R/fuse_ind_computation.R
fuse.RdThis index takes into account species functional uniqueness (also called Functional Originality), species specialisation and species IUCN status.
fuse(sp_dist, sp_faxes_coord, nb_NN = 5, GE, standGE = FALSE)a dist object provided by funct.dist,
daisy or dist.ktab.
a data frame with the coordinates of the species on a multidimensional space based on a selected number of axes derived from a Principal Coordinate Analysis (PCoA). The species are in rows and the PCOA axes are in column.
a numerical value giving the number of nearest neighbor to
consider. Default: nb_NN = 5.
a numerical vector giving the IUCN status rank (DD = NA, LC = 0, NT = 1, VU = 2, EN = 3, CR = 4) or the IUCN extinction probability associated with each status. See Mooers et al. (2008) for further information. For example, DD = NA, LC = 0, NT = 0.1, VU = 0.4, EN = 0.666, and CR = 0.999).
a logical value to standardize the GE values.
A data frame with species in rows and the following metrics in columns:
FUSE: functionally unique, specialized and endangered (see Pimiento et al. (2020);
FUn_std: functional uniqueness standardized between 0 and 1 (see Mouillot et al. (2013);
FSp_std: functional specialization standardized between 0 and 1 (see Mouillot et al. (2013);
Mouillot et al. (2013) Rare species support vulnerable functions in
high-diversity ecosystems. PLoS Biology, 11, e1001569.
Pimiento et al. (2020) Functional diversity of marine megafauna in the
Anthropocene. Science Advances, 6, eaay7650.
Violle et al. (2007) Let the concept of trait be functional! Oikos,
116, 882-892.
# Load species traits data:
sp_tr <- read.csv(system.file('extdata', 'data_traits_MMA_ursus.csv',
package = 'mFD'), dec = ',', sep = ';', header = TRUE, row.names = 1,
na.strings='NA')
# Trait compilation and ordination:
dimorphism <- ordered(sp_tr$dimorphism)
breeding_site <- ordered(sp_tr$breeding_site)
social_behavior <- ordered(sp_tr$social_behavior)
weight_max <- log(sp_tr$adult_weight_max)
social_group <- log(sp_tr$social_group_mean)
# Trait Matrix construction:
sp_tr_end <- data.frame(
main_diet = sp_tr$main_diet,
foraging_water_depth = sp_tr$foraging_water_depth,
foraging_location = sp_tr$foraging_location,
fasting_strategy = sp_tr$fasting_strategy,
female_sexual_maturity = sp_tr$female_sexual_maturity,
weaning = sp_tr$weaning,
gestation = sp_tr$gestation, inter_litter = sp_tr$inter_litter,
breeding_site = sp_tr$breeding_site,
social_group = sp_tr$social_group_mean,
social_behavior = sp_tr$social_behavior,
weight_max = sp_tr$adult_weight_max,
dimorphism = sp_tr$dimorphism)
rownames(sp_tr_end) <- rownames(sp_tr)
# Function weigthing vector:
v <- c(0.25, 0.25, 0.25, 0.25, 0.20, 0.20, 0.20, 0.20, 0.20, 0.5, 0.5, 0.5,
0.5)
# Gower distance calculation:
sp_tr_end$main_diet <- as.factor(sp_tr_end$main_diet)
sp_tr_end$foraging_water_depth <- as.factor(sp_tr_end$foraging_water_depth)
sp_tr_end$foraging_location <- as.factor(sp_tr_end$foraging_location)
sp_tr_end$breeding_site <- as.factor(sp_tr_end$breeding_site)
sp_tr_end$social_behavior <- as.factor(sp_tr_end$social_behavior)
sp_dist_tr <- cluster::daisy(sp_tr_end, metric = c('gower'),
type = list(symm = c(4)), weights = v)
# Principal coordinate analyses
Pcoa <- ade4::dudi.pco(ade4::quasieuclid(sp_dist_tr), scann = FALSE,
nf = 40)
#> Warning: Zero distance(s)
sp_faxes_coord <- Pcoa$li[1:40]
# FUSE calculation:
FUSE_res <- mFD::fuse(
sp_dist = sp_dist_tr,
sp_faxes_coord = as.matrix(sp_faxes_coord),
nb_NN = 5,
GE = sp_tr$IUCN_num,
standGE = TRUE)
FUSE_res
#> FUSE FUn_std FSp_std
#> Arctocephalus_australis 0.00000000 0.4066626897 0.44574291
#> Arctocephalus_forsteri 0.00000000 0.5170579368 0.51871477
#> Arctocephalus_galapagoensis 0.65704590 0.5592652556 0.47871747
#> Arctocephalus_gazella 0.00000000 0.6208798411 0.56465339
#> Arctocephalus_philippii 0.00000000 0.2779525182 0.44247109
#> Arctocephalus_pusillus 0.00000000 0.2442786896 0.37884040
#> Arctocephalus_townsendi 0.00000000 0.5852680899 0.64653619
#> Arctocephalus_tropicalis 0.00000000 0.2297455947 0.32036900
#> Balaena_mysticetus 0.00000000 0.7452467855 0.57306402
#> Balaenoptera_acutorostrata 0.00000000 0.4460157412 0.41489069
#> Balaenoptera_bonaerensis 0.13238904 0.2184186166 0.32978308
#> Balaenoptera_borealis 0.41103021 0.2139234148 0.39976514
#> Balaenoptera_edeni 0.00000000 0.4661991166 0.27554077
#> Balaenoptera_musculus 0.80941909 0.6292520413 0.70171703
#> Balaenoptera_omurai NA 0.2386976599 0.41958574
#> Balaenoptera_physalus 0.56665878 0.3536749038 0.52385972
#> Berardius_arnuxii NA 0.3691785951 0.24980784
#> Berardius_bairdii NA 0.3306752012 0.23813008
#> Callorhinus_ursinus 0.48846635 0.5012945401 0.60635396
#> Caperea_marginata 0.00000000 0.1832726206 0.40111351
#> Cephalorhynchus_commersonii 0.00000000 0.1835307609 0.17480251
#> Cephalorhynchus_eutropia 0.01817766 0.0069987566 0.06626082
#> Cephalorhynchus_heavisidii 0.01830039 0.0083171263 0.06542231
#> Cephalorhynchus_hectori 0.01749032 0.0070959999 0.01634259
#> Cystophora_cristata 0.45529572 0.5865158316 0.43824460
#> Delphinapterus_leucas 0.00000000 0.6739629047 0.32847428
#> Delphinus_capensis NA 0.0264311644 0.16472623
#> Delphinus_delphis 0.00000000 0.3984163792 0.16127757
#> Dugong_dugon 0.38031579 0.5379056252 0.30543867
#> Enhydra_lutris 0.71394550 0.7016950229 0.45056295
#> Erignathus_barbatus 0.00000000 0.5531416419 0.35107768
#> Eschrichtius_robustus 0.00000000 0.8271900919 0.61300225
#> Eubalaena_australis 0.00000000 0.3144018773 0.78268639
#> Eubalaena_glacialis 0.53448288 0.2810689133 0.54593451
#> Eubalaena_japonica 0.64071030 0.4661757614 0.54157645
#> Eumetopias_jubatus 0.23895925 0.4516548620 0.56433150
#> Feresa_attenuata 0.00000000 0.2955099743 0.27261560
#> Globicephala_macrorhynchus 0.00000000 0.5255589486 0.35104810
#> Globicephala_melas 0.00000000 0.4990595861 0.35763988
#> Grampus_griseus 0.00000000 0.5233269607 0.29251186
#> Halichoerus_grypus 0.00000000 0.1032026841 0.35586820
#> Histriophoca_fasciata 0.00000000 0.6521823871 0.28824480
#> Hydrurga_leptonyx 0.00000000 0.6622353793 0.44212015
#> Hyperoodon_ampullatus NA 0.2547878402 0.12270144
#> Hyperoodon_planifrons 0.00000000 0.2557952131 0.12249240
#> Indopacetus_pacificus NA 0.2850555343 0.28554866
#> Kogia_breviceps NA 0.2839209537 0.25751272
#> Kogia_sima NA 0.1456685909 0.25492545
#> Lagenodelphis_hosei 0.00000000 0.7241772659 0.51940242
#> Lagenorhynchus_acutus 0.00000000 0.4544319444 0.19736356
#> Lagenorhynchus_albirostris 0.00000000 0.0907709847 0.14280471
#> Lagenorhynchus_australis 0.00000000 0.0010393047 0.21058380
#> Lagenorhynchus_cruciger 0.00000000 0.0020371106 0.15621825
#> Lagenorhynchus_obliquidens 0.00000000 0.3327438642 0.20430708
#> Lagenorhynchus_obscurus 0.00000000 0.4240208007 0.17545748
#> Leptonychotes_weddellii 0.00000000 0.5404210014 0.55524903
#> Lissodelphis_borealis 0.00000000 0.5812804661 0.50809556
#> Lissodelphis_peronii 0.00000000 0.2947422923 0.43157141
#> Lobodon_carcinophaga 0.00000000 0.5833807958 0.41597696
#> Lontra_felina 0.59408663 0.5749777422 0.35413972
#> Megaptera_novaeangliae 0.00000000 0.3564239828 0.45460052
#> Mesoplodon_bidens NA 0.2401439269 0.23803164
#> Mesoplodon_bowdoini NA 0.0644576583 0.20799830
#> Mesoplodon_carlhubbsi NA 0.0008237359 0.07159363
#> Mesoplodon_densirostris NA 0.2058523276 0.19967333
#> Mesoplodon_europaeus NA 0.1358313979 0.09000617
#> Mesoplodon_ginkgodens NA 0.0013549553 0.07202895
#> Mesoplodon_grayi NA 0.0544755693 0.20125592
#> Mesoplodon_hectori NA 0.0533639848 0.20213100
#> Mesoplodon_layardii NA 0.0156247025 0.09936896
#> Mesoplodon_mirus NA 0.2615344649 0.02711371
#> Mesoplodon_perrini NA 0.0007873510 0.07105382
#> Mesoplodon_peruvianus NA 0.0022081471 0.07148019
#> Mesoplodon_stejnegeri NA 0.0019316220 0.07240253
#> Mesoplodon_traversii NA 0.0000000000 0.09237153
#> Mirounga_angustirostris 0.00000000 1.0000000000 1.00000000
#> Mirounga_leonina 0.00000000 0.6948598959 0.62780483
#> Monachus_monachus 0.25265231 0.1977684465 0.16152114
#> Monachus_schauinslandi 0.69523452 0.5791027790 0.52972758
#> Monodon_monoceros 0.00000000 0.7032597866 0.45028422
#> Neophoca_cinerea 0.36345229 0.1434988631 0.39804367
#> Neophocaena_phocaenoides 0.32176325 0.5420666711 0.17076625
#> Odobenus_rosmarus NA 0.5803602059 0.45366482
#> Ommatophoca_rossii 0.00000000 0.6659562055 0.34130521
#> Orcaella_brevirostris 0.04133240 0.0101282373 0.04578858
#> Orcaella_heinsohni 0.05624410 0.0292679517 0.08519702
#> Orcinus_orca NA 0.7536273607 0.39332028
#> Otaria_flavescens 0.00000000 0.0808815948 0.34394151
#> Pagophilus_groenlandicus 0.00000000 0.7570041744 0.46023398
#> Peponocephala_electra 0.00000000 0.5314927079 0.48063075
#> Phoca_largha 0.00000000 0.5982829480 0.33477382
#> Phoca_vitulina 0.00000000 0.4543455128 0.37496303
#> Phocarctos_hookeri 0.29111541 0.0782092491 0.35171865
#> Phocoena_dioptrica 0.00000000 0.2513166389 0.41532085
#> Phocoena_phocoena 0.00000000 0.0736635094 0.00000000
#> Phocoena_sinus 0.30989600 0.1864775088 0.14901742
#> Phocoena_spinipinnis 0.11003937 0.2651030237 0.18774230
#> Phocoenoides_dalli 0.00000000 0.2916871646 0.15983045
#> Physeter_macrocephalus 0.54891552 0.7564270292 0.51249076
#> Pontoporia_blainvillei 0.27464151 0.3710816347 0.22018302
#> Pseudorca_crassidens 0.17203888 0.4744533574 0.24712980
#> Pusa_caspica 0.36513400 0.1941091818 0.34349375
#> Pusa_hispida 0.00000000 0.1823213934 0.15240645
#> Sotalia_guianensis 0.01946782 0.0546637568 0.02364730
#> Sousa_chinensis 0.20619793 0.5623262797 0.31006940
#> Sousa_teuszii 0.38826398 0.2726857890 0.15850980
#> Stenella_attenuata 0.00000000 0.4500796407 0.27718723
#> Stenella_clymene 0.00000000 0.3747462296 0.40334210
#> Stenella_coeruleoalba 0.00000000 0.2311412497 0.18363765
#> Stenella_frontalis 0.00000000 0.3490478318 0.23845778
#> Stenella_longirostris 0.00000000 0.5133002403 0.18285982
#> Steno_bredanensis 0.00000000 0.1334810508 0.21805988
#> Tasmacetus_shepherdi NA 0.3474343349 0.17676343
#> Trichechus_manatus 0.33814860 0.5037922863 0.24035976
#> Trichechus_senegalensis 0.36824108 0.5315342856 0.28350122
#> Tursiops_aduncus 0.04686502 0.0517896426 0.13834135
#> Tursiops_truncatus 0.00000000 0.3052280508 0.19082721
#> Ursus_maritimus 0.67482557 0.9090386502 0.70012282
#> Zalophus_californianus 0.00000000 0.1204667495 0.62677747
#> Zalophus_wollebaeki 0.32738815 0.0749554707 0.41799919
#> Ziphius_cavirostris 0.00000000 0.1383689569 0.09353647
FUSE_res2 <- mFD::fuse(
sp_dist = sp_dist_tr,
sp_faxes_coord = as.matrix(sp_faxes_coord),
nb_NN = 5,
GE = sp_tr$IUCN_50,
standGE = TRUE)
FUSE_res2
#> FUSE FUn_std FSp_std
#> Arctocephalus_australis 0.0000000000 0.4066626897 0.44574291
#> Arctocephalus_forsteri 0.0000000000 0.5170579368 0.51871477
#> Arctocephalus_galapagoensis 0.4051935747 0.5592652556 0.47871747
#> Arctocephalus_gazella 0.0000000000 0.6208798411 0.56465339
#> Arctocephalus_philippii 0.0000000000 0.2779525182 0.44247109
#> Arctocephalus_pusillus 0.0000000000 0.2442786896 0.37884040
#> Arctocephalus_townsendi 0.0000000000 0.5852680899 0.64653619
#> Arctocephalus_tropicalis 0.0000000000 0.2297455947 0.32036900
#> Balaena_mysticetus 0.0000000000 0.7452467855 0.57306402
#> Balaenoptera_acutorostrata 0.0000000000 0.4460157412 0.41489069
#> Balaenoptera_bonaerensis 0.0022311864 0.2184186166 0.32978308
#> Balaenoptera_borealis 0.2482137302 0.2139234148 0.39976514
#> Balaenoptera_edeni 0.0000000000 0.4661991166 0.27554077
#> Balaenoptera_musculus 0.5062324442 0.6292520413 0.70171703
#> Balaenoptera_omurai NA 0.2386976599 0.41958574
#> Balaenoptera_physalus 0.3468953473 0.3536749038 0.52385972
#> Berardius_arnuxii NA 0.3691785951 0.24980784
#> Berardius_bairdii NA 0.3306752012 0.23813008
#> Callorhinus_ursinus 0.0562359308 0.5012945401 0.60635396
#> Caperea_marginata 0.0000000000 0.1832726206 0.40111351
#> Cephalorhynchus_commersonii 0.0000000000 0.1835307609 0.17480251
#> Cephalorhynchus_eutropia 0.0002983037 0.0069987566 0.06626082
#> Cephalorhynchus_heavisidii 0.0003002586 0.0083171263 0.06542231
#> Cephalorhynchus_hectori 0.0101183562 0.0070959999 0.01634259
#> Cystophora_cristata 0.0520745374 0.5865158316 0.43824460
#> Delphinapterus_leucas 0.0000000000 0.6739629047 0.32847428
#> Delphinus_capensis NA 0.0264311644 0.16472623
#> Delphinus_delphis 0.0000000000 0.3984163792 0.16127757
#> Dugong_dugon 0.0429309730 0.5379056252 0.30543867
#> Enhydra_lutris 0.4434975661 0.7016950229 0.45056295
#> Erignathus_barbatus 0.0000000000 0.5531416419 0.35107768
#> Eschrichtius_robustus 0.0000000000 0.8271900919 0.61300225
#> Eubalaena_australis 0.0000000000 0.3144018773 0.78268639
#> Eubalaena_glacialis 0.3270161133 0.2810689133 0.54593451
#> Eubalaena_japonica 0.3945009065 0.4661757614 0.54157645
#> Eumetopias_jubatus 0.0041331511 0.4516548620 0.56433150
#> Feresa_attenuata 0.0000000000 0.2955099743 0.27261560
#> Globicephala_macrorhynchus 0.0000000000 0.5255589486 0.35104810
#> Globicephala_melas 0.0000000000 0.4990595861 0.35763988
#> Grampus_griseus 0.0000000000 0.5233269607 0.29251186
#> Halichoerus_grypus 0.0000000000 0.1032026841 0.35586820
#> Histriophoca_fasciata 0.0000000000 0.6521823871 0.28824480
#> Hydrurga_leptonyx 0.0000000000 0.6622353793 0.44212015
#> Hyperoodon_ampullatus NA 0.2547878402 0.12270144
#> Hyperoodon_planifrons 0.0000000000 0.2557952131 0.12249240
#> Indopacetus_pacificus NA 0.2850555343 0.28554866
#> Kogia_breviceps NA 0.2839209537 0.25751272
#> Kogia_sima NA 0.1456685909 0.25492545
#> Lagenodelphis_hosei 0.0000000000 0.7241772659 0.51940242
#> Lagenorhynchus_acutus 0.0000000000 0.4544319444 0.19736356
#> Lagenorhynchus_albirostris 0.0000000000 0.0907709847 0.14280471
#> Lagenorhynchus_australis 0.0000000000 0.0010393047 0.21058380
#> Lagenorhynchus_cruciger 0.0000000000 0.0020371106 0.15621825
#> Lagenorhynchus_obliquidens 0.0000000000 0.3327438642 0.20430708
#> Lagenorhynchus_obscurus 0.0000000000 0.4240208007 0.17545748
#> Leptonychotes_weddellii 0.0000000000 0.5404210014 0.55524903
#> Lissodelphis_borealis 0.0000000000 0.5812804661 0.50809556
#> Lissodelphis_peronii 0.0000000000 0.2947422923 0.43157141
#> Lobodon_carcinophaga 0.0000000000 0.5833807958 0.41597696
#> Lontra_felina 0.3649494018 0.5749777422 0.35413972
#> Megaptera_novaeangliae 0.0000000000 0.3564239828 0.45460052
#> Mesoplodon_bidens NA 0.2401439269 0.23803164
#> Mesoplodon_bowdoini NA 0.0644576583 0.20799830
#> Mesoplodon_carlhubbsi NA 0.0008237359 0.07159363
#> Mesoplodon_densirostris NA 0.2058523276 0.19967333
#> Mesoplodon_europaeus NA 0.1358313979 0.09000617
#> Mesoplodon_ginkgodens NA 0.0013549553 0.07202895
#> Mesoplodon_grayi NA 0.0544755693 0.20125592
#> Mesoplodon_hectori NA 0.0533639848 0.20213100
#> Mesoplodon_layardii NA 0.0156247025 0.09936896
#> Mesoplodon_mirus NA 0.2615344649 0.02711371
#> Mesoplodon_perrini NA 0.0007873510 0.07105382
#> Mesoplodon_peruvianus NA 0.0022081471 0.07148019
#> Mesoplodon_stejnegeri NA 0.0019316220 0.07240253
#> Mesoplodon_traversii NA 0.0000000000 0.09237153
#> Mirounga_angustirostris 0.0000000000 1.0000000000 1.00000000
#> Mirounga_leonina 0.0000000000 0.6948598959 0.62780483
#> Monachus_monachus 0.1497520468 0.1977684465 0.16152114
#> Monachus_schauinslandi 0.4302127336 0.5791027790 0.52972758
#> Monodon_monoceros 0.0000000000 0.7032597866 0.45028422
#> Neophoca_cinerea 0.2192750379 0.1434988631 0.39804367
#> Neophocaena_phocaenoides 0.0362881475 0.5420666711 0.17076625
#> Odobenus_rosmarus NA 0.5803602059 0.45366482
#> Ommatophoca_rossii 0.0000000000 0.6659562055 0.34130521
#> Orcaella_brevirostris 0.0240062354 0.0101282373 0.04578858
#> Orcaella_heinsohni 0.0058839286 0.0292679517 0.08519702
#> Orcinus_orca NA 0.7536273607 0.39332028
#> Otaria_flavescens 0.0000000000 0.0808815948 0.34394151
#> Pagophilus_groenlandicus 0.0000000000 0.7570041744 0.46023398
#> Peponocephala_electra 0.0000000000 0.5314927079 0.48063075
#> Phoca_largha 0.0000000000 0.5982829480 0.33477382
#> Phoca_vitulina 0.0000000000 0.4543455128 0.37496303
#> Phocarctos_hookeri 0.1750436555 0.0782092491 0.35171865
#> Phocoena_dioptrica 0.0000000000 0.2513166389 0.41532085
#> Phocoena_phocoena 0.0000000000 0.0736635094 0.00000000
#> Phocoena_sinus 0.3098959997 0.1864775088 0.14901742
#> Phocoena_spinipinnis 0.0018432814 0.2651030237 0.18774230
#> Phocoenoides_dalli 0.0000000000 0.2916871646 0.15983045
#> Physeter_macrocephalus 0.0642642678 0.7564270292 0.51249076
#> Pontoporia_blainvillei 0.0302045496 0.3710816347 0.22018302
#> Pseudorca_crassidens 0.0029361868 0.4744533574 0.24712980
#> Pusa_caspica 0.2193438717 0.1941091818 0.34349375
#> Pusa_hispida 0.0000000000 0.1823213934 0.15240645
#> Sotalia_guianensis 0.0003188826 0.0546637568 0.02364730
#> Sousa_chinensis 0.0035493076 0.5623262797 0.31006940
#> Sousa_teuszii 0.3882639834 0.2726857890 0.15850980
#> Stenella_attenuata 0.0000000000 0.4500796407 0.27718723
#> Stenella_clymene 0.0000000000 0.3747462296 0.40334210
#> Stenella_coeruleoalba 0.0000000000 0.2311412497 0.18363765
#> Stenella_frontalis 0.0000000000 0.3490478318 0.23845778
#> Stenella_longirostris 0.0000000000 0.5133002403 0.18285982
#> Steno_bredanensis 0.0000000000 0.1334810508 0.21805988
#> Tasmacetus_shepherdi NA 0.3474343349 0.17676343
#> Trichechus_manatus 0.0379151532 0.5037922863 0.24035976
#> Trichechus_senegalensis 0.0414988099 0.5315342856 0.28350122
#> Tursiops_aduncus 0.0007741038 0.0517896426 0.13834135
#> Tursiops_truncatus 0.0000000000 0.3052280508 0.19082721
#> Ursus_maritimus 0.0811703393 0.9090386502 0.70012282
#> Zalophus_californianus 0.0000000000 0.1204667495 0.62677747
#> Zalophus_wollebaeki 0.1982794545 0.0749554707 0.41799919
#> Ziphius_cavirostris 0.0000000000 0.1383689569 0.09353647
FUSE_res3 <- mFD::fuse(
sp_dist = sp_dist_tr,
sp_faxes_coord = as.matrix(sp_faxes_coord),
nb_NN = 5,
GE = sp_tr$IUCN_100,
standGE = TRUE)
FUSE_res3
#> FUSE FUn_std FSp_std
#> Arctocephalus_australis 0.0000000000 0.4066626897 0.44574291
#> Arctocephalus_forsteri 0.0000000000 0.5170579368 0.51871477
#> Arctocephalus_galapagoensis 0.5992815838 0.5592652556 0.47871747
#> Arctocephalus_gazella 0.0000000000 0.6208798411 0.56465339
#> Arctocephalus_philippii 0.0000000000 0.2779525182 0.44247109
#> Arctocephalus_pusillus 0.0000000000 0.2442786896 0.37884040
#> Arctocephalus_townsendi 0.0000000000 0.5852680899 0.64653619
#> Arctocephalus_tropicalis 0.0000000000 0.2297455947 0.32036900
#> Balaena_mysticetus 0.0000000000 0.7452467855 0.57306402
#> Balaenoptera_acutorostrata 0.0000000000 0.4460157412 0.41489069
#> Balaenoptera_bonaerensis 0.0054747614 0.2184186166 0.32978308
#> Balaenoptera_borealis 0.3731209005 0.2139234148 0.39976514
#> Balaenoptera_edeni 0.0000000000 0.4661991166 0.27554077
#> Balaenoptera_musculus 0.7405518753 0.6292520413 0.70171703
#> Balaenoptera_omurai NA 0.2386976599 0.41958574
#> Balaenoptera_physalus 0.5159872370 0.3536749038 0.52385972
#> Berardius_arnuxii NA 0.3691785951 0.24980784
#> Berardius_bairdii NA 0.3306752012 0.23813008
#> Callorhinus_ursinus 0.1087457494 0.5012945401 0.60635396
#> Caperea_marginata 0.0000000000 0.1832726206 0.40111351
#> Cephalorhynchus_commersonii 0.0000000000 0.1835307609 0.17480251
#> Cephalorhynchus_eutropia 0.0007324479 0.0069987566 0.06626082
#> Cephalorhynchus_heavisidii 0.0007372515 0.0083171263 0.06542231
#> Cephalorhynchus_hectori 0.0157191188 0.0070959999 0.01634259
#> Cystophora_cristata 0.1007823971 0.5865158316 0.43824460
#> Delphinapterus_leucas 0.0000000000 0.6739629047 0.32847428
#> Delphinus_capensis NA 0.0264311644 0.16472623
#> Delphinus_delphis 0.0000000000 0.3984163792 0.16127757
#> Dugong_dugon 0.0832219750 0.5379056252 0.30543867
#> Enhydra_lutris 0.6522096715 0.7016950229 0.45056295
#> Erignathus_barbatus 0.0000000000 0.5531416419 0.35107768
#> Eschrichtius_robustus 0.0000000000 0.8271900919 0.61300225
#> Eubalaena_australis 0.0000000000 0.3144018773 0.78268639
#> Eubalaena_glacialis 0.4866156416 0.2810689133 0.54593451
#> Eubalaena_japonica 0.5841787823 0.4661757614 0.54157645
#> Eumetopias_jubatus 0.0101348519 0.4516548620 0.56433150
#> Feresa_attenuata 0.0000000000 0.2955099743 0.27261560
#> Globicephala_macrorhynchus 0.0000000000 0.5255589486 0.35104810
#> Globicephala_melas 0.0000000000 0.4990595861 0.35763988
#> Grampus_griseus 0.0000000000 0.5233269607 0.29251186
#> Halichoerus_grypus 0.0000000000 0.1032026841 0.35586820
#> Histriophoca_fasciata 0.0000000000 0.6521823871 0.28824480
#> Hydrurga_leptonyx 0.0000000000 0.6622353793 0.44212015
#> Hyperoodon_ampullatus NA 0.2547878402 0.12270144
#> Hyperoodon_planifrons 0.0000000000 0.2557952131 0.12249240
#> Indopacetus_pacificus NA 0.2850555343 0.28554866
#> Kogia_breviceps NA 0.2839209537 0.25751272
#> Kogia_sima NA 0.1456685909 0.25492545
#> Lagenodelphis_hosei 0.0000000000 0.7241772659 0.51940242
#> Lagenorhynchus_acutus 0.0000000000 0.4544319444 0.19736356
#> Lagenorhynchus_albirostris 0.0000000000 0.0907709847 0.14280471
#> Lagenorhynchus_australis 0.0000000000 0.0010393047 0.21058380
#> Lagenorhynchus_cruciger 0.0000000000 0.0020371106 0.15621825
#> Lagenorhynchus_obliquidens 0.0000000000 0.3327438642 0.20430708
#> Lagenorhynchus_obscurus 0.0000000000 0.4240208007 0.17545748
#> Leptonychotes_weddellii 0.0000000000 0.5404210014 0.55524903
#> Lissodelphis_borealis 0.0000000000 0.5812804661 0.50809556
#> Lissodelphis_peronii 0.0000000000 0.2947422923 0.43157141
#> Lobodon_carcinophaga 0.0000000000 0.5833807958 0.41597696
#> Lontra_felina 0.5413762905 0.5749777422 0.35413972
#> Megaptera_novaeangliae 0.0000000000 0.3564239828 0.45460052
#> Mesoplodon_bidens NA 0.2401439269 0.23803164
#> Mesoplodon_bowdoini NA 0.0644576583 0.20799830
#> Mesoplodon_carlhubbsi NA 0.0008237359 0.07159363
#> Mesoplodon_densirostris NA 0.2058523276 0.19967333
#> Mesoplodon_europaeus NA 0.1358313979 0.09000617
#> Mesoplodon_ginkgodens NA 0.0013549553 0.07202895
#> Mesoplodon_grayi NA 0.0544755693 0.20125592
#> Mesoplodon_hectori NA 0.0533639848 0.20213100
#> Mesoplodon_layardii NA 0.0156247025 0.09936896
#> Mesoplodon_mirus NA 0.2615344649 0.02711371
#> Mesoplodon_perrini NA 0.0007873510 0.07105382
#> Mesoplodon_peruvianus NA 0.0022081471 0.07148019
#> Mesoplodon_stejnegeri NA 0.0019316220 0.07240253
#> Mesoplodon_traversii NA 0.0000000000 0.09237153
#> Mirounga_angustirostris 0.0000000000 1.0000000000 1.00000000
#> Mirounga_leonina 0.0000000000 0.6948598959 0.62780483
#> Monachus_monachus 0.2283726931 0.1977684465 0.16152114
#> Monachus_schauinslandi 0.6345952150 0.5791027790 0.52972758
#> Monodon_monoceros 0.0000000000 0.7032597866 0.45028422
#> Neophoca_cinerea 0.3298536309 0.1434988631 0.39804367
#> Neophocaena_phocaenoides 0.0703478821 0.5420666711 0.17076625
#> Odobenus_rosmarus NA 0.5803602059 0.45366482
#> Ommatophoca_rossii 0.0000000000 0.6659562055 0.34130521
#> Orcaella_brevirostris 0.0371819980 0.0101282373 0.04578858
#> Orcaella_heinsohni 0.0115106174 0.0292679517 0.08519702
#> Orcinus_orca NA 0.7536273607 0.39332028
#> Otaria_flavescens 0.0000000000 0.0808815948 0.34394151
#> Pagophilus_groenlandicus 0.0000000000 0.7570041744 0.46023398
#> Peponocephala_electra 0.0000000000 0.5314927079 0.48063075
#> Phoca_largha 0.0000000000 0.5982829480 0.33477382
#> Phoca_vitulina 0.0000000000 0.4543455128 0.37496303
#> Phocarctos_hookeri 0.2640009489 0.0782092491 0.35171865
#> Phocoena_dioptrica 0.0000000000 0.2513166389 0.41532085
#> Phocoena_phocoena 0.0000000000 0.0736635094 0.00000000
#> Phocoena_sinus 0.3098959997 0.1864775088 0.14901742
#> Phocoena_spinipinnis 0.0045236417 0.2651030237 0.18774230
#> Phocoenoides_dalli 0.0000000000 0.2916871646 0.15983045
#> Physeter_macrocephalus 0.1239917183 0.7564270292 0.51249076
#> Pontoporia_blainvillei 0.0587425276 0.3710816347 0.22018302
#> Pseudorca_crassidens 0.0072022892 0.4744533574 0.24712980
#> Pusa_caspica 0.3310632694 0.1941091818 0.34349375
#> Pusa_hispida 0.0000000000 0.1823213934 0.15240645
#> Sotalia_guianensis 0.0007830123 0.0546637568 0.02364730
#> Sousa_chinensis 0.0087042852 0.5623262797 0.31006940
#> Sousa_teuszii 0.3882639834 0.2726857890 0.15850980
#> Stenella_attenuata 0.0000000000 0.4500796407 0.27718723
#> Stenella_clymene 0.0000000000 0.3747462296 0.40334210
#> Stenella_coeruleoalba 0.0000000000 0.2311412497 0.18363765
#> Stenella_frontalis 0.0000000000 0.3490478318 0.23845778
#> Stenella_longirostris 0.0000000000 0.5133002403 0.18285982
#> Steno_bredanensis 0.0000000000 0.1334810508 0.21805988
#> Tasmacetus_shepherdi NA 0.3474343349 0.17676343
#> Trichechus_manatus 0.0735594963 0.5037922863 0.24035976
#> Trichechus_senegalensis 0.0804618871 0.5315342856 0.28350122
#> Tursiops_aduncus 0.0019004117 0.0517896426 0.13834135
#> Tursiops_truncatus 0.0000000000 0.3052280508 0.19082721
#> Ursus_maritimus 0.1560437697 0.9090386502 0.70012282
#> Zalophus_californianus 0.0000000000 0.1204667495 0.62677747
#> Zalophus_wollebaeki 0.2973796407 0.0749554707 0.41799919
#> Ziphius_cavirostris 0.0000000000 0.1383689569 0.09353647