Biology subjects

Branco, M.

Publications and source records attributed to Branco, M..

10 recordsLinked to original sources

bioRxiv2025

Resprouting sustains cork oak seedlings while recent grazing limits resprouting and survival

Regeneration failure is a bottleneck in Mediterranean oak woodlands. Cattle can hinder or promote recruitment, depending on grazing location, timing and intensity. Herbivory theory predicts that repeated defoliation and trampling deplete seedling reserves, whereas resprouting can extend survival; yet field studies rarely separate intensity from recency or combine long-run grazing records with individual fates and microhabitat/climate context. We test how management-driven heterogeneity shapes cork oak seedling survival and resprouting by combining 12 years of paddock-level grazing records with individual tracking of 8431 seedlings across 24 paddocks. Bayesian mixed-effects survival models related seedling lifespan to grazing history x pressure (moderate [≤]150; high >150 LSU ha-1 days yr-1) and to key covariates, including seedling height, resprouting status, shrub distance, cattle dung counts (as a proxy of very recent grazing), and 1-month SPEI (as recent water balance). Bayesianlogistic mixed models were then used to relate resprouting probability to grazing treatments. Survival was lower in grazed than ungrazed paddocks and declined along management gradients: median lifespan fell from 460 (moderate grazing) to 256 days (high), and from 460 (old grazing; two-year absence) to 199 days (recent). A two-year cattle absence increased survival under moderate pressure but was insufficient where pressure was high, indicating legacy effects and that recovery windows must scale with pressure. Resprouting dominated persistence: resprouters lived >5x longer than non-resprouters (2351 vs 460 days). Taller seedlings lived longer, and shrub proximity conferred a modest benefit. Climate modulated outcomes: wetter recent periods (higher SPEI) markedly boosted survival. Cattle reduced the odds of resprouting, with the strongest penalty under recent use. By disentangling grazing intensity from recency and linking both to seedling survival and resprouting, we show why recruitment falters under continuous, heavy grazing and when it can recover. Because drought intensifies cattle impacts, managers should combine moderate stocking rates with multi-year rest periods to rebuild oak bud banks and below-ground reserves; a two-year hiatus can help under moderate pressure but appears insufficient where pressure is high. Aligning rotational plans with drought outlooks and tracking simple field cues (seedling height, recent resprouting) offers a practical path to reconcile production with regeneration in Mediterranean wood-pastures. HighlightsO_LITwelve years of grazing records linked to 8431 cork oak seedling fates C_LIO_LIRecent grazing reduced survival and resprouting versus a two-year cattle absence C_LIO_LIHigh grazing shortened lifespan; two-year rest helped only under moderate pressure C_LIO_LIResprouting was the strongest survival correlate; resprouters lived over 5x longer C_LIO_LIWetter short-term water balance increased cork oak seedling longevity C_LI

ecology↗

bioRxiv2025

Population genomics of incipient allochronic divergence in the Pine Processionary Moth

Allochronic divergence is a key evolutionary mechanism that can frequently lead to incipient speciation. Although theoretical models suggest that such divergence is notably facilitated by small population size and genetic polymorphisms influencing reproductive timing, though constrained by genetic load, empirical validation remains limited. We investigated these predictions by re-analyzing a case of allochronic differentiation between two sympatric populations of pine processionary moth (Thaumetopoea pityocampa) in Portugal, using whole genome resequencing (IndSeq and PoolSeq) of those two populations and eight allopatric ones. We inferred the demographic history of those populations, assessed their genetic load, and searched for genomic regions associated with life cycle differences. Our analyses revealed a recent split between the sympatric allochronic populations, accompanied by a strong reduction in gene flow, bottlenecks, inbreeding, and accumulation of deleterious variants. Genome scans identified several loci associated with life cycle variation, including genes putatively involved in circadian rhythm regulation, predominantly located on the Z chromosome. We discuss how these empirical genomic findings support theoretical expectations that assortative mating driven by differences in reproductive timing, underpinned by polymorphisms in circadian genes, along with genetic drift and purge of genetic load at high-impact sites, can promote the onset and persistence of allochronic divergence.

evolutionary biology↗

bioRxiv2025

A Chromosome-Level Assembly of the Pine Processionary Moth (Thaumetopoea pityocampa) genome

We present a chromosome-level genome assembly and annotation of the pine processionary moth, Thaumetopoea pityocampa (Lepidoptera: Notodontidae), a key forest pest that is a public health concern. The nuclear genome spans 615.9 Mb, scaffolded into 50 chromosome scale and 115 smaller scaffolds, with high completeness (BUSCO score: 98.9%) that provides a decisive improvement over the previous assembly (537 Mb; 68,292 contigs; BUSCO 83.6%). Coverage differences in resequenced males and females allowed identification of the Z chromosome and several W-linked contigs. As ex-pected from previous studies, we found that synteny was largely conserved with related Lepidoptera, although chromosomal fissions may explain the higher chromosome number of 49 autosomes com-pared to typical lepidopteran karyotypes. We also integrated into the assembly linkage map, allowing estimation of a genome-wide male recombination rate of 5.06 cM/Mb, varying from 11.6 cM/Mb to 1.98 cM/Mb from the smallest to the largest chromosomes. Repetitive elements represented 49.1% of this new assembly, dominated by LINEs (45.1% of classified repeats). Finally, gene prediction identified 12,898 gene models, among which 17 circadian rhythm genes were manually curated. Ex-pert annotation further allowed to identify 51 genes of the odorant receptor (OR) family as well as a total of 236 detoxification genes, including 78 CYPs, 56 CCEs, 30 GSTs, 23 UGTs and 49 ABCs. Overall, this assembly represents the first chromosome-level genome for a member of the Thaume-topoeinae subfamily, significantly expanding the currently limited set of genomic resources avail-able for Notodontidae. The fully annotated assembly is publicly accessible through the LepidoDB database (https://bipaa.genouest.org/is/lepidodb/) and will serve as a valuable resource for research on population genomics of this species.

genomics↗

bioRxiv2025

Worldwide spread of Hylurgus ligniperda (Coleoptera: Scolytinae), and the potential role of bridgehead invasions

Hylurgus ligniperda (F.) is a highly successful invader among bark beetles (Scolytinae) and forest insects in general. Native to the western Palearctic region, it has become established in every continent where its host plants (Pinus spp.) occur. Especially in southern hemisphere regions with large pine plantations, it is often highly abundant. As a repeat invader with a wealth of information on various aspects relevant for biological invasions, it is highly suitable as a model organism for studying the role of international trade, the planting of non-native trees, and the potential occurrence of bridgehead invasions (where abundant non-native populations precipitate further invasions). In the present study, our specific objectives were to reconstruct the worldwide invasions of H. ligniperda and the pathways involved by using a multi-pronged approach including population genetics, analysis of historic interception data generated from inspections of imports, and records of establishments in the literature. Our review of the native and non-native ranges of H. ligniperda and the chronology of establishments revealed at least 13 separate invasions of non-native regions, beginning with Madeira (Portugal) before 1850, and, most recently, eastern China in 2019. We compared the population genetics of 464 specimens from eight countries in the native range and eight countries in the non-native range. Sequencing of the mitochondrial COI gene revealed the presence of 29 haplotypes in six well-supported clades, based on a Bayesian analysis. Non-native populations had significantly lower haplotype diversity (mean h = 0.219) than populations in the native range (mean h = 0.691). Countries in the non-native range had an average of about two haplotypes compared with about four haplotypes in native countries. In the non-native range, only one or two haplotypes were dominant, and these differed among invaded regions except for haplotype HL-H3 which occurred in Australia, New Zealand and China as well as in four countries in southern Europe, and HL-H4 which was dominant in New Zealand, California, New York State, and eastern China as well as two countries in southern Europe. Analyses of interceptions of H. ligniperda with imports arriving in five countries revealed that between 74% and 99% of interceptions originated from other non-native regions while in the USA, most interceptions were linked to imports from the native range beginning in the 1970s. Based on the combined evidence of the chronology of invasions, interception data, and analysis of haplotype distribution, we conclude that the early invasions (before 1950) probably all originated from the native range, while several of the more recent invasions probably originated from parts of the non-native range (suggestive of a bridgehead effect). However, it cannot be determined with certainty what the original sources of each of the invading populations were.

ecology↗

bioRxiv2025

Recreating coronary vascularization and sympathetic innervation of myocardium on a human pluripotent stem cell-derived heart organoid

Coronary vascularization and sympathetic innervation of the myocardium is a concomitant event during embryonic heart development and both systems are crucial to ensure normal adult heart function. Here we describe a self-organized hiPSC-derived heart organoid that recreates both the coronary vascular plexus and the sympathetic neuronal network of the ventricle myocardium, with a physiologically relevant in-vivo-like structural organization and function. Through modulation of PDGF-{beta} and VEGF signalling pathways, we attained a heart organoid that incorporates 1) an external epicardial layer (mesothelium) of DACH1, NR2F2 and WT1 positive cells, 2) a sub-epicardial space from where a functional primary coronary vascular plexus of CD31+/DACH1+ cells emerge, 3) a compact myocardial region adjacent to the epicardium, enriched in proliferative cardiomyocytes and ECM deposition, and 4) a sympathetic neuronal network that controls heart organoid contraction. Therefore, the human heart organoid described herein, is a unique model to study new regenerative medicine-based approaches to restore innervation and promote re-vascularization in adult heart after ischemic events and to perform adult and developmental cardiotoxicity studies.

developmental biology↗

bioRxiv2023

Distribution of the invasive Anisandrus maiche (Coleoptera: Scolytinae) in Switzerland, first record in Europe of its ambrosia fungus Ambrosiella cleistominuta, and its new association with Xylosandrus crassiusculus

In 2022, two independent insect surveys in canton Ticino (southern Switzerland) revealed the widespread occurrence of the invasive ambrosia beetle Anisandrus maiche from southern to central-upper Ticino. This species is native to east Asia and has previously been found as a non-native invasive species in the United States, Canada, western Russia, Ukraine and, in 2021, in northern Italy. Here, we present the results of several trapping studies using different trap types (bottle traps, funnel traps and Polytrap intercept traps) and attractants and a map of the distribution of the species. In total, 685 specimens of A. maiche, all female, were trapped, and the identity of selected individuals was confirmed by morphological and molecular identification based on three mitochondrial and nuclear markers (COI, 28S and CAD). Traps checked from early April to early September 2022 in intervals of two to four weeks showed that flights of A. maiche occurred mainly from June to mid-August. Isolation of fungal associates of A. maiche from beetles trapped alive revealed the presence of four fungal species, including the ambrosia fungus Ambrosiella cleistominuta, the known mutualists of A. maiche. The identity of A. cleistominuta was confirmed by comparing DNA sequences of its nuclear, internal transcribed spacer (ITS) gene with reference sequences in NCBI and BOLDSYSTEMS. This represents the first record of A. cleistominuta in Europe. Ambrosiella cleistominuta was also found in association with another non-native invasive ambrosia beetle, Xylosandrus crassiusculus, at a botanic garden in central Ticino. As ambrosia beetles usually show a high degree of fidelity with only one mutualistic fungus (in the case of X. crassiusculus normally Ambrosiella roeperi), this association is highly unusual and probably the result of lateral transfer among these non-native invasive species. Of the other fungal associates isolated from A. maiche in Ticino, Fusarium lateritium is of note as there is a possibility that A. maiche could act as a vector of this plant pathogen. We highlight several research needs that should be addressed to gain insight into the potential impact of these non-native species and to overcome problems with heteroplasmy in COI sequences in studies of invasion and population genetics of ambrosia beetles.

ecology↗

bioRxiv2021

The cohesin regulator Stag1 promotes cell plasticity through heterochromatin regulation.

Several studies have shown a role for Stag proteins in cell identity. Our understanding of how Stag proteins contribute to cell identity have largely been focused on its roles in chromosome topology as part of the cohesin complex and the impact on protein-coding gene expression. Furthermore, several Stag paralogs exist in mammalian cells with non-reciprocal chromosome structure and cohesion functions. Why cells have so many Stag proteins and what specific functions each Stag protein performs to support a given cell state are poorly understood. Here we reveal that Stag1 is the dominant paralog in mouse embryonic stem cells (mESC) and is required for pluripotency. Through the discovery of diverse, naturally occurring Stag1 isoforms in mESCs, we shed new light not only on the unique ends of Stag1 but also the critical role that their levels play in stem cell identity. Furthermore, we revel a new role for Stag1, and specifically its unique N-terminal end, in regulating nucleolar integrity and safeguarding mESCs from totipotency. Stag1 is localised to repressive perinucleolar regions, bound at repeats and interacts with Nucleolin and TRIM28. Loss of the Stag1 N-terminus, leads to decreased LINE-1 and rRNA expression and disruption of nucleolar structure and function which consequently leads to activation of the two-cell-like (2C-LC)-specific transcription factor DUX and conversion of pluripotent mESCs to totipotent 2C-LCs. Our results move beyond protein-coding gene regulation via chromatin loops into a new role for Stag1 in repeat regulation and nucleolar structure, and offer fresh perspectives on how Stag proteins contribute to cell identity and disease.

cell biology↗

bioRxiv2020

Search for top-down and bottom-up drivers of latitudinal trends in insect herbivory in oak trees in Europe

AimThe strength of species interactions is traditionally expected to become stronger toward the Equator. However, recent studies have reported opposite or inconsistent latitudinal trends in the bottom-up (plant quality) and top-down (natural enemies) forces driving insect herbivory, possibly because these forces have rarely been studied concomitantly. This makes previous attempts to understand the effect of large scale climatic gradients on insect herbivory unsuccessful. LocationEurope Time period2018-2019 Major taxa studiedQuercus robur MethodsWe used scholar-based citizen science to simultaneously test for latitudinal variation in plant-herbivore-natural enemy interactions. We further investigated the underlying climatic factors associated with variation in herbivory, leaf chemistry and attack rates in Quercus robur across its complete latitudinal range in Europe. We quantified insect herbivory and the occurrence of specialist herbivores as well as leaf chemistry and bird attack rates on dummy caterpillars on 261 oak trees. ResultsClimatic factors rather than latitude per se were the best predictors of the large-scale (geographical) variation in the incidence of gall-inducers and leaf-miners as well as of leaf nutritional quality. However, insect herbivory, plant chemical defences (leaf phenolics) and bird attack rates were not influenced by latitude or climatic factors. The incidence of leaf-miners increased with increasing concentrations of hydrolysable tannins and decreased with those of condensed tannins, whereas the incidence of gall-inducers increased with increasing leaf soluble sugar concentration and decreased with increasing leaf C:N ratios. However, neither other traits nor bird attack rates varied with insect herbivory. Main conclusionsThese findings help to refine our understanding of the bottom-up and top-down mechanisms driving geographical variation in plant-herbivore interactions, and urge for further examination of the drivers of insect herbivory on trees.

ecology↗

bioRxiv2019

Can school children support ecological research? Lessons from the ‘Oak bodyguard’ citizen science project

Scientific knowledge in the field of ecology is increasingly enriched by data acquired by the general public participating in citizen science (CS) programs. Yet, doubts remain about the reliability of such data, in particular when acquired by school children. We built upon an ongoing CS program - Oak bodyguards - to assess the ability of European schoolchildren to accurately estimate the strength of biotic interactions in terrestrial ecosystems. We used standardized protocols to estimate predation rates on artificial caterpillars and insect herbivory on oak leaves and compared estimates made by school children, trained and untrained professional scientists (with no or limited expertise in predation or herbivory assessment). Compared to trained scientists, both schoolchildren and untrained professional scientists overestimated predation rates, but assessments made by the latter were more consistent. School children overestimated insect herbivory, as did untrained professional scientists. Thus, raw data acquired by school children participating in CS programs cannot be used and require several quality checks. However, such data are of no less value than data collected by untrained professional scientists and can be calibrated for bias.

scientific communication and education↗

bioRxiv2018

Unravelling associations between tree seedling performance, herbivory, competition, and facilitation in high nature value farmlands

Herbivory, plant facilitation, and competition have complex impacts on tree regeneration which are seldom investigated together. Grazing exclosure experiments have allowed to quantify the effects of large herbivores on tree regeneration dynamics but have often ignored the effect of herbivorous insects. We experimentally tested how folivory (percentage of leaf damaged by insects), and microenvironment (tree-canopy cover and herbs) jointly alter performance (growth and survival) of seedlings of two dominant Mediterranean oak-species within ungulate exclosures. An agroforestry system dominated by cork oak (Quercus suber) and holm oak (Q. rotundifolia) was assessed in south-east Portugal. We aimed also to determine whether the two oak-species differ in the interdependences between folivory, microenvironment, covaring factors, and seedling performance. Unexpectedly, under the low-moderate insect defoliation occurred in our 3-year field study, growth and survival of cork and holm oak-seedlings were positively associated with herbivory damage. Herb removal increased oak folivory by 1.4 times. Herb removal was also positively associated with growth, directly and indirectly through its negative effect on oak folivory. Tree-canopy favored insect folivory upon cork oak seedlings directly and upon holm oak indirectly via decreasing light availability. Folivory was threefold greater upon cork than upon holm oak-seedlings. Our study shows that tree-canopy, herbs, and covarying factors can affect cork and holm oak-seedling performances through complex pathways, which markedly differ for the two species. The combined effect of insect herbivory and positive and negative plant-plant interactions need to be integrated into future tree regeneration efforts toward tackling the regeneration crisis of oak agroforestry systems of the Mediterranean.

ecology↗