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