Biodiversity Data Journal :
Research Article
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Corresponding author: Henrique Niza (hmniza@fc.ul.pt), Marta Bento (mabento@fc.ul.pt), Luis F. Lopes (filipe.lopes@ihmt.unl.pt), Alexandra Cartaxana (macartaxana@edu.ulisboa.pt), Alexandra M. Correia (amcorreia@fc.ul.pt)
Academic editor: Dimitris Poursanidis
Received: 18 May 2021 | Accepted: 24 Jul 2021 | Published: 24 Sep 2021
© 2021 Henrique Niza, Marta Bento, Luis Lopes, Alexandra Cartaxana, Alexandra Correia
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Niza H, Bento M, Lopes LF, Cartaxana A, Correia AM (2021) A picture is worth a thousand words: using digital tools to visualise marine invertebrate diversity data along the coasts of Mozambique and São Tomé & Príncipe. Biodiversity Data Journal 9: e68817. https://doi.org/10.3897/BDJ.9.e68817
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The amount of biological data available in online repositories is increasing at an exponential rate. However, data on marine invertebrate biodiversity resources from Mozambique and São Tomé and Príncipe are still sparse and scattered. Online repositories are useful instruments for biodiversity research, as they provide a fast access to data from different sources. The use of interactive platforms comprising web mapping are becoming more important, not only for the scientific community, but also for conservation managers, decision-makers and the general public as they allow data presentation in simple and understandable visual schemes. The main goal of this study was to create an interactive online digital map (hosted and available at MARINBIODIV Atlas), through the collection of data from various sources, to visualise marine invertebrate occurrences and distribution across different habitats, namely mangroves, seagrasses, corals and other coastal areas, in Mozambique and São Tomé and Príncipe. The acquired biodiversity data were managed and structured to be displayed as spatial data and to be disseminated using the geographic information system ArcGIS, where data can be accessed, filtered and mapped. The ArcGIS web mapping design tools were used to produce interactive maps to visualise marine invertebrate diversity information along the coasts of Mozambique and São Tomé and Príncipe, through different habitats, offering the foundation for analysing species incidence and allocation information. Understanding the spatial occurrences and distribution of marine invertebrates in both countries can provide a valuable baseline, regarding information and trends on their coastal marine biodiversity.
biodiversity, coastal marine fauna, macroinvertebrates, Mozambique channel, online mapping, São Tomé and Príncipe
There is an exponential increase in the amount of biological data available in online repositories. In biodiversity studies, digital repositories are useful resources because they provide centralisation of available global knowledge, enable prompt accessibility, incorporate data from multiple sources around the world, allow more holistic data analysis and accurate reproducible studies (
Maps are suitable tools to communicate complex spatial information, being extremely useful to explore contents and for raising awareness about different issues. For instance, maps on species occurrences and spatial patterns are mandatory tools to provide biodiversity information for environmental resource management. The increase of georeferenced species occurrence data enables the use of geographic information system (GIS) tools that can be applied for geographic data representations through, for example, the creation of accurate distribution maps. High quality, robust and consistent data and information on species occurrences at different spatial and temporal levels, allow the use of GIS to manage digital biodiversity data from various sources to analyse it and display it in a spatially explicit manner (
For greater accessibility, web mapping is the method of using interactive maps made accessible on the internet by GIS. These may implement filters that allow the user to choose the data to be displayed, deriving different levels of information. For the scientific community, the public and policy-makers, the use of interactive platforms consisting of web maps is becoming increasingly important, as they allow up-to-date data to be presented using clear and understandable visual systems (
The growth of human populations within coastal areas has increased due to rural-urban migration, with people relocating to more urbanised and economic centres. This migration increases human pressure on the environment due to land and marine-based human activities. As a result, coastal and marine living resources and their habitats are being adversely lost or damaged, reducing marine biodiversity (
The main objectives of this study were to: 1) integrate comprehensive data on marine invertebrates from mangroves, seagrasses, corals and other coastal areas of Mozambique (MOZ) and São Tomé and Príncipe (STP) into an interactive GIS mapping system and 2) disseminate this information online through the web mapping MARine INvertebrate BIODIVersity (MARINBIODIV Atlas) along the coasts of Mozambique and São Tomé and Príncipe. We explored existing digital records of marine biodiversity from MOZ and STP to generate species occurrence distribution maps and made these available online through a web map - MARINBIODIV Atlas. These data increased our understanding of marine invertebrate biodiversity along the coasts of MOZ and STP contributing with baseline information on coastal marine invertebrate occurrences and distribution in both countries. Further, the MARINBIODIV Atlas provides a new tool for science, policy-making and legislating, as well as for engaging Mozambican and São Tomé and Príncipe’s citizens with science and the preservation of their natural resources.
This study comprised the use of digital tools: (1) to create an interactive geographic data representation of marine invertebrate species occurrences and distribution and respective habitats, across the coastal zones of MOZ and STP in ArcGIS Desktop (ArcMap 10.7.1), by a comprehensive compilation of biodiversity data contained in digital repositories, NHC records and scientific literature and (2) to construct an interactive digital platform map (MARINBIODIV Atlas) for online dissemination using ArcGIS Online, specifically designed for web mapping (Fig.
The biodiversity database was created by combining and organising data from MOZ and STP on marine invertebrates, as well as aggregating global biodiversity data from digital repositories. Annelida, Arthropoda, Cnidaria, Echinodermata and Mollusca were chosen as the phyla that were most representative of the study areas and habitats. Specifically, data were gathered from worldwide open-source information from online digital biodiversity repositories, such as GBIF (Suppl. material
Geographic analysis, using QGIS, entailed steps, such as geographical data processing and merging different habitat layers. Habitat data collected from images instead were georeferenced using the inbuilt QGIS Georeferencer function. In this case, the georeferencing process – which involves taking a raster image coverage, assigning a coordinate system and coordinates to it and translating, transforming and warping it into a position relative to some other spatial data – was accomplished by assigning real-world coordinates to specific pixels on the raster obtained by the coordinates on the map image itself.
For georeferencing, a total of nine ground control points were used in the raster relative to São Tomé Island and eight ground control points for the raster relative to Príncipe Island (Fig.
The habitats studied encompassed mangroves, seagrasses and corals present in the coastal zones of MOZ and STP. The spatial datasets mapping the coastal habitats, added as layers, were downloaded from the UN Environment World Conservation Monitoring Centre website at http://data.unep-wcmc.org and the ReefBase website at http://reefbase.org/gis_maps/datasets.aspx. The datasets, used for each habitat, were as follows: Coral - Global Distribution of Coral Reefs (Dataset ID: WCMC-008): the dataset shows the global distribution of coral reefs in tropical and subtropical regions, composed of one set of polygon occurrence data, with a temporal range from 1954 to 2018 and the reference system WGS 1984 (version 4.0 - November 2018); Coral Bleaching (Dataset: ReefBase): the dataset provides point occurrence data of observation details of coral bleaching around the world, with a temporal scope since early 2002; Monitoring Sites (Dataset: ReefBase): the dataset provides point occurrence data on coral reef monitoring sites locations from major reef monitoring programmes. Reefs Location (Dataset: ReefBase): the dataset provides point occurrence data on coral reef locations; Marine Protected Areas (Dataset: ReefBase): the dataset provides point occurrence data on marine protected areas with coral reef zones. Mangrove: World Atlas of Mangroves (Dataset ID: WCMC-011): the dataset shows the global distribution of mangroves and it was produced mostly from satellite imagery, composed of one set of polygon occurrence data, with a temporal series mainly from 1999 to 2003 and the reference system WGS 1984 (version 2.0 – December 2017); Global Distribution of Mangroves USGS (Dataset ID: WCMC 010): the dataset shows the global distribution of mangrove forests derived from earth observation satellite imagery, composed of one set of polygon occurrence data, with a temporal range from 1997 to 2000 and the reference system WGS 1984 (version 1.3 – June 2015); Global Mangrove Watch (Dataset ID: GMW-001): the dataset shows a global baseline map of mangroves using satellite imagery, composed of one set of polygon occurrence data, with a temporal array from 1996 to 2016. Data retrieved on 4 April 2019 (version 2.0). Seagrass: Global Distribution of Seagrasses (Dataset ID: WCMC-013-014): the dataset shows the global distribution of seagrasses, composed of two subsets of point and polygon occurrence data, with a temporal range from 1934 to 2015 and the reference system WGS 1984 (version 6.0 - June 2018). The search was expanded to the scientific literature to resolve the lack of habitat information in São Tomé and Príncipe.
The layers with the same geometry type, for example, "Point" or "Polygon," were merged into a single layer using the command "Merge Vector Layers" to combine all data corresponding to each habitat (corals, mangroves and seagrasses) in a single shapefile.
The process of vectorisation generated several thousands of small polygons in some places, which created overlapping polygons. To correct these, a dissolve operation was performed with Mapshaper software. (
The input layers “Global Distribution of Coral Reefs”, “Coral Bleaching”, “Monitoring Sites”, “Reefs Location” and “Marine Protected Areas” were merged into a point data layer named “Coral point-data”. Both input layers “Global Distribution of Mangroves USGS” and “Global Mangrove Watch” were merged into a polygon data layer named “Mangrove polygon-data”. All layers created manually were also joined to their respective habitat layers. Region layers were downloaded from public domain map data available online: administrative boundaries, divisions and outline of MOZ and STP as ESRI Shape file format latitude and longitude coordinates at GADM data website at https://gadm.org/data.html; Mozambican and São Tomé and Príncipe EEZ as Shapefile format at Marine Regions website at www.marineregions.org.
The data were imported to ArcMap as a CSV file with latitude and longitude coordinates stored in separated columns. Point coordinates’ longitude and latitude were mapped to X and Y fields, respectively. The coordinate reference system used was EPSG:4326 or WGS 1984. The ArcMap layouts are specifically designed to provide a foundation for web mapping species occurrences and distribution data across MOZ and STP habitats. Based on point data and/or polygon data, the arrangement of combined data corresponding to the three habitat layers (corals, mangroves and seagrass) provides the basis for the filtering of habitat types.
To promote online data dissemination and make it user-friendly, a digital platform web map (MARINBIODIV Atlas) was developed to visualise marine invertebrate diversity along the coasts of Mozambique and São Tomé and Príncipe, by using the complete cloud-based ArcGIS mapping software, ArcGIS Online, designed for web mapping and exploring data through filtering and mapping different layers of information.
MARINBIODIV Atlas web map is an interactive digital platform that can be used to visualise the occurrences and distribution of invertebrate species along the coastlines of MOZ and STP. It provides a variety of filter layers to manipulate the data, allowing the visualisation of occurrences against specific criteria (e.g. type of habitat, taxonomic classification, amongst others). The web map contains 11 layers that can be selected or unselected to filter the data in display. These layers are grouped in three main sub-groups: 1) species occurrences, 2) habitats and 3) MOZ and STP boundaries. To provide geographical context, the continents and oceans are also represented in the background (Figs
The web map's homepage uses a full-screen canvas template, presenting part of Africa, as well as the Atlantic and Indian Oceans comprising the study areas. Filtering can be done through the collapsible layers' menu, at the top right side of the map, which includes five layers (species occurrences, MOZ and STP areas and EEZ). The occurrences in the map are clustered, i.e. symbols scale proportionally to the number of occurrences of a given species at a location. Species, genus or family can be searched through the filter symbol at the top left of the map (Fig.
The species occurrence layers are separated into 13 main classes, represented by specific symbols: barnacle, bivalve, cephalopod, coral, crab, echinoderm, gastropod, lobster, medusa, sea anemone, sea spider, shrimp and worm (Fig.
Habitats are divided into three groups: corals, mangroves and seagrasses, with polygon-data and point-data layers, each represented with specific symbology (Figs
Fig.
The interactive digital platform is hosted and available at MARINBIODIV Atlas.
Marine biodiversity is essential to human well-being providing essential services, such as nutrient cycling, ecosystem stability, food, medicinal resources and recreation, amongst others. Thus, it is of the utmost importance to gather existing knowledge and transmit it to decision-makers so that governments, together with the civil society, safeguard biodiversity health. We compiled and integrated data on marine invertebrates from mangroves, seagrasses and corals along the coastal zones of Mozambique and São Tome and Príncipe. These data were incorporated into a web platform to assemble an interactive map, MARINBIODIV Atlas, on the occurrence and distribution of marine invertebrates across different habitats in MOZ and STP, to disseminate and share the obtained information with the scientific community, conservation managers, policy-makers and the general public. As biodiversity loss continues and limited resources are available to preserve and protect biodiversity, replication of this type of approach in other regions and other species (e.g. fishes) is important (
MARINBIODIV Atlas was developed using the ArcGIS Online software, which allowed the creation and combination of multiple habitat layers, as well as other information layers and to define marker symbology. One of the major challenges for the development of this Atlas was related to the preparation of habitat shapefiles, compiled from multiple, varying scale and quality data sources. While some used consistent methodology across all regions, others were less consistent, including observational data from different regional, national and international sources. These factors generated a mismatch in the position of the layers in relation to the coastline, which was corrected as far as possible, by creating representative polygons, based on satellite imagery. Overall, most polygons used in this work are relatively well spatially aligned to the coastline layer. In spite of our best efforts to reduce spatial representation bias, accuracy may vary amongst locations because layer sources were different and related errors were not consistent across datasets, including cloud cover, background noise, Landsat scanline error and misclassification of certain areas due to striping artifacts, amongst others. Nevertheless, precision is best measured on the seaward side when compared to the landward side due to the presence of terrestrial vegetation (
Habitat mapping is an effective method to gain a better understanding of biodiversity in a given region. Mangroves, seagrasses and corals were the only habitats mapped along the MOZ and STP coastlines. The lack of other mapped habitat types may generate limitations to fully assess the ecological and biological significance of these marine regions. To avert these constraints, data from “open sea” and “other coastal areas” were also included in MARINBIODIV Atlas. Data gaps related to habitat mapping might be explained by a lack of research financing and geopolitical instability. These generally hinder data collection and monitoring programmes aimed at improving representation and understanding of those countries' biodiversity and ecosystems, resulting in less available information (
Marine invertebrates are a major component of marine habitats, encompassing a highly diverse group (
Nearshore habitats are extremely important socioeconomically, particularly in the western Indian Ocean, because 65 million people live within 10 kilometres of the coast in the greater Indian Ocean region (
By being freely accessible, the MARINBIODIV Atlas can be further used to develop new research projects, to create teaching or dissemination tools, to write books, articles and brochures for outreach, amongst other work programmes. The significance of this study lies in its ability to provide clear baseline biodiversity data and digital resources that can be used to model the distribution of marine invertebrate species and estimate the size of species ranges in mangroves, seagrasses and corals along the coasts of Mozambique and São Tomé and Príncipe in order to predict extinction risk and, hopefully, to advance biodiversity conservation strategies.
Due to an overwhelming and continual increase in data available online, integration of biodiversity data from multiple sources, formatted according to international standards, is vital for data analysis and critical for extracting knowledge for the field of biological sciences (
Further development of this study could have broader implications, such as providing a framework or baseline information for more detailed ecological research, resulting in the identification of natural areas and ecological networks to provide information for habitat preservation and restoration, strategic land-use planning, as well as marine invertebrate monitoring, management and conservation.
Special thanks are given to Luiz Coutinho for technical support, for lodging the ArcGIS web map produced here and making it available online. This work is part of the project COBIO-NET (Coastal biodiversity and food security in peri-urban Sub-Saharan Africa: assessment, capacity building and regional networking in contrasting Indian and Atlantic Oceans), funded by AGA KHAN Foundation and Fundação para a Ciência e a Tecnologia (FCT) (50:50). LF Lopes and M Bento acknowledge the financial support of Fundação para a Ciência e Tecnologia (Ref. GHTM–UID/Multi/04413/2013 and SFRH/BD/147875/2019, respectively). Additional support was provided by FCUL (Faculdade de Ciências, Universidade de Lisboa) and MNHNC (Museu Nacional de História Natural e da Ciência, Universidade de Lisboa), with human resources and digital space to lodge the Web Map on an ESRI platform. This publication was funded by the European Union's Horizon 2020 Research and Innovation Programme under grant agreement N810139: Project Portugal Twinning for Innovation and Excellence in Marine Science and Earth Observation – PORTWIMS.
H. Niza: Methodology, Software, Validation, Investigation, Data Curation, Writing - Original Draft, Writing - Review & Editing, Visualisation. M. Bento: Methodology, Validation, Investigation, Data Curation, Writing - Review & Editing, Visualisation. L.F. Lopes: Conceptualisation, Supervision, Writing - Original Draft, Writing - Review & Editing, Visualisation, Project administration. A. Cartaxana: Investigation, Supervision, Writing - Review & Editing, Visualisation. A.M. Correia: Conceptualisation, Supervision, Writing - Original Draft, Writing - Review & Editing, Visualisation, Project administration.
Mozambique and São Tomé and Príncipe occurrence data