Molecular phylogeny of land and freshwater planarians (Tricladida, Platyhelminthes): from freshwater to land and back

The suborder Tricladida (phylum Platyhelminthes) comprises the well-known free-living flatworms, taxonomically grouped into three infraorders according to their ecology: Maricola (marine planarians), Paludicola (freshwater planarians), and Terricola (land planarians). Molecular analyses have demonstrated that the Paludicola are paraphyletic, the Terricola being the sister group of one of the three paludicolan families, the Dugesiidae. However, neither 18S rDNA nor COI based trees have been able to resolve the relationships among species of Terricola and Dugesiidae, particularly the monophyly of Terricola. Here, we present new molecular data including sequences of nuclear genes (18S rDNA, 28S rDNA) and a mitochondrial gene (COI) of a wider sample of dugesiid and terricolan species. The new sequences have been analyzed, together with those previously obtained, in independent and concatenated analyses using maximum likelihood and bayesian methods. The results show that, although some parts of the trees remain poorly resolved, they support a monophyletic origin for Terricola followed by a likely return of some species to freshwater habitats. Relationships within the monophyletic group of Dugesiidae are clearly resolved, and relationships among some terricolan subfamilies are also clearly established and point to the need for a thorough revision of Terricola taxonomy.     

5S rRNA sequences of 12 species of flatworms: implications for the phylogeny of the Platyhelminthes

5S rRNAs from 12 species of free living and parasitic platyhelminthes were sequenced. In the phylogenetic analysis, attention was focused on the statistical estimates of the trees corresponding to existing phylogenetic hypotheses. The available 5S rRNA data agree well with widely accepted views on the relationships between the Acoela, Polycladida, Tricladida, and Neorhabdocoela; our analysis of the published 18S rRNA sequences also demonstrated good correspondence between these views and molecular data. With available 5S rRNA data the hypothesis that the dalyellioid turbellarians is the sister group of the Neodermata is less convincing than the hypotheses proposing the Neodermata as the sister group of the Neorhabdocoela, or of the Seriata, or of the branch uniting them. A relatively low rate of base replacement in parasitic flatworms, probably, accounts for the uncertain position of the Neodermata, while a relatively high rate in planarians may explain a relatively too early divergence of the Tricladida in several published phylogenetic trees constructed from various rRNA data.     

A robust molecular phylogeny of the Tricladida (Platyhelminthes: Seriata) with a discussion on morphological synapomorphies.

The suborder Tricladida (Platyhelminthes: Turbellaria, Seriata) comprises most well-known species of free-living flatworms. Four infraorders are recognized: (i) the Maricola (marine planarians); (ii) the Cavernicola (a group of primarily cavernicolan planarians); (iii) the Paludicola (freshwater planarians); and (iv) the Terricola (land planarians). The phylogenetic relationships among these infraorders have been analysed using morphological characters, but they remain uncertain. Here we analyse the phylogeny and classification of the Tricladida, with additional, independent, molecular data from complete sequences of 18S rDNA and 18S rRNA. We use maximum parsimony and neighbour-joining methods and the characterization of a unique gene duplication event involving the Terricola and the dugesiids to reconstruct the phylogeny. The results show that the Maricola is monophyletic and is the primitive sister group to the rest of the Tricladida (the Paludicola plus the Terricola). The Paludicola are paraphyletic since the Terricola and one paludicolan family, the Dugesiidae, share a more recent common ancestor than the dugesiids with other paludicolans (dendrocoelids and planariids). A reassessment of morphological evidence may confirm the apparent redundancy of the existing infraorders Paludicola and Terricola. In the meantime, we suggest replacing the Paludicola and Terricola with a new clade, the Continenticola, which comprises the families Dugesiidae, Planariidae, Dendrocoelidae and the Terricola.     

Evolution and systematics of the feliform Carnivora

Recent studies have improved our knowledge about the evolution and phylogeny of feliform taxa. Detailed study on new fossil remains of extinct feliform nimravides allows a new hypothesis concerning interrelationships within this family. Many factors indicate lack of sister relationships of Nimravinae and Barbourofelinae. However, only further investigations may bring full acceptance of this hypothesis. The paraphyly of Viverridae has been resolved by excluding the taxa Nandinia, Prionodon and Cryptoprocta and Fossa, which today are placed basally to all remaining Feliformia (family Nandiniidae), as sister taxon of Felidae (family Prionodontidae) and as Malagasy Carnivora lineage basal to hyaenid–herpestid clade, respectively. Still, incongruence among results concerning the systematic position of these taxa exhibits the necessity of further investigation. Detailed study revealed inconsistencies within genet and genet-like taxa phylogeny, which have still to be resolved. Malagasy Carnivora belong to a separate lineage, which originated from herpestid–hyaenid ancestors and colonised Madagascar during a single colonisation event. However, interrelationships among Malagasy Carnivora are poorly resolved. The situation of the social mongooses clade was resolved by including ethologic data to phylogenetic analyses; however, there is little information on solitary mongooses, which have a paraphyletic status today. Felid morphology and taxonomic revision attained during recent years show greater evolutionary differentiation. Nevertheless, no clear taxonomy has been achieved. New investigating methods are required. In the hyaenid family, which includes only four living species, some investigations related to the ecomorphological evolutionary path have been performed. The comparisons of fossil and subfossil remains with modern feliforms, combined with recent molecular methods, may improve our knowledge.     

Molecular phylogeny of Geoplaninae (Platyhelminthes) challenges current classification: proposal of taxonomic actions

Despite likely being the most diverse group within the Tricladida, the systematics of land planarians (Geoplanidae) has received minor attention. The most species‐rich ingroup, the subfamily Geoplaninae, is restricted to the Neotropics. The systematics of Geoplaninae remains uncertain. Unique features supporting the genera are scanty; moreover, parts of the known species have been poorly described, making comparative studies difficult. Likewise the evolutionary relationships among land planarians remain insufficiently understood. In the present study, a phylogenetic hypothesis for selected taxa of Geoplaninae based on the molecular data is presented and discussed in the light of morphological features. Our phylogenetic inference is based on the fragments of three nuclear regions (18S, 28S rDNA and EF‐1α) and a mitochondrial marker (cytochrome oxidase I) for which we considered three optimality criteria (parsimony, maximum likelihood and Bayesian inference). Although our data provide little support for most basal nodes, our phylogenetic trees show a number of well‐supported clades, unveiling morphologically homogeneous groups. According to these results, we propose to separate Geoplana into Barreirana (formerly considered a subgenus), Cratera gen. n., Imbira gen. n., Matuxia gen. n., Obama gen. n. and Paraba gen. n., emend the diagnoses of Barreirana, Geoplana, Notogynaphallia, Pasipha and Xerapoa and review the classification of the species within these genera. For Geoplana goetschi sensu Marcus, (1951), a new name is proposed.     

Multigene phylogeny of the southern bull-kelp genus Durvillaea (Phaeophyceae: Fucales)

Durvillaea (southern bull-kelp) is an economically and ecologically important brown algal genus that dominates many exposed, rocky coasts in the cold-temperate Southern Hemisphere. Of its five currently-recognized species, four are non-buoyant and restricted to the south-western Pacific, whereas one is both buoyant and widely distributed. Durvillaea has had an unsettled taxonomic history. Although its position within the brown algae (Phaeophyceae) has now been largely resolved through the use of molecular techniques, the taxonomic status of several Durvillaea species/morphotypes remains unresolved. Previous molecular phylogenetic studies of phaeophycean taxa have included few Durvillaea samples, and have consequently paid little or no attention to variation within this genus. The current study presents phylogenetic analyses of four genetic markers (mitchondrial: COI; chloroplast: rbcL; and nuclear: 18S and 28S) to resolve phylogenetic relationships within Durvillaea. Results support the monophyly of solid-bladed taxa D. willana, D. potatorum, and D. sp. A (an undescribed species from the Antipodes Islands), whereas the widespread, buoyant D. antarctica is paraphyletic, with solid-bladed D.chathamensis placed sister to a D. antarctica clade from northern NZ but within D. antarctica sensu lato. The phylogenetic and ecological diversity detected within D. antarctica indicate that it is a species complex of five deeply divergent clades. Under a phylogenetic species concept, Durvillaea can be interpreted as a complex of nine distinct evolutionary lineages, only one of which has an intercontinental distribution ('subantarctic'D. antarctica).     

Ascidian molecular phylogeny inferred from mtDNA data with emphasis on the Aplousobranchiata

We explored the usefulness of mtDNA data in assessing phylogenetic relationships within the Ascidiacea. Although ascidians are a crucial group in studies of deuterostome evolution and the origin of chordates, little molecular work has been done to ascertain the evolutionary relationships within the class, and in the studies performed to date the key group Aplousobranchiata has not been adequately represented. We present a phylogenetic analysis based on mitochondrial cytochrome c oxidase subunit I (COI) sequences of 37 ascidian species, mainly Aplousobranchiata (26 species). Our data retrieve the main groups of ascidians, although Phlebobranchiata appeared paraphyletic in some analyses. Aplousobranch ascidians consistently appeared as a derived group, suggesting that their simple branchial structure is not a pleisiomorphic feature. Relationships between the main groups of ascidians were not conclusively determined, the sister group of Aplousobranchiata was the Stolidobranchiata or the Phlebobranchiata, depending on the analysis. Therefore, our data could not confirm an Enterogona clade (Aplousobranchiata+Phlebobranchiata). All of the tree topologies confirmed previous ideas, based on morphological and biochemical characters, suggesting that Cionidae and Diazonidae are members of the clade Aplousobranchiata, with Cionidae occupying a basal position within them in our analyses. Within the Aplousobranchiata, we found some stable clades that provide new data on the evolutionary relationships within this large group of ascidians, and that may prompt a re-evaluation of some morphological characters.     

Retroposed elements and their flanking regions resolve the evolutionary history of xenarthran mammals (armadillos, anteaters, and sloths)

Armadillos, anteaters, and sloths (Order Xenarthra) comprise 1 of the 4 major clades of placental mammals. Isolated in South America from the other continental landmasses, xenarthrans diverged over a period of about 65 Myr, leaving more than 200 extinct genera and only 31 living species. The presence of both ancestral and highly derived anatomical features has made morphoanatomical analyses of the xenarthran evolutionary history difficult, and previous molecular analyses failed to resolve the relationships within armadillo subfamilies. We investigated the presence/absence patterns of retroposons from approximately 7,400 genomic loci, identifying 35 phylogenetically informative elements and an additional 39 informative rare genomic changes (RGCs). DAS-short interspersed elements (SINEs), previously described only in the Dasypus novemcinctus genome, were found in all living armadillo genera, including the previously unsampled Chlamyphorus, but were noticeably absent in sloths. The presence/absence patterns of the phylogenetically informative retroposed elements and other RGCs were then compared with data from the DNA sequences of the more than 12-kb flanking regions of these retroposons. Together, these data provide the first fully resolved genus tree of xenarthrans. Interestingly, multiple evidence supports the grouping of Chaetophractus and Zaedyus as a sister group to Euphractus within Euphractinae, an association that was not previously demonstrated. Also, flanking sequence analyses favor a close phylogenetic relationship between Cabassous and Tolypeutes within Tolypeutinae. Finally, the phylogenetic position of the subfamily Chlamyphorinae is resolved by the noncoding sequence data set as the sister group of Tolypeutinae. The data provide a stable phylogenetic framework for further evolutionary investigations of xenarthrans and important information for defining conservation priorities to save the diversity of one of the most curious groups of mammals.     

Evolutionary Analysis of Mitogenomes from Parasitic and Free-Living Flatworms

Mitochondrial genomes (mitogenomes) are useful and relatively accessible sources of molecular data to explore and understand the evolutionary history and relationships of eukaryotic organisms across diverse taxonomic levels. The availability of complete mitogenomes from Platyhelminthes is limited; of the 40 or so published most are from parasitic flatworms (Neodermata). Here, we present the mitogenomes of two free-living flatworms (Tricladida): the complete genome of the freshwater species Crenobia alpina (Planariidae) and a nearly complete genome of the land planarian Obama sp. (Geoplanidae). Moreover, we have reanotated the published mitogenome of the species Dugesia japonica (Dugesiidae). This contribution almost doubles the total number of mtDNAs published for Tricladida, a species-rich group including model organisms and economically important invasive species. We took the opportunity to conduct comparative mitogenomic analyses between available free-living and selected parasitic flatworms in order to gain insights into the putative effect of life cycle on nucleotide composition through mutation and natural selection. Unexpectedly, we did not find any molecular hallmark of a selective relaxation in mitogenomes of parasitic flatworms; on the contrary, three out of the four studied free-living triclad mitogenomes exhibit higher A+T content and selective relaxation levels. Additionally, we provide new and valuable molecular data to develop markers for future phylogenetic studies on planariids and geoplanids.     

Evolution,biogeography and systematics of the western Palaearctic Zamenis ratsnakes

The phylogenetic relationships between western Palaearctic Zamenis and Rhinechis ratsnakes have been troubled, with recent estimates based on the supermatrix approach questioning their monophyly and providing contradictory results. In this study, we generated a comprehensive molecular data set for Zamenis and closely related ratsnakes to assess their phylogenetic and systematic relationships and infer their spatial and temporal modes of diversification. We obtained a fully resolved and well‐supported phylogeny, which is consistent across markers, taxon‐sets and phylogenetic methods. The close phylogenetic relationship between Rhinechis and Zamenis is well‐established. However, the early branching pattern within this clade, and the position of R. scalaris and Z. hohenackeri, remains poorly supported. The Persian ratsnake Z. persicus is sister to the Mediterranean species Z. situla, Z. longissimus and Z. lineatus, of which Z. situla is sister to a clade containing the latter two species. These results are consistent with a recent phylogenomic study on ratsnakes based on hundreds of loci. Whereas, topological tests based on our data and evidence from such phylogenomic study strongly rejected previous phylogenetic estimates based on the supermatrix approach and demonstrate that these “mega‐phylogenies”, with hundreds of taxa and high levels of missing data, have recovered inconsistent relationships with spurious nodal support. Biogeographical and molecular dating analyses suggest an origin of the ancestor of Rhinechis and Zamenis in the Aegean region with early cladogenesis during the Late Miocene associated with the Aegean arch formation and support a scenario of east‐to‐west diversification. Finally, while we have little morphological and phylogenetic evidence for the distinctiveness between Rhinechis and Zamenis, a classification of them in a single genus, and the designation of Zamenis scalaris (Schinz, 1822), reflects better their evolutionary relationships.     

Correction: Revised molecular phylogeny,global biogeography,and diversification of palms subfamily Coryphoideae (Arecaceae) based on low copy nuclear and plastid regions

Coryphoideae are palmate-leaved palms from the family Arecaceae consisting of 46 genera representing 421 species. Although several phylogenetic analyses based on different genomic regions have been carried out on Coryphoideae, a fully resolved molecular phylogenetic tree has not been reported yet. To achieve this, we applied two phylogenetic reconstruction methods: Maximum Likelihood and Bayesian Inference, using amplified sampling by retrieving chloroplast and nuclear DNA sequences from NCBI and adding newly produced sequences from Indian accession into the dataset. The same dataset (chloroplast + nuclear DNA sequences) was used to estimate divergence times and the evolutionary history of Coryphoideae with a Bayesian uncorrelated, lognormal relaxed-clock approach and a Statistical Divergence-Vicariance Analysis method, respectively. The phylogenetic analyses based on a combined chloroplast and nuclear DNA sequence dataset showed well-resolved relationships within the subfamily. Both phylogenetic trees divide Coryphoideae into two main groups: CSPT (Crysophileae, Sabaleae, Phoeniceae, and Trachycarpeae) and the Syncarpous group. These main groups are segregated into eight tribes (Trachycarpeae, Phoeniceae, Sabaleae, Crysophileae, Borasseae, Corypheae, Caryoteae, and Chuniophoeniceae) and four subtribes (Rhapidine, Livistoninae, Hyphaeninae, and Lataniinae) with strong support-values. Most previously unresolved and doubtful relationships within tribes Trachycarpeae and Crysophilieae are now resolved and well-supported. The reconstructed phylogenetic trees support all previous systematic revisions of the subfamily. All Indian sampled species of Arenga, Bentinckia, Hyphaene, and Trachycarpus show close relation with their respective congeneric species. Molecular dating results and integration of biogeography suggest that Coryphoideae originated in Laurasia at ~95.12 Ma and then diverged into the tropical and subtropical regions of the whole world. This study offers the correct combination of nuclear and plastid regions to test the current and future systematic revisions.

     

Phylogenetic relationships of Danio within the order Cypriniformes: a framework for comparative and evolutionary studies of a model species

The evolutionary relationships of species of Danio and the monophyly and phylogenetic placement of the genus within the family Cyprinidae and subfamily Rasborinae provide fundamentally important phyloinformatics necessary for direct evaluations of an array of pertinent questions in modern comparative biology. Although the genus Danio is not one of the most diverse within the family, Danio rerio is one of the most important model species in biology. Many investigations have used this species or presumed close relatives to address specific questions that have lasting impact on the hypothesis and theory of development in vertebrates. Largely lacking from this approach has been a holistic picture of the exact phylogenetic or evolutionary relationships of this species and its close relatives. One thing that has been learned over the previous century is that many organismal attributes (e.g., developmental pathways, ecologies, behaviors, speciation) are historically constrained and their origins and functions are best explained via a phylogenetic approach. Herein, we provide a molecular evaluation of the phylogenetic placement of the model species Danio rerio within the genus Danio and among hypothesized closely related species and genera. Our analysis is derived from data using two nuclear genes (RAG1, rhodopsin) and five mitochondrial genes (ND4, ND4L, ND5, COI, cyt b) evaluated using parsimony, maximum likelihood, and Bayesian analyses. The family Cyprinidae is resolved as monophyletic but the subfamily Rasborinae (priority over Danioinae) is an unnatural assemblage. Danio is identified as a monophyletic group sister to a clade inclusive of the genera Chela, Microrasbora, Devario, and Inlecypris, not Devario nor Esomus as hypothesized in previous studies. Danio rerio is sister to D. kyathit among the species of Danio evaluated in this analysis. Microrasbora and Rasbora are non-monophyletic assemblages; however, Boraras is monophyletic.     

Molecular phylogeny of Sinocyclocheilus (Cypriniformes: Cyprinidae) inferred from mitochondrial DNA sequences

More than 10 species within the freshwater fish genus Sinoncyclocheilus adapt to caves and show different degrees of degeneration of eyes and pigmentation. Therefore, this genus can be useful for studying evolutionary developmental mechanisms, role of natural selection and adaptation in cave animals. To better understand these processes, it is indispensable to have background knowledge about phylogenetic relationships of surface and cave species within this genus. To investigate phylogenetic relationships among species within this genus, we determined nucleotide sequences of complete mitochondrial cytochrome b gene (1140 bp) and partial ND4 gene (1032 bp) of 31 recognized ingroup species and one outgroup species Barbodes laticeps. Phylogenetic trees were reconstructed using maximum parsimony, Bayesian, and maximum likelihood analyses. Our phylogenetic results showed that all species except for two surface species S. jii and S. macrolepis clustered as five major monophyletic clades (I, II, III, IV, and V) with strong supports. S. jii was the most basal species in all analyses, but the position of S. macrolepis was not resolved. The cave species were polyphyletic and occurred in these five major clades. Our results indicate that adaptation to cave environments has occurred multiple times during the evolutionary history of Sinocyclocheilus. The branching orders among the clades I, II, III, and IV were not resolved, and this might be due to early rapid radiation in Sinocyclocheilus. All species distributed in Yunnan except for S. rhinocerous and S. hyalinus formed a strongly supported monophyletic group (clade V), probably reflecting their common origins. This result suggested that the diversification of Sinocyclocheilus in Yunnan may correlate with the uplifting of Yunnan Plateau.     

Integrating genomic and phenotypic data to evaluate alternative phylogenetic and species delimitation hypotheses in a recent evolutionary radiation of grasshoppers

Although resolving phylogenetic relationships and establishing species limits are primary goals of systematics, these tasks remain challenging at both conceptual and analytical levels. Here, we integrated genomic and phenotypic data and employed a comprehensive suite of coalescent‐based analyses to develop and evaluate competing phylogenetic and species delimitation hypotheses in a recent evolutionary radiation of grasshoppers (Chorthippus binotatus group) composed of two species and eight putative subspecies. To resolve the evolutionary relationships within this complex, we first evaluated alternative phylogenetic hypotheses arising from multiple schemes of genomic data processing and contrasted genetic‐based inferences with different sources of phenotypic information. Second, we examined the importance of number of loci, demographic priors, number and kind of phenotypic characters and sex‐based trait variation for developing alternative species delimitation hypotheses. The best‐supported topology was largely compatible with phenotypic data and showed the presence of two clades corresponding to the nominative species groups, one including three well‐resolved lineages and the other comprising a four‐lineage polytomy and a well‐differentiated sister taxon. Integrative species delimitation analyses indicated that the number of employed loci had little impact on the obtained inferences but revealed the higher power provided by an increasing number of phenotypic characters and the usefulness of assessing their phylogenetic information content and differences between sexes in among‐taxa trait variation. Overall, our study highlights the importance of integrating multiple sources of information to test competing phylogenetic hypotheses and elucidate the evolutionary history of species complexes representing early stages of divergence where conflicting inferences are more prone to appear.     

Phylogenetic, morphological, and chemotaxonomic incongruence in the North American endemic genus Echinacea

The study of recently formed species is important because it can help us to better understand organismal divergence and the speciation process. However, these species often present difficult challenges in the field of molecular phylogenetics because the processes that drive molecular divergence can lag behind phenotypic divergence. In the current study we show that species of the recently diverged North American endemic genus of purple coneflower, Echinacea, have low levels of molecular divergence. Data from three nuclear loci and two plastid loci provide neither resolved topologies nor congruent hypotheses about species-level relationships. This lack of phylogenetic resolution is likely due to the combined effects of incomplete lineage sorting, hybridization, and backcrossing following secondary contact. The poor resolution provided by molecular markers contrasts previous studies that found well-resolved and taxonomically supported relationships from metabolic and morphological data. These results suggest that phenotypic canalization, resulting in identifiable morphological species, has occurred rapidly within Echinacea. Conversely, molecular signals have been distorted by gene flow and incomplete lineage sorting. Here we explore the impact of natural history on the genetic organization and phylogenetic relationships of Echinacea.     

Novel classification and biogeography of Leptolejeunea (Lejeuneaceae,Marchantiophyta) with implications for the origin and evolution of the Asian evergreen broad-leaved forests

Although recent molecular phylogenetic analyses have greatly improved our understanding of the classification of the large liverwort family Lejeuneaceae, the frequent incongruencies between morphology-based taxonomy and molecular phylogeny have hindered our understanding of evolutionary diversification within the group. Here we focus on Leptolejeunea (Spruce) Steph., a pantropical epiphyllous genus in Lejeuneaceae with 40 species. Phylogenetic studies on the genus have been hampered by insufficient taxon sampling, leaving the deep phylogenetic relationships within this group unresolved. We present the most comprehensive phylogenetic analysis of the genus to date with sampling of over 80% of species, including the enigmatic Leptolejeunea spinistipula (Mizut.) X.L.He endemic to Borneo. Based on data from three molecular markers with representatives of Leptolejeunea and its allies, Leptolejeunea appeared to be monophyletic following the exclusion of L. spinistipula and its transfer to Soella R.L.Zhu, L.Shu, Qiong He & Y.M.Wei. A total-evidence approach was taken to resolve the backbone phylogeny of Leptolejeunea and a first infrageneric classification of Leptolejeunea, including a new subgenus and three new sections, is proposed based on integrated molecular and morphological evidence. Reconstruction of the evolutionary history showed a wide ancestral area of Leptolejeunea during the Paleogene that arose in mainland Asia, followed by an accelerated speciation rate. Across the biogeographical history of Leptolejeunea, long-distance dispersal had profound effects on population expansion. Our findings suggest that Australasia is a source of biodiversity of Asian evergreen broad-leaved forests that have been established since the Oligocene and rose after the early Miocene.     

A multi-locus phylogeny for Phytophthora utilizing markers derived from complete genome sequences.

Phytophthora species are devastating plant pathogens in both agricultural and natural environments. Due to their significant economic and environmental impact, there has been increasing interest in Phytophthora genetics and genomics, culminating in the recent release of three complete genome sequences (P. ramorum, P. sojae, and P. infestans). In this study, genome and other large sequence databases were used to identify over 225 potential genetic markers for phylogenetic analyses. Here, we present a genus-wide phylogeny for 82 Phytophthora species using seven of the most informative loci (approximately 8700 nucleotide sites). Our results support the division of the genus into 10 well-supported clades. The relationships among these clades were rigorously evaluated using a number of phylogenetic methods. This is the most comprehensive study of Phytophthora relationships to date, and many newly discovered species have been included. A more resolved phylogeny of Phytophthora species will allow for better interpretations of the overall evolutionary history of the genus.     

A multi-locus phylogeny for Phytophthora utilizing markers derived from complete genome sequences

Phytophthora species are devastating plant pathogens in both agricultural and natural environments. Due to their significant economic and environmental impact, there has been increasing interest in Phytophthora genetics and genomics, culminating in the recent release of three complete genome sequences (P. ramorum, P. sojae, and P. infestans). In this study, genome and other large sequence databases were used to identify over 225 potential genetic markers for phylogenetic analyses. Here, we present a genus-wide phylogeny for 82 Phytophthora species using seven of the most informative loci (approximately 8700 nucleotide sites). Our results support the division of the genus into 10 well-supported clades. The relationships among these clades were rigorously evaluated using a number of phylogenetic methods. This is the most comprehensive study of Phytophthora relationships to date, and many newly discovered species have been included. A more resolved phylogeny of Phytophthora species will allow for better interpretations of the overall evolutionary history of the genus.