• Changes in technology and imperfect detection of nest contents impedes reliable estimates of population trends in burrowing seabirds

      Lavers, JL; Hutton, I; Bond, A (Elsevier, 2019-03-01)
      One of the most fundamental aspects of conservation biology is understanding trends in the abundance of species and populations. This influences conservation interventions, threat abatement, and management by implicitly or explicitly setting targets for favourable conservation states, such as an increasing or stable population. Burrow-nesting seabirds present many challenges for determining abundance reliably, which is further hampered by variability in the quality of previous surveys. We used burrow scopes to determine the population status of Flesh-footed Shearwaters (Ardenna carneipes) at their largest colony on Lord Howe Island, Australia, in 2018. We estimated a breeding population of 22,654 breeding pairs (95% CI: 8159–37,909). Comparing burrow scope models used in 2018 found more than half of burrow contents (20/36 burrows examined) were classified differently. If this detection probability is applied retroactively to surveys in 2002 and 2009, we estimate that the Flesh-footed Shearwater population on Lord Howe has decreased by up to 50% in the last decade, but uncertainty around previous surveys’ ability to reliably determine burrow contents means a direct comparison is not possible. The decline in burrow density between 2018 and previous years adds further evidence that the population may not be stable. Our results highlight a need for regular surveys to quantify detection probability so that as video technology advances, previous population estimates remain comparable. We urge caution when comparing population counts of burrowing seabirds using different technologies, to ensure comparisons are meaningful.
    • Cladistics

      Kitching, I; Forey, PL; Williams, DM (Elsevier, 2017-01-01)
      Cladistics is a class of methods of biological classification that groups taxa hierarchically into discrete sets and subsets. This article presents the principles and concepts of cladistics and describes the principal analytical methods. The operations by which observations of organisms are coded for analysis are explained, followed by the methods for reconstructing the hierarchical relationships among taxa (usually expressed as branching diagrams termed cladograms). Statistics and principles for determining the degree of fit between data and cladograms are discussed, which permit choices to be made among competing cladograms.
    • Detection of ultrafine plastics ingested by seabirds using tissue digestion.

      Lavers, JL; Stivaktakis, G; Hutton, I; Bond, AL (Elsevier, 2019-04-06)
      Plastic debris is a major global threat to marine ecosystems and species. However, our knowledge of this issue may be incomplete due to a lack of a standardized method for quantifying ingested ultrafine particles (1 μm - 1 mm) in wildlife. This study provides the first quantification of ultrafine plastic in seabirds using chemical and biological digestion treatments to extract plastic items from seabird gizzards. The alkaline agent, potassium hydroxide, outperformed the enzyme corolase, based on cost and efficiency (e.g., digestion time). Ultrafine plastics were observed in 7.0% of Flesh-footed Shearwater (Ardenna carneipes) gizzards collected from Lord Howe Island, Australia and accounted for 3.6% of all plastic items recovered (13 out of 359 items). Existing methods for extracting ingested plastic from seabirds do not account for ultrafine particles, therefore our results indicate current seabird plastic loads, and the associated physical and biological impacts, are underestimated.
    • Early colonisation of urban indoor carcasses by blow flies (Diptera: Calliphoridae): An experimental study from central Spain

      Martin-Vega, D; Martín Nieto, C; Cifrián, B; Baz, A; Díaz-Aranda, LM (Elsevier, 2017-09-01)
      Due to their ubiquity and synanthropy, blow flies (Diptera: Calliphoridae) are generally the first colonisers of cadavers and, therefore, frequently used to estimate a minimum post-mortem interval (minPMI). Whereas in outdoor situations blow flies are expected to locate and colonise exposed cadavers within hours or even minutes after death, it is usually assumed that the colonisation of a cadaver indoors might be delayed for an uncertain period of time. This uncertainty severely limits the informativity of minPMI estimates based on entomological evidence. Moreover, these limitations are emphasised by the lack of experimental data on insect colonisation of indoor carrion and by the fact that most of the forensic cases involving entomological evidence have been reported to occur indoors. In this study we investigate the early colonisation of pig carcasses placed indoors in a building located in the centre of an urban environment in central Spain. Three carcasses were placed in three equal rooms with a window half opened during five experimental trials: summer 2013, autumn 2013, winter 2014, spring 2014 and summer 2014. The species composition and their contribution to the carrion colonisation differed among seasons. Calliphora vicina Robineau–Desvoidy was the sole coloniser of carcasses in winter and colonised the carcasses within the first 24–48 h in every season, although Lucilia sericata (Meigen) was the first coloniser of most summer carcasses. On the other hand, Calliphora vomitoria (L.) and Chrysomya albiceps (Wiedemann) colonised the carcasses significantly later in spring and in spring and summer, respectively, with a delay of several days. In autumn, however, there were no significant differences in the colonisation times by C. vicina, L. sericata and Ch. albiceps. C. vicina and L. sericata showed a clear preference for ovipositing in the natural orifices of the carcasses, whereas Ch. albiceps oviposited more frequently on the trunk and legs.
    • Impact of sample degradation and inhibition on field-based DNA identification of human remains

      Dawnay, N; Flamson, R; Hall, MJR; Steadman, DW (Elsevier, 2018-07-25)
      The advent of DNA technologies for field-based application promises to provide rapid intelligence to aid investigations. Their validation and adoption by enforcement groups have demonstrated utility in sample screening and prioritisation, but field application in some areas of forensic science, such as human remains identification, is little evidenced. Assessing the ability of such approaches to provide meaningful data is critical as decomposition is likely to complicate analysis and limit the effective use of such field-based DNA interventions. This research assessed the ability to collect viable DNA data in the field using the ParaDNA Field Instrument and Intelligence Test chemistry. Different sample collection methods were assessed; direct from skin surface; direct from exposed tissue; indirect from muscle swab transferred to FTA card; and from larvae on the donors. Samples were collected and processed on-site at the Anthropology Research Facility, University of Tennessee. The data show that the muscle tissue provided the most effective sample template and, using this approach, it was possible to generate STR profiles from human remains in under two hours from the time of sample collection. STR profile data were collected up to four days from donor placement (114 Accumulated Degree Days). After this time there was a rapid decrease in the quality of the profiles collected due to the onset of decomposition. The data also show that effective sample recovery was not possible from the surface of the skin, exposed tissue or from carrion larvae. Inhibition studies in the laboratory suggest that by-products of the decomposition process are the primary mode of failure. Together these data suggests a possible application for screening and prioritisation in criminal casework but highlights issues that may affect the success of the approach.
    • Probing recalcitrant problems in polyclad evolution and systematics with novel mitochondrial genome resources

      Kenny, NJ; Noreña, C; Damborenea, C; Grande, C (Elsevier, 2018-02)
      For their apparent morphological simplicity, the Platyhelminthes or “flatworms” are a diverse clade found in a broad range of habitats. Their body plans have however made them difficult to robustly classify. Molecular evidence is only beginning to uncover the true evolutionary history of this clade. Here we present nine novel mitochondrial genomes from the still undersampled orders Polycladida and Rhabdocoela, assembled from short Illumina reads. In particular we present for the first time in the literature the mitochondrial sequence of a Rhabdocoel, Bothromesostoma personatum (Typhloplanidae, Mesostominae). The novel mitochondrial genomes examined generally contained the 36 genes expected in the Platyhelminthes, with all possessing 12 of the 13 protein-coding genes normally found in metazoan mitochondrial genomes (ATP8 being absent from all Platyhelminth mtDNA sequenced to date), along with two ribosomal RNA genes. The majority presented possess 22 transfer RNA genes, and a single tRNA gene was absent from two of the nine assembled genomes. By comparison of mitochondrial gene order and phylogenetic analysis of the protein coding and ribosomal RNA genes contained within these sequences with those of previously sequenced species we are able to gain a firm molecular phylogeny for the inter-relationships within this clade. Our phylogenetic reconstructions, using both nucleotide and amino acid sequences under several models and both Bayesian and Maximum Likelihood methods, strongly support the monophyly of Polycladida, and the monophyly of Acotylea and Cotylea within that clade. They also allow us to speculate on the early emergence of Macrostomida, the monophyly of a “Turbellarian-like” clade, the placement of Rhabditophora, and that of Platyhelminthes relative to the Lophotrochozoa (=Spiralia). The data presented here therefore represent a significant advance in our understanding of platyhelminth phylogeny, and will form the basis of a range of future research in the still-disputed classifications within this taxon.
    • Towards the identification of ancestrally shared regenerative mechanisms across the Metazoa: A Transcriptomic case study in the Demosponge Halisarca caerulea

      Kenny, NJ; de Goeij, JM; de Bakker, DM; Whalen, CG; Berezikov, E; Riesgo, A (Elsevier, 2018-02)
      Regeneration is an essential process for all multicellular organisms, allowing them to recover effectively from internal and external injury. This process has been studied extensively in a medical context in vertebrates, with pathways often investigated mechanistically, both to derive increased understanding and as potential drug targets for therapy. Several species from other parts of the metazoan tree of life, including Hydra, planarians and echinoderms, noted for their regenerative capabilities, have previously been targeted for study. Less well-documented for their regenerative abilities are sponges. This is surprising, as they are both one of the earliest-branching extant metazoan phyla on Earth, and are rapidly able to respond to injury. Their sessile lifestyle, lack of an external protective layer, inability to respond to predation and filter-feeding strategy all mean that regeneration is often required. In particular the demosponge genus Halisarca has been noted for its fast cell turnover and ability to quickly adjust its cell kinetic properties to repair damage through regeneration. However, while the rate and structure of regeneration in sponges has begun to be investigated, the molecular mechanisms behind this ability are yet to be catalogued. Here we describe the assembly of a reference transcriptome for Halisarca caerulea, along with additional transcriptomes noting response to injury before, shortly following (2 h post-), and 12 h after trauma. RNAseq reads were assembled using Trinity, annotated, and samples compared, to allow initial insight into the transcriptomic basis of sponge regenerative processes. These resources are deep, with our reference assembly containing > 92.6% of the BUSCO Metazoa set of genes, and well-assembled (N50s of 836, 957, 1688 and 2032 for untreated, 2 h, 12 h and reference transcriptomes respectively), and therefore represent excellent qualitative resources as a bedrock for future study. The generation of transcriptomic resources from sponges before and following deliberate damage has allowed us to study particular pathways within this species responsible for repairing damage. We note particularly the involvement of the Wnt cascades in this process in this species, and detail the contents of this cascade, along with cell cycle, extracellular matrix and apoptosis-linked genes in this work. This resource represents an initial starting point for the continued development of this knowledge, given H. caerulea's ability to regenerate and position as an outgroup for comparing the process of regeneration across metazoan lineages. With this resource in place, we can begin to infer the regenerative capacity of the common ancestor of all extant animal life, and unravel the elements of regeneration in an often-overlooked clade.
    • The use of anthropogenic marine debris as a nesting material by brown boobies (Sula leucogaster)

      Grant, ML; Lavers, JL; Stuckenbrock, S; Sharp, PB; Bond, AL (Elsevier, 2018-10-11)
      Marine debris is pervasive worldwide, and affects biota negatively. We compared the characteristics of debris incorporated within brown booby (Sula leucogaster) nests throughout their pantropical distribution by assessing the type, colour and mass of debris items within nests and in beach transects at 18 sites, to determine if nests are indicators of the amount of debris in local marine environments. Debris was present in 14.4% of nests surveyed, with the proportion of nests with debris varying among sites (range: 0–100%). There was minimal overlap between the type or colour of debris found in nests and on adjacent beaches at individual sites. This suggests that brown boobies do not select debris uniformly across their distribution. We propose that the nests of brown boobies can be used as a sentinel of marine debris pollution of their local environment.