Large Variation in the Ratio of Mitochondrial to Nuclear Mutation Rate across Animals: Implications for Genetic Diversity and the Use of Mitochondrial DNA as a Molecular Marker

Total-evidence phylogenetic analysis resolves the evolutionary timescale of mantis shrimps (Stomatopoda) and provides insights into their molecular and morphological evolutionary rates

The crustacean order Stomatopoda comprises approximately 500 species of mantis shrimps. These marine predators, common in tropical and subtropical waters, possess sophisticated visual systems and specialized hunting appendages. In this study, we infer the evolutionary relationships within Stomatopoda using a combined data set of 77 morphological characters, whole mitochondrial genomes, and three nuclear markers. Our data set includes representatives from all seven stomatopod superfamilies, including the first sequence data from Erythrosquilloidea. Using a Bayesian relaxed molecular clock with fossil-based calibration priors, we estimate that crown-group unipeltatan stomatopods appeared ∼ 143 (95 % credible interval 199-98) million years ago in the Mesozoic. Additionally, our results support the hypothesis that specialized smashing and spearing appendages appeared early in the evolutionary history of Unipeltata. We found no evidence of a correlation between rates of morphological and molecular evolution across the phylogeny, but identified very high levels of among-lineage rate variation in the morphological characters. Our total-evidence analysis recovered evolutionary signals from both molecular and morphological data sets, demonstrating the merit in combining these sources of information for phylogenetic inference and evolutionary analysis.

Horizontal transmission of functionally diverse transposons is a major source of new introns

Since the discovery of spliceosomal introns in eukaryotic genomes, the proximate molecular and evolutionary processes that generate new introns have remained a critical mystery. Specialized transposable elements (TEs), introners, are thought to be one of the major drivers of intron gain in diverse eukaryotes. However, the molecular mechanism(s) and evolutionary processes driving introner propagation within and between lineages remain elusive. Here, we analyze 8,716 genomes, revealing 1,093 introner families in 201 species spanning 1.7 billion years of evolution. Introners are derived from functionally diverse TEs including families of terminal-inverted-repeat DNA TEs, retrotransposons, cryptons, and helitrons as well as mobile elements with unknown molecular mechanisms. We identify eight cases where introners recently transferred between divergent host species and show that giant viruses that integrate into genomes may facilitate introner transfer across lineages. We propose that ongoing intron gain is primarily a consequence of TE activity in eukaryotes, thereby resolving a key mystery of genome structure evolution.

Speciation in the Peninsular Indian Flying Lizard (Draco dussumieri) Follows Climatic Transition and Not Physical Barriers

Marked with high levels of endemism and in situ radiations, the Western Ghats mountains make for a compelling backdrop to examine processes that lead to the formation and maintenance of species. Regional geographic barriers and paleoclimatic fluctuations have been implicated as drivers of speciation, but their roles have not been explicitly tested in a phylogenomic framework. We integrated mitochondrial DNA, genome-wide SNPs and climatic data to examine the influence of geographic barriers and climatic transitions in shaping phylogeography and potential speciation in the Peninsular Indian Flying lizard (Draco dussumieri). We found strong evidence for two independently evolving, geographically distinct, northern and southern lineages within D. dussumieri that diverged during the early Pleistocene, and a gradient of admixed populations across a broad hybrid zone in the Central Western Ghats. Migrations after initial divergence were continuous, but gene flow remained consistently below thresholds required to homogenise lineages. We found more support for isolation by environment (especially rainfall regimes) than by distance. The range-break between lineages occurs at a transition zone in the Central Western Ghats that separates dissimilar rainfall regimes with no physical barriers. This limit is potentially an ecological barrier, which nevertheless was permeable during glacial maxima. We hypothesise that similar phylogeographic patterns will emerge in other widespread, wet-adapted species in the Western Ghats that presumably endured the same climatic processes.

Whole-genomic comparison reveals complex population dynamics and parasitic adaptation of Echinococcus granulosus sensu stricto

Cystic echinococcosis (CE), caused by Echinococcus granulosus sensu stricto (s.s.), poses a substantial risk to both humans and domestic animals globally. Here, we compared the whole genomes of 111 E. granulosus s.s. samples from China. Genomic variation data revealed frequent cross-fertilization in the hermaphroditic E. granulosus. The G1 and G3 genotypes represent distinct mitochondrial lineages, while showing no differentiation in the nuclear genome, suggesting mito-nuclear discordance caused by historical geographic separation and subsequent fusion. Population structure, demographic history, and gene flow among populations reflected the transmission route of E. granulosus s.s. from the Middle East to Qinghai-Xizang Plateau through the migration of nomadic people, followed by introgression during secondary contact. Genomic variations highlighted selection signatures within the genome prone to balancing selection, particularly impacting genes encoding membrane-related proteins, representing a potential evolutionary strategy for adaptation to parasitic life. Balancing selection pressure on the gene-coding sodium/bile acid cotransporter led to its high level of genetic stability, which may play a crucial role in the survival and development of E. granulosus during the parasitic stage, making it a potential drug target for the treatment of CE. Meanwhile, other genomic regions under strong balancing selection may provide potential targets for protective immunity. These findings offer valuable insights into the complex dynamics and adaptive evolution of E. granulosus s.s. in China.IMPORTANCEEchinococcus granulosus sensu stricto (s.s.) is the primary cause of cystic echinococcosis (CE), a parasitic disease affecting humans and livestock with significant health and economic impacts. Previous studies on this parasite relied on mitochondrial DNA to classify its genotypes and understand its genetic diversity. However, these studies cannot capture the full complexity of its evolutionary dynamics and adaptation strategies. Our research employs comprehensive genome-wide sequencing, offering a more nuanced view of its genetic landscape. We discovered that cross-fertilization appears to be a prevalent reproductive strategy in the hermaphroditic E. granulosus, underpinning the observed deep mitochondrial divergence between genotypes G1 and G3, as well as gene flow among populations. The transmission history of E. granulosus s.s. in China and its widespread genetic mixing were likely facilitated by the migrations of nomadic peoples. Furthermore, we identified genes under balancing selection, including the gene involved in the uptake of host bile acids, which play a crucial role in the parasite's survival and development, potentially offering new targets for intervention. Our research advances the understanding of the genetic diversity and evolutionary strategies of E. granulosus, laying the foundation for improved control measures of CE.

Distinct latitudinal patterns of molecular rates across vertebrates

The latitudinal diversity gradient (LDG) is the most notable global biodiversity pattern, but its underlying mechanisms remain unresolved. The evolutionary speed hypothesis (ESH) posits that molecular rates play a crucial role in shaping the LDG, suggesting that higher temperatures accelerate molecular rates, thereby facilitating rapid speciation and accumulation of biodiversity in the tropics. However, whether ESH can explain the LDG across diverse taxonomic groups remains debated, and systematic examinations of its two key predictions using consistent datasets and methodologies across vertebrates are lacking. Here, we tested ESH using molecular rates from mitochondrial (5,424 species) and nuclear (1,512 species) genomes across major vertebrate groups, including fishes, amphibians, reptiles, mammals, and birds. Our findings revealed distinct latitudinal patterns in the absolute synonymous substitution rate (dS), which were influenced by thermoregulatory strategies. Specifically, the dS increases with ambient temperature and decreases with latitude in ectotherms but shows no correlation in most endotherms. These distinct patterns are likely attributed to different key predictors of dS between thermogroups, with temperature playing a major role only in ectotherms. For mitochondrial genes, absolute nonsynonymous substitution rates (dN) increase with temperature, likely driven by mutation rates in ectotherms and purifying selection in endotherms. However, neither mitochondrial dS nor dN correlates with diversification rates across vertebrates, contradicting the second prediction of ESH. For nuclear rates, the ESH was supported in reptiles and amphibians but not in mammals, birds, or fishes. In conclusion, our results provide limited support for ESH in vertebrates, underscoring the intricate processes that shape the LDG.

Introgression and Genetic Diversity Between Two Cactophilic Drosophila (Drosophila repleta group) Species: A Case Study of an Isolated Population from the Sandstone Hills in the Southeast of Brazil

Introgressive hybridization involves the integration of genetic material from one population into another genetically distinct population. Despite its widespread occurrence in nature, the mechanisms and consequences of introgression remain poorly understood. In this study, we examine the hypothesis that the mitochondrial gene COI from Drosophila antonietae has been introgressed into the gene pool of a specific population of D. gouveai. Additionally, we extended our analysis to include other genes associated with the COX complex, such as mitochondrial (COII) and nuclear genes (CoVa, CG9603, and levy), across various populations of both species from different locations. We estimated indices of genetic diversity, constructed haplotype networks in both mitochondrial and nuclear genes, and performed selection tests to assess the evolutionary dynamics of mitochondrial genes. Our results confirm the hypothesis of a historical secondary contact between D. gouveai and D. antonietae in the region of Analândia, SP, showing asymmetric unidirectional introgression, with signs of positive selection in the mitochondrial genes.

Phylogenomic Analysis of Wide-Ranging Least Shrews Refines Conservation Priorities and Supports a Paradigm for Evolution of Biota Spanning Eastern North America and Mesoamerica

Anthropogenic global change is impacting the evolutionary potential of biodiversity in ways that have been difficult to predict. Distinct evolutionary units within species may respond differently to the same environmental trends, reflecting unique geography, ecology, adaptation, or drift. Least shrews (Cryptotis parvus group) have a widespread distribution across North America, yet systematic relationships and ongoing evolutionary processes remain unresolved. Westernmost peripheral populations have been prioritized for conservation, but little is known of their evolutionary histories or population trajectories. The broad range of this group of species is coincident with many other temperate taxa, presenting a hypothesis that diversification of least shrews follows a repeated process through the Pleistocene, leading to regionally diagnosable conservation units. We use genomic data and niche modeling to delimit species and conservation units of least shrews. Our results show that least shrews warrant recognition as multiple distinct species, along with geographically discrete infraspecific lineages of C. parvus (sensu stricto). Western peripheral populations are evolutionarily distinct based on nuclear, but not mitochondrial data, possibly reflecting mitochondrial capture during the last glacial phase. This population represents a relict conservation unit, consistent with both an "adaptive unit" and "management unit" based on non-neutral and neutral divergence, respectively. Hindcast niche modeling supports growing evidence for a shared process of diversification among co-distributed biota, and forecast modeling suggests continued future loss of suitable environmental niche in peripheral regions. Given mito-nuclear discordance among samples of parapatric lineages, future environmental perturbation may continue to impact the genomic integrity of important conservation units, making ecological and genomic monitoring a critical need.

Advances in research on mitochondrial dysfunction in neurodegenerative diseases

Given the high energy demand of the nervous system, mitochondrial dysfunction is a key factor in the pathogenesis of neurodegenerative diseases. Thus, a comprehensive understanding of its mechanisms and potential therapeutic targets is essential. This review discusses the roles of mitochondrial oxidative stress, mitochondrial dynamics alterations, and mtDNA damage in Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), and multiple sclerosis (MS). In addition, it summarizes the contributions of novel technological approaches in detecting mitochondrial dysfunction, which assist in disease diagnosis. We also emphasize emerging therapeutic strategies and drugs aimed at enhancing mitochondrial quality control and reducing oxidative stress, thereby laying the groundwork for innovative therapeutic approaches in neurodegenerative disease treatment.

Multi-tissue metabolomics reveal mtDNA- and diet-specific metabolite profiles in a mouse model of cardiometabolic disease

RATIONALE

Excess consumption of sugar- and fat-rich foods has heightened the prevalence of cardiometabolic disease, which remains a driver of cardiovascular disease- and type II diabetes-related mortality globally. Skeletal muscle insulin resistance is an early feature of cardiometabolic disease and is a precursor to diabetes. Insulin resistance risk varies with self-reported race, whereby African-Americans have a greater risk of diabetes development relative to their White counterparts. Self-reported race is strongly associated with mitochondrial DNA (mtDNA) haplogroups, and previous reports have noted marked differences in bioenergetic and metabolic parameters in cells belonging to distinct mtDNA haplogroups, but the mechanism of these associations remains unknown. Additionally, distinguishing nuclear DNA (nDNA) and mtDNA contributions to cardiometabolic disease remains challenging in humans. The Mitochondrial-Nuclear eXchange (MNX) mouse model enables in vivo preclinical investigation of the role of mtDNA in cardiometabolic disease development, and has been implemented in studies of insulin resistance, fatty liver disease, and obesity in previous reports.

METHODS

Six-week-old male C57nDNA:C57mtDNA and C3HnDNA:C3HmtDNA wild-type mice, and C57nDNA:C3HmtDNA and C3HnDNA:C57mtDNA MNX mice, were fed sucrose-matched high-fat (45% kcal fat) or control diet (10% kcal fat) until 12 weeks of age (n = 5/group). Mice were weighed weekly and total body fat was collected at euthanasia. Gastrocnemius skeletal muscle and plasma metabolomes were characterized using untargeted dual-chromatography mass spectrometry; both hydrophilic interaction liquid chromatography (HILIC) and C18 columns were used, in positive- and negative-ion modes, respectively.

RESULTS

Comparative analyses between nDNA-matched wild-type and MNX strains demonstrated significantly increased body fat percentage in mice possessing C57mtDNA regardless of nDNA background. High-fat diet in mice possessing C57mtDNA was associated with differential abundance of phosphatidylcholines, lysophosphatidylcholines, phosphatidylethanolamines, and glucose. Conversely, high-fat diet in mice possessing C3HmtDNA was associated with differential abundance of phosphatidylcholines, cardiolipins, and alanine. Glycerophospholipid metabolism and beta-alanine signaling pathways were enriched in skeletal muscle and plasma, indicating mtDNA-directed priming of mitochondria towards oxidative stress and increased fatty acid oxidation in C57nDNA:C57mtDNA wild-type and C3HnDNA:C57mtDNA MNX mice, relative to their nDNA-matched counterparts. In mtDNA-matched mice, C57mtDNA was associated with metabolite co-expression related to the pentose phosphate pathway and sugar-related metabolism; C3HmtDNA was associated with branched chain amino acid metabolite co-expression.

CONCLUSIONS

These results reveal novel nDNA-mtDNA interactions that drive significant changes in metabolite levels. Alterations to key metabolites involved in mitochondrial bioenergetic dysfunction and electron transport chain activity are implicated in elevated beta-oxidation during high-fat diet feeding; abnormally elevated rates of beta-oxidation may be a key driver of insulin resistance. The results reported here support the hypothesis that mtDNA influences cardiometabolic disease-susceptibility by modulating mitochondrial function and metabolic pathways.

Evolutionary history and divergence times of Tettigoniidae (Orthoptera) inferred from mitochondrial phylogenomics

Background

Advances in high-throughput sequencing technology have led to a rapid increase in the number of sequenced mitochondrial genomes (mitogenomes), ensuring the emergence of mitochondrial phylogenomics, as a powerful tool for understanding the evolutionary history of various animal groups.

Methods

In this study, we utilized high-throughput sequencing technology to assemble and annotate the mitogenomes of Letana rubescens (Stål) and Isopsera denticulata Ebner. We described the characteristics of the mitochondrial genes of these two species. Utilizing 13 PCGs and 2 rRNA genes, we reconstructed the phylogenetic relationships of Tettigoniidae by combining published data with our newly generated data. We used likelihood mapping, signal-to-noise ratio (SNR), and saturation analysis across different datasets to ensure the robustness of our inferred topologies.

Results and conclusion

Selective pressure analysis on the 13 protein-coding genes (PCGs) and 2 ribosomal RNA (rRNA) genes revealed that only ND1 and COX1 contained positively selected sites, while negative selection dominated across all genes, indicating that mitochondrial genes primarily function to maintain genetic integrity. Additionally, we assessed the evolutionary rates of the 13 PCGs and two rRNA genes across five major subfamilies using mean pairwise identity analysis. Phylogenetic results of our study provide more precise insights into the relationships within Tettigoniidae, spanning subfamilies, tribes, genera, and species. We further estimated the divergence times of Tettigoniidae using four fossil calibration nodes in MCMCTree, dating the origin of katydids to the early Paleogene period (approximately 60.86 Mya), and identifying the divergence nodes for five major subfamilies.

Increased mitochondrial mutation heteroplasmy induces aging phenotypes in pluripotent stem cells and their differentiated progeny

The mitochondrial genome (mtDNA) is an important source of inherited extranuclear variation. Clonal increases in mtDNA mutation heteroplasmy have been implicated in aging and disease, although the impact of this shift on cell function is challenging to assess. Reprogramming to pluripotency affects mtDNA mutation heteroplasmy. We reprogrammed three human fibroblast lines with known heteroplasmy for deleterious mtDNA point or deletion mutations. Quantification of mutation heteroplasmy in the resulting 76 induced pluripotent stem cell (iPSC) clones yielded a bimodal distribution, creating three sets of clones with high levels or absent mutation heteroplasmy with matched nuclear genomes. iPSC clones with elevated deletion mutation heteroplasmy show altered growth dynamics, which persist in iPSC-derived progenitor cells. We identify transcriptomic and metabolic shifts consistent with increased investment in neutral lipid synthesis as well as increased epigenetic age in high mtDNA deletion mutation iPSC, consistent with changes occurring in cellular aging. Together, these data demonstrate that high mtDNA mutation heteroplasmy induces changes occurring in cellular aging.

Effects of Wolbachia on mitochondrial DNA variation in Aedes albopictus (Diptera: Culicidae)

Wolbachia species are symbiotic bacteria that are commonly found in arthropods and nematodes and live inside their cells. In nature, endosymbiont-host interactions and dynamics are complex, often depending on environmental conditions and evolutionary history. Both Wolbachia and mitochondrial DNA are maternally inherited in cells, and after a long period of coexistence, the presence of Wolbachia may have an impact on mitochondrial sequence diversity, thereby confounding mtDNA-based host phylogeny. The universal and typing primers for the wsp gene were used for PCR amplification, the number of positive samples was counted, and the infection pattern was analysed. The mitochondrial DNA diversity of four groups (Wolbachia-infected and uninfected samples, as well as between singly and double infected samples.) was analysed. PACo and ParaFitGlobal tests were used to explore evolutionary associations. The overall prevalence of Wolbachia in the 22 natural populations was 94.2 %, with Type A, Type B and A × B mixed infections detected in Aedes albopictus and coinfection between wAlbA and wAlbB prevalent. The mitochondrial DNA haplotype associated with Wolbachia (Hap1) became the dominant haplotype and was the most abundant and widely distributed in the population. The linkage map showed the predominant haplotype, Hap1, was more closely associated with wAlbA than with wAlbB. Neutral evolution deviated significantly from zero. The diversity of mtDNA COI genes associated with Wolbachia infection was reduced. Wolbachia infection may lead to the selective sweep of mitochondrial DNA in Ae. albopictus.

High-Throughput Sequencing Enables Rapid Analyses of Nematode Mitochondrial Genomes from an Environmental Sample

Mitochondrial genomes serve as essential tools in evolutionary biology, phylogenetics, and population genetics due to their maternal inheritance, lack of recombination, and conserved structure. Traditional morphological methods for identifying nematodes are often insufficient for distinguishing cryptic species complexes. This study highlights recent advancements in nematode mitochondrial genome research, particularly the impact of long-read sequencing technologies such as Oxford Nanopore. These technologies have facilitated the assembly of mitochondrial genomes from mixed soil samples, overcoming challenges associated with designing specific primers for long PCR amplification across different groups of parasitic nematodes. In this study, we successfully recovered and assembled eleven nematode mitochondrial genomes using long-read sequencing, including those of two plant-parasitic nematode species. Notably, we detected Heterodera cruciferae in Victoria, expanding its known geographic range within Australia. Additionally, short-read sequencing data from a previous draft genome study revealed the presence of the mitochondrial genome of Heterodera filipjevi. Comparative analyses of Heterodera mitogenomes revealed conserved protein-coding genes essential for oxidative phosphorylation, as well as gene rearrangements and variations in transfer RNA placement, which may reflect adaptations to parasitic lifestyles. The consistently high A+T content and strand asymmetry observed across species align with trends reported in related genera. This study demonstrates the utility of long-read sequencing for identifying coexisting nematode species in agricultural fields, providing a rapid, accurate, and comprehensive alternative to traditional diagnostic methods. By incorporating non-target endemic species into public databases, this approach enhances biodiversity records and informs biosecurity strategies. These findings reinforce the potential of mitochondrial genomics to strengthen Australia's as well as the global biosecurity framework against plant-parasitic nematode threats.

Negative global-scale association between genetic diversity and speciation rates in mammals

Genetic diversity is critical for species evolution and their adaptability to global changes, while speciation rate is critical for explaining large-scale patterns of species richness. Exploring correlates of variation in genetic diversity and speciation rates across species is a major interest of evolutionary biologists, but these two questions have mostly been investigated independently. Here, we assess the relationship between intra-specific genetic diversity and speciation rate for 1897 mammal species (~one third of the total diversity) covering all mammalian orders. We find a negative association between mitochondrial genetic diversity and speciation rate across mammalian clades globally. This association is not accounted for by differences in the ecological attributes of species. Our findings suggest a systematic link between micro- and macroevolutionary processes that need to be better understood and considered when investigating determinants of either genetic diversity or speciation rates.

Estimation of Species Abundance Based on the Number of Segregating Sites Using Environmental DNA (eDNA)

The advance of environmental DNA (eDNA) has enabled rapid and non-invasive species detection in aquatic environments. While most studies focus on species detection, recent works explored using eDNA concentration to quantify species abundance. However, the differential individual DNA contribution to eDNA samples could easily obscure the eDNA concentration-species abundance relationship. We propose using the number of segregating sites as a proxy for estimating species abundance. Segregating sites reflect the genetic diversity of the population, which is less sensitive to differential individual DNA contribution than eDNA concentration. We examined the relationship between the number of segregating sites and species abundance in silico, in vitro, and in situ experiments, using two brackish goby species, Acanthogobius hasta and Tridentiger bifasciatus. Analyses of the simulated and in vitro data with DNA mixed from a known number of individuals showed a strong correlation between the number of segregating sites and species abundance (R2 > 0.9; p < 0.01). In the in situ experiments, we analysed eDNA samples collected from mesocosm. The results further validated that the correlation (R2 = 0.70, p < 0.01) was not affected by biotic factors, including body size and feeding behaviour (p > 0.05). The cross-validation test results also showed that the number of segregating sites predicted species abundance with less bias and variability than the eDNA concentration. Overall, the number of segregating sites is less affected by differential DNA contribution among individuals compared to eDNA concentration. This advancement can significantly enhance the proficiency of estimating species abundance using eDNA.

Mitophagy at the oocyte-to-zygote transition promotes species immortality

The quality of inherited mitochondria determines embryonic viability 1 , metabolic health during adulthood and future generation endurance. The oocyte is the source of all zygotic mitochondria 2 , and mitochondrial health is under strict developmental regulation during early oogenesis 3-5 . Yet, fully developed oocytes exhibit the presence of deleterious mitochondrial DNA (mtDNA) 6,7 and mitochondrial dysfunction from high levels of endogenous reactive oxygen species 8 and exogenous toxicants 9 . How fully developed oocytes prevent transmission of damaged mitochondria to the zygotes is unknown. Here we discover that the onset of oocyte-to-zygote transition (OZT) developmentally triggers a robust and rapid mitophagy event that we term mitophagy at OZT (MOZT). We show that MOZT requires mitochondrial fragmentation, activation of the macroautophagy system and the mitophagy receptor FUNDC1, but not the prevalent mitophagy factors PINK1 and BNIP3. Oocytes upregulate expression of FUNDC1 in response to diverse mitochondrial insults, including mtDNA mutations and damage, uncoupling stress, and mitochondrial dysfunction, thereby promoting selection against damaged mitochondria. Loss of MOZT leads to increased inheritance of deleterious mtDNA and impaired bioenergetic health in the progeny, resulting in diminished embryonic viability and the extinction of descendent populations. Our findings reveal FUNDC1-mediated MOZT as a mechanism that preserves mitochondrial health during the mother-to-offspring transmission and promotes species continuity. These results may explain how mature oocytes from many species harboring mutant mtDNA give rise to healthy embryos with reduced deleterious mtDNA.

Reassessing Hybridisation in Australian Tetragonula Stingless Bees Using Multiple Genetic Markers

We re-examined reports of hybridisation in three cryptic stingless bee species in the genus Tetragonula in South East Queensland, Australia (T. carbonaria, T. davenporti and T. hockingsi). Previous studies on this group using microsatellite markers proposed that hybridisation occasionally takes place. In contrast, we find that using 1745 SNPs we could reliably separate the three species, with no evidence of contemporary (or recent) hybridisation. We found identical amplicon sequences of the nuclear gene EF1alpha across most individuals of the three species, but low and moderate species-specific polymorphisms in the nuclear gene Opsin and the mitochondrial 16S rRNA gene, respectively, with no cases of mito-nuclear discordance at these genes. We confirm that nuclear divergence across these species is low, based on 10-26 kb of non-coding sequence flanking EF1alpha and Opsin (0.7%-1% pairwise difference between species). However, we find mitogenomes to be far more diverged than nuclear genomes (21.6%-23.6% pairwise difference between species). Based on these comprehensive analyses of multiple marker types, we conclude there is no ongoing gene flow among the Tetragonula species of South East Queensland, despite their morphological similarity to one another and the low nuclear divergence among them. The higher resolution provided by multiple SNP markers may lead to lower estimates of contemporary hybridisation more generally.

Intraspecific genetic variation in the lymphatic filariasis vector Mansonia dives (Diptera: Culicidae) in Thailand: Hidden species or genetically divergent populations?

Mansonia dives is recognized as a vector for brugian filariasis in Thailand. A recent study analyzing the cytochrome c oxidase subunit I (COI) gene revealed two distinct clades within the Ma. dives population in Thailand. This study aimed to examine the genetic diversity and structure of Ma. dives using the COI gene and the internal transcribed spacer 2 (ITS2) region to determine the presence of distinct species or genetically divergent populations. We analyzed 60 COI and 60 ITS2 sequences from Ma. dives populations in Narathiwat, Ranong, Tak, and Trat. The results showed a nucleotide diversity of 0.019 and a haplotype diversity of 0.979 for the COI gene, while the ITS2 region displayed a nucleotide diversity of 0.005 and a haplotype diversity of 0.545. Phylogenetic and haplotype network analyses of the COI gene identified two genetic lineages: one confined to Trat and another encompassing the other sites. However, species delimitation methods suggested that these genetic differences were insufficient to classify the lineages as distinct species. In contrast, the ITS2 analysis indicated a uniform genetic pattern across all populations. We conducted neutrality tests and mismatch distribution to examine the demographic history. For the COI gene, Tajima's D was slightly positive and non-significant (0.014), while Fu's Fs was negative (-9.750), indicating a potential expansion phase. Conversely, for the ITS2 region, Tajima's D and Fu's Fs were positive and non-significant, suggesting that the population might be in equilibrium or undergoing contraction. Moreover, the mismatch distribution analysis for the ITS2 region was inconclusive. The apparent discrepancies between these markers indicate the presence of genetically divergent populations, rather than distinct species.

DNA repair pathways in the mitochondria

Mitochondria contain their own small, circular genome that is present in high copy number. The mitochondrial genome (mtDNA) encodes essential subunits of the electron transport chain. Mutations in the mitochondrial genome are associated with a wide range of mitochondrial diseases and the maintenance and replication of mtDNA is crucial to cellular health. Despite the importance of maintaining mtDNA genomic integrity, fewer DNA repair pathways exist in the mitochondria than in the nucleus. However, mitochondria have numerous pathways that allow for the removal and degradation of DNA damage that may prevent accumulation of mutations. Here, we briefly review the DNA repair pathways present in the mitochondria, sources of mtDNA mutations, and discuss the passive role that mtDNA mutagenesis may play in cancer progression.

High genetic variation, low differentiation, and Pleistocene expansions of the migratory and endangered long-nosed tequila bat, Leptonycteris nivalis, inferred using both maternal and paternal genetic markers

Tequila bats (genus Leptonycteris) have gained attention for their critical role in pollinating different plant species, especially Agave spp. and columnar cacti. Leptonycteris nivalis is the largest nectar-feeding bat in the Americas, and the females exhibit migratory behavior during the breeding season. Due to its relatively small and seemingly declining population sizes, this species is protected by government agencies in the United States and Mexico. We conducted population genetics and phylogeographic analyses to elucidate the genetic structure and demographic history of the species using two mitochondrial markers and a Y chromosome-associated gene, to describe both maternal and paternal lineages. We estimated high haplotypic diversity measures for the different markers (Dloop-Hd = 0.775; Cyt-b-Hd = 0.937; DBY -Hd = 0.946). We found that geographic genetic differentiation is very low, and there is high connectivity among localities. The estimated divergence time between L. nivalis and L. yerbabuenae, the other species in the genus found in Mexico, aligns with previous estimates for the genus (6.91-9.43 mya). A demographic expansion was detected approximately at 600 ka-700 ka (thousands of years ago). The historical demographic changes observed in L. nivalis appear to be associated with environmental shifts during the Pleistocene, which likely impacted the distribution range of the plants that these bats feed on, such as Agave species.

Direct Measurement of the Mutation Rate and Its Evolutionary Consequences in a Critically Endangered Mollusk

The rate at which mutations arise is a fundamental parameter of biology. Despite progress in measuring germline mutation rates across diverse taxa, such estimates are missing for much of Earth's biodiversity. Here, we present the first estimate of a germline mutation rate from the phylum Mollusca. We sequenced three pedigreed families of the white abalone Haliotis sorenseni, a long-lived, large-bodied, and critically endangered mollusk, and estimated a de novo mutation rate of 8.60 × 10-9 single nucleotide mutations per site per generation. This mutation rate is similar to rates measured in vertebrates with comparable generation times and longevity to abalone, and higher than mutation rates measured in faster-reproducing invertebrates. The spectrum of de novo mutations is also similar to that seen in vertebrate species, although an excess of rare C > A polymorphisms in wild individuals suggests that a modifier allele or environmental exposure may have once increased C > A mutation rates. We use our rate to infer baseline effective population sizes (Ne) across multiple Pacific abalone and find that abalone persisted over most of their evolutionary history as large and stable populations, in contrast to extreme fluctuations over recent history and small census sizes in the present day. We then use our mutation rate to infer the timing and pattern of evolution of the abalone genus Haliotis, which was previously unknown due to few fossil calibrations. Our findings are an important step toward understanding mutation rate evolution and they establish a key parameter for conservation and evolutionary genomics research in mollusks.

A footworm in the door: revising Onchocerca phylogeny with previously unknown cryptic species in wild North American ungulates

Onchocerca is an important genus of vector-borne filarial nematodes that infect both humans and animals worldwide. Many Onchocerca spp., most of medical and veterinary health relevance, are the focus of a variety of diagnostic and molecular research. However, despite the importance of these parasites, there is growing evidence of previously unexplored genetic diversity of these nematodes, particularly among wild ungulate hosts in North America. These understudied parasites prevent us from comprehending the evolutionary history of the genus Onchocerca, monitoring potential One Health threats, and improving our filarioid diagnostic capabilities. In order to fill these knowledge gaps, we identified five uncharacterized Onchocerca lineages and compared them with other well-known filarioid species using single and concatenated gene regions (i.e., nd5, cox1, 12S, 18S, 28S, hsp70, MyoHC, rbp1). Phylogenetic analyses revealed that the novel Onchocerca lineages of wild North American ungulates segregate into two clades. One clade comprised Onchocerca lineages II, IV, and V and other species found mainly in domestic animals and humans, and the second comprised Onchocerca lineages I and III and other species from a variety of hosts including cervids, bovids, and equids. The formation of two clearly separate clades supports the idea of at least two independent expansion events of ancestral Onchocerca spp. into the North American continent via the Bering land bridge. Cophylogenetic analysis shows evidence of ancestral Onchocerca spp. of Bovidae host-switching to wild Cervidae and giving rise to the novel Onchocerca spp. Lastly, pairwise analysis confirms informative molecular markers of diagnostic relevance in both mitochondrial and nuclear gene regions of filarioid nematodes. The overall information provides greater context to the genus Onchocerca and emphasizes the need to discover, characterize, and monitor neglected parasites, especially those of wildlife origin.

Mitochondrial genomes of the European sardine (Sardina pilchardus) reveal Pliocene diversification, extensive gene flow and pervasive purifying selection

The development of management strategies for the promotion of sustainable fisheries relies on a deep knowledge of ecological and evolutionary processes driving the diversification and genetic variation of marine organisms. Sustainability strategies are especially relevant for marine species such as the European sardine (Sardina pilchardus), a small pelagic fish with high ecological and socioeconomic importance, especially in Southern Europe, whose stock has declined since 2006, possibly due to environmental factors. Here, we generated sequences for 139 mitochondrial genomes from individuals from 19 different geographical locations across most of the species distribution range, which was used to assess genetic diversity, diversification history and genomic signatures of selection. Our data supported an extensive gene flow in European sardine. However, phylogenetic analyses of mitogenomes revealed diversification patterns related to climate shifts in the late Miocene and Pliocene that may indicate past divergence related to rapid demographic expansion. Tests of selection showed a significant signature of purifying selection, but positive selection was also detected in different sites and specific mitochondrial lineages. Our results showed that European sardine diversification has been strongly driven by climate shifts, and rapid changes in marine environmental conditions are likely to strongly affect the distribution and stock size of this species.

Phylogenetics and species delimitation of the recluse spider, Loxosceles rufescens (Araneae: Sicariidae) populations invading Bangkok, Thailand

The Mediterranean recluse spider, Loxosceles rufescens, has been discovered for the first time inhabiting human dwellings in Bangkok, Thailand. Expeditions across 39 localities revealed five establishments with L. rufescens populations. The highest density was recorded in a storage house on Yaowarat Road, located in the heart of Bangkok's Chinatown, where 315 individuals were found, including adults, juveniles, and spiderlings. This medically significant spider's presence in such a densely populated urban area raises concerns about potential envenomation risks. Thirteen specimens of L. rufescens were extracted for DNA and sequenced for molecular phylogenetic analyses. COI and ITS2 markers were used to investigate relationships within L. rufescens and across available Loxosceles species sequences. Results indicate COI is superior for resolving species-level genetic clusters compared to ITS2. Surprisingly, L. rufescens individuals from the same house were found in significantly distant COI lineages, suggesting mtDNA may not be suitable for studying intra-specific phylogeography in this case. Species delimitation methods ABGD and ASAP demonstrated promising results for both COI and ITS2, while bPTP and GMYC tended to overestimate species numbers. ITS2 exhibited high sequence similarity in L. rufescens, suggesting potential utility as a barcoding marker for identification of this globally distributed species. Genetic distance analyses revealed a potential barcoding gap (K2P) of 8-9 % for COI and <2 % for ITS2 in Loxosceles. This study contributes valuable sequence data for the medically important genus Loxosceles and highlights the need for integrative approaches in understanding its evolution and spread. The findings have important implications for pest management strategies and public health in urban environments.

MtDNA genetic diversity and phylogeographic insights into giant domestic pigeon (Columba livia domestica) breeds: connections between Central Europe and the Middle East

Humans have selectively bred domestic pigeons (Columba livia domestica) to create breeds with a diversity of shapes, colors and other attributes. Since Darwin, the domestic pigeon has always been a popular model species for scientific research because of its richness of form, colouration and behaviour. It is believed that the world's squab pigeon industry uses breeds and hybrids from the Mediterranean region. An exception is the indigenous giant pigeon breeds of the Carpathian Basin, whose origin is not known. Therefore, our aims were 1) to understand the phylogenetic relationships of giant pigeons, which sheds light on the origin of Hungarian breeds and their relationship to the Mediterranean giant pigeon breed group; 2) to contribute molecular genetic data to the genealogy of 2 Iraqi pigeon breeds close to the pigeon domestication center, including the culturally important Iraqi Red Pigeon, and 3) to compare the genetic diversity of European and Middle Eastern domestic pigeon populations and to draw conclusions on the phylogenetic relationships between pigeon breeds and molecular clues to their different breeding practices of both regions. A 655-bp-long sequence of the cytochrome oxidase 1 (COI) region of the mitochondrial DNA was studied in a total of 276 pigeons (19 breeds). A total of 27 haplotypes were found, of which 22 were unique. The highest genetic diversity was found in the Carpathian Basin, and the lowest in the Iraqi region. STRUCTURE analysis revealed low structurality, K=3 was the most likely. The majority of the samples belong to the most ancient haplotype H_2=219, however the Jacobin pigeon is on a very separate evolutionary branch with a large number of mutations. None of the 19 breeds investigated in this study have been previously studied in phylogenetics, and most of these breeds have potential as squab pigeons, and have good meat forms for utilization, therefore the results of this study may also be of help to the squab pigeon industry.

Unravelling the role of mitochondrial DNA in hybrid incompatibility within species of the Anopheles gambiae complex

Isolation mechanisms between mosquito species of the Anopheles gambiae complex, which includes major malaria vectors, remain poorly understood. In some cases, pre-zygotic barriers have been shown to limit gene flow between species of the complex, leading to a low level of hybridisation in nature. Post-zygotic mechanisms manifest with F1 hybrid males fully sterile and F1 hybrid females with reduced fertility. Genetic approaches combined with DNA sequencing techniques have highlighted the involvement of genomic regions in hybrid incompatibility with a predominant role of the X chromosome. In addition, differences in the phenotype of F1 hybrid males have been identified depending on the directionality of the parental cross used to generate them. All these studies have focused on the interaction of nuclear DNA elements in hybrid individuals. Given the role that mitochondrial DNA plays in genetic incompatibilities within other organisms and its unique inheritance pattern, commonly maternal, we conducted a genetic study that relied on the introgression of mitochondrial DNA between Anopheles gambiae and Anopheles arabiensis. The findings indicate that the mitochondrial switch does not appear to restore the fertility of F1 hybrid males, suggesting that mitochondrial DNA may not play a role in hybrid incompatibilities in these Anopheles species.

Accelerated differentiation of neo-W nuclear-encoded mitochondrial genes between two climate-associated bird lineages signals potential co-evolution with mitogenomes

There is considerable evidence for mitochondrial-nuclear co-adaptation as a key evolutionary driver. Hypotheses regarding the roles of sex-linkage have emphasized Z-linked nuclear genes with mitochondrial function (N-mt genes), whereas it remains contentious whether the perfect co-inheritance of W genes with mitogenomes could hinder or facilitate co-adaptation. Young (neo-) sex chromosomes that possess relatively many N-mt genes compared to older chromosomes provide unprecedented hypothesis-testing opportunities. Eastern Yellow Robin (EYR) lineages in coastal and inland habitats with different climates are diverged in mitogenomes, and in a ~ 15.4 Mb nuclear region enriched with N-mt genes, in contrast with otherwise-similar nuclear genomes. This nuclear region maps to passerine chromosome 1A, previously found to be neo-sex in the inland EYR genome. To compare sex-linked Chr1A-derived genes between lineages, we assembled and annotated the coastal EYR genome. We found that: (i) the coastal lineage shares a similar neo-sex system with the inland lineage, (ii) neo-W and neo-Z N-mt genes are not more diverged between lineages than are comparable non-N-mt genes, and showed little evidence for broad positive selection, (iii) however, W-linked N-mt genes are more diverged between lineages than are their Z-linked gametologs. The latter effect was ~7 times stronger for N-mt than non-N-mt genes, suggesting that W-linked N-mt genes might have diverged between lineages under environmental selection through co-evolution with mitogenomes. Finally, we identify a candidate gene driver for divergent selection, NDUFA12. Our data represent a rare example suggesting a possible role for W-associated mitochondrial-nuclear interactions in climate-associated adaptation and lineage differentiation.

Genomics-Informed Range Predictions Under Global Warming Reveal Reduced Adaptive Diversity Whilst Buffering Range Shifts for a Marine Snail

Understanding the genetic basis of local adaptation in thermal performance is useful for predicting species distribution shifts under anthropogenic climate change. Many species are distributed across multiple biogeographic regions, and the uniquely adapted populations in each region may respond to future ocean warming with distinct distribution changes. In the present study, we investigated phylogeographic patterns, thermal sensitivity, and genetic differentiation in the intertidal snail Littorina brevicula along China's coast. Whole-genome sequencing results based on a newly assembled chromosome-level genome revealed two genetic lineages, with a north-south divergence that is linked to the thermal environment. Within each lineage, individuals could be further subdivided into genetic subgroups that differ at key genomic loci underpinning differences in upper heat tolerance. Heat stress drives adaptive divergence across multiple levels of organization, from the individual to the biogeographic level. Taking into account genetic diversity associated with variation in heat tolerance, a physiological species distribution model (pSDM) was applied to predict the distributions of the different genetic subgroups in response to climate change. Both northern and southern lineages were predicted to experience declines in habitat suitability under a 4°C future warming scenario, and that a genotypic subset of snails from the southern lineage may even be driven to extinction. These findings illustrate that even when a species' range is maintained, it can nonetheless experience a significant decrease in adaptive diversity as a result of climate change. The integrated approach presented here, which considered both physiological and adaptive genetic variation at the level of individuals within a biogeographical context, provided new insights into how marine species can respond to global warming.

The Phylogeography and Diversification of an Endemic Trapdoor Spider Genus, Stasimopus Simon 1892 (Araneae, Mygalomorphae, Stasimopidae) in the Karoo, South Africa

The genus Stasimopus is endemic to South Africa but has never undergone a phylogeographic review. This study aims to unravel the phylogeographic patterns and history of the many Stasimopus species which occur in the greater Karoo region. A fossil-calibrated phylogeny was produced based on three gene regions (CO1, 16S and EF-1ɣ) for Stasimopus (Cor-k-lid trapdoor spiders) specimens collected in the Karoo region, to infer dates of origin and diversification. Demographic analyses were performed on species with sufficient sample sizes (> 4). Haplotype networks were constructed for each gene region and plotted on a map to infer phylogeographic patterns. Lastly, Mantel tests were performed to test for isolation by distance. It was found that 15 species occur in the Karoo and that the genus radiation in the area is in the early Palaeocene. Most diversification occurred between the late Eocene and the Miocene, coinciding with significant changes in climate. Several species show signals of demographic expansions. Isolation by distance was detected, but only with a slight correlation. It is apparent that aridification has played a vital role in the diversification of the genus in the Karoo region. This is a shared biogeographic influence between the mygalomorph fauna of the Karoo and arid region of western Australia. Stasimopus has radiated from the late Eocene and through the Miocene resulting in 15 extant species in the region. The Tankwa Karoo has been identified as a possible Pleistocene glacial cycle refugia for the species S. leipoldti. Many of the species in the Karoo are short-range endemics, making them of high conservation concern. This study provided vital information as the Karoo is undergoing further desertification due to factors such as climate change, which may affect the future of short-range endemic spiders.

Novel Megaptera novaeangliae (Humpback whale) haplotype chromosome-level reference genome

The sequencing of a kidney sample (KW2013002) from a stranded Megaptera novaeangliae (Humpback whale) calf is the first chromosome-level reference genome for this species1. The calf, a 457 cm and 2,500 lbs male, was found stranded in Hawai'i Kai, HI, in 2013 and was marked as abandoned/orphaned. In 2023, 1 g of kidney was sequenced with PacBio long-read DNA sequencing, chromatin conformation capture (Hi-C), RNA sequencing, and mitochondrial sequencing to comprehensively characterize the genome and transcriptome of M. novaeangliae. Data validation includes a synteny analysis, mitochondrial annotation, and a comparison of BUSCO scores (scaffold v. reference genome and Balaenoptera musculus (Blue whale) v. M. novaeangliae). BUSCO analysis was performed on an M. novaeangliae scaffold-level assembly to determine genomic completeness of the reference genome, with a scaffold BUSCO score of 91.2% versus a score of 95.4%. Synteny analysis was performed using the B. musculus genome as comparison to determine chromosome-level coverage and structure. Further, a time-based phylogenetic tree was constructed using the sequenced data and publicly available genomes.

Drivers of interlineage variability in mitogenomic evolutionary rates in Platyhelminthes

Studies of forces driving interlineage variability in the evolutionary rates (both sequence and architecture) of mitochondrial genomes often produce contradictory results. Flatworms (Platyhelminthes) exhibit the fastest-evolving mitogenomic sequences among all bilaterian phyla. To test the effects of multiple factors previously associated with different aspects of mitogenomic evolution, we used mitogenomes of 223 flatworm species, phylogenetic multilevel regression models, and causal inference. Thermic host environment (endothermic vs. ectothermic) had nonsignificant impacts on both sequence evolution and mitogenomic size. Mitogenomic gene order rearrangements (GORR) were mostly positively correlated with mitogenomic size (R2 ≈ 20-30%). Longevity was not (negatively) correlated with sequence evolution in flatworms. The predominantly free-living "turbellaria" exhibited much shorter branches and faster-evolving mitogenomic architecture than parasitic Neodermata. As a result, "parasitism" had a strong explanatory power on the branch length variability (>90%), and there was a negative correlation between GORR and branch length. However, the stem branch of Neodermata comprised 63.6% of the total average branch length. This evolutionary period was also marked by a high rate of gene order rearrangements in the ancestral Neodermata. We discuss how this period of rapid evolution deep in the evolutionary history may have decoupled sequence evolution rates from longevity and GORR, and overestimated the explanatory power of "parasitism". This study shows that impacts of variables often vary across lineages, and stresses the importance accounting for the episodic nature of evolutionary patterns in studies of mitogenomic evolution.

Genomic landscape of introgression from the ghost lineage in a gobiid fish uncovers the generality of forces shaping hybrid genomes

Extinct lineages can leave legacies in the genomes of extant lineages through ancient introgressive hybridization. The patterns of genomic survival of these extinct lineages provide insight into the role of extinct lineages in current biodiversity. However, our understanding on the genomic landscape of introgression from extinct lineages remains limited due to challenges associated with locating the traces of unsampled 'ghost' extinct lineages without ancient genomes. Herein, we conducted population genomic analyses on the East China Sea (ECS) lineage of Chaenogobius annularis, which was suspected to have originated from ghost introgression, with the aim of elucidating its genomic origins and characterizing its landscape of introgression. By combining phylogeographic analysis and demographic modelling, we demonstrated that the ECS lineage originated from ancient hybridization with an extinct ghost lineage. Forward simulations based on the estimated demography indicated that the statistic γ of the HyDe analysis can be used to distinguish the differences in local introgression rates in our data. Consistent with introgression between extant organisms, we found reduced introgression from extinct lineage in regions with low recombination rates and with functional importance, thereby suggesting a role of linked selection that has eliminated the extinct lineage in shaping the hybrid genome. Moreover, we identified enrichment of repetitive elements in regions associated with ghost introgression, which was hitherto little known but was also observed in the re-analysis of published data on introgression between extant organisms. Overall, our findings underscore the unexpected similarities in the characteristics of introgression landscapes across different taxa, even in cases of ghost introgression.

Genome variations in sea cucumbers: Insights from genome survey sequencing and comparative analysis of mitochondrial genomes

Sea cucumbers, marine benthic invertebrates, play crucial roles in maintaining the stability of marine ecosystems and hold key evolutionary positions. However, information regarding their genomes remains limited. Here, we conducted genome survey analyses on seven species from four orders. Results indicated that Colochirus anceps, Colochirus quadrangularis, and Pseudocolochirus violaceus within the order Dendrochirotida have significantly larger genomes (2238-3754 Mbp) compared to conventional sea cucumber genomes, accompanied by a very high proportion of repeat sequences (69.39-72.52 %). While Holothuria edulis and Holothuria atra exhibited similar genome sizes comparable to those of other species within the order Holothuriida, heterozygosity and repeat content varied among all the six species in this order. The representative species Apostichopus californicus of the order Synallactida possesses the smallest genome size (573.45Mbp) within its order, but its heterozygosity (2.24 %) is significantly higher than that of other species. The representative species Synapta maculata of the order Apodida exhibited a normal genome size (900.97 Mbp), lower proportion of repeat sequences (42.19 %), and lower heterozygosity (0.84 %), making it the species with the least challenges for genome sequencing and assembly in the future among all surveyed species. Subsequently, we compiled genomic information from a total of 19 sea cucumber genomes, both newly sequenced and previously reported, revealing a significant linear relationship (P = 0.0001) between genome size and the proportion of repeat sequences in sea cucumbers. Additionally, phylogenetic and comparative analysis of mitochondrial genomes among them indicated extensive rearrangements within the order Apodida, leading to significant discrepancies between mitochondrial and nuclear genome phylogenies.

Assessment of the Genetic Diversity of the Monogenean Gill Parasite Lamellodiscus echeneis (Monogenea) Infecting Wild and Cage-Reared Populations of Sparus aurata (Teleostei) from the Mediterranean Sea

The diplectanid monogenean Lamellodiscus echeneis (Wagener, 1857) is a specific and common gill parasite of the gilthead seabream Sparus aurata Linnaeus, 1758, in the Mediterranean Sea. Few isolated molecular studies of this monogenean have been conducted, and its population structure and genetic diversity are poorly understood. This study represents the first analysis of the population genetics of L. echeneis, isolated from wild and cage-reared gilthead seabream from fifteen localities in both the Southern (Tunisia) and Northern (Italy and Spain) regions of the Mediterranean Sea, using nuclear ITS rDNA markers and a partial fragment of the mitochondrial gene cytochrome oxidase subunit I (COI). The phylogenetic trees based on the newly obtained dataset and the previously published sequences of L. echeneis corroborated the spread of only a single species throughout the Mediterranean Sea. The star-like haplotypes network, inferred by COI sequences, suggested a recent population expansion of L. echeneis. This is supported by the observed high haplotype diversity (Hd = 0.918) and low nucleotide diversity (Pi = 0.01595). Population structure-based AMOVA for two groups (the Adriatic Sea and the rest of the Mediterranean Sea) attributed 35.39% of the total variation to differences within populations, 16.63% to differences among populations within groups, and 47.99% to differences among groups. Fixation indices were significant, with a high FST value (0.64612), likely related to the divergence of the parasite populations from the Adriatic Sea and other Mediterranean regions. Phylogenetic analyses grouped all samples into the main clade corresponding to L. echeneis from several localities. This study provides insight into the genetic variation between L. echeneis populations, and did not show a clear genetic structure between populations of L. echeneis throughout Tunisian, Italian, and Spanish localities, which can be attributed to the considerable gene flow between the populations favoured by the potential for host dispersion within the Mediterranean Sea. Finally, haplotypes shared between wild and cage-reared hosts provided evidence for the potential for cross-infection between wild and farmed hosts in the Mediterranean Sea.

Mitochondrial Variation in Anopheles gambiae and Anopheles coluzzii: Phylogeographic Legacy and Mitonuclear Associations With Metabolic Resistance to Pathogens and Insecticides

Mitochondrial DNA has been a popular marker in phylogeography, phylogeny, and molecular ecology, but its complex evolution is increasingly recognized. Here, we investigated mitochondrial DNA variation in Anopheles gambiae and Anopheles coluzzii, in relation to other species in the Anopheles gambiae complex, by assembling the mitogenomes of 1,219 mosquitoes across Africa. The mitochondrial DNA phylogeny of the Anopheles gambiae complex was consistent with previously reported highly reticulated evolutionary history, revealing important discordances with the species tree. The three most widespread species (An. gambiae, An. coluzzii, and Anopheles arabiensis), known for extensive historical introgression, could not be discriminated based on mitogenomes. Furthermore, a monophyletic clustering of the three saltwater-tolerant species (Anopheles merus, Anopheles melas, and Anopheles bwambae) in the Anopheles gambiae complex also suggested that introgression and possibly selection shaped mitochondrial DNA evolution. Mitochondrial DNA variation in An. gambiae and An. coluzzii across Africa revealed significant partitioning among populations and species. A peculiar mitochondrial DNA lineage found predominantly in An. coluzzii and in the hybrid taxon of the African "far-west" exhibited divergence comparable to the interspecies divergence in the Anopheles gambiae complex, with a geographic distribution matching closely An. coluzzii's geographic range. This phylogeographic relict of the An. coluzzii and An. gambiae split was associated with population and species structure, but not with the rare Wolbachia occurrence. The lineage was significantly associated with single nucleotide polymorphisms in the nuclear genome, particularly in genes associated with pathogen and insecticide resistance. These findings underline potential mitonuclear coevolution history and the role played by mitochondria in shaping metabolic responses to pathogens and insecticides in Anopheles.

Mitoclone2: an R package for elucidating clonal structure in single-cell RNA-sequencing data using mitochondrial variants

Clonal cell population dynamics play a critical role in both disease and development. Due to high mitochondrial mutation rates under both healthy and diseased conditions, mitochondrial genomic variability is a particularly useful resource in facilitating the identification of clonal population structure. Here we present mitoClone2, an all-inclusive R package allowing for the identification of clonal populations through integration of mitochondrial heteroplasmic variants discovered from single-cell sequencing experiments. Our package streamlines the investigation of this phenomenon by providing: built-in compatibility with commonly used tools for the delineation of clonal structure, the ability to directly use multiplexed BAM files as input, annotations for both human and mouse mitochondrial genomes, and helper functions for calling, filtering, clustering, and visualizing variants.

Evolution and maintenance of mtDNA gene content across eukaryotes

Across eukaryotes, most genes required for mitochondrial function have been transferred to, or otherwise acquired by, the nucleus. Encoding genes in the nucleus has many advantages. So why do mitochondria retain any genes at all? Why does the set of mtDNA genes vary so much across different species? And how do species maintain functionality in the mtDNA genes they do retain? In this review, we will discuss some possible answers to these questions, attempting a broad perspective across eukaryotes. We hope to cover some interesting features which may be less familiar from the perspective of particular species, including the ubiquity of recombination outside bilaterian animals, encrypted chainmail-like mtDNA, single genes split over multiple mtDNA chromosomes, triparental inheritance, gene transfer by grafting, gain of mtDNA recombination factors, social networks of mitochondria, and the role of mtDNA dysfunction in feeding the world. We will discuss a unifying picture where organismal ecology and gene-specific features together influence whether organism X retains mtDNA gene Y, and where ecology and development together determine which strategies, importantly including recombination, are used to maintain the mtDNA genes that are retained.

Deciphering tissue-specific expression profiles of mitochondrial genome-encoded tRNAs and rRNAs through transcriptomic profiling in buffalo

BACKGROUND

Mitochondria, essential for cellular energy production through oxidative phosphorylation (OXPHOS), integrate mt-DNA and nuclear-encoded genes. This cooperation extends to the mitochondrial translation machinery, involving crucial mtDNA-encoded RNAs: 22 tRNAs (mt-tRNAs) as adapters and two rRNAs (mt-rRNAs) for ribosomal assembly, enabling mitochondrial-encoded mRNA translation. Disruptions in mitochondrial gene expression can strongly impact energy generation and overall animal health. Our study investigates the tissue-specific expression patterns of mt-tRNAs and mt-rRNAs in buffalo.

MATERIAL AND METHODS

To investigate the expression patterns of mt-tRNAs and mt-rRNAs in different tissues and gain a better understanding of tissue-specific variations, RNA-seq was performed on various tissues, such as the kidney, heart, brain, and ovary, from post-pubertal female buffaloes. Subsequently, we identified transcripts that were differentially expressed in various tissue comparisons.

RESULTS

The findings reveal distinct expression patterns among specific mt-tRNA and mt-rRNA genes across various tissues, with some exhibiting significant upregulation and others demonstrating marked downregulation in specific tissue contexts. These identified variations reflect tissue-specific physiological roles, underscoring their significance in meeting the unique energy demands of each tissue. Notably, the brain exhibits the highest mtDNA copy numbers and an abundance of mitochondrial mRNAs of our earlier findings, potentially linked to the significant upregulation of mt-tRNAs in brain. This suggests a plausible association between mtDNA replication and the regulation of mtDNA gene expression.

CONCLUSION

Overall, our study unveils the tissue-specific expression of mitochondrial-encoded non-coding RNAs in buffalo. As we proceed, our further investigations into tissue-specific mitochondrial proteomics and microRNA studies aim to elucidate the intricate mechanisms within mitochondria, contributing to tissue-specific mitochondrial attributes. This research holds promise to elucidate the critical role of mitochondria in animal health and disease.

High heteroplasmy is associated with low mitochondrial copy number and selection against non-synonymous mutations in the snail Cepaea nemoralis

Molluscan mitochondrial genomes are unusual because they show wide variation in size, radical genome rearrangements and frequently show high variation (> 10%) within species. As progress in understanding this variation has been limited, we used whole genome sequencing of a six-generation matriline of the terrestrial snail Cepaea nemoralis, as well as whole genome sequences from wild-collected C. nemoralis, the sister species C. hortensis, and multiple other snail species to explore the origins of mitochondrial DNA (mtDNA) variation. The main finding is that a high rate of SNP heteroplasmy in somatic tissue was negatively correlated with mtDNA copy number in both Cepaea species. In individuals with under ten mtDNA copies per nuclear genome, more than 10% of all positions were heteroplasmic, with evidence for transmission of this heteroplasmy through the germline. Further analyses showed evidence for purifying selection acting on non-synonymous mutations, even at low frequency of the rare allele, especially in cytochrome oxidase subunit 1 and cytochrome b. The mtDNA of some individuals of Cepaea nemoralis contained a length heteroplasmy, including up to 12 direct repeat copies of tRNA-Val, with 24 copies in another snail, Candidula rugosiuscula, and repeats of tRNA-Thr in C. hortensis. These repeats likely arise due to error prone replication but are not correlated with mitochondrial copy number in C. nemoralis. Overall, the findings provide key insights into mechanisms of replication, mutation and evolution in molluscan mtDNA, and so will inform wider studies on the biology and evolution of mtDNA across animal phyla.

Genetic Variation among the Partial Gene Sequences of the Ribosomal Protein Large-Two, the Internal Transcribed Spacer, and the Small Ribosomal Subunit of Blastocystis sp. from Human Fecal Samples

In the present study, we compared the genetic variability of fragments from the internal transcribed spacer region (ITS) and the small subunit ribosomal DNA (SSUrDNA) as nuclear markers, in contrast with the ribosomal protein large two (rpl2) loci, placed in the mitochondrion-related organelles (MROs) within and among human fecal samples with Blastocystis. Samples were analyzed using polymerase chain reaction (PCR)-sequencing, phylogenies, and genetics of population structure analyses were performed. In total, 96 sequences were analyzed, i.e., 33 of SSUrDNA, 35 of rpl2, and 28 of ITS. Only three subtypes (STs) were identified, i.e., ST1 (11.4%), ST2 (28.6%), and ST3 (60%); in all cases, kappa indexes were 1, meaning a perfect agreement among ST assignations. The topologies of phylogenetic inferences were similar among them, clustering to each ST in its specific cluster; discrepancies between phylogeny and assignment of STs were not observed. The STRUCTURE v2.3.4 software assigned three subpopulations corresponding to the STs 1-3, respectively. The population indices were consistent with those previously reported by other groups. Our results suggest the potential use of the ITS and rpl2 genes as molecular markers for Blastocystis subtyping as an alternative approach for the study of the genetic diversity observed within and between human isolates of this microorganism.

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

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

Mitonuclear interactions impact aerobic metabolism in hybrids and may explain mitonuclear discordance in young, naturally hybridizing bird lineages

Understanding genetic incompatibilities and genetic introgression between incipient species are major goals in evolutionary biology. Mitochondrial genes evolve rapidly and exist in dense gene networks with coevolved nuclear genes, suggesting that mitochondrial respiration may be particularly susceptible to disruption in hybrid organisms. Mitonuclear interactions have been demonstrated to contribute to hybrid dysfunction between deeply divergent taxa crossed in the laboratory, but there are few empirical examples of mitonuclear interactions between younger lineages that naturally hybridize. Here, we use controlled hybrid crosses and high-resolution respirometry to provide the first experimental evidence in a bird that inter-lineage mitonuclear interactions impact mitochondrial aerobic metabolism. Specifically, respiration capacity of the two mitodiscordant backcrosses (with mismatched mitonuclear combinations) differs from one another, although they do not differ significantly from the parental groups or mitoconcordant backcrosses as we would expect of mitonuclear disruptions. In the wild hybrid zone between these subspecies, the mitochondrial cline centre is shifted west of the nuclear cline centre, which is consistent with the direction of our experimental results. Our results therefore demonstrate asymmetric mitonuclear interactions that impact the capacity of cellular mitochondrial respiration and may help to explain the geographic discordance between mitochondrial and nuclear genomes observed in the wild.

Phylogeographic Pattern of the Assassin Bug Sycanus bifidus Inferred from Mitochondrial Genomes and Nuclear Genes

The assassin bug Sycanus bifidus has a wide distribution across southern China. This study explored its distribution and evolution by analyzing mitochondrial and nuclear ribosomal RNA genes, revealing how Pleistocene climate and geological changes shaped its phylogeography. We identified two main clades, A and B, that diverged in the Middle Pleistocene. Hainan Island's populations form a unique group within Clade A, suggesting that the Qiongzhou Strait served as a dispersal corridor during glaciation. Rising sea levels likely separated the Hainan population afterward. Ecological niche modeling showed that both populations have been viable since the last interglacial period, with demographic analyses indicating possible expansions during the Middle and Late Pleistocene, driven by favorable climates. This study highlights the significant effects of Pleistocene sea-level and climatic changes on the distribution and evolution of S. bifidus in China.

Microbiome and mitogenomics of the chigger mite Pentidionis agamae: potential role as an Orientia vector and associations with divergent clades of Wolbachia and Borrelia

BACKGROUND

Trombiculid mites are globally distributed, highly diverse arachnids that largely lack molecular resources such as whole mitogenomes for the elucidation of taxonomic relationships. Trombiculid larvae (chiggers) parasitise vertebrates and can transmit bacteria (Orientia spp.) responsible for scrub typhus, a zoonotic febrile illness. Orientia tsutsugamushi causes most cases of scrub typhus and is endemic to the Asia-Pacific Region, where it is transmitted by Leptotrombidium spp. chiggers. However, in Dubai, Candidatus Orientia chuto was isolated from a case of scrub typhus and is also known to circulate among rodents in Saudi Arabia and Kenya, although its vectors remain poorly defined. In addition to Orientia, chiggers are often infected with other potential pathogens or arthropod-specific endosymbionts, but their significance for trombiculid biology and public health is unclear.

RESULTS

Ten chigger species were collected from rodents in southwestern Saudi Arabia. Chiggers were pooled according to species and screened for Orientia DNA by PCR. Two species (Microtrombicula muhaylensis and Pentidionis agamae) produced positive results for the htrA gene, although Ca. Orientia chuto DNA was confirmed by Sanger sequencing only in P. agamae. Metagenomic sequencing of three pools of P. agamae provided evidence for two other bacterial associates: a spirochaete and a Wolbachia symbiont. Phylogenetic analysis of 16S rRNA and multi-locus sequence typing genes placed the spirochaete in a clade of micromammal-associated Borrelia spp. that are widely-distributed globally with no known vector. For the Wolbachia symbiont, a genome assembly was obtained that allowed phylogenetic localisation in a novel, divergent clade. Cytochrome c oxidase I (COI) barcodes for Saudi Arabian chiggers enabled comparisons with global chigger diversity, revealing several cases of discordance with classical taxonomy. Complete mitogenome assemblies were obtained for the three P. agamae pools and almost 50 SNPs were identified, despite a common geographic origin.

CONCLUSIONS

P. agamae was identified as a potential vector of Ca. Orientia chuto on the Arabian Peninsula. The detection of an unusual Borrelia sp. and a divergent Wolbachia symbiont in P. agamae indicated links with chigger microbiomes in other parts of the world, while COI barcoding and mitogenomic analyses greatly extended our understanding of inter- and intraspecific relationships in trombiculid mites.

Phylogeography and population structure of Lagocephalus spadiceus (Richardson, 1845) (Tetraodontiformes, Tetraodontidae) in the South China Sea

The climate fluctuations during the Late Pleistocene significantly influenced the phylogeographic structure and historical dynamics of marine fishes in the marginal seas of the western Pacific Ocean. The puffer fish, Lagocephalus spadiceus, holds substantial nutritional and economic value in the South China Sea. To investigate the demographic history and population structure of the L. spadiceus, the mitochondrial DNA COI and Cyt b gene datasets from 300 individuals across eight populations in the South China Sea were sequenced. Our findings revealed high haplotype diversity (0.874 ± 0.013) and low nucleotide diversity (0.00075 ± 0.00058). The phylogenetic tree and haplotype networks revealed no significant genetic differentiation along the northern coast of South China Sea. Neutrality tests, mismatch distribution analyses, and Bayesian skyline plots suggested that L. spadiceus underwent population expansion during the Late Pleistocene. Both ocean currents and climate change significantly influenced the geographical distribution and genetic population structure of L. spadiceus.

Mitochondrial genome comparison and phylogenetic position of Fannia pusio among the Calyptratae flies

Fannia pusio, the chicken dung fly species, remains unexplored despite its forensic, sanitary, and veterinary importance in the Nearctic and Neotropical regions. In this study, we obtained the complete mitochondrial genome of Fannia pusio for the first time using next-generation sequencing. We compared it with previously published mitogenomes of the genus from the Palearctic region, and its phylogenetic position was studied based on the concatenated protein-coding genes (PCGs) dataset of Calyptratae flies. The circular mitochondrial genome of F. pusio is 16,176 bp in length, with a high A + T content (78.3%), whose gene synteny, codon usage analysis, and amino acid frequency are similar to previously reported Fannia mitogenomes. All PCGs underwent purifying selection except the nad2 gene. Interspecific K2P distances of PCGs of Fannia yielded an average of 12.4% (8.1%-21.1%). The Fannia genus is monophyletic and closely related to Muscidae based on molecular data. Further taxonomic sampling is required to deep into the phylogenetic relationships of the originally proposed species-groups and subgroups within the genus. These results provide a valuable dataset for studying the mitochondrial genome evolution and a resource for the taxonomy and systematics of Fannia.

Insights into the mitochondrial cytochrome oxidase I (mt-COI) gene and wing morphometrics of Anopheles baimaii (Diptera: Culicidae) in malaria-endemic islands of Thailand

Anopheles baimaii (Diptera: Culicidae) significantly contributes to the transmission of parasites causing malaria in Southeast Asia and South Asia. This study examined the morphological (wing shape) and molecular (mitochondrial gene) variations of An. baimaii in four of Thailand's border islands, and also investigated the presence of Plasmodium parasites in these mosquitoes. No Plasmodium infections were detected in the samples. Significant differences in wing shape were observed in most island populations (p < 0.05). A single-linkage tree, constructed using Mahalanobis distances, clustered the populations into two groups based on geographical locations. Genetic variation in An. baimaii was also analyzed through cytochrome c oxidase subunit I (COI) gene sequences. This analysis identified 22 segregating sites and a low nucleotide diversity of 0.004. Furthermore, 18 distinct haplotypes were identified, indicating a high haplotype diversity of 0.825. Neutrality tests for the overall population revealed a significantly negative Fu's Fs value (-5.029), indicating a population expansion. In contrast, Tajima's D yielded a negative value (-1.028) that did not reach statistical significance. The mismatch distribution analysis exhibited a bimodal pattern, and the raggedness index was 0.068, showing no significant discrepancy (p = 0.485) between observed and expected distributions. Pairwise genetic differentiation assessments demonstrated significant differences between all populations (p < 0.05). These findings provide valuable insights into the COI gene and wing morphometric variations in An. baimaii across Thailand's islands, offering critical information for understanding the adaptations of this malaria vector and guiding future comprehensive research.

Genome copy number predicts extreme evolutionary rate variation in plant mitochondrial DNA

Nuclear and organellar genomes can evolve at vastly different rates despite occupying the same cell. In most bilaterian animals, mitochondrial DNA (mtDNA) evolves faster than nuclear DNA, whereas this trend is generally reversed in plants. However, in some exceptional angiosperm clades, mtDNA substitution rates have increased up to 5,000-fold compared with closely related lineages. The mechanisms responsible for this acceleration are generally unknown. Because plants rely on homologous recombination to repair mtDNA damage, we hypothesized that mtDNA copy numbers may predict evolutionary rates, as lower copy numbers may provide fewer templates for such repair mechanisms. In support of this hypothesis, we found that copy number explains 47% of the variation in synonymous substitution rates of mtDNA across 60 diverse seed plant species representing ~300 million years of evolution. Copy number was also negatively correlated with mitogenome size, which may be a cause or consequence of mutation rate variation. Both relationships were unique to mtDNA and not observed in plastid DNA. These results suggest that homologous recombinational repair plays a role in driving mtDNA substitution rates in plants and may explain variation in mtDNA evolution more broadly across eukaryotes. Our findings also contribute to broader questions about the relationships between mutation rates, genome size, selection efficiency, and the drift-barrier hypothesis.

Whole genome sequencing reveals stepping-stone dispersal buffered against founder effects in a range expanding seabird

Many species are shifting their ranges in response to climate-driven environmental changes, particularly in high-latitude regions. However, the patterns of dispersal and colonization during range shifting events are not always clear. Understanding how populations are connected through space and time can reveal how species navigate a changing environment. Here, we present a fine-scale population genomics study of gentoo penguins (Pygoscelis papua), a presumed site-faithful colonial nesting species that has increased in population size and expanded its range south along the Western Antarctic Peninsula. Using whole genome sequencing, we analysed 129 gentoo penguin individuals across 12 colonies located at or near the southern range edge. Through a detailed examination of fine-scale population structure, admixture, and population divergence, we inferred that gentoo penguins historically dispersed rapidly in a stepping-stone pattern from the South Shetland Islands leading to the colonization of Anvers Island, and then the adjacent mainland Western Antarctica Peninsula. Recent southward expansion along the Western Antarctic Peninsula also followed a stepping-stone dispersal pattern coupled with limited post-divergence gene flow from colonies on Anvers Island. Genetic diversity appeared to be maintained across colonies during the historical dispersal process, and range-edge populations are still growing. This suggests large numbers of migrants may provide a buffer against founder effects at the beginning of colonization events to maintain genetic diversity similar to that of the source populations before migration ceases post-divergence. These results coupled with a continued increase in effective population size since approximately 500-800 years ago distinguish gentoo penguins as a robust species that is highly adaptable and resilient to changing climate.

Whole-genome resequencing confirms the genetic effects of dams on an endangered fish Hemibagrus guttatus (Siluriformes: Bagridae): A case study in a tributary of the Pearl River

Dam construction in riverine ecosystems has fragmented natural aquatic habitats and has altered environmental conditions. As a result, damming has been demonstrated to threaten aquatic biodiversity by reducing species distribution ranges and hindering gene exchange, leading to the inability to adapt to environmental changes. Knowledge of the contemporary genetic diversity and genetic structure of fish populations that are separated by dams is vital to developing effective conservation strategies, particularly for endangered fish species. We chose the Lianjiang River, a tributary of the Pearl River, as a case study to assess the effects of dams on the genetic diversity and genetic structure of an endangered fish species, Hemibagrus guttatus, using whole-genome resequencing data from 63 fish samples. The results indicated low levels of genetic diversity, high levels of inbreeding and decreasing trend of effective population size in fragmented H. guttatus populations. In addition, there were significant genetic structure and genetic differentiation among populations, suggesting that the dams might have affected H. guttatus populations. Our findings may benefit management and conservation practices for this endangered species that is currently suffering from the effects of dam construction.