Cladogram Topology Research Articles

Evolution, Inheritance, and Strata Formation of the W Chromosome in Duck (Anas platyrhynchos)

Abstract The nonrecombining female-limited W chromosome is predicted to experience unique evolutionary processes. Difficulties in assembling W chromosome sequences have hindered the identification of duck W-linked sequences and their evolutionary footprint. To address this, we conducted three initial contig-level genome assemblies and developed a rigorous pipeline by which to successfully expand the W-linked data set, including 11 known genes and 24 newly identified genes. Our results indicate that the W chromosome expression may not be subject to female-specific selection; a significant convergent pattern of upregulation associated with increased female-specific selection was not detected. The genetic stability of the W chromosome is also reflected in the strong evolutionary correlation between it and the mitochondria; the complete consistency of the cladogram topology constructed from their gene sequences proves the shared maternal coevolution. By detecting the evolutionary trajectories of W-linked sequences, we have found that recombination suppression started in four distinct strata, of which three were conserved across Neognathae. Taken together, our results have revealed a unique evolutionary pattern and an independent stratum evolutionary pattern for sex chromosomes.

The Coral of Plants

The present article has two primary objectives. First, the article provides a historical overview of graphical tools used in the past centuries for summarizing the classification and phylogeny of plants. It is emphasized that each published diagram focuses on only a single or a few aspects of the present and past of plant life on Earth. Therefore, these diagrams are less useful for communicating general knowledge in botanical research and education. Second, the article offers a solution by describing the principles and methods of constructing a lesser- known image type, the coral, whose potential usefulness in phylogenetics was first raised by Charles Darwin. Cladogram topology, phylogenetic classification and nomenclature, diversity of taxonomic groups, geological timescale, paleontological records, and other relevant information on the evolution of Archaeplastida are simultaneously condensed for the first time into the same figure – the Coral of Plants. This image is shown in two differently scaled parts to efficiently visualize as many details as possible, because the evolutionary timescale is much longer, and the extant diversity is much lower for red and green algae than for embryophytes. A fundamental property of coral diagrams, that is their self-similarity, allows for the redrawing of any part of the diagram at smaller scales.

The last Pleistocene glaciations phylogeography episode of Phaneroptera falcata (Poda, 1761) (Orthoptera: Tettigoniidae) in the Volga River basin based on the mtDNA Cytochrome C Oxidase subunit 1 (COI) gene fragment

This study is to research the phylogeography of Phaneroptera falcata (Poda, 1761) in the Volga river basin based on the mtDNA Cytochrome C Oxidase subunit 1 (COI) gene fragment at the last Pleistocene glaciation episode. The studied location is the Volga river basin, a territory within the central and partially southern parts of European Russia; it includes the rivers Volga, Oka, Khoper and Don basins. We used the traditional molecular phylogeography methods: mtDNA COI gene fragment from the key locations within the studied area was sequenced and then analyzed (cladogram topology, haplotype diversity, cladogram calibration etc.). The phylogenetic tree shows the dispersion of our samples over the following regions: Lower Volga, Middle Volga, Lower Oka, Middle Oka, Upper Oka, Don basin, Khoper basin. Nine haplotypes determined from our samples; they are grouped into 7 haplogroups. Six of them are in the basins of the main rivers of the Volga region: three haplogroups - on the Oka (Upper, Middle and Lower Oka respectively), haplogroups of the Khoper and Don basins, and the haplogroup of the Middle Volga combining two subgroups – Lower and Middle Volga basins. The distribution of found haplogroups correlates with big river basins in the Volga area (Volga, Oka, Khoper, Don).

Phylogenetic signal analysis in the basicranium of Ursidae (Carnivora, Mammalia).

Ursidae is a monophyletic group comprised of three subfamilies: Tremarctinae, Ursinae and Ailuropodinae, all of which have a rich geographical distribution. The phylogenetic relationships within the Ursidae group have been underexamined, especially regarding morphological traits such as the basicranium. Importantly, the basicranium is a highly complex region that covers a small portion of the skull, combining both structural and functional aspects that determine its morphology. Phylogenetic hypotheses of the Ursidae (including Tremarctinae) have been made based on morphological characters that considers skull, mandible and teeth features, while specific characters of the auditory region and basicranium have not been taken into account. To do this, we analyse the shape and size macroevolution of the basicranium of Ursidae, testing its morphological disparity in a phylogenetic context, which is quantified by means of the phylogenetic signal. We investigated phylogenetical autocorrelation by shape (depicted by Principal Components Analysis scores from previous published analyses) and basicranium size (depicted by centroid size, CS) using an orthonormal decomposition analysis and Abouheif C mean. The main advantages of these methods are that they rely exclusively on cladogram topology and do not require branch-length estimates. Also, an optimisation of the ancestral nodes was performed using TNT 1.5 software. In relation to the phylogenetic signal, both methods showed similar results: the presence of autocorrelation was detected in PC1 and PC2, while in PC3, PC4 and PC5 and in the size of the basicranium (CS), the absence of autocorrelation occurred. The most significant nodes (where there is autocorrelation) are the basal nodes ‘Ursidae’ and ‘Ursinae-Tremarctinae’. Within this last group, distinctive basicranium morphology is observed, being more conservative in Tremarctinae than in Ursinae. The differences between these subfamilies could be related to historical events involving varying food and environmental preferences. The high phylogenetic signal in the node Tremarctinae probably indicates that the basicranium configuration of these bears was obtained early in their evolutionary history. Finally, our results of the basicranium and skull length ratios indicate that in Tremarctinae, the basicranium size was not determined by phylogeny but instead by other factors, such as adaptive responses to climatic changes and competition with other carnivores.

Phylogeny of Genus Cupuladria (Bryozoa, Cheilostomata) in the Neogene of Tropical America

We used 57 morphometric characters to discriminate 17 extant and fossil Cupuladria species and analyzed their phylogenetic relationships in relation to extant Discoporella species. Data were gathered from 496 extant and fossil Cupuladria specimens ranging in age from early Miocene to Recent and distributed from the Caribbean to tropical eastern Pacific. A first series of discriminant analyses distinguished three morphological groups: Cupuladria with vicarious avicularia, Cupuladria without vicarious avicularia, and Discoporella. Further discriminant analyses identified 17 species of Cupuladria. Cladistic analyses of these three groups yielded four equally parsimonious trees. All of the consensus trees exhibited the same topology, dividing the 25 tropical American cupuladriids into four distinct monophyletic clades, including Discoporella, and are consistent with previous molecular phylogenies except that there are no molecular data for the CV2 clade. Diversification of species was higher in the CV1 and CV2 clades than CNV clade, and involved mostly Caribbean species. Cupuladria with vicarious clade 1 (CV1) includes: C. monotrema, C. pacificiensis, C. exfragminis, C. cheethami, C. biporosa, and four new species: C. pervagata, C. floridensis, C. colonensis and C. dominicana. Cupuladria with vicarious clade 2 (CV2) includes: C. multesima, C. incognita, and three new species C. collyrida, C. veracruxiensis and C. planissima. Cupuladria clade without vicarious (CNV) includes: C. surinamensis, C. panamensis, and one new species C. gigas. The stratigraphic occurrence of species is consistent with cladogram topology within clades. However hypothesized cladistic relations among clades are the reverse of their stratigraphic occurrence with younger clade CNV appearing as the hypothetical ancestor of the two older clades CV1 and CV2. More extensive collections of early to middle Miocene specimens of Cupuladria and Discoporella will be required to resolve this apparent paradox.

Phylogeny of Genus Cupuladria (Bryozoa, Cheilostomata) in the Neogene of Tropical America

We used 57 morphometric characters to discriminate 17 extant and fossil Cupuladria species and analyzed their phylogenetic relationships in relation to extant Discoporella species. Data were gathered from 496 extant and fossil Cupuladria specimens ranging in age from early Miocene to Recent and distributed from the Caribbean to tropical eastern Pacific. A first series of discriminant analyses distinguished three morphological groups: Cupuladria with vicarious avicularia, Cupuladria without vicarious avicularia, and Discoporella. Further discriminant analyses identified 17 species of Cupuladria. Cladistic analyses of these three groups yielded four equally parsimonious trees. All of the consensus trees exhibited the same topology, dividing the 25 tropical American cupuladriids into four distinct monophyletic clades, including Discoporella, and are consistent with previous molecular phylogenies except that there are no molecular data for the CV2 clade. Diversification of species was higher in the CV1 and CV2 clades than CNV clade, and involved mostly Caribbean species. Cupuladria with vicarious clade 1 (CV1) includes: C. monotrema, C. pacificiensis, C. exfragminis, C. cheethami, C. biporosa, and four new species: C. pervagata, C. floridensis, C. colonensis and C. dominicana. Cupuladria with vicarious clade 2 (CV2) includes: C. multesima, C. incognita, and three new species C. collyrida, C. veracruxiensis and C. planissima. Cupuladria clade without vicarious (CNV) includes: C. surinamensis, C. panamensis, and one new species C. gigas. The stratigraphic occurrence of species is consistent with cladogram topology within clades. However hypothesized cladistic relations among clades are the reverse of their stratigraphic occurrence with younger clade CNV appearing as the hypothetical ancestor of the two older clades CV1 and CV2. More extensive collections of early to middle Miocene specimens of Cupuladria and Discoporella will be required to resolve this apparent paradox.

Cladistic analysis of the Paleozoic bryozoan families Monticuliporidae and Mesotrypidae

A set of 127 binary and multistate characters, weighted by the number of derived character states, degree of covariation, and level of homoplasy, was used in a cladistic analysis of type species representing 12 genera previously assigned to families Monticuliporidae and Mesotrypidae. The most parsimonious tree consisted of a 10-genus monophyletic crown group with the remaining two genera forming a basal paraphyletic stem group. The composition of the monticuliporid crown group is broadly similar to two earlier classifications while stem group membership matches the family Mesotrypidae. Phenetic groupings, based on overall morphological similarity, have memberships that are similar to those of clades but provide no means of determining the polarity of evolutionary relationships either within or between them. Finally, only the observed stratigraphic ranges of the type species of genera provide a statistically significant match with cladistic branching sequence, perhaps because current composite generic ranges reflect the mixing of species belonging to different genera. Based on cladogram topology, we propose the placement of all 12 genera into a single family Monticuliporidae.

<i>Oreonax</i> – not a genus

We summarize our re-examination and extension of the Groves (2001) parsimony analysis of Woolly monkeys, genus Lagothrix, which led him to conclude that the species flavicauda is not most closely related to lagotricha but to Ateles, the Spider monkeys. As a consequence, Groves further proposed that the Yellow-tailed woolly monkey should be assigned to a separate genus, Oreonax, previously erected by Oldfield Thomas (1927). Our analysis, while closely following his methods, samples a greater diversity of species and sub-species representing all the living ateline genera and makes minor revisions in Groves’ data matrix of craniodental characteristics. With this broader analysis we show that Groves’ cladistic results cannot be replicated except by duplicating his study using only a restricted range of taxa. A more wide ranging taxonomic sampling fails to link consistently flavicauda and other ateline species, in any particular cladogram topology, while the overall craniodental morphology of flavicauda does not separate it from lagotricha. Groves’ cladistic conclusion is likely to be an artifact stemming from a chance combination of the particular taxa used as a study group and selection of characters that may not be appropriate in intergeneric comparison. There is thus no justification for recognizing Oreonax as a distinct genus, and its usage should be rejected.

Molecular Markers Reject Monophyly of the Subgenera of <I>Satyrium</I> (Orchidaceae)

Abstract Satyrium is a morphologically anomalous genus. Although clearly a member of the terrestrial orchid subfamily Orchidoideae, its phylogenetic relationships within the subfamily are uncertain. Morphologically it has always been placed in tribe Diseae, albeit associated with different subtribes, but recent molecular studies suggest a closer relationship to Orchideae. The infrageneric classification of Satyrium is equally problematic, and several different classifications are available. The only infrageneric classification based on a phylogenetic analysis of morphological characters resulted in recognition of the three subgenera Brachysaccium, Bifidum, and Satyrium. DNA sequence data from nuclear (ITS1, 5.8S, and ITS2) and plastid (trnL intron, trnL-F intergenic spacer, and part of the matK gene and trnK intron) genome are used to test the monophyly of these subgenera. Topologies of cladograms resulting from parsimony analysis of separate datasets show several cases of incongruence, some of which are ...

A New Brontothere (Brontotheriidae, Perissodactyla, Mammalia) from the Eocene of the Ily Basin of Kazakstan and a Phylogeny of Asian “Horned” Brontotheres

A new genus and species of “horned” brontothere, Aktautitan hippopotamopus, from the Ily Basin of Kazakstan is described from three skulls and nearly complete postcranial material. This material occurs in fluvio-lacustrine red beds of the upper part of the Eocene (Irdinmanhan) Kyzylbulak Formation at Aktau Mountain. Trackways occurring in the overlying layers are also attributed to this new brontothere. Additionally, several misleading problems in the taxonomy of Asian horned brontotheres are addressed. We conclude that Protitan khaitshinus Yanovskaya, 1980 is a junior objective synonym of Metatitan relictus Granger and Gregory, 1943. Protitan reshetovi Yanovskaya, 1980 is removed from the genus Protitan and possibly belongs within Metatitan. Brachydiastematherium transylvanicum Böckh and Maty, 1876, the only bona fide European brontothere, known from a single partial mandible, is morphologically consistent with Metatitan Granger and Gregory, 1943. Although B. transylvanicum is known from very fragmentary material, it is possible that Metatitan is a junior synonym of Brachydiastematherium. The first cladistic phylogeny of middle and late Eocene Asian horned brontotheres was constructed with 40 characters and 17 taxa. Aktautitan, Metatitan, Brachydiastematherium, and Embolotherium form a monophyletic clade, with Aktautitan hippopotamopus as the most basal member of this clade. Within this clade, there are two monophyletic trichotomies: a Metatitan relictus, M. primus, Brachydiastematherium transylvanicum clade and a “Metatitan” progressus, Embolotherium andrewsi, E. grangeri clade. The cladogram topology suggests that the elevated frontonasal horns shared by Aktautitan and Metatitan represent the ancestral morphology of the bizarre “battering-ram” of Embolotherium. We extend the subfamily name Embolotheriinae to include these taxa. The unusually shortened distal limb segments of A. hippopotamopus resemble those of a phylogenetically disparate group of large ungulates that have convergently evolved hippolike limb proportions. We conclude that these limb proportions probably do not indicate a semiaquatic lifestyle, as had been previously surmised.

Genets and ‘genet-like’ taxa (Carnivora, Viverrinae): phylogenetic analysis, systematics and biogeographic implications

The subfamily Viverrinae is a taxon of uncertain systematic status. This study consists of cladistic analyses based on morphological characters of specimens belonging to the genera Genetta, Osbornictis, Poiana and Prionodon. Two levels of analysis are carried out, one concerning generic relationships (intergeneric analysis) and one dealing with the interrelationships of species within the genus Genetta (intrageneric analysis). In the first analysis, different outgroups were used in order to test the ingroup topology. With regard to the intergeneric analysis, Osbornictis, Poiana and Prionodon, together with Genetta johnstoni, constitute a monophyletic group (including Nandinia), which is the sister-group of a clade formed by the other species of genets. Thus, the genus Genetta is regarded as paraphyletic. Prionodon appears to be a derived taxon. The Poiana–Prionodon clade is well supported, especially by ultrastructural hair characters. The cladogram topology in the intrageneric analysis indicates an ecological transition from the rain forest genets to the savanna genets. This supports a rain forest origin of the genus Genetta, a conclusion which may be generalized to the entire study group. © 2002 The Linnean Society of London, Zoological Journal of the Linnean Society, 2002, 134, 317–334.

Phylogenetic relationships in Selaginellaceae based on RBCL sequences

A phylogenetic framework is developed for the clubmoss family Selaginellaceae based on maximum parsimony analyses of molecular data. The chloroplast gene rbcL was sequenced for 62 species, which represent nearly 10% of living species diversity in the family. Taxa were chosen to reflect morphological, geographical, and ecological diversity. The analyses provide support for monophyly of subgenera Selaginella and Tetragonostachys. Stachygynandrum and Heterostachys are polyphyletic. Monophyly of Ericetorum is uncertain. Results also indicate a large number of new groupings not previously recognized on morphological grounds. Some of these new groups seem to have corresponding morphological synapomorphies, such as the presence of rhizophores (distinctive root-like structures), aspects of rhizophore development, and leaf and stem morphology. Others share distinctive ecological traits (e.g., xerophytism). For many groups, however, no morphological, ecological, or physiological markers are known. This could reflect patchy sampling and a lack of detailed knowledge about many species. Despite a lengthy fossil record dating from the Carboniferous Period, cladogram topology indicates that most of the living tropical species are probably the products of more recent diversifications. Resurrection plants, extreme xerophytes characterized by aridity-driven inrolling of branches and rapid revival on rehydration, have evolved at least three times in quite different clades.

The relationships of vascular plants.

Recent phylogenetic research indicates that vascular plants evolved from bryophyte-like ancestors and that this involved extensive modifications to the life cycle. These conclusions are supported by a range of systematic data, including gene sequences, as well as evidence from comparative morphology and the fossil record. Within vascular plants, there is compelling evidence for two major clades, which have been termed lycophytes (clubmosses) and euphyllophytes (seed plants, ferns, horsetails). The implications of recent phylogenetic work are discussed with reference to life cycle evolution and the interpretation of stratigraphic inconsistencies in the early fossil record of land plants. Life cycles are shown to have passed through an isomorphic phase in the early stages of vascular plant evolution. Thus, the gametophyte generation of all living vascular plants is the product of massive morphological reduction. Phylogenetic research corroborates earlier suggestions of a major representational bias in the early fossil record. Mega-fossils document a sequence of appearance of groups that is at odds with that predicted by cladogram topology. It is argued here that the pattern of appearance and diversification of plant megafossils owes more to changing geological conditions than to rapid biological diversification.

AN EIGENVECTOR METHOD FOR ESTIMATING PHYLOGENETIC INERTIA.

We propose a new method to estimate and correct for phylogenetic inertia in comparative data analysis. The method, called phylogenetic eigenvector regression (PVR) starts by performing a principal coordinate analysis on a pairwise phylogenetic distance matrix between species. Traits under analysis are regressed on eigenvectors retained by a broken-stick model in such a way that estimated values express phylogenetic trends in data and residuals express independent evolution of each species. This partitioning is similar to that realized by the spatial autoregressive method, but the method proposed here overcomes the problem of low statistical performance that occurs with autoregressive method when phylogenetic correlation is low or when sample size is too small to detect it. Also, PVR is easier to perform with large samples because it is based on well-known techniques of multivariate and regression analyses. We evaluated the performance of PVR and compared it with the autoregressive method using real datasets and simulations. A detailed worked example using body size evolution of Carnivora mammals indicated that phylogenetic inertia in this trait is elevated and similarly estimated by both methods. In this example, Type I error at α = 0.05 of PVR was equal to 0.048, but an increase in the number of eigenvectors used in the regression increases the error. Also, similarity between PVR and the autoregressive method, defined by correlation between their residuals, decreased by overestimating the number of eigenvalues necessary to express the phylogenetic distance matrix. To evaluate the influence of cladogram topology on the distribution of eigenvalues extracted from the double-centered phylogenetic distance matrix, we analyzed 100 randomly generated cladograms (up to 100 species). Multiple linear regression of log transformed variables indicated that the number of eigenvalues extracted by the broken-stick model can be fully explained by cladogram topology. Therefore, the broken-stick model is an adequate criterion for determining the correct number of eigenvectors to be used by PVR. We also simulated distinct levels of phylogenetic inertia by producing a trend across 10, 25, and 50 species arranged in "comblike" cladograms and then adding random vectors with increased residual variances around this trend. In doing so, we provide an evaluation of the performance of both methods with data generated under different evolutionary models than tested previously. The results showed that both PVR and autoregressive method are efficient in detecting inertia in data when sample size is relatively high (more than 25 species) and when phylogenetic inertia is high. However, PVR is more efficient at smaller sample sizes and when level of phylogenetic inertia is low. These conclusions were also supported by the analysis of 10 real datasets regarding body size evolution in different animal clades. We concluded that PVR can be a useful alternative to an autoregressive method in comparative data analysis.

A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. IV. Nested analyses with cladogram uncertainty and recombination.

We previously developed an analytical strategy based on cladistic theory to identify subsets of haplotypes that are associated with significant phenotypic deviations. Our initial approach was limited to segments of DNA in which little recombination occurs. In such cases, a cladogram can be constructed from the restriction site data to estimate the evolutionary steps that interrelate the observed haplotypes to one another. The cladogram is then used to define a nested statistical design for identifying mutational steps associated with significant phenotypic deviations. The central assumption behind this strategy is that a mutation responsible for a particular phenotypic effect is embedded within the evolutionary history that is represented by the cladogram. The power of this approach depends on the accuracy of the cladogram in portraying the evolutionary history of the DNA region. This accuracy can be diminished both by recombination and by uncertainty in the estimated cladogram topology. In a previous paper, we presented an algorithm for estimating the set of likely claodgrams and recombination events. In this paper we present an algorithm for defining a nested statistical design under cladogram uncertainty and recombination. Given the nested design, phenotypic associations can be examined using either a nested analysis of variance (for haploids or homozygous strains) or permutation testing (for outcrossed, diploid gene regions). In this paper we also extend this analytical strategy to include categorical phenotypes in addition to quantitative phenotypes. Some worked examples are presented using Drosophila data sets. These examples illustrate that having some recombination may actually enhance the biological inferences that may derived from a cladistic analysis. In particular, recombination can be used to assign a physical localization to a given subregion for mutations responsible for significant phenotypic effects.