Biology subjects

Murdock, D.

Publications and source records attributed to Murdock, D..

3 recordsLinked to original sources

bioRxiv2024

The relationship between microbial community succession, decay, and anatomical character loss in non-biomineralised animals

A fundamental assumption of hypothesis-driven decay experiments is that, during decay, the loss of anatomy follows a sequence broadly controlled by the intrinsic compositional properties of tissues. Recent work investigating the succession of postmortem endogenous microbial communities (thanatomicrobiome) challenges this assumption. These studies suggest the thanatomicrobiome exhibits a predictable, clock-like succession in response to physical and chemical environmental changes within a carcass. Therefore, it is possible that reproducible sequences of character loss during decay are controlled by thanatomicrobiome succession dynamics. If so, exceptionally preserved fossil anatomy would reflect a succession of ancient contemporaneous microbial communities, about which we know nothing, rendering decay experiments uninformative. Here, we investigate two questions: (1) what is the role of exogenous and endogenous bacteria during formation of the thanatomicrobiome and (2) do thanatomicrobiome successions control the sequence of anatomical character loss within a decaying carcass? Our analysis shows that the thanatomicrobiome is dominated by endogenous bacteria and that, even in the presence of inoculum, exogenous bacteria do not invade the carcass and replace native bacteria (while the carcass is intact). This confirms that the use of environmental inoculum in decay experiments introduces an inadvisable confounding variable. Secondly, we find no correlation between thanatomicrobiome successions and the sequence of anatomical character loss, supporting that fossil non-biomineralised characters correlate with their propensity to decay in extant relatives. These findings indicate that the inability to model ancient bacteria does not invalidate decay experiments. We also present a synthesis of the role of bacteria in non-biomineralised fossilisation.

paleontology↗

bioRxiv2022

Putting the F in FBD analyses: tree constraints or morphological data ?

1The fossilized birth-death (FBD) process provides an ideal model for inferring phylogenies from both extant and fossil taxa. Using this approach, fossils (with or without character data) are directly considered as part of the tree. This leads to a statistically coherent prior on divergence times, where the variance associated with node ages reflects uncertainty in the placement of fossil taxa in the phylogeny. Since fossils are typically not associated with molecular sequences, additional information is required to place fossils in the tree. Previously, this information has been provided in two different forms: using topological constraints, where the user specifies monophyletic clades based on established taxonomy, or so-called total-evidence analyses, which use a morphological data matrix with data for both fossil and extant specimens in addition to the molecular alignment. In this work, we use simulations to evaluate these different approaches to handling fossil placement in FBD analyses, both in ideal conditions and in datasets including uncertainty or even errors. We also explore how rate variation in fossil recovery or diversification rates impacts these approaches. We find that the extant topology is well recovered under all methods of fossil placement. Divergence times are similarly well recovered across all methods, with the exception of constraints which contain errors. These results are consistent with expectations: in FBD inferences, divergence times are mostly informed by fossil ages, so variations in the position of fossils strongly impact these estimates. On the other hand, the placement of extant taxa in the phylogeny is driven primarily by the molecular alignment. We see similar patterns in datasets which include rate variation, however one notable difference is that relative errors in extant divergence times increase when more variation is included in the dataset, for all approaches using topological constraints, and particularly for constraints with errors. Finally, we show that trees recovered under the FBD model are more accurate than those estimated using non-FBD (i.e., non-time calibrated) inference. This result holds even with the use of erroneous fossil constraints and model misspecification under the FBD. Overall, our results underscore the importance of core taxonomic research, including morphological data collection and species descriptions, irrespective of the approach to handling phylogenetic uncertainty using the FBD process.

evolutionary biology↗

bioRxiv2021

Genetic Sex Validation for Sample Tracking in Clinical Testing

BackgroundNext generation DNA sequencing (NGS) has been rapidly adopted by clinical testing laboratories for detection of germline and somatic genetic variants. The complexity of sample processing in a clinical DNA sequencing laboratory creates multiple opportunities for sample identification errors, demanding stringent quality control procedures. MethodsWe utilized DNA genotyping via a 96-SNP PCR panel applied at sample acquisition in comparison to the final sequence, for tracking of sample identity throughout the sequencing pipeline. The 96-SNP PCR panels inclusion of sex SNPs also provides a mechanism for a genotype-based comparison to recorded sex at sample collection for identification. This approach was implemented in the clinical genomic testing pathways, in the multi-center Electronic Medical Records and Genomics (eMERGE) Phase III program ResultsWe identified 110 inconsistencies from 25,015 (0.44%) clinical samples, when comparing the 96-SNP PCR panel data to the test requisition-provided sex. The 96-SNP PCR panel genetic sex predictions were confirmed using additional SNP sites in the sequencing data or high-density hybridization-based genotyping arrays. Results identified clerical errors, samples from transgender participants and stem cell or bone marrow transplant patients and undetermined sample mix-ups. ConclusionThe 96-SNP PCR panel provides a cost-effective, robust tool for tracking samples within DNA sequencing laboratories, while the ability to predict sex from genotyping data provides an additional quality control measure for all procedures, beginning with sample collections. While not sufficient to detect all sample mix-ups, the inclusion of genetic versus reported sex matching can give estimates of the rate of errors in sample collection systems.

genomics↗