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Dennis, A.

Publications and source records attributed to Dennis, A..

5 recordsLinked to original sources

Mitochondrial genomes of three Melampus species (Ellobiidae; Gastropoda) and a proposed mitochondrial control region for Euthyneura

Melampus bidentatus was recently divided into three genetically divergent cryptic species: M. bidentatus, M. jaumei and M. gundlachi. We have assembled and annotated a mitochondrial genome for each of these species. Comparisons with other taxa showed that these three species possess a gene order that is distinct from the conserved gene order found in the six (out of nine available) Ellobiid genera. Among the species with a derived gene order, mean nucleotide divergence over all genes was on average 1.57x higher than among mitogenomes with the conserved gene order. This suggests varying evolutionary rates of mitochondrial genes in this family. We also use comparisons among 130 mitochondrial genomes within Euthyneura to support the presence of a control region preceding the Isoleucin-tRNA, including in the novel genomes presented here.

genomics↗

Intergenerational Effects of Early Life Starvation on Life-History, Consumption, and Transcriptomes of a Holometabolous Insect

Intergenerational effects, also known as parental effects in which the offspring phenotype is influenced by the parental phenotype, can occur in response to factors that occur not only in early but also in late parental life. However, little is known about how these parental life stage-specific environments interact with each other and with the offspring environment to influence offspring phenotype, particularly in organisms that realize distinct niches across ontogeny. We examined the effects of parental larval starvation and adult reproductive environment on offspring traits under matching or mismatching offspring larval starvation conditions using the holometabolous, haplo-diploid insect Athalia rosae (turnip sawfly). We show that the parental larval starvation treatment had trait-dependent intergenerational effects on both life-history and consumption traits of offspring larvae, partly in interaction with offspring conditions and sex, while there was no significant effect of parental adult reproductive environment. In addition, while offspring larval starvation led to numerous gene- and pathway-level expression differences, parental larval starvation impacted fewer genes and only the ribosomal pathway. Our findings reveal that parental starvation evokes complex intergenerational effects on offspring life-history traits, consumption patterns as well as gene expression, although the effects are less pronounced than those of offspring starvation.

ecology↗

Identification of hidden population structure in time-scaled phylogenies

Population structure influences genealogical patterns, however data pertaining to how populations are structured are often unavailable or not directly observable. Inference of population structure is highly important in molecular epidemiology where pathogen phylogenetics is increasingly used to infer transmission patterns and detect outbreaks. Discrepancies between observed and idealised genealogies, such as those generated by the coalescent process, can be quantified, and where significant differences occur, may reveal the action of natural selection, host population structure, or other demographic and epidemiological heterogeneities. We have developed a fast non-parametric statistical test for detection of cryptic population structure in time-scaled phylogenetic trees. The test is based on contrasting estimated phylogenies with the theoretically expected phylodynamic ordering of common ancestors in two clades within a coalescent framework. These statistical tests have also motivated the development of algorithms which can be used to quickly screen a phylogenetic tree for clades which are likely to share a distinct demographic or epidemiological history. Epidemiological applications include identification of outbreaks in vulnerable host populations or rapid expansion of genotypes with a fitness advantage. To demonstrate the utility of these methods for outbreak detection, we applied the new methods to large phylogenies reconstructed from thousands of HIV-1 partial pol sequences. This revealed the presence of clades which had grown rapidly in the recent past, and was significantly concentrated in young men, suggesting recent and rapid transmission in that group. Furthermore, to demonstrate the utility of these methods for the study of antimicrobial resistance, we applied the new methods to a large phylogeny reconstructed from whole genome Neisseria gonorrhoeae sequences. We find that population structure detected using these methods closely overlaps with the appearance and expansion of mutations conferring antimicrobial resistance.

evolutionary biology↗

The relative influence of niche versus neutral processes on Ediacaran communities

A fundamental question in community ecology is the relative influence of niche versus neutral processes in determining ecosystem dynamics. The extent to which these processes structured early animal communities is yet to be explored. Here we use spatial point process analyses (SPPA) to determine the influence of niche versus neutral processes on early total-group metazoan paleocommunities from the Ediacaran Period [~]565 million years in age. Preservation of these sessile organisms in large in-situ populations on exposed bedding planes enables inference of the most likely underlying processes governing their spatial distributions by SPPA. We conducted comprehensive spatial mapping of six of the largest Ediacaran paleocommunities in Newfoundland, Canada and Charnwood Forest, UK using LiDAR, photogrammetry and a laser-line probe. For each paleocommunity we determined the best-fit spatial model for each univariate and bivariate species distribution, comparing four sets of spatial models (complete spatial randomness, dispersal, habitat, and combined dispersal with habitat) using goodness-of-fit tests. Random and dispersal models are considered neutral processes while habitat and combined models are considered niche processes. We find the dynamics of these paleocommunities to be dominated by neutral processes, with limited influence from niche processes. Our findings are consistent with community model predictions of when neutral dynamics dominate, but are in stark contrast to the niche-dominated communities of the modern marine realm. Thus, while the underlying processes determining metazoan community assembly appear to have been in place since the appearance of the first macroscopic, complex animals, the dynamics of these early metazoan communities were fundamentally different to those of extant communities.\n\nSignificance statementThe extent to which habitat and dispersal processes structure the earliest animal communities found during the Ediacaran Period [~]565 million years ago, is unknown. In this study we analyse six of the largest and most diverse fossil assemblages from Newfoundland, Canada and Charnwood Forest, UK, using spatial point processes analyses to determine the relative influence of habitat processes (niche) and dispersal processes (neutral) on the spatial distribution of taxa. The vast majority of Ediacaran taxon distributions were controlled by neutral processes, in striking contrast to niche-dominated modern marine ecosystems, but consistent with model predictions of when neutral dynamics dominate communities. Thus the underlying processes determining metazoan community assembly have been in place since the appearance of the first macroscopic, complex animals.

ecology↗

High quality whole genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena)

The harbour porpoise (Phocoena phocoena) is a highly mobile cetacean found in waters across the Northern hemisphere. It occurs in coastal water and inhabits water basins that vary broadly in salinity, temperature, and food availability. These diverse habitats could drive differentiation among populations. Here we report the first harbour porpoise genome, assembled de novo from a Swedish Kattegat individual. The genome is one of the most complete cetacean genomes currently available, with a total size of 2.7 Gb and 50% of the total length found in just 34 scaffolds. Using the largest 122 scaffolds, we were able to validate a high level of homology to the chromosome-level genome assembly of the closest related species for which such resource was available, the domestic cattle (Bos taurus). The draft annotation comprises 22,154 predicted gene models, which we further annotated through matches to the NCBI nucleotide database, GO categorization, and motif prediction. To infer the adaptive abilities of this species, as well as their population history, we performed a Bayesian skyline analysis, and produced results that are concordant with the demographic history of this species, including expansion and fragmentation events. Overall, this genome assembly, together with the draft annotation, represents a crucial addition to the limited genetic markers currently available for the study of porpoises and Phocoenidae conservation, phylogeny, and evolution.

genomics↗