scholarly journals Base-substitution mutation rate across the nuclear genome of Alpheus snapping shrimp and the timing of isolation by the Isthmus of Panama

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Katherine Silliman ◽  
Jane L. Indorf ◽  
Nancy Knowlton ◽  
William E. Browne ◽  
Carla Hurt
Keyword(s):  
Gene Flow ◽  
Mutation Rate ◽  
Substitution Rate ◽  
Nuclear Genome ◽  
Mutation Rates ◽  
Parameter Estimates ◽  
Reduced Representation ◽  
Snapping Shrimp ◽  
Isthmus Of Panama ◽  
Species Pairs

Abstract Background The formation of the Isthmus of Panama and final closure of the Central American Seaway (CAS) provides an independent calibration point for examining the rate of DNA substitutions. This vicariant event has been widely used to estimate the substitution rate across mitochondrial genomes and to date evolutionary events in other taxonomic groups. Nuclear sequence data is increasingly being used to complement mitochondrial datasets for phylogenetic and evolutionary investigations; these studies would benefit from information regarding the rate and pattern of DNA substitutions derived from the nuclear genome. Results To estimate the genome-wide neutral mutation rate (µ), genotype-by-sequencing (GBS) datasets were generated for three transisthmian species pairs in Alpheus snapping shrimp. A range of bioinformatic filtering parameters were evaluated in order to minimize potential bias in mutation rate estimates that may result from SNP filtering. Using a Bayesian coalescent approach (G-PhoCS) applied to 44,960 GBS loci, we estimated µ to be 2.64E−9 substitutions/site/year, when calibrated with the closure of the CAS at 3 Ma. Post-divergence gene flow was detected in one species pair. Failure to account for this post-split migration inflates our substitution rate estimates, emphasizing the importance of demographic methods that can accommodate gene flow. Conclusions Results from our study, both parameter estimates and bioinformatic explorations, have broad-ranging implications for phylogeographic studies in other non-model taxa using reduced representation datasets. Our best estimate of µ that accounts for coalescent and demographic processes is remarkably similar to experimentally derived mutation rates in model arthropod systems. These results contradicted recent suggestions that the closure of the Isthmus was completed much earlier (around 10 Ma), as mutation rates based on an early calibration resulted in uncharacteristically low genomic mutation rates. Also, stricter filtering parameters resulted in biased datasets that generated lower mutation rate estimates and influenced demographic parameters, serving as a cautionary tale for the adherence to conservative bioinformatic strategies when generating reduced-representation datasets at the species level. To our knowledge this is the first use of transisthmian species pairs to calibrate the rate of molecular evolution from GBS data.

scholarly journals Base-substitution mutation rate across the nuclear genome of Alpheus snapping shrimp and the timing of isolation by the Isthmus of Panama

2020 ◽  
Author(s):  
Katherine Silliman ◽  
Jane L. Indorf ◽  
Nancy Knowlton ◽  
William E. Browne ◽  
Carla Hurt
Keyword(s):  
Mutation Rate ◽  
Sequence Data ◽  
Nuclear Genome ◽  
Base Substitution ◽  
Snapping Shrimp ◽  
Isthmus Of Panama ◽  
Species Pairs ◽  
Genotype By Sequencing ◽  
Independent Calibration ◽  
Taxonomic Groups

AbstractThe formation of the Isthmus of Panama and final closure of the Central American Seaway (CAS) provides an independent calibration point for examining the rate of DNA substitutions. This vicariant event has been widely used to estimate the substitution rate across mitochondrial genomes and to date evolutionary events in other taxonomic groups. Nuclear sequence data is increasingly being used to complement mitochondrial datasets for phylogenetic and evolutionary investigations; these studies would benefit from information regarding the rate and pattern of DNA substitutions derived from the nuclear genome. To estimate this genomewide neutral mutation rate (μ), genotype-by-sequencing (GBS) datasets were generated for three transisthmian species pairs in Alpheus snapping shrimp. Using a Bayesian coalescent approach (G-PhoCS) applied to 44,960 GBS loci, we estimated μ to be 2.64E-9 substitutions/site/year, when calibrated with the closure of the CAS at 3 Ma. This estimate is remarkably similar to experimentally derived mutation rates in model arthropod systems, strengthening the argument for a recent closure of the CAS. To our knowledge this is the first use of transisthmian species pairs to calibrate the rate of molecular evolution from GBS data.

scholarly journals Single-sperm sequencing reveals the accelerated mitochondrial mutation rate in male Daphnia pulex (Crustacea, Cladocera)

2017 ◽  
Vol 284 (1863) ◽  
pp. 20171548 ◽  
Author(s):  
Sen Xu ◽  
Kenny Van Tran ◽  
Swatantra Neupane ◽  
Marelize Snyman ◽  
Trung Viet Huynh ◽  
...  
Keyword(s):  
Mutation Rate ◽  
Daphnia Pulex ◽  
Nuclear Genome ◽  
Mutation Rates ◽  
Mtdna Mutation ◽  
Mitochondrial Mutation ◽  
Mtdna Mutations ◽  
Cell Divisions ◽  
Female Rate ◽  
Dna Replication Errors

Mutation rate in the nuclear genome differs between sexes, with males contributing more mutations than females to their offspring. The male-biased mutation rates in the nuclear genome is most likely to be driven by a higher number of cell divisions in spermatogenesis than in oogenesis, generating more opportunities for DNA replication errors. However, it remains unknown whether male-biased mutation rates are present in mitochondrial DNA (mtDNA). Although mtDNA is maternally inherited and male mtDNA mutation typically does not contribute to genetic variation in offspring, male mtDNA mutations are critical for male reproductive health. In this study, we measured male mtDNA mutation rate using publicly available whole-genome sequences of single sperm of the freshwater microcrustacean Daphnia pulex . Using a stringent mutation detection pipeline, we found that the male mtDNA mutation rate is 3.32 × 10 −6 per site per generation. All the detected mutations are heteroplasmic base substitutions, with 57% of mutations converting G/C to A/T nucleotides. Consistent with the male-biased mutation in the nuclear genome, the male mtDNA mutation rate in D. pulex is approximately 20 times higher than the female rate per generation. We propose that the elevated mutation rate per generation in male mtDNA is consistent with an increased number of cell divisions during male gametogenesis.

scholarly journals Likelihood-Based Estimation of Microsatellite Mutation Rates

Genetics ◽  
2003 ◽  
Vol 164 (2) ◽  
pp. 781-787 ◽  
Author(s):  
John C Whittaker ◽  
Roger M Harbord ◽  
Nicola Boxall ◽  
Ian Mackay ◽  
Gary Dawson ◽  
...  
Keyword(s):  
Mutation Rate ◽  
Mutation Rates ◽  
Parameter Estimates ◽  
Step Size ◽  
Exponential Relationship ◽  
Length Increase ◽  
Microsatellite Evolution ◽  
Competing Models ◽  
Allele Length ◽  
Microsatellite Mutation

Abstract Microsatellites are widely used in genetic analyses, many of which require reliable estimates of microsatellite mutation rates, yet the factors determining mutation rates are uncertain. The most straightforward and conclusive method by which to study mutation is direct observation of allele transmissions in parent-child pairs, and studies of this type suggest a positive, possibly exponential, relationship between mutation rate and allele size, together with a bias toward length increase. Except for microsatellites on the Y chromosome, however, previous analyses have not made full use of available data and may have introduced bias: mutations have been identified only where child genotypes could not be generated by transmission from parents' genotypes, so that the probability that a mutation is detected depends on the distribution of allele lengths and varies with allele length. We introduce a likelihood-based approach that has two key advantages over existing methods. First, we can make formal comparisons between competing models of microsatellite evolution; second, we obtain asymptotically unbiased and efficient parameter estimates. Application to data composed of 118,866 parent-offspring transmissions of AC microsatellites supports the hypothesis that mutation rate increases exponentially with microsatellite length, with a suggestion that contractions become more likely than expansions as length increases. This would lead to a stationary distribution for allele length maintained by mutational balance. There is no evidence that contractions and expansions differ in their step size distributions.

scholarly journals Evaluating the role of contracting and expanding rainforest in initiating cycles of speciation across the Isthmus of Panama

2012 ◽  
Vol 279 (1742) ◽  
pp. 3520-3526 ◽  
Author(s):  
Brian Tilston Smith ◽  
Amei Amei ◽  
John Klicka
Keyword(s):  
Bird Species ◽  
Tropical Regions ◽  
Isthmus Of Panama ◽  
Species Pairs ◽  
The Matrix ◽  
High Species Richness ◽  
The Rich ◽  
The Tropics ◽  
The Impact

Climatic and geological changes across time are presumed to have shaped the rich biodiversity of tropical regions. However, the impact climatic drying and subsequent tropical rainforest contraction had on speciation has been controversial because of inconsistent palaeoecological and genetic data. Despite the strong interest in examining the role of climatic change on speciation in the Neotropics there has been few comparative studies, particularly, those that include non-rainforest taxa. We used bird species that inhabit humid or dry habitats that dispersed across the Panamanian Isthmus to characterize temporal and spatial patterns of speciation across this barrier. Here, we show that these two assemblages of birds exhibit temporally different speciation time patterns that supports multiple cycles of speciation. Evidence for these cycles is further corroborated by the finding that both assemblages consist of ‘young’ and ‘old’ species, despite dry habitat species pairs being geographically more distant than pairs of humid habitat species. The matrix of humid and dry habitats in the tropics not only allows for the maintenance of high species richness, but additionally this study suggests that these environments may have promoted speciation. We conclude that differentially expanding and contracting distributions of dry and humid habitats was probably an important contributor to speciation in the tropics.

Patterns of morphological diversity among and within arcid bivalve species pairs separated by the Isthmus of Panama

2001 ◽  
Vol 75 (3) ◽  
pp. 590-606 ◽  
Author(s):  
Peter B. Marko ◽  
Jeremy B. C. Jackson
Keyword(s):  
Morphological Variation ◽  
Fossil Record ◽  
Eastern Pacific ◽  
Nominal Species ◽  
Western Atlantic ◽  
Isthmus Of Panama ◽  
Species Pairs ◽  
Recent Species ◽  
Discriminant Analyses ◽  
Collection Sites

Geminate species are morphologically similar sister-species found on either side of the Isthmus of Panama. The existence of all geminates in the tropical Eastern Pacific ocean and the Caribbean Sea is most often explained by vicariance: closure of the Central American Seaway 3.1 to 3.5 Ma simultaneously isolated populations of species with amphi-American distributions. In this paper, we test the potential of morphological measurements for discriminating between Recent geminate species pairs from three genera (Arca, Arcopsis, and Barbatia) in the bivalve family Arcidae and examine the prospects for distinguishing nominal species in the fossil record. Fourteen morphological variables were used to characterize shell shape and multivariate methods were used to discriminate between five Recent species pairs. Collection sites were also used as a priori groups for discrimination to describe patterns of intraspecific morphological variation and to evaluate differences among samples from different geographic regions.On average, 84 percent of specimens within geminate pairs are classified correctly following five separate discriminant analyses with nominal species as the grouping variable. Although all but one arcid species pair are discriminated with high statistical significance, some collection sites within species are highly morphologically distinct. Overall, a large proportion of specimens from each collection locality (79 percent on average) can be classified correctly to site although no single site possessed a multivariate centroid that was significantly different from all other conspecific centroids. The distinctiveness of some collection sites, however, raises the possibility that some nominal species may harbor cryptic species, indicating the need for wider geographic surveys of both molecular and morphological variation within geminate species pairs.The eigenvalue coefficients derived from the Recent samples of one geminate pair (Arca mutabilis and A. imbricata) were used to assess the potential for identifying arcid species in the fossil record. Discriminant analyses of fossil Arca indicate that the forms that characterize Recent A. mutabilis and A. imbricata are present in the fossil record as far back as the Late Early Miocene, in the Cantaure Formation of Venezuela. Because a deep water connection between the Eastern Pacific and Western Atlantic existed until the Middle Miocene, the morphological differences associated with Recent A. mutabilis and A. imbricata likely existed well before the rising Isthmus affected ocean circulation patterns in tropical America. Therefore, despite great overall morphological similarity, these putative geminate species likely have a time of divergence that is at least four times older than final seaway closure. The geographic distribution of fossils also suggests that morphological forms associated with each Recent species had amphi-American distributions both before and after isthmus formation but are now geographically restricted to either side of the isthmus in the Recent fauna.

scholarly journals Mutation rate analysis via parent–progeny sequencing of the perennial peach. II. No evidence for recombination-associated mutation

2016 ◽  
Vol 283 (1841) ◽  
pp. 20161785 ◽  
Author(s):  
Long Wang ◽  
Yanchun Zhang ◽  
Chao Qin ◽  
Dacheng Tian ◽  
Sihai Yang ◽  
...  
Keyword(s):  
Mutation Rate ◽  
Recombination Rate ◽  
Mutation Rates ◽  
Recombination Rates ◽  
Rate Analysis ◽  
A Genome ◽  
Break Points ◽  
New Mutations

Mutation rates and recombination rates vary between species and between regions within a genome. What are the determinants of these forms of variation? Prior evidence has suggested that the recombination might be mutagenic with an excess of new mutations in the vicinity of recombination break points. As it is conjectured that domesticated taxa have higher recombination rates than wild ones, we expect domesticated taxa to have raised mutation rates. Here, we use parent–offspring sequencing in domesticated and wild peach to ask (i) whether recombination is mutagenic, and (ii) whether domesticated peach has a higher recombination rate than wild peach. We find no evidence that domesticated peach has an increased recombination rate, nor an increased mutation rate near recombination events. If recombination is mutagenic in this taxa, the effect is too weak to be detected by our analysis. While an absence of recombination-associated mutation might explain an absence of a recombination–heterozygozity correlation in peach, we caution against such an interpretation.

Evolution of mutation rate and virulence among human retroviruses

1994 ◽  
Vol 346 (1317) ◽  
pp. 333-343 ◽  
Keyword(s):  
Immune System ◽  
Mutation Rate ◽  
Hiv Infections ◽  
Molecular Data ◽  
Mutation Rates ◽  
Rapid Progression ◽  
Human T Cell ◽  
Large Numbers ◽  
The Individual ◽  
Multicellular Organisms

High mutation rates are generally considered to be detrimental to the fitness of multicellular organisms because mutations untune finely tuned biological machinery. However, high mutation rates may be favoured by a need to evade an immune system that has been strongly stimulated to recognize those variants that reproduced earlier during the infection, hiv infections conform to this situation because they are characterized by large numbers of viruses that are continually breaking latency and large numbers that are actively replicating throughout a long period of infection. To be transmitted, HIVS are thus generally exposed to an immune system that has been activated to destroy them in response to prior viral replication in the individual. Increases in sexual contact should contribute to this predicament by favouring evolution toward relatively high rates of replication early during infection. Because rapid replication and high mutation rate probably contribute to rapid progression of infections to aids, the interplay of sexual activity, replication rate, and mutation rate helps explain why HIV-1 has only recently caused a lethal pandemic, even though molecular data suggest that it may have been present in humans for more than a century. This interplay also offers an explanation for geographic differences in progression to cancer found among infections due to the other major group of human retroviruses, human T-cell lymphotropic viruses (HTLV). Finally, it suggests ways in which we can use natural selection as a tool to control the aids pandemic and prevent similar pandemics from arising in the future.

scholarly journals Transfer RNA genes experience exceptionally elevated mutation rates

2018 ◽  
Vol 115 (36) ◽  
pp. 8996-9001 ◽  
Author(s):  
Bryan P. Thornlow ◽  
Josh Hough ◽  
Jacquelyn M. Roger ◽  
Henry Gong ◽  
Todd M. Lowe ◽  
...  
Keyword(s):  
Mutation Rate ◽  
Trna Gene ◽  
Gene Evolution ◽  
Purifying Selection ◽  
Mutation Rates ◽  
Model Organisms ◽  
Biological Synthesis ◽  
Human Populations ◽  
Trna Genes ◽  
Simple Method

Transfer RNAs (tRNAs) are a central component for the biological synthesis of proteins, and they are among the most highly conserved and frequently transcribed genes in all living things. Despite their clear significance for fundamental cellular processes, the forces governing tRNA evolution are poorly understood. We present evidence that transcription-associated mutagenesis and strong purifying selection are key determinants of patterns of sequence variation within and surrounding tRNA genes in humans and diverse model organisms. Remarkably, the mutation rate at broadly expressed cytosolic tRNA loci is likely between 7 and 10 times greater than the nuclear genome average. Furthermore, evolutionary analyses provide strong evidence that tRNA genes, but not their flanking sequences, experience strong purifying selection acting against this elevated mutation rate. We also find a strong correlation between tRNA expression levels and the mutation rates in their immediate flanking regions, suggesting a simple method for estimating individual tRNA gene activity. Collectively, this study illuminates the extreme competing forces in tRNA gene evolution and indicates that mutations at tRNA loci contribute disproportionately to mutational load and have unexplored fitness consequences in human populations.

Y-chromosomal microsatellite mutation rates: Differences in mutation rate between and within loci

2004 ◽  
Vol 23 (2) ◽  
pp. 117-124 ◽  
Author(s):  
B. Myhre Dupuy ◽  
M. Stenersen ◽  
T. Egeland ◽  
B. Olaisen
Keyword(s):  
Mutation Rate ◽  
Mutation Rates ◽  
Microsatellite Mutation

scholarly journals Direct estimate of the spontaneous mutation rate uncovers the effects of drift and recombination in theChlamydomonas reinhardtiiplastid genome

2015 ◽  
Author(s):  
Rob W Ness ◽  
Susanne A Kraemer ◽  
Nick Colegrave ◽  
Peter D Keightley
Keyword(s):  
Mutation Rate ◽  
Genetic Drift ◽  
Plastid Genome ◽  
De Novo ◽  
Spontaneous Mutation ◽  
Genome Structure ◽  
Nuclear Genome ◽  
De Novo Mutation ◽  
Direct Estimate ◽  
Plastid Genomes

Plastids perform crucial cellular functions, including photosynthesis, across a wide variety of eukaryotes. Since endosymbiosis, plastids have maintained independent genomes that now display a wide diversity of gene content, genome structure, gene regulation mechanisms, and transmission modes. The evolution of plastid genomes depends on an input ofde novomutation, but our knowledge of mutation in the plastid is limited to indirect inference from patterns of DNA divergence between species. Here, we use a mutation accumulation experiment, where selection acting on mutations is rendered ineffective, combined with whole-plastid genome sequencing to directly characterize de novo mutation inChlamydomonas reinhardtii. We show that the mutation rates of the plastid and nuclear genomes are similar, but that the base spectra of mutations differ significantly. We integrate our measure of the mutation rate with a population genomic dataset of 20 individuals, and show that the plastid genome is subject to substantially stronger genetic drift than the nuclear genome. We also show that high levels of linkage disequilibrium in the plastid genome are not due to restricted recombination, but are instead a consequence of increased genetic drift. One likely explanation for increased drift in the plastid genome is that there are stronger effects of genetic hitchhiking. The presence of recombination in the plastid is consistent with laboratory studies inC. reinhardtiiand demonstrates that although the plastid genome is thought to be uniparentally inherited, it recombines in nature at a rate similar to the nuclear genome.

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