Tropical tree species diversity: a test of the Janzen-Connell model

To test the premises and predictions of the Janzen-Connell model (Janzen's spacing mechanism), seeds of the rainforest canopy tree, Brosimum alicastrum, were placed at different distances from the parent tree and their removal observed over 3 weeks. The number and density of naturally occurring seeds at different distances from the parent tree were also estimated. Predation was not greater near the parent tree, except on the very small spatial scale: the proportion of experimental seeds removed was greater 1 m from the trunk than it was 5–25 m from the trunk. Predation was negatively correlated with seed density, not positively as the Janzen-Connell model assumes-presumably due to predator satiation. The density of seeds after predation peaked 5 m from the tree trunk, but this is well within the crown radius of the parent tree. There is a peak in the number of potential recruits at a distance of 10 m from the parent tree, due to the peaked initial distribution of seeds. This peak is caused by the interaction between the seed density curve and the increasing area of an annulus around the parent tree at increasing distances, not by the product of the density curve and the predation curve. However, it is important to realize that it is not the presence of a peak in recruitment away from the parent that is essential to maintaining tropical tree species diversity, but frequency-dependent recruitment induced by poor recruitment near conspecifics. Predator satiation seems to be an important factor in the survival of B. alicastrum seeds, possibly at several spatial scales. The number of seeds produced by the tree is negatively correlated with the loss to predators, and trees that have a fruiting conspecific nearby also suffer lower levels of predation. Seed predation increases as one moves from the forest edge into the interior, creating an edge effect that may have long-term effects on the forest composition and tree species diversity. More studies are needed, for other species, other localities, and larger spatial and temporal scales, on both the Janzen-Connell mechanism and this edge effect.     

Heterozygote excess in a self-incompatible and partially clonal forest tree species -- Prunus avium L

Wild cherry (Prunus avium L.), a partially asexual self-incompatible forest tree, shows heterozygote excess, which is a poorly studied phenomenon. In three natural populations, we found significant heterozygote excess at almost all investigated loci (eight microsatellites and markers for the self-incompatibility locus). We examined four hypotheses to account for this observed heterozygote excess. First, negative F(IS) can result from a lack of selfed progeny in small populations of outcrossing species. A second explanation for negative F(IS) is selection during the life cycle of the most heterozygous individuals. A third explanation is negative assortative mating when reproduction occurs between individuals bearing phenotypes more dissimilar than by chance. The last explanation for negative F(IS) relies on asexual reproduction. Expectations for each hypothesis were tested using empirical data. Patterns of F(IS) differed among loci. Nevertheless, our experimental results did not confirm the small sample size hypothesis. Although one locus is probably under a hitch-hiking effect from the SI locus, we rejected the effect of the self-incompatibility locus for the genome as a whole. Similarly, although one locus showed a clear pattern consistent with the selection of heterozygous individuals, the heterosis effect over the whole genome was rejected. Finally, our results revealed that clonality probably explains significant negative F(IS) in wild cherry populations when considering all individuals. More theoretical effort is needed to develop expectations and hypotheses, and test them in the case of species combining self-incompatibility and partially asexual reproduction.     

Sexual incompatibility in Rosaceae fruit tree species: molecular interactions and evolutionary dynamics

Fruit crops have a growing economic importance worldwide and molecular genetics might be useful in solving many problems that arise during commercial production. One of the fields that have attracted intense attention is the molecular basis of self-incompatibility that may result in low fruit set. In tree fruits of the Rosaceae family, the incompatibility reactions take place between the pistil S-ribonuclease (S-RNase) and the pollen-expressed S-haplotype specific F-box (SFB) proteins. In most cases, the loss of self-incompatibility was associated with mutations in the S-RNase or SFB genes. A total of 27 non-functional S-haplotypes have been identified and characterized, most (24) of which emerged as a consequence of natural mutations. In the Prunoideae, most haplotypes are pollen-part mutants (50 %), while 8 are stylar-part mutants (36 %), one haplotype shows both pollen- and stylar-part mutations, and molecular changes for two haplotypes still have not been clarified. In contrast, non-functional natural haplotypes in the Maloideae are all stylar-part mutants. The analysis of such mutants may shed light on underlying molecular mechanisms as was the case with the establishment of the general inhibitor model that describes interactions between pollen and pistil S-proteins. However, several other molecules were supposed to contribute to the molecular interactions, at least in Solanaceae, a family with a similar self-incompatibility system. This review also endeavours to delineate the evolutionary implications of the S-locus mutations and collect limited data on non-S-locus molecular interactions and signaling events after self- and cross-pollination of fruit tree species.     

Development of microsatellite markers in Annona crassiflora Mart., a Brazilian Cerrado fruit tree species

Annona crassiflora Mart. (Annonaceae) is a native fruit species of the region of Brazilian Cerrado with a high agronomic potential, although without any traces of domestication. A set of 10 microsatellite primer pairs was developed from an enriched genome library (TC13). An average of 19.3 alleles per locus was detected. Observed heterozygosity estimates were consistently lower than those obtained for gene diversity, evidencing a departure from Hardy-Weinberg expected proportions. The reported set of markers showed to be highly informative and constitutes a powerful tool for the development of genetic characterization studies in A. crassiflora.     

Maximum tree: a consistent estimator of the species tree

We propose a model based approach to use multiple gene trees to estimate the species tree. The coalescent process requires that gene divergences occur earlier than species divergences when there is any polymorphism in the ancestral species. Under this scenario, speciation times are restricted to be smaller than the corresponding gene split times. The maximum tree (MT) is the tree with the largest possible speciation times in the space of species trees restricted by available gene trees. If all populations have the same population size, the MT is the maximum likelihood estimate of the species tree. It can be shown the MT is a consistent estimator of the species tree even when the MT is built upon the estimates of the true gene trees if the gene tree estimates are statistically consistent. The MT converges in probability to the true species tree at an exponential rate.     

The probability distribution of ranked gene trees on a species tree

The properties of random gene tree topologies have recently been studied under a coalescent model that treats a species tree as a fixed parameter. Here we develop the analogous theory for random ranked gene tree topologies, in which both the topology and the sequence of coalescences for a random gene tree are considered. We derive the probability distribution of ranked gene tree topologies conditional on a fixed species tree. We then show that similar to the unranked case, ranked gene trees that do not match either the ranking or the topology of the species tree can have greater probability than the matching ranked gene tree.     

Towards patterns tree of gene coexpression in eukaryotic species

MOTIVATION: Cellular pathways behave coordinated regulation activity, and some reported works also have affirmed that genes in the same pathway have similar expression pattern. However, the complexity of biological systems regulation actually causes expression relationships between genes to display multiple patterns, such as linear, non-linear, local, global, linear with time-delayed, non-linear with time-delayed, monotonic and non-monotonic, which should be the explicit representation of cellular inner regulation mechanism in mRNA level. To investigate the relationship between different patterns, our work aims to systematically reveal gene-expression relationship patterns in cellular pathways and to check for the existence of dominating gene-expression pattern. By a large scale analysis of genes expression in three eukaryotic species, Saccharomyces cerevisiae, Caenorhabditis elegans and Human, we constructed gene coexpression patterns tree to systematically and hierarchically illustrate the different patterns and their interrelations. RESULTS: The results show that the linear is the dominating expression pattern in the same pathway. The time-shifted pattern is another important relationship pattern. Many genes from the different pathway also present coexpression patterns. The non-linear, non-monotonic and time-delayed relationship patterns reflect the remote interactions between the genes in cellular processes. Gene coexpression phenomena in the same pathways are diverse in different species. Genes in S.cerevisiae and C.elegans present strong coexpression relationships, especially in C.elegans, coexpression is more universal and stronger due to its special array of genes. However in Human, gene coexpression is not apparent and the human genome involves more complicated functional relationships. In conclusion, different patterns corresponding to different coordinating behaviors coexist. The patterns trees of different species give us comprehensive insight and understanding of genes expression activity in the cellular society.     

AUGIST: inferring species trees while accommodating gene tree uncertainty

SUMMARY: AUGIST (accomodating uncertainty in genealogies while inferring species tress) is a new software package for inferring species trees while accommodating uncertainty in gene genealogies. It is written for the Mesquite software system and provides sampling procedures to incorporate uncertainty in gene tree reconstruction while providing confidence estimates for inferred species trees. AVAILABILITY: http://www.lycaenid.org/augist/     

Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree

Phylogenetic trees from multiple genes can be obtained in two fundamentally different ways. In one, gene sequences are concatenated into a super-gene alignment, which is then analyzed to generate the species tree. In the other, phylogenies are inferred separately from each gene, and a consensus of these gene phylogenies is used to represent the species tree. Here, we have compared these two approaches by means of computer simulation, using 448 parameter sets, including evolutionary rate, sequence length, base composition, and transition/transversion rate bias. In these simulations, we emphasized a worst-case scenario analysis in which 100 replicate datasets for each evolutionary parameter set (gene) were generated, and the replicate dataset that produced a tree topology showing the largest number of phylogenetic errors was selected to represent that parameter set. Both randomly selected and worst-case replicates were utilized to compare the consensus and concatenation approaches primarily using the neighbor-joining (NJ) method. We find that the concatenation approach yields more accurate trees, even when the sequences concatenated have evolved with very different substitution patterns and no attempts are made to accommodate these differences while inferring phylogenies. These results appear to hold true for parsimony and likelihood methods as well. The concatenation approach shows >95% accuracy with only 10 genes. However, this gain in accuracy is sometimes accompanied by reinforcement of certain systematic biases, resulting in spuriously high bootstrap support for incorrect partitions, whether we employ site, gene, or a combined bootstrap resampling approach. Therefore, it will be prudent to report the number of individual genes supporting an inferred clade in the concatenated sequence tree, in addition to the bootstrap support.     

A polynomial time algorithm for calculating the probability of a ranked gene tree given a species tree

ABSTRACT: BACKGROUND: The ancestries of genes form gene trees which do not necessarily have the same topology as the species tree due to incomplete lineage sorting. Available algorithms determining the probability of a gene tree given a species tree require exponential computational runtime. RESULTS: In this paper, we provide a polynomial time algorithm to calculate the probability of a ranked gene tree topology for a given species tree, where a ranked tree topology is a tree topology with the internal vertices being ordered. The probability of a gene tree topology can thus be calculated in polynomial time if the number of orderings of the internal vertices is a polynomial number. However, the complexity of calculating the probability of a gene tree topology with an exponential number of rankings for a given species tree remains unknown. CONCLUSIONS: Polynomial algorithms for calculating ranked gene tree probabilities may become useful in developing methodology to infer species trees based on a collection of gene trees, leading to a more accurate reconstruction of ancestral species relationships.     

Dihydrofolate reductase gene as a versatile expression marker.

The Escherichia coli dihydrofolate reductase (DHFR) gene has been used as a genetic marker specifying trimethoprim resistance (TmpR). In order to use the DHFR gene as a versatile expression marker, we have constructed three types of plasmids: promoter cloning vector, terminator cloning vector, and the plasmid containing the DHFR gene cassette. In these systems, the selection of recombinant plasmids was carried out just by examining the TmpR phenotype of the transformed cells. Then, levels of the enzymatic activity of DHFR were measured to evaluate the efficiency of promoters and terminators in the fused DNA fragment. An expression plasmid which resulted in the E. coli host cells being able to produce DHFR up to 20% of total cellular proteins was also constructed by changing the promoter and Shine-Dalgarno sequences of the DHFR gene.     

Nitrogen stress response of a hybrid species: a gene expression study

Background and Aims

Low soil fertility limits growth and productivity in many natural and agricultural systems, where the ability to sense and respond to nutrient limitation is important for success. Helianthus anomalus is an annual sunflower of hybrid origin that is adapted to desert sand-dune substrates with lower fertility than its parental species, H. annuus and H. petiolaris. Previous studies have shown that H. anomalus has traits generally associated with adaptation to low-fertility habitats, including a lower inherent relative growth rate and longer leaf lifetime.

Methods

Here, a cDNA microarray is used to identify gene expression differences that potentially contribute to increased tolerance of low fertility of the hybrid species by comparing the nitrogen stress response of all three species with high- and low-nutrient treatments.

Key Results

Relative to the set of genes on the microarray, the genes showing differential expression in the hybrid species compared with its parents are enriched in stress-response genes, developmental genes, and genes involved in responses to biotic or abiotic stimuli. After a correction for multiple comparisons, five unique genes show a significantly different response to nitrogen limitation in H. anomalus compared with H. petiolaris and H. annuus. The Arabidopsis thaliana homologue of one of the five genes, catalase 1, has been shown to affect the timing of leaf senescence, and thus leaf lifespan.

Conclusions

The five genes identified in this analysis will be examined further as candidate genes for the adaptive stress response in H. anomalus. Genes that improve growth and productivity under nutrient stress could be used to improve crops for lower soil fertility which is common in marginal agricultural settings.     

Geographic variation in advertisement calls in a tree frog species: gene flow and selection hypotheses

Background

In a species with a large distribution relative to its dispersal capacity, geographic variation in traits may be explained by gene flow, selection, or the combined effects of both. Studies of genetic diversity using neutral molecular markers show that patterns of isolation by distance (IBD) or barrier effect may be evident for geographic variation at the molecular level in amphibian species. However, selective factors such as habitat, predator, or interspecific interactions may be critical for geographic variation in sexual traits. We studied geographic variation in advertisement calls in the tree frog Hyla japonica to understand patterns of variation in these traits across Korea and provide clues about the underlying forces for variation.

Methodology

We recorded calls of H. japonica in three breeding seasons from 17 localities including localities in remote Jeju Island. Call characters analyzed were note repetition rate (NRR), note duration (ND), and dominant frequency (DF), along with snout-to-vent length.

Results

The findings of a barrier effect on DF and a longitudinal variation in NRR seemed to suggest that an open sea between the mainland and Jeju Island and mountain ranges dominated by the north-south Taebaek Mountains were related to geographic variation in call characters. Furthermore, there was a pattern of IBD in mitochondrial DNA sequences. However, no comparable pattern of IBD was found between geographic distance and call characters. We also failed to detect any effects of habitat or interspecific interaction on call characters.

Conclusions

Geographic variations in call characters as well as mitochondrial DNA sequences were largely stratified by geographic factors such as distance and barriers in Korean populations of H. japoinca. Although we did not detect effects of habitat or interspecific interaction, some other selective factors such as sexual selection might still be operating on call characters in conjunction with restricted gene flow.     

Establishing zebrafish as a novel exercise model: swimming economy, swimming-enhanced growth and muscle growth marker gene expression

Background

Zebrafish has been largely accepted as a vertebrate multidisciplinary model but its usefulness as a model for exercise physiology has been hampered by the scarce knowledge on its swimming economy, optimal swimming speeds and cost of transport. Therefore, we have performed individual and group-wise swimming experiments to quantify swimming economy and to demonstrate the exercise effects on growth in adult zebrafish.

Methodology/Principal Findings

Individual zebrafish (n = 10) were able to swim at a critical swimming speed (U_crit) of 0.548±0.007 m s⁻¹ or 18.0 standard body lengths (BL) s⁻¹. The optimal swimming speed (U_opt) at which energetic efficiency is highest was 0.396±0.019 m s⁻¹ (13.0 BL s⁻¹) corresponding to 72.26±0.29% of U_crit. The cost of transport at optimal swimming speed (COT_opt) was 25.23±4.03 µmol g⁻¹ m⁻¹. A group-wise experiment was conducted with zebrafish (n = 83) swimming at U_opt for 6 h day⁻¹ for 5 days week⁻¹ for 4 weeks vs. zebrafish (n = 84) that rested during this period. Swimming zebrafish increased their total body length by 5.6% and body weight by 41.1% as compared to resting fish. For the first time, a highly significant exercise-induced growth is demonstrated in adult zebrafish. Expression analysis of a set of muscle growth marker genes revealed clear regulatory roles in relation to swimming-enhanced growth for genes such as growth hormone receptor b (ghrb), insulin-like growth factor 1 receptor a (igf1ra), troponin C (stnnc), slow myosin heavy chain 1 (smyhc1), troponin I2 (tnni2), myosin heavy polypeptide 2 (myhz2) and myostatin (mstnb).

Conclusions/Significance

From the results of our study we can conclude that zebrafish can be used as an exercise model for enhanced growth, with implications in basic, biomedical and applied sciences, such as aquaculture.     

Assessment of Prunus persica fruit softening using a proteomics approach

Fruit ripening in Prunus persica involves a number of physiological changes, being one of the most significant the mesocarp softening in melting varieties. In order to get a better understanding of the molecular processes involved in this phenomenon, the protein accumulation patterns in firm and soft fruit of three peach and two nectarine melting flesh varieties were assessed using 2D gel analysis. A General Linear Model (GLM) two-way analysis of variance determined that 164 of the 621 protein spots analyzed displayed a differential accumulation associated with the softening process. Among them, only 14 proteins changed their accumulation in all the varieties assessed, including proteins mostly involved in carbohydrates and cell wall metabolism as well as fruit senescence. The analysis among varieties showed that 195 and 189 spots changed within the firm and soft fruit conditions, respectively. Despite the changes in relative abundance in the spot proteins, the proteome is conserved among varieties and during the transition from firm to soft fruit. Only two spots proteins exhibited a qualitative change in all the conditions assessed. These results are in agreement with the notion that Prunus persica commercial varieties have a narrow genetic background.