Comparative transcriptome analysis reveals lineage- and environment-specific adaptations in cacti from the Brazilian Atlantic Forest.

MAIN CONCLUSION: Natural selection influenced adaptive divergence between Cereus fernambucensis and Cereus insularis, revealing key genes governing abiotic stress responses and supporting neoteny in C. insularis. Uncovering the molecular mechanisms driving adaptive divergence in traits related to habitat adaptation remains a central challenge. In this study, we focused on the cactus clade, which includes Cereus sericifer F.Ritter, Cereus fernambucensis Lem., and Cereus insularis Hemsley. These allopatric species inhabit distinct relatively drier regions within the Brazilian Atlantic Forest, each facing unique abiotic conditions. We leveraged whole transcriptome data and abiotic variables datasets to explore lineage-specific and environment-specific adaptations in these species. Employing comparative phylogenetic methods, we identified genes under positive selection (PSG) and examined their association with non-synonymous genetic variants and abiotic attributes through a PhyloGWAS approach. Our analysis unveiled signatures of selection in all studied lineages, with C. fernambucensis northern populations and C. insularis showing the most PSGs. These PSGs predominantly govern abiotic stress regulation, encompassing heat tolerance, UV stress response, and soil salinity adaptation. Our exclusive observation of gene expression tied to early developmental stages in C. insularis supports the hypothesis of neoteny in this species. We also identified genes associated with abiotic variables in independent lineages, suggesting their role as environmental filters on genetic diversity. Overall, our findings suggest that natural selection played a pivotal role in the geographic range of these species in response to environmental and biogeographic transitions.

Unravelling phylogenetic relationships of the tribe Cereeae using target enrichment sequencing.

BACKGROUND AND AIMS: Cactaceae are succulent plants, quasi-endemic to the American continent, and one of the most endangered plant groups in the world. Molecular phylogenies have been key to unravelling phylogenetic relationships among major cactus groups, previously hampered by high levels of morphological convergence. Phylogenetic studies using plastid markers have not provided adequate resolution for determining generic relationships within cactus groups. This is the case for the tribe Cereeae s.l., a highly diverse group from tropical America. Here we aimed to reconstruct a well-resolved phylogenetic tree of tribe Cereeae and update the circumscription of suprageneric and generic groups in this tribe. METHODS: We integrated sequence data from public gene and genomic databases with new target sequences (generated using the customized Cactaceae591 probe set) across representatives of this tribe, with a denser taxon sampling of the subtribe Cereinae. We inferred concatenated and coalescent phylogenetic trees and compared the performance of both approaches. KEY RESULTS: Six well-supported suprageneric clades were identified using different datasets. However, only genomic datasets, especially the Cactaceae591, were able to resolve the contentious relationships within the subtribe Cereinae. CONCLUSIONS: We propose a new taxonomic classification within Cereeae based on well-resolved clades, including new subtribes (Aylosterinae subtr. nov., Uebelmanniinae subtr. nov. and Gymnocalyciinae subtr. nov.) and revised subtribes (Trichocereinae, Rebutiinae and Cereinae). We emphasize the importance of using genomic datasets allied with coalescent inference to investigate evolutionary patterns within the tribe Cereeae.

Revisiting phylogeny, systematics, and biogeography of a Pleistocene radiation.

PREMISE: Pilosocereus (Cactaceae) is an important dry forest element in all subregions and transitional zones of the neotropics, with the highest diversity in eastern Brazil. The genus is subdivided into informal taxonomic groups; however, most of these are not supported by recent molecular phylogenetic inferences. This lack of confidence is probably due to the use of an insufficient number of loci and the complexity of cactus diversification. Here, we explored the species relationships in Pilosocereus in more detail, integrating multilocus phylogenetic approaches with the assessment of the ancestral range and the effect of geography on diversification shifts. METHODS: We used 28 nuclear, plastid, and mitochondrial loci from 54 plant samples of 31 Pilosocereus species for phylogenetic analyses. We used concatenated and coalescent phylogenetic trees and Bayesian models to estimate the most likely ancestral range and diversification shifts. RESULTS: All Pilosocereus species were clustered in the same branch, except P. bohlei. The phylogenetic relationships were more associated with the geographic distribution than taxonomic affinities among taxa. The genus began diversifying during the Plio-Pleistocene transition in the Caatinga domain and experienced an increased diversification rate during the Calabrian age. CONCLUSIONS: We recovered a well-supported multispecies coalescent phylogeny. Our results refine the pattern of rapid diversification of Pilosocereus species across neotropical drylands during the Pleistocene and highlight the need for taxonomic rearrangements in the genus. We recovered a pulse of diversification during the Pleistocene that was likely driven by multiple dispersal and vicariance events within and among the Caatinga, Cerrado, and Atlantic Forest domains.

Monitoring of Circulating Tumor DNA Predicts Response to Treatment and Early Progression in Follicular Lymphoma: Results of a Prospective Pilot Study.

PURPOSE: Follicular lymphoma (FL) is the most frequent indolent non-Hodgkin lymphoma. Around 20% of patients suffer early disease progression within 24 months (POD24) of diagnosis. This study examined the significance of circulating tumor DNA (ctDNA) in predicting response to therapy and POD24 in patients with FL. EXPERIMENTAL DESIGN: We collected 100 plasma samples, before and during the treatment, from 36 patients with FL prospectively enrolled in 8 Spanish hospitals. They were treated with a chemotherapy-rituximab regimen and followed up for a median of 3.43 years. We performed targeted deep sequencing in cell-free DNA (cfDNA) and tumor genomic DNA from 31 diagnostic biopsy samples. RESULTS: Of the alterations detected in the diagnostic tissue samples, 73% (300/411) were also identified in basal cfDNA. The mean numbers of alterations per basal cfDNA sample in patients who suffered progression of disease within 24 months (POD24-pos) or did not achieve complete response (non-CR) were significantly higher than in POD24-neg or CR patients (unpaired samples t test, P = 0.0001 and 0.001, respectively). Pretreatment ctDNA levels, as haploid genome equivalents per milliliter of plasma, were higher in patients without CR (P = 0.02) and in POD24-pos patients compared with POD24-neg patients (P < 0.001). Dynamic analysis showed that ctDNA levels decreased dramatically after treatment, although the reduction was more significant in patients with CR and POD24-neg patients. CONCLUSIONS: Basal ctDNA levels are associated with the risk of early progression and response to treatment in FL. cfDNA monitoring and genotyping during treatment and follow-up predict response to treatment and early progression.

Coalescent-based species delimitation meets deep learning: Insights from a highly fragmented cactus system.

Delimiting species boundaries is a major goal in evolutionary biology. An increasing volume of literature has focused on the challenges of investigating cryptic diversity within complex evolutionary scenarios of speciation, including gene flow and demographic fluctuations. New methods based on model selection, such as approximate Bayesian computation, approximate likelihoods, and machine learning are promising tools arising in this field. Here, we introduce a framework for species delimitation using the multispecies coalescent model coupled with a deep learning algorithm based on convolutional neural networks (CNNs). We compared this strategy with a similar ABC approach. We applied both methods to test species boundary hypotheses based on current and previous taxonomic delimitations as well as genetic data (sequences from 41 loci) in Pilosocereus aurisetus, a cactus species complex with a sky-island distribution and taxonomic uncertainty. To validate our method, we also applied the same strategy on data from widely accepted species from the genus Drosophila. The results show that our CNN approach has a high capacity to distinguish among the simulated species delimitation scenarios, with higher accuracy than ABC. For the cactus data set, a splitter hypothesis without gene flow showed the highest probability in both CNN and ABC approaches, a result agreeing with previous taxonomic classifications and in line with the sky-island distribution and low dispersal of P. aurisetus. Our results highlight the cryptic diversity within the P. aurisetus complex and show that CNNs are a promising approach for distinguishing complex evolutionary histories, even outperforming the accuracy of other model-based approaches such as ABC.

Maintaining genetic integrity with high promiscuity: Frequent hybridization with low introgression in multiple hybrid zones of Melocactus (Cactaceae).

Hybridization and introgression between species in contact/hybrid zones provide important insight into the genetic and ecological mechanisms of speciation. Cactaceae represents the most important radiation of true succulent angiosperms in the New World. This diversification continues to date, with species experiencing few intrinsic barriers to gene flow and the frequent occurrence of natural hybridization. Here, we used RAD-Seq single-nucleotide polymorphism (SNP) data to investigate the genetic architecture of hybridization in four hybrid zones hosting Melocactus concinnus and four congeneric species (M. ernestii, M. glaucescens, M. paucispinus, and M. zehntneri). Our results revealed that M. concinnus is highly promiscuous in sympatric areas and hybridizes with various species distributed in Morro do Chapéu (Diamantina Plateau, Bahia), eastern Brazil. However, the contemporary genomic introgression among the investigated species is very low (c. 2-5%), confirming that even in the face of hybridization, Melocactus species maintain their genetic integrity. The genomic cline approach showed a large fraction of loci deviating from a model of neutral introgression, where most of the loci are consistent with selection favoring parental genotypes. Our results suggest the occurrence of weak premating but strong postmating reproductive isolation in the analyzed cactus species. Furthermore, as most of the Melocactus species are restricted in distribution, hybridization might negatively affect their integrity if hybrids replace the parental species.

Weak population structure and no genetic erosion in Pilosocereus aureispinus: A microendemic and threatened cactus species from eastern Brazil.

Succulent cacti (Cactaceae) are among the most threatened taxonomic groups assessed to date. Here we evaluated the genetic diversity and population structure of a narrow endemic columnar cactus Pilosocereus aureispinus. This species is only found in a small area of c. 300 km2 of rocky savanna from eastern Brazil and it is currently classified as vulnerable (VU) on the International Union for Conservation of Nature (IUCN) red list. Eight microsatellite loci were genotyped for 91 individuals from four localities of the known P. aureispinus range. In contrast with expectations for narrow endemic species, we found relatively high levels of genetic diversity (e.g., HE = 0.390 to 0.525; HO = 0.394 to 0.572) and very low population structure based on the variation of six loci. All the analyzed individuals were clustered in one unique genetic group in assignment tests. We also generated the sequences of two plastid markers (trnT-trnL and psbD-trnT) and found no variation on a subsample of 39 individuals. We used Landsat 8 images and Normalized Difference Vegetation Index to estimate a potential extent of occurrence of c. 750 km2 for this species. Our results showed that P. aureispinus is not suffering from erosion of nuclear genetic variability due to its narrow distribution. However, we advocate that because of the extremely limited extent of occurrence, the ongoing anthropogenic disturbances in its habitat, and phylogenetic distinctiveness of P. aureispinus, this species should be classified as endangered (EN) on the IUCN Red List.

Lineage-specific evolutionary rate in plants: Contributions of a screening for Cereus (Cactaceae).

PREMISE OF THE STUDY: Predictable chloroplast DNA (cpDNA) sequences have been listed for the shallowest taxonomic studies in plants. We investigated whether plastid regions that vary between closely allied species could be applied for intraspecific studies and compared the variation of these plastid segments with two nuclear regions. METHODS: We screened 16 plastid and two nuclear intronic regions for species of the genus Cereus (Cactaceae) at three hierarchical levels (species from different clades, species of the same clade, and allopatric populations). RESULTS: Ten plastid regions presented interspecific variation, and six of them showed variation at the intraspecific level. The two nuclear regions showed both inter- and intraspecific variation, and in general they showed higher levels of variability in almost all hierarchical levels than the plastid segments. DISCUSSION: Our data suggest no correspondence between variation of plastid regions at the interspecific and intraspecific level, probably due to lineage-specific variation in cpDNA, which appears to have less effect in nuclear data. Despite the heterogeneity in evolutionary rates of cpDNA, we highlight three plastid segments that may be considered in initial screenings in plant phylogeographic studies.

Occurrence of fat embolism after liposuction surgery with or without lipografting: an experimental study.

BACKGROUND: Liposuction in plastic surgery consists of the removal of excess fatty tissue in healthy individuals. In recent decades, this procedure has become more common worldwide. Associated with liposuction, lipografting has also been used for improving body contours, and has become known as liposculpture. Liposuction sometimes causes complications, including fat embolism, as described in the medical literature. The present study aims at ascertaining whether there is intravascular mobilization of fat after mechanical liposuction surgery and/or fat graft when carried out using one of the most common specific procedures used for liposuction, the superwet technique. METHODS: A total of 30 Wistar rats were included in this study. Before the surgery, the animals were placed in the supine position and anesthetized with thiopental for 50 to 60 minutes, as it is generally performed in clinical practice. The animals were divided in the following 3 groups. Group A, consisting of 10 rats, served as controls, and were only anesthetized. Group B consisted of 10 rats, which underwent only liposuction. Group C also comprised 10 rats, which were liposuctioned and then lipografted in the dorsal region. Blood was collected just before and again, 48 hours after the procedure. After 48 hours, the animals were killed, and the lungs, kidneys, liver, and brain were histologically examined. RESULTS: All the collected samples were analyzed microscopically with 2 different stains, namely, hematoxylin and eosin, and Sudan black. Fat particles were found in the lungs of 3 animals in group B (those that underwent only liposuction) and in 6 animals of group C (liposuction and lipografting). No fat particles were found in any organ of the control group. CONCLUSIONS: With this experiment, the authors showed that there is a risk of systemic mobilization of fat after liposuction surgery and that this risk is even higher when fat grafts are also carried out.

Phenotypic variation of the Aedeagus of Drosophila serido vilela & sene (Diptera: Drosophilidae).

Drosophila serido Vilela & Sene is a polytypic and cactophilic species with broad geographic distribution in Brazil. The morphology of the aedeagi of eight natural populations of D. serido was analyzed. Based on features of their aedeagi, populations of D. serido were discriminated with an efficiency of nearly 75%. The analysis using the Mantel test suggests that the morphological divergence of D. serido is correlated with the geographic distance among populations. There is no single cause to explain the observed pattern; therefore, the results were discussed considering the three main hypotheses to explain the aedeagus evolution: lock and key, pleiotropy and sexual selection. Alternatively, the aedeagus variability of D. serido might be related to environmental causes, such as temperature and/or host cacti.

Tratamento cirúrgico do paciente com síndrome de Barraquer-Simon: revisão bibliográfica e relato de caso / Surgical treatment of patient with Barraquer-Simon syndrome: review of literature and related case

Barraquer e Simon descreveram no começo do século uma doença caracterizada por progressiva atrofia da gordura do tecido subcutâneo, limitada à parte superior do corpo, incluindo face. É uma síndrome rara, de origem obscura, também conhecida como lipodistrofia céfalotorácica. Os pacientes com a síndrome perdem progressivamente sua gordura subcutânea em direção craniocaudal simetricamente, começando na face e progredindo até uma determinada área da coxa. Freqüentemente estes pacientes apresentam uma hipertrofia de tecido celular subcutâneo nas suas extremidades inferiores. A doença começa no final da primeira década de vida ou no começo da segunda década, e é rara em pacientes do sexo masculino. Os autores descrevem um caso da síndrome de Barraquer-Simon com envolvimento facial e torácico, sem outras anomalias. Durante o seguimento cirúrgico, foram realizadas lipoenxertias, cirurgia para colocação de bioimplantes malares e cirurgia ortognática. A síndrome de Barraquer-Simon, classificada como lipodistrofia parcial, ainda é pouco compreendida. Mais estudos serão necessários para confirmar a base genética.

Barraquer and Simon described at the beginning of the century a disease characterized by progressive atrophy of the fat tissue of the sub-cutaneous limited to upper body including face. It is a rare syndrome of obscure origin, also known as lipodystrophy cefalochest. The patients with the syndrome gradually lose their fat sub-cutaneous toward craniocaudal symmetrically, starting on the face and progresses to a certain area of the thigh. Often these patients have a hypertrophy of cellular sub-cutaneous tissue in their lower extremities. The disease begins at the end of the first decade of life or at the beginning of the second decade, and is rare in patients male. The authors describe a case of the syndrome Barraquer-Simon involvement with facial and chest with no other abnormalities. During the surgical follow up, was performed lipoenxertias, surgery for placement of bioimplantes malares and surgery orthognathic. The syndrome Barraquer-Simon, classified as partial lipodystrophy, is still little understood. More studies are needed to confirm the genetic basis.

Phenotypic variation of the Aedeagus of Drosophila serido vilela & sene (Diptera: Drosophilidae) / Variação fenotípica do edeago de Drosophila serido vilela & sene (Diptera: Drosophilidae)

Drosophila serido Vilela & Sene é uma espécie cactofílica e politípica, com ampla distribuição geográfica no Brasil. A morfologia do edeago de indivíduos provenientes de oito populações naturais de D. serido foi avaliada. De acordo com as características dos seus edeagos, as populações de D. serido foram discriminadas com eficiência de aproximadamente 75 por cento. O resultado do teste de Mantel sugere que a divergência morfológica de D. serido é correlacionada com a distância geográfica das populações. A explicação para o padrão observado não é única. Por esta razão, os resultados foram discutidos considerando-se as três principais hipóteses para explicar a evolução do edeago: chave-fechadura, pleiotropia e seleção sexual. Alternativamente, a variabilidade encontrada nos edeagos de D. serido poderia estar relacionada a fatores ambientais, tais como temperatura e/ou cacto hospedeiro.

Drosophila serido Vilela & Sene is a polytypic and cactophilic species with broad geographic distribution in Brazil. The morphology of the aedeagi of eight natural populations of D. serido was analyzed. Based on features of their aedeagi, populations of D. serido were discriminated with an efficiency of nearly 75 percent. The analysis using the Mantel test suggests that the morphological divergence of D. serido is correlated with the geographic distance among populations. There is no single cause to explain the observed pattern; therefore, the results were discussed considering the three main hypotheses to explain the aedeagus evolution: lock and key, pleiotropy and sexual selection. Alternatively, the aedeagus variability of D. serido might be related to environmental causes, such as temperature and/or host cacti.

Molecular characterization of SSS139, a new satellite DNA family in sibling species of the Drosophila buzzatii cluster

We characterized sequences of a novel SSS139 RsaI satellite DNA family in Drosophila gouveai and Drosophila seriema, two members of the Drosophila buzzatii cluster (D. repleta group). The sequences were AT-rich (69 percent) with a monomer unit length of about 139 bp and contained two direct subrepeats of 14 bp and 16 bp, suggesting that it might have originated by the duplication of smaller sequences. Southern and dot-blot hybridization analyses also detected SSS139 in other Drosophila buzzatii cluster species (D. koepferae, D. antonietae, D. borborema and D. serido) but not in D. buzzatii. These results agree with the marginal phylogenetic position of D. buzzatii within the D. buzzatii cluster.

Low rates of homogenization of the DBC-150 satellite DNA family restricted to a single pair of microchromosomes in species from the Drosophila buzzatii cluster.

A satellite DNA family, termed DBC-150, comprises slightly GC-rich repeat units of approximately 150 bp that were isolated (by DNA digestions or PCR) from the genome of all seven Drosophila species from the buzzatii cluster (repleta group). The presence of subrepeats suggests that part of the extant DBC-150 monomer originated by the duplication of small sequence motifs. The DBC-150 family is compared to the previously described pBuM satDNA family, an abundant component of the genome of five species of the cluster. The two families are different in several aspects, including primary structure, A + T content, intraspecific and interspecific variability and rates of homogenization (or nucleotide spread). The data indicate a lower rate of homogenization (and absence of complete concerted evolution) of the DBC-150 compared to the pBuM family. FISH on metaphase chromosomes revealed that the DBC-150 family is located exclusively in the microchromosomes. To our knowledge this is the first record of a complex Drosophila satDNA restricted to a single pair of microchromosomes. The observed low rates of homogenization of the DBC-150 family might be related to a presumed reduction or suppression of meiotic recombination in the microchromosomes.

Aedeagus morphology as a discriminant marker in two closely related Cactophilic species of Drosophila (Diptera; Drosophilidae) in South America

Drosophila serido e D. antonietae são espécies crípticas pertencentes ao ''cluster'' Drosophila buzzatii. Morfologicamente, elas podem ser discriminadas apenas por diferenças quantitativas. Neste trabalho, nós analisamos o comprimento e a média da curvatura equalizada de quatro regiões do edeago de indivíduos de D. antonietae e D. serido. Os espécimes de D. serido e D. antonietae foram discriminados com 96,74% de eficiência. Apenas com base na variável que mais contribuiu para discriminação dos grupos (média da curvatura equalizada do arco IV do edeago), nós observamos significativa divergência morfológica intraespecífica em D. serido em relação a D. antonietae, o que está em concordância com outros marcadores. A alta divergência morfológica apenas na média da curvatura equalizada do arco IV do edeago mostra que essa região do edeago evoluiu mais rápido que as demais desde a divergência entre as duas espécies. A importância do presente estudo para o entendimento das bases genética que controlam a formação do edeago, nas espécies do ''cluster'' Drosophila buzzatii, é discutida.

Aedeagus morphology as a discriminant marker in two closely related cactophilic species of Drosophila (Diptera; Drosophilidae) in South America.

Drosophila serido and D. antonietae are sibling species belonging to the Drosophila buzzatii cluster. Morphologically, they can only be discriminated by quantitative traits. In this paper we analyze the length and equalized average curvature of four regions of the aedeagus of D. antonietae and D. serido. Specimens of D. serido and D. antonietae were classified correctly 96.74% of the time. Based only on the variable that most contributed to the discrimination of the groups (equalized average curvature of the arch IV of the aedeagus), we observed significant intraspecific morphological divergence in D. serido in relation to the D. antonietae, in agreement with other markers. The high morphological divergence in equalized average curvature of the arch IV of the aedeagus shows that this region evolved faster than others, since the divergence of the two species. The importance of the present study to the understanding of the genetic basis that controls the formation of the aedeagus, in the species of the Drosophila buzzatii cluster, is discussed.

On the pBuM189 satellite DNA variability among South American populations of Drosophila buzzatii.

The pBuM189 satellite DNA was analysed in Drosophila buzzatii populations that cover most of the species distribution in South America. This satDNA consists of A + T-rich monomers of 189 bp and previous studies showed a fast rate of evolutionary change of this component of D. buzzatii genome. A total of 63 pBuM189 repetition units from 14 D. buzzatii populations (9 from Brazil and 5 from Argentina) were studied. The average nucleotide variability among the 63 repeats is 4.2 %. At least one repeat (Juan/4) seems to be part of another pBuM189 satDNA subfamily. The nucleotide alignment of all 63 repeats revealed no specific nucleotide substitutions, or indels, that could discriminate each population or groups of geographically close populations. Such lack of satDNA interpopulational differentiation is congruent with previous mtDNA data that indicate a high gene flow and very little population differentiation throughout most of the D. buzzatii distribution in South America. Gene flow might have been possible during glaciation events in the Pleistocene, such as the one occurred between 13,000 and 18,000 years ago, when D. buzzatii probably had a more continuous distribution than what is observed today.