scholarly journals Mitochondrial substitution rates estimation for molecular clock analyses in modern birds based on full mitochondrial genomes

2019 ◽  
Author(s):  
Angel Arcones ◽  
Raquel Ponti ◽  
David R. Vieites
Keyword(s):  
Mitochondrial Dna ◽  
Molecular Clock ◽  
Bird Species ◽  
Divergence Times ◽  
Mitochondrial Genomes ◽  
Fixed Rate ◽  
D Loop ◽  
Standard Clock ◽  
Complete Mitochondrial Genomes ◽  
Mtdna Marker

AbstracttiMitochondrial DNA (mtDNA) is a very popular resource in the study of evolutionary processes in birds, and especially to infer divergence times between lineages. These inferences rely on rates of substitution in the mtDNA genes that, ideally, are specific for the studied taxa. But as such values are often unavailable many studies fixed rate values generalised from other studies, such as the popular “standard molecular clock”. However the validity of these universal rates across all bird lineages and for the different mtDNA has been severely questioned. Thus, we here performed the most comprehensive calibration of the mtDNA molecular clock in birds, with the inclusion of complete mitochondrial genomes for 622 bird species and 25 reliable fossil calibrations. The results show variation in the rates between lineages and especially between markers, contradicting the universality of the standard clock. Moreover, we provide especific rates for every mtDNA marker (except D-loop) in each of the sampled avian orders, which should help improve future estimations of divergence times between bird species or populations.

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.

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.

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.

scholarly journals Characterization of four mitochondrial genomes of family Neritidae (Gastropoda: Neritimorpha) and insight into its phylogenetic relationships

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jian-tong Feng ◽  
Li-ping Xia ◽  
Cheng-rui Yan ◽  
Jing Miao ◽  
Ying-ying Ye ◽  
...  
Keyword(s):  
Molecular Clock ◽  
Gene Order ◽  
Phylogenetic Relationships ◽  
Evolutionary Relationships ◽  
Mitochondrial Genomes ◽  
Phylogenetic Resolution ◽  
Relaxed Molecular Clock ◽  
Insight Into ◽  
Complete Mitochondrial Genomes

AbstractNeritidae is one of the most diverse families of Neritimorpha and possesses euryhaline properties. Members of this family usually live on tropical and subtropical coasts and are mainly gregarious. The phylogenetic relationships between several subclasses of Gastropoda have been controversial for many years. With an increase in the number of described species of Neritidae, the knowledge of the evolutionary relationships in this family has improved. In the present study, we sequenced four complete mitochondrial genomes from two genera (Clithon and Nerita) and compared them with available complete mitochondrial genomes of Neritidae. Gene order exhibited a highly conserved pattern among three genera in the Neritidae family. Our results improved the phylogenetic resolution within Neritidae, and more comprehensive taxonomic sampling of subclass Neritimorpha was proposed. Furthermore, we reconstructed the divergence among the main lineages of 19 Neritimorpha taxa under an uncorrelated relaxed molecular clock.

scholarly journals Ten complete mitochondrial genomes of Gymnocharacini (Stethaprioninae, Characiformes): evolutionary relationships and a repetitive element in the Control Region (D-loop)

2020 ◽  
Author(s):  
Rubens Pasa ◽  
Fabiano Bezerra Menegídio ◽  
Igor Henrique Rodrigues-Oliveira ◽  
Iuri Batista da Silva ◽  
Matheus Lewi Cruz Bonaccorsi de Campos ◽  
...  
Keyword(s):  
Neotropical Region ◽  
Rrna Genes ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Raw Data ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Species Complexes ◽  
D Loop ◽  
Complete Mitochondrial Genomes

AbstractWe are presenting the complete mitogenomes of eight fish species/cytotypes from Neotropical region belonging to the Astyanax and Psalidodon genus: A. aeneus, A. altiparanae, P. fasciatus (from two locations - Upper Paraná and São Francisco river basins), A. lacustris, P. rivularis (two cytotypes) and P. rioparanaibano. We perform the whole-genome sequencing for six of these species in a Novaseq 6000 - by Illumina, meanwhile two genomes were assembled from raw data available in databases. Plus, we reassembled and annotated the mitochondrial genomes for A. mexicanus and P. paranae, both already described and with raw data available online. All the genomes presented the same organization, with 13 protein-coding genes, 22 tRNA genes and two rRNA genes. Aiming to contribute to the understanding of the several cryptic species complexes and phylogeny of the genus, we perform Bayesian analysis using the 13 protein-coding genes from these species, plus Deuterodon giton and using a Brycon species as outgroup.

scholarly journals Comparative Characterization of the Complete Mitochondrial Genomes of the Three Apple Snails (Gastropoda: Ampullariidae) and the Phylogenetic Analyses

2018 ◽  
Vol 19 (11) ◽  
pp. 3646 ◽  
Author(s):  
Huirong Yang ◽  
Jia-en Zhang ◽  
Jun Xia ◽  
Jinzeng Yang ◽  
Jing Guo ◽  
...  
Keyword(s):  
Control Strategies ◽  
Phylogenetic Analyses ◽  
Mitochondrial Protein ◽  
Evolutionary Process ◽  
Economic Losses ◽  
Mitochondrial Genomes ◽  
Pomacea Canaliculata ◽  
Bayesian Phylogenetic Analysis ◽  
D Loop ◽  
Complete Mitochondrial Genomes

The apple snails Pomacea canaliculata, Pomacea diffusa and Pomacea maculate (Gastropoda: Caenogastropoda: Ampullariidae) are invasive pests causing massive economic losses and ecological damage. We sequenced and characterized the complete mitochondrial genomes of these snails to conduct phylogenetic analyses based on comparisons with the mitochondrial protein coding sequences of 47 Caenogastropoda species. The gene arrangements, distribution and content were canonically identical and consistent with typical Mollusca except for the tRNA-Gln absent in P. diffusa. An identifiable control region (d-loop) was absent. Bayesian phylogenetic analysis indicated that all the Ampullariidae species clustered on the same branch. The genus Pomacea clustered together and then with the genus Marisa. The orders Architaenioglossa and Sorbeoconcha clustered together and then with the order Hypsogastropoda. Furthermore, the intergenic and interspecific taxonomic positions were defined. Unexpectedly, Ceraesignum maximum, Dendropoma gregarium, Eualetes tulipa and Thylacodes squamigerus, traditionally classified in order Hypsogastropoda, were isolated from the order Hypsogastropoda in the most external branch of the Bayesian inference tree. The divergence times of the Caenogastropoda indicated that their evolutionary process covered four geological epochs that included the Quaternary, Neogene, Paleogene and Cretaceous periods. This study will facilitate further investigation of species identification to aid in the implementation of effective management and control strategies of these invasive species.

scholarly journals Ten Complete Mitochondrial Genomes of Gymnocharacini (Stethaprioninae, Characiformes). Insights Into Evolutionary Relationships and a Repetitive Element in the Control Region (D-loop)

2021 ◽  
Vol 9 ◽  
Author(s):  
Rubens Pasa ◽  
Fabiano Bezerra Menegídio ◽  
Igor Henrique Rodrigues-Oliveira ◽  
Iuri Batista da Silva ◽  
Matheus Lewi Cruz Bonaccorsi de Campos ◽  
...  
Keyword(s):  
Control Region ◽  
Repetitive Element ◽  
Evolutionary Relationships ◽  
Mitochondrial Genomes ◽  
D Loop ◽  
Complete Mitochondrial Genomes

scholarly journals Ancient mitogenomics elucidates diversity of extinct West Indian tortoises

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Christian Kehlmaier ◽  
Nancy A. Albury ◽  
David W. Steadman ◽  
Eva Graciá ◽  
Richard Franz ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Molecular Clock ◽  
Late Holocene ◽  
West Indian ◽  
Distinct Species ◽  
Galapagos Islands ◽  
Mitochondrial Genomes ◽  
Galápagos Islands ◽  
The Bahamas ◽  
Complete Mitochondrial Genomes

AbstractWe present 10 nearly complete mitochondrial genomes of the extinct tortoise Chelonoidis alburyorum from the Bahamas. While our samples represent morphologically distinct populations from six islands, their genetic divergences were shallow and resembled those among Galápagos tortoises. Our molecular clock estimates revealed that divergence among Bahamian tortoises began ~ 1.5 mya, whereas divergence among the Galápagos tortoises (C. niger complex) began ~ 2 mya. The inter-island divergences of tortoises from within the Bahamas and within the Galápagos Islands are much younger (0.09–0.59 mya, and 0.08–1.43 mya, respectively) than the genetic differentiation between any other congeneric pair of tortoise species. The shallow mitochondrial divergences of the two radiations on the Bahamas and the Galápagos Islands suggest that each archipelago sustained only one species of tortoise, and that the taxa currently regarded as distinct species in the Galápagos should be returned to subspecies status. The extinct tortoises from the Bahamas have two well-supported clades: the first includes one sample from Great Abaco and two from Crooked Island; the second clade includes tortoises from Great Abaco, Eleuthera, Crooked Island, Mayaguana, Middle Caicos, and Grand Turk. Tortoises belonging to both clades on Great Abaco and Crooked Island suggest late Holocene inter-island transport by prehistoric humans.

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