Strong phylogeographic relationships among three goat breeds from the Canary Islands

2004 ◽  
Vol 71 (3) ◽  
pp. 257-262 ◽  
Author(s):  
Marcel Amills ◽  
Juan Capote ◽  
Anna Tomàs ◽  
Lucía Kelly ◽  
Gabriela Obexer-Ruff ◽  
...  
Keyword(s):  
Canary Islands ◽  
Dairy Products ◽  
Phylogeographic Structure ◽  
Mitochondrial Haplotype ◽  
Domestic Goat ◽  
Loop Region ◽  
D Loop ◽  
Identity Test ◽  
Migratory Movements ◽  
Single Cluster

We partially sequenced the mitochondrial D-loop region in 47 individuals from eleven Spanish and foreign goat breeds. Phylogenetic analysis of these sequences allowed us to identify a particular D-loop haplotype shared by individuals from the Palmera, Majorera and Tinerfeña Canarian breeds. Genotyping of 281 goats from 17 different breeds by PCR-HpaII RFLP evidenced that the geographical distribution of this haplotype is restricted to the Canary Islands. This ancestral mitochondrial haplotype might originate in the domestic goat herds brought by the native Canarian inhabitants approximately 3000 years ago. Although we observed other miscellaneous D-loop haplotypes in the Palmera, Majorera and Tinerfeña breeds, any of them allowed us to group individuals from these three populations in a single cluster, a feature that suggests that these haplotypes might have diverse origins. The remarkable degree of phylogeographic structure of the Canary goat breeds with regard to other Spanish and foreign populations might be attributed to the isolation of these breeds in the Canary Islands for approximately 2500 years, without exposure to the migratory movements and commercial trading events that probably affected the genesis of most domestic goat breeds worldwide. The Canarian D-loop haplotype can be efficiently genotyped by using DNA isolated from milk and cheese samples, which paves the way for the future establishment of a Canary breed identity test for these dairy products.

scholarly journals Maternal variability of Croatian Spotted goat (Capra hircus)

2019 ◽  
Vol 64 (No. 6) ◽  
pp. 248-254
Author(s):  
Ivana Drzaic ◽  
Ino Curik ◽  
Dinko Novosel ◽  
Vlatka Cubric-Curik
Keyword(s):  
Mitochondrial Dna ◽  
Nucleotide Diversity ◽  
Population Expansion ◽  
Capra Hircus ◽  
Phylogeographic Structure ◽  
Goat Breed ◽  
Loop Region ◽  
D Loop ◽  
Mtdna Diversity

Abstract: This study provides the first characterization of maternal ancestry and mitochondrial DNA (mtDNA) diversity in the Croatian Spotted goat (CSG), the most important autochthonous goat breed in Croatia. CSG (n = 25) were randomly sampled from seven herds and a 660-bp fragment from the mtDNA D-loop region was sequenced. Those sequences were compared with 122 corresponding GenBank sequences from goat populations in Albania, Austria, Egypt, Greece, Italy, Romania and Switzerland. CSG showed a great polymorphism (only three out of 17 haplotypes were shared) with high a haplotype (Hd = 0.967 ± 0.019) and nucleotide diversity (π = 0.01305 ± 0.00068). When compared with Mediterranean and ancient goats, all of the 25 CSG were randomly scattered inside haplogroup A showing the weak phylogeographic structure with within-breed variance accounting for 91.76% of the genetic variation. In addition, population expansion tests (mismatch distribution and Fu’s Fs statistic) supported these results suggesting at least one population expansion.

scholarly journals Phylogeographic Structure of Freshwater Tor sp. in River Basins of Sabah, Malaysia

Fishes ◽  
2021 ◽  
Vol 6 (4) ◽  
pp. 44
Author(s):  
Helena Biun ◽  
Ahemad Sade ◽  
Rolando Robert ◽  
Kenneth Francis Rodrigues
Keyword(s):  
Isolation By Distance ◽  
In Situ Conservation ◽  
Haplotype Network ◽  
Phylogeographic Structure ◽  
Loop Region ◽  
Mtdna Sequence ◽  
Population Structuring ◽  
D Loop ◽  
Main Barrier

We characterized the genetic diversity, phylogeography, and demography of Tor sp. (Cyprinidae) from Sabah, Malaysian Borneo, by examining nucleotide variation in the D-loop region of the mtDNA. Sequence analysis of 18 populations (N = 173) yielded 35 unique mtDNA haplotypes with mean haplotype and nucleotide diversity of 0.833 and 0.023, respectively. Phylogenetic reconstructions using Bayesian, neighbor-joining, and maximum parsimony methods, as well as haplotype network, revealed four well-defined clades, namely, the eastern, central, northwestern, and southwestern clades, which corresponded to evolutionarily significant units (ESUs). These ESUs were estimated to have become separated since the late Miocene to Pliocene era (between 5 and 1 million years ago), with the central highlands of Sabah Crocker Trusmadi Range (CTR) constituting the main barrier to genetic exchange between clades. Analysis of molecular variance (AMOVA) and pairwise genetic differentiation showed significant population structuring (Φct = 0.575–1.000, p < 0.05). We further identified eight major groups of river systems harboring reproductively isolated Tor subpopulations. Neutrality statistics and Bayesian skyline plots (BSP) suggested constant population size over time for most Tor populations. Tor sp. in Sabah is comprised of four ESUs (eastern, central, northwestern, and southwestern ESUs), and that each ESU can be compartmentalized into 1–4 MUs. Due to isolation by distance, the highest number of MU occurs in the low-elevation drainages of Eastern Sabah, which is the largest in terms of land area. The evidence provided by this study supports the hypothesis that the four ESU represent genetically distinct subpopulations of Tor and highlight the urgent need for the in situ conservation of these subpopulations.

scholarly journals Mitochondrial D-loop mutations can be detected in sporadic malignant tumours in dogs

2014 ◽  
Vol 58 (4) ◽  
pp. 631-637 ◽  
Author(s):  
Brygida Ślaska ◽  
Magdalena Surdyka ◽  
Adam Brodzki ◽  
Sylwia Nisztuk ◽  
Artur Gurgul ◽  
...  
Keyword(s):  
Head And Neck ◽  
Mitochondrial Haplotype ◽  
Malignant Tumours ◽  
Head And Neck Tumours ◽  
Tissue Samples ◽  
Epithelial Cancers ◽  
Loop Region ◽  
Sex Type ◽  
D Loop ◽  
Polymorphic Variants

Abstract The aim of this study was to identify mutations in the D-loop region of mtDNA in head, neck, and limb tumours in dogs, and determination of their relationship with the process of neoplastic transformation. Blood and tumour tissue samples from 19 dogs with diagnosed sporadic malignant tumours were analysed. DNA extraction, amplification, and sequencing of the mtDNA D-loop, and bioinformatic analyses were performed. Five mutations and 19 polymorphisms were observed in 68.42% of all tumours. Polymorphic variants were noted in 42.86% of the head and neck tumours and in 58.33% of the limb tumours. Mutations were observed in 21.05% of dogs. The mutations were found in 28.57% of the head and neck tumours and in 16.66% of the limb tumours. The mutations were identified in 50% of the studied epithelial cancers. In the mesenchymal tumours, no mutations in the D-loop region were observed. Mitochondrial haplotype A17 was found in over 40% cases of limb tumours. No association between the age, breed, sex, type of tumour, and detected polymorphic variants were observed. Different mutational changes in the D-loop sequences of mtDNA identified in the blood and tumour tissues may indicate a relationship between the type of tumour and individual changes in the D-loop nucleotide sequences of mtDNA.

scholarly journals Phylogeography of the Central american red brocket deer, Mazama temama (Artiodactyla, Cervidae) in southeastern Mexico

2021 ◽  
Vol 16 (2) ◽  
pp. 369-382
Author(s):  
Ricardo Serna-Lagunes ◽  
Dayana Kristel Romero-Ramos ◽  
Christian Alejandro Delfín-Alfonso ◽  
Juan Salazar-Ortiz
Keyword(s):  
Multidimensional Scaling ◽  
Mismatch Distribution ◽  
Haplotype Network ◽  
Phylogeographic Structure ◽  
Scaling Analysis ◽  
Evolutionary Divergence ◽  
Multidimensional Scaling Analysis ◽  
Loop Region ◽  
D Loop ◽  
Tajima’S D

Anthropogenic threats have increasingly isolated the populations of Mazama temama (Erxleben, 1777) and limited the gene flow in this species. Knowledge of the phylogeographic structure of this species is therefore essential for its conservation. Thus, in this study, we describe the phylogeographic structure of two M. temama populations of Veracruz and Oaxaca, Mexico. We sequenced the D-Loop region of the mitochondrial DNA of 16 individuals, in order to estimate the diversity and genetic differentiation (FST), Tajima’s D index, "Mismatch distribution" test; a phylogram and a haplotype network was constructed and we performed multidimensional scaling analysis to test the hypothesis of association between geographic distance and genetic diversity. The haplotypic and nucleotide diversity was high, indicating divergent populations (FST = 0.223), while the Tajima’s D index (-1,03300; P &gt; 0.10) determined disequilibrium in the D-Loop region, derived from a population expansion that was evidenced in the "Mismatch distribution" test and confirmed with the haplotype network in the form of a star. Four lineages were identified in the phylogram (Veracruz n = 3, Oaxaca n = 1), evidencing geographic and reproductive isolation between the two populations. This was confirmed by the multidimensional scaling analysis, which evidenced recent evolutionary divergence between the populations analyzed, which are considered evolutionary units of conservation.

scholarly journals Mitochondrial DNA Methylation and Human Diseases

2021 ◽  
Vol 22 (9) ◽  
pp. 4594
Author(s):  
Andrea Stoccoro ◽  
Fabio Coppedè
Keyword(s):  
Dna Methylation ◽  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Nuclear Dna ◽  
Epigenetic Modification ◽  
Nuclear Genome ◽  
Epigenetic Modifications ◽  
Human Diseases ◽  
Loop Region ◽  
D Loop

Epigenetic modifications of the nuclear genome, including DNA methylation, histone modifications and non-coding RNA post-transcriptional regulation, are increasingly being involved in the pathogenesis of several human diseases. Recent evidence suggests that also epigenetic modifications of the mitochondrial genome could contribute to the etiology of human diseases. In particular, altered methylation and hydroxymethylation levels of mitochondrial DNA (mtDNA) have been found in animal models and in human tissues from patients affected by cancer, obesity, diabetes and cardiovascular and neurodegenerative diseases. Moreover, environmental factors, as well as nuclear DNA genetic variants, have been found to impair mtDNA methylation patterns. Some authors failed to find DNA methylation marks in the mitochondrial genome, suggesting that it is unlikely that this epigenetic modification plays any role in the control of the mitochondrial function. On the other hand, several other studies successfully identified the presence of mtDNA methylation, particularly in the mitochondrial displacement loop (D-loop) region, relating it to changes in both mtDNA gene transcription and mitochondrial replication. Overall, investigations performed until now suggest that methylation and hydroxymethylation marks are present in the mtDNA genome, albeit at lower levels compared to those detectable in nuclear DNA, potentially contributing to the mitochondria impairment underlying several human diseases.

scholarly journals Genetic Diversity of Maternal Lineage in the Endangered Kiso Horse Based on Polymorphism of the Mitochondrial DNA D-Loop Region

2014 ◽  
Vol 76 (11) ◽  
pp. 1451-1456 ◽  
Author(s):  
Masaki TAKASU ◽  
Namiko ISHIHARA ◽  
Teruaki TOZAKI ◽  
Hironaga KAKOI ◽  
Masami MAEDA ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Maternal Lineage ◽  
Loop Region ◽  
D Loop
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