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17 pages, 2547 KiB  
Article
A Host Cell Vector Model for Analyzing Viral Protective Antigens and Host Immunity
by Sun-Min Ahn, Jin-Ha Song, Seung-Eun Son, Ho-Won Kim, Gun Kim, Seung-Min Hong, Kang-Seuk Choi and Hyuk-Joon Kwon
Int. J. Mol. Sci. 2025, 26(15), 7492; https://doi.org/10.3390/ijms26157492 (registering DOI) - 2 Aug 2025
Viewed by 218
Abstract
Avian influenza A viruses (IAVs) pose a persistent threat to the poultry industry, causing substantial economic losses. Although traditional vaccines have helped reduce the disease burden, they typically rely on multivalent antigens, emphasize humoral immunity, and require intensive production. This study aimed to [...] Read more.
Avian influenza A viruses (IAVs) pose a persistent threat to the poultry industry, causing substantial economic losses. Although traditional vaccines have helped reduce the disease burden, they typically rely on multivalent antigens, emphasize humoral immunity, and require intensive production. This study aimed to establish a genetically matched host–cell system to evaluate antigen-specific immune responses and identify conserved CD8+ T cell epitopes in avian influenza viruses. To this end, we developed an MHC class I genotype (B21)-matched host (Lohmann VALO SPF chicken) and cell vector (DF-1 cell line) model. DF-1 cells were engineered to express the hemagglutinin (HA) gene of clade 2.3.4.4b H5N1 either transiently or stably, and to stably express the matrix 1 (M1) and nucleoprotein (NP) genes of A/chicken/South Korea/SL20/2020 (H9N2, Y280-lineage). Following prime-boost immunization with HA-expressing DF-1 cells, only live cells induced strong hemagglutination inhibition (HI) and virus-neutralizing (VN) antibody titers in haplotype-matched chickens. Importantly, immunization with DF-1 cells transiently expressing NP induced stronger IFN-γ production than those expressing M1, demonstrating the platform’s potential for differentiating antigen-specific cellular responses. CD8+ T cell epitope mapping by mass spectrometry identified one distinct MHC class I-bound peptide from each of the HA-, M1-, and NP-expressing DF-1 cell lines. Notably, the identified HA epitope was conserved in 97.6% of H5-subtype IAVs, and the NP epitope in 98.5% of pan-subtype IAVs. These findings highlight the platform’s utility for antigen dissection and rational vaccine design. While limited by MHC compatibility, this approach enables identification of naturally presented epitopes and provides insight into conserved, functionally constrained viral targets. Full article
(This article belongs to the Special Issue Molecular Research on Immune Response to Virus Infection and Vaccines)
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19 pages, 30070 KiB  
Article
Introgressive Hybridization and a Natural Barrier: Molecular Analyses Lay Out a Conservation Blueprint for the Critically Endangered Vietnamese Pond Turtle (Mauremys annamensis)
by Hanh T. Ngo, Timothy E. M. McCormack, Ha V. Hoang, Luan T. Nguyen, Thuy T. Nguyen, Van T. H. Nguyen, Hao T. Do, Ha L. T. Trinh, Thomas Ziegler, Mary E. Blair and Minh D. Le
Diversity 2025, 17(4), 260; https://doi.org/10.3390/d17040260 - 7 Apr 2025
Viewed by 853
Abstract
The critically endangered Vietnamese Pond Turtle (Mauremys annamensis), an endemic species occurring in a small lowland area in central Vietnam, has been virtually extirpated from its natural range. As a result, reintroduction of held individuals worldwide, especially from Europe, the United [...] Read more.
The critically endangered Vietnamese Pond Turtle (Mauremys annamensis), an endemic species occurring in a small lowland area in central Vietnam, has been virtually extirpated from its natural range. As a result, reintroduction of held individuals worldwide, especially from Europe, the United States, and Vietnam, will play a vital role in species recovery programs. Nevertheless, the discordance between different molecular markers in inferring the placements of two closely related species, M. annamensis and M. mutica, and the existence of two distinct mitochondrial lineages within M. annamensis, have hindered conservation strategies to properly maintain the genetic integrity of held populations to release individuals back to their natural habitat in the future. In this study, we sequenced 732 bps of a mitochondrial gene (ND4) and 1038 bps of an intron fragment of the RNA fingerprint protein 35 (R35) gene for 18 samples collected from the local trade in five provinces in Vietnam and 20 samples from founders in the Turtle Conservation Centre, Cuc Phuong National Park, Vietnam. DNA sequences analyzed by Bayesian Inference, Maximum Likelihood, and NeighborNet methods show that the Vietnamese Pond Turtle is a well-defined species and that the population of M. mutica from Hainan Island likely evolved through introgression between a lineage distantly related to true M. mutica and M. annamensis and a lineage closely related to the two mitochondrial haplotypes of M. annamensis. Interestingly, our analyses of samples collected from the local trade and those with known localities reveal that the two extant mitochondrial lineages within M. annamensis are geographically isolated and evolutionarily significant. Based upon the new findings, we recommend genetic screening for all held populations in Vietnam and elsewhere and that animals with different genetic histories be managed separately. In addition, it is important to use other molecular markers, such as microsatellites and single nucleotide polymorphisms (SNPs), to determine potential hybrids between the two mitochondrial haplotypes and remove them from conservation breeding programs before releasing the turtles back to their natural habitat. Full article
(This article belongs to the Section Biodiversity Conservation)
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15 pages, 1040 KiB  
Article
Characterization of Streptococcus pyogenes Strains from Tonsillopharyngitis and Scarlet Fever Resurgence, 2023—FIRST Detection of M1UK in Bulgaria
by Emma Keuleyan, Theodor Todorov, Deyan Donchev, Ani Kevorkyan, Radoslava Vazharova, Alexander Kukov, Georgi Todorov, Boriana Georgieva, Iskra Altankova and Yordanka Uzunova
Microorganisms 2025, 13(1), 179; https://doi.org/10.3390/microorganisms13010179 - 16 Jan 2025
Cited by 2 | Viewed by 1927
Abstract
Recently a resurgence of Streptococcus pyogenes infections has arisen, with concerns around the highly virulent M1UK lineage. Our aim was to characterize S. pyogenes, the immune responses it causes, and to determine the presence of the M1UK lineage in Sofia, [...] Read more.
Recently a resurgence of Streptococcus pyogenes infections has arisen, with concerns around the highly virulent M1UK lineage. Our aim was to characterize S. pyogenes, the immune responses it causes, and to determine the presence of the M1UK lineage in Sofia, Bulgaria. In our study, the infections were confirmed by culture testing or rapid antigen test. Identification was performed by MALDI-TOF and was followed up by antibiotic susceptibility testing (EUCAST). Virulence factors were identified using multiplex PCR and whole genome sequencing (WGS). Immune responses were measured through detection of serum complement levels, lymphocyte subsets, and cytokine profiling. Out of 82 children, 38 had scarlet fever and the rest had streptococcal pharyngitis. Strains were susceptible to penicillin (β-lactams), macrolides, clindamycin, tetracyclines, co-trimoxazole, fluoroquinolones, and linezolid. Superantigen profiles were identified: SpeA + SpeJ (45%), SpeC, and SpeI + SpeH (27.5% each). A novel Multilocus sequence typing (MLST) haplotype in the mutS gene (d90b) was found in four strains. The M1UK lineage was detected for the first time in Bulgaria. We observed an increase in complement fractions C3 and C4 and a decrease in T lymphocytes. A significant increase in the levels of IFN-γ, IL-6, and IL-10 with corresponding reduction in IL-17A were revealed. In conclusion, the studied S. pyogenes strains were characterized by their susceptibility to antibiotics and the predominance of SpeA superantigen; for the first time in Bulgaria the presence of M1UK and a novel SNP variation in the mutS gene (d90b) were found. A mixed pattern of pro- and anti-inflammatory immune responses in patients was observed. Full article
(This article belongs to the Section Medical Microbiology)
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12 pages, 2213 KiB  
Article
A Genetic Make Up of Italian Lipizzan Horse Through Uniparental Markers to Preserve Historical Pedigrees
by Alessandra Crisà, Irene Cardinali, Andrea Giontella, Maurizio Silvestrelli, Hovirag Lancioni and Luca Buttazzoni
Biology 2024, 13(12), 1087; https://doi.org/10.3390/biology13121087 - 23 Dec 2024
Cited by 1 | Viewed by 1034
Abstract
Lipizzan is a famous horse breed dating back to 1580 when the original stud of Lipica was established by the Hasburg Archduke Charles II. Currently, the Italian State Stud of Lipizzan Horses (ASCAL) is a conservation nucleus managed through strict mating rules where [...] Read more.
Lipizzan is a famous horse breed dating back to 1580 when the original stud of Lipica was established by the Hasburg Archduke Charles II. Currently, the Italian State Stud of Lipizzan Horses (ASCAL) is a conservation nucleus managed through strict mating rules where mitochondrial DNA sequences are used to verify the correct assignment of mares to a historical pedigree maternal lineage. Here, we analyzed the D-loop sequences of Lipizzan horses from the ASCAL in Monterotondo (Rome, Italy) in order to confirm their pedigree assignment to known female founder families. The concurrent investigation of the paternal counterpart based on variation in the male-specific region of the Y chromosome (MSY) showed a prevalence of HT02 (80%), typical of the Neapolitan/Oriental wave. The mtDNA polymorphisms identified shaped nine haplotypes that were unequivocally assigned to each of nine classical mare families of the stud (Africa, Almerina, Argentina, Deflorata, Djebrin, Fistula, Ivanka, Sardinia, Spadiglia), while the Europa and Theodorosta families shared a tenth haplotype. New polymorphisms were identified in a not previously studied region (np 16100–16350). The mtDNA phylogenetic analysis revealed that the Lipizzans of the Monterotondo stud belong to six haplogroups (B, C, G, L, M, Q), out of the 18 recorded for the equine species. This work enabled us to identify and preserve ten haplotypes from the historical maternal lines in a small stud kept in genetic segregation for over 100 years. Full article
(This article belongs to the Section Conservation Biology and Biodiversity)
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20 pages, 6682 KiB  
Article
Landscape Heterogeneity Drives Genetic Diversity in the Highly Dispersive Moss Funaria hygrometrica Hedw.
by Mahmoud Magdy, Olaf Werner, Jairo Patiño and Rosa María Ros
Plants 2024, 13(19), 2785; https://doi.org/10.3390/plants13192785 - 4 Oct 2024
Viewed by 2217
Abstract
Funaria hygrometrica, a cosmopolitan moss species known for its remarkable dispersal capacity, was selected as the focal organism to investigate the relationship between landscape features and genetic diversity. Our study encompassed samples collected from two distinct regions: the Spanish Sierra Nevada Mountains [...] Read more.
Funaria hygrometrica, a cosmopolitan moss species known for its remarkable dispersal capacity, was selected as the focal organism to investigate the relationship between landscape features and genetic diversity. Our study encompassed samples collected from two distinct regions: the Spanish Sierra Nevada Mountains (SN), characterized by a diverse landscape with an altitudinal difference of nearly 3500 m within a short distance, and the Murcia Region (MU) in Southeast Spain, characterized by a uniform landscape akin to the lowlands of Sierra Nevada. Genotyping analysis targeted three genetic regions: the nuclear ribosomal internal transcribed spacer (nrITS), the chloroplast rps3-rpl16 region, and the mitochondrial rpl5-rpl16 spacer. Through this analysis, we aimed to assess genetic variability and population structure across these environmentally contrasting regions. The Sierra Nevada populations exhibited significantly higher haplotype diversity (Hd = 0.78 in the highlands and 0.67 overall) and nucleotide diversity (π% = 0.51 for ITS1) compared to the Murcia populations (Hd = 0.35, π% = 0.14). Further investigation unveiled that samples from the lowlands of Sierra Nevada showed a closer genetic affinity to Murcia than to the highlands of Sierra Nevada. Furthermore, the genetic differentiation between highland and lowland populations was significant (ΦST = 0.55), with partial Mantel tests and ResistanceGA analysis revealing a strong correlation between ITS1-based genetic diversity and landscape features, including altitude and bioclimatic variables. Our study elucidated potential explanations for the observed genetic structuring within F. hygrometrica samples’ populations. These included factors such as a high selfing rate within restricted habitats, a limited average dispersal distance of spores, hybrid depression affecting partially incompatible genetic lineages, and recent migration facilitated via human activities into formerly unoccupied areas of the dry zones of Southeast Spain. Full article
(This article belongs to the Special Issue Responses and Adaptations of Bryophytes to a Changing World)
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12 pages, 3830 KiB  
Article
Genome-Wide Association Studies Reveal That the Abietane Diterpene Isopimaric Acid Promotes Rice Growth through Inhibition of Defense Pathways
by Xiaomeng Luo, Liping Bai, Jiaqi Huang, Luying Peng, Juan Hua and Shihong Luo
Int. J. Mol. Sci. 2024, 25(17), 9161; https://doi.org/10.3390/ijms25179161 - 23 Aug 2024
Viewed by 1132
Abstract
Plants are an important source for the discovery of novel natural growth regulators. We used activity screening to demonstrate that treatment of Nipponbare seeds with 25 μg/mL isopimaric acid significantly increased the resulting shoot length, root length, and shoot weight of rice seedlings [...] Read more.
Plants are an important source for the discovery of novel natural growth regulators. We used activity screening to demonstrate that treatment of Nipponbare seeds with 25 μg/mL isopimaric acid significantly increased the resulting shoot length, root length, and shoot weight of rice seedlings by 11.37 ± 5.05%, 12.96 ± 7.63%, and 27.98 ± 10.88% and that it has a higher activity than Gibberellin A3 (GA3) at the same concentration. A total of 213 inbred lines of different rice lineages were screened, and we found that isopimaric acid had different growth promotional activities on rice seedlings of different varieties. After induction with 25 μg/mL isopimaric acid, 15.02% of the rice varieties tested showed increased growth, while 15.96% of the varieties showed decreased growth; the growth of the remaining 69.02% did not show any significant change from the control. In the rice varieties showing an increase in growth, the shoot length and shoot weight significantly increased, accounting for 21.88% and 31.25%. The root length and weight significantly increased, accounting for 6.25% and 3.13%. Using genome-wide association studies (GWASs), linkage disequilibrium block, and gene haplotype significance analysis, we identified single nucleotide polymorphism (SNP) signals that were significantly associated with the length and weight of shoots on chromosomes 2 and 8, respectively. After that, we obtained 17 candidate genes related to the length of shoots and 4 candidate genes related to the weight of shoots. Finally, from the gene annotation data and gene tissue-specific expression; two genes related to this isopimaric acid regulation phenotype were identified as OsASC1 (LOC_Os02g37080) on chromosome 2 and OsBUD13 (LOC_Os08g08080) on chromosome 8. Subcellular localization analysis indicated that OsASC1 was expressed in the plasma membrane and the nuclear membrane, while OsBUD13 was expressed in the nucleus. Further RT-qPCR analysis showed that the relative expression levels of the resistance gene OsASC1 and the antibody protein gene OsBUD13 decreased significantly following treatment with 25 μg/mL isopimaric acid. These results suggest that isopimaric acid may inhibit defense pathways in order to promote the growth of rice seedlings. Full article
(This article belongs to the Section Molecular Plant Sciences)
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12 pages, 1703 KiB  
Article
Use of Wing Geometric Morphometric Analysis and mtDNA to Identify Africanization of Apis mellifera in the Central Highlands of Ecuador
by Diego Masaquiza, Lino Curbelo Rodríguez, José Zapata, Joffre Monar, Maritza Vaca, Leonardo Porrini, Martin Eguaras, Martin Daniele, Dora Romero and Amilcar Arenal
Insects 2024, 15(8), 628; https://doi.org/10.3390/insects15080628 - 20 Aug 2024
Viewed by 1895
Abstract
Seventy-five samples were collected from 15 beehives in the central highlands of Ecuador (Tungurahua–Chimborazo) to assess Africanization in managed bee populations using wing geometric morphometric and mitochondrial DNA analyses. The results indicated that when grouping the apiaries based on altitudinal floors into 2600–2800, [...] Read more.
Seventy-five samples were collected from 15 beehives in the central highlands of Ecuador (Tungurahua–Chimborazo) to assess Africanization in managed bee populations using wing geometric morphometric and mitochondrial DNA analyses. The results indicated that when grouping the apiaries based on altitudinal floors into 2600–2800, 2801–3000, and 3001–3274 m above sea level, differences (p < 0.001) were observed. The morphotypes were similar in the first two floors, but the third indicated that altitude plays a crucial role in the differentiation of populations. When comparing with the pure subspecies, we found differences (p < 0.001); the nearest Mahalanobis distance was for Apis mellifera scutellata (D2 = 3.51), with 95.8% Africanization via father in the area. The maternal origin of all patterns belonged to lineage A (A. m. scutellata), with seven haplotypes. The most frequent haplotypes were A26 and A1; however, the A1q haplotype was not detected at the national level or in nearby countries. The identified haplotypes do not coincide with A4, which is predominant in South Africa and Brazil. The results indicate a double origin due to their presence in North Africa and the Iberian Peninsula. The formation of specific morphological groups within ecoregions is suggested. Full article
(This article belongs to the Section Insect Ecology, Diversity and Conservation)
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12 pages, 2069 KiB  
Article
New COI-COII mtDNA Region Haplotypes in the Endemic Honey Bees Apis mellifera intermissa and Apis mellifera sahariensis (Hymenoptera: Apidae) in Algeria
by Amira Chibani Bahi Amar, Nacera Tabet Aoul, Riad Fridi, Alain Vignal and Kamila Canale-Tabet
Insects 2024, 15(7), 549; https://doi.org/10.3390/insects15070549 - 20 Jul 2024
Viewed by 2035
Abstract
The practice of beekeeping in Algeria is of great cultural, social, and economic importance. However, the importation of non-local subspecies reported by beekeepers has disrupted the natural geographical distribution area and the genetic diversity of the native honey bees. To assess the genetic [...] Read more.
The practice of beekeeping in Algeria is of great cultural, social, and economic importance. However, the importation of non-local subspecies reported by beekeepers has disrupted the natural geographical distribution area and the genetic diversity of the native honey bees. To assess the genetic diversity of A. m. intermissa and A. m. sahariensis, and their relationships with African and European subspecies, the COI-COII intergenic region was analyzed in 335 individuals, 68 sampled in Algeria, 71 in Europe, Madagascar, and the South West Indian Ocean archipelagos, and 196 sequences recovered from GenBank. The results show the presence of the A lineage exclusively in Algerian samples with the identification of 24 haplotypes of which 16 are described for the first time. These haplotypes were found to be shared by both subspecies, with A74 being the most common haplotype in the population studied. The sequence comparison indicates the existence of three polymorphisms of the COI-COII marker: P0Q, P0QQ, and P0QQQ. One new haplotype was identified in the M lineage in samples from France. No evidence of genetic introgression within the Algerian honey bee population was detected. These data enhance our knowledge of the genetic diversity and emphasize the importance of protecting these local subspecies. Full article
(This article belongs to the Section Insect Molecular Biology and Genomics)
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18 pages, 2079 KiB  
Article
Haplotype Diversity in mtDNA of Honeybee in the Czech Republic Confirms Complete Replacement of Autochthonous Population with the C Lineage
by Aleš Knoll, Lucie Langová, Antonín Přidal and Tomáš Urban
Insects 2024, 15(7), 495; https://doi.org/10.3390/insects15070495 - 2 Jul 2024
Cited by 2 | Viewed by 1453
Abstract
The study aimed to analyze the genetic diversity in the Czech population of Apis mellifera using mitochondrial DNA markers, tRNAleu-cox2 intergenic region and cox1 gene. A total of 308 samples of bees were collected from the entire Czech Republic (from colonies [...] Read more.
The study aimed to analyze the genetic diversity in the Czech population of Apis mellifera using mitochondrial DNA markers, tRNAleu-cox2 intergenic region and cox1 gene. A total of 308 samples of bees were collected from the entire Czech Republic (from colonies and flowers in 13 different regions). Following sequencing, several polymorphisms and haplotypes were identified. Analysis of tRNAleu-cox2 sequences revealed three DraI haplotypes (C, A1, and A4). The tRNAleu-cox2 region yielded 10 C lineage haplotypes, one of which is a newly described variant. Three A lineage haplotypes were identified, two of which were novel. A similar analysis of cox1 sequences yielded 16 distinct haplotypes (7 new) within the population. The most prevalent tRNAleu-cox2 haplotype identified was C1a, followed by C2a, C2c, C2l, and C2d. For the cox1 locus, the most frequent haplotypes were HpB02, HpB01, HpB03, and HpB04. The haplotype and nucleotide diversity indices were high in both loci, in tRNAleu-cox2 with values of 0.682 and 0.00172, respectively, and in cox1 0.789 and 0.00203, respectively. The Tajima’s D values were negative and lower in tRNAleu-cox2 than in cox1. The most frequent haplotypes were uniformly distributed across all regions of the Czech Republic. No haplotype of the indigenous M lineage was identified. High diversity and the occurrence of rare haplotypes indicate population expansion and continuous import of tribal material of the C lineage. Full article
(This article belongs to the Section Insect Molecular Biology and Genomics)
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23 pages, 2053 KiB  
Article
Phylogeography of Ara militaris (Military Macaw): Implications for Conservation
by Francisco A. Rivera-Ortíz, Salomón Sanabria-Urbán, David A. Prieto-Torres, Adolfo G. Navarro-Sigüenza, María del C. Arizmendi and Ken Oyama
Diversity 2023, 15(10), 1035; https://doi.org/10.3390/d15101035 - 26 Sep 2023
Cited by 4 | Viewed by 4783
Abstract
The Military Macaw (Ara militaris) is an endangered bird species with disjunct geographic distribution across the Neotropics, consisting of three recognized subspecies: One in Mexico (A. m. mexicanus) and two in South America (A. m. militaris and A. [...] Read more.
The Military Macaw (Ara militaris) is an endangered bird species with disjunct geographic distribution across the Neotropics, consisting of three recognized subspecies: One in Mexico (A. m. mexicanus) and two in South America (A. m. militaris and A. m. bolivianus). However, due to the limited phenotypic differentiation between these allopatric taxa, their taxonomic status has been the subject of debate. In this study, we explored mitochondrial DNA (mtDNA) variability to determine the phylogeographical pattern through phylogenetic and ecological modelling analyses. We also aimed to describe the evolutionary relationships of twelve A. militaris populations. We identified 41 haplotypes in the 300 bp region of the Cytochrome b (Cyt-b) gene of the mtDNA and low nucleotide diversity. The observed phylogeographic structure suggests the existence of two clades: One composed of A. m. militaris and A. m. bolivianus and another consisting solely of A. m. mexicanus. The A. m. mexicanus clade further divides into two recognized subclades: Sierra Madre Oriental and northeastern portion of the Sierra Madre Occidental. Ecological analyses revealed that the niche similarity between these lineages was lower than expected by chance. Additionally, results from low cross-prediction tests indicated that the two lineages have inhabited different environmental spaces since the Late Pleistocene. This divergence may be associated with a steep ecological gradient and contemporary geographical barrier. Based on our results, we suggest that at least the A. m. mexicanus has a divergent evolutionary history; therefore, it should be considered as a different evolutionarily significant and management unit. We recommend that future conservation strategies in Mexico incorporate effective protection measures, including habitat preservation and the reduction of illegal trade, to ensure the preservation of viable populations. Full article
(This article belongs to the Special Issue Ecology and Conservation of Parrots)
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12 pages, 1510 KiB  
Article
The Origins of the Royal Spanish Surname Castilla: Genetics and Genealogy
by Ana María López-Parra, María Soledad Mesa, Fernando Castilla and Eduardo Arroyo-Pardo
Genealogy 2023, 7(3), 52; https://doi.org/10.3390/genealogy7030052 - 31 Jul 2023
Cited by 1 | Viewed by 5426
Abstract
In most Western European societies, surnames pass from generation to generation and in cases where surnames are shared by fathers to children, the Y chromosome passes down from fathers to male offspring in the same way as surnames do. The aim of this [...] Read more.
In most Western European societies, surnames pass from generation to generation and in cases where surnames are shared by fathers to children, the Y chromosome passes down from fathers to male offspring in the same way as surnames do. The aim of this study was to ascertain the patrilineal relationship between individuals with the surname “Castilla” and their respective Y-chromosome haplotypes. The toponymic surname “Castilla” is part of the Spanish royal family. Genealogical studies of this surname have allowed the formulation of different hypotheses about its origin, most of which were centered in Burgos. To shed some light on the origin of the surname Castilla and to investigate the possible co-ancestry behind the living carriers of this surname, markers located in the Y chromosome-specific region were analyzed in a sample of 102 men whose paternal surname was Castilla. The study aimed to establish the minimum number of founders and the expansion time of the lineages from our sample. Two major haplogroups were identified: R1b and E1b1b-M81. The high frequency of the E1b1b-M81 haplogroup in comparison to that of the general Spanish population, its low haplotype diversity, and its young TMRCA (323+/− 255 years CE) are compatible with the historical timing of the obligation to use surnames. However, the coincidence of the most common haplogroup in the Castilla sample and the most frequent haplogroup in the Spanish general population, R1b, makes it difficult to identify founder haplotypes/haplogroups in the history of the Castilla surname. Full article
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12 pages, 1742 KiB  
Article
Haplotypes of the tRNAleu-COII mtDNA Region in Russian Apis mellifera Populations
by Milyausha D. Kaskinova, Luisa R. Gaifullina and Elena S. Saltykova
Animals 2023, 13(14), 2394; https://doi.org/10.3390/ani13142394 - 24 Jul 2023
Cited by 6 | Viewed by 1997
Abstract
Analysis of the mtDNA tRNAleu-COII locus is a widely used tool to establish belonging to a particular evolutionary lineage of Apis mellifera L. (lineages A, M, C, O, and Y). In Russia, most of the area was once inhabited by Apis mellifera mellifera [...] Read more.
Analysis of the mtDNA tRNAleu-COII locus is a widely used tool to establish belonging to a particular evolutionary lineage of Apis mellifera L. (lineages A, M, C, O, and Y). In Russia, most of the area was once inhabited by Apis mellifera mellifera from the M evolutionary lineage, but the introduction of bee subspecies from the southern regions of Russia (A. m. caucasica, A. m. carnica) and from abroad (A. m. carnica, A. m. ligustica) led to fragmentation of their native range. In this study, the results of assessing the haplotype number for the tRNAleu-COII locus of mtDNA in Russian Apis mellifera populations were presented. We analyzed 269 colonies from 19 regions of Russia. As a result, two evolutionary lineages were identified: the East European lineage C (26.4%) and the Northwestern European lineage M (73.6%). A total of 29 haplotypes were identified, 8 of them were already reported, and 21 were found to be novel. From the C lineage, haplotypes C1, C2, C2c, C2j, and C3 were predominant. All M lineage samples from Russia belong to the M17 and M4’ haplogroups but have only minor variations in the form of nucleotide substitutions. An analysis of publications devoted to the tRNAleu-COII locus haplotypes, as well as an analysis of the available tRNAleu-COII sequences in GenBank, showed that there is still a problem with the haplotype nomenclature. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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20 pages, 4700 KiB  
Article
Comparison of the Efficiency of Single-Locus Species Delimitation Methods: A Case Study of a Single Lake Fish Population in Comparison against the Barcodes from International Databases
by Dmitry P. Karabanov, Alexey A. Kotov, Elena A. Borovikova, Yulia V. Kodukhova and Xiaowei Zhang
Water 2023, 15(10), 1851; https://doi.org/10.3390/w15101851 - 12 May 2023
Cited by 8 | Viewed by 3829
Abstract
To date, a rather large set of both mathematical theories for species delimitation, based on single-locus genetic data, and their implementations as software products, has been accumulated. Comparison of the efficiencies of different delineation methods in the task of accumulating and analyzing data [...] Read more.
To date, a rather large set of both mathematical theories for species delimitation, based on single-locus genetic data, and their implementations as software products, has been accumulated. Comparison of the efficiencies of different delineation methods in the task of accumulating and analyzing data with reference to different taxa in different regions, is vital. The aim of this study was to compare the efficiency of fifteen single-locus species delimitation methods using the example of a fish species found in a single lake in European Russia (Lake Plescheyevo) with reference to other sequences of revealed taxa deposited in international databases. We analyzed 186 original COI sequences belonging to 24 haplotypes, and 101 other sequences previously deposited in GenBank and BOLD. Comparison of all 15 alternative taxonomies demonstrated that all methods adequately separate only the genera, while the number of delimited mOTUs differed from 16 (locMin) to 43 (HwM/CoMa). We can assume that the effectiveness of each method is correlated with the number of matches based on Ctax and MatchRatio criteria. The most comparable results were provided by bGMYC, mPTP, STACEY, KoT and ASAP and the most synchronous results were obtained from bGMYC, mPTP, STACEY and ASAP. We believe that these results are maximally realistic in the number of revealed mOTUs. A high genetic diversity, resulting in the existence of several mOTUs and phylogenetic lineages within many species, demonstrates the usefulness of the “polymorphic species” concept, which does not underestimate species richness and does not prevent the rational use and protection of biodiversity. Full article
(This article belongs to the Special Issue Biogeography and Speciation of Aquatic Organisms)
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10 pages, 1146 KiB  
Article
Evaluating the Utility of Five Gene Fragments for Genetic Diversity Analyses of Mytella strigata Populations
by Chenxia Zuo, Tingting Zhang, Chenchen Zhang, Daotan Zhao, Yi Zhu, Xiaojie Ma, Haiyan Wang, Peizhen Ma and Zhen Zhang
Fishes 2023, 8(1), 34; https://doi.org/10.3390/fishes8010034 - 3 Jan 2023
Cited by 5 | Viewed by 2717
Abstract
Mytella strigata (Hanley, 1843) is an invasive mussel species that has rapidly spread in China in recent years. Here, we tested the utility of three mitochondrial gene fragments, COI, 12S, and 16S, and two nuclear gene fragments, D1 28S and [...] Read more.
Mytella strigata (Hanley, 1843) is an invasive mussel species that has rapidly spread in China in recent years. Here, we tested the utility of three mitochondrial gene fragments, COI, 12S, and 16S, and two nuclear gene fragments, D1 28S and 18S-ITS1, for characterizing the levels of genetic diversity among and within populations using 191 M. strigata specimens collected in China to aid ongoing efforts to identify the origin of the invasion as well as molecular genetic studies. M. strigata exhibited two sex-associated haplogroups according to the COI and 12S sequences. The ratio of female-lineage to male-lineage COI and 12S sequences was 149:22 and 72:7, and the genetic distances between haplogroups were 6.56 and 9.17, respectively. Only one haplotype was detected among the 18S-ITS1 sequences (413 bp), and three haplotypes were detected among the D1 28S sequences (296 bp). The haplotype diversity of both the female-lineage COI and 12S sequences was greater than 0.5, and the nucleotide diversity of the 12S, 16S, D1 28S, and 18S-ITS1 sequences was less than 0.005 in all six populations in China. Our findings indicated that COI is the most useful gene fragment for genetic diversity studies of M. strigata populations; D1 28S and 18S-ITS1 sequences would be useful for species identification because of their low intraspecific diversity. Our genetic analysis of the COI sequences revealed Colombia as the most likely origin of M. strigata in China and showed that the invasive populations in China have recently experienced or are currently experiencing a population bottleneck. Full article
(This article belongs to the Special Issue Mollusk Genetic Diversity and Breeding Technology)
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13 pages, 943 KiB  
Article
The Spatial Pattern of the Two Genetic Lineages of the Field Vole in Lithuania
by Petras Prakas, Dalius Butkauskas, Jevgenija Vaišvilienė, Laima Balčiauskienė and Linas Balčiauskas
Diversity 2022, 14(10), 820; https://doi.org/10.3390/d14100820 - 29 Sep 2022
Cited by 2 | Viewed by 1956
Abstract
The phylogeography of the filed vole (Microtus agrestis) in Eurasia was thoroughly examined using mitochondrial DNA (mtDNA) of the cytochrome b (cytb) gene. However, the former conclusions about genetic variability and the contact zone of eastern and western genetic [...] Read more.
The phylogeography of the filed vole (Microtus agrestis) in Eurasia was thoroughly examined using mitochondrial DNA (mtDNA) of the cytochrome b (cytb) gene. However, the former conclusions about genetic variability and the contact zone of eastern and western genetic lineages in Lithuania were based on the analysis of a very limited number of individuals. In the present study, we examined 74 M. agrestis individuals trapped in four sites in the eastern, northern, and western parts of the country using sequence analysis of cytb and D-loop. Totals of 25 new cytb haplotypes and 19 new D-loop haplotypes were identified for this species. Higher nucleotide diversity was observed for D-loop (π = 0.01147 ± 0.00070) as compared to cytb (π = 0.00694 ± 0.00039). The phylogenetic analysis based on both loci revealed the presence of two genetic lineages, i.e., the eastern and western ones, which were mixed in Lithuanian samples, with the exception of the Rusnė site in the west of the country. Only the western lineage was observed in this island population of M. agrestis; the sample differed in low genetic variability and genetic differentiation from other investigated samples. We found D-loop to be an appropriate locus for the evaluation of the genetic variability of M. agrestis. Full article
(This article belongs to the Special Issue Advances in Diversity and Conservation of Terrestrial Small Mammals)
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