scholarly journals Mitogenomes Reveal Multiple Colonization of Mountains by Rattus in Sundaland

2020 ◽  
Author(s):  
Miguel Camacho-Sanchez ◽  
Jennifer A Leonard
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Purifying Selection ◽  
High Elevation ◽  
Mitochondrial Genomes ◽  
Tropical Mountains ◽  
Weak Evidence ◽  
History Of ◽  
Phylogenetic Framework ◽  
Complete Mitochondrial Genomes

Abstract Tropical mountains are cradles of biodiversity and endemism. Sundaland, tropical Southeast Asia, hosts 3 species of Rattus endemic to elevations above 2000 m with an apparent convergence in external morphology: Rattus korinchi and R. hoogerwerfi from Sumatra, and R. baluensis from Borneo. A fourth one, R. tiomanicus, is restricted to lowland elevations across the whole region. The origins of these endemics are little known due to the absence of a robust phylogenetic framework. We use complete mitochondrial genomes from the 3 high altitude Rattus, and several related species to determine their relationships, date divergences, reconstruct their history of colonization, and test for selection on the mitochondrial DNA. We show that mountain colonization happened independently in Borneo (<390 Kya) and Sumatra (~1.38 Mya), likely from lowland lineages. The origin of the Bornean endemic R. baluensis is very recent and its genetic diversity is nested within the diversity of R. tiomanicus. We found weak evidence of positive selection in the high-elevation lineages and attributed the greater nonsynonymous mutations on these branches (specially R. baluensis) to lesser purifying selection having acted on the terminal branches in the phylogeny.

scholarly journals Evolutionary History of Chimpanzees Inferred from Complete Mitochondrial Genomes

2010 ◽  
Vol 28 (1) ◽  
pp. 615-623 ◽  
Author(s):  
A. Bjork ◽  
W. Liu ◽  
J. O. Wertheim ◽  
B. H. Hahn ◽  
M. Worobey
Keyword(s):  
Evolutionary History ◽  
Mitochondrial Genomes ◽  
History Of ◽  
Complete Mitochondrial Genomes

scholarly journals Comparative Analysis of Complete Mitochondrial Genomes of Three Gerres Fishes (Perciformes: Gerreidae) and Primary Exploration of Their Evolution History

2020 ◽  
Vol 21 (5) ◽  
pp. 1874 ◽  
Author(s):  
Huiting Ruan ◽  
Min Li ◽  
Zhenhai Li ◽  
Jiajie Huang ◽  
Weiyuan Chen ◽  
...  
Keyword(s):  
Purifying Selection ◽  
Living Environment ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Marine Fishery ◽  
Gc Skew ◽  
The Difference ◽  
Early Paleogene ◽  
Complete Mitochondrial Genomes

Mitochondrial genome is a powerful molecule marker to explore phylogenetic relationships and reveal molecular evolution in ichthyological studies. Gerres species play significant roles in marine fishery, but its evolution has received little attention. To date, only two Gerres mitochondrial genomes were reported. In the present study, three mitogenomes of Gerres (Gerres filamentosus, Gerres erythrourus, and Gerres decacanthus) were systemically investigated. The lengths of the mitogenome sequences were 16,673, 16,728, and 16,871 bp for G. filamentosus, G. erythrourus, and G. decacanthus, respectively. Most protein-coding genes (PCGs) were initiated with the typical ATG codon and terminated with the TAA codon, and the incomplete termination codon T/TA could be detected in the three species. The majority of AT-skew and GC-skew values of the 13 PCGs among the three species were negative, and the amplitude of the GC-skew was larger than the AT-skew. The genetic distance and Ka/Ks ratio analyses indicated 13 PCGs were suffering purifying selection and the selection pressures were different from certain deep-sea fishes, were which most likely due to the difference in their living environment. The phylogenetic tree was constructed by molecular method (Bayesian Inference (BI) and maximum Likelihood (ML)), providing further supplement to the scientific classification of fish. Three Gerres species were differentiated in late Cretaceous and early Paleogene, and their evolution might link with the geological events that could change their survival environment.

scholarly journals The Genetic Diversity of the Nguni Breed of African Cattle (Bos spp.): Complete Mitochondrial Genomes of Haplogroup T1

PLoS ONE ◽  
2013 ◽  
Vol 8 (8) ◽  
pp. e71956 ◽  
Author(s):  
K. Ann Horsburgh ◽  
Stefan Prost ◽  
Anna Gosling ◽  
Jo-Ann Stanton ◽  
Christy Rand ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Genomes ◽  
African Cattle ◽  
Complete Mitochondrial Genomes

scholarly journals A simple centrifugation protocol leads to a 55-fold mitochondrial DNA enrichment and paves the way for future mitogenomic research

2017 ◽  
Author(s):  
Jan Niklas Macher ◽  
Vera Zizka ◽  
Alexander Martin Weigand ◽  
Florian Leese
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genomes ◽  
Shotgun Metagenomics ◽  
Fold Enrichment ◽  
Speed Up ◽  
Mitochondrial Origin ◽  
Reduced Costs ◽  
Mock Communities ◽  
Centrifugation Protocol ◽  
Complete Mitochondrial Genomes

AbstractDNA (meta)barcoding is used to study biodiversity and is available for standardised assessments. However, it suffers from PCR bias, which can lead to the loss of specific taxa. PCR-free techniques such as shotgun metagenomics are therefore thought to be more suited for biodiversity assessments, but are currently limited by incomplete reference libraries.The technique of ‘mitogenome-skimming’ or ‘mitogenomics’, in which complete mitochondrial genomes are sequenced, is ideal to bridge the techniques of (meta)barcoding and metagenomics. However, without the enrichment of mitochondria, roughly 99 % of all sequencing reads are of non-mitochondrial origin and mostly useless for common applications, e.g. species identification.Here, we present a simple centrifugation protocol that leads to an average 140-fold enrichment of mitochondrial DNA. By sequencing six ‘mock’- communities – comprising the freshwater taxa Corbicula fluminea, Gammarus roeselii and Hydropsyche exocellata each – we recovered whole mitochondrial genomes of these species and the acanthocephalan endoparasite Pomphorhynchus laevis.The presented protocol will greatly speed up building reference libraries for whole mitochondrial genomes, as dozens of species could be sequenced on a single MiSeq run. Subsequently, it will also allow biodiversity assessments using mitogenomics at greatly reduced costs in comparison to mitogenomic approaches without prior enrichment for mitochondria.

The Complete Mitochondrial Genomes of two Flying Fishes, Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii

2020 ◽  
Author(s):  
Liyan Qu ◽  
Heng Zhang ◽  
Fengying Zhang ◽  
Wei Wang ◽  
Fenghua Tang ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Flying Fishes ◽  
Complete Mitochondrial Genomes

Background: Genome-scale approaches have played a significant role in the analysis of evolutionary relationships. Because of rich polymorphisms, high evolutionary rate and rare recombination, mitochondrial DNA sequences are commonly considered as effective markers for estimating population genetics, evolutionary and phylogenetic relationships. Flying fishes are important components of epipelagic ecosystems. Up to now, only few complete mitochondrial genomes of flying fishes have been reported. In the present study, the complete mitochondrial DNA sequences of the Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii had been determined. Methods: Based on the published mitogenome of Cheilopogon atrisignis (GenBank: KU360729), fifteen pairs of primers were designed by the software Primer Premier 5.0 to get the complete mitochondrial genomes of two flying fishes. According to the reported data, the phylogenetic position of two flying fishes were detected using the conserved 12 protein-coding genes. Result: The complete mitochondrial genomes of Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii are determined. They are 16532bp and 16525bp in length, respectively. And they both consists of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and a control region. The OL regions are conserved in these two flying fishes and might have no function. From the tree topologies, we found C.p. japonicus and H. rondeletii clustered in a group. The findings of the study would contribute to the phylogenetic classification and the genetic conservation management of C.p. japonicus and H. rondeletii.

Genetic diversity and demographic history of the giant river catfish Sperata seenghala inferred from mitochondrial DNA markers

2016 ◽  
Vol 28 (6) ◽  
pp. 920-926 ◽  
Author(s):  
Priyanka Kumari ◽  
A. Pavan-Kumar ◽  
Gulshan Kumar ◽  
Absar Alam ◽  
Janmejay Parhi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Dna Markers ◽  
Demographic History ◽  
History Of ◽  
Sperata Seenghala

scholarly journals Molecular Evolution and Recombination in Gender-Associated Mitochondrial DNAs of the Manila Clam Tapes philippinarum

Genetics ◽  
2003 ◽  
Vol 164 (2) ◽  
pp. 603-611 ◽  
Author(s):  
Marco Passamonti ◽  
Jeffrey L Boore ◽  
Valerio Scali
Keyword(s):  
Mitochondrial Dna ◽  
Molecular Evolution ◽  
Single Gene ◽  
Mitochondrial Genomes ◽  
Uniparental Inheritance ◽  
Doubly Uniparental Inheritance ◽  
Tapes Philippinarum ◽  
Mitochondrial Dnas ◽  
History Of ◽  
Mitochondrial Dna Heteroplasmy

Abstract Doubly uniparental inheritance (DUI) provides an intriguing system for addressing aspects of molecular evolution and intermolecular recombination of mitochondrial DNA. For this reason, a large sequence analysis has been performed on Tapes philippinarum (Bivalvia, Veneridae), which has mitochondrial DNA heteroplasmy that is consistent with a DUI. The sequences of a 9.2-kb region (containing 29 genes) from 9 individuals and the sequences of a single gene from another 44 individuals are analyzed. Comparisons suggest that the two sex-related mitochondrial genomes do not experience a neutral pattern of divergence and that selection may act with varying strength on different genes. This pattern of evolution may be related to the long, separate history of M and F genomes within their tissue-specific “arenas.” Moreover, our data suggest that recombinants, although occurring in soma, may seldom be transmitted to progeny in T. philippinarum.

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