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.
Highlights
During the last two decades, one of the fields that took the most benefit of the explosive growth of bioinformatic tools was phylogenetics, which uses molecular data to establish evolutionary relationships among species [1,2]
SplitsTree4 contains methods specialized in the creation of recombination and hybridization networks, and were used in some studies with plants [67], where the obtained network revealed conflicting phylogenetic signals, such as rapid radiation or ancient hybridization events, within five Betoideae genera distributed in the Macaronesian Islands and in the western Mediterranean region
Considering (i) the inherent drawbacks of the targeted molecular marker-based techniques, namely, the high effort required for finding a considerable number of informative loci; (ii) their little resolving power at low taxonomic levels, which ignores many population-level effects, and (iii) increasingly affordable sequencing costs resulting from the continuous advancement of next-generation sequencing (NGS) technologies, phylogenomics emerges as an promising alternative tool for studying evolutionary relationships based on comparative analysis of genome-scale data [92]
Summary
During the last two decades, one of the fields that took the most benefit of the explosive growth of bioinformatic tools was phylogenetics, which uses molecular data to establish evolutionary relationships among species [1,2]. Large amounts of genetic data are retrievable from public repositories, such as GenBank [3], which stores and organizes molecular sequences, while making them publicly accessible and ready to use. Other biology focused databases include EMBL (European Molecular Biology Laboratory) [4], UniProt (Universal Protein resource) [5], DDBJ Bank of Japan) [6] and many others, all of them available online, allowing an ever-growing global network of information that continues to expand, giving researchers an almost never-ending flow of new data. An issue that arose from the high output of data was its processing. The past two dIenct.aJ.dMesol.hSacvi. e20b19e,e2n0,axsFtOonRiPsEhEinRgR,EwVIiEtWh more than a million-fold improvement in the rate of seque6nocfe generation [7], with the introduction of Generation Sequencing (NGS), which is fuorfthbeiroddiisvceursssiteyd b[6e8lo].w.TWheithtesrurechstrainalexetnradoermdiincarliynqeaugaenstitoyfofthseequMenaccaersobneeinsigancreIastleadn,dtsheanreumobfteern ocfhbairoaicntfeorirzmedatibcys toococulspryeiqnugirdeidffetroenhtahnadbleitastusc; hshhoiwghinlgevsetrliskionfginmfoorrmphaotiloong,icaallsdoifgfreerwencaensdamthoenirg asnpaelyciteics;cfarpeqacuietyntdrraarmityataicnadllybeiminpgrporveesde.nCt iunrrfeewntlayn, adlmsmoastllapllospyusltaetmioantsic[6st5u].dOievsehratvheespoamstedtyecpaedoefs, brieosineaforcrmh ahtaicssfaoncaulsyesdisoanndmiut ilstipcolemfmacoentstoofmiaslkaenudsseaonfdmhuoltwiplteheoypthioanvse. had a relevant role in the estaAblnisohumtsetnatnodfinegcoalroegaifcoarlsatnuddieevs oolfuetvioonluatriyonthaenodrsiepse[c6ia8t,i6o9n].is the Macaronesian Region (i.e., Azores, MadeDiraif,feSreelnvtapgaetst,eCrnasnoafriceosl,oannizdatCioanbowiVtherindethaerMchaipcaerlaognoessi;aFnigRuergeio1nAh)atvheabt eeenncoanmopnagssoeinsgasgurbejaectt noufmdbeebraotfe.enSdoemmeicolfintehaegeissl.aTnhdessewiistlhainndsthbieslorneggiotonthaereMneedairtetrhraenmeaaninBlaasnind,bwioditihvetrhseityclhoosetsspt obte[i8n]g, wFhuiechrteisvcehnaturarcateinritzheedCbaynhairgyhIlselvaneldsso,fwehnidcehmdiissmta,nacneds orenplyrecsae.n9ts aknmexwceesllteonftmaraeiantloansdtuAdyfriecvao(lFuitgiounr.e T1hAe)a.iTmhoisf tphriosxsitmudityyims taoyrehvaivewe ftahceilpitraetseedntdkisnpoewrslieodngeanodn tchoelotrneiezaotfiolinfewanitdhetvhoeluintifoluneonfcCe aobfooVceeradneic bcioudrrivenertssit(yNuosritnhgA, atlsacnatsice-asntuddCieasn, tahreyrceuprtrileensts[9),] wanhdilethneovrathsc-uealasrteprllaynttrsa[d1e0]w, winhdischmsahyowhahvieghfolsetveerlesd otfheenddiesmseimsmin, awtiiothnsoefvaenraclersatrnagles-preesctireisctferdomsptehceiecsoonctcinuerrnitnagnidn dnieffaerrbeynCt haanbairtyatIss,laannddst.hFuosrctohnisstriteuatseoan, giotohdasmboedenelpsryospteomsedtothuantdferresqtuanendtpcaotltoenrnizsaotifodnievveersnitfiscfartoimontwheitchoinnttihniesnatracnhdipcelloasgeoa.rWcheipweillalgdoesbmataey thheavreelecvoanntcriebouftceudtttiongth-eedhgiegbhioniunmfobrmeraotifcsentodoelms ainc dspmeectihesodinolsoogmiees toofpthroevliedsesaisboeltatteerdunMdaecrasrtaonndeisniagn oIfstlhanedesvo[7lu0]t.ionary history of the recent radiated groups of the Macaronesian Region
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