First detection of an ocellate octopus in the Revillagigedos ecoregion, a biodiversity hotspot located in the Tropical East Pacific Province.

Eupatorium lindleyanum is a widely utilized traditional medicinal plant with diverse pharmacological activities, extensive distribution, and abundant resources, making it a promising candidate for industrial and scientific research. However, limited genomic resources and unclear genetic relationships have hindered its development. To date, molecular studies on E. lindleyanum are scarce, and no detailed mitochondrial genome analyses have been reported for congeneric species. In this study, we present the first complete assembly and annotation of the mitochondrial and plastid genomes of E. lindleyanum, investigating their potential for phylogenetic reconstruction within Asteraceae. Using Illumina NovaSeq and Nanopore PromethION platforms, 13.4Gb and 12Gb of raw sequencing data were generated, respectively. The mitochondrial genome of E. lindleyanum is a 299,285bp circular DNA molecule with a GC content of 45.06%, encoding 32 unique protein-coding genes, 17 tRNA genes, and 3 rRNA genes. The plastid genome of E. lindleyanum, a typical quadripartite circular structure, is 151,377bp in length with a GC content of 37.60%, comprising 80 unique protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Codon usage analysis revealed a preference for A or T at the third codon position in mitochondrial genes. The mitochondrial genome contains 73 simple sequence repeats, 31 tandem repeats, 274 dispersed repeats, and 504 predicted RNA editing sites. Additionally, 11,245bp of homologous sequences were identified between the mitochondrial and plastid genomes, accounting for 3.76% of the mitochondrial genome. Comparative analysis with E. chinense demonstrated significant structural variation within mitochondrial genomes of the Eupatorium genus, highlighting potential evolutionary mechanisms such as gene loss and functional compensation. Phylogenetic reconstruction using mitochondrial genome data further confirmed its utility in resolving evolutionary patterns and relationships, providing complementary insights to traditional plastid-based approaches. These findings provide foundational genomic resources for E. lindleyanum, offering critical insights into the evolution of mitochondrial genomes in the genus Eupatorium. This study also contributes to understanding the evolutionary mechanisms and environmental adaptability of E. lindleyanum, paving the way for future research on its genetic and functional diversity.

ABSTRACTClarion Island, in the Revillagigedo Archipelago off the Pacific Coast of Mexico, hosts a unique assemblage of vertebrates. Introduced species have caused significant ecological damage, and Spiny‐tailed Iguanas (Ctenosaura pectinata) were assumed to have been introduced in recent times, prompting plans for eradication. To investigate the origin of the Ctenosaura population on Clarion Island, we conducted phylogenetic analyses of the Clarion Island and mainland populations using a portion of the mitochondrial DNA gene ND4. We estimated the date of divergence of the Clarion Island population from mainland Mexico populations using a relaxed‐clock method. Phylogenetic analyses reveal that Clarion iguanas are sister to mainland C. brachylopha populations in northwestern Mexico, a species recently resurrected out of C. pectinata. We estimated a divergence of approximately 425,600 years ago for the Clarion population—predating human colonization of the Americas. These findings support natural dispersal, likely through rafting on vegetation mats, as the mechanism of colonization. Iguanas are well known for their ability to colonize islands, and this represents their second‐longest overwater dispersal (> 1100 km); slightly greater than the distance of the Galapagos Islands from mainland Ecuador. Our findings demonstrate that Spiny‐tailed Iguanas are native to Clarion Island and should be considered an integral part of the island's native fauna. Conservation plans must prioritize the protection of this population, which we identify as an evolutionarily significant unit (ESU). Further genetic sampling and analyses are needed to determine the population's genetic variation and taxonomic status. Our findings challenge prior assumptions and emphasize the need for evidence‐based conservation strategies to preserve the integrity of oceanic island ecosystems.

Molecular identification of ornamental loaches (Cypriniformes, Cobitoidei) of North East India using mitochondrial genes

Background:Prunus plants are widely distributed across Asia and Europe, yet their intricate phylogenetic relationships pose significant challenges for systematic studies and interspecies identification. Objectives: To clarify the mitochondrial and chloroplast genomes of Prunus salicina var. cordata, and to reveal its evolutionary relationship and historical gene flow with domesticated cherries. Methods: In this study, we assembled, annotated, and analyzed the first mitochondrial and chloroplast genomes of P. salicina var. cordata, a species within the Prunus genus. Results: The mitochondrial genome was found to be 484,858 base pairs in length, exhibiting a typical circular conformation. Phylogenetic analysis revealed a close evolutionary relationship between P. domestica and P. salicina, suggesting historical gene flow between these two species last genomes; mitochondrial genomes; phylogeny analysis. Conclusions: To provide a genomic basis for resolving the phylogenetic controversies within the Li-associated plants, elucidating their evolutionary mechanisms, and formulating breeding strategies.

The mitochondrial gene coding for the small rRNA (15S rRNA) of yeast has been isolated and its nucleotide sequence has been determined. A segment of mtDNA carrying the 15S rRNA gene was isolated from a ρ − mutant, strain P2. This ρ − genome has a tandemly repeated unique sequence of 5.5 kbp and carries the genetic markers par R 454 and ts1297 + . The position and orientation of this mtDNA with respect to the wild-type ( ρ + ) mtDNA have been established (Wesolowski et al. 1980). When digested by the restriction endonuclease Hpa II, the mtDNA produced 12 fragments, and two of these fragments (800 bp and 1100 bp) contained sequences homologous to the 15S rRNA sequence. This region of both strands was sequenced after 5′-end labeling and strand separation of various restriction fragments. SEQUENCE OF THE MITOCHONDRIAL 15S rRNA GENE Figure 1 shows the sequence of the 15S rRNA gene and the sequences immediately before and after the gene. Since many regions of this sequence showed obvious homology with the Escherichia coli 16S rRNA sequence, it was aligned with the bacterial sequence. Maximum homology was obtained when some stretches of sequence were considered as additions or deletions with respect to the bacterial sequence: About 44% of the bacterial sequence was homologous to the mitochondrial gene sequence. The mitochondrial sequence contains many internal inverted repeats and can be folded into base-paired structures. Figure 2 shows one of the possible secondary structures of the 15S rRNA, as deduced from the gene sequence. Although this structure may not represent...

ObjectiveGlarea lozoyensis is a filamentous fungus used for industrial production of the antifungal drug caspofungin. Previously, the mitochondrial genome (mitogenome) of a mutant strain ATCC 74030 was reported. The purpose of the current study is to test if mutagen treatments have caused changes on the mitogenome of the fungus. MethodsThe mitogenome of the wild strain ATCC 20868 was assembled and compared with the published mitogenome of ATCC 74030. PCR assays were done for both strains. Additional analyses were done using correct mitogenome sequences. ResultsWe successfully assembled the mitogenome of the wild strain ATCC 20868. Initial comparison of the mitogenomes of the wild and mutant strains indicated six variable nucleotide sites and two regions with length variations. PCR assays and subsequent sequencing, however, showed no difference between the two strains. The differences observed from initial comparison were due to sequence errors present in the published mitogenome of ATCC 74030. Interestingly, three intron-containing tRNAs and a rnpB gene were detected in the mitogenome of the fungus. Obvious repetitive elements were identified within the G. lozoyensis mitogenome, and duplication events were identified between its mitochondrial and nuclear genomes. ConclusionWe verified that there existed erroneous sequences in the published mitogenome of ATCC 74030; mutagens did not cause variations on the mitogenome of G. lozoyensis. We reported the authentic mitogenome sequence of G. lozoyensis and found frequent gene transfer between mitochondrial and nuclear genomes in the fungus.

Many methods, based on morphological, molecular or chemical characters, have been used to address the question of species taxonomic status. Integrative taxonomy aims to define stronger supported taxonomic hypotheses by considering complementary datasets from different characters. By following an integrative approach, the present study includes molecular, chemical and morphological criteria to establish the taxonomic status of two rare and doubtful cuckoo bumblebee taxa: Bombus (Psithyrus) barbutellus and Bombus (Psithyrus) maxillosus . These two sympatric taxa are discriminated by few morphological criteria (mainly wing darkness and hair length). We used these morphological character diagnoses to establish an a priori status of our samples (23 specimens). We developed a combined molecular dataset from one nuclear gene, elongation factor 1 α ( EF‐1α ), and one mitochondrial gene, cytochrome c oxidase subunit I ( COI ), spanning 1623 bp, and a chemical dataset of sexual marking pheromones (73 compounds). The molecular data were subjected to maximum‐likelihood and Bayesian phylogenetic inference under partitioned model and maximum parsimony. The chemical data were analysed by clustering and the two‐group k ‐means method to test divergences between the two species. The resulting phylogenetic trees show no consistent divergence between the two taxa. Moreover, we found no divergence in the sexual marking pheromones in the clustering and two‐group k ‐means analyses. These converging results support the conspecificity of both taxa. Nonetheless, our determinations using the traditional morphological criteria separated our samples into two taxa. We conclude that the morphological criteria seem to relate to intraspecific variations: B. maxillosus is regarded as a syn.n. of B. barbutellus .

BackgroundSargassum polycystum C. Agardh and Sargassum plagiophyllum C. Agardh are inhabitants of tropical coastal areas, their populations are negatively influenced by global warming and marine environment changes. The mitochondrial and chloroplast genomes of these species have not been sequenced.ResultsThe mitochondrial genomes of S. polycystum and S. plagiophyllum were 34,825 bp and 34,862 bp, respectively, and their corresponding chloroplast genomes were 124,493 bp and 124,536 bp, respectively. The mitochondrial and chloroplast genomes of these species share conserved synteny, sequence regions and gene number when compared with the organellar genomes of other Sargassum species. Based on sequence analysis of 35 protein-coding genes, we deduced that S. polycystum and S. plagiophyllum were closely related with S. ilicifolium; these species diverged approximately 0.3 million years ago (Ma; 0.1–0.53 Ma) during the Pleistocene period (0.01–2.59 Ma). Rates of synonymous and non-synonymous substitutions in the mitochondrial genome of the Sargassum genus were 3 times higher than those in the chloroplast genome. In the mitochondrial genome, rpl5, rpl31 and rps11 had the highest synonymous substitution rates. In the chloroplast genome, psaE, rpl14 and rpl27 had the highest synonymous substitution rates.ConclusionsPhylogenetic analysis confirms the close relationship between the two sequenced species and S. ilicifolium. Both synonymous and non-synonymous substitution rates show significant divergence between the group of mitochondrial genomes versus the group of chloroplast genomes. The deciphering of complete mitochondrial and chloroplast genomes is significant as it advances our understanding of the evolutionary and phylogenetic relationships between species of brown seaweeds.

The mitochondrial and nuclear genomes of Coprinus stercorarius and C. cinereus were compared to assess their evolutionary relatedness and to characterize at the molecular level changes that have occurred since they diverged from a common ancestor. The mitochondrial genome of C. stercorarius (91.1 kb) is approximately twice as large as that of C. cinereus (43.3 kb). The pattern of restriction enzyme recognition sites shows both genomes to be circular, but reveals no clear homologies; furthermore, the order of structural genes is different in each species. The C. stercorarius mitochondrial genome contains a region homologous to a probe derived from the yeast mitochondrial var1 gene, whereas its nuclear genome does not. By contrast, the C. cinereus nuclear, but not mitochondrial, genome contains a region homologous to the var1 probe. Only a small fraction of either the nuclear or mitochondrial genomes, perhaps corresponding to the coding sequences, is capable of forming duplexes in interspecies solution reassociations, as measured by binding to hydroxylapatite. Those sequences capable of reassociating were found to have approximately 15% divergence for the mitochondrial genomes and 7%-15% divergence for the nuclear genomes, depending on the conditions of reassociation.

Barbouriidae Christoffersen, 1987 is a family comprised of 4 genera and 11 species of enigmatic shrimps restricted to anchialine or marine caves whose evolutionary history and relationships remain elusive. We investigated the evolutionary relationships among members of Barbouriidae with the inclusion of four genera and nine species, and newly collected material from Belize, the Bahamas, and the Yucatán Peninsula, Mexico. Phylogenetic analyses based on seven mitochondrial and nuclear gene regions and genetic distances calculated using partial 16S gene regions have identified a need to revisit the relationships and classification within Barbouriidae. More specifically, we find evidence to suggest Janicea Manning & Hart, 1984 as a junior synonym of Parhippolyte Borradaile, 1900, B. yanezi Mejía, Zarza & López, 2008 as a synonym of Barbouria cubensis (von Martens, 1872), and define two new subfamilies, Calliasmatinae Holthuis, 1973 and Barbouriinae Christoffersen, 1987. Included is a dichotomous key for the species of Barbouriidae that summarizes previous literature and includes new morphological characters. Our findings shed light on existing inaccuracies and gaps in molecular data from barbouriids. We also provide further clarity into evolutionary relationships among genera of Barbouriidae and their allies, suggesting phylogeographic divisions within the family. Our findings suggest an early Atlantic-Pacific divide among genera originating from a shallow-water reef ancestor.

Species complexes are often taxonomically challenging because the evolutionary relationships among closely related taxa may not be well reflected by morphological divergence. Molecular data can be a powerful tool in resolving these ambiguities. Using nuclear restriction fragment length polymorphisms (RFLPs), we examined genetic variation among 22 populations of the Acacia microbotrya complex and assessed its congruence with five taxa previously identified using morphological criteria. Four distinct genetic clusters were consistently detected across multiple analytical approaches (Bayesian, UPGMA, maximum likelihood, and principle coordinate). These genetic clusters were strongly congruent with each of four morphologically defined taxa, Acacia amblyophylla, Acacia daphnifolia, A. microbotrya and A. microbotrya (Dandaragan variant). From this, we suggest that the Dandaragan variant warrants formal recognition at the same taxonomic level as the other three taxa. Individuals of the fifth morphologically defined species, Acacia splendens, were not consistently assigned to any one genetic cluster having affinities with A. microbotrya (Dandaragan variant) and A. amblyophylla, although at the population level it showed closest affinity to A. microbotrya (Dandaragan variant). Despite strong genetic and morphological differentiation of these taxa in allopatric regions, we detected a hybrid zone of genetic admixture between A. microbotrya and A. daphnifolia where their geographic ranges overlap. Together, these results highlight a complex evolutionary history of fragmentation, divergence and hybridisation in the A. microbotrya complex. While further work is required to resolve the phylogenetic status of A. splendens, this study provides compelling evidence for the recognition of these four genetic clusters as distinct evolutionary entities in the A. microbotrya complex that should be treated as separate units for conservation, commercial or management purposes.

Animal phylogeny

Microphilypnus and Leptophilypnion are miniaturized genera within the family Eleotridae. The evolutionary relationships among these taxa are still poorly understood, and molecular analyses are restricted to mitochondrial genes, which have not been conclusive. We compiled both mitochondrial and nuclear genes to study the phylogenetic position of Microphilypnus and the evolutionary history and relationships of eleotrids. We propose that Microphilypnus and Leptophilypnus (a non-miniature genus) are not sister groups as suggested by previous studies, but rather separate lineages that arose in the early Eocene, with Leptophilypnus recovered as a sister group to the other analyzed eleotrids. In fact, Microphilypnus is currently associated with the Neotropical clade Guavina/Dormitator/Gobiomorus. We also identified a well-supported clade that indicated Gobiomorus and Hemieleotris as paraphyletic groups, besides a close relationship among Calumia godeffroyi, Bunaka gyrinoides, Eleotris and Erotelis species. This is the first comprehensive report about the evolutionary relationships in members of the family Eleotridae, including multiloci and multispecies approaches. Therefore, we provided new insights about the phylogenetic position of some taxa absent in previous studies, such as the miniature genus Microphilypnus and a recently described species of Eleotris from South America.

At the crossroads of two biodiversity hotspots; the biogeographic patterns of Shimba Hills, Kenya Beryl A. Bwong The Shimba Hills of Kenya (SHK) is geographically located at the cross roads of two major biodiversity hotspots; the Coastal Forests of Eastern Africa (CFEA) and the Eastern Afromontane Biodiversity Region, specifically the neighbouring Eastern Arc Mountains (EAM). Results from old and recent collections of its flora and fauna indicate that Shimba Hills harbour species associated with EAM and CFEA as well as taxa that have affinity with West African Guineo-Congolian forest. However, the link between SHK and these biodiversity hotspots has never been tested appropriately using phylogenetic approaches. Using 16S mtDNA, demographic analysis and species distribution modelling, I sought to understand the phylogeographic affiliation of Shimba Hills with the neighbouring CFEA and EAM using its amphibian assemblage. Three main questions were explored, namely: a) Which are the closest relatives of SHK amphibian populations? b) Do amphibian species currently occurring in SHK have similar phylogeographic patterns to each other? c) Which historical processes, if any, account for the observed patterns of genetic diversity? I found that SHK and indeed the entire study area have a complex biogeographic history and no single pattern can explain the current amphibian assemblage in the area. Shimba Hills are more closely affiliated to the CFEA than to the EAM. Two previously undocumented putative phylogeographic breaks are recovered from the study area; one from the Kenya north coast and another in the Tanga region in Tanzania. Historical habitat stability and connectivity appear to play a significant role in species diversification in the area. Additionally, I also report on some fundamental findings on Shimba Hills amphibians during this study; Using a combination of molecular, morphological, spatial and bioacoustics methods the taxonomic status of the only endemic amphibian from Shimba Hills, Hyperolius rubrovermiculatus, is confirmed and description of a new species from the north eastern Tanzania is proposed. Secondly the taxonomic status of a Callulina rediscovered in Shimba Hills after 50 years is confirmed and I also propose the description of three new species of Callulina from the neighbouring Eastern Arc Mountains in Tanzania. Finally, I took the opportunity to compile the first ever annotated checklist of amphibians of Shimba Hills National Reserve where a new country record for the Ribbon Caecilian (Scolecomorphus vittatus) and other interesting discoveries are discussed. The reserve plus the entire SHK area contains the highest number of amphibian diversity for any known locality in Kenya. Therefore its continued conservation will ensure about 30% of Kenya’s amphibian species are preserved. Key words: Coastal forests, Eastern Arc Mountains, Phylogeography, species distribution modelling, checklist, Amphibians.

Ma, K. Y., Chan, T. ‐Y & Chu, K. H. (2011). Refuting the six‐genus classification of Penaeus s.l. (Dendrobranchiata, Penaeidae): a combined analysis of mitochondrial and nuclear genes. —Zoologica Scripta, 40, 498–508.The taxonomic revision in 1997 of the shrimps formerly classified in Penaeus s.l. has been one of the most controversial issues on systematics of the decapods in recent years. Since Pérez Farfante & Kensley (Penaeoid and Sergestoid Shrimps and Prawns of the World, 1997) split this long‐accepted taxon into six genera, much debate has been devoted to their proposed new classification scheme; this has taken place because there are serious doubts whether the said scheme could reflect the evolutionary relationships among the 29 Penaeus s.l. species. Although these shrimps can be easily separated into several groups morphologically, whether these subdivisions are truly monophyletic and warrant a generic rank continues to be hotly debated among taxonomists. This study examined a total of 2425 bp sequences from three nuclear protein genes (enolase, phosphoenolpyruvate carboxykinase and sodium–potassium ATPase α‐subunit), and the mitochondrial 16S and 12S rRNA gene of 18 Penaeus s.l. shrimps and 13 other species in the family Penaeidae. Our phylogenetic analyses strongly support the monophyly of Penaeus s.l. and, concurring with previous studies that used the mitochondrial genes alone, the paraphyly of both Penaeus s.s. (sensu Pérez Farfante & Kensley, Penaeoid and Sergestoid Shrimps and Prawns of the World, 1997) and Melicertus, rendering them non‐natural groupings. Our study reveals two lineages: Penaeus s.s. + Fenneropenaeus + Litopenaeus + Farfantepenaeus and Melicertus + Marsupenaeus, which exhibit genetic divergences comparable with those among other penaeid genera. However, all the morphological characters, which are emphasized by Pérez Farfante and Kensley and used to separate Penaeus s.l., do not correlate with the grouping revealed by the present, perhaps decisive, phylogenetic result. Such disparity may arise from selection on the morphology of genitalia and convergent evolution. Our molecular data clearly refute the six‐genus classification, and we advocate the restoration of the old Penaeus genus (=Penaeus s.l.) definition which is the only classification scheme with both the morphological and the molecular data being in agreement.