Phylogenetic positions of seven poorly known species of Ferula (Apiaceae) with remarks on the phylogenetic utility of the plastid trnH-psbA,trnS-trnG,and atpB-rbcL intergenic spacers

Ferula L. is one of the most species-rich and taxonomically difficult genera of Apiaceae. In this study, we obtained nrDNA ITS sequences of seven poorly known species of Ferula (Ferula anatolica, Ferula sp. (tentatively identified as F. candelabrum by collectors), F. drudeana, F. huber-morathii, F. marmarica, F. talassica, and F. tunetana) and explored their phylogenetic positions using 148 ITS sequences of the subtribe Ferulinae from GenBank. Five of these newly sequenced species fall into three groups, corresponding to clades recognized in earlier molecular studies. Ferula sp. are added to clade, which is mostly composed of Central Asian species. This placement showed that identification as F. candelabrum was erroneous. The second clade, which is mostly composed of Mediterranean taxa, includes two species from North Africa: F. marmarica and F. tunetana. Despite the well-supported monophyly of this clade, the relationships inside this group need to be revised, as broadly distributed F. communis is paraphyletic with respect to other species. Ferula drudeana and F. huber-morathii, two narrow endemics from Turkey, are placed in the Central Asian clade. Two species, F. anatolica and F. talassica, do not fall into any of the recognized clades. In addition, we examined the sequence variation of three potentially highly variable pDNA regions, the trnH-psbA, trnS-trnG, and atpB-rbcL intergenic spacers, for a subset of 18 specimens. The resulting pDNA and ITS based phylogenetic trees were incongruent, as supported by significant ILD tests. The cause of this incongruence can be manifold, including hybridization, a lack of a phylogenetic signal, and homoplastic substitutions. Our analyses suggest that only trnS-trnG can be added to the list of pDNA markers used for phylogenetic studies of Ferula, as it has the highest number of parsimony informative characters and is easy to amplify from degraded material.     

Unraveling the phylogeny of polygrammoid ferns (Polypodiaceae and Grammitidaceae): exploring aspects of the diversification of epiphytic plants

We explore the phylogeny of the polygrammoid ferns using nucleotide sequences derived from three plastid loci for each of 98 selected species. Our analyses recovered four major monophyletic lineages: the loxogrammoids, two clades consisting of taxa restricted to the Old World, and a largely neotropical clade that also includes the pantropical Grammitidaceae. The loxogrammoid lineage diverges first and is sister to a large clade comprising the three remaining species-rich lineages. One paleotropical clade includes the drynarioid and selligueoid ferns, whereas the second paleotropical clade includes the platycerioids, lepisoroids, microsoroids, and their relatives. The grammitids nest within the neotropical clade, although the sister taxon of this circum-tropic, epiphytic group remains ambiguous. Microsorum and Polypodium, as traditionally defined, were recovered as polyphyletic. The relatively short branch lengths of the deepest clades contrast with the long branch lengths leading to the terminal groups. This suggests that the polygrammoid ferns arose through an old, rapid radiation. Our analysis also reveals that the rate of substitution in the grammitids is remarkably higher relative to other polygrammoids. Disparities in substitution rate may be correlated with one or more features characterizing grammitids, including species richness, chlorophyllous spores, and an extended gametophytic phase.     

Detecting phylogenetic incongruence using BIONJ: an improvement of the ILD test

The problem of testing for congruence between phylogenetic data has long been debated among phylogeneticists, but reaches a critical point with the availability of large amount of biological sequences. Notably in prokaryotes, where the amount of lateral transfers is believed to be important, the inference of phylogenies using multiple genes requires testing for incongruence before concatenating the genes. On another scale, incongruence tests can be used to detect recombination points within single gene alignments. The incongruence length difference test (ILD), based on parsimony, has been proved to be useful for finding incongruent data sets, but its application remains limited to small data sets for computational time reasons. Here, we have adapted the principle of ILD to the BIONJ algorithm. This algorithm is based on a tree length minimisation criterion and is suitable to replace parsimony in this test when used with uncorrected distance (model-free approach). We show that this new test, ILD-BIONJ, while being much faster, is often more accurate than the ILD test, especially when the alignments compared are simulated under different evolutionary models.     

The 185/333 gene family is a rapidly diversifying host-defense gene cluster in the purple sea urchin Strongylocentrotus purpuratus

The genome of the purple sea urchin contains numerous large gene families with putative immunological functions. One gene family, known as 185/333, is characterized by extraordinary molecular diversity resulting from single nucleotide polymorphisms and the presence or the absence of 27 large blocks of sequences known as elements. The mosaic composition of elements, known as element patterns, that is present within the members of this gene family is encoded entirely in the second of two exons. Many of the elements correspond to one of six types of repeats that are present throughout the genes. The sequence diversity and variation in element patterns led us to investigate the evolution of the 185/333 gene family. The work presented here suggests that the element patterns are the result of both recombination and duplication and/or deletion of intragenic repeats. Each element is composed of a limited number of similar but distinct sequences, and their distribution among the 185/333 genes suggests frequent recombination within this gene family. Phylogenetic analyses of five 185/333 elements and two regions of the intron were performed using two tests: incongruence length difference and incongruence permutation. Results indicated that each pair of sequence segments was incongruent, suggesting that recombination occurs frequently along the length of the genes, including both the intron and the second exon, and that recombination is not restricted to intact elements. Paradoxically, the high level of similarity among the elements indicated that the 185/333 genes appear to be the result of a recent diversification. These results add to the growing body of evidence suggesting that invertebrate immune systems are not simple and static, but are dynamic and highly complex, and may employ group-specific mechanisms for diversification.     

The use of colour characters in phylogenetic reconstruction

The use of coloration as a source of characters in phylogenetic reconstruction is investigated using 54 published data sets. Studies were divided into two categories based on a priori postulated roles of the coloration: (1) aposematic and mimetic coloration and (2) nonaposematic, nonmimetic coloration plus dual signals. Colour characters superficially appear to provide similar phylogenetic signal to morphological ones in the case of aposematic and mimetic coloration but significantly less in other situations. However, the data indicated that the apparent signal in the aposematic/mimetic studies tends to be in greater conflict with the morphological signal. It is proposed that this reflects constraints in the evolution of colour characters that are part of aposematic/mimetic patterns and not that they are necessarily good indicators of phylogeny.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 193–202.     

The surfactant lipid transporter ABCA3 is N-terminally cleaved inside LAMP3-positive vesicles

ABCA3 mutations cause fatal surfactant deficiency and interstitial lung disease. ABCA3 protein is a lipid transporter indispensible for surfactant biogenesis and storage in lamellar bodies (LB). The protein folds in endoplasmic reticulum and is glycosylated in Golgi en route to the membrane of mature LB and their precursor multivesicular bodies (MVB). In immunoblots, C-terminally labeled ABCA3 appears as two protein bands of 150 and 190 kDa. Using N- and C-terminal protein tags and hindering ABCA3 processing we show that the 150 kDa protein represents the mature ABCA3 whose N-terminus is cleaved by a cysteine protease inside MVB/LB.

Structured summary

MINT-7996633: Calnexin (uniprotkb:P27824) and ABCA3 (uniprotkb:Q99758) colocalize (MI:0403) by fluorescence microscopy (MI:0416)MINT-7996380, MINT-7996593, MINT-7996607: LAMP3 (uniprotkb:Q9UQV4) and ABCA3 (uniprotkb:Q99758) colocalize (MI:0403) by fluorescence microscopy (MI:0416)     

Phylogenetic utility of the first two introns of the S7 ribosomal protein gene in African electric fishes (Mormyroidea: Teleostei) and congruence with other molecular markers

A series of recent molecular systematic studies of the African electric fishes (Mormyroidea) have challenged many aspects of their traditional taxonomy and precladistic hypotheses of their phylogeny. However, poor resolution of some interrelationships within the subfamily Mormyrinae in these studies highlights the need for additional data and analyses. Here we evaluate the phylogenetic information content of nucleotide sequences from the first two introns of the low‐copy nuclear S7 ribosomal protein gene in 40 mormyroid species. Alignment of S7 sequences from 38 taxa within the subfamily Mormyrinae is non‐problematic, but these are difficult to align with sequences of Petrocephalus bovei (Petrocephalinae) and Gymnarchus niloticus (Gymnarchidae), which we exclude from our analysis. There are no significant differences in base frequencies among these sequences and base compositional bias is low. Maximum parsimony (MP) analysis on the S7 dataset, designating Myomyrus macrops as the outgroup, generates a phylogenetic hypothesis for these taxa with a low level of homoplasy (RI = 0.87). We examine agreement between the S7 data with previously published mitochondrial (12S/16S, cytochrome b) and nuclear (rag 2) datasets for the same taxa by means of incongruence length difference tests and partitioned Bremer support (decay) analysis. While we find significant agreement between the S7 dataset and the others, MP analysis of the S7 data alone and in combination with the other datasets indicates two novel relationships within the Mormyrinae: (1) Mormyrus is the sister group to Brienomyrus brachyistius and Isichthys henryi, and (2) Hippopotamyrus pictus is the sister group of a clade, previously recovered, containing Marcusenius senegalensis. S7 data provide additional support for a number of clades recovered in the earlier molecular studies, some of which conflict with current mormyrid taxonomy. Inferred indels and a single inversion in the S7 fragment provide supplemental character support for many of these relationships. These phylogenetic results strengthen recent hypotheses concerning the evolution of electric organ structure in these fishes. The evolutionary characteristics of this nuclear marker and its phylogenetic utility in this group suggests that it could be widely useful for systematic studies at the subfamilial level in teleost fishes. © 2003 The Linnean Society of London. Biological Journal of the Linnean Society, 2003, 78 , 273–292.     

Phylogeny of Barnadesioideae (Asteraceae) inferred from DNA sequence data and morphology

Subfamily Barnadesioideae (Asteraceae) consists of nine genera and 91 species endemic to South America. They include annual and perennial herbs, arching shrubs and trees up to 30 m tall. Presumed sister to all other Asteraceae, its intergeneric relationships are key to understanding the early evolution of the family. Results of the only molecular study on the subfamily conflict with relationships inferred from morphology. We investigate inter- and intrageneric relationships in Barnadesioideae with novel DNA sequence data and morphological characters using parsimony, likelihood and Bayesian inference. All results verify Barnadesioideae as monophyletic and sister to the rest of the family. A basal split within the subfamily is recognized, with Chuquiraga, Doniophyton and Duseniella in one clade, and Arnaldoa, Barnadesia, Dasyphyllum, Fulcaldea, Huarpea and possibly Schlechtendalia in another. The largest genus, Dasyphyllum, is revealed as biphyletic with the two clades separating along subgeneric and geographic lines. Schlechtendalia, suggested as the earliest diverging lineage of the subfamily by morphological studies and parsimony analyses, is found in a more derived position under model-based inference methods. Competing phylogenetic hypotheses, both previous and present, are evaluated using likelihood-based tests. Evolutionary trends within Barnadesioideae are inferred: hummingbird pollination has developed convergently at least three times. An early vicariance in the subfamily’s distribution is revealed. X = 9 is supported as the ancestral base chromosome number for both Barnadesioideae and the family as a whole.     

系统发育分析中检测数据不相合性的方法

在进行生物系统发育研究的过程中,不同性质或来源的数据产生的结果之间往往存在差异,这种数据的不相合性已经成为我们重建系统发育历史的重要影响因素.本文介绍了数据不相合性存在的范围和成因,目前用于检测数据不相合性的主要方法:ILD检测,SH检测,PABA检测和PCI系数检测等,并对这些方法进行了比较,讨论了对不相合性数据的处理方法.