A hierarchical view of convergent evolution in microbial eukaryotes

Distinguishing convergent evolution from other causes of similarity in organisms is necessary for reconstructing phylogenetic relationships, inferring patterns of character evolution, and investigating the forces of natural selection. In contrast to animals and land plants, the pervasiveness and adaptive significance of convergent evolution in microbes has yet to be systematically explored or articulated. Convergent evolution in microbial eukaryotes, for instance, often involves very distantly related lineages with relatively limited repertoires of morphological features. These large phylogenetic distances weaken the role of ancestral developmental programs on the subsequent evolution of morphological characters, making convergent evolution between very distantly related lineages fundamentally different from convergent evolution between closely related lineages. This suggests that examples of convergence at different levels in the phylogenetic hierarchy offer different clues about the causes and processes of macroevolutionary diversification. Accordingly (and despite opinions to the contrary), I recognize three broad and overlapping categories of phenotypic convergence-"parallel", "proximate" and "ultimate"-that represent either (1) subcellular analogues, (2) subcellular analogues to multicellular systems (and vice versa), or (3) multicellular analogues. Microbial eukaryotes living in planktonic environments, interstitial environments, and the intestinal environments of metazoan hosts provide compelling examples of ultimate convergence. After describing selected examples in microbial eukaryotes, I suggest some future directions needed to more fully understand the hierarchical structure of convergent evolution and the overall history of life.     

Genetic evidence for the convergent evolution of light skin in Europeans and East Asians

Human skin pigmentation shows a strong positive correlation with ultraviolet radiation intensity, suggesting that variation in skin color is, at least partially, due to adaptation via natural selection. We investigated the evolution of pigmentation variation by testing for the presence of positive directional selection in 6 pigmentation genes using an empirical F(ST) approach, through an examination of global diversity patterns of these genes in the Centre d'Etude du Polymorphisme Humain (CEPH)-Diversity Panel, and by exploring signatures of selection in data from the International HapMap project. Additionally, we demonstrated a role for MATP in determining normal skin pigmentation variation using admixture mapping methods. Taken together (with the results of previous admixture mapping studies), these results point to the importance of several genes in shaping the pigmentation phenotype and a complex evolutionary history involving strong selection. Polymorphisms in 2 genes, ASIP and OCA2, may play a shared role in shaping light and dark pigmentation across the globe, whereas SLC24A5, MATP, and TYR have a predominant role in the evolution of light skin in Europeans but not in East Asians. These findings support a case for the recent convergent evolution of a lighter pigmentation phenotype in Europeans and East Asians.     

Molecular evolution and phylogeny of the angiosperm ycf2 gene

Much of the recent progress in understanding angiosperm phylogeny has been achieved using multi-gene or plastid genome datasets. However, it is largely unclear what size of dataset is required to achieve suffi-cient resolution. The ycf2 gene is the largest plastid gene in angiosperms and it was used as part of multigene datasets in several earlier investigations into angiosperm relationships. In this study, we show that the ycf2 gene alone can provide a generally well-supported phylogeny that is consistent with those inferred from the most comprehensive multigene or plastid genome datasets. The phylogenetic signal of the ycf2 gene is likely de-rived from the combination of its long sequence length and low rate of nucleotide substitution. The ycf2 gene may provide a low-cost alternative to comprehensive multigene or genome datasets for investigating angiosperm relationships.     

Genetics and evolution of triatomines: from phylogeny to vector control

Triatomines are hemipteran bugs acting as vectors of the protozoan parasite Trypanosoma cruzi. This parasite causes Chagas disease, one of the major parasitic diseases in the Americas. Studies of triatomine genetics and evolution have been particularly useful in the design of rational vector control strategies, and are reviewed here. The phylogeography of several triatomine species is now slowly emerging, and the struggle to reconcile the phenotypic, phylogenetic, ecological and epidemiological species concepts makes for a very dynamic field. Population genetic studies using different markers indicate a wide range of population structures, depending on the triatomine species, ranging from highly fragmented to mobile, interbreeding populations. Triatomines transmit T. cruzi in the context of complex interactions between the insect vectors, their bacterial symbionts and the parasites; however, an integrated view of the significance of these interactions in triatomine biology, evolution and in disease transmission is still lacking. The development of novel genetic markers, together with the ongoing sequencing of the Rhodnius prolixus genome and more integrative studies, will provide key tools to expanding our understanding of these important insect vectors and allow the design of improved vector control strategies.     

Molecular phylogeny and plumage evolution in gulls (Larini)

We used DNA sequence data of the mitochondrial control region and cytochrome b gene to assess phylogenetic relationships among 32 gull species and two outgroup representatives. We tentatively estimated divergence times from transversional substitutions calibrated against DNA–DNA hybridization data. Several strongly supported species groups are identified, but the relationships between these species groups and the rooting of the gull tree remain unresolved. Geographical range extension appears as a factor of speciation, but several related, well‐differentiated species seem to have evolved within comparatively restricted areas. Some plumage characters used in the past for delimiting species groups appear inappropriate. The dark hooded species, for instance, do not constitute a natural assemblage. Molecular data also allowed the identification of several striking plumage convergences that had obscured the true relationships between gull species until now. For example, the dark tropical gulls analysed here each belong to totally different clades and are independent examples of convergent plumage evolution under common environmental constraints. The reverse situation also happened, with two arctic‐distributed species, the ivory gull (Pagophila eburnea) and the Sabine’s gull (Xema sabini), appearing as sister taxa despite completely different plumage features. Molecular data have thus significantly improved our understanding of gull evolution.     

Delimitation and phylogeny of Aletris (Nartheciaceae) with implications for perianth evolution

Aletris,containing approximately 21 species,is the largest genus in Nartheciaceae,and is disjunctively distributed in eastern Asia and eastern North America.Its delimitation has been controversial beca...     

Molecular phylogeny and evolution of the freshwater eel, genus Anguilla

A molecular phylogenetic analysis was conducted on all of the known catadromous eel species of the genus Anguilla to assess their relationships and evolutionary history. The analyses of a total of 1427 bp of the mitochondrial 16S ribosomal RNA and 1140 bp of the complete cytochrome b gene sequences suggested that the genus Anguilla was monophyletic in origin, with A. borneensis as the most basal species. Four clades/species groups that correspond to their geographical ranges were indicated, Indo-Atlantic (three species), Oceania (two species), tropical Pacific (two species), and Indo-Pacific (five species), with ambiguous positions for A. japonica and A. reinhardti. This grouping conflicts with that of a previous morphological study, since the broad undivided maxillary and short-fin type, which were thought to be phylogenetically important, were paraphyletic in the molecular analysis. However, the molecular phylogeny and the present geographic distribution of species suggested historical dispersion of the genus Anguilla according to the Tethys corridor hypothesis, which proposed that anguillid eels originated near present-day Indonesia and dispersed westward along paleo-circumglobal equatorial currents. The westward-moving strain entered the paleo-Atlantic through the Tethys Sea and was ancestral to present-day European and American species.     

Comparative morphology and molecular phylogeny of aplanochytrids (Labyrinthulomycota)

Aplanochytrids comprise one of three major subgroups within the Labyrinthulomycota. We have surveyed the diversity of aplanochytrids and have discovered that most isolates are difficult to identify to species because of character plasticity and ambiguity. Ten isolates were studied using molecular phylogenies based on small subunit ribosomal gene sequences (SSU rDNA) and morphological characters derived from light microscopy, SEM and TEM (e.g., colony size, colony shape, colony pattern, agar penetration, cell shape, cell surface patterns, cell inclusion characteristics and ectoplasmic net morphology). Of these isolates, we could positively identify two of them to species, namely Aplanochytrium yorkensis (Perkins, 1973) Leander and Porter, 2000 and A. minuta (Watson and Raper, 1957) Leander and Porter, 2000. We used standardized conditions for growing aplanochytrid isolates in order to minimize environmentally induced phenotypic plasticity in our comparative studies of morphology. By mapping the morphological characters listed above onto a conservative phylogenetic topology derived from SSU rDNA sequences, we were able to identify several synapomorphies (e.g., gross colony characteristics and cell surface patterns) that serve as valuable taxonomic characters for the identification of species and specific clades of aplanochytrids.     

Marmot phylogeny revisited: molecular evidence for a diphyletic origin of sociality

We established the phylogeny of 11 species of the genus Marmota based on the entire sequence of the mitochondrial cytochrome b ( cyt-b ) gene (1.1 kb) and a partial sequence of the NADH dehydrogenase subunit 4 ( ND4 ) gene (1.2 kb). In three species ( Marmota caligata , Marmota olympus , and Marmota bobac ) full-sized nuclear pseudogenes of the mitochondrial cyt-b were identified. The mitochondrial cyt-b genes and the three pseudogenes form separate clusters in the maximum parsimony dendrogram. This finding suggests that the pseudogenes originated from a single transfer to the nucleus that may have occurred prior to the radiation of the genus Marmota . Notably, compared with their functional mitochondrial equivalents the pseudogenes show a much lower substitution rate. In the dendrograms deduced from the mitochondrial sequences two distinct clusters become apparent: one cluster consists of the North-west American species, the other contains the Eurasian species together with the North American species Marmota monax . The position of M. monax as a member of the Eurasian clade is in accordance with the evolution of chromosome numbers. The results are of special interest with respect to the evolution of social systems in the genus that vary from solitary species ( M. monax ) to highly social species living in family groups (e.g. Marmota marmota ). The molecular phylogeny suggests a diphyletic origin of high sociality in the genus Marmota .     

Evidence for convergent nucleotide evolution and high allelic turnover rates at the complementary sex determiner gene of Western and Asian honeybees

Our understanding of the impact of recombination, mutation, genetic drift, and selection on the evolution of a single gene is still limited. Here we investigate the impact of all these evolutionary forces at the complementary sex determiner (csd) gene that evolves under a balancing mode of selection. Females are heterozygous at the csd gene and males are hemizygous; diploid males are lethal and occur when csd is homozygous. Rare alleles thus have a selective advantage, are seldom lost by the effect of genetic drift, and are maintained over extended periods of time when compared with neutral polymorphisms. Here, we report on the analysis of 17, 19, and 15 csd alleles of Apis cerana, Apis dorsata, and Apis mellifera honeybees, respectively. We observed great heterogeneity of synonymous (piS) and nonsynonymous (piN) polymorphisms across the gene, with a consistent peak in exons 6 and 7. We propose that exons 6 and 7 encode the potential specifying domain (csd-PSD) that has accumulated elevated nucleotide polymorphisms over time by balancing selection. We observed no direct evidence that balancing selection favors the accumulation of nonsynonymous changes at csd-PSD (piN/piS ratios are all <1, ranging from 0.6 to 0.95). We observed an excess of shared nonsynonymous changes, which suggest that strong evolutionary constraints are operating at csd-PSD resulting in the independent accumulation of the same nonsynonymous changes in different alleles across species (convergent evolution). Analysis of csd-PSD genealogy revealed relatively short average coalescence times ( approximately 6 Myr), low average synonymous nucleotide diversity (piS < 0.09), and a lack of trans-specific alleles that substantially contrasts with previously analyzed loci under strong balancing selection. We excluded the possibility of a burst of diversification after population bottlenecking and intragenic recombination as explanatory factors, leaving high turnover rates as the explanation for this observation. By comparing observed allele richness and average coalescence times with a simplified model of csd-coalescence, we found that small long-term population sizes (i.e., N(e) < 10(4)), but not high mutation rates, can explain short maintenance times, implicating a strong historical impact of genetic drift on the molecular evolution of highly social honeybees.     

Crystal structure of creatininase from Pseudomonas putida: a novel fold and a case of convergent evolution

Creatinine amidohydrolase (creatininase; EC 3.5.2.10) from Pseudomonas putida, a homohexameric enzyme with a molecular mass of 28.4 kDa per subunit, is a cyclic amidohydrolase catalysing the reversible conversion of creatinine to creatine. The enzyme plays a key role in the bacterial degradation of creatinine. The three-dimensional structure of creatininase from P.putida was determined and refined to 2.1A. The structure shows the six subunits arranged as a trimer of dimers and definitely disproves previous reports that the enzyme has an octameric quaternary structure. Each monomer consists of a central, four-stranded, parallel beta-sheet flanked by two alpha-helices on both sides of the beta-sheet. This topology is unique within the superfamily of amidohydrolases. Moreover, creatininase possesses a novel fold with no close structural relatives within the Protein Data Bank. Each creatininase monomer contains a binuclear zinc centre near the C termini of the beta-strands and the N termini of the main alpha-helices. These zinc ions indicate the location of the active site unambiguously. The active site is entirely buried and is not accessible from the solution without movement of parts of the protein. The two zinc ions are bridged by a water molecule and by an aspartate residue, which acts as a bidentate ligand. They differ from each other in the number and the spatial arrangement of their ligands. One of them is tetrahedrally and the other trigonal-bipyramidally ligated. Using two water molecules of the first coordination sphere as anchor points, a creatinine-water adduct resembling the transition state of the hydrolysation reaction was modelled into the active site. The resulting complex in combination with structural comparisons with other amidohydrolases enabled us to identify the most probable candidate for the catalytic base and to suggest a putative reaction mechanism. Surprisingly these structural comparisons revealed a similarity in the active-site arrangement between creatininase and the hydantoinase-like cyclic amidohydrolases that was unexpected, given the completely unrelated primary and tertiary structures. In particular, the zinc-bridging aspartate residue of creatininase is a spatially and functionally analogue to a carboxylated lysine residue found in dihydroorotase and the hydantoinases. Hence, creatininase and the hydantoinase-like cyclic amidohydrolases represent a further example of convergent evolution within the enzyme class of hydrolases.     

On the evolution of adult head structures and the phylogeny of Hydraenidae (Coleoptera, Staphyliniformia)

External and internal head structures of adults of Orchymontiinae, Prosthetopinae, Hydraeninae and Ochthebiinae were studied and those of Ochthebius semisericeus and Limnebius truncatellus are described in detail. The results are evaluated with respect to their relevance for a reconstruction of hydraenid phylogeny and also compared with structural features found in adults of other staphyliniform families. The monophyly of Hydraenidae is supported by the presence of a plate‐like, trilobed premento‐hypopharyngeal extension, an unusual origin of m. tentoriohypopharyngalis, dorsal tentorial arms firmly fused with the head capsule, modified basal antennomeres, and palpigers connected by a transverse sclerotized bar. Orchymontiinae are monophyletic and the basal sister group of the remaining Hydraenidae. The presence of a ventral transverse genal bulge and of a pubescent antennal club with more than two antennomeres (reversal in some prosthetopines: e.g. Mesoceration abstrictum) are possible apomorphies of Hydraenidae excluding Orchymontiinae. Prosthetopinae are probably monophyletic and the sister group of Ochthebiinae + Hydraeninae. The latter clade is characterized by a distinct cupula formed by antennomere VI, a loose five‐segmented pubescent antennal club, and a modified antennal musculature. The presence of an unusual tentorio‐pharyngeal dilator is a shared derived feature of Ochthebiinae and the genus Davidraena. The monophyly of Ochthebiinae was confirmed and Ochtheosus is the sister group of the remaining ochthebiine genera, which are characterized by a perforated wall‐like structure formed by the posterior tentorial arms. The absence of this tentorial modification and the fimbriate galea are plesiomorphies retained in Ochtheosus. Calobius differs strongly from other subgenera of Ochthebius and a generic status may be appropriate. The monophyly of Hydraeninae is not supported. Hydraena was confirmed as a clade and Laeliaena and Limnebius are sister groups. The latter genus is characterized by several autapomorphies. The basal position of Orchymontiinae and Prosthetopinae suggests a Gondwanan origin of Hydraenidae and a primary preference for life in running water. Important evolutionary changes of head structures are complex transformations of the antennae and related structures. Yet, the use of the antennae as accessory breathing organs is not a groundplan feature of the family. The results of this study strengthen the case of staphylinoid affinities of Hydraenidae.     

A method for molecular phylogeny construction by direct use of nucleotide sequence data

Summary A method for molecular phylogeny construction is newly developed. The method, called the stepwise ancestral sequence method, estimates molecular phylogenetic trees and ancestral sequences simultaneously on the basis of parsimony and sequence homology. For simplicity the emphasis is placed more on parsiomony than on sequence homology in the present study, though both are certainly important. Because parsimony alone will sometimes generate plural candidate trees, the method retains not one but five candidates from which one can then single out the final tree taking other criteria into account.The properties and performance of the method are then examined by simulating an evolving gene along a model phylogenetic tree. The estimated trees are found to lie in a narrow range of the parsimony criteria used in the present study. Thus, other criteria such as biological evidence and likelihood are necessary to single out the correct tree among them, with biological evidence taking precedence over any other criterion. The computer simulation also reveals that the method satisfactorily estimates both tree topology and ancestral sequences, at least for the evolutionary model used in the present study.     

Molecular information on bowerbird phylogeny and the evolution of exaggerated male characteristics

Mitochondrial DNA cytochrome b sequences of 849 base pairs are reported from eight species of Australian bowerbirds. These sequences are used with three from the literature (Edwards et al., 1991) to investigate bowerbird phylogeny using maximum parsimony and maximum likelihood methods. With respect to the three outgroup species, bowerbirds are shown to be monophyletic with high confidence using the bootstrap. The monogamous Ailuroedus crassirostris (which does not clear display courts) is indicated as the sister group to other bowerbirds. The maypole-builders (Amblyornis macgregoriae and Prionodura newtoniana) are significantly supported as a clade indicating a common origin for maypole type bowers, despite large differences in the design of these species' bowers. The avenue-builders (Sericulus chrysocephalus, Ptilonorhynchus violaceus, Chlamydera maculata and C. nuchalis) are also monophyletic. The pattern of divergence in avenue builders accords with the predictions of Gilliard's (1956, 1963) “transferral effect”. The transference hypothesis is not supported by evidence suggesting that the dull plumage of Scenopoeetes is an ancestral condition in bowerbirds. The use of sticks to build bowers could have had a single evolutionary origin and been secondarily lost in Scenopoeetes, or evolved independently in the avenue and maypole builders.     

Chromosome and breeding system evolution of the genus Mercurialis (Euphorbiaceae): implications of ITS molecular phylogeny

 The internal transcribed spacers (ITS1 and ITS2) of nuclear ribosomal DNA were amplified and sequenced from 19 samples representing all species of the genus Mercurialis and two outgroup species, Ricinus communis and Acalypha hispida. The length of ITS1 in the ingroups ranged from 223 to 246 bp and ITS2 from 210 to 218 bp. Sequence divergence between pairs of species ranged from 1.15% to 25.88% among the ingroup species in the combined data of ITS1 and ITS2. Heuristic phylogenetic analyses using Fitch parsimony on the combined data of ITS1 and ITS2 with gaps treated as missing generated 45 equally parsimonious trees. The strict consensus tree was principally concordant with morphological classification. Within the genus, the ITS sequences recognised two main infrageneric clades: the M. perennis complex including three Eurasian stoloniferous species (M.␣leiocarpa, M. ovata and M. perennis) and the western Mediterranean group including eight both annual and perennial species. Of the western Mediterranean clade, the annual and perennial species grouped respectively into two different groups, and the annual life form is revealed as a synapomorphic character derived from perennial, whereas in the Eurasian clade ITS phylogeny suggested M. leiocarpa as basal clade sister to M.␣perennis and M. ovata. ITS phylogeny failed to resolve the relationships among the different cytotypes of M. ovata and M. perennis. ITS phylogeny also suggested rapid karyotypic evolution for the genus. The karyotypic divergence among the perennial species of western Mediterranean region did not corroborate the nucleotide sequence divergence among the species. Optimisation of chromosome numbers onto the ITS phylogeny suggested x=8 to be the ancestral basic chromosome number of the genus. ITS phylogeny confirmed that the androdioecy of M. ambigua is derived from dioecy. The nucleotide heterozygosity and additivity in ITS sequences clearly confirm the interspecific hybridisation in the genus Mercurialis. Received December 22, 2001; accepted May 21, 2002?Published online: November 14, 2002 Address of the authors: Martin Kr?henbühl, Yong-Ming Yuan (correspondence) and Philippe Küpfer, Institut de Botanique, Laboratoire de botanique évolutive, Université de Neuchatel, Emile-Argand 11, CH-2007 Neuchatel, Suisse. (e-mail: yong-ming.yuan@unine.ch)     

Parasite histories and novel phylogenetic tools: alternative approaches to inferring parasite evolution from molecular markers

Parasitological research is often contingent on the knowledge of the phylogeny/genealogy of the studied group. Although molecular phylogenetics has proved to be a powerful tool in such investigations, its application in the traditional fashion, based on a tree inference from the primary nucleotide sequences may, in many cases, be insufficient or even improper. These limitations are due to a number of factors, such as a scarcity/ambiguity of phylogenetic information in the sequences, an intricacy of gene relationships at low phylogenetic levels, or a lack of criteria when deciding among several competing coevolutionary scenarios. With respect to the importance of a precise and reliable phylogenetic background in many biological studies, attempts are being made to extend molecular phylogenetics with a variety of new data sources and methodologies. In this review, selected approaches potentially applicable to parasitological research are presented and their advantages as well as drawbacks are discussed. These issues include the usage of idiosyncratic markers (unique features with presumably low probability of homoplasy), such as insertion of mobile elements, gene rearrangements and secondary structure features; the problem of ancestral polymorphism and reticulate relationships at low phylogenetic levels; and the utility of a molecular clock to facilitate discrimination among alternative scenarios in host-parasite coevolution.     

The phylogeny of rotifers: molecular,ultrastructural and behavioural data

This work discusses the nature and significance of molecular, ultrastructural, and behavioural characters that can be used in phylogenetic analyses of rotifers.Recent molecular research has demonstrated the presence of very small amounts of 4-hydroxyproline in rotifers, probably arising from acetyl-cholinesterase or glycoproteins. Thus, rotifers appear to be the first known Metazoa without collagen.Ultrastructural work also has made some interesting discoveries. (1) The myelinic cuticle of the integument and pharynx of gastrotrichs is present in the pharynx of at least two rotifers (Philodina and Brachionus) and some Annelida. (2) The intracytoplasmic lamina (IL) of the syncytial ingestive integument of Acanthocephala is similar to the IL of the syncytial stomach of Bdelloidea. (3) The fibrous terminal web of primitive epidermal ciliated cells may have evolved in the skeletal IL of the syncytial, aciliated integument of rotifers. (4) Using the ultrastructural features of the skeletal, IL of the integument, I derived two possible dendograms of rotifer evolution. (5) These models and other ultrastructural data predict that Bdelloidea should be separated from Monogononta, while Seison has several characters which suggest that it should be more closely aligned to the Monogononta than previously proposed.Molecular and ultrastructural data suggest that rotifers are primitive Metazoa, probably derived by neoteny from ancestral, ciliated larvae. Finally, I argue that information on sensory organs and the behaviour of rotifers may offer unique insights into the evolution of the phylum.     

A molecular phylogeny of minivets (Passeriformes: Campephagidae: Pericrocotus): implications for biogeography and convergent plumage evolution

Jønsson, K. A., Irestedt, M., Ericson, P. G. P. & Fjeldså, J. (2009). A molecular phylogeny of minivets (Passeriformes: Campephagidae: Pericrocotus ): implications for biogeography and convergent plumage evolution.— Zoologica Scripta, 39 , 1–8.
Minivets are conspicuous and mostly intensely colourful birds inhabiting wooded environments in tropical and subtropical South and Southeast Asia and temperate East Asia. We present a robust phylogeny of the group based on nuclear and mitochondrial DNA data including all 12 recognized species and also many subspecies representing disjunct populations in the Oriental mainland and in Indonesia. The study indicates that minivets radiated within mainland Asia and dispersed to the Indonesian archipelago. We also demonstrate that in accordance with studies on other bird groups, plumage characters are highly plastic and that the diversity of plumage patterns and colouration represents an example of convergent evolution.     

Karyological evolution and molecular phylogeny in Macaronesian dendroid spurges (Euphorbia subsect. Pachycladae)

 Euphorbia subsect. Pachycladae is a taxon of primarily Macaronesian distribution, defined by morphological and biogeographical criteria. On the basis of morphological data, it is a heterogeneous group within which at least three complexes of species can be distinguished. To ascertain whether it is a natural group and discover its phylogenetic relations, we performed a cladistic analysis of the sequences of ribosomal nuclear DNA and a karyological study. The results of the two studies are concordant and show that the sub-section is polyphyletic and includes three different groups. The first monophyletic group is made up of the Macaronesian endemics E. atropurpurea complex and E. lamarckii complex, which form a polytomy with E. dendroides as the basal species. The lauroid species E. longifolia and E. stygiana represent the second monophyletic group, which derive from Mediterranean forms of E. sect. Helioscopia Dumort. Both species are paleopolyploid (2n=44) with highly symmetrical karyotypes. Finally, E. balsamifera, with a Canarian, African and Arabian distribution, remains isolated in a basal position. Its karyotype, with 2n=20 chromosomes, differs from the Macaronesian model and displays analogies with African cactiform spurges. On the basis of the results, some hypotheses are formulated about speciation processes in the three groups. Received March 3, 2001 Accepted October 28, 2001     

Property and efficiency of the maximum likelihood method for molecular phylogeny

Summary The maximum likelihood (ML) method for constructing phylogenetic trees (both rooted and unrooted trees) from DNA sequence data was studied. Although there is some theoretical problem in the comparison of ML values conditional for each topology, it is possible to make a heuristic argument to justify the method. Based on this argument, a new algorithm for estimating the ML tree is presented. It is shown that under the assumption of a constant rate of evolution, the ML method and UPGMA always give the same rooted tree for the case of three operational taxonomic units (OTUs). This also seems to hold approximately for the case with four OTUs. When we consider unrooted trees with the assumption of a varying rate of nucleotide substitution, the efficiency of the ML method in obtaining the correct tree is similar to those of the maximum parsimony method and distance methods. The ML method was applied to Brown et al.'s data, and the tree topology obtained was the same as that found by the maximum parsimony method, but it was different from those obtained by distance methods.