Biology subjects

Lopes-Lima, M.

Publications and source records attributed to Lopes-Lima, M..

6 recordsLinked to original sources

bioRxiv2025

Forest conversion to cashew orchards delays the diel activity of diurnal mammals in West Africa

Land-use change is the main driver of biodiversity loss worldwide. However, less is known about how species adapt their behavior to persist in human-altered habitats. We addressed this gap by examining mammal responses in terms of habitat use and diel activity patterns to forest conversion into cashew orchards in West Africa. We surveyed mammals using camera-trapping in 12 forest sites and 12 cashew orchards in the Cantanhez National Park in southwest Guinea-Bissau, West Africa. We grouped mammals into (1) diurnal and cathemeral and (2) nocturnal species according to their diel activity periods and assessed their use and diel activity between habitat types. Based on 709 trap-days, we obtained 842 records of 12 diurnal or cathemeral species (18.3% of the records) and 13 nocturnal species (81.7%). Mammal habitat use was similar between forests and cashew orchards for both diurnal/cathemeral and nocturnal species. However, the peak of diurnal/cathemeral species shifted from the morning period ([~]11h00) in the forests to the afternoon period in the cashew orchards ([~]16h30), resulting in little overlap in activity of diurnal/cathemeral species between habitat types. No differences were observed in the diel activity of nocturnal mammals. Although mammals can make use of altered habitats, diurnal species are able to delay their activity, probably to avoid direct contact with humans. Our study highlights the ability of species in adapting their behaviour to persist in newly human-modified landscapes in the tropics.

ecology↗

bioRxiv2025

Mammal responses to habitat degradation induced by cashew expansion in West Africa

Tropical landscapes are perishing due to high rates of land-use change. In West Africa, Guinea-Bissau lost 77% of its closed-canopy forest over the last 25 years, mostly to the expansion of cashew monoculture. To date, understanding how species cope with such changes remains a conservation priority for the region. Here we examine mammal species composition, richness, and abundance, in addition to trophic-guild abundance across closed-canopy sub-humid forests and cashews orchards in the Cantanhez National Park, southwest Guinea-Bissau. Mammals were surveyed using one camera trap at each of the 24 sites, half in forest and half in cashew orchards, and their local and landscape-scale variables were measured. Based on 709 trap-nights, we collected 842 records from 25 mammal species. Local habitat structure--including canopy openness, floor obstruction, density of both lianas, palms and trees, tree species richness and height--sharply contrasted between forests and cashew orchards. As expected, mammal species composition differed between forests and cashew orchards, and the estimated, but not the observed, species richness declined towards cashew-like habitats. Although overall mammal abundance remained unaffected by the variables considered, carnivores were more abundant in cashew-like habitats, whereas insectivores and herbivores were more abundant in forest-like habitats. Human activity and distance to forest did not affect the response variables considered. Forest conversion into cashew orchards negatively affects mammals by profoundly changing the local habitat structure. Guild-level responses further unveiled specificity in their vulnerability to this form of land-use change, alerting for a potential disruption in the ecosystem functioning. We emphasize the need for policies that limit monoculture expansion, while safeguarding the remaining forests, thus maximising biodiversity persistence across the Afrotropics.

ecology↗

bioRxiv2023

The Crown Pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)

Contiguous assemblies are fundamental to decipher the exact composition of extant genomes. In molluscs, this task is considerably challenging owing to their large size, heterozygosity, and widespread content of repetitive content. Consequently, the usage of long-read sequencing technologies is fundamental to achieve high contiguity and quality. The first genome assembly of Margaritifera margaritifera (Linnaeus, 1758) (Mollusca: Bivalvia: Unionida), a culturally relevant, widespread, and highly threatened species of freshwater mussels, has been produced recently. However, the current genome is highly fragmented since the assembly relied solely on short-read approaches. To overcome this caveat, here, a new improved reference genome assembly is produced using a combination of PacBio CLR long reads and Illumina paired-end short reads. This novel genome assembly is 2.4 Gb long, organized into 1,700 scaffolds with a contig N50 length of 3.4Mbp. The ab initio gene prediction resulted in a total of 48,314 protein-coding genes. This new assembly represents a substantial improvement and is an essential resource for studying this species unique biological and evolutionary features that ultimately will help to promote its conservation.

genomics↗

bioRxiv2023

PacBio Hi-Fi genome assembly of the Iberian dolphin freshwater mussel Unio delphinus Spengler, 1793

Mussels of order Unionida are a group of strictly freshwater bivalves with nearly 1,000 described species widely dispersed across world freshwater ecosystems. They are highly threatened showing the highest record of extinction events within faunal taxa. Conservation is particularly concerning in species occurring in the Mediterranean biodiversity hotspot that are exposed to multiple anthropogenic threats, possibly acting in synergy. That is the case of the dolphin freshwater mussel Unio delphinus Spengler, 1793, endemic to the western Iberian Peninsula with recently strong population declines. To date, only four genome assemblies are available for the order Unionida and only one European species. We present the first genome assembly of Unio delphinus. We used the PacBio HiFi to generate a highly contiguous genome assembly. The assembly is 2.5 Gb long, possessing 1254 contigs with a contig N50 length of 10 Mbp. This is the most contiguous freshwater mussel genome assembly to date and is an essential resource for investigating the species biology and evolutionary history that ultimately will help to support conservation strategies.

bioinformatics↗

bioRxiv2020

The Crown Pearl: a draft genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)

Since historical times, the inherent human fascination with pearls turned the freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758) into a highly valuable cultural and economic resource. Although pearl harvesting in M. margaritifera is nowadays residual, other human threats have aggravated the species conservation status, especially in Europe. This mussel presents a myriad of rare biological features, e.g. high longevity coupled with low senescence and Doubly Uniparental Inheritance of mitochondrial DNA, for which the underlying molecular mechanisms are poorly known. Here, the first draft genome assembly of M. margaritifera was produced using a combination of Illumina Paired-end and Mate-pair approaches. The genome assembly was 2,4 Gb long, possessing 105,185 scaffolds and a scaffold N50 length of 288,726 bp. The ab initio gene prediction allowed the identification of 35,119 protein-coding genes. This genome represents an essential resource for studying this species unique biological and evolutionary features and ultimately will help to develop new tools to promote its conservation.

genomics↗

bioRxiv2020

Towards a taxonomically unbiased EU Biodiversity Strategy for 2030

Through the Habitats Directive (92/43/EEC) and the LIFE projects financial investments, Europe has been the world’s experimental arena for biological conservation. With an estimated budget of €20 billion/year, the EU Biodiversity Strategy for 2030 has set an ambitious goal of reaching 30% Protected Areas and ensure no deterioration in conservation trends and status of all protected species. We analyzed LIFE projects focused on animals from 1992 to 2018 and we found that investment towards vertebrates has been six times higher than that for invertebrates (€970 vs €150 million), with birds and mammals alone accounting for 72% species and 75% total budget. Budget allocation is primarily explained by species’ popularity. We propose a roadmap to achieve unbiased conservation targets for 2030 and beyond.Competing Interest StatementThe authors have declared no competing interest.View Full Text

ecology↗