Biology subjects

Pineiro, R.

Publications and source records attributed to Pineiro, R..

8 recordsLinked to original sources

bioRxiv2025

A higher load of deleterious mutations has a detrimental effect on tree growth in maritime pine

A high proportion of deleterious mutations in the genome is predicted to cause a reduction in fitness known as genetic load. In plants, most studies focus on how detrimental mutations increase as a consequence of population bottlenecks, for instance in cultivated species as a negative outcome of domestication or at the margin of species ranges. However, the actual adverse effect of genetic load on individual phenotypes remains little characterised, especially in wild plant species with large populations and long lifespans. We estimated genetic load based on genomic data in populations of the conifer maritime pine (Pinus pinaster, Ait.), and examined its association with phenotypic traits related to growth, phenology, and water-use efficiency measured under common garden conditions. Our results revealed a strong negative correlation between genetic load and tree height on the Mediterranean island of Corsica, thus suggesting a negative cumulative effect of deleterious mutations on tree growth at the regional scale. Our study is one of the first to experimentally demonstrate adverse phenotypic effects (reduced tree growth) of genetic load in a long-lived plant.

evolutionary biology↗

bioRxiv2025

The frequency and importance of polyploidy in tropical rainforest tree radiations

O_LIThe presence of two or more copies of the genome in an organism, termed polyploidy, is a crucial force in plant evolution, generating genetic, phenotypic and ecological diversity. The Amazonian tree flora is the most species-rich on Earth, and largely arose as a result of rapid evolutionary radiations. While polyploidy is an important catalyst of rapid radiations, it remains poorly studied in tropical tree radiations. C_LIO_LIWe examined ploidy variation across Inga (Fabaceae), a characteristic Amazonian tree radiation, using DNA sequence data from 1305 loci for 189/282 Inga species. We then tested whether polyploid species experience more positive selection than diploids, particularly in loci underlying chemical defence against herbivory, which is a key ecological pressure affecting rainforest tree diversification. C_LIO_LIWe show that tetraploidy occurs in 14% (N=27) of the Inga species we sequenced, with several widespread species showing geographical ploidy variation, alongside minimal phylogenetic signal in ploidy which suggests recurrent polyploidisation. Interestingly, we found more loci under selection in polyploids than diploids, most notably in chemical defence loci. C_LIO_LIOur results show that polyploidy has arisen independently in several Inga species, and that polyploidisation can lead to elevated selection in chemical defence, helping to shape ecological interactions and influence diversification in Inga. C_LI

evolutionary biology↗

bioRxiv2025

Intraline genomic heterogeneity of the triple-negative breast cancer MDA-MB-231 cell line

Cancer cell lines are valuable models for studying tumor biology, yet their genomic evolution during culture can compromise experimental reproducibility. We conducted a detailed genomic analysis of the triple-negative breast cancer cell line MDA-MB-231, examining sublines obtained from different sources, at various time points, and across distinct passages. We introduce the concept of intraline heterogeneity (ILH) to highlight the genomic variability observed among these sublines. Our analyses revealed extensive genomic diversity, including differences in single nucleotide variants (SNVs) and copy number alterations (CNAs). In particular, CNAs exhibited remarkable heterogeneity, with pronounced chromosomal gains and losses between sublines, underscoring the impact of genomic instability on ILH. These findings suggest that ILH may influence experimental outcomes, emphasizing the importance of considering passage-specific genomic characterization to ensure consistency and reliability in cancer research.

genomics↗

bioRxiv2023

Do Reticulate Relationships Between Tropical Trees Drive Diversification? Insights from Inga (Fabaceae)

Evolutionary radiations underlie much of the species diversity of life on Earth, particularly within the worlds most species-rich tree flora - that of the Amazon rainforest. Hybridisation occurs in many radiations, with effects ranging from homogenisation of species to generation of genetic and phenotypic novelty that fuels speciation, but the influence of hybridisation on Amazonian tree radiations has been little studied. We address this using the ubiquitous, species-rich, neotropical tree genus Inga, which typifies rapid radiations of rainforest trees. We assess patterns of gene tree incongruence to ascertain whether hybridisation was associated with rapid radiation in Inga. Given the importance of insect herbivory in structuring rainforest tree communities (and hence the potential for hybridisation to promote adaptation through admixture of defence traits), we also test whether introgression of loci underlying chemical defences against herbivory occurred during the radiation of Inga. Our phylogenomic analyses of 189/288 Inga species using >1300 target capture loci showed widespread introgression in Inga. Specifically, we found widespread phylogenetic incongruence explained by introgression, with phylogenetic networks recovering multiple introgression events across Inga and up to 20% of shared, likely introgressed, genetic variation between some species. In addition, most defence chemistry loci showed evidence of positive selection and marginally higher levels of introgression. Overall, our results suggest that introgression has occurred widely over the course of Ingas history, likely facilitated by extensive dispersal across Amazonia, and that in some cases introgression of chemical defence loci may influence adaptation in Inga.

evolutionary biology↗

bioRxiv2022

Modelling metastasis in zebrafish unveils regulatory interactions of cancer-associated fibroblasts with circulating tumour cells

The dynamic intercommunication between tumour cells and cells from the microenvironment, such as cancer-associated fibroblast (CAFs), is a key factor driving breast cancer (BC) metastasis. Clusters of circulating tumour cells (CTCs), known to bare a higher efficiency at establishing metastases, are found in the blood of BC patients, often accompanied by CAFs in heterotypic CTC-clusters. Previously we have shown the utility of CTC-clusters models and the zebrafish embryo as a model of metastasis to understand the biology of breast cancer CTC-clusters. In this work, we use the zebrafish embryo to study the interactions between CTCs in homotypic clusters and CTC-CAFs in heterotypic CTC-clusters to identify potential pro-metastatic traits derived from CTC-CAF communication. We found that upon dissemination CAFs seem to exert a pro-survival and pro-proliferative effect on the CTCs, but only when CTCs and CAFs remain joined as cell clusters. Our data indicate that the clustering of CTC and CAF allows the establishment of physical interactions that when maintained over time favour the selection of CTCs with a higher capacity to survive and proliferate upon dissemination. Importantly, this effect seems to be dependent on the survival of disseminated CAFs and was not observed in the presence of normal fibroblasts. Moreover, we show that CAFs can exert regulatory effects on the CTCs without being involved in promoting tumour cell invasion, and these effects are differential based on the BC cell molecular phenotype, and the crosstalk between tumour cells and CAFs, i.e. paracrine or physical interaction. Lastly, we show that the physical communication between BC cells and CAFs leads to the production of soluble factors involved in BC cell survival and proliferation. These findings suggest the existence of a CAF-regulatory effect on CTC survival and proliferation sustained by cell-to-cell contacts and highlight the need to understand the molecular mechanisms that mediate the interaction between the CTCs and CAFs in clusters enhancing the metastatic capacity of CTCs.

cancer biology↗

bioRxiv2022

Red blood cells protein profile is modified in breast cancer patients

Metastasis is the primary cause of death for most breast cancer patients who succumb to the disease. During the haematogenous dissemination, circulating tumor cells interact with different blood components. Thus, there are micro-environmental and systemic processes contributing to cancer regulation. We have published that Red Blood Cells (RBCs) that accompany circulating tumor cells have prognostic value in metastatic breast cancer patients. Although the principal known role of RBCs is gas transport, it has been recently assigned additional functions as regulatory cells on circulation. Hence, to explore their potential contribution to tumor progression, we characterized the proteomic composition of RBCs from 53 breast cancer patients, compared with 33 healthy donors. RBCs from breast cancer patients showed a different proteomic profile compared to healthy donors. The differential proteins were mainly related to extracellular components, proteasome, and metabolism. Besides, LAMP2 emerge as a new RBCs marker with diagnostic and prognostic potential for metastatic patients. Seemingly, RBCs are acquiring modifications in their proteomic composition that probably represents the systemic cancer disease, conditioned by the tumor microenvironment.

cancer biology↗

bioRxiv2019

Contrasting dates of rainforest fragmentation in Africa inferred from trees with different dispersal abilities

The rainforests of Tropical Africa have fluctuated over time. Although today the forest cover is continuous in Central Africa this may have not always been the case, as the scarce fossil record in this region suggests that more arid conditions might have significantly reduced the density of trees during the Ice Ages. Our aim was to investigate whether the dry ice-age periods left a genetic signature on tree species that can be used to date the past fragmentation of the rainforest. We sequenced reduced representation libraries of 182 samples representing five Legume tree species that are widespread in African rainforests and seven outgroups. Phylogenetic analyses identified an early divergent lineage for all species in West Africa (Upper Guinea), and two clades in Central Africa: Lower Guinea-North and Lower Guinea-South. As the structure separating the Northern and Southern clades cannot be explained by geographic barriers, we tested other hypotheses using demographic model testing. The best estimates recovered using {partial}a{partial}I indicate that the two clades split between the Upper Pliocene and the Pleistocene, a date compatible with forest fragmentation driven by ice-age climatic oscillations. Furthermore, we found remarkably older split dates for the shade-tolerant tree species with non-assisted seed dispersal than for light-demanding long-distance wind-dispersed trees. We also show that the genetic diversity significantly declines with the distance from ice-age refugia in the two long-distance dispersed species only. Different recolonisation abilities after recurrent cycles of forest fragmentation seem to explain why we observe congruent genetic spatial structures across species with contrasted timescales.\n\nSIGNIFICANCE STATEMENTAlthough today the rainforest cover is continuous in Central Africa, the scarce fossil record suggests that arid conditions during the Ice Ages might have reduced the density of trees during the Ice Ages. However, the vast majority of the fossil pollen records preserved in Tropical Africa is too young to inform about this period. Investigating whether the past climate change left a genetic signature on trees can thus be useful to date past forest fragmentation. However, most genetic studies available to date lack resolution as they use limited numbers of loci. In this study we use modern DNA technology to study five Legume trees. Our results show significant differentiation of the populations of each species at a date compatible with forest fragmentation driven by ice-age climatic oscillations. Contrasted timescales were obtained for each species, which probably reflects their different recolonisation abilities after forest fragmentation.

evolutionary biology↗

bioRxiv2019

Population genomics of the widespread African savannah trees Afzelia africana and Afzelia quanzensis (Caesalpinioideae, Fabaceae) reveals no significant past fragmentation of their distribution ranges

Few studies have addressed the evolutionary history of tree species from African savannahs at large geographic scales, particularly in the southern hemisphere (Zambezian region). Afzelia (Fabaceae: Caesalpinioideae) contains economically important timber species, including two species widely distributed in African savannahs: A. africana in the Sudanian region and A. quanzensis in the Zambezian region. To characterize the population genetic diversity and structure of these two species across their distribution ranges, we used nuclear microsatellites (simple sequence repeats, SSRs) and genotyping-by-sequencing (GBS) markers. Six SSR loci were genotyped in 241 A. africana and 113 A. quanzensis individuals, while 2,800 and 3,841 high-quality single nucleotide polymorphisms (SNPs) were identified in 30 A. africana and 12 A. quanzensis individuals, respectively. Both species appeared to be outcrossing (selfing rate ~ 0%). The spatial genetic structure was consistent with isolation-by-distance expectations based on both SSR and SNP data, suggesting that gene dispersal is spatially restricted in both species (bLd (SSR)= -0.005 and -0.007 and bLd (SNP)= -0.008 and -0.006 for A. africana and A. quanzensis, respectively). Bayesian clustering of SSR genotypes failed to identify genetic structure within species. In contrast, SNP data resolved intraspecific genetic clusters in both species, illustrating the higher resolving power of GBS at shallow levels of divergence. However, the clusters identified by SNPs revealed low levels of differentiation and no clear geographical entities. These results suggest that, although gene flow has been restricted over short distances in both species, populations have remained connected throughout the large, continuous Savannah landscapes. The absence of clear phylogeographic discontinuities, also found in a few other African savannah trees, indicates that their distribution ranges have not been significantly fragmented during past climate changes, in contrast to patterns commonly found in African rainforest trees.

plant biology↗