Appendix S4: Supplementary methods
Phylogenetic host specificity and sampling effort
Methods
Using the phylogeny of our 35 focal primate species, we “infected” whole clades of primates with a hypothetical parasite and estimated NRI. We then removed one host species at random and re-estimated NRI. This reflects a scenario in which a parasite is a phylogenetic host specialist but due to poor sampling some host species are effectively missing the parasite which could spuriously cause us to accept the null hypothesis of no significant phylogenetic host specificity. We repeated randomly removing primate host species without replacement and estimating NRI until only two primates remained “infected” (NRI cannot be estimated for just one host species). We repeated this infecting a different primate clade each time, using all clades with more than two species. We then repeated the whole procedure 1000 times and calculated the proportion of these 1000 iterations which resulted in the correct result, i.e., a significant NRI value. This was the power of the NRI method to detect significant phylogenetic host specificity.
To determine the power of the NRI method to accept the null hypothesis of no significant phylogenetic host specificity in a parasite, we “infected” primates with a hypothetical parasite randomly across the phylogeny of our 35 focal primate species and estimated NRI. We then removed one host species at random and re-estimated NRI. This reflects a scenario in which a parasite is a phylogenetic host generalist but due to poor sampling some host species are effectively missing the parasite which could cause a spurious signal of phylogenetic host specificity. We repeated randomly removing primate host species without replacement and estimating NRI until only two primates remained “infected”. We then repeated the whole

procedure 1000 times and calculated the proportion of these 1000 iterations which resulted in the correct result, i.e., a non-significant NRI value.
Results
As the proportion of missing parasites increased, the power of NRI to correctly define a parasite as a phylogenetic host specialist or generalist decreased (Figure S1). For phylogenetic host specialists, power to detect significant phylogenetic host specialism remained greater than
95% until around 60% of parasites were removed at random. Our methods have even higher power to correctly identify phylogenetic host generalists; power remained greater than 90% for all simulations, i.e., even with 80% of parasites removed at random, phylogenetic host generalism was correctly detected over 90% of the time (Figure S1).
To determine how much of an issue poor-sampling may be in our analyses we used the jackknife 1 method in the R package vegan (Oksanen et al.
2011) to estimate how many hosts each parasite in our dataset should have, and from this we estimated an upper and lower bound on the number of hosts “missing” from each parasite (Table S1). Our jackknife estimates show that none of our parasites are expected to be “missing” more than 56% of their primate host species ( Hepatocystis kochi is missing the greatest percentage of hosts at 55.19%) indicating that sampling effort should not affect our results or conclusions about phylogenetic host specificity
(Table S1). Importantly this also indicates that we have not biased our results by including only
35 primate species, rather than using the whole primate phylogeny.
References
Oksanen J., Blanchet F.G., Kindt R., Legendre P., O'Hara R.B., Simpson G.L.
, et al.
(2011). vegan: community ecology package. R package version 1.17-11.

Figure S1: Figure showing the power of the net relatedness index (NRI) to either detect significant phylogenetic host specificity in a parasite, i.e., where the parasite has more closelyrelated host species than expected by chance (left hand panel) or to detect non-significant phylogenetic host specificity in a parasite, i.e., where the parasite does not have more closelyrelated host species than expected by chance (right hand panel). Power is defined as the % of simulations where NRI was correctly significant (left hand panel) or non-significant (right hand panel). Proportion missing = the number of hosts the parasite was randomly removed from.

Table S1: Predicted numbers of host species for each parasite with > 1 host in our subset of 35 well-sampled primates, estimated using the “jackknife 1” method from the R package vegan
(Oksanen et al.
2011).
Parasite Name
Acanthocheilonema gracile
Alphavirus Chikungunya
Alphavirus Mayaro
Alphavirus Semliki forest virus
Ascaridia galli
Ascaris lumbricoides
Athesmia foxi
Babesia pitheci
Bacillus anthracis
Balantidium coli
Bertiella studeri
Blastocystis hominis
Brodenia laciniata
Brugia malayi
Cercopithifilaria kenyensis
Chilomastix mesnili
Colobenterobius guerezae
Controrchis biliophilus
Coxiella burnetti
Deltaretrovirus STLV
Dengue virus group Dengue 2
Dientamoeba fragilis
Dipetalonema atelense
Dipetalonema caudispina
Dipetalonema gracile
Dipetalonema marmosetae
Dipetalonema nicollei
Dipetalonema obtusa
Dipetalonema parvum
Dipetalonema streptocercum
Dipetalonema vanhoofi
Dirofilaria aethiops
Dirofilaria magnilarvatum
Ebolavirus Zaire ebolavirus
Endolimax nana
Entamoeba chattoni
Jackknife
2
2
2
2
6
2
2
2
2
8
4
2
3
2
2
15
9
2
2
2
16
N hosts estimate SE % missing min % max %
3
5
4.00
8.00
1.22
1.94
25.00
37.50
-8.10
17.54
42.58
49.68
4
6
2
4.80
9.00
2.00
0.80
3.39
0.00
16.67
33.33
0.00
0.00
-6.97
0.00
28.57
51.58
0.00
7
2
2
3
2
6
3
3
2
15
10.38
3.00
4.00
2.00
20.76
9.84 1.64
2.00 0.00
3.00 0.71
3.80 0.80
2.50
2.36
0.00
1.22
0.00
2.35
0.50
42.17
0.00
25.00
0.00
27.75
28.88
0.00
33.33
21.05
20.00
25.12
0.00
52.89
0.00
-8.10 42.58
0.00
18.52
0.00
35.10
14.65 39.04
0.00 0.00
12.77 46.05
0.00 34.78
0.00 33.33
16.11
2.00
2.75
3.00
23.64
3.00 0.71
4.50 1.32
2.00 0.00
3.00 0.71
24.78
9.33 3.20
2.00 0.00
2.50 0.50
2.00 0.00
3.00
3.00 0.71
2.00 0.00
2.67 0.67
2.75 0.75
10.77
5.71
3.41
0.00
0.75
0.71
3.03
5.48
0.71
1.60
1.21
44.14
0.00
27.27
33.33
32.31
33.33
33.33
0.00
33.33
39.46
35.71
0.00
20.00
0.00
33.33
33.33
0.00
25.00
27.27
25.71
30.00
29.12 53.91
0.00 0.00
0.00 42.86
12.77 46.05
22.34 40.01
12.77 46.05
5.57 48.48
0.00 0.00
12.77 46.05
22.27 50.43
2.22 52.12
0.00 0.00
0.00 33.33
0.00 0.00
12.77 46.05
12.77 46.05
0.00 0.00
0.00 40.00
0.00 42.86
12.76 35.32
11.15 42.25

Entamoeba coli
Entamoeba dispar
Entamoeba hartmanni
Entamoeba histolytica
Enterobius brevicauda
Enterobius vermicularis
Entopolypoides macaci
Filariopsis arator
Filariopsis barretoi
Filaroides barretoi
Flavivirus Japanese encephalitis
Flavivirus St. Louis encephalitis
Flavivirus West Nile Virus
Flavivirus Yellow Fever
Flavivirus Zika
Giardia duodenalis
Hepadnavirus Hepatitis B
Hepatocystis cercopitheci
Hepatocystis kochi
Hepatocystis semnopitheci
Hepatocystis simiae
Hepatovirus Hepatitis A
Hymenolepis diminuta
Influenza A2
Iodamoeba butschlii
Klebsiella pneumoniae
Leipertrema foxi
Lentivirus SIV
Loa loa
Longistriata dubia
Lymphocryptovirus Human herpesvirus 4
Mastadenovirus SV
Microfilaria obtusa
Microfilaria panamensis
Molineus elegans
Molineus torulosus
Molineus vexillarius
Moniezia rugosa
Morbillivirus measles
Mycobacterium bovis
Necator americanus
Nochtia nochti
25.00
0.00
0.00
0.00
25.00
25.00
0.00
0.00
25.00
0.00
42.17
0.00
0.00
34.78
42.86
33.33
33.33
30.42
33.33
0.00
28.36
33.33
25.00
33.33
33.33
39.59
25.00
28.95
33.33
0.00
41.22
30.48
33.33
25.24
27.32
0.00
36.00
20.00
33.33
33.33
0.00
33.33
28.77 2.92
3.00 0.71
14.71 2.30
24.77 2.56
2.00 0.00
6.25 1.79
3.75 0.75
3.00 0.71
3.00 0.71
3.00 0.00
4.50 1.06
3.00 0.71
3.00 0.71
28.14 4.43
2.67 0.67
12.67 1.83
3.00 0.71
2.00 0.00
18.71 5.83
2.00 0.00
7.67 2.40
10.50 2.81
4.50 1.32
3.00 0.71
18.68 2.70
3.00 0.71
2.00 0.00
16.75 2.53
4.50 1.06
2.67 0.67
2.67 0.67
3.00 0.00
2.00 0.00
2.00 0.00
2.67 0.67
2.67 0.67
3.00 0.00
2.00 0.00
2.67 0.67
2.00 0.00
13.83 3.40
2.00 0.00
3
2
2
2
8
2
2
2
2
2
3
2
13
2
2
12
2
5
6
3
2
3
2
2
2
17
2
9
2
2
11
4
3
2
2
3
20
2
11
18
2
3
22.62 36.89
12.77 46.05
11.37 35.36
18.95 34.12
0.00 0.00
10.41 50.22
0.00 33.33
12.77 46.05
12.77 46.05
0.00 0.00
12.77 46.05
12.77 46.05
12.77 46.05
28.31 47.81
0.00 40.00
16.92 37.93
12.77 46.05
0.00 0.00
14.60 55.19
0.00 0.00
5.00 50.35
22.01 54.91
5.57 48.48
12.77 46.05
18.68 39.20
12.77 46.05
0.00 0.00
15.60 37.77
12.77 46.05
0.00 40.00
0.00 40.00
0.00
0.00
0.00
0.00
0.00 0.00
0.00 40.00
0.00 40.00
0.00
0.00
0.00
0.00
0.00 40.00
0.00 0.00
23.36 53.57
0.00 0.00

2
2
2
2
4
2
5
13
2
5
4
2
3
3
3
4
3
2
2
2
2
3
4
3
2
4
6
2
3
2
3
7
4
2
2
3
3
2
2
Oesophagostomum aculeatum
Oesophagostomum apiostomum
Oesophagostomum bifurcum
Oesophagostomum brumpti
Oesophagostomum stephanostomum
Orthobunyavirus Bakau
Tanjong Rabok
Orthobunyavirus Bunyamwera
Orthopoxvirus monkeypox
Papillomavirus SA-12
Parabronema bonnei
Pentatrichomonas hominis
Physaloptera caucasia
Plasmodium brasilianum
Plasmodium coatneyi
Plasmodium cynomolgi
Plasmodium falciparum
Plasmodium fieldi
Plasmodium georgesi
Plasmodium gonderi
Plasmodium inui
Plasmodium knowlesi
Plasmodium petersi
Plasmodium reichenowi
Plasmodium rodhani
Plasmodium schwetzi
Plasmodium simium
Plasmodium vivax
Pneumocystis carinii
Pneumovirus Human respiratory syncytial virus
Polyomavirus SV-12
Primasubulura jacchi
Prosthenorchis elegans
Protospirura muricola
Raillietina dermeriensis
Respirovirus Human parainfluenza virus 3
Retortamonas intestinalis
Rotavirus rotavirus A
Rubulavirus Human parainfluenza virus 2
Salmonella bredene
30.43
40.00
23.53
0.00
0.00
0.00
40.00
30.77
0.00
0.00
0.00
15.66
22.12
25.00
11.76
40.00
0.00
20.00
0.00
0.00
0.00
25.00
20.00
33.33
0.00
33.33
33.33
33.33
33.33
0.00
33.33
39.13
33.33
0.00
33.33
33.33
40.00
33.33
0.00
2.88 0.88
6.67 1.76
7.85 1.31
2.00 0.00
2.00 0.00
3.00 0.00
6.67 1.76
4.33 1.49
2.00 0.00
3.00 0.00
3.00 0.00
5.93 0.93
16.69 1.85
2.67 0.67
5.67 0.67
6.67 1.76
2.00 0.00
2.50 0.50
2.00 0.00
4.00 0.00
2.00 0.00
2.67 0.67
2.50 0.50
3.00 0.71
2.00 0.00
4.50 1.06
6.00 1.63
4.50 1.32
4.50 1.06
2.00 0.00
4.50 1.32
11.50 3.52
6.00 2.00
2.00 0.00
3.00 0.71
4.50 1.32
5.00 1.15
3.00 0.71
2.00 0.00
0.00 46.67
18.41 52.55
8.27 34.44
0.00 0.00
0.00 0.00
0.00 0.00
18.41 52.55
-5.54 48.49
0.00
0.00
0.00
0.00
0.00
0.00
0.00 27.08
12.44 29.88
0.00 40.00
0.00 21.05
18.41 52.55
0.00 0.00
0.00 33.33
0.00
0.00
0.00
0.00
0.00
0.00
0.00 40.00
0.00 33.33
12.77 46.05
0.00 0.00
12.77 46.05
8.40 47.60
5.57 48.48
12.77 46.05
0.00 0.00
5.57 48.48
12.30 53.39
0.00 50.00
0.00 0.00
12.77 46.05
5.57 48.48
21.98 51.26
12.77 46.05
0.00 0.00

2
2
2
3
6
6
3
2
6
2
2
3
2
4
2
2
16
4
3
12
2
13
2
2
4
2
2
3
2
2
7
2
2
2
7
15
2
3
5
7
2
3
Salmonella muenster
Salmonella poona
Schistosoma haematobium
Schistosoma mansoni
Schistosoma mattheei
Shigella flexerni
Simplexvirus Cercopithecine herpesvirus 1
Simplexvirus Herpes simplex virus 1
Spumavirus Simian foamy virus
Streptopharagus armatus
Streptopharagus baylisi
Streptopharagus pigmentatus
Strongyloides fulleborni
Strongyloides stercoralis
Subulura distans
Ternidens deminutus
Tetrapetalonema atelensis
Tetrapetalonema marmosetae
Tetrapetalonema parvum
Toxoplasma gondii
Treponema endemicum
Treponema pallidum
Treponema pertenue
Trichospirura leptostoma
Trichostrongylus colubriformis
Trichuris dispar
Trichuris trichiura
Trypanosoma conorrhini
Trypanosoma cruzi
Trypanosoma cyclops
Trypanosoma devei
Trypanosoma hippicum
Trypanosoma lambrechti
Trypanosoma minasense
Trypanosoma mycetae
Trypanosoma primatum
Trypanosoma rangeli
Trypanosoma saimirii
Trypanosoma venezuelense
Trypanoxyuris callithricis
Trypanoxyuris microon
Trypanoxyuris minutus
2.00 0.00
3.00 0.00
9.20 2.04
7.91 1.35
3.83 0.83
3.00 0.71
3.00 0.71
2.00 0.00
11.44 2.39
3.00 0.71
3.80 0.80
9.82 1.63
20.86 2.39
2.00 0.00
4.50 1.32
7.67 1.54
2.50 0.50
10.50 3.57
2.00 2.00
2.67 0.67
2.00 0.00
6.00 2.00
2.67 0.67
2.00 0.00
5.00 1.15
2.00 0.00
16.83 2.16
2.00 0.00
18.33 2.88
2.00 0.00
2.75 0.75
2.00 0.00
2.67 0.67
22.22 4.83
5.33 1.49
3.50 0.50
9.33 1.67
2.80 0.80
2.00 0.00
4.50 1.06
2.67 0.67
4.86 0.86
0.00
0.00
0.00
0.00
16.21 46.62
8.54 35.25
0.00 35.71
12.77 46.05
12.77 46.05
0.00 0.00
22.66 49.41
12.77 46.05
0.00 34.78
14.57 38.88
18.79 35.50
0.00 0.00
5.57 48.48
18.39 45.69
0.00 33.33
-1.02 50.25
#DIV/0! 50.00
0.00 40.00
0.00 0.00
0.00 50.00
0.00 40.00
0.00 0.00
21.98 51.26
0.00 0.00
18.19 36.80
0.00 0.00
15.87 38.72
0.00 0.00
0.00 42.86
0.00 0.00
0.00 40.00
8.02 40.85
-4.10 41.38
0.00 25.00
21.74 45.45
0.00 44.44
0.00 0.00
12.77 46.05
0.00 40.00
0.00 30.00
0.00
0.00
34.78
24.18
21.74
33.33
33.33
0.00
28.69
0.00
29.09
0.00
27.27
0.00
25.00
28.00
25.00
14.29
35.71
28.57
0.00
33.33
25.00
17.65
20.00
33.33
0.00
25.00
0.00
33.33
25.00
0.00
40.00
0.00
38.83
33.33
21.05
28.74
28.10
0.00
33.33
34.78

Trypanoxyuris sceleratus
Varicellovirus Cercopithecine herpesvirus 9
Watsonius deschieni
2
3
2
2.00 0.00
3.00 0.00
2.00 0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00