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Ancient DNA (aDNA) is increasingly being used to investigate questions such as the phylogenetic relationships and divergence times of extant and extinct species. If aDNA samples are sufficiently old, expected branch lengths (in units of nucleotide substitutions) are reduced relative to contemporary samples. This can be accounted for by incorporating sample ages into phylogenetic analyses. Existing methods that use tip (sample) dates infer gene trees rather than species trees, which can lead to incorrect or biased inferences of the species tree. Methods using a multispecies coalescent (MSC) model overcome these issues. We developed an MSC model with tip dates and implemented it in the program BPP. The method performed well for a range of biologically realistic scenarios, estimating calibrated divergence times and mutation rates precisely. Simulations suggest that estimation precision can be best improved by prioritizing sampling of many loci and more ancient samples. Incorrectly treating ancient samples as contemporary in analyzing simulated data, mimicking a common practice of empirical analyses, led to large systematic biases in model parameters, including divergence times. Two genomic datasets of mammoths and elephants were analyzed, demonstrating the method's empirical utility.

The multispecies coalescent (MSC) model accommodates genealogical fluctuations across the genome and provides a natural framework for comparative analysis of genomic sequence data from closely related species to infer the history of species divergence and gene flow. Given a set of populations, hypotheses of species delimitation (and species phylogeny) may be formulated as instances of MSC models (e.g. MSC for 1 species versus MSC for 2 species) and compared using Bayesian model selection. This approach, implemented in the program bpp , has been found to be prone to over-splitting. Alternatively, heuristic criteria based on population parameters (such as population split times, population sizes, and migration rates) estimated from genomic data may be used to delimit species. Here, we develop hierarchical merge and split algorithms for heuristic species delimitation based on the genealogical divergence index (⁠ g d i ⁠) and implement them in a Python pipeline called hhsd. We characterize the behavior of the g d i under a few simple scenarios of gene flow. We apply the new approaches to a dataset simulated under a model of isolation by distance as well as 3 empirical datasets. Our tests suggest that the new approaches produced sensible results and were less prone to oversplitting. We discuss possible strategies for accommodating paraphyletic species in the hierarchical algorithm, as well as the challenges of species delimitation based on heuristic criteria. [ABSTRACT FROM AUTHOR]

Promoting agency – people's ability to form intentions and to act on them freely – must become a primary objective for Behavioural Public Policy (BPP). Contemporary BPPs do not directly pursue this objective, which is problematic for many reasons. From an ethical perspective, goals like personal autonomy and individual freedom cannot be realised without nurturing citizens' agency. From an efficacy standpoint, BPPs that override agency – for example, by activating automatic psychological processes – leave citizens 'in the dark', incapable of internalising and owning the process of behaviour change. This may contribute to non-persistent treatment effects, compensatory negative spillovers or psychological reactance and backfiring effects. In this paper, we argue agency-enhancing BPPs can alleviate these ethical and efficacy limitations to longer-lasting and meaningful behaviour change. We set out philosophical arguments to help us understand and conceptualise agency. Then, we review three alternative agency-enhancing behavioural frameworks: (1) boosts to enhance people's competences to make better decisions; (2) debiasing to encourage people to reduce the tendency for automatic, impulsive responses; and (3) nudge+ to enable citizens to think alongside nudges and evaluate them transparently. Using a multi-dimensional framework, we highlight differences in their workings, which offer comparative insights and complementarities in their use. We discuss limitations of agency-enhancing BPPs and map out future research directions. [ABSTRACT FROM AUTHOR]

SUMMARY: Ghost introgression, or the transfer of genetic material from extinct or unsampled lineages to sampled species, has attracted much attention. However, conclusive evidence for ghost introgression, especially in plant species, remains scarce. Here, we newly assembled chromosome‐level genomes for both Carya sinensis and Carya cathayensis, and additionally re‐sequenced the whole genomes of 43 C. sinensis individuals as well as 11 individuals representing 11 diploid hickory species. These genomic datasets were used to investigate the reticulation and bifurcation patterns within the genus Carya (Juglandaceae), with a particular focus on the beaked hickory C. sinensis. By combining the D‐statistic and BPP methods, we obtained compelling evidence that supports the occurrence of ghost introgression in C. sinensis from an extinct ancestral hickory lineage. This conclusion was reinforced through the phylogenetic network analysis and a genome scan method VolcanoFinder, the latter of which can detect signatures of adaptive introgression from unknown donors. Our results not only dispel certain misconceptions about the phylogenetic history of C. sinensis but also further refine our understanding of Carya's biogeography via divergence estimates. Moreover, the successful integration of the D‐statistic and BPP methods demonstrates their efficacy in facilitating a more precise identification of introgression types. Significance Statement: Hybridization and introgression are widely recognized as significant factors in plant evolution, but the possibility of carrying ancient traits from ancestors that are now extinct (i.e., ghost introgression) has been mostly overlooked in plants. In this study, we employed whole‐genome sequencing datasets using a new combined method to spot this for the first time in hickory trees and anticipate more ghost introgression events to be discovered following this methodology. [ABSTRACT FROM AUTHOR]

A recent study on the freshwater planarian fauna of Corsica and Sardinia established that the formerly presumed single species Dugesia benazzii subsumed a complex of species. In that study, a thorough integrative taxonomic approach, combining molecular, morphological, and karyological data, uncovered the presence of two new endemic species. For the present study, additional samplings were conducted on Corsica, covering several new localities. The data obtained were added to our previous datasets, which included information on specimens collected from both islands. By taking a similar integrative approach to the prior study, we here describe another new endemic species from Corsica, Dugesia xeropotamica. Although our results support the separate status of this new species, it also turned out that the evolutionary relationships among species of the Corso-Sardinian clade remain unclear, because the relationships are not well resolved. Additionally, we corroborate the presence of Dugesia mariae on the Tyrrhenian islets of Montecristo and Molara, representing new records for this group of Dugesia species in the region of the Tyrrhenian Sea. In all, our findings indicate that the evolutionary and biogeographical history of Dugesia species in this region of the Western Mediterranean is more intricate than previously thought. [ABSTRACT FROM AUTHOR]

Analyses of genome sequence data have revealed pervasive interspecific gene flow and enriched our understanding of the role of gene flow in speciation and adaptation. Inference of gene flow using genomic data requires powerful statistical methods. Yet current likelihood-based methods involve heavy computation and are feasible for small datasets only. Here, we implement the multispecies-coalescent-with-migration model in the Bayesian program bpp, which can be used to test for gene flow and estimate migration rates, as well as species divergence times and population sizes. We develop Markov chain Monte Carlo algorithms for efficient sampling from the posterior, enabling the analysis of genome-scale datasets with thousands of loci. Implementation of both introgression and migration models in the same program allows us to test whether gene flow occurred continuously over time or in pulses. Analyses of genomic data from Anopheles mosquitoes demonstrate rich information in typical genomic datasets about the mode and rate of gene flow.

The multispecies coalescent (MSC) model accommodates both species divergences and within-species coalescent and provides a natural framework for phylogenetic analysis of genomic data when the gene trees vary across the genome. The MSC model implemented in the program bpp assumes a molecular clock and the Jukes-Cantor model, and is suitable for analyzing genomic data from closely related species. Here we extend our implementation to more general substitution models and relaxed clocks to allow the rate to vary among species. The MSC-with-relaxed-clock model allows the estimation of species divergence times and ancestral population sizes using genomic sequences sampled from contemporary species when the strict clock assumption is violated, and provides a simulation framework for evaluating species tree estimation methods. We conducted simulations and analyzed two real datasets to evaluate the utility of the new models. We confirm that the clock-JC model is adequate for inference of shallow trees with closely related species, but it is important to account for clock violation for distant species. Our simulation suggests that there is valuable phylogenetic information in the gene-tree branch lengths even if the molecular clock assumption is seriously violated, and the relaxed-clock models implemented in bpp are able to extract such information. Our Markov chain Monte Carlo algorithms suffer from mixing problems when used for species tree estimation under the relaxed clock and we discuss possible improvements. We conclude that the new models are currently most effective for estimating population parameters such as species divergence times when the species tree is fixed.

The outcome of species delimitation depends on many factors, including conceptual framework, study design, data availability, methodology employed and subjective decision making. Obtaining sufficient taxon sampling in endangered or rare taxa might be difficult, particularly when non‐lethal tissue collection cannot be utilized. The need to avoid overexploitation of the natural populations may thus limit methodological framework available for downstream data analyses and bias the results. We test species boundaries in rare North American trapdoor spider genus Cyclocosmia Ausserer (1871) inhabiting the Southern Coastal Plain biodiversity hotspot with the use of genomic data and two multispecies coalescent model methods. We evaluate the performance of each methodology within a limited sampling framework. To mitigate the risk of species over splitting, common in taxa with highly structured populations, we subsequently implement a species validation step via genealogical diversification index (gdi), which accounts for both genetic isolation and gene flow. We delimited eight geographically restricted lineages within sampled North American Cyclocosmia, suggesting that major river drainages in the region are likely barriers to dispersal. Our results suggest that utilizing BPP in the species discovery step might be a good option for datasets comprising hundreds of loci, but fewer individuals, which may be a common scenario for rare taxa. However, we also show that such results should be validated via gdi, in order to avoid over splitting. see also the Perspective by Kristen M. Martinet and Luke J. Harmon [ABSTRACT FROM AUTHOR]

Watermarking is exclusively done for ownership authentication and identity integrity. There are various watermarking techniques for hiding crucial patients' data while digital medical image transmission but most lack resistance against many unwanted attacks. The proposed technique focuses on robustness, reversible data hiding with tamper localization, and recovery for medical images. Firstly, ANN is used to create a watermark creation by feature extraction, and the medical image is divided into ROI and RONI. Then, hybrid watermarking uses SLT and RS Vector. SHA-3, AES andLZW are used for reliability and confidentiality. Pre-processing is done to reduce the disordered pixels for minimal visual distortion and contrast enhancement. The tampered data recovery of the ROI from the watermarked image at the receiver's end is located by the difference matrix between the ROI bits after applying ANN and the bits extracted from the background. Experimental results demonstrate that in comparison with < 30 existing articles, the proposed technique achieves high robustness against < 20 attacks along with tamper detection and recovery of ROI, preserving the visual quality of the cover image. [ABSTRACT FROM AUTHOR]

Previous phylogenetic analyses of the grass-specialist leafhopper tribe Chiasmini have resolved relationships among genera but have included few representatives of individual genera. Here the phylogeny of 20 Chinese species belonging to 8 chiasmine genera was investigated by combining DNA sequence data from two mitochondrial genes (COI, 16S) and two nuclear genes (H3, 28S). In both maximum likelihood (ML) and Bayesian inference (BI) analyses, relationships among genera were largely consistent with prior analyses, with most members of the tribe placed into two sister clades: (Exitianus + Nephotettix) and the remaining five sampled genera. To examine morphology-based species definitions in the taxonomically difficult genus Exitianus Ball, 1929, one mitochondrial gene (COI) and one nuclear gene (ITS2) were used to infer the phylogenetic relationships and status of two common and widespread species and compare the performance of different molecular species-delimitation methods. These analyses divide the included populations into two well-supported clades corresponding to current morphological species concepts but some inconsistencies occurred under the jMOTU, ABGD and bPTP methods depending on the which gene and analytical parameter values were selected. Considering the variable results yielded by methods employing single loci, the BPP method, which combines data from multiple loci, may be more reliable in Exitianus.

In recent years, the study of hybridization and introgression has made significant progress, with ghost introgression—the transfer of genetic material from extinct or unsampled lineages to extant species—emerging as a key area for research. Accurately identifying ghost introgression, however, presents a challenge. To address this issue, we focused on simple cases involving 3 species with a known phylogenetic tree. Using mathematical analyses and simulations, we evaluated the performance of popular phylogenetic methods, including HyDe and PhyloNet/MPL, and the full-likelihood method, Bayesian Phylogenetics and Phylogeography (BPP), in detecting ghost introgression. Our findings suggest that heuristic approaches relying on site-pattern counts or gene-tree topologies struggle to differentiate ghost introgression from introgression between sampled non-sister species, frequently leading to incorrect identification of donor and recipient species. The full-likelihood method BPP uses multilocus sequence alignments directly—hence taking into account both gene-tree topologies and branch lengths, by contrast, is capable of detecting ghost introgression in phylogenomic datasets. We analyzed a real-world phylogenomic dataset of 14 species of Jaltomata (Solanaceae) to showcase the potential of full-likelihood methods for accurate inference of introgression. [ABSTRACT FROM AUTHOR]

Gene flow between species, although usually deleterious, is an important evolutionary process that can facilitate adaptation and lead to species diversification. It also makes estimation of species relationships difficult. Here, we use the full-likelihood multispecies coalescent (MSC) approach to estimate species phylogeny and major introgression events in Heliconius butterflies from whole-genome sequence data. We obtain a robust estimate of species branching order among major clades in the genus, including the ‘melpomene-silvaniform’ group, which shows extensive historical and ongoing gene flow. We obtain chromosome-level estimates of key parameters in the species phylogeny, including species divergence times, present-day and ancestral population sizes, as well as the direction, timing, and intensity of gene flow. Our analysis leads to a phylogeny with introgression events that differ from those obtained in previous studies. We find that Heliconius aoede most likely represents the earliest-branching lineage of the genus and that ‘silvaniform’ species are paraphyletic within the melpomene-silvaniform group. Our phylogeny provides new, parsimonious histories for the origins of key traits in Heliconius, including pollen feeding and an inversion involved in wing pattern mimicry. Our results demonstrate the power and feasibility of the full-likelihood MSC approach for estimating species phylogeny and key population parameters despite extensive gene flow. The methods used here should be useful for analysis of other difficult species groups with high rates of introgression.

The Indonesian government has set a roadmap to achieve a carbon neutral energy transition by 2060. In supporting this program, PT XYZ as a power generation company is focusing on building new power plants. Current power plant development only focuses on conventional concepts, namely price affordability and security of supply. However, in achieving a carbon neutral energy transition, it is necessary to add the pillar of acceptability. This acceptability pillar can be applied in the development of new projects by considering ESG factors (Environmental, Social, and Governance) which has an impact on the project's financial model. With the assignment allocation of 130 power generation projects from state own enterprise to PT XYZ assubholding, the author's suggestion is that PT XYZ should conduct a comprehensive study that evaluates the impact of ESG factors onfinancial model. This consideration aims to support the transition programnet zero emission, preventing environmental damage, allocating budgets efficiently, ensuring the long-term stability of the company's BPP, and maximizing company value. Although there are some opinions that consider ESG to be a burden, this research aims to evaluate or analyze that ESG is not a burden but a benefit for the development of new projects. The method used is to consider significant ESG factorsfinancial model projects, as well as assessing financial feasibility using methods such asInternal Rate of Return (IRR) andNet Present Value (NPV). This analysis takes into account the existence of limits on buying and selling prices set by state own enterprise (Persero) to prevent significant increases in BPP subsidies. Feasibility analysis of adding ESG factors to the construction of new generating projects provides the conclusion that ESG factors have savings benefits for PT XYZ. [ABSTRACT FROM AUTHOR]

Genomic data are informative about the history of species divergence and interspecific gene flow, including the direction, timing, and strength of gene flow. However, gene flow in opposite directions generates similar patterns in multilocus sequence data, such as reduced sequence divergence between the hybridizing species. As a result, inference of the direction of gene flow is challenging. Here, we investigate the information about the direction of gene flow present in genomic sequence data using likelihood-based methods under the multispecies-coalescent-with-introgression model. We analyze the case of two species, and use simulation to examine cases with three or four species. We find that it is easier to infer gene flow from a small population to a large one than in the opposite direction, and easier to infer inflow (gene flow from outgroup species to an ingroup species) than outflow (gene flow from an ingroup species to an outgroup species). It is also easier to infer gene flow if there is a longer time of separate evolution between the initial divergence and subsequent introgression. When introgression is assumed to occur in the wrong direction, the time of introgression tends to be correctly estimated and the Bayesian test of gene flow is often significant, while estimates of introgression probability can be even greater than the true probability. We analyze genomic sequences from Heliconius butterflies to demonstrate that typical genomic datasets are informative about the direction of interspecific gene flow, as well as its timing and strength. [ABSTRACT FROM AUTHOR]

Recent analyses suggest that cross-species gene flow or introgression is common in nature, especially during species divergences. Genomic sequence data can be used to infer introgression events and to estimate the timing and intensity of introgression, providing an important means to advance our understanding of the role of gene flow in speciation. Here, we implement the multispecies-coalescent-with-introgression model, an extension of the multispecies-coalescent model to incorporate introgression, in our Bayesian Markov chain Monte Carlo program Bpp. The multispecies-coalescent-with-introgression model accommodates deep coalescence (or incomplete lineage sorting) and introgression and provides a natural framework for inference using genomic sequence data. Computer simulation confirms the good statistical properties of the method, although hundreds or thousands of loci are typically needed to estimate introgression probabilities reliably. Reanalysis of data sets from the purple cone spruce confirms the hypothesis of homoploid hybrid speciation. We estimated the introgression probability using the genomic sequence data from six mosquito species in the Anopheles gambiae species complex, which varies considerably across the genome, likely driven by differential selection against introgressed alleles.

Despite being one of the most world's widely used and mass-produced compounds, bisphenol A (BPA) has a wide range of toxic effects. Bisphenol P (BPP), an alternative to BPA, has been detected in many foods. The effects of BPP dietary exposure on gut microbiota and the intestinal barrier were unclear. We designed three batches of animal experiments: The first studied mice were exposed to BPP (30 µg/kg BW/day) for nine weeks and found that they gained weight and developed dysbiosis of the gut microbiota. The second, using typical human exposure levels (L, 0.3 µg/kg BW/day BPP) and higher concentrations (M, 30 µg/kg BW/day BPP; H, 3000 µg/kg BW/day BPP), caused gut microbiota dysbiosis in mice, activated the Lipopolysaccharide (LPS) /TLR4/NF-κB signaling pathway, triggered an inflammatory response, increased intestinal permeability, and promoted bacterial translocation leading to intestinal barrier disruption. The third treatment used a combination of antibiotics and alleviated intestinal inflammation and injury. This study demonstrated the mechanism of injury and concentration effects of intestinal damage caused by BPP exposure, providing reference data for BPP use and control and yielding new insights for human disease prevention.

The 'sinistral Phalloceros group' consists of three species, P. aspilos , P. leptokeras and P. tupinamba , that belong to Phalloceros , a genus of freshwater fish endemic to South America. They inhabit the Paraíba do Sul Basin and coastal drainages in south-eastern Brazil. This group is diagnosed by large hooks in the medial portion of the gonopodial appendices in males and the sinistral direction of the urogenital papilla in females. We conducted a phylogeographic analysis of mitochondrial (COI and Cytb) and nuclear (RAG1) haplotypes of 36 individuals sampled from 11 localities to test the hypothesis that the biogeographic history of sinistral Phalloceros was mediated by connections of coastal basins caused by lowered sea-levels during the Quaternary. We evaluated the taxonomic status of these nominal taxa by integrating molecular species delimitation methods and morphological data. Our results suggest that the three nominal taxa are synonyms, and P. leptokeras is designated as the valid species name. The geographic expansion of the P. leptokeras lineage began in the coastal region (~2.3 Mya). The phylogeographic relationships among populations partially corroborate the palaeodrainage model, but also suggest that P. leptokeras colonized the inland Paraíba do Sul drainage, overcoming the Serra do Mar mountains. [ABSTRACT FROM AUTHOR]

We investigate the control system's computational task scheduling problem within limited time and with limited CPU cores in the cloud server. We employ a neural network model to estimate the runtime consumption of linear quadratic regulators (LQR) under varying numbers of CPU cores. Building upon this, we model the task scheduling problem as a two-dimensional bin packing problem (2D BPP) and formulate the BPP as a Markov Decision Process (MDP). By studying the characteristics of the MDP, we simplify the action space, design an efficient reward function, and propose a Double DQN-based algorithm with a simplified action space. Experimental results demonstrate that the proposed approach has improved training efficiency and learning performance compared to other packing algorithms, effectively addressing the challenges of task scheduling in the context of the control system. [ABSTRACT FROM AUTHOR]

Recent simulation studies examining the performance of Bayesian species delimitation as implemented in the bpp program have suggested that bpp may detect population splits but not species divergences and that it tends to over-split when data of many loci are analyzed. Here, we confirm these results and provide the mathematical justifications. We point out that the distinction between population and species splits made in the protracted speciation model (PSM) has no influence on the generation of gene trees and sequence data, which explains why no method can use such data to distinguish between population splits and speciation. We suggest that the PSM is unrealistic as its mechanism for assigning species status assumes instantaneous speciation, contradicting prevailing taxonomic practice. We confirm the suggestion, based on simulation, that in the case of speciation with gene flow, Bayesian model selection as implemented in bpp tends to detect population splits when the amount of data (the number of loci) increases. We discuss the use of a recently proposed empirical genealogical divergence index (gdi) for species delimitation and illustrate that parameter estimates produced by a full likelihood analysis as implemented in bpp provide much more reliable inference under the gdi than the approximate method phrapl. We distinguish between Bayesian model selection and parameter estimation and suggest that the model selection approach is useful for identifying sympatric cryptic species, while the parameter estimation approach may be used to implement empirical criteria for determining species status among allopatric populations.

The multispecies coalescent provides a natural framework for accommodating ancestral genetic polymorphism and coalescent processes that can cause different genomic regions to have different genealogical histories. The Bayesian program BPP includes a full-likelihood implementation of the multispecies coalescent, using transmodel Markov chain Monte Carlo to calculate the posterior probabilities of different species trees. BPP is suitable for analyzing multilocus sequence data sets and it accommodates the heterogeneity of gene trees (both the topology and branch lengths) among loci and gene tree uncertainties due to limited phylogenetic information at each locus. Here, we provide a practical guide to the use of BPP in species tree estimation. BPP is a command-line program that runs on linux, macosx, and windows. This protocol shows how to use both BPP 3.4 (http://abacus.gene.ucl.ac.uk/software/) and BPP 4.0 (https://github.com/bpp/).

Cluster flies of the genus Pollenia are known as mass invaders of human dwellings, but are important plant pollinators in the temperate climatic zone. Despite being the most species-rich and widespread genus in Polleniidae, no study to date has tested infrageneric relationships using molecular data. Here we use three molecular markers, COI , Ef-1α and CAD to reconstruct the phylogenetic relationships between 18 West Palaearctic species of Pollenia , representing eight predefined morphological species groups, using both maximum likelihood and Bayesian approaches. We show several instances where morphological and molecular results are congruent, but also instances where they are discordant. We develop a COI barcode reference library for 18 species, containing newly generated data (87 sequences) and sequences retrieved from the Barcode of Life Data System (BOLD). We analyse this dataset using both Automatic Barcode Gap Discovery (ABGD) and Bayesian Phylogenetics & Phylogeography (BPP) methods to validate morphological species hypotheses and delimit species. The results of these species delimitation analyses were, in most cases, identical and aligned with predefined morphological species concepts. Based on the results of our analyses, we synonymize P. moravica (stat. rev.) with P. amentaria and assign 191 unidentified sequences from BOLD to named morphospecies. [ABSTRACT FROM AUTHOR]

Copyright of Jurnal Indonesia Sosial Teknologi is the property of Publikasi Indonesia and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Species delimitation in herbaceous bamboos has been complex and, in some genera, a great part of its diversity has been confirmed only based on genetic information, as is the case of the genus Raddia. It includes nine species, all occurring in Brazil, but only R. portoi predominates in dry forests of the Northeast associated with the Caatinga phytogeographic domain. This species is morphologically close to R. angustifolia, which is known for a single location in the Atlantic Forest in Southern Bahia, and is considered to be threatened by extinction. Besides problems with taxonomic focus, actions for its conservation are complicated because it is not certain if it must be considered an independent species or included in the more widespread R. portoi. In this study, we used coalescent multispecies (MSC) theory approaches combined with genetic structure analyses in an attempt to delimit these two species. Different analyses were congruent and the species delimitation using MSC inferred distinct lineages supporting their recognition as two species. These results solved the taxonomic doubts and also showed the power of these approaches to delimit species as lineages, even in groups with weak morphological divergence and low genetic variability, and also impacting our knowledge for conservation purposes. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Engineering Sciences & Information Technology is the property of Arab Journal of Sciences & Research Publishing (AJSRP) and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Phylogenomic analyses under the multispecies coalescent model assume no recombination within locus and free recombination among loci. Yet, in real data sets intralocus recombination causes different sites of the same locus to have different genealogical histories so that the model is misspecified. The impact of recombination on various coalescent‐based phylogenomic analyses has not been systematically examined. Here, we conduct a computer simulation to examine the impact of recombination on several Bayesian analyses of multilocus sequence data, including species tree estimation, species delimitation (by Bayesian selection of delimitation models) and estimation of evolutionary parameters such as species divergence and introgression times, population sizes for modern and extinct species, and cross‐species introgression probabilities. We found that recombination, at rates comparable to estimates from the human being, has little impact on coalescent‐based species tree estimation, species delimitation and estimation of population parameters. At rates 10 times higher than the human rate, recombination may affect parameter estimation, causing positive biases in introgression times and ancestral population sizes, although species divergence times and cross‐species introgression probabilities are estimated with little bias. Overall, the simulation suggests that phylogenomic inferences under the multispecies coalescent model are robust to realistic amounts of intralocus recombination. [ABSTRACT FROM AUTHOR]

The biogeography and genetic structure of species endemic to the high-elevation sky islands (tepuis) of the Guiana Shield in eastern and southern Venezuela and adjacent areas of Brazil and Guyana are poorly known. We investigated the phylogeography and population structure of the tepui brush finch (Atlapetes personatus) as an exemplar of that biota. Mitochondrial DNA sequences revealed three monophyletic clades that correspond to major morphological subspecies groups occurring in eastern, southern and north-western regions of the Pantepui. Differentiation among the clades accounted for 95% of the total genetic variance. DNA sequences from three nuclear loci also showed marked divergence among those three regions. Estimates of gene flow between regions and sampled populations were all less than one individual per generation. Consequently, these subspecies groups ought to be recognized as species-level taxa. The results suggest there is more large-scale biogeographical structure within the Pantepui region than generally recognized. Additionally, within two of the three regions, genetic variance among tepuis was substantial at both mitochondrial and nuclear loci. Many of the sampled populations appear to be genetically independent units that are almost cryptic morphologically. The sampled tepuis might be islands of habitat for this taxon and for conservation purposes. [ABSTRACT FROM AUTHOR]

Full-likelihood implementations of the multispecies coalescent with introgression (MSci) model treat genealogical fluctuations across the genome as a major source of information to infer the history of species divergence and gene flow using multilocus sequence data. However, MSci models are known to have unidentifiability issues, whereby different models or parameters make the same predictions about the data and cannot be distinguished by the data. Previous studies of unidentifiability have focused on heuristic methods based on gene trees and do not make an efficient use of the information in the data. Here we study the unidentifiability of MSci models under the full-likelihood methods. We characterize the unidentifiability of the bidirectional introgression (BDI) model, which assumes that gene flow occurs in both directions. We derive simple rules for arbitrary BDI models, which create unidentifiability of the label-switching type. In general, an MSci model with k BDI events has 2 k unidentifiable modes or towers in the posterior, with each BDI event between sister species creating within-model parameter unidentifiability and each BDI event between nonsister species creating between-model unidentifiability. We develop novel algorithms for processing Markov chain Monte Carlo samples to remove label-switching problems and implement them in the bpp program. We analyze real and synthetic data to illustrate the utility of the BDI models and the new algorithms. We discuss the unidentifiability of heuristic methods and provide guidelines for the use of MSci models to infer gene flow using genomic data. [ABSTRACT FROM AUTHOR]

Abstract Background Deep mitochondrial divergences were observed in Scandinavian populations of the terrestrial to semi-aquatic annelid Fridericia magna (Clitellata: Enchytraeidae). This raised the need for testing whether the taxon is a single species or a complex of cryptic species. Results A total of 62 specimens from 38 localities were included in the study, 44 of which were used for species delimitation. First, the 44 specimens were divided into clusters using ABGD (Automatic Barcode Gap Discovery) on two datasets, consisting of sequences of the mitochondrial markers COI and 16S. For each dataset, the worms were divided into six not completely congruent clusters. When they were combined, a maximum of seven clusters, or species hypotheses, were obtained, and the seven clusters were used as input in downstream analyses. We tested these hypotheses by constructing haplowebs for two nuclear markers, H3 and ITS, and in both haplowebs the specimens appeared as a single species. Multi-locus species delimitation analyses performed with the Bayesian BPP program also mainly supported a single species. Furthermore, no apparent morphological differences were found between the clusters. Two of the clusters were partially separated from each other and the other clusters, but not strongly enough to consider them as separate species. All 62 specimens were used to visualise the Scandinavian distribution, of the species, and to compare with published COI data from other Fridericia species. Conclusion We show that the morphospecies Fridericia magna is a single species, harbouring several distinct mitochondrial clusters. There is partial genetic separation between some of them, which may be interpreted as incipient speciation. The study shows the importance of rigorous species delimitation using several independent markers when deep mitochondrial divergences might give the false impression of cryptic speciation.

Multispecies coalescent (MSC) is the extension of the single-population coalescent model to multiple species. It integrates the phylogenetic process of species divergences and the population genetic process of coalescent, and provides a powerful framework for a number of inference problems using genomic sequence data from multiple species, including estimation of species divergence times and population sizes, estimation of species trees accommodating discordant gene trees, inference of cross-species gene flow and species delimitation. In this review, we introduce the major features of the MSC model, discuss full-likelihood and heuristic methods of species tree estimation and summarize recent methodological advances in inference of cross-species gene flow. We discuss the statistical and computational challenges in the field and research directions where breakthroughs may be likely in the next few years. [ABSTRACT FROM AUTHOR]

Species delimitation can be difficult when the divergence between focal taxa is in the incipient stage of speciation, because conflicting results are expected among different data sets, and the species limits can differ depending on the species concept applied. We studied speciation history and investigated the impact on taxonomic decision-making when using different types of data in a Taiwanese endemic sister-species pair of stag beetles, Lucanus miwai and Lucanus yulaoensis , from sky island habitats. We showed that the two geographical taxa can be diagnosed by male mandibular shape. We found two mitochondrial co1 lineages with pairwise sequence divergence > 3%; however, L. miwai might not be monophyletic. The result of our multispecies coalescent-based species delimitation using five nuclear loci supported the evolutionary independence of the two sister species, but the calculated values of the genealogical divergence index (gdi) corresponded to the ambiguous zone of species delimitation. We also showed that post-divergence gene flow is unlikely. Our study demonstrates challenges in the delineation of incipient species, but shows the importance of understanding the speciation history and adopting integrative approaches to reconcile seemingly conflicting results before making evolutionarily relevant taxonomic decisions. [ABSTRACT FROM AUTHOR]

The nudibranch genus Doto is taxonomically problematic in particular, and some species are described on the notion of strict monophagy. Here we perform species delimitation on NE Atlantic species, as well as placing them phylogenetically, using two markers: the mitochondrial COI and the nuclear H3. We also study the morphology of the species including radular ultrastructure and review food specificity. Specimens were first divided into potential species using ABDG on both markers, these groups were used as input species for species delimitation analyses using BPP, and analyses were performed with both markers combined and on H3 only. The analyses delimit 11 and eight species, respectively. With the exception of one species for which only COI was available, the differences are found in D. fragilis, which is split into three groups when COI is included and lumped into one with only H3. Doto hystrix is nested within these groups. We also found that specimens from Sweden seemingly close to D. maculata in external morphology have identical sequences as D. coronata. Analysis of food preferences of the species involved in the study contradicts the notion of strict monophagy within Doto. [ABSTRACT FROM AUTHOR]

Species delimitation in herbaceous bamboos has been complex and, in some genera, a great part of its diversity has been confirmed only based on genetic information, as is the case of the genus Raddia. It includes nine species, all occurring in Brazil, but only R. portoi predominates in dry forests of the Northeast associated with the Caatinga phytogeographic domain. This species is morphologically close to R. angustifolia, which is known for a single location in the Atlantic Forest in Southern Bahia, and is considered to be threatened by extinction. Besides problems with taxonomic focus, actions for its conservation are complicated because it is not certain if it must be considered an independent species or included in the more widespread R. portoi. In this study, we used coalescent multispecies (MSC) theory approaches combined with genetic structure analyses in an attempt to delimit these two species. Different analyses were congruent and the species delimitation using MSC inferred distinct lineages supporting their recognition as two species. These results solved the taxonomic doubts and also showed the power of these approaches to delimit species as lineages, even in groups with weak morphological divergence and low genetic variability, and also impacting our knowledge for conservation purposes.

Abstract Background Recent studies have demonstrated that Bayesian species delimitation based on the multispecies coalescent model can produce inaccurate results by misinterpreting population splits as species divergences. An approach based on the genealogical divergence index (gdi) was shown to be a viable alternative, especially for delimiting allopatric populations where gene flow is low. We implemented these analyses to assess species boundaries in Southeast Asian toads, a group that is understudied and characterized by numerous unresolved species complexes. Results Multilocus phylogenetic analyses showed that deep evolutionary relationships including the genera Sigalegalephrynus, Ghatophryne, Parapelophryne, Leptophryne, Pseudobufo, Rentapia, and Phrynoides remain unresolved. Comparison of genetic divergences revealed that intraspecific divergences among allopatric populations of Pelophyrne signata (Borneo vs. Peninsular Malaysia), Ingerophrynus parvus (Peninsular Malaysia vs. Myanmar), and Leptophryne borbonica (Peninsular Malaysia, Java, Borneo, and Sumatra) are consistent with interspecific divergences of other Southeast Asian bufonid taxa. Conversely, interspecific divergences between Pelophryne guentheri/P. api, Ansonia latiffi/A. leptopus, and I. gollum/I. divergens were low (

Nephotettix leafhoppers are widely distributed and some members of this genus are important vectors of rice pathogens. Species delimitation in this group has proven difficult because traditional morphological characters tend to exhibit substantial variation within populations, and the morphology-based species classification of this genus has not previously been tested using molecular data. This study analysed DNA sequence data from three mitochondrial genes (COI , Cytb and 16S) and two nuclear genes (ITS2 , H3) to infer the phylogenetic relationships and status of five previously recognized Nephotettix species and compare the performance of different molecular species-delimitation methods using single loci and multiple loci. The analysis supports the monophyly of Nephotettix and divided the included haplotypes into five well-supported subclades. Data from the three mitochondrial genes were usually consistent with morphology in supporting recognition of five species. However, data from the two nuclear genes usually lumped the haplotypes into a single species, probably due to the relatively small numbers of variable and parsimony-informative nucleotide positions present in these loci. The jMOTU and ABGD analyses of single mitochondrial loci gave the most consistent results with morphology. Considering the variable results yielded by various methods employing single loci, the BPP method, which combines data from multiple loci, may be more reliable in Nephotettix. [ABSTRACT FROM AUTHOR]

This paper develops an efficient color image compression method based on the DCT and a new color base. Digital color images are commonly represented in RGB space. Generally, it is noted that a strong correlation exists between the three planes R, G, and B of a color image. The reduction of this correlation certainly offers an advantage in the compression of RGB images. In this context, there is an infinite number of possible spaces to represent the RGB image. The main contributions of this paper are summarized in two main points. First, we design an optimized color space B1B2B3 using the Bat algorithm (BA) to pass from the RGB space to space more appropriate for each image. This space is produced by maximizing the energy of the image in the plane B1 more than in B2 and B3. Second, we produce optimized thresholds appropriate to each plane of the converted image. The Bat algorithm optimizes the cost function to compute thresholds to partially reduce the number of the less significant DCT coefficients that correspond to the lower quantity of energy. The reported results against those of recent methods prove that the proposed method presents high performances in terms of peak signal to noise ratio (PSNR) on the commonly used test color images as well as the test medical images in literature. [ABSTRACT FROM AUTHOR]

BPP nets, a subclass of finite Place/Transition Petri nets, are equipped with some causal behavioral semantics, which are variations of fully-concurrent bisimilarity [3], inspired by weak [28] or branching bisimulation [12] on labeled transition systems. Then, we introduce novel, efficiently decidable, distributed semantics, inspired by team bisimulation [17] and h-team bisimulation [19], and show how they relate to these variants of fully-concurrent bisimulation. [ABSTRACT FROM AUTHOR]

One must compress data prior to sending it to the internet since it helps minimize time and the cost. The main aim of the essay is to develop and design a systemic and a secure method for encrypting data, so as it can be used in executing a lossless compacting steganography method. The technique can be used to decrease the amount of every transmitted data aiding fast transmission while using slow internet or take a small space ion a disk. The paper proposes a compacting with stenography method which might be used to hide of data with significant security and also a perfect invisibility while using a combination of RSA (Rivest–Shamir–Adleman) cryptography method and also used steganography proficiency which are Huffman coding, Run-length encoding (RLE), or Discrete Wavelet Transform (DWT) with Least Significant Bits (LSB) steganography technique. The first step is grounded on the RSA skill to both decrypts and encrypt confidential messages. The next step is compression, which is Huffman coding based techniques that will be used to compress the sensitive data through lossless technology, RLE, which is a more natural way to compress data or DWT based that compacts cover image through lossy compression in order reducing the cover image's dimensions. LSB will then be used to implant the encrypted pieces of information in the compacted cover image. This system shows high ranking performance and a systematic system as compared to other states [1-5] of the structure that uses simulation outcomes. [ABSTRACT FROM AUTHOR]

Abstract Background Coalescent methods that use multi-locus sequence data are powerful tools for identifying putatively reproductively isolated lineages, though this approach has rarely been used for the study of microbial groups that are likely to harbor many unrecognized species. Among microbial symbionts, integrating genetic species delimitation methods with trait data that could indicate reproductive isolation, such as host specificity data, has rarely been used despite its potential to inform species limits. Here we test the ability of an integrative approach combining genetic and host specificity data to delimit species within the avian malaria parasite genus Leucocytozoon in central Alaska. Results We sequenced seven nuclear loci for 69 Leucocytozoon samples and used multiple species delimitation methods (GMYC and BPP models), tested for differences in host infection patterns among putative species based on 406 individual infections, and characterized parasite morphology. We found that cryptic morphology has masked a highly diverse Leucocytozoon assemblage, with most species delimitation methods recovering support for at least 21 separate species that occur sympatrically and have divergent host infection patterns. Reproductive isolation among putative species appears to have evolved despite low mtDNA divergence, and in one instance two Leucocytozoon cytb haplotypes that differed by a single base pair (~ 0.2% divergence) were supported as separate species. However, there was no consistent association between mtDNA divergence and species limits. Among cytb haplotypes that differed by one to three base pairs we observed idiosyncratic patterns of nuclear and ecological divergence, with cytb haplotype pairs found to be either conspecific, reproductively isolated with no divergence in host specificity, or reproductively isolated with divergent patterns of host specialization. Conclusion Integrating multi-locus genetic species delimitation methods and non-traditional ecological data types such as host specificity provide a novel view of the diversity of avian malaria parasites that has been missed previously using morphology and mtDNA barcodes. Species delimitation methods show that Leucocytozoon is highly species-rich in Alaska, and the genus is likely to harbor extraordinary species-level diversity worldwide. Integrating genetic and ecological data will be an important approach for understanding the diversity and evolutionary history of microbial symbionts moving forward.