Dataset Information

A Post-pleistocene Calibrated Mutation Rate from Insect Museum Specimens.

ABSTRACT: Quantifying the age of recent species divergence events can be challenging in the absence of calibration points within many groups. The katydid species Neoconocephalus lyristes provides the opportunity to calibrate a post-Pleistocene, taxa specific mutation rate using a known biogeographic event, the Mohawk-Hudson Divide. DNA was extracted from pinned museum specimens of N. lyristes from both Midwest and Atlantic populations and the mitochondrial gene COI sequenced using primers designed from extant specimens. Coalescent analyses using both strict and relaxed molecular clock models were performed in BEAST v1.8.2. The assumption of a strict molecular clock could not be rejected in favor of the relaxed clock model as the distribution of the standard deviation of the clock rate strongly abutted zero. The strict molecular clock model resulted in an intraspecific calculated mutation rate of 14.4-17.3 %/myr, a rate substantially higher than the common rates of sequence evolution observed for insect mitochondrial DNA sequences. The rate, however, aligns closely with mutation rates estimated from other taxa with similarly recent lineage divergence times.

SUBMITTER: Ney G

PROVIDER: S-EPMC6072552 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature

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A Post-pleistocene Calibrated Mutation Rate from Insect Museum Specimens.

Ney Gideon G Frederick Katy K Schul Johannes J

PLoS currents 20180713

Quantifying the age of recent species divergence events can be challenging in the absence of calibration points within many groups. The katydid species <i>Neoconocephalus lyristes</i> provides the opportunity to calibrate a post-Pleistocene, taxa specific mutation rate using a known biogeographic event, the Mohawk-Hudson Divide. DNA was extracted from pinned museum specimens of <i>N. lyristes</i> from both Midwest and Atlantic populations and the mitochondrial gene COI sequenced using primers de ...[more]

PMID: 30116653

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Project description:Unlocking the vast genomic diversity stored in natural history collections would create unprecedented opportunities for genome-scale evolutionary, phylogenetic, domestication and population genomic studies. Many researchers have been discouraged from using historical specimens in molecular studies because of both generally limited success of DNA extraction and the challenges associated with PCR-amplifying highly degraded DNA. In today's next-generation sequencing (NGS) world, opportunities and prospects for historical DNA have changed dramatically, as most NGS methods are actually designed for taking short fragmented DNA molecules as templates. Here we show that using a standard multiplex and paired-end Illumina sequencing approach, genome-scale sequence data can be generated reliably from dry-preserved plant, fungal and insect specimens collected up to 115 years ago, and with minimal destructive sampling. Using a reference-based assembly approach, we were able to produce the entire nuclear genome of a 43-year-old Arabidopsis thaliana (Brassicaceae) herbarium specimen with high and uniform sequence coverage. Nuclear genome sequences of three fungal specimens of 22-82 years of age (Agaricus bisporus, Laccaria bicolor, Pleurotus ostreatus) were generated with 81.4-97.9% exome coverage. Complete organellar genome sequences were assembled for all specimens. Using de novo assembly we retrieved between 16.2-71.0% of coding sequence regions, and hence remain somewhat cautious about prospects for de novo genome assembly from historical specimens. Non-target sequence contaminations were observed in 2 of our insect museum specimens. We anticipate that future museum genomics projects will perhaps not generate entire genome sequences in all cases (our specimens contained relatively small and low-complexity genomes), but at least generating vital comparative genomic data for testing (phylo)genetic, demographic and genetic hypotheses, that become increasingly more horizontal. Furthermore, NGS of historical DNA enables recovering crucial genetic information from old type specimens that to date have remained mostly unutilized and, thus, opens up a new frontier for taxonomic research as well.

Project description:Sylvilagus floridanus Papillomavirus (SfPV) causes growth of large horn-like tumors on rabbits. SfPV was described in cottontail rabbits (probably Sylvilagus floridanus) from Kansas and Iowa by Richard Shope in 1933, and detected in S. audubonii in 2011. It is known almost exclusively from the US Midwest. We explored the University of Kansas Natural History Museum for historical museum specimens infected with SfPV, using molecular techniques, to assess if additional wild species host SfPV, and whether SfPV occurs throughout the host range, or just in the Midwest. Secondary aims were to detect distinct strains, and evidence for strain spatio-temporal specificity. We found 20 of 1395 rabbits in the KU collection SfPV symptomatic. Three of 17 lagomorph species (S. nuttallii, and the two known hosts) were symptomatic, while Brachylagus, Lepus and eight additional Sylvilagus species were not. 13 symptomatic individuals were positive by molecular testing, including the first S. nuttallii detection. Prevalence of symptomatic individuals was significantly higher in Sylvilagus (1.8%) than Lepus. Half of these specimens came from Kansas, though new molecular detections were obtained from Jalisco-Mexico's first-and Nebraska, Nevada, New Mexico, and Texas, USA. We document the oldest lab-confirmed case (Kansas, 1915), pre-dating Shope's first case. SfPV amplification was possible from 63.2% of symptomatic museum specimens. Using multiple methodologies, rolling circle amplification and, multiple isothermal displacement amplification in addition to PCR, greatly improved detection rates. Short sequences were obtained from six individuals for two genes. L1 gene sequences were identical to all previously detected sequences; E7 gene sequences, were more variable, yielding five distinct SfPV1 strains that differing by less than 2% from strains circulating in the Midwest and Mexico, between 1915 and 2005. Our results do not clarify whether strains are host species specific, though they are consistent with SfPV specificity to genus Sylvilagus.

Dataset Information

A Post-pleistocene Calibrated Mutation Rate from Insect Museum Specimens.

Publications

A Post-pleistocene Calibrated Mutation Rate from Insect Museum Specimens.

Similar Datasets

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