2× genomes - depth does matter

Table 1 Number of dubious duplications at the eutherian node involving various species as 'orphans'

Species	Isolated sp(i)	sp(i)versus >5	sp(i)versus >5 - no sp(i)	sp(i)versus >10	sp(i)versus >10 - no sp(i)
2× coverage genomes
Sorex araneus	621	591	581	563	557
Erinaceus europaeus	565	531	523	498	493
Ochotona princeps	376	343	337	308	302
Cavia porcellus	344	308	302	280	274
Echinops telfairi	272	246	235	237	227
Myotis lucifugus	192	168	156	146	137
Tupaia belangeri	192	159	150	132	126
Spermophilus tridecemlineatus	182	142	140	110	108
Oryctolagus cuniculus	149	114	108	93	88
Otolemur garnettii	125	100	97	79	76
Loxodonta africana	109	77	64	70	59
Microcebus murinus	112	90	86	62	59
Felis catus	98	73	70	57	54
Dasypus novemcinctus	15	6	0	4	0
High-coverage genomes
Bos taurus	200	168	131	148	112
Canis familiaris	156	120	94	93	71
Mus musculus	129	100	94	75	70
Equus caballus	134	110	78	86	58
Rattus norvegicus	73	52	37	37	28
Pongo pygmaeus	34	25	21	17	14
Macaca mulatta	62	44	24	28	14
Pan troglodytes	24	13	7	10	5
Homo sapiens	14	7	5	4	3
One-tail Mann-Whitney test
P-value	0.016	0.016	0.005	0.014	0.005

See Figure 7 and text for details. Different columns correspond to cases where one side of a duplication at the eutherian node involved: an orphan species (isolated sp(i)), or one orphan species versus more than five (sp(i) versus >5) or more than ten (sp(i) versus >10) species on the other side of the duplication. The column labeled with 'no sp(i)' indicates the cases where the orphan species is absent from the other side of the duplication node (this requires perfect reciprocal complementary gene losses and, hence, corresponds to a species-overlap score of zero). Values are sorted according to the last column.

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