Supplementary material

Table S1. Results of the GLMs of each iteration of the R simulation.

Iteration	F	P-value
1	15.87380	0.0001886
2	13.77843	0.0004577
3	14.28849	0.0003678
4	16.44167	0.0001491
5	16.64354	0.0001372
6	15.96820	0.0001813
7	15.70402	0.0002024
8	14.33750	0.0003602
9	15.46239	0.0002239
10	16.94157	0.0001214
11	15.24768	0.0002450
12	14.22673	0.0003776
13	14.45194	0.0003430
14	16.38215	0.0001528
15	13.20255	0.0005874
16	15.87191	0.0001887
17	15.83485	0.0001917
18	16.15088	0.0001681
19	15.31126	0.0002385
20	16.73986	0.0001319
21	15.88018	0.0001881
22	16.99329	0.0001189
23	17.10959	0.0001134
24	16.44908	0.0001486
25	14.59410	0.0003229
26	15.25806	0.0002439
27	16.93161	0.0001219
28	15.90318	0.0001863
29	17.16106	0.0001110
30	14.87201	0.0002870
31	16.38513	0.0001526
32	14.11087	0.0003968
33	15.94987	0.0001827
34	16.57312	0.0001412
35	14.77301	0.0002993
36	16.60928	0.0001392
37	15.68984	0.0002036
38	15.30413	0.0002393
39	15.18370	0.0002517
40	16.29127	0.0001586
41	15.17999	0.0002521
42	14.66412	0.0003135
43	17.06356	0.0001155
44	15.34724	0.0002350
45	16.44511	0.0001489
46	17.90958	0.0000820
47	16.39928	0.0001517
48	17.85242	0.0000839
49	16.91699	0.0001227
50	16.20052	0.0001647
51	14.95050	0.0002777
52	14.67240	0.0003124
53	15.15019	0.0002553
54	14.97637	0.0002747
55	15.12759	0.0002577
56	11.44695	0.0012773
57	15.54780	0.0002160
58	14.66722	0.0003130
59	17.07447	0.0001150
60	16.25443	0.0001611
61	15.18368	0.0002517
62	12.72306	0.0007244
63	15.89902	0.0001866
64	17.81338	0.0000852
65	16.84256	0.0001265
66	17.87743	0.0000831
67	14.84943	0.0002898
68	15.81197	0.0001935
69	15.90828	0.0001859
70	14.98558	0.0002736
71	15.37662	0.0002321
72	14.80798	0.0002949
73	14.84017	0.0002909
74	17.62686	0.0000919
75	14.68079	0.0003112
76	16.31414	0.0001571
77	15.96180	0.0001818
78	15.20197	0.0002498
79	15.21139	0.0002488
80	14.83042	0.0002921
81	15.91928	0.0001851
82	14.33157	0.0003611
83	14.21144	0.0003801
84	17.38221	0.0001015
85	15.94298	0.0001832
86	13.03641	0.0006315
87	15.63172	0.0002086
88	14.82947	0.0002922
89	15.15164	0.0002551
90	14.23562	0.0003762
91	14.70269	0.0003084
92	17.13729	0.0001121
93	15.53734	0.0002170
94	12.09541	0.0009558
95	15.52079	0.0002185
96	15.21391	0.0002485
97	16.30743	0.0001576
98	15.33222	0.0002365
99	15.34555	0.0002351
100	15.72400	0.0002007

Table S2. Specimen information, extraction results, library preparation details, Illumina sequencing statistics, locus assembly, and raw sequence data deposition for Columbicola wing lice from small New World ground-doves.

Louse.taxa	Extract.Code	Host.species	Host.Collection.code	Collection.location	Collection.date	DNA.extraction.date	DNA.yield..ng.uL.	Sonication.instrument	Library.preparation.kit	Sequencing.platform	Sequencing.Kit	Sequencing.cycles	Bar.code	Sequencing.pool	Read.length	Paired.end	Number.of.raw.Reads	Predicted.sequencing.depth	Read.duplication	Number.of.reads.after.pre.processing	Sequencing.depth.after.pre.processing	Number.of.genes.assembled.with.BowTie2..1.058.Genes.Targeted.	NCBI.SRA	NCBI.BioSample	NCBI.BioProject	Chosen.for.Phylonet.analyses..1.means.yes.
Physconelloides emersoni emersoni	Pheme.Memel.5.26.2015.8	Metriopelia melanoptera	KGM445	Argentina: Jujay	11-Oct-2001	26-May-15	0.853	Covaris M220	Kapa Biosystems	Illumina HiSeq2500	HiSeq SBS V. 4	161	ATTCCT	4	160nt	yes	118843526	95.07000	23.70	96244932	77.00000	1058	SRP076185	SAMN04633184	PRJNA318056	1
Physconelloides emersoni emersoni	Pheme.Memel.6.15.2015.5	Metriopelia melanoptera	KGM511	Bolivia: Lago Poopo, Oruro	2-Nov-2001	15-Jun-15	0.379	Covaris M220	Kapa Biosystems	Illumina HiSeq2500	HiSeq SBS V. 4	161	CAGATC	1	160nt	yes	78198304	62.56000	37.67	50415214	40.33000	1052	SRP076185	SAMN04633188	PRJNA318056	0
Physconelloides emersoni emersoni	Pheme.Memel.3.16.2016.2	Metriopelia melanoptera	REW273	Peru: Puno	21-Oct-2002	16-Mar-16	0.417	Covaris M220	Kapa Biosystems	Illumina HiSeq2500	HiSeq SBS V. 4	161	CGTCTCGTGA	2	160nt	yes	63517384	50.81000	17.90	51240446	40.99000	1057	SRP076185	SAMN05099560	PRJNA318056	0
Physconelloides emersoni emersoni	Pheme.Memel.3.16.2016.8	Metriopelia melanoptera	ASEC004	Ecuador: Pichincha	23-Jan-2016	16-Mar-16	0.333	Covaris M220	Kapa Biosystems	Illumina HiSeq2500	HiSeq SBS V. 4	161	GAGAGTACTA	3	160nt	yes	36399076	29.12000	12.17	28968590	23.17000	1058	SRP076185	SAMN05099566	PRJNA318056	0
Physconelloides eurysema eurysema 3	Pheur.Clpre.3.14.2016.5	Claravis pretiosa	5172	Brazil: Para	2-Jun-2013	14-Mar-16	0.579	Covaris M220	Kapa Biosystems	Illumina HiSeq2500	HiSeq SBS V. 4	161	CCGGTGGAAT	1	160nt	yes	35524478	28.42000	26.60	27317070	21.85000	1050	SRP076185	SAMN05099551	PRJNA318056	0
Physconelloides eurysema eurysema 3	Pheur.Clpre.3.14.2016.11	Claravis pretiosa	GES470	Mexico: Campeche	16-Mar-1998	14-Mar-16	0.212	Covaris M220	Kapa Biosystems	Illumina HiSeq2500	HiSeq SBS V. 4	161	TCTCGACGTT	2	160nt	yes	42423630	33.94000	27.43	33041298	26.43000	1058	SRP076185	SAMN05099557	PRJNA318056	1
Physconelloides eurysema eurysema 3	Pheur.Clpre.3.16.2016.5	Claravis pretiosa	6414	Brazil: Para	1-Aug-2014	16-Mar-16	0.090	Covaris M220	Kapa Biosystems	Illumina HiSeq2500	HiSeq SBS V. 4	161	AGGAGAATCA	3	160nt	yes	40120794	32.10000	14.05	31896742	25.52000	1058	SRP076185	SAMN05099563	PRJNA318056	0
Physconelloides eurysema eurysema 3	Pheur.Clpre.5.26.2015.6	Claravis pretiosa	GES382	Mexico: Campeche	16-Mar-1998	26-May-15	0.973	Covaris M220	Kapa Biosystems	Illumina HiSeq2500	HiSeq SBS V. 4	161	GAGTGG	4	160nt	yes	63821562	51.06000	20.82	49744786	39.80000	1058	SRP076185	SAMN04633182	PRJNA318056	0
Physconelloides eurysema eurysema 3	Pheur.Clpre.6.15.2015.8	Claravis pretiosa	REW176	Peru: Cajamarca	7-Sep-2002	15-Jun-15	0.189	Covaris M220	Kapa Biosystems	Illumina HiSeq2500	HiSeq SBS V. 4	161	TTAGGC	1	160nt	yes	51392388	41.11000	17.67	37130950	29.70000	1058	SRP076185	SAMN04633191	PRJNA318056	0
Physconelloides eurysema eurysema 3	Pheur.Cobuc.3.16.2016.4	Columbina buckleyi	RCF998	Peru: Cajamarca	15-Feb-1999	16-Mar-16	0.522	Covaris M220	Kapa Biosystems	Illumina HiSeq2500	HiSeq SBS V. 4	161	ACTTCCGCAC	3	160nt	yes	36856494	29.49000	10.56	33206986	26.57000	1058	SRP076185	SAMN05099562	PRJNA318056	0
Physconelloides eurysema eurysema 3	Pheur.Cobuc.6.15.2015.1	Columbina buckleyi	REW170	Peru: Cajamarca	5-Sep-2002	15-Jun-15	0.515	Covaris M220	Kapa Biosystems	Illumina HiSeq2500	HiSeq SBS V. 4	161	CGATGT	1	160nt	yes	61157596	48.93000	51.75	36504910	29.20000	1058	SRP076185	SAMN04633185	PRJNA318056	0
Physconelloides eurysema eurysema 3	Pheur.Cocru.3.16.2016.9	Columbina cruziana	ASEC008	Ecuador: Manabi	29-Jan-2016	16-Mar-16	0.481	Covaris M220	Kapa Biosystems	Illumina HiSeq2500	HiSeq SBS V. 4	161	GCTCCTCTTG	3	160nt	yes	44058524	35.25000	7.95	35529848	28.42000	1057	SRP076185	SAMN05099567	PRJNA318056	0
Physconelloides eurysema eurysema 3	Pheur.Cocru.6.15.2015.2	Columbina cruziana	REW85	Peru: Lima	8-Aug-2002	15-Jun-15	0.887	Covaris M220	Kapa Biosystems	Illumina HiSeq2500	HiSeq SBS V. 4	161	TGACCA	1	160nt	yes	61326000	49.06000	71.40	26000756	20.80000	1046	SRP076185	SAMN04633186	PRJNA318056	0
Physconelloides eurysema eurysema 3	Pheur.Comin.3.14.2016.9	Columbina minuta	JK06-367	Panama: Charco Azul	2-Mar-2006	14-Mar-16	0.499	Covaris M220	Kapa Biosystems	Illumina HiSeq2500	HiSeq SBS V. 4	161	TGTTACCTAC	2	160nt	yes	32144260	25.72000	25.74	24668212	19.73000	1058	SRP076185	SAMN05099555	PRJNA318056	0
Physconelloides eurysema eurysema 3	Pheur.Copas.3.14.2016.4	Columbina passerina	5048	Brazil: Amazonas	11-Jul-2013	14-Mar-16	0.520	Covaris M220	Kapa Biosystems	Illumina HiSeq2500	HiSeq SBS V. 4	161	ACCGCCTATT	1	160nt	yes	41362350	33.09000	13.07	33206986	26.57000	1056	SRP076185	SAMN05099550	PRJNA318056	0
Physconelloides eurysema eurysema 3	Pheur.Copas.3.14.2016.7	Columbina passerina	5050	Brazil: Amazonas	11-Jul-2013	14-Mar-16	0.294	Covaris M220	Kapa Biosystems	Illumina HiSeq2500	HiSeq SBS V. 4	161	GCAGGCGTAT	1	160nt	yes	48354288	38.68000	17.09	38250780	30.60000	1050	SRP076185	SAMN05099553	PRJNA318056	0
Physconelloides eurysema eurysema 3	Pheur.Copas.3.14.2016.10	Columbina passerina	GES233	Mexico: Campeche	2-Mar-1998	14-Mar-16	0.323	Covaris M220	Kapa Biosystems	Illumina HiSeq2500	HiSeq SBS V. 4	161	TAGCGGCACT	2	160nt	yes	46626818	37.30000	30.13	35850772	28.68000	1058	SRP076185	SAMN05099556	PRJNA318056	0
Physconelloides eurysema eurysema 3	Pheur.Copas.3.16.2016.1	Columbina passerina	6469	Brazil: Rondonia	7-Oct-2014	16-Mar-16	0.610	Covaris M220	Kapa Biosystems	Illumina HiSeq2500	HiSeq SBS V. 4	161	TAAGAGCGCC	2	160nt	yes	49146294	39.32000	10.47	39663616	31.73000	1058	SRP076185	SAMN05099559	PRJNA318056	0
Physconelloides eurysema eurysema 3	Pheur.Copas.3.16.2016.7	Columbina passerina	ASEC001	Ecuador: Pichincha, Calacali	20-Jan-2016	16-Mar-16	0.387	Covaris M220	Kapa Biosystems	Illumina HiSeq2500	HiSeq SBS V. 4	161	CTACAACGGC	3	160nt	yes	35742462	28.59000	10.13	28679204	22.94000	1058	SRP076185	SAMN05099565	PRJNA318056	0
Physconelloides eurysema eurysema 3	Pheur.Cotal.3.14.2016.2	Columbina talpacoti	4741	Brazil: Santa Catarina	31-Oct-2013	14-Mar-16	0.197	Covaris M220	Kapa Biosystems	Illumina HiSeq2500	HiSeq SBS V. 4	161	TTGTTGGCGG	1	160nt	yes	24481602	19.59000	38.76	17876904	14.30000	1048	SRP076185	SAMN05099548	PRJNA318056	0
Physconelloides eurysema eurysema 3	Pheur.Cotal.3.14.2016.6	Columbina talpacoti	GMS1950	Panama: Torti	18-Feb-2006	14-Mar-16	0.731	Covaris M220	Kapa Biosystems	Illumina HiSeq2500	HiSeq SBS V. 4	161	CTAACGATCG	1	160nt	yes	49810804	39.85000	12.18	40316768	32.25000	1058	SRP076185	SAMN05099552	PRJNA318056	0
Physconelloides eurysema eurysema 3	Pheur.Cotal.3.16.2016.3	Columbina talpacoti	6370	Brazil: Sao Paulo	1-Jun-2014	16-Mar-16	0.231	Covaris M220	Kapa Biosystems	Illumina HiSeq2500	HiSeq SBS V. 4	161	TTCTCCTTCA	2	160nt	yes	51734340	41.39000	14.29	41941080	33.55000	1050	SRP076185	SAMN05099561	PRJNA318056	0
Physconelloides eurysema eurysema 3	Pheur.Cotal.3.16.2016.12	Columbina talpacoti	SMD739	Panama: Felipillo	19-Feb-2006	16-Mar-16	0.207	Covaris M220	Kapa Biosystems	Illumina HiSeq2500	HiSeq SBS V. 4	161	ACATGGTCCA	3	160nt	yes	34980054	27.98000	11.28	27853084	22.28000	1057	SRP076185	SAMN05099570	PRJNA318056	0
Physconelloides eurysema eurysema 4	Pheur.Coinc.6.15.2015.7	Columbina inca	MCZ 01-149	Costa Rica: Guanacaste	10-Dec-2001	15-Jun-15	0.887	Covaris M220	Kapa Biosystems	Illumina HiSeq2500	HiSeq SBS V. 4	161	ATCACG	1	160nt	yes	53047444	42.44000	22.31	34924128	27.94000	1052	SRP076185	SAMN04633190	PRJNA318056	1
Physconelloides eurysema eurysema 1	Pheur.Comin.6.15.2015.10	Columbina minuta	MCZ 01-335	Costa Rica: Guanacaste	10-Dec-2001	15-Jun-15	0.363	Covaris M220	Kapa Biosystems	Illumina HiSeq2500	HiSeq SBS V. 4	161	GATCAG	1	160nt	yes	46622380	37.30000	12.96	31194444	24.96000	1052	SRP076185	SAMN04633192	PRJNA318056	0
Physconelloides eurysema eurysema 1	Pheur.Copas.3.14.2016.8	Columbina passerina	299	USA: Texas (captive)	27-Apr-2000	14-Mar-16	0.967	Covaris M220	Kapa Biosystems	Illumina HiSeq2500	HiSeq SBS V. 4	161	GCCTTCAGGA	2	160nt	yes	44144898	35.32000	8.11	35767700	28.61000	1058	SRP076185	SAMN05099554	PRJNA318056	1
Physconelloides eurysema eurysema 1	Pheur.Copas.3.16.2016.6	Columbina passerina		USA: Illinois, McClean, Bloomington	19-Oct-2015	16-Mar-16	0.105	Covaris M220	Kapa Biosystems	Illumina HiSeq2500	HiSeq SBS V. 4	161	AGCTCAACGA	3	160nt	yes	40646734	32.52000	19.80	31553360	25.24000	1050	SRP076185	SAMN05099564	PRJNA318056	0
Physconelloides eurysema eurysema 2	Pheur.Cosqu.3.14.2016.1	Columbina squammata	4702	Brazil: Para	1-Sep-2010	14-Mar-16	0.464	Covaris M220	Kapa Biosystems	Illumina HiSeq2500	HiSeq SBS V. 4	161	AGTATAGCGC	1	160nt	yes	33666308	26.93000	23.60	25793048	20.63000	1058	SRP076185	SAMN05099547	PRJNA318056	1
Physconelloides eurysema eurysema 2	Pheur.Cosqu.3.14.2016.12	Columbina squammata	4780	Brazil: Para	15-Aug-2013	14-Mar-16	0.162	Covaris M220	Kapa Biosystems	Illumina HiSeq2500	HiSeq SBS V. 4	161	GGCGAAGGTT	2	160nt	yes	49091816	39.27000	41.21	35989584	28.79000	1054	SRP076185	SAMN05099558	PRJNA318056	0
Physconelloides eurysema eurysema 5	Pheur.Urcam.3.14.2016.3	Uropelia campestris	4887	Brazil: Para	20-Aug-2013	14-Mar-16	2.500	Covaris M220	Kapa Biosystems	Illumina HiSeq2500	HiSeq SBS V. 4	161	AACCGAGTTA	1	160nt	yes	43813494	35.05000	16.04	34834472	27.87000	1058	SRP076185	SAMN05099549	PRJNA318056	1
Physconelloides robbinsi robbinsi	Phrob.Mecec.5.26.2015.7	Metriopelia ceciliae	REW153	Peru: Caras	28-Aug-2002	26-May-15	1.280	Covaris M220	Kapa Biosystems	Illumina HiSeq2500	HiSeq SBS V. 4	161	ACTGAT	4	160nt	yes	80808714	64.65000	17.87	63931800	51.15000	1058	SRP076185	SAMN04633183	PRJNA318056	1
Physconelloides robbinsi robbinsi	Phrob.Mecec.6.15.2015.6	Metriopelia ceciliae	REW151	Peru: Caras	28-Aug-2002	15-Jun-15	0.940	Covaris M220	Kapa Biosystems	Illumina HiSeq2500	HiSeq SBS V. 4	161	CTTGTA	1	160nt	yes	13580582	10.86000	39.22	7260590	5.81000	1032	SRP076185	SAMN04633189	PRJNA318056	0
Physconelloides robbinsi robbinsi	Phrob.Mecec.3.16.2016.10	Metriopelia ceciliae	REW150	Peru: Caras	28-Aug-2002	16-Mar-16	0.167	Covaris M220	Kapa Biosystems	Illumina HiSeq2500	HiSeq SBS V. 4	161	TAGGCATCGG	3	160nt	yes	34801206	27.84000	19.67	27053634	21.64000	1058	SRP076185	SAMN05099568	PRJNA318056	0
Physconelloides robbinsi robbinsi	Phrob.Mecec.3.16.2016.11	Metriopelia ceciliae	REW294	Peru: Tacna	25-Oct-2002	16-Mar-16	0.257	Covaris M220	Kapa Biosystems	Illumina HiSeq2500	HiSeq SBS V. 4	161	CAACCTAACA	3	160nt	yes	33983950	27.19000	14.41	26808390	21.45000	1058	SRP076185	SAMN05099569	PRJNA318056	0
Columbicola passerinae passerinae 1	Cosp.Coinc.11.2.2016.9	Columbina inca	MCZ 01-149	Costa Rica	10-Dec-2001	2-Nov-2016	0.324	Covaris M220	Hyper Library (Kapa Biosystems)	Illumina HiSeq4000	HiSeq4000 v.1	151	TCCTTAACCCGG	2	150 bp	yes	45454206	34.09065	15.47	34876801	26.15760	1031	SRR5998819	SAMN07573751	PRJNA400795	0
Columbicola passerinae passerinae 1	Cosp.Comin.11.2.2016.16	Columbina minuta	JMD733	Panama: Felipillo	19-Feb-2006	2-Nov-2016	0.501	Covaris M220	Hyper Library (Kapa Biosystems)	Illumina HiSeq4000	HiSeq4000 v.1	151	GAAAGAGAGTCC	1	150 bp	yes	47902092	35.92657	31.25	34645037	25.98378	1037	SRR5998828	SAMN07573758	PRJNA400795	0
Columbicola passerinae passerinae 1	Cosp.Comin.11.2.2016.4	Columbina minuta	JLK258	Peru: Loreto	15-Jun-2001	2-Nov-2016	0.231	Covaris M220	Hyper Library (Kapa Biosystems)	Illumina HiSeq4000	HiSeq4000 v.1	151	TGATGCAACCGG	1	150 bp	yes	31447878	23.58591	15.03	23729175	17.79688	1037	SRR5998812	SAMN07573746	PRJNA400795	0
Columbicola passerinae passerinae 1	Cosp.Copas.11.7.2016.12	Columbina passerina	GES233	Mexico: Yucatan	2-Mar-1998	7-Nov-2016	0.268	Covaris M220	Hyper Library (Kapa Biosystems)	Illumina HiSeq4000	HiSeq4000 v.1	151	GGGCCAACCCTT	1	150 bp	yes	37641540	28.23116	34.47	26218767	19.66408	1037	SRR5998808	SAMN07573769	PRJNA400795	0
Columbicola passerinae passerinae 1	Cosp.Copas.11.7.2016.14	Columbina passerina	ASEC001	Ecuador: Pichincha: Calicali	20-Jan-2016	7-Nov-2016	0.343	Covaris M220	Hyper Library (Kapa Biosystems)	Illumina HiSeq4000	HiSeq4000 v.1	151	CCCGGAACCCTT	1	150 bp	yes	45388822	34.04162	28.00	32058302	24.04373	1036	SRR5998802	SAMN07573771	PRJNA400795	0
Columbicola passerinae passerinae 1	Cosp.Copas.11.7.2016.15	Columbina passerina	n/a	USA: IL: McClean: Bloomington	19-Oct-2015	7-Nov-2016	0.402	Covaris M220	Hyper Library (Kapa Biosystems)	Illumina HiSeq4000	HiSeq4000 v.1	151	CTTCCAACCCGG	2	150 bp	yes	42180932	31.63570	17.18	32311708	24.23378	1037	SRR5998801	SAMN07573772	PRJNA400795	0
Columbicola passerinae passerinae 1	Cosp.Copas.11.7.2016.8	Columbina passerina	5049	Brazil: Amazonas	11-Jul-2013	7-Nov-2016	0.475	Covaris M220	Hyper Library (Kapa Biosystems)	Illumina HiSeq4000	HiSeq4000 v.1	151	GTACTGATCCTT	1	150 bp	yes	39632690	29.72452	16.79	29508201	22.13115	1037	SRR5998804	SAMN07573765	PRJNA400795	0
Columbicola passerinae passerinae 1	Cosp.Copic.11.2.2016.1	Columbina picui	CCW880	Bolivia: Santa Cruz	n/a	2-Nov-2016	0.219	Covaris M220	Hyper Library (Kapa Biosystems)	Illumina HiSeq4000	HiSeq4000 v.1	151	AACGTTGTGTCC	1	150 bp	yes	32596536	24.44740	17.31	24402171	18.30163	1031	SRR5998813	SAMN07573743	PRJNA400795	0
Columbicola passerinae passerinae 1	Cosp.Copic.11.2.2016.3	Columbina picui	KGM292	Argentina: Cordoba	26-Apr-2001	2-Nov-2016	0.260	Covaris M220	Hyper Library (Kapa Biosystems)	Illumina HiSeq4000	HiSeq4000 v.1	151	GCGGAGATCCGG	2	150 bp	yes	47314896	35.48617	12.25	35586948	26.69021	1036	SRR5998811	SAMN07573745	PRJNA400795	0
Columbicola passerinae passerinae 1	Cosp.Cosqu.11.7.2016.1	Columbina squammata	4703	Brazil: Para	1-Sep-2010	7-Nov-2016	0.521	Covaris M220	Hyper Library (Kapa Biosystems)	Illumina HiSeq4000	HiSeq4000 v.1	151	ATTCTGAAGTCC	2	150 bp	yes	48517638	36.38823	15.39	36766169	27.57463	1037	SRR5998825	SAMN07573759	PRJNA400795	0
Columbicola passerinae passerinae 1	Cosp.Cosqu.11.7.2016.5	Columbina squammata	4781	Brazil: Para	15-Aug-2013	7-Nov-2016	0.156	Covaris M220	Hyper Library (Kapa Biosystems)	Illumina HiSeq4000	HiSeq4000 v.1	151	AACATTAGCCGG	1	150 bp	yes	72675376	54.50653	14.09	52631931	39.47395	1033	SRR5998806	SAMN07573763	PRJNA400795	0
Columbicola passerinae passerinae 1	Cosp.Cotal.11.2.2016.15	Columbina talpacoti	GMS1870	Panama: Torti	13-Feb-2006	2-Nov-2016	0.502	Covaris M220	Hyper Library (Kapa Biosystems)	Illumina HiSeq4000	HiSeq4000 v.1	151	GGCGGTTGGGCC	2	150 bp	yes	46266960	34.70022	14.42	35674625	26.75597	1037	SRR5998827	SAMN07573757	PRJNA400795	0
Columbicola passerinae passerinae 1	Cosp.Cotal.11.7.2016.2	Columbina talpacoti	JMD732	Panama: Felipillo	19-Feb-2006	7-Nov-2016	0.601	Covaris M220	Hyper Library (Kapa Biosystems)	Illumina HiSeq4000	HiSeq4000 v.1	151	GTCGTCAACCGG	1	150 bp	yes	35243764	26.43282	15.97	26727002	20.04525	1037	SRR5998826	SAMN07573760	PRJNA400795	0
Columbicola passerinae passerinae 1	Cosp.Urcam.11.7.2016.4	Uropelia campestris	4789	Brazil: Para	15-Aug-2013	7-Nov-2016	0.104	Covaris M220	Hyper Library (Kapa Biosystems)	Illumina HiSeq4000	HiSeq4000 v.1	151	GACCGTAGCCTT	1	150 bp	yes	74749204	56.06190	17.66	52886962	39.66522	1036	SRR5998830	SAMN07573762	PRJNA400795	0
Columbicola passerinae passerinae 1	Cosp.Urcam.11.7.2016.6	Uropelia campestris	4888	Brazil: Para	20-Aug-2013	7-Nov-2016	0.335	Covaris M220	Hyper Library (Kapa Biosystems)	Illumina HiSeq4000	HiSeq4000 v.1	151	CGTCAGTTGTCC	2	150 bp	yes	49864818	37.39861	17.87	39286712	29.46503	1037	SRR5998805	SAMN07573764	PRJNA400795	0
Columbicola passerinae passerinae 1	Copas1	Columbina picui		Argentina: Salta			NA					NA		NA			NA	NA	NA	NA	NA	1037	SRR3161931	SAMN04103775	PRJNA296666	1
Columbicola passerinae passerinae 2	Cosp.Clpre.11.2.2016.14	Claravis pretiosa	REW178	Peru: Cajamarca	7-Sep-2002	2-Nov-2016	0.304	Covaris M220	Hyper Library (Kapa Biosystems)	Illumina HiSeq4000	HiSeq4000 v.1	151	CATGGCCGGTCC	2	150 bp	yes	41944386	31.45829	16.97	31984684	23.98851	1036	SRR5998822	SAMN07573756	PRJNA400795	0
Columbicola passerinae passerinae 2	Cosp.Clpre.11.7.2016.11	Claravis pretiosa	CO-14	Mexico: Campeche	19-Mar-1998	7-Nov-2016	0.514	Covaris M220	Hyper Library (Kapa Biosystems)	Illumina HiSeq4000	HiSeq4000 v.1	151	CTGGCTAGCCTT	1	150 bp	yes	45739438	34.30458	21.00	33977515	25.48314	1037	SRR5998809	SAMN07573768	PRJNA400795	0
Columbicola passerinae passerinae 2	Cosp.Clpre.11.7.2016.3	Claravis pretiosa	REW166	Peru: Cajamarca: Jaen	5-Sep-2002	7-Nov-2016	0.443	Covaris M220	Hyper Library (Kapa Biosystems)	Illumina HiSeq4000	HiSeq4000 v.1	151	TTGCATGTGGCC	1	150 bp	yes	40306124	30.22959	20.84	30250586	22.68794	1037	SRR5998829	SAMN07573761	PRJNA400795	0
Columbicola passerinae passerinae 2	Cosp.Clpre.11.7.2016.9	Claravis pretiosa	5178	Brazil: Para	7-Jun-2013	7-Nov-2016	0.334	Covaris M220	Hyper Library (Kapa Biosystems)	Illumina HiSeq4000	HiSeq4000 v.1	151	GTCACGTACCTT	1	150 bp	yes	42960738	32.22055	44.09	27071367	20.30353	1037	SRR5998803	SAMN07573766	PRJNA400795	0
Columbicola passerinae passerinae 2	Cosp.Cobuc.11.2.2016.13	Columbina buckleyi	REW187	Peru: Cajamarca	7-Sep-2002	2-Nov-2016	0.638	Covaris M220	Hyper Library (Kapa Biosystems)	Illumina HiSeq4000	HiSeq4000 v.1	151	CCTGTTGACCGG	2	150 bp	yes	36749634	27.56223	17.85	28306675	21.23001	1034	SRR5998821	SAMN07573755	PRJNA400795	0
Columbicola passerinae passerinae 2	Cosp.Cobuc.11.2.2016.2	Columbina buckleyi	RCF998	Peru	n/a	2-Nov-2016	0.403	Covaris M220	Hyper Library (Kapa Biosystems)	Illumina HiSeq4000	HiSeq4000 v.1	151	GCAGTGTTGGCC	1	150 bp	yes	32833854	24.62539	25.53	24018454	18.01384	1037	SRR5998814	SAMN07573744	PRJNA400795	0
Columbicola passerinae passerinae 2	Cosp.Cocru.11.2.2016.11	Columbina cruziana	REW84	Peru: Lima: Hatillo	8-Aug-2002	2-Nov-2016	0.386	Covaris M220	Hyper Library (Kapa Biosystems)	Illumina HiSeq4000	HiSeq4000 v.1	151	CAGTACGCGGCC	1	150 bp	yes	42659324	31.99449	41.41	28547754	21.41082	1037	SRR5998823	SAMN07573753	PRJNA400795	0
Columbicola passerinae passerinae 2	Cosp.Cocru.11.7.2016.16	Columbina cruziana	ASEC006	Ecuador: Manabi: Cerro Seco	29-Jan-2016	7-Nov-2016	0.353	Covaris M220	Hyper Library (Kapa Biosystems)	Illumina HiSeq4000	HiSeq4000 v.1	151	GAAGGAACCCGG	2	150 bp	yes	49782620	37.33696	15.47	38438694	28.82902	1036	SRR5998831	SAMN07573773	PRJNA400795	0
Columbicola passerinae passerinae 2	Cosp.Cotal.11.2.2016.8	Columbina talpacoti	n/a	Bolivia	5-May-2002	2-Nov-2016	0.482	Covaris M220	Hyper Library (Kapa Biosystems)	Illumina HiSeq4000	HiSeq4000 v.1	151	AAATTAACCCTT	2	150 bp	yes	48092106	36.06908	15.46	36474253	27.35569	1037	SRR5998816	SAMN07573750	PRJNA400795	0
Columbicola passerinae passerinae 2	Cosp.Cotal.11.7.2016.10	Columbina talpacoti	6471	Brazil: Rondonia	7-Oct-2014	7-Nov-2016	0.304	Covaris M220	Hyper Library (Kapa Biosystems)	Illumina HiSeq4000	HiSeq4000 v.1	151	ACTACCAACCGG	2	150 bp	yes	45408470	34.05635	13.86	34842969	26.13223	1037	SRR5998810	SAMN07573767	PRJNA400795	0
Columbicola passerinae passerinae 2	Copas2	Columbina cruziana		Peru			NA					NA		NA			NA	NA	NA	NA	NA	1037	SRR3161930	SAMN04103774	PRJNA296666	1
Columbicola drowni drowni	Cosp.Memel.11.2.2016.6	Metriopelia melanoptera	KGM 443	Argentina: Jujuy	10-Oct-2001	2-Nov-2016	0.501	Covaris M220	Hyper Library (Kapa Biosystems)	Illumina HiSeq4000	HiSeq4000 v.1	151	TACCGGCGCCGG	2	150 bp	yes	46552564	34.91442	12.95	35613935	26.71045	1039	SRR5998818	SAMN07573748	PRJNA400795	0
Columbicola drowni drowni	Cosp.Memel.11.7.2016.13	Metriopelia melanoptera	ASEC003	Ecuador: Pichincha: Secas	23-Jan-2016	7-Nov-2016	0.570	Covaris M220	Hyper Library (Kapa Biosystems)	Illumina HiSeq4000	HiSeq4000 v.1	151	TACTACGGCCTT	2	150 bp	yes	54926416	41.19481	19.90	41232463	30.92435	1039	SRR5998807	SAMN07573770	PRJNA400795	0
Columbicola drowni drowni	Codro	Metriopelia melanoptera		Argentina: Jujuy			NA					NA		NA			NA	NA	NA	NA	NA	1039	SRR3161922	SAMN04103766	PRJNA296666	1
Columbicola gymnopeliae gymnopeliae	Cosp.Mecec.11.2.2016.10	Metriopelia ceciliae	REW192	Peru: Cajamarca	13-Sep-2002	2-Nov-2016	0.494	Covaris M220	Hyper Library (Kapa Biosystems)	Illumina HiSeq4000	HiSeq4000 v.1	151	GCTCGGCCGGCC	1	150 bp	yes	44362564	33.27192	16.95	33757698	25.31827	1038	SRR5998820	SAMN07573752	PRJNA400795	1
Columbicola gymnopeliae gymnopeliae	Cosp.Mecec.11.2.2016.12	Metriopelia ceciliae	REW150	Peru: Caras	28-Aug-2002	2-Nov-2016	0.561	Covaris M220	Hyper Library (Kapa Biosystems)	Illumina HiSeq4000	HiSeq4000 v.1	151	CATAGCTTCCGG	2	150 bp	yes	39654522	29.74089	12.77	30602281	22.95171	1037	SRR5998824	SAMN07573754	PRJNA400795	0
Columbicola gymnopeliae gymnopeliae	Cogym	Metriopelia ceciliae		Peru: Cajamarca			NA					NA		NA			NA	NA	NA	NA	NA	1037	SRR3161923	SAMN04103767	PRJNA296666	0
Columbicola altamimiae altamimiae	Cosp.Meaym.11.2.2016.5	Metriopelia aymara	KGM 431	Argentina: Salta	6-Oct-2001	2-Nov-2016	0.606	Covaris M220	Hyper Library (Kapa Biosystems)	Illumina HiSeq4000	HiSeq4000 v.1	151	TTACTTCTCCGG	1	150 bp	yes	35598232	26.69867	13.33	26911929	20.18395	1031	SRR5998817	SAMN07573747	PRJNA400795	1
Columbicola altamimiae altamimiae	Cosp.Meaym.11.2.2016.7	Metriopelia aymara	KGM 510	Bolivia: Oruro: Lago Poopo	2-Nov-2001	2-Nov-2016	0.168	Covaris M220	Hyper Library (Kapa Biosystems)	Illumina HiSeq4000	HiSeq4000 v.1	151	ATGATCGGCCTT	2	150 bp	yes	46193236	34.64493	15.82	34544913	25.90868	1031	SRR5998815	SAMN07573749	PRJNA400795	0
Columbicola altamimiae altamimiae	Coalt	Metriopelia aymara		Argentina: Salta			NA					NA		NA			NA	NA	NA	NA	NA	1031	SRR3161921	SAMN04103765	PRJNA296666	0

Figs. S1-S12

Click the links below (in blue) to visualize each plot. Individuals used for the phylonet analyses are asterisked.

Columbicola

Fig. S1. sppIDer results of Columbicola altamimiae samples

*coalt (Species coverage)

coalt (Coverage across the genomes)

coalt (Mapping quality)

Cosp_Meaym_11_2_2016_5 (Species coverage)

Cosp_Meaym_11_2_2016_5 (Coverage across the genomes)

Cosp_Meaym_11_2_2016_5 (Mapping quality)

Cosp_Meaym_11_2_2016_7 (Species coverage)

Cosp_Meaym_11_2_2016_7 (Coverage across the genomes)

Cosp_Meaym_11_2_2016_7 (Mapping quality)

Fig. S2. sppIDer results of Columbicola drowni_drowni samples

*Codro (Species coverage)

Codro (Coverage across the genomes)

Codro (Mapping quality)

Cosp_Memel_11_7_2016_13 (Species coverage)

Cosp_Memel_11_7_2016_13 (Coverage across the genomes)

Cosp_Memel_11_7_2016_13 (Mapping quality)

Cosp_Memel_11_2_2016_6 (Species coverage)

Cosp_Memel_11_2_2016_6 (Coverage across the genomes)

Cosp_Memel_11_2_2016_6 (Mapping quality)

Fig. S3. sppIDer results of Columbicola gymnopeliae samples

cogym (Species coverage)

cogym (Coverage across the genomes)

cogym (Mapping quality)

*Cosp_Mecec_11_2_2016_10 (Species coverage)

Cosp_Mecec_11_2_2016_10 (Coverage across the genomes)

Cosp_Mecec_11_2_2016_10 (Mapping quality)

Cosp_Mecec_11_2_2016_12 (Species coverage)

Cosp_Mecec_11_2_2016_12 (Coverage across the genomes)

Cosp_Mecec_11_2_2016_12 (Mapping quality)

Fig. S4. sppIDer results of Columbicola passerinae 1 samples

*copas1 (Species coverage)

copas1 (Coverage across the genomes)

copas1 (Mapping quality)

Cosp_Coinc_11_2_2016_9 (Species coverage)

Cosp_Coinc_11_2_2016_9 (Coverage across the genomes)

Cosp_Coinc_11_2_2016_9 (Mapping quality)

Cosp_Comin_11_2_2016_16 (Species coverage)

Cosp_Comin_11_2_2016_16 (Coverage across the genomes)

Cosp_Comin_11_2_2016_16 (Mapping quality)

Cosp_Comin_11_2_2016_4 (Species coverage)

Cosp_Comin_11_2_2016_4 (Coverage across the genomes)

Cosp_Comin_11_2_2016_4 (Mapping quality)

Cosp_Copas_11_7_2016_8 (Species coverage)

Cosp_Copas_11_7_2016_8 (Coverage across the genomes)

Cosp_Copas_11_7_2016_8 (Mapping quality)

Cosp_Copas_11_7_2016_12 (Species coverage)

Cosp_Copas_11_7_2016_12 (Coverage across the genomes)

Cosp_Copas_11_7_2016_12 (Mapping quality)

Cosp_Copas_11_7_2016_14 (Species coverage)

Cosp_Copas_11_7_2016_14 (Coverage across the genomes)

Cosp_Copas_11_7_2016_14 (Mapping quality)

Cosp_Copas_11_7_2016_15 (Species coverage)

Cosp_Copas_11_7_2016_15 (Coverage across the genomes)

Cosp_Copas_11_7_2016_15 (Mapping quality)

Cosp_Copic_11_2_2016_1 (Species coverage)

Cosp_Copic_11_2_2016_1 (Coverage across the genomes)

Cosp_Copic_11_2_2016_1 (Mapping quality)

Cosp_Copic_11_2_2016_3 (Species coverage)

Cosp_Copic_11_2_2016_3 (Coverage across the genomes)

Cosp_Copic_11_2_2016_3 (Mapping quality)

Cosp_Cosqu_11_7_2016_1 (Species coverage)

Cosp_Cosqu_11_7_2016_1 (Coverage across the genomes)

Cosp_Cosqu_11_7_2016_1 (Mapping quality)

Cosp_Cosqu_11_7_2016_5 (Species coverage)

Cosp_Cosqu_11_7_2016_5 (Coverage across the genomes)

Cosp_Cosqu_11_7_2016_5 (Mapping quality)

Cosp_Cotal_11_2_2016_15 (Species coverage)

Cosp_Cotal_11_2_2016_15 (Coverage across the genomes)

Cosp_Cotal_11_2_2016_15 (Mapping quality)

Cosp_Cotal_11_7_2016_2 (Species coverage)

Cosp_Cotal_11_7_2016_2 (Coverage across the genomes)

Cosp_Cotal_11_7_2016_2 (Mapping quality)

Cosp_Urcam_11_7_2016_6 (Species coverage)

Cosp_Urcam_11_7_2016_6 (Coverage across the genomes)

Cosp_Urcam_11_7_2016_6 (Mapping quality)

Cosp_Urcam_11_7_2016_4 (Species coverage)

Cosp_Urcam_11_7_2016_4 (Coverage across the genomes)

Cosp_Urcam_11_7_2016_4 (Mapping quality)

Fig. S5. sppIDer results of Columbicola passerinae 2 samples

*Copas2 (Species coverage)

Copas2 (Coverage across the genomes)

Copas2 (Mapping quality)

Cosp_Clpre_11_2_2016_14 (Species coverage)

Cosp_Clpre_11_2_2016_14 (Coverage across the genomes)

Cosp_Clpre_11_2_2016_14 (Mapping quality)

Cosp_Clpre_11_7_2016_3 (Species coverage)

Cosp_Clpre_11_7_2016_3 (Coverage across the genomes)

Cosp_Clpre_11_7_2016_3 (Mapping quality)

Cosp_Clpre_11_7_2016_9 (Species coverage)

Cosp_Clpre_11_7_2016_9 (Coverage across the genomes)

Cosp_Clpre_11_7_2016_9 (Mapping quality)

Cosp_Clpre_11_7_2016_11 (Species coverage)

Cosp_Clpre_11_7_2016_11 (Coverage across the genomes)

Cosp_Clpre_11_7_2016_11 (Mapping quality)

Cosp_Cobuc_11_2_2016_13 (Species coverage)

Cosp_Cobuc_11_2_2016_13 (Coverage across the genomes)

Cosp_Cobuc_11_2_2016_13 (Mapping quality)

Cosp_Cobuc_11_2_2016_2 (Species coverage)

Cosp_Cobuc_11_2_2016_2 (Coverage across the genomes)

Cosp_Cobuc_11_2_2016_2 (Mapping quality)

Cosp_Cocru_11_2_2016_11 (Species coverage)

Cosp_Cocru_11_2_2016_11 (Coverage across the genomes)

Cosp_Cocru_11_2_2016_11 (Mapping quality)

Cosp_Cocru_11_7_2016_16 (Species coverage)

Cosp_Cocru_11_7_2016_16 (Coverage across the genomes)

Cosp_Cocru_11_7_2016_16 (Mapping quality)

Cosp_Cotal_11_7_2016_10 (Species coverage)

Cosp_Cotal_11_7_2016_10 (Coverage across the genomes)

Cosp_Cotal_11_7_2016_10 (Mapping quality)

Cosp_Cotal_11_2_2016_8 (Species coverage)

Cosp_Cotal_11_2_2016_8 (Coverage across the genomes)

Cosp_Cotal_11_2_2016_8 (Mapping quality)

Physconelloides

Fig. S6. sppIDer results of Physconelloides eurysema 1 samples

*Pheur_Copas_3_14_2016_8 (Species coverage)

Pheur_Copas_3_14_2016_8 (Coverage across the genomes)

Pheur_Copas_3_14_2016_8 (Mapping quality)

Pheur_Copas_3_16_2016_6 (Species coverage)

Pheur_Copas_3_16_2016_6 (Coverage across the genomes)

Pheur_Copas_3_16_2016_6 (Mapping quality)

Pheur_Comin_6_15_2015_10 (Species coverage)

Pheur_Comin_6_15_2015_10 (Coverage across the genomes)

Pheur_Comin_6_15_2015_10 (Mapping quality)

Fig. S7. sppIDer results of Physconelloides eurysema 2 samples

*Pheur_Cosqu_3_14_2016_1 (Species coverage)

Pheur_Cosqu_3_14_2016_1 (Coverage across the genomes)

Pheur_Cosqu_3_14_2016_1 (Mapping quality)

Pheur_Cosqu_3_14_2016_12 (Species coverage)

Pheur_Cosqu_3_14_2016_12 (Coverage across the genomes)

Pheur_Cosqu_3_14_2016_12 (Mapping quality)

Fig. S8. sppIDer results of Physconelloides eurysema 3 samples

Pheur2_Clpre_5_26_2015_6 (Species coverage)

Pheur2_Clpre_5_26_2015_6 (Coverage across the genomes)

Pheur2_Clpre_5_26_2015_6 (Mapping quality)

Pheur_Clpre_6_15_2015_8 (Species coverage)

Pheur_Clpre_6_15_2015_8 (Coverage across the genomes)

Pheur_Clpre_6_15_2015_8 (Mapping quality)

Pheur_Cotal_3_14_2016_2 (Species coverage)

Pheur_Cotal_3_14_2016_2 (Coverage across the genomes)

Pheur_Cotal_3_14_2016_2 (Mapping quality)

Pheur_Copas_3_14_2016_4 (Species coverage)

Pheur_Copas_3_14_2016_4 (Coverage across the genomes)

Pheur_Copas_3_14_2016_4 (Mapping quality)

Pheur2_Clpre_3_14_2016_5 (Species coverage)

Pheur2_Clpre_3_14_2016_5 (Coverage across the genomes)

Pheur2_Clpre_3_14_2016_5 (Mapping quality)

Pheur_Cotal_3_14_2016_6 (Species coverage)

Pheur_Cotal_3_14_2016_6 (Coverage across the genomes)

Pheur_Cotal_3_14_2016_6 (Mapping quality)

Pheur_Copas_3_14_2016_7 (Species coverage)

Pheur_Copas_3_14_2016_7 (Coverage across the genomes)

Pheur_Copas_3_14_2016_7 (Mapping quality)

Pheur1_Comin_3_14_2016_9 (Species coverage)

Pheur1_Comin_3_14_2016_9 (Coverage across the genomes)

Pheur1_Comin_3_14_2016_9 (Mapping quality)

Pheur_Copas_3_14_2016_10 (Species coverage)

Pheur_Copas_3_14_2016_10 (Coverage across the genomes)

Pheur_Copas_3_14_2016_10 (Mapping quality)

*Pheur2_Clpre_3_14_2016_11 (Species coverage)

Pheur2_Clpre_3_14_2016_11 (Coverage across the genomes)

Pheur2_Clpre_3_14_2016_11 (Mapping quality)

Pheur_Copas_3_16_2016_1 (Species coverage)

Pheur_Copas_3_16_2016_1 (Coverage across the genomes)

Pheur_Copas_3_16_2016_1 (Mapping quality)

Pheur_Cotal_3_16_2016_3 (Species coverage)

Pheur_Cotal_3_16_2016_3 (Coverage across the genomes)

Pheur_Cotal_3_16_2016_3 (Mapping quality)

Pheur2_Cobuc_3_16_2016_4 (Species coverage)

Pheur2_Cobuc_3_16_2016_4 (Coverage across the genomes)

Pheur2_Cobuc_3_16_2016_4 (Mapping quality)

Pheur2_Clpre_3_16_2016_5 (Species coverage)

Pheur2_Clpre_3_16_2016_5 (Coverage across the genomes)

Pheur2_Clpre_3_16_2016_5 (Mapping quality)

Pheur_Copas_3_16_2016_7 (Species coverage)

Pheur_Copas_3_16_2016_7 (Coverage across the genomes)

Pheur_Copas_3_16_2016_7 (Mapping quality)

Pheur2_Cocru_3_16_2016_9 (Species coverage)

Pheur2_Cocru_3_16_2016_9 (Coverage across the genomes)

Pheur2_Cocru_3_16_2016_9 (Mapping quality)

Pheur_Cotal_3_16_2016_12 (Species coverage)

Pheur_Cotal_3_16_2016_12 (Coverage across the genomes)

Pheur_Cotal_3_16_2016_12 (Mapping quality)

Pheur_Cobuc_6_15_2015_1 (Species coverage)

Pheur_Cobuc_6_15_2015_1 (Coverage across the genomes)

Pheur_Cobuc_6_15_2015_1 (Mapping quality)

Pheur_Cocru_6_15_2015_2 (Species coverage)

Pheur_Cocru_6_15_2015_2 (Coverage across the genomes)

Pheur_Cocru_6_15_2015_2 (Mapping quality)

Pheur_Cotal_6_15_2015_4 (Species coverage)

Pheur_Cotal_6_15_2015_4 (Coverage across the genomes)

Pheur_Cotal_6_15_2015_4 (Mapping quality)

Fig. S9. sppIDer results of Physconelloides eurysema 4 samples

*Pheur_Coinc_6_15_2015_7 (Species coverage)

Pheur_Coinc_6_15_2015_7 (Coverage across the genomes)

Pheur_Coinc_6_15_2015_7 (Mapping quality)

Fig. S10. sppIDer results of Physconelloides eurysema 5 samples

*Pheur_Urcam_3_14_2016_3 (Species coverage)

Pheur_Urcam_3_14_2016_3 (Coverage across the genomes)

Pheur_Urcam_3_14_2016_3 (Mapping quality)

Fig. S11. sppIDer results of Physconelloides robbinsi samples

*Pheme_Memel_5_26_2015_8 (Species coverage)

Pheme_Memel_5_26_2015_8 (Coverage across the genomes)

Pheme_Memel_5_26_2015_8 (Mapping quality)

Phrob_Mecec_3_16_2016_10 (Species coverage)

Phrob_Mecec_3_16_2016_10 (Coverage across the genomes)

Phrob_Mecec_3_16_2016_10 (Mapping quality)

Phrob_Mecec_3_16_2016_11 (Species coverage)

Phrob_Mecec_3_16_2016_11 (Coverage across the genomes)

Phrob_Mecec_3_16_2016_11 (Mapping quality)

Phrob_Mecec_6_15_2015_6 (Species coverage)

Phrob_Mecec_6_15_2015_6 (Coverage across the genomes)

Phrob_Mecec_6_15_2015_6 (Mapping quality)

Fig. S12. sppIDer results of Physconelloides emersoni samples

*Phrob_Mecec_5_26_2015_7 (Species coverage)

Phrob_Mecec_5_26_2015_7 (Coverage across the genomes)

Phrob_Mecec_5_26_2015_7 (Mapping quality)

Pheme_Memel_3_16_2016_2 (Species coverage)

Pheme_Memel_3_16_2016_2 (Coverage across the genomes)

Pheme_Memel_3_16_2016_2 (Mapping quality)

Pheme_Memel_3_16_2016_8 (Species coverage)

Pheme_Memel_3_16_2016_8 (Coverage across the genomes)

Pheme_Memel_3_16_2016_8 (Mapping quality)

Pheme_Memel_6_15_2015_5 (Species coverage)

Pheme_Memel_6_15_2015_5 (Coverage across the genomes)

Pheme_Memel_6_15_2015_5 (Mapping quality)

Table S3. Summmary statistics of the assemblies of the putatively introgressed reads detected by sppIDer.

Sample.id	Number.of.contigs.assembled	Minimum.length..assembled.contigs.	Maximun.length..assembled.contigs.	Mean.length..assembled.contigs.	Median.length..assembled.contigs.	Number.of.assembled.contigs.shorter.than.the.smaller.reference.locus..Physconelloides.90bp..Columbicola.99bp.
Cosp_Clpre_11_2_2016_14	5291	78	762	259	253	2
Cosp_Cocru_11_7_2016_16	2972	78	886	261	253	2
Cosp_Copas_11_7_2016_15	3208	78	1220	273	255	2
Cosp_Cotal_11_7_2016_10	3161	78	679	260	253	7
Cosp_Memel_11_2_2016_6	6443	78	730	258	251	8
Copas2	12078	78	750	279	274	3
Cosp_Clpre_11_7_2016_3	3665	78	734	253	246	9
Cosp_Coinc_11_2_2016_9	2990	78	1051	264	254	4
Cosp_Copic_11_2_2016_1	4023	78	839	258	248	2
Cosp_Cotal_11_2_2016_8	4476	78	810	260	252	3
Cosp_Urcam_11_7_2016_6	3053	78	1115	270	255	2
Copas1	10054	78	1237	278	274	32
Cosp_Clpre_11_7_2016_9	2766	78	701	252	246	1
Cosp_Comin_11_2_2016_16	4203	78	1221	264	249	1
Cosp_Copic_11_2_2016_3	9501	78	733	262	254	3
Cosp_Meaym_11_2_2016_5	3837	78	634	255	246	2
Cosp_Urcam_11_7_2016_4	14335	78	850	263	257	22
Cosp_Clpre_11_7_2016_11	4666	78	789	254	247	3
Cosp_Comin_11_2_2016_4	5257	78	897	261	249	3
Cosp_Cosqu_11_7_2016_1	3978	78	1195	271	255	2
Cosp_Meaym_11_2_2016_7	5580	78	758	260	253	23
Cosp_Cobuc_11_2_2016_13	2817	78	744	260	253	4
Cosp_Copas_11_7_2016_8	4913	78	1106	260	248	4
Cosp_Cosqu_11_7_2016_5	14986	78	885	261	255	27
Cosp_Mecec_11_2_2016_10	4318	78	654	256	248	2
Coalt	14714	78	985	279	273	18
Cosp_Cobuc_11_2_2016_2	3225	78	721	255	247	3
Cosp_Copas_11_7_2016_12	3694	78	905	262	247	2
Cosp_Cotal_11_2_2016_15	4338	78	1018	269	254	2
Cosp_Mecec_11_2_2016_12	2712	78	756	261	253	2
Codro	18497	78	825	283	279	3
Cosp_Cocru_11_2_2016_11	2849	78	767	253	245	3
Cosp_Copas_11_7_2016_14	4883	78	1117	260	248	2
Cosp_Cotal_11_7_2016_2	3700	78	1120	265	248	3
Cosp_Memel_11_7_2016_13	3606	78	728	261	253	2
Cogym	13355	78	835	278	273	2
Pheur_Cosqu_3_14_2016_1	9144	78	1664	292	269	21
Pheur_Urcam_3_14_2016_3	9584	78	1374	290	273	7
Pheur_Cotal_3_14_2016_6	18320	78	1583	311	277	112
Pheur1_Comin_3_14_2016_9	10296	78	1762	293	269	15
Pheur_Clpre_3_14_2016_11	14465	78	1173	284	269	274
Pheme_Memel_3_16_2016_2	18891	78	1752	284	274	186
Pheur_Clpre_3_16_2016_5	16311	78	1601	297	273	43
Pheur_Comin_6_15_2015_10	10279	78	1314	323	291	1
Phrob_Mecec_3_16_2016_10	9188	78	1245	288	270	7
Pheur_Cobuc_6_15_2015_1	12189	78	1255	286	269	44
Pheme_Memel_6_15_2015_5	20288	78	1886	287	276	302
Pheur_Clpre_5_26_2015_6	18517	78	1978	297	275	12
Pheme_Memel_5_26_2015_8	1511	314	2952	797	689	0
Phrob_Mecec_5_26_2015_7	26223	77	2503	312	286	372
Pheur_Coinc_6_15_2015_7	20933	78	1400	285	273	174
Phrob_Mecec_6_15_2015_6	1919	78	686	265	258	4
Pheur_Cotal_6_15_2015_4	1854	78	859	268	261	10
Pheur_Cocru_6_15_2015_2	5288	78	912	274	263	12
Pheur_Cotal_3_16_2016_12	14272	78	1720	308	274	14
Phrob_Mecec_3_16_2016_11	9922	78	1126	287	270	7
Pheur_Cocru_3_16_2016_9	9454	78	1489	301	270	15
Pheme_Memel_3_16_2016_8	11031	78	2042	298	271	23
Pheur_Copas_3_16_2016_7	15506	78	1949	298	273	67
Pheur_Copas_3_16_2016_6	13697	78	1282	291	271	22
Pheur_Cobuc_3_16_2016_4	2369	218	1471	469	414	0
Pheur_Copas_3_16_2016_1	17798	78	1892	307	274	103
Pheur_Cosqu_3_14_2016_12	1948	400	1584	627	572	0
Pheur_Copas_3_14_2016_10	14332	78	1450	300	275	100
Pheur_Copas_3_14_2016_8	7425	78	1291	287	266	19
Pheur_Copas_3_14_2016_7	27741	78	1315	274	269	1340
Pheur_Clpre_3_14_2016_5	13253	78	1718	293	270	15
Pheur_Copas_3_14_2016_4	18657	78	2312	309	275	172
Pheur_Cotal_3_14_2016_2	13466	78	1325	289	269	26
Pheur_Clpre_6_15_2015_8	20711	78	1338	293	275	15

Table S4. Summmary of pairwise genetic distances (uncorrected) between samples of Columbicola and Physconelloides.

Genus	Interspecific..max.	Interspecific..min.	Interspecific..mean.	Intraspecific..max.	Intraspecific..min.	Intraspecific..mean.
Physconelloides	2.99	0.74	2.53	2.91	0.002	1.19
Columbicola	1.50	0.55	1.01	0.36	0.050	0.18

Fig. S13. Examples of individual gene trees (Columbicola)

Fig. S14. Examples of individual gene trees (Physconelloides)