A

                              Guide to  

                         the mtDNA of Squirrels

                        

  
------------------------------------------------------------------------------------------ GenBank ------- Useable complete (or nearly so) mtDNA sequences of Squirrels on the GenBank database (March 2018) Total 6+3+33+1+10 = 53 ------------- Group V (6 sequences) JQ230001 05-MAR-2013 Pteromys volans Siberian flying squirrel JQ743657 31-MAR-2014 Petaurista alborufus Red and white giant flying squirrel JX572159 21-MAR-2016 Petaurista hainana Hainan giant flying squirrel KC447305 01-FEB-2015 Hylopetes phayrei Indochinese flying squirrel KX528208 28-JAN-2017 Petaurista yunanensis Yunnan giant flying squirrel KX710106 30-OCT-2016 Hylopetes alboniger Particolored flying squirrel ------------- Group IV (3 sequences) KP698974 10-JUN-2015 Ictidomys tridecemlineatus Thirteen-lined ground squirrel KP698975 31-AUG-2016 Callospermophilus lateralis Golden-mantled ground squirrel KR534854 13-JUN-2015 Spermophilus dauricus Daurian ground squirrel ------------- Group III (2+3+8+2+2+3+1+3+1+8 = 33) - Exilisciurus (2 sequence) KR911801 19-APR-2016 Exilisciurus exilis Least pygmy squirrel KY117546 30-AUG-2017 Exilisciurus exilis Least pygmy squirrel - Rubisciurus (3 sequences) KR911790 19-APR-2016 Rubrisciurus rubriventer Sulawesi giant squirrel KR911791 19-APR-2016 Rubrisciurus rubriventer Sulawesi giant squirrel KR911792 19-APR-2016 Rubrisciurus rubriventer Sulawesi giant squirrel - Prosciurillus (8 sequences) KR911784 19-APR-2016 Prosciurillus leucomus Whitish dwarf squirrel KR911785 19-APR-2016 Prosciurillus leucomus Whitish dwarf squirrel KR911786 19-APR-2016 Prosciurillus leucomus Whitish dwarf squirrel KR911787 19-APR-2016 Prosciurillus weberi Weber's dwarf squirrel KR911788 19-APR-2016 Prosciurillus weberi Weber's dwarf squirrel KR911793 19-APR-2016 Prosciurillus abstrusus Secretive dwarf squirrel KR911794 19-APR-2016 Prosciurillus murinus Celebes dwarf squirrel KR911795 19-APR-2016 Prosciurillus murinus Celebes dwarf squirrel - Hyosciurus (2 sequences) KR911796 19-APR-2016 Hyosciurus ileile Lowland long-nosed squirrel KR911797 19-APR-2016 Hyosciurus heinrichi Montane long-nosed squirrel - Tamiops (2 sequences) KP027416 29-MAR-2015 Tamiops swinhoei Swinhoe's striped squirrel KP708710 10-FEB-2016 Tamiops maritimus Maritime striped squirrel - Dremonys (3 sequences) KC447304 01-FEB-2015 Dremomys rufigenis Asian red-cheeked squirrel KP708711 31-JUL-2017 Dremomys pernyi Perny's long-nosed squirrel KR911798 19-APR-2016 Dremomys everetti Bornean mountain ground squirrel - Nannosciurus (1 sequence) KT001463 19-APR-2016 Nannosciurus melanotis Black-eared squirrel - Sundasciurus (3 sequences) KY117586 30-AUG-2017 Sundasciurus brookei Brooke's squirrel KY117587 30-AUG-2017 Sundasciurus lowii Low's squirrel KY117588 30-AUG-2017 Sundasciurus sp. FPF-2017 - Lariscus (1 sequence) KR911799 19-APR-2016 Lariscus insignis Three-striped ground squirrel - Callosciurus (8 sequences) KM502568 26-OCT-2014 Callosciurus erythraeus Pallas's squirrel KR911800 19-APR-2016 Callosciurus adamsi Ear-spot squirrel KY117538 30-AUG-2017 Callosciurus erythraeus Pallas's squirrel KY117539 30-AUG-2017 Callosciurus finlaysonii Finlayson's squirrel KY117540 30-AUG-2017 Callosciurus finlaysonii Finlayson's squirrel (frandseni) KY117541 30-AUG-2017 Callosciurus notatus Plantain squirrel KY117542 30-AUG-2017 Callosciurus notatus Plantain squirrel KY117543 30-AUG-2017 Callosciurus prevostii Prevost's squirrel ---------- Group II (1 sequence) KF575124 27-FEB-2014 Ratufa bicolor Black giant squirrel ---------- GROUP I (10 sequences) KU962990 31-MAR-2017 Sciurus vulgaris Eurasian Red squirrel KC992999 02-NOV-2015 Sciurus vulgaris fuscoater Eurasian red squirrel KC993000 02-NOV-2015 Sciurus vulgaris fuscoater Eurasian red squirrel KC993001 02-NOV-2015 Sciurus vulgaris fuscoater Eurasian red squirrel KC993002 02-NOV-2015 Sciurus vulgaris fuscoater Eurasian red squirrel KC993003 02-NOV-2015 Sciurus vulgaris fuscoater Eurasian red squirrel KC993004 02-NOV-2015 Sciurus vulgaris fuscoater Eurasian red squirrel KC993005 02-NOV-2015 Sciurus vulgaris fuscoater Eurasian red squirrel KC993006 02-NOV-2015 Sciurus vulgaris fuscoater Eurasian red squirrel KC993007 02-NOV-2015 Sciurus vulgaris fuscoater Eurasian red squirrel --------------------------------------------------------------------------------- Humanin sequences: ------------------ Group V (6 sequences) JQ230001 05-MAR-2013 Pteromys volans Siberian flying squirrel ATGGCTTAACGAGGGTTTAACTGTCTCTTACTCTCAATCAGTGAAATTGACCTTTCCGTGAAGAGGCGGAAAT.. M..A..X..R..G..F..N..C..L..L..L..S..I..S..E..I..D..L..S..V..K..R..R..K..X.. JQ743657 31-MAR-2014 Petaurista alborufus Red and white giant flying squirrel ATGGCTTAACGAGGGTTCAACTGTCTCTTACTCCCAATCAGTGAAATTGACCTCCCCGTGAAGAGGCGGGGAT.. M..A..X..R..G..F..N..C..L..L..L..P..I..S..E..I..D..L..P..V..K..R..R..G..X.. JX572159 21-MAR-2016 Petaurista hainana Hainan giant flying squirrel ATGGCTTGACGAGGGTTCAACTGTCTCTTACTCCCAATCAGTGAAATTGACCTCCCCGTGAAGAGGCGGGGAT.. M..A..W..R..G..F..N..C..L..L..L..P..I..S..E..I..D..L..P..V..K..R..R..G..X.. KC447305 01-FEB-2015 Hylopetes phayrei Indochinese flying squirrel ATGGCTTAACGAGGGTTTAACTGTCTCTTACTTTTAATCAGTGAAATTGACCTTTCCGTGAAGAGGCGGAAAT.. M..A..X..R..G..F..N..C..L..L..L..L..I..S..E..I..D..L..S..V..K..R..R..K..X.. KX528208 28-JAN-2017 Petaurista yunanensis Yunnan giant flying squirrel ATGGCTTAACGAGGGTTTAACTGTCTCTTACTCCCAATCAGTGAAATTGACCTCCCCGTGAAGAGGCGGGGAT.. M..A..X..R..G..F..N..C..L..L..L..P..I..S..E..I..D..L..P..V..K..R..R..G..X.. KX710106 30-OCT-2016 Hylopetes alboniger Particolored flying squirrel ATGGCTTAACGAGGGTTTAACTGTCTCTTACTTTCAATCAGTGAAATTGACCTTTCCGTGAAGAGGCGGAAAT.. M..A..X..R..G..F..N..C..L..L..L..S..I..S..E..I..D..L..S..V..K..R..R..K..X.. ---------------- Group IV (3 sequences) KP698974 10-JUN-2015 Ictidomys tridecemlineatus Thirteen-lined ground squirrel ATGGCTTGACGAGGGTTTAACTGTCTCTTACTTTTAATCAGTGAAATTGACCTTCCCGTGAAGAGGCGGGAAT.. M..A..W..R..G..F..N..C..L..L..L..L..I..S..E..I..D..L..P..V..K..R..R..E..X.. KP698975 31-AUG-2016 Callospermophilus lateralis Golden-mantled ground squirrel ATGGCTCAACGAGGGTTTAACTGTCTCTTACTTTTGATCAGTGAAATTGACCTCCCCGTGAAGAGGCGGGAAT.. M..A..Q..R..G..F..N..C..L..L..L..L..I..S..E..I..D..L..P..V..K..R..R..E..X.. KR534854 13-JUN-2015 Spermophilus dauricus Daurian ground squirrel ATGGCCCCACGAGGGTTTAACTGTCTCTTACTTTTAATCAGTGAAATTGACCCTCCCGTGAAGAGGCGGGGAT.. M..A..P..R..G..F..N..C..L..L..L..L..I..S..E..I..D..P..P..V..K..R..R..G..X.. ---------------- Group III - Exilisciurus (2 sequence) KR911801 19-APR-2016 Exilisciurus exilis Least pygmy squirrel ATGGCCAAACGAGGGTTTGACTGTCTCTTACTTTTAATCAGTGAAATTGACCTTCCCGTGAAGAGGCGGGAAT.. M..A..K..R..G..F..D..C..L..L..L..L..I..S..E..I..D..L..P..V..K..R..R..E..X.. KY117546 30-AUG-2017 Exilisciurus exilis Least pygmy squirrel ATGGCCAAACGAGGGTTTGACTGTCTCTTACTTTTAATCAGTGAAATTGACCTTCCCGTGAAGAGGCGGGAAT.. M..A..K..R..G..F..D..C..L..L..L..L..I..S..E..I..D..L..P..V..K..R..R..E..X.. - Rubisciurus (3 sequences) KR911790 19-APR-2016 Rubrisciurus rubriventer Sulawesi giant squirrel ATGGCCAAACGAGGGTTTATCTGTCTCTTACTTCCAATCAGTGAAATTGACCTTCCCGTGAAGAGGCGGGAAT.. M..A..K..R..G..F..I..C..L..L..L..P..I..S..E..I..D..L..P..V..K..R..R..E..X.. KR911791 19-APR-2016 Rubrisciurus rubriventer Sulawesi giant squirrel ATGGCCAAACGAGGGTTTATCTGTCTCTTACTTCCAATCAGTGAAATTGACCTTCCCGTGAAGAGGCGGGAAT.. M..A..K..R..G..F..I..C..L..L..L..P..I..S..E..I..D..L..P..V..K..R..R..E..X.. KR911792 19-APR-2016 Rubrisciurus rubriventer Sulawesi giant squirrel ATGGCCAAACGAGGGTTTATCTGTCTCTTACTTCCAATCAGTGAAATTGACCTTCCCGTGAAGAGGCGGGAAT.. M..A..K..R..G..F..I..C..L..L..L..P..I..S..E..I..D..L..P..V..K..R..R..E..X.. - Prosciurillus (8 sequences) KR911787 19-APR-2016 Prosciurillus weberi Weber's dwarf squirrel ATGGCCAAACGAGGGTTTATCTGTCTCTTACTTTCAATCAGTGAAATTGACCTTCCCGTGAAGAGGCGGGAAT.. M..A..K..R..G..F..I..C..L..L..L..S..I..S..E..I..D..L..P..V..K..R..R..E..X.. KR911788 19-APR-2016 Prosciurillus weberi Weber's dwarf squirrel ATGGCCAAACGAGGGTTTATCTGTCTCTTACTTTCAATCAGTGAAATTGACCTTCCCGTGAAGAGGCGGGAAT.. M..A..K..R..G..F..I..C..L..L..L..S..I..S..E..I..D..L..P..V..K..R..R..E..X.. KR911793 19-APR-2016 Prosciurillus abstrusus Secretive dwarf squirrel ATGGCTAAACGAGGGTTTATCTGTCTCTTACTTTCAATCAGTGAAATTGACCTTCCCGTGAAGAGGCGGGAAT.. M..A..K..R..G..F..I..C..L..L..L..S..I..S..E..I..D..L..P..V..K..R..R..E..X.. KR911794 19-APR-2016 Prosciurillus murinus Celebes dwarf squirrel ATGGCTAAACGAGGGTTTATCTGTCTCTTACTTTTAATCAGTGAAATTGACCTTCCCGTGAAGAGGCGGGAAT.. M..A..K..R..G..F..I..C..L..L..L..L..I..S..E..I..D..L..P..V..K..R..R..E..X.. KR911795 19-APR-2016 Prosciurillus murinus Celebes dwarf squirrel ATGGCTAAACGAGGGTTTATCTGTCTCTTACTTTTAATCAGTGAAATTGACCTTCCCGTGAAGAGGCGGGAAT.. M..A..K..R..G..F..I..C..L..L..L..L..I..S..E..I..D..L..P..V..K..R..R..E..X.. KR911784 19-APR-2016 Prosciurillus leucomus Whitish dwarf squirrel ATGGCCAAACGAGGGTTTATCTGTCTCTTACTTTCAATCAGTGAAATTGACCTTCCCGTGAAGAGGCGGGAAT.. M..A..K..R..G..F..I..C..L..L..L..S..I..S..E..I..D..L..P..V..K..R..R..E..X.. KR911785 19-APR-2016 Prosciurillus leucomus Whitish dwarf squirrel ATGGCCAAACGAGGGTTTATCTGTCTCTTACTTTCAATCAGTGAAATTGACCTTCCCGTGAAGAGGCGGGAAT.. M..A..K..R..G..F..I..C..L..L..L..S..I..S..E..I..D..L..P..V..K..R..R..E..X.. KR911786 19-APR-2016 Prosciurillus leucomus Whitish dwarf squirrel ATGGCCAAACGAGGGTTTATCTGTCTCTTACTTTCAATCAGTGAAATTGACCTTCCCGTGAAGAGGCGGGAAT.. M..A..K..R..G..F..I..C..L..L..L..S..I..S..E..I..D..L..P..V..K..R..R..E..X.. - Hyosciurus (2 sequences) KR911796 19-APR-2016 Hyosciurus ileile Lowland long-nosed squirrel ATGGCCAAACGAGGGTTTATCTGTCTCTTACTTTTAATCAGTGAAATTGACCTTTCCGTGAAGAGGCGGGAAT.. M..A..K..R..G..F..I..C..L..L..L..L..I..S..E..I..D..L..S..V..K..R..R..E..X.. KR911797 19-APR-2016 Hyosciurus heinrichi Montane long-nosed squirrel ATGGCCAAACGAGGGTTTATCTGTCTCTTACTTTTAATCAGTGAAATTGACCTTCCCGTGAAGAGGCGGGAAT.. M..A..K..R..G..F..I..C..L..L..L..L..I..S..E..I..D..L..P..V..K..R..R..E..X.. - Tamiops (2 sequences) KP027416 29-MAR-2015 Tamiops swinhoei Swinhoe's striped squirrel ATGGCTAAACGAGGGTTTATCTGTCTCTTACTTTCAATCAGTGAAATTGACCTCCCCGTGAAGAGGCGGGAAT.. M..A..K..R..G..F..I..C..L..L..L..S..I..S..E..I..D..L..P..V..K..R..R..E..X.. KP708710 10-FEB-2016 Tamiops maritimus Maritime striped squirrel ATGGTTAAAGGAGGGTTCATCTGTCTCTTACTTTCAATCAGTGAAATTGACCTTCCCGTGAAGAGCGGGAATC.. M..V..K..G..G..F..I..C..L..L..L..S..I..S..E..I..D..L..P..V..K..S..G..N..X.. - Dremonys (3 sequences) KP708711 31-JUL-2017 Dremomys pernyi Perny's long-nosed squirrel ATGGCCAAACGAGGGTTTATCTGTCTCTTACTTTTAATCAGTGAAATTGACCTTCCCGTGAAGAGGCGGGAAT.. M..A..K..R..G..F..I..C..L..L..L..L..I..S..E..I..D..L..P..V..K..R..R..E..X.. KC447304 01-FEB-2015 Dremomys rufigenis Asian red-cheeked squirrel ATGGCCAAACGAGGGTTTATCTGTCTCTTACTTTTAATCAGTGAAATTGACCTTCCCGTGAAGAGGCGGGAAT.. M..A..K..R..G..F..I..C..L..L..L..L..I..S..E..I..D..L..P..V..K..R..R..E..X.. KR911798 19-APR-2016 Dremomys everetti Bornean mountain ground squirrel ATGGCCAAACGAGGGTTTATCTGTCTCTTACTTTTAATCAGTGAAATTGACCTTCCCGTGAAGAGGCGGGAAT.. M..A..K..R..G..F..I..C..L..L..L..L..I..S..E..I..D..L..P..V..K..R..R..E..X.. - Nannosciurus (1 sequence) KT001463 19-APR-2016 Nannosciurus melanotis Black-eared squirrel ATGGCCAAACGAGGGTTTATCTGTCTCTTGCTTTCAATCAGTGAAATTGACCTTCCCGTGAAGAGGCGGGAAT.. M..A..K..R..G..F..I..C..L..L..L..S..I..S..E..I..D..L..P..V..K..R..R..E..X.. - Sundasciurus (3 sequences) KY117586 30-AUG-2017 Sundasciurus brookei Brooke's squirrel ATGGCCAAACGAGGGTTTATCTGTCTCTTACTTTTAATCAGTGAAATTGACCTTCCCGTGAAGAGGCGGGAAT.. M..A..K..R..G..F..I..C..L..L..L..L..I..S..E..I..D..L..P..V..K..R..R..E..X.. KY117587 30-AUG-2017 Sundasciurus lowii Low's squirrel ATGGCCAAACGAGGGTTTATCTGTCTCTTACTTTTAATCAGTGAAATTGACCTTCCCGTGAAGAGGCGGGAAT.. M..A..K..R..G..F..I..C..L..L..L..L..I..S..E..I..D..L..P..V..K..R..R..E..X.. KY117588 30-AUG-2017 Sundasciurus sp. FPF-2017 ATGGCAAAACGAGGGTTTATCTGTCTCTTACTTTTGATCAGTGAAATTGACCTTCCCGTGAAGAGGCGGGAAT.. M..A..K..R..G..F..I..C..L..L..L..L..I..S..E..I..D..L..P..V..K..R..R..E..X.. - Lariscus (1 sequence) KR911799 19-APR-2016 Lariscus insignis Three-striped ground squirrel ACGGCTAGACGAGGGTTAATCTGTCTCTTACTTTTAATCAGTGAAATTGACCTTCCCGTGAAGAGGCGGGAAT.. T..A..R..R..G..L..I..C..L..L..L..L..I..S..E..I..D..L..P..V..K..R..R..E..X.. - Callosciurus (8 sequences) KM502568 26-OCT-2014 Callosciurus erythraeus Pallas's squirrel ACGGCTAAACGAGGGTTAATCTGTCTCTTACTCTTAATCAGTGAAATTGACCTCCCCGTGAAGAGGCGGGGAT.. T..A..K..R..G..L..I..C..L..L..L..L..I..S..E..I..D..L..P..V..K..R..R..G..X.. KR911800 19-APR-2016 Callosciurus adamsi Ear-spot squirrel ACGGCTAGACGAGGGTTAATCTGTCTCTTACTTTTAATCAGTGAAATTGACCTTCCCGTGAAGAGGCGGGAAT.. T..A..R..R..G..L..I..C..L..L..L..L..I..S..E..I..D..L..P..V..K..R..R..E..X.. KY117538 30-AUG-2017 Callosciurus erythraeus Pallas's squirrel ACGGCTAAACGAGGGTTAATCTGTCTCTTACTTTTAATCAGTGAAATTGACCTTCCCGTGAAGAGGCGGGAAT.. T..A..K..R..G..L..I..C..L..L..L..L..I..S..E..I..D..L..P..V..K..R..R..E..X.. KY117539 30-AUG-2017 Callosciurus finlaysonii Finlayson's squirrel ACGGCTAAACGAGGGTTAATCTGTCTCTTACTTTTAATCAGTGAAATTGACCTTCCCGTGAAGAGGCGGGAAT.. T..A..K..R..G..L..I..C..L..L..L..L..I..S..E..I..D..L..P..V..K..R..R..E..X.. KY117540 30-AUG-2017 Callosciurus finlaysonii Finlayson's squirrel ACGGCTAAACGAGGGTTAATCTGTCTCTTACTTTTAATCAGTGAAATTGACCTTCCCGTGAAGAGGCGGGAAT.. T..A..K..R..G..L..I..C..L..L..L..L..I..S..E..I..D..L..P..V..K..R..R..E..X.. KY117541 30-AUG-2017 Callosciurus notatus Plantain squirrel ACGGCTAGACGAGGGTTAATCTGTCTCTTACTTTTAATCAGTGAAATTGACCTCCCCGTGAAGAGGCGGGGAT.. T..A..R..R..G..L..I..C..L..L..L..L..I..S..E..I..D..L..P..V..K..R..R..G..X.. KY117542 30-AUG-2017 Callosciurus notatus Plantain squirrel ACGGCTAAACGAGGGTTAATCTGTCTCTTACTTTTAATCAGTGAAATTGACCTCCCCGTGAAGAGGCGGGGAT.. T..A..K..R..G..L..I..C..L..L..L..L..I..S..E..I..D..L..P..V..K..R..R..G..X.. KY117543 30-AUG-2017 Callosciurus prevostii Prevost's squirrel ACGGCTAAACGAGGGTTAATCTGTCTCTTACTTTTAATCAGTGAAATTGACCTTCCCGTGAAGAGGCGGGAAT.. T..A..K..R..G..L..I..C..L..L..L..L..I..S..E..I..D..L..P..V..K..R..R..E..X.. ---------------- GROUP II (1 sequence) KF575124 27-FEB-2014 Ratufa bicolor Black giant squirrel ATGGCTGGACGAGGGTTCAACTGTCTCTTACTCCTAATCTGTGAAATTGACCTCCCTGTGAAAAGGCAGGGAT.. M..A..G..R..G..F..N..C..L..L..L..L..I..C..E..I..D..L..P..V..K..R..Q..G..X.. ---------------- GROUP I (10 sequences) KU962990 31-MAR-2017 Sciurus vulgaris Eurasian Red squirrel ATGGCCCCACGAGGGTTAAACTGTCTCTTACTTTTAATCAGTGAACTTGACCTTCCCGTGAAGAGGCGGGGAT.. M..A..P..R..G..L..N..C..L..L..L..L..I..S..E..L..D..L..P..V..K..R..R..G..X.. KC992999 02-NOV-2015 Sciurus vulgaris fuscoater Eurasian red squirrel ATGGCCCCACGAGGGTTAAACTGTCTCTTACTTTTAATCAGTGAACTTGACCTTCCCGTGAAGAGGCGGGGAT.. M..A..P..R..G..L..N..C..L..L..L..L..I..S..E..L..D..L..P..V..K..R..R..G..X.. KC993000 02-NOV-2015 Sciurus vulgaris fuscoater Eurasian red squirrel ATGGCCCCACGAGGGTTAAACTGTCTCTTACTTTTAATCAGTGAACTTGACCTTCCCGTGAAGAGGCGGGGAT.. M..A..P..R..G..L..N..C..L..L..L..L..I..S..E..L..D..L..P..V..K..R..R..G..X.. KC993001 02-NOV-2015 Sciurus vulgaris fuscoater Eurasian red squirrel ATGGCCCCACGAGGGTTAAACTGTCTCTTACTTTTAATCAGTGAACTTGACCTTCCCGTGAAGAGGCGGGGAT.. M..A..P..R..G..L..N..C..L..L..L..L..I..S..E..L..D..L..P..V..K..R..R..G..X.. KC993002 02-NOV-2015 Sciurus vulgaris fuscoater Eurasian red squirrel ATGGCCCCACGAGGGTTAAACTGTCTCTTACTTTTAATCAGTGAACTTGACCTTCCCGTGAAGAGGCGGGGAT.. M..A..P..R..G..L..N..C..L..L..L..L..I..S..E..L..D..L..P..V..K..R..R..G..X.. KC993003 02-NOV-2015 Sciurus vulgaris fuscoater Eurasian red squirrel ATGGCCCCACGAGGGTTAAACTGTCTCTTACTTTTAATCAGTGAACTTGACCTTCCCGTGAAGAGGCGGGGAT.. M..A..P..R..G..L..N..C..L..L..L..L..I..S..E..L..D..L..P..V..K..R..R..G..X.. KC993004 02-NOV-2015 Sciurus vulgaris fuscoater Eurasian red squirrel ATGGCCCCACGAGGGTTAAACTGTCTCTTACTTTTAATCAGTGAACTTGACCTTCCCGTGAAGAGGCGGGGAT.. M..A..P..R..G..L..N..C..L..L..L..L..I..S..E..L..D..L..P..V..K..R..R..G..X.. KC993005 02-NOV-2015 Sciurus vulgaris fuscoater Eurasian red squirrel ATGGCCCCACGAGGGTTAAACTGTCTCTTACTTTTAATCAGTGAACTTGACCTTCCCGTGAAGAGGCGGGGAT.. M..A..P..R..G..L..N..C..L..L..L..L..I..S..E..L..D..L..P..V..K..R..R..G..X.. KC993006 02-NOV-2015 Sciurus vulgaris fuscoater Eurasian red squirrel ATGGCCCCACGAGGGTTAAACTGTCTCTTACTTTTAATCAGTGAACTTGACCTTCCCGTGAAGAGGCGGGGAT.. M..A..P..R..G..L..N..C..L..L..L..L..I..S..E..L..D..L..P..V..K..R..R..G..X.. KC993007 02-NOV-2015 Sciurus vulgaris fuscoater Eurasian red squirrel ATGGCCCCACGAGGGTTAAACTGTCTCTTACTTTTAATCAGTGAACTTGACCTTCCCGTGAAGAGGCGGGGAT.. M..A..P..R..G..L..N..C..L..L..L..L..I..S..E..L..D..L..P..V..K..R..R..G..X.. ------------------------------------------------------------------------------------------ Papers: ------- Molecular phylogeny and biogeography of Petaurista inferred from the cytochrome b gene, with implications for the taxonomic status of P. caniceps, P. marica and P. sybilla. Li S, He K, Yu FH, Yang QS. PLoS One. 2013 Jul 26;8(7):e70461. Free download at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3724786/ Abstract The polymorphic genus Petaurista includes a group of diverse species and subspecies that are adapted for gliding and arboreal life. This morphological diversity has resulted in taxonomic discrepancies, and molecular phylogenetic studies have been limited by taxon sampling. To clarify this controversial taxonomy, we used the cytochrome b gene to reconstruct the phylogeny to obtain a more accurate picture of the evolutionary relationships, species differentiation and divergence pattern of Petaurista. The results revealed a significant inconsistency between taxonomic designations, phylogeny and genetic distances. When 6 recognized species were included, species delimitation revealed 15 putative species, a finding that warrants a comprehensive morphological diagnosis and a re-assessment of the species status. The validity of P. caniceps and P. marica was discussed. An estimation of the molecular divergence time demonstrated that the diversification and speciation of Petaurista began during the later Miocene and may have been affected by the uplifting of the Qinghai-Tibet plateau and subsequent climate change. --------------- Evolutionary history of endemic Sulawesi squirrels constructed from UCEs and mitogenomes sequenced from museum specimens. Hawkins MT, Leonard JA, Helgen KM, McDonough MM, Rockwood LL, Maldonado JE. BMC Evol Biol. 2016 Apr 14;16:80. Free download at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4831120/ Abstract BACKGROUND: The Indonesian island of Sulawesi has a complex geological history. It is composed of several landmasses that have arrived at a near modern configuration only in the past few million years. It is the largest island in the biodiversity hotspot of Wallacea-an area demarcated by the biogeographic breaks between Wallace's and Lydekker's lines. The mammal fauna of Sulawesi is transitional between Asian and Australian faunas. Sulawesi's three genera of squirrels, all endemic (subfamily Nannosciurinae: Hyosciurus, Rubrisciurus and Prosciurillus), are of Asian origin and have evolved a variety of phenotypes that allow a range of ecological niche specializations. Here we present a molecular phylogeny of this radiation using data from museum specimens. High throughput sequencing technology was used to generate whole mitochondrial genomes and a panel of nuclear ultraconserved elements providing a large genome-wide dataset for inferring phylogenetic relationships. RESULTS: Our analysis confirmed monophyly of the Sulawesi taxa with deep divergences between the three endemic genera, which predate the amalgamation of the current island of Sulawesi. This suggests lineages may have evolved in allopatry after crossing Wallace's line. Nuclear and mitochondrial analyses were largely congruent and well supported, except for the placement of Prosciurillus murinus. Mitochondrial analysis revealed paraphyly for Prosciurillus, with P. murinus between or outside of Hyosciurus and Rubrisciurus, separate from other species of Prosciurillus. A deep but monophyletic history for the four included species of Prosciurillus was recovered with the nuclear data. CONCLUSIONS: The divergence of the Sulawesi squirrels from their closest relatives dated to ~9.7-12.5 million years ago (MYA), pushing back the age estimate of this ancient adaptive radiation prior to the formation of the current conformation of Sulawesi. Generic level diversification took place around 9.7 MYA, opening the possibility that the genera represent allopatric lineages that evolved in isolation in an ancient proto-Sulawesian archipelago. We propose that incongruence between phylogenies based on nuclear and mitochondrial sequences may have resulted from biogeographic discordance, when two allopatric lineages come into secondary contact, with complete replacement of the mitochondria in one species. ----------------------- The effects of Cenozoic global change on squirrel phylogeny. Mercer JM, Roth VL. Science. 2003 Mar 7;299(5612):1568-72. Free download at: https://pdfs.semanticscholar.org/7596/8d20494c825146c94e2dae29c7002fd3c63d.pdf Abstract By modifying habitats and creating bridges and barriers between landmasses, climate change and tectonic events are believed to have important consequences for diversification of terrestrial organisms. Such consequences should be most evident in phylogenetic histories of groups that are ancient, widespread, and diverse. The squirrel family (Sciuridae) is one of very few mammalian families endemic to Eurasia, Africa, and North and South America and is ideal for examining these issues. Through phylogenetic and molecular-clock analyses, we infer that arrival and diversification of squirrels in Africa, on Sunda Shelf islands, across Beringea, and across the Panamanian isthmus coincide in timing and location with multiple well-documented sea-level, tectonic, and paleontological events. These precise correspondences point to an important role for global change in the diversification of a major group of mammals. ------------------------------------------------------------------------------------------ An expanded mammal mitogenome dataset from Southeast Asia. Gigascience. 2017 Aug 1;6(8):1-8. Mohd Salleh F, Ramos-Madrigal J, Peñaloza F, Liu S1, Mikkel-Holger SS, Riddhi PP, Martins R, Lenz D, Fickel J, Roos C, Shamsir MS, Azman MS, Burton KL, Stephen JR, Wilting A, Gilbert MTP. Gigascience. 2017 Aug 1;6(8):1-8. A free dwonload at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737531/ Abstract Southeast (SE) Asia is 1 of the most biodiverse regions in the world, and it holds approximately 20% of all mammal species. Despite this, the majority of SE Asia's genetic diversity is still poorly characterized. The growing interest in using environmental DNA to assess and monitor SE Asian species, in particular threatened mammals-has created the urgent need to expand the available reference database of mitochondrial barcode and complete mitogenome sequences. We have partially addressed this need by generating 72 new mitogenome sequences reconstructed from DNA isolated from a range of historical and modern tissue samples. Approximately 55 gigabases of raw sequence were generated. From this data, we assembled 72 complete mitogenome sequences, with an average depth of coverage of ×102.9 and ×55.2 for modern samples and historical samples, respectively. This dataset represents 52 species, of which 30 species had no previous mitogenome data available. The mitogenomes were geotagged to their sampling location, where known, to display a detailed geographical distribution of the species. Our new database of 52 taxa will strongly enhance the utility of environmental DNA approaches for monitoring mammals in SE Asia as it greatly increases the likelihoods that identification of metabarcoding sequencing reads can be assigned to reference sequences. This magnifies the confidence in species detections and thus allows more robust surveys and monitoring programmes of SE Asia's threatened mammal biodiversity. The extensive collections of historical samples from SE Asia in western and SE Asian museums should serve as additional valuable material to further enrich this reference database. ------------------------------------------------------------------------------------------ Genetic characterization of Callosciurus (Rodentia: Sciuridae) Asiatic squirrels introduced in Argentina M. GABRIELLI, Y. P. CARDOSO, V. BENITEZ, A. C. GOZZI, M. L. GUICHÓN, & M. S. LIZARRALDE Italian Journal of Zoology, 2014, 328–343, Vol. 81, No. 3. A free download at: https://www.tandfonline.com/doi/pdf/10.1080/11250003.2014.940006 Abstract Squirrels have been traded in the pet market for several decades, and numerous species have established in the wild. The Asiatic speciesCallosciurus erythraeus and Callosciurus finlaysonii have been introduced into other parts of Asia, in Europe and South America. In this study, (1) we conducted a genetic characterization of C. erythraeus introduced into Argentina and compared them with native and introduced populations in Asia, and (2) we analyzed genetic variation among the four invasion foci in Argentina in order to corroborate that the pathway of invasion was a single introduction event in the country and subsequent translocations. We analyzed mitochondrial (cytochrome b, Cyt b; cytochrome oxidase c subunit I, COI and D-loop) and nuclear (recombination activating gene I, RAGI) DNA markers using the classical method (DNA barcoding gap analysis) and also the Automatic Barcode Gap Discovery method (ABGD). The markers D-loop, COI, and RAG1 indicated that the introduced squirrels from the different invasion foci formed a monophyletic group that, together with only one haplotype for the D-loop and COI markers, supported the hypothesis of one introduction event into Argentina followed by subsequent translocations. Unexpectedly, sequences from squirrels captured in Argentina were more related to C. finlaysonii than to C. erythraeus for D-loop and Cyt b markers. However, intraspecific variation among sequences of C. erythraeus belonging to different subspecies or collected in different regions was large and comparable with the distance to the sequences from Argentina. The ABGD method also indicated large genetic variability within C. erythraeus and close proximity between squirrels from Argentina and C. finlaysonii. The complex taxonomy of Callosciurus , as occurs with the sister species C. erythraeus and C. finlaysonii, requires a thorough systematic revision. A simultaneous analysis of diagnostic morphological characters and genetic markers is needed and will provide new insight regarding the worldwide invasion of Asiatic squirrels. ------------------------------------------------------------------------------------------ Complete mitochondrial genome of the black giant squirrel Ratufa bicolor (Rodentia: Sciuridae). Kong L, Wang W, Cong H, Liu Z, Li Y. Mitochondrial DNA. 2015;26(5):759-60. Abstract The complete mitochondrial genome of black giant squirrel (Ratufa bicolor) from Hainan Island was sequenced and characterized in detail. The 16,563?bp genome was composed of 13 protein-coding genes, 22 tRNAs, 2 rRNAs and 2 non-coding regions. The mitochondrial genome of R. bicolor presented in this report will be useful for species identification, conversation and clarifying the controversial taxonomic status of genus Ratufa. ------------------------------------------------------------------------------------------ Assessment of Human Impact on the Genetic Diversity of Tropical Forest Taxa A thesis submitted to the University of Manchester for the degree of Doctor of Philosophy in the Faculty of Life Sciences 2015 SALISA JUMPA A free download at: https://www.research.manchester.ac.uk/portal/files/54573619/FULL_TEXT.PDF ------------------------------------------------------------------------------------------ Conserved microsatellite markers of high cross-species utility for flying, ground and tree squirrels Salisa Jumpa,Deborah A. Dawson,Gavin J. Horsburgh,Catherine Walton Conservation Genet Resour (2015) 7:599–603 A free download at: https://link.springer.com/content/pdf/10.1007%2Fs12686-015-0439-1.pdf Abstract Many squirrel species around the world are threatened by forest loss and fragmentation. To facilitate studies of squirrel biodiversity, particularly of flying squirrels in Southeast Asia, we identified Hylopetes, Menetes, Glaucomys and Sciurus squirrel microsatellite sequences with homologs in a second squirrel species (Spermophilus tridecemlineatus), designed 40 consensus markers and tested three squirrel species. When tested in four individuals per species, 26 markers were variable in Hylopetes phayrei, 25 markers in H. lepidus and 25 markers in Menetes berdmorei. Eleven markers were selected from 14 that were polymorphic in all three species. Cross-species utility was confirmed for these 11 markers in seven additional squirrel species, including: the flying squirrels H. phayrei, H. lepidus, H. spadiceus and Petaurista petaurista; a ground squirrel, M. berdmorei; and the tree squirrels, Callosciurus caniceps and C. finlaysoni. The other markers that were variable in one or multiple species are also useful for those specific species. ------------------------------------------------------------------------------------------ Mitochondrial Genetic Diversity of Eurasian Red Squirrels (Sciurus vulgaris) from Denmark. Madsen CL, et al. J Hered. 2015 Nov-Dec;106(6):719-27. A free download at: https://academic.oup.com/jhered/article/106/6/719/2622876 Abstract Melanistic Eurasian red squirrels Sciurus vulgaris are commonly found on the Danish island of Funen. They are thought to represent native Danish squirrel types and are presently under threat from admixture with introduced red squirrels. In response, a conservation program was started in 2009 that involves the translocation of melanistic squirrels from Funen to the squirrel-free island of Langeland. Using mitochondrial DNA of 101 historical and modern samples from throughout Denmark, we assess for the first time population structure and mitochondrial genetic diversity of Danish squirrels compared to its larger pan-Eurasian distribution. We find that Danish squirrels have low levels of genetic diversity, especially melanistic individuals. Bayesian skyline reconstructions show that Danish squirrels have most probably experienced a severe bottleneck within the last 200 years. Also, fine-scale genetic structure was found between squirrels from the regions of Funen, Zealand and Jutland, which mimics the insular geography of Denmark. Additional nuclear DNA analyses will be required to determine the precise admixture levels between original Danish and introduced squirrels and to locate unmixed candidate populations for specific conservation efforts. ------------------------------------------------------------------------------------------