Publications by authors named "Melo-Ferreira J"
Article Synopsis
- A genomic database encompassing all eukaryotic species on Earth is crucial for scientific advancements, yet most species lack genomic data.
- The Earth BioGenome Project (EBP) was initiated in 2018 by global scientists to compile high-quality reference genomes for approximately 1.5 million recognized eukaryotic species.
- The European Reference Genome Atlas (ERGA) launched a Pilot Project to create a decentralized model for reference genome production by testing it on 98 species, providing valuable insights into scalability, equity, and inclusiveness for genomic projects.
Article Synopsis
- The European Reference Genome Atlas (ERGA) consortium seeks to create a comprehensive reference genome catalogue for all eukaryotic species in Europe, utilizing a collaborative network for sample collection.
- The ERGA Pilot project highlights the consortium's capabilities by establishing the Sampling and Sample Processing committee (SSP), which focuses on setting standards, prioritizing species for genome sequencing, and developing collection guidelines.
- The manuscript shares insights on implementing standardized procedures and best practices, showcasing the importance of FAIR and CARE principles in enhancing genomic resource support and workflow efficiency.
Article Synopsis
- Portugal has a lot of different plants and animals because of its unique geography and history, but these species are in danger from things like climate change and over-exploitation.
- Researchers in Portugal are working together through a project called Biogenome Portugal to study and document biodiversity, which means looking closely at the genes of different species.
- The goal is to create a library of genetic information to help protect endangered species and promote conservation efforts in Portugal, especially for unique plants and animals found only there.
Article Synopsis
- The Spotted-Wing Drosophila (Drosophila suzukii), an invasive pest causing harm to soft-skinned fruits, first appeared in Portugal in 2012, prompting this study on its genomic traits in relation to its global spread.
- Analysis of three Portuguese populations revealed connections to other Southern European populations, indicating a Mediterranean invasion path, while variations in genetic diversity suggest differing colonization histories.
- The study identified ten genes linked to the pest's invasive success and six genes showing local adaptation, including one related to insecticide resistance, highlighting the need for further research on adaptive traits in these Portuguese populations.
Guanylate binding proteins (GBPs) are an evolutionarily ancient family of proteins that are widely distributed among eukaryotes. They belong to the dynamin superfamily of GTPases, and their expression can be partially induced by interferons (IFNs). GBPs are involved in the cell-autonomous innate immune response against bacterial, parasitic and viral infections.
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- Anthropogenic factors like climate change are significantly influencing insect behavior and survival, particularly in pests, though specific impacts on certain pests remain under-researched.
- One such pest, which poses a threat to soft-skinned small fruits, is facing challenges from cold temperatures, causing issues like dehydration and immune system stress.
- The review discusses this pest's adaptive strategies for surviving cold seasons, including behaviors, reproductive adaptations, and metabolic changes, while also considering how ongoing climate change may enhance its spread and what measures can be taken to mitigate this issue.
Article Synopsis
- - The study investigates how genetic variations in specific genes affect the seasonal color change in white-tailed jackrabbits, influencing their camouflage against changing snow cover.
- - Researchers found that the ability to adapt to diminished snow cover relies on different alleles of genes such as endothelin receptor type B, corin serine peptidase, and agouti signaling protein, which show evidence of selection.
- - The findings indicate that while reduced snow cover may threaten the rabbits' camouflage, populations with genetic diversity for darker pelage could adapt quickly, offering insights for conservation efforts in the face of climate change.
Article Synopsis
- - The study examines the transcytosis process of immunoglobulins IgA and IgM across epithelial barriers, focusing on the polymeric immunoglobulin receptor (pIgR), its variants, and its evolutionary significance in lagomorphs versus other mammals.
- - Researchers sequenced pIgR genes from various leporid species and aligned them with sequences from all mammalian orders, discovering that the lagomorph pIgR evolves at a higher rate and shows strong positive selection in certain domains.
- - The findings suggest that the unique evolutionary patterns of pIgR in lagomorphs may be linked to species-specific adaptations or expansions of IgA genes, necessitating further research to better understand the underlying evolutionary mechanisms.*
Article Synopsis
- - Recent evolutionary changes in marine brown algae, specifically in the Fucus genus, reveal complexities in speciation due to climate shifts and genetic mixing between populations.
- - Research indicates that isolation of certain F. vesiculosus populations likely led to the development of new hermaphrodite species through a process of parapatric speciation, along with observed patterns of gene flow.
- - Findings suggest that reproductive systems, especially self-fertilizing traits in hermaphrodites, play a critical role in maintaining species boundaries amidst extensive sympatry.
Article Synopsis
- TLR8 is missing in hares but present in European rabbits, while TLR7 is absent in rabbits and shows significant variation in hares.
- The study indicates that TLR7 and TLR8 in lagomorphs have evolved more rapidly compared to other mammals, potentially due to extensive interactions with viruses and their positioning in dynamic areas of the genome.
Guanylate binding proteins (GBPs) are paramount in the host immunity by providing defense against invading pathogens. Multigene families related to the immune system usually show that the duplicated genes can either undergo deletion, gain new functions, or become non-functional. Here, we show that in muroids, the genes followed an unusual pattern of gain and loss of genes.
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- * Researchers found that a split between hare populations occurred about 20,000 years ago, allowing for rapid local adaptations, with distinct genetic signatures linked to environmental traits like coat color and body size.
- * The findings indicate that adaptive genetic variants are mostly unique to mountain hares but can also result from hybridization with other hare species, highlighting the role of both standing genetic variation and introgression in their evolution since the last ice age.
Article Synopsis
- The study investigates how genetic variation influences adaptive traits, focusing on the winter coat colors of least weasels (Mustela nivalis) that adapt for camouflage in different snowy environments.
- Researchers used whole-genome sequencing to analyze samples from two regions in Europe where the weasels show distinct white and brown winter coat morphs.
- An association was found between coat color and the MC1R pigmentation gene, with a specific amino acid change linked to the brown morph, indicating that single gene changes can significantly impact seasonal camouflage.
Fc receptor-like (FCRL) molecules comprise a large family of receptors, homologous to the receptors for the Fc portion of immunoglobulins (FCR). Within this family, an unusual gene known to exist in mice, rats and dogs, termed , encodes a chimeric protein with both Ig-like FCRL and type B scavenger-receptor cysteine-rich (SRCR)-like domains. In mice, is located next to the and genes.
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- Hybridization plays a key role in the adaptive evolution of hares (Lepus), with extensive gene flow observed across the 32 existing species, influencing their ecological adaptations.
- Researchers analyzed whole exome sequences from 15 hare species to understand the impact of introgression, uncovering significant allele sharing that indicates both ancient and recent hybridization events along the Lepus lineage.
- The findings suggest that ancient hybridization has created a genetic legacy, contributing to adaptations in response to seasonal environments, particularly in genes related to circadian rhythm, pigmentation, and thermoregulation.
Article Synopsis
- Immune-response (IR) genes are critical for species survival against diverse pathogens, but existing genomic data from Old World camelids contain inconsistencies that hinder detailed studies on these genes.
- Recent research improved genome assemblies for three Old World camel species, utilizing advanced computational methods for better accuracy and annotation.
- Findings indicated significant differences in nucleotide diversity among species and IR gene groups, with domestic Bactrian camels showing the highest diversity, and the major histocompatibility complex having the most variability among immune gene types.
Article Synopsis
- The study focuses on how the mountain hare changes its coat color from brown in summer to white in winter for better camouflage, analyzing skin transcription changes during this molt process.
- Researchers identified 632 different genes that are differentially expressed at three stages of the molt—brown, intermediate, and white—with significant changes occurring early in the process.
- The findings highlight similarities in gene regulation between mountain and snowshoe hares, emphasizing the evolutionary significance of coat color adaptation while also noting differences that may relate to seasonal and nutritional factors.
Article Synopsis
- Researchers have created the first de novo draft reference genome for the mountain hare (Lepus timidus), allowing for better understanding of hare-specific variations compared to previous studies that relied on the European rabbit genome.
- The genome assembly includes 32,294 scaffolds totaling 2.7 Gb, which were refined down to 4,205 scaffolds when aligned with rabbit chromosomes, showcasing a significant reduction in complexity.
- The study annotated 24,578 protein-coding genes and found similar genetic diversity metrics between the new hare genome and analyses using the rabbit genome, indicating that the hare reference genome is a valuable tool for future genetic studies on this species.
Article Synopsis
- Toll-like receptors (TLRs), particularly TLR5, play a crucial role in the immune system by recognizing bacterial proteins like flagellin, and this study focuses on the evolutionary rates of TLR5 across different mammalian groups.
- Researchers analyzed TLR5 substitution rates across several animal groups (Euungulata, Carnivora, Chiroptera, etc.) using various evolutionary models and found that certain lineages like Lagomorpha, Rodentia, Carnivora, and Chiroptera have higher substitution rates.
- The study suggests that the faster evolution of TLR5 in these groups may be due to factors like neofunctionalization, pseudogenization, or an evolutionary "arms race" with parasites
Introgression drives repeated evolution of winter coat color polymorphism in hares.
Proc Natl Acad Sci U S A
November 2019
Article Synopsis
- Many species of mammals and birds adapt to seasonal changes by altering their fur or feather color, with some maintaining nonwhite winter morphs suited to less snowy environments.
- An introduction of mountain hares to the Faroe Islands in 1855 resulted in a rapid shift from winter-white to winter-gray coat color due to selective pressures, providing insight into the genetics behind this trait.
- Genomic analysis revealed that the winter-gray coloration is linked to introgression from a noncolor changing species and highlights the role of regulatory changes and positive selection in this adaptation.
Article Synopsis
- Studying the Cape hare (Lepus capensis) helps understand how large species distributions relate to major diversity patterns across different regions, utilizing genetic analysis of microsatellites and DNA sequences from various samples.
- The research identifies five distinct evolutionary lineages of the Cape hare across different regions: north-western Africa, eastern Africa, southern Africa, the Near East, and the Arabian Peninsula, indicating a significant evolutionary divergence between African and Asian groups.
- The findings emphasize the impact of environmental changes, like desert aridification and savannah habitat fluctuations, on species evolution and highlight the importance of integrating evolutionary insights for biodiversity conservation.
Article Synopsis
- Selection and demographic processes influence the patterns of genetic exchange between species, particularly in cases of invasive species like the Iberian hare, which replaced the arctic L. timidus.
- The study utilizes whole-genome sequencing to analyze nuclear introgression alongside mitochondrial DNA patterns, revealing that while average introgression varies, they both adhere to a shared post-glacial replacement model.
- Findings suggest that while demographic factors primarily explain genetic patterns, selection plays a role in certain immune and metabolic genes, potentially alleviating negative impacts from hybridization.
Snowshoe hares () maintain seasonal camouflage by molting to a white winter coat, but some hares remain brown during the winter in regions with low snow cover. We show that cis-regulatory variation controlling seasonal expression of the gene underlies this adaptive winter camouflage polymorphism. Genetic variation at clustered by winter coat color across multiple hare and jackrabbit species, revealing a history of recurrent interspecific gene flow.
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- * With climate change reducing snow cover, species such as the snowshoe hare and Arctic fox face challenges as their winter white coat contrasts sharply with dark backgrounds, raising concerns for their survival and conservation.
- * The review highlights that SCC moulting primarily serves for camouflage, with photoperiod influencing when animals change color, but many mechanisms behind this adaptation remain unclear, necessitating further research for effective population management under changing climates.