Biology subjects

Michael Lynch

Publications and source records attributed to Michael Lynch.

5 recordsLinked to original sources

bioRxiv2016

Genome-wide biases in the rate and molecular spectrum of spontaneous mutations in Vibrio cholerae and Vibrio fischeri

The vast diversity in nucleotide composition and architecture among bacterial genomes may be partly explained by inherent biases in the rates and spectra of spontaneous mutations. Bacterial genomes with multiple chromosomes are relatively unusual but some are relevant to human health, none more so than the causative agent of cholera, Vibrio cholerae. Here, we present the genome-wide mutation spectra in wild-type and mismatch repair (MMR) defective backgrounds of two Vibrio species, the low-GC% squid symbiont V. fischeri and the pathogen V. cholerae, collected under conditions that greatly minimize the efficiency of natural selection. In apparent contrast to their high diversity in nature, both wild-type V. fischeri and V. cholerae have among the lowest rates for base-substitution mutations (bpsms) and insertion-deletion mutations (indels) that have been measured, below 10-3/genome/generation. V. fischeri and V. cholerae have distinct mutation spectra, but both are AT-biased and produce a surprising number of multi-nucleotide indels. Furthermore, the loss of a functional MMR system caused the mutation spectra of these species to converge, implying that the MMR system itself contributes to species-specific mutation patterns. Bpsm and indel rates varied among genome regions, but do not explain the more rapid evolutionary rates of genes on chromosome 2, which likely result from weaker purifying selection. More generally, the very low mutation rates of Vibrio species correlate inversely with their immense population sizes and suggest that selection may not only have maximized replication fidelity but also optimized other polygenic traits relative to the constraints of genetic drift.

Genetics↗

bioRxiv2016

Promoter architecture and sex-specific gene expression in the microcrustacean Daphnia pulex revealed by large-scale profiling of 5′-mRNA ends

Large-scale identification of transcription start sites (TSSs) using Cap Analysis of Gene Expression (CAGE) has yielded insight into promoter location, architecture, and regulation for a small set of taxa representing major model organisms, including human. However, comparative and evolutionary genomics studies of cis-regulatory control of transcription initiation for a wider spectrum of Metazoa are still outstanding. To broaden our understanding of core promoter structure in species from metazoan clades with currently scant genome data, we sought to characterize the landscape of cis-regulatory elements in the microcrustacean water flea Daphnia pulex, an important model organism for studies in ecology, toxicology, and genetics. We performed CAGE from total RNA derived from three states: sexual females, asexual females, and males, reflecting distinct sexes and modes of reproduction. We mapped over 120 million CAGE reads to the D. pulex genome and generated a Daphnia promoter atlas containing 12,662 unique promoters. Characterization of the transcription initiation sites showed the expected enrichment of the CA-dinucleotide at TSSs [-1,1] (associated with Initiator-motif containing promoters) but also significant over-representation of GN-dinucleotides. Overall, these data suggest that D. pulex initiation sites are among the most GC-rich yet observed in metazoans. Computational de novo motif discovery around CAGE-identified TSSs revealed eight putative core promoter elements, including the canonical TATA (TATAWAA) and Initiator (CAGWY) motifs, as well as statistically significant motifs with no obvious orthologs in other metazoans. Analysis of the differentially-expressed genes suggests that a considerable number of cell cycle genes (each with net negative regulatory effects on meiosis) are upregulated in asexual females, providing a glimpse of the molecular events that underpin the cyclical parthenogenesis in D. pulex. Taken together, this work provides the first picture of transcription initiation and promoter architecture within Crustacea. The Daphnia promoter atlas we present here provides a basis for future study among Daphnia spp. as well as for comparative genomic analyses of metazoan transcriptional control.

Genomics↗

bioRxiv2016

Estimating seven coefficients of pairwise relatedness using population genomic data

Population structure can be described by genotypic correlation coefficients between groups of individuals, the most basic of which are the pair-wise relatedness coefficients between any two individuals. There are nine pair-wise relatedness coefficients in the most general model, and we show that these can be reduced to seven coefficients for biallelic loci. Although all nine coefficients can be estimated from pedigrees, six coefficients have been beyond empirical reach. We provide a numerical optimization procedure that estimates them from population-genomic data. Simulations show that the procedure is nearly unbiased, even at 3x coverage, and errors in five of the seven coefficients are statistically uncorrelated. The remaining two coefficients have a negative correlation of errors, but their sum provides an unbiased assessment of the overall correlation of heterozygosity between two individuals. Application of these new methods to four populations of the freshwater crustacean Daphnia pulex reveal the occurrence of half-siblings in our samples, as well as a number of identical individuals that are likely obligately asexual clone-mates. Statistically significant negative estimates of these pair-wise relatedness coefficients, including inbreeding coefficents that were typically negative, underscore the difficulties that arise when interpreting genotypic correlations as estimations of the probability that alleles are identical by descent.

Evolutionary Biology↗

bioRxiv2015

Low base-substitution mutation rate in the germline genome of ciliate Tetrahymena thermophila

Mutation is the ultimate source of all genetic variation and is, therefore, central to evolutionary change. Previous work on Paramecium tetraurelia found an unusually low germline base-substitution mutation rate in this ciliate. Here, we tested the generality of this result among ciliates using Tetrahymena thermophila. We sequenced the genomes of 10 lines of T. thermophila that had each undergone approximately 1,000 generations of mutation accumulation (MA). We applied an existing mutation-calling pipeline and developed a new probabilistic mutation detection approach that directly models the design of an MA experiment and accommodates the noise introduced by mismapped reads. Our probabilistic mutation-calling method provides a straightforward way of estimating the number of sites at which a mutation could have been called if one was present, providing the denominator for our mutation rate calculations. From these methods, we find that T. thermophila has a germline base-substitution mutation rate of 7.61 x 10-12 per site, per cell division, which is consistent with the low base-substitution mutation rate in P. tetraurelia. Over the course of the evolution experiment, genomic exclusion lines derived from the MA lines experienced a fitness decline that cannot be accounted for by germline base-substitution mutations alone, suggesting that other genetic or epigenetic factors must be involved. Because selection can only operate to reduce mutation rates based upon the \"visible\" mutational load, asexual reproduction with a transcriptionally silent germline may allow ciliates to evolve extremely low germline mutation rates.

Evolutionary Biology↗

bioRxiv2014

The rate and molecular spectrum of spontaneous mutations in the GC-rich multi-chromosome genome of Burkholderia cenocepacia

Spontaneous mutations are ultimately essential for evolutionary change and are also the root cause of many diseases. However, until recently, both biological and technical barriers have prevented detailed analyses of mutation profiles, constraining our understanding of the mutation process to a few model organisms and leaving major gaps in our understanding of the role of genome content and structure on mutation. Here, we present a genome-wide view of the molecular mutation spectrum in Burkholderia cenocepacia, a clinically relevant pathogen with high %GC-content and multiple chromosomes. We find that B. cenocepacia has low genome-wide mutation rates with insertion-deletion mutations biased towards deletions, consistent with the idea that deletion pressure reduces prokaryotic genome sizes. Unlike prior studies of other organisms, mutations in B. cenocepacia are not AT-biased, which suggests that at least some genomes with high %GC-content experience unusual base-substitution mutation pressure. Importantly, we also observe variation in both the rates and spectra of mutations among chromosomes and elevated G:C>T:A transversions in late-replicating regions. Thus, although some patterns of mutation appear to be highly conserved across cellular life, others vary between species and even between chromosomes of the same species, potentially influencing the evolution of nucleotide composition and genome architecture.

Evolutionary Biology↗