Supplementary Information

Table A – Platanista samples collected for this study and sequences obtained from GenBank that were included in the analyses, with details of the year and location of origin, museum, record number and which sequences and haplotypes were obtained.

Study ID / Sub-species / Tissue / Country of Origin / Location of Origin / Year Collected / Museum/ Source / Museum No. / Control Region / cytb /
Partial / Complete /
PL67 / minor / bone / Pakistan / Punjab / 1970s? / Pakistan MNH / - / - / - / -
PL55 / minor / dried skin & bone / Pakistan / Begari, Sindh / 1978 / Stuttgart SMN / 42497 / Y (D) / - / -
PL56 / minor / dried skin & bone / Pakistan / Begari, Sindh / 1978 / Stuttgart SMN / 42498 / Y (D& SA) / Y (SA)
Hap-1 / Y (SA)
Hap-4
PL57 / minor / dried skin & bone / Pakistan / Tappu Island, Sukkur / Nov-1969 / Stuttgart SMN / 45631 / Y (D& SA) / Y (SA)
Hap-1 / -
PL58 / minor / dried skin & bone / Pakistan / Tappu Island, Sukkur / Nov-1969 / Stuttgart SMN / 45632 / Y (D& SA) / Y (SA)
Hap-1 / Y (SA)
Hap-4
PL59 / minor / dried skin & bone / Pakistan / Tappu Island, Sukkur / Nov-1969 / Stuttgart SMN / 45633 / Y (D& SA) / Y (SA)
Hap-1 / -
PL60 / minor / dried skin & bone / Pakistan / Tappu Island, Sukkur / Nov-1969 / Stuttgart SMN / 45634 / Y (D) / - / -
PL61 / minor / dried skin & bone / Pakistan / Tappu Island, Sukkur / Nov-1969 / Stuttgart SMN / 45635 / Y (D) / - / Y (SA)
Hap-4
PL62 / minor / dried skin & bone / Pakistan / Tappu Island, Sukkur / Nov-1969 / Stuttgart SMN / 45636 / Y (D& SA) / Y (SA)
Hap-1 / -
PL63 / minor / dried skin & bone / Pakistan / Chak, Guddu-Sukkur / 1972 / Stuttgart SMN / 45637 / Y (D) / - / -
PL64 / minor / dried skin & bone / Pakistan / Chak, Guddu-Sukkur / 1972 / Stuttgart SMN / 45638 / Y (D) / - / -
PL65 / minor / dried skin & bone / Pakistan / Chak, Guddu-Sukkur / 1974 / Stuttgart SMN / 45639 / Y (D& SA) / Y (SA)
Hap-1 / Y (SA)
Hap-3
PL66 / minor / dried skin & bone / Pakistan / Chak, Guddu-Sukkur / 1974 / Stuttgart SMN / 45640 / Y (D& SA) / Y (SA)
Hap-1 / Y (SA)
Hap-4
PL53 / minor / dried skin & bone / Pakistan / Chak, Guddu-Sukkur / 1976 / Stuttgart SMN / 45641 / Y (D& SA) / Y (SA)
Hap-1 / -
PL52 / minor / dried skin & bone / Pakistan / Chak, Guddu-Sukkur / 1976 / Stuttgart SMN / 45642 / Y (D) / - / -
PL51 / minor / dried skin & bone / Pakistan / Chak, Guddu-Sukkur / 1976 / Stuttgart SMN / 45643 / Y (D) / - / -
PL50 / minor / dried skin & bone / Pakistan / Guddu-Sukkur / Apr-1977 / Stuttgart SMN / 45644 / - / - / -
PL49 / minor / dried skin & bone / Pakistan / Guddu-Sukkur / Apr-1977 / Stuttgart SMN / 45645 / - / - / -
PL48 / minor / dried skin & bone / Pakistan / Guddu-Sukkur / Apr-1977 / Stuttgart SMN / 45646 / Y (D& SA) / Y (SA)
Hap-1 / Y (SA)
Hap-3
PL47 / minor / dried skin & bone / Pakistan / Guddu-Sukkur / Apr-1977 / Stuttgart SMN / 45647 / Y (D& SA) / Y (SA)
Hap-1 / -
PL40 / minor / dried skin & bone / Pakistan / Tappu Island, Sukkur / 1969 / Stuttgart SMN / 46802 / Y (SA) / Y (SA)
Hap-2 / Y (SA)
Hap-4
PL41 / minor / bone / Pakistan / Chak, Guddu-Sukkur / 1972 / Stuttgart SMN / 46833 / - / - / -
PL42 / minor / bone / Pakistan / Chak, Guddu-Sukkur / 1972 / Stuttgart SMN / 46834 / Y (D) / - / Y (SA)
Hap-4
PL43 / minor / bone / Pakistan / Chak, Guddu-Sukkur / 1972 / Stuttgart SMN / 46835 / - / - / -
PL44 / minor / bone / Pakistan / Chak, Guddu-Sukkur / 1972 / Stuttgart SMN / 46836 / - / - / -
PL45 / minor / bone / Pakistan / Chak, Guddu-Sukkur / 1972 / Stuttgart SMN / 46837 / Y (SA) / Y (SA)
Hap-1 / -
PL46 / minor / bone / Pakistan / Chak, Guddu-Sukkur / 1957 / Stuttgart SMN / 46844 / - / - / -
PL4 / minor / bone / Pakistan / Guddu-Sukkur / 1969 or 1970 / NM Scotland / 1991.43.4 / - / - / -
PL5 / minor / bone / Pakistan / Guddu-Sukkur / 1969 or 1970 / NM Scotland / 1991.43.5 / - / - / -
PL6 / minor / bone / Pakistan / Guddu-Sukkur / 1969 or 1970 / NM Scotland / 1991.43.6 / - / - / -
PL7 / minor / bone / Pakistan / Guddu-Sukkur / 1969 or 1970 / NM Scotland / 1991.43.7 / - / - / -
PL8 / minor / bone / Pakistan / Guddu-Sukkur / 1969 or 1970 / NM Scotland / 1991.43.8 / - / - / -
PL9 / minor / bone / Pakistan / Guddu-Sukkur / 1969 or 1970 / NM Scotland / 1991.43.9 / - / - / -
PL2 / minor / bone / Pakistan / Guddu-Sukkur / 1975 / NM Scotland / 1991.43.2 / Y (SA) / Y (SA)
Hap-1 / -
PL3 / minor / bone / Pakistan / Guddu-Sukkur / 1975 / NM Scotland / 1991.43.3 / Y (SA) / Y (SA)
Hap-1 / -
PL1 / minor / bone / Pakistan / Guddu-Sukkur / 1975 / NM Scotland / 1991.43.1 / Y (D& SA) / Y (SA)
Hap-1 / -
PL28 / minor / bone / Pakistan / Indus River / late 1800s / NHM, London / 1874.4.13.4 / - / - / -
PM1 / minor / fresh tissue / Pakistan / Sukkur / 2001 / SWFSC / PM012001 / Y (SA) / Y (SA)
Hap-1 / Y (SA)
Hap-3
PM2 / minor / fresh tissue / Pakistan / Sukkur / 2002 / SWFSC / PM012002 / Y (SA) / Y (SA)
Hap-1 / Y (SA)
Hap-4
PL16 / gangetica / dried skin & bone / India / Gela bil, Assam / Dec-1969 / Stuttgart SMN / 45648 / Y (D) / - / -
PL15 / gangetica / dried skin & bone / India / Gela bil, Assam / Dec-1969 / Stuttgart SMN / 45649 / - / - / -
PL14 / gangetica / dried skin & bone / India / Gela bil, Assam / Dec-1969 / Stuttgart SMN / 45650 / - / - / -
PL12 / gangetica / dried skin & bone / India / Gela bil, Assam / Dec-1969 / Stuttgart SMN / 45651 / - / - / -
PL13 / gangetica / dried skin & bone / India / Gela bil, Assam / Dec-1969 / Stuttgart SMN / 45652 / - / - / -
PL11 / gangetica / dried skin & bone / India / Gela bil, Assam / Dec-1969 / Stuttgart SMN / 45653 / Y (D) / - / -
PL18 / gangetica / dried skin & bone / India / Gela bil, Assam / Dec-1969 / Stuttgart SMN / 45654 / - / - / -
PL17 / gangetica / dried skin & bone / India / Ganges River / N/K / Stuttgart SMN / 26397 / Y (D) / - / -
PL22 / gangetica / bone / India / Hooghly River / 1866 / NM Scotland / 1948.53 / - / - / -
PL20 / gangetica / bone / India / Hooghly River / 1860s / NM Scotland / 1991.44.1 / - / - / -
PL21 / gangetica / bone / India / Hooghly River / 1860s / NM Scotland / 1991.44.2 / - / - / -
PL19 / gangetica / bone / India / Uttar Pradesh / 1880 / NM Scotland / 1991.44.4 / - / - / -
PL31 / gangetica / bone / India / River Hooghly, Calcutta / 28-Dec-1865 / NHM, London / 1874.6.1.1 / - / - / -
PL30 / gangetica / dried tissue & bone / India / Calcutta / late 1800s / NHM, London / 1884.3.29.1 / - / - / -
PL32 / gangetica / dried tissue & bone / India / Benares, Ganges River / 13-Dec-1895 / NHM, London / 1895.5.20.2 / - / - / -
PL33 / gangetica / bone / India / Ganges River / 1843 / NHM, London / 1843.8.18.5 / - / - / -
PL29 / gangetica / bone / India / Benares, Ganges River / N/K / NHM, London / GERM 334A / - / - / -
PL27 / gangetica / dried tissue & bone / India / River Jumna, Kiola near Mattra / 14-Apr-1897 / NHM, London / 1897.6.30.1 / - / - / -
PL38 / unknown / bone / N/K / N/K / N/K / NM Scotland / 1981.57.510 / - / - / -
PL36 / unknown / bone / N/K / N/K / N/K / NM Scotland / 1991.49 / - / - / -
PL37 / unknown / bone / N/K / N/K / N/K / NM Scotland / - / - / - / -
PL35 / unknown / bone / N/K / N/K / 1800s? / University of St. Andrews / 1 / - / - / -
PL34 / unknown / bone / N/K / N/K / 1800s? / University of St. Andrews / 2 / - / - / -
PL25 / unknown / dried tissue & tooth / N/K / N/K / Late 1800s / Cambridge, UMZ / C.64.B / - / - / -
PL24 / unknown / dried tissue & tooth / N/K / N/K / 1881 / Cambridge, UMZ / C.62.A / - / - / -
PL23 / unknown / dried tissue / N/K / N/K / Late 1800s / Cambridge, UMZ / C.63.A / - / - / -
AJ554058 / minor / N/A / Pakistan / N/K / - / (Arnason et al. 2004) / - / Y (GenB) / Y (GenB)
Hap-3 / Y (GenB)
Hap-3
AY102527 / gangetica / N/A / India / Ganges River, Patna, Bihar / - / (Verma et al. 2004) / - / Y (GenB) / Y (GenB)
Hap-4 / -
AY102528 / gangetica / N/A / Bangladesh / Kaptai Lake, Karnaphuli River / - / (Verma et al. 2004) / - / Y (GenB) / Y (GenB)
Hap-4 / -
AY102529 / gangetica / N/A / India / Ganges River, Patna, Bihar / - / (Verma et al. 2004) / - / Y (GenB) / Y (GenB)
Hap-4 / -
AY102530 / gangetica / N/A / India / Ganges River, Patna, Bihar / - / (Verma et al. 2004) / - / Y (GenB) / Y (GenB)
Hap-4 / -
AY102531 / gangetica / N/A / India / Ganges River, Patna, Bihar / - / (Verma et al. 2004) / - / Y (GenB) / Y (GenB)
Hap-4 / -
AY102532 / gangetica / N/A / Bangladesh / Kaptai Lake, Karnaphuli River / - / (Verma et al. 2004) / - / Y (GenB) / Y (GenB)
Hap-4 / -
AY102533 / gangetica / N/A / India / Ganges River, Patna, Bihar / - / (Verma et al. 2004) / - / Y (GenB) / Y (GenB)
Hap-4 / -
AY102534 / gangetica / N/A / India / Ganges River, Patna, Bihar / - / (Verma et al. 2004) / - / Y (GenB) / Y (GenB)
Hap-6 / -
AY102535 / gangetica / N/A / India / Ganges River, Patna, Bihar / - / (Verma et al. 2004) / - / Y (GenB) / Y (GenB)
Hap-6 / -
AY102536 / gangetica / N/A / India / Ganges River, Patna, Bihar / - / (Verma et al. 2004) / - / Y (GenB) / Y (GenB)
Hap-5 / -
AY102537 / gangetica / N/A / India / Ganges River, Patna, Bihar / - / (Verma et al. 2004) / - / Y (GenB) / Y (GenB)
Hap-5 / -
AY102538 / gangetica / N/A / India / N/K / - / (Verma et al. 2004) / - / Y (GenB) / Y (GenB)
Hap-5 / -
AY102539 / gangetica / N/A / India / N/K / - / (Verma et al. 2004) / - / Y (GenB) / Y (GenB)
Hap-5 / -
Gachal-7 / minor / N/A / Pakistan / Sindh / - / (Gachal 2001) / - / - / - / Y
Hap-4
Gachal-6 / minor / N/A / Pakistan / Sindh / - / (Gachal 2001) / - / - / - / Y partial
Gachal-5 / minor / N/A / Pakistan / Sindh / - / (Gachal 2001) / - / - / - / Y partial
Gachal-2 / minor / N/A / Pakistan / Sindh / - / (Gachal 2001) / - / - / - / Y partial
AY102512 / gangetica / N/A / India / Kurzi, Patna, Ganges River / - / (Verma et al. 2004) / - / - / - / Y (GenB)
Hap-2
AY102513 / gangetica / N/A / India / Digha, Patna, Ganges River / - / (Verma et al. 2004) / - / - / - / Y (GenB)
Hap-2
AY102514 / gangetica / N/A / India / Durja, Patna, Ganges River / - / (Verma et al. 2004) / - / - / - / Y (GenB)
Hap-2
AY102515 / gangetica / N/A / India / Patna, Ganges River / - / (Verma et al. 2004) / - / - / - / Y (GenB)
Hap-2
AY102516 / gangetica / N/A / India / Patna, Ganges River / - / (Verma et al. 2004) / - / - / - / Y (GenB)
Hap-2
AY102517 / gangetica / N/A / India / Durja, Patna, Ganges River / - / (Verma et al. 2004) / - / - / - / Y (GenB)
Hap-2
AY102518 / gangetica / N/A / India / Balughat, Patna, Ganges River / - / (Verma et al. 2004) / - / - / - / Y (GenB)
Hap-2
AY102519 / gangetica / N/A / India / Patna, Ganges River / - / (Verma et al. 2004) / - / - / - / Y (GenB)
Hap-2
AY102520 / gangetica / N/A / Indi / Kasmar, Pahleza, Patna, Ganges River / - / (Verma et al. 2004) / - / - / - / Y (GenB)
Hap-2
AY102521 / gangetica / N/A / India / Ghagha Ghat, Patna, Ganges River / - / (Verma et al. 2004) / - / - / - / Y (GenB)
Hap-4
AY102522 / gangetica / N/A / India / Bangladesh / - / (Verma et al. 2004) / - / - / - / Y (GenB)
Hap-4
AY102523 / gangetica / N/A / India / Durja, Patna, Ganges River / - / (Verma et al. 2004) / - / - / - / Y (GenB)
Hap-4
AY102524 / gangetica / N/A / India / Digha, Patna, Ganges River / - / (Verma et al. 2004) / - / - / - / Y (GenB)
Hap-4
AY102525 / gangetica / N/A / India / Pahleza ghat, Patna, Ganges River / - / (Verma et al. 2004) / - / - / - / Y (GenB)
Hap-4
AY102526 / gangetica / N/A / Bangladesh / N/K / - / (Verma et al. 2004) / - / - / - / Y (GenB)
Hap-4
AF158376 / gangetica / N/A / Bangladesh / Dhaka / - / (Yang et al. 2002) / - / - / Y (GenB)
Hap-1
AF334483 / gangetica / N/A / probably originated Bangladesh. / Stored in National Science Museum Tokyo, Japan, / - / (Hamilton et al. 2001) / - / - / Y (GenB)
AF304070 / gangetica / N/A / India / 100km upstream Patna, Ganges River / - / (Cassens et al. 2000) / - / - / Y (GenB)
Hap-2

Museums: Staatliches Museum für Naturkunde Stuttgart, Bell-Pettigrew Museum of Natural History University of St. Andrews, Cambridge University Museum of Zoology, National Museums of Scotland (Edinburgh), Pakistan Natural History Museum, SWFSC, Southwest Fisheries Science Center, N/K = not known, N/A = not applicable. Partial control region sequences, 458bp; Complete control region sequence, 586bp; Cytb= cytochrome b sequence. D=sequence produced by work at Durham University, SA= sequence produced by work at the University of St. Andrews, GenB = Sequence downloaded from GenBank.

Table B - Primers for Platanista mitochondrial control and cytochrome b regions.

Primer name / Gene / sequence
CRPL3F / CR / GGTTGCGGGCCTATTCCGTCCGTGA
CRPL3R / CR / GGGGATTAGTGGAGTACTATGTCCTGT
CRPL2F / CR / TATATATGCTATGTATAATCGTGCA
CRPL2R / CR / GAGAAATACCAACTGTACTGAGTCC
PL d1 F / CR / CTATACCTCACCGCCAGCAC
PL int R / CR / GCAACCATCGTGATGTCTTA
PL int F / CR / CGTGGGGGTAGCTAATTATGA
PL d1 R / CR / TCAGTGTCTTGCTTTTTGAGATG
PLtRNAcytBF / Cytb / ccatgaccaatgacatgaaaa
PLtRNAcyt BintR / Cytb / gttggatggaattcctgtgg
PLtRNAcyt BintF / Cytb / cacgaaacaggctcaaacaa
PLtRNAcytBR / Cytb / AGGGTATTTCGTTATACTACG