Genomics offer clues to how forest trees responded to the last Ice Age

Persistent, colder climates in the last Ice Age contributed to limiting the distribution of certain commercially and medicinally-important forest species such as cobra saffron (nagkesar) to smaller forest patches that are present day ‘biodiversity hotspots’, scientists said in a recent paper. In contrast, species that survive in the Northern Hemisphere’s cooler climate showed resilience to the glaciation hurdles and expanded their spread later.

Scientists at IISER Bhopal, College of Forestry, Ponnampet, Kodagu, and College of Agriculture Hassan, UAS, Bengaluru, decoded the genome sequence of cobra saffron (Mesua ferrea) and compared its demographic history to 12 other tropical forest tree species and two northern species (silver birch and olives) using existing public genomic datasets of those species. Researchers stress on addressing the paucity of genomic datasets of tree species endemic to India, especially as such data enable prediction and modeling of the extent of the impact on forests due to harsher conditions; they also feed into conservation policies and actions, including the People’s Biodiversity Register (PBR) and the Indian Initiative for Earth Biogenome Sequencing.

The scientists write in the study that they find evidence of a “substantial bottleneck” in the tropical forest plants during Mid-Pleistocene glaciations, which occurred between 115,000 to 20,000 years ago. The genomic analysis revealed a reduced effective population size of most forest plants in the last glacial period (occurring during the Mid-Pleistocene glaciations) when persistent, colder, and drier climates adversely impacted these forest species. Effective population size is a theoretical concept and serves as a proxy for actual population size, explained study’s corresponding author Nagarjun Vijay of IISER-Bhopal.

“It is known that tropical forest species show a decline in effective population size in this period. So we were expecting to see a decline in the effective population size for cobra saffron and the 12 other tropical forest tree species, and our analysis did show that reduction. However, the two northern species, the cold-adapted silver birch, and olive, show an increase in the population size; they could spring back from the effects of the harsh cold climate and expand their spread later,” Vijay at IISER-Bhopal’s Computational Evolutionary Genomics Lab in the Department of Biological Sciences, told Mongabay-India.

The most recent periods of global cooling, or ice ages, took place during the Pleistocene. According to the International Commission on Stratigraphy, this geologic period began about 2.6 million and lasted until about 11,700 years ago. The Pleistocene is the earlier and major of the two epochs that constitute the Quaternary Period. Throughout the past 2.6 million years, the Quaternary Period has seen a waxing and waning of glacial-interglacial cycles. The times with large ice sheets are “glacial periods” (or ice ages), and times without large ice sheets are “interglacial periods.”

Hemmed in biodiversity hotspots and protected forests

Nagarjun Vijay, whose group looks into large genomic datasets to understand the patterns of evolution and the processes driving these patterns, explained that the decline in effective population size started in the Pleistocene for most of the species and it continued into the last glacial period; however, the reduction intensified in the last glacial period (115,000 to 20,000 years ago) because the decline had been going on for a few thousand years and populations were splitting apart.

“So the last glacial period was more important in the context that the plants that had adapted, they did so before the last glacial (silver birch) while the other species (nagkesar) that did not have the chance to do so, they continued their decline,” noted Vijay.

Nagkesar is found across biodiversity hotspots of the Western Ghats and northeast India and in parts of southeast Asia. It is used for timber, biofuel, and traditional medicine. The researchers collected leaves of cobra saffron from sacred groves in Kodagu, Karnataka, in the Western Ghats for their study to commemorate the critical role of sacred groves in the conservation of ancient flora.

“Due to the inability of dispersal, germination, and proliferation, their (tropical forest trees’) propagation might have been restricted in the glaciations. This might have led to the depletion of wide distribution across large landscapes to smaller forest patches, what we see as hotspots of biodiversity today,” observed Vijay. “Fragmentation of the geographic distribution (mountains as barriers, for example) could also have contributed to the observed decline in effective population size,” he said.

The ones that revived from the ice age bottleneck

But there were exceptions among the forest trees in the study sample. Faidherbia albida, a deciduous legume tree, is an important component of agroforestry systems in semi-arid tropics. F. albida could adapt to the subsequent drier climates and spring back from the bottleneck around the last glacial period.

“Glaciation periods are cyclically followed by de-glaciation events where we see an increase in temperatures. Due to the meltdown of large ice sheets following the increase in temperature, low-lying areas get flooded. Later we do see rapid regeneration, germination, and proliferation of vegetation. But these also would be restricted to the areas which already had seeds spread out in the area. Because distributions of these forest plants were restricted, even though these plants were able to survive, eventually, their numbers could not be the same as they used to be. Some plants, such as Faidherbia albida, were able to resurrect from these bottlenecks and, due to adaptations to the drier climates, could regain their numbers considerably,” he said.

Faidherbia has shown many phenotypic adaptations, such as a highly developed tap root system, making it highly resistant to drought and drier conditions. This plant attracts multiple insect species, which makes its breeding more efficient and is more successful in sustaining in the wild. “Useful plants generally get used by people extensively and eventually become part of agroforestry. This plant is also an important part of agroforestry due to its widespread uses, but it is still part of forests and is found in wild conditions,” elaborated Vijay.

Need to expand genomic datasets of endemic tree species

A decade ago in a 2011 review Forest tree genomics: growing resources and applications, authors David B. Neale and Antoine Kremer wrote that forest trees are found in both a domesticated and undomesticated (wild) state, and they are among the most genetically diverse plants. They underscored the advent of next-generation sequencing technologies, the enormous genetic diversity in forest trees, and the need to mitigate the effects of climate change as factors that would bolster genomic research in forest trees.

Vijay emphasises that the paucity of genomic datasets of tree species endemic to India motivated them to sequence the genome of cobra saffron. “Future efforts using the ever-increasing genomic datasets will allow the exploration of more intricate hypotheses. Studying past demographic history and responses of these forest species gives us clues about each species’ adaptations and tolerance. These estimates further help in species-specific models of forest bio communities for long-term monitoring of forest landscapes. It also becomes easier to predict and model the extent of the impact on forests due to harsher conditions, which is important in current unprecedented global climate change,” he said.

And integration of data from historical demographic models with present-day effects of climate change is required to realise the practical implications for conservation efforts fully. “A lot more work is required to understand how a paleoclimate response might be different from the present climate change. For instance, the pace and magnitude of climate change might result in very different responses. Nonetheless, paleoclimate responses provide a system to study the effect of climate change on diverse species,” he said, adding that systematic comparative efforts are needed.

Sandeep Sen, postdoctoral researcher, at Ashoka Trust for Research in Ecology and the Environment (ATREE), Bangalore, adds that in terms of policy, genomic datasets will directly contribute to designing future in situ conservation networks and help prioritise populations to archive ex-situ, especially for endemic species and the ones with low population size, it will be possible to identify a population/ individuals with high adaptation potential.

“Also, genome-based approaches may help select better reproductive materials to use in the wake of climate change by considering their evolutionary responses. In simple terms, we may know which populations might perform well under drought or a warming climate which can be used for assisted migrations, silviculture, etc.,” Sen, who was not associated with the study, told Mongabay-India.

Suma Arun Dev of Kerala Forest Research Institute, who has worked on deciphering the genetic diversity of teak from the natural areas, says protected forests conserve populations that have adapted to environmental stressors. Her research using genomic tools has shown that teak populations distributed in protected areas have adaptive alleles (one of two or more versions of a gene) that help the particular population survive environmental stressors. Their studies of 18 wild teak populations spanning south and central India found the central Indian populations “more vulnerable” to climate change than the south Indian counterparts.

Targeting such populations can help resource managers design and implement management and conservation strategies, said Arun Dev, who was not involved in the cobra saffron study.

Simultaneously, these datasets will foster the development of new research areas (locating medicinally important genes, etc.). “However, it is essential to pay more attention to access and benefit-sharing (ABS) related issues associated with forest genetic resources,” Sen cautioned.

Vijay said incentivising a model that links traditional knowledge with genetic/genomic resources may work. “Unfortunately, recognition of traditional knowledge and proper documentation of local communities’ role has not become a part of the academic scientific discourse. International genomic repositories have helped foster an open environment for data sharing (14 of the 15 species used in our study are from international databases),” he said. A national framework for e-PBRs may help solve some of the latency, according to Vijay. A national framework for e-PBRs is envisaged under the NISARG Bharat (National Initiative for Sustained Assessment of Resource Governance), one of the critical components of the National Mission on Biodiversity and Human Well-being.

 

Banner image: Forest canopy in the Nilgiris, southern India. Photo by L. Shyamal/Wikimedia Commons.