TY  - JOUR
A1  - Patel, Riddhi P.
A1  - Förster, Daniel W.
A1  - Kitchener, Andrew C.
A1  - Rayan, Mark D.
A1  - Mohamed, Shariff W.
A1  - Werner, Laura
A1  - Lenz, Dorina
A1  - Pfestorf, Hans
A1  - Kramer-Schadt, Stephanie
A1  - Radchuk, Viktoriia
A1  - Fickel, Jörns
A1  - Wilting, Andreas
T1  - Two species of Southeast Asian cats in the genus Catopuma with diverging histories: an island endemic forest specialist and a widespread habitat generalist
JF  - Royal Society Open Science
N2  - 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 onmorphological 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 PeninsularMalaysia 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.
KW  - Felidae
KW  - Southeast Asia
KW  - last glacial maximum
KW  - Toba volcanic eruption
KW  - hybrid capture
KW  - next generation sequencing
Y1  - 2016
U6  - https://doi.org/10.1098/rsos.160350
SN  - 2054-5703
VL  - 3
SP  - 741
EP  - 752
PB  - Royal Society
CY  - London
ER  - 
TY  - JOUR
A1  - Teasdale, Matthew David
A1  - van Doorn, N. L.
A1  - Fiddyment, S.
A1  - Webb, C. C.
A1  - Hofreiter, Michael
A1  - Collins, Matthew J.
A1  - Bradley, Daniel G.
T1  - Paging through history: parchment as a reservoir of ancient DNA for next generation sequencing
JF  - Philosophical transactions of the Royal Society of London : B, Biological sciences
N2  - Parchment represents an invaluable cultural reservoir. Retrieving an additional layer of information from these abundant, dated livestock-skins via the use of ancient DNA (aDNA) sequencing has been mooted by a number of researchers. However, prior PCR-based work has indicated that this may be challenged by cross-individual and cross-species contamination, perhaps from the bulk parchment preparation process. Here we apply next generation sequencing to two parchments of seventeenth and eighteenth century northern English provenance. Following alignment to the published sheep, goat, cow and human genomes, it is clear that the only genome displaying substantial unique homology is sheep and this species identification is confirmed by collagen peptide mass spectrometry. Only 4% of sequence reads align preferentially to a different species indicating low contamination across species. Moreover, mitochondrial DNA sequences suggest an upper bound of contamination at 5%. Over 45% of reads aligned to the sheep genome, and even this limited sequencing exercise yield 9 and 7% of each sampled sheep genome post filtering, allowing the mapping of genetic affinity to modern British sheep breeds. We conclude that parchment represents an excellent substrate for genomic analyses of historical livestock.
KW  - parchment
KW  - next generation sequencing
KW  - ancient DNA
KW  - ZooMS
KW  - sheep
Y1  - 2015
U6  - https://doi.org/10.1098/rstb.2013.0379
SN  - 0962-8436
SN  - 1471-2970
VL  - 370
IS  - 1660
PB  - Royal Society
CY  - London
ER  -