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Biology subjects

Irmak, S.

Publications and source records attributed to Irmak, S..

2 recordsLinked to original sources

The best of two worlds: using stacked generalization for integrating expert range maps in species distribution models

Species distribution models (SDMs) are powerful tools for assessing suitable habitat across large areas and at fine spatial resolution. Yet, the usefulness of SDMs for mapping species realized distributions is often limited, since data biases or missing information on dispersal barriers or biotic interactions hinder them from accurately delineating species range limits. One way to overcome this limitation is to integrate SDMs with expert range maps, which provide coarse-scale information on the extent of species ranges that is complementary to information offered by SDMs. Here, we propose a new approach for integrating expert range maps in SDMs based on an ensemble method called stacked generalization. Specifically, our approach relies on training a meta-learner regression model using predictions from one or more SDM algorithms alongside the distance of training points to expert-defined ranges as predictor variables. We demonstrate our approach with an occurrence dataset for 49 bat species covering four biodiversity hotspots in the Eastern Mediterranean, Western Asia, and Central Asia. Our approach offers a flexible method to integrate expert range maps with any combination of SDM modeling algorithms, thus facilitating the use of algorithm ensembles. In addition, it provides a novel, data-driven way to account for uncertainty in expert-defined ranges not requiring prior knowledge about their accuracy, which is often lacking. Our approach holds considerable promise for better understanding species distributions, and thus for biogeographical research and conservation planning. In addition, our work highlights the overlooked potential of stacked generalization as an ensemble method in species distribution modeling.

ecology↗

A Clade-D Auxin Response Factor is a Major Regulator of Auxin Signaling in Physcomitrium patens.

Auxin Response Factors (ARFs) are a family of transcription factors that are responsible for regulating gene expression in response to changes in auxin level. The analysis of ARF sequence and activity indicates that there are two major groups-activators and repressors. One clade of ARFs, clade-D, is sister to clade-A activating ARFs, but are unique in that they lack a DNA binding domain. Clade-D ARFs are present in lycophytes and bryophytes but absent in pteridophytes and spermatophytes. The transcriptional activity of clade-D ARFs, as well as how they regulate gene expression, is not well understood. Here, we report that clade-D ARFs are transcriptional activators in the model bryophyte P. patens and have a major role in the development of this species. {Delta}arfd1,d2 protonemata exhibit a delay in filament branching, as well as a delay in a key cell differentiation event. Additionally, leafy gametophore development in {Delta}arfd1,d2 lines lag behind wild-type. We present evidence that ARFd1 interacts with activating, but not repressing, ARFs. An ARFd1 hypomorph, arfd1T653L, cannot multimerize. Therefore, we propose a model by which clade-D ARFs enhance gene expression by oligomerizing to DNA-bound archetypal ARFs.

plant biology↗