Does long-distance pollen dispersal preclude inbreeding in tropical trees? Fragmentation genetics of Dysoxylum malabaricum in an agro-forest landscape.

Tropical trees often display long-distance pollen dispersal, even in highly fragmented landscapes. Understanding how patterns of spatial isolation influence pollen dispersal and interact with background patterns of fine-scale spatial genetic structure (FSGS) is critical for evaluating the genetic consequences of habitat fragmentation. In the endangered tropical timber tree Dysoxylum malabaricum (Meliaceae), we apply eleven microsatellite markers with paternity and parentage analysis to directly estimate historic gene flow and contemporary pollen dispersal across a large area (216 km(2)) in a highly fragmented agro-forest landscape. A comparison of genetic diversity and genetic structure in adult and juvenile life stages indicates an increase in differentiation and FSGS over time. Paternity analysis and parentage analysis demonstrate high genetic connectivity across the landscape by pollen dispersal. A comparison between mother trees in forest patches with low and high densities of adult trees shows that the frequency of short-distance mating increases, as does average kinship among mates in low-density stands. This indicates that there are potentially negative genetic consequences of low population density associated with forest fragmentation. Single isolated trees, in contrast, frequently receive heterogeneous pollen from distances exceeding 5 km. We discuss the processes leading to the observed patterns of pollen dispersal and the implications of this for conservation management of D. malabaricum and tropical trees more generally.

Jack of all trades: Genome assembly of Wild Jack and comparative genomics of Artocarpus.

Artocarpus (Moraceae), known as breadfruits for their diverse nutritious fruits, is prized for its high-quality timber, medicinal value, and economic importance. Breadfruits are native to Southeast Asia but have been introduced to other continents. The most commonly cultivated species are Artocarpus heterophyllus (Jackfruit) and Artocarpus altilis (Breadfruit). With numerous smaller but nutritionally comparable fruits on a larger tree, Artocarpus hirsutus, also called "Wild Jack" or "Ayani", is an elusive forest species endemic to Indian Western Ghats. In this study, we sequenced and assembled the whole genome of Artocarpus hirsutus sampled from the sacred groves of Coorg, India. To decipher demographic and evolutionary history, we compared our Wild Jack genome with previously published Jackfruit and Breadfruit genomes. Demographic history reconstruction indicates a stronger effect of habitat rather than phylogeny on the population histories of these plants. Repetitive genomic regions, especially LTR Copia, strongly affected the demographic trajectory of A. heterophyllus. Upon further investigation, we found a recent lineage-specific accumulation of LTR Copia in A. heterophyllus, which had a major contribution to its larger genome size. Several genes from starch, sucrose metabolism, and plant hormone signal transduction pathways, in Artocarpus species had signatures of selection and gene family evolution. Our comparative genomic framework provides important insights by incorporating endemic species such as the Wild Jack.

Erratum to: Elephants also like coffee: Trends and drivers of human-elephant conflicts in coffee agroforestry landscapes of Kodagu, Western Ghats, India.

Kodagu district produces 2% of the world's coffee, in complex, multistoried agroforestry systems. The forests of the district harbour a large population of the Asian elephant (Elephas maximus). The combined effects of high elephant density and major landscape changes due to the expansion of coffee cultivation are the cause of human-elephant conflicts (HEC). Mitigation strategies, including electric fences and compensation schemes implemented by the Forest Department have met with limited success. Building on previous studies in the area, we assessed current spatial and temporal trends of conflict, analysed local stakeholders' perceptions and identified factors driving elephants into the estates. Our study, initiated in May 2007, shows that the intensity of HEC has increased over the last 10 years, exhibiting new seasonal patterns. Conflict maps and the lack of correlation between physical features of the coffee plantations and elephant visits suggest elephants move along corridors between the eastern and western forests of the district, opportunistically foraging when crossing the plantations. Dung analyses indicate elephants have selectively included ripe coffee berries in their diet. This is, to our knowledge, the first report of wild elephants feeding on coffee berries. If this new behaviour spreads through the population, it will compound an already severe conflict situation. The behavioural plasticity, the multiplicity of stakeholders involved, the difficulty in defining the problem and the limits of technical solutions already proposed suggest that HEC in Kodagu has the ingredients of a "wicked" problem whose resolution will require more shared understanding and problem solving work amongst the stakeholders.

Elephants also like coffee: trends and drivers of human-elephant conflicts in coffee agroforestry landscapes of Kodagu, Western Ghats, India.

Kodagu district produces 2% of the world's coffee, in complex, multistoried agroforestry systems. The forests of the district harbour a large population of the Asian elephant (Elephas maximus). The combined effects of high elephant density and major landscape changes due to the expansion of coffee cultivation are the cause of human-elephant conflicts (HEC). Mitigation strategies, including electric fences and compensation schemes implemented by the Forest Department have met with limited success. Building on previous studies in the area, we assessed current spatial and temporal trends of conflict, analysed local stakeholders' perceptions and identified factors driving elephants into the estates. Our study, initiated in May 2007, shows that the intensity of HEC has increased over the last 10 years, exhibiting new seasonal patterns. Conflict maps and the lack of correlation between physical features of the coffee plantations and elephant visits suggest elephants move along corridors between the eastern and western forests of the district, opportunistically foraging when crossing the plantations. Dung analyses indicate elephants have selectively included ripe coffee berries in their diet. This is, to our knowledge, the first report of wild elephants feeding on coffee berries. If this new behaviour spreads through the population, it will compound an already severe conflict situation. The behavioural plasticity, the multiplicity of stakeholders involved, the difficulty in defining the problem and the limits of technical solutions already proposed suggest that HEC in Kodagu has the ingredients of a "wicked" problem whose resolution will require more shared understanding and problem solving work amongst the stakeholders.

The genome sequence of Mesua ferrea and comparative demographic histories of forest trees.

Mesua ferrea (Family: Calophyllaceae) is a tropical forest plant used for timber, biofuel, and traditional medicine. Colloquially, it is known as Nagkesar (Cobra saffron) and is the state flower of Tripura (India). In this study, we perform the whole-genome assembly of Mesua ferrea using ~180X coverage paired-end Illumina data. Our de novo assembly is 614 Mega-base pair (Mbp), has an N50 of 392 Kilo-base pairs (Kbp), and an assembly quality comparable to other published Malpighiales genomes. Further, we collate the genomic datasets of 14 additional forest tree species to compare the temporal dynamics of Effective Population Size (Ne) and find evidence of a substantial bottleneck in all tropical forest plants during Mid-Pleistocene glaciations. The availability of this high-quality draft genome assembly will prove to be a useful resource for functional and comparative genomic studies.