Homology as a parsimony problem: a dynamic homology approach for morphological data

The primary data used to reconstruct phylogenies comes organized in the conceptual grid of homology correspondences, and the construction of this theory‐rich grid depends in part on knowledge of relationships. This situation is not satisfactory as a conceptual system, because the evidence is not clearly delimited from the results. I explore the testing of alternative hypotheses of morphological correspondences in a quantitative cladistic context. The varying homology assessments implied by classical criteria of homology (topological equivalence, or position and connections; composition of structures, or commonality in details of construction) can be expressed as regular characters in a cladistic analysis. Doing so provides adequate transformation costs for changes in schemas of correspondences. Correspondences imply evolutionary transformations, and multiple schemas of correspondences can be compared according to the evolutionary transformations that they imply. The method is used to test the correspondences in sclerites of the male copulatory organs of spiders of the subfamily Amaurobioidinae (Arachnida, Araneae, Anyphaenidae). The correspondences of three sclerites are tested, in a data set of 93 species having one, two or three sclerites, using a simultaneous analysis of all the morphological characters. Most parsimonious trees are identified together with the correspondences they imply. Once the correspondences are integrated in the phylogenetic analysis, it is easy to evaluate the robustness of trees or decay in optimality after changes in anatomical interpretations. A Bremer support for anatomical interpretations is proposed, calculated as the increase in tree length when the specific interpretation is not used. © The Willi Hennig Society 2007.     

Amino acid sequence versus morphological data and the interordinal relationships of mammals

To a large extent, the mutual affinities of the mammalian orders continue to puzzle systematists, even though comparative anatomy and amino acid sequencing offer a massive data base from which these relationships could potentially be adduced. In the present paper the consistency index--the number of character states less the number of characters in a data set, divided by the total number of changes in the character states on a cladogram--was used to examine the relative resolving powers of recently published morphological and molecular- sequence data. Consistency indices were calculated for previously published alpha crystallin A chain and myoglobin amino acid-sequence cladograms and for four original amino acid-sequence cladograms (alpha crystallin A, myoglobin, and alpha and beta hemoglobin); these were found to be comparable to the consistency indices of morphologically based cladograms. Qualitative comparisons between the morphologically based and molecularly based trees were also made; only moderate congruence between the two was observed. Moreover, there was a general lack of congruence between the cladograms specified by each of the four proteins. Amino acid-sequence and morphological data agreed on the placement of edentates as an early eutherian offshoot and on the grouping of hyracoids, proboscideans, and sirenians. Otherwise there was only limited congruence: morphology strongly supported the grouping of lagomorphs and rodents and the alliance of pholidotes and edentates, but sequence analyses did not. The placement of tubulidentates differed widely among proteins. Morphology indicated the close association of sirenians with proboscideans; proteins suggested a pairing of sirenians with hyracoids. Sequence data did not identify many (morphologically well-diagnosed) orders as monophyletic (e.g., Lagomorpha).(ABSTRACT TRUNCATED AT 250 WORDS)      

Reassessment of homology of morphological characters in tetractinellid sponges based on molecular data

In sponges, as in other taxa with simple organization, the evaluation and use of morphological characters is difficult. Phylogenetic analysis of the first 850 nucleotides from the 5' end of the 28S rRNA gene is used here to assess the homology of spicules used in the classification of the subclass Tetractinellida. A single well-supported MP tree was obtained. The monophyly of the nine Tetractinellida species studied confirms the tetraxon megasclere as a morphological synapomorphy for the Tetractinellida. Two species are reallocated, Penares helleri as a Geodiidae, now thought to have lost sterraster microscleres, and Stryphnus mucronatus to the Streptosclerophorida. SEM micrographs of Stryphnus microscleres show that the morphology of the sanidasters is compatible with the hypothesis that they are homologous with streptoscleres and confirm this reallocation. Two other synapomorphies are confirmed within the tetractinellid clade, the simultaneous presence of tetraxon megasclere and aster-type microsclere (Astrophorida) and the loss of the streptosclere and persistence of the euaster s.s. microscleres (Euastrophorida) evidenced by the reallocation of Stryphnus mucronatus. The streptosclere microscleres cannot be evaluated in terms of homology because Streptosclerophorida may be paraphyletic (although these nodes are not supported by reliable bootstrap proportions) contrary to the currently accepted classification.     

Concordance of molecular and morphological data: The example of the Acoela

Morphological features of the Acoela appear to be quite plastic, including those of the copulatory organs, which provide the principle characteristics used for the systematics of this group. Consequently, classification schemes of the Acoela comprise numerous polyphyletic groupings. In this review, we detail recent revisions of acoel systematics using molecular sequence data and new and reevaluated morphological characteristics. Gene trees are discordant with traditional systematic schemes but strongly concordant with new morphological characteristics obtained through the use of transmission electron microscopy and confocal laser scanning microscopy, namely, characteristics of body-wall and copulatory organ musculature, sperm, sperm ducts, sagittocysts, and immunocytochemistry of the nervous system. This merger of molecular and morphological data has led to significant changes in acoel classification, including a major emendation of the largest family of the Acoela, the Convolutidae, whereby half of its members were transferred to a newly created family, the Isodiametridae.     

The gonangulum: A reassessment of its morphology,homology, and phylogenetic significance

The gonangulum is a sclerite in the female genitalic region of insects. Its presence or full development has long been considered an apomorphy supporting Zygentoma + Pterygota. Recent studies of female genitalia in several insect orders (K.-D. Klass and co-workers) revealed many new data on the gonangulum and homologous sclerotisations (laterocoxa LC9). Herein the gonangulum area is described (including articulations, muscle attachments, sulci) and compared among Archaeognatha, Zygentoma, Odonata, Dermaptera, Dictyoptera, and Notoptera. A wider perspective is provided to the topic by addressing some novel issues: identification of LC9 sclerotisations in non-insect taxa and in insects that secondarily lack an ovipositor; occurrence of homonomous sclerotisations in other abdominal segments of both sexes; morphological interpretation of LC9; and the role of paedomorphosis in LC9 evolution. As a result, there is currently no support for any insect lineage from this character system. For gonangulum-related characters both a significant intra-ordinal variation and frequent homoplasy are demonstrated using various Odonata, Dermaptera, and Dictyoptera as examples. Divergent fates of LC9 in simplified genitalia are shown using a dermapteran and an odonatan. We view all this as a showcase of how a renewed and more detailed examination of a character system can dramatically change the phylogenetic evidence drawn from it.     

The fine structure of ‘homology’

There is long-standing conflict between genealogical and developmental accounts of homology. This paper provides a general framework that shows that these accounts are compatible and clarifies precisely how they are related. According to this framework, understanding homology requires both (a) an abstract genealogical account that unifies the application of the term to all types of characters used in phylogenetic systematics and (b) locally enriched accounts that apply only to specific types of characters. The genealogical account serves this unifying role by relying on abstract notions of ‘descent’ and ‘character’. As a result, it takes for granted the existence of such characters. This requires theoretical justification that is provided by enriched accounts, which incorporate the details by which characters are inherited. These enriched accounts apply to limited domains (e.g. genes and proteins, or body parts), providing the needed theoretical justification for recognizing characters within that domain. Though connected to the genealogical account of homology in this way, enriched accounts include phenomena (e.g. serial homology, paralogy, and xenology) that fall outside the scope of the genealogical account. They therefore overlap, but are not nested within, the genealogical account. Developmental accounts of homology are to be understood as enriched accounts of body part homology. Once they are seen in this light, the conflict with the genealogical account vanishes. It is only by understanding the fine conceptual structure undergirding the many uses of the term ‘homology’ that we can understand how these uses hang together.     

The role of the Src homology domains in morphological transformation by v-src.

The Src homology (SH2 and SH3) domains of v-Src are required for transformation of Rat-2 cells and for wild-type (morphr) transformation of chicken embryo fibroblasts (CEFs). We report herein that the N-terminal domains of v-Src, when expressed in trans, cannot complement the transformation defect of a deletion mutant lacking the "unique," SH3, and SH2 regions. However, the same regions of Src can promote transformation when translocated to the C terminus of v-Src, although the transformation of CEFs is somewhat slower. We conclude that the SH3 and SH2 domains must be present in cis to the catalytic domain to promote transformation but that transformation is not dependent on the precise intramolecular location of these domains. In CEFSs and in Rat-2 cells, the expression of wild-type v-Src results in tyrosine phosphorylation of proteins that bind to the v-Src SH3 and SH2 domains in vitro; mutations in the SH2 or SH3 and SH2 domains prevent the phosphorylation of these proteins. These findings are most consistent with models in which the SH3 and SH2 domains of v-Src directly or indirectly target the catalytic domain to substrates involved in transformation. However, the N-terminal domains of v-Src can promote tyrosine phosphorylation of certain proteins, in particular p130Cas, even when expressed in the absence of the catalytic domain, indicating that the N-terminal domains of v-Src have effects that are independent of the catalytic domain.     

Protein structure prediction constrained by solution X-ray scattering data and structural homology identification

Here we perform a systematic exploration of the use of distance constraints derived from small angle X-ray scattering (SAXS) measurements to filter candidate protein structures for the purpose of protein structure prediction. This is an intrinsically more complex task than that of applying distance constraints derived from NMR data where the identity of the pair of amino acid residues subject to a given distance constraint is known. SAXS, on the other hand, yields a histogram of pair distances (pair distribution function), but the identities of the pairs contributing to a given bin of the histogram are not known. Our study is based on an extension of the Levitt-Hinds coarse grained approach to ab initio protein structure prediction to generate a candidate set of C(alpha) backbones. In spite of the lack of specific residue information inherent in the SAXS data, our study shows that the implementation of a SAXS filter is capable of effectively purifying the set of native structure candidates and thus provides a substantial improvement in the reliability of protein structure prediction. We test the quality of our predicted C(alpha) backbones by doing structural homology searches against the Dali domain library, and find that the results are very encouraging. In spite of the lack of local structural details and limited modeling accuracy at the C(alpha) backbone level, we find that useful information about fold classification can be extracted from this procedure. This approach thus provides a way to use a SAXS data based structure prediction algorithm to generate potential structural homologies in cases where lack of sequence homology prevents identification of candidate folds for a given protein. Thus our approach has the potential to help in determination of the biological function of a protein based on structural homology instead of sequence homology.     

Native 3D structure of eukaryotic 80s ribosome: morphological homology with E. coli 70S ribosome

A three-dimensional reconstruction of the eukaryotic 80S monosome from a frozen-hydrated electron microscopic preparation reveals the native structure of this macromolecular complex. The new structure, at 38A resolution, shows a marked resemblance to the structure determined for the E. coli 70S ribosome (Frank, J., A. Verschoor, Y. Li, J. Zhu, R.K. Lata, M. Radermacher, P. Penczek, R. Grassucci, R.K. Agrawal, and Srivastava. 1996b. In press; Frank, J., J. Zhu, P. Penczek, Y. Li, S. Srivastava ., A. Verschoor, M. Radermacher, R. Grassucci, R.K. Lata, and R. Agrawal. 1995. Nature (Lond.).376:441-444.) limited to a comparable resolution, but with a number of eukaryotic elaborations superimposed. Although considerably greater size and intricacy of the features is seen in the morphology of the large subunit (60S vs 50S), the most striking differences are in the small subunit morphology (40S vs 30S): the extended beak and crest features of the head, the back lobes, and the feet. However, the structure underlying these extra features appears to be remarkably similar in form to the 30S portion of the 70S structure. The intersubunit space also appears to be strongly conserved, as might be expected from the degree of functional conservation of the ribosome among kingdoms (Eukarya, Eubacteria, and Archaea). The internal organization of the 80S structure appears as an armature or core of high-density material for each subunit, with the two cores linked by a single bridge between the platform region of the 40S subunit and the region below the presumed peptidyltransferase center of the 60S subunit. This may be equated with a close contact of the 18S and 28S rRNAs in the translational domain centered on the upper subunit:subunit interface.     

Discovering local structure in gene expression data: the order-preserving submatrix problem.

This paper concerns the discovery of patterns in gene expression matrices, in which each element gives the expression level of a given gene in a given experiment. Most existing methods for pattern discovery in such matrices are based on clustering genes by comparing their expression levels in all experiments, or clustering experiments by comparing their expression levels for all genes. Our work goes beyond such global approaches by looking for local patterns that manifest themselves when we focus simultaneously on a subset G of the genes and a subset T of the experiments. Specifically, we look for order-preserving submatrices (OPSMs), in which the expression levels of all genes induce the same linear ordering of the experiments (we show that the OPSM search problem is NP-hard in the worst case). Such a pattern might arise, for example, if the experiments in T represent distinct stages in the progress of a disease or in a cellular process and the expression levels of all genes in G vary across the stages in the same way. We define a probabilistic model in which an OPSM is hidden within an otherwise random matrix. Guided by this model, we develop an efficient algorithm for finding the hidden OPSM in the random matrix. In data generated according to the model, the algorithm recovers the hidden OPSM with a very high success rate. Application of the methods to breast cancer data seem to reveal significant local patterns.     

The 5S rRNA loop E: chemical probing and phylogenetic data versus crystal structure.

A significant fraction of the bases in a folded, structured RNA molecule participate in noncanonical base pairing interactions, often in the context of internal loops or multi-helix junction loops. The appearance of each new high-resolution RNA structure provides welcome data to guide efforts to understand and predict RNA 3D structure, especially when the RNA in question is a functionally conserved molecule. The recent publication of the crystal structure of the "Loop E" region of bacterial 5S ribosomal RNA is such an event [Correll CC, Freeborn B, Moore PB, Steitz TA, 1997, Cell 91:705-712]. In addition to providing more examples of already established noncanonical base pairs, such as purine-purine sheared pairings, trans-Hoogsteen UA, and GU wobble pairs, the structure provides the first high-resolution views of two new purine-purine pairings and a new GU pairing. The goal of the present analysis is to expand the capabilities of both chemical probing and phylogenetic analysis to predict with greater accuracy the structures of RNA molecules. First, in light of existing chemical probing data, we investigate what lessons could be learned regarding the interpretation of this widely used method of RNA structure probing. Then we analyze the 3D structure with reference to molecular phylogeny data (assuming conservation of function) to discover what alternative base pairings are geometrically compatible with the structure. The comparisons between previous modeling efforts and crystal structures show that the intricate involvements of ions and water molecules in the maintenance of non-Watson-Crick pairs render the process of correctly identifying the interacting sites in such pairs treacherous, except in cases of trans-Hoogsteen A/U or sheared A/G pairs for the adenine N1 site. The phylogenetic analysis identifies A/A, A/C, A/U and C/A, C/C, and C/U pairings isosteric with sheared A/G, as well as A/A and A/C pairings isosteric with both G/U and G/G bifurcated pairings. Thus, each non-Watson-Crick pair could be characterized by a phylogenetic signature of variations between isosteric-like pairings. In addition to the conservative changes, which form a dictionary of pairings isosterically compatible with those observed in the crystal structure, concerted changes involving several base pairs also occur. The latter covariations may indicate transitions between related but distinctive motifs within the loop E of 5S ribosomal RNA.     

The phylogenetic position of early hexapod lineages: morphological data contradict molecular data

Abstract. A review of different studies on the phylogenetic relationships of the early Hexapoda lineages shows that analyses based on molecular sequence data have led to labile and sometimes incongruous results, introducing doubt as to the reliability of the cladograms as a whole. In a recent analysis using molecular data, the Collembola, usually considered as early branching hexapods, appear to occupy a position outside the assemblage of Crustacea and Insecta, leading to the rejection of the traditional view of hexapod monophyly. However, many morphological features, as well as the results of cladistic analyses based on morphological and developmental information, contradict these conclusions. More generally, it appears that in the present state of the analytical strategies, hypotheses concerning arthropod phylogenies obtained from morphological and developmental criteria and combined analyses involving molecular and morphological data provide more reliable results than those generated by molecular information alone.     

The importance of colony structure versus shoot morphology for the water balance of 22 subarctic bryophyte species

Questions: What are the water economy strategies of the dominant subarctic bryophytes in terms of colony and shoot traits? Can colony water retention capacity be predicted from morphological traits of both colonies and separate shoots? Are suites of water retention traits consistently related to bryophyte habitat and phylogenetic position? Location: Abisko Research Station, North Sweden. Methods: We screened 22 abundant subarctic bryophyte species from diverse habitats for water economy traits of shoots and colonies, including desiccation rates, water content at field capacity, volume and density (mg cm^?3) of water‐saturated and oven‐dried patches, evaporation rate (g·m^?2·s^?1) and cell wall thickness. The relationships between these traits and shoot and colony desiccation rates were analysed with Spearman rank correlations. Subsequent multivariate (cluster followed by PCA) analyses were based on turf density, turf and shoot desiccation rate, cell wall thickness and amount of external and internal water. Results: Individual shoot properties, i.e. leaf cell wall properties, water retention capacity and desiccation rate, did not correspond with colony water retention capacity. Colony desiccation rate depended on density of water‐saturated colonies, and was marginally significantly negatively correlated with species individual shoot desiccation rate but not related to any other shoot or colony trait. Multivariate analyses based on traits assumed to determine colony desiccation rate revealed six distinct species groups reflecting habitat choice and phylogenetic relationships. Conclusions: General relationships between shoot and colony traits as determinants of water economy will help to predict and upscale changes in hydrological function of bryophyte‐dominated peatlands undergoing climate‐induced shifts in species abundance, and feedbacks of such species shifts on permafrost insulation and carbon sequestration functions.     

Phylogeny, evolution and systematics of Moehringia (Caryophyllaceae) as inferred from molecular and morphological data: a case of homology reassessment

The phylogeny of the genus Moehringia (Caryophyllaceae) is investigated by means of analyzing nuclear (ITS) and chloroplast (matK) sequence data in combination with morphological characters. Parsimony and Bayesian methods yield consistent results, and a common phylogenetic signal is shared by the nuclear and chloroplast data. Morphological characters are affected by a high level of homoplasy, but they provide valuable information when analyzed in combination with the molecular data. Moehringia is paraphyletic to Arenaria with the Iberian taxa belonging to Moehringia sect. Pseudomoehringia McNeill more closely related to Arenaria. This cladistic evidence led us to reinterpret the homology of the key character used in most, if not all, floras, to separate Moehringia from Arenaria, i.e., the seed strophiole. Thorough anatomical studies were carried out to elucidate the ontogeny of the strophiole, which proved different in Moehringia s. str. and the Iberian taxa. Within Moehringia s. str., two sister clades are recognized (i.e., Moehringia sect. Moehringia and M. sect. Latifoliae much as recognized by McNeill, whereas representatives of M. sect. Diversifoliae are assigned to either groups), and biogeographical events related to the Würm glaciation are considered to play a fundamental role in the evolution and present distribution of the genus. The variation of the strophiole is regarded as adaptability to ecological conditions and dispersal agents. We also propose two new combinations and two replacement names: Arenaria glochidisperma (J.M. Mont.) Fior et P.O. Karis, comb. nov., Arenaria tejedensis (Willk.) Fior et P.O. Karis, comb. nov., Arenaria suffruticosa Fior et P.O. Karis, nom. nov. for Moehringia intricata Willk., and Arenaria funiculata Fior et P.O. Karis, nom. nov. for Moehringia fontqueri Pau. © The Willi Hennig Society 2007.     

Functional morphology and homology in the odontocete nasal complex: Implications for sound generation

The site and physiologic mechanism(s) responsible for the generation of odontocete biosonar signals have eluded investigators for decades. To address these issues we subjected postmortem toothed whale heads to interrogation using medical imaging techniques. Most of the 40 specimens (from 19 species) were examined using X-ray computed tomography (CT) and/or magnetic resonance imaging (MR). Interpretation of scan images was aided by subsequent dissection of the specimens or, in one case, by cryosectioning. In all specimens we described a similar tissue complex and identified it as the hypothetical biosonar signal generator. This complex includes a small pair of fatty bursae embedded in a pair of connective tissue lips, a cartilaginous blade, a stout ligament, and an array of soft tissue air sacs. Comparing and contrasting the morphologic patterns of nasal structures across species representing every extant odontocete superfamily reveals probable homologous relationships, which suggests that all toothed whales may be making their biosonar signals by a similar mechanism. © 1996 Wiley-Liss, Inc.     

On the necessity of an archetypal concept in morphology: With special reference to the concepts of “structure” and “homology”

Morphological elements, or structures, are sorted into four categories depending on their level of anatomical isolation and the presence or absence of intrinsically identifying characteristics. These four categories are used to highlight the difficulties with the concept of structure and our ability to identify or define structures. The analysis is extended to the concept of homology through a discussion of the methodological and philosophical problems of the current concept of homology. It is argued that homology is fundamentally a similarity based concept rather than a phylogenetic concept, and a proposal is put forth to return to a comparative context for homology. It is shown that for both the concepts of structure and homology ana priori assumption of stable underlying patterns (i.e. archetypes) is essential.     

Allozymic, morphological, phenological, linguistic, plant use, and nutritional data ofBenincasa Hispida (Cucurbitaceae)

Benincasa hispida, from tropical Asia, is cultivated primarily for its edible fruit. To explore its domestication and ethnobotany, we made collections from two regions where it may have been domesticated: (1) Southern China/Southeast Asia, represented by southern Yunnan Province (China) and northern Laos; and (2) the Indian subcontinent, represented by southeastern Nepal. Domestication has resulted in diverse fruit sizes, shapes, and colors; seed sizes and shapes; and, in some accessions, the loss of tendrils. Modern cultivars have larger fruit, earlier flowers, and lower nutritional content than traditional cultivars. Allozyme diversity was low, divergence between these two regions was low, and these results do not clarify the place of domestication. The greater morphological diversity of plants from Yunnan and Laos, as compared to Nepal, suggests domestication in the former region. In all accessions, male flowers precede females.Benincasa hispida is prominent in some traditional stories and rituals.