Miracle-dz/UniFAR-FTUs huggingface dataset:
Improving intraspecific allele networks inferred by maximum parsimony

Allele (or haplotype) networks are often used in phylogeographic studies to display genetic variation within a species or a group of closely related species. A global maximum parsimony approach to infer allele networks, arguably the method of choice to display genetic variation at the intraspecific level, consists in inferring all most parsimonious trees from a DNA sequence alignment and combining the corresponding phylograms into a single graph. However, it has been suggested that, while classic phylogenetic programs generate a single phylogram per most parsimonious tree, deriving all possible phylograms from them would allow identifying additional most parsimonious paths among alleles, thereby improving this network inference method. We test this prediction by analysing both simulated and empirical DNA sequence alignments. For this purpose, a computer program, CPN, was developed to implement the entire procedure, starting with a set of most parsimonious trees and combining all derived phylograms into a network. We show that including all possible most parsimonious phylograms indeed often results in finding additional most parsimonious paths in the network graph, thereby improving the search for a global maximum parsimony solution. We highly recommend the use of this approach in future phylogeographic studies, to ensure that all most parsimonious paths are included in the allele network, instead of an arbitrarily selected subset of those.
Método generalizado de análise de dialelos desbalanceados

A general procedure for estimation of general and specific combining ability in diallelic crosses with unequal number of replications for treatments (parents and F1 hybrid combinations), evaluated in a design with restricted randomization, is presented. In this case, the estimates of adjusted means are interdependent and heterocedastic, demanding the use of the GaussMarcov generalized linear model. The objective of this study was the theoretical deduction of the model and its application to a practical example. A complete diallel crossing without reciprocals was performed, including five parents: CB 511687-1, CB 733753, Diamante Negro, Rosinha G-2 and Compuesto Chimaltenango 2. The parents CB 511687-1, CB 733753 and Diamante Negro contribute genetically for resistance while Rosinha G-2 and Compuesto Chimaltenango 2 contribute for susceptibility of dry bean to common bacterial blight. Most of the crosses analyzed showed partial dominance for susceptibility of bean to Xanthomonas axonopodis pv. phaseoli.
Suitability of Random Amplified Polymorphic DNA for Genetic Markers in the Aphid Parasitoid, Aphelinus asychis Walker

Abstract The repeatability, variability, transmission, and linkage relationships of random amplified polymerphic DNA (RAPD) fragments were examined using six inbred lines of the haplodiploid parasitoid, Aphelinus asychis, originally collected on one date from a single held in southern France. Repeatability of RAPD fragments could be adequately judged using two replicate amplifications of the same individual in the same amplification run. Thirty-one of 136 repeatable fragments generated by 14 primers were polymorphic among lines. Segregation ratios in Fz males did not differ from 1:1 and extrachromosomal transmission was not observed. However, 5 nonparental bands that would increase the apparent number of loci by 16.2% in outbreeding populations were detected in hybrid F 1 females. In addition, linkage analysis indicates that the 31 polymorphic bands represent 19 presence-absence loci and 6 biallelic, fragment length polymorphism (FLP) or FLP-like loci. Four linkage groups were detected. Our main conclusion is that RAPD polymerphisms cannot be used as genetic markers unless information identifying nonparental bands and FLP and FLP-like loci is obtained. This information can be obtained during the course of typical population surveys in haplodiploid species because of male haploidy. In diploid species though, crossing experiments or DNA hybridization tests to establish homology are necessary prior to working with unpedigreed populations.
AVIAN SEED DISPERSAL OF THREE NEOTROPICAL GAP-DEPENDENT PLANTS'

In cloud forest at Monteverde, Costa Rica, I investigated the reproductive consequences of avian seed dispersal for three species of gap-dependent plants: Phytolacca rivinoides (Phytolaccaceae), Witheringia solanacea, and W. coccoloboides (Solanaceae). Of six bird species that consumed fruits of these plants, only three (Myadestes melanops (Muscicapidae), Phainoptila melanoxantha (Ptilogonatidae), and Semnornisfrantzii (Cap- itonidae)), dispersed seeds in viable condition. Other species discarded most seeds before swallowing fruit pulp, or destroyed seeds in the gut. I estimated the quality of dispersal service provided by the "legitimate" disperser species by comparing the seed shadows they produced with the spatial and temporal distributions of establishment sites for the plants. I estimated seed shadows from data on gut passage rates of seeds and on movement patterns of radio-tracked birds. Seed shadows produced by all three effective dispersers were extensive, with few seeds deposited near the parent plant, and some seeds moved >500 m. Seeds of the species examined establish in forest gaps formed by treefalls or landslides. Establishment success varies with gap size and age, but the relationship is different for each species; both Witheringia species establish well in gaps as small as 15 m2 or as old as 6 mo, whereas P. rivinoides establishes well only in gaps > 70 m2 or < 4 mo old. Consequently, establishment sites for all three plants are both rare and ephemeral, but to differing degrees. Seeds that are not dispersed to suitable habitat patches can remain dormant in the soil until a gap is formed overhead; seed dormancy experiments showed no significant decrease in viability of seeds buried for up to 27 mo. To determine consequences of dispersal and dormancy for plant reproductive success, I developed a simulation model that uses data on seed shadows, germination requirements, seed dormancy, and forest dynamic processes to estimate reproductive output (total off- spring produced during an individual plant's lifetime) and relative "fitness" (an estimator that discounts the contribution of offspring produced after a long period of dormancy). Results show that (1) dispersal by any of the three legitimate dispersers increases repro- ductive output 16-36 times, even without seed dormancy. (2) Dormancy capabilities up to 2 yr enhance both reproductive output and "fitness," but greater capabilities increase only reproductive output. (3) Without dispersal, dormancy has little effect on either re- productive output or fitness. Thus, both dispersal and dormancy ("dispersal" in time) are essential to these gap-dependent plants, but long-term seed dormancy may be relatively unimportant.
Molecular data support Ramalina ovalis as a distinct lineage (Ramalinaceae, Ascomycota)

Abstract Ramalina celastri is a highly variable, widely distributed pan-subtropical lichen species. In Australasia the species had been separated into two subspecies; R. celastri subsp. celastri and R. celastri subsp. ovalis. This study compares morphological variation, substratum preference and sequences of the internal transcribed spacer (ITS) and intergenic spacer (IGS) regions of ribosomal DNA from a range of specimens from New Zealand and one from Australia. Bayesian and ML trees generated using the sequence data form two well-supported clades corresponding to the two previously recognized subspecies. Molecular, morphological and geographical differences support the recognition of R. ovalis at the species rank.
Phytoplankton size distribution and growth rates in the Alboran Sea (SW Mediterranean): short term variability related to mesoscale hydrodynamics

The short term variability of the size distribution and growth rates of the phytoplankton community was studied during several visits at three stations located across the anticyclonic gyre of the Western Alboran Sea in May 1998. Chlorophyll a (Chl a) concentration was fractionated in three size classes, picoplankton ( 20 μm). Biovolume and cell carbon estimations, based on cell cytometry and microscopy counts, image analysis and published conversion values, were carried out for seven groups of autotrophic organisms. Carbon:chlorophyll a (C:Chl a) ratios in combination with 14 C uptake experiments were used to calculate phytoplankton growth rates. Temporal differences among stations in the size structure and composition of the phytoplankton community were related to hydrographic phenomena. At the beginning of the survey, the proportion of the three chlorophyll size fractions ranged between 20 and 40% for all the stations; this situation changed dramatically after a nutrient upwelling event which occurred at the station closest to the coast, located at the northern edge of the anticyclonic gyre, and was associated with an increase in the biomass of the whole phytoplankton community (mainly due to diatoms) and with a shift in the microplankton proportion from 35 to 60% of the integrated Chl a. In contrast, the pico- and nanoplankton fractions increased their dominance in the oligotrophic waters of the centre of the gyre (between 75 and 95% of the integrated total Chl a, mainly accounted for by Synechococcus and small flagellates). At all the stations, picoplanktonic cells were generally more abundant in the upper layers of the photic zone while nano- and microplanktonic organisms tended to be more important with depth. Maximum phytoplankton growth rates ranged from 0.45 to 1.41 day -1 and did not present significant differences among stations, in spite of their different hydrographic and nutrient conditions. In particular, average duplication times of 0.9 day at the oligotrophic central station indicate that phytoplankton was actively growing there. Growth rates averaged for the photic layer were not associated with the phytoplankton composition and size distribution but were positively correlated with the available irradiance. These findings suggest a physiological acclimation of the phytoplankton community to the light conditions and may be relevant for the parameterization of primary production models. The C:Chl a ratio decreased with depth and increased from high to low nutrient stations and with the fraction size.
The evolution of density‐dependent dispersal in a noisy spatial population model

It is well-known that dispersal is advantageous in many different ecological situations, e.g. to survive local catastrophes where populations live in spatially and temporally heterogeneous habitats. However, the key question, what kind of dispersal strategy is optimal in a particular situation, has remained unanswered. We studied the evolution of density-dependent dispersal in a coupled map lattice model, where the population dynamics are perturbed by external environmental noise. We used a very flexible dispersal function to enable evolution to select from practically all possible types of monotonous density-dependent dispersal functions. We treated the parameters of the dispersal function as continuously changing phenotypic traits. The evolutionary stable dispersal strategies were investigated by numerical simulations. We pointed out that irrespective of the cost of dispersal and the strength of environmental noise, this strategy leads to a very weak dispersal below a threshold density, and dispersal rate increases in an accelerating manner above this threshold. Decreasing the cost of dispersal increases the skewness of the population density distribution, while increasing the environmental noise causes more pronounced bimodality in this distribution. In case of positive temporal autocorrelation of the environmental noise, there is no dispersal below the threshold, and only low dispersal below it, on the other hand with negative autocorrelation practically all individual disperses above the threshold. We found our results to be in good concordance with empirical observations.
Effects of fluvalinate on two‐spotted spider mite dispersal, fecundity and feeding

Residual deposits of fluvalinate caused two‐spotted spider mite, Tetranychus urticae Koch, dispersal by running off (run‐off) and spinning down (spin‐down) from treated leaves. Run‐off occured at concentrations from 0.0005 g a.i. 1−1 and reached a peak at 0.01 g a.i. 1−1. Spin‐down was more predominant at concentrations above 0.01 g a. i. 1−1. Spin‐down and run‐off proportions varied with fluvalinate formulation. Oviposition was temporarily suppressed on fluvalinate‐treated leaves, presumably because of an irritant effect which reduced feeding. An emulsifiable concentrate formulation caused the largest reductions in oviposition. Oviposition returned to the level exhibited by untreated mites two days after removal from treated surfaces. Oviposition and feeding were positively correlated and both declined reciprocally with increasing fluvalinate concentration.
A phylogenetic re-evaluation of morphological variations of starch grains among Poaceae species

Starch forms transparent grains, referred to as starch grains (SGs), in amyloplasts. Despite the simple glucose polymer composition of starch, SGs exhibit different morphologies depending on plant species, especially in the endosperm of the family Poaceae. In previous comprehensive work, SG morphologies of Poaceae endosperm were classified into four types: compound grains, bimodal simple grains, uniform simple grains and a mixed configuration comprised of compound and simple grains. Despite these observations, the phylogenetic relationships among the SG types remained unclear. In this report, we analyzed the previous observations with respect to current knowledge of the molecular phylogeny of Poaceae to determine how SG morphological types are clustered and scattered in the phylogenetic tree. We also obtained clear images of SGs of 26 species belonging to the four genera Hordeum, Elymus, Triticum and Bromus. Previously published work indicated that the SG morphologies of these genera were clustered in the phylogenetic tree and specific for the bimodal simple grain type. However, our work identified novel morphological types of SGs within Bromus in addition to the known bimodal simple grain type. A discussion of the molecular phylogenetic analysis and the remarkable intrageneric variation found in this study will contribute to a greater understanding of SG morphological diversity.
The Secondary Association of Chromosomes

1. A detailed account is given of the behaviour of the chromosomes from diplotene to second anaphase in Dahlia Merckii (2n=36), D. coccinea (2n=32), D. coronata (2n=32) and D. variabilis (2n=64). 2. Two kinds of chromosome association are found in these species:a) Primary Association, arising from particulate pairing at zygotene and determining segregation at metaphase.b) Secondary Association, arising at pro-metaphase and due to the general affinity of homologous chromosomes. This does not affect segregation. The chromosomes first associate at pro-metaphase when they are in close proximity to each other.3. As first described by DARLINGTON, the primary association of chromosomes at metaphase is shown to be solely due to the mainten-ance of chiasmata formed at pachytene. Only those chromosome pairs or multivalents which are materially connected by chiasmata survive the strong repulsion phase of diakinesis. This repulsion results in the radial dispersion of the bivalents to the periphery of the nucleus, coupled with an equal aversion between the pairs and the members of each pair. The repulsion is fully maintained until mid-diaknesis, and then gradually diminishes to pro-metaphase, when the close proximity and general affinity of homologous chromosome results in groups of secondarily associated chromosomes at metaphase. The frequency and size of the group is characteristic for a given species. The importance of the diakinetic Phase in differentiating primary and secondary association is emphasised.4. The theory of secondary association is discussed and evidence from the literature presented. It is claimed that secondary association is evidence of more remote affinities than can ever be expressed in primary association in a poly-ploid. This is proved by the occurrence of true (primary) association in triploid Pyrus between chromosomes which only show secondary association in the diploid form.5. The effects of fixation, the correlation between allopolyploidy and secondary association and finally the value of secondary association as a criterion of homology are discussed.
SOME BASIC ASPECTS OF THE ACTIVITY OF ELECTRIC PLATES

The most conspicuous manifestations of the activity of electric organs are: (a) the electrical discharge itself; (b) variations of the electrical conductivity of the tissue; (c) thermal effects; (d) chemical (metabolic) transformations. Every individual feature of the total discharge is more or less closely associated with the species of fish examined, with its shape and dimensions, and with the struct,ural arrangement of the physiological units (or electric plates) composing the organ. However, on the cellular dimension scale, the behavior of these plates shows a striking unity, and is generally considered as an ordinary bioelectric phenomenon. The classical conceptions of nerve physiology are applicable here, and these, combined with our rapidly progressing knowledge of neuromuscular transmission mechanisms, have been used for explaining the production of electricity in these organs. Here, briefly exposed for each essential manifestation of activity, are the most significant facts in favor of the unitary conception, together with some details concerning our experimental contribution to this problem.
Novel schizophrenia risk genesand gene expression

ZNF804A was (at the time this work started) one of only a few robustly implicated schizophrenia susceptibility genes, due to replicated genome-wide significant evidence for association between a polymorphism in the gene and schizophrenia. Determining the function of the ZNF804A protein, which is currently unknown, may provide a way of elucidating the pathophysiology of this relatively common, complex disorder. Based on the hypothesis that the ZNF804A protein regulates gene expression or splicing, the aim of this thesis was to identify genes that exhibit altered expression or splicing in brain tissue from mice in which the orthologue Zfp804a carries a nonsense mutation. No robust evidence was obtained that showed the effects of the mutation on differential expression in individual genes. Although this finding does not support the hypothesis that ZNF804A acts directly to regulate gene expression, the results may reflect the possibility that effects on gene expression may be too subtle to be detected using the methods applied. Evidence was obtained to show the mutation affected the alternative splicing of a number of individual genes, which could suggest a role for ZNF804A in the direct or indirect regulation of alternative splicing. Through RNA sequencing, I identified a novel transcript in Zfp804a with an alternative exon upstream of the Refseq exon 1. I also showed that a proportion of the significant splicing differences identified in mutants were artefacts of strain differences in gene sequences that are likely to affect the efficiency of hybridisation on the exon array. Genes identified as differentially spliced between mutants and wildtypes were enriched in axon guidance and cell adhesion pathways, both thought to be important during development. The findings of this thesis suggest the novel hypothesis that ZNF804A effects risk for schizophrenia via aberrant splicing in the above pathways that are critical to normal brain development. Further studies with increased power are required to understand the effects on gene expression.
MANDUCA QUINQUEMACULATA'S OPTIMIZATION OF INTRA-PLANT OVIPOSITION TO PREDATION, FOOD QUALITY, AND THERMAL CONSTRAINTS

To examine the hypothesis that intra-plant oviposition preferences of Man- duca quinquemaculata on Nicotiana attenuate optimize predation risk and nutritional needs of developing larvae and eggs, we measured oviposition behavior of adults and larval mortality, movement, performance, and body temperatures at different leaf positions in a natural population. Nearly 70% of the eggs were oviposited on young central stem leaves of elongated plants. Intra-plant movement was very rare in the first and common in the second to fourth larval instars. The oviposition preference for, and larval movement toward, younger leaves was correlated with a 40% lower predation risk and a 6.3-fold greater mass gain, suggesting higher nutritive value despite 2. 1-fold higher nicotine concentrations and 4.6-fold higher polyphenol oxidase activities. The predatory bug, Geocoris pallens, which consumed eggs and larvae with instar- and leaf position-specific preferences, was respon- sible for the vast majority of M. quinquemaculata mortality and may shape the moth's oviposition preference.
AN IMPROVED LABORATORY METHOD FOR REARING LARGE NUMBERS OF SPRUCE BUDWORM, CHORISTONEURA FUMIFERANA (LEPIDOPTERA: TORTRICIDAE)

Abstract Larvae are reared on a synthetic diet in 1 oz. ribbed plastic cups. To eliminate the task of placing individual larvae on food, small gauze patches containing 25–40 larvae are placed in the cups prior to emergence from hibernacula. Larvae establish feeding sites between the ribs and are relatively undisturbed by others in the cup until the fifth instar. For maintenance of rearing stock the number of larvae is reduced to six to eight per cup, and they are allowed to pupate in the cups. Up to 100 pairs of pupae are placed in screened cages for adult emergence, mating, and oviposition. When the adults emerge balsam fir foliage is introduced and most of the eggs are deposited on the needles. Needles or twigs with egg clusters are transferred to large dishes the inside of which is painted black. The dish is tightly sealed with parafilm to which small gauze patches are attached and then placed under artificial lighting. The newly-hatched larvae are attracted toward the light and spin hibernacula in the gauze. The parafilm and gauze are sealed in plastic bags for cold storage treatment. By this system up to 10,000 larvae per week are easily produced.A discussion on the selection of rearing stock, rearing conditions, rearing containers, and the use of anti-fungal agents is included in the report.