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Molecular phylogenetics of Micromeria (Lamiaceae) in the Canary Islands, diversification and inter-island colonization patterns inferred from nuclear genes
Abstract
Here we reconstruct the evolutionary history of Micromeria in the Canary Islands using eight nuclear markers. Our results show two centers of diversification for Micromeria, one in the eastern islands Gran Canaria and Lanzarote, the other in the western islands, Tenerife, La Palma and El Hierro. Suggested directions of inter-island colonization are the following: Gran Canaria to Lanzarote and La Gomera; Tenerife to La Palma (from the paleoisland of Teno), to El Hierro (from the younger, central part), and to La Gomera and Madeira (from the paleoislands). Colonization of La Gomera probably occurred several times from Gran Canaria and Tenerife. The taxonomic implications of these results are discussed. Incongruence among the different markers was evaluated and, using next generation sequencing, we investigated if this incongruence is due to gene duplication.
Copyright © 2015 Elsevier Inc. All rights reserved.
... They grow on all of the Canary Islands and in all ecological zones. As in many other Canarian taxa, molecular data show two main lineages of Micromeria on the Canary Islands archipelago [28,29]. One includes the species found on the eastern islands of Gran Canaria, Lanzarote and Fuerteventura; the other contains taxa from the western islands of Tenerife, La Palma, and El Hierro (Fig. 1). ...
... One includes the species found on the eastern islands of Gran Canaria, Lanzarote and Fuerteventura; the other contains taxa from the western islands of Tenerife, La Palma, and El Hierro (Fig. 1). Taxa from La Gomera belong to both lineages: M. lepida and M. gomerensis are part of the eastern lineage, while M. pedro-luisii is part of the western lineage [29]. ...
... varia). These taxa occupy all islands except La Palma and have been recently separated based on molecular phylogenetic analyses [26,27,29] (Fig. 1). ...
Background
Especially on islands closer to the mainland, such as the Canary Islands, different lineages that originated by multiple colonization events could have merged by hybridization, which then could have promoted radiation events (Herben et al., J Ecol 93: 572–575, 2005; Saunders and Gibson, J Ecol 93: 649–652, 2005; Caujapé-Castells, Jesters, red queens, boomerangs and surfers: a molecular outlook on the diversity of the Canarian endemic flora, 2011). This is an alternative to the scenario where evolution is mostly driven by drift (Silvertown, J Ecol 92: 168–173, 2004; Silvertown et al., J Ecol 93: 653–657, 2005). In the former case hybridization should be reflected in the genetic structure and diversity patterns of island species. In the present work we investigate Micromeria from the Canary Islands by extensively studying their phylogeographic pattern based on 15 microsatellite loci and 945 samples. These results are interpreted according to the hypotheses outlined above. ResultsGenetic structure assessment allowed us to genetically differentiate most Micromeria species and supported their current classification. We found that populations on younger islands were significantly more genetically diverse and less differentiated than those on older islands. Moreover, we found that genetic distance on younger islands was in accordance with an isolation-by-distance pattern, while on the older islands this was not the case. We also found evidence of introgression among species and islands. Conclusions
These results are congruent with a scenario of multiple colonizations during the expansion onto new islands. Hybridization contributes to the grouping of multiple lineages into highly diverse populations. Thus, in our case, islands receive several colonization events from different sources, which are combined into sink populations. This mechanism is in accordance with the surfing syngameon hypothesis. Contrary to the surfing syngameon current form, our results may reflect a slightly different effect: hybridization might always be related to colonization within the archipelago as well, making initial genetic diversity to be high to begin with. Thus the emergence of new islands promotes multiple colonization events, contributing to the establishment of hybrid swarms that may enhance adaptive ability and radiation events. With time, population sizes grow and niches start to fill. Consequently, gene-flow is not as effective at maintaining the species syngameon, which allows genetic differentiation and reproductive isolation to be established between species. This process contributes to an even further decrease in gene-flow between species.
... only one species, M. varia bentham (1834: 374), is distributed among all islands though different subspecies have been described for each, highlighting the morphological variation present in this species. Phylogenetic evidence (Puppo et al. 2014(Puppo et al. , 2015 however, suggests that M. hyssopifolia plants from Tenerife and el Hierro are not closely related. Similarly, it seems that individuals from la Palma referred to M. lasiophylla are not closely related to those from Tenerife and rather constitute two different taxa. ...
... gomerensis P. Pérez (1978: 179). However, molecular analyses revealed that each subspecies of M. varia present in la gomera constitutes independent lineages (Puppo et al. 2015) deriving from different colonization events. Micromeria varia subsp. ...
... gomerensis and both subspecies of M. lepida most likely resulted from colonization from gran Canaria while M. varia subsp. varia probably originated from Tenerife (Puppo et al. 2015). ...
Based on recent molecular evidence, one new species and one new subspecies of Micromeria are described for the Canary Islands: M. pedro-luisii and M. hierrensis subsp. incana. Six new combinations are proposed: M. canariensis, M. canariensis subsp. meridialis, M. gomerensis, M. rupestris, M. herpyllomorpha subsp. palmensis, and M. hierrensis. Three new hybrids are described for La Gomera: M. lepida subsp. bolleana × M. gomerensis, M. lepida subsp. bolleana × M. pedro-luisii, and M. lepida subsp. lepida × M. pedro-luisii. A new name is also given to the taxon from Madeira: M. maderensis. A revised key to the species present in the Canary archipelago is provided.
... Notably, a number of molecular-based studies have revealed sharp genetic discontinuities within and between islands in both narrowly distributed and widespread Canarian endemic plant lineages (Rumeu et al., 2014;Jaén-Molina et al., 2015;Puppo et al., 2015;García-Verdugo et al., 2017). These results emphasize the value of comprehensive sampling of populations and genomes for a thorough understanding of evolution prior to the implementation of the necessary components of an effective conservation strategy (Caujapé-Castells et al., unpublished;Díaz-Bertrana and Saturno, 2017). ...
... Northern Tenerife has been subjected to a number of geologic events such as volcanic landslides and avalanches in different periods of time from 2.2 Ma (Tigaiga landslide) to 170 ka (formation of Las Cañadas Caldera) (Ancochea et al., 1990;Watts and Masson, 1995;Ablay and Hürlimann, 2000) that likely have caused recent disruptions of gene flow in taxa that formerly constituted a continuum of populations. For instance, the populations of Bystropogon (Trusty et al., 2005), and some populations of Micromeria (Puppo et al., 2015) or Canarina canariensis (Mairal et al., 2015), presently distributed in Teno and Anaga may be the remnants of a larger ancestral distribution area affected by these volcanic events. In the case of Navaea phoenicea (Malvaceae), a palaeo-endemic with a similar distribution to SVV, González De (2016) finds modest levels of gene flow mediated by pollinators among Anaga and Teno. ...
Islands provide unique opportunities to integrated research approaches to study evolution and conservation because boundaries are circumscribed, geological ages are often precise, and many taxa are greatly imperiled. We combined morphological and hybridization studies with high-throughput genotyping platforms to streamline relationships in the endangered monophyletic and highly diverse lineage of Solanum in the Canarian archipelago, where three endemic taxa are currently recognized. Inter-taxa hybridizations were performed, and morphological expression was assessed with a common-garden approach. Using the eggplant Single Primer Enrichment Technology (SPET) platform with 5,093 probes, 74 individuals of three endemic taxa (Solanum lidii, S. vespertilio subsp. vespertilio, and S. vespertilio subsp. doramae) were sampled for SNPs. While morphological and breeding studies showed clear distinctions and some continuous variation, inter-taxon hybrids were fertile and heterotic for vigor traits. SPET genotyping revealed 1,421 high-quality SNPs and supported four, not three, distinct taxonomic entities associated with post-emergence geological, ecological and geographic factors of the islands. Given the lack of barriers to hybridization among all the taxa and their molecular differences, great care must be taken in population management. Conservation strategies must take account of the sexual and breeding systems and genotypic distribution among populations to successfully conserve and restore threatened/endangered island taxa, as exemplified by Solanum on the Canary Islands.
... Many studies have been published on the relationship of the various archipelagos to the mainland as well as relationships within and between archipelagos [7][8][9][10]. In the first case, the Canarian and Madeiran flora exhibits a clear affinity to the western Mediterranean, its main source region, whereas the Azores archipelago displays important relationships with Atlantic and Boreal Europe, and Cape Verde is related to the Saharan Tropical African flora [11][12][13]. ...
... In the case of R. cortusifolius, however, genetic differences among populations indicate that this taxon is actually a complex comprising several species having a common origin from a single colonisation of Macaronesia followed by subsequent inter-archipelago dispersal [14]. The close floristic relationship between the Canary Islands and Madeira shown in numerous studies is more often due to dispersal events from the Canaries to Madeira than vice versa [8][9][10][11][15][16][17][18][19][20]. Studies focusing on plant taxa of the Azores have revealed their origins to be in south-western Europe [21], Madeira [22,23] and the Canary Islands [19,24]. ...
The Macaronesian Scrophularia lowei is hypothesized to have arisen from the widespread S. arguta on the basis of several phylogenetic studies of the genus, but sampling has been limited. Although these two annual species are morphologically distinct, the origin of S. lowei is unclear because genetic studies focused on this Macaronesian species are lacking. We studied 5 S. lowei and 25 S. arguta populations to determine the relationship of both species and to infer the geographical origin of S. lowei. The timing of S. lowei divergence and differentiation was inferred by dating analysis of the ITS region. A phylogenetic analysis of two nuclear (ITS and ETS) and two chloroplast (psbJ–petA and psbA–trnH) DNA regions was performed to study the relationship between the two species, and genetic differentiation was analysed by AMOVA. Haplotype network construction and Bayesian phylogeographic analysis were conducted using chloroplast DNA regions and a spatial clustering analysis was carried out on a combined dataset of all studied regions. Our results indicate that both species constitute a well-supported clade that diverged in the Miocene and differentiated in the Late Miocene-Pleistocene. Although S. lowei constitutes a well-supported clade according to nDNA, cpDNA revealed a close relationship between S. lowei and western Canarian S. arguta, a finding supported by the spatial clustering analysis. Both species have strong population structure, with most genetic variability explained by inter-population differences. Our study therefore supports a recent peripatric speciation of S. lowei—a taxon that differs morphologically and genetically at the nDNA level from its closest relative, S. arguta, but not according to cpDNA, from the closest Macaronesian populations of that species. In addition, a recent dispersal of S. arguta to Madeira from Canary Islands or Selvagens Islands and a rapid morphological differentiation after the colonization to generate S. lowei is the most likely hypothesis to explain the origin of the last taxon.
... 8.2 Mya). Puppo et al. (2015) also date the origin of Micromeria (Lamiaceae) some 8.4 Mya, which was followed by a radiation burst originating in the central islands some 6.4 Mya (Fig. 1B). ...
... 0.8 My BP) originated a tsunami that reached 100 m asl in Agaete, on the NW of Gran Canaria (Carracedo et al., 2009).The prevalence of the Westerlies (Rognon and Coude-Gaussen, 1996) in several epochs of the late Pleistocene (ca. 18,000 years BP) probably determined colonization waves from the Western islands to Eastern islands (e.g. as in the case of Micromeria rupestris [Lamiaceae] endemic to Lanzarote, Puppo et al., 2015), and from the islands to the mainland (see Caujapé-Castells 2004, 2011. ...
... Finally, La Palma and El Hierro emerged within the last 3.5 and 1.1 Ma, respectively (Guillou et al., 1996;Carracedo et al., 2001). The repeated volcanic activity, formation of new territories, large-scale landslides and sea level variations (Carracedo, 1994), would have led to isolation, local extinctions and (re)colonization of the species communities, consequently shaping their evolutionary trajectories (see Gübitz et al., 2005;Mairal et al., 2015;Puppo et al. 2015;Noguerales et al., 2024). ...
... Ricinus communis is most commonly known as the Castor Oil plant which is a perennial flowering plant species of the monotypic genus Ricinus from subtribe Ricinae. Recinus is currently being studied by many researchers, and its pharmacological value and importance is very impressive [87,88]. ...
An informal group of scientists from multiple nations formed the Angiosperm Phylogeny Group (APG), in which experts work together for the development of taxonomy of angiosperms. The group took into account all new information about diverse plant species using a high steering phylogenetic investigation. The APG has developed four classification systems from 1998 through 2003 and 2009 up until 2016. Since, the previously classified angiosperm species and their wild relatives were not fully based on monophyletic grouping, the classification has a lot of shortcoming and faults. According to the Angiosperm Phylogeny Group system, the Phyllanthaceae of order Malpighiales is most important with Euphorbiaceae sensu lato as a pantropical family comprised of hundreds of genera and thousands of species. It has several physical characteristics which are the same as Euphorbiaceae sensu stricto. The most important characteristics include unisexual flowers and a syncarpous ovary. Further, the flowers have an axile-apical placentation without pistillode (rudimentary pistil). In the Middle East region, the critical taxonomic review of six important genera from 10 taxa of sub-families Phyllanthaceae and Euphorbiaceae were studied for various characteristics using the latest nomenclature, type citation, and keys for each genus and species. Euphorbia are very rich in natural plant products which have an incredible chemical composition and functional diversity. Compounds were found highly significant and have been the subject of extensive research globally. Further, the genetic composition of Euphorbia is diverse, maturing in various growth forms, cyathial features, and habitats. The molecular characterization of the family Euphorbiaceae also showed a diverse species composition. The members of the family Euphorbiaceae exhibit a palisadal exotegmen with cellular bundles in association with vascular bundles on inner integument as synapomorphies for several major clades. Within current studies on phylogeny and classification of Euphorbia subg. Esula are burning topics comprised of diverse species that make the genus most significant in the kingdom plantae..
... Recent molecular analyses (Puppo et al. 2014a(Puppo et al. , 2015 revealed that species of Micromeria within each island of the Canary Islands are more closely related to each other than taxa from other islands, supporting each taxon as a single-island endemic. To incorporate this new molecular evidence, a taxonomic revision of Micromeria in the Canaries was published in 2015 (Puppo & Meimberg 2015a, 2015b. ...
Based on molecular and morphological evidence, a new species of Micromeria is described for Tenerife, Canary Islands. Micromeria tenensis is endemic to the massif of Teno, occurring between 100–1000 m elevation. It is characterized by having more or less pendulous branches, tomentose stems and leaves, hispid calyx, and calyx apices triangular to lanceolate, densely white hispid.
... Thus, genetic differentiation has also been recently detected in non-species-rich lineages, encompassing (1) widespread floristic elements that are thought not to be taxonomically diverse (González-Pérez et al., 2014;García-Verdugo et al., 2015;Puppo et al., 2015;Valtueña et al., 2016) and (2) taxa that are endangered but have populations on two or more islands and have thus not received so much attention as the single island endemics (SIE thereafter) (Rumeu et al., 2014;Jaén-Molina et al., 2015;Gramazio et al., 2020). These recent and ongoing investigations provide compelling evidence that many diversification processes remain to be discovered in the Canarian flora, and some of them may result in urgent taxonomic and conservation reassessments. ...
We studied four currently recognized endemics of Ruta (Rutaceae) from the Canary Islands, an oceanic biodiversity hotspot, to identify genetic variation, reconstruct evolutionary relationships and clarify the taxonomic delimitation of several recently discovered populations. We analysed four plastid DNA regions for a thorough population sampling of Ruta oreojasme on Gran Canaria, R. pinnata on Tenerife and La Palma and R. microcarpa and the only known population of the recently described R. nanocarpa on La Gomera. Bayesian clock dating analysis, haplotype network and ancestral area reconstructions were carried out. Our results reveal a complex, extremely dynamic and largely overlooked pattern of colonization and evolutionary history of Ruta in the archipelago. Thirty haplotypes were found, but only one of them was shared across more than one island. Species divergence and all colonization events in the Canary Islands were dated from the late Pliocene to the Pleistocene, and R. oreojasme has an earlier origin than its Canarian congeners. Multiple secondary colonization events between and within islands account for the diversification of R. pinnata and R. microcarpa. Our data cannot discard a possible independent origin of R. oreojasme and do not support the currently accepted circumscription of R. pinnata and R. microcarpa. Rather, the high levels of genetic differentiation detected suggest the existence of ongoing diversification processes and of new taxa. Urgent population-level conservation efforts should be undertaken, especially focused on the single population on La Gomera that can be attributed to R. microcarpa, R. nanocarpa and genetically distinct populations from La Palma and the palaeo-islands of Tenerife.
... Finally, La Palma and El Hierro emerged within the last 3.5 and 1.1 Ma, respectively (Guillou et al., 1996;Carracedo et al., 2001). The repeated volcanic activity, formation of new territories, large-scale landslides and sea level variations (Carracedo, 1994), would have led to isolation, local extinctions and (re)colonization of the species communities, consequently shaping their evolutionary trajectories (see Gübitz et al., 2005;Mairal et al., 2015;Puppo et al. 2015;Noguerales et al., 2024). ...
Island archipelagos are global biodiversity hotspots since they often foster high concentrations of diverse lineages and endemic species. Here, we examine the population genetics of the endemic Bolle’s Laurel Pigeon Columba bollii , a frugivorous bird inhabiting subtropical laurel forests. We genotyped ten microsatellite loci using DNA obtained from moulted tail feathers collected at eight sampling sites on the four western islands of the Canarian archipelago. Analyses including F-statistics, Bayesian clustering approaches, isolation by distance tests and population graph topologies, were used to infer the genetic diversity and the population differentiation within and among insular populations. Additionally, we evaluated the effect of null alleles on data analysis. Low genetic diversity was found in all populations of Bolle’s Laurel Pigeon, with no significant differences in diversity among them. However, significant genetic differentiation was detected among all populations, with pigeons from La Palma and El Hierro exhibiting the closest affinity. Bayesian clustering supported population separation between islands, and also detected fine-scale structure within the Tenerife and La Gomera populations. Present-day pigeon movements appear to occur between islands, however, this has not been sufficient to remove the signature of genetic divergence among the populations of Bolle’s Laurel Pigeon, which was moderately linked to geographical distance. According to metapopulation structure, this study suggests that the evolutionary history of C. bollii is closely related to the geological past of these oceanic islands and the distribution range of its habitat, the laurel forest. Finally, conservation implications for the species are discussed.
... However, such synonyms or erroneously reported species are also maintained in an appendix to allow checking for the existence of these taxa in the future. For highly debated taxa, we also consider current scientific literature on plant phylogenetics (e.g., [66] for the genus Micromeria). ...
The flora of the Canary Islands has been subject to botanical studies for more than 200 years. Several biodiversity databases are available for the archipelago. However, there are various drivers of change in real biodiversity and the knowledge about it constantly needs to be kept track of. Island floras are both: exposed to species loss and to species introductions, either through natural processes or by anthropogenic drivers. Additionally, the evolution of endemic plant species plays a substantial role. Endemic species are sensitive to population decline due to small population sizes and possible low competitiveness against incoming species. Additionally, there is continuous progress in systematics and taxonomy. Species names or their taxonomic attribution can be modified. Here, we check published plant lists for the Canary Islands and literature, and compile currently accepted taxa into an updated checklist. For this FloCan checklist, several sources were compiled, checked for completeness and quality, and their taxonomy was updated. We illustrate how far plant names are considered in regional or global databases. This work represents the current state of knowledge on Canary Island plant diversity, including introduced and recently described taxa. We provide a comprehensive and updated basis for biogeographical and macroecological studies. Particularly, the number of non-native species is being extended substantially. The adaptation to standard international nomenclature supports integration into large-scale studies.
... Our results suggest that the largest and most diverse islands (Gran Canaria and Tenerife) seem to have played a major role during the diversification of this lineage, in accordance to a previous biogeographic pattern detected for several Canarian plant lineages (i.e. Aeonium, Cheirolophus or Micromeria, Mort et al., 2002;Vitales et al., 2014;Puppo et al., 2015;Curto et al., 2017), which suggests that the central Canaries were the centers of diversification to both the older easternmost islands and to the younger westernmost islands (Sanmartín et al., 2008(Sanmartín et al., , 2010. In line with the fact that the complex geological history of the islands played an important role in generating patterns of genetic diversity (Marrero and Francisco Ortega, 2001;Caujapé-Castells et al. 2017), these two islands also host a higher variety of habitats at present, most of which must have been formed during the last 2 Ma due to volcanic activity (García-Talavera, 1999). ...
With a wide distribution range including Europe and Asia, Lotus (Leguminosae) represents the largest genus within Loteae. It is particularly diverse in the Mediterreanean region and in the five archipelagos of Macaronesia (Atlantic Ocean). However, little is known about the relationships among the 14 sections currently recognized within Lotus and about the timing and patterns of its colonization in the Macaronesian region. In this investigation, we use four DNA regions (nuclear ribosomal ITS plus three plastid regions) in the most comprehensive sampling of Lotus species to date (some endemic species within the Canary Islands were poorly represented in previous phylogenetic analyses) to infer relationships within this genus and to establish patterns of colonization in Macaronesia. Divergence time estimates and habitat reconstruction analyses indicate that Lotus likely diverged about 7.86 Ma from its sister group, but all colonization events to Macaronesia occurred more recently (ranging from the last 0.23 to 2.70 Ma). The diversification of Lotus in Macaronesia involved between four and six independent colonization events from four sections currently distributed in Africa and Europe. A major aspect shaping the current distribution of taxa involved intra-island colonization of mainly new habitats and inter-island colonization of mostly similar habitats, with Gran Canaria and Tenerife as the major sources of diversification and of further colonization events. Section Pedrosia is the most diverse in terms of colonization events, number of species, and habitat heterogeneity, including a back-colonization event to the continent. Subsections within Pedrosia radiated into diverse habitat types recently (late Pleistocene, ca 0.23–0.29 Ma) and additional molecular markers and sampling would be necessary to understand the most recent dispersal events of this group within the Canary Islands and Cape Verde
... Many of the phylogenetic and biogeographical studies dealing with endemic plant groups in the Canary Islands have revealed the prevalence of strongly supported monophyletic lineages (e.g. Fernández-Palacios and Whittaker, 2008;Kim et al., 2008;Guzmán and Vargas, 2010;Vitales et al., 2014;Puppo et al., 2015), which are considered to be the result of a single colonization event from the mainland followed by rapid diversification and spread across the islands (Silvertown et al., 2005). Several models that are not mutually exclusive have been proposed to explain this pattern (Carine, 2005;Herben et al., 2005;Silvertown et al., 2005;Sanmartín et al., 2008). ...
Background and Aims
Several biogeographic models have been proposed to explain the colonization and diversification patterns of Macaronesian lineages. In this study, we calculated the diversification rates and explored what model better explains the current distribution of the 15 endemic species to the Canary Islands belonging to Helianthemum sect. Helianthemum (Cistaceae).
Methods
We performed robust phylogenetic reconstructions based on genotyping-by-sequencing (GBS) data and analysed the timing, the biogeographical history and the ecological niche conservatism of this endemic Canarian clade.
Key Results
Our phylogenetic analyses provide strong support for the monophyly of this clade, and retrieved five lineages not currently restricted to a single island. The pristine colonization event took place in the Pleistocene (c. 1.82 Ma) via dispersal to Tenerife by a Mediterranean ancestor.
Conclusions
The rapid and abundant diversification (0.75-1.85 spp. Ma-1) undergone by this Canarian clade seems the result of complex inter-island dispersal events followed by allopatric speciation driven mostly by niche conservatism, i.e. inter-island dispersal towards niches featuring similar environmental conditions. Nevertheless, significant instances of ecological niche shifts have also been observed in some lineages, remarkably contributing to the overall diversification history of this clade.
https://academic.oup.com/aob/advance-article-abstract/doi/10.1093/aob/mcaa090/5835303
... Many of the phylogenetic and biogeographical studies dealing with endemic plant groups in the Canary Islands have revealed the prevalence of strongly supported monophyletic lineages (e.g. Fernández-Palacios and Whittaker, 2008;Kim et al., 2008;Guzmán and Vargas, 2010;Vitales et al., 2014;Puppo et al., 2015), which are considered to be the result of a single colonization event from the mainland followed by rapid diversification and spread across the islands (Silvertown et al., 2005). Several models that are not mutually exclusive have been proposed to explain this pattern (Carine, 2005;Herben et al., 2005;Silvertown et al., 2005;Sanmartín et al., 2008). ...
Background and aims:
Several biogeographic models have been proposed to explain the colonization and diversification patterns of Macaronesian lineages. In this study, we calculated the diversification rates and explored what model better explains the current distribution of the 15 endemic species to the Canary Islands belonging to Helianthemum sect. Helianthemum (Cistaceae).
Methods:
We performed robust phylogenetic reconstructions based on genotyping-by-sequencing (GBS) data and analysed the timing, the biogeographical history and the ecological niche conservatism of this endemic Canarian clade.
Key results:
Our phylogenetic analyses provide strong support for the monophyly of this clade, and retrieved five lineages not currently restricted to a single island. The pristine colonization event took place in the Pleistocene (c. 1.82 Ma) via dispersal to Tenerife by a Mediterranean ancestor.
Conclusions:
The rapid and abundant diversification (0.75-1.85 spp. Ma-1) undergone by this Canarian clade seems the result of complex inter-island dispersal events followed by allopatric speciation driven mostly by niche conservatism, i.e. inter-island dispersal towards niches featuring similar environmental conditions. Nevertheless, significant instances of ecological niche shifts have also been observed in some lineages, remarkably contributing to the overall diversification history of this clade.
... The raw data were allocated to the correct read direction and paired amplicons were merged using the De Novo Assamble tool with the highest sensitivity. The sequencing quality was checked manually, inspecting the peaks in the electropherogram (Puppo et al. 2015). Merged amplicons were trimmed to 650 bp sequences by removal of the primer sequences. ...
DNA barcoding constitutes a supplemental genetically based characterization tool for the identification of species. Traditionally, the barcodes are generated with a length of 650 bp using standardized Sanger sequencing, but with the introduction of high-throughput sequencing (HTS) methods new opportunities for sequencing are available. To use HTS for barcode collection and identification, the amplification of shorter fragments is preferred. Reference DNA midi-barcodes of wild bees were produced using the Illumina MiSeq as well as the Sanger method. Although DNA midi-barcodes derived from Illumina were comparatively shorter (418 bp), their sequences were coherent to the morphological assignment of species. The Illumina barcodes proved to be effective and dealt better with some general limitations of DNA barcoding.
... According to the data of Bräuchler et al. (2010), section Pineolentia and section Micromeria have the same clade, and this shows that they have a common ancestor. The data of Puppo et al. (2014Puppo et al. ( , 2015 contributed to sections Pineolentia and Micromeria. M. pineolens shares the same clade with the Canary Islands section Micromeria specimens. ...
A new species, Micromeria aybalae H.Duman & Dirmenci (Lamiaceae), Micromeria Benth. sect. Micromeria, is described from Muğla Province in southwestern Turkey. A description, taxonomic note, distribution map, habitat, and nrDNA ITS and cpDNA trnL-F based phylogeny are presented. The differences between the new species and its allies, Micromeria cremnophila Boiss. & Heldr. s.l. and M. hispida Benth., are discussed, and an identification key is provided for the Turkish Micromeria.
... In the present study, chloroplast diversity reveals a strong genetic divergence between eastern islands (Gran Canaria, Fuerteventura, and Lanzarote) and western islands (EI Hierro, La Palma, La Gomera, and Tenerife), which is partially congruent with the pattern of nuclear genetic diversity. This east-west genetic split has been found in other Canarian plant lineages such as Canarina canariensis (Mairal et al., 2015), Phoenix canariensis (Saro et al., 2015), Micromeria species (Puppo et al., 2015), and Euphorbia species (Sun et al., 2016). ...
Kleinia neriifolia Haw. is an endemic species on the Canarian archipelago, this species is widespread in the coastal thicket of all the Canarian islands. In the present study, genetic diversity and population structure of K. neriifolia were investigated using chloroplast gene sequences and nuclear SSR (simple sequence repeat). The differentiation among island populations, the historical demography, and the underlying evolutionary scenarios of this species are further tested based on the genetic data. Chloroplast diversity reveals a strong genetic divergence between eastern islands (Gran Canaria, Fuerteventura, and Lanzarote) and western islands (EI Hierro, La Palma, La Gomera, Tenerife), this west–east genetic divergence may reflect a very beginning of speciation. The evolutionary scenario with highest posterior probabilities suggests Gran Canaria as oldest population with a westward colonization path to Tenerife, La Gomera, La Palma, and EI Hierro, and eastward dispersal path to Lanzarote through Fuerteventura. In the western islands, there is a slight decrease in the effective population size toward areas of recent colonization. However, in the eastern islands, the effective population size increase in Lanzarote relative to Gran Canaria and Fuerteventura. These results further our understanding of the evolution of widespread endemic plants within Canarian archipelago.
... The genetic divergence between the "eastern" islands and the "western" islands has been revealed in numerous groups such as Canarina canariensis 9 and Phoenix canariensis 24 . In the present study, the west-east split corresponded to species differentiation between E. regis-jubae and E. lamarckii, which could be interpreted as an inter-island colonization and diversification in the archipelago 10,25 . E. regis-jubae and E. lamarckii are xerophilous and thermophilous species with a marked invasive capacity and appear to live in similar ecological conditions because both are very common constituents of the coastal belt vegetation at low elevations in the arid and semi-arid infracanarian bioclimatic belt 15 . ...
Diversification between islands and ecological radiation within islands are postulated to have occurred in the Euphorbia species (sect. Aphyllis subsect. Macaronesicae) on the Canary Islands. In this study, the biogeographical pattern of 11 species of subsect. Macaronesicae and the genetic differentiation among five species were investigated to distinguish the potential mode and mechanism of diversification and speciation. The biogeographical patterns and genetic structure were examined using statistical dispersal-vicariance analysis, Bayesian phylogenetic analysis, reduced median-joining haplotype network analysis, and discriminant analysis of principal components. The gene flow between related species was evaluated with an isolation-with-migration model. The ancestral range of the species of subsect. Macaronesicae was inferred to be Tenerife and the Cape Verde Islands, and Tenerife-La Gomera acted as sources of diversity to other islands of the Canary Islands. Inter-island colonization of E. lamarckii among the western islands and a colonization of E. regis-jubae from Gran Canaria to northern Africa were revealed. Both diversification between islands and radiation within islands have been revealed in the Euphorbia species (sect. Aphyllis subsect. Macaronesicae) of the Canary Islands. It was clear that this group began the speciation process in Tenerife-La Gomera, and this process occurred with gene flow between some related species.
... ). Similar patterns with the central Canaries as centres of dispersal events within the archipelago have been described in other animal and plant studies(Francisco-Ortega et al. 2002;G omez et al. 2003;Sanmart ın et al. 2008; Mairal et al. 2015;Puppo et al. 2015). Moreover, a spatio-temporal pattern of colonization comparable to Canarina, showing Tenerife as the centre of dispersal events to adjacent islands in the last 1 Ma, can be found in the Canarian lineage of Cistus[0.33 ...
Geographical isolation by oceanic barriers and climatic stability has been postulated as some of the main factors driving diversification within volcanic archipelagos. However, few studies have focused on the effect that catastrophic volcanic events have had on patterns of within-island diversification in geological time. This study employed data from the chloroplast (cpDNA haplotypes) and the nuclear (AFLPs) genomes to examine patterns of genetic variation in Canarina canariensis, an iconic plant species associated with the endemic laurel forest of the Canary Islands. We found a strong geographic population structure, with a first divergence around 0.8 Ma that has Tenerife as its central axis and
divides Canarian populations into eastern and western clades. Genetic diversity was greatest in the geologically stable "paleo-islands" of Anaga, Teno and Roque del Conde; these areas were also inferred as the ancestral location of migrant alleles towards other disturbed areas within Tenerife or the nearby islands using a Bayesian approach to phylogeographic clustering. Oceanic barriers, in contrast, appear to have played a lesser role in structuring genetic variation, with intra-island levels of genetic diversity larger than those between islands. We argue that volcanic eruptions and landslides after the merging of the paleoislands 3.5 million years ago played key roles in generating genetic boundaries within Tenerife, with the paleo-islands acting as refugia against extinction, and as cradles and
sources of genetic diversity to other areas within the archipelago.
Micromeria silicii, a new species from St. Andrea (Svetac) and Biševo Islands of Dalmatia (Croatia) is described and illustrated. Previously, it was attributed to M. microphylla, but careful morphological investigation allowed to differentiate it from the latter. In order to emphasize the relationships with the other taxa currentelly attributed to M. microphylla group were examined also M. acropolitana, M. cypria, M. carpatha, M. hispida, M. sphaciotica and M. rodriguezii, which are distributed in various territories of the Mediterranean area. All these species were studied from the taxonomical, nomenclatural and chorological point of view, as well as a new icononography was provided for some of them. Besides, an analitical key for all investigated species is given too.
Premise of the study:
Oceanic islands offer the opportunity to understand evolutionary processes underlying rapid diversification. Along with geographic isolation and ecological shifts, a growing body of genomic evidence has suggested that hybridisation can play an important role in island evolution. Here we use genotyping-by-sequencing (GBS) to understand the roles of hybridisation, ecology, and geographic isolation in the radiation of Canary Island Descurainia (Brassicaceae).
Methods:
We carried out GBS for multiple individuals of all Canary Island species and two outgroups. Phylogenetic analyses of the GBS data were performed using both super-matrix and gene tree approaches and hybridisation events were examined using D-statistics and Approximate Bayesian Computation (ABC). Climatic data were analysed to examine the relationship between ecology and diversification.
Key results:
Analysis of the supermatrix dataset resulted in a fully resolved phylogeny. Species networks suggest a hybridisation event has occurred for D. gilva, with these results being supported by ABC analysis. Strong phylogenetic signals for temperature and precipitation indicate one major ecological shift within Canary Island Descurainia.
Conclusions:
Inter-island dispersal played a significant role in the diversification of Descurainia, with evidence of only one major shift in climate preferences. Despite weak reproductive barriers and the occurrence of hybrids, hybridisation appears to have played only a limited role in the diversification of the group, with a single instance detected. The results highlight the need to use phylogenetic network approaches that can simultaneously accommodate ILS and gene flow when studying groups prone to hybridisation; patterns that might otherwise be obscured in species trees. This article is protected by copyright. All rights reserved.
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Rafael G. Albaladejo, Sara Martín-Hernanz, J. Alfredo Reyes-Betancort, Arnoldo Santos-Guerra, María Olangua-Corral and Abelardo Aparicio Reconstruction of the spatio-temporal diversification and ecological niche evolution of Helianthemum (Cistaceae) in the Canary Islands using genotyping-by-sequencing data, Annals of Botany, Volume 127, Issue 5, 16 April 2021, Pages 597–611, https://doi.org/10.1093/aob/mcaa090
Island species are particularly vulnerable to extinction and decline due to a range of factors, including isolation, small population sizes, climate change, or the introduction of alien species. Given their high levels of biodiversity, the preservation and protection of island endemic species are fundamental to reducing the loss of global diversity. Therefore, species delimitation, description and identification are among the most important tasks in conservation biology. However, determining species boundaries in some cases can be challenging, especially in groups that have radiated recently, where frequently used molecular markers do not have enough discrimination power. Thus, it is important to look for new approaches with higher resolution. In the present study, we test the use of retrotransposon-based molecular markers to investigate the taxonomic status of five endemic and endangered Lotus species in the Canary Islands. Our analysis revealed that the five species conform different entities, in concordance with their morphological differences, and shown that the technique named inter-Primer Binding Site (iPBS) is a reliable molecular marker system that allows to discriminate among Lotus and has a potential value for taxonomy and conservation.
Inferring the processes responsible for the rich endemic diversity of oceanic island floras is important for our understanding of plant evolution and setting practical conservation priorities. This requires an accurate knowledge of phylogenetic relationships, which have often been difficult to resolve due to a lack of genetic variation.
We employed genotyping‐by‐sequencing (GBS) to investigate how geographical isolation, habitat shifts, and hybridisation have contributed to the evolution of diversity observed in Argyranthemum Webb (Asteraceae), the largest genus of flowering plants endemic to the Macaronesian archipelagos.
Species relationships were resolved, and biogeographical stochastic mapping identified intra‐island speciation as the most frequent biogeographic process underlying diversification, contrary to the prevailing view in Argyranthemum and the Canary Islands. D‐statistics revealed significant evidence of hybridisation between lineages co‐occurring on the same island, however there was little support for the hypothesis that hybridisation may be responsible for the occurrence of nonmonophyletic multi‐island endemic (MIE) species.
Geographic isolation, habitat shifts and hybridisation have all contributed to the diversification of Argyranthemum, with intra‐island speciation found to be more frequent than previously thought. Morphological convergence is also proposed to explain the occurrence of nonmonophyletic MIE species. This study reveals greater complexity in the evolutionary processes generating Macaronesian endemic diversity.
Micromeria Bentham (1829: sub t. 1282) (Lamiaceae) is a monophyletic and taxonomically intricate genus, represented by
nearly 70 species. These are distributed from the Macaronesian-Mediterranean region to southern Africa, India, and China
(Morales 1991b, Govaerts 1999, Harley et al. 2004, Bräuchler et al. 2005, 2008; Puppo & Meimberg 2015, Puppo et al.
2014, 2015).
Micromeria microphylla (d’Urville) Bentham (1834: 377) was described by d’Urville (1822: 327) as Thymus
microphyllus, and is spread in the Mediterranean region (mainland Italy, Sicily, Maltese Islands, Balearic Islands). This species
is a pubescent dwarf shrub 10–30 cm, with filiform, procumbent or ascending stems; leaves 3–6 × 2–4 mm, triangular-ovate
to elliptical, the upper sometimes narrowly elliptical, rounded or cuneate at base, acute, entire, flat, subsessile; verticillasters
with 1-6 usually erect-patent flowers; peduncles or pedicels ca ½ as long as subtending leaves; calyx 2.5–3.5 mm, patentpubescent, villous in throat; teeth ca ½ as long as tube, lanceolate-acuminate to-subulate, unequal; corolla 5–8 mm, purple
(Chater & Guinea 1972, Greuter et al. 1986, Mus & Rosselló 1987, Bolòs & Vigo 1996, Morales 1991a, 2010, Pignatti
2018).
Bräuchler (in Bräuchler et al. 2008: 393) had previously lectotypified the name Thymus microphyllus using a specimen
held at P (see below). However, the type designated by this author is ineffective, being contrary to Art. 9.12 (this and all
articles in the following refer to the ICN, Turland et al. 2018). The aim of this paper is revise the typification of the name.
Micromeria rodriguezii es una especie endémica de las Islas Baleares (Mediterráneo occidental). Una población de esta especie se ha encontrado en la provincia de Castellón (España), en el margen de un camino forestal. Se proporciona un estudio de la morfología de las plantas de esta población, así como su estado de conservación en la Comunidad Valenciana. Debido a que esta es la única población ibérica conocida hasta el momento, se debe elaborar un plan de manejo y conservación para garantizar su conservación.
Some aspects concerning the typification of the Linnaean name Satureja graeca, basionym of Micromeria graeca (Lamiaceae)
are discussed. This name had previously been “typified” by Siddiqi in 1985 from a specimen kept at LINN, and also
later by Morales in 1991 from another specimen preserved in the same Linnaean herbarium. However, it is not sure that these
specimens are part of Linnaeus’s original material so neither cannot be considered a lectotype. An illustration published by
Morison in 1699 and cited by Linnaeus in the protologue of Satureja graeca is designated as the lectotype of the name.
As found in other oceanic islands, the Canary Islands include a large number of single island endemic species, some of which form clades that are broadly distributed within the archipelago. The genus Micromeria (Lamiaceae), for instance, includes groups of morphologically similar but ecologically diverse species on each island, representing a great model to investigate niche shifts and adaptation within the Canary Archipelago. Previous attempts to reconstruct phylogenetic relationships within the genus did not lead to robust phylogenies, presumably due to introgression and/or incomplete lineage sorting. In this study, we use a newly developed RAD-sequencing method to improve phylogenetic resolution and to better understand relationships among the Canary Island endemic Micromeria. Overall, we obtained 3571 loci that were genotyped for a total of 46 individuals of Micromeria. Our data reconstructed a highly resolved phylogeny, and corroborated the latest species reclassification of the M. varia s.l. species complex, the taxonomically most complicated group within the genus. Furthermore, taxa occupying similar ecological conditions in different islands, were shown to be closely related. This is the case of taxa from the laurel forest from La Gomera and Gran Canaria, suggesting that the laurel forest likely worked as a filter, only allowing the establishment of colonizers already pre-adapted to these conditions. We also found introgression between these species so it is also possible that the genes that facilitated the adaptation to laurel forest were swapped between Gran Canaria and La Gomera. The observations obtained in this study also allowed us to explain the role of introgression in the origin of M. varia s.l. species complex.
Recently, the authors presented a proposal to conserve the names Micromeria varia Bentham (1834: 374) with a conserved type and M. hyssopifolia Webb & Berthelot (1844: 72) against Thymus ericifolius Roth (1800: 50) (Puppo et al. 2014a) to avoid disruption of current usage of these two well established names. This proposal, however, was not recommended by the Nomenclature Committee (Applequist 2016) and subsequently turned down by the General Committee (Wilson 2017). While regretting this decision, we are prepared to accept the taxonomic and nomenclatural implications.
Geological history of oceanic islands can have a profound effect on the evolutionary history of insular flora, especially in complex islands such as Tenerife in the Canary Islands. Tenerife results from the secondary connection of three paleo-islands by a central volcano, and other geological events that further shaped it. This geological history has been shown to influence the phylogenetic history of several taxa, including genus Micromeria (Lamiaceae). Screening 15 microsatellite markers in 289 individuals representing the eight species of Micromeria present in Tenerife, this study aims to assess the genetic diversity and structure of these species and its relation with the geological events on the island. In addition, we evaluate the extent of hybridization among species and discuss its influence on the speciation process. We found that the species restricted to the paleo-islands present lower levels of genetic diversity but the highest levels of genetic differentiation suggesting that their ranges might have contracted over time. The two most widespread species in the island, M. hyssopifolia and M. varia, present the highest genetic diversity levels and a genetic structure that seems correlated with the geological composition of the island. Samples from M. hyssopifolia from the oldest paleo-island, Adeje, appear as distinct while samples from M. varia segregate into two main clusters corresponding to the paleo-islands of Anaga and Teno. Evidence of hybridization and intraspecific migration between species was found. We argue that species boundaries would be retained despite hybridization in response to the habitat's specific conditions causing postzygotic isolation and preserving morphological differentiation.
Arlequin ver 3.0 is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework. Arlequin 3 introduces a completely new graphical interface written in C++, a more robust semantic analysis of input files, and two new methods: a Bayesian estimation of gametic phase from multi-locus genotypes, and an estimation of the parameters of an instantaneous spatial expansion from DNA sequence polymorphism. Arlequin can handle several data types like DNA sequences, microsatellite data, or standard multilocus genotypes. A Windows version of the software is freely available on http://cmpg.unibe.ch/software/arlequin3.
Premise of the study:
Geographic isolation, habitat shifts, and hybridization have contributed to the diversification of oceanic island floras. We investigated the contribution of these processes to the diversification of Pericallis, a genus endemic to Macaronesia.
Methods:
Data from the chloroplast psaI-accD and trnV-ndhC regions and the nuclear ribosomal internal transcribed spacer region (ITS) were sampled for multiple accessions of all taxa and used to establish phylogenetic hypotheses. Habitat preferences were optimized to investigate habitat shifts, and divergence times were estimated. Species nonmonophyly was investigated using Bayes factors.
Key results:
Much of the diversification in Pericallis has occurred recently, within the past 1.7 Ma. Three habitat shifts have occurred in the evolution of the genus. However, geographic isolation has played a greater role in its diversification. Novel allopatric patterns were revealed within some species, highlighting the significance of geographic isolation in the evolution of Pericallis. One species (P. appendiculata) that resolved as monophyletic in the ITS analysis was polyphyletic in the chloroplast analysis. Bayes factors provide strong support for the nonmonophyly of P. appendiculata haplotypes, and their phylogenetic placement suggests that ancient hybridization is responsible for the haplotype diversity observed.
Conclusions:
Multiple markers and extensive sampling provided new insights into the evolution of Pericallis. In contrast to previous studies, our results reveal a more significant role for allopatry than habitat shifts and new evidence for ancient hybridization in the evolution of Pericallis. Our study highlights the power of broad taxon sampling for unraveling diversity patterns and processes within oceanic island radiations.
The bioclimates, ombrotypes, thermotypes, bioclimatic belts, climatophilous vegetation seres and potential natural vegetation of Gran Canada were established and mapped. Due to salic substrates in the SW of the island, the potential natural vegetation map shows significant differences from the climatophilous seres map. Phytosociological tables of the terminal communities of each climatophilous sere are shown. The new association Pistacio lentisci - Oleetum cerasiformis is described.
Micromeria Benth. (Lamiaceae, Nepetoideae) is a very common genus in the Mediterranean region. To test the monophyly of the genus and to elucidate its phylogenetic placement within subtribe Menthinae (Dumort) Endl. of tribe Mentheae Dumort we performed parsimony analysis of trnK intron sequence data of 51 accessions representing 15 genera of Nepetoideae and two genera of subfamily Ajugoideae. Tree topology reveals a well-supported "core group" indicating four distinct lineages. The first one comprises three species of Satureja L. s.str., the second one includes taxa of the genus Clinopodium L. from both the Old and the New World, paraphyletic with respect to Monarda L. and two species of Micromeria section Pseudomelissa Benth. A third group contains all samples of the remaining Micromeria species. Within this monophyly, a western lineage including taxa from NW Africa, the Balearic, and the Canary Islands, is sister to an eastern lineage with species distributed from SE Asia to the western Mediterranean. In a further clade the genera Thymbra L., Thymus L., and Origanum L. are grouped together. Combined analysis using a reduced dataset of trnK/trnL-F sequences increased support for the infrageneric resolution within Micromeria. Based on the phylogenetic reconstructions there is evidence that the genus as currently circumscribed is polyphyletic. Results are discussed in the context of morphology, karyology, and biogeography, outlining the necessity of removing section Pseudomelissa from Micromeria.
No comprehensive revision of Micromeria is available and uncertainties about the taxonomy of the genus have lasted for a long time. Since the last synopsis many new data from both morphological and molecular genetic studies have been accumulated and, consequently, the number of accepted taxa and the delimitation of the genus have changed considerably. The authors provide a review of recent and unpublished research on the genus, a new circumscription and description of the genus and an updated distribution map. All published Micromeria names are listed with a reference to their current taxonomic position. Names of taxa currently placed in Micromeria are provided with type citations. A new combination, M. cristata subsp. kosaninii, is validated, along with the new name M. longipedunculata for the illegitimate M. parviflora of Reichenbach. The author standard abbreviation E. F. Chapm. is proposed for one of the authors of M. graeca subsp. cypria and 24 names are typified. Taxonomic problems needing special attention in future research are identified.
Sideritis L. subgenus Marrubiastrum (Lamiaceae) comprises 24 species of Macaronesian endemic perennials. The constituent taxa encompass a wide array of life forms that have exploited all ecological zones present in the Macaronesian archipelagos of Madeira and the Canary Islands. Though recently revised, an explicit phylogeny of the subgenus is still lacking. This group is especially intriguing because it exhibits the largest aneuploid series ever reported in oceanic island plants. The present study uses a chloroplast DNA restriction site analysis to elucidate the pattern of evolution within and among the islands. The insular taxa form a strongly supported monophyletic group, indicating a single colonization of Macaronesia. Monophyly of the sections is not supported. Integrating geographical and ecological distribution with the cpDNA phylogeny reveals a pattern of diversification within the islands consistent with adaptive radiation. Most other Macaronesian plant groups studied thus far have diversified by inter-island colonization between similar ecological zones. An analysis of chromosome number suggests a bimodal pattern of chromosomal change in the island subgenus, with one clade showing a decreasing aneuploid series and a second clade exhibiting aneuploid increase. The rate of change appears markedly amplified relative to that of the continental subgenus. This extreme level of chromosomal diversity stands in stark contrast to a general pattern of chromosomal stasis in island plants. Communicating Editor: John V. Freudenstein
The Macaronesian clade of Crassulaceae comprises four genera (Aichryson, Aeonium, Greenovia, and Monanthes) that are largely endemic to Macaronesia, a region encompassing the Azores, Madeira, and the Cape Verde, Canary, and Salvage Islands. The monophyly of this clade has been supported by recent family-level phylogenetic analyses; however, the relationships within the clade remain uncertain. To resolve relationships within the Macaronesian clade, we sequenced several chloroplast DNA regions (matK and the trnL-trnF and psbA-trnH spacer regions) and the nuclear rDNA ITS region. Parsimony analyses of separate ITS and cpDNA data sets recover three major clades, corresponding to Aichryson, the perennial species of Monanthes, and Aeonium (including Greenovia). Congruence tests revealed significant heterogeneity between the ITS and cpDNA data sets. Comparison of the topologies resulting from analyses of these separate data sets indicated five instances of incongruence between the ITS and cpDNA that may be the result of cpDNA capture events. Those five cpDNA sequences that appear to be the result of hybridization were removed, and a combined cpDNA/ITS data set was constructed and analyzed. Parsimony analyses of this combined data set again resolve three major clades that correspond to Aichryson, Monanthes, and Aeonium (including Greenovia); however, the combined analyses provide greater resolution and higher internal support than the analyses of the separate data sets. Given this estimate of phylogeny, the Macaronesian clade most likely evolved from herbaceous, continental ancestors; the woody habit evolved once in Aichryson tortuosum and again in the ancestor of the Aeonium clade. Combined analyses of cpDNA and ITS for a large sampling of the Macaronesian Crassulaceae also confirms recent conclusions that Aeonium originated in Macaronesia and not in Africa and that the east African species, A. leucoblepharum, is of recent origin and represents long-distance dispersal from Macaronesia to Africa. Communicating Editor: Paul Wilson
The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic, and statistical refinements permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is described for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position Specific Iterated BLAST (PSLBLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities.
Understanding the evolutionary history of living organisms is a central problem in biology. Until recently the ability to infer evolutionary relationships was limited by the amount of DNA sequence data available, but new DNA sequencing technologies have largely removed this limitation. As a result, DNA sequence data are readily available or obtainable for a wide spectrum of organisms, thus creating an unprecedented opportunity to explore evolutionary relationships broadly and deeply across the Tree of Life. Unfortunately, the algorithms used to infer evolutionary relationships are NP-hard, so the dramatic increase in available DNA sequence data has created a commensurate increase in the need for access to powerful computational resources. Local laptop or desktop machines are no longer viable for analysis of the larger data sets available today, and progress in the field relies upon access to large, scalable high-performance computing resources. This paper describes development of the CIPRES Science Gateway, a web portal designed to provide researchers with transparent access to the fastest available community codes for inference of phylogenetic relationships, and implementation of these codes on scalable computational resources. Meeting the needs of the community has included developing infrastructure to provide access, working with the community to improve existing community codes, developing infrastructure to insure the portal is scalable to the entire systematics community, and adopting strategies that make the project sustainable by the community. The CIPRES Science Gateway has allowed more than 1800 unique users to run jobs that required 2.5 million Service Units since its release in December 2009. (A Service Unit is a CPU-hour at unit priority).
The use of single copy nuclear markers is of increasing importance in plant phylogenetics. The generally higher level of variability compared to chloroplast DNA and the ability to use incongruence in a multilocus analysis to determine reticulation patterns makes these kinds of sequence based markers especially useful for species level investigations. However, the prevalence of gene duplication that results from the high frequency of polyploidization events during the evolution of higher plants can impede marker development especially for groups lacking model organisms. Here, we present the strategy and results of marker development for phylogenetic analysis in Micromeria, using publicly available DNA sequences and ESTs from related genera from Lamiaceae, subfamily Nepetoideae. By eliminating markers with signatures of duplication during four steps of marker development, we were able to select 19 primer pairs that resulted in orthologous products for all the species studied. This corresponds to 23% of the initial 84 primer pairs designed. Using an initial sampling of eight individuals, we tested the markers for support of phylogenetic hypotheses related to the evolution of Micromeria on the Canary Islands. While some hypotheses were supported by all markers, an east west split, with a closer relationship between the species of Tenerife and Madeira on one hand and the ones from Gran Canaria and the eastern islands on the other is supported by 12 markers but contradicted by the remaining seven. This indicates that reticulation and inter-island gene flow played a role in the evolution of Micromeria.
Computational evolutionary biology, statistical phylogenetics and coalescent-based population genetics are becoming increasingly
central to the analysis and understanding of molecular sequence data. We present the Bayesian Evolutionary Analysis by Sampling
Trees (BEAST) software package version 1.7, which implements a family of Markov chain Monte Carlo (MCMC) algorithms for Bayesian
phylogenetic inference, divergence time dating, coalescent analysis, phylogeography and related molecular evolutionary analyses.
This package includes an enhanced graphical user interface program called Bayesian Evolutionary Analysis Utility (BEAUti)
that enables access to advanced models for molecular sequence and phenotypic trait evolution that were previously available
to developers only. The package also provides new tools for visualizing and summarizing multispecies coalescent and phylogeographic
analyses. BEAUti and BEAST 1.7 are open source under the GNU lesser general public license and available at http://beast-mcmc.googlecode.com and http://beast.bio.ed.ac.uk
Analysis of sequence data from the internal transcribed spacers (ITS) and 5.8S region of nuclear ribosomal DNA show that Canarian and Madeiran brooms (Genisteae) of the genera Teline, Adenocarpus, and Genista are related to Mediterranean species and not to species from adjacent parts of Morocco. Each separate colonization of the islands has resulted in contrasting patterns of adaptation and radiation. The genus Teline is polyphyletic, with both groups (the "T. monspessulana group" and the "T. linifolia group") separately nested within Genista. Genista benehoavensis (La Palma) and G. tenera (Madeira) form, with G. tinctoria of Europe, a single clade characterized by vestigially arillate seeds. The Canarian species of Adenocarpus have almost identical sequence to the Mediterranean A. complicatus and are likely to be the result of island speciation after a very recent colonization event. This Canarian/Mediterranean A. complicatus group is sister to the afrotropical montane A. mannii which is probably derived from an earlier colonization from the Mediterranean, possibly via the Red Sea hills. The independent colonization and subsequent radiation of the two Teline groups in the Canary Islands make an interesting comparison: the phylogenies both show geographical structuring, each with a central and western island division of taxa. Within the "T. monspessulana group" there is some evidence that both continental and Madeiran taxa could be derived from the Canary Islands, although it is likely that near contemporaneous speciation occurred via rapid colonization of the mainland and islands. The finding of two groups within Teline also has implications for patterns of hybridization in those parts of the world where Teline species are invasive; in California members of the T. monspessulana group hybridize readily, but no hybrids have been recorded with T. linifolia which has been introduced in the same areas.
The 14 species of Crambe L. sect. Dendrocrambe DC. (Brassicaceae) form a monophyletic group endemic to the Canary and Madeira archipelagos. Both parsimony and maximum likelihood analyses of sequence data from the two internal transcribed spacer regions of nuclear ribosomal DNA were used to estimate phylogenetic relationships within this section. These analyses support the monophyly of three major clades. No clade is restricted to a single island, and therefore it appears that inter-island colonization has been the main avenue for speciation in these two archipelagos. The two species endemic to Fuerteventura (C. sventenii) and Madeira (C. fruticosa) comprise a clade, providing the first evidence for a floristic link between the Eastern Canary Islands and the archipelago of Madeira. Both maximum likelihood and weighted parsimony analyses show that this clade is sister to the two other clades, although bootstrap support for this relationship is weak. Parsimony optimizations of ecological zones and island distribution suggest a colonization route from the low-altitude areas of the lowland scrub toward the high-elevation areas of the laurel and pine forests. In addition, Tenerife is likely the ancestral island for species endemic to the five westernmost islands of Gran Canaria, La Gomera, El Hierro, La Palma, and Tenerife.
A molecular phylogenetic analysis of the Macaronesian endemic species of Convolvulus was undertaken using data from the nuclear ribosomal internal transcribed spacer (ITS) regions. The results of the analysis support two introductions into Macaronesia from distantly related clades within Convolvulus and a subsequent back-colonization to the continent from within one of the clades. Hypothesized relationships between Macaronesian species and New World taxa and between the Canarian endemic C. caput-medusae and the Moroccan C. trabutianus are refuted. Both Macaronesian clades are shown to have Mediterranean sister groups although one is predominantly western Mediterranean and the other predominantly eastern Mediterranean in distribution. The patterns of colonization into Macaronesia demonstrated by Convolvulus and also by other multiple colonizing genera conform to either a pattern of phylogenetic distinctiveness or a checkerboard distribution of island lineages. Both are consistent with the hypothesis that niche preemption is responsible for the limited number of colonizations into the region. A review of sister group relationships demonstrates that, in common with Convolvulus, most Macaronesian groups have sister groups distributed in the near-continent (i.e., western Mediterranean). Disjunct sister group relationships (including Eastern Mediterranean disjunctions) occur in only 18% of groups.
PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.
Motivation: DnaSP is a software package for a comprehensive analysis of DNA polymorphism data. Version 5 implements a number of new features
and analytical methods allowing extensive DNA polymorphism analyses on large datasets. Among other features, the newly implemented
methods allow for: (i) analyses on multiple data files; (ii) haplotype phasing; (iii) analyses on insertion/deletion polymorphism
data; (iv) visualizing sliding window results integrated with available genome annotations in the UCSC browser.
Availability: Freely available to academic users from: http://www.ub.edu/dnasp
Contact: jrozas{at}ub.edu
Arlequin ver 3.0 is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework. Arlequin 3 introduces a completely new graphical interface written in C++, a more robust semantic analysis of input files, and two new methods: a Bayesian estimation of gametic phase from multi-locus genotypes, and an estimation of the parameters of an instantaneous spatial expansion from DNA sequence polymorphism. Arlequin can handle several data types like DNA sequences, microsatellite data, or standard multi-locus genotypes. A Windows version of the software is freely available on http://cmpg.unibe.ch/software/arlequin3.
We present here a framework for the study of molecular variation within a single species. Information on DNA haplotype divergence is incorporated into an analysis of variance format, derived from a matrix of squared-distances among all pairs of haplotypes. This analysis of molecular variance (AMOVA) produces estimates of variance components and F-statistic analogs, designated here as phi-statistics, reflecting the correlation of haplotypic diversity at different levels of hierarchical subdivision. The method is flexible enough to accommodate several alternative input matrices, corresponding to different types of molecular data, as well as different types of evolutionary assumptions, without modifying the basic structure of the analysis. The significance of the variance components and phi-statistics is tested using a permutational approach, eliminating the normality assumption that is conventional for analysis of variance but inappropriate for molecular data. Application of AMOVA to human mitochondrial DNA haplotype data shows that population subdivisions are better resolved when some measure of molecular differences among haplotypes is introduced into the analysis. At the intraspecific level, however, the additional information provided by knowing the exact phylogenetic relations among haplotypes or by a nonlinear translation of restriction-site change into nucleotide diversity does not significantly modify the inferred population genetic structure. Monte Carlo studies show that site sampling does not fundamentally affect the significance of the molecular variance components. The AMOVA treatment is easily extended in several different directions and it constitutes a coherent and flexible framework for the statistical analysis of molecular data.
Numerous island-inhabiting species of predominantly herbaceous angiosperm genera are woody shrubs or trees. Such "insular woodiness" is strongly manifested in the genus Echium, in which the continental species of circummediterranean distribution are herbaceous, whereas endemic species of islands along the Atlantic coast of north Africa are woody perennial shrubs. The history of 37 Echium species was traced with 70 kb of noncoding DNA determined from both chloroplast and nuclear genomes. In all, 239 polymorphic positions with 137 informative sites, in addition to 27 informative indels, were found. Island-dwelling Echium species are shown to descend from herbaceous continental ancestors via a single island colonization event that occurred < 20 million years ago. Founding colonization appears to have taken place on the Canary Islands, from which the Madeira and Cape Verde archipelagos were invaded. Colonization of island habitats correlates with a recent origin of perennial woodiness from herbaceous habit and was furthermore accompanied by intense speciation, which brought forth remarkable diversity of forms among contemporary island endemics. We argue that the origin of insular woodiness involved response to counter-selection of inbreeding depression in founding island colonies.
The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons,
a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST
programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering
the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program
that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining
statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using
this matrix. The resulting Position-Specific Iterated BLAST (PSIBLAST) program runs at approximately the same speed per iteration
as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST
is used to uncover several new and interesting members of the BRCT superfamily.
The Gonosperminae (Asteraceae) are composed of three genera endemic to the Canary Islands (GONOSPERMUM: Less., and LUGOA: DC.) and southern Africa (INULANTHERA: Källersjö), and they are considered an example of a floristic link between these two regions. Phylogenetic analyses of ITS sequences reveal that the Canarian genera are not sister to INULANTHERA: and do not support the monophyly of the Gonosperminae. These results, coupled with previous phylogenetic studies of other groups, suggest that many of the putative biogeographic links between Macaronesia and southeast Africa need to be evaluated by rigorous phylogenetic analyses. INULANTHERA: forms part of the basal southern African radiation of the Anthemideae, and therefore it is closely related to other taxa from this region. Maximum likelihood and weighted parsimony analyses support a monophyletic group in the Canary Islands, that includes LUGOA:, Gonospermum, and three TANACETUM: species endemic to the island of Gran Canaria. Bootstrap support for the monophyly of this Canarian group is weak, and it collapses in the strict consensus tree based on unweighted parsimony. LUGOA: is nested within Gonospermum, and both interisland colonization among the western islands of La Gomera, El Hierro, La Palma and Tenerife, and radiation on the central island of Gran Canaria have been the major patterns of species diversification for these Canarian endemics.
Most evolutionary studies of oceanic islands have focused on the Pacific Ocean. There are very few examples from the Atlantic archipelagos, especially Macaronesia, despite their unusual combination of features, including a close proximity to the continent, a broad range of geological ages, and a biota linked to a source area that existed in the Mediterranean basin before the late Tertiary. A chloroplast DNA (cpDNA) restriction site analysis of Argyranthemum (Asteraceae: Anthemideae), the largest endemic genus of plants of any volcanic archipelago in the Atlantic Ocean, was performed to examine patterns of plant evolution in Macaronesia. cpDNA data indicated that Argyranthemum is a monophyletic group that has speciated recently. The cpDNA tree showed a weak correlation with the current sectional classification and insular distribution. Two major cpDNA lineages were identified. One was restricted to northern archipelagos--e.g., Madeira, Desertas, and Selvagens--and the second comprised taxa endemic to the southern archipelago--e.g., the Canary Islands. The two major radiations identified in the Canaries are correlated with distinct ecological habitats; one is restricted to ecological zones under the influence of the northeastern trade winds and the other to regions that are not affected by these winds. The patterns of phylogenetic relationships in Argyranthemum indicate that interisland colonization between similar ecological zones is the main mechanism for establishing founder populations. This phenomenon, combined with rapid radiation into distinct ecological zones and interspecific hybridization, is the primary explanation for species diversification.
MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types—e.g. morphological, nucleotide, and protein—and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters.
Availability: http://morphbank.ebc.uu.se/mrbayes
Contact: fredrik.ronquist@ebc.uu.se
*
To whom correspondence should be addressed.
Combined analysis of multiple phylogenetic data sets can reveal emergent character support that is not evident in separate analyses of individual data sets. Previous parsimony analyses have shown that this hidden support often accounts for a large percentage of the overall phylogenetic signal in cladistic studies. Here, reanalysis of a large comparative genomic data set for yeast (genus Saccharomyces) demonstrates that hidden support can be an important factor in maximum likelihood analyses of multiple data sets as well. Emergent signal in a concatenation of 106 genes was responsible for up to 64% of the likelihood support at a particular node (the difference in log likelihood scores between optimal topologies that included and excluded a supported clade). A grouping of four yeast species (S. cerevisiae, S. paradoxus, S. mikatae, and S. kudriavzevii) was robustly supported by combined analysis of all 106 genes, but separate analyses of individual genes suggested numerous conflicts. Forty-eight genes strictly contradicted S. cerevisiae + S. paradoxus + S. mikatae + S. kudriavzevii in separate analyses, but combined likelihood analyses that included up to 45 of the "wrong" data sets supported this group. Extensive hidden support also emerged in a combined likelihood analysis of 41 genes that each recovered the exact same topology in separate analyses of the individual genes. These results show that isolated analyses of individual data sets can mask congruence and distort interpretations of clade stability, even in strictly model-based phylogenetic methods. Consensus and supertree procedures that ignore hidden phylogenetic signals are, at best, incomplete.
A novel source of nuclear DNA information from random amplified polymorphisms (RAPD) and a wide-range mitochondrial DNA information (cytochrome b, cytochrome oxidase, and 12s rRNA sequence, RFLP from 4-base and 6-base recognition endonucleases) are used to reconstruct the population phylogeny of the western Canary Island lizard, Gallotia galloti, which, for geological reasons, has been subject to dispersal but not vicariance. Interpretation of DNA phylogenies in terms of colonization sequence indicates that G. galloti arose in Tenerife and dispersed westward in two independent pathways: north from north Tenerife to La Palma, and south from south Tenerife to Gomera to Hierro. The direction and timing of colonization by DNA divergence is entirely compatible with geological time and sequence of island origin.
A novel source of nuclear DNA information from random amplified polymorphisms (RAPD) and a wide-range mitochondrial DNA information (cytochrome b, cytochrome oxidase, and 12s rRNA sequence, RFLP from 4-base and 6-base recognition endonucleases) are used to reconstruct the population phylogeny of the western Canary Island lizard, Gallotia galloti, which, for geological reasons, has been subject to dispersal but not vicariance. Interpretation of DNA phylogenies in terms of colonization sequence indicates that G. galloti arose in Tenerife and dispersed westward in two independent pathways: north from north Tenerife to La Palma, and south from south Tenerife to Gomera to Hierro. The direction and timing of colonization by DNA divergence is entirely compatible with geological time and sequence of island origin.
AimUsing phylogenetic and morphometric approaches, our study aims to understand the diversification process of the two groups of Micromeria species in Tenerife: the species restricted to the palaeoislands, and the species widely distributed in the younger part of the island.LocationTenerife, Canary Islands.Methods
We calculated a calibrated phylogeny and a Neighbor-Net network based on eight nuclear loci from 37 samples: 22 of the 8 species currently recognized in Tenerife, and 15 of their closest relatives occurring in neighbouring islands and continental populations. We performed a principal components analysis (PCA) of 27 morphological characters from 54 specimens sampled from Tenerife.ResultsOur phylogeny showed that the species from Tenerife can be subdivided into three main clades: one composed of the species inhabiting the palaeoisland of Anaga (M. teneriffae, M. glomerata and M. rivas-martinezii); another composed of the species present in the palaeoisland of Teno (M. densiflora); and a third group that includes all the central species (M. hyssopifolia, M. varia, M. lachnophylla and M. lasiophylla). Morphometric analyses indicated two main groups corresponding to the palaeoisland species and the central ones.Main conclusionsOur study points to a relationship between the diversification in Micromeria and the geological history of Tenerife. We conclude that Micromeria first arrived in Anaga where it diversified, subsequently colonized Teno and from there occupied the central part, presumably after the formation of the Teide volcano. The species of Micromeria in Tenerife constitute an interesting example of how species diversification on oceanic islands can be shaped by the island's geological history, which probably contributed to the high levels of endemism on Tenerife.
Macaronesia is a biogeographical region comprising five Atlantic Oceanic archipelagos: the Azores, Madeira, Selvagen (Savage Islands), Canaries and Cape Verde. It has strong affinities with the Atlantic coast of the Iberian Peninsula and the north-western fringes of Africa. This paper re-evaluates the biogeographical history and relationships of Macaronesia in the light of geological evidence, which suggests that large and high islands may have been continuously available in the region for very much longer than is indicated by the maximum surface area of the oldest current island (27 Ma) – possibly for as long as 60 million years. We review this literature, attempting a sequential reconstruction of Palaeo-Macaronesia from 60 Ma to the present. We consider the implications of these geological dynamics for our understanding of the history of colonization of the present islands of Macaronesia. We also evaluate the role of these archipelagos as stepping stones and as both repositories of palaeo-endemic forms and crucibles of neo-endemic radiations of plant and animal groups. Our principal focus is on the laurel forest communities, long considered impoverished relicts of the Palaeotropical Tethyan flora. This account is therefore contextualized by reference to the long-term climatic and biogeographical history of Southern Europe and North Africa and by consideration of the implications of changes in land–sea configuration, climate and ocean circulation for Macaronesian biogeography. We go on to provide a synthesis of the more recent history of Macaronesian forests, which has involved a process of impoverishment of the native elements of the biota that has accelerated since human conquest of the islands. We comment briefly on these processes and on the contemporary status and varied conservation opportunities and threats facing these forests across the Macaronesian biogeographical region.
Argyranthemum coronopifolium (Willd.) C. J. Humphries, a rare endemic of Ten–erife in the Canary Islands, has a disjunct distribution which coincides with the two largest Tertiary basalt massives, Teno and Anaga. No morphological differentiation was found between the Teno and Anaga populations. The disjunction is believed to be due to barriers caused by lava flows in the intermediate region of North Tenerife. A. coronopifolium is shown to be hybridizing with the widespread A. frutescens (L.) Schultz Bip. in both Anaga and Teno. The hybridization was analysed phenetically by Wells' distance method and principal coordinate analysis. Geographical barriers between the species are shown to be broken down by road side immigration of A. frutescens into the area of A. coronopifolium, and the possibility of swamping is discussed. The trend of increasing hybridization is connected to the development of tourism in the Canary Islands.
Phylogenetic relationships among species of Aeonium were studied using morphological characters and chloroplast DNA RFLPs. Cladistic analysis of weighted morphological data indicates that the small, herbaceous and least woody species are basal in the genus. Chloroplast DNA data gave similar results, supporting the separation of the herbaceous or small, woody species from the large, hapaxanth rosettes, rosette trees, and branched subshrubs with yellow, white or red flowers as well as the only (herbaceous) species with axillary inflorescences. The relationships among the species descending from a polytomy that comprises all species of the genus as well as a polytomy which comprises 18 of the 26 species studied, are only very incompletely resolved, except for two monophyletic clades that contain the branched subshrubs with yellow flowers (A. sect. Aeonium) and the branched subshrubs and rosette trees with white or red flowers (A. sect. Leuconium), respectively. Cladistic analysis of the combined morphological and chloroplast DNA data improved resolution considerably. Four monophyletic clades are distinguished, each of which, except for three species, comprises only one of the five main growth-form types. Although Aeonium is generally regarded as an outstanding example of adaptive radiation, this mode of speciation seems to have been of minor significance in the evolution of the genus, because each growth-form apparently evolved only once. Instead, island speciation in the absence of major ecological shifts, is probably more important in the evolution of the genus.
Islands have long provided model systems in which ecologists and evolutionary biologists have develo-ped, tested and refined models for species diversity (Whittaker and Fernández-Palacios 2007). In two recent papers, Emerson and Kolm (2005a, b) have presented and discussed multiple regression analyses from two oceanic archipelagos, the Canaries and Hawaii, demon-strating for plants and arthropods that islands of greater species richness also have higher proportions of single island endemics (SIEs). They claim this as evidence that higher species richness of a taxon drives higher rates of diversification in that taxon, i.e. that ''diversity begets diversity''. Their analysis is interesting, but given that it is an analysis of proportions of SIEs not rate of species production, it is ultimately inconclusive as to mechan-isms leading to the relationship. It might tell us, as inferred by Emerson and Kolm (2005a, b), that high species richness creates the conditions for high rates of speciation through: 1) competitive interactions, 2) genetic drift due to small population sizes, and 3) greater community structural complexity. But it could also be that the relationship is a by-product of circum-stances not adequately captured in their analyses. Herein, we develop an alternative model, positing that the opportunities for speciation have a broadly predictable relationship to the life cycle of oceanic islands. We term our model the island immaturity Á speciation pulse (IISP) model of island evolution. Intrinsic to this model is that opportunity drives speciation rate and that opportunity is greatest at a relatively early stage of an island's life cycle, when intrinsic carrying capacity exceeds species richness by the greatest margin, i.e. when there is greatest ''vacant niche space''. As islands mature, both richness and endemism increase in tandem, but as islands decline in their old age, opportunities for speciation diminish, in tandem with a reduced carrying capacity (and reduced numbers of SIEs). Our argument is that the mechanisms identified by Emerson and Kolm (2005a, b), whilst each having a role in island evolution, make for an incomplete set of key island mechanisms and that in particular they neglect the likely importance of compe-titive release early in the life cycle of an island, and of the subsequent decline in carrying capacity, for the propor-tions of single island endemics (see Peck et al. 1999). In setting out the IISP model, we describe the observations on which it is based, and then examine what we expect in terms of critical rates, and emergent patterns of SIEs, comparing our model with that put forward by Emerson and Kolm (2005a, b). We illustrate our model with reference to data for the arthropods and plants of the Canary Islands (cf. Emerson and Kolm 2005a).
Aim MacArthur and Wilson’s dynamic equilibrium model of island biogeography provides a powerful framework for understanding the ecological processes acting on insular populations. However, their model is known to be less successful when applied to systems and processes operating on evolutionary and geological timescales. Here, we present a general dynamic model (GDM) of oceanic island biogeography that aims to provide a general explanation of biodiversity patterns through describing the relationships between fundamental biogeographical processes – speciation, immigration, extinction – through time and in relation to island ontogeny.
Location Analyses are presented for the Azores, Canaries, Galápagos, Marquesas and Hawaii.
Methods We develop a theoretical argument from first principles using a series of graphical models to convey key properties and mechanisms involved in the GDM. Based on the premises (1) that emergent properties of island biotas are a function of rates of immigration, speciation and extinction, (2) that evolutionary dynamics predominate in large, remote islands, and (3) that oceanic islands are relatively short‐lived landmasses showing a characteristic humped trend in carrying capacity (via island area, topographic variation, etc.) over their life span, we derive a series of predictions concerning biotic properties of oceanic islands. We test a subset of these predictions using regression analyses based largely on data sets for native species and single‐island endemics (SIEs) for particular taxa from each archipelago, and using maximum island age estimates from the literature. The empirical analyses test the power of a simple model of diversity derived from the GDM: the log(Area) + Time + Time ² model (ATT ² ), relative to other simpler time and area models, using several diversity metrics.
Results The ATT ² model provides a more satisfactory explanation than the alternative models evaluated (for example the standard diversity–area models) in that it fits a higher proportion of the data sets tested, although it is not always the most parsimonious solution.
Main conclusions The theoretical model developed herein is based on the key dynamic biological processes (migration, speciation, extinction) combined with a simple but general representation of the life cycle of oceanic islands, providing a framework for explaining patterns of biodiversity, endemism and diversification on a range of oceanic archipelagos. The properties and predictions derived from the model are shown to be broadly supported (1) by the empirical analyses presented, and (2) with reference to previous phylogenetic, ecological and geological studies.
New age determinations from Tenerife, together with those previously published (93 in all), provide a fairly comprehensive picture of the volcanic evolution of the island. The oldest volcanic series, with ages starting in the late Miocene, are formed mainly by basalts with some trachytes and phonolites which appear in Anaga, Teno and Roque del Conde massifs. In Anaga (NE), three volcanic cycles occurred: one older than 6.5 Ma, a second one between 6.5 and 4.5 Ma, with a possible gap between 5.4 and 4.8 Ma, and a late cycle around 3.6 Ma. In Teno (NW), after some undated units, the activity took place between 6.7 and 4.5 Ma, with two main series separated by a possible pause between 6.2 and 5.6 Ma. In the zone of Roque del Conde (S), the ages are scattered between 11.6 and 3.5 Ma. Between 3.3 and 1.9 Ma, the whole island underwent a period of volcanic quiescence and erosion.
Determining accurate phylogenetic relationships among the members of the woody Sonchus alliance presents challenges because of an insufficient level of molecular variation and the convergent evolution of similar morphological traits in island settings. To obtain a better resolved phylogeny and to test the potential role of hybridization and introgression, we sequenced all members of the alliance with multiple populations for the ITS of nrDNA and over 4000 base pairs of coding and noncoding regions of cpDNA. The cpDNA phylogeny is not well resolved in the core members of the alliance (i.e., subg. Dendrosonchus and genus Taeckholmia), but like the ITS tree, it has identified basal lineages of monotypic genera. The cpDNA data set was not significantly different from that of ITS, and subsequent combined analysis provided a better resolved and supported phylogeny within the alliance. The combined ML tree identified the same basal lineages, suggested nonmonophyly of Dendrosonchus and Taeckholmia, and did not support either Boulos' or Aldridge's infrasubgeneric classification system. Assessment of the role of hybridization and introgression was limited due to poor resolution in the cpDNA phylogeny. The combined analysis supports a Gran Canaria origin for the alliance and two subsequent long distance dispersal events to Madeira and Cape Verde islands.
It has been argued that niche pre-emption is not the only possible explanation for monophyly among Macaronesian endemic plants because (i) interspecific competition is diffuse, not species-specific, (ii) the radiations in question may not in fact be monophyletic, and (iii) later colonists may have hybridized with earlier ones, making a small and undetected contribution to the gene pool of lineages that appear to be monophyletic. The niche pre-emption mechanism does not, however, require species-specific competitive interactions. It merely proposes that the clade created by adaptive radiation will occupy more niche space than the original colonist could on its own. Members of the clade will then collectively inhibit establishment by new colonists more effectively than can a colonist that has not radiated. The monophyly of many larger radiations in the Macaronesian flora is well established and new studies tend to confirm this pattern. A few later-arriving colonists may have undetectably hybridized with earlier arrivals, but this is only a genetic interpretation of the essential idea behind pre-emption, i.e. that early arrivals so outnumber later colonists that the latter cannot establish. We do not therefore believe that hybridization provides an alternative explanation of why groups with multiple colonization failed to radiate in Macaronesia.
Although the subfamily Nepetoideae (Lamiaceae) is considered to be monophyletic, relationships between tribes, subtribes and genera within the subfamily are poorly understood as complex and possibly homoplasious morphological characters make taxa difficult to delimit. DNA sequence data from three regions (chloroplast: trnK intron; trnL-F; nuclear: ITS) in total including 278 accessions, representing 38 out of 40 genera of subtribe Menthinae and 11 outgroup genera, were used to reconstruct the evolutionary history, test previous hypotheses of classification, explain biogeographic patterns and elucidate character evolution. Using maximum parsimony (MP) and Bayesian analysis phylogenetic reconstructions based on nuclear and chloroplast sequence data were incongruent, consequently the data were analyzed separately.
Woody Sonchus and five related genera (Babcockia, Taeckholmia, Sventenia, Lactucosonchus, and Prenanthes) of the Macaronesian islands have been regarded as an outstanding example of adaptive radiation in angiosperms. Internal transcribed spacer region of the nuclear rDNA (ITS) sequences were used to demonstrate that, despite the extensive morphological and ecological diversity of the plants, the entire alliance in insular Macaronesia has a common origin. The sequence data place Lactucosonchus as sister group to the remainder of the alliance and also indicate that four related genera are in turn sister groups to subg. Dendrosonchus and Taeckholmia. This implies that the woody members of Sonchus were derived from an ancestor similar to allied genera now present on the Canary Islands. It is also evident that the alliance probably occurred in the Canary Islands during the late Miocene or early Pliocene. A rapid radiation of major lineages in the alliance is consistent with an unresolved polytomy near the base and low ITS sequence divergence. Increase of woodiness is concordant with other insular endemics and refutes the relictural nature of woody Sonchus in the Macaronesian islands.
Reconstructing phylogenies from intraspecific data (such as human mitochondrial DNA variation) is often a challenging task because of large sample sizes and small genetic distances between individuals. The resulting multitude of plausible trees is best expressed by a network which displays alternative potential evolutionary paths in the form of cycles. We present a method ("median joining" [MJ]) for constructing networks from recombination-free population data that combines features of Kruskal's algorithm for finding minimum spanning trees by favoring short connections, and Farris's maximum-parsimony (MP) heuristic algorithm, which sequentially adds new vertices called "median vectors", except that our MJ method does not resolve ties. The MJ method is hence closely related to the earlier approach of Foulds, Hendy, and Penny for estimating MP trees but can be adjusted to the level of homoplasy by setting a parameter epsilon. Unlike our earlier reduced median (RM) network method, MJ is applicable to multistate characters (e.g., amino acid sequences). An additional feature is the speed of the implemented algorithm: a sample of 800 worldwide mtDNA hypervariable segment I sequences requires less than 3 h on a Pentium 120 PC. The MJ method is demonstrated on a Tibetan mitochondrial DNA RFLP data set.
The prevalence of woody species in oceanic islands has attracted the attention of evolutionary biologists for more than a century. We used a phylogeny based on sequences of the internal-transcribed spacer region of nuclear ribosomal DNA to trace the evolution of woodiness in Pericallis (Asteraceae: Senecioneae), a genus endemic to the Macaronesian archipelagos of the Azores, Madeira, and Canaries. Our results show that woodiness in Pericallis originated independently at least twice in these islands, further weakening some previous hypotheses concerning the value of this character for tracing the continental ancestry of island endemics. The same data suggest that the origin of woodiness is correlated with ecological shifts from open to species-rich habitats and that the ancestor of Pericallis was an herbaceous species adapted to marginal habitats of the laurel forest. Our results also support Pericallis as closely related to New World genera of the tribe Senecioneae.
Recently, the Canary Islands have become a focus for studies of the colonization and the diversification of different organisms. Some authors have considered Canarian endemisms as relicts of Tertiary origin, but new molecular data suggest a general pattern of continental dispersion followed by in situ speciation. Recent phylogeographic studies are revealing variants of the simple stepping-stone colonization model that seems to hold for many Hawaiian groups. Many factors can generate deviations from such a pattern: the stochastic nature of colonization, competitive exclusion, phylogenetic constraints on adaptive evolution and extinction. An understanding of island colonization and diversification can best be developed from an ecosystem level synthesis as more data for the Canarian archipelago come to hand.
Current routine genotyping methods typically do not provide haplotype information, which is essential for many analyses of fine-scale molecular-genetics data. Haplotypes can be obtained, at considerable cost, experimentally or (partially) through genotyping of additional family members. Alternatively, a statistical method can be used to infer phase and to reconstruct haplotypes. We present a new statistical method, applicable to genotype data at linked loci from a population sample, that improves substantially on current algorithms; often, error rates are reduced by > 50%, relative to its nearest competitor. Furthermore, our algorithm performs well in absolute terms, suggesting that reconstructing haplotypes experimentally or by genotyping additional family members may be an inefficient use of resources.
By their very nature oceanic island ecosystems offer great opportunities for the study of evolution and have for a long time been recognized as natural laboratories for studying evolution owing to their discrete geographical nature and diversity of species and habitats. The development of molecular genetic methods for phylogenetic reconstruction has been a significant advance for evolutionary biologists, providing a tool for answering questions about the diversity among the flora and fauna on such islands. These questions relate to both the origin and causes of species diversity both within an archipelago and on individual islands. Within a phylogenetic framework one can answer fundamental questions such as whether ecologically and/or morphologically similar species on different islands are the result of island colonization or convergent evolution. Testing hypotheses about ages of the individual species groups or entire community assemblages is also possible within a phylogenetic framework. Evolutionary biologists and ecologists are increasingly turning to molecular phylogenetics for studying oceanic island plant and animal communities and it is important to review what has been attempted and achieved so far, with some cautionary notes about interpreting phylogeographical pattern on oceanic islands.
The phylogeny and population history of Meladema diving beetles (Coleoptera, Dytiscidae) were examined using mitochondrial DNA sequence from 16S ribosomal RNA and cytochrome oxidase I genes in 51 individuals from 22 populations of the three extant species (M. imbricata endemic to the western Canary Islands, M. lanio endemic to Madeira and M. coriacea widespread in the Western Mediterranean and on the western Canaries), using a combination of phylogenetic and nested clade analyses. Four main lineages are observed within Meladema, representing the three recognized species plus Corsican populations of M. coriacea. Phylogenetic analyses demonstrate the sister relationship of the two Atlantic Island taxa, and suggest the possible paraphyly of M. coriacea. A molecular clock approach reveals that speciation within the genus occurred in the Early Pleistocene, indicating that the Atlantic Island endemics are not Tertiary relict taxa as had been proposed previously. Our results point to past population bottlenecks in all four lineages, with recent (Late-Middle Pleistocene) range expansion in non-Corsican M. coriacea and M. imbricata. Within the Canary Islands, M. imbricata seems to have independently colonized La Gomera and La Palma from Tenerife (although a colonization of La Palma from La Gomera cannot be discarded), and M. coriacea has independently colonized Tenerife and Gran Canaria from separate mainland lineages. In the Mediterranean basin this species apparently colonized Corsica on a single occasion, relatively early in its evolutionary history (Early Pleistocene), and has colonized Mallorca recently on multiple occasions. On the only island where M. coriacea and M. imbricata are broadly sympatric (Tenerife), we report evidence of bidirectional hybridization between the two species.
Nuclear DNA contents for 104 Macaronesian angiosperms, with particular attention on Canary Islands endemics, were analysed using propidium iodide flow cytometry. Prime estimates for more than one-sixth of the whole Canarian endemic flora (including representatives of 11 endemic genera) were obtained. The resulting 1C DNA values ranged from 0.19 to 7.21 pg for Descurainia bourgeauana and Argyranthemum frutescens, respectively (about 38-fold difference). The majority of species, however, possessed (very) small genomes, with C-values <1.6 pg. The tendency towards small nuclear DNA contents and genome sizes was confirmed by comparing average values for Macaronesian and non-Macaronesian representatives of individual families, genera and major phylogenetic lineages. Our data support the hypothesis that the insular selection pressures in Macaronesia favour small C-values and genome sizes. Both positive and negative correlations between infrageneric nuclear DNA amount variation and environmental conditions on Tenerife were also found in several genera.
Molecular phylogenetic analyses of Macaronesian Lotus and related genera were conducted to assess their biogeographic history and taxonomy. Macaronesian Lotus, which are typically classified within one of two subgenera, Lotus subgenus Pedrosia or L. subg. Rhyncholotus, are diagnosed by the presence of a forked or toothed style and differences in corolla morphology. Maximum parsimony and Bayesian analyses of internal transcribed spacer sequences identify a well-supported northwest African-Cape Verde Island clade that includes all members of Lotus subgenus Pedrosia+L. subg. Rhyncholotus. There is modest support for two independently nested clades containing the Canary Island species and two non-Canarian species, Lotus assakensis from Africa and Lotus azoricus endemic to the Azores. Biogeographic reconstruction based on a parsimony topology unequivocally identifies an African origin for the Canary Island group with subsequent back dispersal to the African continent and a single dispersal event to the Azores. A phylogeographic assessment of colonization and diversification patterns suggests that geographic isolation via interisland colonization of ecologically similar habitats is the primary mode of species diversification in Canary Island Lotus.
Abstract A molecular phylogenetic study of Bystropogon L'Her. (Lamiaceae) is presented. We performed a cladistic analysis of nucleotide sequences of the internal transcribed spacers (ITS), of the nuclear ribosomal DNA, and of the trnL gene and trnL-trnF intergenic spacer of the chloroplast DNA. Bystropogon odoratissimus is the only species endemic to the Canary Islands that occurs in the three palaeo-islands of Tenerife. This species is not part of an early diverging lineage of Bystropogon and we suggest that it has a recent origin. This phylogenetic pattern is followed by most of the species endemic to the palaeo-islands of Tenerife. The two sections currently recognized in Bystropogon form two monophyletic groups. Taxa belonging to the section Bystropogon clade show interisland colonization limited to the Canary Islands with ecological shifts among three ecological zones. Taxa from the section Canariense clade show interisland colonization both within the Canary Islands and between the Canary Islands and Madeira. Speciation events within this clade are mostly limited to the laurel forest. The genus has followed a colonization route from the Canaries towards Madeira. This route has also been followed by at least five other plant genera with species endemic to Macaronesia. Major incongruences were found between the current infrasectional classification and the molecular phylogeny, because the varieties of Bystropogon origanifolius and Bystropogon canariensis do not form two monophyletic groups. The widespread B. origanifolius appears as progenitor of the other species in section Bystropogon with a more restricted distribution.
The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known that more complex evolutionary scenarios are poorly described by such models. Further, even when evolution proceeds in a tree-like manner, analysis of the data may not be best served by using methods that enforce a tree structure but rather by a richer visualization of the data to evaluate its properties, at least as an essential first step. Thus, phylogenetic networks should be employed when reticulate events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved, and, even in the absence of such events, phylogenetic networks have a useful role to play. This article reviews the terminology used for phylogenetic networks and covers both split networks and reticulate networks, how they are defined, and how they can be interpreted. Additionally, the article outlines the beginnings of a comprehensive statistical framework for applying split network methods. We show how split networks can represent confidence sets of trees and introduce a conservative statistical test for whether the conflicting signal in a network is treelike. Finally, this article describes a new program, SplitsTree4, an interactive and comprehensive tool for inferring different types of phylogenetic networks from sequences, distances, and trees.