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Figure 2 in Cicada minimum age tree: Cryptic speciation and exponentially increasing base substitution rates in recent geologic time

Figure 2. Cicada timetree built by BEAST v1.X, applying 1,534 bp COI sequence. OUTs with isolate number: our own analyzed specimens shown in Table 1, and others: from GenBank/DDJB. In outgroup Hemiptera; #: analyzed family by Johnson et al. (2018); % analyzed family by Misof et al. (2014). Inserted figure: Base substitution rate (= rate median shown at each node; substitutions per site per million year; s/s/myr) vs age (= posterior age shown at each node) diagram. Red approximate curve with its formula was drawn by Excel function, with the intersection for the curve = 0.0128 s/s/myr, the rate median shown on Tracer.

Figure 4 in Cicada minimum age tree: Cryptic speciation and exponentially increasing base substitution rates in recent geologic time

Figure 4. Number of base changes of transition and tansversion vs corrected pairwide distance diagram for whole mitochondrial gene.

Figure 1 in Cicada minimum age tree: Cryptic speciation and exponentially increasing base substitution rates in recent geologic time

Figure 1. Simplified cicada timetree built by BEAST v1.X, applying a 1,534 bp in maximum COI sequence. Inserted figure: Base substitution rate (= ratemedian shown at each node; substitutions per siteper millionyear; s/s/ myr) vsage (= posterior age shown at each node) diagram. Red approximate curve with its formula was drawn by an Excel function, with the intersection for the curve = 0.0128 s/s/myr, the rate median shown on Tracer.

Figure 3 in Cicada minimum age tree: Cryptic speciation and exponentially increasing base substitution rates in recent geologic time

Figure 3. Cicada timetree built by BEAST v1.X, applying 1,534 bp COI and 874 bp 18S rRNA sequences. OUTswith isolate number: our own analyzed specimens shown in Table 1, and others: from GenBank/DDJB. In outgroup Hemiptera; #: analyzed family by Johnson et al. (2018); % analyzed family by Misof et al. (2014). Inserted figure: Base substitution rate (= rate median shown at each node; substitutions per site per million year; s/s/myr) vs age (= posterior age shown at each node) diagram. Red approximatecurve with its formulawas drawn by Excel function, with the intersection for the curve = 0.0114 s/s/myr, the rate median shown on Tracer. Note that this rate is a little slower than thatsolely of COI in Figures 1 and 2, reflecting slowerrate of 18S rRNAthan COI (see Osozawa et al. 2017a).

opencc-zeroJan 2024View details →

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Main model fits and substitution rate predictions for: A quantitative genetic model of background selection in humans

Across the human genome, there are large-scale fluctuations in genetic diversity caused by the indirect effects of selection. This can be thought of as a "linked selection signal" that reflects the impact of selection varying according to the placement of functional regions and recombination rates along the genome. Previous work has shown that negative selection against the steady influx of new deleterious mutations into conserved regions is the predominant mode of selection in humans. However, the theoretic model that underpins these results, classic Background Selection theory, is only applicable when new mutations are so deleterious that they cannot fix in the population. Here, we develop a statistical method based on a quantitative genetics view of the linked selection, which models the effects of weak draft created according to how polygenic additive fitness variance is distributed along the genome. We use a recent model that jointly predicts the equilibrium fitness variance and substitution rates due to both strong and weakly deleterious mutations, we estimate the distribution of fitness effects (DFE) and mutation rate across three human populations. While our model can accommodate weaker selection, we initially find evidence across three human populations of very strong selection against deleterious mutations consistent with previous work. However, the corollary predicted substitution rates for conserved regions are unreasonably low, and in disagreement with observed rates. We hypothesize this could be due to selected sites experiencing a further diminished population size due to selective interference. When we account for this in our method, we find evidence of weakly deleterious mutations in conserved regions which brings the predicted substitution rate into agreement with observations. However, these models lead to implausibly large mutation rate estimates. Overall, while our model of the genomic linked selection signal brings us a step towards uniting population and quantitative genetic selection models with the substitution process, our work suggests considerable uncertainty remains about the processes generating fitness variance in humans.

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Main model fits and substitution rate predictions for: A quantitative genetic model of background selection in humans

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publicJan 2024View details →

opencc-zeroAug 2021View details →

Correlates of substitution rate variation in a robust Procellariiform seabird phylogeny

Molecular substitution rates vary among branches and can lead to inaccurate reconstructions of evolutionary relationships and obscure the true phylogeny of affected clades. Body mass is often assumed to have a major influence on substitution rate, though other factors such as population size, life history traits, and flight demands are also thought to have an influence. Birds of the order Procellariiformes—which encompasses petrels, storm-petrels and albatrosses—show a striking 900-fold difference in body mass between the smallest and largest members, divergent life history traits, and substantial heterogeneity in mitochondrial substitution rates. Here, we used genome-scale nuclear DNA sequence data from 4365 ultraconserved element loci (UCEs) in 51 procellariiform species to examine whether phylogenetic reconstruction using genome-wide datasets is robust to the presence of rate heterogeneity, and to identify predictors of substitution rate variation. Our results provide a backbone phylogeny for procellariiform seabirds and resolves several controversies about the evolutionary history of the order, demonstrating that albatrosses are basal, storm-petrels are paraphyletic and diving petrels nestled within the Procellariidae. We find evidence of rate variation; however, all phylogenetic analyses using both concatenation and multispecies coalescent approaches recovered the same branching topology, including analyses implementing different clock models, and analyses of the most and least clock-like loci. Overall, we find that rate heterogeneity is little impacted by body mass and age at first breeding, but moderately impacted by longevity and hand-wing index, a proxy for wing shape and flight efficiency. Our results indicate that substitution rate may be the product of interactions among many, potentially taxon-specific, variables.

opencc-zeroJul 2023View details →

Data for dating in the dark: Elevated substitution rates in cave cockroaches (Blattodea: Nocticolidae) have negative impacts on molecular date estimates

Rates of nucleotide substitution vary substantially across the Tree of Life, with potentially confounding effects on phylogenetic and evolutionary analyses. A large acceleration in mitochondrial substitution rate occurs in the cockroach family Nocticolidae, which predominantly inhabit subterranean environments. To evaluate the impacts of this among-lineage rate heterogeneity on estimates of phylogenetic relationships and evolutionary timescales, we analysed nuclear ultraconserved elements (UCEs) and mitochondrial genomes from nocticolids and other cockroaches. Substitution rates were substantially elevated in nocticolid lineages compared with other cockroaches, especially in mitochondrial protein-coding genes. This disparity in evolutionary rates is likely to have led to different evolutionary relationships being supported by mitochondrial genomes and UCE loci. Furthermore, analyses using relaxed-clock models inferred much deeper divergence times compared with a flexible local clock. Our phylogenetic analysis of UCEs, which is the first genome-scale study to include all nine major cockroach families, unites Corydiidae and Nocticolidae and places Anaplectidae as the sister lineage to the rest of Blattoidea. We uncover an extraordinary level of genetic divergence in Nocticolidae, including two highly distinct clades that separated ~115 million years ago despite both containing representatives of the genus Nocticola. The results of our study highlight the potential impacts of high among-lineage rate variation on estimates of phylogenetic relationships and evolutionary timescales.

publicDec 2023View details →

Data for dating in the dark: Elevated substitution rates in cave cockroaches (Blattodea: Nocticolidae) have negative impacts on molecular date estimates

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publicMar 2022View details →

Correlates of substitution rate variation in a robust Procellariiform seabird phylogeny

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publicJun 2021View details →

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

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opencc-zeroDec 2016View details →

Data from: The complex effects of demographic history on the estimation of substitution rate: concatenated gene analysis results in no more than twofold overestimation

Our recent estimation of the divergence time and isolation of Death Valley pupfishes, including the iconic Devil's Hole pupfish (DHP), rewrote widespread assumptions about this group. These species were previously assumed to be relic populations isolated over millions of years; our genomic analyses indicated recent colonization of Devil's Hole within the past 105–830 years and frequent gene flow among Death Valley populations [1]. These results understandably attracted substantial attention given the iconic battle for conservation and intense management of DHP [2]; nonetheless, a young age for this species should not diminish its conservation value. Indeed, we argue that the unique natural history of this species makes it a prime candidate for exhibiting one of the fastest mutation rates observed in any vertebrate [3].

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Life history traits impact the nuclear rate of substitution but not the mitochondrial rate in isopods.

Alignements from the paper "Life history traits impact the nuclear rate of substitution but not the mitochondrial rate in isopods" submitted to Molecular Biology and Evolution.File "concatenation_382NuclearGenes.fas" corresponds to the concatenation of 382 nuclear genes for 26 Isopod species. File "concatenation_12MtGenes.fas" corresponds to the concatenation of 12 mitochondrial protein coding genes (cytb, cox1, cox2, cox3, atp6, nad1, nad2, nad3, nad4, nad4l, nad5, nad6 ). Genes were aligned with PRANK (Löytynoja and Goldman, 2008) and sites ambiguously aligned were removed with Gblocks (Castresana, 2000). File "Opsine1_cds.fas" corresponds to the alignement of the coding part of the Opsin 1 gene for 26 Isopod species. Intron has been removed as well as non-sens mutations. 26 Mitochondrial genomes: we reconstructed mitochondrial genomes using both the de novo transcriptome assemblies from Francois et al. (2016) and low coverage genome sequencing reads available for 22 species from Lef ebure et al. (2017). Since mitochondrial genomes are present in multiple copies per cell, a very low sequencing effort is sufficient to yield a high coverage for mitochondrial sequences. Using the DNA-seq reads, mitogenomes were assembled with MITObim (Hahn et al. 2013) using the COI gene as a seed to build the complete mitogenome. All annotated genome have been deposited in the ENA project PRJEB14193.

opencc-by-4.0Sep 2018View details →

opencc-zeroNov 2021View details →

Nucleotide substitutions during speciation may explain substitution rate variation

Although molecular mechanisms associated with the generation of mutations are highly conserved across taxa, there is widespread variation in mutation rates between evolutionary lineages. When phylogenies are reconstructed based on nucleotide sequences, such variation is typically accounted for by the assumption of a relaxed molecular clock, which is just a statistical distribution of mutation rates without much underlying biological mechanism. Here, we propose that variation in accumulated mutations may be partly explained by an elevated mutation rate during speciation. Using simulations, we show how shifting mutations from branches to speciation events impacts inference of branching times in phylogenetic reconstruction. Furthermore, the resulting nucleotide alignments are better described by a relaxed than by a strict molecular clock. Thus, elevated mutation rates during speciation potentially explain part of the variation in substitution rates that is observed across the tree of life.

opencc-zeroApr 2022View details →

Parthenogenesis doubles the rate of amino acid substitution in Whiptail mitochondria

Sexual reproduction is ubiquitous in the natural world, suggesting that sex must have extensive benefits to overcome the cost of males compared to asexual reproduction. One hypothesized advantage of sex with strong theoretical support is that sex plays a role in removing deleterious mutations from the genome. Theory predicts that transitions to asexuality should lead to the suppression of recombination and segregation and, in turn, weakened natural selection, allowing for the accumulation of slightly deleterious mutations. We tested this prediction by estimating the dN/dS ratios in asexual vertebrate lineages in the genus Aspidoscelis using whole mitochondrial genomes from seven asexual and five sexual species. We found higher dN/dS ratios in asexual Aspidoscelis species, indicating that asexual whiptails accumulate non-synonymous substitutions due to weaker purifying selection. Additionally, we estimated nucleotide diversity and found that asexuals harbor significantly less diversity. Thus, despite their recent origins, slightly deleterious mutations accumulated rapidly enough in asexual lineages to be detected. We provided empirical evidence to corroborate the connection between asexuality and increased amino acid substitutions in asexual vertebrate lineages.

opencc-zeroJun 2022View details →

Genome-structural analyses support an allotetraploid origin of the walnut family from within Myricaceae and shared genome duplications reveal substitution rate variation

In lineages of allopolyploid origin, entire parental subgenomes may coexist, with two or more sets of homoeologous chromosomes that differ in gene content and syntenic structure. Presence or absence of genes, and microsynteny along chromosomal blocks, can be used to differentiate subgenomes and can be coded as phylogenetic data. We assembled chromosome-level genomes of representative species across an ancient allopolyploid lineage, the walnut family (Juglandaceae), with Myrica and other Fagales as outgroups, and used genome-structural data to infer a phylogeny. Microsynteny (with various collinear block sizes) and gene content analyses, using the dominant or recessive progenitor subgenomes or both, all yielded identical topologies that place Engelhardia (a SE Asian and Central American clade) with Platycarya, an enigmatic monospecific taxon endemic in East Asia, but well-represented in the Paleocene-Eocene of North America and Europe. Morphological studies including fossils also found the Platycarya/Engelhardia clade because of leaf architecture, floral morphology, and nut walls without lacunae, but DNA-alignment-based phylogenetics carried out here and in previous studies never detected this uniformly wind-dispersed clade, instead grouping Platycarya with Carya and Juglans. The novel analyses further reveal the family's hybrid origin from extinct or unsampled progenitors nested within Myricaceae and that Rhoiptelea chiliantha, the Chinese sister species to all other Juglandaceae, contains proportionally more genes related to DNA repair and evolved at a rate 2.6- to 3.5-times slower than the remaining species. Our results have implications for the molecular clock hypothesis and suggest that genomic structure contains so-far undervalued phylogenetic signal.

publicApr 2022View details →

Parthenogenesis doubles the rate of amino acid substitution in Whiptail mitochondria

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publicJul 2017View details →

Data from: The complex effects of demographic history on the estimation of substitution rate: concatenated gene analysis results in no more than twofold overestimation

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publicJun 2022View details →

Genome-structural analyses support an allotetraploid origin of the walnut family from within Myricaceae and shared genome duplications reveal substitution rate variation

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