Mitochondrial Control Region Genes Research Articles

Novel Insights Into the Genetic Population Connectivity of Transient Whale Sharks (Rhincodon typus) in Pacific Panama Provide Crucial Data for Conservation Efforts

The whale shark (Rhincodon typus) is an endangered and highly migratory species, of which solitary individuals or aggregations are observed in oceans worldwide and for which conservation efforts are hindered by a lack of comprehensive data on genetic population connectivity. Tissue samples were collected from wandering whale sharks in Pacific Panama to determine genetic diversity, phylogeographic origin, and possible global and local connectivity patterns using a 700–800 bp fragment of the mitochondrial control region gene. Genetic diversity among samples was high, with five new haplotypes and nine polymorphic sites identified among the 15 sequences. Haplotype diversity (Hd= 0.83) and nucleotide diversity (π = 0.00516) were similar to those reported in other studies. Our sequences, in particular haplotypesPTY1andPTY2, were similar to those previously reported in the Arabian Gulf and the Western Indian Ocean populations (a novel occurrence in the latter case). HaplotypesPTY3,PTY4, andPTY5were similar to populations in Mexico and the Gulf of California. In contrast, the only populations to which our Panamanian sequences were genetically dissimilar were those from the Atlantic Ocean. The absence of reference sequences in GenBank from southern sites in the Eastern Tropical Pacific, such as Galapagos (Ecuador), Gorgona and Malpelo Islands (Colombia), and Coco Island (Costa Rica), reduced our capacity to genetically define regional patterns. Genetic differentiation and connectivity were also assessed using an analysis of molecular variance (AMOVA), which showed a similar population structure (five groups) to the neighbor-joining tree. Other population features based on neutrality tests, such as Tajima’s D and Fu’sFsstatistics, showed positive values for Panama of 0.79 and 1.61, respectively. Positive values of these statistics indicate a lack of evidence for population expansion among the sampled individuals. Our results agree with previous reports suggesting that whale sharks can travel over long distances and that transboundary conservation measures may be effective for species protection.

Genetic Diversity and Phylogenetic of Longtail Tuna (Thunnus tonggol) Landed in Pabean Fish Market, Surabaya

Indonesia is the biggest tuna exporter in Southeast Asia. With a high number of tuna catch, it is worried that the catch will decrease tuna population, specifically longtail tuna. To anticipate the decrease, there needs to be a conservation program to protect longtail tunas from scarcity. One method used to protect longtail tuna is by genetic conservation. The aim of this research is to understand the genetic and phylogenetic variety of the longtail tuna in Pabean Surabaya Fish Market. The polymerase chain reaction was used to amplify segment of the mitochondrial control region gene from members of these sample, used forward primer CRK 5’-AGCTC AGCGC CAGAG CGCCG GTCTT GTAAA-3’ and reverse primer CRE 5’-CCTGA AGTAG GAACC AGATG-3’. Based on the sequencing process, 28 out of 29 samples longtail tuna were analyzed successfully. The results of the 28 sample analysis of longtail tuna based on its genetic variety and phylogenetic tree reconstruction showed a haplotype variety (Hd) score of 1,00000, and nucleotide (π) variety of 0,1939. Genetic variety value showed that longtail tuna has great adaption capabilities toward environmental changes time to time. Phylogenetic tree reconstruction results showed 7 clades with a genetic range of 0,005 – 0,035, which shows that all samples are closely related. The results of this study can be used as basic information in forming regulations on longtail tuna sustainable management and genetic conservation.

Molecular identification of redfish (genus Sebastes) in the White Sea indicates patterns of introgressive hybridisation

The rare occurrence of redfish (genus Sebastes) in the White Sea encouraged Rolskii et al. (Polar Biol 43:385–389, 2020) to investigate the species identity of two animals captured near the Sredniy Island at 40 m depth. They reported that their morphological description proved unreliable and that genetic evidence “clearly demonstrated” these redfish belong to S. norvegicus. This was inferred using the S7 and the mitochondrial control region genes. However, while their S7 matched one S. norvegicus reference sequence, the S. norvegicus mitochondrial reference sequences used to infer species identity were previously shown to cluster with S. mentella. Therefore, both of their redfish samples belong to a S. norvegicus × S. mentella (deep-pelagic) hybrid which presents an interesting perspective into the complex species dynamics in this group.

Morphological and genetic characterization of Sardinian trout Salmo cettii Rafinesque, 1810 and their conservation implications

The morphological and genetic structure of Western Mediterranean trout Salmo cettii inhabiting basins in Sardinia was completed to assist the design of its conservation programmes. Genetic analysis of protein-coding LDH-C1 plus sequencing mitochondrial control region gene and analyses of morphological characters described 253 specimens from seven localities in two basins in Southwest Sardinia. Nuclear and mitochondrial analyses revealed all of the fish were pure-bred native S. cettii, with no introgression from allochthonous S. trutta. The novel 18 mtDNA control region haplotypes were clustered in an ‘insular’ clade, strictly related to the Adriatic haplogroup, and depicted a radial network around two ancestral haplotypes. Completion of discriminant analysis using data on body pigmentation and quantitative morphologic parameters revealed three phenotypic groups within the fish. Each population and phenotype, characterised by high values of nucleotide and haplotype diversity, were not genetically differentiated and not geographically structured according to the two hydrological basins. Geometric morphometric analysis, based on 15 landmarkers, revealed pronounced and highly significant differences in body shape morphology between populations, suggesting S. cettii is locally adapting to extreme environmental conditions and so future management plans for these populations should treat the two basins as distinct morphological units.

Genetic structure and diffusion of population of <i>Coilia ectenes taihuensis</i> in Lake Nansi inferred from the mitochondrial control region

为推断南四湖湖鲚种群来源,采用线粒体控制区(D-loop)基因序列测定技术,对3个不同水域湖鲚(Coilia ectenes taihuensis)种群的遗传结构特征及其变异进行研究,并分析它们之间的系统发育关系. 结果表明3个不同湖鲚种群的平均单倍型多样性和核苷酸多样性分别为0.9646和0.0097,除3个单倍型共享外,不同地理单元中具有较高的单倍型多样性.AMOVA和成对F_st值分析均表明,不同湖泊群体间未发现明显的遗传分化,各地理单元中的单倍型相互散布在不同的种群中.系统发育分析结果显示,不同湖泊湖鲚种群的单倍型形成3个分支,但每一地理群体没有显示出明显的地理位置与单倍型间的对应关系.结合南四湖历史资料和当前渔业监测结果,推测湖鲚为2002年实施长江向南四湖应急补水时洪泽湖湖鲚迁移扩散进而在南四湖建群的.;The genetic structure and genetic variation of three populations of Coilia ectenes taihuensis in different lakes are investigated using the mitochondrial control region gene. Results show that the hapotype diversity(h) and mean nucleotide diversity(π) of the populations of different lakes are 0.9646 and 0.0097, respectively. 30 hapotypes were detected out of 45 individuals from the three populations. Only three of these haplotypes were shared among three lakes which contributed much to the genetic diversity. The AMOVA analysis and the pairwise F_st values revealed no significance among three populations of C. ectenes taihuensis. NJ and Bayesian analyses revealed that individuals of three populations formed three clades with poor support, but no clear relationships between haplotypes and geographical regions. We inferred that C. ectenes taihuensis populations in Lake Nansi originate from lakes in the Yangtze River by the ecological urgent water diversion in 2002.

Comparison of D-Loop Gene for Subspecies Confirmation of Tigers (Panthera Tigris)

Tiger (Panthera tigris), the biggest cat species and the top predator has fallen into endangered category. In the present study, we confirmed the subspecies of tiger with help of DNA based methods. The mitochondrial control region gene (D–loop) sequence was utilized for this purpose. DNA was extracted from tiger blood sample originally obtained from mini zoo of Rohtak, Haryana. The D–loop sequence was amplified and submitted to GenBank with accession number HM362438. Based on D–loop sequence identity and phylogenetic analysis Panthera tigris tigris (Indian tiger) was differentiated from other Panthera tigris subspecies (Panthera tigris amoyensis, Panthera tigris corbetti, Panthera tigris sumatrae and Panthera tigris altacia) from different parts of the world. The present report also describes an easier, quicker and non hazardous protocol for the isolation of genomic DNA from tiger blood. All copyrights reserved to Nexus® academic publishers

Molecular Identification and Historic Demography of the Marine Tucuxi (Sotalia guianensis) at the Amazon River’s Mouth by Means of Mitochondrial Control Region Gene Sequences and Implications for Conservation

In 2005, three fishermen, with artisan fishing vessels and drift gillnets, accidentally captured around 200 dolphins between Vigia and Salinópolis in the Amazon River estuary. The dolphins died and they then prepared their vaginas and penises in order to sell them in the Ver-ao-Peso market in the city of Belem within the Brazilian state of Pará. We randomly sampled a minimal quantity of tissue of these sexual organs from 78 of these 200 dolphins and we determined the following results after sequencing 689 base pairs (bp) from the mitochondrial control region gene: (1) 96.15% (75/78) of these dolphins belonged to the species Sotalia guianensis. The other species detected were Steno brenadensis, Stenella coeruleoalba and Tursiops truncatus; (2) The levels of gene diversity found in this sample of S. guianensis were high (33 haplotypes, haplotype diversity of 0.917 and nucleotide diversity of 0.0045) compared to gene diversities found in other Brazilian S. guianensis locations; (3) All the population genetics methods employed indicated a clear population expansion in this population. This population expansion could have begun 400,000 years ago; (4) The haplotype divergence within this population could have begun around 2.1 millions of years ago (MYA), with posterior splits around 2.0–1.8 MYA, 1.7–1.8 MYA, 1–1.5 MYA, 0.6–0.8 MYA, 0.4–0.2 MYA and 0.16–0.02 MYA, all during the Pleistocene.

Mitochondrial DNA analysis reveals a unique population structure of the amphidromous sculpin Cottus pollux middle-egg type (Teleostei: Cottidae)

In this study, we examined nucleotide sequences from the first half of the mitochondrial control region gene to test for genetic differentiation in an amphidromous sculpin, Cottus pollux middle-egg type (ME) (Cottidae), obtained from 19 localities across its distribution range. Spatial analysis of molecular variance revealed five divergent groups of related haplotypes among this populations. Analysis with Migrate software revealed that gene flow was quite restricted among the groups, although it occurred practically between neighboring groups. It has previously been reported that the population structure among the amphidromous fishes of the various islands is low or non-existent, and is characterized mainly by the duration of the pelagic larval life. However, the present study demonstrated that the various C. pollux ME populations were different both among the islands, and within the island of the Japanese Archipelago. Our finding indicate that the unique population structure of C. pollux ME may be influenced not only by the extent of the pelagic larval phase of the species but also by the seasonal differentiation of its dispersal phase.

Historical population dynamics and demography of the eastern Atlantic pomacentrid Chromis limbata (Valenciennes, 1833)

Recent studies have focused on the relationship between the marine fauna of the eastern Atlantic and the Mediterranean Sea, but within the Atlantic, little is known about genetic relationships between populations of the Macaronesian islands. In this study, we tested whether the paleo-climatology and paleo-oceanography of the region could predict the genetic relationships among three eastern Atlantic populations (Azores, Madeira, and Canaries) of a damselfish, Chromis limbata, and compared our results with its Mediterranean and adjacent Atlantic sister species, Chromis chromis. We combined phylogeographic and coalescent approaches using the fast evolving mitochondrial control region gene. No population structure was found for the three archipelagos. The coalescence time estimated for C. limbata (0.857–1.17 Mya) was much greater than that estimated for C. chromis. We propose that this difference reflects differences in glaciating extents in the Northeastern Atlantic and the Mediterranean. Diversity indexes (Hd and genetic distances) together with historical demographic parameters of C. limbata ( Θ and g) revealed a more stable population history when compared to C. chromis. Our results suggest that the Macaronesian populations of C. limbata have probably been less affected by the last glaciation than the Mediterranean populations of C. chromis. Migration across the three archipelagos was estimated and a prevailing northwest trend was detected. This result supports the idea of a colonization of the Azores by warm water fish from Madeira or the westernmost Canary islands which acted as major glacial refugia for the tropical and subtropical marine fauna during the glaciations.