Biology subjects

Silva, C. N. S.

Publications and source records attributed to Silva, C. N. S..

4 recordsLinked to original sources

bioRxiv2023

Environmental determinants of suitable habitat and the prediction of a southern shift in the future distribution of spiny lobsters, genus Jasus

Climate change is altering environmental conditions which is affecting species habitats globally. As a result, many species are shifting their habitat ranges poleward to ensure that they remain within their optimal thermal range. On average, marine species have shifted their ranges poleward by approximately 72km to track their optimal thermal conditions compared to 17km for terrestrial species. These range shifts are pushing some species out of their currently fished areas. This will require nations and fishery companies to predict the most likely areas their target species could move to and obtain permits to fish in those new areas. Spiny lobsters (genus Jasus) are likely to shift their ranges poleward as they are distributed within a relatively tight latitudinal band, but there is limited information about the extent of any potential range shifts. The aims of this study were to identify the environmental variables that characterise the current habitat locations of lobsters within the genus Jasus, and to predict their potential distribution by modelling future suitable habitat under the RCP45, RCP60, and RCP85 climate scenarios using MaxEnt. There were 16 environmental variables used for modelling suitable habitat for the present (2000-2014), while only four environmental variables were available for modelling in two future time periods (2040-2050 and 2090-2100). There was a predicted overall southern shift in suitable habitat locations for all species. The most important environmental variable identified for species distributed along continental shelves (J. edwardsii and J. lalandii) was benthic temperature. Benthic nutrients (silicate, nitrate, and phosphate) were the most important variables for species distributed around islands and on seamounts (J. paulensis, J. frontalis, and J. tristani). Approximately 90% of Jasus lobsters present range contained highly suitable habitat locations. The percent of highly suitable locations under the RCP45 and RCP60 scenarios were higher than the present percentages for each species, while under the RCP85 scenario, there was a decrease of highly suitable habitat for most species in 2040-2050 period, while for the 2090- 2100 period, there was an increase in the percent of highly suitable habitats. This study provides evidence that Jasus populations might become more abundant in the southern extents of their current range as they track their optimum habitat conditions.

ecology↗

bioRxiv2023

Genomic evidence for West Antarctic Ice Sheet collapse during the Last Interglacial Period

The marine-based West Antarctic Ice Sheet (WAIS) is considered vulnerable to irreversible collapse under future climate trajectories and its tipping point may even lie within the mitigated warming scenarios of 1.5-2 {degrees}C of the United Nations Paris Agreement. Knowledge of ice loss during similarly warm past climates, including the Last Interglacial, when global sea levels were 5-10 m higher than today, and global average temperatures of 0.5-1.5 {degrees}C warmer than preindustrial levels, could resolve this uncertainty. Here we show, using a panel of genome-wide, single nucleotide polymorphisms of a circum-Antarctic octopus, persistent, historic signals of gene flow only possible with complete WAIS collapse. Our results provide the first empirical evidence that the tipping point of WAIS loss could be reached even under stringent climate mitigation scenarios. One-Sentence SummaryHistorical gene flow in marine animals indicate the West Antarctic Ice Sheet collapsed during the Last Interglacial.

evolutionary biology↗

bioRxiv2022

A scalable open-source framework for machine learning based image collection, annotation and classification: a case study for automatic fish species identification

Citizen science platforms, social media and multiple smart phone applications enable collection of large amounts of georeferenced images. This provides a huge opportunity in biodiversity and ecological research, but also creates challenges for efficient data handling and processing. Recreational and small-scale fisheries is one of the fields that could be revolutionised by efficient, widely accessible and machine learning based processing of georeferenced images. The majority of non-commercial inland and coastal fisheries are considered data poor and are rarely assessed, yet they provide multiple societal benefits and can have large ecological impacts. Given that large quantities of fish observations and images are being collected by fishers every day, artificial intelligence (AI) and computer vision applications offer a great opportunity to improve data collection, automate analyses and inform management. Yet, to date, many AI image analysis applications in fisheries are focused on the commercial sector and are not publicly available for community use. In this study we present an open-source modular framework for large scale image storage, handling, annotation and automatic classification, using cost- and labour-efficient methodologies. The tool is based on TensorFlow Lite Model Maker library and includes data augmentation and transfer learning techniques, applied to different convolutional neural network models. We demonstrate the implementation of this framework in an example case study for automatic fish species identification from images taken through a recreational fishing smartphone application. The framework presented here is highly customisable for further advancement and community based image collection and annotation.

ecology↗

bioRxiv2018

Genetic potential for disease resistance in a critically endangered frog decimated by chytridiomycosis.

Southern corroboree frogs (Pseudophryne corroboree) have been driven to functional extinction in the wild after the emergence of the amphibian fungal pathogen Batrachochytrium dendrobatidis (Bd) in southeastern Australia in the 1980s. This species is currently maintained in a captive assurance colony and is managed to preserve the genetic diversity of the founding populations. However, it is unlikely that self-sustaining wild populations can be re-established unless Bd resistance increases. We performed a Bd-challenge study to investigate the association between genetic variants of the major histocompatibility complex class IA (MHC) and genome-wide single nucleotide polymorphisms (SNPs). We also investigated differences in Bd susceptibility among individuals and populations, and the genetic diversity and population genetic structure of four natural P. corroboree populations. We found several MHC alleles and SNPs associated with Bd infection load and survival, provide evidence of significant structure among populations, and identified population-level differences in the frequency of influential variants. We also detected evidence of positive selection acting on the MHC and a subset of SNPs as well as evidence of high genetic diversity in P. corroboree populations. We suggest that low interbreeding rates may have contributed to the demise of this species by limiting the spread of Bd resistance genes. However, our findings demonstrate that despite dramatic declines there is potential to restore high levels of genetic diversity in P. corroboree. Additionally, we show that there are immunogenetic differences among captive southern corroboree frogs, which could be manipulated to increase disease resistance and mitigate the key threatening process, chytridiomycosis.

genomics↗