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Scleractinian corals are the main modern builders of coral reefs, which are major hot spots of marine biodiversity. Southern Atlantic reef corals are understudied compared to their Caribbean and Indo‐Pacific counterparts and many hypotheses about their population dynamics demand further testing. We employed thousands of single nucleotide polymorphisms (SNPs) recovered via ezRAD to characterize genetic population structuring and species boundaries in the amphi‐Atlantic hard coral genus Favia. Coalescent‐based species delimitation (BFD* – Bayes Factor Delimitation) recovered F. fragum and F. gravida as separate species. Although our results agree with depth‐related genetic structuring in F. fragum, they did not support incipient speciation of the 'tall' and 'short' morphotypes. The preferred scenario also revealed a split between two main lineages of F. gravida, one from Ascension Island and the other from Brazil. The Brazilian lineage is further divided into a species that occurs throughout the Northeastern coast and another that ranges from the Abrolhos Archipelago to the state of Espírito Santo. BFD* scenarios were corroborated by analyses of SNP matrices with varying levels of missing data and by a speciation‐based delimitation approach (DELINEATE). Our results challenge current notions about Atlantic reef corals because they uncovered surprising genetic diversity in Favia and rejected the long‐standing hypothesis that Abrolhos Archipelago may have served as a Pleistocenic refuge during the last glaciations. [ABSTRACT FROM AUTHOR]

In many organizational interactions,the employee and the organization have different understandings of the obligations of each party and how to fulfill their obligations.Divergence of these perceptions can lead to misunderstandings,conflicts and even breaches of contract.The main purpose of this study is to "provide a framework for stabilizing the employee-organization relationship,studied:Snapp".This research is applied-developmental in terms of purpose and mixed method in terms of approach and descriptive-survey in terms of data collection method.The statistical population used in this study were Snapp managers and experts in middle and senior levels and the sample size was 15 Snapp organizational experts.To select these people,targeted sampling and snowball sampling methods were used.In this study,interpretive structural modeling(ISM) and MICMAC analysis were used to identify the criteria and explore the relationships between them,After studying the literature and conducting in-depth semi-structured interviews with the sample size.Findings of the study showed the extraction of six components "employee characteristics,cultural characteristics,structural factors, governance model, policy rationality and environmental context" in a four-level ISM graph. Environmental contexts and policy rationality were identified as the most effective components and employee characteristics as the most impressive component in stabilizing the relationship between the employee and the organization.

Our understanding of speciation processes in marine environments remains very limited and the role of different reproductive barriers are still debated. While physical barriers were considered important drivers causing reproductive isolation, recent studies highlight the importance of climatic and hydrological changes creating unsuitable habitat conditions as factors promoting population isolation. Although speciation in marine fish has been investigated from different perspectives, these studies often have a limited geographical extant. Therefore, data on speciation within widely distributed species are largely lacking. Species complexes offer valuable opportunities to study the initial stages of speciation. Herein we study speciation within the Mugil cephalus species complex (MCSC) which presents a unique opportunity due to its circumglobal distribution. We used a whole-genome shotgun analysis approach to identify SNPs among the 16 species within the MCSC. We inferred the phylogenetic relationships within the species complex followed by a time-calibration analysis. Subsequently, we estimated the ancestral ranges within the species complex to explore their biogeographical history. Herein, we present a fully resolved and well-supported phylogeny of the MCSC. Its origin is dated at around 3.79 Ma after which two main clades emerged: one comprising all West Atlantic and East Pacific species and the other all East Atlantic and Indo-Pacific species. Rapid dispersal following an initial founder colonization from the West to the East Atlantic led to the population of all major realms worldwide in less than 2 Myr. Physical and climatic barriers heavily impacted the ancestral distribution ranges within the MCSC and triggered the onset of speciation., (Copyright © 2025. Published by Elsevier Inc.)

Accurate delimitation of species and their relationships is a fundamental issue in evolutionary biology and taxonomy and provides essential implications for conservation management. Scleractinian corals are difficult to identify because of their ecophenotypic and geographic variation and their morphological plasticity. Furthermore, phylogenies based on traditional loci are often unresolved at the species level because of uninformative loci. Here, we attempted to resolve these issues and proposed a consistent species definition method for corals by applying the genome-wide technique Restriction-site Associated DNA sequencing (RADseq) to investigate phylogenetic relationships and species delimitation within the genus Leptastrea. We collected 77 colonies from nine localities of the Indo-Pacific and subjected them to genomic analyses. Based on de novo clustering, we obtained 44,162 SNPs (3701 loci) from the holobiont dataset and 62,728 SNPs (9573 loci) from the reads that map to coral transcriptome to reconstruct a robust phylogenetic hypothesis of the genus. Moreover, nearly complete mitochondrial genomes and ribosomal DNA arrays were retrieved by reference mapping. We combined concatenation-based phylogenetic analyses with coalescent-based species tree and species delimitation methods. Phylogenies suggest the presence of six distinct species, three corresponding to known taxa, namely Leptastrea bottae, Leptastrea inaequalis, Leptastrea transversa, one characterized by a remarkable skeletal variability encompassing the typical morphologies of Leptastrea purpurea and Leptastrea pruinosa, and two distinct and currently undescribed species. Therefore, based on the combination of genomic, morphological, morphometric, and distributional data, we herein described Leptastrea gibbosa sp. n. from the Pacific Ocean and Leptastrea magaloni sp. n. from the southwestern Indian Ocean and formally considered L. pruinosa as a junior synonym of L. purpurea. Notably, mitogenomes and rDNA yielded a concordant yet less resolved phylogeny reconstruction compared to the ones based on SNPs. This aspect demonstrates the strength and utility of RADseq technology for disentangling species boundaries in closely related species and in a challenging group such as scleractinian corals. [ABSTRACT FROM AUTHOR]

A proactive approach to conservation must be predictive, anticipating how habitats will change and which species are likely to decline or prosper. We use composite species distribution modelling to identify suitable habitats for 18 members of the North American Atlantic Coastal Plain Flora (ACPF) since the Last Glacial Maximum and project these into the future. We then use Scirpus longii (Cyperaceae), a globally imperiled ACPF sedge with many of the characteristics of extinction vulnerability, as a case study. We integrate phylogeographical and population genetic analyses and species distribution modelling to develop a broad view of its current condition and prognosis for conservation. We use genotyping‐by‐sequencing to characterize the genomes of 142 S. longii individuals from 20 populations distributed throughout its range (New Jersey to Nova Scotia). We measure the distribution of genetic diversity in the species and reconstruct its phylogeographical history using the snapp and rase models. Extant populations of S. longii originated from a single refugium south of the Laurentide ice sheet around 25 ka. The genetic diversity of S. longii is exceedingly low, populations exhibit little genetic structure and the species is slightly inbred. Projected climate scenarios indicate that nearly half of extant populations of S. longii will be exposed to unsuitable climate by 2070. Similar changes in suitable habitat will occur for many other northern ACPF species—centres of diversity will shift northward and Nova Scotia may become the last refuges for those species not extinguished. [ABSTRACT FROM AUTHOR]

Aim: The Sarracenia alata pitcher plant and inquiline species comprise an ecological community. These inquilines span the continuum in their ecological association with the host pitcher plant, from species that contain little‐to‐no interaction with the plant to species that are completely dependent on the plant for their entire life cycle. We are interested in testing if degree of ecological dependence is positively correlated with a shared evolutionary history, and in identifying members of this community that display concordant phylogeographic structure. Location: Southeastern United States. Methods: We collected genome‐wide sequence data from a set of arthropods that are ecologically associated with the plant to estimate comparative phylogeographic patterns among the species. We estimated species tree distributions from biallelic unlinked SNP data and used phylogeographic concordance factors (PCFs) to test degree of phylogeographic concordance among community members. In addition, for each species we conducted an analysis of molecular variance and calculated FST values to identify population genetic structure across the landscape, and compared these traditional values to the tree‐based approach. Results: Obligate members of the pitcher plant community display concordant phylogeographic patterns, suggesting their ecological dependence has manifested itself into a shared evolutionary history. In contrast, two spider species do not contain significant population genetic structure or similar phylogeographic histories, highlighting their loose association with the host pitcher plant. Main conclusion: The S. alata pitcher plant system should be considered an evolutionary community, where multiple members sharing strong ecological interactions also display concordant phylogeographic structure. This work demonstrates that PCFs provide an important quantitative measure into assessing community structure and illustrates how simulations can be used to assess significance of shared patterns of phylogeographic structure across the landscape. [ABSTRACT FROM AUTHOR]

The avian genus Calandrella (larks) was recently suggested to be non-monophyletic, and was divided into two genera, of which Calandrella sensu stricto comprises 4–5 species in Eurasia and Africa. We analysed mitochondrial cytochrome b (cyt b ) and nuclear Restriction-site Associated DNA (RAD) sequences from all species, and for cyt b we studied 21 of the 22 recognised subspecies, with the aim to clarify the phylogenetic relationships within the genus and to compare large-scale nuclear sequence patterns with a widely used mitochondrial marker. Cyt b indicated deep splits among the currently recognised species, although it failed to support the interrelationships among most of these. It also revealed unexpected deep divergences within C. brachydactyla , C. blanfordi / C. erlangeri , C. cinerea , and C. acutirostris . It also suggested that both C. brachydactyla and C. blanfordi , as presently circumscribed, are paraphyletic. In contrast, most of the many subspecies of C. brachydactyla and C. cinerea were unsupported by cyt b , although two populations of C. cinerea were found to be genetically distinct. The RAD data corroborated the cyt b tree (for the smaller number of taxa analysed) and recovered strongly supported interspecific relationships. However, coalescence analyses of the RAD data, analysed in SNAPP both with and without an outgroup, received equally strong support for two conflicting topologies. We suggest that the tree rooted with an outgroup – which is not recommended for SNAPP – is more trustworthy, and suggest that the reliability of analyses performed without any outgroup species should be thoroughly evaluated. We also demonstrate that degraded museum samples can be phylogenetically informative in RAD analyses following careful bioinformatic treatment. We note that the genus Calandrella is in need of taxonomic revision. [ABSTRACT FROM AUTHOR]

A common challenge in phylogenetic reconstruction is to find enough suitable genomic markers to reliably trace splitting events with short internodes. Here, we present phylogenetic analyses based on genomewide single-nucleotide polymorphisms ( SNPs) of an enigmatic avian radiation, the subspecies complex of Afrocanarian blue tits ( Cyanistes teneriffae). The two sister species, the Eurasian blue tit ( Cyanistes caeruleus) and the azure tit ( Cyanistes cyanus), constituted the out-group. We generated a large data set of SNPs for analysis of population structure and phylogeny. We also adapted our protocol to utilize degraded DNA from old museum skins from Libya. We found strong population structuring that largely confirmed subspecies monophyly and constructed a coalescent-based phylogeny with full support at all major nodes. The results are consistent with a recent hypothesis that La Palma and Libya are relic populations of an ancient Afrocanarian blue tit, although a small data set for Libya could not resolve its position relative to La Palma. The birds on the eastern islands of Fuerteventura and Lanzarote are similar to those in Morocco. Together they constitute the sister group to the clade containing the other Canary Islands (except La Palma), in which El Hierro is sister to the three central islands. Hence, extant Canary Islands populations seem to originate from multiple independent colonization events. We also found population divergences in a key reproductive trait, viz. sperm length, which may constitute reproductive barriers between certain populations. We recommend a taxonomic revision of this polytypic species, where several subspecies should qualify for species rank. [ABSTRACT FROM AUTHOR]

Young species complexes that are widespread across ecologically disparate regions offer important insights into the process of speciation because of their relevance to how local adaptation and gene flow influence diversification. We used mitochondrial DNA and up to 28 152 genomewide single nucleotide polymorphisms from polytypic barking frogs ( Craugastor augusti complex) to infer phylogenetic relationships and test for the signature of introgressive hybridization among diverging lineages. Our phylogenetic reconstructions suggest (i) a rapid Pliocene- Pleistocene radiation that produced at least nine distinct lineages and (ii) that geographic features of the arid Central Mexican Plateau contributed to two independent northward expansions. Despite clear lineage differentiation (many private alleles and high between-lineage FST scores), D-statistic tests, which differentiate introgression from ancestral polymorphism, allowed us to identify two putative instances of reticulate gene flow. Partitioned D-statistics provided evidence that these events occurred in the same direction between clades but at different points in time. After correcting for geographic distance, we found that lineages involved in hybrid gene flow interactions had higher levels of genetic variation than independently evolving lineages. These findings suggest that the nature of hybrid compatibility can be conserved overlong periods of evolutionary time and that hybridization between diverging lineages may contribute to standing levels of genetic variation. [ABSTRACT FROM AUTHOR]

The ability of 18-crown-6 (18C6) to form noncovalent complexes with cationic groups in the gas phase has been leveraged in numerous, largely orthogonal mass spectrometry-based applications. Although the fundamental interaction between 18C6 and a charged group in the gas phase is quite strong, the strength of attachment of 18C6 to large molecules is more difficult to predict because intramolecular binding of the cation can be competitive. Herein, we demonstrate in experiments with model peptides that 18C6 adducts are not strongly attached to flexible molecules with numerous potential hydrogen bonding sites. 18C6 adduct stability is increased if intramolecular charge complexation is inhibited by sterics or competitive binding. It is demonstrated with molecular mechanics that significant structural changes occur upon loss of 18C6 in model peptides. Examination of the loss of 18C6 adducts from proteins following collisional activation reveals that lower charge states lose the most 18C6. The degree of 18C6 adduct stability may reflect the degree of structural reorganization that occurs following collisional activation, suggesting that lower charge states represent structures that are not similar to gas phase idealized states. In this regard, 18C6 may serve the function of protecting solution phase protein structure. Collisional activation of holomyoglobin with 18C6 adducts attached reveals that heme loss occurs primarily after 18C6 loss, further supporting the notion that 18C6 protects native structure by solvating charged sites. [Figure not available: see fulltext.] [ABSTRACT FROM AUTHOR]

The multispecies coalescent provides an elegant theoretical framework for estimating species trees and species demographics from genetic markers. However, practical applications of the multispecies coalescent model are limited by the need to integrate or sample over all gene trees possible for each genetic marker. Here we describe a polynomial-time algorithm that computes the likelihood of a species tree directly from the markers under a finite-sites model of mutation effectively integrating over all possible gene trees. The method applies to independent (unlinked) biallelic markers such as well-spaced single nucleotide polymorphisms, and we have implemented it in SNAPP, a Markov chain Monte Carlo sampler for inferring species trees, divergence dates, and population sizes. We report results from simulation experiments and from an analysis of 1997 amplified fragment length polymorphism loci in 69 individuals sampled from six species of Ourisia (New Zealand native foxglove). [ABSTRACT FROM PUBLISHER]

While the inference of species trees from molecular sequences has become a common type of analysis in studies of species diversification, few programs so far allow for the use of single-nucleotide polymorphisms (SNPs) for the same purpose. In this book chapter, I discuss the use of the Bayesian program SNAPP, which infers the species tree by mathematically integrating over all possible genealogies at each SNP. In particular, I focus on a molecular clock model developed for SNAPP, allowing the inference of divergence times together with the species tree topology and the population size, directly from SNP datasets in variant call format. With the growing availability of SNP datasets for multiple closely related species, this approach is becoming increasingly relevant for the reconstruction of the temporal framework of recent species diversification., (© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

In this work, the effect of two key structural parameters, number of arms and arm length, of star-shaped "structurally nanoengineered antimicrobial peptide polymers" (SNAPPs) on their antimicrobial activity and biocompatibility, is investigated. A library of star-shaped SNAPPs is prepared, containing varying arm numbers and arm lengths. Antimicrobial assays are then performed to assess the capacity of the SNAPPs to disrupt the membrane, inhibit the growth, and kill pathogenic bacteria. A major finding of the study is that increasing arm number and length of SNAPPs enhanced antimicrobial activity, which can be respectively attributed to the higher local concentrations of polypeptide arms and increased α-helical content. SNAPP architecture is shown to affect the bacteria membrane state and therefore mechanism of killing. Two more potent structures with up to twice the antimicrobial activity of the previously reported SNAPP are discovered in this process. Toxicities of the SNAPPs also increase with arm number and arm length, however therapeutic index calculations identified a 16-arm SNAPP and an easier to prepare 4-arm SNAPP as the best therapeutic agents. The biocompatibility of the SNAPP with the best biological activity is also evaluated in vivo, showing no markers of systemic damage in mice., (© 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)