{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,11]],"date-time":"2026-02-11T19:08:23Z","timestamp":1770836903182,"version":"3.50.1"},"reference-count":116,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2019,6,6]],"date-time":"2019-06-06T00:00:00Z","timestamp":1559779200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["FCT \/  Aga Khan Development Network (AKDN) CVAgrobiodiversity\/333111699"],"award-info":[{"award-number":["FCT \/  Aga Khan Development Network (AKDN) CVAgrobiodiversity\/333111699"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Over the previous decades, numerous studies focused on how oceanic islands have contributed to determine the phylogenetic relationships and times of origin and diversification of different endemic lineages. The Macaronesian Islands (i.e., Azores, Madeira, Selvagens, Canaries, and Cabo Verde), harbour biotas with exceptionally high levels of endemism. Within the region, the vascular plants and reptiles constitute two of the most important radiations. In this study we compare relevant published phylogenetic data and diversification rates retrieved within Cabo Verde endemic lineages and discuss the importance of choosing appropriate phylogeny-based methods to investigate diversification dynamics on islands. From this selective literature-based review, we summarize the software packages used in Macaronesian studies and discuss their adequacy considering the published data to obtain well-supported phylogenies in the target groups. We further debate the importance of Next Generation Sequencing (NGS), to investigate the evolutionary processes of diversification in the Macaronesian Islands. Analysis of genomic data provides phylogenetic resolution for rapidly evolving species radiations, suggesting a great potential to improve the phylogenetic signal and divergence time estimates in insular lineages. The most important Macaronesian reptile radiations provide good case-studies to compare classical phylogenetic methods with new tools, such as phylogenomics, revealing a high value for research on this hotspot area.<\/jats:p>","DOI":"10.3390\/ijms20112782","type":"journal-article","created":{"date-parts":[[2019,6,7]],"date-time":"2019-06-07T03:56:31Z","timestamp":1559879791000},"page":"2782","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Shortcomings of Phylogenetic Studies on Recent Radiated Insular Groups: A Meta-Analysis Using Cabo Verde Biodiversity"],"prefix":"10.3390","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9373-6302","authenticated-orcid":false,"given":"Maria M.","family":"Romeiras","sequence":"first","affiliation":[{"name":"LEAF, Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal"},{"name":"Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749-016 Lisbon, Portugal"}]},{"given":"Ana Rita","family":"Pena","sequence":"additional","affiliation":[{"name":"Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749-016 Lisbon, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6812-5710","authenticated-orcid":false,"given":"Tiago","family":"Menezes","sequence":"additional","affiliation":[{"name":"CIBIO, Research Centre in Biodiversity and Genetic Resources, Azores Group, InBIO Associate Laboratory, Universidade dos A\u00e7ores, 9501-855 Ponta Delgada, Azores, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4717-9429","authenticated-orcid":false,"given":"Raquel","family":"Vasconcelos","sequence":"additional","affiliation":[{"name":"CIBIO, Research Centre in Biodiversity and Genetic Resources, InBIO Associate Laboratory, Universidade do Porto, 4485-661 Vair\u00e3o, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1505-2140","authenticated-orcid":false,"given":"Filipa","family":"Monteiro","sequence":"additional","affiliation":[{"name":"LEAF, Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal"},{"name":"Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749-016 Lisbon, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5408-5212","authenticated-orcid":false,"given":"Oct\u00e1vio S.","family":"Paulo","sequence":"additional","affiliation":[{"name":"Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749-016 Lisbon, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5555-2388","authenticated-orcid":false,"given":"M\u00f3nica","family":"Moura","sequence":"additional","affiliation":[{"name":"CIBIO, Research Centre in Biodiversity and Genetic Resources, Azores Group, InBIO Associate Laboratory, Universidade dos A\u00e7ores, 9501-855 Ponta Delgada, Azores, Portugal"}]}],"member":"1968","published-online":{"date-parts":[[2019,6,6]]},"reference":[{"key":"ref_1","unstructured":"L\u00f3pez-Fern\u00e1ndez, H., Duque, P., Henriques, S., V\u00e1zquez, N., dez-Riverola, F., Vieira, C.P., Reboiro-Jato, M., and Viera, J. 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