scholarly journals Evolutionary rates are correlated between cockroach symbiont and mitochondrial genomes

2019 ◽  
Author(s):  
Daej A. Arab ◽  
Thomas Bourguignon ◽  
Zongqing Wang ◽  
Simon Y. W. Ho ◽  
Nathan Lo
Keyword(s):  
Evolutionary Rates ◽  
Mitochondrial Genomes ◽  
Genome Data ◽  
Branch Lengths ◽  
Species Pairs ◽  
Molecular Evolutionary Rates ◽  
Bacterial Endosymbionts ◽  
Multiple Strains ◽  
Selection Factors ◽  
Host Evolution

AbstractBacterial endosymbionts evolve under strong host-driven selection. Factors influencing host evolution might affect symbionts in similar ways, potentially leading to correlations between the molecular evolutionary rates of hosts and symbionts. Although there is evidence of rate correlations between mitochondrial and nuclear genes, similar investigations of hosts and symbionts are lacking. Here we demonstrate a correlation in molecular rates between the genomes of an endosymbiont (Blattabacterium cuenoti) and the mitochondrial genomes of their hosts (cockroaches). We used partial genome data for multiple strains of B. cuenoti to compare phylogenetic relationships and evolutionary rates for 55 cockroach/symbiont pairs. The phylogenies inferred for B. cuenoti and the mitochondrial genomes of their hosts were largely congruent, as expected from their identical maternal and cytoplasmic mode of inheritance. We found a correlation between evolutionary rates of the two genomes, based on comparisons of root-to-tip distances and on comparisons of the branch lengths of phylogenetically independent species pairs. Our results underscore the profound effects that long-term symbiosis can have on the biology of each symbiotic partner.

scholarly journals Evolutionary rates are correlated between cockroach symbionts and mitochondrial genomes

2020 ◽  
Vol 16 (1) ◽  
pp. 20190702 ◽  
Author(s):  
Daej A. Arab ◽  
Thomas Bourguignon ◽  
Zongqing Wang ◽  
Simon Y. W. Ho ◽  
Nathan Lo
Keyword(s):  
Evolutionary Rates ◽  
Mitochondrial Genomes ◽  
Genome Data ◽  
Branch Lengths ◽  
Species Pairs ◽  
Molecular Evolutionary Rates ◽  
Bacterial Endosymbionts ◽  
Multiple Strains ◽  
Selection Factors ◽  
Host Evolution

Bacterial endosymbionts evolve under strong host-driven selection. Factors influencing host evolution might affect symbionts in similar ways, potentially leading to correlations between the molecular evolutionary rates of hosts and symbionts. Although there is evidence of rate correlations between mitochondrial and nuclear genes, similar investigations of hosts and symbionts are lacking. Here, we demonstrate a correlation in molecular rates between the genomes of an endosymbiont ( Blattabacterium cuenoti ) and the mitochondrial genomes of their hosts (cockroaches). We used partial genome data for multiple strains of B. cuenoti to compare phylogenetic relationships and evolutionary rates for 55 cockroach/symbiont pairs. The phylogenies inferred for B. cuenoti and the mitochondrial genomes of their hosts were largely congruent, as expected from their identical maternal and cytoplasmic mode of inheritance. We found a correlation between evolutionary rates of the two genomes, based on comparisons of root-to-tip distances and on comparisons of the branch lengths of phylogenetically independent species pairs. Our results underscore the profound effects that long-term symbiosis can have on the biology of each symbiotic partner.

scholarly journals Evolutionary rates are correlated between Buchnera endosymbionts and mitochondrial genomes of their aphid hosts

2020 ◽  
Author(s):  
Daej A. Arab ◽  
Nathan Lo
Keyword(s):  
Mitochondrial Genomes ◽  
Factors Affecting ◽  
Genome Data ◽  
Branch Lengths ◽  
Species Pairs ◽  
Bacterial Endosymbionts ◽  
Sap Feeding ◽  
Widespread Phenomenon ◽  
Multiple Strains ◽  
Selection Factors

AbstractThe evolution of bacterial endosymbiont genomes is strongly influenced by host-driven selection. Factors affecting host genome evolution will potentially affect endosymbiont genomes in similar ways. One potential outcome is correlations in molecular rates between the genomes of the symbiotic partners. Recently, we presented the first evidence of such a correlation between the mitochondrial genomes of cockroaches and the genome of their endosymbiont (Blattabacterium cuenoti). Here we investigate whether similar patterns are found in additional host-symbiont partners. We use partial genome data from multiple strains of bacterial endosymbionts, B. aphidicola and Sulcia mulleri, and the mitochondrial genomes of their sap-feeding insect hosts. Both endosymbionts show phylogenetic congruence with the mitochondria of their hosts, a result that is expected due to their identical mode of inheritance. We compared root-to-tip distances and branch lengths of phylogenetically independent species pairs. Both analyses show a highly significant correlation of molecular rates between genomes of Buchnera and mitochondrial genomes of their hosts. A similar correlation was detected between Sulcia and their hosts, but was not statistically significant. Our results indicate that evolutionary rate correlations between hosts and long-term symbionts may be a widespread phenomenon.

Numt identification and removal with RtN!

2020 ◽  
Vol 36 (20) ◽  
pp. 5115-5116 ◽  
Author(s):  
August E Woerner ◽  
Jennifer Churchill Cihlar ◽  
Utpal Smart ◽  
Bruce Budowle
Keyword(s):  
Mitochondrial Genome ◽  
Massively Parallel Sequencing ◽  
Sequence Similarity ◽  
Variant Calling ◽  
Supplementary Information ◽  
Mitochondrial Genomes ◽  
Sequencing Data ◽  
Read Mapping ◽  
Genome Data ◽  
Mitochondrial Sequences

Abstract Motivation Assays in mitochondrial genomics rely on accurate read mapping and variant calling. However, there are known and unknown nuclear paralogs that have fundamentally different genetic properties than that of the mitochondrial genome. Such paralogs complicate the interpretation of mitochondrial genome data and confound variant calling. Results Remove the Numts! (RtN!) was developed to categorize reads from massively parallel sequencing data not based on the expected properties and sequence identities of paralogous nuclear encoded mitochondrial sequences, but instead using sequence similarity to a large database of publicly available mitochondrial genomes. RtN! removes low-level sequencing noise and mitochondrial paralogs while not impacting variant calling, while competing methods were shown to remove true variants from mitochondrial mixtures. Availability and implementation https://github.com/Ahhgust/RtN Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Evolutionary rates of mitochondrial genomes correspond to diversification rates and to contemporary species richness in birds and reptiles

2010 ◽  
Vol 277 (1700) ◽  
pp. 3587-3592 ◽  
Author(s):  
Soo Hyung Eo ◽  
J. Andrew DeWoody
Keyword(s):  
Species Richness ◽  
Nuclear Data ◽  
Synonymous Substitution ◽  
Evolutionary Rates ◽  
Rate Variation ◽  
Substitution Rates ◽  
Diversification Rates ◽  
Extinction Process ◽  
Molecular Evolutionary Rates ◽  
Speciation Rates

Rates of biological diversification should ultimately correspond to rates of genome evolution. Recent studies have compared diversification rates with phylogenetic branch lengths, but incomplete phylogenies hamper such analyses for many taxa. Herein, we use pairwise comparisons of confamilial sauropsid (bird and reptile) mitochondrial DNA (mtDNA) genome sequences to estimate substitution rates. These molecular evolutionary rates are considered in light of the age and species richness of each taxonomic family, using a random-walk speciation–extinction process to estimate rates of diversification. We find the molecular clock ticks at disparate rates in different families and at different genes. For example, evolutionary rates are relatively fast in snakes and lizards, intermediate in crocodilians and slow in turtles and birds. There was also rate variation across genes, where non-synonymous substitution rates were fastest at ATP8 and slowest at CO 3. Family-by-gene interactions were significant, indicating that local clocks vary substantially among sauropsids. Most importantly, we find evidence that mitochondrial genome evolutionary rates are positively correlated with speciation rates and with contemporary species richness. Nuclear sequences are poorly represented among reptiles, but the correlation between rates of molecular evolution and species diversification also extends to 18 avian nuclear genes we tested. Thus, the nuclear data buttress our mtDNA findings.

Wing shape and environmental energy are associated with molecular evolutionary rates in a large avian radiation

2020 ◽  
Author(s):  
David Alejandro Duchêne ◽  
Paola Montoya ◽  
Carlos Daniel Cadena
Keyword(s):  
Uv Radiation ◽  
Positive Association ◽  
Evolutionary Rates ◽  
Wing Morphology ◽  
Geographic Ranges ◽  
Molecular Evolutionary Rates ◽  
Strong Positive Association ◽  
Genomic Regions ◽  
Avian Family

AbstractAmong the macroevolutionary drivers of molecular evolutionary rates, metabolic demands and environmental energy have been a central topic of discussion. The large number of studies examining these associations have found mixed results, and have rarely explored the interactions among various factors impacting molecular evolutionary rates. Taking the diverse avian family Furnariidae as a case study, we examined the association between several estimates of molecular evolutionary rates with a proxy of metabolic demands imposed by flight (wing morphology) and proxies of environmental energy across the geographic ranges of species (temperature and UV radiation). We found a strong positive association between molecular rates in genomic regions that can change the coded amino-acid with wing morphology, environmental temperature, and UV radiation. Strikingly, however, we did not find evidence of such associations with molecular rates at sites not impacting amino-acids. Our results suggest that the demands of flight and environmental energy primarily impact genome evolution by placing selective constraints, instead of being associated with basal mutation rates.

scholarly journals Divergence time of the two regional medaka populations in Japan as a new time scale for comparative genomics of vertebrates

2009 ◽  
Vol 5 (6) ◽  
pp. 812-816 ◽  
Author(s):  
Davin H. E. Setiamarga ◽  
Masaki Miya ◽  
Yusuke Yamanoue ◽  
Yoichiro Azuma ◽  
Jun G. Inoue ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Molecular Clock ◽  
Divergence Time ◽  
Evolutionary Rates ◽  
Implicit Assumption ◽  
Molecular Evolutionary Rates ◽  
Clock Analysis ◽  
The Japanese Archipelago ◽  
Two Populations ◽  
Rates Of Molecular Evolution

The southern and northern Japanese populations of the medaka fish provide useful tools to gain insights into the comparative genomics and speciation of vertebrates, because they can breed to produce healthy and fertile offspring despite their highly divergent genetic backgrounds compared with those of human–chimpanzee. Comparative genomics analysis has suggested that such large genetic differences between the two populations are caused by higher molecular evolutionary rates among the medakas than those of the hominids. The argument, however, was based on the assumption that the two Japanese populations diverged approximately at the same time (4.0–4.7 Myr ago) as the human–chimpanzee lineage (5.0–6.0 Myr ago). This can be misleading, because the divergence time of the two populations was calculated based on estimated, extremely higher molecular evolutionary rates of other fishes with an implicit assumption of a global molecular clock. Here we show that our estimate, based on a Bayesian relaxed molecular-clock analysis of whole mitogenome sequences from 72 ray-finned fishes (including 14 medakas), is about four times older than that of the previous study (18 Myr). This remarkably older estimate can be reconciled with the vicariant events of the Japanese archipelago, and the resulting rates of molecular evolution are almost identical between the medaka and hominid lineages. Our results further highlight the fact that reproductive isolation may not evolve despite a long period of geographical isolation.

scholarly journals Theoretical foundation of the RelTime method for estimating divergence times from variable evolutionary rates

2017 ◽  
Author(s):  
Koichiro Tamura ◽  
Qiqing Tao ◽  
Sudhir Kumar
Keyword(s):  
Relative Rate ◽  
Molecular Data ◽  
Evolutionary Rates ◽  
Divergence Times ◽  
Computationally Efficient ◽  
Molecular Sequence ◽  
Branch Lengths ◽  
Variable Evolutionary Rates ◽  
Relationship Of ◽  
The Relationship

AbstractRelTime estimates divergence times by relaxing the assumption of a strict molecular clock in a phylogeny. It showed excellent performance in estimating divergence times for both simulated and empirical molecular sequence datasets in which evolutionary rates varied extensively throughout the tree. RelTime is computationally efficient and scales well with increasing size of datasets. Until now, however, RelTime has not had a formal mathematical foundation. Here, we show that the basis of the RelTime approach is a relative rate framework (RRF) that combines comparisons of evolutionary rates in sister lineages with the principle of minimum rate change between an evolutionary lineage and its descendants. We present analytical solutions for estimating relative lineage rates and divergence times under RRF. We also discuss the relationship of RRF with other approaches, including the Bayesian framework. We conclude that RelTime will be also useful for phylogenies with branch lengths derived not only from molecular data, but also morphological and biochemical traits.

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