An analysis of species boundaries and biogeographic patterns in a cryptic species complex: the rotifer--Brachionus plicatilis

Since the advent of molecular phylogenetics, there is increasing evidence that many small aquatic and marine invertebrates--once believed to be single, cosmopolitan species--are in fact cryptic species complexes. Although the application of the biological species concept is central to the identification of species boundaries in these cryptic complexes, tests of reproductive isolation do not frequently accompany phylogenetic studies. Because different species concepts generally identify different boundaries in cryptic complexes, studies that apply multiple species concepts are needed to gain a more detailed understanding of patterns of diversification in these taxa. Here we explore different methods of empirically delimiting species boundaries in the salt water rotifer Brachionus plicatilis by comparing reproductive data (i.e., the traditional biological species concept) to phylogenetic data (the genealogical species concept). Based on a high degree of molecular sequence divergence and largely concordant genetic patterns in COI and ITS1, the genealogical species hypothesis indicates the existence of at least 14 species--the highest estimate for the group thus far. A test of the genealogical species concept with biological crosses shows a fairly high level of concordance, depending on the degree of reproductive success used to draw boundaries. The convergence of species concepts in this group suggests that many of the species within the group may be old. Although the diversity of the group is higher than previously understood, geographic distributions remain broad. Efficient passive dispersal has resulted in global distributions for many species with some evidence of isolation by distance over large geographic scales. These patterns concur with expectations that micro-meiofauna (0.1-1mm) have biogeographies intermediate to microbial organisms and large vertebrates. Sympatry of genetically distant strains is common.     

Molecular evidence of a peripatric origin for two sympatric species of field crickets (Gryllus rubens and G. texensis) revealed from coalescent simulations and population genetic tests

Species pairs that differ primarily in characters involved in mating interactions and are largely sympatric raise intriguing questions about the mode of speciation. When species divergence is relatively recent, the footprint of the demographic history during speciation might be preserved and used to reconstruct the biogeography of species divergence. In this study, patterns of genetic variation were examined throughout the geographical range of two cryptic sister taxa of field crickets, Gryllus texensis and G. rubens; mitochondrial cytochrome oxidase I (COI) was sequenced in 365 individuals sampled from 48 localities. Despite significant molecular divergence between the species, they were not reciprocally monophyletic. We devised several analyses to statistically explore what historical processes might have given rise to this genealogical structure. The analyses indicated that the biogeographical pattern of genetic variation does not support a model of recent gene flow between species. Instead, coalescent simulations suggested that the genealogical structure within G. texensis, namely a deep split between two geographically overlapping clades, reflects historical substructure within G. texensis. Additional tests that consider the concentration of G. rubens haplotypes in one of the two G. texensis genetic clusters suggest a model of speciation in which G. rubens was derived from one lineage of a geographically subdivided ancestor. These results indicate that, despite the contemporary sympatry of G. texensis and G. rubens, the data are indicative of an peripatric origin in which G. rubens was derived from one of the two historical partitions in the species currently recognized as G. texensis. This proposed model of species divergence suggests how the interplay of geography and selection may give rise to new species, although this requires testing with multilocus data. Specifically, the model highlights how that geographical partitioning of ancestral variation in the past may augment the selectively driven divergence of characters involved in the reproductive isolation of the species today.     

Positive directional selection in the proline-rich antigen (PRA) gene among the human pathogenic fungi Coccidioides immitis, C. posadasii and their closest relatives

In this study, we investigate the possibility of selection acting on the proline-rich antigen (PRA) gene in natural populations of the two human pathogens, Coccidioides immitis and Coccidioides posadasii, and three of their close relatives, Chrysosporium lucknowense, Chrysosporium queenslandicum, and Uncinocarpus reesii. We addressed the following questions: Is diversifying selection acting on PRA in the pathogenic species as a result of avoidance of the host's immune system, and has adaptation to a pathogenic life style lead to positive directional selection and increased rate of evolution in PRA between the species? For these purposes, we amplified and sequenced from 40 individuals belonging to the five species, the entire coding region of the PRA gene, as well as partial sequences from the coding region of each of the three housekeeping genes glyderaldehyde-3-phosphate dehydrogenase, glutamine synthetase A, and hexokinase A. We used likelihood-based methods to compare models of different types of selective pressure among codons to analyze the mode of evolution of the genes and found that the PRA gene evolves under positive selection, but the investigated parts of the housekeeping genes evolve primarily under purifying selection. We found a very low level of intraspecific variability and no evidence of diversifying selection, suggesting that the increased rate of evolution in the PRA gene is not a result of avoidance of the host's immune system. Neither did likelihood-based analyses suggest that selection was stronger on the branch separating pathogenic and nonpathogenic species. Instead, we suggest that positive selection act on PRA as a consequence of spore cell-wall morphogenesis unique to each species.     

Molecular phylogeny of litostome ciliates (Ciliophora, Litostomatea) with emphasis on free-living haptorian genera

The monophyly of the litostomes was tested using nine newly sequenced and four previously unpublished small subunit ribosomal RNA (SSrRNA) gene sequences from free-living Haptoria as well as from endosymbiotic Trichostomatia: the vestibuliferids Balantidium coli and Isotricha prostoma, the cyclotrichiid Mesodinium pulex, and the haptorids Loxophyllum rostratum, Dileptus sp., Enchelyodon sp., Enchelys polynucleata, Epispathidium papilliferum (isolates A and B), Spathidium stammeri, Arcuospathidium muscorum, Arcuospathidium cultriforme, and the unusual Teuthophrys trisulca. Phylogenetic analyses depicted the litostomes as a monophyletic group consisting of the trichostomes (subclass Trichostomatia) and the free-living haptorians (subclass Haptoria). The cyclotrichiids Mesodinium and Myrionecta (order Cyclotrichiida) branched either basally within or outside the Litostomatea. In most analyses, the haptorians did not receive support as a monophyletic group. Instead, Dileptus branched basally to all litostome taxa, and Epispathidium papilliferum grouped with the Subclass Trichostomatia. Some subgroupings, however, of haptorian genera corresponded to suggested superfamilial taxa (e.g., orders Spathidiida and Pleurostomatida). Within the monophyletic trichostomes, we can distinguish three clades: (1) an Australian clade; (2) the order Entodiniomorphida; and (3) the order Vestibuliferida. However, Balantidium, currently classified in the Vestibuliferida, did not group with the other vestibuliferids, suggesting that this order may be paraphyletic.     

Molecular evaluation of nominal species in the Ceratitis fasciventris, C. anonae, C. rosa complex (Diptera: Tephritidae)

Ceratitis fasciventris, C. anonae and C. rosa form a complex of economically important fruit fly pests infesting a variety of crops in African countries. Hitherto only adult males of these species can be distinguished easily by morphological characters. Other stages cannot, and for some taxa the taxonomic interpretation and species boundaries remain unclear. In order to clarify phylogenetic relationships and taxonomic status of these species, sequences of mitochondrial (16S, COI, ND6) and nuclear markers (period, ITS1) were analysed in specimens of the three morphospecies throughout the distribution of the complex. Maximum likelihood trees did not recover monophyletic groups corresponding to the morphospecies. Conversely, ND6 and COI divided West African C. fasciventris specimens in two consistent and bootstrap supported clades, involving specimens from Benin and from Mali/Ivory Coast, while the nuclear gene fragments per and ITS1 recovered a well-supported clade corresponding to C. fasciventris from Kenya/Uganda. Hence, the phylogenetic relationships and taxonomic interpretation of the complex appear more intricate than previously hypothesised. The current molecular data do not allow to identify C. fasciventris, C. anonae and C. rosa as distinct phylogenetic species but rather suggest that the morphospecies C. fasciventris is itself a complex of cryptic taxa.     

Molecular phylogenetic analysis of the genus Strongyloides and related nematodes

Strongyloides spp., parasitic nematodes of humans and many other terrestrial vertebrates, display an unusual heterogonic lifecycle involving alternating parasitic and free-living adult reproductive stages. A number of other genera have similar lifecycles, but their relationships to Strongyloides have not been clarified. We have inferred a phylogeny of 12 species of Strongyloides, Parastrongyloides, Rhabdias and Rhabditophanes using small subunit ribosomal RNA gene (SSU rDNA) sequences. The lineage leading to Strongyloides appears to have arisen within parasites of terrestrial invertebrates. Inferred lifecycle evolution was particularly dynamic within these nematodes. Importantly, the free-living Rhabditophanes sp. KR3021 is placed within a clade of parasitic taxa, suggesting that this species may represent a reversion to a non-parasitic lifecycle. Species within the genus Strongyloides are very closely related, despite the disparity of host species parasitised. The highly pathogenic human parasite Strongyloides fuelleborni kelleyi is not supported as a subspecies of the primate parasite S. fuelleborni fuelleborni, but is most likely derived from a local zoonotic source.     

Phylogeny and cryptic diversity in geckos (Phyllopezus; Phyllodactylidae; Gekkota) from South America's open biomes

The gecko genus Phyllopezus occurs across South America's open biomes: Cerrado, Seasonally Dry Tropical Forests (SDTF, including Caatinga), and Chaco. We generated a multi-gene dataset and estimated phylogenetic relationships among described Phyllopezus taxa and related species. We included exemplars from both described Phyllopezus pollicaris subspecies, P. p. pollicaris and P. p.przewalskii. Phylogenies from the concatenated data as well as species trees constructed from individual gene trees were largely congruent. All phylogeny reconstruction methods showed Bogertia lutzae as the sister species of Phyllopezus maranjonensis, rendering Phyllopezus paraphyletic. We synonymized the monotypic genus Bogertia with Phyllopezus to maintain a taxonomy that is isomorphic with phylogenetic history. We recovered multiple, deeply divergent, cryptic lineages within P. pollicaris. These cryptic lineages possessed mtDNA distances equivalent to distances among other gekkotan sister taxa. Described P. pollicaris subspecies are not reciprocally monophyletic and current subspecific taxonomy does not accurately reflect evolutionary relationships among cryptic lineages. We highlight the conservation significance of these results in light of the ongoing habitat loss in South America's open biomes.     

Mitochondrial genes reveal cryptic diversity in plant-breeding frogs from Madagascar (Anura, Mantellidae, Guibemantis)

One group of mantellid frogs from Madagascar (subgenus Pandanusicola of Guibemantis) includes species that complete larval development in the water-filled leaf axils of rainforest plants. This group consists of six described species: G. albolineatus, G. bicalcaratus, G. flavobrunneus, G. liber, G. pulcher, and G. punctatus. We sequenced the 12S and 16S mitochondrial rRNA genes ( approximately 1.8 kb) from multiple specimens (35 total) of all six species to assess phylogenetic relationships within this group. All reconstructions strongly supported G. liber as part of the Pandanusicola clade, even though this species does not breed in plant leaf axils. This result confirms a striking reversal of reproductive specialization. However, all analyses also indicated that specimens assigned to G. liber include genetically distinct allopatric forms that do not form a monophyletic group. Most other taxa that were adequately sampled (G. bicalcaratus, G. flavobrunneus, and G. pulcher) likewise consist of several genetically distinct lineages that do not form monophyletic groups. These results suggest that many of the recognized species in this group are complexes of cryptic species.     

DNA barcoding of the endemic New Zealand leafroller moth genera, Ctenopseustis and Planotortrix

Molecular techniques such as DNA barcoding have become popular in assisting species identification especially for cryptic species complexes. We have analysed data from a 468-bp region of the mitochondrial cytochrome oxidase subunit I (COI) gene from 200 specimens of 12 species of endemic New Zealand leafroller moths (Tortricidae) from the genera Planotortrix and Ctenopseustis to assess whether the DNA barcoding region can distinguish these species. Among the 200 sequences analysed, 72 haplotypes were recovered, with each genus forming a separate major clade. Maximum likelihood phylogenetic methods were used to test whether species fell into reciprocally monophyletic clades. The optimal phylogeny showed that four species within the genus Ctenopseustis (C. obliquana, C. herana, C. filicis and C. fraterna) and three within Planotortrix (P. octo, P. excessana and P. avicenniae) are polyphyletic. Shimodaira-Hasegawa tests rejected a null hypothesis of monophyly for the species C. obliquana, C. herana, P. octo and P. excessana. Comparisons of within and between species levels of sequence divergence for the same set of seven species showed cases where maximum levels of within-species divergence were greater than some levels of between-species divergence. DNA barcoding using this region of the COI gene is able to distinguish the two genera and some species within each genus; however, many species cannot be identified using this method. Finally, we discuss the possible reasons for this polyphyly, including incomplete lineage sorting, introgression, horizontal gene transfer and incorrect taxonomy.     

Molecular systematics and phylogeography of the cryptic species complex Baetis rhodani (Ephemeroptera, Baetidae)

Genetic studies have highlighted cryptic diversity in many well-known taxa including aquatic insects, with the general implication that there are more species than are currently recognised. Baetis rhodani Pictet are among the most widespread, abundant and ecologically important of all European mayflies (Ephemeroptera), and used widely as biological indicators of stream quality. Traditional taxonomy and systematics have never fully resolved differences among suspected cryptic species in the B. rhodani complex because morphological characters alone do not allow reliable distinction. This is particularly true among larvae, the life-stage used most widely in monitoring. Here, we assess the molecular diversity of this complex in one of the largest such studies of cryptic species in the order Ephemeroptera to date. Phylogenies were constructed using data from the mitochondrial cytochrome oxidase subunit I (COI) gene. Two monophyletic groups were recovered consisting of one major haplogroup and a second clade of 6 smaller but distinct haplogroups. Haplogroup divergence ranged from 0.2-3% (within) to 8-19% (among) with the latter values surpassing maxima typically reported for other insects, and provides strong evidence for cryptic species in the B. rhodani complex. The taxonomic status of these seven haplogroups remains undefined. Their distributions across Western Europe reveal no obvious geographic pattern, suggesting widespread diffusion of genetic lineages since the last glacial maximum. The implications of these findings are far-reaching given the ecological and bioindicator significance of what now appears to be several taxa.     

Phylogenetic relationships of Moxostoma and Scartomyzon (Catostomidae) based on mitochondrial cytochrome b sequence data

A recent phylogenetic study based on morphological, biochemical and early life history characters resurrected the genus Scartomyzon (jumprock suckers, c . eight−10 species) from Moxostoma (redhorse suckers, c . 10–11 species) and advanced the understanding of relationships among species in these two genera, and the genealogical affinities of these genera with other evolutionary lineages within the tribe Moxostomatini in the subfamily Catostominae. To further examine phylogenetic relationships among moxostomatin suckers, the complete mitochondrial (mt) cytochrome b gene was sequenced from all species within this tribe and representative outgroup taxa from the Catostomini and other catostomid subfamilies. Phylogenetic analysis of gene sequences yielded two monophyletic clades within Catostominae: Catostomus + Deltistes + Xyrauchen + Erimyzon + Minytrema and Moxostoma + Scartomyzon + Hypentelium + Thoburnia . Within the Moxostomatini, Thoburnia was either unresolved or polyphyletic; Thoburnia atripinnis was sister to a monophyletic Hypentelium . In turn, this clade was sister to a monophyletic clade containing Scartomyzon and Moxostoma . Scartomyzon was never resolved as monophyletic, but was always recovered as a polyphyletic group embedded within Moxostoma , rendering the latter genus paraphyletic if ' Scartomyzon ' continues to be recognized. Relationships among lineages within the Moxostoma and' Scartomyzon 'clade were resolved as a polytomy. To better reflect phylogenetic relationships resolved in this analysis, the following changes to the classification of the tribe Moxostomatini are proposed: subsumption of' Scartomyzon 'into Moxostoma ; restriction of the tribe Moxostomatini to Moxostoma ; resurrect the tribe Erimyzonini, containing Erimyzon and Minytrema , classified as incertae sedis within Catostominae; retain the tribe Thoburniini.     

Testing dispersal and cryptic diversity in a widely distributed groundwater amphipod (Niphargus rhenorhodanensis)

Theories about colonization and evolution in groundwater have assumed that the fragmented structure of groundwater strongly limits dispersal. The high number of endemic and allopatric species in groundwater supports this hypothesis, but the occurrence of widely distributed groundwater taxa calls into question its universality. These widely distributed taxa might also be sets of cryptic species because extreme conditions of life in groundwater promote cryptic diversity by inducing convergent morphological evolution. Niphargus rhenorhodanensis is a widely distributed and ubiquitous groundwater amphipod which supposedly colonized the Alps after Quaternary glaciations. We tested the dispersal and the cryptic species hypotheses within this species using a phylogeographic approach based on two mitochondrial genes (COI and 16S) and a nuclear gene (28S). Results support the view that poor dispersal is a main evolutionary factor in groundwater. All genes independently supported the existence of numerous cryptic and mostly allopatric units within N. rhenorhodanensis, indicating that its apparently wide distribution range is an artefact generated by cryptic diversity. We reject the hypothesis of a recent and global colonization of the Alps and argue that some N. rhenorhodanensis lineages probably survived glaciations near or within the Alps.     

Mitochondrial DNA sequences of the Afro-Arabian spiny-tailed lizards (genus Uromastyx; family Agamidae): phylogenetic analyses and evolution of gene arrangements

Approximately 1.7 kbp of mitochondrial DNA were sequenced from 29 individuals assignable to 11 Uromastyx species or subspecies and two other agamids. U. ocellata and U. ornata had an insertion between the glutamine and isoleucine tRNA genes, which could be folded into a stable stem-and-loop structure, and the insertion for U. ornata additionally retained a sequence similar to the glutamine tRNA gene. This corroborates the role of tandem duplication in reshaping mitochondrial gene arrangements, and supports the idea that the origin of light-strand replication could be relocated within mitochondrial genomes. Molecular phylogeny from different tree-building methods consistently placed African and Arabian taxa in mutually monophyletic groups, excluding U. hardwickii inhabiting India and Pakistan. Unlike previous studies based on morphology , U. macfadyeni did not cluster with morphologically similar Arabian taxa, suggesting convergent evolution to be responsible for the morphological similarities. Divergence times estimated among the Uromastyx taxa, together with geological and palaeontological evidence, suggest that the Uromastyx agamids originated from Central Asia during the Eocene and colonized Africa after its connection with Eurasia in the early Miocene. Their radiation may have been facilitated by repeated aridification of North Africa since the middle Miocene, and geological events such as the expansion of the Red Sea and the East African Rift Valley.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 85 , 247–260.     

A test for concordance between the multilocus genealogies of genes and microsatellites in the pathogenic fungus Coccidioides immitis

Uncovering the correct phylogeny of closely related species requires analysis of multiple gene genealogies or, alternatively, genealogies inferred from the multiple alleles found at highly polymorphic loci, such as microsatellites. However, a concern in using microsatellites is that constraints on allele sizes may occur, resulting in homoplasious distributions of alleles, leading to incorrect phylogenies. Seven microsatellites from the pathogenic fungus Coccidioides immitis were sequenced for 20 clinical isolates chosen to represent the known genetic diversity of the pathogen. An organismal phylogeny for C. immitis was inferred from microsatellite-flanking sequence polymorphisms and other restriction fragment length polymorphism-containing loci. Two microsatellite genetic distances were then used to determine phylogenies for C. immitis, and the trees found by these three methods were compared. Congruence between the organismal and microsatellite phylogenies occurred when microsatellite distances were based on simple allele frequency data. However, complex mutation events at some loci made distances based on stepwise mutation models unreliable. Estimates of times of divergence for the two species of C. immitis based on microsatellites were significantly lower than those calculated from flanking sequence, most likely due to constraints on microsatellite allele sizes. Flanking-sequence insertions/deletions significantly decreased the accuracy of genealogical information inferred from microsatellite loci and caused interspecific length homoplasies at one of the seven loci. Our analysis shows that microsatellites are useful phylogenetic markers, although care should be taken to choose loci with appropriate flanking sequences when they are intended for use in evolutionary studies.     

Comparative ITS and AFLP analysis of diploid Cardamine (Brassicaceae) taxa from closely related polyploid complexes

BACKGROUND AND AIMS: Diploid representatives from the related polyploid complexes of Cardamine amara, C. pratensis and C. raphanifolia (Brassicaceae), were studied to elucidate phylogenetic relationships among the complexes and among the individual taxa included. METHODS: Two independent molecular data sets were used: nucleotide sequences from the internal transcribed spacers (ITS) of nrDNA, and amplified fragment length polymorphism (AFLP) markers. Seventeen diploid taxa from the studied groups were sampled. KEY RESULTS: Both ITS and AFLP analyses provided congruent results in inferred relationships, and revealed two main lineages. While the C. amara group, consisting of C. wiedemanniana and four subspecies of C. amara, was resolved as a well-supported monophyletic group, taxa from the C. pratensis and C. tenera groups (the latter representing diploid taxa of the complex of C. raphanifolia) all appeared together in a single clade/cluster with no support for the recognition of either of the groups. Intra-individual polymorphisms and patterns of nucleotide variation in the ITS region in C. uliginosa and C. tenera, together with the distribution of AFLP bands, indicate ancient hybridization and introgression among these Caucasian diploids. CONCLUSIONS: The lack of supported hierarchical structure suggests that extensive reticulate evolution between these groups, even at the diploid level, has occurred (although an alternative explanation, namely ancestral polymorphism in ITS data, cannot be completely excluded). Several implications for the investigation of the polyploid complexes of concern are drawn. When tracing origins of polyploid taxa, a much more complex scenario should be expected, taking into account all relatives as potential parents, irrespective of the group in which they are classified.     

Recombination within sympatric cryptic species of the insect pathogenic fungus Metarhizium anisopliae

Metarhizium anisopliae is an insect pathogenic fungus with a worldwide distribution. It is being developed and used as a biocontrol agent against a wide range of insect pests but relatively little is known of the life history of this fungus. We tested hypotheses concerning reproductive isolation and recombination in a sample of heat-active (ability to grow at 37 degrees C) and cold-active (ability to grow at 8 degrees C) sympatrically occurring isolates of M. anisopliae from Ontario, Canada by assaying nucleotide sequence variation at six polymorphic loci: the internally transcribed spacer (ITS) region of the nuclear ribosomal DNA repeat, and portions of calmodulin (CAL), chitin synthase (CHS), subtilisin-like protease (PR1), neutral trehalase (NTL) and actin (ACT)-encoding genes. The most parsimonious trees constructed showed a topology consistent with the heat-active and cold-active isolates as two monophyletic groups. We then applied Genealogical Concordance Phylogenetic Species Recognition (GCPSR) to the genealogical trees and concluded that the transition from concordance among branches to incongruity among branches delimited two species of M. anisopliae within Ontario. The GCPSR of two species was supported by intraspecific incongruity within each species when tested using the Partition Homogeneity test, indicating recombination. The GCPSR of two species also corresponded to the heat-active and cold-active groups. As the groups are morphologically indistinguishable we applied the term 'cryptic species'. Therefore, the sympatrically occurring heat-active and cold-active isolates represent different cryptic species with a history of recombination among isolates within each species.     

Comparative genomic analysis of human fungal pathogens causing paracoccidioidomycosis

Paracoccidioides is a fungal pathogen and the cause of paracoccidioidomycosis, a health-threatening human systemic mycosis endemic to Latin America. Infection by Paracoccidioides, a dimorphic fungus in the order Onygenales, is coupled with a thermally regulated transition from a soil-dwelling filamentous form to a yeast-like pathogenic form. To better understand the genetic basis of growth and pathogenicity in Paracoccidioides, we sequenced the genomes of two strains of Paracoccidioides brasiliensis (Pb03 and Pb18) and one strain of Paracoccidioides lutzii (Pb01). These genomes range in size from 29.1 Mb to 32.9 Mb and encode 7,610 to 8,130 genes. To enable genetic studies, we mapped 94% of the P. brasiliensis Pb18 assembly onto five chromosomes. We characterized gene family content across Onygenales and related fungi, and within Paracoccidioides we found expansions of the fungal-specific kinase family FunK1. Additionally, the Onygenales have lost many genes involved in carbohydrate metabolism and fewer genes involved in protein metabolism, resulting in a higher ratio of proteases to carbohydrate active enzymes in the Onygenales than their relatives. To determine if gene content correlated with growth on different substrates, we screened the non-pathogenic onygenale Uncinocarpus reesii, which has orthologs for 91% of Paracoccidioides metabolic genes, for growth on 190 carbon sources. U. reesii showed growth on a limited range of carbohydrates, primarily basic plant sugars and cell wall components; this suggests that Onygenales, including dimorphic fungi, can degrade cellulosic plant material in the soil. In addition, U. reesii grew on gelatin and a wide range of dipeptides and amino acids, indicating a preference for proteinaceous growth substrates over carbohydrates, which may enable these fungi to also degrade animal biomass. These capabilities for degrading plant and animal substrates suggest a duality in lifestyle that could enable pathogenic species of Onygenales to transfer from soil to animal hosts.     

THE PHYLOGENY OF CAULERPA BASED ON RDNA INTERNAL TRANSCRIBED SPACER SEQUENCES

Phylogenetic hypotheses for the pantropical marine green algal genus, Caulerpa , were inferred based on analyses of nuclear-encoded rDNA internal transcribed spacer (ITS) sequences. Results of these analyses were used to assess the correspondence between rDNA phylogeny and traditional sectional taxonomy, to identify synapomorphic morphological characters (including assimilator morphology and chloroplast ultrastructure), and to examine marine biogeographic hypotheses for the genus. Ribosomal DNA ITS sequences were aligned for thirty-three species and intraspecific taxa of Caulerpa. Results indicate limited correspondence between phylogeny and sectional taxonomy for the genus, (e.g., the sections Filicoideae and Sedoideae were not monophyletic). In contrast, chloroplast morphology could be mapped to the tree topology with limited homoplasy. Pantropical isolates of the filicoidean species, Caulerpa sertularioides and Caulerpa mexicana each formed monophyletic groups. Caulerpa reyesii was included as a derived taxon within the Caulerpa taxifolia clade, suggesting that these species were conspecific and affirmed the lack of correspondence between phylogeny and assimilator morphology. Isolates and various intraspecific taxa of Caulerpa racemosa did not form a monophyletic group. Instead, these taxa formed a heterogeneous assemblage with other sedoidean and filicoidean taxa. Within the C. sertularioides clade, Caribbean and Atlantic isolates formed a basal paraphyletic group, whereas eastern and western Pacific isolates formed a more derived monophyletic group. Therefore, these results are not consistent with an Indo-West Pacific origin of this species.     

Acanthocephalan phylogeny and the evolution of parasitism

The study of parasite evolution relies on the identification of free-living sister taxa of parasitic lineages. Most lineages of parasitic helminths are characterized by an amazing diversity of species that complicates the resolution of phylogenetic relationships. Acanthocephalans offer a potential model system to test various long-standing hypotheses and generalizations regarding the evolution of parasitism in metazoans. The entirely parasitic Acanthocephala have a diversity of species that is manageable with regards to constructing global phylogenetic hypotheses, exhibit variation in hosts and habitats, and are hypothesized to have close phylogenetic affinities to the predominately free-living Rotifera. In this paper, I review and test previous hypotheses of acanthocephalan phylogenetic relationships with analyses of the available 18S rRNA sequence database. Maximum-parsimony and maximum-likelihood inferred trees differ significantly with regard to relationships among acanthocephalans and rotifers. Maximum-parsimony analysis results in a paraphyletic Rotifera, placing a long-branched bdelloid rotifer as the sister taxon of Acanthocephala. Maximum-likelihood analysis results in a monophyletic Rotifera. The difference between the two optimality criteria is attributed to long-branch attraction. The two analyses are congruent in terms of relationships within Acanthocephala. The three sampled classes are monophyletic, and the Archiacanthocephala is the sister taxon of a Palaeacanthocephala + Eoacanthocephala clade. The phylogenetic hypothesis is used to assess the evolution of host and habitat preferences. Acanthocephalan lineages have exhibited multiple radiations into terrestrial habitats and bird and mammal definitive hosts from ancestral aquatic habitats and fish definitive hosts, while exhibiting phylogenetic conservatism in the type of arthropod intermediate host utilized.