Assessing the accuracy of ancestral protein reconstruction methods

The phylogenetic inference of ancestral protein sequences is a powerful technique for the study of molecular evolution, but any conclusions drawn from such studies are only as good as the accuracy of the reconstruction method. Every inference method leads to errors in the ancestral protein sequence, resulting in potentially misleading estimates of the ancestral protein's properties. To assess the accuracy of ancestral protein reconstruction methods, we performed computational population evolution simulations featuring near-neutral evolution under purifying selection, speciation, and divergence using an off-lattice protein model where fitness depends on the ability to be stable in a specified target structure. We were thus able to compare the thermodynamic properties of the true ancestral sequences with the properties of “ancestral sequences” inferred by maximum parsimony, maximum likelihood, and Bayesian methods. Surprisingly, we found that methods such as maximum parsimony and maximum likelihood that reconstruct a “best guess” amino acid at each position overestimate thermostability, while a Bayesian method that sometimes chooses less-probable residues from the posterior probability distribution does not. Maximum likelihood and maximum parsimony apparently tend to eliminate variants at a position that are slightly detrimental to structural stability simply because such detrimental variants are less frequent. Other properties of ancestral proteins might be similarly overestimated. This suggests that ancestral reconstruction studies require greater care to come to credible conclusions regarding functional evolution. Inferred functional patterns that mimic reconstruction bias should be reevaluated.     

Origin of Mediterranean insular endemics in the Boraginales: integrative evidence from molecular dating and ancestral area reconstruction

Aim The presence of numerous reliable fossils and the occurrence of many endemic island species make the Boraginales particularly suitable for integrative biogeographical studies. In this paper we aim to elucidate the time frame and events associated with the origin of selected borages endemic to the Mediterranean climate zone. More specifically, we describe and examine the alternative palaeo‐ and neoendemic hypotheses for their origin. Location Corsica and Sardinia (continental fragment islands) and the Canary Islands (an oceanic island archipelago). Methods Eighty‐nine accessions, representing 30 genera from five families ascribed to the Boraginales, were examined for six chloroplast DNA regions. We used an integrative approach including phylogenetic analyses (Mr Bayes ), Bayesian molecular dating (T3 package) with four fossil constraints on nodes, and biogeographical reconstructions (diva ) to elucidate the temporal and spatial origins of the Corso‐Sardinian and Canary Island endemics. Results Species of Echium endemic to the Canary Islands diverged from their continental sister clade during the Miocene (15.3 ± 5.4 Ma), probably after the rise of the oldest islands (c. 20 Ma). Corso‐Sardinian endemics of Borago diverged from their primarily North African sister clade during the late Miocene‐Pliocene (c. 6.9 ± 3.6 Ma), well after the initial fragmentation of the islands (c. 30 Ma). Similarly, Corso‐Sardinian endemics of Anchusa diverged from the South African Anchusa capensis during the Pliocene–Pleistocene (c. 2.7 ± 2.1 Ma). Main conclusions The present study reveals an Anatolian origin for Anchusa, Borago and Echium and underlines the importance of the Eastern Mediterranean region as a possible reservoir for plant evolution in the Mediterranean Basin. For Anchusa and Borago, the divergence from their respective sister clades on the two types of islands post‐dated the formation of the islands, thus supporting the neo‐endemic hypothesis, whereas the dating results for the origin of Echium endemics were less conclusive.     

History can matter: non-Markovian behavior of ancestral lineages

Although most of the important evolutionary events in the history of biology can only be studied via interspecific comparisons, it is challenging to apply the rich body of population genetic theory to the study of interspecific genetic variation. Probabilistic modeling of the substitution process would ideally be derived from first principles of population genetics, allowing a quantitative connection to be made between the parameters describing mutation, selection, drift, and the patterns of interspecific variation. There has been progress in reconciling population genetics and interspecific evolution for the case where mutation rates are sufficiently low, but when mutation rates are higher, reconciliation has been hampered due to complications from how the loss or fixation of new mutations can be influenced by linked nonneutral polymorphisms (i.e., the Hill-Robertson effect). To investigate the generation of interspecific genetic variation when concurrent fitness-affecting polymorphisms are common and the Hill-Robertson effect is thereby potentially strong, we used the Wright-Fisher model of population genetics to simulate very many generations of mutation, natural selection, and genetic drift. This was done so that the chronological history of advantageous, deleterious, and neutral substitutions could be traced over time along the ancestral lineage. Our simulations show that the process by which a nonrecombining sequence changes over time can markedly deviate from the Markov assumption that is ubiquitous in molecular phylogenetics. In particular, we find tendencies for advantageous substitutions to be followed by deleterious ones and for deleterious substitutions to be followed by advantageous ones. Such non-Markovian patterns reflect the fact that the fate of the ancestral lineage depends not only on its current allelic state but also on gene copies not belonging to the ancestral lineage. Although our simulations describe nonrecombining sequences, we conclude by discussing how non-Markovian behavior of the ancestral lineage is plausible even when recombination rates are not low. As a result, we believe that increased attention needs to be devoted to the robustness of evolutionary inference procedures that rely upon the Markov assumption.     

Retrospective coalescent methods and the reconstruction of metapopulation histories in the sea

Phylogeographic analyses are a key interface between ecological and evolutionary ways of knowing because such analyses integrate the cumulative effects of demographic (ecological) processes over geological (evolutionary) time scales. Newly developed coalescent methods allow evolutionary ecologists to overcome some limitations associated with inferring population history from classic methods such as Wright’s F _ST. Here we briefly contrast classic and coalescent methods for looking backward in time through a population genetic lens, focusing on the key advantages of the isolation-with-migration (IM) class of coalescent methods for distinguishing ancient connectedness from actual recurrent contemporary gene flow as causes of genetic similarity or differentiation among populations. Making this critical distinction can lead to the discovery of otherwise obscured histories underlying conventional patterns of spatial variation. We illustrate the importance of these insights using analyses of Pacific fishes, snails, and sea stars in which population sizes and divergence times are more important than rates of contemporary gene flow as determinants of population genetic differentiation. We then extend the IM method to genetic data from two model metapopulation species (California abalone, Australian damselfish). The analyses show the potential use of non-equilibrium IM methods for differentiating among metapopulation models that make different predictions about population parameters and have different implications for the design of marine protected areas and other conservation goals. At face value, the results largely rule out classic metapopulation dynamics (dominated by extinction and colonization rather than connectivity via ongoing recurrent gene flow) but, at the same time, do not strongly support a modern marine metapopulation dynamic (ecologically significant connectivity between demes). However, the results also highlight the need for much more data (i.e., loci) sampled on different spatial scales in order to determine whether metapopulation dynamics might exist on smaller scales than are typically sampled by most phylogeographers and landscape geneticists.     

A geographic mosaic of evolutionary lineages within the insular endemic newt Euproctus montanus

Islands are hotspots of biodiversity, with a disproportionately high fraction of endemic lineages, often of ancient origin. Nevertheless, intra‐island phylogeographies are surprisingly scarce, leading to a scanty knowledge about the microevolutionary processes induced on island populations by Plio‐Pleistocene climatic oscillations, and the manner in which these processes contributed to shape their current genetic diversity. We investigated the phylogeography, historical demography and species distribution models of the Corsican endemic newt Euproctus montanus (north‐western Mediterranean). As for many island endemics, the continuous distribution of E. montanus throughout its range has hitherto been considered as evidence for a single large population, a belief that also guided the species' categorization for conservation purposes. Instead, we found a geographic mosaic of ancient evolutionary lineages, with five main clades of likely Pliocene origin (2.6–5.8 My), all but one restricted to northern Corsica. Moreover, the copresence between main lineages in the same population was limited to a single case. As also suggested by growing literature on intra‐island phylogeographic variation, it seems that the extensive use of simplifying assumption on the population structure and historical demography of island populations—both in theoretical and applicative studies—should be carefully reconsidered, a claim that is well exemplified by the case presented here.     

Hair removal methods: A comparative study for dermoscopy images

Removal and restoration of hair and hair-like regions within skin lesion images is needed so features within lesions can be more effectively analyzed for benign lesions, cancerous lesions, and for cancer discrimination. This paper refers to “melanoma texture” as a rationale for supporting the need for the proposed hair detection and repair techniques, which incompletely represents why hair removal is an important operation for skin lesion analysis. A comparative study of the state-of-the-art hair-repaired methods with a novel algorithm is also proposed by morphological and fast marching schemes. The hair-repaired techniques are evaluated in terms of computational, performance and tumor-disturb patterns (TDP) aspects. The comparisons have been done among (i) linear interpolation, inpainting by (ii) non-linear partial differential equation (PDE) and (iii) exemplar-based repairing techniques. The performance analysis of hair detection quality, was based on the evaluation of the hair detection error (HDE), quantified by statistical metrics and manually used to determine the hair lines from a dermatologist as the ground truth. The results are presented on a set of 100 dermoscopic images. For the two characteristics measured in the experiments the best method is the fast marching hair removal algorithm (HDE: 2.98%, TDP: 4.21%). This proposed algorithm repaired the texture of the melanoma, which becomes consistent with human vision. The comparisons results obtained, indicate that hair-repairing algorithm based on the fast marching method achieve an accurate result.     

A comparative study in methods of cryoprotection for human semen

A comparative study using either glycerol or an egg yolk-citrate-glycerol mix for cryoprotection under the conditions described showed the latter to give a significantly better post-thaw motility. The greatest drop was noted within the first hour, suggesting that freezability of a sample could be judged accurately by rethawing at that time.Controlled studies using scanning electron microscopy clearly showed a greater head disruption after freezing with glycerol and looped tails after centrifugation, which could account for some of the findings of the first part of the study.These findings are reviewed and it is recommended that seminal samples are not centrifuged and that a complex medium be employed for seminal freezing and storing.     

Towards the reconstruction of the bilaterian ancestral pre-MHC region

In this article, we describe how we reconstructed a precise, minimal proto-MHC region in the ancestor of euchordates, which was based on a comparison of the MHC-paralogy group of vertebrate with the MHC-like chromosome of cephalochordates. This deduced ancestral region was compared with the genomes of extant species, other deuterostomes and protostomes. Our analysis revealed statistically significant traces of conservation in these species, suggesting that a proto-MHC region existed at the origin of all bilaterian species. We also propose a new approach to reconstruct ancestral genomes, which combines both stringent statistical testing and phylogenetic analysis.     

The origin of animals: an ancestral reconstruction of the unicellular-to-multicellular transition

How animals evolved from a single-celled ancestor, transitioning from a unicellular lifestyle to a coordinated multicellular entity, remains a fascinating question. Key events in this transition involved the emergence of processes related to cell adhesion, cell–cell communication and gene regulation. To understand how these capacities evolved, we need to reconstruct the features of both the last common multicellular ancestor of animals and the last unicellular ancestor of animals. In this review, we summarize recent advances in the characterization of these ancestors, inferred by comparative genomic analyses between the earliest branching animals and those radiating later, and between animals and their closest unicellular relatives. We also provide an updated hypothesis regarding the transition to animal multicellularity, which was likely gradual and involved the use of gene regulatory mechanisms in the emergence of early developmental and morphogenetic plans. Finally, we discuss some new avenues of research that will complement these studies in the coming years.     

A comparative study of clustering methods for molecular data

The research aim is to use three clustering technologies for establishing molecular data model of large size sets by comparison between low energy samples (LES) and local molecular samples (LMS). Hierarchical cluster of multi-level tree distance relation, competitive learning network of similar inputs falling into the same cluster and topological SOM are used to analyze 6,242 LES and 5,000 LMS. Our experiments show that in SOM, there are 24 to 25 Davies-Boulding clustering index and color map cluster units in the LES more than 10 to 12 in the LMS, which is consistent with the results of hierarchical cluster and competitive learning network in the rough. The hierarchical cluster reflects the biggest inter-cluster distance about 30 for the LES is far larger than that of LMS about 10. The intra-cluster distance of LES about 15 is also far bigger than that of LMS about 3. In SOM, there are more cluster borders of high values (black) reflecting large distance and more clusters in the D-matrix and U-matrix of LES than that of LMS, due to the biggest standard deviation range from -8 to 10 of samples feature of the LES is bigger than that of LMS from -2.5 to 2.5.     

Evolution of protein specificity: insights from ancestral protein reconstruction

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A comparative study of the purine- and pyrimidine-metabolising enzymes of a range of trypanosomatids

A range of trypanosomatids (amastigotes and cultured promastigotes of Leishmania mexicana mexicana, cultured promastigotes of L. m. amazonensis, L. donovani and L. tarentolae, culture forms of Crithidia fasciculata, Herpetomonas muscarum muscarum and H. m. ingenoplastis and procyclic trypomastigotes of Trypanosoma brucei brucei) have been surveyed for the presence of purine- and pyrimidine-metabolising enzymes. Several common features were observed, including the presence of nucleosidases, catabolic phosphorylases, phosphoribosyltransferases, kinases and cytidine deaminase and the apparent absence of AMP deaminase, anabolic purine phosphorylase and cytosine deaminase. Significant differences between species were discovered, notably in adenine and adenosine metabolism. Nucleoside phosphotransferase active on inosine was detected in insect trypanosomatids but not in L. m. mexicana.     

Aeroallergens: a comparative study of two monitoring methods

Olive and grass pollen grains are the major causes of hay fever in the Mediterranean region. A number of samplers and methods have been developed in recent years in order to obtain reliable data regarding airborne allergen concentrations. This paper reports on a detailed comparison of two samplers—Cyclone and ChemVol—and on the parameters that could influence their efficiency. Airborne concentrations of two key olive and grass allergens, Ole e 1 and Phl p 5, respectively, were monitored over two years with different weather patterns, 2012 and 2014. Allergenic particles were quantified by ELISA assay, and results were compared with pollen concentrations monitored using a Hirst-type volumetric spore trap over the same study periods. The influence of weather-related parameters on local airborne pollen and allergen concentrations was also analysed. Although a positive correlation was detected between results obtained using the two samplers during the pollen season, results for the cumulative annual Allergen Index varied considerably. The two samplers revealed a positive correlation between pollen concentrations and both minimum temperature during the warmer year (2012) and maximum temperature during the cooler year (2014); a negative significant correlation was observed in both cases with rainfall and relative humidity. In summary, although some differences were observed between the two samplers studied, both may be regarded as suitable for allergen detection.     

Estimating the number of ancestral lineages using a maximum-likelihood method based on rejection sampling

Estimating the number of ancestral lineages of a sample of DNA sequences at time t in the past can be viewed as a variation on the problem of estimating the time to the most recent common ancestor. To estimate the number of ancestral lineages, we develop a maximum-likelihood approach that takes advantage of a prior model of population demography, in addition to the molecular data summarized by the pattern of polymorphic sites. The method relies on a rejection sampling algorithm that is introduced for simulating conditional coalescent trees given a fixed number of ancestral lineages at time t. Computer simulations show that the number of ancestral lineages can be estimated accurately, provided that the number of mutations that occurred since time t is sufficiently large. The method is applied to 986 present-day human sequences located in hypervariable region 1 of the mitochondrion to estimate the number of ancestral lineages of modern humans at the time of potential admixture with the Neanderthal population. Our estimates support a view that the proportion of the modern population consisting of Neanderthal contributions must be relatively small, less than approximately 5%, if the admixture happened as recently as 30,000 years ago.     

A comparative study of laboratory methods for the preparation of arabic acid

Different methods of precipitation of arabic acid from natural gum arabic are compared in terms of yield and molecular weight derived from gel chromatography experiments. All of the precipitation methods used gave products which were closely similar in terms of $\text{M}$_n, but precipitation with HCl/acetone and HAc/ethanol gave low yields (25 and 3%, respectively).