Envisaging a global infrastructure to exploit the potential of digitised collections.

Tens of millions of images from biological collections have become available online over the last two decades. In parallel, there has been a dramatic increase in the capabilities of image analysis technologies, especially those involving machine learning and computer vision. While image analysis has become mainstream in consumer applications, it is still used only on an artisanal basis in the biological collections community, largely because the image corpora are dispersed. Yet, there is massive untapped potential for novel applications and research if images of collection objects could be made accessible in a single corpus. In this paper, we make the case for infrastructure that could support image analysis of collection objects. We show that such infrastructure is entirely feasible and well worth investing in.

Assessing the conservation of Miombo timber species through an integrated index of anthropogenic and climatic threats.

AIM: Angolan Miombo woodlands, rich in timber species of the Leguminosae family, go through one of the highest rates of deforestation in sub-Saharan Africa. This study presents, on the basis of updated information of the distribution of Leguminosae timber species native to Angola, an integrated index framing the main threats for trees, which aims to support new conservation measures. LOCATION: Sub-Saharan Africa, Republic of Angola. METHODS: The current distribution areas of six Leguminosae timber species (i.e., Afzelia quanzensis, Brachystegia spiciformis, Guibourtia coleosperma, Isoberlinia angolensis, Julbernardia paniculata, and Pterocarpus angolensis) were predicted through ensemble modeling techniques. The level of threat to each species was analyzed, comparing the species potential distribution with a threat index map and with the protected areas. The threat index of anthropogenic and climatic factors encompasses the effects of population density, agriculture, proximity to roads, loss of tree cover, overexploitation, trends in wildfires, and predicted changes in temperature and precipitation. RESULTS: Our results revealed that about 0.5% of Angola's area is classified as of "Very high" threat, 23.9% as "High" threat, and 66.5% as "Moderate" threat. Three of the studied species require special conservation efforts, namely B. spiciformis and I. angolensis, which have a large fraction of predicted distribution in areas of high threat, and G. coleosperma since it has a restricted distribution area and is one of the most valuable species in international markets. The priority areas for the conservation of Leguminosae timber species were found in Benguela and Huíla. MAIN CONCLUSIONS: This study provides updated data that should be applied to inform policymakers, contributing to national conservation planning and protection of native flora in Angola. Moreover, it presents a methodological approach for the predictions of species distribution and for the creation of a threat index map that can be applied in other poorly surveyed tropical regions.

A database of the global distribution of alien macrofungi.

BACKGROUND: Human activities are allowing the ever-increasing dispersal of taxa to beyond their native ranges. Understanding the patterns and implications of these distributional changes requires comprehensive information on the geography of introduced species. Current knowledge about the alien distribution of macrofungi is limited taxonomically and temporally, which severely hinders the study of human-mediated distribution changes for this taxonomic group. NEW INFORMATION: Here, we present a database on the global alien distribution of macrofungi species. Data on the distribution of alien macrofungi were searched in a large number of data sources, including scientific publications, grey literature and online databases. The database compiled includes 1966 records (i.e. species x region combinations) representing 2 phyla, 7 classes, 22 orders, 82 families, 207 genera, 648 species and 31 varieties, forms or subspecies. Dates of introduction records range from 1753 to 2018. Each record includes the location where the alien taxon was identified and, when available, the date of first observation, the host taxa or other important information. This database is a major step forward to the understanding of human-mediated changes in the distribution of macrofungal taxa.

Modelling landscape constraints on farmland bird species range shifts under climate change.

Several studies estimating the effects of global environmental change on biodiversity are focused on climate change. Yet, non-climatic factors such as changes in land cover can also be of paramount importance. This may be particularly important for habitat specialists associated with human-dominated landscapes, where land cover and climate changes may be largely decoupled. Here, we tested this idea by modelling the influence of climate, landscape composition and pattern, on the predicted future (2021-2050) distributions of 21 farmland bird species in the Iberian Peninsula, using boosted regression trees and 10-km resolution presence/absence data. We also evaluated whether habitat specialist species were more affected by landscape factors than generalist species. Overall, this study showed that the contribution of current landscape composition and pattern to the performance of species distribution models (SDMs) was relatively low. However, SDMs built using either climate or climate plus landscape variables yielded very different predictions of future species range shifts and, hence, of the geographical patterns of change in species richness. Our results indicate that open habitat specialist species tend to expand their range, whereas habitat generalist species tend to retract under climate change scenarios. The effect of incorporating landscape factors were particularly marked on open habitat specialists of conservation concern, for which the expected expansion under climate change seems to be severely constrained by land cover change. Overall, results suggest that particular attention should be given to landscape change in addition to climate when modelling the impacts of environmental changes for both farmland specialist and generalist bird distributions.

Ichthyological collection of the Museu Oceanográfico D. Carlos I.

The collection of the Museu Oceanográfico D. Carlos I is a historical specimen, instrument, and document collection that has been housed at the Aquário Vasco da Gama since 1935. The collection is largely the result of several scientific campaigns conducted by Dom Carlos de Bragança between 1896 and 1907. Specifically, the ichthyological collection consists of 675 surviving catalogue records of specimens caught, acquired or offered to D. Carlos I between 1892 to 1907, and includes the type specimen for Odontaspis nasutus Bragança, 1904 (junior synonym of Mitsukurina owstoni Jordan, 1898), along with several specimens of deep sea species. All specimens were captured in coastal Portuguese waters, and were preserved in alcohol, formalin, or mounted.

The collection of birds from Mozambique at the Instituto de Investigação Científica Tropical of the University of Lisbon (Portugal).

The Instituto de Investigação Científica Tropical of the University of Lisbon, which resulted from the recent merger (in 2015) of the former state laboratory Instituto de Investigação Científica Tropical in the University of Lisbon, holds an important collection of bird skins from the Portuguese-speaking African Countries (Angola, Mozambique, São Tomé and Príncipe, Guinea Bissau and Cape Verde), gathered as a result of several scientific expeditions made during the colonial period. In this paper, the subset from Mozambique is described, which was taxonomically revised and georeferenced. It contains 1585 specimens belonging to 412 taxa, collected between 1932 and 1971, but mainly in 1948 (43% of specimens) and 1955 (30% of specimens). The collection covers all eleven provinces of the country, although areas south of the Zambezi River are better represented than those north of the river. The provinces with the highest number of specimens were Maputo, Sofala, and Gaza. Although it is a relatively small collection with a patchy coverage, it adds significantly to Global Biodiversity Information Facility, with 15% of all records available before and during the collecting period (1830-1971) being the second largest dataset for that period for Mozambique.

Networks of global bird invasion altered by regional trade ban.

Wildlife trade is a major pathway for introduction of invasive species worldwide. However, how exactly wildlife trade influences invasion risk, beyond the transportation of individuals to novel areas, remains unknown. We analyze the global trade network of wild-caught birds from 1995 to 2011 as reported by CITES (Convention on International Trade in Endangered Species of Wild Fauna and Flora). We found that before the European Union ban on imports of wild-caught birds, declared in 2005, invasion risk was closely associated with numbers of imported birds, diversity of import sources, and degree of network centrality of importer countries. After the ban, fluxes of global bird trade declined sharply. However, new trade routes emerged, primarily toward the Nearctic, Afrotropical, and Indo-Malay regions. Although regional bans can curtail invasion risk globally, to be fully effective and prevent rerouting of trade flows, bans should be global.

Exploring the floristic diversity of tropical Africa.

BACKGROUND: Understanding the patterns of biodiversity distribution and what influences them is a fundamental pre-requisite for effective conservation and sustainable utilisation of biodiversity. Such knowledge is increasingly urgent as biodiversity responds to the ongoing effects of global climate change. Nowhere is this more acute than in species-rich tropical Africa, where so little is known about plant diversity and its distribution. In this paper, we use RAINBIO - one of the largest mega-databases of tropical African vascular plant species distributions ever compiled - to address questions about plant and growth form diversity across tropical Africa. RESULTS: The filtered RAINBIO dataset contains 609,776 georeferenced records representing 22,577 species. Growth form data are recorded for 97% of all species. Records are well distributed, but heterogeneous across the continent. Overall, tropical Africa remains poorly sampled. When using sampling units (SU) of 0.5°, just 21 reach appropriate collection density and sampling completeness, and the average number of records per species per SU is only 1.84. Species richness (observed and estimated) and endemism figures per country are provided. Benin, Cameroon, Gabon, Ivory Coast and Liberia appear as the botanically best-explored countries, but none are optimally explored. Forests in the region contain 15,387 vascular plant species, of which 3013 are trees, representing 5-7% of the estimated world's tropical tree flora. The central African forests have the highest endemism rate across Africa, with approximately 30% of species being endemic. CONCLUSIONS: The botanical exploration of tropical Africa is far from complete, underlining the need for intensified inventories and digitization. We propose priority target areas for future sampling efforts, mainly focused on Tanzania, Atlantic Central Africa and West Africa. The observed number of tree species for African forests is smaller than those estimated from global tree data, suggesting that a significant number of species are yet to be discovered. Our data provide a solid basis for a more sustainable management and improved conservation of tropical Africa's unique flora, and is important for achieving Objective 1 of the Global Strategy for Plant Conservation 2011-2020. In turn, RAINBIO provides a solid basis for a more sustainable management and improved conservation of tropical Africa's unique flora.

The collection of birds from São Tomé and Príncipe at the Instituto de Investigação Científica Tropical of the University of Lisbon (Portugal).

The former Instituto de Investigação Científica Tropical-IICT (Lisbon, Portugal), recently integrated into the University of Lisbon, gathers important natural history collections from Portuguese-speaking African countries. In this study, we describe the bird collection from the Democratic Republic of São Tomé and Príncipe, which was fully taxonomically checked and georeferenced. The IICT bird collection contains 5598 specimens, of which 559 are from São Tomé and Príncipe, representing 85 taxa, including 19 endemic species and 13 endemic subspecies of birds. The specimens were collected between 1946 and 1973, although 43% of the records are from 1954 and 45% are from 1970. The geographic distribution of samples covers the whole territory, with a higher number of records from São Tomé than from Príncipe. The districts with highest number of records are Pagué (equivalent to Príncipe Island), and Água Grande and Mé-Zochi on São Tomé. Despite the relatively low number of specimens per taxon, the importance of the collection is considerable due to the high number of endemic and threatened species represented. Furthermore, it adds valuable information to the GBIF network, especially for a country whose two islands are each an Endemic Bird Area and for which substantial gaps in ornithological knowledge remain.

RAINBIO: a mega-database of tropical African vascular plants distributions.

The tropical vegetation of Africa is characterized by high levels of species diversity but is undergoing important shifts in response to ongoing climate change and increasing anthropogenic pressures. Although our knowledge of plant species distribution patterns in the African tropics has been improving over the years, it remains limited. Here we present RAINBIO, a unique comprehensive mega-database of georeferenced records for vascular plants in continental tropical Africa. The geographic focus of the database is the region south of the Sahel and north of Southern Africa, and the majority of data originate from tropical forest regions. RAINBIO is a compilation of 13 datasets either publicly available or personal ones. Numerous in depth data quality checks, automatic and manual via several African flora experts, were undertaken for georeferencing, standardization of taxonomic names and identification and merging of duplicated records. The resulting RAINBIO data allows exploration and extraction of distribution data for 25,356 native tropical African vascular plant species, which represents ca. 89% of all known plant species in the area of interest. Habit information is also provided for 91% of these species.

The Botanic Mission to Mozambique (1942-1948): contributions to knowledge of the medicinal flora of Mozambique.

This article reviews the historical and scientific findings of the Botanic Mission to Mozambique (1942-1948) under the Tropical Botanic Garden of the Instituto de Investigação Científica Tropical, in Lisbon, highlighting the collectors' field notes with the aim of identifying the traditional medicinal uses of Mozambican flora. Having collated information on 71 taxa (70 species and one genus), the medicinal usage of 34 species presumably not yet reported in Mozambique was identified, including five whose therapeutic use still had not yet been described in the African continent. Overall, 58 uses presumably not yet reported in Mozambique were recorded.

Documenting biogeographical patterns of African timber species using herbarium records: a conservation perspective based on native trees from Angola.

In many tropical regions the development of informed conservation strategies is hindered by a dearth of biodiversity information. Biological collections can help to overcome this problem, by providing baseline information to guide research and conservation efforts. This study focuses on the timber trees of Angola, combining herbarium (2670 records) and bibliographic data to identify the main timber species, document biogeographic patterns and identify conservation priorities. The study recognized 18 key species, most of which are threatened or near-threatened globally, or lack formal conservation assessments. Biogeographical analysis reveals three groups of species associated with the enclave of Cabinda and northwest Angola, which occur primarily in Guineo-Congolian rainforests, and evergreen forests and woodlands. The fourth group is widespread across the country, and is mostly associated with dry forests. There is little correspondence between the spatial pattern of species groups and the ecoregions adopted by WWF, suggesting that these may not provide an adequate basis for conservation planning for Angolan timber trees. Eight of the species evaluated should be given high conservation priority since they are of global conservation concern, they have very restricted distributions in Angola, their historical collection localities are largely outside protected areas and they may be under increasing logging pressure. High conservation priority was also attributed to another three species that have a large proportion of their global range concentrated in Angola and that occur in dry forests where deforestation rates are high. Our results suggest that timber tree species in Angola may be under increasing risk, thus calling for efforts to promote their conservation and sustainable exploitation. The study also highlights the importance of studying historic herbarium collections in poorly explored regions of the tropics, though new field surveys remain a priority to update historical information.

Spatial modeling of factor analysis scores: the case of heavy metal biomonitoring in mainland Portugal.

The use of mosses as biomonitors operates as an indicator of their concentration in the environment, becoming a methodology which provides a significant interpretation in terms of environmental quality. The different types of pollution are variables that can not be measured directly in the environment - latent variables. Therefore, we propose the use of factor analysis to estimate these variables in order to use them for spatial modelling. On the contrary, the main aim of the commonly used principal components analysis method is to explain the variability of observed variables and it does not permit to explicitly identify the different types of environmental contamination. We propose to model the concentration of each heavy metal as a linear combination of its main sources of pollution, similar to the case of multiple regression where these latent variables are identified as covariates, though these not being observed. Moreover, through the use of geostatistical methodologies, we suggest to obtain maps of predicted values for the different sources of pollution. With this, we summarize the information acquired from the concentration measurements of the various heavy metals, and make possible to easily determine the locations that suffer from a particular source of pollution.

A Missão Botânica de Moçambique (1942-1948): contribuições para o conhecimento da flora medicinal de Moçambique / The Botanic Mission to Mozambique (1942-1948): contributions to knowledge of the medicinal flora of Mozambique

O artigo revisita o espólio histórico-científico aduzido pela Missão Botânica de Moçambique (1942-1948) à guarda do Jardim Botânico Tropical do Instituto de Investigação Científica Tropical (Lisboa), destacando os cadernos de campo dos seus coletores, com o objetivo de identificar os usos medicinais tradicionais da flora moçambicana. Tendo-se coligido informação relativa a 71 taxa (setenta espécies e um género), identificou-se a utilização medicinal de 34 espécies presumivelmente ainda não reportada para Moçambique, entre as quais, cinco cujo uso terapêutico ainda não havia sido atribuído ao continente africano. No total registaram-se 58 utilizações presumivelmente ainda não relatadas em Moçambique.

This article reviews the historical and scientific findings of the Botanic Mission to Mozambique (1942-1948) under the Tropical Botanic Garden of the Instituto de Investigação Científica Tropical, in Lisbon, highlighting the collectors’ field notes with the aim of identifying the traditional medicinal uses of Mozambican flora. Having collated information on 71 taxa (70 species and one genus), the medicinal usage of 34 species presumably not yet reported in Mozambique was identified, including five whose therapeutic use still had not yet been described in the African continent. Overall, 58 uses presumably not yet reported in Mozambique were recorded.

The collection and database of Birds of Angola hosted at IICT (Instituto de Investigação Científica Tropical), Lisboa, Portugal.

The bird collection of the Instituto de Investigação Cientítica Tropical (Lisbon, Portugal) holds 5598 preserved specimens (skins), mainly from Angola, Mozambique, Guinea-Bissau, São Tomé and Principe, and Cape Verde. The subset collection from Angola includes 1560 specimens, which were taxonomically revised and georeferenced for the publication of this data paper. The collection contains a total of 522 taxa, including 161 species and 361 subspecies. Two species are classified by the IUCN Red List as Endangered - the wattled crane (Grus carunculata) and the Gabela bush-shrike (Laniarius amboimensis) - and two are classified as vulnerable - African penguin (Spheniscus demersus) and the white-headed vulture (Trigonoceps occipitalis). The temporal span of the database ranges between 1943 and 1979, but 32% are from years 1958-1959, and 25% from years 1968-1969. The spatial coverage of the collection is uneven, with 2/3 of the records representing only four of the eighteen provinces of the country, namely Huíla, Moxico, Namibe and Cuanza Sul. It adds, however, valuable information for the Huíla area of the Angolan Scarp, which is probably a biodiversity hotspot of global conservation priority. Furthermore, this georeferenced database adds invaluable bird information to the GBIF network, for one of the countries with highest but less known biodiversity in Africa.

Spatio-temporal patterns of Cu contamination in mosses using geostatistical estimation.

Several recent studies have reported temporal trends in metal contamination in mosses, but such assessments did not evaluate uncertainty in temporal changes, therefore providing weak statistical support for time comparisons. Furthermore, levels of contaminants in the environment change in both space and time, requiring space-time modelling methods for map estimation. We propose an indicator of spatial and temporal variation based on space-time estimation by indicator kriging, where uncertainty at each location is estimated from the local distribution function, thereby calculating variability intervals for comparison between several biomonitoring dates. This approach was exemplified using copper concentrations in mosses from four Portuguese surveys (1992, 1997, 2002 and 2006). Using this approach, we identified a general decrease in copper contamination, but spatial patterns were not uniform, and from the uncertainty intervals, changes could not be considered significant in the majority of the study area.

Assessment of human exposure to environmental heavy metals in soils and bryophytes of the central region of Portugal.

This study intends to identify the spatial patterns of variation for some metals and metalloids, in soils and mosses, in the central region of Portugal. The purposes were: (i) to identify relationships amongst five elements (Cu, Pb, Zn, Cr and As) in three different media (topsoil, bottom soil and bryophytes) and with some site-specific characteristics, using Multiple Correspondence Analysis; (ii) to define spatial patterns of variation for the associations identified by Multiple Correspondence Analysis using Variography and Ordinary Kriging; and (iii) to assess atmospheric deposition as a source of heavy metals to the topsoil by crossing results with the biomonitors. The results indicated relatively low metal concentrations in soils and mosses. Some metal associations and dissociations were identified. The spatial patterns of variation of bottom and topsoil are distinct. There is some evidence that different site-specific characteristics control the spatial distribution of different elements. The areas within the central region of Portugal with a higher vulnerability to metal contamination were identified.

Application of indicator kriging to the complementary use of bioindicators at three trophic levels.

The use of biological indicators is widespread in environmental monitoring, although it has long been recognised that each bioindicator is generally associated with a range of potential limitations and shortcomings. To circumvent this problem, this study adopted the complementary use of bioindicators representing different trophic levels and providing different type of information, in an innovative approach to integrate knowledge and to estimate the overall health state of ecosystems. The approach is illustrated using mercury contamination in primary producers (mosses), primary consumers (domestic pigeons and red-legged partridges) and top predators (Bonelli's eagles) in southern Portugal. Indicator kriging geostatistics was used to identify the areas where mercury concentration was higher than the median for each species, and to produce an index that combines mercury contamination across trophic levels. Spatial patterns of mercury contamination were consistent across species. The combined index provided a new level of information useful in incorporating measures of overall environmental contamination into pollution studies.

Detection of exposition risk to arsenic in Portugal assessed by air deposition in biomonitors and water contamination.

Human exposure risk to environmental arsenic is evaluated by combining drinking water and atmospheric deposition, assessed tap water analysis and a moss biomonitoring survey. Water analyses are assessed through mandatory national and European regulations for the supplying areas. Moss concentrations were determined as part of a biomonitoring survey performed at a national level in 2002. For each of the parameters, continuous maps of indicator values were determined applying geostatistical methods, namely indicator kriging. The exposure risk of human populations was determined afterwards combining the indicator values of water and biomonitoring values. The identified regions of accumulated water and atmospheric exposure are in the inland north and central areas of the country.

Transplants of aquatic mosses as biomonitors of metals released by a mine effluent.

Transplants of the aquatic moss Fontinalis antipyretica Hedw. were used to assess the contamination of an industrial effluent discharge on a river located in south Portugal. The sampling program was run for 2 years, using a newly developed transplant device in ten stations, and the elements analysed were Cu, Zn, Pb, Fe, Ni, Ca, K, and Mg. An increase of water contamination by Cu, Zn was detected, and to a lesser extent, Pb. The increase was verified in the extra and intracellular moss fraction, especially for soluble Cu in the first 4 km after the discharge point, and also for particulate metal at the first station after the discharge. The effects of metal contamination could be related to changes in the intracellular concentrations of Mg, indicating possible stress effects.