scholarly journals Genetic variation of Nigerian cattle inferred from maternal and paternal genetic markers

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10607
Author(s):  
David H. Mauki ◽  
Adeniyi C. Adeola ◽  
Said I. Ng’ang’a ◽  
Abdulfatai Tijjani ◽  
Ibikunle Mark Akanbi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Markers ◽  
Bos Indicus ◽  
Haplotype Diversity ◽  
Population History ◽  
Genetic Introgression ◽  
High Genetic Diversity ◽  
African Cattle ◽  
D Loop ◽  
Mtdna Lineages

The African cattle provide unique genetic resources shaped up by both diverse tropical environmental conditions and human activities, the assessment of their genetic diversity will shade light on the mechanism of their remarkable adaptive capacities. We therefore analyzed the genetic diversity of cattle samples from Nigeria using both maternal and paternal DNA markers. Nigerian cattle can be assigned to 80 haplotypes based on the mitochondrial DNA (mtDNA) D-loop sequences and haplotype diversity was 0.985 + 0.005. The network showed two major matrilineal clustering: the dominant cluster constituting the Nigerian cattle together with other African cattle while the other clustered Eurasian cattle. Paternal analysis indicates only zebu haplogroup in Nigerian cattle with high genetic diversity 1.000 ± 0.016 compared to other cattle. There was no signal of maternal genetic structure in Nigerian cattle population, which may suggest an extensive genetic intermixing within the country. The absence of Bos indicus maternal signal in Nigerian cattle is attributable to vulnerability bottleneck of mtDNA lineages and concordance with the view of male zebu genetic introgression in African cattle. Our study shades light on the current genetic diversity in Nigerian cattle and population history in West Africa.

scholarly journals Mitochondrial DNA D-loop sequence variability reveals high haplotype diversity and multiple maternal origins in twelve indigenous goat populations from Tanzania.

2021 ◽  
Author(s):  
Athumani Nguluma
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Haplotype Diversity ◽  
Capra Hircus ◽  
Maternal Origin ◽  
High Genetic Diversity ◽  
Ecological Zones ◽  
Goat Population ◽  
D Loop ◽  
Indigenous Goats

The Small East African (SEA) goat (Capra hircus) breeds are widely distributed in different agro-ecological zones of Tanzania. We report the genetic diversity, maternal origin, and phylogenetic relationship among the 12 Tanzanian indigenous goats populations, namely Fipa (n = 44), Songwe (n = 34), Tanga (n = 33), Pwani (n = 40), Newala (n = 49), Lindi (n = 46), Gogo (n = 73), Pare (n = 67), Maasai (n = 72), Sukuma (n = 67), and Ujiji (n = 67), based on the mitochondrial DNA (mtDNA) D-loop. High haplotype (Hd = 0.9619-0.9945) and nucleotide (π = 0.0120-0.0162) diversities were revealed from a total of 389 haplotypes. The majority of the haplotypes (h = 334) drawn from all the goat populations belonged to Haplogroup A which was consistent with the global scenario on the genetic pattern of maternal origin of all goat breeds in the world. Haplogroup G comprised of 45 haplotypes drawn from all populations except the Ujiji goat population while Haplogroup B with 10 haplotypes was dominated by Ujiji goats (41%). Tanzanian goats shared four haplotypes with the Kenyan goats and two with goats from South Africa, Namibia, and Mozambique. There was no sharing of haplotypes observed between individuals from Tanzanian goat populations with individuals from North or West Africa. The indigenous goats in Tanzania have high genetic diversity defined by 389 haplotypes and multiple maternal origins of haplogroup A, B and G. There is a lot of intermixing and high genetic variation within populations which represent an abundant resource for selective breeding in the different agro-ecological regions of the country.

scholarly journals Phylogeography of the Brittle Star Ophiura sarsii Lütken, 1855 (Echinodermata: Ophiuroidea) from the Barents Sea and East Atlantic

Diversity ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 40
Author(s):  
Evgeny Genelt-Yanovskiy ◽  
Yixuan Li ◽  
Ekaterina Stratanenko ◽  
Natalia Zhuravleva ◽  
Natalia Strelkova ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Barents Sea ◽  
Haplotype Diversity ◽  
Brittle Star ◽  
The Arctic ◽  
Coi Gene ◽  
High Genetic Diversity ◽  
Svalbard Archipelago ◽  
Mitochondrial Coi ◽  
The Barents Sea

Ophiura sarsii is a common brittle star species across the Arctic and Sub-Arctic regions of the Atlantic and the Pacific oceans. Ophiurasarsii is among the dominant echinoderms in the Barents Sea. We studied the genetic diversity of O.sarsii by sequencing the 548 bp fragment of the mitochondrial COI gene. Ophiurasarsii demonstrated high genetic diversity in the Barents Sea. Both major Atlantic mtDNA lineages were present in the Barents Sea and were evenly distributed between the northern waters around Svalbard archipelago and the southern part near Murmansk coast of Kola Peninsula. Both regions, and other parts of the O.sarsii range, were characterized by high haplotype diversity with a significant number of private haplotypes being mostly satellites to the two dominant haplotypes, each belonging to a different mtDNA clade. Demographic analyses indicated that the demographic and spatial expansion of O.sarsii in the Barents Sea most plausibly has started in the Bølling–Allerød interstadial during the deglaciation of the western margin of the Barents Sea.

Genealogical relationship inference to identify areas of intensive poaching of the Orange-fronted Parakeet (Eupsittula canicularis)

BMC Zoology ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Gabriela Padilla-Jacobo ◽  
Tiberio C. Monterrubio-Rico ◽  
Horacio Cano-Camacho ◽  
María Guadalupe Zavala-Páramo
Keyword(s):  
Genetic Diversity ◽  
Dna Sequences ◽  
Haplotype Diversity ◽  
Coastal Region ◽  
Central American ◽  
Illegal Trade ◽  
Wild Populations ◽  
High Genetic Diversity ◽  
Genealogical Relationship ◽  
Genetic Pool

Abstract Background The Orange-fronted Parakeet (Eupsittula canicularis) is the Mexican psittacine that is most captured for the illegal pet trade. However, as for most wildlife exploited by illegal trade, the genetic diversity that is extracted from species and areas of intensive poaching is unknown. In this study, we analyzed the genetic diversity of 80 E. canicularis parakeets confiscated from the illegal trade and estimated the level of extraction of genetic diversity by poaching using the mitochondrial DNA sequences of cytochrome b (Cytb). In addition, we analyzed the genealogical and haplotypic relationships of the poached parakeets and sampled wild populations in Mexico, as a strategy for identifying the places of origin of poached parakeets. Results Poached parakeets showed high haplotype diversity (Hd = 0.842) and low nucleotide diversity (Pi = 0.00182). Among 22 haplotypes identified, 18 were found exclusively in 37 individuals, while four were detected in the remaining 43 individuals and shared with the wild populations. A rarefaction and extrapolation curve revealed that 240 poached individuals can include up to 47 haplotypes and suggested that the actual haplotype richness of poached parakeets is higher than our analyses indicate. The geographic locations of the four haplotypes shared between poached and wild parakeets ranged from Michoacan to Sinaloa, Mexico. However, the rare haplotypes detected in poached parakeets were derived from a recent genetic expansion of the species that has occurred between the northwest of Michoacan and the coastal region of Colima, Jalisco and southern Nayarit, Mexico. Conclusions Poached parakeets showed high genetic diversity, suggesting high extraction of the genetic pool of the species in central Mexico. Rarefaction and extrapolation analyses suggest that the actual haplotype richness in poached parakeets is higher than reflected by our analyses. The poached parakeets belong mainly to a very diverse genetic group of the species, and their most likely origin is between northern Michoacan and southern Nayarit, Mexico. We found no evidence that poachers included individuals from Central American international trafficking with individuals from Mexico in the sample.

Gene flow from multiple sources maintains high genetic diversity and stable population history of Common MoorhenGallinula chloropusin China

Ibis ◽  
2018 ◽  
Vol 160 (4) ◽  
pp. 855-869 ◽  
Author(s):  
Luzhang Ruan ◽  
Wei Xu ◽  
Yuqing Han ◽  
Chaoying Zhu ◽  
Bicai Guan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Population History ◽  
Stable Population ◽  
Multiple Sources ◽  
High Genetic Diversity ◽  
History Of

scholarly journals Retraction Note: Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of wild almond species

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Karim Sorkheh ◽  
Mehrana Koohi Dehkordi ◽  
Sezai Ercisli ◽  
Attila Hegedus ◽  
Júlia Halász
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Dna Markers ◽  
High Genetic Diversity ◽  
Link Type ◽  
New Generation ◽  
Wild Almond

Editor's Note: this Article has been retracted; the Retraction Note is available at https://www.nature.com/articles/s41598-020-72522-x

scholarly journals The patterns of admixture, divergence, and ancestry of African cattle populations determined from genome-wide SNP data

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
N. Z. Gebrehiwot ◽  
E. M. Strucken ◽  
H. Aliloo ◽  
K. Marshall ◽  
J. P. Gibson
Keyword(s):  
Genetic Diversity ◽  
Bos Taurus ◽  
Large Population ◽  
Bos Indicus ◽  
Principal Component ◽  
Effective Population ◽  
Indigenous Cattle ◽  
Cattle Breeds ◽  
African Cattle ◽  
Snp Data

Abstract Background Humpless Bos taurus cattle are one of the earliest domestic cattle in Africa, followed by the arrival of humped Bos indicus cattle. The diverse indigenous cattle breeds of Africa are derived from these migrations, with most appearing to be hybrids between Bos taurus and Bos indicus. The present study examines the patterns of admixture, diversity, and relationships among African cattle breeds. Methods Data for ~ 40 k SNPs was obtained from previous projects for 4089 animals representing 35 African indigenous, 6 European Bos taurus, 4 Bos indicus, and 5 African crossbred cattle populations. Genetic diversity and population structure were assessed using principal component analyses (PCA), admixture analyses, and Wright’s F statistic. The linkage disequilibrium and effective population size (Ne) were estimated for the pure cattle populations. Results The first two principal components differentiated Bos indicus from European Bos taurus, and African Bos taurus from other breeds. PCA and admixture analyses showed that, except for recently admixed cattle, all indigenous breeds are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus. The African zebu breeds had highest proportions of Bos indicus ancestry ranging from 70 to 90% or 60 to 75%, depending on the admixture model. Other indigenous breeds that were not 100% African Bos taurus, ranged from 42 to 70% or 23 to 61% Bos indicus ancestry. The African Bos taurus populations showed substantial genetic diversity, and other indigenous breeds show evidence of having more than one African taurine ancestor. Ne estimates based on r2 and r2adj showed a decline in Ne from a large population at 2000 generations ago, which is surprising for the indigenous breeds given the expected increase in cattle populations over that period and the lack of structured breeding programs. Conclusion African indigenous cattle breeds have a large genetic diversity and are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus. This provides a rich resource of potentially valuable genetic variation, particularly for adaptation traits, and to support conservation programs. It also provides challenges for the development of genomic assays and tools for use in African populations.

The genetic crisis of the Mexican Bolson Tortoise (Gopherus flavomarginatus: Testudinidae)

2012 ◽  
Vol 33 (1) ◽  
pp. 45-53 ◽  
Author(s):  
Cinthya Alejandra Ureña-Aranda ◽  
Alejandro Espinosa de los Monteros
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
20Th Century ◽  
Chihuahuan Desert ◽  
Haplotype Diversity ◽  
Genetic Homogeneity ◽  
Significant Percentage ◽  
Tectonic Processes ◽  
D Loop ◽  
Demographic Growth

Gopherus flavomarginatus (Testudinidae) is endemic to a series of discontinuous, isolated basins collectively known as the Bolson de Mapimí in the Chihuahuan Desert. Its numbers declined after catastrophic levels of exploitation during the mid-20th century. However currently, the Bolson Tortoise appears to be on a path to recovery owing to intensive, sustained conservation efforts. We sequenced an 842-bp-long fragment of the D-loop from 76 individuals distributed throughout the species’ range. The results revealed only two haplotypes. An AMOVA showed that 95% of the variance occurred among populations, whereas the remaining 5% was explained by genetic differences within populations. Tectonic processes together with ecological transformation during the Pleistocene and Holocene may be responsible for the reduction in this species’ genetic variation. A bottleneck during which a significant percentage of the haplotype diversity was lost would result in genetic homogeneity. Although there is demographic growth, the lack of genetic diversity is indicative of the potential crisis that the Bolson Tortoise is facing, and awareness must be brought to this situation.

scholarly journals Mitochondrial DNA-based diversity study of Hungarian brown hares (Lepus europaeus Pallas 1778)

2016 ◽  
pp. 23-29
Author(s):  
Noémi Soós ◽  
Szilvia Kusza
Keyword(s):  
Mitochondrial Dna ◽  
Large Scale ◽  
Haplotype Diversity ◽  
Lepus Europaeus ◽  
Brown Hare ◽  
High Genetic Diversity ◽  
Ongoing Research ◽  
European Continent ◽  
Hair Samples ◽  
D Loop

The brown hare being an important game species which is widespread across the European continent has been in focus of many population genetic studies. However only a few comprising researches can be found on the diversity of Central-European populations. The aim of our large scale long term ongoing study is to fill this gap of information on the species by describing the genetic history and structure of the brown hare populations of the area using both mitochondrial DNA markers and genomic skin and hair colour regulating genes. This article gives forth a part of our results concerning the mitochondrial DNA diversity of Hungarian brown hares based on amplification of a 512 bp long D-loop sequence. N=39 tissue or hair samples have been collected from 15 sampling sites on the Hungarian Great Plain. We have described a high level of haplotype diversity (Hd=0.879±0.044) based on a 410 bp alignment of our sequences. We have found 17 haplotypes within our sample set with the nucleotid diversity of π=0.01167±0.0022. Our ongoing research shows high genetic diversity for the brown hare in the studied region and a second alignment with 156 sequences downloaded from GenBank indicates a geographic pattern of haplotypes among the studied populations though these results need confirmation by our further analyses.

scholarly journals Genetic Diversity of Mitochondrial DNA Cytochrome b in Indonesian Native and Local Cattle Populations

2020 ◽  
Vol 25 (2) ◽  
pp. 39
Author(s):  
Peni Wahyu Prihandini ◽  
A Primasari ◽  
M Luthfi ◽  
J Efendy ◽  
D Pamungkas
Keyword(s):  
Genetic Diversity ◽  
Bos Taurus ◽  
Phylogenetic Analyses ◽  
Bos Indicus ◽  
Haplotype Diversity ◽  
Genetic Distances ◽  
Conservation Strategies ◽  
Bos Javanicus ◽  
Reverse Primer ◽  
Relationship Of

Information on the genetic diversity of native and local cattle in Indonesia is vital for the development of breeding and conservation strategies. This study was aimed to assess the genetic diversity and phylogenetic relationship of the Indonesian native (Bali) and local [(Donggala, Madura, Sragen, Galekan, Rambon, dan Peranakan Ongole Grade x Bali (POBA)] cattle populations. Genomic DNA was extracted from blood samples (n= 75). Partial sequences of mtDNA cyt<em> b</em>, 464 bp, were amplified using the polymerase chain reaction technique (forward primer: L14735 and reverse primer: H15149). Thirty-four reference sequences of <em>Bos taurus</em>, <em>Bos indicus</em>, and <em>Bos javanicus</em> were included in the phylogenetic analyses. A total of 55 polymorphic sites and 13 haplotypes were observed in the whole breeds. No variable sites of mtDNA cyt<em> b</em> were observed in Galekan (kept in BCRS) and Rambon cattle. Overall haplotype diversity and nucleotide diversity were 0.515 ± 0.070 and 0.0184 ± 0.0045, respectively. The highest (0.092) and the lowest (0.000) genetic distances were between Bali and Donggala cattle populations and among Galekan (kept in BCRS), Rambon, and POBA cattle populations, respectively. Both mtDNA network and phylogenetic analyses revealed two major maternal lineages (A and B) of the studied population. Most of the sampled individuals (69.33%, present in haplotype H8-H19) were linked to lineage B, which belonged to the same cluster with <em>Bos javanicus</em>. Overall, most of the Indonesian native and local cattle populations had a considerable genetic diversity and shared a common maternal origin with <em>Bos javanicus</em>.

Sign in / Sign up

Export Citation Format

Share Document