Wavelet-based multifractal analysis and fractal Signature of SARS-Cov-2 Coronavirus Variants genomes.

In this paper, the SARS-CoV-2 coronavirus variants of concern and of interest genomes are analyzed using the wavelet transform modulus maxima lines (WTMM) method. The goal is to track the monofractal behavior of the virus genomes and to investigate the Long-Range-Correlation (LRC) character through the estimation of the Hurst exponent. The obtained results demonstrate the multifractal and the anti-correlated characters in the variants of concern for the Knucleotidic and GC DNA coding. The fractal signatures of SARS-CoV-2 coronavirus variants are investigated through the indicator matrix maps of the genomes, they exhibit the same patterns for the variants (Alpha, Delta) and (Eta, Lota, Kappa) with moving positions, while the variants Beta, Gamma and Epsilon have different indicator matrixes. The fractal dimensions of SARS-CoV-2 variants are oscillating aroundI, except the Epsilon variant from USA, where the fractal dimension is 1.70.

Evolution under domestication of correlated characters in populations of Stenocereus stellatus (Pfeiff.) Riccob., under different forms of management in central Mexico: genetic diversity, damage, and defense mechanisms

Across the process of domestication, human selection produces changes in target attributes as well as changes that are not necessarily desired by humans due to pleiotropic or linked genes. In this paper we addressed, correlated changes between genetic diversity, damage level, defense mechanisms (resistance and tolerance), and fitness due to the domestication process of Stenocereus pruinosus (Otto ex Pfeiff.) Buxbaum and Stenocereus stellatus (Pfeiff.) Riccobono, an endemic columnar cactus of south-central Mexico. One hundred eighty individuals of S. stellatus from wild, in situ managed, and cultivated populations of Valle de Tehuacán and Mixteca Baja, Puebla, were sampled, and attributes including damage level, defense mechanisms and fitness (number of fruits) were measured. The DNA of 176 individuals was extracted to amplify and analyze five microsatellites in order to estimate genetic diversity and structure. As expected, cultivated populations showed a significantly higher damage level, as well as lower resistance and genetic diversity. Depending on the form of management, correlations between genetic diversity and the rest of the attributes exhibited different patterns. In wild populations, genetic diversity was positively correlated with damage and negatively with resistance; in situ managed populations exhibited the opposite pattern, and in cultivated populations, no correlations were found between these attributes. We propose a hypothetic model of human selection to explain the variation in these correlations. No differences in genetic diversity and tolerance were detected between regions; however, the populations of Valle de Tehuacán exhibited more damage and more resistance. In both regions, populations showed a positive correlation between fitness and resistance and a negative correlation between damage and resistance, suggesting the existence of a defense mechanism to ensure fitness. Also, non-regional differentiation suggests an eventual gene flow due to pollinators, human movement of branches, or a common ancestry before the domestication process.

Predicting and Analyzing the Response to Selection on Correlated Characters

The breeder’s equation generally provides robust predictions for the short-term evolution of single characters. When selection targets two or more characters simultaneously, there are often large discrepancies between predicted and observed responses. We assessed how well this standard model predicts responses to bivariate selection on wing color pattern characteristics in the tropical butterfly Bicyclus anynana. In separate laboratory selection experiments, two sets of serially repeated eyespots were subjected to ten generations of concerted and antagonistic selection for either size or color composition. We compared predicted and actual selection responses over successive generations, using the phenotypic data, selection differentials, and estimates of the genetic variance-covariance matrix G. We found differences in the precision of predictions between directions of selection but did not find any evidence of systematic biases in our predictions depending on the direction of selection. Our investigation revealed significant environmental effects on trait evolution across generations. When these were accounted for, predictions using the standard model improved considerably. In the experiment on eyespot size, secondary splitting of selection lines allowed the estimation of changes in G after nine generations of selection. Changes were not in general agreement with expectations from the breeder’s equation. A contour plot of prediction errors across trait space suggests that directional epistasis in the eyespot genotype-phenotype map might occur but estimates of changes in G are too model-dependent to verify whether they agree with that hypothesis. Altogether, our results underscore the need for quantitative genetics to investigate and estimate potential effects of multivariate non-linear genotype-phenotype maps and of environmental effects on G.

Foxed intra- and interspecific differentiation in Leptogorgia (Octocorallia: Gorgoniidae). A description of a new species based on multiple sources of evidence

The challenges of delimiting and identifying marine invertebrate species impede estimations of true biodiversity. This is particularly true in the case of gorgonian diversity, in which only classical morphological characters (e.g. branching pattern, size and colouration of the colony and sclerites, etc.), which can be homoplastic and continuous, have been used. In this study, using an integrative taxonomic approach, we analysed two morphs initially considered as two eco-typical variants of Leptogorgia alba Duchassaing and Michelotti, 1864, living sympatrically in the littoral area of Ecuador. We explored the use of classical morphological and morphometric characters to delimit species in combination with the analyses of molecular markers (mtMutS, CoxII-Igr-CoxI, ITSs, and 28S rRNA) to infer phylogenetic relationships. Based on our results, two species should be considered, L. alba and a new species, L. manabiensis n. sp., which showed distinguishing morphological features that cannot be attributed to phenotypic plasticity. Both species also showed significant differences in morphometric, non-correlated characters in all size classes. The phylogenetic analyses showed a polyphyletic L. alba - L. manabiensis n. sp. species complex, and ancestral polymorphism and incomplete lineage sorting as possible evolutionary processes leading to this pattern. In conclusion, the combination of morphological and morphometric evidences provides the best support for the identification and delimitation of these challenging species. In addition, molecular analyses, mainly supported by nuclear markers, allow fundamental aspects of the evolutionary history of these organisms to be discerned.

Resolving the status of Pyriporoides and Daisyella (Bryozoa: Cheilostomata), with the systematics of some additional taxa of Calloporoidea having an ooecial heterozooid

Based on the examination of type and newly discovered specimens, the scope of the calloporid genus Pyriporoides Hayward & Thorpe, 1989 is expanded to include Daisyella Gordon, 1989. All species of Pyriporoides have colonies of branching uniserial runners and acleithral ovicells that are borne on and/or develop concurrently with a distal heterozooid, not the distal autozooid. The ooecial heterozooid is usually kenozooidal but can be avicularian. Correlated characters include, inter alia: a raised granular rim that encloses a generally well-developed cryptocystal shelf, and a longitudinally elongate opesia that may be constricted and asymmetrical. Articulated perioral/pericryptocystal spines are present as well as occasional accessory spines borne on the lateral gymnocyst. Pyriporoides is mostly austral in distribution, ranging from the southern Indian Ocean and New Zealand’s subantarctic islands to West Antarctica, with an outlier in the northeast Atlantic. Three additional genera, one little known, two new to science, have species with small, mostly spot-like, colonies that share most of the zooidal characters of Pyriporoides and so are described and discussed in this context. These genera are Apiophragma Hayward & Ryland, 1993, Olisthella n. gen. and Bryobrownius n. gen. A cladistic analysis of the taxa described herein plus selected outgroup species of Calloporidae and Pyrisinellidae identified an apparent clade within or derived from Calloporidae, the significance of which is discussed.

Closing the gap between rocks and clocks using total-evidence dating

Total-evidence dating (TED) allows evolutionary biologists to incorporate a wide range of dating information into a unified statistical analysis. One might expect this to improve the agreement between rocks and clocks but this is not necessarily the case. We explore the reasons for such discordance using a mammalian dataset with rich molecular, morphological and fossil information. There is strong conflict in this dataset between morphology and molecules under standard stochastic models. This causes TED to push divergence events back in time when using inadequate models or vague priors, a phenomenon we term ‘deep root attraction’ (DRA). We identify several causes of DRA. Failure to account for diversified sampling results in dramatic DRA, but this can be addressed using existing techniques. Inadequate morphological models also appear to be a major contributor to DRA. The major reason seems to be that current models do not account for dependencies among morphological characters, causing distorted topology and branch length estimates. This is particularly problematic for huge morphological datasets, which may contain large numbers of correlated characters. Finally, diversification and fossil sampling priors that do not incorporate all the available background information can contribute to DRA, but these priors can also be used to compensate for DRA. Specifically, we show that DRA in the mammalian dataset can be addressed by introducing a modest extra penalty for ghost lineages that are unobserved in the fossil record, for instance by assuming rapid diversification, rare extinction or high fossil sampling rate; any of these assumptions produces highly congruent divergence time estimates with a minimal gap between rocks and clocks. Under these conditions, fossils have a stabilizing influence on divergence time estimates and significantly increase the precision of those estimates, which are generally close to the dates suggested by palaeontologists. This article is part of the themed issue ‘Dating species divergences using rocks and clocks’.

Multiple morphological clocks and total-evidence tip-dating in mammals

Morphological integration predicts that correlated characters will coevolve; thus, each distinct suite of correlated characters might be expected to evolve according to a separate clock or ‘pacemaker’. Characters in a large morphological dataset for mammals were found to be evolving according to seven separate clocks, each distinct from the molecular clock. Total-evidence tip-dating using these multiple clocks inflated divergence time estimates, but potentially improved topological inference. In particular, single-clock analyses placed several meridiungulates and condylarths in a heterodox position as stem placentals, but multi-clock analyses retrieved a more plausible and orthodox position within crown placentals. Several shortcomings (including uneven character sampling) currently impact upon the accuracy of total-evidence dating, but this study suggests that when sufficiently large and appropriately constructed phenotypic datasets become more commonplace, multi-clock approaches are feasible and can affect both divergence dates and phylogenetic relationships.