scholarly journals Two partial mitochondrial gene sequences (COI and 12S-rRNA) suggested that Ceramaster japonicus (Sladen, 1889) and Ceramaster patagonicus (Sladen, 1889) (Asteroidea: Goniasteridae) from the Japanese waters are probably of the same species

Zoosymposia ◽  
2019 ◽  
Vol 15 (1) ◽  
pp. 129-140
Author(s):  
DAVIN H.E. SETIAMARGA ◽  
RENA SHIBA ◽  
YUKI KAMITO ◽  
MASAKI YAMAMOTO ◽  
NAZIFA NAZIHA BT. RAZALI ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Population Structure ◽  
Mitochondrial Gene ◽  
Haplotype Network ◽  
12S Rrna ◽  
National Museum ◽  
Network Analyses ◽  
Morphological Studies ◽  
The Pacific ◽  
Japanese Waters

Our recent morphological studies on the echinoderm collection of the National Museum of Nature and Science, Tokyo (NMST), indicated that the goniasterid starfishes Ceramaster japonicus (Sladen, 1889) and Ceramaster patagonicus (Sladen, 1889) are distributed in the Pacific Oceanside of Japan. In this study, we studied the NMST samples of C. japonicus and C. patagonicus from Japan, by using two mitochondrial DNA genes, the COI and 12S-rRNA, as markers to test relationships between these species in Japan. C. patagonicus sequences from GenBank were mined and included in the analyses. Results of phylogenetic and haplotype network analyses of both genes (final sequence lengths: COI = 317 bp, 12S = 477 bp) suggested that "Ceramaster patagonicus" and "Ceramaster japonicus" from Japanese waters are almost certainly synonymous without any population structure inside Japan.

scholarly journals Tracing Worldwide Turkey Genetic Diversity Using D-loop Sequence Mitochondrial DNA Analysis

Animals ◽  
2019 ◽  
Vol 9 (11) ◽  
pp. 897 ◽  
Author(s):  
Amado Manuel Canales Vergara ◽  
Vincenzo Landi ◽  
Juan Vicente Delgado Bermejo ◽  
Amparo Martínez ◽  
Patricia Cervantes Acosta ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Rural Areas ◽  
Dna Analysis ◽  
Meleagris Gallopavo ◽  
Haplotype Network ◽  
Network Analyses ◽  
The Usa ◽  
D Loop ◽  
Genetic Value

According to recent archeological evidence, turkey (Meleagris gallopavo gallopavo) domestication may have occurred in Mexico around 2000 years ago. However, little is known about the phylogenetic and genealogical background underlying domestic turkey populations. This study aimed to further understand the domestication process and identify inter- or intraspecific connections between turkey populations to determine their origins, trace their global expansion, and define the species’ genetic value. Ninety-three domestic turkeys (local breeds) were sampled from populations in Brazil, Mexico, USA, Spain, Italy, Iran, and Egypt. Publicly available sequences from previous studies were also included. Standard mitochondrial DNA, genetic diversity, and haplotype network analyses were performed. Seventy-six polymorphic sites were identified. Turkeys from Mexico showed the greatest number of polymorphic sites (40), while turkeys from Italy and Brazil reported only one site each. Nucleotide diversity was also highest in Mexico and the USA (π = 0.0175 and 0.0102, respectively) and lowest in Brazil and Italy. Of the six major haplogroups defined, the Mexican and USA populations appeared to have remained more stable and diverse than the other populations. This may be due to conservative husbandry policies in the rural areas of other populations, which have prevented the introduction of commercial turkey lines.

scholarly journals Wolbachia affects mitochondrial population structure in two systems of closely related Palaearctic blue butterflies

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Alena Sucháčková Bartoňová ◽  
Martin Konvička ◽  
Jana Marešová ◽  
Martin Wiemers ◽  
Nikolai Ignatev ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Population Structure ◽  
Species Complex ◽  
Mitochondrial Gene ◽  
Mitochondrial Structure ◽  
Distribution Ranges ◽  
Mitochondrial Population ◽  
Two Systems ◽  
History Of ◽  
Mitochondrial Phylogeny

AbstractThe bacterium Wolbachia infects many insect species and spreads by diverse vertical and horizontal means. As co-inherited organisms, these bacteria often cause problems in mitochondrial phylogeny inference. The phylogenetic relationships of many closely related Palaearctic blue butterflies (Lepidoptera: Lycaenidae: Polyommatinae) are ambiguous. We considered the patterns of Wolbachia infection and mitochondrial diversity in two systems: Aricia agestis/Aricia artaxerxes and the Pseudophilotes baton species complex. We sampled butterflies across their distribution ranges and sequenced one butterfly mitochondrial gene and two Wolbachia genes. Both butterfly systems had uninfected and infected populations, and harboured several Wolbachia strains. Wolbachia was highly prevalent in A. artaxerxes and the host’s mitochondrial structure was shallow, in contrast to A. agestis. Similar bacterial alleles infected both Aricia species from nearby sites, pointing to a possible horizontal transfer. Mitochondrial history of the P. baton species complex mirrored its Wolbachia infection and not the taxonomical division. Pseudophilotes baton and P. vicrama formed a hybrid zone in Europe. Wolbachia could obscure mitochondrial history, but knowledge on the infection helps us to understand the observed patterns. Testing for Wolbachia should be routine in mitochondrial DNA studies.

scholarly journals Phylogeography of the planktonic shrimp Lucifer hanseni Nobili 1905 in the Indo-Malayan Archipelago

2016 ◽  
Vol 97 (1) ◽  
pp. 129-140
Author(s):  
Mary Mar Noblezada ◽  
Hiroomi Miyamoto ◽  
Wilfredo L. Campos ◽  
Fatimah MD. Yusoff ◽  
Shuhei Nishida
Keyword(s):  
Ribosomal Rna ◽  
Solomon Islands ◽  
Nuclear Gene ◽  
Haplotype Network ◽  
Andaman Sea ◽  
Phylogeographic Structure ◽  
12S Rrna ◽  
28S Rrna ◽  
Network Analyses ◽  
Low Genetic Diversity

Using partial sequences of two mitochondrial genes, cytochrome c oxidase subunit I (COI) and 12S ribosomal RNA (12S rRNA), and one nuclear gene, 28S ribosomal RNA (28S rRNA), we investigated population genetics of the holoplanktonic shrimp Lucifer hanseni Nobili, 1905 in the Indo-Malayan Archipelago (IMA), encompassing Andaman Sea, Malacca Strait, Gulf of Thailand, Borneo Island, Philippines (hereafter collectively referred to as the Thailand-Malaysia-Philippine area: TMP), Celebes Sea (CS), and the waters near islands in the Western Pacific (WP) including Palau, Papua New Guinea and Solomon Islands. The samples from the TMP showed the highest number of haplotypes. Significant phylogeographic structure was found in the L. hanseni populations (ΦST = 0.832 for COI, 0.159 for 12S rRNA, 0.783 for 28S rRNA). The total number of haplotypes was 46 in COI, 28 in 12S rRNA and 23 in 28S rRNA. The haplotype network analyses revealed two major clades for COI (subgroups: TMP + CS, WP) and for 12S rRNA and 28S rRNA (TMP, CS + WP). The CS and WP populations appeared isolated from the TMP populations. The samples from the CS showed low genetic diversity compared with the other samples at both haplotype and nucleotide levels, suggesting that the population CS experienced bottleneck events. This is the first demonstration of significant genetic structure of a holoplanktonic metazoan in IMA, which is suggested to be synergistically influenced by historical events (vicariance) and contemporary oceanographic circulations and corroborates the results of previous studies on other benthic/demersal animals with mero-planktonic phases.

Mitochondrial DNA reveals high genetic divergence between populations of Chalcides mertensi Klausewitz, 1954 (Reptilia: Scincidae) from Tunisia

2013 ◽  
Vol 34 (3) ◽  
pp. 389-399
Author(s):  
Massimo Giovannotti ◽  
Paola Nisi Cerioni ◽  
Andrea Splendiani ◽  
Mohsen Kalboussi ◽  
Paolo Ruggeri ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Divergence ◽  
Nadh Dehydrogenase ◽  
Mitochondrial Gene ◽  
Rflp Analysis ◽  
12S Rrna ◽  
Rrna Gene ◽  
Gene Encoding ◽  
Sidi Bouzid ◽  
Exhaustive Study

Genetic diversity of four populations of Chalcides mertensi (Klausewitz, 1954) from Tunisia was analyzed by means of the Restriction Fragment Length Polymorphism (RFLP) analysis of two fragments of mitochondrial DNA (mtDNA) encompassing NADH dehydrogenase subunits 1 and 2 (ND-1/2) and NADH dehydrogenase subunits 3, 4 and 4L (ND-3/4). Phylogenetic relationships between haplotypes were inferred by analysing the sequence of 396 base pairs at the 5′ end of the mitochondrial gene encoding cytochrome b and a segment of 12S rRNA gene (386 bp). The results of this study highlighted a pronounced genetic divergence between the populations from northern (Ain Soltane and Tabarka) and southern (Kasserine and Sidi Bouzid) Tunisia, that the phylogenetic analysis recovered as two distinct taxonomic entities. These two groups of populations can therefore be ascribed to two distinct taxa, with southern populations probably representing the typical C. mertensi, whereas northern individuals are likely to represent a new species of grass swimming Chalcides. The divergence between these two taxonomic entities can be referred to palaeogeographic and palaeoclimatic events that have affected northwestern Africa during the last 10 Million years. The analysed populations show a low genetic variability that can be related to the past climatic and geologic events and the colonization processes that took place with environmental amelioration, and to the peripheral position of these populations in the distributional range of the species. However, a more exhaustive study, including Algerian and Moroccan skink populations will be necessary in order to clarify these issues.

scholarly journals Genetic diversity and its conservation implications of Vitex rotundifolia (Lamiaceae) populations in East Asia

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6194 ◽  
Author(s):  
Yiqi Sun ◽  
Hong Yang ◽  
Qiaoyan Zhang ◽  
Luping Qin ◽  
Pan Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Population Differentiation ◽  
Haplotype Diversity ◽  
Haplotype Network ◽  
Conservation Strategy ◽  
Nuclear Ribosomal Dna ◽  
Wild Plants ◽  
Intergenic Spacers ◽  
Network Analyses

Vitex rotundifolia is an important coastal and medicinal plant, and is recorded in the List of the Important Wild Plants for Conservation in China and Japan. However, an effective conservation strategy is lacking. In the present study, the genetic diversity and population structure were analyzed using phylogeographical methods based on the trnH-psbA and trnG-trnS intergenic spacers of the chloroplast DNA (cpDNA) sequences from 157 individuals from 25 sampling sites for V. rotundifolia and V. trifolia plus the internal transcribed spacer (ITS) of the nuclear ribosomal DNA (nrDNA) sequences of 177 individuals from 27 sampling sites. The results showed that V. rotundifolia and V. trifolia had eight cpDNA and two nrDNA haplotypes, respectively, and the V. rotundifolia has a low level of genetic diversity (haplotype diversity hd,cp = 0.360, hd,nr = 0.440), a more pronounced genetic differentiation among populations (population differentiation at the species level (GST) = 0.201, population differentiation at the allele level (NST) = 0.462), and an insignificantly different phylogeographical structure (NST > GST, P > 0.05). In addition, haplotype network analyses indicated that V. rotundifolia and V. trifolia have distinct haplotypes. Divergence dating based on BEAST software analyses showed that most cpDNA clades diverged in the late Pleistocene era. Demographic analysis indicated that V. rotundifolia underwent a rapid demographic expansion. Some scientific strategies are suggested for resource conservation of V. rotundifolia based on its genetic diversity and population structure.

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