A new paper in Science examining the genomes of modern pygmies in the island of Flores found similarities with Neanderthal and Denisovan  sequences, but nothing else unexpected, which would suggest that the modern pygmies have no genetic link with the island’s most famous pygmy, Homo floresiensis.

Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia
Tucci et al.
Science, doi: 10.1126/science.aar8486

Flores Island, Indonesia, was inhabited by the small-bodied hominin species Homo floresiensis, which has an unknown evolutionary relationship to modern humans. This island is also home to an extant human pygmy population. Here we describe genome-scale single-nucleotide polymorphism data and whole-genome sequences from a contemporary human pygmy population living on Flores near the cave where H. floresiensis was found. The genomes of Flores pygmies reveal a complex history of admixture with Denisovans and Neanderthals but no evidence for gene flow with other archaic hominins. Modern individuals bear the signatures of recent positive selection encompassing the FADS (fatty acid desaturase) gene cluster, likely related to diet, and polygenic selection acting on standing variation that contributed to their short-stature phenotype. Thus, multiple independent instances of hominin insular dwarfism occurred on Flores.

Source: Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia | Science, 03 August 2018

See also:

• Modern Flores Island pygmies show no genetic link to extinct ‘hobbits’ | Science Daily, 02 August 2018
• No evidence of ‘hobbit’ ancestry in genomes of Flores Island pygmies | Eureka Alert, 02 August 2018