Cheppudira. G. Kushalappa

Deforestation and biodiversity loss in agroecosystems are generally the result of rational choices, not of a lack of awareness or knowledge. Despite both scientific evidence and traditional knowledge that supports the value of diverse production systems for ecosystem services and resilience, a trend of agroecosystem intensification is apparent across tropical regions. These transitions happen in spite of policies that prohibit such transformations. We present a participatory modelling study run to (1) understand the drivers of landscape transition and (2) explore the livelihood and environmental impacts of tenure changes in the coffee agroforestry systems of Kodagu (India). The components of the system, key actors and resources, and their interactions were defined with stakeholders, following the companion modelling (ComMod) approach. The underlying ecological processes driving the system were validated through expert knowledge and scientific literature. The conceptual model was transformed into a role-playing game and validated by eight workshops with a total of 57 participants. Two scenarios were explored, a No Policy Change as baseline, and a Restitution of Rights where rights to cut the native trees are handed over to farmers. Our results suggest that the landscape transition is likely to continue unabated unless there is a change to the current policy framework. However, the Restitution of Rights risks speeding up the process rather than reversing it, as inter alia, the differential growth rate between exotic and native tree species, kick in.

Estimating demographic histories using genomic datasets has proven to be useful in addressing diverse evolutionary questions. Despite improvements in inference methods and availability of large genomic datasets, quality control steps to be performed prior to the use of sequentially Markovian coalescent (SMC) based methods remains understudied. While various filtering and masking steps have been used by previous studies, the rationale for such filtering and its consequences have not been assessed systematically. In this study, we have developed a reusable pipeline called “CoalQC”, to investigate potential sources of bias (such as repeat regions, heterogeneous coverage, and callability). First, we demonstrate that genome assembly quality can affect the estimation of demographic history using the genomes of several species. We then use the CoalQC pipeline to evaluate how different repeat classes affect the inference of demographic history in the plant species Populus trichocarpa. Next, we assemble a draft genome by generating whole-genome sequencing data for Mesua ferrea (sampled from Western Ghats, India), a multipurpose forest plant distributed across tropical south-east Asia and use it as an example to evaluate several technical (sequencing technology, PSMC parameter settings) and biological aspects that need to be considered while comparing demographic histories. Finally, we collate the genomic datasets of 14 additional forest tree species to compare the temporal dynamics of Ne and find evidence of a strong bottleneck in all tropical forest plants during Mid-Pleistocene glaciations. Our findings suggest that quality control prior to the use of SMC based methods is important and needs to be standardised.

Abstract:  Although sacred groves are important for conservation in India, the landscape that surrounds them has a vital influence on biodiversity within them. Research has focused on tree diversity inside these forest patches. In a coffee‐growing region of the Western Ghats, however, landscape outside sacred groves is also tree covered because planters have retained native trees to provide shade for coffee plants. We examined the diversity of trees, birds, and macrofungi at 58 sites—10 forest‐reserve sites, 25 sacred groves, and 23 coffee plantations— in Kodagu district. We measured landscape composition and configuration around each site with a geographic information system. To identify factors associated with diversity we constructed multivariate models by using a decision‐tree technique. The conventional measures of landscape fragmentation such as patch size did not influence species richness. Distance of sacred groves from the forest reserve had a weak influence. The measures of landscape structure (e.g., tree cover in the surroundings) and stand structure (e.g., variability in canopy height) contributed to the variation in species richness explained by multivariate models. We suggest that biodiversity present within sacred groves has been influenced by native tree cover in the surrounding landscape. To conserve this biodiversity the integrity of the tree‐covered landscape matrix will need to be conserved.