Description
Molecular Phylogenetics and Evolution is dedicated to bringing Darwin's dream - to "have fairly true genealogical trees of each great kingdom of Nature" - within grasp. The journal provides a forum for molecular studies that advance our understanding of phylogeny and evolution. This journal plays an important role by publishing the results of molecular studies that identify the actual clades to which different species and higher taxa belong. Such knowledge will further the development of phylogenetically more accurate taxonomic classifications and ultimately lead to a unified classification for all the ramifying lines of life.
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Molecular phylogenetics and evolution
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1055-7903
OCLC
23325059
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Periodical, Internet resource
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Elsevier
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Publications in this journal
Authors: Gael J. Kergoat, Bruno P. Le Ru, Gwenaelle Genson, Corinne Cruaud, Arnaud Couloux, Alex Delobel
Molecular Phylogenetics and Evolution. 59(3):746-760.
Though for a long time it was hypothesized that the extraordinary diversity of phytophagous insects was better explained by a synchronous pattern of co-diversification with plants, the results ofThough for a long time it was hypothesized that the extraordinary diversity of phytophagous insects was better explained by a synchronous pattern of co-diversification with plants, the results of recent studies have led to question this theory, suggesting that the diversification of insects occurred well after that of their hosts. In this study we address this issue by investigating the timing of diversification of a highly specialized group of seed beetles, which mostly feeds on legume plants from the tribe Indigofereae. To that purpose, a total of 130 specimens were sequenced for six genes and analyzed under a Bayesian phylogenetic framework. Based on the resulting trees we performed several analyses that allowed a better definition of the group boundaries and to investigate the status of several taxa through the use of molecular species delimitation analyses in combination with morphological evidences. In addition the evolution of host plant use was reconstructed and different molecular-dating approaches were carried out in order to assess the ages of several clades of interest. The resulting framework suggests a more ancient than previously thought origin for seed beetles, and a pattern of rapid host plant colonization. These findings call for further similar studies in other highly specialized groups of phytophagous insects.
Authors: M. Hill, A. Allenby, B. Ramsby, C. Schönberg, A. Hill
Molecular Phylogenetics and Evolution. 59:81-88.
Authors: Sylvia Schäffer, Tobias Pfingstl, Stephan Koblmüller, Kathrin A Winkler, Christian Sturmbauer, Günther Krisper
Molecular Phylogenetics and Evolution. 55(3):318-334.
a b s t r a c t The soil and moss dwelling oribatid mite family Scutoverticidae is considered to represent an assemblage of distantly related but morphologically similar genera. We used nucleotidea b s t r a c t The soil and moss dwelling oribatid mite family Scutoverticidae is considered to represent an assemblage of distantly related but morphologically similar genera. We used nucleotide sequences of one mitochon-drial (COI) and two nuclear (28S rDNA, ef-1a) genes, and 79 morphological characters to elucidate the phylogenetic relationships among 11 nominal plus two undescribed European mite species of the family Scutoverticidae with a particular focus on the genus Scutovertex. Both molecular genetic and morpholog-ical data revealed a paraphyletic genus Scutovertex, with S. pictus probably representing a distinct genus, and Provertex kuehnelti was confirmed as member of the family Scutoverticidae. Molecular genetic data confirmed several recently described Scutovertex species and thus the high species diversity within this genus in Europe and suggest that S. sculptus represents a complex of several cryptic species exhibiting marked genetic, but hardly any morphological divergence.
Authors: Stephan Koblmüller, Bernd Egger, Christian Sturmbauer, Kristina M Sefc
Molecular Phylogenetics and Evolution. 55(1):318-334.
a b s t r a c t The evolutionary history of the endemic Lake Tanganyika cichlid tribe Tropheini, the sister group of the species flocks of Lake Malawi and the Lake Victoria region, was reconstructeda b s t r a c t The evolutionary history of the endemic Lake Tanganyika cichlid tribe Tropheini, the sister group of the species flocks of Lake Malawi and the Lake Victoria region, was reconstructed from 2009 bp DNA sequence of two mitochondrial genes (ND2 and control region) and from 1293 AFLP markers. A period of rapid cladogenesis at the onset of the diversification of the Tropheini produced a multitude of special-ized, predominantly rock-dwelling aufwuchs-feeders that now dominate in Lake Tanganyika's shallow habitat. Nested within the stenotopic rock-dwellers is a monophyletic group of species, which also utilize more sediment-rich habitat. Most of the extant species date back to at least 0.7 million years ago. Several instances of disagreement between AFLP and mtDNA tree topology are attributed to ancient incomplete lineage sorting, introgression and hybridization. A large degree of correspondence between AFLP cluster-ing and trophic types indicated fewer cases of parallel evolution of trophic ecomorphology than previ-ously inferred from mitochondrial data.
Authors: Stephan Koblmüller, Ulrich K Schliewen, Nina Duftner, Kristina M Sefc, Cyprian Katongo, Christian Sturmbauer
Molecular Phylogenetics and Evolution. 49(1):153-169.
a b s t r a c t The Haplochromini are by far the most species-rich cichlid fish tribe that originated along with the so-called primary radiation of the Lake Tanganyika cichlid species flock, i.e. ata b s t r a c t The Haplochromini are by far the most species-rich cichlid fish tribe that originated along with the so-called primary radiation of the Lake Tanganyika cichlid species flock, i.e. at the same time during which the majority of the endemic Lake Tanganyika cichlid tribes emerged. Unlike the other tribes, the haplo-chromines are not restricted to Lake Tanganyika but distributed throughout Africa, except for the north-western part of the continent. Haplochromine cichlids seeded the adaptive radiation of cichlid fishes in Lakes Malawi, Kivu, Victoria, Turkana, as well as in the now extinct paleo-Lake Makgadikgadi. Here we present a comprehensive phylogenetic and phylogeographic analysis of haplochromine cichlids that is based upon DNA sequences of two mitochondrial gene segments of riverine taxa covering all major Afri-can biogeographic regions where haplochromines are found. Our analysis revealed that six lineages of haplochromines originated within a short period of time, about 5.3–4.4 MYA. These haplochromine lin-eages show a highly complex phylogeographic pattern, probably severely influenced by climate-and/or geology-induced changes of the environment, with river capture events most likely playing an important role for species dispersal.
Authors: Frank E Rheindt, Janette A Norman, Les Christidis
Molecular phylogenetics and evolution. 48(1):150-6.
We investigated mitochondrial and nuclear DNA in the small tyrant-flycatcher genus Zimmerius (Tyrannidae) and show that molecular data are in strong disagreement with morphology-based taxonomy, butWe investigated mitochondrial and nuclear DNA in the small tyrant-flycatcher genus Zimmerius (Tyrannidae) and show that molecular data are in strong disagreement with morphology-based taxonomy, but in good concordance with vocal characters. Our molecular data identified two independent cases of well-supported polyphyletic species arrangements within this genus that indicate the following taxonomic changes: elevation of Z. acer and Z. albigularis to species level, separation of northern populations of Z. chrysops as a species and inclusion of southern populations of Z. chrysops into Z. viridiflavus. Although polyphyly has rarely been encountered in bird systematics it has previously been shown for two other tyrannid genera and suggests that tyrannid taxonomy may be poorly resolved, presumably as a consequence of the conserved plumage patterns observed in many tyrannid genera. Our study suggests that vocalizations can be a better indicator of taxonomic limits than plumage pattern in tyrannids.
Authors: Jinliang Zhao, Chenhong Li, Lili Zhao, Weiwei Wang, Yang Cao
Molecular phylogenetics and evolution.
Authors: Takashi Nakada, Kazuharu Misawa, Hisayoshi Nozaki
Molecular phylogenetics and evolution. 48(1):281-91.
The taxonomy of Volvocales (Chlorophyceae, Chlorophyta) was traditionally based solely on morphological characteristics. However, because recent molecular phylogeny largely contradicts theThe taxonomy of Volvocales (Chlorophyceae, Chlorophyta) was traditionally based solely on morphological characteristics. However, because recent molecular phylogeny largely contradicts the traditional subordinal and familial classifications, no classification system has yet been established that describes the subdivision of Volvocales in a manner consistent with the phylogenetic relationships. Towards development of a natural classification system at and above the generic level, identification and sorting of hundreds of sequences based on subjective phylogenetic definitions is a significant step. We constructed an 18S rRNA gene phylogeny based on 449 volvocalean sequences collected using exhaustive BLAST searches of the GenBank database. Many chimeric sequences, which can cause fallacious phylogenetic trees, were detected and excluded during data collection. The results revealed 21 strongly supported primary clades within phylogenetically redefined Volvocales. Phylogenetic classification following PhyloCode was proposed based on the presented 18S rRNA gene phylogeny along with the results of previous combined 18S and 26S rRNA and chloroplast multigene analyses.
Authors: V A Funk, Raymund Chan
Molecular phylogenetics and evolution. 48(1):47-60.
The tribe Arctotideae (African Daisies), of the flowering plant family Compositae (Asteraceae), is a diverse and interesting group with a primarily southern African distribution (ca. 13 genera, 215The tribe Arctotideae (African Daisies), of the flowering plant family Compositae (Asteraceae), is a diverse and interesting group with a primarily southern African distribution (ca. 13 genera, 215 species) and many species in the Cape Floristic Region. It is divided into two subtribes: Arctotidinae (ca. 5 genera, 85 species) and Gorteriinae (ca. 8 genera, 130 species). The monophyly of the genera within the subtribe Gorteriinae and their relationship to one another was investigated using 71 samples/212 sequences including 64/141 of which are newly reported from three phylogenetic markers, two from chloroplast DNA (trnL-F and ndhF) and one from the nuclear genome (ITS). The outgroup was composed of seven members from the sister subtribe. Results show the subtribe Gorteriinae to be divided into three monophyletic groups, the Gazania-Hirpicium-Gorteria group, the Didelta group, and the Berkheya-Cullumia group. Within these three groups are 13 sub-groups, one of which has sub-clades. The genus Berkheya Ehrh. is paraphyletic, falling into five different sub-groups. The two monotypic genera, Cuspidia and Heterorhachis are not nested within any of the Berkheya clades. Hirpicium and Cullumia each have most of their taxa in a monophyletic group, but they also have one or two taxa associated with other clades. Four of the five sub-groups of Berkheya have morphologically recognizable shared characters, such as habit and spines that have been recognized by past studies. However, the grouping of one species with Didelta is difficult to explain. Support for the major clades and most of the sub-groups is strong but the relationships among some of the terminal taxa are variable.
Authors: Catherine R Linnen, Brian D Farrell
Molecular phylogenetics and evolution. 48(1):240-57.
Neodiprion Rohwer (Hymenoptera: Diprionidae) is a Holarctic genus of conifer-feeding sawflies with a remarkable amount of inter- and intraspecific diversity in host use, behavior, and development.Neodiprion Rohwer (Hymenoptera: Diprionidae) is a Holarctic genus of conifer-feeding sawflies with a remarkable amount of inter- and intraspecific diversity in host use, behavior, and development. This variation is thought to play a central role in Neodiprion diversification, but speciation hypotheses remain untested due to a lack of a robust phylogenetic estimate. Here, we utilize sequence data from three nuclear genes (CAD, ANL43, EF1alpha) to obtain a phylogenetic estimate for the genus. These analyses suggest that: (1) North American and Eurasian Neodiprion are monophyletic sister clades, (2) the sertifer group is paraphyletic with respect to the monophyletic lecontei group, and (3) on at least two occasions, dispersal from eastern to western North America proceeded via southern host bridges. Based on these results and host biogeography, we revise a previous scenario for the evolution of Neodiprion and suggest maximum ages for the genus and for the lecontei group (25 My and 14 My, respectively). In addition, because a previous study reported rampant mitochondrial introgression in the lecontei group, we assess its prevalence in the sertifer group. Analysis of three mitochondrial genes (COI, tRNA-leucine, and COII) reveals that mito-nuclear discordance is prevalent in the sertifer group, and patterns of species monophyly are consistent with those expected under frequent mitochondrial introgression. As was the case for lecontei group species, we find that introgression appears to be most pronounced between species that occasionally share hosts, suggesting that divergent host use is an important barrier to gene flow in Neodiprion. Finally, we suggest that the lack of phylogenetic resolution and prevalence of species non-monophyly in the non-Pinus feeding Neodiprion may result from the rapid divergence (possibly with gene flow) of these species following their entry into a novel adaptive zone.
Authors: Urban Olsson, Per Sundberg, Per Alström, Magnus Gelang, Per G P Ericson
Molecular phylogenetics and evolution. 48(1):383-5.
Authors: Nina Rønsted, George D Weiblen, V Savolainen, James M Cook
Molecular phylogenetics and evolution. 48(1):12-22.
We conducted the first molecular phylogenetic study of Ficus section Malvanthera (Moraceae; subgenus Urostigma) based on 32 Malvanthera accessions and seven outgroups representing other sections ofWe conducted the first molecular phylogenetic study of Ficus section Malvanthera (Moraceae; subgenus Urostigma) based on 32 Malvanthera accessions and seven outgroups representing other sections of Ficus subgenus Urostigma. We used DNA sequences from the nuclear ribosomal internal and external transcribed spacers (ITS and ETS), and the glyceraldehyde-3-phosphate dehydrogenase (G3pdh) region. Phylogenetic analysis using maximum parsimony, maximum likelihood and Bayesian methods recovered a monophyletic section Malvanthera to the exclusion of the rubber fig, Ficus elastica. The results of the phylogenetic analyses do not conform to any previously proposed taxonomic subdivision of the section and characters used for previous classification are homoplasious. Geographic distribution, however, is highly conserved and Melanesian Malvanthera are monophyletic. A new subdivision of section Malvanthera reflecting phylogenetic relationships is presented. Section Malvanthera likely diversified during a period of isolation in Australia and subsequently colonized New Guinea. Two Australian series are consistent with a pattern of dispersal out of rainforest habitat into drier habitats accompanied by a reduction in plant height during the transition from hemi-epiphytic trees to lithophytic trees and shrubs. In contradiction with a previous study of Pleistodontes phylogeny suggesting multiple changes in pollination behaviour, reconstruction of changes in pollination behaviour on Malvanthera, suggests only one or a few gains of active pollination within the section.
Authors: Yvonne C F Su, Gavin J D Smith, Richard M K Saunders
Molecular phylogenetics and evolution. 48(1):188-206.
Phylogenetic relationships within the magnoliid basal angiosperm genus Pseuduvaria (Annonaceae) are investigated using chloroplast DNA sequences from five regions: psbA-trnH spacer, trnL-F, matK,Phylogenetic relationships within the magnoliid basal angiosperm genus Pseuduvaria (Annonaceae) are investigated using chloroplast DNA sequences from five regions: psbA-trnH spacer, trnL-F, matK, rbcL, and atpB-rbcL spacer. Over 4000 nucleotides from 51 species (of the total 53) were sequenced. The five cpDNA datasets were analyzed separately and in combination using maximum parsimony (MP), maximum likelihood (ML), and Bayesian methods. The phylogenetic trees constructed using all three phylogenetic methods, based on the combined data, strongly support the monophyly of Pseuduvaria following the inclusion of Craibella phuyensis. The trees generated using MP were less well resolved, but relationships are similar to those obtained using the other methods. ML and Bayesian analyses recovered trees with short branch lengths, showing five main clades. This study highlights the evolutionary changes in seven selected morphological characters (floral sex, stamen and carpel numbers, inner petal color, presence of inner petal glands, flowering peduncle length, and monocarp size). Although floral unisexuality is ancestral within the genus, several evolutionary lineages reveal reversal to bisexuality. Other phylogenetic transitions include the evolution of sapromyophily, and fruit-bat frugivory and seed dispersal, thus allowing a wide range of adaptations for species survival.
Authors: R P Brown, B Terrasa, V Pérez-Mellado, J A Castro, P A Hoskisson, A Picornell, M M Ramon
Molecular phylogenetics and evolution. 48(1):350-8.
Phylogenetic relationships and timings of major cladogenesis events are investigated in the Balearic Island lizards Podarcislilfordi and P.pityusensis using 2675bp of mitochondrial and nuclear DNAPhylogenetic relationships and timings of major cladogenesis events are investigated in the Balearic Island lizards Podarcislilfordi and P.pityusensis using 2675bp of mitochondrial and nuclear DNA sequences. Partitioned Bayesian and Maximum Parsimony analyses provided a well-resolved phylogeny with high node-support values. Bayesian MCMC estimation of node dates was investigated by comparing means of posterior distributions from different subsets of the sequence against the most robust analysis which used multiple partitions and allowed for rate heterogeneity among branches under a rate-drift model. Evolutionary rates were systematically underestimated and thus divergence times overestimated when sequences containing lower numbers of variable sites were used (based on ingroup node constraints). The following analyses allowed the best recovery of node times under the constant-rate (i.e., perfect clock) model: (i) all cytochrome b sequence (partitioned by codon position), (ii) cytochrome b (codon position 3 alone), (iii) NADH dehydrogenase (subunits 1 and 2; partitioned by codon position), (iv) cytochrome b and NADH dehydrogenase sequence together (six gene-codon partitions), (v) all unpartitioned sequence, (vi) a full multipartition analysis (nine partitions). Of these, only (iv) and (vi) performed well under the rate-drift model. These findings have significant implications for dating of recent divergence times in other taxa. The earliest P.lilfordi cladogenesis event (divergence of Menorcan populations), occurred before the end of the Pliocene, some 2.6Ma. Subsequent events led to a West Mallorcan lineage (2.0Ma ago), followed 1.2Ma ago by divergence of populations from the southern part of the Cabrera archipelago from a widely-distributed group from north Cabrera, northern and southern Mallorcan islets. Divergence within P.pityusensis is more recent with the main Ibiza and Formentera clades sharing a common ancestor at about 1.0Ma ago. Climatic and sea level changes are likely to have initiated cladogenesis, with lineages making secondary contact during periodic landbridge formation. This oscillating cross-archipelago pattern in which ancient divergence is followed by repeated contact resembles that seen between East-West refugia populations from mainland Europe.
Authors: Omar Rota-Stabelli, Maximilian J Telford
Molecular phylogenetics and evolution. 48(1):103-11.
The choice of an appropriate outgroup is a fundamental prerequisite when the difference between two conflicting phylogenetic hypotheses depends on the position of the root. This is the case for theThe choice of an appropriate outgroup is a fundamental prerequisite when the difference between two conflicting phylogenetic hypotheses depends on the position of the root. This is the case for the myriapods that may group either with Pancrustacea forming a clade called Mandibulata, in accordance with morphological characters, or with chelicerates to form Myriochelata (also called Paradoxopoda) as has recently been proposed by mitochondrial and ribosomal RNA gene phylogenies. In order to understand the impact that outgroup choice may have on phylogenetic reconstruction, we have investigated compositional heterogeneity and genetic distance in mtDNA sequences of several different outgroups to the arthropods, selected from deuterostomes, lophotrochozoans and ecdysozoans, and have used them to root a phylogenetically balanced and compositionarily homogeneous arthropod dataset. Results indicate that some outgroups, in particular from lophotrochozoans, nematodes and an onychophoran have G+C content and strand specific biases which are very different from those of arthropods, suggesting that the use of such outgroups may interfere with the stationarity of the model to create a random outgroup effect. We suggest a multi criterion approach for the selection of optimal outgroup species on the basis of (1) low substitution rate, (2) ingroup-like G+C composition, (3) a new strand bias estimator called the skew index, (4) the ability of the outgroup to avoid a "random branching effect" and (5) phylogenetic proximity to arthropods. Inference of phylogeny using various outgroups shows that use of phylogenetically distant and compositionally distinct lophotrochozoans as outgroups strongly supports Myriochelata and use of more closely related, but fast evolving nematodes supports Mandibulata. A dataset comprising multiple ecdysozoan outgroups also supports Mandibulata, unless the compositionally distant Onychophora are included. A group of the best outgroups selected according to our multi criteria selection, and including the most closely related, least genetically distant and most compositionally similar outgroup, a priapulid worm, supports Mandibulata. We conclude that support for the Myriochelata hypothesis from mitochondrial sequences may depend on the nature of the outgroup sequences rather than a true phylogenetic signal. Finally, we advocate a careful analysis and an objective choice of outgroup when dealing with derived sequences, such as mitochondrial genomes.
Authors: M Virgilio, T Backeljau, N Barr, M DE Meyer
Molecular phylogenetics and evolution. 48(1):270-80.
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 speciesCeratitis 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.
Authors: Alexandra Pavlova, Robert M Zink, Sergei V Drovetski, Sievert Rohwer
Molecular phylogenetics and evolution. 48(1):61-73.
Climatic fluctuations during the Quaternary resulted in a dynamic history of species' range shifts, fragmentations and expansions. Some of these events left traces in the genetic structures of plantsClimatic fluctuations during the Quaternary resulted in a dynamic history of species' range shifts, fragmentations and expansions. Some of these events left traces in the genetic structures of plants and animals. Recent avian phylogeographic studies demonstrated that Holarctic birds responded idiosyncratically to Pleistocene climate fluctuations. We present phylogeographic analyses of the Holarctic collared sand martin (Riparia riparia) and the Asian pale sand martin (Riparia diluta), which were considered conspecific until recently. Mitochondrial and nuclear sequences confirm species status of the pale sand martin; the two species diverged sometime between late Pliocene and middle Pleistocene, but precise dates could not be provided without calibration of the substitution rate. Within the pale sand martin, we found two mitochondrial clades that are likely to have diverged in the Pleistocene, one from Central Siberia, and the other restricted to Mongolia. The two clades were sympatric with the collared sand martin in Buryatiya and Mongolia, respectively. The mitochondrial gene genealogy and phi(st) analysis of the collared sand martin haplotypes indicate recent, but not ongoing, gene exchange between North America and Eurasia, and restricted gene flow between western and eastern Siberia that likely resulted from historic fragmentation of the species' range during the last glacial maximum.
Authors: Oive Tinn, Todd H Oakley
Molecular phylogenetics and evolution. 48(1):157-67.
Dating evolutionary origins of taxa is essential for understanding rates and timing of evolutionary events, often inciting intense debate when molecular estimates differ from first fossilDating evolutionary origins of taxa is essential for understanding rates and timing of evolutionary events, often inciting intense debate when molecular estimates differ from first fossil appearances. For numerous reasons, ostracods present a challenging case study of rates of evolution and congruence of fossil and molecular divergence time estimates. On the one hand, ostracods have one of the densest fossil records of any metazoan group. However, taxonomy of fossil ostracods is controversial, owing at least in part to homoplasy of carapaces, the most commonly fossilized part. In addition, rates of evolution are variable in ostracods. Here, we report evidence of extreme variation in the rate of molecular evolution in different ostracod groups. This rate is significantly elevated in Halocyprid ostracods, a widespread planktonic group, consistent with previous observations that planktonic groups show elevated rates of molecular evolution. At the same time, the rate of molecular evolution is slow in the lineage leading to Manawa staceyi, a relict species that we estimate diverged approximately 500 million years ago from its closest known living relative. We also report multiple cases of significant incongruence between fossil and molecular estimates of divergence times in Ostracoda. Although relaxed clock methods improve the congruence of fossil and molecular divergence estimates over strict clock models, incongruence is present regardless of method. We hypothesize that this observed incongruence is driven largely by problems with taxonomy of fossil Ostracoda. Our results illustrate the difficulty in consistently estimating lineage divergence times, even in the presence of a voluminous fossil record.
Authors: M Daly, A Chaudhuri, L Gusmão, E Rodríguez
Molecular phylogenetics and evolution. 48(1):292-301.
Sea anemones (order Actiniaria) are among the most diverse and successful members of the anthozoan subclass Hexacorallia, being found at all depths and latitudes and in all marine habitats. MembersSea anemones (order Actiniaria) are among the most diverse and successful members of the anthozoan subclass Hexacorallia, being found at all depths and latitudes and in all marine habitats. Members of this group exhibit the greatest variation in anatomy, biology, and life history in Hexacorallia, and lack any morphological synapomorphy. Nonetheless, previous molecular phylogenetic studies have found that Actiniaria is monophyletic with respect to other extant hexacorallians. However, relationships within Actiniaria have remained unresolved, as none of these earlier works have included sufficient taxon sampling to estimate relationships within Actiniaria. We have analyzed sequences from two mitochondrial and two nuclear markers for representatives of approximately half of the family-level diversity within the order, and present the first phylogenetic tree for Actiniaria. We concur with previous studies that have suggested that molecular evolution is unusually slow in this group. We determine that taxonomic groups based on the absence of features tend not to be recovered as monophyletic, but that at least some classical anatomical features define monophyletic groups.
Authors: Lara D Shepherd, Barbara R Holland, Leon R Perrie
Molecular phylogenetics and evolution. 48(1):176-87.
A previous study of the relationships amongst three subgroups of the Austral Asplenium ferns found conflicting signal between the two chloroplast loci investigated. Because organelle genomes likeA previous study of the relationships amongst three subgroups of the Austral Asplenium ferns found conflicting signal between the two chloroplast loci investigated. Because organelle genomes like those of chloroplasts and mitochondria are thought to be non-recombining, with a single evolutionary history, we sequenced four additional chloroplast loci with the expectation that this would resolve these relationships. Instead, the conflict was only magnified. Although tree-building analyses favoured one of the three possible trees, one of the alternative trees actually had one more supporting site (six versus five) and received greater support in spectral and neighbor-net analyses. Simulations suggested that chance alone was unlikely to produce strong support for two of the possible trees and none for the third. Likelihood permutation tests indicated that the concatenated chloroplast sequence data appeared to have experienced recombination. However, recombination between the chloroplast genomes of different species would be highly atypical, and corollary supporting observations, like chloroplast heteroplasmy, are lacking. Wider taxon sampling clarified the composition of the Austral group, but the conflicting signal meant analyses (e.g., morphological evolution, biogeographic) conditional on a well-supported phylogeny could not be performed.
Authors: Hirotoshi Sato, Noriaki Murakami
Molecular phylogenetics and evolution. 48(1):326-34.
Among the higher fungi, reproductively isolated cryptic species exist that are morphologically difficult to distinguish owing to a lack of taxonomically useful morphological characters. Mating testsAmong the higher fungi, reproductively isolated cryptic species exist that are morphologically difficult to distinguish owing to a lack of taxonomically useful morphological characters. Mating tests are helpful for detecting reproductive isolation between cryptic species, but are often difficult to perform for higher fungi, especially ectomycorrhizal fungi. In order to identify cryptic species of the ectomycorrhizal genus Strobilomyces more efficiently, lineages were defined based on the nucleotide sequence of two mitochondrial genes. Then the gene flow among lineages was measured using cleaved amplified polymorphic sequences (CAPS) markers designed for single copy nuclear genes. No heterozygosity was observed between different lineages, but within the same lineage heterozygosity was present at the ratio expected given Hardy Weinberg equilibrium. These results show that the mtDNA lineages are separate Mendelian populations, possibly cryptic species that are reproductively isolated from each other.
Authors: Anna M Goebel, Tom A Ranker, Paul Stephen Corn, Richard G Olmstead
Molecular phylogenetics and evolution.
The Anaxyrus boreas species group currently comprises four species in western North America including the broadly distributed A. boreas, and three localized species, Anaxyrus nelsoni, AnaxyrusexsulThe Anaxyrus boreas species group currently comprises four species in western North America including the broadly distributed A. boreas, and three localized species, Anaxyrus nelsoni, Anaxyrusexsul and Anaxyrus canorus. Phylogenetic analyses of the mtDNA 12S rDNA, cytochrome oxidase I, control region, and restriction sites data, identified three major haplotype clades. The Northwest clade (NW) includes both subspecies of A. boreas and divergent minor clades in the middle Rocky Mountains, coastal, and central regions of the west and Pacific Northwest. The Southwest (SW) clade includes A. exsul, A. nelsoni, and minor clades in southern California. Anaxyrus canorus, previously identified as paraphyletic, has populations in both the NW and SW major clades. The Eastern major clade (E) includes three divergent lineages from southern Utah, the southern Rocky Mountains, and north of the Great Basin at the border of Utah and Nevada. These results identify new genetic variation in the eastern portion of the toad's range and are consistent with previous regional studies from the west coast. Low levels of control region sequence divergence between major clades (2.2-4.7% uncorrected pair-wise distances) are consistent with Pleistocene divergence and suggest that the phylogeographic history of the group was heavily influenced by dynamic Pleistocene glacial and climatic changes, and especially pluvial changes, in western North America. Results reported here may impact conservation plans in that the current taxonomy does not reflect the diversity in the group.
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