J. Cotton

Publications178
h-index47
Citations7,777
Highly Influential Citations386
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Genomic Insights into the Origin of Parasitism in the Emerging Plant Pathogen Bursaphelenchus xylophilus
TLDR
A high-quality draft genome sequence from an inbred line of B. xylophilus is presented, and the lack of proteins homologous to effectors from other plant parasitic nematodes confirms the distinctive molecular basis of plant parasitism in the Bursaphelenchus lineage.
Genome-wide signatures of convergent evolution in echolocating mammals
TLDR
This first attempt to detect genome-wide convergent sequence evolution across divergent taxa reveals the phenomenon to be much more pervasive than previously recognized.
Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance.
TLDR
It is shown that whole-genome sequence data reveals genetic structure within these lines not shown by multilocus typing, and suggests that drug resistance has emerged multiple times in this closely related set of lines, providing additional power to track the drug resistance and epidemiology of an important human pathogen.
The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode
TLDR
The complete genome sequence of G. pallida is presented, together with transcriptomic data from most of the nematode life cycle, particularly focusing on the life cycle stages involved in root invasion and establishment of the biotrophic feeding site.
Tempo and Mode of Diversification of Lake Tanganyika Cichlid Fishes
TLDR
Although the results indicate a dominant role for the environment in shaping cichlid diversification, differences in the timing of diversification among the Tanganyikan tribes indicate that biological differences were still important for the dynamics of species build-up in the lake.
Comparative Genomics of the Apicomplexan Parasites Toxoplasma gondii and Neospora caninum: Coccidia Differing in Host Range and Transmission Strategy
TLDR
The ecological niches occupied by these species are influenced by a relatively small number of gene products which operate at the host-parasite interface and that the dominance of vertical transmission in N. caninum may be associated with the evolution of reduced virulence in this species.
The Ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records
TLDR
The two historical records of life both suggest that although the cradle of Metazoa lies in the Cryogenian, and despite the explosion of ecology that occurs in the Cambrian, it is the emergence of bilaterian taxa in the Ediacaran that sets the tempo and mode of macroevolution for the remainder of geological time.
Supertrees disentangle the chimerical origin of eukaryotic genomes.
TLDR
A novel supertree-based phylogenetic signal-stripping method is used to recover supertrees of life based on phylogenies for up to 5,741 single gene families distributed across 185 genomes and rejects all but two of the current hypotheses for the origin of eukaryotes.
Genomic Confirmation of Hybridisation and Recent Inbreeding in a Vector-Isolated Leishmania Population
TLDR
Patterns of linkage disequilibrium indicate that this population reproduced primarily clonally following the original hybridisation event, but that some recombination also occurred, the first quantitative estimate of these events during the Leishmania life cycle.
Phylogenomic Analyses Elucidate the Evolutionary Relationships of Bats
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