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A Holling Functional Response Model for Mapping QTLs Governing Interspecific Interactions

ABSTRACT: Genes play an important role in community ecology and evolution, but how to identify the genes that affect community dynamics at the whole genome level is very challenging. Here, we develop a Holling type II functional response model for mapping quantitative trait loci (QTLs) that govern interspecific interactions. The model, integrated with generalized Lotka-Volterra differential dynamic equations, shows a better capacity to reveal the dynamic complexity of inter-species interactions than classic competition models. By applying the new model to a published mapping data from a competition experiment of two microbial species, we identify a set of previously uncharacterized QTLs that are specifically responsible for microbial cooperation and competition. The model can not only characterize how these QTLs affect microbial interactions, but also address how change in ecological interactions activates the genetic effects of the QTLs. This model provides a quantitative means of predicting the genetic architecture that shapes the dynamic behavior of ecological communities.

SUBMITTER: Zhang X

PROVIDER: S-EPMC8554200 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundHolling (Can Entomol 91(5):293-320, 1959) was the first to describe a functional response between a predator's consumption-rate and the density of its prey. The same concept can be applied to the habitat selection of herbivores, specifically, the change in relative habitat use with the change in habitat availability. Functional responses in habitat selection at a home-range scale have been reported for several large herbivores. However, a link to Holling's original functional response types has never been drawn, although it could replace the current phenomenological view with a more mechanistically based understanding of functional responses.MethodsIn this study, discrete choice models were implemented as mixed-effects baseline-category logit models to analyze the variation in habitat selection of a large herbivore at seasonal and diurnal scales. Thus, changes in the use of land cover types with respect to their availability were investigated by monitoring 11 land cover types commonly used by roe deer (Capreolus capreolus) in the Bavarian Forest National Park, Germany. Functional response curves were then fitted using Holling's formulas.ResultsStrong evidence of non-linear functional responses was obtained for almost all of the examined land cover types. The shape of the functional response curves varied depending on the season, the time of day, and in some cases between sexes. These responses could be referenced to Holling's types, with a predominance of type II.ConclusionsOur results indicate that Holling's types can be applied to describe general patterns of the habitat selection behavior of herbivores. Functional responses in habitat selection may occur in situations requiring a trade-off in the selection of land cover types offering different resources, such as due to the temporally varying physiological needs of herbivores. Moreover, two associated parameters defining the curves (prey density and predation rate) can aid in the identification of temporal variations and in determinations of the strength of the cost-benefit ratio for a specific land cover type. Application of our novel approach, using Holling's equations to describe functional responses in the habitat selection of herbivores, will allow the assignment of general land cover attraction values, independent of availability, thus facilitating the identification of suitable habitats.

Project description:BACKGROUND: Marker Assisted Selection (MAS) is well suited to a perennial crop like oil palm, in which the economic products are not produced until several years after planting. The use of DNA markers for selection in such crops can greatly reduce the number of breeding cycles needed. With the use of DNA markers, informed decisions can be made at the nursery stage, regarding which individuals should be retained as breeding stock, which are satisfactory for agricultural production, and which should be culled. The trait associated with oil quality, measured in terms of its fatty acid composition, is an important agronomic trait that can eventually be tracked using molecular markers. This will speed up the production of new and improved oil palm planting materials. RESULTS: A map was constructed using AFLP, RFLP and SSR markers for an interspecific cross involving a Colombian Elaeis oleifera (UP1026) and a Nigerian E. guinneensis (T128). A framework map was generated for the male parent, T128, using Joinmap ver. 4.0. In the paternal (E. guineensis) map, 252 markers (199 AFLP, 38 RFLP and 15 SSR) could be ordered in 21 linkage groups (1815 cM). Interval mapping and multiple-QTL model (MQM) mapping (also known as composite interval mapping, CIM) were used to detect quantitative trait loci (QTLs) controlling oil quality (measured in terms of iodine value and fatty acid composition). At a 5% genome-wide significance threshold level, QTLs associated with iodine value (IV), myristic acid (C14:0), palmitic acid (C16:0), palmitoleic acid (C16:1), stearic acid (C18:0), oleic acid (C18:1) and linoleic acid (C18:2) content were detected. One genomic region on Group 1 appears to be influencing IV, C14:0, C16:0, C18:0 and C18:1 content. Significant QTL for C14:0, C16:1, C18:0 and C18:1 content was detected around the same locus on Group 15, thus revealing another major locus influencing fatty acid composition in oil palm. Additional QTL for C18:0 was detected on Group 3. A minor QTL for C18:2 was detected on Group 2. CONCLUSION: This study describes the first successful detection of QTLs for fatty acid composition in oil palm. These QTLs constitute useful tools for application in breeding programmes.

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A Holling Functional Response Model for Mapping QTLs Governing Interspecific Interactions

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