Data-Mining Discovery of Pattern and Process in Ecological Systems

ABSTRACT Most ecologists use statistical methods as their main analytical tools when analyzing data to identify relationships between a response and a set of predictors; thus, they treat all analyses as hypothesis tests or exercises in parameter estimation. However, little or no prior knowledge about a system can lead to creation of a statistical model or models that do not accurately describe major sources of variation in the response variable. We suggest that under such circumstances data mining is more appropriate for analysis. In this paper we 1) present the distinctions between data-mining (usually exploratory) analyses and parametric statistical (confirmatory) analyses, 2) illustrate 3 strengths of data-mining tools for generating hypotheses from data, and 3) suggest useful ways in which data mining and statistical analyses can be integrated into a thorough analysis of data to facilitate rapid creation of accurate models and to guide further research.     

Seed dispersal by ants in the semi-arid Caatinga of North-East Brazil

BACKGROUND AND AIMS: Myrmecochory is a conspicuous feature of several sclerophyll ecosystems around the world but it has received little attention in the semi-arid areas of South America. This study addresses the importance of seed dispersal by ants in a 2500-km(2) area of the Caatinga ecosystem (north-east Brazil) and investigates ant-derived benefits to the plant through myrmecochory. METHODS: Seed manipulation and dispersal by ants was investigated during a 3-year period in the Xingó region. Both plant and ant assemblages involved in seed dispersal were described and ant behaviour was characterized. True myrmecochorous seeds of seven Euphorbiaceae species (i.e. elaiosome-bearing seeds) were used in experiments designed to: (1) quantify the rates of seed cleaning/removal and the influence of both seed size and elaiosome presence on seed removal; (2) identify the fate of seeds dispersed by ants; and (3) document the benefits of seed dispersal by ants in terms of seed germination and seedling growth. KEY RESULTS: Seed dispersal by ants involved one-quarter of the woody flora inhabiting the Xingó region, but true myrmecochory was restricted to 12.8 % of the woody plant species. Myrmecochorous seeds manipulated by ants faced high levels of seed removal (38-84 %) and 83 % of removed seeds were discarded on ant nests. Moreover, seed removal positively correlated with the presence of elaiosome, and elaiosome removal increased germination success by at least 30 %. Finally, some Euphorbiaceae species presented both increased germination and seedling growth on ant-nest soils. CONCLUSIONS: Myrmecochory is a relevant seed dispersal mode in the Caatinga ecosystem, and is particularly frequent among Euphorbiaceae trees and shrubs. The fact that seeds reach micro-sites suitable for establishment (ant nests) supports the directed dispersal hypothesis as a possible force favouring myrmecochory in this ecosystem. Ecosystems with a high frequency of myrmecochorous plants appear not to be restricted to regions of nutrient-impoverished soil or to fire-prone regions.     

Producing sons reduces lifetime reproductive success of subsequent offspring in pre-industrial Finns

Life-history theory states that reproductive events confer costs upon mothers. Many studies have shown that reproduction causes a decline in maternal condition, survival or success in subsequent reproductive events. However, little attention has been given to the prospect of reproductive costs being passed onto subsequent offspring, despite the fact that parental fitness is a function of the reproductive success of progeny. Here we use pedigree data from a pre-industrial human population to compare offspring life-history traits and lifetime reproductive success (LRS) according to the cost incurred by each individual's mother in the previous reproductive event. Because producing a son versus a daughter has been associated with greater maternal reproductive cost, we hypothesize that individuals born to mothers who previously produced sons will display compromised survival and/or LRS, when compared with those produced following daughters. Controlling for confounding factors such as socio-economic status and ecological conditions, we show that those offspring born after elder brothers have similar survival but lower LRS compared with those born after elder sisters. Our results demonstrate a maternal cost of reproduction manifested in reduced LRS of subsequent offspring. To our knowledge, this is the first time such a long-term intergenerational cost has been shown in a mammal species.     

Survival against the odds: ontogenetic changes in selective pressure mediate growth-mortality trade-offs in a marine fish

For organisms with complex life cycles, variation among individuals in traits associated with survival in one life-history stage can strongly affect the performance in subsequent stages with important repercussions on population dynamics. To identify which individual attributes are the most influential in determining patterns of survival in a cohort of reef fish, we compared the characteristics of Pomacentrus amboinensis surviving early juvenile stages on the reef with those of the cohort from which they originated. Individuals were collected at hatching, the end of the planktonic phase, and two, three, four, six and eight weeks post-settlement. Information stored in the otoliths of individual fish revealed strong carry-over effects of larval condition at hatching on juvenile survival, weeks after settlement (i.e. smaller-is-better). Among the traits examined, planktonic growth history was, by far, the most influential and long-lasting trait associated with juvenile persistence in reef habitats. However, otolith increments suggested that larval growth rate may not be maintained during early juvenile life, when selective mortality swiftly reverses its direction. These changes in selective pressure may mediate growth-mortality trade-offs between predation and starvation risks during early juvenile life. Ontogenetic changes in the shape of selectivity may be a mechanism maintaining phenotypic variation in growth rate and size within a population.     

Anti-predator defence and the complexity-stability relationship of food webs

The mechanism for maintaining complex food webs has been a central issue in ecology because theory often predicts that complexity (higher the species richness, more the interactions) destabilizes food webs. Although it has been proposed that prey anti-predator defence may affect the stability of prey-predator dynamics, such studies assumed a limited and relatively simpler variation in the food-web structure. Here, using mathematical models, I report that food-web flexibility arising from prey anti-predator defence enhances community-level stability (community persistence and robustness) in more complex systems and even changes the complexity-stability relationship. The model analysis shows that adaptive predator-specific defence enhances community-level stability under a wide range of food-web complexity levels and topologies, while generalized defence does not. Furthermore, while increasing food-web complexity has minor or negative effects on community-level stability in the absence of defence adaptation, or in the presence of generalized defence, in the presence of predator-specific defence, the connectance-stability relationship may become unimodal. Increasing species richness, in contrast, always lowers community-level stability. The emergence of a positive connectance-stability relationship however necessitates food-web compartmentalization, high defence efficiency and low defence cost, suggesting that it only occurs under a restricted condition.     

Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites

Detection of positive Darwinian selection has become ever more important with the rapid growth of genomic data sets. Recent branch-site models of codon substitution account for variation of selective pressure over branches on the tree and across sites in the sequence and provide a means to detect short episodes of molecular adaptation affecting just a few sites. In likelihood ratio tests based on such models, the branches to be tested for positive selection have to be specified a priori. In the absence of a biological hypothesis to designate so-called foreground branches, one may test many branches, but a correction for multiple testing becomes necessary. In this paper, we employ computer simulation to evaluate the performance of 6 multiple test correction procedures when the branch-site models are used to test every branch on the phylogeny for positive selection. Four of the methods control the familywise error rates (FWERs), whereas the other 2 control the false discovery rate (FDR). We found that all correction procedures achieved acceptable FWER except for extremely divergent sequences and serious model violations, when the test may become unreliable. The power of the test to detect positive selection is influenced by the strength of selection and the sequence divergence, with the highest power observed at intermediate divergences. The 4 correction procedures that control the FWER had similar power. We recommend Rom's procedure for its slightly higher power, but the simple Bonferroni correction is useable as well. The 2 correction procedures that control the FDR had slightly more power and also higher FWER. We demonstrate the multiple test procedures by analyzing gene sequences from the extracellular domain of the cluster of differentiation 2 (CD2) gene from 10 mammalian species. Both our simulation and real data analysis suggest that the multiple test procedures are useful when multiple branches have to be tested on the same data set.     

Indirect benefits for choosy female grasshoppers (Chorthippus biguttulus)?

Since direct benefits are likely to be absent in the grasshopper Chorthippus biguttulus, indirect genetic benefits are a potential explanation for costly female preference. Choosy females may improve their fitness in terms of enhanced attractiveness of sons alone or additionally by improved viability of offspring. We tested the predictions of these two hypotheses by comparing attractiveness-related song traits and viability in offspring of attractive and unattractive grasshopper males. The experiment was conducted with larvae reared under semi natural lab conditions in one year and under natural conditions in the field in the following year. If reared under natural conditions no significant differences in viability and song traits between offspring of attractive and unattractive males could be found. Offspring reared in the lab produced calling songs with a significantly more exact song rhythm when sired by attractive males than offspring of unattractive males. Offspring of attractive males should thus have a theoretical advantage in mate choice, which, however, did not translate into higher attractiveness values in acoustic female choice experiments. Therefore our experiments could not resolve whether female choice in C. biguttulus evolved according to the sexy son hypothesis. Since viability in offspring of attractive males did not differ from offspring of unattractive males, “good genes” seems unlikely to be the underlying mechanism of female choice.     

Fruit removal efficiency and success: influence of crop size in a neotropical treelet

The reproductive success of animal-dispersed plants is closely linked to the number of seeds that they are able to disperse. The fruit crop size hypothesis states that a plant with large fruit crop size will attract more dispersers than a plant with a smaller fruit crop, which may result in more seeds being dispersed from the foremost. In this study, we experimentally examined the effect of crop size and other factors on primary seed dispersal in a neotropical shrub/tree, Casearia corymbosa (Flacourtiaceae). We used two predictive variables of reproductive success, which produce an accurate picture of seed dispersal ratio: fruit removal efficiency (proportion of a fruit crop removed by frugivores) and fruit removal success (relative contribution of each individual tree to the number of fruits removed in the population). We established two levels of fruit crop size at the C. corymbosa individuals, using plants with large (150 fruits) and small crops (50 fruits). We found that individual plants with larger crops had significantly higher values of fruit removal efficiency (92.6%) and success (5%) than plants with smaller crops (69.3% and 1.3%, respectively). Fruit removal efficiency was related to vegetation type, plant height and fruit width, but the variance explained by these variables was low ( < 8%). Fruit removal success was significantly related to crop size ( > 90% of the variance explained). These results suggest that fruit removal efficiency and success are strongly related to fruit crop size of C. corymbosa plants.     

Investigating Devonian trees as geo‐engineers of past climates: linking palaeosols to palaeobotany and experimental geobiology

We present the rationale for a cross‐disciplinary investigation addressing the ‘Devonian plant hypothesis’ which proposes that the evolutionary appearance of trees with deep, complex rooting systems represents one of the major biotic feedbacks on geochemical carbon cycling during the Phanerozoic. According to this hypothesis, trees have dramatically enhanced mineral weathering driving an increased flux of Ca²⁺ to the oceans and, ultimately, a 90% decline in atmospheric CO₂ levels through the Palaeozoic. Furthermore, experimental studies indicate a key role for arbuscular mycorrhizal fungi in soil–plant processes and especially in unlocking the limiting nutrient phosphorus in soil via Ca‐phosphate dissolution mineral weathering. This suggests co‐evolution of roots and symbiotic fungi since the Early Devonian could well have triggered positive feedbacks on weathering rates whereby root–fungal P release supports higher biomass forested ecosystems. Long‐standing areas of uncertainty in this paradigm include the following: (1) limited fossil record documenting the origin and timeline of the evolution of tree‐sized plants through the Devonian; and (2) the effects of the evolutionary advance of trees and their in situ rooting structures on palaeosol geochemistry. We are addressing these issues by integrating palaeobotanical studies with geochemical and mineralogical analyses of palaeosol sequences at selected sites across eastern North America with a particular focus on drill cores from Middle Devonian forests in Greene County, New York State.