Molecular phylogenetic analysis of class Colpodea (phylum Ciliophora) using broad taxon sampling

The ciliate class Colpodea provides a powerful case in which a molecular genealogy can be compared to a detailed morphological taxonomy of a microbial group. Previous analyses of the class using the small-subunit rDNA are based on sparse taxon sampling, and are therefore of limited use in comparisons with morphologically-based classifications. Taxon sampling is increased here to include all orders within the class, and more species within previously sampled orders and in the species rich genus Colpoda. Results indicate that the Colpodea may be paraphyletic, although there is no support for deep nodes. The orders Bursariomorphida, Grossglockneriida, and Sorogenida are monophyletic. The orders Bryometopida, Colpodida, and Cyrtolophosidida, and the genus Colpoda, are not monophyletic. Although congruent in many aspects, the conflict between some nodes on this single gene genealogy and morphology-based taxonomy suggests the need for additional markers as well as a reassessment of the Colpodea taxonomy.     

A phylogenetic analysis of the phylum Fibrobacteres

Members of the phylum Fibrobacteres are highly efficient cellulolytic bacteria, best known for their role in rumen function and as potential sources of novel enzymes for bioenergy applications. Despite being key members of ruminants and other digestive microbial communities, our knowledge of this phylum remains incomplete, as much of our understanding is focused on two recognized species, Fibrobacter succinogenes and F. intestinalis. As a result, we lack insights regarding the environmental niche, host range, and phylogenetic organization of this phylum. Here, we analyzed over 1000 16S rRNA Fibrobacteres sequences available from public databases to establish a phylogenetic framework for this phylum. We identify both species- and genus-level clades that are suggestive of previously unknown taxonomic relationships between Fibrobacteres in addition to their putative lifestyles as host-associated or free-living. Our results shed light on this poorly understood phylum and will be useful for elucidating the function, distribution, and diversity of these bacteria in their niches.     

树鼩进化分类地位的分子证据

树鼩隶属攀鼩目,广泛分布于东南亚、南亚和中国南部等地区。由于其独特的特点,如体型小、脑-体重比例高、生殖周期短、寿命短和饲养成本低等,在生物医学研究中被认为是可望替代灵长类动物的新型实验动物。然而,关于树鼩与灵长类动物的亲缘关系一直存在争议。明确树鼩的分类地位是创建实验动物的重要研究基础。该文介绍了近年来关于树鼩分类地位探讨的分子证据。在现有的研究中,大部分核DNA序列研究,包括近期树鼩全基因组序列分析,都支持树鼩是灵长动物的近缘旁系群,然而绝大部分基于线粒体DNA序列的研究却显示树鼩与啮齿动物的亲缘关系更为接近。这样的分歧主要是由于线粒体序列和核基因数据的差异以及不同的算法导致。综合现有不同DNA数据的研究结果,作者认为树鼩作为灵长类的近亲这一结论应该成为共识。     

Molecular phylogenetic and embryological evidence that feeding larvae have been reacquired in a marine gastropod

Evolutionary transitions between different modes of development in marine invertebrates are thought to be biased toward the loss of feeding larvae. Because the morphology of feeding larvae is complex and nonfeeding larvae or encapsulated embryos with benthic development often have simplified morphologies, it is presumed to be easier to lose a larval stage than to reacquire it. Some authors have gone so far as to suggest that feeding larvae, morphologically similar to the ancestral feeding larvae, cannot be reacquired. However, the larval structures of some groups, most notably gastropods, are often retained in the encapsulated embryos of species that hatch as benthic juveniles. Therefore the re-evolution of feeding larvae using the same structures may be possible in these groups. Here we present the first well-substantiated case for the recent re-evolution of feeding larvae within a clade of direct-developers. DNA sequence data show that Crepipatella fecunda, a species of calyptraeid gastropod with planktotrophic development, is nested within a clade of species with direct development, and that Crepipatella dilatata, a species with direct development, appears to be paraphyletic with respect to C. fecunda. Observation of the embryos of C. dilatata shows that the features necessary for larval feeding and swimming are retained in the encapsulated veligers, suggesting that heterochronic shifts in hatching time and changes in nurse-egg allotment could have resulted in the re-evolution of feeding larvae in this species.     

A molecular phylogenetic approach to the phylum Cycliophora provides further evidence for cryptic speciation in Symbion americanus

Cryptic speciation is a phenomenon that has been reported in a wide range of marine invertebrates, including the American cycliophoran Symbion americanus . Although cryptic speciation is often proposed based on phylogeographical analyses, here we demonstrate the utility of multilocus molecular phylogenetic approaches in identifying cryptic lineages within the phylum Cycliophora. Thirteen individuals from three putative cryptic lineages of S. americanus , as well as two individuals each from the European species S. pandora and a new species of Symbion living on Homarus gammarus , were sequenced for up to 4.8 kb of genomic DNA over four loci (COI, 16S rRNA, 18S rRNA and 28S rRNA). Phylogenetic analyses of individual loci as well as combined data clearly support a division between American and European cycliophorans. Moreover, the American cycliophorans consistently form three well-supported clades, which is congruent with the presence of three putative reproductively isolated lineages in a species complex. Further studies are necessary to more precisely describe the evolution of reproductive isolation within S. americanus .     

Biometric evidence that sexual selection has shaped the hominin face

We consider sex differences in human facial morphology in the context of developmental change. We show that at puberty, the height of the upper face, between the lip and the brow, develops differently in males and females, and that these differences are not explicable in terms of sex differences in body size. We find the same dimorphism in the faces of human ancestors. We propose that the relative shortening in men and lengthening in women of the anterior upper face at puberty is the mechanistic consequence of extreme maxillary rotation during ontogeny. A link between this developmental model and sexual dimorphism is made for the first time, and provides a new set of morphological criteria to sex human crania. This finding has important implications for the role of sexual selection in the evolution of anthropoid faces and for theories of human facial attractiveness.     

Molecular evidence for deep phylogenetic divergence in Mandrillus sphinx

Mandrills (Mandrillus sphinx) are forest primates indigenous to western central Africa. Phylogenetic analysis of 267 base pairs (bp) of the cytochrome b gene from 53 mandrills of known and 17 of unknown provenance revealed two phylogeographical groups, with haplotypes differentiated by 2.6% comprising seven synonymous transitions. The distribution of the haplotypes suggests that the Ogooué River, Gabon, which bisects their range, separates mandrill populations in Cameroon and northern Gabon from those in southern Gabon. The haplotype distribution is also concordant with that of two known mandrill simian immunodeficiency viruses, suggesting that these two mandrill phylogroups have followed different evolutionary trajectories since separation.     

Molecular phylogenetic evidence for the evolution of specialization in anemonefishes.

Anemonefishes (genera: Amphiprion and Premnas; family Pomacentridae) are a group of 28 species of coral reef fishes that are found in obligate symbiosis with large tropical sea anemones. A phylogenetic hypothesis based on morphological analyses of this group suggests that the ancestral anemonefish was a generalist with similar morphology to other pomacentrids, and that it gave rise to other anemonefish species that were more specialized for living with particular species of host anemones. To test this hypothesis we constructed a molecular phylogeny for the anemonefishes by sequencing 1140 base pairs of the cytochrome b gene and 522 base pairs of the 16S rRNA gene for six species of anemonefishes (representatives of all subgenera and species complexes) and two other pomacentrid species. Three methods of phylogenetic analysis all strongly supported the conclusion that anemonefishes are a monophyletic group. The molecular phylogeny differs from the tree based on morphological data in that the two species of specialized anemonefishes (Premnas biaculeatus and Amphiprion ocellaris) were assigned to a basal position within the clade, and the extreme host generalist (Amphiprion clarkii) to a more derived position. Thus, the initial anemonefish ancestors were probably host specialists and subsequent speciation events led to a combination of generalist and specialist groups. Further phylogenetic studies of additional anemonefish species are required to substantiate this hypothesis.     

Molecular phylogeny of the Haplosporidia based on two independent gene sequences

The phylogenetic position of the Haplosporidia has confounded taxonomists for more than a century because of the unique morphology of these parasites. We collected DNA sequence data for small subunit (SSU) ribosomal RNA and actin genes from haplosporidians and other protists for conducting molecular phylogenetic analyses to help elucidate relationships of taxa within the group, as well as placement of this group among Eukaryota. Analyses were conducted using DNA sequence data from more than 100 eukaryotic taxa with various combinations of data sets including nucleotide sequence data for each gene separately and combined, as well as SSU ribosomal DNA data combined with translated actin amino acids. In almost all analyses, the Haplosporidia was sister to the Cercozoa with moderate bootstrap and jackknife support. Analysis with actin amino acid sequences alone grouped haplosporidians with the foraminiferans and cercozoans. The haplosporidians Minchinia and Urosporidium were found to be monophyletic, whereas Haplosporidium was paraphyletic. "Microcell" parasites, Bonamia spp. and Mikrocytos roughleyi, were sister to Minchinia, the most derived genus, with Haplosporidium falling between the "microcells" and the more basal Urosporidium. Two recently discovered parasites, one from abalone in New Zealand and another from spot prawns in British Columbia, fell at the base of the Haplosporidia with very strong support, indicating a taxonomic affinity to this group.     

Molecular evidence for the phylogenetic position ofHanabusaya asiatica Nakai (Campanulaceae), an endemic species in Korea

The phylogenetic relationship of the Korean endemic genus,Hanabusaya, to other campanulaceous genera has been controversial since it was described by Nakai in 1911. Three genera of Campanuloideae,Symphyandra, Adenophora, andCampanula, have been considered closely related by various taxonomists on the basis of anther shape, gross morphology, and pollen characters, respectively. We have tested these competing taxonomic hypotheses using the internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA from 12 taxa representing 7 genera of Campanulaceae. The molecular phylogeny indicates strongly thatHanabusaya is more closely allied toAdenophora than toCampanula orSymphyandra. The phylogenetic affinity ofHanabusaya andAdenophora is supported by a 100% bootstrap value and a high decay index (13). The average sequence divergence value (Kimura’s 2-parameter method) betweenHanabusaya and theAdenophora species is 2.58. The value is significantly (about ten times) lower than the ones observed betweenHanabusaya and the species ofCampanula (average of 23.52) and betweenHanabusaya andSymphyandra (24.95). The ITS sequence phylogeny suggests that some morphological characters, such as fused anthers and corolla shape, are homoplastic in the Campanulaceae genera.     

Molecular evidence on the species status and phylogenetic relationships of Spiranthes parksii, an endangered orchid from Texas

New genetic information on the taxonomic status of an endangered species may have strong implications for its continued protection and that of other listed taxa with questionable species status. While analyzing a more comprehensive project on the molecular phylogeny of North American Spiranthes (Orchidaceae), lack of genetic differentiation between endangered S. parksii, endemic only to Texas, and a common local congener, S. cernua, was discovered. To confirm these results in a comparative context, we focused parsimony analyses on a subset of data from local Spiranthes and the same congeners found elsewhere, expanded by additional local samples of the two focal species. Four DNA sequence segments (two chloroplast, one mitochondrial, one nuclear ribosomal) totaling 3191 base pairs were used separately and together to verify that S. parksii is nested within the same clade as S. cernua, and thus likely to be the same species. Our results concur with another recent investigation using AFLP and microsatellite data that also suggests S. parksii is not unique genetically. Therefore, based on empirical data and the phylogenetic species concept, endangered S. parksii is merely an aberrant local phenotype of and a synonym for S. cernua sensu lato. Our results should be considered during the current review of this orchid’s listing status, despite some recent policy changes on consideration of genetic data after listing.     

Ontogenetic evidence for the Paleozoic ancestry of salamanders

The phylogenetic positions of frogs, salamanders, and caecilians have been difficult to establish. Data matrices based primarily on Paleozoic taxa support a monophyletic origin of all Lissamphibia but have resulted in widely divergent hypotheses of the nature of their common ancestor. Analysis that concentrates on the character states of the stem taxa of the extant orders, in contrast, suggests a polyphyletic origin from divergent Paleozoic clades. Comparison of patterns of larval development in Paleozoic and modern amphibians provides a means to test previous phylogenies based primarily on adult characteristics. This proves to be highly informative in the case of the origin of salamanders. Putative ancestors of salamanders are recognized from the Permo-Carboniferous boundary of Germany on the basis of ontogenetic changes observed in fossil remains of larval growth series. The entire developmental sequence from hatching to metamorphosis is revealed in an assemblage of over 600 specimens from a single locality, all belonging to the genus Apateon. Apateon forms the most speciose genus of the neotenic temnospondyl family Branchiosauridae. The sequence of ossification of individual bones and the changing configuration of the skull closely parallel those observed in the development of primitive living salamanders. These fossils provide a model of how derived features of the salamander skull may have evolved in the context of feeding specializations that appeared in early larval stages of members of the Branchiosauridae. Larvae of Apateon share many unique derived characters with salamanders of the families Hynobiidae, Salamandridae, and Ambystomatidae, which have not been recognized in any other group of Paleozoic amphibians.     

Genetic evidence for the Mongolian ancestry of Kalmyks

The Kalmyks are an ethnic group along the lower Volga River in Russia who are thought to have migrated there from Mongolia about 300 years ago. To investigate their origins, we studied mtDNA and Y-chromosome variation in 99 Kalmyks. Both mtDNA HV1 sequences and Y-chromosome SNP haplogroups indicate a close relationship of Kalmyks with Mongolians. In addition, genetic diversity for both mtDNA and the Y chromosome are comparable in Kalmyks, Mongolians, and other Central Asian groups, indicating that the Kalmyk migration was not associated with a substantial bottleneck. The so-called "Genghis Khan" Y-chromosome short tandem repeat (STR) haplotype was found in high frequency (31.3%) among Kalmyks, further supporting a strong genetic connection between Kalmyks and Mongolians. Genetic analyses of even recent, relatively well-documented migrations such as of the Kalmyks can therefore lead to new insights concerning such migrations.     

Molecular phylogenetic analyses indicate that the Ixodes ricinus complex is a paraphyletic group

The Ixodes ricinus species complex is a group of ticks distributed in almost all geographic regions of the world. Lyme borreliosis spirochetes are primarily transmitted by tick species within this complex. It has been hypothesized that the Lyme vector ticks around the world are closely related and represent a monophyletic group. This implies that vector competence in ixodid ticks for Lyme agents might have evolved only once. To test this hypothesis, we used a molecular phylogenetic approach. Two fragments of mitochondrial 16S ribosomal deoxyribonucleic acid were sequenced from 11 species in the I. ricinus complex and from 16 other species of Ixodes. Phylogenetic analysis using Bayesian methodology indicated that the I. ricinus complex is not a monophyletic group unless 3 additional Ixodes species are included in it. The known major vectors of Lyme disease agents in different areas of the world are not sister taxa. This suggests that acquisition of the ability to transmit borreliosis agents in species of Ixodes may have multiple origins.     

On universal common ancestry, sequence similarity, and phylogenetic structure: the sins of P-values and the virtues of Bayesian evidence

Life is a chemical reaction. Three major transitions in early evolution are considered without recourse to a tree of life. The origin of prokaryotes required a steady supply of energy and electrons, probably in the form of molecular hydrogen stemming from serpentinization. Microbial genome evolution is not a treelike process because of lateral gene transfer and the endosymbiotic origins of organelles. The lack of true intermediates in the prokaryote-to-eukaryote transition has a bioenergetic cause. This article was reviewed by Dan Graur, W. Ford Doolittle, Eugene V. Koonin and Christophe Malaterre.     

A molecular phylogenetic framework for the phylum Ctenophora using 18S rRNA genes.

This paper presents the first molecular phylogenetic analysis of the phylum Ctenophora, by use of 18S ribosomal RNA sequences from most of the major taxa. The ctenophores form a distinct monophyletic group that, based on this gene phylogeny, is most closely related to the cnidarians. Our results suggest that the ancestral ctenophore was tentaculate and cydippid-like and that the presently recognized order Cydippida forms a polyphyletic group. The other ctenophore orders that we studied (Lobata, Beroida, and Platyctenida) are secondarily derived from cydippid-like ancestors, a conclusion that is also supported by developmental and morphological data. The very short evolutionary distances between characterized ctenophore 18S rRNA gene sequences suggests that extant ctenophores are derived from a recent common ancestor. This has important consequences for future studies and for an understanding of the evolution of the metazoans.