Stromule formation is dependent upon plastid size, plastid differentiation status and the density of plastids within the cell

Stromules are motile extensions of the plastid envelope membrane, whose roles are not fully understood. They are present on all plastid types but are more common and extensive on non-green plastids that are sparsely distributed within the cell. During tomato fruit ripening, chloroplasts in the mesocarp tissue differentiate into chromoplasts and undergo major shifts in morphology. In order to understand what factors regulate stromule formation, we analysed stromule biogenesis in tobacco hypocotyls and in two distinct plastid populations in tomato mesocarp. We show that increases in stromule length and frequency are correlated with chromoplast differentiation, but only in one plastid population where the plastids are larger and less numerous. We used tobacco hypocotyls to confirm that stromule length increases as plastids become further apart, suggesting that stromules optimise the plastid-cytoplasm contact area. Furthermore, we demonstrate that ectopic chloroplast components decrease stromule formation on tomato fruit chromoplasts, whereas preventing chloroplast development leads to increased numbers of stromules. Inhibition of fruit ripening has a dramatic impact on plastid and stromule morphology, underlining that plastid differentiation status, and not cell type, is a significant factor in determining the extent of plastid stromules. By modifying the plastid surface area, we propose that stromules enhance the specific metabolic activities of plastids. This is an electronic version of an Article published in The Plant Journal, August 2004, Volume 39, pp. 655-667. Copyright 2004 Blackwell Publishing Ltd and The Society for Experimental Biology.

Nonparametric Evaluation of Quantitative Traits in Population-Based Association Studies when the Genetic Model is Unknown

Statistical association between a single nucleotide polymorphism (SNP) genotype and a quantitative trait in genome-wide association studies is usually assessed using a linear regression model, or, in the case of non-normally distributed trait values, using the Kruskal-Wallis test. While linear regression models assume an additive mode of inheritance via equi-distant genotype scores, Kruskal-Wallis test merely tests global differences in trait values associated with the three genotype groups. Both approaches thus exhibit suboptimal power when the underlying inheritance mode is dominant or recessive. Furthermore, these tests do not perform well in the common situations when only a few trait values are available in a rare genotype category (disbalance), or when the values associated with the three genotype categories exhibit unequal variance (variance heterogeneity). We propose a maximum test based on Marcus-type multiple contrast test for relative effect sizes. This test allows model-specific testing of either dominant, additive or recessive mode of inheritance, and it is robust against variance heterogeneity. We show how to obtain mode-specific simultaneous confidence intervals for the relative effect sizes to aid in interpreting the biological relevance of the results. Further, we discuss the use of a related all-pairwise comparisons contrast test with range preserving confidence intervals as an alternative to Kruskal-Wallis heterogeneity test. We applied the proposed maximum test to the Bogalusa Heart Study dataset, and gained a remarkable increase in the power to detect association, particularly for rare genotypes. Our simulation study also demonstrated that the proposed non-parametric tests control family-wise error rate in the presence of non-normality and variance heterogeneity contrary to the standard parametric approaches. We provide a publicly available R library nparcomp that can be used to estimate simultaneous confidence intervals or compatible multiplicity-adjusted p-values associated with the proposed maximum test.

Aspects of migration, size structure and mortality of juvenile Nile perch in the Mwanza Gulf of Lake Victoria

A detailed study of the early life of fishes forms one of the very important aspects with respect to recruitment mechanism and proper uneterstanding of the dynamics leading to sustainance of fish populations. It should be the central theme of the fisheries biologist and managers to extract the bilogical information relevant to the proper understanding of this part of the population. A number of studies in the Mwanza gulf and Lake Victoria have emphasized the need to monitor the fishery by conducting observations of stock size, migration, catch effort data and growth of big specimen (Acere 1981, Goudsward et al 1984, Asila. Ogari 1988 and Okemwa 1984). The present paper discusses the preliminary information on the size structure, mortality and migration of juvenile Nile perch. The long term objectives of the programme is aimed at describing the size structure, growth, mortality, recruitment pattern and population dynamics of the Nile perch up to 30 cm total length in the, Mwanza Gulf.

Early post-fledgling survival in a fragmented population of a tropical cooperative breeding passerine

During the last years tropical forest has been a target of intense study especially due to its recent big scale destruction. Although a lot still needs to be explored, we start realizing how negative can the impact of our actions be for the ecosystem. Subsequently, the living community have been developing strategies to overcome this problem avoiding bottlenecks or even extinctions. Cooperative breeding (CB) has been recently pointed out as one of those strategies. CB is a breeding system where more than two individuals raise one brood. In most of the cases, extra individuals are offspring that delay their dispersal and independent breeding what allows them to help their parents raising their siblings in the subsequent breeding season. Such behavior is believed to be due, per example, to the lack of mates or breeding territories (ecological constraints hypothesis), a consequence of habitat fragmentation and/or disturbance. From this point, CB is easily promoted by a higher reproductive success of group vs pairs or single individuals. Accordingly, during this thesis I explore the early post-fledging survival of a cooperative breeding passerine, namely the impact of individual/habitat quality in its survival probability during the dependence period of the chicks. Our study species is the Cabanis’s greenbul (Phyllastrephus cabanisi), a medium-sized, brownish passerine, classified within the Pycnonotidae family. It is found over part of Central Africa in countries such as Angola, Democratic Republic of the Congo, Mozambique and Kenya, inhabiting primary and secondary forests, as well as woodland of various types up to 2700m of altitude. Previous studies have concluded that PC is a facultative cooperative breeder. This study was conducted in Taita Hills (TH) at the Eastern Arc Mountains (EAM), a chain of mountains running from Southeast Kenya to the South of Tanzania. TH comprises an area of 430 ha and has been suffering intense deforestation reflecting 98% forest reduction over the last 200 years. Nowadays its forest is divided in fragments and our study was based in 5of those fragments. We access the post-fledging survival through radio-telemetry. The juvenile survey was done through the breeding females in which transmitters were placed with a leg-loop technique. Ptilochronology is consider to be the study of feather growth bars and has been used to study the nutritional state of a bird. This technique considers that the feather growth rate is positively proportional to the individual capability of ingesting food and to the food availability. This technique is therefore used to infer for individual/habitat quality. Survival was lowest during the first 5 days post-fledging representing 53.3%. During the next 15 days, risk of predation decreased with only 14.3% more deceased individuals. This represents a total of only 33% survived individuals in the end of the 50 days. Our results showed yet a significant positive relationship between flock size and post-fledging survival as well as between ptilochronology values and post-fledgling survival. In practice, these imply that on this population, as bigger the flock, as greater the post fledging survival and that good habitat quality or good BF quality, will lead to a higher juvenile survival rate. We believe that CB is therefore an adaptive behaviour to the lack of mates/breeding territory originated from the mass forest destruction and disturbance. Such results confirms the critical importance of habitat quality in the post-fledging survival and, for the first time, demonstrates how flock size influences the living probability of the juveniles and therefore how it impacts the (local) population dynamics of this species. In my opinion, future research should be focus in disentangle individual and habitat quality from each other and verify which relationship exist between them. Such study will allow us to understand which factor has a stronger influence in the post-fledging survival and therefore redirect our studies in that direction. In order to confirm the negative impact of human disturbance and forest fragmentation, it would be of major relevance to compare the reproductive strategies and reproductive success of populations living in intact forests and disturbed patches.

When is bigger better? The effects of group size on the evolution of helping behaviours.

Understanding the evolution of sociality in humans and other species requires understanding how selection on social behaviour varies with group size. However, the effects of group size are frequently obscured in the theoretical literature, which often makes assumptions that are at odds with empirical findings. In particular, mechanisms are suggested as supporting large-scale cooperation when they would in fact rapidly become ineffective with increasing group size. Here we review the literature on the evolution of helping behaviours (cooperation and altruism), and frame it using a simple synthetic model that allows us to delineate how the three main components of the selection pressure on helping must vary with increasing group size. The first component is the marginal benefit of helping to group members, which determines both direct fitness benefits to the actor and indirect fitness benefits to recipients. While this is often assumed to be independent of group size, marginal benefits are in practice likely to be maximal at intermediate group sizes for many types of collective action problems, and will eventually become very small in large groups due to the law of decreasing returns. The second component is the response of social partners on the past play of an actor, which underlies conditional behaviour under repeated social interactions. We argue that under realistic conditions on the transmission of information in a population, this response on past play decreases rapidly with increasing group size so that reciprocity alone (whether direct, indirect, or generalised) cannot sustain cooperation in very large groups. The final component is the relatedness between actor and recipient, which, according to the rules of inheritance, again decreases rapidly with increasing group size. These results explain why helping behaviours in very large social groups are limited to cases where the number of reproducing individuals is small, as in social insects, or where there are social institutions that can promote (possibly through sanctioning) large-scale cooperation, as in human societies. Finally, we discuss how individually devised institutions can foster the transition from small-scale to large-scale cooperative groups in human evolution.

The impact of household size on poverty: An analysis of various low-income townships in the Northern Free State region, South Africa

Poverty is a multi-dimensional socio-economic problem in most sub-Saharan African countries. The purpose of this study is to analyse the relationship between household size and poverty in low-income communities. The Northern Free State region in South Africa was selected as the study region. A sample of approximately 2 900 households was randomly selected within 12 poor communities in the region. A poverty line was calculated and 74% of all households were found to live below the poverty line. The Pearson’s chi-square test indicated a positive relationship between household size and poverty in eleven of the twelve low-income communities. Households below the poverty line presented larger households than those households above the poverty line. This finding is in contradiction with some findings in other African countries due to the fact that South Africa has higher levels of modernisation with less access to land for subsistence farming. Effective provision of basic needs, community facilities and access to assets such as land could assist poor households with better quality of life. Poor households also need to be granted access to economic opportunities, while also receiving adult education regarding financial management and reproductive health.

Population structure and growth of the hermit crab Pagurus brevidacylus (Anomura : Paguridae) from the northern coast of São Paulo, Brazil

The hermit crab Paguras brevidactylus (Crustacea: Anomura: Paguridea) from the infralittoral area of Anchieta Island, Ubatuba, was characterized by population Structure (size, sex ratio, reproduction and recruitment) and growth. Animals were collected monthly during 1999 by SCUBA diving. A total of 1525 individuals was collected (633 males and 892 females), 695 of them were ovigerous females. Overall sex ratio was 0.7:1 in favour of females. The crabs showed a unimodal distribution with males significantly larger than females. Ovigerous females were collected during all months and in high percentages from 1.0 mm of shield length, demonstrating intense and Continuous reproduction. The longevity was approximately 24 months for males and 18 for females, which showed larger growth rate and reached sexual maturity earlier (two months) than males. The low number of males in this Population may be due to the longer life span. Moreover, the sexual dimorphism favours males during the intra- and interspecific fights by shell, food, reproduction and territory. Females demonstrated a short life cycle and intense reproduction.

Population structure and sexual maturity of the calico box crab Hepatus epheliticus Linnaeus (Brachyura, Hepatidae) from Yucatan Peninsula, Mexico

The calico box crab Hepatus epheliticus is an abundant species from shallow and continental shelf waters of the Atlantic coast of USA and Mexico. Information about population structure and sexual maturity is absent, even though this crab is caught to be used as bait for the octopus fishery in the Campeche Bank, Mexico. In order to achieve such information, a total of 768 individuals were collected from January to March 2010 through baited traps installed in the Yucatan Peninsula, Mexico. Our results showed that sex ratio is biased towards more males than females (1:0.55), contradicting to that reported in other brachyuran crabs. The absence of ovigerous females suggests that they did not enter into the traps during embryogenesis. Males reached a larger maximum size than females (64.0 +/- 6.15 and 58.4 +/- 5.60 mm carapace width, respectively). The general scheme of growth being positive allometric throughout ontogeny of both sexes. Males presented a transition phase from juveniles to adult corresponding to the puberty moult. The estimation of the onset of functional sexual maturity revealed a steady situation for the population, with 21.5 and 13.8% of males and females, respectively, morphologically immature at the time of catch. This study constitutes the first report on population structure and sexual maturity in a population of the calico box crab H. epheliticus.

Population structure of pond-raised Macrobrachium amazonicum with different stocking and harvesting strategies

The effect of size-grading of juveniles prior to stocking, as well as selective harvesting, on the population structure of pond-raised Macrobrachium amazonicum was studied. A randomized-complete-blocks design with 4 treatments and 3 replicates was used. The treatments were: upper size-graded juveniles, lower size-graded juveniles, ungraded juveniles (traditional), and ungraded juveniles with selective harvesting. Twelve 0.01 ha earthen ponds were stocked at 40 juveniles m(-2), according to the relevant treatment. Every three weeks, random samples from each pond were obtained for biometry, and after 3.5 months, the ponds were drained and completely harvested. Animals were then counted, weighed, and sexed; males were sorted as Translucent Claw (TC), Cinnamon Claw (CC), Green Claw 1 (GC1), and Green Claw 2 (GC2), and females as Virgin (VF), Berried (BE), and Open (OF). The prawns developed rapidly in the ponds. attaining maturity and differentiating into male morphotypes after about 2 months in all treatments. The fast-growing juveniles (upper grading fraction) mostly did not constitute the dominant males (CC] and GC2) in the adult population. Population development was slower in ponds stocked with Lower prawns, whereas selective harvesting increased the frequency of GC1 and reduced the final mean weight of GC2 males. The proportion of males increased throughout the culture period, but was generally not affected by the stocking or harvesting strategies. Grading juveniles and selective harvesting slightly altered the population dynamics and structure, although the general population development showed similar patterns in ponds stocked with upper, lower, and ungraded juveniles, or selectively harvested. (C) 2010 Elsevier B.V. All rights reserved.

Population estimates and behavioral analyses of managed cat (Felis Catus) colonies located in Miami-Dade County, Florida, parks

The purpose of my study was to collect data on managed cat (Felis catus) colonies located in two Miami-Dade County, Florida, parks, in order to test the following assertions put forward by proponents of the colonies: 1) Managed cat colonies will decline in size over time and 2) The territorial behavior of cats living in established cat colonies will prevent additional cats from joining. I collected observational and photographic capture-recapture data in order to track colony population dynamics. Behavioral data were also collected in order to understand the role that cat behavior plays in influencing colony population dynamics. My results do not support the assertion that colonies will decline over time. Instead, my findings demonstrate that the establishment of colonies on public lands encourages dumping of cats and creates an attractive nuisance. Furthermore, my behavioral analysis suggests that territorial behavior does not play a role in excluding new cats.

Sex-biased differences in the effects of host individual, host population and environmental traits driving tick parasitism in red deer

The interactions between host individual, host population, and environmental factors modulate parasite abundance in a given host population. Since adult exophilic ticks are highly aggregated in red deer (Cervus elaphus) and this ungulate exhibits significant sexual size dimorphism, life history traits and segregation, we hypothesized that tick parasitism on males and hinds would be differentially influenced by each of these factors. To test the hypothesis, ticks from 306 red deer-182 males and 124 females-were collected during 7 years in a red deer population in south-central Spain. By using generalized linear models, with a negative binomial error distribution and a logarithmic link function, we modeled tick abundance on deer with 20 potential predictors. Three models were developed: one for red deer males, another for hinds, and one combining data for males and females and including "sex" as factor. Our rationale was that if tick burdens on males and hinds relate to the explanatory factors in a differential way, it is not possible to precisely and accurately predict the tick burden on one sex using the model fitted on the other sex, or with the model that combines data from both sexes. Our results showed that deer males were the primary target for ticks, the weight of each factor differed between sexes, and each sex specific model was not able to accurately predict burdens on the animals of the other sex. That is, results support for sex-biased differences. The higher weight of host individual and population factors in the model for males show that intrinsic deer factors more strongly explain tick burden than environmental host-seeking tick abundance. In contrast, environmental variables predominated in the models explaining tick burdens in hinds.

Population parameters of the smooth lantern shark, Etmopterus pusillus, in southern Portugal (NE Atlantic)

Etmopterus pusillus is a deep water lantern shark with a widespread global distribution that is caught in large quantities in some areas, but is usually discarded due to the low commercial value. In this work, the population biology was studied and life history parameters determined for the first time in this species. Age was estimated from sections of the second dorsal spine and validated by marginal increment analysis. Males attained a maximum age of 13 years, while 17-year-old females were found. Several growth models were fitted and compared for both size and weight at age data, showing that even though this is a small sized species, it has a relatively slow growth rate. This species matures late and at a relatively large size: at 86.81% and 79.40% of the maximum observed sizes and at 58.02% and 54.40% of the maximum observed ages for males and females, respectively. It has a low fecundity, with a mean ovarian fecundity of 10.44 oocytes per reproductive cycle. The estimated parameters indicate that this species has a vulnerable life cycle, typical of deep water squalid sharks. Given the high fishing pressures that it is suffering in the NE Atlantic, the smooth lantern shark may be in danger of severe declines in the near future. (c) 2007 Elsevier B.V. All rights reserved.

Juniperus navicularis - a study of Portuguese population structure and fitness

Juniperus navicularis Gand. is a dioecious endemic conifer that constitutes the understory of seaside pine forests in Portugal, areas currently threatened by increasing urban expansion. The aim of this study is to assess the conservation status of previously known populations of this species located on its core area of distribution. The study was performed in south-west coast of Portugal. Three populations varying in size and pine density were analyzed. Number of individuals, population density, spatial distribution and individual characteristics of junipers were estimated. Female cone, seed characteristics and seed viability were also evaluated. Results suggest that J. navicularis populations are vulnerable because seminal recruitment is scarce, what may lead to a reduction of genetic variability due solely to vegetative propagation. This vulnerability seems to be strongly determined by climatic constraints toward increasing aridity. Ratio between male and female shrubs did not differ from 1:1 in any population. Deviations from 1:1 between mature and non-mature plants were found in all populations, denoting population ageing. Very low seed viability was observed. A major part of described Juniperus navicularis populations have disappeared through direct habitat loss to urban development, loss of fitness in drier and warmer locations and low seed viability. This study is the first to address J. navicularis conservation, and represents a valuable first step toward this species preservation.

Using sclerochronology to estimate the growth rate in Pinna nobilis: a case study of Les Alfaques Bay population (Ebro Delta, Spain).

Pinna nobilis is the biggest Mediterranean bivalve, endemic and semi-infaunal. Provide hard substrates to colonize, increasing the spatial heterogeneity of the softbottom communities. P. nobilis suffer a drastic decline due to the anthropogenic pressures. It’s included in the Habitats Directive, in the Barcelona Convention, and in the red lists of many Mediterranean countries. Estimates the growth rate allows to understand the population dynamics of species and yield knowledge to improve protection efforts. In this study a new methodology based on sclerochronology was used to estimate the age and the growth rate of a P. nobilis population located in Les Alfaques bay. The shells of 35 specimens were cataloged. A subsample of 20 individuals was selected, and one valve of each specimens was cut into radial sections along PAMS (Posterior Adductor Muscle Scar) to study the inner register. Thus, the positions of PAMS obscured by nacre were identified, and the number of missing records was estimated by the width of the calcitic layer in the anterior part of the shell. The first growth curve for the Les Alfaques bay population was calculated from the length/age data. To simulate the growth rate of this population, the growth model based on the modified Von Bertalanffy equation was used. Shallow water usually hosts small sized populations of P. nobilis, while in deeper waters specimens reaches larger size. In Les Alfaques bay the population is composed by large size individuals though it’s located in shallows waters. This unusual size pattern is probably due to a sand bar that offers protection from hydrodynamic stress, allowing individuals to elongate more. This study contributes to the knowledge on P. nobilis biology and, with the aim to monitor this species, the growth curve could be used as baseline for future studies on habitat characteristics that may affect the population structure and dynamics in Les Alfaques Bay.

Applied genomics in livestock: genome-wide association studies and population genomics analysis in pig and rabbit breeds

The domestication and selection processes in pigs and rabbits have resulted in the constitution of multiple breeds with broad phenotypic diversity. Population genomics analysis and Genome-wide association study analysis can be utilized to gain insights into the ancestral origins, genetic diversity, and the presence of lethal mutations across these diverse breeds. In this thesis, we analysed the dataset obtained from three Italian Pig breeds to detect deleterious alleles. We screened the dataset for genetic markers showing homozygous deficiency using two approaches single marker and haplotype-based approach. Moreover, Genome-wide association study analyses were performed to detect genetic markers associated with pigs' reproductive traits. In rabbits, we investigated the application of SNP bead chip for detection signatures of selection in rabbits using different methods. This analysis was implemented for the first time in different fancy and meet rabbit breeds. Multiple approaches were utilized for the detection of the selection of signatures including Fst analysis, ROH analysis, PCAdapt analysis, and haplotype-based analysis. The analysis in pigs was able to identify five putative deleterious SNPs and nine putative deleterious haplotypes in the analysed Italian Pig breeds. The genomic regions of the detected putative deleterious genomic markers harboring loss of function variants such as the Frameshift variant, start lost, and splice donor variant. Those variants are close to important candidate genes such as IGF2BP1, ADGRL4, and HGF. In rabbits, multiple genomic regions were detected to be under selection of signature. These genomic regions harbor candidate genes associated with coat color phenotype (MC1R, TYR, and ASIP), hair structure (LIPH), and body size (HMGA2 and COL2A1). The described results in rabbits and pigs could be used to improve breeding programs by excluding the deleterious genetic markers carriers and incorporating candidate genes for coat color, body size, and meat production in rabbit breeding programs to enhance desired traits