sugar beet root rot in Heilongjiang Province, China

Introduction

Sugar beet (Beta vulgaris L.) is an economically important crop grown worldwide, but its production is threatened by root rot diseases caused by soil-borne fungi. This study aimed to identify and characterize a new pathogen causing root rot in sugar beet in Heilongjiang Province, China.

Methods

During 2019 and 2023, isolates were obtained from infected sugar beet roots showing symptoms of red-brown or black lesions and tissue necrosis. The pathogenicity of the causal organism was confirmed by Koch's postulates. The isolates were characterized based on morphological features and multilocus phylogenetic analyses. To evaluate potential control measures for this new pathogen in field conditions, the fungicides pyraclostrobin, boscalid, and fluconazole were tested for their efficacy in inhibiting the growth of this new pathogen in vitro.

Results

The newly discovered pathogen was found to differ from previously described taxa in conidial morphology, molecular features, and disease index. Thus, the pathogen was determined to be a new species, which we called Diaporthe betae sp. nov. All three fungicides demonstrated significant inhibitory effects, with fluconazole showing the strongest activity and pyraclostrobin the second-highest efficacy.

Discussion

The discovery of this new pathogenic fungus will help researchers elucidate the pathogenesis of sugar beet root rot and provide a theoretical basis for performing targeted monitoring, preventing diseases and implementing control measures.

Just the tip of the iceberg: uncovering a hyperdiverse clade of African Russula (Basidiomycota, Russulales, Russulaceae) species with signs of evolutionary habitat adaptations

The diversity within the ectomycorrhizal genus Russula (Basidiomycota) in West Africa is largely unexplored. The study area was Benin, where only ten out of the 159 species endemic to tropical Africa have been previously reported. We focused on "Afrovirescentinae", which is a monophyletic lineage within Russulasubgen.Heterophyllidiaesister tosubsect.Virescentinae. The phylogenetic placement of this clade was analysed using sequence data from ITS, LSU, mtSSU, tef1, rpb1 and rpb2 regions. Ten "Afrovirescentinae" species are recognised, described and illustrated from Benin. Four of them, R.carmesina, R.hiemisilvae, R.inflata and R.sublaevis, were previously published. Five species, Russulaacrialbida sp. nov., R.beenkenii sp. nov., R.coronata sp. nov., R.florae sp. nov. and R.spectabilis sp. nov., are newly described. Species within this group are characterised by densely reticulated spore ornamentation, but they exhibit considerable variation in field appearance and pileipellis structure. In gallery forests, their basidiomata are ephemeral, small and their basidiospores have prominent ornamentation; while in savannah woodlands, the basidiomata are fleshy, large and basidiospores present low ornamentation. We suggest that these morphological traits may represent evolutionary adaptations to a specific environmental condition. We analysed the species richness, ecological range and distribution of the "Afrovirescentinae" clade globally based on data from the UNITE database, estimating a total diversity of 94 species primarily distributed in sub-Saharan Africa, but also in the Neotropics. Four additional previously described species not detected in Benin were assigned to this clade, based on holotype sequencing. Several species are widely distributed across tropical Africa and do not show specificity regarding their associated plant symbionts.

Characterization of Complete Mitochondrial Genome of Badri Breed of Bos indicus (Bovidae: Bovinae): Selection Pressure and Comparative Analysis

High-altitude mammals are often subject to specific environmental obstacles, which exert selective pressure on their physiological and morphological traits, hence driving their evolutionary processes. It is anticipated that these circumstances will lead to the adaptive evolution of protein-coding genes (PCGs) in the mitochondrial genome, which play a crucial role in the oxidative phosphorylation system. In this study, we have generated the complete mitochondrial genome of the Badri breed of Bos indicus inhabiting a high-altitude environment to test the signatures of adaptive evolution on PCGs and their phylogenetic relationships. The complete mitogenome of the Badri breed is 16,339 bp and most tRNAs showed typical clover-leaf secondary structure with a few exceptions, like trnS1 and trnS2 without DHU arm and trnK without DHU loop. Comparative analysis of PCGs indicated that cox1 is the most conserved, while atp6 is the most variable gene. Moreover, the ratios of non-synonymous to synonymous substitution rates indicated the purifying selection (Ka/Ks < 1) in the protein-coding genes that shape the diversity in mitogenome of Bos indicus. Furthermore, Branch-site model (BSM) suggested that cox1, cox2, nad3, nad4L, and nad6 underwent stronger purifying selection (ω < 1) than other PCGs in 15 breeds of 4 species, including Badri. BSM also detected 10 positive sites in PCGs and one in 13 PCGs concatenated dataset. Additional analyses in Datamonkey indicated 11 positive sites and 23 purifying sites in the concatenated dataset, a relaxation of selection strength in nad3, and no evidence of episodic diversifying selection in any PCGs. Phylogeny revealed the sister relationship of the Badri with other breeds of Bos indicus as well as Bos frontalis (Gayal-2). The mitogenome of the Badri breed is an important genomic resource for conservation genetics of this species and also contributes to the understanding of the adaptive evolution of mitochondrial protein coding genes.

First autochthonous case of Opisthorchis felineus in Austria

BACKGROUND

Opisthorchis felineus is a feline pathogen with zoonotic potential that can be a causative agent of human opisthorchiasis and cholangiocarcinoma. In Europe, O. felineus is particularly endemic in Eastern European countries, while this parasite has also been sporadically detected in Germany, Italy and northern Poland. Parts of Asia, such as Russia, Ukraine and Kazakhstan, are also affected.

METHODS

A 7-year-old female neutered European Shorthair cat, without any traveling history, presented in May 2023 with weight loss, anorexia and vomiting.

RESULTS

The cat showed increased liver enzyme activities, hyperbilirubinemia and hyperammonemia consistent with the suspected diagnosis of cholangitis with consecutive hepatoencephalopathy. Eggs of O. felineus were detected by routine cytological examination of bile smears and PCR confirmed O. felineus.

CONCLUSIONS

This is the first report of autochthonous O. felineus infection in Austria.

Detection and phylogenetic analysis of blood-associated pathogens from spleen samples of wild raccoons (Procyon lotor) in Germany

Raccoons (Procyon lotor) originated in North America and have been introduced to Europe. Due to their close contact with human settlements, they are important reservoirs for zoonotic pathogens, such as Baylisascaris procyonis. The relevance and prevalence of vector-borne pathogens have not yet been fully elucidated. In this study, we screened 285 spleen samples of raccoons, collected between 2019 and 2022 in Germany. The samples were analysed by PCR to detect Mycoplasma spp., Anaplasmataceae, Bartonella spp., Babesia spp., Rickettsia spp., Filarioidea, Trypanosomatida and Hepatozoon spp., and positive PCR products were sequenced. In total, 104 samples were positive for Mycoplasma spp. (36.49%), making this the first study to detect Mycoplasma spp. in raccoons outside of North America. Three samples were positive for Babesia spp. (1.05%) and two for Anaplasma phagocytophilum (0.7%). Phylogenetic analysis revealed that the Mycoplasma spp. detected all belong to the haemotrophic mycoplasmas cluster and were grouped within a single phylogenetic clade. Two different Babesia spp. were detected, one of which was closely related to Babesia canis, while the other was more closely related to Babesia sp. from ruminants. It is unclear whether the pathogens detected have an impact on the health of raccoons or whether they may serve as a reservoir for other animals.

The Mitochondrial Genome of Melipona fasciculata (Apidae, Meliponini): Genome Organization and Comparative Analyses, Phylogenetic Implications and Divergence Time Estimations

The native stingless bee Melipona fasciculata is economically and ecologically important to the Brazilian Northeast, providing a sustainable source of income to family farmers and being considered an effective pollinator in most ecosystems and crops. This study describes, for the first time, the mitogenome of the species and its phylogenetic position. The mitochondrial genome was sequenced using a MiSeq Sequencer (Illumina Inc.) and compared with other GenBank bee mitogenomes. The length of the mitochondrial DNA, excluding most of the control region, is 14,753 bp, and contains 13 protein-coding genes (PCGs), 21 transfer RNAs, 2 ribosomal RNAs (16S and 12S), and 1 AT-rich region. The GC-content of the M. fasciculata mitogenome was 13.4%. Of the 36 coding regions, 12 tRNAs and 9 PCGs were encoded in the heavy strand, and 9 tRNAs, 4 PCGs and 2 rRNAs were encoded in the light strand. The relative orientation and gene order was the same as other stingless bee mitogenomes. Phylogenetic inference produced well-resolved relationships with high statistical support for concordant branch topologies, under different optimization schemes and model parameters, within and among Melipona, Bombus, Apis, and related clades of Hymenoptera. In general, our divergence time estimates, which were based on the concatenated gene sequences (PCGs + rRNAs) from various groups, overlapped estimations captured by Bayesian analysis from different studies. The divergence time among Melipona species was estimated to occur during the Oligocene, approximately 24 Mya (95% HPD 14-36 Mya). Our results represent a valuable addition to help understanding not only the taxonomy and evolution of Brazilian stingless bee species, but also to uncover historical dispersal and isolation patterns in Meliponinae.

Organelle genome assembly, annotation, and comparative analyses of Typha latifolia and T. domingensis: two keystone species for wetlands worldwide

Typha is a cosmopolitan aquatic plant genus that includes species with widespread global distributions. In previous studies, a revised molecular phylogeny was inferred using seven plastid loci from nine Typha species across different geographic regions. By utilizing complete organellar genomes, we aim to provide a more comprehensive dataset that offers a robust phylogenetic signal for resolving Typha species evolutionary relationships. Here, we assembled T. latifolia and T. domingensis mitochondrial genomes (mitogenomes) using a combination of short-read and long-read data (PacBio, ONT). The mitogenomes of both species are assembled into single circular molecules of 395,136 bp and 395,140 bp in length, respectively, with a similar GC content of 46.7%. A total of 39 protein-coding genes, 17 tRNA genes, and 3 rRNA genes were annotated in both mitogenomes. The plastid genomes (plastomes) of both species possess typical quadripartite structures observed across most plants, with sizes of 161,545 bp and 161,230 bp. The overall average GC content of the plastomes of both species was 36.6%. The comparative analysis of the plastome and mitogenome revealed that 12 mitogenome DNA fragments share similar sequences with in the repeat regions of the corresponding plastomes, suggesting a past transfer of repeat regions into the mitogenome. Additionally, the mitogenomes of the two Typha species exhibited high sequence conservation with several syntenic blocks. Phylogenetic analysis of the organellar genomes of the two Typha species and 10 related species produced congruent phylogenetic trees. The availability of these organellar genomes from two Typha species provide valuable genetic resources for studying the evolution of Typhaceae and will improve taxonomic classifications within the family.

Phylogeography, taxonomy, and conservation of the endangered brown howler monkey, Alouatta guariba (Primates, Atelidae), of the Atlantic Forest

The brown howler, Alouatta guariba, endemic to the Atlantic Forest of Brazil and Argentina, is threatened by habitat loss and fragmentation, hunting, and its susceptibility to yellow fever. Two subspecies have been recognized, but their names, validity, and geographic ranges have been controversial. We obtained samples covering the species' entire distribution in Brazil and Argentina to clarify these issues by investigating their genetic diversity and structure and assessing their evolutionary history. We analyzed, for the first time, a set of ten microsatellite markers (N = 153), plus mitochondrial DNA (mtDNA) segments of the control region (N = 207) and cytochrome b gene (N = 116). The microsatellite data support two to three genetic clusters with biological significance. The southern populations (Argentina, Santa Catarina, and Rio Grande do Sul) presented a homogeneous genetic component, and populations from São Paulo (SP) to the north presented another component, although most presented ∼20% of the southern component. With K = 3, SP emerged as a third component while sharing some ancestry with Rio de Janeiro and Argentina. The mtDNA phylogenies revealed three main clades that diverged almost simultaneously around 250 thousand years ago (kya). Clades A and B are from central SP to the north and east, while clade C is from SP to the south and southwest. Samples from SP presented haplotypes in all three clades, sometimes in the same population. The demographic history of the species estimated with the Bayesian skyline plot of the mtDNA showed a strong expansion ∼40-20 kya and a strong reduction over the last ∼4-2 kya. Although the genetic clusters identified here deserve appropriate management strategies as conservation units, the absence of (i) concordance between the mtDNA and microsatellite data, (ii) reciprocal monophyly in the mtDNA, and (iii) clear-cut non-genetic diagnostic characters advises against considering them as different taxonomic entities. None of the previous taxonomic proposals were corroborated by our data. Our results elucidate the taxonomy of the Atlantic Forest brown howler, indicating it should be considered a monotypic species, A. guariba. We also clarify the evolutionary history of the species regarding its intraspecific genetic diversity, which is crucial information for its conservation and population management.

The complete mitogenome dataset of the heptageniid mayfly Afronurus levis (Ephemeroptera: Heptageniidae: Ecdyonurinae) from South Korea

The Heptageniidae family stands out as one of the most abundant and widespread among mayflies, distinguished by its unique mitochondrial characteristics in intergenic spacers and duplication of transfer RNA (tRNA) genes. In this dataset, we present the complete mitochondrial genome sequence of Afronurus levis (Navás, 1912), a member of the Heptageniidae family of mayflies. The total length of the A. levis mitogenome was determined to be 15,362 base pairs, encompassing 13 protein-coding genes (PCGs), 23 tRNA genes, and two ribosomal RNA genes. An additional trnM gene was detected in the A. levis genome, consistent with observations in other Heptageniid species. The base composition of the A. levis mitogenome was determined to be 31.7 % A, 32.7 % T, 14.1% G, and 21.5 % C. Phylogenetic analysis using PCGs confirmed that the newly sequenced A. levis mitogenome clusters within the genus Afronurus, showing closer proximity to that of A. drepanophyllus.

Mitogenomics providing new insights into the phylogenetic structure of subfamily Panchaetothripinae (Thripidae: Terebrantia)

Complete mitochondrial genome of two species of subfamily Panchaetothripinae, Astrothrips tumiceps (16,467 bp) and Monilothrips kempi (14,773 bp) are generated by Next-Generation Sequencing Method. In this study, the detailed annotation of these mitogenomes as well as comparative analyses are carried out to explore the codon usage, gene composition, and phylogenetic relationship of subfamilies of family Thripidae. Moreover, the gene rearrangement of subfamily Panchaetothripinae of family Thripidae is also studied. Both the mitogenomes featured by 37 genes including 13 PCGs, 22 tRNAs, 2 rRNAs and with single putative control region with a positive AT-skew and negative GC-skew. trnS1 without DHU arm in both species, trnV without DHU arm in M. kempi, and trnE without TΨC loop in As. tumiceps. Further, codon based comparative analysis depicted the existence of natural selection pressure on all the PCGs in all the subfamilies of family Thripidae. The phylogenetic analyses, using the Bayesian inference (BI) and Maximum likelihood (ML) supported the monophyly of two suborders and family Phlaeothripidae. The family Thripidae is recovered as paraphyletic and subfamily Panchaetothripinae is in sister relationship with family Aeolothripidae and Stenurothripidae rather than the other subfamilies of family Thripidae. The gene order of the order Thysanoptera is highly rearranged, while few members of the subfamily Panchaetothripinae showed similar gene order to family Stenurothripidae. Therefore, this study suggests that the phylogenetic relationship between the subfamily Panchaetothripinae and other families is uncertain, necessitating a whole genome-based study to clarify the position of Panchaetothripinae within the suborder Terebrantia.

A comprehensive study on the mitochondrial genome of Volva habei and exploring phylogenetic relationships in Littorinimorpha

In order to enrich our taxonomic and systematic comprehension of Ovulidae within the evolutionary framework of Littorinimorpha. we present a comprehensive analysis of the mitochondrial genome (mitogenome) sequence of Volva habei using next-generation sequencing technology (GenBank accession number OR492307). The mitogenome spans a total length of 16,519 bp, encompassing a complete set of 37 genes, including 13 protein-coding genes (PCGs), 22 tRNAs and two rRNAs, demonstrating a distinct AT bias. Notably, trnS2 lacks a dihydrouracil (DHU) arm, thus preventing the formation of a typical secondary structure. In contrast, the remaining tRNAs exhibit a characteristic cloverleaf-like secondary structure. Comparative analysis with ancestral gastropods reveals substantial differences in three gene clusters (or genes), incorporating fifteen tRNAs and eight PCGs. Of particular significance are the observed inversions and translocations, representing the predominant types of rearrangements in V. habei. Phylogenetic analysis strongly supports the monophyletic grouping of all Littorinimorpha species, with V. habei forming a distinct Ovulidae clade. It is noteworthy that V. habei forms a sister group with Cypraeidae, collectively belonging to the Cypraeoidea. In summary, this study not only advances our comprehension of the entire mitochondrial dataset for Calyptraeoidea but also provides novel insights into the phylogenetic relationships within Littorinimorpha.

New insights on the Xylaria species (Ascomycota, Xylariales) with bright-coloured exudates: Xylaria aurantiorubroguttata sp. nov. and revision of X. haemorrhoidalis and X. anisopleura type collections

A new species of Xylaria is described based on morphological characters of both sexual and asexual morphs, and molecular data based on nuclear rDNA internal transcribed spacer, α-actin, β-tubulin and RNA polymerase subunit II sequences. Xylaria aurantiorubroguttata is characterized by the presence of both upright, cylindrical, long-stipitate and globose to subglobose, short-stipitate stromata, immature stromatal stages producing at first orange and then red drops, and ascospores with a slightly oblique, straight half spore-length germ slit. We provide also new morphological descriptions for X. haemorrhoidalis (holotype) and X. anisopleura (isosyntype), two Xylaria species belonging to X. polymorpha complex together with X. aurantiorubroguttata.

Chloroplast Genome and Description of Borodinellopsis insignis sp. nov. (Chlamydomonadales, Chlorophyta), a Rare Aerial Alga from China

The genus Borodinellopsis is extremely rare and is the subject of limited research and reports. It currently comprises only two species, Borodinellopsis texensis and Borodinellopsis oleifera, which differ from other globose algae due to their unique centrally radiating chloroplasts. In this study, we describe a new specimen in detail based on morphological data and phylogenetic analysis and identify it as B. insignis. B. insignis and B. texensis exhibit a high degree of similarity, likely due to their shared characteristics of centrally radiating chloroplasts and flagella that are significantly longer than the cell body. A phylogenetic tree constructed based on the 18S rDNA sequence indicates that B. insignis and B. texensis form a branch that is distinct from other genera, such as Tetracystis, Spongiococcum, and Chlorococcum. Phylogenetic analysis of the ITS sequence, the rbcL gene, and the tufA gene reveals that B. insignis is significantly different from B. texensis, in that it has oil droplets, smaller vegetative cells and zoospores, and distinct habitats. It is also different from B.oleifera as it has smaller vegetative cells and zoospores, turns red after cultivation, has longer flagella, and resides in different habitats. The chloroplast genomes of B. texensis and B. insignis further show significant differences, with the phylogenetic tree constructed based on the analysis of 49 protein-coding genes forming two separate branches. The collinearity of the chloroplast genomes in B. texensis and B. insignis is poor, with 15 out of the 31 homologous modules displaying inversions and complex rearrangements. Given these differences, we classify this alga as a new species and named it Borodinellopsis insignis sp. nov.

Insight into the Phylogenetic Relationships of Phasmatodea and Selection Pressure Analysis of Phraortes liaoningensis Chen & He, 1991 (Phasmatodea: Lonchodidae) Using Mitogenomes

Stick and leaf insects are a group among the Insecta that are famous for their extraordinary mimicry ability. Since the establishment of the Phasmatodea, their internal classification has been constantly revised. Mitochondrial genes as molecular markers have been widely used for species classification, but the phylogenetic relationships within the Phasmatodea remain to be thoroughly discussed. In the present study, five mitogenomes of Phasmatodea ranging from 15,746 bp to 16,747 bp in length were sequenced. Bayesian inference (BI) and maximum likelihood (ML) analyses were carried out based on a 13 PCGs data matrix (nt123) and a combined matrix of 13 PCGs and two rRNA genes (nt123_rRNA). The present study supports the conclusion that Phylliidae was the basal group of Neophasmatodea and confirms the monophyly of Lonchodinae and Necrosciinae, but it shows that Lonchodidae was polyphyletic. A sister group of Bacillidae and Pseudophasmatidae was also recovered. The phylogenetic tree based on the nt_123 dataset showed higher node support values. The construction of a divergent time tree in this study supported the conclusion that extant Phasmatodea originated in the Jurassic (170 Mya) and most lineages diverged after the Cretaceous-Paleogene extinction event. To explore whether the mitochondrial genes of Phraortes liaoningensis collected from high latitudes where low temperatures occur for eight months of the year are under selection pressure, this study used the branch-site model and the branch model to analyze the selection pressure on the 13 mitochondria protein-coding genes (PCGs). We found that both ND2 and ND4L of Ph. liaoningensis exhibited positive selection sites using the branch-site model. This study shows that a low-temperature environment causes mitochondrial genes to be selected to meet the energy requirements for survival.

The Complete Mitochondrial Genome of Nephropsis grandis: Insights into the Phylogeny of Nephropidae Mitochondrial Genome

The systematic phylogeny of Pleocyemata species, particularly within the family Nephropidae, remains incomplete. In order to enhance the taxonomy and systematics of Nephropidae within the evolutionary context of Pleocyemata, we embarked upon a comprehensive study aiming to elucidate the phylogenetic position of Nephropsis grandis. Consequently, we determined the complete mitochondrial DNA sequence for N. grandis. The circular genome spans a length of 15,344 bp and exhibits a gene composition analogous to that observed in other metazoans, encompassing a comprehensive set of 37 genes. Additionally, the genome features an AT-rich region. The rRNAs exhibited the highest AT content among the 37 genes (70.41%), followed by tRNAs (67.42%) and protein-coding genes (PCGs) (62.76%). The absence of a dihydrouracil arm in trnS1 prevented the formation of the canonical cloverleaf secondary structure. Selective pressure analysis indicated that the PCGs underwent purifying selection. The Ka/Ks ratios for cox1, cox2, cox3, and cob were considerably lower compared to other PCGs, implying strong purifying selection acting upon these particular genes. The mitochondrial gene order in N. grandis was consistent with the reported order in ancestral Pleocyemata. Phylogenetic revealed that N. grandis forms a cluster with the genus Metanephrops, and this cluster further groups with Homarus and the genus Nephrops within the Nephropidae family. These findings provide robust support for N. grandis as an ancestral member of the Nephropidae family. This study highlights the significance of employing complete mitochondrial genomes in phylogenetic analysis and deepens our understanding of the evolution of the Nephropidae family.

Phylogenetic and divergence analysis of Pentatomidae, with a comparison of the mitochondrial genomes of two related species (Hemiptera, Pentatomidae)

Pentatomidae, the most diverse family of Pentatomoidea, is found worldwide. Currently, the phylogenetic relationships among Pentatomidae tribes remain unstable, and subfamily divergence has not been estimated. Here, we sequenced and analyzed the complete mitochondrial genomes of two species of Lelia, and studied the phylogenetic relationships among Pentatominae tribes. We also selected three available fossil as the calibration points in the family, and preliminarily discussed the divergence time of Pentatomidae. Trees of Pentatomidae were reconstructed using the Bayesian inference method. Divergence times of Pentatominae were estimated based on the nucleotide sequences of protein-coding genes with a relaxed clock log-normal model in BEASTv.1.8.2. The results showed that the gene arrangements, nucleotide composition, and codon preferences were highly conserved in Lelia. Further, a phylogenetic analysis recovered Eysarcorini, Strachiini, Phyllocephalini, and Menidini as monophyletic with strong support, however, the monophyly of Antestiini, Nezarini, Carpocorini, Pentatomini and Cappaeini were rejected. Moreover, Pentatominae diverged from Pentatomidae soon after the origin of the Cretaceous Period, at approximately 110.38 Ma. This study enriches the mitochondrial genome database of Pentatomidae and provides a reference for further phylogenetic studies, and provides a more accurate estimate of divergence time.

Comparative Phylogenomic Study of Malaxidinae (Orchidaceae) Sheds Light on Plastome Evolution and Gene Divergence

Malaxidinae is one of the most confusing groups in the Orchidaceae classification. Previous phylogenetic analyses have revealed that the relationships between the taxa in Malaxidinae have not yet been reliably established, using only a few plastome regions and nuclear ribosomal internal transcribed spacer (nrITS). In the present study, the complete plastomes of Oberonia integerrima and Crepidium purpureum were assembled using high-throughput sequencing. Combined with publicly available complete plastome data, this resulted in a dataset of 19 plastomes, including 17 species of Malaxidinae. The plastome features and phylogenetic relationships were compared and analyzed. The results showed the following: (1) Malaxidinae species plastomes possess the quadripartite structure of typical angiosperms, with sizes ranging from 142,996 to 158,787 bp and encoding from 125 to 133 genes. The ndh genes were lost or pseudogenized to varying degrees in six species. An unusual inversion was detected in the large single-copy region (LSC) of Oberonioides microtatantha. (2) Eight regions, including ycf1, matK, rps16, rpl32, ccsA-ndhD, clpP-psbB, trnFGAA-ndhJ, and trnSGCU-trnGUCC, were identified as mutational hotspots. (3) Based on complete plastomes, 68 protein-coding genes, and 51 intergenic regions, respectively, our phylogenetic analyses revealed the genus-level relationships in this subtribe with strong support. The Liparis was supported as non-monophyletic.

The Complete Mitochondrial Genome of the Siberian Scoter Melanitta stejnegeri and Its Phylogenetic Relationship in Anseriformes

The Siberian Scoter (Melanitta stejnegeri) is a medium sea duck distinct from M. deglandi due to the absence of hybridization and differences in morphological characteristics. However, knowledge of its phylogenetic relationships within Anseriformes is limited due to a lack of molecular data. In this study, the complete mitogenome of M. stejnegeri was firstly sequenced, then annotated and used to reconstruct the phylogenetic relationships of 76 Anseriformes species. The complete mitogenome of M. stejnegeri is 16,631 bp and encodes 37 typical genes: 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and 1 non-coding control region. Its mitogenome organization is similar to that of other Anseriformes species. The phylogenetic relationships within the genus Melanitta are initially clarified, with M. americana at the base. M. stejnegeri and M. deglandi are sister groups, clustering with M. fusca and M. perspicillata in order. Phylogenetic analysis suggests that Mareca falcata and M. strepera are sister groups, differing from previous studies. Results firstly indicate that Clangula hyemalis and Somateria mollissima are sister groups, suggesting a potentially skewed phylogenetic relationship may have been overlooked in earlier analyses relying solely on mitochondrial genomes. Our results provide new mitogenome data to support further phylogenetic and taxonomic studies of Anseriformes.

Resolving phylogenetic relationships and taxonomic revision in the Pseudogastromyzon (Cypriniformes, Gastromyzonidae) genus: molecular and morphological evidence for a new genus, Labigastromyzon

The Pseudogastromyzon genus, consisting of species predominantly distributed throughout southeastern China, has garnered increasing market attention in recent years due to its ornamental appeal. However, the overlapping diagnostic attributes render the commonly accepted criteria for interspecific identification unreliable, leaving the phylogenetic relationships among Pseudogastromyzon species unexplored. In the present study, we undertake molecular phylogenetic and morphological examinations of the Pseudogastromyzon genus. Our phylogenetic analysis of mitochondrial genes distinctly segregated Pseudogastromyzon species into two clades: the Pseudogastromyzon clade and the Labigastromyzon clade. A subsequent morphological assessment revealed that the primary dermal ridge (specifically, the second ridge) within the labial adhesive apparatus serves as an effective and precise interspecific diagnostic characteristic. Moreover, the distributional ranges of Pseudogastromyzon and Labigastromyzon are markedly distinct, exhibiting only a narrow area of overlap. Considering the morphological heterogeneity of the labial adhesive apparatus and the substantial division within the molecular phylogeny, we advocate for the elevation of the Labigastromyzon subgenus to the status of a separate genus. Consequently, we have ascertained the validity of the Pseudogastromyzon and Labigastromyzon species, yielding a total of six valid species. To facilitate future research, we present comprehensive descriptions of the redefined species and introduce novel identification keys.

Ecological Changes Exacerbating the Spread of Invasive Ticks has Driven the Dispersal of Severe Fever with Thrombocytopenia Syndrome Virus Throughout Southeast Asia

Severe fever with thrombocytopenia syndrome virus (SFTSV) is a tick-borne virus recognized by the World Health Organization as an emerging infectious disease of growing concern. Utilizing phylodynamic and phylogeographic methods, we have reconstructed the origin and transmission patterns of SFTSV lineages and the roles demographic, ecological, and climatic factors have played in shaping its emergence and spread throughout Asia. Environmental changes and fluctuations in tick populations, exacerbated by the widespread use of pesticides, have contributed significantly to its geographic expansion. The increased adaptability of Lineage L2 strains to the Haemaphysalis longicornis vector has facilitated the dispersal of SFTSV through Southeast Asia. Increased surveillance and proactive measures are needed to prevent further spread to Australia, Indonesia, and North America.

The Phylogenetic Relationships of Major Lizard Families Using Mitochondrial Genomes and Selection Pressure Analyses in Anguimorpha

Anguimorpha, within the order Squamata, represents a group with distinct morphological and behavioral characteristics in different ecological niches among lizards. Within Anguimorpha, there is a group characterized by limb loss, occupying lower ecological niches, concentrated within the subfamily Anguinae. Lizards with limbs and those without exhibit distinct locomotor abilities when adapting to their habitats, which in turn necessitate varying degrees of energy expenditure. Mitochondria, known as the metabolic powerhouses of cells, play a crucial role in providing approximately 95% of an organism's energy. Functionally, mitogenomes (mitochondrial genomes) can serve as a valuable tool for investigating potential adaptive evolutionary selection behind limb loss in reptiles. Due to the variation of mitogenome structures among each species, as well as its simple genetic structure, maternal inheritance, and high evolutionary rate, the mitogenome is increasingly utilized to reconstruct phylogenetic relationships of squamate animals. In this study, we sequenced the mitogenomes of two species within Anguimorpha as well as the mitogenomes of two species in Gekkota and four species in Scincoidea. We compared these data with the mitogenome content and evolutionary history of related species. Within Anguimorpha, between the mitogenomes of limbless and limbed lizards, a branch-site model analysis supported the presence of 10 positively selected sites: Cytb protein (at sites 183 and 187), ND2 protein (at sites 90, 155, and 198), ND3 protein (at site 21), ND5 protein (at sites 12 and 267), and ND6 protein (at sites 72 and 119). These findings suggested that positive selection of mitogenome in limbless lizards may be associated with the energy requirements for their locomotion. Additionally, we acquired data from 205 mitogenomes from the NCBI database. Bayesian inference (BI) and Maximum Likelihood (ML) trees were constructed using the 13 mitochondrial protein-coding genes (PCGs) and two rRNAs (12S rRNA and 16S rRNA) from 213 mitogenomes. Our phylogenetic tree and the divergence time estimates for Squamata based on mitogenome data are consistent with results from previous studies. Gekkota was placed at the root of Squamata in both BI and ML trees. However, within the Toxicofera clade, due to long-branch attraction, Anguimorpha and (Pleurodonta + (Serpentes + Acrodonta)) were closely related groupings, which might indicate errors and also demonstrate that mitogenome-based phylogenetic trees may not effectively resolve long-branch attraction issues. Additionally, we reviewed the origin and diversification of Squamata throughout the Mesozoic era, suggesting that Squamata originated in the Late Triassic (206.05 Mya), with the diversification of various superfamilies occurring during the Cretaceous period. Future improvements in constructing squamate phylogenetic relationships using mitogenomes will rely on identifying snake and acrodont species with slower evolutionary rates, ensuring comprehensive taxonomic coverage of squamate diversity, and increasing the number of genes analyzed.

Comparative Analysis of Codon Usage Bias in Six Eimeria Genomes

The codon usage bias (CUB) of genes encoded by different species' genomes varies greatly. The analysis of codon usage patterns enriches our comprehension of genetic and evolutionary characteristics across diverse species. In this study, we performed a genome-wide analysis of CUB and its influencing factors in six sequenced Eimeria species that cause coccidiosis in poultry: Eimeria acervulina, Eimeria necatrix, Eimeria brunetti, Eimeria tenella, Eimeria praecox, and Eimeria maxima. The GC content of protein-coding genes varies between 52.67% and 58.24% among the six Eimeria species. The distribution trend of GC content at different codon positions follows GC1 > GC3 > GC2. Most high-frequency codons tend to end with C/G, except in E. maxima. Additionally, there is a positive correlation between GC3 content and GC3s/C3s, but a significantly negative correlation with A3s. Analysis of the ENC-Plot, neutrality plot, and PR2-bias plot suggests that selection pressure has a stronger influence than mutational pressure on CUB in the six Eimeria genomes. Finally, we identified from 11 to 15 optimal codons, with GCA, CAG, and AGC being the most commonly used optimal codons across these species. This study offers a thorough exploration of the relationships between CUB and selection pressures within the protein-coding genes of Eimeria species. Genetic evolution in these species appears to be influenced by mutations and selection pressures. Additionally, the findings shed light on unique characteristics and evolutionary traits specific to the six Eimeria species.

Identification of pre-flexion fish larvae from the western South Atlantic using DNA barcoding and morphological characters

Knowledge on species composition is the first step necessary for the proper conservation and management of biological resources and ecologically relevant species. High species diversity and a lack of diagnostic characters for some groups can impose difficulties for taxonomic identification through traditional methodologies, and ichthyoplankton (fish larvae and eggs) are a good example of such a scenario. With more than 35.000 valid species of fishes worldwide and overall similar anatomies in early developmental stages in closely related groups, fish larvae are often hard to be identified at the species or even more encompassing taxonomic levels. To overcome this situation, molecular techniques have been applied, with different markers tested over the years. Cytochrome c oxidase I (COI) is the most commonly used marker and now has the broadest public reference libraries, providing consistent results for species identification in different metazoan studies. Here we sequenced the mitochondrial COI-5P fragment of 89 fish larvae collected in the Campos Basin, coastal southeastern Brazil, and compared these sequences with references deposited in public databases to obtain taxonomic identifications. Most specimens identified are species of the Blenniiformes, with Parablennius and Labrisomus the most frequently identified genera. Parablennius included two species (P. marmoreus and P. pilicornis), while Labrisomus included three species (L. cricota, L. conditus and L. nuchipinnis). Anatomy of these molecularly identified specimens were then analyzed with the intention of finding anatomical characters that might be diagnostically informative amongst the early development stage (pre-flexion) larvae. Ventral pigmentation patterns are proposed as useful markers to identify Labrisomus species. However, additional specimens are needed to confirm if the character holds stability through the geographic distribution of the species.

A novel deep-benthic sea cucumber species of Benthodytes (Holothuroidea, Elasipodida, Psychropotidae) and its comprehensive mitochondrial genome sequencing and evolutionary analysis

BACKGROUND

The holothurians, commonly known as sea cucumbers, are marine organisms that possess significant dietary, nutritional, and medicinal value. However, the National Center for Biotechnology Information (NCBI) currently possesses only approximately 70 complete mitochondrial genome datasets of Holothurioidea, which poses limitations on conducting comprehensive research on their genetic resources and evolutionary patterns. In this study, a novel species of sea cucumber belonging to the genus Benthodytes, was discovered in the western Pacific Ocean. The genomic DNA of the novel sea cucumber was extracted, sequenced, assembled and subjected to thorough analysis.

RESULTS

The mtDNA of Benthodytes sp. Gxx-2023 (GenBank No. OR992091) exhibits a circular structure spanning 17,386 bp, comprising of 13 protein-coding genes (PCGs), 24 non-coding RNAs (2 rRNA genes and 22 tRNA genes), along with two putative control regions measuring 882 bp and 1153 bp, respectively. It exhibits a high AT% content and negative AT-skew, which distinguishing it from the majority of sea cucumbers in terms of environmental adaptability evolution. The mitochondrial gene homology between Gxx-2023 and other sea cucumbers is significantly low, with less than 91% similarity to Benthodytes marianensis, which exhibits the highest level of homology. Additionally, its homology with other sea cucumbers is below 80%. The mitogenome of this species exhibits a unique pattern in terms of start and stop codons, featuring only two types of start codons (ATG and ATT) and three types of stop codons including the incomplete T. Notably, the abundance of AT in the Second position of the codons surpasses that of the First and Third position. The gene arrangement of PCGs exhibits a relatively conserved pattern, while there exists substantial variability in tRNA. Evolutionary analysis revealed that it formed a distinct cluster with B. marianensis and exhibited relatively distant phylogenetic relationships with other sea cucumbers.

CONCLUSIONS

These findings contribute to the taxonomic diversity of sea cucumbers in the Elasipodida order, thereby holding significant implications for the conservation of biological genetic resources, evolutionary advancements, and the exploration of novel sea cucumber resources.

A new species of the genus Luciogobius Gill, 1859 (Teleostei, Oxudercidae) from Taiwan

A new species, Luciogobiusopisthoproctus sp. nov., is described based on 18 specimens collected from Daxi Creek (Yilan) and Babian Creek (Taitung) in Taiwan. The new species is characterized by having a yellowish body with scattered spots on the sides, a black blotch on the caudal fin, the absence of free pectoral-fin rays, and more than 40 vertebrae. The new species can be distinguished from congeners by the following combination of characters: AAA distance (anus to anal-fin origin) shorter than twice the body depth at anus, 4.2-7.2% of standard length (SL); pre-anus length 80.0-92.8% of pre-anal-fin length; snout length 39.7-62.7% of AAA distance; abdominal vertebrae 20-22; caudal vertebrae 20-22; first anal-fin pterygiophore usually inserted behind the second haemal spine.

Mitochondrial Genome Characteristics Reveal Evolution of Acanthopsetta nadeshnyi (Jordan and Starks, 1904) and Phylogenetic Relationships

In the present study, the mitochondrial genomic characteristics of Acanthopsetta nadeshnyi have been reported and have depicted the phylogenetic relationship among Pleuronectidae. Combined with a comparative analysis of 13 PCGs, the TN93 model was used to review the neutral evolution and habitat evolution catalysis of the mitogenome to verify the distancing and purification selectivity of the mitogenome in Pleuronectidae. At the same time, a species differentiation and classification model based on mitogenome analysis data was established. This study is expected to provide a new perspective on the phylogenetic relationship and taxonomic status of A. nadeshnyi and lay a foundation for further exploration of environmental and biological evolutionary mechanisms.

Purifying selection drove the adaptation of mitochondrial genes along with correlation of gene rearrangements and evolutionary rates in two subfamilies of Whitefly (Insecta: Hemiptera)

Insect mitochondrial genomes (mitogenomes) are usually represented by a conserved gene order. Whiteflies exhibit gene rearrangement in their mitogenomes; however, understanding how nucleotide substitution rates shape gene rearrangement in whiteflies is unclear due to the limited number of mitogenomes. Additionally, the mechanisms by which selection pressure drives adaptations in mitochondrial genes in the two subfamilies of whiteflies are not yet known. Here, we analyzed 18 whitefly mitogenomes, including one newly generated mitogenome, to compare nucleotide substitution rates, selection pressure, and gene arrangements. The newly generated mitogenome is reported along with reannotation of Pealius mori and comparisons to other whitefly mitogenomes. Comparative studies on nucleotide composition of 18 whiteflies revealed the positive GC skewness, confirming the reversal of strand asymmetry. We found 11 rearranged gene orders within two subfamilies of whiteflies with 8-18 breakpoints of gene rearrangements. Members of the subfamily Aleyrodinae exhibit more complex pathways in the evolution of gene order as compared to the subfamily Aleurodicinae. Our findings also revealed that the increase or reduction of nucleotide substitution rates does not have an impact on any of the gene rearrangement scenarios depicting neutral correlation. Selection pressure analysis revealed that the mitogenomes from members of both the subfamilies Aleurodicinae and Aleyrodinae are characterized by intense purifying selection pressure.

Differential Mitochondrial Genome Expression of Four Hylid Frog Species under Low-Temperature Stress and Its Relationship with Amphibian Temperature Adaptation

Extreme weather poses huge challenges for animals that must adapt to wide variations in environmental temperature and, in many cases, it can lead to the local extirpation of populations or even the extinction of an entire species. Previous studies have found that one element of amphibian adaptation to environmental stress involves changes in mitochondrial gene expression at low temperatures. However, to date, comparative studies of gene expression in organisms living at extreme temperatures have focused mainly on nuclear genes. This study sequenced the complete mitochondrial genomes of five Asian hylid frog species: Dryophytes japonicus, D. immaculata, Hyla annectans, H. chinensis and H. zhaopingensis. It compared the phylogenetic relationships within the Hylidae family and explored the association between mitochondrial gene expression and evolutionary adaptations to cold stress. The present results showed that in D. immaculata, transcript levels of 12 out of 13 mitochondria genes were significantly reduced under cold exposure (p < 0.05); hence, we put forward the conjecture that D. immaculata adapts by entering a hibernation state at low temperature. In H. annectans, the transcripts of 10 genes (ND1, ND2, ND3, ND4, ND4L, ND5, ND6, COX1, COX2 and ATP8) were significantly reduced in response to cold exposure, and five mitochondrial genes in H. chinensis (ND1, ND2, ND3, ND4L and ATP6) also showed significantly reduced expression and transcript levels under cold conditions. By contrast, transcript levels of ND2 and ATP6 in H. zhaopingensis were significantly increased at low temperatures, possibly related to the narrow distribution of this species primarily at low latitudes. Indeed, H. zhaopingensis has little ability to adapt to low temperature (4 °C), or maybe to enter into hibernation, and it shows metabolic disorder in the cold. The present study demonstrates that the regulatory trend of mitochondrial gene expression in amphibians is correlated with their ability to adapt to variable climates in extreme environments. These results can predict which species are more likely to undergo extirpation or extinction with climate change and, thereby, provide new ideas for the study of species extinction in highly variable winter climates.

Phylogenomics and plastomics offer new evolutionary perspectives on Kalanchoideae (Crassulaceae)

BACKGROUND AND AIMS

Kalanchoideae is one of three subfamilies within Crassulaceae and contains four genera. Despite previous efforts, the phylogeny of Kalanchoideae remains inadequately resolved with persistent issues including low support, unstructured topologies and polytomies. This study aimed to address two central objectives: (1) resolving the pending phylogenetic questions within Kalanchoideae by using organelle-scale 'barcodes' (plastomes) and nuclear data; and (2) investigating interspecific diversity patterns among Kalanchoideae plastomes.

METHODS

To explore the plastome evolution in Kalanchoideae, we newly sequenced 38 plastomes representing all four constituent genera (Adromischus, Cotyledon, Kalanchoe and Tylecodon). We performed comparative analyses of plastomic features, including GC and gene contents, gene distributions at the IR (inverted repeat) boundaries, nucleotide divergence, plastomic tRNA (pttRNA) structures and codon aversions. Additionally, phylogenetic inferences were inferred using both the plastomic dataset (79 genes) and nuclear dataset (1054 genes).

KEY RESULTS

Significant heterogeneities were observed in plastome lengths among Kalanchoideae, strongly correlated with LSC (large single copy) lengths. Informative diversities existed in the gene content at SSC/IRa (small single copy/inverted repeat a), with unique patterns individually identified in Adromischus leucophyllus and one major Kalanchoe clade. The ycf1 gene was assessed as a shared hypervariable region among all four genera, containing nine lineage-specific indels. Three pttRNAs exhibited unique structures specific to Kalanchoideae and the genera Adromischus and Kalanchoe. Moreover, 24 coding sequences revealed a total of 41 lineage-specific unused codons across all four constituent genera. The phyloplastomic inferences clearly depicted internal branching patterns in Kalanchoideae. Most notably, by both plastid- and nuclear-based phylogenies, our research offers the first evidence that Kalanchoe section Eukalanchoe is not monophyletic.

CONCLUSIONS

This study conducted comprehensive analyses on 38 newly reported Kalanchoideae plastomes. Importantly, our results not only reconstructed well-resolved phylogenies within Kalanchoideae, but also identified highly informative unique markers at the subfamily, genus and species levels. These findings significantly enhance our understanding of the evolutionary history of Kalanchoideae.

Isospora and Lankesterella Parasites (Eimeriidae, Apicomplexa) of Passeriform Birds in Europe: Infection Rates, Phylogeny, and Pathogenicity

Wild birds are common hosts to numerous intracellular parasites such as single-celled eukaryotes of the family Eimeriidae (order Eucoccidiorida, phylum Apicomplexa). We investigated the infection rates, phylogeny, and pathogenicity of Isospora and Lankesterella parasites in wild and captive passerine birds. Blood and tissue samples of 815 wild and 15 deceased captive birds from Europe were tested using polymerase chain reaction and partial sequencing of the mitochondrial cytochrome b and cytochrome c oxidase I and the nuclear 18S rRNA gene. The infection rate for Lankesterella in wild birds was 10.7% compared to 5.8% for Isospora. Chromogenic in situ hybridization with probes targeting the parasites' 18S rRNA was employed to identify the parasites' presence in multiple organs, and hematoxylin-eosin staining was performed to visualize the parasite stages and assess associated lesions. Isospora parasites were mainly identified in the intestine, spleen, and liver. Extraintestinal tissue stages of Isospora were accompanied by predominantly lymphohistiocytic inflammation of varying severity. Lankesterella was most frequently detected in the spleen, lung, and brain; however, infected birds presented only a low parasite burden without associated pathological changes. These findings contribute to our understanding of Isospora and Lankesterella parasites in wild birds.

Effectiveness of multigene analysis for associating dimorphic partners in flat wasps (Hymenoptera, Bethylidae, Dissomphalus)

DNA sequences have proved valuable for associating males and females of the same dimorphic species in Hymenoptera. These molecular associations, however, depend on the used DNA sequences and the analysis methods. In the present study, we evaluated the molecular associations on 23 species of Dissomphalus (Hymenoptera, Bethylidae) using the three most common DNA sequences in molecular studies of Hymenoptera (28S rRNA, COI and ITS2). Our results indicated the male-female association with these three markers. COI, however, showed to be more suitable than the other markers because there was no overlap of genetic variation among species. In contrast, the 28S rRNA showed overlapping of genetic distance limits, indicating that the distance matrix is not enough to assign a sexual conspecificity. We were able to perform female association to the described species D. verus Mugrabi & Azevedo, demonstrating that phylogenetic analysis is a valuable tool for associating the sexes of dimorphic species.

Describe the morphology and mitochondrial genome of Mecidea indica Dallas, 1851 (Hemiptera, Pentatomidae), with its phylogenetic position

We here describe the external morphology and complete mitochondrial genome characteristics of Mecidea indica Dallas, 1851, and clarify the evolutionary rate and divergence time. The M. indica mitochondrial genome length is 15,670 bp, and it exhibits a typical high A+T-skew (76.31%). The sequence shows strong synteny with the original gene arrangement of Drosophila yakuba Burla, 1954 without rearrangement. The M. indica mitochondrial genome characteristics were analyzed, and phylogenetic trees of Pentatomidae were reconstructed using Bayesian methods based on different datasets of the mitochondrial genome datasets. Phylogenetic analysis shows that M. indica belongs to Pentaotominae and form a sister-group with Anaxilaus musgravei Gross, 1976, and Asopinae is highly supported as monophyletic. Molecular clock analysis estimates a divergence time of Pentatomidae of 122.75 Mya (95% HPD: 98.76-145.43 Mya), within the Mesozoic Cretaceous; the divergence time of M. indica and A. musgravii was no later than 50.50 Mya (95% HPD: 37.20-64.80 Mya). In addition, the divergence time of Asopinae was 62.32 Mya (95% HPD: 47.08-78.23 Mya), which was in the Paleogene of the Cenozoic era. This study is of great significance for reconstructing the phylogeny of Pentatomidae and providing insights into its evolutionary history.

Characterization of the complete mitochondrial genome of Desmaulus extinctorium (Littorinimorpha, Calyptraeoidea, Calyptraeidae) and molecular phylogeny of Littorinimorpha

For the purpose of determining the placement of Calyptraeidae within the Littorinimorpha, we hereby furnish a thorough analysis of the mitochondrial genome (mitogenome) sequence of Desmaulus extinctorium. This mitogenome spans 16,605 base pairs and encompasses the entire set of 37 genes, including 13 PCGs, 22 tRNAs and two rRNAs, with an evident AT bias. Notably, tRNASer1 and tRNASer2 lack dihydrouracil (DHU) arms, resulting in an inability to form a secondary structure. Similarly, tRNAAla lacks a TΨC arm, rendering it incapable of forming a secondary structure. In contrast, the remaining tRNAs demonstrate a characteristic secondary structure reminiscent of a cloverleaf. A comparison with ancestral gastropods reveals distinct differences in three gene clusters (or genes), encompassing 15 tRNAs and eight PCGs. Notably, inversions and translocations represent the major types of rearrangements observed in D. extinctorium. Phylogenetic analysis demonstrates robust support for a monophyletic grouping of all Littorinimorpha species, with D. extinctorium representing a distinct Calyptraeoidea clade. In summary, this investigation provides the first complete mitochondrial dataset for a species of the Calyptraeidae, thus providing novel insights into the phylogenetic relationships within the Littorinimorpha.

Adaptive evolution of mitochondrial genomes in Triplophysa cavefishes

Extreme conditions in caves pose survival challenges for cave dwellers, who gradually develop adaptive survival features. Cavefishes are one of the most successful animals among cave dwellers. Triplophysa cavefishes are an important group of cavefishes, and they show remarkable adaptability to the extreme environments of caves. However, there is a limited understanding of their adaptation mechanisms. In this study, eight complete mitochondrial genomes of Triplophysa cavefishes were newly obtained, and their genomic characteristics, including the base composition, base bias, and codon usage, were analyzed. Phylogenetic analysis was carried out based on 13 mitochondrial protein-coding genes from 44 Nemacheilidae species. This showed that Triplophysa cavefishes and non-cavefishes separate into two reciprocally monophyletic clades, suggesting a single origin of the cave phenotype. Positive selection analysis strongly suggested that the selection pressure in cavefishes is higher than that in non-cavefishes. Furthermore, the ND5 gene in cavefishes showed evidence of positive selection, which suggests that the gene may play an important role in the adaptation of cavefishes to the cave environment. Protein structure analysis of the ND5 subunit implied that the sites of positive selection in cavefishes might allow them to acquire lower ND5 protein stability, compared to that in non-cavefishes, which might help the accumulation of nonsynonymous (mildly deleterious) mutations. Together, our study revealed the genetic signatures of cave adaptation in Triplophysa cavefishes from the perspective of energy metabolism.

A Guide to Phylogenomic Inference

Phylogenomics aims at reconstructing the evolutionary histories of organisms taking into account whole genomes or large fractions of genomes. Phylogenomics has significant applications in fields such as evolutionary biology, systematics, comparative genomics, and conservation genetics, providing valuable insights into the origins and relationships of species and contributing to our understanding of biological diversity and evolution. This chapter surveys phylogenetic concepts and methods aimed at both gene tree and species tree reconstruction while also addressing common pitfalls, providing references to relevant computer programs. A practical phylogenomic analysis example including bacterial genomes is presented at the end of the chapter.

Diversification dynamics of a common deep-sea octocoral family linked to the Paleocene-Eocene thermal maximum

The deep-sea has experienced dramatic changes in physical and chemical variables in the geological past. However, little is known about how deep-sea species richness responded to such changes over time and space. Here, we studied the diversification dynamics of one of the most diverse octocorallian families inhabiting deep sea benthonic environments worldwide and sustaining highly diverse ecosystems, Primnoidae. A newly dated species-level phylogeny was constructed to infer their ancestral geographic locations and dispersal rates initially. Then, we tested whether their global and regional (the Southern Ocean) diversification dynamics were mediated by dispersal rate and abiotic factors as changes in ocean geochemistry. Finally, we tested whether primnoids showed changes in speciation and extinction at discrete time points. Our results suggested primnoids likely originated in the southwestern Pacific Ocean during the Lower Cretaceous ∼112 Ma, with further dispersal after the physical separation of continental landmasses along the late Mesozoic and Cenozoic. Only the speciation rate of the Southern Ocean primnoids showed a significant correlation to ocean chemistry. Moreover, the Paleocene-Eocene thermal maximum marked a significant increase in the diversification of primnoids at global and regional scales. Our results provide new perspectives on the macroevolutionary and biogeographic patterns of an ecologically important benthic organism typically found in deep-sea environments.

The Phylogenetic Relationship of Lamiinae (Coleoptera: Cerambycidae) Using Mitochondrial Genomes

Lamiinae is the largest subfamily of the Cerambycidae (longhorn beetles), with approximately 21,863 described species. Previous phylogenetic studies of Lamiinae showed that this subfamily was monophyletic, but the relationship between the tribes of Lamiinae is still controversial. Partial molecular data and species morphological characteristics are not sufficient to resolve species phylogenetic studies perfectly. At the same time, the full mitochondrial genome contains more comprehensive genetic data. Benefiting from the development of next-generation sequencing (NGS), mitochondrial genomes can be easily acquired and used as reliable molecular markers to investigate phylogenetic relationships within Cerambycidae. Using NGS technology, we obtained 11 mitochondrial genome sequences of Lamiinae species. Based on this newly generated mitochondrial genome dataset matrix, we reconstructed the phylogeny of Lamiinae. The Bayesian Inference and Maximum Likelihood analyses strongly support the monophyly of four tribes (Lamiini, Batocerini, Mesosini, and Saperdini), whereas the tribe Acanthocinini was identified as paraphyletic. Other mitochondrial structural features were also observed: the start codon in the nad1 gene of all 11 mitochondrial genomes is TTG; 17-22 bp intergenic spacers (IGS) with a 'TACTA' motif were found between trnS2 and nad1. Moreover, two long IGS were found in Mesosa myops and Batocera sp. Tandem repeats were found in the IGS of Batocera sp.

Characterization of complete mitochondrial genome of three Horse flies of the genus Tabanus (Diptera: Tabanidae): comparative analysis

BACKGROUND

Tabanidae (Horse-Flies or Deer-Flies) are one of the most economically important as well as medically significant haematophagous insect family within the order Diptera. Members of this group are also responsible for the mortality of substantial number of live-stock every year. Due to their pathogen transmission potential and vector competencies makes them an important insect group to study. Till now, mitochondrial genome of 18 species of tabanids were available.

METHODS AND RESULTS

The complete mitogenome of three species T. diversifrons (15,809 bp), T. rubidus (15,878 bp) and T. tenens (15,872 bp) were generated by Next generation sequencing method. They consist 37 genes, with a positive AT skew and a negative GC skew. The gene order of these three species is similar to the typical gene arrangement of infra-order Tabanomorpha. Most of the tRNAs showed typical clover-leaf secondary structure except trnS1, which lacks the DHU arm. The sliding window analysis showed that the nad4L is the most conserved while atp8, and nad6 are the most variable genes. Moreover, the ratios of non-synonymous to synonymous substitution rates indicated that all PCGs under the purifying selection. Phylogeny revealed Chrysops and Haematopota are monophyletic while species of Hybomitra are nested within the polyphyletic clade of Tabanus. T. diversifrons exhibits sister relationship with Atylotus miser. Two morphologically divergent species T. rubidus and T. tenens are found to be genetically similar and indistinguishable by mitochondrial genome.

CONCLUSIONS

The hypervariable genes like atp8 and nad6 can be used as molecular markers for the identification of recently diverged lineages of family Tabanidae. Further, to address uncertainties arising from the two morphological divergent species, it is imperative to obtain data from nuclear gene markers.

Distinguish Dianthus species or varieties based on chloroplast genomes

Most plants belonging to the widely distributed genus Dianthus are used for gardening. Interspecific hybridization of different Dianthus species leads to blurred genetic backgrounds. To obtain more genomic resources and understand the phylogenetic relationships among Dianthus species, the chloroplast genomes of 12 Dianthus species, including nine Dianthus gratianopolitanus varieties, were analyzed. The chloroplast genomes of these 12 species exhibited similar sizes (149,474-149,735 bp), with Dianthus caryophyllus having a chloroplast genome size of 149,604 bp marked by a significant contraction in inverted repeats. In the chloroplast genome of Dianthus, we identified 124-126 annotated genes, including 83-84 protein-coding genes. Notably, D. caryophyllus had 83 protein-coding genes but lacked rpl2. The repeat sequences of the chloroplast genome were consistent among species, and variations in the sequence were limited and not prominent. However, notable gene replacements were observed in the boundary region. Phylogenetic analysis of Dianthus indicated that D. caryophyllus and D. gratianopolitanus were most closely related, suggesting that the degree of variation within nine Dianthus varieties was no less than the variation observed between species. These differences provide a theoretical foundation for a more comprehensive understanding of the diversity within Dianthus species.

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.