mtDNA Sequences Research Articles

Indian Red Jungle fowl reveals a genetic relationship with South East Asian Red Jungle fowl and Indian native chicken breeds as evidenced through whole mitochondrial genome sequences.

Background: Native chickens are dispersed in a wide geographical range and have hereditary assets that are kept by farmers for various purposes. Mitochondrial DNA (mtDNA) is a widely utilized marker in molecular studies because of its quick advancement, matrilineal legacy, and simple molecular structure. Method and Results: We performed NGS sequencing to investigate mitochondrial genomes and to evaluate the hereditary connections, diversity, and measure of gene stream estimation in Indian native chicken breeds and Red Jungle fowl. The chicken breeds were genotyped using the D-loop region and 23 haplotypes were identified. When compared to Indian native breeds, more haplotypes were identified in the NADH dehydrogenase subunits, Cytochrome c oxidase, Cytochrome b, ATP synthase subunit 6, and Ribosomal RNA genes. The phylogenetic examination indicated that the analyzed chicken breeds were divided into six significant clades, namely A, B, C, D, E, and F, of which the F clade indicated the domestication of chicken breeds in India. Additionally, our work affirmed that the Indian Red Jungle Fowl is the origin for both reference Red Jungle Fowl as well as all Indian breeds, which is reflected in the dendrogram as well as network analysis based on the whole mtDNA and D-loop region. Indian Red Jungle Fowl is distributed as an outgroup, suggesting that this ancestry was reciprocally monophyletic. Conclusion: The mtDNA sequences of Indian native chickens provided novel insights into adaptation mechanisms and the significance of important mtDNA variations in understanding the maternal lineages of native birds.

Nuclear DNA segments homologous to mitochondrial DNA are obstacles for detecting heteroplasmy in sugar beet (Beta vulgaris L.).

Heteroplasmy, the coexistence of multiple mitochondrial DNA (mtDNA) sequences in a cell, is well documented in plants. Next-generation sequencing technology (NGS) has made it feasible to sequence entire genomes. Thus, NGS has the potential to detect heteroplasmy; however, the methods and pitfalls in heteroplasmy detection have not been fully investigated and identified. One obstacle for heteroplasmy detection is the sequence homology between mitochondrial-, plastid-, and nuclear DNA, of which the influence of nuclear DNA segments homologous to mtDNA (numt) need to be minimized. To detect heteroplasmy, we first excluded nuclear DNA sequences of sugar beet (Beta vulgaris) line EL10 from the sugar beet mtDNA sequence. NGS reads were obtained from single plants of sugar beet lines NK-195BRmm-O and NK-291BRmm-O and mapped to the unexcluded mtDNA regions. More than 1000 sites exhibited intra-individual polymorphism as detected by genome browsing analysis. We focused on a 309-bp region where 12 intra-individual polymorphic sites were closely linked to each other. Although the existence of DNA molecules having variant alleles at the 12 sites was confirmed by PCR amplification from NK-195BRmm-O and NK-291BRmm-O, these variants were not always called by six variant-calling programs, suggesting that these programs are inappropriate for intra-individual polymorphism detection. When we changed the nuclear DNA reference, a numt absent from EL10 was found to include the 309-bp region. Genetic segregation of an F2 population from NK-195BRmm-O x NK-291BRmm-O supported the numt origin of the variant alleles. Using four references, we found that numt detection exhibited reference dependency, and extreme polymorphism of numts exists among sugar beet lines. One of the identified numts absent from EL10 is also associated with another intra-individual polymorphic site in NK-195mm-O. Our data suggest that polymorphism among numts is unexpectedly high within sugar beets, leading to confusion about the true degree of heteroplasmy.

Heth longquani sp. n.—(Rhigonematomorpha: Hethidae)—obligate commensalistic nematode of camballoid millipede (Spirostreptida: Cambalopsidae) from Viet Nam

A new nematode species, Heth longquani sp. n. (Hethidae, Ransonematoidea, Rhigonematomorpha, Rhabditida) is described from the camballoid millipede, Chonecambala crassicauda from Thanh Hóa province, Viet Nam. The morphological features of this new species were studied with brightfield and scanning electron microscopies. Partial sequences of LSU rDNA and Cox1 mtDNA are provided. The phylogeny of the nematodes of the genus Heth Cobb, 1898 is discussed.

From rookeries to foraging grounds: understanding regional connectivity and genetic diversity in hawksbill turtles

This study investigated the genetic structure, diversity, and migratory patterns of hawksbill turtles (Eretmochelys imbricata) from two nesting locations in Papua New Guinea (PNG) using mitochondrial DNA (mtDNA) sequencing and satellite telemetry. Tissue samples collected from nesting female hawksbill turtles (n=75) in PNG revealed a total of 6 haplotypes from the Conflict Group site and 5 haplotypes from Kavieng site, with the Conflict Group and Kavieng samples significantly differing from one another and all other known Asia-Pacific stocks. This finding expands our understanding of the genetic stock structure of hawksbill turtles in the Asia-Pacific region, resulting in 9 Management Units (MUs) now published. Satellite tracking of 15 hawksbill turtles revealed that all individuals migrated from the Conflict Group westerly towards foraging areas in eastern Australia (93%) and PNG (7%). With a mean migration path distance of 1241 ± 108 km, three distinct migration strategies were used by the 10 hawksbill turtles that made it to their foraging grounds in the I) eastern Torres Strait, II) Far North Queensland, and III) western PNG waters. A broad scope of home-range strategies and sizes (95% UD) were used, and in comparison to other studies further postulates that hawksbills are connected to non-specific foraging grounds associated with food source availability. This study provides for the first time in PNG essential insights into hawksbill turtle population structure and connectivity in the western Pacific region, highlighting the importance of effectively conserving and managing this critically endangered species as distinct population stocks. Furthermore, we make recommendations for national and regional conservation strategies and transboundary management to ensure the long-term survival and recovery of western Pacific’s hawksbill turtle populations.

An extended mtDNA phylogeography for the alpine newt illuminates the provenance of introduced populations

Abstract Many herpetofauna species have been introduced outside of their native range. MtDNA barcoding is regularly used to determine the provenance of such populations. The alpine newt has been introduced across the Netherlands, the United Kingdom and Ireland. However, geographical mtDNA structure across the natural range of the alpine newt is still incompletely understood and certain regions are severely undersampled. We collect mtDNA sequence data of over seven hundred individuals, from both the native and the introduced range. The main new insights from our extended mtDNA phylogeography are that 1) haplotypes from Spain do not form a reciprocally monophyletic clade, but are nested inside the mtDNA clade that covers western and eastern Europe; and 2) haplotypes from the northwest Balkans form a monophyletic clade together with those from the Southern Carpathians and Apuseni Mountains. We also home in on the regions where the distinct mtDNA clades meet in nature. We show that four out of the seven distinct mtDNA clades that comprise the alpine newt are implicated in the introductions in the Netherlands, United Kingdom and Ireland. In several introduced localities, two distinct mtDNA clades co-occur. As these mtDNA clades presumably represent cryptic species, we urge that the extent of genetic admixture between them is assessed from genome-wide nuclear DNA markers. We mobilized a large number of citizen scientists in this project to support the collection of DNA samples by skin swabbing and underscore the effectiveness of this sampling technique for mtDNA barcoding.

Mitochondrial DNA analyses revealed distinct lineages in an alpine mammal, Siberian ibex (Capra sibirica) in Xinjiang, China.

Maternal lineages of mitochondrial DNA (mtDNA) are recognized as important components of intra and interspecific biodiversity and help us to disclose the phylogeny and divergence times of many taxa. Species of the genus Capra are canonical mountain dwellers. Among these is the Siberian ibex (Capra sibirica), which is regarded as a relic species whose intraspecific classification has been controversial so far. We collected 58 samples in Xinjiang, China, and analyzed the mtDNA genes to shed light on the intraspecific relationships of the C. sibirica populations and estimate the divergence time. Intriguingly, we found that the mtDNA sequences of C. sibirica split into two main lineages in both phylogenetic and network analyses: the Southern lineage, sister to Capra falconeri, consisting of samples from Ulugqat, Kagilik (both in Xinjiang), India, and Tajikistan; and the Northern lineage further divided into four monophyletic clades A-D corresponding to their geographic origins. Samples from Urumqi, Sawan, and Arturk formed a distinct monophyletic clade C within the Northern lineage. The genetic distance between the C. sibirica clades ranges from 3.0 to 8.6%, with values of F ST between 0.839 and 0.960, indicating notable genetic differentiation. The split of the genus Capra occurred approximately 6.75 Mya during the late Miocene. The Northern lineage diverged around 5.88 Mya, followed by the divergence of Clades A-D from 3.30 to 1.92 Mya during the late Pliocene and early Pleistocene. The radiation between the Southern lineage and C. falconeri occurred at 2.29 Mya during the early Pleistocene. Our results highlight the importance of extensive sampling when relating to genetic studies of alpine mammals and call for further genomic studies to draw definitive conclusions.

Novel single-cell mtDNA sequencing technology reveals hidden mutations in oocytes, blastoids, and stem cells

Novel single-cell mtDNA sequencing technology reveals hidden mutations in oocytes, blastoids, and stem cells

Expanding the mutational spectrum of ZTTK syndrome: A de novo variant with global developmental delay and malnutrition in a Chinese patient.

Zhu-Tokita-Takenouchi-Kim (ZTTK, OMIM 617140) syndrome is a severe multisystem developmental disorder characterized by intellectual disability, developmental delay, cortical malformations, epilepsy, visual problems, musculoskeletal abnormalities, and congenital malformations. ZTTK syndrome is caused by a heterozygous pathogenic variant of the SON gene (NM_138927) at chromosome 21q22.1. The purpose of this study was to investigate the pathogenesis of a 6-month-old Chinese child who exhibited global developmental delay, muscle weakness, malnutrition, weight loss, and strabismus, brain abnormality, immunological system abnormalities. The little girl was tested for medical exome sequencing (MES) and mtDNA sequencing in trio. And, the mutation was validated by Sanger sequencing. A novel de novo frameshift variant, c.1845_1870del26 (p.G616Sfs*61), in the SON gene was found in the proband. We described a 6-month-old Chinese child with global developmental delay caused by pathogenic de novo mutation c.1845_1870del26 (p.G616Sfs*61) in the SON. Apart from a founder mutation, we reviewed the phenotypic abnormalities and genotypes in 79 individuals. The data showed that global developmental delay is accompanied by other system disorders. Our findings expanded the mutational spectrum of ZTTK syndrome and provide genetic counseling of baby with global developmental delay.

Establishing a Sequencing Method for the Whole Mitochondrial DNA of Domestic Dogs.

In human beings, whole mitochondrial DNA (mtDNA) sequencing has been widely used in many research fields, including medicine, forensics, and genetics. With respect to the domestic dog (Canis lupus familiaris), which is commonly recognized as being an additional member of the traditional human family structure, research studies on mtDNA should be developed to expand and improve our collective knowledge of dog medicine and welfare as it seems that there is still room for further development in these areas. Moreover, a simple and robust method for sequencing whole mtDNA that can be applied to various dog breeds has not yet been described in the literature. In the present study, we aim to establish such a method for the whole mtDNA sequencing of the domestic dog. In the experiments we conducted, oral mucosa DNA samples obtained from six Japanese domestic dogs were used as a template. We designed four primer pairs that could amplify approximately 5 kbp from each region of the mtDNA and validated several PCR conditions. Subsequently, the PCR amplicons were pooled and subjected to library preparation. The sequencing of the libraries was performed using next-generation sequencing (NGS), followed by bioinformatics analysis. Our results demonstrate that the proposed method can be used to perform highly accurate resequencing. We believe that this method may be useful for future research conducted to better understand dog medicine and welfare.

The complete mitochondrial genome of Trigonisca nataliae (Hymenoptera, Apidae) assemblage reveals heteroplasmy in the control region

The evolution of mitochondrial genomes in the stingless bees is surprisingly dynamic, making them a model system to understand mitogenome structure, function, and evolution. Out of the seven mitogenomes available in this group, five exhibit atypical characteristics, including extreme rearrangements, rapid evolution and complete mitogenome duplication. To further explore the mitogenome diversity in these bees, we utilized isolated mtDNA and Illumina sequencing to assemble the complete mitogenome of Trigonisca nataliae, a species found in Northern Brazil. The mitogenome of T. nataliae was highly conserved in gene content and structure when compared to Melipona species but diverged in the control region (CR). Using PCR amplification, cloning and Sanger sequencing, six different CR haplotypes, varying in size and content, were recovery. These findings indicate that heteroplasmy, where different mitochondrial haplotypes coexist within individuals, occurs in T. nataliae. Consequently, we argue that heteroplasmy might indeed be a common phenomenon in bees that could be associated with variations in mitogenome size and challenges encountered during the assembly process.

Metastatic pattern of ovarian cancer delineated by tracing the evolution of mitochondrial DNA mutations

Ovarian cancer (OC) is the most lethal gynecologic tumor and is characterized by a high rate of metastasis. Challenges in accurately delineating the metastatic pattern have greatly restricted the improvement of treatment in OC patients. An increasing number of studies have leveraged mitochondrial DNA (mtDNA) mutations as efficient lineage-tracing markers of tumor clonality. We applied multiregional sampling and high-depth mtDNA sequencing to determine the metastatic patterns in advanced-stage OC patients. Somatic mtDNA mutations were profiled from a total of 195 primary and 200 metastatic tumor tissue samples from 35 OC patients. Our results revealed remarkable sample-level and patient-level heterogeneity. In addition, distinct mtDNA mutational patterns were observed between primary and metastatic OC tissues. Further analysis identified the different mutational spectra between shared and private mutations among primary and metastatic OC tissues. Analysis of the clonality index calculated based on mtDNA mutations supported a monoclonal tumor origin in 14 of 16 patients with bilateral ovarian cancers. Notably, mtDNA-based spatial phylogenetic analysis revealed distinct patterns of OC metastasis, in which a linear metastatic pattern exhibited a low degree of mtDNA mutation heterogeneity and a short evolutionary distance, whereas a parallel metastatic pattern showed the opposite trend. Moreover, a mtDNA-based tumor evolutionary score (MTEs) related to different metastatic patterns was defined. Our data showed that patients with different MTESs responded differently to combined debulking surgery and chemotherapy. Finally, we observed that tumor-derived mtDNA mutations were more likely to be detected in ascitic fluid than in plasma samples. Our study presents an explicit view of the OC metastatic pattern, which sheds light on efficient treatment for OC patients.

Genetic diversity of mtDNA in the grey wolf population of Belarus threatened by wolf-dog admixture

Hybridisation with domestic species is one of the prominent threats to conser-vation of numerous valuable species in Belarus, in particular the grey wolf (Canis lupus Linnaeus, 1758), the population of which has previously shown unusually divergent genotypes, indicating a possible admixture with free-ranging dogs (Canis lupus familiaris Linnaeus, 1758). Such admixture could threaten the future of the species already weakened by anthropogenic pressure. Reports of hybrids in Belarus based on morphological characteristics have been steadily increasing in frequency since 2010, which can be tied with a growing food availability for feral dogs and low population density of grey wolf facili-tating hybridisation. A limited number of genetic studies with sampling that partially covered Belarus did not detect any traces of hybridisation. Here we report our estimate of genetic diversity in the Belarusian population of grey wolf according to control region (D-loop) mtDNA sequence analysis. We ana-lysed tissue samples from 35 specimens harvested during legal hunts across 25 administrative districts from all 6 regions of Belarus between 2009 and 2022, with 9 of the specimens reported to have morphological characteristics of wolf–dog hybrids. We detected 6 haplotypes among those 35 specimens, 4 of which were found among the likely wolf–dog hybrids. Clade analysis of the obtained sequences with 100 confirmed sequences of wolves, dogs, and their hybrids from the NCBI Genbank database has shown the presence of possible wolf–dog hybrids in our sample. The Belarusian wolf population has shown a low nucleotide and a relatively high haplotype diversity. The discovered genet-ic diversity data of the Belarusian wolf population is mostly in line with studies of similar wolf populations across Europe. The persistence of large wolf meta-populations across Eastern Europe and Russia, combined with the high mobility of the animal, seems to be the probable cause of genetic diversity of wolf populations in Belarus, but some degree of wolf–dog hybridisation could also explain the observed genetic heterogeneity, which invites further research based on nuclear markers.

P-706 Non-invasive analysis of mitochondrial DNA mutation for embryo evaluation.

Abstract Study question Is it possible to amplify whole mitochondrial DNA (mtDNA) and detect all mtDNA mutation in human embryo from spent media after embryo culture? Summary answer We were able to amplify whole mtDNA from 43% of spent medium after 24-hour culture. The most of mtDNA mutation in embryo could be detected. What is known already Preimplantation genetic testing for aneuploidy (PGT-A) with embryo biopsy is now commonly used to improve pregnancy rate. However, invasive embryo biopsy requires highly trained embryologist and induced higher risk of pre-eclampsia. Therefore, non-invasive methods with cell-free DNA in spent medium have been studied. Our group previously showed euploid or viable embryos at post-implantation stage have lower number of non-synonymous mtDNA mutations and this may help to select the best blastocyst to transfer. Although cell-free DNA is reported to contain mtDNA, it remains unclear whether mtDNA mutations number can be assessed from cell-free DNA. Study design, size, duration Donated low grade blastocysts were cultured for additional 24 hours with new media, cell-free mtDNA were obtained from the spent culture medium (non-invasive samples). For comparison, trophectoderm cells were biopsied from each embryo (invasive sample). The mtDNA selective amplifications were done to both samples. We performed mtDNA sequencing by next generation sequencing (NGS) and compared mtDNA mutations between non-invasive and invasive samples to clarify the capability of non-invasive assessment for mtDNA mutation. Participants/materials, setting, methods Under the ethical review of Yokohama City University and informed consent with patients, we collected human blastocysts which were discarded because of slow development or morphologically low-grade. We extracted whole DNA from biopsy and medium samples and selectively amplified mtDNA by long-range PCR for two overlapping amplicons. The mtDNA sequencing with NGS was performed to successfully amplified mtDNA. The 90% or more heteroplasmy level non-synonymous mutations were investigated. Main results and the role of chance We collected 34 discarded embryos from 13 patients. All embryos were cultured individually for additional 24 hours with 20 μl drop of newly prepared media. Amplified mtDNA were visualized by the presence of 8 kb band following agarose gel-apheresis for two fragments PCR. Both fragments were detected in 41% (14/34) of non-invasive samples and all invasive samples. Only one fragment was detected in 14% (5/34) of non-invasive samples. The completely amplified non-invasive samples and corresponding invasive samples were performed mtDNA sequencing with NGS. In results, 13 non-synonymous mutations were identified in invasive samples. All of these mutations were also detected in non-invasive samples. Although the number and location of mutations completely matched between the invasive and non-invasive samples in 78.5% (11/14) embryos, in other 3 embryos, mtDNA mutation numbers were higher in non-invasive samples even though no mutation existed in invasive samples. This means, if selective mtDNA amplification is completed, mtDNA mutations can be evaluated from the non-invasive samples with a probability of about 80% but include 20% false positive mtDNA mutations. To realize this, we need to improve the mtDNA amplification method. Limitations, reasons for caution We can used only clinically discarded embryos because ethical restriction. And it was necessary to additional 24-hours culture to obtain individually cultured spent media because embryos are co-cultured until they are donated. Because of small number of samples available, we keep collecting more samples for more accurate evaluation. Wider implications of the findings If the mtDNA mutations can be analyzed from spent medium, high-quality embryos can be selected without invasive embryo biopsy and complicated procedure. If this non-invasive mtDNA analysis can be performed to clinical embryo for embryo transfer, it may contribute to further improvement of pregnancy rate without any invasion to embryo. Trial registration number the Japan Society for the Promotion of Science (JSPS) KAKENHI Grant-in-Aid for Scientific Research C (Grant Number JP21K09474) and Early-Career Scientists (Grant Number JP20K18169)

Clinical and bi-genomic DNA findings of patients suspected to have mitochondrial diseases.

Background: Mitochondrial diseases are the most common group of inherited metabolic disorders, causing difficulties in definite diagnosis due to clinical and genetic heterogeneity. Clinical components are predominantly associated with pathogenic variants shown in nuclear or mitochondrial genomes that affect vital respiratory chain function. The development of high-throughput sequencing technologies has accelerated the elucidation of the genetic etiology of many genetic diseases that previously remained undiagnosed. Methods: Thirty affected patients from 24 unrelated families with clinical, radiological, biochemical, and histopathological evaluations considered for mitochondrial diseases were investigated. DNA isolated from the peripheral blood samples of probands was sequenced for nuclear exome and mitochondrial DNA (mtDNA) analyses. MtDNA sequencing was also performed from the muscle biopsy material in one patient. For segregation, Sanger sequencing is performed for pathogenic alterations in five other affected family members and healthy parents. Results: Exome sequencing revealed 14 different pathogenic variants in nine genes encoding mitochondrial function peptides (AARS2, EARS2, ECHS1, FBXL4, MICOS13, NDUFAF6, OXCT1, POLG, and TK2) in 12 patients from nine families and four variants in genes encoding important for muscle structure (CAPN3, DYSF, and TCAP) in six patients from four families. Three probands carried pathogenic mtDNA variations in two genes (MT-ATP6 and MT-TL1). Nine variants in five genes are reported for the first time with disease association: (AARS2: c.277C>T/p.(R93*), c.845C>G/p.(S282C); EARS2: c.319C>T/p.(R107C), c.1283delC/p.(P428Lfs*); ECHS1: c.161G>A/p.(R54His); c.202G>A/p.(E68Lys); NDUFAF6: c.479delA/p.(N162Ifs*27); and OXCT1: c.1370C>T/p.(T457I), c.1173-139G>T/p.(?). Conclusion: Bi-genomic DNA sequencing clarified genetic etiology in 67% (16/24) of the families. Diagnostic utility by mtDNA sequencing in 13% (3/24) and exome sequencing in 54% (13/24) of the families prioritized searching for nuclear genome pathologies for the first-tier test. Weakness and muscle wasting observed in 17% (4/24) of the families underlined that limb-girdle muscular dystrophy, similar to mitochondrial myopathy, is an essential point for differential diagnosis. The correct diagnosis is crucial for comprehensive genetic counseling of families. Also, it contributes to making treatment-helpful referrals, such as ensuring early access to medication for patients with mutations in the TK2 gene.

The Phylogeny of Bornean Swamp Buffalo (Bubalus bubalis) Analysis Based on D-loop Mitochondrial DNA Sequence Variation

Swamp buffalo ( Bubalus bubalis ) is one of the Indonesian germplasm that adapts well to Borneo Island. This study aimed to determine the genetic diversity, phylogenetic tree, and phylogeographic structure of Bornean swamp buffalo based on control region (D-loop) mitochondrial DNA sequences. A total of 120 animals were collected from three populations in Indonesia, i.e., the North, East, and South of Kalimantan Provinces. Along 1140 bp of D-loop mtDNA gene of Bornean swamp buffaloes was amplified with a design primer of F: 5'-CAA CAC CCA AAG CTG AAG TT-3’ and R: 5'-CGC TCC TCT TAG TCT CGT TG-3’. Therefore, the forward and reverse sequencing was performed to visualize the full length of D-loop mtDNA gene sequence (1140 bp). Results showed that a total of 47 haplotypes were detected in the animal study, with haplotype and nucleotide diversities of 0.936 and 0.005, respectively. Consequently, two haplogroups were observed in the animal study, i.e., Haplogroup A (North) and Haplogroup B (East and South). Based on structure analysis, Bornean swamp buffaloes were comparable to filing swamp buffaloes of China based on structure. According to the analysis of molecular (AMOVA), the geographical component contributed over 56.44% of the total mtDNA sequence variations. In conclusion, it was discovered that the haplogroups of buffalo from the East and South populations were identical.

Central American Trachemys revisited: New sampling questions current understanding of taxonomy and distribution (Testudines: Emydidae)

Using 3226-bp-long mtDNA sequences and five nuclear loci (Cmos, ODC, R35, Rag1, Rag2, together 3409 bp), we examine genetic differentiation and relationships of Central American slider turtles (Trachemys grayi, T. venusta). Our investigation also included samples from taxa endemic to North America (T. gaigeae, T. scripta), the Antilles (T. decorata, T. decussata, T. stejnegeri, T. terrapen), and South America (T. dorbigni, T. medemi plus the two T. venusta subspecies endemic to northern South America). Our mitochondrial phylogeny retrieves all studied species as distinct, with three well-supported clades in a polytomy: (1) the Central and South American species (T. grayi + T. venusta) + (T. dorbigni + T. medemi), (2) the Antillean species, and (3) T. gaigeae + T. scripta. Our nuclear DNA analyses also suggest three distinct but conflicting clusters: (1) T. scripta plus the Antillean species, (2) T. gaigeae, and (3) the Central and South American species T. dorbigni, T. grayi, T. medemi, and T. venusta. However, in the mitochondrial phylogeny, T. gaigeae is the little divergent sister taxon of T. scripta. This conflicting placement of T. gaigeae suggests a distinct evolutionary trajectory and old hybridization with T. scripta and mitochondrial capture. Despite prominent color pattern differences, genetic divergences within T. grayi and T. venusta are shallow and the taxonomic diversity of each species with several currently recognized subspecies could be overestimated. Finally, we provide for the first time evidence for the occurrence of T. grayi along the Caribbean versant of Costa Rica.

Historical genomes elucidate European settlement and the African diaspora in Delaware

The 17th-century colonization of North America brought thousands of Europeans to Indigenous lands in the Delaware region, which comprises the eastern boundary of the Chesapeake Bay in what is now the Mid-Atlantic region of the United States.1 The demographic features of these initial colonial migrations are not uniformly characterized, with Europeans and European-Americans migrating to the Delaware area from other countries and neighboring colonies as single persons or in family units of free persons, indentured servants, or tenant farmers.2 European colonizers also instituted a system of racialized slavery through which they forciblytransported thousands of Africans to the Chesapeake region. Historical information about African-descended individuals in the Delaware region is limited, with a population estimate of less than 500 persons by 1700 CE.3,4 To shed light on the population histories of this period, we analyzed low-coverage genomes of 11 individuals from the Avery's Rest archaeological site (circa 1675-1725 CE), located in Delaware. Previous osteological and mitochondrial DNA (mtDNA) sequence analyses showed a southern group of eight individuals of European maternal descent, buried 15-20 feet from a northern group of three individuals of African maternal descent.5 Autosomal results further illuminate genomic similarities to Northwestern European reference populations or West and West-Central African reference populations, respectively. We also identify three generations of maternal kin of European ancestry and a paternal parent-offspring relationship between an adult and child of African ancestry. These findings expand our understanding of the origins and familial relationships in late 17th and early 18th century North America.

Macroscopic sarcocystosis in a pig carcass from an Italian abattoir.

Different food-safety institutions, including the European Food Safety Authority, encourage monitoring and characterising Sarcocystis spp. in animals and foodstuffs; among meat-producing animals, domestic pigs (Sus scrofa domesticus) can host two different Sarcocystis spp., that is Sarcocystis miescheriana and the zoonotic Sarcocystis suihominis. Herein, we report for the first time the presence of macrocysts of Sarcocystis miescheriana in a domestic pig resulting in carcass condemnation. In North-West Italy, in June 2022 the carcass of a clinically healthy sow was condemned due to the detection of multifocal macroscopic whitish fusiform lesions. Affected muscle samples were submitted to histological and molecular analyses targeting the mtDNA cox1 and 18S rRNA genes. At gross examination and histology, well demarcated, oval or elongated macrocysts up to 8mm in length characterized by a calcified central core surrounded by fibrosis were detected. The molecular amplification and sequencing of the cox1 mtDNA and 18S rRNA genes revealed the presence of Sarcocystis miescheriana DNA in all sampled macrocysts. Our study provides the first molecularly confirmed case of Sarcocystis miescheriana infection in a domestic pig in Italy. The present report highlights the need to increase data related to the occurrence and the prevalence of Sarcocystis spp. in meat-producing animals, and in wild and domestic pigs in particular, taking into account the zoonotic potential of Sarcocystis suihominis and the possible financial losses related to carcass discard due to macroscopic Sarcocystis spp. cysts.

Actinarctus doryphorus (Tanarctidae) DNA barcodes and phylogenetic reinvestigation of Arthrotardigrada with new A. doryphorus and Echiniscoididae sequences.

Little is still known about the diversity and evolution of marine arthrotardigrades, as they are generally difficult to sample, resulting in a limited amount of molecular data for barcoding and phylogenetic studies. With the current study, we provide the first investigation into COI haplotype diversity in a marine tanarctid and at the same time readdress arthrotardigrade phylogeny. Specifically, we provide COI mtDNA, 18S and 28S rDNA sequences from a population of Actinarctus doryphorus (Tanarctidae) sampled off the coast of Roscoff, France and further provide new 18S sequences from two marine echiniscoidids. A. doryphorus COI sequences confirmed the presence of a single species and further revealed five haplotypes shared among nine sequenced individuals. Our 18S and 28S rDNA datasets were individually and combined analysed with Bayesian inference and Maximum Likelihood. Actinarctus doryphorus was placed together with Tanarctus sequences within a maximally supported Tanarctidae, confirming previous interpretations that the clade is distinct from Halechiniscidae. Although several studies in recent decades have concluded that the marine arthrotardigrades are paraphyletic, recent studies have argued that the clade may not be paraphyletic. Our phylogenetic analyses consistently inferred Arthrotardigrada as paraphyletic, as the clade includes the monophyletic Echiniscoidea. Accordingly, we propose that it is time to suppress the order Arthrotardigrada as it clearly does not reflect tardigrade phylogeny.

Validating the occurrence of the giant mottled eel (Anguilla marmorata) in the Galápagos Islands.

The giant mottled eel (Anguilla marmorata) is distributed mostly in the Indo-West Pacific. However, a few records indicate the presence of this eel in the Tropical Central and East Pacific. In April 2019, an eel specimen was caught in a small stream in San Cristobal Island, Galápagos. Morphological and molecular characters (16S and Cytb mtDNA sequences) confirmed the species as A. marmorata Quoy & Gaimard, 1824. The re-discovery of A. marmorata in Galápagos supports the hypothesis of an eastward range expansion from the west, probably through the North Equatorial Counter-Current.