Analysis of the Gut Microbiota by High-Throughput Sequencing of the V5–V6 Regions of the 16S rRNA Gene in Donkey

Considerable evidence suggests that the gut microbiota is complex in many mammals and gut bacteria communities are essential for maintaining gut homeostasis. To date the research on the gut microbiota of donkey is surprisingly scarce. Therefore, we performed high-throughput sequencing of the 16S rRNA genes V5–V6 hypervariable regions from gut fecal material to characterize the gut microbiota of healthy donkeys and compare the difference of gut microbiota between male and female donkeys. Sixty healthy donkeys (30 males and 30 females) were enrolled in the study, a total of 915,691 validated reads were obtained, and the bacteria found belonged to 21 phyla and 183 genera. At the phylum level, the bacterial community composition was similar for the male and female donkeys and predominated by Firmicutes (64 % males and 64 % females) and Bacteroidetes (23 % males and 21 % females), followed by Verrucomicrobia, Euryarchaeota, Spirochaetes, and Proteobacteria. At the genus level, Akkermansia was the most abundant genus (23 % males and 17 % females), followed by Sporobacter, Methanobrevibacter, and Treponema, detected in higher distribution proportion in males than in females. On the contrary, Acinetobacter and Lysinibacillus were lower in males than in females. In addition, six phyla and 15 genera were significantly different between the male and female donkeys for species abundance. These findings provide previously unknown information about the gut microbiota of donkeys and also provide a foundation for future investigations of gut bacterial factors that may influence the development and progression of gastrointestinal disease in donkey and other animals.     

Application of DFT methods to the study of the coordination environment of the VO2+ ion in V?proteins

Density functional theory (DFT) methods were used to simulate the environment of vanadium in several V proteins, such as vanadyl-substituted carboxypeptidase (sites A and B), vanadyl-substituted chloroplast F(1)-ATPase (CF(1); site 3), the reduced inactive form of vanadium bromoperoxidase (VBrPO; low- and high-pH sites), and vanadyl-substituted imidazole glycerol phosphate dehydratase (IGPD; sites α, β, and γ). Structural, electron paramagnetic resonance, and electron spin echo envelope modulation parameters were calculated and compared with the experimental values. All the simulations were performed in water within the framework of the polarizable continuum model. The angular dependence of [Formula: see text] and [Formula: see text] on the dihedral angle θ between the V=O and N-C bonds and on the angle φ between the V=O and V-N bonds, where N is the coordinated aromatic nitrogen atom, was also found. From the results it emerges that it is possible to model the active site of a vanadium protein through DFT methods and determine its structure through the comparison between the calculated and experimental spectroscopic parameters. The calculations confirm that the donor sets of sites B and A of vanadyl-substituted carboxypeptidase are [[Formula: see text], H(2)O, H(2)O, H(2)O] and [N(His)(||), N(His)(⊥), [Formula: see text], H(2)O], and that the donor set of site 3 of CF(1)-ATPase is [[Formula: see text], OH(Thr), H(2)O, H(2)O, [Formula: see text]]. For VBrPO, the coordination modes [N(His)(||), N(His)(∠), OH(Ser), H(2)O, H(2)O(ax)] for the low-pH site and [N(His)(||), N(His)(∠), OH(Ser), OH(-), H(2)O(ax)] or [N(His)(||), N(His)(∠), [Formula: see text], H(2)O] for the high-pH site, with an imidazole ring of histidine strongly displaced from the equatorial plane, can be proposed. Finally, for sites α, β, and γ of IGPD, the subsequent deprotonation of one, two, and three imidazole rings of histidine and the participation of a carboxylate group of a glutamate residue ([N(His)(||), [Formula: see text], H(2)O, H(2)O], [N(His)(||), N(His)(||), [Formula: see text], H(2)O], and [N(His)(||), N(His)(||), [Formula: see text], OH(-), [Formula: see text]], respectively) seems to be the most plausible hypothesis.     

Analysis of the disulfide bond arrangement of the HIV-1 envelope protein CON-S gp140 ΔCFI shows variability in the V1 and V2 regions

Disulfide bonding of cysteines is one of the most important protein modifications, and it plays a key role in establishing/maintaining protein structures in biologically active forms. Therefore, the determination of disulfide bond arrangement is one important aspect to understanding the chemical structure of a protein and defining its functional domains. Herein, aiming to understand how the HIV-1 envelope protein's structure influences its immunogenicity, we used an MS-based approach, liquid chromatography electrospray ionization Fourier transform ion cyclotron resonance (LC/ESI-FTICR) mass spectrometry, to determine the disulfide linkages on an oligomeric form of the group M consensus HIV-1 envelope protein (Env), CON-S gp140 ΔCFI. This protein has marked improvement in its immunogenicity compared to monomeric gp120 and wild-type forms of gp140 Envs. Our results demonstrate that the disulfide connectivity in the N-terminal region of CON-S gp140 ΔCFI is different from the disulfide bonding previously reported in the monomeric form of gp120 HIV-1 Env. Additionally, heterogeneity of the disulfide bonding was detected in this region. These data suggest that the V1/V2 region does not have a single, conserved disulfide bonding pattern and that variability could impact immunogenicity of expressed Envs.     

Substitution Reaction on the Indole Ring of ( – )-Indolactam V,the Fundamental Structure of Teleocidins

We isolated a temperature-sensitive mutant which did not exhibit derepression of acid phosphatase and invertase at the restrictive temperature. The mutation was mapped in the cryl gene, the structural gene for the catalytic subunit of adenylate cyclase. On electron microscopic observation of the mutant cells at the restrictive temperature, it was observed that they accumulated carbohydrate particles in the cytoplasm. Isolated particles had a rosette-like structure of 40 to 60 nm in diameter, and were identified as glycogen. After 2 hr incubation at the restrictive temperature, glycogen particles occupied most of the cytoplasmic space and the vacuoles were observed to be fragmented.     

Identification of binding partners interacting with the α1-N-propeptide of type V collagen

The predominant form of type V collagen is the [α1(V)]?α2(V) heterotrimer. Mutations in COL5A1 or COL5A2, encoding respectively the α1(V)- and α2(V)-collagen chain, cause classic EDS (Ehlers-Danlos syndrome), a heritable connective tissue disorder, characterized by fragile hyperextensible skin and joint hypermobility. Approximately half of the classic EDS cases remain unexplained. Type V collagen controls collagen fibrillogenesis through its conserved α1(V)-N-propeptide domain. To gain an insight into the role of this domain, a yeast two-hybrid screen among proteins expressed in human dermal fibroblasts was performed utilizing the N-propeptide as a bait. We identified 12 interacting proteins, including extracellular matrix proteins and proteins involved in collagen biosynthesis. Eleven interactions were confirmed by surface plasmon resonance and/or co-immunoprecipitation: α1(I)- and α2(I)-collagen chains, α1(VI)-, α2(VI)- and α3(VI)-collagen chains, tenascin-C, fibronectin, PCPE-1 (procollagen C-proteinase enhancer-1), TIMP-1 (tissue inhibitor of metalloproteinases-1), MMP-2 (matrix metalloproteinase 2) and TGF-β1 (transforming growth factor β1). Solid-phase binding assays confirmed the involvement of the α1(V)-N-propeptide in the interaction between native type V collagen and type VI collagen, suggesting a bridging function of this protein complex in the cell-matrix environment. Enzymatic studies showed that processing of the α1(V)-N-propeptide by BMP-1 (bone morphogenetic protein 1)/procollagen C-proteinase is enhanced by PCPE-1. These interactions are likely to be involved in extracellular matrix homoeostasis and their disruption could explain the pathogenetic mechanism in unresolved classic EDS cases.     

Method of fixing the heterotic effect—implementation on plants (on the hundredth anniversary of the birth of V.A. Strunnikov)

The article is devoted to the 100th anniversary of the outstanding world-renown Russian scientist Vladimir Alexandrovich Strunnikov, Academician, Professor, Head of Group of Developmental Cytology and Sex Regulation at Koltzov Institute of Developmental Biology and Head of genetic studies on silkworms in a number of sericulture institutes in CIS. Laureate of the State Prize of the USSR (1981), Hero of Socialist Labor (1990), awarded the I.I. Mechnikov Gold Medal, Academy of Sciences of the USSR (1981), founder of the theory explaining the origin of heterosis. One of his most significant achievements is the “Methods of Fixing the Heterosis Effect,” which makes it possible to abandon the production of hybrid seed and increase the yield of many crops by 20–50%. Fixing the gene complexes that determine the heterosis effect will become the “springboard” that will allow obtaining even more productive heterotic hybrids on the basis of new-generation varieties. The efficiency of this method in plant objects at the organismal and molecular levels was shown in the All-Russia Research Institute of Rice. A modification of this method reducing its laboriousness and increasing its efficiency was developed.     

Comprehensive Mass Spectrometric Mapping of the Hydroxylated Amino Acid residues of the α1(V) Collagen Chain

Aberrant expression of the type V collagen α1(V) chain can underlie the connective tissue disorder classic Ehlers-Danlos syndrome, and autoimmune responses against the α1(V) chain are linked to lung transplant rejection and atherosclerosis. The α1(V) collagenous COL1 domain is thought to contain greater numbers of post-translational modifications (PTMs) than do similar domains of other fibrillar collagen chains, PTMs consisting of hydroxylated prolines and lysines, the latter of which can be glycosylated. These types of PTMs can contribute to epitopes that underlie immune responses against collagens, and the high level of PTMs may contribute to the unique biological properties of the α1(V) chain. Here we use high resolution mass spectrometry to map such PTMs in bovine placental α1(V) and human recombinant pro-α1(V) procollagen chains. Findings include the locations of those PTMs that vary and those PTMs that are invariant between these α1(V) chains from widely divergent sources. Notably, an unexpectedly large number of hydroxyproline residues were mapped to the X-positions of Gly-X-Y triplets, contrary to expectations based on previous amino acid analyses of hydrolyzed α1(V) chains from various tissues. We attribute this difference to the ability of tandem mass spectrometry coupled to nanoflow chromatographic separations to detect lower-level PTM combinations with superior sensitivity and specificity. The data are consistent with the presence of a relatively large number of 3-hydroxyproline sites with less than 100% occupancy, suggesting a previously unknown mechanism for the differential modification of α1(V) chain and type V collagen properties.     

Molecular Determinants of Mechanical Properties of V.?cholerae Biofilms at?the Air-Liquid Interface

Biofilm formation increases both the survival and infectivity of Vibrio cholerae, the causative agent of cholera. V. cholerae is capable of forming biofilms on solid surfaces and at the air-liquid interface, termed pellicles. Known components of the extracellular matrix include the matrix proteins Bap1, RbmA, and RbmC, an exopolysaccharide termed Vibrio polysaccharide, and DNA. In this work, we examined a rugose strain of V. cholerae and its mutants unable to produce matrix proteins by interfacial rheology to compare the evolution of pellicle elasticity in real time to understand the molecular basis of matrix protein contributions to pellicle integrity and elasticity. Together with electron micrographs, visual inspection, and contact angle measurements of the pellicles, we defined distinct contributions of the matrix proteins to pellicle morphology, microscale architecture, and mechanical properties. Furthermore, we discovered that Bap1 is uniquely required for the maintenance of the mechanical strength of the pellicle over time and contributes to the hydrophobicity of the pellicle. Thus, Bap1 presents an important matrix component to target in the prevention and dispersal of V. cholerae biofilms.     

Role of adhesion molecules in recruitment of Vδ1 T cells from the peripheral blood to the tumor tissue of esophageal cancer patients

 The mechanism responsible for tissue specific localization of γδ T cell subsets is not well understood. In order to explain the sequestration of specific γδ T cell subsets in the peripheral blood and tumor tissue of patients with esophageal cancer, we examined the function and expression of adhesion molecules on these cells. A hierarchy in the expression of adhesion molecules was observed. In vitro activated γδ T cells showed dominant expression of LFA-1 (CD11a), VLA-α4 (CD49d), intermediate expression of VLA-α5 (CD49e) and L-selectin (CD62L), but low expression of CD44v6 and α_Eβ₇ (CD103). It was observed that the γδ T cells use LFA-1, L-selectin and CD44v6 to bind to squamous cell carcinoma (SCC) cells, whereas they adhere to fibroblast cells using LFA-1, VLA-α4 and VLA-α5. Vδ1 T cell subsets from the peripheral blood γδ T cells utilize a larger array of adhesion molecules, namely LFA-1, VLA-α4, VLA-α5, L-selectin and α_Eβ_7, to bind to SCC cells compared to the restricted usage of LFA-1, L-selectin and CD44v6 by the Vδ2 T cells. Flow cytometric analysis of tumor infiltrating lymphocytes from the esophageal tumors confirmed the selective accumulation of Vδ1⁺γδ T cells in the tumor compartment. It thus appears that adhesion molecules expressed on these lymphocytes play an important role in the recruitment and retention of Vδ1 T cells in the tumor milieu. Received: 27 November 2000 / Accepted: 1 March 2001     

C-terminal modification of osteopontin inhibits interaction with the αVβ3-integrin

Osteopontin (OPN) is a multifunctional phosphorylated protein containing the integrin binding sequence Arg-Gly-Asp through which it interacts with several integrin receptors, such as the α(V)β(3)-integrin. OPN exists in many different isoforms differing in phosphorylation status that are likely to interact differently with integrins. The C-terminal region of OPN is particularly well conserved among mammalian species, which suggests an important functional role of this region. In this study, we show that modification of the extreme C terminus of OPN plays an important regulatory role for the interaction with the α(V)β(3)-integrin. It is demonstrated that highly phosphorylated OPN has a much reduced capability to promote cell adhesion via the α(V)β(3)-integrin compared with lesser phosphorylated forms. The cell attachment promoted by highly phosphorylated OPN could be greatly increased by both dephosphorylation and proteolytic removal of the C terminus. Using recombinantly expressed OPN containing a tag in the N or C terminus, it is shown that a modification in the C-terminal part significantly reduces the adhesion of cells to OPN via the α(V)β(3)-integrin, whereas modification of the N terminus does not influence the binding. The inhibited binding of the α(V)β(3)-integrin to OPN could be restored by proteolytic removal of the C terminus by thrombin and plasmin. These data illustrate a novel mechanism regulating the interaction of OPN and the α(V)β(3)-integrin by modification of the highly conserved C-terminal region of the protein.     

Macropinocytosis of the PDGF β-receptor promotes fibroblast transformation by H-RasG12V

Receptor tyrosine kinase (RTK) signaling is frequently increased in tumor cells, sometimes as a result of decreased receptor down-regulation. The extent to which the endocytic trafficking routes can contribute to such RTK hyperactivation is unclear. Here, we show for the first time that fibroblast transformation by H-RasG12V induces the internalization of platelet-derived growth factor β-receptor (PDGFRβ) by macropinocytosis, enhancing its signaling activity and increasing anchorage-independent proliferation. H-RasG12V transformation and PDGFRβ activation were synergistic in stimulating phosphatidylinositol (PI) 3-kinase activity, leading to receptor macropinocytosis. PDGFRβ macropinocytosis was both necessary and sufficient for enhanced receptor activation. Blocking macropinocytosis by inhibition of PI 3-kinase prevented the increase in receptor activity in transformed cells. Conversely, increasing macropinocytosis by Rabankyrin-5 overexpression was sufficient to enhance PDGFRβ activation in nontransformed cells. Simultaneous stimulation with PDGF-BB and epidermal growth factor promoted macropinocytosis of both receptors and increased their activation in nontransformed cells. We propose that H-Ras transformation promotes tumor progression by enhancing growth factor receptor signaling as a result of increased receptor macropinocytosis.     

Molecular interplays involved in the cellular uptake of octaarginine on cell surfaces and the importance of syndecan-4 cytoplasmic V domain for the activation of protein kinase Cα

Arginine-rich cell-penetrating peptides (CPPs) are promising carriers for the intracellular delivery of various bioactive molecules. However, many ambiguities remain about the molecular interplays on cell surfaces that ultimately lead to endocytic uptake of CPPs. By treatment of cells with octaarginine (R8), enhanced clustering of syndecan-4 on plasma membranes and binding of protein kinase Cα (PKCα) to the cytoplasmic domain of syndecan-4 were observed; these events potentially lead to the macropinocytic uptake of R8. The cytoplasmic V domain of syndecan-4 made a significant contribution to the cellular uptake of R8, whereas the cytoplasmic C1 and C2 domains were not involved in the process.     

Validation of the MERIS products on large European lakes: Peipsi,Vänern and Vättern

The Medium Resolution Imaging Spectrometer (MERIS/Envisat) was launched in March 2002 for coastal zone monitoring. Preliminary data from MERIS show that its imagery of large lakes is superior to that of other common ocean colour sensors. The main objective of the present study is to evaluate the MERIS data on large European lakes, Vänern and Vättern in Sweden and Peipsi in Estonia/Russia. In these lakes, coloured dissolved organic matter (CDOM) can be a major contributor to the optical properties of the water. Another characteristic of the waters under investigation is the large temporal and spatial variability in the concentrations of chlorophyll (C _Chl) and suspended sediments (C _TSS). Potentially toxic cyanobacterial blooms occur in Lake Peipsi in late summer. We have compared the MERIS products from the latest reprocessing (finished in March 2006) with available in situ data. There is a reasonably good correlation between the MERIS algal_2 product and the measured C _chl over all three lakes, but no correlation was found for other optically active substances. A significant portion of the pixels (up to 90%) are flagged as invalid results after atmospheric correction.     

Residual Structures in the Acid-Unfolded States of Vλ6 Proteins Affect Amyloid Fibrillation

Many proteins form amyloid-like fibrils in vitro under partially or highly unfolding conditions. Recently, we showed that the residual structure in highly unfolded state is closely related to amyloid fibril formation in hen lysozyme. Thus, to better understand the role of the residual structure on amyloid fibril formation, we focused on AL amyloidosis, which results from the extracellular deposition of monoclonal immunoglobulin light-chain variable domains (V_Ls) as insoluble fibrils. We examined the relationship between the residual structure and amyloid fibril formation on three λ6 recombinant V_L (rVλ6) proteins, wild type, Jto, and Wil. Although rVλ6 proteins are highly unfolded in pH 2, ¹⁵N NMR transverse relaxation experiments revealed nonrandom structures in regions, which include some hydrophobic residues and a single disulfide bond, indicating the existence of residual structure in rVλ6 proteins. However, the residual structure of Wil was markedly disrupted compared with those of the other proteins, despite there being no significant differences in amino acid sequences. Fibrillation experiments revealed that Wil had a longer lag time for fibril formation than the others. When the single disulfide bond was reduced and alkylated, the residual structure was largely disrupted and fibril formation was delayed in all three rVλ6 proteins. It was suggested that the residual structure in highly unfolded state has a crucial role in amyloid fibril formation in many proteins, even pathogenic ones.     

The 125th anniversary of the first postulation of the soil origin of endophytic bacteria – a tribute to M.L.V. Galippe

Aims

In spite of the important role played by herbivory in plant community structure and the fact that it constitutes one of the most important ecological disturbance processes in the dynamics of both natural and anthropic systems, few studies have concentrated on the consequences of browsing on vegetation spatial patterns. The main objective of this study was to examine the role of domestic livestock pressure in the spatial distribution pattern and interspecific competition of two sand dune shrubs: Retama monosperma and the endangered species Thymus carnosus.

Methods

We compared three areas featuring different intensities of livestock pressure. Two 25 × 25 m plots were established in each study area, and the crown heights, diameters and x, y coordinates of every individual in each plot were recorded.

Results

Livestock activity produced a considerable effect, not only on plant cover and size (larger and higher crowns of both species in non herbivory plots) but also on spatial pattern. Whereas light herbivory lead to a random spatial pattern for both species, high herbivory resulted in a repulsion one.

Conclusions

Under high and no livestock pressure, T. carnosus is displaced by R. monosperma, creating a repulsion point pattern distribution between the two species. However, when livestock disturbance was low, our data reveal relatively higher T. carnosus cover values than in the other livestock pressure scenarios, along with a random distribution pattern.     

Effect of cortisone on the developmental pattern of the neutral and the acid β-galactosidases of the small intestine of the rat

1. The developmental pattern and effect of cortisone on acid beta-galactosidase and neutral beta-galactosidase were studied in postnatal rats by a recently proposed method for their independent determination. 2. After birth the acid beta-galactosidase activity increases in the ileum, whereas it decreases slightly in the jejunum. On day 16 after birth the activity in the ileum decreases and in 20-day-old rats activity in both parts of the intestine decreases to adult values. In suckling animals the activity in the ileum exceeds the jejunal activity severalfold and in adult animals the activity in the jejunum is slightly higher than that in the ileum. 3. Neutral beta-galactosidase activity is high after birth and decreases in both jejunum and ileum after day 20 after birth. In 12-20-day-old rats activity in both parts is essentially the same, but in adult animals jejunal activity exceeds ileal activity four-to five-fold. 4. Cortisone (0.5, 2.0 or 5.0mg/100g body wt. daily for 4 days) does not influence the activity of either enzyme in 60-day-old rats. Acid beta-galactosidase activity is decreased after cortisone treatment in 8-, 12-, 16-and 18-day-old rats, with sensitivity to cortisone increasing with the approach of weaning. No effect of cortisone on acid beta-galactosidase is seen in 8-day-old rats. Neutral beta-galactosidase activity is increased in the ileum of 8-, 12-, 16- and 18-day old rats, but only in the jejunum of 8-and 12-day-old rats.     

Human Vκ immunoglobulin gene number: Implications for the origin of antibody diversity

To assess the relative contributions of germline versus somatically mutated genes in the human immune system, we have examined the size of the kappa light-chain variable region (V_κ) gene pool. Two cloned kappa subgroup 1 (V_κ1) gene probes detected the same family of 15 to 20 crosshybridizing restriction fragments in human DNA, whereas flanking region probes detected fewer hybridizing fragments. Most of the hybridizing bands represent single-copy genes, as judged by a “gene titration” experiment. Furthermore, the number of hybridization bands is a good estimate of the haploid gene number, since we observed little polymorphism of restriction sites in the V_κ locus of eight unrelated people. A cloned V_κ3 probe hybridized to essentially the same 15–20 genes in human DNA as the V_κ1 probes. These results strongly suggest that a discrete family of 15–20 genes constitutes a large proportion of the V genes from three of the four V_κ subgroups. The small number of V_κ genes in the human genome supports the idea that somatic mutation plays a major role in the origin of antibody diversity in man.     

Gymnosperm Phylogeny — A commentary on the views of S. V. Meyen

In his important contribution to the literature on gymnosperm phylogeny, “Basic Features of Gymnosperm Systematics and Phylogeny as Evidenced by the Fossil Record,” Meyen (1984) uses the classical comparative method of the morphologist and the “congregational” method, i.e., grouping by common characters, of the taxonomist. The latter may have led him to categorize some taxa on the basis of superficially similar, non-homologous characters because he used no apparently objective method to distinguish homoplasy. For this and other reasons, Meyen’s hypothesis of evolutionary relationship among gymnosperms cannot, at present, be accepted as any nearer the truth than several competing proposals. The major innovation of Meyen’s proposed phylogeny is the recognition of the clade, Ginkgoopsida, coordinate with Cycadopsida and Pinopsida. Ginkgoopsida encompasses Calamopityaceae, Callistophytales, Glossopteridales, Peltaspermales, Caytoniales, and Ginkgoales, among others. These taxa are considered to be related because, in Meyen’s view, they share the common character of primary platyspermy — i.e., the presumed platyspermic seed-type of the basal group, Calamopityaceae, is considered to have evolved directly from the pteridophytic condition of an ancestral form. This basis for Ginkgoopsida is weakened by the facts that no seeds have been discovered in organic connection with any calamopityacean and, except for the poorly-preserved seed-like structure,Spermolithus, all seeds that occur earlier in the geologic record than fossils of the Calamopityaceae are radiospermic. It is possible, therefore, that even if the platyspermic seed,Lyrasperma, found in association with the calamopityacean,Stenomyelon, were borne by that plant, it is secondarily platyspermic, having evolved from a radiospermic ancestor. The foundation upon which Ginkgoopsida was erected seems, therefore, to be rather tenuous. Other characters used by Meyen, both reproductive and vegetative are discussed. Some which he considers significant, are interpreted to be unimportant in denoting phylogeny, while others are interpreted to support alternative hypotheses. Meyen proposes that the Ginkgoopsida evolved from archaeopterid progymnosperms. This viewpoint seems to be based largely on his erroneous belief thatArchaeopteris was probably a seed plant that bore compound leaves. There is no definitive evidence that supports the view thatArchaeopteris bore seeds. On the other hand, there is strong evidence to support the contention thatArchaeopteris produced simple leaves (Carluccio et al., 1966; Beck, 1971), not compound leaves. Meyen’s phylogenetic proposal is based on data that can be and, in part, have been differently interpreted by others. Consequently, it deserves the careful and critical evaluation of all students of gymnosperm phylogeny.