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Matrix 45949 of Study 22736

About Citation title: "Diversification rates of the ?Old Endemic? murine rodents of Luzon Island, Philippines are inconsistent with incumbency-mediated cladogenesis and ecological opportunity".
About Study name: "Diversification rates of the ?Old Endemic? murine rodents of Luzon Island, Philippines are inconsistent with incumbency-mediated cladogenesis and ecological opportunity".
About This study is part of submission 22736 (Status: Published).

Matrices

Title: Murinae RAxML Alignment

Description: Concatenated Matrix of CYTB, GHR, IRBP, BRCA1, RAG1, ACP5, and FGB7 used in RAxML reconstruction (converted to .nex)

Rows

Taxon Label Row Segments Characters 1?–30
Hapalomys delacouri R5237  (none) ATGACAAACATCCGAAAATCACACCCACTA
Crateromys australis  (none) ATGACAATCATCCGAAAAACCCACCCACTA
Batomys hamiguitan  (none) ATGACAAACATCCGAAAAACCCACCCATTA
Batomys salomonseni  (none) ATGACAAACATCCGAAAAACCCACCCATTA
Crateromys heaneyi  (none) ATGACAAATATCCGAAAAACCCACCCTCTA
Abditomys latidens  (none) ATGACAAACATTCGAAAAACTCACCCCCTA
Chrotomys sibuyanensis  (none) ATGACAAACATCCGAAAAACACACCCCCTT
Apomys gracilirostris  (none) ATGACAAACATCCGAAAAACACACCCCCTC
Lophiomys imhausi  (none) ATGAAAATTATACGAAAATCACACCCACTT
Carpomys melanurus  (none) ATGACAAACATCCGAAAAATTCACCCATTA
Carpomys phaeurus  (none) ATGACAAACATCCGAAAAATTCACCCATTA
Musseromys gulantang  (none) ATGACAAACATCCGAAAAACTCACCCACTA
Musseromys inopinatus  (none) ATGACAAACATCCGAAAAACCCACCCACTA
Musseromys anacuao  (none) ATGACAAACATCCGAAAAACTCACCCATTA
Musseromys beneficus  (none) ATGACAAACATCCGAAAAACTCACCCATTA
Crunomys melanius  (none) ATGACAAACATCCGAAAATCCCACCCTCTA
Crunomys suncoides  (none) ATGACAAACATCCGAAAATCCCACCCTCTA
Bullimus gamay  (none) ATGACAAACATTCGAAAGTCCCATCCCCTG
Bullimus bagobus  (none) ATGACAAACATTCGAAAATCTCATCCCCTA
Bullimus luzonicus  (none) ATGACAAACATTCGAAAATCTCATCCCCTA
Rattus everetti  (none) ATGACAAACATCCGAAAATCTCACCCTCTA
Tarsomys apoensis  (none) ATGACAAACATCCGAAAATCTCACCCTCTG
Limnomys bryophilus  (none) ATGACAAACATCCGAAAATCTCACCCCTTA
Limnomys sibuanus  (none) ATGACAAACATTCGAAAATATCATCCCCTA
Rhynchomys banahao  (none) ATGACAAACATCCGAAAAACACATCCTCTT
Rhynchomys isarogensis  (none) ATGACAAACATCCGAAAAACACATCCTCTT
Rhynchomys soricoides  (none) ATGACAAACATCCGAAAAACACATCCTCTT
Rhynchomys tapulao  (none) ATGACAAACATCCGAAAAACACATCCTCTT
Archboldomys luzonensis  (none) ATGACAAACATCCGAAAAACACATCCTCTT
Archboldomys maximus  (none) ------------------ACACACCCCCTT
Apomys sierrae  (none) ATGACAAACATCCGAAAAACGCACCCTCTC
Apomys magnus  (none) ATGACAAACATCCGAAAAACACACCCTCTC
Apomys iridensis  (none) ------------------------------
Apomys zambalensis  (none) ATGACAAACATCCGAAAAACGCACCCTCTC
Apomys aurorae  (none) ATGACAAACATCCGAAAAACGCACCCCCTC
Apomys minganensis  (none) ------------------------------
Apomys abrae  (none) ---------------------CATCCTCTT
Apomys datae  (none) ATGACAAATATCCGAAAAACACACCCTCTT
Apomys brownorum  (none) ATGACAAACATCCGAAAAACACACCCCCTC
Apomys lubangensis  (none) ------------------------------
Apomys sacobianus  (none) ATGACAAACATCCGAAAAACACACCCCCTC
Apomys banahao  (none) ATGACAAACATCCGAAAAACACATCCCCTC
Apomys musculus  (none) ATGACAAACATCCGAAAGACACATCCCCTT
Apomys microdon  (none) ATGACAAACATCCGAAAAACACATCCACTT
Soricomys montanus  (none) ATGACAAACATCCGAAAAGCACATCCCCTA
Soricomys musseri  (none) ATGACAAACATCCGAAAAACCCACCCTCTC
Soricomys leonardocoi  (none) ATGACAAACATCCGAAAAACACATCCCCTT
Soricomys kalinga  (none) ATGACAAACATCCGAAAAACACACCCTCTC
Chrotomys silaceus  (none) ATGACAAACATCCGAAAAACACACCCCCTT
Chrotomys gonzalesi  (none) ATGACAAACATCCGAAAAACACACCCCCTT
Chrotomys mindorensis  (none) ATGACAAACATCCGAAAAACACACCCCCTT
Chrotomys whiteheadi  (none) ATGACAAACATCCGAAAAACACACCCCCTT
Phloeomys cumingi  (none) ATGACAAACATCCGAAAAACCCACCCACTA
Phloeomys pallidus  (none) ATGACATACATCCGAAAAACTCACCCACTA
Crateromys schadenbergi  (none) ATGACAAACATCCGAAAAACCCATCCCCTA
Batomys granti  (none) ATGACAAACATCCGAAAAACCCACCCACTA
Batomys uragon  (none) ATGACAAACATCCGAAAAACCCACCCACTG
Uranomys ruddi  (none) ---------------AAATCCCACCCTTTA
Gerbillus gerbillus  (none) ATG{AT}CAAACATT{CT}GAAAAATTCAC
Meriones shawi  (none) ------------------------------
Mylomys dybowskii  (none) ATGACAAACATCCGAAAAACTCACCCACTA
Micaelamys namaquensis  (none) ATGATAAACATCCGAAAAACCCATCCCCTA
Hapalomys delacouri ZIN98922  (none) ------AATATCCGAAAATCACATCCACTA
Oenomys hypoxanthus  (none) ATGACAAACATCCGAAAAACTCACCCCTTA
Micromys minutus  (none) ATGACAATCATCCGAAAAACCCACCCCTTA
Lemniscomys barbarus  (none) ATGACAAACATTCGAAAAACTCATCCTCTA
Mus pahari  (none) ATGACAAACATACGAAAAACACATCCACTA
Dephomys defua  (none) ------------------------------
Chiromyscus chiropus  (none) ------------------------CCCCTA
Maxomys moi  (none) ATGACAGATATACGAAAAACCCATCCCCTA
Maxomys hellwaldii  (none) ATGACAAACATCCGAAAATCCCACCCTCTA
Maxomys dollmani  (none) ATGACAAACATCCGAAAATCCCACCCTCTA
Maxomys bartelsii  (none) ------------------------------
Maxomys whiteheadi  (none) ATGACAAACATCCGAAAATCCCACCCCTTA
Maxomys hylomyoides  (none) ------------------------------
Maxomys musschenbroekii  (none) ATGACAAACATTCGAAAATCCCACCCCCTA
Crunomys celebensis  (none) ATGACAAATATCCGCAAATCCCATCCCTTA
Maxomys panglima  (none) ATGACAAACATCCGAAAAACCCATCCCCTA
Maxomys cf hellwaldii  (none) ------------------------------
Maxomys surifer  (none) ---------ATCCGAAAAACCCATCCCTTA
Maxomys pagensis  (none) ------------------------------
Maxomys rajah  (none) ------------------------------
Waiomys mamasae  (none) ATGACAAACACCCGAAAAACCCATCCTCTA
Niviventer cremoriventer  (none) ------------------------------
Sommeromys macrorhinos  (none) ATGACAAACATACGTAAAACCCACCCCCTA
Niviventer excelsior  (none) ATGACAAACATCCGAAAAACCCACCCCCTC
Niviventer culturatus  (none) ATGACAAACATCCGAAAAACTCATCCCTTA
Niviventer confucianus  (none) ATGACAAATATCCGAAAAACCCATCCCCTT
Paruromys dominator  (none) ATGACAAACATTCGAAAATCTCACCCCTTA
Saxatilomys paulinae  (none) ATGACAAACATCCGAAAAACCCACCCTTTA
Leopoldamys sabanus  (none) ------------------------------
Leopoldamys edwardsi  (none) ------------------ACCCACCCTCTA
Leopoldamys neilli  (none) ------------CGAAAAACTCACCCCCTC
Dacnomys millardi  (none) ------------------------------
Paucidentomys vermidax  (none) ------------------------------
Tateomys rhinogradoides  (none) ---------------------CACCCTCTA
Echiothrix centrosa  (none) ATGACAAACATCCGAAAAACCCACCCACTA
Melasmothrix naso  (none) ATGACAAACATCCGAAAAGCCCACCCCTTA
Hyorhinomys stuempkei  (none) ATGACAAACACCCGAAAAACCCACCCCCTG
Tateomys macrocercus  (none) ---------------------CACCCACTA
Berylmys berdmorei  (none) ------------CGAAAATCCCACCCTCTA
Berylmys bowersi  (none) ATGACAAACATCCGAAAATCCCACCCTCTA
Srilankamys ohiensis  (none) ATGACAAACATCCGAAAATCCCACCCCCTC
Rattus norvegicus  (none) ATGACAAACATCCGAAAATCTCACCCCCTA
Bandicota bengalensis  (none) ATGACAAACATTCGAAAATCCCACCCTCTA
Bandicota savilei  (none) ------------CGAAAATCCCACCCTCTA
Sundamys muelleri  (none) ------------------------------
Diplothrix legata  (none) ATGGCAAACATTCGAAAATCCCACCCTCTA
Rattus praetor  (none) ATGACAAACATTCGAAAATCCCACCCTCTG
Rattus villosissimus  (none) ATGACAAACATTCGAAAATCTCACCCTCTA
Arvicanthis neumanni  (none) ATGACAAACATCCGAAAAACACACCCCCTA
Dasymys incomtus  (none) ATGACAAACATCCGAAAGACCCACCCCTTA
Mus musculus  (none) ATGACAAACATACGAAAAACACACCCATTA
Mus spicilegus  (none) ---ACAAACATACGAAAAACACATCCATTA
Mus caroli  (none) ATGACAAACATCCGAAAAACACATCCACTA
Mus cookii  (none) ATGACAAACATCCGAAAAACACACCCATTA
Stochomys longicaudatus  (none) ATGACAAACATACGAAAAACCCACCCCCTA
Hybomys univittatus  (none) ATGACAAACATCCGAAAAACACACCCTCTC
Golunda elliotti  (none) ATGACAAACATCCGAAAAACCCACCCACTA
Grammomys ibeanus  (none) ATGACAAACACCCGAAAAACCCACCCCTTA
Parotomys brantsii  (none) ATGACAAACATCCGAAAAACTCACCCCCTT
Otomys angoniensis  (none) ATGACAAACATCCGAAAAACCCACCCCCTA
Otomys denti  (none) ATGACAAACATCCGAAAAACCCACCCTCTA
Chiropodomys gliroides  (none) ------------------------------
Malacomys longipes  (none) ATGACAAACATACGAAAATCTCACCCACTA
Zyzomys argurus  (none) ATGACAAACATTCGAAAAACACATCCACTA
Apodemus latronum  (none) ------AACATCCGAAAAACCCATCCACTT
Apodemus semotus  (none) ATGACAAATATCCGAAAAACACACCCACTT
Apodemus speciosus  (none) ATGACAAACATCCGAAAAACACATCCATTA
Mammelomys lanosus  (none) ATGACAAACATCCGAAAATCACATCCGTTA
Apodemus mystacinus  (none) ATGACAAACATACGTAAAACACATCCATTA
Chiruromys vates  (none) ATGATTCACATTCGAAAAACACACCCCCTA
Hyomys goliath  (none) ATGACAAACATCCGAAAAACACACCCACTA
Macruromys major  (none) ATGACACACATCCGAAAAACCCACCCTTTA
Apodemus flavicollis  (none) ATGACAAACATTCGAAAAACACACCCCCTA
Apodemus sylvaticus  (none) ATGACAAACATTCGAAAAACACACCCACTA
Heimyscus fumosus  (none) ATGACAAACATCCGAAAATCTCACCCATTA
Mallomys rothschildi  (none) ATGAAAAACATTCGAAAAACACACCCACTA
Apodemus agrarius  (none) ATGACAAACATCCGAAAAACTCACCCCCTA
Hylomyscus parvus  (none) ATGACAAACATCCGAAAAACACACCCATTA
Praomys degraaffi  (none) ATGACAAACATCCG?AAAACCCACCCACTA
Praomys jacksoni  (none) ATGACAAACATCCGAAAAACCCACCCACTT
Zelotomys hildegardeae  (none) ATGACAAACATCCGAAAAACCCACCCACTA
Praomys misonnei  (none) ------------------ACCCACCCACTA
Praomys tullbergi  (none) ATGACAAACATCCGAAAAACCCACCCACTA
Pogonomys macrourus  (none) ATGACAAACATTCGAAAAACCCACCCTTTA
Mastacomys fuscus  (none) ATGACAAACATACGAAAAACACACCCCCTA
Pseudomys australis  (none) ATGACAAACATACGAAAAACACATCCCTTG
Lorentzimys nouhuysi  (none) ATGATAAACATCCGAAAAACACACCCCCTA
Leporillus conditor  (none) ------------------ACCCACCCACTC
Uromys caudimaculatus  (none) ------------------------------
Paramelomys levipes  (none) ------------------------------
Notomys fuscus  (none) ATGACAAACATCCGAAAAACACATCCCTTA
Pogonomys loriae  (none) ATGACAAACATCCGAAAAACTCACCCCTTA
Leggadina forresti  (none) ATGACAAACATCCGAAAAACACACCCCTTA
Conilurus penicillatus  (none) ------------------------------
Pseudohydromys ellermani  (none) ATGACAAACATCCGAAAAACACACCCCCTA
Xeromys myoides  (none) ATGACAAACATCCGAAAAACACATCCCCTA
Leptomys elegans  (none) ATGACAAACATTCGAAAAACACACCCCTTA
Crossomys moncktoni  (none) ATGACAAACATCCGAAAAACACACCCTTTA
Hydromys chrysogaster  (none) ATGACAAACATCCGAAAAACACACCCCCTA
Parahydromys asper  (none) ATGACAAACATCCGAAAAACACACCCCTTA
Solomys salebrosus  (none) ------------------------CCCCTA
Melomys rufescens  (none) ATGACAAACATTCGAAAAACACACCCCCTA
Rattus exulans  (none) ATGACAAACATTCGAAAATCTCATCCTCTA
Rattus tanezumi  (none) ATGACAAACATTCGAAAATCACACCCCCTA
Apomys camiguinensis  (none) ATGACAAACATCCGAAAAACACACCCTCTT
Apomys hylocoetes  (none) ATGACAAACATCCGAAAAACACATCCCCTT
Apomys insignis  (none) ATGACAAACATCCGAAAAACACATCCCCTT
Tokudaia osimensis  (none) ------------------------------
Vandeleuria oleracea  (none) ------------------------------
Millardia kathleenae  (none) ------------------------------
Anisomys imitator  (none) ------------------------------
Pogonomys sylvestris  (none) ------------------------------
Abeomelomys sevia  (none) ------------------------------
Mesembriomys gouldii  (none) ------------------------------
Paraleptomys sp  (none) ------------------------------
Microhydromys richardsoni  (none) ------------------------------
Myomyscus brockmani  (none) ------------------------------
Mastomys erythroleucus  (none) ------------------------------
Mastomys hildebrandtii  (none) ------------------------------
Stenocephalomys albipes  (none) ------------------------------
Colomys goslingi  (none) ------------------------------
Hylomyscus stella  (none) ------------------------------
Grammomys macmillani  (none) ------------------------------
Grammomys dolichurus  (none) ------------------------------
Margaretamys elegans  (none) ------------------------------
Bunomys chrysocomus  (none) ------------------------------
Rattus tiomanicus  (none) ------------------------------
Rattus rattus  (none) ------------------------------
Rattus verecundus  (none) ------------------------------
Rattus leucopus  (none) ------------------------------
Rattus novaguineae  (none) ------------------------------
Otomys anchietae  (none) ------------------------------
Lemniscomys striatus  (none) ------------------------------
Rhabdomys pumilio  (none) ------------------------------
Arvicanthis niloticus  (none) ------------------------------
Gerbilliscus robustus  (none) ------------------------------
Acomys ignitus  (none) ------------------------------
Mus terricolor  (none) ------------------------------
Mus booduga  (none) ------------------------------
Mus cervicolor  (none) ------------------------------
Rattus sordidus  (none) ------------------------------
Rattus giluwensis  (none) ------------------------------

Columns

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