Data from: Two species of Southeast Asian cats in the genus Catopuma with diverging histories: an island endemic forest specialist and a widespread habitat generalist

Background. The bay cat Catopuma badia is endemic to Borneo, whereas its
sister species the Asian golden cat Catopuma temminckii is distributed
from the Himalayas and southern China through Indochina, Peninsular
Malaysia and Sumatra. Based on morphological data, up to five subspecies
of the Asian golden cat have been recognized, but a taxonomic assessment,
including molecular data and morphological characters, is still lacking.
Results. We combined molecular data (whole mitochondrial genomes),
morphological data (pelage) and species distribution projections (up to
the Late Pleistocene) to infer how environmental changes may have
influenced the distribution of these sister species over the past 120 000
years. The molecular analysis was based on sequenced mitogenomes of 3 bay
cats and 40 Asian golden cats derived mainly from archival samples. Our
molecular data suggested a time of split between the two species
approximately 3.16 Ma and revealed very low nucleotide diversity within
the Asian golden cat population, which supports recent expansion of the
population. Discussion. The low nucleotide diversity suggested a
population bottleneck in the Asian golden cat, possibly caused by the
eruption of the Toba volcano in Northern Sumatra (approx. 74 kya),
followed by a continuous population expansion in the Late
Pleistocene/Early Holocene. Species distribution projections, the
reconstruction of the demographic history, a genetic isolation-by-distance
pattern and a gradual variation of pelage pattern support the hypothesis
of a post-Toba population expansion of the Asian golden cat from south
China/Indochina to Peninsular Malaysia and Sumatra. Our findings reject
the current classification of five subspecies for the Asian golden cat,
but instead support either a monotypic species or one comprising two
subspecies: (i) the Sunda golden cat, distributed south of the Isthmus of
Kra: C. t. temminckii and (ii) Indochinese, Indian, Himalayan and Chinese
golden cats, occurring north of the Isthmus: C. t. moormensis.