Biology subjects

Martin, M. D.

Publications and source records attributed to Martin, M. D..

21 records · Page 2Linked to original sources

bioRxiv2022

The genomic basis of the plant island syndrome in Darwin's giant daisies

Oceanic archipelagos comprise multiple disparate environments over small geographic areas and are isolated from other biotas. These conditions have led to some of the most spectacular adaptive radiations, which have been key to our understanding of evolution, and offer a unique chance to characterise the genomic basis underlying rapid and pronounced phenotypic changes. Repeated patterns of evolutionary change in plants on oceanic archipelagos, i.e. the plant island syndrome, include changes in leaf morphology, acquisition of perennial life-style, and change of ploidy. Here, we describe the genome of the critically endangered and Galapagos endemic Scalesia atractyloides Arnot., obtaining a chromosome-resolved 3.2-Gbp assembly with 43,093 candidate gene models. Using a combination of fossil transposable elements, k-mer spectra analyses and orthologue assignment, we identify the two ancestral subgenomes and date their divergence and the polyploidization event, concluding that the ancestor of all Scalesia species on the Galapagos was an allotetraploid. There are a comparable number of genes and transposable elements across the two subgenomes, and while their synteny has been mostly conserved, we find multiple inversions that may have facilitated adaptation. We identify clear signatures of selection across genes associated with vascular development, life-growth, adaptation to salinity and changes in flowering time, thus finding compelling evidence for a genomic basis of island syndrome in Darwins giant daisy radiation. This work advances understanding of factors influencing subgenome divergence in polyploid genomes, and characterizes the quick and pronounced genomic changes in a specular and diverse radiation of an iconic island plant radiation.

evolutionary biology↗

bioRxiv2020

Runs of homozygosity in killer whale genomes provide a global record of demographic histories

Runs of homozygosity (ROH) occur when offspring receive the same ancestral haplotype from both parents, and, accordingly, reduce individual heterozygosity. Their distribution throughout the genome contains information on the probability of inbreeding mediated by mating system and population demography. Here, we investigate variation in killer whale demographic history as reflected in genome-wide heterozygosity, using a global dataset of 26 genomes. We find an overall pattern of lower heterozygosity in genomes sampled at high latitudes, with hundreds of short ROH (< 1Mbp) reflecting high background relatedness due to coalescence of haplotypes during bottlenecks associated with founder events during post-glacial range expansions. Across most of the species range, intermediate length ROH (1-10Mb) revealed long-term inbreeding in 22 of the 26 sampled killer whale genomes, consistent with the high social philopatry observed in all populations studied to date. Inbreeding coefficients (FROH) were comparable to those reported in other taxa with long-term low population size, such as bonobos and the Native American Karitiana of the Brazilian Amazon. The extreme outlier in this dataset, a Scottish killer whale, was homozygous over one-third of the autosomes (41.6%) with a distinct distribution of ROH length, indicating generations of inbreeding. This exceeds autozygosity in emblematic examples of long-term inbreeding, such as the Altai Neanderthal, and eastern lowland and mountain gorillas. The fate of this Scottish killer whale population, in which no calves have been born in over two decades, may be inextricably linked to its demographic history and consequential inbreeding depression.

evolutionary biology↗

bioRxiv2020

On the origin and evolution of RNA editing in metazoans

Extensive adenosine-to-inosine (A-to-I) editing of nuclear-transcribed RNAs is the hallmark of metazoan transcriptional regulation, and is fundamental to numerous biochemical processes. Here we explore the origin and evolution of this regulatory innovation, by quantifying its prevalence in 22 species that represent all major transitions in metazoan evolution. We provide substantial evidence that extensive RNA editing emerged in the common ancestor of extant metazoans. We find the frequency of RNA editing varies across taxa in a manner independent of metazoan complexity. Nevertheless, cis-acting features that guide A-to-I editing are under strong constraint across all metazoans. RNA editing seems to preserve an ancient mechanism for suppressing the more recently evolved repetitive elements, and is generally nonadaptive in protein-coding regions across metazoans, except for Drosophila and cephalopods. Interestingly, RNA editing preferentially target genes involved in neurotransmission, cellular communication and cytoskeleton, and recodes identical amino acid positions in several conserved genes across diverse taxa, emphasizing broad roles of RNA editing in cellular functions during metazoan evolution that have been previously underappreciated.

evolutionary biology↗