PHYLOGENY OF CARTERIA (CHLOROPHYCEAE) INFERRED FROM MOLECULAR AND ORGANISMAL DATA1

Comparative ultrastructural data have shown that at least two distinct groups exist within Carteria. Similarly, interpretations of variation in gross morphological features have led to the discovery of morphologically distinct groups within the genus. Partial sequences from the nuclear-encoded small- and large-subunit ribosomal RNA molecules of selected Carteria taxa were studied as a means of 1) testing hypotheses that distinct groups of species exist within the genus and 2) assessing monophyly of the genus. Parsimony analysis of the sequence data suggests that three Carteria species, C. lunzensis, C. crucifera, and C. olivieri, form a monophyletic group that is the basal sister group to all other ingroup flagellate taxa (including species of Chlamydomonas, Haematococcus, Stephanosphaera, Volvox, and Eudorina). Two other Carteria taxa, C. radiosa and Carteria sp. (UTEX isolate LB 762), form a clade that is the sister group to a clade that includes Haematococcus spp., Chlamydomonas spp., and Stephanosphaera. Thus, the sequence data support the interpretations of ultrastructural evidence that described two distinct Carteria lineages. Moreover, the sequence data suggest that these two Carteria groups do not form a monophyletic assemblage. Parsimony analysis of a suite of organismal (morphological, ultra-structural, life history, and biochemical) character data also suggest two distinct lineages among the five Carteria taxa; however, the organismal data are ambiguous regarding monophyly of these Carteria taxa. When the two independent data sets are pooled, monophyly of Carteria is not supported; therefore, the weight of available evidence, both molecular and organismal, fails to support the concept of Carteria as a natural genus.     

Phylogenetic resolution and systematics of the Asian tree frogs,Rhacophorus (Rhacophoridae,Amphibia)

Li, J.T., Li, Y., Murphy, R.W., Rao, D.‐Q. & Zhang, Y.‐P. (2012). Phylogenetic resolution and systematics of the Asian tree frogs, Rhacophorus (Rhacophoridae, Amphibia). —Zoologica Scripta, 41, 557–570. The treefrog genus Rhacophorus, a large genus with 80 species, has a wide range, occurring eastward from India to China, Japan, South‐east Asia, the Greater Sunda Islands and the Philippines. The phylogenetic relationships and taxonomic recognition of many species are very controversial. To stabilize the taxonomy, the phylogenetic relationships among about 52 species are investigated from 96 samples using mtDNA sequence data. Matrilineal relationships based on maximum likelihood and Bayesian inference methods resolve three well‐supported lineages (A, B and C), although the phylogenetic relationships among three lineages remain ambiguous. Analyses support recognition of two previously assigned subgenera, Leptomantis and Rhacophorus, and these correspond to lineages A and B, respectively. Given that we have three strongly supported lineages, that these lineages are morphologically distinct, and the constrained geographic distributions of these groups, we recognize each lineage as a taxon. Subgenus Leptomantis includes species mainly from Malaysia, Indonesia and the Philippines. Subgenus Rhacophorus contains a mix of species occurring in India, Indochina and southern China. Lineage C accommodates species distributed mostly in East Asia, including Japan and China. Based on genetic and morphological data from type localities, the taxonomic recognition of some species needs to be reconsidered. Rhacophorus pingbianensis and Polypedates spinus are considered as junior synonyms of Rhacophorus duboisi. Specimens of Rhacophorus rhodopus from Vietnam and Hainan, China likely represent an undescribed, cryptic species.     

Phylogeny of Dendroctonus bark beetles (Coleoptera: Curculionidae: Scolytinae) inferred from morphological and molecular data

Bark beetles in the genus Dendroctonus may attack and kill several species of coniferous trees, some of them causing major economic losses in temperate forests throughout North and Central America. For this reason, they have been widely studied. However, various aspects of the taxonomy and evolutionary history of the group remain contentious. The genus has been subdivided in species groups according to morphological, biological, karyological or molecular attributes, but the evolutionary affinities among species and species groups within the genus remain uncertain. In this study, phylogenetic relationships among Dendroctonus species were reassessed through parsimony‐based cladistic analysis of morphological and DNA sequence data. Phylogenetic inference was based on 36 morphological characters and on mitochondrial DNA sequences of the cytochrome oxidase I (COI) gene. Analyses were carried out for each dataset, as well as for the combined data analysed simultaneously, under equal and implied weights. According to the combined analysis, the genus Dendroctonus is a monophyletic group defined by at least three synapomorphic characters and there are four main lineages of varied composition and diversity within the genus. Within these lineages, several monophyletic groups match, to some extent, species groups defined by previous authors, but certain groups proposed by those authors are polyphyletic or paraphyletic.     

EVOLUTIONARY CONSEQUENCES OF THE LOSS OF PHOTOSYNTHESIS IN CHLAMYDOMONADACEAE: PHYLOGENETIC ANALYSIS OF Rrn18 (18S rDNA) IN 13 POLYTOMA STRAINS (CHLOROPHYTA)1

Complete sequences of the Rrn 18 genes were obtained from 13 strains of the nonphotosynthetic algal genus Polytoma. Phylogenetic analyses showed that these strains formed two clades. One clade shows only modest sequence diversity but is represented by strains collected at widely dispersed sites in Europe and America. The other clade consists of a single isolate from the Canary Islands. Both clades lie well within the extended clade that includes all species of Chlamydomonas for which sequence data are available. The two Polytoma clades are separated from each other by several green species, suggesting that the extant nonphotosynthetic Chlamydomonadaceae arose from photosynthetic ancestors at least twice. These results suggest that nonphotosynthetic mutants are capable of establishing lineages that can spread widely but have a higher probability of extinction than their photosynthetic congeners.     

Phylogeography and phylogenetic relationships of Malagasy tree and ground boas

Three species of boid snakes are recognized in Madagascar, namely the genus Sanzinia (one species and two subspecies) and the genus Acrantophis (two species). In the present study, we studied the patterns of genetic variation of these species across Madagascar using a fragment of the mitochondrial 16S rRNA gene in 77 specimens. To support the phylogenetic relationships of the lineages identified, three further gene fragments (cytochrome b, 12S rRNA and c‐mos) were analyzed in a reduced but representative set of samples. The results obtained corroborate that the genus Sanzinia includes two highly divergent mitochondrial lineages that evolved independently from each other on the east versus the west side of Madagascar. Each of these lineages presents a further subdivision that separates northern from southern groups. The nuclear marker showed no variation among the Malagasy boas, indicating either very low substitution rates in this gene or relatively recent speciation events coupled with high mitochondrial substitution rates. Because the broad geographic sampling detected no admixture among haplotypic lineages within Sanzinia, it is hypothesized that these may represent distinct species. Deviant haplotypes of snakes morphologically similar to Acrantophis dumerili indicate that this taxon may be a complex of two species as well. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 640–652.     

Multiple cryptic species of sympatric generalists within the avian blood parasite Haemoproteus majoris

The avian haemosporidian parasite Haemoproteus majoris has been reported to infect a wide range of passerine birds throughout the Holarctic ecozone. Five cytochrome b (cyt b) lineages have been described as belonging to the morphological species H. majoris, and these form a tight phylogenetic cluster together with 13 undescribed lineages that differ from each other by < 1.2% in sequence divergence. Records in a database (MalAvi) that contains global findings of haemosporidian lineages generated by universal primers suggest that these lineages vary substantially in host distribution. We confirm this pattern in a data set collected at Lake Kvismaren, Sweden, where three of the generalist lineages have local transmission. However, whether these lineages represent intraspecific mitochondrial diversity or clusters of cryptic species has previously not been examined. In this study, we developed novel molecular markers to amplify the partial segments of four nuclear genes to determine the level of genetic diversity and gene phylogenies among the five morphologically described cyt b lineages of H. majoris. All five cyt b lineages were strongly associated with unique nuclear alleles at all four nuclear loci, indicating that each mitochondrial lineage represents a distinct biological species. Within lineages, there was no apparent association between nuclear alleles and host species, indicating that they form genetically unstructured populations across multiple host species.     

Colonization and speciation on volcanic islands: phylogeography of the flightless grasshopper genus Arminda (Orthoptera,Acrididae) on the Canary Islands

Abstract Volcanic archipelagos represent excellent areas to study colonization and speciation processes. The grasshopper genus Arminda is one of many endemic taxa of the Canary Islands. It consists of seven wingless species, most of which are single‐island endemics. We sequenced two mitochondrial (12s rRNA, ND5) and two nuclear gene fragments (28s rRNA, ITS2) to reconstruct the colonization pattern of the genus. Our results are in accordance with a stepping‐stone colonization model from east to west, corresponding to the prevailing ocean currents, but alternative hypotheses cannot be fully rejected. The populations of A. brunneri from Tenerife belong to two different lineages (east and west) consistent with the geological history of the island. It remains to be tested whether these lineages represent different species and whether further lineages exist on this island. The five clades of the four western islands (A. brunneri group) have approximately similar branch lengths. The short internodes between these lineages resulted in a poorer phylogenetic resolution. Specimens from La Palma were genetically distinct and are subsequently described as a new species, Arminda palmae sp.n. Our results suggest in situ speciation on Gran Canaria, which was accompanied by a stronger degree of morphological diversification than the inter‐island speciation processes. The aberrant species A. canariensis has formerly been assigned to a monotypic subgenus Chopardminda, which is now synonymized with Arminda syn.n. based on its phylogenetic position. Gran Canaria seems to be the only island where Arminda species occur sympatrically, although allopatric speciation seems likely due to the long history of volcanism and erosion on the island.     

Taxonomic revision of Chlamydomonas subg. Amphichloris (Volvocales,Chlorophyceae), with resurrection of the genus Dangeardinia and descriptions of Ixipapillifera gen. nov. and Rhysamphichloris gen. nov.

Chlamydomonas (Cd.) is one of the largest but most polyphyletic genera of freshwater unicellular green algae. It consists of 400–600 morphological species and requires taxonomic revision. Toward reclassification, each morphologically defined classical subgenus (or subgroup) should be examined using culture strains. Chlamydomonas subg. Amphichloris is characterized by a central nucleus between two axial pyrenoids, however, the phylogenetic structure of this subgenus has yet to be examined using molecular data. Here, we examined 12 strains including six newly isolated strains, morphologically identified as Chlamydomonas subg. Amphichloris, using 18S rRNA gene phylogeny, light microscopy, and mitochondria fluorescent microscopy. Molecular phylogenetic analyses revealed three independent lineages of the subgenus, separated from the type species of Chlamydomonas, Cd. reinhardtii. These three lineages were further distinguished from each other by light and fluorescent microscopy—in particular by the morphology of the papillae, chloroplast surface, stigmata, and mitochondria—and are here assigned to three genera: Dangeardinia emend., Ixipapillifera gen. nov., and Rhysamphichloris gen. nov. Based on the molecular and morphological data, two to three species were recognized in each genus, including one new species, I. pauromitos. In addition, Cd. deasonii, which was previously assigned to subgroup “Pleiochloris,” was included in the genus Ixipapillifera as I. deasonii comb. nov.     

Phylogenetic Analysis of Burkholderia Species by Multilocus Sequence Analysis

Burkholderia comprises more than 60 species of environmental, clinical, and agro-biotechnological relevance. Previous phylogenetic analyses of 16S rRNA, recA, gyrB, rpoB, and acdS gene sequences as well as genome sequence comparisons of different Burkholderia species have revealed two major species clusters. In this study, we undertook a multilocus sequence analysis of 77 type and reference strains of Burkholderia using atpD, gltB, lepA, and recA genes in combination with the 16S rRNA gene sequence and employed maximum likelihood and neighbor-joining criteria to test this further. The phylogenetic analysis revealed, with high supporting values, distinct lineages within the genus Burkholderia. The two large groups were named A and B, whereas the B. rhizoxinica/B. endofungorum, and B. andropogonis groups consisted of two and one species, respectively. The group A encompasses several plant-associated and saprophytic bacterial species. The group B comprises the B. cepacia complex (opportunistic human pathogens), the B. pseudomallei subgroup, which includes both human and animal pathogens, and an assemblage of plant pathogenic species. The distinct lineages present in Burkholderia suggest that each group might represent a different genus. However, it will be necessary to analyze the full set of Burkholderia species and explore whether enough phenotypic features exist among the different clusters to propose that these groups should be considered separate genera.     

Examining the phylogeny of the Australasian Lymnaeidae (Heterobranchia: Pulmonata: Gastropoda) using mitochondrial, nuclear and morphological markers

We examined the species groups relationships of the freshwater snail genus Austropeplea using mitochondrial, nuclear and morphological markers in addition to traditional methods of shell shape analysis. Based primarily on the results of a combined molecular and morphological analysis, samples of the nominal species A. tomentosa form distinct lineages. The New Zealand populations of A. tomentosa are a very distinct lineage from any of the Australian populations attributed to A. tomentosa. Furthermore, within the Australian group, three lineages, south Australia, Tasmania and eastern Australia, appear to have undergone recent and/or rapid speciation events. Samples assigned to A. lessoni were resolved as two distinct lineages, representing the eastern and northern Australian populations. Kutikina hispida was resolved within the Australian A. tomentosa clade. Molecular results for A. viridis suggests that it is also composed of at least two distinct lineages that could be treated as species. Incongruence observed between the single mitochondrial, nuclear and morphological topologies highlight the importance of using a number of different datasets in the delimitation of species-group taxa.     

Long forsaken species diversity in the Middle American lizard Holcosus undulatus (Teiidae)

Numerous reptile species have been divided into subspecies. Although this classification may capture the morphological variation within species, it often conceals significant species diversity because many subspecies actually represent species under lineage‐based species concepts. The lizard Holcosus undulatus is a common, widely distributed, monotypic species in Middle America. However, 12 subspecies of this taxon were recognized until the early 1970s. We used two lineage‐based methods for species delimitation to re‐evaluate species limits within H. undulatus with DNA sequence and morphological data. We included all the previously recognized subspecies of H. undulatus except H. u. miadis. Holcosus undulatus was exclusive. In addition, H. u. amphigrammus, H. u. gaigeae, H. u. hartwegi, H. u. parvus, H. u. pulcher, H. u. sinister, H. u. stuarti, H. u. thomasi and H. u. undulatus were supported as distinct evolutionary lineages based on the molecular and morphological evidence. We therefore elevate all of these subspecies to species rank. In addition, two separate mitochondrial lineages may represent cryptic, undescribed species within H. undulatus. The morphological distinctness and allopatry of H. u. miadis and H. u. pulcher, as well as the high genetic divergence of the latter species, suggest that they also represent distinct evolutionary species. Our results also suggest that additional species diversity may still be hidden within the H. u. amphigrammus, H. u. parvus, H. u. sinister and H. u. undulatus lineages. This work supports resurrection of overlooked diversity within Holcosus, which has important implications for the conservation of this genus in Middle America. © 2015 The Linnean Society of London     

Deep phylogeographic structure may indicate cryptic species within the Sparid genus Spondyliosoma

Two geographically nonoverlapping species are currently described within the sparid genus Spondyliosoma: Spondyliosoma cantharus (Black Seabream) occurring across Mediterranean and eastern Atlantic waters from NW Europe to Angola and S. emarginatum (Steentjie) considered endemic to southern Africa. To address prominent knowledge gaps this study investigated range-wide phylogeographic structure across both species. Mitochondrial DNA sequences revealed deep phylogeographic structuring with four regionally partitioned reciprocally monophyletic clades, a Mediterranean clade and three more closely related Atlantic clades [NE Atlantic, Angola and South Africa (corresponding to S. emarginatum)]. Divergence and distribution of the lineages reflects survival in, and expansion from, disjunct glacial refuge areas. Cytonuclear differentiation of S. emarginatum supports its validity as a distinct species endemic to South African waters. However, the results also indicate that S. cantharus may be a cryptic species complex wherein the various regional lineages represent established/incipient species. A robust multilocus genetic assessment combining morphological data and detailing interactions among lineages is needed to determine the full diversity within Spondyliosoma and the most adequate biological and taxonomic status.     

Species delimitation in Neotropical fishes of the genus Characidium (Teleostei,Characiformes)

Neotropical darters of the genus Characidium have a complex systematic history with several examples of sympatry throughout their distribution range in Neotropical freshwaters. Although various species within the genus have been used as models to investigate chromosomal evolution and biogeography, species boundaries and relationships still remain uncertain. Here, we use mitochondrial DNA sequences to perform species delimitation analyses within Characidium and test previous hypotheses of species richness within the Characidium zebra complex and among sympatric morphotypes of C. alipioi. Results indicate high genetic distances within tested species complexes and revealed the presence of strongly supported lineages such as the large C. lauroi group from southeastern Brazil. This suggests that the evolutionary history of these groups may be correlated with biogeographic history. Analyses also reveal that three geographically isolated populations of C. zebra represent a single species, leading us to reject prior hypothesis of multiple species. Species delimitation using mitochondrial data strongly supports the presence of two sympatric species within C. alipioi in southeastern Brazil despite limited morphological variation and conserved chromosomal patterns. These results provide a framework to further the study of systematics and evolution within Characidium.     

Unravelling evolutionary lineages among South African velvet worms (Onychophora: Peripatopsis) provides evidence for widespread cryptic speciation

The endemic South African velvet worm genus Peripatopsis currently contains eight recognized species described from variable morphological characters and the current taxonomy is unsatisfactory. In an attempt to investigate evolutionary relationships within Peripatopsis, we collected 137 individuals from 34 sample localities for six of the eight species. Sequence data derived from two partial mitochondrial (mt)DNA gene loci (COI and 12S rRNA), as well as partial sequence data from the ribosomal nuclear 18S rDNA locus in combination with gross morphological characters and scanning electron microscopy (SEM), was used to examine evolutionary relationships. Phylogenetic relationships were investigated using minimum evolution (ME) and Bayesian inferences (BI). Additionally, we also undertook a maximum likelihood (ML) analyses on the combined DNA sequence data set. The combined DNA evidence topologies derived from the ME, BI, and ML was highly congruent and was characterized by the presence of multiple lineages within recognized taxa. Peripatopsis clavigera, Peripatopsis moseleyi, and Peripatopsis sedgwicki each comprised two evolutionary lineages; Peripatopsis capensis comprised three; and Peripatopsis balfouri comprised six operational taxonomic units respectively. Genealogical exclusivity at both mtDNA and nuclear DNA among the geographically coherent groups coupled with pronounced sequence divergence suggested a two‐fold increase in the number of species within Peripatopsis. Previously used gross morphological characters (such as the number of leg pairs and colour) were either highly variable within operational taxonomic units, or were invariant, suggesting that alternative morphological characters are necessary for species discrimination. SEM results revealed potentially useful diagnostic characters that can discriminate between at least discriminate some of the newly‐identified lineages. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society 2009, 97 , 200–216.     

An integrative approach to the evolution of shrimps of the genus Palaemon (Decapoda,Palaemonidae)

Shrimps of the genus Palaemon Weber, 1795 comprise of 86 species with a wide morphological and ecological variability along the tropical and temperate regions. Studies based on molecular data have indicated that despite a recent taxonomic rearrangement, it may remain not monophyletic. On the other hand, cladistic, morphological analyses have suggested the presence of synapomorphies, implying a natural status for the genus. In this work, a broad taxonomic and molecular sampling is applied to verify whether Palaemon is a monophyletic taxon and, based on the recovered phylogeny, identify geographical and morphological patterns related to the lineages. Partial sequences of 16S rRNA, histone H3 and 18S rRNA from 60 species of Palaemon and 15 species from other genera of Palaemonidae were analysed. In addition, previously used characters as well as novel diagnostic characters were scrutinized. The present phylogeny indicates that the species of Palaemon fall into three distinct lineages and that the colonization of America and Europe likely occurred multiple times. Morphological characters allow for the identification of at least four monophyletic groups in Palaemon; two of which are monospecific at the moment. Based on the present results, it may become necessary to establish two new genera (to accommodate Palaemon concinnus and Palaemon mercedae, respectively), as well as re‐erect the genus Alaocaris Holthuis, 1949 for Palaemon antrorum, potentially including a further six American species.     

Mitochondrial DNA phylogeny of North American field crickets: perspectives on the evolution of life cycles,songs, and habitat associations

North American field crickets (genus Gryllus) exhibit a diversity of life cycles, habitat associations, and calling songs. However, patterns of evolution for these ecological and behavioral traits remain uncertain in the absence of a robust phylogenetic framework. Analyses of morphological variation have provided few clues about species relationships in the genus Gryllus. Here we use comparisons of mitochondrial DNA restriction site maps for 29 individuals representing 11 species (including potential outgroups) to examine relationships among eastern North American field crickets. Initially chosen as likely outgroup taxa, the two European species of Gryllus do not obviously fall outside of an exclusively North American clade and (based on amount of sequence divergence) appear to have diverged from North American lineages at about the same time that major North American lineages diverged from each other. The egg-overwintering crickets comprise a strongly supported monophyletic group, but relationships among these three closely related species cannot be resolved. The mtDNA data are consistent with a single origin of egg diapause and do not support a model of recent life cycle divergence and allochronic speciation for Gryllus pennsylvanicus and G. veletis. The two crickets are not sister species, despite remarkable similarity in morphology, habitat, and calling song. This conclusion is consistent with published data on allozyme variation in North American field crickets. The habitat associations of eastern North American field crickets have been labile, but calling songs sometimes have remained virtually unchanged across multiple speciation events.     

Phylogeny,genetic diversity and phylogeography of the genus Codoma (Teleostei,Cyprinidae)

This study represents a thorough analysis of Codoma, a monotypic genus endemic to north‐western Mexico. A previous morphological analysis of the species concluded that there exists several morphological groups in Codoma ornata, suggesting diversity in Codoma could be underestimated. No studies have examined the genetic diversity in Codoma ornata to test this hypothesis and identify independent lineages. We present a phylogeographic analysis using one mitochondrial and two nuclear genes, and specimens from across nine major drainages in both the Chihuahuan Desert and the Sierra Madre Occidental of western Mexico. All genes and analyses recovered populations of Codoma in a well‐supported clade and sister to Tampichthys, and this clade sister to Cyprinella. Analyses of both mitochondrial and nuclear genes indicated Codoma is not monotypic and recover more diversity in the genus than currently recognized. The four (mitochondrial) and five (nuclear) genetically distinct lineages are consistent with those groups outlined in the prior morphological study of the genus. Composition and distribution of these major lineages is also consistent with prior biogeographic hypothesis for other fishes in the region, supporting an ancestral Rio Grande system extending south towards central Mexico. Fragmentation of this paleosystem was followed by allopatric speciation in the Chihuahuan Desert. These results suggest a scenario of long‐term isolation in four major regions (upper Conchos, lower Conchos, Nazas, upper Mezquital). Resolution of the diversity and biogeography of these lineages has many implications for various biological disciplines, especially for evolutionary and conservation studies.     

<Emphasis Type="Italic">Cleistocybe</Emphasis>, a new genus of Agaricales

A new clitocyboid genus of Agaricales, Cleistocybe, is described to accommodate the isolated evolutionary position of the new species Cleistocybe vernalis inferred by a previously published multigene phylogenetic study. Cleistocybe is distinguished from other clitocyboid lineages by a combination of morphological characters, including lamellae that become gray in age, an interwoven hymenophoral trama with divergent elements when young, strongly interwoven pileipellis with pigmented and encrusted hyphae, white spore deposit, a distinct or ephemeral fibrillose to submembranous partial veil, and smooth, inamyloid basidiospores that are inequilateral in profile view. Cleistocybe encompasses two species, C. vernalis and Clitocybe gomphidioides, based on morphological comparisons with C. vernalis. Clitocybe subvelosa is confirmed as conspecific with C. gomphidioides based on morphological and ITS sequence comparisons of type collections. Cleistocybe is known only from western North America in coniferous forests and appears most closely related to the ectomycorrhizal genus Catathelasma and the saprotrophic genera Callistosporium, Macrocybe, and Pleurocollybia based on nLSU-rDNA phylogenetic analysis. Together these lineages constitute the Catathelasma clade.