Brindle_Opie_tables_figures_ESM from Postcopulatory sexual selection influences baculum evolution in primates and carnivores

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Brindle & Opie. Postcopulatory sexual selection influences baculum evolution in primates and carnivores. Supplementary information on data, methods and analyses

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Electronic Supplementary Material
Postcopulatory sexual selection influences baculum evolution in
primates and carnivores
Matilda Brindle and Christopher Opie
Proceedings of the Royal Society B: Biological Sciences (DOI 10.1098/rspb.2016-1736)
These supplementary materials provide information additional to that
contained in the main paper on: trait data, ancestral state reconstructions
using additional data and the variable rates model, and other analyses.
Notes on Trait Data
a) Baculum data
When more than one data point was available, the mean baculum length was
used.
b) Body mass data
All body masses are those of adult males, aside from species in which no
body size dimorphism exists.
c) Intromission data
‘Long’ intromission was defined as that which continued for longer than 180
seconds and ‘short’ intromission was defined as that which continued for less
than 180 seconds (following Dixson [1]).
d) Mating system data
Primates for which more than one mating system was cited in the literature
were coded as such. If the polymorphism included polygamy, the species
was removed from the dataset before analyses were run as this effectively
meant it fell on both sides of the binary grouping variable (‘polygamy’ versus
‘other’).
e) Breeding seasonality data
Primates were classed as ‘seasonal breeders’ if over 67% of births occurred
over a peak three-month period [2].
Mammalian Ancestral State Reconstructions

Species within the orders Pholidota and Xenarthra have been consistently
excluded from literature describing the mammalian orders in which the
baculum is present, suggesting that a baculum is not present in these orders.
However, since it was not possible to find a source explicitly stating that this
was the case, these orders were excluded from our main reconstruction of the
evolution of the baculum across mammals. Similarly, species within the
orders Afrosoricida and Eulipotyphla have been consistently defined as
orders in which a baculum is present and it has not been possible to find any
indication that this is not the case for all species within the order [3,4].
However, since no source has directly stated that all species within these
orders have a baculum, they too were excluded from our main reconstruction
of bacular evolution.
This approach, although cautious, may not be as accurate as if these orders
were to be included. For this reason, we re-ran exactly the same multistate
analysis across the mammalian phylogeny, this time including Pholidota,
Xenarthra, Afrosoricida and Eulipotyphla. The results of this analysis (table
S1) produce a more specific time frame for the first evolution of the baculum,
suggesting an initial appearance after node 2, but before node 4 (see figure
S1). Another notable change in this version of the analysis is that the baculum
is indicated to be absent at node 5, rather than present as in the original
analysis. This is understandable given the addition of an entire order in
which a baculum is absent to this clade.
Baculum Absent
Baculum Present
Mean Probability
Standard Error
Mean Probability
Standard Error
Root
1.00
0.0000
0.00
0.0000
Node 1
1.00
0.0001
0.00
0.0001
Node 2
0.92
0.0005
0.08
0.0005
Node 3
1.00
0.0000
0.00
0.0000
Node 4
0.00
0.0000
1.00
0.0000
Node 5
0.89
0.0005
0.11
0.0005
Node 6
0.01
0.0000
0.99
0.0000
Node A
0.03
0.0000
0.97
0.0000
Table S1. Probability of baculum presence or absence at the root and seven
nodes of the mammalian phylogeny.

Ancestral State Reconstructions: variable rates model
A single time-calibrated phylogenetic tree is required to use the variable rates
model. Tree Annotator, a programme available in the BEAST software
package [6], was used to create a single maximum clade credibility (MCC)
tree from the block of 10,000 trees used in the variable rates analyses [7].
Figure S1. Mammal phylogeny [5] with the ancestral nodes (R = root, nodes 1-6)
used for reconstruction (table 1, table S1). Node A is only relevant when the
orders Eulipotyphla and Pholidota are included in the analyses (table S1).
Orders are colour coded: grey = no species with bacula, blue = all species have
bacula, light blue = mixed, some species with bacula. Taxa names are grey if
they were excluded from the main analyses (table 1), but are included in the
broader analysis (table S1).
0.025.050.075.0100.0125.0150.0175.0
Afrosoricida
Dermoptera
Dasyuromorphia
Notoryctemorphia
Carnivora
Xenarthra
Diprotodontia
Rodentia
Proboscidea
Tubulidentata
Cetartiodactyla
Hyracoidea
Perissodactyla
Microbiotheria
Paucituberculata
Macroscelidea
Didelphimorphia
Monotremata
Scandentia
Lagomorpha
Chiroptera
Eulipotyphla
Peramelemorphia
Pholidota
Primates
Sirenia
0.025.050.075.0100.0125.0150.0175.0
Afrosoricida
Dermoptera
Dasyuromorphia
Notoryctemorphia
Carnivora
Xenarthra
Diprotodontia
Rodentia
Proboscidea
Tubulidentata
Cetartiodactyla
Hyracoidea
Perissodactyla
Microbiotheria
Paucituberculata
Macroscelidea
Didelphimorphia
Monotremata
Scandentia
Lagomorpha
Chiroptera
Eulipotyphla
Peramelemorphia
Pholidota
Primates
Sirenia
mya$
1$
2$
3$
4$
5$
6$
R$
A

Melursus_ursinus
Felis_silvestris
Urocyon_cinereoargenteus
Bassariscus_astutus
Hydrictis_maculicollis
Ailuropoda_melanoleuca
Canis_lupus
Vulpes_zerda
Meles_meles
Mellivora_capensis
Zalophus_californianus
Mustela_itatsi
Ursus_arctos
Aonyx_cinerea
Martes_martes
Vulpes_macrotis
Mustela_altaica
Neofelis_nebulosa
Mustela_nudipes
Puma_concolor
Phoca_vitulina
Lynx_canadensis
Panthera_onca
Panthera_leo
Nasua_narica
Cystophora_cristata
Mirounga_leonina
Martes_flavigula
Canis_latrans
Potos_flavus
Procyon_cancrivorus
Vormela_peregusna
Vulpes_vulpes
Neophoca_cinerea
Otaria_byronia
Mydaus_javanensis
Mephitis_mephitis
Mustela_africana
Martes_zibellina
Lontra_longicaudis
Callorhinus_ursinus
Mirounga_angustirostris
Mustela_lutreola
Phoca_groenlandica
Ursus_maritimus
Lontra_canadensis
Spilogale_putorius
Odobenus_rosmarus
Monachus_schauinslandi
Prionailurus_viverrinus
Crocuta_crocuta
Martes_pennanti
Lobodon_carcinophaga
Eira_barbara
Mustela_frenata
Martes_foina
Eumetopias_jubatus
Halichoerus_grypus
Leptailurus_serval
Lutra_lutra
Mustela_eversmannii
Nyctereutes_procyonoides
Proteles_cristatus
Felis_catus
Pteronura_brasiliensis
Meles_anakuma
Mustela_strigidorsa
Vulpes_lagopus
Hyaena_hyaena
Martes_americana
Procyon_lotor
Ictonyx_libyca
Leopardus_pardalis
Taxidea_taxus
Helarctos_malayanus
Lutrogale_perspicillata
Mustela_kathiah
Mustela_sibirica
Galictis_vittata
Mustela_erminea
Erignathus_barb atus
Canis_aureus
Phoca_fasciata
Bassariscus_sumichrasti
Mustela_nivalis
Ictonyx_striatus
Gulo_gulo
Lynx_rufus
Ailurus_fulgens
Ursus_thibetanus
Nasua_nasua
Panthera_tigris
Urocyon_littoralis
Hydrurga_leptonyx
Ursus_americanus
Arctonyx_collaris
Pusa_hispida
Enhydra_lutris
Melogale_personata
Arctocephalus_tropicalis
Prionailurus_bengalensis
Conepatus_mesoleucus
Neovison_vison
Leptonychotes_weddellii
Panthera_pardus
Mustela_nigripes
Poecilogale_albinucha
Mustela_putorius
Figure S2. A carnivore phylogeny [7] scaled to reflect the rate of bacular evolution [8].
Darker red branches indicate lower rates of evolution; blue branches indicate
particularly high rates of evolution.

Aotus_lemurinus
Saguinus_fuscicollis
Macaca_fuscata
Loris_tardigradus
Pongo_abelii
Papio_papio
Cercocebus_torquatus
Eulemur_mongoz
Pithecia_pithecia
Lemur_catta
Nasalis_larvatus
Papio_cynocephalus
Allenopithecus_nigroviridis
Papio_hamadryas
Saguinus_oedipus
Alouatta_palliata
Macaca_silenus
Gorilla_beringei
Homo_sapiens
Galago_moholi
Galagoides_demidoff
Leontopithecus_rosalia
Callithrix_pygmaea
Eulemur_rubriventer
Cercopithecus_ascanius
Hylobates_lar
Symphalangus_syndactylus
Eulemur_fulvus_fulvus
Cacajao_calvus
Macaca_mulatta
Macaca_fascicularis
Lagothrix_lagotricha
Callithrix_jacchus
Hapalemur_griseus
Perodicticus_potto
Pan_paniscus
Miopithecus_talapoin
Pongo_pygmaeus
Papio_ursinus
Eulemur_macaco_macaco
Cebus_apella
Galago_senegalensis
Semnopithecus_entellus
Otolemur_garnettii
Nycticebus_coucang
Hylobates_agilis
Cheirogaleus_major
Mandrillus_leucophaeus
Microcebus_murinus
Trachypithecus_obscurus
Hylobates_moloch
Gorilla_gorilla_gorilla
Otolemur_crassicaudatus
Erythrocebus_patas
Aotus_trivirgatus
Theropithecus_gelada
Saimiri_sciureus
Eulemur_coronatus
Papio_anubis
Cheirogaleus_medius
Colobus_guereza
Nycticebus_pyg maeus
Callithrix_argentata
Trachypithecus_cristatus
Macaca_radiata
Macaca_nemestrina
Mandrillus_sphinx
Chlorocebus_aethiops
Pan_troglodytes_troglodytes
Saguinus_midas
Macaca_arctoides
Figure S3. A primate phylogeny [7] scaled to reflect the rate of testes evolution [8].
Darker red branches indicate lower rates of evolution; blue branches indicate
particularly high rates of evolution.

Callorhinus_ursinus
Felis_silvestris
Spilogale_putorius
Vulpes_lagopus
Canis_lupus
Martes_pennanti
Neovison_vison
Nyctereutes_procyonoides
Suricata_suricatta
Mustela_erminea
Puma_concolor
Acinonyx_jubatus
Ursus_americanus
Mellivora_capensis
Lycalopex_culpaeus
Felis_chaus
Mephitis_mephitis
Panthera_onca
Ursus_arctos
Lycalopex_griseus
Mustela_nivalis
Mustela_frenata
Chrysocyon_brachyurus
Taxidea_taxus
Urocyon_cinereoargenteus
Vulpes_vulpes
Lynx_lynx
Ursus_maritimus
Crocuta_crocuta
Eumetopias_jubatus
Canis_aureus
Meles_meles
Canis_latrans
Procyon_lotor
Helogale_parvula
Felis_catus
Mustela_putorius
Genetta_genetta
Gulo_gulo
Spilogale_gracilis
Cynictis_penicillata
Lontra_canadensis
Panthera_leo
Herpestes_javanicus
Figure S4. A carnivore phylogeny [7] scaled to reflect the rate of testes evolution [8].
Darker red branches indicate lower rates of evolution; blue branches indicate
particularly high rates of evolution.

Continuous Regression
These analyses suggest that testes mass (a proxy for postcopulatory selection
pressure) is not a significant predictor of baculum length in primates or
carnivores.
Correlated Evolution
It was not possible to test for correlated evolution between baculum presence
and intromission duration in carnivores. Since the Hyaenidae family are the
only carnivores in which a baculum is completely absent, the sample was not
large enough to produce meaningful results. For this reason, carnivores are
only included in analyses examining baculum length.
Hypothesis Testing
Species were divided into groups by creating binary variables and regressing
baculum length onto these (following Organ et al. [9]). Adult male body mass
was included as a predictor variable in order to account for its effect on
baculum length.
Unfortunately it was not possible to gather enough data on carnivore mating
systems or seasonality to allow meaningful replications of the tests conducted
with primates.
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Table S2. Phylogenetic regression between baculum length and testes mass in
primates and carnivores.

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Baculum Presence: 0 = Absent
1 = Present

Intromission Duration: 0 = Short (<180 seconds)
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