Biology subjects

Ramakrishnan, U.

Publications and source records attributed to Ramakrishnan, U..

3 recordsLinked to original sources

bioRxiv2018

Empowering conservation practice with efficient and economical genotyping from poor quality samples

O_LIModerate to high density genotyping (100+ SNPs) is widely used to determine and measure individual identity, relatedness, fitness, population structure and migration in wild populations. C_LIO_LIHowever, these important tools are difficult to apply when high-quality genetic material is unavailable. Most genomic tools are developed for high quality DNA sources from labor medical settings. As a result, most genetic data from market or field settings is limited to easily amplified mitochondrial DNA or a few microsatellites. C_LIO_LITo enable genotyping in conservation contexts, we used next-generation sequencing of multiplex PCR products from very low-quality DNA extracted from feces, hair, and cooked samples. We demonstrated utility and wide-ranging potential application in endangered wild tigers and tracking commercial trade in Caribbean queen conch. C_LIO_LIWe genotyped 100 SNPs from degraded tiger samples to identify individuals, discern close relatives, and detect population differentiation. Co-occurring carnivores do not amplify (e.g. Indian wild dog/Dhole) or are monomorphic (e.g. leopard). 62 SNPs from conch fritters and field-collected samples were used to test relatedness and detect population structure. C_LIO_LIWe provide proof-of-concept for a rapid, simple, cost-effective, and scalable method (for both samples and number of loci), a framework that can be applied to other conservation scenarios previously limited by low quality DNA samples. These approaches provide a critical advance for wildlife monitoring and forensics, open the door to field-ready testing, and will strengthen the use of science in policy decisions and wildlife trade. C_LI

genomics↗

bioRxiv2017

Coalescent theory of migration network motifs

Natural populations display a variety of spatial arrangements, each potentially with a distinctive impact on genetic diversity and genetic differentiation among subpopulations. Although the spatial arrangement of populations can lead to intricate migration networks, theoretical developments have focused mainly on a small subset of such networks, emphasizing the island-migration and stepping-stone models. In this study, we investigate all small network motifs: the set of all possible migration networks among populations subdivided into at most four subpopulations. For each motif, we use coalescent theory to derive expectations for three quantities that describe genetic variation: nucleotide diversity, FST, and half-time to equilibrium diversity. We describe the impact of network properties on these quantities, finding that motifs with a large mean node degree have the largest nucleotide diversity and the longest time to equilibrium, whereas motifs with small density have the largest FST. In addition, we show that the motifs whose pattern of variation is most strongly influenced by loss of a connection or a subpopulation are those that can be split easily into several disconnected components. We illustrate our results using two example datasets--sky island birds of genus Brachypteryx and Indian tigers--identifying disturbance scenarios that produce the greatest reduction in genetic diversity; for tigers, we also compare the benefits of two assisted gene flow scenarios. Our results have consequences for understanding the effect of geography on genetic diversity and for designing strategies to alter population migration networks to maximize genetic variation in the context of conservation of endangered species.

genetics↗

bioRxiv2016

Protected corridors preserve tiger genetic diversity and minimize extinction into the next century

Habitat loss is the greatest threat to large carnivores around the world. Maintenance of functional connectivity in fragmented landscapes will be important for long-term species persistence. Here, we merge landscape genetics analyses and spatially-explicit simulations to understand future persistence and extinction of tigers (Panthera tigris) in Central India. Tigers in this landscape are restricted to Protected Areas (PAs) and forest fragments embedded within a mosaic of agricultural fields and human settlements. We examined current population connectivity of tigers across nine reserves (using 116 non-invasively sampled individuals and 12 microsatellites). Genetic data was used to infer resistance-to-movement. Our results suggest that dense human settlements and roads with high traffic are detrimental to tiger movement. We used landscape genetic simulations to model 86 different scenarios that incorporated impacts of future land-use change on inferred population connectivity and extinction. Our results confirm that genetic variability (heterozygosity) will decrease in the future and small and/or isolated PAs will have a high risk of local extinction. The average extinction risk of small PAs reduced by 23-70% on adding a 5 km buffer around exiting boundaries. Unplanned development results in 35% lower heterozygosity and 56% higher average extinction probability for tigers even within protected areas. Increasing tiger numbers in such a scenario decreases extinction probability just by 12 % (from 56% to 44%). Scenarios where habitat connectivity was enhanced and maintained, stepping-stone populations were introduced/maintained, and tiger numbers were increased, led to low overall extinction probability (between 3-21%). Our simulations provide a means to quantitatively evaluate the effects of different land-use change scenarios on connectivity and extinction, linking basic science to land-use change policy and planned infrastructure development.

genetics↗