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Table 3 Sequences from previous studies included in the mt dataset.

From: Revisiting the taxonomy of the Rattini tribe: a phylogeny-based delimitation of species boundaries

Voucher Nominal species Origin of specimen Cytb COI Phylogenetic species
RrHu1 R. rattus Huahine, Society Islands [GenBank: EF186469] [GenBank: EF186584] R1
RrSamoa2 R. rattus Samoa [GenBank: EF186475] [GenBank: EF186590] R1
RrRa18 R. rattus Raiatea, Society Islands [GenBank: EF186474] [GenBank: EF186589] R1
ABTC50177 R. rattus Sideia Is., Papua New Guinea [GenBank: EF186472] [GenBank: EF186587] R1
ABTC64906 R. rattus diardi (1) Kuala Lumpur, Malaysia [GenBank: EF186413] [GenBank: EF186528] R3
ABTC64907 R. rattus diardi Kuala Lumpur, Malaysia [GenBank: EF186409] [GenBank: EF186524] R3
ABTC64908 R. rattus diardi Kuala Lumpur, Malaysia [GenBank: EF186410] [GenBank: EF186525] R3
ABTC64909 R. rattus diardi Kuala Lumpur, Malaysia [GenBank: EF186411] [GenBank: EF186526] R3
ABTC64910 R. rattus diardi Kuala Lumpur, Malaysia [GenBank: EF186412] [GenBank: EF186527] R3
ABTC 8529 R. kandianus (2) Sri Lanka [GenBank: EF186444] [GenBank: EF18655] R3
ABTC 8536 R. kandianus Sri Lanka [GenBank: EF186445] [GenBank: EF186560] R3
ABTC 8540 R. kandianus Sri Lanka [GenBank: EF186446] [GenBank: EF186561] R3
ABTC 8487 R. tanezumi Amami Island, Japan [GenBank: EF186508] [GenBank: EF186623] R2
ABTC 8562 R. tanezumi Amami Island, Japan [GenBank: EF186510] [GenBank: EF186625] R2
ABTC47981 R. tanezumi Yogyakarta, Indonesia [GenBank: EF186493] [GenBank: EF186608] R2
ABTC47982 R. tanezumi Yogyakarta, Indonesia [GenBank: EF186494] [GenBank: EF186609] R2
ABTC47983 R. tanezumi Yogyakarta, Indonesia [GenBank: EF186495] [GenBank: EF186610] R2
ABTC47984 R. tanezumi Yogyakarta, Indonesia [GenBank: EF186502] [GenBank: EF186617] R2
ABTC47985 R. tanezumi Yogyakarta, Indonesia [GenBank: EF186503] [GenBank: EF186618] R2
ABTC47986 R. tanezumi Yogyakarta, Indonesia [GenBank: EF186504] [GenBank: EF186619] R2
ABTC47987 R. tanezumi Yogyakarta, Indonesia [GenBank: EF186505] [GenBank: EF186620] R2
ABTC47988 R. tanezumi Yogyakarta, Indonesia [GenBank: EF186506] [GenBank: EF186621] R3
ABTC47989 R. tanezumi Yogyakarta, Indonesia [GenBank: EF186507] [GenBank: EF186622] R2
ABTC47992 R. tanezumi Jakarta, Indonesia [GenBank: EF186490] [GenBank: EF186605] R3
ABTC47993 R. tanezumi Jakarta, Indonesia [GenBank: EF186491] [GenBank: EF186606] R2
ABTC47994 R. tanezumi Jakarta, Indonesia [GenBank: EF186492] [GenBank: EF186607] R5
ABTC47995 R. tanezumi Jakarta, Indonesia [GenBank: EF186496] [GenBank: EF186611] R3
ABTC47996 R. tanezumi Jakarta, Indonesia [GenBank: EF186497] [GenBank: EF186612] R3
ABTC47997 R. tanezumi Jakarta, Indonesia [GenBank: EF186498] [GenBank: EF186613] R3
ABTC47998 R. tanezumi Jakarta, Indonesia [GenBank: EF186499] [GenBank: EF186614] R3
ABTC47999 R. tanezumi Jakarta, Indonesia [GenBank: EF186500] [GenBank: EF186615] R3
ABTC48000 R. tanezumi Jakarta, Indonesia [GenBank: EF186501] [GenBank: EF186616] R3
ABTC48004 R. tanezumi Northern Sulawesi, Indonesia [GenBank: EF186511] [GenBank: EF186626] R3
ABTC48005 R. tanezumi Northern Sulawesi, Indonesia [GenBank: EF186512] [GenBank: EF186627] R3
ABTC 8489 R. flavipectus (3) Hong Kong, China [GenBank: EF186440] [GenBank: EF186555] R2
Chat2 R. exulans Chatham Islands, New Zealand [GenBank: EF186426] [GenBank: EF186541] R8
CI 6 R. exulans Aitutaki, Cook Islands [GenBank: EF186414] [GenBank: EF186529] R8
Fiji1 R. exulans Fiji [GenBank: EF186417] [GenBank: EF186532] R8
Hawaii3 R. exulans Hawaii [GenBank: EF186418] [GenBank: EF186533] R8
Hu38 R. exulans Huahine, Society Islands [GenBank: EF186420] [GenBank: EF186535] R8
Kap6 R. exulans Kapiti Island, New Zealand [GenBank: EF186425] [GenBank: EF186540] R8
Ra22 R. exulans Raiatea, Society Islands [GenBank: EF186429] [GenBank: EF186544] R8
RNZAwa01 R. exulans Great Barrier Island, New Zealand [GenBank: EF186424] [GenBank: EF186539] R8
Samoa 3 R. exulans Manua, Samoa [GenBank: EF186430] [GenBank: EF186545] R8
Taku5 R. exulans Takutea, Cook Islands [GenBank: EF186416] [GenBank: EF186531] R8
UaHuka4 R. exulans UaHuka, Marquesas Islands [GenBank: EF186422] [GenBank: EF186537] R8
ABTC 8480 R. exulans Thailand [GenBank: EF186434] [GenBank: EF186549] R8
ABTC 8553 R. exulans Thailand [GenBank: EF186432] [GenBank: EF186547] R8
ABTC 8559 R. exulans Thailand [GenBank: EF186433] [GenBank: EF186548] R8
ABTC43078 R. exulans Yuro, Papua New Guinea [GenBank: EF186427] [GenBank: EF186542] R8
ABTC48011 R. exulans Cibodas Forest, Java, Indonesia [GenBank: EF186421] [GenBank: EF186536] R8
ABTC48895 R. exulans Nagada Harbour, Papua New Guinea [GenBank: EF186428] [GenBank: EF186543] R8
ABTC65753 R. hoffmanni Tangoa, Sulawesi, Indonesia [GenBank: EF186443] [GenBank: EF186558] -
ABTC65754 R. hoffmanni Tangoa, Sulawesi, Indonesia [GenBank: EF186441] [GenBank: EF186556] -
ABTC65809 R. hoffmanni Mt Nokilalaki, Sulawesi, Indonesia [GenBank: EF186442] [GenBank: EF186557] -
Rargen_1266 R. argentiventer** Bangkok, Thailand O.Verneau, unpublished - R6
Rsikki_866 R. sikkimensis **(4) Mocchan, Vietnam O.Verneau, unpublished - R7
ABTC48025 R. tiomanicus Cibodas Forest, Java, Indonesia [GenBank: EF186514] [GenBank: EF186629] R5
ABTC48026 R. tiomanicus Cibodas Forest, Java, Indonesia [GenBank: EF186513] [GenBank: EF186628] R5
Rn Ra 15 R. norvegicus Raiatea, Society Islands [GenBank: EF186462] [GenBank: EF186577] R9
Rn Hu 21 R. norvegicus Huahine, Society Islands [GenBank: EF186461] [GenBank: EF186576] R9
  1. "Nominal species" stands for the identification given to the specimen by the curator or the collector ([25] and F. Catzeflis, pers. comm.).
  2. "Phylogenetic species" relies on the DNA-based species delimitation method (see also Figure 3).
  3. (1) Rattus rattus diardi: Robins et al [25] reports that the specimens ABTC64906-64910 are identified by the South Australian Museum as the subspecies Rattus rattus diardi (not diardii) as listed by Ellerman [71] on the basis on R. r. diardi after Jentink [72]. As already mentioned by Robins et al., [25], R. diardii (after Jentink 1880) is however considered as a synonym for R. tanezumi by Musser and Carleton [16] but there is no 1880 reference in their bibliography.
  4. (2) R. kandianus is listed as a synonym of R. rattus [16], (3) R. flavipectus of R. tanezumi [16], (4) R. sikkimensis of R. andamanensis [16].
  5. ** indicates that specimens are no more available in the mammal tissue collection housed at the Institut des Sciences de l'Evolution de Montpellier [73].
  6. Mismatches between nominal species and phylogenetic species are highlighted in bold.