Changed number of the collection of Permian ammonoids from Novaya Zemlya housed in the cited collection repository of the Borissiak Paleontological Institute,Russian Academy of Sciences

The development of views on the phylogeny of the family Cyclolobidae Zittel, 1895 is discussed. The generic composition is emended, phylogenetic links are indicated, a new version of the phylogenetic scheme is proposed, and phylogeny of the key genera is traced at species level. The sutural ontogeny of the genus Mexicoceras is examined, its placement in the family Cyclolobidae is supported, and its position in the phylogenetic reconstruction of the family is determined.     

The use of DNA barcodes to estimate phylogenetic diversity in forest communities of southern China

To elucidate potential ecological and evolutionary processes associated with the assembly of plant communities, there is now widespread use of estimates of phylogenetic diversity that are based on a variety of DNA barcode regions and phylogenetic construction methods. However, relatively few studies consider how estimates of phylogenetic diversity may be influenced by single DNA barcodes incorporated into a sequence matrix (conservative regions vs. hypervariable regions) and the use of a backbone family‐level phylogeny. Here, we use general linear mixed‐effects models to examine the influence of different combinations of core DNA barcodes (rbcL, matK, ITS, and ITS2) and phylogeny construction methods on a series of estimates of community phylogenetic diversity for two subtropical forest plots in Guangdong, southern China. We ask: (a) What are the relative influences of single DNA barcodes on estimates phylogenetic diversity metrics? and (b) What is the effect of using a backbone family‐level phylogeny to estimate topology‐based phylogenetic diversity metrics? The combination of more than one barcode (i.e., rbcL + matK + ITS) and the use of a backbone family‐level phylogeny provided the most parsimonious explanation of variation in estimates of phylogenetic diversity. The use of a backbone family‐level phylogeny showed a stronger effect on phylogenetic diversity metrics that are based on tree topology compared to those that are based on branch lengths. In addition, the variation in the estimates of phylogenetic diversity that was explained by the top‐rank models ranged from 0.1% to 31% and was dependent on the type of phylogenetic community structure metric. Our study underscores the importance of incorporating a multilocus DNA barcode and the use of a backbone family‐level phylogeny to infer phylogenetic diversity, where the type of DNA barcode employed and the phylogenetic construction method used can serve as a significant source of variation in estimates of phylogenetic community structure.     

Cyprinid phylogeny based on Bayesian and maximum likelihood analyses of partitioned data: implications for Cyprinidae systematics

Cyprinidae is the biggest family of freshwater fish, but the phylogenetic relationships among its higher-level taxa are not yet fully resolved. In this study, we used the nuclear recombination activating gene 2 and the mitochondrial 16S ribosomal RNA and cytochrome b genes to reconstruct cyprinid phylogeny. Our aims were to (i) demonstrate the effects of partitioned phylogenetic analyses on phylogeny reconstruction of cyprinid fishes; (ii) provide new insights into the phylogeny of cyprinids. Our study indicated that unpartitioned strategy was optimal for our analyses; partitioned analyses did not provide better-resolved or -supported estimates of cyprinid phylogeny. Bayesian analyses support the following relationships among the major monophyletic groups within Cyprinidae: (Cyprininae, Labeoninae), ((Acheilognathinae, ((Leuciscinae, Tincinae), Gobioninae)), Xenocyprininae). The placement of Danioninae was poorly resolved. Estimates of divergence dates within the family showed that radiation of the major cyprinid groups occurred during the Late Oligocene through the Late Miocene. Our phylogenetic analyses improved our understanding of the evolutionary history of this important fish family.     

The phylogeny of the world's bulbuls (Pycnonotidae) inferred using a supermatrix approach

The bulbuls comprise an ecologically important group of frugivorous, seed‐dispersing birds found in Asia and Africa. Although several studies have examined the phylogenetic relationships of subsets of bulbul species, a comprehensive phylogeny of the family Pycnonotidae has hitherto been lacking. We used publicly available sequences generated from previous phylogenetic studies, augmented by new sequences from several unstudied taxa, to create a supermatrix from which to infer the phylogeny of the family. In all, we compared 121 of the 130 bulbul species. Our tree supports the monophyly of the family and comprises an exclusively African and a predominantly Asian clade. Several genera were found not to be monophyletic and we suggest taxonomic changes to provide a more accurate classification based on phylogeny.     

Assessing whether alpha-tubulin sequences are suitable for phylogenetic reconstruction of Ciliophora with insights into its evolution in euplotids

The current understanding of ciliate phylogeny is mainly based on analyses of a single gene, the small subunit ribosomal RNA (SSU-rDNA). However, phylogenetic trees based on single gene sequence are not reliable estimators of species trees, and SSU-rDNA genealogies are not useful for resolution of some branches within Ciliophora. Since congruence between multiple loci is the best tool to determine evolutionary history, we assessed the usefulness of alpha-tubulin gene, a protein-coding gene that is frequently sequenced, for ciliate phylogeny. Here, we generate alpha-tubulin gene sequences of 12 genera and 30 species within the order Euplotida, one of the most frequently encountered ciliate clades with numerous apparently cosmopolitan species, as well as four genera within its putative sister order Discocephalida. Analyses of the resulting data reveal that: 1) the alpha-tubulin gene is suitable phylogenetic marker for euplotids at the family level, since both nucleotide and amino acid phylogenies recover all monophyletic euplotid families as defined by both morphological criteria and SSU-rDNA trees; however, alpha-tubulin gene is not a good marker for defining species, order and subclass; 2) for seven out of nine euplotid species for which paralogs are detected, gene duplication appears recent as paralogs are monophyletic; 3) the order Euplotida is non-monophyletic, and the family Uronychiidae with sequences from four genera, is non-monophyletic; and 4) there is more genetic diversity within the family Euplotidae than is evident from dargyrome (geometrical pattern of dorsal "silverline system" in ciliates) patterns, habit and SSU-rDNA phylogeny, which indicates the urgent need for taxonomic revision in this area.     

Complete mitochondrial genome sequence and phylogenetic position of the Amu Darya sturgeon,Pseudoscaphirhynchus kaufmanni (Acipenseriformes: Acipenseridae)

In this study, we successfully assembled the complete mitochondrial genome of the Amu Darya sturgeon Pseudoscaphirhynchus kaufmanni. Based on this mitochondrial genome and previously published mitochondrial genomes of members of the Acipenseridae family, we assessed the phylogenetic position of P. kaufmanni using maximum likelihood and Bayesian inference for phylogeny reconstruction. The resultant phylogenetic trees were well-resolved, with congruence between different phylogenetic methods. This robust phylogenetic analysis elucidated the relationship among the four acipenserid genera and strongly supported the division of the family into three main clades. Evaluation of molecular phylogeny using maximum likelihood and Bayesian analysis led to the following conclusions: (a) the most basal position within the Acipenseridae remains in the clade containing Acipenser oxyrinchus and Acipenser sturio; (b) the genus Scaphirhynchus belongs to the Atlantic clade and is a sister group of the remaining species of the clade; and (c) the close relationship between P. kaufmanni and Acipenser stellatus is well supported.     

A Re-assessment of Relationships within Epacridaceae

An extensive database of predominantly morphological characters has been assembled for the family Epacridaceae. Problems of homology across the family and its outgroups were encountered for several characters. A phylogenetic analysis, using only those characters for which we were fairly confident of our assessment of homology, was undertaken to establish broad relationships within the family as a basis for a re-assessment of the supra-generic classification. The resultant phylogeny is weakly resolved and lacks robustness in the basal clades. Previous classifications of the family are assessed in the light of this analysis, and an alternative arrangement of four tribes is proposed.     

Molecular phylogeny of Anthelidae and other bombycoid taxa (Lepidoptera: Bombycoidea)

Abstract.  Based on DNA sequences of the fusion protein carbamoylphosphate synthetase/aspartate transcarbamylase/dihydroorotase (CAD; 680 bp) and elongation factor-1α (Ef-1α; 1240 bp); the first molecular phylogeny of the moth family Anthelidae and its placement within the Bombycoidea sensu Brock (1971) (= bombycoid complex sensu Minet, 1994 ) is proposed. The results strongly support the monophyly of the family Anthelidae and its subfamilies Munychryiinae and Anthelinae, but demonstrate the vast polyphyly of its main genus Anthela Walker, 1855. The proposed phylogeny suggests that grass feeding, as apparent from some pest records, probably is an ancestral trait within the subfamily Anthelinae. Evolutionary relationships of the family Anthelidae and of most parts of the Bombycoidea remain obscure. However, the results contradict many of the widely accepted phylogenetic hypotheses within the Bombycoidea proposed by Minet (1994 : Entomologica scandinavica , 25, 63–88). The Brahmaeidae are paraphyletic relative to the Lemoniidae ( syn.nov. ), and the current concept of Bombycidae is polyphyletic, with the bombycid subfamily Apatelodinae being part of a monophylum comprising Brahmaeidae / Lemoniidae, Eupterotidae and Apatelodidae ( stat.rev .).     

A molecular approach to arthrotardigrade phylogeny (Heterotardigrada,Tardigrada)

The marine order Arthrotardigrada (class Heterotardigrada, phylum Tardigrada) is known for its conspicuously high morphological diversity and has been traditionally recognized as the most ancestral group within the phylum. Despite its potential importance in understanding the evolution of the phylum, the phylogenetic relationships of Arthrotardigrada have not been clarified. This study conducted molecular phylogenetic analyses of the order encompassing all families except Neoarctidae using nuclear 18S and 28S rRNA fragments. Data from two rare families, Coronarctidae and Renaudarctidae, were included for the first time. The analyses confirmed the monophyly of Heterotardigrada and inferred Coronarctidae as the sister group to all other heterotardigrade taxa. Furthermore, the results support a monophyletic Renaudarctidae + Stygarctidae clade, which has been previously suggested on morphology. Our data indicated that two subfamilies currently placed in Halechiniscidae are only distantly related to this family. We propose that these taxa are each elevated to family level (Styraconyxidae (new rank) and Tanarctidae (new rank)). The morphology of tardigrades is discussed in the context of the inferred phylogeny.     

Using 18S rDNA to resolve diaptomid copepod (Copepoda: Calanoida: Diaptomidae) phylogeny: an example with the North American genera

The phylogenetic relationships among the numerous genera of diaptomid copepods remain elusive due to difficulties in obtaining sufficient numbers of phylogenetically informative morphological characters for cladistic analysis. Molecular phylogenetic techniques offer high potential to resolve phylogenetic relationships in the absence of sufficient morphological characters because of the ease in which many characters can be unambiguously coded. I present the first molecular phylogeny for diaptomid copepod genera using 18S rDNA. Specifically, I test Light’s (1939) hypothesis regarding the interrelationships among the North American diaptomid genera. The 18S phylogeny is remarkably consistent with Light’s hypothesis. The endemic North American genera represent a monophyletic group exclusive of the non-endemic genera. Moreover, his hypothesized basal genus for the North America genera, Hesperodiaptomus, is the basal genus in this analysis. However, his Leptodiaptomus group is not reciprocally monophyletic with his Hesperodiaptomus group, but is rather a derived member of the latter group. Finally, the genus Mastigodiaptomus is found to be more closely allied with the non-endemic genera, as Light suggested. This phylogeny contributes heavily to the understanding of phylogenetic relationships among North American diaptomids and has large implications for the systematics of diaptomids in general. The use of 18S rDNA sequences in phylogenetic analyses of diaptomid copepods can be used to confirm the monophyly of recognized genera, the interrelationships among genera, and subsequent biogeographic interpretation of the family’s diversification. The use of molecular data, such as 18S rDNA sequences, to test phylogenetic hypotheses based on a very limited number of morphological characters will be a particularly useful approach to phylogenetic analysis in this system.     

Brassicaceae phylogeny and trichome evolution

To estimate the evolutionary history of the mustard family (Brassicaceae or Cruciferae), we sampled 113 species, representing 101 of the roughly 350 genera and 17 of the 19 tribes of the family, for the chloroplast gene ndhF. The included accessions increase the number of genera sampled over previous phylogenetic studies by four-fold. Using parsimony, likelihood, and Bayesian methods, we reconstructed the phylogeny of the gene and used the Shimodaira-Hasegawa test (S-H test) to compare the phylogenetic results with the most recent tribal classification for the family. The resultant phylogeny allowed a critical assessment of variations in fruit morphology and seed anatomy, upon which the current classification is based. We also used the S-H test to examine the utility of trichome branching patterns for describing monophyletic groups in the ndhF phylogeny. Our phylogenetic results indicate that 97 of 114 ingroup accessions fall into one of 21 strongly supported clades. Some of these clades can themselves be grouped into strongly to moderately supported monophyletic groups. One of these lineages is a novel grouping overlooked in previous phylogenetic studies. Results comparing 30 different scenarios of evolution by the S-H test indicate that five of 12 tribes represented by two or more genera in the study are clearly polyphyletic, although a few tribes are not sampled well enough to establish para- or polyphyly. In addition, branched trichomes likely evolved independently several times in the Brassicaceae, although malpighiaceous and stellate trichomes may each have a single origin.     

A PHYLOGENETIC PERSPECTIVE ON THE EVOLUTION OF SEXUAL DICHROMATISM IN TANAGERS (THRAUPIDAE): THE ROLE OF FEMALE VERSUS MALE PLUMAGE

The evolution of sexual dichromatism in tanagers (family Thraupidae) was studied from a phylogenetic perspective using a molecular-based phylogeny. Mapping patterns of sexual dimorphism in plumage onto the phylogeny reveals that changes in female plumage occur more frequently than changes in male plumage. Possible explanations for this pattern include sexual selection acting on female plumage and natural selection for background matching. The results of this study and other recent phylogenetic and comparative studies suggest that factors affecting female plumage are important in shaping patterns of sexual dimorphism.     

Functional divergence in the Arabidopsis LOB-domain gene family

The Arabidopsis LOB-domain (LBD) gene family is composed by 43 members divided in two classes based on amino acid conservation within the LOB-domain. The LOB domain is known to be responsible for DNA binding and protein-protein interactions. There is very little functional information available for most genes in the LBD family and many lbd single mutants do not exhibit conspicuous phenotypes. One plausible explanation for the limited loss-of-function phenotypes observed in this family is that LBD genes exhibit significant functional redundancy. Here we discuss an example of one phylogenetic subgroup of the LBD family, in which genes that are closely related based on phylogeny exhibit distinctly different expression patterns and do not have overlapping functions. We discuss the challenges of using phylogenetic analyses to predict redundancy in gene families.     

An ant colony optimization algorithm for phylogenetic estimation under the minimum evolution principle

Background  

Distance matrix methods constitute a major family of phylogenetic estimation methods, and the minimum evolution (ME) principle (aiming at recovering the phylogeny with shortest length) is one of the most commonly used optimality criteria for estimating phylogenetic trees. The major difficulty for its application is that the number of possible phylogenies grows exponentially with the number of taxa analyzed and the minimum evolution principle is known to belong to the -hard class of problems.     

An automated phylogenetic key for classifying homeoboxes

When novel gene sequences are discovered, they are usually identified, classified, and annotated based on aggregate measures of sequence similarity. This method is prone to errors, however. Phylogenetic analysis is a more accurate basis for gene classification and ortholog identification, but it is relatively labor-intensive and computationally demanding. Here we report and demonstrate a rapid new method for gene classification based on phylogenetic principles. Given the phylogeny of a minimal sample of gene family members, our method automatically identifies amino acids that are phylogenetically characteristic of each class of sequences in the family; it then classifies a novel sequence based on the presence of these characteristic attributes in its sequence. Using a subset of homeobox protein sequences as a test case, we show that our method approximates classification based on full-scale phylogenetic analysis with very high accuracy in a tiny fraction of the time.     

The phylogeny of Xantusiid lizards: The concern for analysis in the search for a best estimate of phylogeny

In the onrush of molecular-based phylogenetic hypotheses, previous morphological-based phylogenies are being ignored, discarded, or even treated with disdain. Coupled with this implicit superiority of molecular data is the sometimes tendency to construct a phylogeny from the molecular data with less than analytical rigor. This paper examines the phylogenetic relationships within the lizard family Xantusiidae employing both molecular and morphological data. The analysis focuses on four analytical points of the molecular data and on the phylogenetics synthesis of the two data sets. We conclude that the phylogeny of xantusiid lizards is not yet a robust hypothesis.     

Relationships within the family Actiniidae (Cnidaria,Actiniaria) based on molecular characters

Current sea anemone systematics is based on relatively few morphological characters, and potentially could benefit from the use of molecular characters. In this paper, the phylogenetic relationships of 12 species from 6 genera in the family Actiniidae have been investigated using electrophoretically separated isozymes. A numerical cladistic analysis has produced an estimated phylogeny. The implications of this phylogeny for the taxonomic use of certain morphological characters are discussed.     

Molecular Phylogenetic Studies of Caribbean Palms (Arecaceae) and Their Relationships to Biogeography and Conservation

The Caribbean Islands are one of the world’s 34 biodiversity hotspots, remarkable for its biological richness and the high level of threat to its flora and fauna. The palms (family Arecaceae) are well represented in the West Indies, with 21 genera (three endemic) and 135 species (121 endemic). We provide an overview of phylogenetic knowledge of West Indian Palms, including their relationships within a plastid DNA-based phylogeny of the Arecaceae. We present new data used to reconstruct the phylogeny of tribe Cryosophileae, including four genera found in the West Indies, based on partial sequences of the low-copy nuclear genes encoding phosphoribulokinase (PRK) and subunit 2 of RNA polymerase II (RPB2). Recently published phylogenetic studies of tribe Cocoseae, based on PRK sequences, and tribes Cyclospatheae and Geonomateae, based on PRK and RPB2 sequences, also provide information on the phylogenetic relationships of West Indian palms. Results of these analyses show many independent origins of the West Indian Palm flora. These phylogenetic studies reflect the complex envolutionary history of the West Indies and no single biogeographical pattern emerges for these palms. The present day distributions of West Indian palms suggest complicated evolutionary interchange among islands, as well as between the West Indies and surrounding continents. We identified six palm lineages that deserve conservation priority. Species-level phylogenies are needed for Copernicia, Sabal, and Roystonea before we can build a more complete understanding of the origin and diversification of West Indian palms. An erratum to this article can be found at     

Phylogeny and biogeography of the core babblers (Aves: Timaliidae)

The avian family Timaliidae is a species rich and morphologically diverse component of African and Asian tropical forests. The morphological diversity within the family has attracted interest from ecologists and evolutionary biologists, but systematists have long suspected that this diversity might also mislead taxonomy, and recent molecular phylogenetic work has supported this hypothesis. We produced and analyzed a data set of 6 genes and almost 300 individuals to assess the evolutionary history of the family. Although phylogenetic analysis required extensive adjustment of program settings, we ultimately produced a well-resolved phylogeny for the family. The resulting phylogeny provided strong support for major subclades within the family but extensive paraphyly of genera. Only 3 genera represented by more than 3 species were monophyletic. Biogeographic reconstruction indicated a mainland Asian origin for the family and most major clades. Colonization of Africa, Sundaland, and the Philippines occurred relatively late in the family's history and was mostly unidirectional. Several putative babbler genera, such as Robsonius, Malia, Leonardina, and Micromacronus are only distantly related to the Timaliidae.