Comparative transcriptomics and gene expression divergence associated with homoploid hybrid speciation in Argyranthemum.

Ecological isolation is increasingly thought to play an important role in speciation, especially for the origin and reproductive isolation of homoploid hybrid species. However, the extent to which divergent and/or transgressive gene expression changes are involved in speciation is not well studied. In this study, we employ comparative transcriptomics to investigate gene expression changes associated with the origin and evolution of two homoploid hybrid plant species, Argyranthemum sundingii and A. lemsii (Asteraceae). As there is no standard methodology for comparative transcriptomics, we examined five different pipelines for data assembly and analysing gene expression across the four species (two hybrid and two parental). We note biases and problems with all pipelines, and the approach used affected the biological interpretation of the data. Using the approach that we found to be optimal, we identify transcripts showing DE between the parental taxa and between the homoploid hybrid species and their parents; in several cases, putative functions of these DE transcripts have a plausible role in ecological adaptation and could be the cause or consequence of ecological speciation. Although independently derived, the homoploid hybrid species have converged on similar expression phenotypes, likely due to adaptation to similar habitats.

Geographical isolation, habitat shifts and hybridisation in the diversification of the Macaronesian endemic genus Argyranthemum (Asteraceae).

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.

Independent homoploid hybrid speciation events in the Macaronesian endemic genus Argyranthemum.

Well-characterized examples of homoploid hybrid speciation (HHS) are rare in nature, yet they offer the potential to study a number of evolutionary processes. In this study, we investigate putative homoploid hybrid species in the genus Argyranthemum (Asteraceae), a group of plants endemic to the Macaronesian archipelagos of the North Atlantic Ocean. We specifically address a number of knowledge gaps surrounding the origin(s) of A. sundingii and A. lemsii, which are thought to be derived from the same parental cross. Comparisons of leaf morphology suggest that A. sundingii and A. lemsii are distinct from their parental progenitors and distinguishable from each other based on leaf area. Ecological niche modelling (ENM) demonstrated that the homoploid hybrid species occupy novel habitats that are intermediate relative to the parental species. Nuclear simple sequence repeat markers (SSRs) and single nucleotide polymorphism (SNP) data indicate that the homoploid hybrid species are distinct from the parental taxa, while population-level sampling of chloroplast SSRs and approximate Bayesian computation show that A. sundingii and A. lemsii are independently derived from the same parental cross. As such, Argyranthemum represents an example of independent homoploid hybrid speciation events with evidence of divergence in leaf morphology and adaptation to novel intermediate habitats. On oceanic islands, which are often typified by steep ecological gradients and inhabited by recently derived species with weak reproductive barriers, multiple HHS events from the same parental cross are not only possible but also likely to have played a more important role in oceanic island radiations than we currently think.

Transcriptome sequencing and simple sequence repeat marker development for three Macaronesian endemic plant species.

PREMISE OF THE STUDY: Oceanic islands offer unparalleled opportunities to investigate evolutionary processes such as adaptation and speciation. However, few genomic resources are available for oceanic island endemics. In this study, we publish transcriptome sequences from three Macaronesian endemic plant species (Argyranthemum broussonetii [Asteraceae], Descurainia bourgaeana [Brassicaceae], and Echium wildpretii [Boraginaceae]) that are representative of lineages that have radiated in the region. In addition, the utility of transcriptome data for marker development is demonstrated. METHODS AND RESULTS: Transcriptomes from the three plant species were sequenced, assembled, and annotated. Between 1972 and 2282 simple sequence repeats (SSRs) were identified for each taxon. Primers were designed and tested for 30 of the candidate SSRs identified in Argyranthemum, of which 12 amplified well across three species and eight were polymorphic. CONCLUSIONS: We demonstrate here that a single transcriptome sequence is sufficient to identify hundreds of polymorphic SSR markers. The SSRs are applicable to a wide range of questions relating to the evolution of island lineages.

How the temperate world was colonised by bindweeds: biogeography of the Convolvuleae (Convolvulaceae).

BACKGROUND: At a global scale, the temperate zone is highly fragmented both between and within hemispheres. This paper aims to investigate how the world's disjunct temperate zones have been colonised by the pan-temperate plant group Convolvuleae, sampling 148 of the c. 225 known species. We specifically determine the number and timing of amphitropical and transoceanic disjunctions, investigate the extent to which disjunctions in Convolvuleae are spatio-temporally congruent with those in other temperate plant groups and determine the impact of long-distance dispersal events on diversification rates. RESULTS: Eight major disjunctions are observed in Convolvuleae: two Northern Hemisphere, two Southern Hemisphere and four amphitropical. Diversity in the Southern Hemisphere is largely the result of a single colonisation of Africa 3.1-6.4 Ma, and subsequent dispersals from Africa to both Australasia and South America. Speciation rates within this monophyletic, largely Southern Hemisphere group (1.38 species Myr(-1)) are found to be over twice those of the tribe as a whole (0.64 species Myr(-1)). Increased speciation rates are also observed in Calystegia (1.65 species Myr(-1)). CONCLUSIONS: The Convolvuleae has colonised every continent of the world with a temperate biome in c. 18 Myr and eight major range disjunctions underlie this broad distribution. In keeping with other temperate lineages exhibiting disjunct distributions, long-distance dispersal is inferred as the main process explaining the patterns observed although for one American-Eurasian disjunction we cannot exclude vicariance. The colonisation of the temperate zones of the three southern continents within the last c. 4 Myr is likely to have stimulated high rates of diversification recovered in this group, with lineage accumulation rates comparable to those reported for adaptive radiations.

Are there any widespread endemic flowering plant species in Macaronesia? Phylogeography of Ranunculus cortusifolius.

PREMISE OF THE STUDY: Oceanic island endemics typically exhibit very restricted distributions. In Macaronesia, only one endemic angiosperm species, Ranunculus cortusifolius, has a distribution spanning the archipelagos of the Azores, Madeira, and Canaries. Earlier work suggested possible differences between archipelagos and the multiple origins of the species. This paper tests the hypothesis that R. cortusifolius is a single widespread Macaronesian endemic species with a single origin. METHODS: Chloroplast (matK-trnK, psbJ-petA) and ITS sequences were generated from across the distribution of R. cortusifolius. Relationships were investigated using Bayesian inference and divergence times estimated using BEAST. Infraspecific variation was investigated using statistical parsimony. The general mixed Yule-coalescent model (GMYC) was further used to identify putative species boundaries based on maternally inherited plastid data. KEY RESULTS: The hypothesis of multiple independent origins of R. cortusifolius is rejected. Divergence of the R. cortusifolius lineage from a western Mediterranean sister group in the late Miocene is inferred. Distinct genotypes were resolved within R. cortusifolius that are endemic to the Azores, Madeira, and the Canaries. Four to five putative species were delimited by different versions of the GMYC model. CONCLUSION: Ranunculus cortusifolius is the result of a single colonization of Macaronesia. The large distances between archipelagos have been effective barriers to dispersal, promoting allopatric diversification at the molecular level with diversification also evident within the Canaries. Isolation has not been accompanied by marked morphological diversification, which may be explained by the typical association of R. cortusifolius with stable and climatically buffered laurel forest communities.

A foundation monograph of Convolvulus L. (Convolvulaceae).

A global revision of Convolvulus L. is presented, Calystegia R.Br. being excluded on pragmatic grounds. One hundred and ninety species are recognised with the greatest diversity in the Irano-Turanian region. All recognised species are described and the majority are illustrated. Distribution details, keys to species identification and taxonomic notes are provided. Four new species, Convolvulusaustroafricanus J.R.I.Wood & R.W.Scotland, sp. nov., Convolvulusiranicus J.R.I.Wood & R.W.Scotland, sp. nov., Convolvuluspeninsularis J.R.I.Wood & R.W.Scotland, sp. nov. and Convolvulusxanthopotamicus J.R.I.Wood & R.W.Scotland, sp. nov., one new subspecies Convolvuluschinensissubsp.triangularis J.R.I.Wood & R.W.Scotland, subsp. nov., and two new varieties Convolvulusequitansvar.lindheimeri J.R.I.Wood & R.W.Scotland, var. nov., Convolvulusglomeratusvar.sachalitarum J.R.I.Wood & R.W.Scotland, var. nov. are described. Convolvulusincisodentatus J.R.I.Wood & R.W.Scotland, nom. nov., is provided as a replacement name for the illegitimate Convolvulusincisus Choisy. Several species treated as synonyms of other species in recent publications are reinstated including Convolvuluschinensis Ker-Gawl., Convolvulusspinifer M.Popov., Convolvulusrandii Rendle and Convolvulusaschersonii Engl. Ten taxa are given new status and recognised at new ranks: Convolvulusnamaquensis (Schltr. ex. A.Meeuse) J.R.I.Wood & R.W.Scotland, stat. nov., Convolvulushermanniaesubsp.erosus (Desr.) J.R.I.Wood & R.W.Scotland, stat. nov., Convolvuluscrenatifoliussubsp.montevidensis (Spreng.) J.R.I.Wood & R.W.Scotland, stat. nov., Convolvulusfruticulosussubsp.glandulosus (Webb) J.R.I.Wood & R.W.Scotland, stat. nov., Convolvuluscapituliferussubsp.foliaceus (Verdc.) J.R.I.Wood & R.W.Scotland, stat. nov., Convolvulushystrixsubsp.ruspolii (Dammer ex Hallier f.) J.R.I.Wood & R.W.Scotland, stat. nov., Convolvulushystrixsubsp.inermis (Chiov.) J.R.I.Wood & R.W.Scotland, stat. nov., Convolvulusrottlerianussubsp.stocksii (Boiss.) J.R.I.Wood & R.W.Scotland, comb. et stat. nov., Convolvuluscalvertiisubsp.ruprechtii (Boiss.) J.R.I.Wood & R.W.Scotland, stat. nov., Convolvuluscephalopodussubsp.bushiricus (Bornm.) J.R.I.Wood & R.W.Scotland, stat. nov. The status of various infraspecific taxa is clarified and numerous taxa are lectotypified. This account represents a new initiative in terms of taxonomic monography, being an attempt to bring together the global approach of the traditional monograph with the more pragmatic and identification-focussed approach of most current floras while at the same time being informed by insights from molecular systematics.

Speciation via floral heterochrony and presumed mycorrhizal host switching of endemic butterfly orchids on the Azorean archipelago.

• Premise of the study: Most orchid species native to the Macaronesian islands reflect immigration from western Europe or North Africa followed by anagenesis. The only putative exception is the butterfly orchids (Platanthera) of the Azores, where three species apparently reflect at least one cladogenetic speciation event. This multidisciplinary study explores the origin, speciation, phenotypic, and genotypic cohesion of these Azorean species and their mainland relatives.• Methods: Plants of Platanthera from 30 localities spanning all nine Azorean islands were compared with those of four continental European relatives for 38 morphometric characters; substantial subsets were also analyzed for plastid microsatellites, and for nrITS of both the orchids and their mycorrhizae.• Key results: Although the three Azorean and four mainland species are all readily distinguished morphometrically using several floral characters, and hybridization appears rare, divergence in ITS and especially plastid sequences is small. Despite occupying similar laurisilva habitats, the Azorean species differ radically in the identities and diversity of their mycorrhizal partners; specialism apparently increases rarity.• Conclusions: Although morphological evidence suggests two invasions of the islands from NW Africa and/or SW Europe, ITS data imply only one. As the molecular data are unable to distinguish among the potential mainland ancestors, two scenarios of relationship are explored that imply different ancestors. Both scenarios require both anagenetic and cladogenetic speciation events, involving homoplastic shifts in overall flower size and (often substantial) changes in the relative dimensions of individual floral organs. Limited genotypic divergence among the three species compared with greater phenotypic divergence suggests comparatively recent speciation. Mycorrhizae may be the most critical factor dictating the respective ecological tolerances, and thus the relative frequencies, of these species. The recent IUCN Red-List amalgamation of Azorean Platanthera taxa into a single species urgently requires reappraisal, as P. micrantha is an excellent indicator species of seminatural laurisilva forest and P. azorica is arguably Europe's rarest orchid.

Allopatric diversification, multiple habitat shifts, and hybridization in the evolution of Pericallis (Asteraceae), a Macaronesian endemic genus.

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.

Cardamine hirsuta: a versatile genetic system for comparative studies.

A major goal in biology is to identify the genetic basis for phenotypic diversity. This goal underpins research in areas as diverse as evolutionary biology, plant breeding and human genetics. A limitation for this research is no longer the availability of sequence information but the development of functional genetic tools to understand the link between changes in sequence and phenotype. Here we describe Cardamine hirsuta, a close relative of the reference plant Arabidopsis thaliana, as an experimental system in which genetic and transgenic approaches can be deployed effectively for comparative studies. We present high-resolution genetic and cytogenetic maps for C. hirsuta and show that the genome structure of C. hirsuta closely resembles the eight chromosomes of the ancestral crucifer karyotype and provides a good reference point for comparative genome studies across the Brassicaceae. We compared morphological and physiological traits between C. hirsuta and A. thaliana and analysed natural variation in stamen number in which lateral stamen loss is a species characteristic of C. hirsuta. We constructed a set of recombinant inbred lines and detected eight quantitative trait loci that can explain stamen number variation in this population. We found clear phylogeographic structure to the genetic variation in C. hirsuta, thus providing a context within which to address questions about evolutionary changes that link genotype with phenotype and the environment.

Molecular phylogenetics and morphological evolution of St. John's wort (Hypericum; Hypericaceae).

Phylogenetic hypotheses for the large cosmopolitan genus Hypericum (St. John's wort) have previously been based on morphology, and molecular studies have thus far included only a few species. In this study, we used 360 sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (nrDNA) for 206 species representing Hypericum (incl. Triadenum and Thornea) and three other genera of Hypericaceae to generate an explicit phylogenetic hypothesis for the genus using parsimony and model-based methods. The results indicate that the small genus Triadenum is nested in a clade within Hypericum containing most of the New World species. Sister to Hypericum is Thornea from Central America. Within Hypericum, three large clades and two smaller grades were found; these are based on their general morphology, especially characters used previously in taxonomy of the genus. Relative to the most recent classification, around 60% of the sections of Hypericum were monophyletic. We used a Bayesian approach to reconstruct ancestral states of selected morphological characters, which resulted in recognition of characters that support major clades within the genus and a revised interpretation of morphological evolution in Hypericum. The shrubby habit represents the plesiomorphic state from which herbs evolved several times. Arborescent species have radiated convergently in high-elevation habitats in tropical Africa and South America.

Systematics, biogeography, and character evolution of the legume tribe Fabeae with special focus on the middle-Atlantic island lineages.

BACKGROUND: Tribe Fabeae comprises about 380 legume species, including some of the most ancient and important crops like lentil, pea, and broad bean. Breeding efforts in legume crops rely on a detailed knowledge of closest wild relatives and geographic origin. Relationships within the tribe, however, are incompletely known and previous molecular results conflicted with the traditional morphology-based classification. Here we analyse the systematics, biogeography, and character evolution in the tribe based on plastid and nuclear DNA sequences. RESULTS: Phylogenetic analyses including c. 70% of the species in the tribe show that the genera Vicia and Lathyrus in their current circumscription are not monophyletic: Pisum and Vavilovia are nested in Lathyrus, the genus Lens is nested in Vicia. A small, well-supported clade including Vicia hirsuta, V. sylvatica, and some Mediterranean endemics, is the sister group to all remaining species in the tribe. Fabeae originated in the East Mediterranean region in the Miocene (23-16 million years ago (Ma)) and spread at least 39 times into Eurasia, seven times to the Americas, twice to tropical Africa and four times to Macaronesia. Broad bean (V. faba) and its sister V. paucijuga originated in Asia and might be sister to V. oroboides. Lentil (Lens culinaris ssp. culinaris) is of Mediterranean origin and together with eight very close relatives forms a clade that is nested in the core Vicia, where it evolved c. 14 Ma. The Pisum clade is nested in Lathyrus in a grade with the Mediterranean L. gloeosperma, L. neurolobus, and L. nissolia. The extinct Azorean endemic V. dennesiana belongs in section Cracca and is nested among Mediterranean species. According to our ancestral character state reconstruction results, ancestors of Fabeae had a basic chromosome number of 2n=14, an annual life form, and evenly hairy, dorsiventrally compressed styles. CONCLUSIONS: Fabeae evolved in the Eastern Mediterranean in the middle Miocene and spread from there across Eurasia, into Tropical Africa, and at least seven times to the Americas. The middle-Atlantic islands were colonized four times but apparently did not serve as stepping-stones for Atlantic crossings. Long-distance dispersal events are relatively common in Fabeae (seven per ten million years). Current generic and infrageneric circumscriptions in Fabeae do not reflect monophyletic groups and should be revised. Suggestions for generic level delimitation are offered.

Big hitting collectors make massive and disproportionate contribution to the discovery of plant species.

Discovering biological diversity is a fundamental goal--made urgent by the alarmingly high rate of extinction. We have compiled information from more than 100,000 type specimens to quantify the role of collectors in the discovery of plant diversity. Our results show that more than half of all type specimens were collected by less than 2 per cent of collectors. This highly skewed pattern has persisted through time. We demonstrate that a number of attributes are associated with prolific plant collectors: a long career with increasing productivity and experience in several countries and plant families. These results imply that funding a small number of expert plant collectors in the right geographical locations should be an important element in any effective strategy to find undiscovered plant species and complete the inventory of the world flora.

Herbaria are a major frontier for species discovery.

Despite the importance of species discovery, the processes including collecting, recognizing, and describing new species are poorly understood. Data are presented for flowering plants, measuring quantitatively the lag between the date a specimen of a new species was collected for the first time and when it was subsequently described and published. The data from our sample of new species published between 1970 and 2010 show that only 16% were described within five years of being collected for the first time. The description of the remaining 84% involved much older specimens, with nearly one-quarter of new species descriptions involving specimens >50 y old. Extrapolation of these results suggest that, of the estimated 70,000 species still to be described, more than half already have been collected and are stored in herbaria. Effort, funding, and research focus should, therefore, be directed as much to examining extant herbarium material as collecting new material in the field.

The ghosts of Gondwana and Laurasia in modern liverwort distributions.

Recent advances in phylogenetics and, in particular, molecular dating, indicate that transoceanic dispersal has played an important role in shaping plant and animal distributions, obscuring any effect of tectonic history. Taxonomic sampling in biogeographic studies is, however, systematically biased towards vertebrates and higher plants and the possibility remains that a much stronger signature of ancient vicariance might be evident among other organisms, particularly among basal land plants. Here, an explicit Bayesian model-based approach was used to investigate global-scale biogeographic patterns among liverwort genera and to determine whether the patterns identified are consistent with the expectations of vicariance or dispersal scenarios. The distribution of each genus was mapped onto the phylograms describing the floristic affinities among areas in order to define the synapomorphic transitions supporting the observed groupings. The probabilities of change in a branch were calculated by implementing the Markov model of BayesTraits. The consistent ambiguity in ancestral state reconstructions returned by the unconstrained, two-rate model indicated that the overall signal in the data was weak, leading us to test the performance of competing, explicit models. The analyses resolved clades of geographic areas that are mostly consistent with the kingdoms traditionally identified for plants and animals, but with strikingly lower rates of endemism. The major split observed in the phylograms is into almost entirely Laurasian and Gondwanan clades. Other patterns recovered by the analyses, including Wallace's line and the South Atlantic Disjunction, have also traditionally been interpreted in terms of vicariance. These observations contrast with the idea that, in spore-dispersed organisms like bryophytes and pteridophytes, dispersal obscures evidence of vicariance. However, some discrepancies between the liverwort trees and expectations from a continental drift scenario were observed, such as the sister-group relationship of the Australian and New Zealand floras, which is supported by the co-occurrence of many genera, often endemic to these two areas. Together with an interpretation of the results within a phylogenetic context, our analyses suggest that patterns, which are at first sight consistent with an ancient vicariance hypothesis, may, in fact, conceal a complex mixture of relictual distributions and more recent, asymmetrical dispersal events. Our results provide a framework for testing specific evolutionary hypotheses concerning the extremely low levels of endemism in bryophytes and in particular, the significance of dispersal and cryptic diversification.

Phylogenetic relationships among Strobilanthes s.l. (Acanthaceae): evidence from ITS nrDNA, trnL-F cpDNA, and morphology.

Chloroplast trnL-F sequence data, nuclear ribosomal internal transcribed spacer (ITS) sequence data, and morphology were used to analyze phylogenetic relationships among members of the subtribe Strobilanthinae. Parsimony and maximum likelihood analyses of trnL-F indicate that the Strobilanthinae are a monophyletic group. While parsimony analysis of ITS recovers a nonmonophyletic subtribe, maximum likelihood analysis of ITS corroborates results from trnL-F and suggests that systematic error is impacting on ITS parsimony analysis. A combined ITS and trnL-F analysis strengthens the signal and also recovers a monophyletic subtribe. All analyses indicate that Hemigraphis, Sericocalyx, and Strobilanthes are nonmonophyletic. With one exception, all morphological characters included in a combined ITS and morphological analysis are homoplastic. The prospect for a new informative generic classification of the Strobilanthinae aiming to recognize and diagnose only monophyletic groups is considered. While some groups can be diagnosed, adequate diagnosis of the majority of groups remains problematic. Consequently, a single expanded genus Strobilanthes sensu lato is proposed at the level of the well-supported and monophyletic Strobilanthinae.

Relationships of the Macaronesian and Mediterranean floras: molecular evidence for multiple colonizations into Macaronesia and back-colonization of the continent in Convolvulus (Convolvulaceae).

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.

Classification or Phylogenetic Estimates?

[m]3ta is a method that seeks to implement a taxic view of homology. The method is consistent with Patterson's tests for discriminating homology from nonhomology. Contrary to the claims of Kluge and Farris, (1999, Cladistics 15, 205-212), m3ta is not a phenetic method-nor does it necessarily place the basal split in a tree between the phenetically most divergent taxa. [m]3ta does not seek to accurately recover phylogeny but rather it seeks to maximize the information content of taxic homology propositions. [m]3ta is a method of classification in which the unit of analysis is the relation of homology. [m]3ta differs from all phylogenetic methods because the units of analyses in phylogenetic methods, including sca, are transformation series.

Taxic and Transformational Homology: Different Ways of Seeing.

Hypotheses of taxic homology are hypotheses of taxa (groups). Hypotheses of transformational homology are hypotheses of transformations between character states within the context of an explicit model of character evolution. Taxic and transformational homology are discussed with respect to secondary loss and reversal in the context of three-taxon statement analysis and standard cladistic analysis. We argue that it is important to distinguish complement relation homologies from those that we term paired homologues. This distinction means that the implementation of three-taxon statement analysis needs modification if all data are to be considered potentially informative. Modified three-taxon statement analysis and standard cladistic analysis yield different results for the example of character reversal provided by Kluge (1994) for both complement relation data and paired homologues. We argue that these different results reflect the different approaches of standard cladistic analysis and modified t.t.s. analysis. In the standard cladistic approach, absence, as secondary loss, can provide evidence for a group. This is because the standard cladistic approach implements a transformational view of homology. In the t.t.s approach discussed in this paper, absence can only be interpreted as secondary loss by congruence with other data; absence alone can never provide evidence for a group. In this respect, the modified t.t.s. approach is compatible with a taxic view of homology.