Northeast India, with its variety of geographical features and topography, provides a plethora of niches for species to evolve and thrive. Among a multitude of factors, past climate change is one of the important factors influencing primate speciation in this region. Populations of various species could have risen or declined in response to these climatic fluctuations. Recent advances in climate modelling as well as genomic data analysis has paved the way for understanding how species accumulate at a particular geographic region. We utilized these methods to explore the primate diversity in the unique region of northeast India. To ascertain these population level changes, we inferred demographic history of nine species of primates found in northeast India with MSMC2 and compared it with species distribution models using past climate data of Pliocene and Pleistocene period. Through this study, we are able to give a detailed picture of how past climatic changes have affected the present species diversity and we show that the primate diversity in northeast India is a mix of species either originated there or have dispersed from mainland southeast Asia. We observe that effective population size has decreased for all the species, but distributions are different for all the four genera, Macaca, Trachypithecus, Hoolock and Nycticebus, and this provides important insights pertaining to present primate diversity in the region. It also gives an idea about how each species is affected differently by climate change, and why it should be given emphasis in framing species-wise conservation models for future climate change.

The Xerces Blue (Glaucopsyche xerces) is considered to be the first butterfly to become extinct at global scale in historical times. It was notable for its chalky lavender wings with conspicuous white spots on the ventral wings. The last individuals were collected in their restricted habitat, in the dunes near the Presidio military base in San Francisco, in 1941. To explore the demographic history of this iconic butterfly and to better understand why it went extinct, we sequenced at medium coverage the genomes of four 80 to 100-year-old Xerces Blue specimens and seven historic specimens of its closest relative, the Silvery Blue (G. lygdamus). We compared these to a novel annotated genome of the Green-Underside Blue (G. alexis). Phylogenetic relationships inferred from complete mitochondrial genomes indicate that Xerces Blue was a distinct species that diverged from the Silvery Blue lineage at least 850,000 years ago. Using nuclear genomes, we show that both species experienced population growth during the MIS 7 interglacial period, but the Xerces Blue decreased to a very low effective population size subsequently, a trend opposite to that observed in the Silvery Blue. Runs of homozygosity in the Xerces Blue were significantly greater than in the Silvery Blue, suggesting a higher incidence of inbreeding. In addition, the Xerces Blue carried a higher proportion of derived, putatively deleterious amino acid-changing alleles than the Silvery Blue. These results demonstrate that the Xerces Blue experienced more than 100 thousand years of population decline, prior to its human-induced final extinction.