Supplementary Table 1. Changes to the multiple sequence alignment of [9]. Only one change was made to non-protein coding sequences (APP), listed in the first row. Alignment changes are represented by smallcase nucleotides in nexus file available in the file "nuc-align.nex" , linked from the supplementary data website, the character positions of which correspond with locations given below in column 3. "AA" = amino acid; "RF" = reading frame.


Gene

Taxa/on

Character(s) in nuc-align.nex

Change

APP

all but Cavia

1381

single gap added to better align 19bp motif in Cavia

adrB2

Sorex

944-948

indels in Sorex and Equus homologized

BDNF

Trichechus

2973-2974

gap characters changed to ? (no AA translation given in genBank AY011451)

BDNF

Trichechus

3042

gap character changed to ? (no AA translation given in genBank AY011451)

CNR1

Didelphis

3652-3654

moved 1 position downstream to fit RF

TYR

Equus

7948-8373

Equus had not been included in Roca et al. (2004) alignment, sequences from AF252540 added

vWF

all

8578-8592

region reidentified as "alignment ambiguous"

vWF

ruminant

9277-9282

moved 1 position downstream to fit RF

vWF

Didelphis and Macropus

9364-9366

moved 3 bases downstream to match indel in Sus

BRCA1

Solenodon

9995-9997

moved 1 position upstream to fit RF

BRCA1

Sorex

9998-10000

moved 1 position upstream to fit RF

BRCA1

Solenodon

10046-10048

moved 1 position downstream to fit RF

BRCA1

phyllostomid

10070-10084

moved 1 position downstream to fit RF

BRCA1

diprotodont

10139-10141

moved 1 position downstream to fit RF

BRCA1

Didelphis and Macropus

10712-10720

moved 1 position downstream to fit RF

BRCA1

all

10730-10732

moved 1 position downstream to fit RF

BRCA1

Echinops

10943-10945

moved 3 positions downstream to match indel in other taxa

BRCA1

Didelphis and Macropus

11141-11149

moved 2 positions downstream to fit RF and match indel in Orycteropus

BRCA1

Didelphis and Tupaia

11315-11317

moved 6 positions upstream to match beginning of indel in cetartiodactyls

BRCA1

Chaetophractus and myrmecophagid

11315-11317

moved 3 positions downstream to match beginning of indel in cetartiodactyls

BRCA1

Manis

11345-11356

moved 3 positions upstream to match indel in marsupials

BRCA1

Orycteropus

11402-11404

moved 3 positions downstream to match indel in Manis

BRCA1

Rousettus

11630-11641

moved 2 positions upstream to fit RF

BRCA1

Tupaia

11891-11896

moved 1 position upstream to fit RF

BRCA1

Erinaceus

12194-12205

moved 1 position downstream to fit RF

BRCA1

strepsirhine

12536-12538

moved 3 positions downstream to match indel in Ochotona and Equus

BRCA1

phyllostomid

12746-12748

moved 3 positions downstream to fit indel in Erinaceus and Lama

BRCA1

ruminant

12830-12832

moved 2 positions upstream to fit RF

IRBP

elephant shrews

13944-13946

moved 1 position downstream to fit RF

IRBP

Didelphis and Ochotona

13950-13952

moved 2 positions upstream to fit RF

IRBP

delphinid

14055-14057

moved 1 position downstream to fit RF

A2AB

Orycteropus and Echinops

14799-14801

moved 3 positions upstream to match termination of indel in bats, carnivorans, and Manis

A2AB

Solenodon and Homo

14832-14834

moved 1 position upstream to fit RF

A2AB

Felis

15030-15032

moved 2 positions upstream to fit RF



Supplementary Table 2. Qualitative character-state corrections to the morphology matrix first published in [17]. Asterisks indicate changes already made by [24].

character

taxon

as coded 2003

revised

11, Transpromontorial sulcus*

Ochotona

internal carotid artery sulcus on ventrum of petrosal present (0)

sulcus absent (1) following Bugge (1974).

20, Alisphenoid contribution to auditory bulla*

Zalambdalestes

present (1)

absent (0) following Wible et al. (2004)

33, Alisphenoid canal*

Leptictis

polymorphic (0,1)

present (0)

33, Alisphenoid canal*

Palaeoparadoxia

present (0)

uncertain (?)

39, hypoglossal foramen

Orycteropus, Sus

absent (0)

present (1)

39, hypoglossal foramen

Sorex

absent (0)

polymorphic (0,1)

48, Foramen rotundum

Didelphis

confluent (0)

distinct (1) following Wible (2003:153), Gregory (1910: 429)

56, Glenoid position

Manis

glenoid poorly defined (2)

even with petrosal (0)

71, Lacrimal foramen

Sylvilagus ("leporid" in present study)

with "fenestra in anterior orbit" comprising state 2 (state 2 also not recorded in Appendix 2B)

previous coding for Sylvilagus results from artefactual loss of lacrimal bone in some specimens. taxon "leporid" is corrected to state "0, lacrimal foramen present."

75, Maxilla in medial orbital wall*

Amblysomus

reduced (0), without incursion of maxilla in orbital wall

maxilla with incursion into medial orbital wall (1)

178, Pedal digit I*

Ukhaatherium

uncertain ("?")

weight bearing ("0")


Supplementary Table 3. Summary of discrepancies between Appendices 1 and 2 of [17].

Character (#, name)

Taxon

Correction

25, ectotympanic shape

Sorex

Erroneously listed as state "1" in description on p. 173; should be state "0"

41, petrosal exposure in braincase

Tapirus

State "0" (petrosal exposed) omitted from printed Appendix 1

43, dorsum subarcuate fossa

cetaceans

State 2 "absent" erroneously included in Appendix 2A. In matrix state "2" was coded as inapplicable (i.e., as missing)

47, crista galli

All

States in Appendix 2B are reversed

47, crista galli

cetaceans

Description for state 2 lacking in Appendix 2B

57, glenoid shape

Sorex

Description of state 2 "glenoid dual" missing in Appendix 2B

71, lacrimal foramen

All

States in Appendix 2B are reversed.

76, premaxillary-frontal contact

cetaceans

Description of state 2 "present over maxilla" missing in Appendix 2B

78, posterior nasals

Arsinoitherium

Description of state 2 "horns" missing in Appendix 2B

89, palatal exposure premaxilla

bats, cetaceans, Tamandua, Ceratotherium

Description of state 0 "premaxilla absent or comprising alveoli only" missing in Appendix 2B; states 1 and 2 in matrix correspond to states 0 and 1 in Appendix 2B

95, incisor enamel

Loxodonta, Palaeoparadoxia

Description of state 2 "enamel reduced, present on apex of tooth only" missing in Appendix 2B

99, tooth replacement

marsupials

Following Luckett (1993), the last premolar of marsupial mammals, and the only tooth with a deciduous precursor, is p/P3, not p/P4 as originally written in Appendix 2B

110, stylar shelf

All

States in Appendix 2B are reversed

124, C2 odontoid shape

All

States 0,1 in Appendix 2B are reversed

124, C2 odontoid shape

cetaceans

State 2 "odontoid missing" was erroneously included in Appendix 2B description for character 124, repeating information from character 123. However, state 2 was originally (and correctly) coded as inapplicable ("?") in matrix

132, scapular shape

All

States in Appendix 2B are reversed

132, scapular shape

talpids

Description of state 2 "scapula long and narrow" missing in Appendix 2B

141, proximal radius

Loxodonta

Described in Appendix 2B as having state 2 "proximal radius articulates in V-shaped notch of ulna", but is coded in matrix as state 0 "proximal radius circular". Correctly coded as state 0 in matrix; with V-shaped notch accounted for in character 142.

164, medial trochanteric ridge

Didelphis

Erroneously listed as state "1"; should be state "0" in description on p. 189

167, fibular facet of calcaneus

All

States in Appendix 2B are reversed

177, projection from ankle

chiropterans

States in Appendix 2B for mega- and microchiropterans are reversed

184, metatarsal length

Macropus

Erroneously given state 2 "long tibia"; should be coded state 1 for relatively long metatarsals