recent extinctions disturb path to equilibrium diversity in Caribbean bats

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Log-likelihood In the format provided by the authors and unedited. recent extinctions disturb path to equilibrium diversity in Caribbean bats Luis Valente, 2, rampal S. etienne 3 and Liliana M. Dávalos 4, 5 * SUPPLEMENTRY INFORMTION VOLUME: RTICLE NUMBER: 0026 Rate 0. 0.2 0.3 0.4-45 -40-35 -30 λ c µ γ λ a Likelihood 20 25 30 35 40 45 ssumed archipelago age (Ma) Supplementary Figure Sensitivity analysis of the DI model with archipelago age. Effect of varying assumed archipelago age on maximum likelihood values and parameter estimates of the DI model, M = 00. γ - per lineage rate of immigration; λ a - per lineage rate of anagenesis; λ c - per lineage rate of cladogenesis; µ - per lineage rate of extinction. NTURE ECOLOGY & EVOLUTION DOI: 0.038/s4559-06-0026 www.nature.com/natecolevol 207 Macmillan Publishers Limited, part of Springer Nature. ll rights reserved.

a 0 20 40 60 80 00 b 0 20 40 60 80 00-2 - 0 2 3 4 5 LLR 0 2 4 6 8 0 LLR Supplementary Fig. 2 - Bootstrap likelihood ratio test. a) distribution of logarithms of the likelihood ratio of diversity-dependent (DD) and diversity-independent (DI) model for islands simulated under DI. b) same as a) but for data simulated under the DI model. Black arrow - logarithm of the likelihood ratio for the real data; red arrow - logarithm of the likelihood ratio for a significance level of a = 0 05. NTURE ECOLOGY & EVOLUTION DOI: 0.038/s4559-06-0026 www.nature.com/natecolevol 2 207 Macmillan Publishers Limited, part of Springer Nature. ll rights reserved.

a b 0 0 20 30 40 50 60 0 0 20 30 40 50 60 70-0. 0.0 0. 0.2 0.3 0.4 μ - λ c 0.0 0. 0.2 0.3 0.4 0.5 μ - λ c Supplementary Figure 3 Distribution of difference between ML rate of extinction (µ) and ML rate of cladogenesis (λ c ). Based on datasets simulated with the parameters of the DI model for T = 20 (a) and T = 45 (b). When µ - λ c > 0, equilibrium dynamics are preferred (0 value marked with dotted line for visibility). NTURE ECOLOGY & EVOLUTION DOI: 0.038/s4559-06-0026 www.nature.com/natecolevol 3 207 Macmillan Publishers Limited, part of Springer Nature. ll rights reserved.

Proportion of equilibrium diversity 0.0 0.2 0.4 0.6 0.8.0.2 20 25 30 35 40 45 ssumed archipelago age (Ma) Supplementary Figure 4 Proportion of extant noctilionoid diversity compared with expected diversity at equilibrium. For all assumed archipelago ages T between 20 and 45 Ma. Black line high human impact scenario; grey line low human impact scenario; blue dotted line equilibrium value. NTURE ECOLOGY & EVOLUTION DOI: 0.038/s4559-06-0026 www.nature.com/natecolevol 4 207 Macmillan Publishers Limited, part of Springer Nature. ll rights reserved.

a b Number of lineages 0 5 0 5 20 25 Number of lineages 0 5 0 5 20 0 0 20 30 40 Time (Ma) 0 0 20 30 40 Time (Ma) Supplementary Figure 5 - Expected future number of independent colonist lineages under the DI model assuming high human impact, starting from current extant number of lineages. Scenario assuming all species went extinct as a result of human activity. a) ssuming archipelago age T = 20 Ma; b) assuming archipelago age T = 45 Ma. Black dotted line prehuman number of lineages. Light and dark shaded areas show the 2.5-97.5 and the 25-75 percentiles, respectively. NTURE ECOLOGY & EVOLUTION DOI: 0.038/s4559-06-0026 www.nature.com/natecolevol 5 207 Macmillan Publishers Limited, part of Springer Nature. ll rights reserved.

a b 0 200 400 600 0 200 400 600 20 40 60 80 Number of species 5 0 5 20 25 Number of colonization events c d 0 200 400 600 0 200 600 000 5 0 5 20 Number of endemic clades 0 2 4 6 8 0 Number of anagenetic species Supplementary Figure 6 Goodness of fit of the DI model, assuming archipelago age T = 20 Ma. Histograms show the total number of (a) species, (b) colonisation events, (c) endemic clades and (d) anagenetic species (endemic species with no relatives on the G) in 5,000 phylogenetic datasets simulated with the ML parameters of the DI model. Black vertical lines indicate median values across simulated datasets and arrows indicate the observed values in the G data. NTURE ECOLOGY & EVOLUTION DOI: 0.038/s4559-06-0026 www.nature.com/natecolevol 6 207 Macmillan Publishers Limited, part of Springer Nature. ll rights reserved.

a 0 00 300 500 b 0 00 300 500 30 40 50 60 70 80 90 Number of colonisation events 50 00 50 200 250 300 350 Number of cladogenesis events c 0 200 400 600 d 0 50 50 250 5 0 5 20 25 30 Number of anagenesis events 50 00 50 200 250 300 Number of extinction events Supplementary Figure 7 Number of events during the course of entire simulation, assuming archipelago age T = 20 Ma. Histograms show the total number of (a) colonisation, (b) cladogenesis, (c) anagenesis and (d) extinction events that took place during the course of 20 million years in each of 5,000 datasets simulated with the ML parameters of the DI model. Black vertical lines indicate median values across simulated datasets. NTURE ECOLOGY & EVOLUTION DOI: 0.038/s4559-06-0026 www.nature.com/natecolevol 7 207 Macmillan Publishers Limited, part of Springer Nature. ll rights reserved.

a b Number of endemic species 0 20 40 60 80 Number of endemic species 0 0 20 30 40 0 5 0 5 20 Time (Ma) 0 5 0 5 20 Time (Ma) Supplementary Figure 8 - Expected future noctilionoid bat endemic diversity in the Greater ntilles for low human impact scenario. Scenario assuming only three species went extinct as a result of human activity. Based on diversity-independent model, starting from current extant diversity, with archipelago ages of T = 20 Ma (a) and T = 45 Ma (b). Black dotted line - pre-human diversity levels; blue dotted line expected number of endemic species at equilibrium. Light and dark shaded areas show the 2.5-97.5 and the 25-75 percentiles, respectively. NTURE ECOLOGY & EVOLUTION DOI: 0.038/s4559-06-0026 www.nature.com/natecolevol 8 207 Macmillan Publishers Limited, part of Springer Nature. ll rights reserved.

Supplementary Table Noctilionoid bat species of the Greater ntilles. Including extinct and extirpated taxa. Taxon Brachyphylla cavernarum Brachyphylla nana nana Brachyphylla nana pumila Erophylla bombifrons Erophylla sezekorni Phyllonycteris aphylla Clade Code (Supplementary Table 2) Source of phylogenetic data Geographical distribution WI Endemic G + Bahamas G + TC G Endemic Status G + Bahamas + TC G Endemic Phyllonycteris major * G Endemic Extinct 2 Phyllonycteris poeyi obtusa Phyllonycteris poeyi poeyi Mormoops blainvillei B G + Bahamas G Endemic WI Endemic Mormoops magna B * G Endemic Extinct 3 Mormoops megalophylla Monophyllus plethodon C D SUPPLEMENTRY INFORMTION WI + Continent Extirpated 3 WI Endemic Extirpated 2 Monophyllus redmani D G + Bahamas + TC Desmodus puntajudensis E * G Endemic Extinct 4,5 Pteronotus macleayii F Pteronotus quadridens F Glossophaga soricina G G + Bahamas G + Bahamas WI + Continent Cubanycteris silvai H a G Endemic Extinct 6 riteus flavescens Phyllops falcatus I I G Endemic G Endemic Phyllops silvai I a G Endemic Extinct 7 Phyllops vetus I a G Endemic Extinct 8 Stenoderma rufum Tonatia saurophila I J G Endemic WI + Continent Extirpated 9 rtibeus anthonyi K a G Endemic Extinct 0 Pteronotus parnellii portoricensis Pteronotus parnellii pusillus L L G Endemic G Endemic Pteronotus pristinus L * WI + Continent Extinct 3 Pteronotus sp. nov. L * G Endemic Extinct Noctilio leporinus Pteronotus parnelli parnellii N M WI + Continent G + Bahamas NTURE ECOLOGY & EVOLUTION DOI: 0.038/s4559-06-0026 www.nature.com/natecolevol 9 207 Macmillan Publishers Limited, part of Springer Nature. ll rights reserved.

Macrotus waterhousii jamaicensis O 2 G Endemic Macrotus waterhousii minor O 2 G + Bahamas + TC Macrotus waterhousii O 2 G Endemic waterhousii (Hispaniola) Macrotus waterhousii O * WI Endemic Extinct 3 waterhousii (Puerto Rico & nguilla) rtibeus jamaicensis P 4 WI + Continent - Lineage extinct from the G archipelago a Source trees deposited in Dryad (doi:0.506/dryad.9mk20) * - Sampled as missing species in clade G - Greater ntilles WI - West Indies TC - Turks & Caicos NTURE ECOLOGY & EVOLUTION DOI: 0.038/s4559-06-0026 www.nature.com/natecolevol 0 207 Macmillan Publishers Limited, part of Springer Nature. ll rights reserved.

Supplementary Table 2 Independent colonisation events of noctilionoid bats in the Greater ntilles. Estimated times of colonisation in millions of years from present. nagenetic clades are those with a single endemic species whereas cladogenetic clades have two or more endemic species. Independent colonisation event Clade code Number of species Time of colonisation 95% CI Clade type Brachyphyllini + Phyllonycterini 9 7.97 5.46-20.45 Cladogenetic Mormoops blainvillei B 2 4.7 9.32-9.37 Cladogenetic Mormoops megalophylla C 4.7 9.32-9.37* Non-endemic Monophyllus D 2 3.94.63-6.22 Cladogenetic Desmodus puntajudensis E 2.39 9.50-6.08 nagenetic Pteronotus macleayii F 2 0.72 8.48-2.94 Cladogenetic Glossophaga soricina G 7.5 5.54-8.74* Non-endemic Cubanycteris H 6.83 5.08-8.78 nagenetic Sternodermatina I 5 6.6 5.20-7.24 Cladogenetic Tonatia saurophila J 4.5 2.84-6.5* Non-endemic rtibeus anthonyi K 3.32.64-5.20 nagenetic Pteronotus parnellii pusillus L 4 2.59 2.42-4.07 Cladogenetic Noctilio leporinus M 2.55.67-3.56* Non-endemic Pteronotus parnellii parnellii N.72.7-2.44 nagenetic Macrotus waterhousii O 4 0.28 0.06-0.58 Cladogenetic rtibeus jamaicensis P 0.03 0.0-0.04 Non-endemic Lineage extinct from the archipelago. * Upper bound for age of colonization. NTURE ECOLOGY & EVOLUTION DOI: 0.038/s4559-06-0026 www.nature.com/natecolevol 207 Macmillan Publishers Limited, part of Springer Nature. ll rights reserved.

Supplementary Table 3 DISIE maximum-likelihood analyses for M = 20. ML parameters of the diversity-independent (DI) and diversity-dependent models (DD) for the two different assumed archipelago ages. Results for consensus dataset. λ c - per lineage rate of cladogenesis; µ - per lineage rate of extinction; K carrying capacity; γ - per lineage rate of immigration; λ a - per lineage rate of anagenesis; LogLik Log likelihood. Dataset rchipelago age (Ma) Model λ c µ K γ λ a LogLik High human impact 20 DI 0.26 0.29-0.37 0.3-6.69 DD 0.4 0.33 5 0.46 0.24-5.44 45 DI 0.29 0.38-0.70 0.33-8.64 DD 0.42 0.40 8 0.76 0.25-7.60 Low human impact 20 DI 0.29 0.32-0.097 0.36-90.70 DD 0.43 0.34 8 0.095 0.30-89.92 45 DI 0.33 0.4-0.8 0.37-92.5 DD 0.43 0.42 25 0.5 0.32-9.64 Contemporary dataset 20 DI 0.22 0.24-0.082 0.34-88.45 DD 0.33 0.27 5 0.084 0.32-87.82 45 DI 0.25 0.33-0.03 0.37-90.05 DD 0.33 0.34 20 0.03 0.33-89.63 NTURE ECOLOGY & EVOLUTION DOI: 0.038/s4559-06-0026 www.nature.com/natecolevol 2 207 Macmillan Publishers Limited, part of Springer Nature. ll rights reserved.

Supplementary Table 4 95% confidence intervals of the ML parameter estimates for the high human impact dataset. Obtained by fitting DISIE models across 00 posterior datasets incorporating phylogenetic uncertainty, for mainland pool size M = 00 species. λ c - per lineage rate of cladogenesis; µ - per lineage rate of extinction; K carrying capacity; γ - per lineage rate of immigration; λ a - per lineage rate of anagenesis. rchipelago age (Ma) Model λ c µ K γ λ a 20 DI 0.24 0.32 0.26-0.38-0.025 0.033 0.5 0.26 DD 0.27 0.38 0.26 0.39 25-0.024 0.032 0. 0.25 45 DI 0.27 0.35 0.36 0.46-0.032 0.040 0.2 0.26 DD 0.29 0.4 0.36 0.47 33-0.03 0.039 0.04 0.24 NTURE ECOLOGY & EVOLUTION DOI: 0.038/s4559-06-0026 www.nature.com/natecolevol 3 207 Macmillan Publishers Limited, part of Springer Nature. ll rights reserved.

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