Mutational Steps Research Articles

Empirical Study of Multi-Objective Risk Portfolio Optimization Based on NSGA-II

The purpose of the article. The application of multi-objective optimization in portfolio management has gained significant attention in asset management. This study aims to uncover the potential advantages of dynamic portfolio optimization using a multi-objective genetic algorithm to address the challenges of ever-changing market conditions. Methodology. By incorporating multi-objective optimization, this paper comprehensively examines three key portfolio objectives: minimizing two risk types and maximizing returns. The approach involves constructing portfolios, initializing the population using the Non-Dominated Sorting Genetic Algorithm II (NSGA-II), and employing crossover and mutation steps to achieve Pareto optimality. Additionally, this study compares the performance of two risk minimization strategies through traditional portfolio backtesting. Results of the research. The results indicate that the multi-objective risk genetic algorithm not only effectively explores the portfolio space but also handles conflicting optimization objectives, thereby enhancing the comprehensiveness and flexibility of investment decisions. However, its performance depended on the chosen risk measurement methods, and the backtesting returns were unstable.

Phylogeography of the Invasive Fruit Fly Species Bactrocera carambolae Drew & Hancock (Diptera: Tephritidae) in South America.

The carambola fruit fly, Bactrocera carambolae Drew & Hancock, is native to Southeast Asia, infests about 150 plant species, and is considered a quarantine pest insect in several regions of the world. Bactrocera carambolae has invaded Suriname, French Guyana, and northern Brazil. In Brazil, it was first recorded in 1996 and has been restricted to the states of Amapá and Roraima due to official control efforts of the Ministry of Agriculture and Food Supply (Ministério da Agricultura e Pecuária-MAPA). This is the first study to estimate the genetic structure and diversity of South American populations of B. carambolae. A total of 116 individuals from 11 localities in Brazil and 7 localities in Suriname were analyzed. Additional sequences available at GenBank from Indonesia (Lampung) and Thailand (San Pa Tong and Muang District) were also used in the analysis. We sequenced a fragment of the mitochondrial gene cytochrome oxidase subunit I. A total of 35 haplotypes were found. Haplotypes from Indonesia were closest to the haplotypes from South America, separated only by a few mutational steps. This suggests that Indonesia is the likely source for the introduction of B. carambolae into South America. The Southeast Asian populations appeared as the most ancestral group in the phylogenetic trees. The high similarity and sharing of several haplotypes among populations within South America indicate a lack of genetic structure. The mismatch distribution and neutrality tests suggest that South American populations have undergone a rapid growth and expansion following a single founder event. The low genetic diversity and the population expansion evidenced by the neutrality tests lend support to the hypothesis of a recent introduction of a single lineage of the carambola fruit fly into South America.

The origin of mutational epistasis.

The interconnected processes of protein folding, mutations, epistasis, and evolution have all been the subject of extensive analysis throughout the years due to their significance for structural and evolutionary biology. The origin (molecular basis) of epistasis-the non-additive interactions between mutations-is still, nonetheless, unknown. The existence of a new perspective on protein folding, a problem that needs to be conceived as an 'analytic whole', will enable us to shed light on the origin of mutational epistasis at the simplest level-within proteins-while also uncovering the reasons why the genetic background in which they occur, a key component of molecular evolution, could foster changes in epistasis effects. Additionally, because mutations are the source of epistasis, more research is needed to determine the impact of post-translational modifications, which can potentially increase the proteome's diversity by several orders of magnitude, on mutational epistasis and protein evolvability. Finally, a protein evolution thermodynamic-based analysis that does not consider specific mutational steps or epistasis effects will be briefly discussed. Our study explores the complex processes behind the evolution of proteins upon mutations, clearing up some previously unresolved issues, and providing direction for further research.

First Histopathological and Molecular Characterization of Giant Thorny-headed Worm, Macracanthorhynchus hirudinaceus (Pallas, 1781) (Acanthocephala: Oligacanthorhynchidae) in Wild Boars, Sus scrofa Linnaeus, 1758 from Eastern Türkiye.

Macracanthorhynchus hirudinaceus (Pallas, 1781) is a zoonotic acanthocephalan that parasitizes the small intestine of wild boars. It is a pathogenic that causes economic losses, and poses a public health threat due to increased emergence. The aims of this study is describes histopathologically the damage caused by M. hirudinaceus in the small intestine of wild boar Sus scrofa Linnaeus, 1758, and molecularly characterize this parasite (sequences, haplotypes, phylogeny) for the first time in Elazig city, Türkiye. A high prevalence of infection was obtained. Upon separating the worms, it was discovered that there were ulcers resembling craters in the center, of the small intestine mucosa, surrounded by edema. The intestine wall where the parasite attached was damaged, with the villi epithelium and lamina propria in the mucosa being destroyed. The genomic DNA was isolated from all M. hirudinaceus samples, and PCR amplified the 489bp gene fragments were sequenced and confirmed that all 21 sequences were M. hirudinaceus. The haplotype analysis of the sequences revealed the presence of a central star-shaped haplotype, in addition to four other haplotypes. After conducting sequence analysis, the genetic differences between the M. hirudinaceus sequences obtained in this study and those reported from Europe and Japan suggest that this parasite is endemic to Türkiye's local wild boar population. Also, four haplotypes were identified, distinguishing it from other haplotypes by 1-5 mutation steps. It is essential to consider the worm's sequences and the formation of haplotypes, since these intrinsic characteristics may impact in the epidemiology and pathology of the worm in the future.

Heterogeneous microbiomes associate with shell-boring Polydora hoplura (Polychaeta, Spionidae) affecting the flat oyster Ostrea edulis

Shell-boring polychaetes belonging to the genus Polydora (Spionidae) infect commercially harvested bivalve molluscs worldwide, reducing their economic value. Due to their limited intraspecific variability, taxonomic identification becomes challenging without molecular approaches. In this study, we identified Polydora hoplura worms infecting flat oysters (Ostrea edulis) in the Gulf of Naples (Italy), providing the first DNA barcode data on the cytochrome c oxidase subunit 1 mitochondrial gene (COI) from its type locality. Three haplotypes with up to ten mutational step differences were detected, suggesting recent introductions from distant populations, including South Africa. The characterization of Polydora associated prokaryotic communities revealed a diverse and fluctuating microbiome linked to these worms, deviating from the usual species-specific pattern observed in other invertebrates. Core and some non-core bacteria could be playing symbiotic roles in nutrient provision, removal of waste products, and antioxidant and detoxifying processes to allow endolithic lifestyle within the borrowed valve chambers. The majority of these microbes though, seem to be acquired horizontally, from an interconnection between the environment and the flat oyster cavity. Indeed, there was a notable detection of opportunistic and potentially pathogenic taxa clusters, including Mycobacterium, Vibrio, Aliiroseovarius and Halarcobacter spp., which in concomitance with the prevalent polydorid infections may prompt implications for the health of the flat oyster host, and for its commercial market, including human consumption. Our study is novel in characterizing bacterial communities associated with shell-boring polychaetes, and sets the bases to propose these parasitic worms as vectors of alterable microbial exchange between oyster hosts and the environment.

Genetic diversity, variation and recombination among the human papillomaviruses (HPVs) genomes isolated in China: a comparative genomic and phylogenetic analysis

ABSTRACT Human papillomaviruses (HPVs) are widespread, sexually transmitted group of viruses that infect most individuals at some stage, causing genital warts and cancers. They are members of the Papillomaviridae family, which contains about 400 HPV types. China is among the high HPV burden countries with reported infections of multiple HPV types, accounting for 17.3% of global deaths and 18.2% of global new cases. Thus, understanding the genetic variation and geographic diversity characteristics of HPVs isolated in China is critical for global HPV prevention strategies. Thus, we analyzed the available HPV genome sequences isolated in China that grouped into two categories (alpha- and gamma-papillomaviruses) based on full-length genomes. The most common were HPV-16, −6, −58, and −52 respectively. In addition, four of the novel strains isolated in China, e.g. TG550, JDFY01, CH2, and L55 clustered with the HPV-mSK 159, 244, 201, and 200 respectively. Our phylogeographic network analysis indicated that the L55, TG550, and CH2 are genetically identical to the mSK 200, 046, and 201 respectively, while JDFY01 appeared separately, connected to the mSK-040 following five mutational steps. Also, we found ten recombination events among HPV-6/11 types within their E1, E2, E7, L1/L2 proteins, and Long Control Region ORFs. We achieved the consensus amino acid sequences of HPV proteins and found a conserved stretch of amino acids within E5A of all HPVs circulating in China. These findings offer valued insights into the genetic relationships, distribution, and evolution of the HPVs in China that may assist in adapting effective HPV preventive measures.

Genetic diversity and population structure of the semiterrestrial crab Armases benedicti (Brachyura, Sesarmidae) along the North Brazilian coast

Abstract For coastal marine species, gene flow patterns are intricately shaped by environmental factors such as oceanographic currents and river plumes. Despite these natural barriers, pelagic larval duration and salinity tolerance potentially facilitate the movement of individuals, resulting in panmixia. This study utilized Cox1 mtDNA data to conduct population genetics and structure analysis of the semiterrestrial crab Armases benedicti along the North Brazilian coast. The haplotype network displayed a star-like configuration, indicating recent mutation events and confirming minimal genetic structure. While DAPC analysis identified three distinct genetic clusters, limited genetic differentiation and negligible structuring were evident between Amapá, the northmost coastal Brazilian state, and Pará (approx. 400 km from the Amapá sampling site). Maranhão (approx. 600 km from Pará) exhibited higher Fst values in all pairwise comparisons but remained just one mutational step away from other sites. Despite coastal barriers affecting genetic connectivity, our findings suggest that A. benedicti populations demonstrate low genetic differentiation, hinting at the minimal impact of the Amazon plume as a barrier to gene flow, possibly due to the species’ adaptability to brackish environments. However, employing more informative genetic markers and conducting complementary ecological studies on larval salinity tolerance remain crucial for a deeper understanding of Armases population dynamics and adaptive strategies.

Improving the performance of mutation-based evolving artificial neural networks with self-adaptive mutations.

Neuroevolution is a promising approach for designing artificial neural networks using an evolutionary algorithm. Unlike recent trending methods that rely on gradient-based algorithms, neuroevolution can simultaneously evolve the topology and weights of neural networks. In neuroevolution with topological evolution, handling crossover is challenging because of the competing conventions problem. Mutation-based evolving artificial neural network is an alternative topology and weights neuroevolution approach that omits crossover and uses only mutations for genetic variation. This study enhances the performance of mutation-based evolving artificial neural network in two ways. First, the mutation step size controlling the magnitude of the parameter perturbation is automatically adjusted by a self-adaptive mutation mechanism, enabling a balance between exploration and exploitation during the evolution process. Second, the structural mutation probabilities are automatically adjusted depending on the network size, preventing excessive expansion of the topology. The proposed methods are compared with conventional neuroevolution algorithms using locomotion tasks provided in the OpenAI Gym benchmarks. The results demonstrate that the proposed methods with the self-adaptive mutation mechanism can achieve better performance. In addition, the adjustment of structural mutation probabilities can mitigate topological bloat while maintaining performance.

Population genetic structure and demographic history of short mackerel, Rastrelliger brachysoma, in the Gulf of Thailand

The short mackerel Rastrelliger brachysoma (Bleeker 1851) is an important fish in the Gulf of Thailand (GoT). The biology of this species has been intensively studied, but its genetic diversity is little known. The genetic diversity, population genetic structure, and demographic history of this species in the GoT were studied using complete mt control region sequences. The CR sequences of 455 mackerel samples collected from 23 localities at four fishing grounds revealed 333 haplotypes with haplotype diversity (h) per population, ranging between 0.8933 and 1.000, with an average of 0.9781. In turn, the nucleotide diversity (µ) ranged between 0.0119 ± 0.0060 and 0.0333 ± 0.0174, with an average of 0.0220 ± 0.00059.A haplotype network analysis showed that all sequences segregated into two subgroups named, clade I and clade II. Two clades were separated by 26 mutational steps. Each clade formed star-like clusters with many haplotypes derived from a common haplotype. Moreover, an analysis of molecular variance (AMOVA) revealed no significant differences among the studied localities, suggesting the presence of a single population in the GoT. Pairwise differences between samples from different fishing regions also indicated no population structure. Both Tajima’s D and Fu’s F S statistics were highly significant for the two clades but nonsignificant for the entire population according to a mismatch distribution analysis. These results confirmed that both clades experienced demographic expansion. The estimated expansion times for clade I and clade II were 1,542.307 years (1.5423 ka BP) and 7,602.541 (7.6025 ka BP) years, respectively.

Discrete SUPPOSe: A new, faster and accurate superresolution method for applications to fluorescence microscopy images

In this article we define Discrete SUPPOSe, a new and faster version of the single shot super resolution SUPPOSe (Superposition of virtual point sources) method. The SUPPOSe method for super-resolution of fluorescent microscope images relies in assuming that the sample source distribution can be modeled as a superposition of virtual point sources of equal intensities distributed in a continuous space, converting the ill posed deconvolution problem into a well posed one. In this work we present a faster new method that consists on discretizing the continuum problem, using a normalized covariance instead of a χ2 for the fitting function and hence transforming the convolution (the main computational time) into a multiplication, and modifying the mutation step of the genetic algorithm. We compare precision, accuracy, resolution and computation time. It is also shown that despite the spatial discretization in Discrete SUPPOSe similar figures for precision, accuracy and resolution are obtained. The algorithm was implemented in Matlab running on a CPU obtaining with a speed improvement factor of more than 15 for one image of 48 × 48 pixels. Processing images in parallel in a 16 cores CPU a 1Mpixel image is computed 240 times faster than the standard SUPPOSe in a 2600 core GPU. Experimental images were used to validate the method.

Genetic diversity and haplotypes of Cysticercus tenuicollis isolates from slaughtered sheep and goats in Elazig and Bingol provinces of Turkey.

The cestode Taenia hydatigena uses canids, primarily dogs, as definitive hosts, whereas the metacestode larval stage cysticercus infects a range of intermediate hosts, including domestic animals such as goats, sheep and pigs. In this study, we aimed to determine the genetic differences and haplotypes of Cysticercus tenuicollis isolates obtained from sheep and goats slaughtered in the Bingol and Elazig provinces of Turkey. C. tenuicollis isolates were collected from 44 sheep and 26 goats slaughtered in slaughterhouses in Bingol and Elazig. After the isolation of total genomic DNA from C. tenuicollis isolates, the genetic characterization of the partial mitochondrial cytochrome oxidase 1 (CO1) gene region (866bp) was amplified using specific primers by polymerase chain reaction (PCR), the products were then sequenced, and haplotype and genetic diversity analyses were carried out. As a result of the haplotype network analyses, 34 different haplotypes were detected around the main haplotype (Hap02) arranged in a star-like configuration and separated from other haplotypes by 1-28 mutation steps and covering 22.85% (16/70) of all isolates. Twenty-seven polymorphic fields were detected, 77.77% (21/27) of which were parsimony-informative, and secondary haplotype and nucleotide diversity were observed. Additionally, we detected high intraspecies haplotype diversity (hd: 0.933) and high nucleotide diversity (π: 0.00383), with 27 different nucleotide variation positions among the haplotypes of the isolates. Tajima's D value was negative, indicating population expansion and/or selection purification. The significantly negative Fu's Fs values indicated recent population expansion or the presence of expected rare haplotypes. The results of this study confirmed that C. tenuicollis isolates clustered in one lineage and were closely related to the relevant reference sequences in different countries, confirming the circulation of C. tenuicollis in different geographical regions.

Genetic diversity and phylogeographic dynamics of avihepadnavirus: a comprehensive full-length genomic view.

Avihepadnavirus is a genus of the Hepadnaviridae family. It primarily infects birds, including species of duck, geese, cranes, storks, and herons etc. To understand the genetic relatedness and evolutionary diversity among avihepadnavirus strains, a comprehensive analysis of the available 136 full-length viral genomes (n = 136) was conducted. The genomes were classified into two major genotypes, i.e., GI and GII. GI viruses were further classified into 8 sub-genotypes including DHBV-I (duck hepatitis B virus-I), DHBV-II (Snow goose Hepatitis B, SGHBV), DHBV-III, RGHBV (rossgoose hepatitis B virus), CHBV (crane hepatitis B virus), THBV (Tinamou hepatitis B virus), STHBV (stork hepatitis B virus), and HHBV (Heron hepatitis B virus). DHBV-I contains two sub-clades DHBV-Ia and DHBV-Ib. Parrot hepatitis B virus (PHBV) stains fall into GII which appeared as a separate phylogenetic branch/clade. All the subtypes of viruses in GI and GII seem to be genetically connected with viruses of DHBV-I by multiple mutational steps in phylogeographic analysis. Furthermore, 16 potential recombination events among different sub-genotypes in GI and one in GII were identified, but none of which is inter-genotypic between GI and GII. Overall, the results provide a whole picture of the genetic relatedness of avihepadnavirus strains, which may assist in the surveillance of virus spreading.

Fault Structure Reconstruction From Magnetic Anomalies Using an Improved Backtracking Search Optimization Algorithm

AbstractFault structure reconstruction is an important aspect of magnetic prospecting as it contributes to understanding tectonic history, hazard assessment, and infrastructure planning. Metaheuristics have proven useful in estimating fault structure parameters from geophysical anomalies. Recently, a modified version of the Backtracking Search Optimization Algorithm (BSA), named mBSA, has been proposed that combines mutation steps of BSA and Differential Evolution (DE) algorithms to achieve a better balance between exploration and exploitation. Here, we present imBSA as an efficient approach that builds on the improvements of mBSA. It uses an adaptive amplitude control factor in the mutation step derived from a normally distributed random number obtained via an exponential function. The performances of these approaches were tested on some widely used benchmark functions such as Rosenbrock, Rastrigin, Griewank, and Himmelblau. Synthetic magnetic fault anomalies were evaluated with and without noise, as well as three real anomalies from the Dehri (India), Perth Basin, and Lachlan Fold Belt (Australia). Prior to the optimizations, the solvability of the model parameters was examined using some error topography images. The obtained solutions in the synthetic cases were evaluated using principal component analysis. In addition, a novel visualization option for high‐dimensional optimization problems was introduced. The experiments showed that imBSA has a faster convergence rate and better optimization statistics compared to BSA and mBSA. Therefore, it is believed to be an efficient and good alternative tool to widely used metaheuristics such as Particle Swarm Optimization and DE in explaining geophysical anomalies and optimization problems in other geoscientific disciplines.

An Approach for Engineering Peptides for Competitive Inhibition of the SARS-COV-2 Spike Protein.

SARS-CoV-2 is the virus responsible for a respiratory disease called COVID-19 that devastated global public health. Since 2020, there has been an intense effort by the scientific community to develop safe and effective prophylactic and therapeutic agents against this disease. In this context, peptides have emerged as an alternative for inhibiting the causative agent. However, designing peptides that bind efficiently is still an open challenge. Here, we show an algorithm for peptide engineering. Our strategy consists of starting with a peptide whose structure is similar to the interaction region of the human ACE2 protein with the SPIKE protein, which is important for SARS-COV-2 infection. Our methodology is based on a genetic algorithm performing systematic steps of random mutation, protein-peptide docking (using the PyRosetta library) and selecting the best-optimized peptides based on the contacts made at the peptide-protein interface. We performed three case studies to evaluate the tool parameters and compared our results with proposals presented in the literature. Additionally, we performed molecular dynamics (MD) simulations (three systems, 200 ns each) to probe whether our suggested peptides could interact with the spike protein. Our results suggest that our methodology could be a good strategy for designing peptides.

Evaluating the Genetic Diversity of the Plasmodium vivax siap2 Locus: A Promising Candidate for an Effective Malaria Vaccine?

Malaria is the deadliest parasitic disease in the world. Traditional control measures have become less effective; hence, there is a need to explore alternative strategies, such as antimalarial vaccines. However, designing an anti-Plasmodium vivax vaccine is considered a challenge due to the complex parasite biology and the antigens´ high genetic diversity. Recently, the sporozoite invasion-associated protein 2 (SIAP2) has been suggested as a potential antigen to be considered in vaccine design due to its significance during hepatocyte invasion. However, its use may be limited by the incomplete understanding of gene/protein diversity. Here, the genetic diversity of pvsiap2 using P. vivax DNA samples from Colombia was assessed. Through PCR amplification and sequencing, we compared the Colombian sequences with available worldwide sequences, revealing that pvsiap2 displays low genetic diversity. Molecular evolutionary analyses showed that pvsiap2 appears to be influenced by directional selection. Moreover, the haplotypes found differ by a few mutational steps and several of them were shared between different geographical areas. On the other hand, several conserved regions within PvSIAP2 were predicted as potential B-cell or T-cell epitopes. Considering these characteristics and its role in hepatocyte invasion, the PvSIAP2 protein emerges as a promising antigen to be considered in a multi-antigen-multi-stage (multivalent) fully effective vaccine against P. vivax malaria.

The First Attempt to Assess the Taxonomic Diversity of the Nepticulidae of Armenia Resulted in the Discovery of New Species and Cryptic Taxa in the Caucasus

A taxonomic review of the Nepticulidae of Armenia is provided for the first time. Currently, the previously little-known fauna of the pygmy moths of Armenia consists of eight genera and 31 species, including seven new species described and illustrated in the current paper as follows: Stigmella armi Stonis, Dobrynina & Remeikis, sp. nov.; Stigmella garnica Stonis, Dobrynina & Remeikis, sp. nov.; Stigmella inopinoides Dobrynina, sp. nov.; Stigmella magicis Stonis & Dobrynina, sp. nov.; Stigmella ararati Stonis, Dobrynina & Remeikis, sp. nov.; Trifurcula vardenisi Stonis, Dobrynina & Remeikis, sp. nov.; and Etainia caucasi Remeikis, sp. nov. The most common Nepticulidae species in Armenia, Stigmella muricatella (Klimesch), still remains a taxonomic puzzle. However, the molecular sequences of the Armenian specimens and a specimen of S. muricatella from Greece were found to be similar, though clearly distinct from the widespread S. rolandi van Nieukerken due to numerous hypothetical mutational steps. Mitotype analysis revealed that the Ectoedemia specimens collected in Armenia do not belong to the expected widespread E. spinosella (Joannis) but are more similar to the less-known E. mahalebella (Klimesch). Moreover, some specimens from Armenia identified by us as Simplimorpha promissa (Staudinger) and Ectoedemia (Zimmermannia) longicaudella Klimesch may actually represent possible cryptic taxa, allopatric subspecies or species. However, from a practical point of view, the description of such difficult-to-diagnose taxa is inappropriate. Thus, we have refrained from describing such new taxa based solely on observed molecular differences.

Sequence and Haplotype Analyses of Ligula intestinalis in Acanthobrama marmid (Cyprinidae) in Turkey

PurposeLigulosis caused by Ligula intestinalis adversely affects the fisheries carried out in the lakes and ponds, causing economic losses in the fish industry. In this study, it was aimed to reveal the molecular characterization of L. intestinalis isolates obtained from woodfish (Acanthobrama marmid) in Keban Dam Lake in Elazig province of Turkey by using mt-CO1 gene sequences and to determine the genetic differences and haplotypes between the isolates.MethodsIn the examination made in terms of L. intestinalis, the intestine of the fish was opened with the help of fine-tipped scissors, the contents were allowed to come out, and the parasites were taken into a petri dish containing phosphate buffered saline (PBS). Then, L. intestinalis plerocercoids were taken into 15 ml falcon tubes containing 70% ethanol and stored at − 20 °C until further analysis. From each isolate, total gDNA was extracted from the plerocercoids. A partial (480 bp) mt-CO1 gene was amplified by PCR and sequenced unidirectionally. The final size of the trimmed sequences was 392 bp for 43 sequences. Sequence and haplotype analyses were performed, followed by phylogenetic analyses.ResultsAll isolates were confirmed as L. intestinalis by BLAST analysis. In addition, 87 nucleotide mutation positions were determined among 43 CO1 gene sequences. As a result of the haplotype network performed for the mt-CO1 gene region of L. intestinalis isolates; arranged in a star-like configuration with the main haplotype (Hap05), separated from other haplotypes by 1–6 mutation steps, and 29 haplotypes were identified, covering 13.9% (6/43) of the total isolates. Also, 75 variable (polymorphic) sites were determined, 52 of which were parsimony informative sites.ConclusionsThe molecular characterization of L. intestinalis in woodfish (A. marmid) was identified for the first time in Turkey.

Addressing Conservation Needs: Genetic Diversity and Population Ecology of the Endemic Tree Spondias tuberosa Arruda.

Spondias tuberosa Arruda (Anacardiaceae), popularly known as umbuzeiro or imbuzeiro, is a fruit tree native to the semiarid region of Brazil. The extractive harvesting of its fruits contributes significantly to the economy, generating an annual revenue of approximately $4,2 million. The present study aimed to assess the spatial pattern, allometric variations, fruit measurements, and genetic diversity of trees within a remaining forest of the Caatinga biome, with a focus on intrapopulation analysis. We used intersimple repeated sequence markers and the second-order function density of neighbours to determine the genetic and spatial structure. The density of neighbours was highest within a 10-meter radius. Biometric analyses revealed average fruit lengths of 31.12 mm (±0.22), diameters of 28.68 mm (±0.25), and fresh masses of 15.56 g (±0.33). Diaspores exhibited an average length, diameter, and thickness of 19.27 mm, 13.95 mm, and 11.14 mm, respectively, with a fresh mass of 2.28 g. Notably, the fresh mass demonstrated the highest coefficient of variation. Ten molecular markers were selected, generating 103 highly polymorphic loci (99.03%) with an average informative content of 0.45. Nei's diversity index (0.37) and Shannon's index (0.55) indicated moderate genetic diversity. Furthermore, Bayesian analysis revealed a population structure with two distinct genetic groups. The Infinite Allele and Mutation Step Models suggested a significant historical decline in population size, indicative of a genetic bottleneck. As a result, proactive in situ conservation strategies, including establishing protected natural areas, become essential, considering the socioeconomic significance of the species. Additionally, it is recommended to establish germplasm banks for ex situ conservation and the development of managed cultivation initiatives to reduce the pressure on native populations of S. tuberosa caused by extraction.

Molecular and morphometric data provide evidence of intraspecific variation in shape and pigmentation pattern in Otocinclus cocama (Siluriformes: Loricariidae) across major river drainages.

Otocinclus cocama, a uniquely colored species of the loricariid catfish genus Otocinclus described solely from the type locality in the lower Ucayali River in northern Peru, is reported occurring in the Tigre River, a tributary to the Marañón River that drains a different section of the Andean Mountain range in the western Amazon. Both populations differ in the number of dark bars spanning the flanks of the body, and we investigated whether these morphotypes constitute distinct species. The body shapes of populations from the Tigre and Ucayali rivers were compared using geometric morphometrics. Although principal component analysis detected a broad overlap between populations, multivariate analysis of variance and linear driscriminat analysis revealed a subtle differentiation between the populations of the two hydrographic basins. Average body shape of the Ucayali River population tend to be slightly higher than that of the Tigre River, with the caudal peduncle stretched vertically in the Ucayali population. Multivariate regression of shape and centroid size revealed an allometric effect of 10.7% (p < 0.001), suggesting that the variation between Tigre and Ucayali populations was purely shape variation. Molecular data of coI, cytb, nd2, and 16S mitochondrial genes indicated a nucleotide diversity range from 0.001 to 0.003, and haplotypic diversity range from 0.600 ± 0.11 to 0.79 ± 0.07. The median-joining haplotype network for the concatenated matrix exhibited two divergent haplogroups related to the geographic area and separated by <10 mutational steps. The molecular species delimitation methods based on distance (automatic barcode gap discovery and assemble species by automatic partitioning) recovered two molecular lineages evolving independently, being one of the lineages formed by individuals from both populations. Tree-based methods (generalized mixed Yule coalescent and Bayesian implementation of the Poisson tree process) recovered similar topologies and supported single lineage recognition. Methods of molecular delimitation of species disclosed the high similarity between the two populations of Otocinclus cocama, further supported by the presence of old haplotypes common to both groups which could indicate that the populations still maintain gene flow. Although the morphological data reveal a subtle variation between both river basins, the molecular data suggest a weak population structuration based on hydrographic areas, but not different species lineages, therefore Otocinclus cocama is composed of a single lineage with two distinct morphotypes.

Range expansion can promote the evolution of plastic generalism in coarse-grained landscapes.

Phenotypic plasticity is one way for organisms to deal with variable environments through generalism. However, plasticity is not found universally and its evolution may be constrained by costs and other limitations such as complexity: the need for multiple mutational steps before the adaptation is realized. Theory predicts that greater experienced heterogeneity, such as organisms may encounter when spatial heterogeneity is fine-grained relative to dispersal, should favor the evolution of a broader niche. Here we tested this prediction via simulation. We found that, contrary to classical predictions, coarse-grained landscapes can be the most favorable for the evolution of plasticity, but only when populations encounter those landscapes through range expansion. During these range expansions, coarse-grained landscapes select for each step in the complex mutational pathway to plastic generalism by blocking the dispersal of specialists. These circumstances provide ecological opportunities for innovative mutations that change the niche. Our results indicate a new mechanism by which range expansion and spatially structured landscapes interact to shape evolution and reveal that the environments in which a complex adaptation has the highest fitness may not be the most favorable for its evolution.