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Large language models overcome the challenges of unstructured text data in ecology
Publication . Castro, Andry; Pinto, João; Reino, Luís; Pipek, Pavel; Capinha, César
The vast volume of currently available unstructured text data, such as research papers, news, and technical report data, shows great potential for ecological research. However, manual processing of such data is labour-intensive, posing a significant challenge. In this study, we aimed to assess the application of three state-of-the-art prompt-based large language models (LLMs), GPT-3.5, GPT-4, and LLaMA-2-70B, to automate the identification, interpretation, extraction, and structuring of relevant ecological information from unstructured textual sources. We focused on species distribution data from two sources: news outlets and research papers. We assessed the LLMs for four key tasks: classification of documents with species distribution data, identification of regions where species are recorded, generation of geographical coordinates for these regions, and supply of results in a structured format. GPT-4 consistently outperformed the other models, demonstrating a high capacity to interpret textual data and extract relevant information, with the percentage of correct outputs often exceeding 90% (average accuracy across tasks: 87–100%). Its performance also depended on the data source type and task, with better results achieved with news reports, in the identification of regions with species reports and presentation of structured output. Its predecessor, GPT-3.5, exhibited slightly lower accuracy across all tasks and data sources (average accuracy across tasks: 81–97%), whereas LLaMA-2-70B showed the worst performance (37–73%). These results demonstrate the potential benefit of integrating prompt-based LLMs into ecological data assimilation workflows as essential tools to efficiently process large volumes of textual data.
Negative and positive impacts of alien macrofungi: a global scale database
Publication . Monteiro, Miguel; Capinha, César; Ferreira, Maria Teresa; Nuñez, Martin A.; Reino, Luís
Advances in ecological research during the last decades have led to an improved understanding of the
impacts of alien species. Despite that, the effects of alien macrofungi have often received little attention
and are still poorly understood. With the aim of reducing this knowledge gap, we compiled a database of
the recorded socio-economic and environmental impacts of alien macrofungi. This database was compiled
from all relevant sources we could identify, through an exhaustive literature review, considering the
identity of known alien taxa and explicit indications of impacts of any kind. In total, 1440 records of both
negative and positive impacts were collected for 374 distinct species in different regions of all continents,
except Antarctica. The most frequently recorded impacts are related to the mutualistic interactions that
these fungi can form with their host plants. In total 47.8% of all records refer to the indirect negative
effect of these interactions, by facilitating the colonization of invasive plants, while 38.5% refer to their
positive contribution to the growth of forestry species. Less frequently recorded negative impacts included
ectomycorrhizal interactions with native plants, plant pathogenicity and human poisoning after ingestion.
Additional positive impacts include the use as a food source by native species and human populations and commercial exploitation. Alien macrofungi are an increasingly prevalent component of human-
dominated ecosystems, having a diverse array of negative and positive impacts on native biota and human
population. Our database provided a first step towards the quantification and mapping of these impacts.
Potential for invasion of traded birds under climate and land-cover change
Publication . Naimi, Babak; Capinha, César; Ribeiro, Joana; Rahbek, Carsten; Strubbe, Diederik; Reino, Luís; Araújo, Miguel B.
Humans have moved species away from their native ranges since the Neolithic, but
globalization accelerated the rate at which species are being moved. We fitted more
than half million distribution models for 610 traded bird species on the CITES list to
examine the separate and joint effects of global climate and land-cover
change on
their potential end-of-
century
distributions. We found that climate-induced
suitability
for modelled invasive species increases with latitude, because traded birds are mainly
of tropical origin and much of the temperate region is ‘tropicalizing.’ Conversely, the
tropics are becoming more arid, thus limiting the potential from cross-continental
invasion
by tropical species. This trend is compounded by forest loss around the tropics
since most traded birds are forest dwellers. In contrast, net gains in forest area across
the temperate region could compound climate change effects and increase the potential
for colonization of low-latitude
birds. Climate change has always led to regional
redistributions of species, but the combination of human transportation, climate, and
land-cover
changes will likely accelerate the redistribution of species globally, increasing
chances of alien species successfully invading non-native
lands. Such process of
biodiversity homogenization can lead to emergence of non-analogue
communities
with unknown environmental and socioeconomic consequences
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Entidade financiadora
Fundação para a Ciência e a Tecnologia
Programa de financiamento
CEEC IND 2017
Número da atribuição
CEECIND/00445/2017/CP1423/CP1645/CT0003