Biology subjects

Cardoso, D.

Publications and source records attributed to Cardoso, D..

7 recordsLinked to original sources

bioRxiv2026

Coordinated Evolutionary Rates in Oxidative Phosphorylation Complexes of Papilionoid Legumes: Cytonuclear Coevolution and Relaxed Selection

Across eukaryotes, mitochondrial (mt) and nuclear genomes coordinate the expression and interaction of gene products to maintain cellular functions. While mitonuclear coevolution has been widely explored in animals, it remains understudied in plants, despite their utility as model systems due to relatively slow mitochondrial evolutionary rates and the presence of plastids. Plants rely on oxidative phosphorylation (OXPHOS) for ATP conversion, which requires cofunctionality and likely coevolution of mitochondrial and nuclear gene products. Here, we investigated evolutionary rate covariation (ERC) between mitochondrial- and nuclear-encoded OXPHOS genes in papilionoid legumes, where plastid-nuclear coevolution and an inversion in plastid DNA have been documented previously. Using 50 legume species spanning 15 papilionoid clades, we estimated evolutionary rates for five gene sets: mt-encoded OXPHOS genes, nuclear-encoded mitochondrial-targeted (N-mt) OXPHOS genes, and three control nuclear gene sets that lack mitochondrial interactions (glycolysis, cell cycle, and cytosolic ribosomal genes). Both mt and N-mt OXPHOS genes exhibited significantly elevated nonsynonymous (dN) and synonymous substitution rates (dS) in the 50-kb inversion clade relative to other legumes, suggesting accelerated mitochondrial substitution rates. Moreover, elevated dN/dS ratios in mt and N-mt OXPHOS genes in this clade were driven by relaxed purifying, not intensified positive selection. ERCs were highest for OXPHOS complexes and genes with physical mitonuclear interactions, as predicted under mitonuclear coevolution. We discuss how these results compare to other cases of cytonuclear coevolution in plants, including plastid-nuclear coevolution in papilionoids, and why dual-targeted, nuclear-encoded genes that repair mt and plastid DNA may underly patterns of molecular evolution in both organelles. Significance StatementMitonuclear interactions are essential for cellular energy production, yet the evolutionary dynamics of these interactions remain poorly understood in plants. This study highlights papilionoid legumes as an important system for understanding how coordinated evolution between mitochondrial and nuclear genes shapes plant genomes. By identifying signatures of mitonuclear coevolution in the 50-kb inversion clade, this work demonstrates how shifts in selective pressures on mitochondrial processes can influence nuclear gene evolution. These findings advance our understanding of cytonuclear coordination in plants and provide a foundation for future studies exploring how interactions among genomic compartments contribute to plant evolution, adaptation, and resilience in agriculturally important lineages.

evolutionary biology↗

bioRxiv2026

Integrating lineage-specific and universal genomic probes illuminates phylogenetic relationships and molecular evolution in Sauvagesieae (Ochnaceae)

Obtaining large and well-resolved phylogenetic trees for neotropical clades is challenging, as many species inhabit remote regions, and sampling often relies on herbarium specimens with highly degraded DNA. Target capture provides an effective solution for retrieving molecular data from fragmentary material. However, data processing using tools generally designed for diploid organisms and single-copy loci is also challenging, particularly when events such as genome duplication and hybridisation have shaped the lineage evolution. We used dual-hybridisation to integrate Ochnaceae-specific and universal probes to reconstruct the phylogenetic relationships of Sauvagesieae, a pantropical clade with ca. 90 species mainly distributed in the northern Andes, the Brazilian Espinhaco Range, and the Amazon-Guyana region. We tested different filtering strategies involving missing data and paralogs to assess probable sources of tree discordance and topological uncertainty. We found no significant benefit in reducing tree discordance after removing entire genes due to the presence of paralogs or a high amount of missing data. Removing fragmentary sequences instead improved alignments and increased branch support of gene trees. By quantifying the proportion of SNPs, analysing the distribution of the allele frequencies, and gene-tree quartet frequencies, we found evidence of polyploidisation and hybridisation, which could reduce resolution at internal nodes, particularly in mountain clades. Our results underscore the importance of exploring the complexities of target-capture data, not only to improve phylogenetic resolution but also to understand the sources of phylogenetic conflict and the underlying molecular evolutionary processes.

genomics↗

bioRxiv2025

Thresholds of drought and terrain complexity shape biomasspatterns in South America's Caatinga

Seasonally Tropical Dry Forests (STDFs) are widespread throughout the world and store significant amounts of carbon; however, they are often overlooked in spatial assessments compared to humid tropical forests. The Caatinga, which is the largest seasonally dry tropical forest in South America, covers approximately 862,000 km{superscript 2} in northeastern Brazil and supports millions of people. Unfortunately, its carbon dynamics has not been thoroughly quantified, especially after centuries of land-use transformation and wood extraction that have significantly diminished its biomass stocks. In this study, we model the potential aboveground biomass (AGB) that Caatinga could sustain under current climatic, atmospheric, and topographic conditions. We integrated data from 301 geo-referenced plots along with high-resolution environmental predictors. The principal Component Analysis revealed two main gradients: a hydro-thermal axis dominated by precipitation, temperature, and severity of drought, and a topographic axis reflecting slope, ruggedness, and terrain position. Random Forest models, validated through both random and spatial cross-validation, explained a significant amount of variation in AGB (R{superscript 2} = 0.81, RMSE = 21 Mg ha). Our findings indicated that AGB is highly sensitive to water availability. In particular, biomass increased sharply when the maximum cumulative water deficit (MCWD) was less than -500 mm and annual rainfall exceeded approximately 1,100 mm. In contrast, elevated vapour pressure deficit (VPD) and potential evapotranspiration (PET) were associated with reduced carbon storage. Topographic heterogeneity further influenced AGB, with rugged and concave terrains supporting potential biomass levels more than twice as high as those found in flat, convex areas. Our predictive map reveals a mosaic of low-biomass cores and localized high-biomass refugia, highlighting the dual influence of hydroclimatic and topographic factors. These findings reposition Caatinga as a heterogeneous and dynamic potential carbon reservoir - historically degraded by changes in land-use but still capable of storing substantial carbon. This research offers critical insights for the restoration, conservation and mitigation efforts for climate change in tropical drylands worldwide.

ecology↗

bioRxiv2024

Well-resolved phylogeny reveals multiple origins of keel flowers during the diversification of papilionoid legumes

O_LIThe butterfly-shaped keel flower is a highly successful floral form in angiosperms. These flowers steer the mechanical interaction with bees and thus are hypothesized to accelerate pollinator-driven diversification. The exceptionally labile evolution of keel flowers in Papilionoideae (Fabaceae) provides a suitable system to test this hypothesis. C_LIO_LIUsing 1,456 low-copy nuclear loci, we confidently resolve the early divergence history of Papilionoideae. Constrained by this backbone phylogeny, we generated a time tree for 3,326 Fabales to evaluate the tempo and mode of diversification within a state-dependent evolutionary framework. C_LIO_LIThe first keel flowers emerged around 59.0 Ma in Papilionoideae, predating the earliest fossil by 3-4 million years. The Miocene diversification of Papilionoideae coincided with rapid evolution of keel flowers. At least six independent origins and thirty-two losses of keel flowers were identified in Papilionoideae, Cercidoideae, and Polygalaceae. However, the state-dependent diversification model was not favored. C_LIO_LILack of radiation associated with keel flowers suggests that diversification within Papilionoideae was not solely driven by pollinator-mediated selection, but instead an outcome of the synergistic effects of multiple innovations including nitrogen fixation and chemical defense as well as dispersal into subtropical and temperate regions. C_LI

evolutionary biology↗

bioRxiv2022

The innovation of the symbiosome has enhanced the evolutionary stability of nitrogen fixation in legumes

O_LINitrogen-fixing symbiosis is globally important in ecosystem functioning and agriculture, yet the evolutionary history of nodulation remains the focus of considerable debate. Recent evidence suggesting a single origin of nodulation followed by massive parallel evolutionary losses raises questions about why a few lineages in the N2-fixing clade retained nodulation and diversified as stable nodulators while most did not. Within legumes, nodulation is restricted to the two most diverse subfamilies, Papilionoideae and Caesalpinioideae, which show stable retention of nodulation across their core clades. C_LIO_LIWe characterize two nodule anatomy types across 128 species in 56 of the 150 genera of the legume subfamily Caesalpinioideae: 1) fixation thread nodules (FTs), where nitrogen-fixing bacteroids are retained within the apoplast in modified infection threads and 2) symbiosomes, where rhizobia are symplastically internalized in the host cell cytoplasm within membrane-bound symbiosomes. C_LIO_LIUsing a robust phylogenomic tree based on 997 genes from 146 caesalpinioid genera, we show that losses of nodulation are more prevalent in lineages with FTs. C_LIO_LIWe propose that evolution of the symbiosome allows for a more intimate and enduring symbiosis through greater compartmentalisation of their rhizobial microsymbionts, resulting in greater evolutionary stability of nodulation across this species-rich pantropical clade of legumes. C_LI

evolutionary biology↗

bioRxiv2021

The chicken or the egg? Plastome evolution and a novel loss of the inverted repeat in papilionoid legumes

The plastid genome (plastome), while surprisingly constant in gene order and content across most photosynthetic angiosperms, exhibits variability in several unrelated lineages. During the diversification history of the legume family Fabaceae, plastomes have undergone many rearrangements, including inversions, expansion, contraction and loss of the typical inverted repeat (IR), gene loss and repeat accumulation in both shared and independent events. While legume plastomes have been the subject of study for some time, most work has focused on agricultural species in the IR-lacking clade (IRLC) and the plant model Medicago truncatula. The subfamily Papilionoideae, which contains virtually all of the agricultural legume species, also comprises most of the plastome variation detected thus far in the family. In this study 33 newly sequenced plastomes of papilionoid legumes and outgroups were evaluated, along with 34 publicly available sequences, to assess plastome structural evolution in the subfamily. In an effort to examine plastome variation across the subfamily, just [~]20% of the sampling represents the IRLC with the remainder selected to represent the early-branching papilionoid clades. A number of IR-related and repeat-mediated changes were identified and examined in a phylogenetic context. Recombination between direct repeats associated with ycf2 resulted in intraindividual plastome heteroplasmy. Although loss of the inverted repeat has not been reported in legumes outside of the IRLC, one genistoid taxon was found to completely lack the typical plastome IR. The role of the IR and non-IR repeats in driving plastome change is discussed. Significance statementComparative genomic approaches employing plastid genomes (plastomes) have revealed that they are more variable across angiosperms than previously suggested. This study examined 64 species of Fabaceae and outgroups, including 33 newly sequenced taxa, to explore plastome structural evolution of the subfamily Papilionoideae in a phylogenetic context. Several unusual features of the inverted repeat highlight the importance of recombination in plastomic structural changes within and between individuals and species.

plant biology↗

bioRxiv2019

Crab fisherman communities in north Brazil: a new high risk population for vampire bat rabies

An outbreak of human rabies transmitted by hematophagous bats occurred in 2018 in the state of Para, Brazil, eastern Amazon, after 14 years with no record of the disease. It is necessary to understand the epidemiological characteristics of these attacks to protect the local population. This study aimed to characterize attacks of humans by vampire bats in the municipality of Sao Joao da Ponta, Para state, Brazil, from 2013 to 2015. All individuals attacked by bats who sought medical care during the study period (n=5) were identified in the Notifiable Diseases Information System (SINAN) database and answered a questionnaire about the circumstances of the attack. Using snowball sampling, seed cases identified other individuals who were attacked in the same period but did not seek medical care (n=61), totalizing 66 people attacked in the same period. The interviewees were male (92.4%), adults between 20 and 50 years old (69.6%) and had completed elementary education (86.3%). Most were rural residents (92.4%) and crab fishermen (79.3%). The interviewees (92.4%) identified the mangrove of the Mae Grande de Curuca extractive reserve as an area conducive to attacks by vampire bats, where groups of fishermen sometimes concentrate for days for crab fishing, often living in improvised dwellings without walls and covered by tarps or straw (88.8%). The wounds were single bites (71.2%) and were located on the lower limbs (93.9%). Overall, 42.4% of participants had been bitten more than four times throughout their life (range 1-23 attacks). Participants were unaware of the risk of contracting rabies by the bite (95.4%). Using Sao Joao da Ponta as a model, this study shows that bat attacks are an essentially occupational problem in the study region. Indeed, for each reported attack, there are 12.2 unreported cases. It is necessary to develop strategies to reach this population for prophylactic treatment.\n\nAuthor SummaryDifferent from which occurs worldwide in relation to rabies transmission, in Amazon region, vampire bat is involved on direct transmission of rabies virus to humans when searching for bloodmeal. It is common in the state of Para, Eastern Amazon, large areas inhabited near forests and mangroves. People living there use forest natural resources as a way of income and sustenance and these working conditions is what our study points out as an important factor for aggressions predisposition. Here this subject is shown as an occupational problem. This study also quantified for the first time underreported humans aggressions by bats in Amazon, using the snowball sampling, which valued the relationship between individuals to reach the target population. Based on these results, rabies surveillance may direct actions for prevention and health education for these individuals, including changes in notifications forms and suggesting pre-exposure prophylaxis in vaccination calendar of the Brazilian Ministry of Health for these individuals exposed to the rabies virus.

epidemiology↗