Parsimony analysis of unaligned sequence data: maximization of homology and minimization of homoplasy,not minimization of operationally defined total cost or minimization of equally weighted transformations

Wheeler (2012) stated that minimization of ad hoc hypotheses as emphasized by Farris (1983) always leads to a preference for trivial optimizations when analysing unaligned sequence data, leaving no basis for tree choice. That is not correct. Farris's framework can be expressed as maximization of homology, a formulation that has been used to overcome the problems with inapplicables (it leads to the notion of subcharacters as a quantity to be co‐minimized in parsimony analysis) and that is known not to lead to a preference for trivial optimizations when analysing unaligned sequence data. Maximization of homology, in turn, can be formulated as a minimization of ad hoc hypotheses of homoplasy in the sense of Farris, as shown here. These issues are not just theoretical but have empirical relevance. It is therefore also discussed how maximization of homology can be approximated under various weighting schemes in heuristic tree alignment programs, such as POY, that do not take into account subcharacters. Empirical analyses that use the so‐called 3221 cost set (gap opening cost three, transversion and transition costs two, and gap extension cost one), the cost set that is known to be an optimal approximation under equally weighted homology in POY, are briefly reviewed. From a theoretical point of view, maximization of homology provides the general framework to understand such cost sets in terms that are biologically relevant and meaningful. Whether or not embedded in a sensitivity analysis, this is not the case for minimization of a cost that is defined in operational terms only. Neither is it the case for minimization of equally weighted transformations, a known problem that is not addressed by Kluge and Grant's (2006) proposal to invoke the anti‐superfluity principle as a rationale for this minimization.     

Modified netting technique for capturing gazelles in Serengeti,Ngorongoro and Loliondo,Tanzania

During serological surveillance of peste des petits ruminants (PPR) disease, it required capture of randomly selected herds of gazelles as part of a study to determine the epidemiological role of these species in the circulation of peste des petits ruminants virus (PPRV). The study targeted capturing 135 Grant's gazelles (Gazella granti) from the Serengeti ecosystem, Tanzania. A modified netting technique was used aiming at providing safe, efficient and cost‐effective method for capture of gazelles. Locally available materials were used, and wildlife professionals guided the process of manufacturing supporting frame for the nets. Twenty (20) black metal pipes, 20 metal bars, four nets and three vehicles were used in the procedure. A total of 136 Grant's gazelles and nine Thomson's gazelles were captured in three missions. The Grant's gazelles were captured as per sample size calculated in all locations: Loliondo (n = 25), Serengeti National Park (n = 44) and Ngorongoro Conservation Area (NCA) (n = 67) using less time and minimum cost than estimated. Injuries of three fawns (2%) inadvertently captured with the groups of adults and sub‐adult animals were recorded. Comparing with 2014 and other studies, modified netting technique showed high animal and operator safety levels with minimal injuries. With this technique, it was possible to capture even flighty animals that behave nervously because of hunting and other human activities, including Thomson's gazelles, a species previously found to be difficult to capture by netting.     

Clarifying Baker's Law

Background

Baker''s Law states that colonization by self-compatible organisms is more likely to be successful than colonization by self-incompatible organisms because of the ability for self-compatible organisms to produce offspring without pollination agents. This simple model has proved very successful in plant ecology and has been applied to various contexts, including colonizing or ruderal species, islands colonizers, invasive species or mating system variation across distribution ranges. Moreover, it is one of the only models in population biology linking two traits of major importance in ecology, namely dispersal and mating system. Although Baker''s Law has stimulated a large number of empirical studies reporting the association of self-fertilization and colonizing ability in various contexts, the data have not established a general pattern for the association of traits.

Scope

In this paper, a critical position is adopted to discuss and clarify Baker''s Law. From the literature referring to Baker''s Law, an analysis made regarding how mating success is considered in such studies and discrepancies with population genetics theory of mating systems are highlighted. The data reporting the association of self-fertilization and colonizing ability are also briefly reviewed and the potential bias in interpretation is discussed. Lastly, a recent theoretical model analysing the link between colonizing ability and self-fertilization is considered.

Conclusions

Evolutionary predictions are actually more complex than Baker''s intuitive arguments. It appears that Baker''s Law encompasses a variety of ecological scenarios, which cannot be considered a priori as equivalent. Questioning what has been considered as self-evident for more than 50 years seems a reasonable objective to analyse in-depth dispersal and mating system traits.     

Reduction of α-Azidopropiophenone by Immobilized Baker's Yeast

Baker's yeast immobilized on montmorillonite K10 and chrysotile reduced α-azidopropiophenone to the corresponding azidoalcohols syn and anti with good chemical yield and enantiomeric excess.     

Influence of strain and cultivation procedure on the performance of simultaneous saccharification and fermentation of steam pretreated spruce

Yeast to be used in simultaneous saccharification and fermentation (SSF) of lignocelluloses materials has to be prepared in a separate cultivation step. The effects of the cultivation procedure on the performance of SSF of steam pretreated softwood were studied in the current work. The yeast used in the SSF was either directly commercially available Baker's yeast (as packaged yeast) or the same strain of yeast produced from the hydrolysate obtained in the pretreatment of the softwood material. A second strain of Saccharomyces cerevisiae TMB3000, isolated from spent sulphite liquor, was also compared with the commercial Baker's yeast. The strains were tested in SSF at substrate loads of 3, 5 and 8% dry weight of water insoluble material. Final ethanol yields were above 85% of the theoretical (based on the available hexoses) in all cases, except for the package yeast for the 8% substrate load, in which case the final yield was less than 65%. The cultivation procedure was found to have a significant impact on the performance during SSF, as well as in small-scale fermentations of hydrolysate liquor without solid material. The Baker's yeast cultivated on the hydrolysate from the steam pretreatment had in all cases a higher productivity, in particular at the highest substrate load. Cultivated Baker's yeast had a slightly higher productivity than TMB3000. The results suggest that the adaptation of the yeast to the inhibitors present in the medium is an important factor that must be considered in the design of SSF processes.     

The founding of Mauritian endemic coffee trees by a synchronous long‐distance dispersal event

The stochastic process of long‐distance dispersal is the exclusive means by which plants colonize oceanic islands. Baker's rule posits that self‐incompatible plant lineages are unlikely to successfully colonize oceanic islands because they must achieve a coordinated long‐distance dispersal of sufficiently numerous individuals to establish an outcrossing founder population. Here, we show for the first time that Mauritian Coffea species are self‐incompatible and thus represent an exception to Baker's rule. The genus Coffea (Rubiaceae) is composed of approximately 124 species with a paleotropical distribution. Phylogenetic evidence strongly supports a single colonization of the oceanic island of Mauritius from either Madagascar or Africa. We employ Bayesian divergence time analyses to show that the colonization of Mauritius was not a recent event. We genotype S‐RNase alleles from Mauritian endemic Coffea, and using S‐allele gene genealogies, we show that the Mauritian allelic diversity is confined to just seven deeply divergent Coffea S‐RNase allelic lineages. Based on these data, we developed an individual‐based model and performed a simulation study to estimate the most likely number of founding individuals involved in the colonization of Mauritius. Our simulations show that to explain the observed S‐RNase allelic diversity, the founding population was likely composed of fewer than 31 seeds that were likely synchronously dispersed from an ancestral mainland species.     

Characterization of eight microsatellite loci in Grant's gazelle (Gazella granti)

Eight microsatellite loci were isolated from a genomic DNA library created from Grant's gazelle (Gazella granti). Observed and expected levels of heterozygosity were computed utilizing 20 individuals from a population in Central Kenya. Tests for Hardy–Weinberg equilibria were conducted and found that two of the eight loci deviated from equilibrium in this population. These markers were developed to analyse the genetic effects of culling and isolation on a game preserve in Kenya.     

BAKER'S LAW REVISITED: REPRODUCTIVE ASSURANCE IN A METAPOPULATION

Baker's Law states that it is more likely for self-compatible than for self-incompatible individuals to establish sexually reproducing colonies after long-distance dispersal, because only the former can do so with a single individual. This hypothesis, proposed by H. G. Baker 40 years ago is based largely on the observation that self-compatibility is particularly frequent among colonists of oceanic islands. Here we argue that the principle of Baker's Law applies equally in the context of a metapopulation in which frequent local extinction is balanced by recolonization of sites by seed dispersal: metapopulation dynamics will select for an ability to self-fertilize. We review several studies that support this hypothesis and present a metapopulation model in which the seed productivity required by obligate outcrossers for their maintenance in a metapopulation is compared with that of selfers. Our model also estimates the reduction in the advantage of reproductive assurance to selfers as a result of perenniality and seed dormancy. In general, selection for reproductive assurance is greatest when the colony occupancy rate, p, is low and is much reduced when p approaches its maximum. This provides an explanation for the observation that many highly successful colonizers, in which p is often high, are self-incompatible. The basic model we present also lends itself to comparisons of metapopulation effects between unisexuality and cosexuality and between different modes of self-incompatibility.     

Comparison of the Baker's yeast process performance in laboratory and production scale

A 215 m³ industrial bubble column reactor for fedbatch production of Baker's yeast was sampled for sugar, to investigate the extent of concentration gradients. The results verify that such gradients exist: the concentration is higher closer to the feeding point. Effects of sugar heterogeneities at different scales were studied by 1)?performing a volumetric scale-down of the industrial process in a laboratory stirred tank reactor (STR); 2) performing the same scaled down process in a Scale-Down Reactor (SDR) with repeated short term exposure of the cells to high sugar concentrations. In this reactor about 10% of the Baker's yeast culture was intermittently exposed to high (0.45–1.9?g?l^?1) concentrations of sugar, for periods of 60 seconds. It was found that physiological parameters of glycolysis and respiration were affected by environmental heterogeneities: 1) A biomass yield reduction of about 6–7% was found, with both the production reactor and the SDR, as compared to the homogeneous reactor. The loss of yield is interpreted in terms of a metabolic by-pass via ethanol, where cells are consuming and producing ethanol with different yields. 2) The maximum respiration rate was higher in cells produced in the production unit and in the SDR. 3) The product quality, expressed as gassing power of the yeast in a dough, was increased for sweet and non-sugar doughs in the SDR, and for sweet doughs in the production reactor. Thus, the SDR, when run with defined glucose gradients, in some aspects resembles the large reactor. It could be regarded as a tool for scale-down and scale-up studies and may be useful in investigations on the scale-up sensitivity of a process.     

Statistical consistency and phylogenetic inference: a brief review

The claim that parsimony can be statistically inconsistent remains the chief criticism of the cladistic approach, and also the main justification for alternative model‐based approaches such as maximum likelihood and Bayesian inference. Despite its refutation in the 1980s, this persistent myth of parsimony's Achilles’ heel is entrenched in the primary literature, and has metastasized into textbooks, as well. Here, I review historical controversies, and offer three short arguments as to why statistical consistency is not only irrelevant to systematics, but to empirical science in general.     

The Use of Baker's Yeast in the Generation of Asymmetric Centers to Produce Chiral Drugs and Other Compounds

ABSTRACT:?

This review gives a general idea about the importance of chiral carbon in medicine and a way to obtain chiral building blocks with Baker's yeast (Saccharomyces cerevisiae) or synthesis of medicaments and other organic compounds. Reactions with these microorganisms are cheaper and easier to be executed than with chemicals (e.g., organometallics). Examples of important and practical reactions catalyzed by enzymes inside Saccharomyces cerevisiae are given and probable mechanisms of action of these enzymes are shown. Although these microbes have advantages such as low cost and availability, there are some concerns that are necessary to be resolved, such as NAD(P)H dosage to choose strains more adequate for reduction reactions.     

OBSERVATIONS ON THE DIETARY CHOICE OF FREE-RANGING JUVENILE OSTRICHES

Cooper, S.M. & Palmer, T. 1994. Observations on the dietary choice of free-ranging juvenile Ostriches. Ostrich 65:251-255.

The dietary selection of juvenile Ostriches in an east African savanna was determined using penned and free-ranging chicks. The young Ostriches displayed an innate preference for selected plant species and showed little change free-ranging chicks. The young Ostriches displayed increasing experience. The most heavily utilized foods were newly emergent grass leaves and the foliage of the woody forbs Indigofera schimperi (Leguminosae) and Aspilia mossambicensis (Comositae) While the diet composition of the Ostrich is similar to that of Grant's gazelle, Ostriches differ in that they eat some silica rich plants not utilized by ungulates; thus Ostriches may be a useful addition to mixed-species game ranching in Africa.     

A falsificationist perspective on the usage of process frequencies in phylogenetics

By referring to Popperian falsificationism, proponents of cladistic parsimony claim the superiority of parsimony over likelihood. They conclude that likelihood as a statistical approach is inconsistent with falsificationism, and base their argumentation on four claims: (1) congruence tests cladograms against observational evidence and represents the most important test in phylogenetics, in which minimum‐step trees represent most corroborated trees; (2) frequency probabilities cannot be used for evaluating degree of corroboration; (3) phylogeny represents a unique process and thus frequencies cannot be applied as they require statistical reference classes that are necessarily general; (4) likelihood is a verificationist approach. After discussing the deficiencies of the cladistic phylogeneticists’ conceptualisation of the congruence test and the presentation of an alternative conceptualisation, it is shown that these four claims cannot be sustained within a falsificationist framework, and that the weighting of characters is a necessity. A differentiation between the theoretical concept of apomorphy and the epistemological concept of character weight is proposed. While apomorphies have to be independent from each other, the weighting of characters is interdependent due to human inability to distinguish organismic traits that are structurally identical though they do not share a common evolutionary origin. The possibility of this epistemological interdependence can best be dealt with by the application of process frequencies. The importance of process frequencies of specific transformation classes is exemplified in reference to Popper's formula for the measure of degree of corroboration and its consistency is shown. Therefore, the application of statistical methods is reasonable. As a consequence, the question whether likelihood or parsimony methods represent the best approaches in phylogenetics remains a genuinely empirical question that cannot be decided only in reference to Popper's falsificationism.     

Clarifying the Taxonomic Identity of a Phylogenetically Important Group of Eukaryotes: Planomonas is a Junior Synonym of Ancyromonas

ABSTRACT. Ancyromonas was first described in 1882 by Saville Kent, with the modern concept of the genus dating from 1979 with the work of Hänel. Since then, organisms assigned to Ancyromonas have been found to be common in diverse ecosystems, and the group's isolated phylogenetic placement renders it of considerable evolutionary interest. However, in 2008 Cavalier‐Smith et al. concluded that all modern accounts of Ancyromonas were of a different organism from that described by Saville Kent, and erected the new genus Planomonas to encompass modern observations of Ancyromonas, and several new species. We critique the rationale for creating this new genus, reexamining the original sources and making additional observations using light and electron microscopy. We find that almost all the differences between the genera are mistaken or insubstantial. In particular, (1) Cavalier‐Smith et al. characterized Ancyromonas sensu Saville Kent as anchoring and Planomonas as gliding, while we find that each type of organism actually does both, and (2) it was claimed that Planomonas is flattened while Ancyromonas sensu Saville Kent is not, but this argument is inconsistent. We treat Planomonas as a junior synonym of Ancyromonas, and Planomonas mylnikovi as a junior synonym of Ancyromonas sigmoides. We transfer Planomonas cephalopora, Planomonas micra, Planomonas howeae and Planomonas limna to Ancyromonas. The genus Ancyromonas therefore includes: A. sigmoides, Ancyromonas cephalopora n. comb., Ancyromonas melba, Ancyromonas sinistra, Ancyromonas micra n. comb., Ancyromonas howeae n. comb., and Ancyromonas limna n. comb.     

Old and New Synthetic Capacities of baker's Yeast

An overview on some recent developments in the use of Baker's yeast as a biocatalyst is given. Some recent examples concerning oxido-reductases, phosphatases and other less defined catalytic activities are discussed.     

Dynamic homology and the likelihood criterion

The use of likelihood as an optimality criterion is explored in the context of dynamic homology. Simple models and procedures are described to allow the analysis of large variable length sequence data sets, alone and in combination with qualitative information (such as morphology). Several approaches are discussed that have different likelihood interpretations in terms of maximum parsimony likelihood and maximum average likelihood. Implementation is discussed and an example in arthropod systematics presented. Topological congruence comparisons with parsimony are made.
© The Willi Hennig Society 2006.     

Sexual dimorphism,mating system,and effect of phylogeny in De Brazza's monkey (Cercopithecus neglectus)

De Brazza's monkey (Cercopithecus neglectus), like other guenons, shows marked sexual dimorphism in an array of features. While strong sexual dimorphism is generally associated with a polygynous mating system, populations of De Brazza's monkeys in Gabon are reportedly monogamous. An explanation of this unique phenomenon is offered here. Patterns of sexual dimorphism are examined for morphology, growth and development, behavior, and ecology, and field and captive studies on the social organization and mating system of De Brazza's monkey and congeneric guenon species are reviewed. Based on the findings, it is postulated that 1) De Brazza's monkeys are not strictly monogamous, but exhibit interpopulational variation in their mating system, from facultative monogamy to mild polygyny; 2) marked sexual dimorphism most likely reflects the effect of the historical-phylogenetic factor; ie, it represents a holdover of a degree of dimorphism established earlier in evolutionary history when the degree of polygyny Was higher; and 3) lessening in the degree of polygyny and a tendency toward monogamy represents a consequence of selection toward small group size. Small group size, a unique antipredator strategy, and failure to form polyspecific associations are ultimately most likely the result of intragroup and interspecific competition and predation pressure.     

The use of parsimony in testing phylogenetic hypotheses

With the advance of cladistic theory differences in principle between it and other systematic techniques are few but of fundamental importance. In the mechanics of classification they are confined to ranking and the rejection of paraphyletic taxa. In cladistic analysis, leading to cladograms, trees and phylogeny reconstruction, inconsistencies in apparent synapomorphies are said to be resolved using Popper's hypothetico-deductive method together with the principle of parsi However, not only do cladists not use Popper's methodology, which is inconsistent with parsimony, but their use of parsimony is invalid as a test of phylo The only accepted extrinsic test of a classification is that enunciated by John Stuart Mill. It has been claimed that cladistic classifications yield the best results when judged by Mill's criteria, but this is only possibly the case with analytic classifications produced by numerical techniques. No satisfactory test exists in normal (synthetic) cladism for distinguishing synapomorphy from homoplasy. The effects of this are particularly dire in cladograms and classifications involving fossils in which a Stufenreihe arrangement is adopted.