scholarly journals Recent population expansion of longtail tuna Thunnus tonggol (Bleeker, 1851) inferred from the mitochondrial DNA markers

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9679
Author(s):  
Noorhani Syahida Kasim ◽  
Tun Nurul Aimi Mat Jaafar ◽  
Rumeaida Mat Piah ◽  
Wahidah Mohd Arshaad ◽  
Siti Azizah Mohd Nor ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Pacific Ocean ◽  
Goodness Of Fit ◽  
Demographic History ◽  
Population Expansion ◽  
Seasonal Migration ◽  
Likelihood Method ◽  
Recent Population Expansion ◽  
D Loop ◽  
Longtail Tuna

The population genetic diversity and demographic history of the longtail tuna Thunnus tonggol in Malaysian waters was investigated using mitochondrial DNA D-loop and NADH dehydrogenase subunit 5 (ND5). A total of 203 (D-loop) and 208 (ND5) individuals of T. tonggol were sampled from 11 localities around the Malaysian coastal waters. Low genetic differentiation between populations was found, possibly due to the past demographic history, dispersal potential during egg and larval stages, seasonal migration in adults, and lack of geographical barriers. The gene trees, constructed based on the maximum likelihood method, revealed a single panmictic population with unsupported internal clades, indicating an absence of structure among the populations studied. Analysis on population pairwise comparison ФST suggested the absence of limited gene flow among study sites. Taken all together, high haplotype diversity (D-loop = 0.989–1.000; ND5 = 0.848–0.965), coupled with a low level of nucleotide diversity (D-loop = 0.019–0.025; ND5 = 0.0017–0.003), “star-like” haplotype network, and unimodal mismatch distribution, suggests a recent population expansion for populations of T. tonggol in Malaysia. Furthermore, neutrality and goodness of fit tests supported the signature of a relatively recent population expansion during the Pleistocene epoch. To provide additional insight into the phylogeographic pattern of the species within the Indo-Pacific Ocean, we included haplotypes from GenBank and a few samples from Taiwan. Preliminary analyses suggest a more complex genetic demarcation of the species than an explicit Indian Ocean versus Pacific Ocean delineation.

scholarly journals Selection on codon usage and base composition in Drosophila americana

2011 ◽  
Vol 8 (1) ◽  
pp. 82-85 ◽  
Author(s):  
Sophie Marion de Procé ◽  
Kai Zeng ◽  
Andrea J. Betancourt ◽  
Brian Charlesworth
Keyword(s):  
Natural Selection ◽  
Codon Usage ◽  
Base Composition ◽  
Maximum Likelihood Method ◽  
Demographic History ◽  
Population Expansion ◽  
Likelihood Method ◽  
Recent Population Expansion ◽  
Coding Sequences ◽  
Biased Gene Conversion

We have used a polymorphism dataset on introns and coding sequences of X-linked loci in Drosophila americana to estimate the strength of selection on codon usage and/or biased gene conversion (BGC), taking into account a recent population expansion detected by a maximum-likelihood method. Drosophila americana was previously thought to have a stable demographic history, so that this evidence for a recent population expansion means that previous estimates of selection need revision. There was evidence for natural selection or BGC favouring GC over AT variants in introns, which is stronger for GC-rich than GC-poor introns. By comparing introns and coding sequences, we found evidence for selection on codon usage bias, which is much stronger than the forces acting on GC versus AT basepairs in introns.

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 Mitochondrial phylogeography of the Mediterranean horseshoe bat on the Balkan Peninsula

2019 ◽  
Vol 71 (4) ◽  
pp. 767-774
Author(s):  
Ivana Budinski ◽  
Vladimir Jovanovic ◽  
Branka Pejic ◽  
Jelena Blagojevic ◽  
Marija Rajicic ◽  
...  
Keyword(s):  
Demographic History ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Balkan Peninsula ◽  
Glacial Refugium ◽  
Recent Population Expansion ◽  
The Balkans ◽  
Loop Region ◽  
The Mediterranean ◽  
Horseshoe Bat

The Balkan Peninsula is identified as one of the major glacial refugia in Europe during the Pleistocene, and it has served as a genetic source for post-glacial recolonization for many temperate species. The aim of this study was to investigate the genetic diversity and phylogeographic patterns of the Mediterranean horseshoe bat, Rhinolophus euryale Blasius 1853, on the Balkan Peninsula. We also analyzed its demographic history and tested the hypothesis that this region was a glacial refugium for this species. We collected 82 samples from 20 localities in the Balkans and Italy and sequenced the mitochondrial D-loop region. Our results revealed low nucleotide but high haplotype diversity, with 20 out of 24 haplotypes reported for the first time. All Balkan and Italian samples belonged to a single genetic clade in the phylogenetic reconstruction, where they clustered together with previously published samples from Turkey, southern France and North Africa. The haplotype network had a star-like pattern that is indicative of recent population expansion. Both mismatch distribution and shallow genetic differentiation also supported the scenario of a sudden demographic expansion. We estimated that expansion within this lineage commenced in the Late Pleistocene. We suggest that the Balkan Peninsula was a glacial refugium for R. euryale.

scholarly journals Limited gene flow and partial isolation phylogeography of Himalayan snowcock Tetraogallus himalayensis based on part mitochondrial D-loop sequences

2011 ◽  
Vol 57 (6) ◽  
pp. 758-767 ◽  
Author(s):  
Xiaoli Wang ◽  
Jiangyong Qu ◽  
Naifa Liu ◽  
Xinkang Bao ◽  
Sen Song
Keyword(s):  
Mitochondrial Dna ◽  
Gene Flow ◽  
Control Region ◽  
Divergence Time ◽  
Population Expansion ◽  
Middle Pleistocene ◽  
Distribution Analysis ◽  
D Loop ◽  
Limited Gene Flow ◽  
Partial Isolation

Abstract Himalayan snowcock Tetraogallus himalayensis are distributed in alpine and subalpine areas in China. We used mitochondrial DNA control-region data to investigate the origin and past demographic change in sixty-seven Himalayan snowcock T. himalayensis. The fragments of 1155 nucleotides from the control region of mitochondrial DNA were sequenced, and 57 polymorphic positions defined 37 haplotypes. A high level of genetic diversity was detected in all populations sampled and may be associated isolation of the mountains and habitat fragmentation and deterioration from Quaternary glaciations. In the phylogenetic tree, all haplotypes grouped into four groups: clade A (Kunlun Mountains clade), clade B (Northern Qinghai-Tibetan Plateau clade), clade C (Tianshan Mountains clade) and clade D (Kalakunlun Mountains clade). We found a low level of gene flow and significant genetic differentiation among all populations. Based on divergence time we suggest that the divergence of Himalayan snowcock occurred in the middle Pleistocene inter-glaciation, and expansion occurred in the glaciation. Analysis of mtDNA D-loop sequences confirmed demographic population expansion, as did our non-significant mismatch distribution analysis. In conclusion, limited gene flow and a pattern of partial isolation phylogeographic was found in geographic populations of T. himalayansis based on the analysis on mtDNA D-loop sequences.

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