Phylogenetic clock models translate inferred amounts of evolutionary change (calculated from either genotypes or phenotypes) into estimates of elapsed time, providing a mechanism for time scaling phylogenetic trees. Relaxed clock models, which accommodate variation in evolutionary rates across branches, are one of the main components of Bayesian dating, yet their consequences for total-evidence phylogenetics have not been thoroughly explored. Here, we combine morphological, molecular (both transcriptomic and Sanger-sequenced), and stratigraphic datasets for all major lineages of echinoids (sea urchins, heart urchins, sand dollars). We then perform total-evidence dated inference under the fossilized birth-death prior, varying two analytical conditions: the choice between autocorrelated and uncorrelated relaxed clocks, which enforce (or not) evolutionary rate inheritance; and the ability to recover ancestor-descendant relationships. Our results show that the latter has no impact on either topology or node ages and highlight a previously unnoticed interaction between the tree and clock models, with analyses implementing an autocorrelated clock precluding the recovery of direct ancestry. On the other hand, tree topology, fossil placement, divergence times, and downstream macroevolutionary inferences (e.g., ancestral state reconstructions) in sea urchins are all strongly affected by the type of relaxed clock implemented. In regions of the tree where molecular rate variation is pervasive and morphological signal relatively uninformative, fossil tips seem to play little to no role in informing divergence times, and instead passively move in and out of clades depending on the ages imposed upon them by molecular data. Our results highlight the extent to which the phylogenetic and macroevolutionary conclusions of total-evidence dated analyses are contingent on the choice of relaxed clock model, highlighting the need for either careful methodological validation or a thorough assessment of sensitivity. Our efforts continue to illuminate the echinoid tree of life, supporting the erection of the order-level clade Apatopygoida to include three living species last sharing a common ancestor with other extant lineages in the Jurassic. Furthermore, they also illustrate how the phylogenetic placement of extinct clades hinges upon the modelling of molecular data, evidencing the extent to which the fossil record remains subservient to phylogenomics.

Sexual dichromatism is relatively rare in anuran amphibians (frogs and toads) but is striking and prevalent in the African reed frogs (Hyperoliidae). In sexually dichromatic hyperoliids, males and females exhibit shared coloration post-metamorphosis, but at the onset of maturity, females undergo a change in color and/or color pattern, whereas males typically retain the juvenile coloration. Hypothesized functions of dichromatism in reed frogs include sexual niche partitioning such that males and females use different habitats and their different colorations provide more effective camouflage in their respective habitats, or alternatively, that color patterns play a role in sex and/or mate recognition in dense breeding choruses. To test these hypotheses, we characterized several aspects of natural history, ecology, and physiology in a population of the sexually dichromatic forest reed frog (Hyperolius tuberculatus) on Bioko Island, Equatorial Guinea. This dataset includes 1) dorsal reflectance measurements for male and female H. tuberculatus and reflectance measurements of the substrates the frogs were found on, 2) microspectrophotometry measurements of H. tuberculatus photoreceptors, and 3) code and custom visual models used to conduct visual modeling analyses using the R package pavo (Maia et al. 2019).

Despite the unprecedented rate of global urbanization, a diverse array of taxa are supported in urban areas. However, the long-term persistence of urban wildlife cannot be guaranteed due to the various adverse effects that come with urbanization, such as resource depletion and reduced gene flow. Accordingly, it is imperative to evaluate the health and viability of urban wildlife, particularly of species that are underrepresented in the existing literature, like herpetofauna. Genomic techniques can provide critical insights into urban wildlife health and population viability. Here, we generated a ddRADseq dataset of 162 Dekay’s brown snakes (Storeria dekayi) among 11 locations with different urbanization magnitudes across New Jersey, USA, and examined the population genetic patterns of this common urban reptile. While genetic diversity was not severely reduced within those populations, we uncovered the presence of genetic differentiation and structuring across them, especially for those from the most urbanized areas. Deviations of interpopulation structure from their geographic distributions might reflect either habitat alteration or human intervention in recent history. Landscape genetic analyses revealed the presence of an isolation-by-distance relationship that was only significant within a short spatial distance of 1,500 m. Most urban populations also displayed lower-than-expected historic migration and diversity rates, but some remained genetically connected and diverse. To conclude, our study can serve as a useful guide for population genomic studies on urban herpetofauna. Based on our results, urbanization is likely to impact interpopulation genetic connectivity, but to have limited effects on intrapopulation genetic diversity of small-bodied, terrestrial urban dwellers.

Supplemental TablesTable S1. Accession database. Plant specimens used in the Paullinieae phylogeny, including their taxonomic classifications, collection details, and herbarium information. Table S3. Sequencing and assembly statistics. Table S4. Anatomical database. Detailed anatomical data for species in the Paullinieae tribe and outgroups, focusing on stem development and vascular variants. The species list included in this database also comprises the curated list of species in Paullinieae by Dr. Pedro Acevedo-Rodríguez, as well as the total number of species accepted in this study. Tree Inference data filesastral.treThis is the species tree infered through ASTRAL with 351 exon gene trees. iqtree.treThis is the maximum likelihood tree with bootstrap support at the nodes with the tips assigned their species names (e.g., Paullinia_atrolineata_b)pau_333s_351g_partitions.contreeThis is the maximum likelihood tree with bootstrap support at the nodes with the sample ID numbers (PAU24)pau_333s_351g.fastaThis is the concatenated alignment of 351 genes across 333 samples. The sample ID names are still present.pau_333s_351g_partitionsThis is the partition gene file, showing the coordinates of each of 351 genes across the concatenated alignment.ChangeSampleNames_iqtree.shThis script uses the function “sed” to find and replace sample ID (e.g., PAU24) in pau_333s_351g_partitions.contree species names (e.g., “Serjania_atrolineata_b”) in a file called iqtree.tre CI-combined_chronograms.treThis is the chronogram infered by treePL, by time calibrating 100 trees with a constrained topology but varying branch lengths.

Supplemental TablesTable S1. Accession database. Plant specimens used in the Paullinieae phylogeny, including their taxonomic classifications, collection details, and herbarium information. Table S3. Sequencing and assembly statistics. Table S4. Anatomical database. Detailed anatomical data for species in the Paullinieae tribe and outgroups, focusing on stem development and vascular variants. The species list included in this database also comprises the curated list of species in Paullinieae by Dr. Pedro Acevedo-Rodríguez, as well as the total number of species accepted in this study. Tree Inference data filesastral.treThis is the species tree infered through ASTRAL with 351 exon gene trees. iqtree.treThis is the maximum likelihood tree with bootstrap support at the nodes with the tips assigned their species names (e.g., Paullinia_atrolineata_b)pau_333s_351g_partitions.contreeThis is the maximum likelihood tree with bootstrap support at the nodes with the sample ID numbers (PAU24)pau_333s_351g.fastaThis is the concatenated alignment of 351 genes across 333 samples. The sample ID names are still present.pau_333s_351g_partitionsThis is the partition gene file, showing the coordinates of each of 351 genes across the concatenated alignment.ChangeSampleNames_iqtree.shThis script uses the function “sed” to find and replace sample ID (e.g., PAU24) in pau_333s_351g_partitions.contree species names (e.g., “Serjania_atrolineata_b”) in a file called iqtree.tre CI-combined_chronograms.treThis is the chronogram infered by treePL, by time calibrating 100 trees with a constrained topology but varying branch lengths.

Understanding patterns of differentiation at microgeographic scales can enhance our understanding of evolutionary dynamics and lead to the development of effective conservation strategies. In particular, high levels of landscape heterogeneity can strongly influence species abundances, genetic structure, and demographic trends. The bearded anole, Anolis pogus, is endemic to the topographically complex island of St. Martin and of conservation concern. Here, we examined genetic diversity and inbreeding, assessed which features of the landscape influence population abundances, tested for population genetic structure across St. Martin, and inferred historical demographic trends. We performed WGS on 54 individuals and conducted abundance surveys of 100 plots throughout the island of St. Martin. Genomic data are hosted elsewhere on NCBI SRA (PRJNA1278788). Hosted here are data from abundance surveys as well as metadata for individuals used to generate WGS libraries. Further, Zenodo provides scripts used to analyse the genomic and abundance data. Our data demonstrate that A. pogus is panmictic on the island of St. Martin, lacking any population structure including isolation by distance. We also find that the species has low levels of inbreeding and has likely recently experienced demographic expansion. Overall, these analyses suggest that A. pogus is unlikely to be of immediate conservation concern. Further, we highlight the role of demographic history and ecological interactions in shaping population structure.

Accurate assessment of historical species ranges is important for conservation science and management. Inaccurate historical species ranges can lead to incorrect assumptions about local extinctions, population trends, and potential sites for reintroductions. Yet, historical knowledge is often lacking for many species. Here, we present body size data on the case of the bearded anole, Anolis pogus, which is long believed to have been recently extirpated from the island of Anguilla. Body size data consists of snout-vent length for adult male and female Anolis pogus, A. schwartzi, and A. gingivinus. These data were generated from a mix of field measurements and samples from natural history collections. We then compared these data with the size distributions of anole fossils found on the island of Anguilla. We show that rather than a two-species community, the fossil size data better corresponds to sexual dimorphism in a single-species community consisting only of A. gingivinus. Thus, fossil data do not support the historical presence of A. pogus as previously suggested. We also generated WGS libraries from archival samples of Anolis pogus allegedly collected on Anguilla. We show that all of these museum samples are actually A. schwartzi and originated from a nearby island, St. Eustatius. Thus, there are no existing collections of A. pogus from the island of Anguilla. Scripts for analyzing these genomic data are archived on Zenodo. Raw sequence data are hosted on NCBI's SRA database.

(All information expressed below is also available in the "read me" text file.) Atlantic reef fishes: distributions and life-history traits Upload date: September 3rd, 2024            DOI for all versions: 10.5281/zenodo.13655553 Isadora Cord¹*, Sergio R. Floeter¹*,**, Gabriel S. Araujo², Juan P. Quimbayo³, D. Ross Robertson⁴, Benjamin C. Victor⁵, Peter Wirtz⁶, Hudson T. Pinheiro², Rui Freitas⁷, Luiz A. Rocha⁸ * joint first authors; ** corresponding author [email protected] ¹Marine Macroecology and Biogeography Lab, Universidade Federal de Santa Catarina, Brazil²Center for Marine Biology, University of São Paulo, São Sebastião, SP, Brazil³University of Florida, USA⁴Smithsonian Tropical Research Institute, Panama⁵Ocean Science Foundation, USA⁶Centro de Ciências do Mar, Universidade do Algarve, Portugal⁷Universidade Técnica do Atlântico, Cabo Verde⁸California Academy of Sciences, San Francisco, CA, USA Introduction to the First EditionThis database includes information on the distribution and life-history traits for 1,628 reef fish species, distributed across 26 sub-provinces of the tropical, sub-tropical, and warm temperate Atlantic Ocean. We followed the definition provided by Floeter et al. (2008) for “reef fish,” including any shallow (<100 m) tropical/subtropical benthic or benthopelagic fishes that consistently associate with hard substrates of coral, algal, or rocky reefs, or occupy adjacent sand substrate. All distributions were verified by the authors, double-checked with online databases, and available literature (peer-reviewed regional checklists and scientific papers; see main refs). Life-history traits were compiled for most species by using a combination of personal data, online databases (e.g. Froese & Pauly, 2023; Robertson & Van Tassell, 2023), and published sources (e.g. Luiz et al. 2015; Pinheiro et al. 2018; Quimbayo et al. 2021).This database is associated with the manuscript Cord et al. (in prep.) “Biogeography and evolution of reef fishes on tropical Mid-Atlantic Ridge islands,” and represents an update that has been in development for 16 years, based on Floeter et al. (2008) “Atlantic reef fish biogeography and evolution”. Data Description:The .xlsx database contains two pages, “traits&distributions” and “acronyms”. The “acronyms” page contains the same table that is available below, as well as a map illustrating the studied areas. The “traits&distributions” page is divided into the following columns:   "A" through "D": Species’ identificationspecies = the complete species names, in the following pattern: “Genus_specific epithet”, e.g. “Acanthurus_bahianus”family, genus = self explanatoryspp = specific epithet   "E" through "AD": Distributions RegionSub-provincesGeographical definitionAcronymWestern Atlantic    Greater CaribbeanCarolinianNorth Carolina State to Mérida (México)CA BermudaBermuda Is.BE Central CaribbeanCentral America and offshore islands (except mentioned elsewhere), Florida KeysCC Southern CaribbeanPanamá to Trinidad and TobagoSCSouthwestern Atlantic   Brazilian ProvinceNorth BrazilGreat Amazon ReefNB Northeastern BrazilRio Grande do Norte to Southern Bahia StateNE Southeastern BrazilEspírito Santo to Paraná StatesSE South BrazilSanta Catarina StateSBBrazilian oceanic islandsRocas Atoll AR Fernando de Noronha FN Trindade Is. TRWarm-temperate Argentinian ProvinceArgentinian Rio Grande do Sul State, from Uruguay to PatagoniaPTMid-Atlantic RidgeSt Paul’s Rocks SP Ascension AS St Helena SHEastern Atlantic   Northeastern AtlanticMediterraneanLevant to Gibraltar MDLusitanaAzores AZ Madeira MA Canaries CNTropical Eastern AtlanticNorthwest AfricaGibraltar to Cape Verde (Senegal)NT Cape Verde Is. CV São Tomé & PríncipeIncludes AnnobonST Tropical West AfricaCape Verde to Moçamedes (Angola)EASouthwest AfricaBenguelaMoçamedes to Cape of Good HopeBN AgulhasCape of Good Hope to Kei RiverCPSouthwestern Indian OceanSouth Africa’s Indian OceanFrom Kei River to Kosi BayIO    "AE" through "AK": Life-history traits“depth_max” = Maximum recorded depth, in meters.“bodysize_max” = Maximum recorded adult body size, in centimeters.“rafter” = Presence (1) or absence (0) of rafting behavior (mostly for the entire genus).“multihabitat” = Usage of other habitats in addition to structural reefs (soft bottoms, seagrass/macroalgae beds, mangroves, and estuaries).“diet” = Diet habits (gc: generalised carnivores; hd: herbivores/detritivores; is: sessile invertivores; mi: mobile invertivores; om: omnivores; pk: planktivores).“groupsize” = Sociability (sol: solitary; pair: pairs of two individuals; smallg: groups of 3 to 10 individuals; medg: groups of 10 to 20 individuals; largeg: groups of over 20 individuals).“spawning” = Spawning modes (att: attached; dem: demersal; live: livebearers; oral: oral; pel: pelagic). Data Sources and Verification:We gathered presence or absence data for 73 families of reef-associated fishes, encompassing 1,637 species in 26 distinct biogeographical units within the Atlantic Basin (see table above). All distributions were strictly verified by the authors, double-checked with online databases and available literature (e.g. Brown et al. 2019; Freitas et al. 2019; Floeter et al. 2023; Pinheiro et al. 2020; Robertson & Van Tassell, 2023; Wirtz et al. 2017). Life-history traits were compiled using personal data, online databases (e.g. Froese & Pauly, 2023; Robertson & Van Tassell, 2023), and published sources (e.g. Luiz et al. 2015; Pinheiro et al. 2018; Quimbayo et al. 2021). All species’ nomenclature was based on Eschmeyer's Catalog of Fishes (Fricke et al. 2024).  Main References:Brown, J., Beard, A., Clingham, E., Fricke, R., Henry, L., & Wirtz, P. (2019). The fishes of St Helena Island, central Atlantic Ocean—new records and an annotated checklist. Zootaxa, 4543(2), 151-194.Freitas, R., Romeiras, M., Silva, L., Cordeiro, R., Madeira, P., González, J.A., Wirtz, P., Falcón, J.M., Brito, A., Floeter, S.R., Afonso, P., Porteiro, F., Viera-Rodríguez, M.A., Neto, A.I., Haroun, R., Farminhão, J.N.M., Rebelo, A.C., Baptista, L., Melo, C.S., Martínez, A., Núñez, J., Berning, B., Johnson, M.E. & Ávila, S.P. (2019). Restructuring of the 'Macaronesia' biogeographic unit: A marine multi-taxon biogeographical approach. Scientific Reports, 9: 15792.Fricke, R., Eschmeyer, W. N. & Fong, J. D. (2024 ). ESCHMEYER'S CATALOG OF FISHES: GENERA/SPECIES BY FAMILY/SUBFAMILY.(http://researcharchive.calacademy.org/research/ichthyology/catalog/ SpeciesByFamily.asp). Electronic version accessed 03 September 2024.Floeter, S.R., Krajewski, J.P., Fiuza, T.M.J., Rocha, L.A. & Carvalho-Filho, A. (2023). Brazilian Reef Fishes. Editora CRV, Curitiba, pp. 320.ISBN 978-65-251-4245-6. DOI: 10.24824/978652514245.6Floeter, S. R., Rocha, L. A., Robertson, D. R., Joyeux, J. C., Smith-Vaniz, W. F., Wirtz, P., Edwards, A. J., Barreiros, J. P., Ferreira, C. E. L., Gasparini, J. L., Brito, A., Falcón, J. M., Bowen, B. W. & Bernardi, G. (2008). Atlantic reef fish biogeography and evolution. Journal of Biogeography, 35: 22-47.Froese R, Pauly D (Eds) (2023) FishBase. [Version 06/2023] http://www.fishbase.org Luiz, O. J., Madin, J. S., Robertson, D. R., Rocha, L. A., Wirtz, P., & Floeter, S. R. (2012). Ecological traits influencing range expansion across large oceanic dispersal barriers: insights from tropical Atlantic reef fishes. Proceedings of the Royal Society B: Biological Sciences, 279(1730), 1033-1040.Munroe, T. A. (1990). Eastern Atlantic tonguefishes (Symphurus: Cynoglossidae, Pleuronectiformes), with descriptions of two new species. Bulletin of Marine Science, 47(2), 464-515.Munroe, T. A. (1991). Western Atlantic Tonguefishes of the Symphurus-Plagusia Complex (Cynoglossidae, Pleuronectiformes), with Descriptions of 2 New Species. Fishery Bulletin.Pinheiro, H. T., Rocha, L. A., Macieira, R. M., Carvalho‐Filho, A., Anderson, A. B., Bender, M. G., ... & Floeter, S. R. (2018). South‐western Atlantic reef fishes: Zoogeographical patterns and ecological drivers reveal a secondary biodiversity centre in the Atlantic Ocean. Diversity and Distributions, 24(7), 951-965.Pinheiro, H. T., Macena, B. C., Francini‐Filho, R. B., Ferreira, C. E., Albuquerque, F. V., Bezerra, N. P., ... & Rocha, L. A. (2020). Fish biodiversity of Saint Peter and Saint Paulʼs Archipelago, Mid‐Atlantic Ridge, Brazil: new records and a species database. Journal of Fish Biology, 97(4), 1143-1153.Quimbayo, J.P., Silva, F.C., Mendes, T.C., Ferrari, D.S., Danielski, S.L., Bender, M.G., Parravicini, V., Kulbicki, M. & Floeter, S.R. (2021). Life-history traits, geographical range and conservation aspects of reef fishes from the Atlantic and Eastern Pacific. Ecology (Data Papers), https://doi.org/10.1002/ecy.3298.Robertson, D. R., & Tornabene, L. (2023). Reef-associated Bony Fishes of the Greater Caribbean: A Checklist (VERSION 5). https://zenodo.org/records/10225031Robertson, D. R., & Van Tassell, J. (2023). Shorefishes of the Greater Caribbean: online information system. Version 3.0 Smithsonian Tropical Research Institute, Balboa, Panamá.Wirtz, P., Bingeman, J., Bingeman, J., Fricke, R., Hook, T. J., & Young, J. (2017). The fishes of Ascension Island, central Atlantic Ocean–new records and an annotated checklist. Journal of the Marine Biological Association of the United Kingdom, 97(4), 783-798. Additional details:Related works Cord et al. (in prep.) and Floeter et al. (2008) Cord, I., Araujo, G. S., Silva, F. C., Kurtz, Y. R., Rocha, C. R., Pinheiro, H. T., Rocha, L. A. & Floeter, S. R. (in prep.). Biogeography and evolution of reef fishes on tropical Mid-Atlantic Ridge islands.Floeter, S. R., Rocha, L. A., Robertson, D. R., Joyeux, J. C., Smith-Vaniz, W. F., Wirtz, P., Edwards, A. J., Barreiros, J. P., Ferreira, C. E. L., Gasparini, J. L., Brito, A., Falcón, J. M., Bowen, B. W. & Bernardi, G. (2008). Atlantic reef fish biogeography and evolution. Journal of Biogeography, 35: 22–47.

(All information expressed below is also available in the "read me" text file.) Atlantic reef fishes: distributions and life-history traits Upload date: September 3rd, 2024            DOI for all versions: 10.5281/zenodo.13655553 Isadora Cord¹*, Sergio R. Floeter¹*,**, Gabriel S. Araujo², Juan P. Quimbayo³, D. Ross Robertson⁴, Benjamin C. Victor⁵, Peter Wirtz⁶, Hudson T. Pinheiro², Rui Freitas⁷, Luiz A. Rocha⁸ * joint first authors; ** corresponding author [email protected] ¹Marine Macroecology and Biogeography Lab, Universidade Federal de Santa Catarina, Brazil²Center for Marine Biology, University of São Paulo, São Sebastião, SP, Brazil³University of Florida, USA⁴Smithsonian Tropical Research Institute, Panama⁵Ocean Science Foundation, USA⁶Centro de Ciências do Mar, Universidade do Algarve, Portugal⁷Universidade Técnica do Atlântico, Cabo Verde⁸California Academy of Sciences, San Francisco, CA, USA Introduction to the First EditionThis database includes information on the distribution and life-history traits for 1,628 reef fish species, distributed across 26 sub-provinces of the tropical, sub-tropical, and warm temperate Atlantic Ocean. We followed the definition provided by Floeter et al. (2008) for “reef fish,” including any shallow (<100 m) tropical/subtropical benthic or benthopelagic fishes that consistently associate with hard substrates of coral, algal, or rocky reefs, or occupy adjacent sand substrate. All distributions were verified by the authors, double-checked with online databases, and available literature (peer-reviewed regional checklists and scientific papers; see main refs). Life-history traits were compiled for most species by using a combination of personal data, online databases (e.g. Froese & Pauly, 2023; Robertson & Van Tassell, 2023), and published sources (e.g. Luiz et al. 2015; Pinheiro et al. 2018; Quimbayo et al. 2021).This database is associated with the manuscript Cord et al. (in prep.) “Biogeography and evolution of reef fishes on tropical Mid-Atlantic Ridge islands,” and represents an update that has been in development for 16 years, based on Floeter et al. (2008) “Atlantic reef fish biogeography and evolution”. Data Description:The .xlsx database contains two pages, “traits&distributions” and “acronyms”. The “acronyms” page contains the same table that is available below, as well as a map illustrating the studied areas. The “traits&distributions” page is divided into the following columns:   "A" through "D": Species’ identificationspecies = the complete species names, in the following pattern: “Genus_specific epithet”, e.g. “Acanthurus_bahianus”family, genus = self explanatoryspp = specific epithet   "E" through "AD": Distributions RegionSub-provincesGeographical definitionAcronymWestern Atlantic    Greater CaribbeanCarolinianNorth Carolina State to Mérida (México)CA BermudaBermuda Is.BE Central CaribbeanCentral America and offshore islands (except mentioned elsewhere), Florida KeysCC Southern CaribbeanPanamá to Trinidad and TobagoSCSouthwestern Atlantic   Brazilian ProvinceNorth BrazilGreat Amazon ReefNB Northeastern BrazilRio Grande do Norte to Southern Bahia StateNE Southeastern BrazilEspírito Santo to Paraná StatesSE South BrazilSanta Catarina StateSBBrazilian oceanic islandsRocas Atoll AR Fernando de Noronha FN Trindade Is. TRWarm-temperate Argentinian ProvinceArgentinian Rio Grande do Sul State, from Uruguay to PatagoniaPTMid-Atlantic RidgeSt Paul’s Rocks SP Ascension AS St Helena SHEastern Atlantic   Northeastern AtlanticMediterraneanLevant to Gibraltar MDLusitanaAzores AZ Madeira MA Canaries CNTropical Eastern AtlanticNorthwest AfricaGibraltar to Cape Verde (Senegal)NT Cape Verde Is. CV São Tomé & PríncipeIncludes AnnobonST Tropical West AfricaCape Verde to Moçamedes (Angola)EASouthwest AfricaBenguelaMoçamedes to Cape of Good HopeBN AgulhasCape of Good Hope to Kei RiverCPSouthwestern Indian OceanSouth Africa’s Indian OceanFrom Kei River to Kosi BayIO    "AE" through "AK": Life-history traits“depth_max” = Maximum recorded depth, in meters.“bodysize_max” = Maximum recorded adult body size, in centimeters.“rafter” = Presence (1) or absence (0) of rafting behavior (mostly for the entire genus).“multihabitat” = Usage of other habitats in addition to structural reefs (soft bottoms, seagrass/macroalgae beds, mangroves, and estuaries).“diet” = Diet habits (gc: generalised carnivores; hd: herbivores/detritivores; is: sessile invertivores; mi: mobile invertivores; om: omnivores; pk: planktivores).“groupsize” = Sociability (sol: solitary; pair: pairs of two individuals; smallg: groups of 3 to 10 individuals; medg: groups of 10 to 20 individuals; largeg: groups of over 20 individuals).“spawning” = Spawning modes (att: attached; dem: demersal; live: livebearers; oral: oral; pel: pelagic). Data Sources and Verification:We gathered presence or absence data for 73 families of reef-associated fishes, encompassing 1,637 species in 26 distinct biogeographical units within the Atlantic Basin (see table above). All distributions were strictly verified by the authors, double-checked with online databases and available literature (e.g. Brown et al. 2019; Freitas et al. 2019; Floeter et al. 2023; Pinheiro et al. 2020; Robertson & Van Tassell, 2023; Wirtz et al. 2017). Life-history traits were compiled using personal data, online databases (e.g. Froese & Pauly, 2023; Robertson & Van Tassell, 2023), and published sources (e.g. Luiz et al. 2015; Pinheiro et al. 2018; Quimbayo et al. 2021). All species’ nomenclature was based on Eschmeyer's Catalog of Fishes (Fricke et al. 2024).  Main References:Brown, J., Beard, A., Clingham, E., Fricke, R., Henry, L., & Wirtz, P. (2019). The fishes of St Helena Island, central Atlantic Ocean—new records and an annotated checklist. Zootaxa, 4543(2), 151-194.Freitas, R., Romeiras, M., Silva, L., Cordeiro, R., Madeira, P., González, J.A., Wirtz, P., Falcón, J.M., Brito, A., Floeter, S.R., Afonso, P., Porteiro, F., Viera-Rodríguez, M.A., Neto, A.I., Haroun, R., Farminhão, J.N.M., Rebelo, A.C., Baptista, L., Melo, C.S., Martínez, A., Núñez, J., Berning, B., Johnson, M.E. & Ávila, S.P. (2019). Restructuring of the 'Macaronesia' biogeographic unit: A marine multi-taxon biogeographical approach. Scientific Reports, 9: 15792.Fricke, R., Eschmeyer, W. N. & Fong, J. D. (2024 ). ESCHMEYER'S CATALOG OF FISHES: GENERA/SPECIES BY FAMILY/SUBFAMILY.(http://researcharchive.calacademy.org/research/ichthyology/catalog/ SpeciesByFamily.asp). Electronic version accessed 03 September 2024.Floeter, S.R., Krajewski, J.P., Fiuza, T.M.J., Rocha, L.A. & Carvalho-Filho, A. (2023). Brazilian Reef Fishes. Editora CRV, Curitiba, pp. 320.ISBN 978-65-251-4245-6. DOI: 10.24824/978652514245.6Floeter, S. R., Rocha, L. A., Robertson, D. R., Joyeux, J. C., Smith-Vaniz, W. F., Wirtz, P., Edwards, A. J., Barreiros, J. P., Ferreira, C. E. L., Gasparini, J. L., Brito, A., Falcón, J. M., Bowen, B. W. & Bernardi, G. (2008). Atlantic reef fish biogeography and evolution. Journal of Biogeography, 35: 22-47.Froese R, Pauly D (Eds) (2023) FishBase. [Version 06/2023] http://www.fishbase.org Luiz, O. J., Madin, J. S., Robertson, D. R., Rocha, L. A., Wirtz, P., & Floeter, S. R. (2012). Ecological traits influencing range expansion across large oceanic dispersal barriers: insights from tropical Atlantic reef fishes. Proceedings of the Royal Society B: Biological Sciences, 279(1730), 1033-1040.Munroe, T. A. (1990). Eastern Atlantic tonguefishes (Symphurus: Cynoglossidae, Pleuronectiformes), with descriptions of two new species. Bulletin of Marine Science, 47(2), 464-515.Munroe, T. A. (1991). Western Atlantic Tonguefishes of the Symphurus-Plagusia Complex (Cynoglossidae, Pleuronectiformes), with Descriptions of 2 New Species. 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Research Article ###This repository contains Supplementary files associated with this research paper:Doré et al., 2025 - Timing is everything: Evolution of ponerine ants highlights how dispersal history shapes modern biodiversity. Nature Communications. In press.__DOI will be updated once the article is published.__https://doi.org/10.1111/XXXX### Research abstract ###     Disentangling the drivers of global biodiversity patterns is a cornerstone of biogeography that remains elusive for many diverse biological groups. Here we present a complete species-level phylogeny of the ant subfamily Ponerinae based on new phylogenomic sequencing and taxonomic grafting. We combine results with a large-scale geographic database to explore the contribution of three main mechanisms in shaping global ponerine biodiversity patterns: time for accumulation, differences in diversification rate, and asymmetric dispersal. We show that extant ponerine ants originated in Gondwana, spread eastward across tropical bioregions, and more recently colonized temperate areas. The relative timing of colonization events was identified as the prominent driver of present-day biodiversity patterns, supporting the time for accumulation hypothesis. Conversely, differences in diversification rates and asymmetrical dispersal histories mitigated the heterogeneity in biodiversity by fueling accumulation of lineages in the least diverse bioregions. These findings suggest that tropical niche conservatism played a major role in shaping the biogeographic and evolutionary history of Ponerinae. Overall, we emphasize the importance of considering the relative timing of past dispersal events and variations in diversification rates over evolutionary time to gain a deeper understanding of Earth’s biodiversity patterns.   ### Contents ###This repository contains five sub-archives: - 01_Supplementary_Data: Supplementary Data S1-S8 of the article including metadata for voucher specimens, fossil calibrations, grafting information, geolocalized occurrences, biogeographic membership, bioregion adjacency matrices, and ready-to-use phylogenies. - 02_Supplementary_Movie: Supplementary Movie 1 - Ponerinae Biogeographic History: Time-lapsed animation of ponerine ant biogeographic and diversification history. - 03_Phylogenetic_inferences: Scripts and files used to carry out phylogenetic inferences. - 04_Divergence_dating: Scripts and files used to carry out divergence dating analyses. - 05_Other_analyses: Script and files used to carry out data curation, tree grafting, and biogeographic and diversification analyses. This is a release of an associated GitHub repository available at https://github.com/MaelDore/Ponerinae_Historical_Biogeography. ### How to cite ###Please cite this research article as:  > Doré, M., Borowiec, M.L., Branstetter, M.G., Camacho, G.P., Fisher, B.L., Longino, J.T., Ward, P.S., & Blaimer, B.B., 2025. Timing is everything: Evolution of ponerine ants highlights how dispersal history shapes modern biodiversity. Nature Communications. In press. https://doi.org/10.1111/XXXX.__DOI will be updated once the article is published.__