Shortcomings of Phylogenetic Studies on Recent Radiated Insular Groups: A Meta-Analysis Using Cabo Verde Biodiversity

Abstract

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.

Keywords: Macaronesia; bioinformatics; divergence times; endemic species; evolution; phylogenetic inference; phylogenomics.

Figure 1

The five archipelagos of the Macaronesian region—Azores, Madeira, Selvagens, Cabo Verde and Canary Islands—with the corresponding distance to the closest mainland point (A), and the diversity of endemic Squamata reptile taxa within this region (B): Chalcides (coeruleopunctatus, sexlineatus, simonyi and viridanus), Chioninia (delalandii, fogoensis, nicolauensis, spinalis boavistensis, spinalis maioensis, spinalis salensis, spinalis santiagoensis, spinalis spinalis, stangeri, vaillanti vaillanti and vaillanti xanthotis), Gallotia (atlantica mahoratae, atlantica atlantica, atlantica laurae, auaritae, bravoana, caesaris caesaris, caesaris gomerae, galloti eisentrauti, galloti galloti, galloti insulanagae, galloti palmae, intermedia, simonyi machadoi and stehlini), Hemidactylus (bouvieri bouvieri, bouvieri ssp., bouvieri razoensis, boavistensis and lopezjuradoi), Tarentola (angustimentalis, bischoffi, boavistensis, bocagei, boettgeri boettgeri, boettgeri hierrensis, caboverdiana caboverdiana, caboverdiana raziana, caboverdiana substituta, darwini, delalandii, gigas gigas, gigas brancoensis, fogoensis, gomerensis, maioensis, nicolauensis, protogigas protogigas, protogigas hartogi and rudis), and Teira dugesii. The three extinct taxa (Chioninia coctei, Gallotia goliath and Gallotia simonyi simonyi) were not included in this representative analysis. Photo of Tarentola maioensis by R. Vasconcelos.

Figure 2

Number of studies (columns) and percentage of studied taxa (red line) within Macaronesian reptile lineages.

Figure 3

Calibration methods used with Macaronesian reptile lineages. Total number of calibration points (columns) and number of unresolved clades (red line). The average percentage of unresolved clades is shown within the columns as the number of unresolved clades/total number of clades.

Figure 4

Divergence times obtained within Macaronesia reptile lineages in a meta-analysis of selected studies. Horizontal bars represent average age estimation (Mya), grey bars indicate minimum and maximum ages estimated (Mya). Asterisks indicate lack of data. Horizontal bar colour indicates the calibration method used: green–mutation rate; black–fossil; brown–mutation rate and geological. The age for the Fogo and Sal islands is shown in a dashed orange line (reference for age; [73]).