Biology subjects

Platt, R. N.

Publications and source records attributed to Platt, R. N..

21 records · Page 2Linked to original sources

bioRxiv2019

The PIWI/piRNA response is relaxed in a rodent that lacks mobilizing transposable elements

Transposable elements (TEs) are genomic parasites that can propagate by inserting copies of themselves into host genomes. Mammalian genomes are typically dominated by LINE retrotransposons and their associated SINEs, and their mobilization in the germline is a challenge to genome integrity. There are genomic defenses against TE proliferation and the PIWI/piRNA defense is among the most well understood. However, the PIWI/piRNA system has been investigated largely in animals with abundant and actively mobilizing TEs and it is unclear how the PIWI/piRNA system functions in the absence of mobilizing TEs. The 13-lined ground squirrel provides an excellent opportunity to examine PIWI/piRNA and TE dynamics within the context of minimal, and possibly nonexistent, TE accumulation. We sequenced RNA and small RNAs pools from the testes of juvenile and adult squirrels and compared results to TE and PIWI/piRNA dynamics in the European rabbit and house mouse. Interestingly in squirrels, despite a lack of young insertions, TEs were still actively transcribed at higher levels compared to mouse and rabbit. All three PIWI proteins were either not expressed, or only minimally expressed, prior to P8 in squirrel testis, but there was little TE expression change with the onset of PIWI expression. We found PIWIs largely did not reduce TE transcription, and the ping-pong cycle was significantly reduced among squirrel LINEs and SINEs compared to the mouse and rabbit. We speculate that, although the PIWI/piRNA system is adaptable to novel TE threats, transcripts from TEs that are no longer threatening receive less attention from PIWI proteins.

evolutionary biology↗

bioRxiv2019

Ancient hybridization and introgression of an invadolysin gene in schistosome parasites

The parasitic blood fluke Schistosoma haematobium causes urogenital schistosomiasis in humans and is a major cause of morbidity and mortality across sub-Saharan Africa. S. haematobium hybridizes with livestock schistosomes, including S. bovis, however the frequency, direction, age and genomic consequences of hybridization are unknown. We sequenced 96 S. haematobium exomes from Niger and the Zanzibar archipelago. and found evidence of an ancient, introgression event between Nigerien S. haematobium and S. bovis occurring 108-613 generations ago. Between 3.3-8.2% of Nigerien S. haematobium genomes are derived from S. bovis alleles, some of which show signatures of directional selection; the strongest signal spans a single gene in the invadolysin gene family, an M8 metalloprotease associated with parasitic life-history traits.

evolutionary biology↗

bioRxiv2017

Conflicting evolutionary histories of the mitochondrial and nuclear genomes in New World Myotis

The rapid diversification of Myotis bats into more than 100 species is one of the most extensive mammalian radiations available for study. Efforts to understand relationships within Myotis have primarily utilized mitochondrial markers and trees inferred from nuclear markers lacked resolution. Our current understanding of relationships within Myotis is therefore biased towards a set of phylogenetic markers that may not reflect the history of the nuclear genome. To resolve this, we sequenced the full mitochondrial genomes of 37 representative Myotis, primarily from the New World, in conjunction with targeted sequencing of 3,648 ultraconserved elements (UCEs). We inferred the phylogeny and explored the effects of concatenation and summary phylogenetic methods, as well as combinations of markers based on informativeness or levels of missing data, on our results. Of the 294 phylogenies generated from the nuclear UCE data, all are significantly different from phylogenies inferred using mitochondrial genomes. Even within the nuclear data, quartet frequencies indicate that around half of all UCE loci conflict with the estimated species tree. Several factors can drive such conflict, including incomplete lineage sorting, introgressive hybridization, or even phylogenetic error. Despite the degree of discordance between nuclear UCE loci and the mitochondrial genome and among UCE loci themselves, the most common nuclear topology is recovered in one quarter of all analyses with strong nodal support. Based on these results, we re-examine the evolutionary history of Myotis to better understand the phenomena driving their unique nuclear, mitochondrial, and biogeographic histories.

evolutionary biology↗