Are monophyly and synapomorphy the same or different? Revisiting the role of morphology in phylogenetics

Species are groups of organisms, marked out by reproductive (replicative) properties. Monophyletic taxa are groups of species, marked out by synapomorphies. In Nelson’s analysis, monophyly and synapomorphy are identical relations. Monophyly and synapomorphy, however, are not equivalent relations. Monophyly is epistemically not accessible, whereas synapomorphy is epistemically accessible through character analysis. Monophyly originates with speciation, the two sister‐species that come into being through the splitting of the ancestral species lineage forming a monophyletic taxon at the lowest level of inclusiveness. Synapomorphy provides the empirical evidence for monophyly, inferred from character analysis in the context of a three‐taxon statement. If synapomorphy and monophyly were equivalent, phylogenetic systematists should find a single tree, instead of multiple equally parsimonious trees. Understanding synapomorphy as the relevant evidence for phylogenetic inference reveals a category mistake in contemporary phylogenetics: the treatment of morphological characters mapped onto molecular trees as synapomorphies and homoplasies. The mapping of morphological characters onto nodes of a molecular tree results in an empirically empty procedure for synapomorphy discovery. Morphological synapomorphies and homoplasies can only be discovered by morphological and combined analyses. The use of morphology in phylogenetic inference in general is defended by examples from Laurales and Squamata in particular. To make empirical evidence scientifically relevant in order to search for concordance, or dis‐concordance, of phylogenetic signal, is certainly more fruitful for phylogenetics than the uncritical mapping of morphological traits on a molecular scaffold. © The Willi Hennig Society 2010.     

Phylogenetic implications of the morphology of the braincase of caecilian amphibians (Gymnophiona)

Caecilian morphology is strongly modified in association with their fossorial mode of life. Currently phylogenetic analyses of characters drawn from the morphology of caecilians lack resolution, as well as complementarity, with results of phylogenetic analyses that employ molecular data. Stemming from the hypothesis derived from the mammal literature that the braincase has the greatest potential (in comparison to other cranial units) to yield phylogenetic information, the braincase and intimately associated stapes of 27 species (23 genera) of extant caecilians were examined using images assembled via microcomputed tomography. Thirty‐four new morphological characters pertaining to the braincase and stapes were identified and tested for congruence with previously recognized morphological characters. The results reveal that when added to previous character matrices, characters of the braincase and stapes resolve generic‐level relationships in a way that is largely congruent with the results of molecular analyses. Analysis of a combined data set of molecular and morphological data provides a framework for conducting ancestral character state reconstructions, which resulted in the identification of 95 new synapomorphies for various clades and taxa, 27 of which appear to be unique for the taxa that possess them. Together these data demonstrate the utility of the application of characters of the braincase and stapes for resolving phylogenetic relationships for a group whose morphology is largely confounded by functional modifications. In addition this study provides evidence of the utility of the braincase in resolving problematic morphology‐based phylogeny outside of Amniota, in an amphibian group. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 166 , 160–201.     

Molecular phylogeny of venus clams (Mollusca,Bivalvia, Veneridae) with emphasis on the systematic position of taxa along the coast of mainland China

Chen, J., Li, Q., Kong, L. & Zheng, X. (2011). Molecular phylogeny of venus clams (Mollusca, Bivalvia, Veneridae) with emphasis on the systematic position of taxa along the coast of mainland China. —Zoologica Scripta, 40, 260–271. Veneridae is the most richly speciose family of heterodont bivalves with high ecological and economic value. Attention to the Veneridae systematics has been raised since traditional conchology‐based ideas on relationships among the venerids were challenged by recent studies using molecular makers and other new approaches and methods. Herein, DNA sequence information from fragments of two mitochondrial genes (COI and 16S) and one nuclear protein‐coding gene (H3) for 135 taxa (128 venerids, five nonvenerid veneroids and two other outgroups) are used to reconstruct the phylogenetic relationships of venus clams under maximum parsimony, maximum likelihood and Bayesian inference approaches. According to our molecular results, the traditional Veneridae is not recovered as monophyletic and most of the nominal subfamilies and genera formed para‐polyphyletic clades. The findings indicate that the current venerid classification cannot validly reflect a natural subdivision. In the present study, the classification of taxa along the coast of mainland China within this family are also revised based on their phylogenetic position and morphological characters. The synonymization of chionine genus Placamen with Clausinella is rejected. Chionine subgenera Anomalodiscus and Cryptonema are given full generic rank again and incorporated into Venerinae and Tapetinae, respectively. Tapetine Marcia hiantina, M. japonica and M. marmorata were distantly related to Katelysia spp., so assigning those three species into the genus Katelysia by some malacologists is rejected herein. Our results also evidence that the synonymization of the genus Tigammona and Periglypta might be inappropriate.     

Relationships among extant and fossil echimyids (Rodentia: Hystricognathi)

The echimyid rodents are the most diverse group of Neotropical hystricognaths, with approximately 40 extant and fossil genera. Craniodental characters are proposed in order to formulate hypotheses of phylogenetic relationships within the Echimyidae. A data matrix of 54 taxa and 50 characters is constructed and submitted to parsimony analyses using PAUP and WinClada programs. Analysis of the complete data set results in 47 448 most parsimonious trees 107 steps long. These trees are summarized in a strict consensus tree, which is taken as the main phylogenetic hypothesis resulting from this study. The monophyly of several currently recognized supraspecific taxa is not corroborated. These are: the subfamilies Eumysopinae, Echimyinae, Myocastorinae and Adelphomyinae; and the genera Proechimys , Echimys and Makalata . Conversely, the monophyly of Dactylomyinae and Trinomys is supported. New associations are proposed: (1) a clade comprising the extant Carterodon , Clyomys and Euryzygomatomys and the fossil Pampamys and Theridomysops placed at the base of the crown-group Echimyidae; (2) a clade uniting Proechimys , Hoplomys and Trinomys , which is the sister-taxon of (3) a clade including Mesomys , Lonchothrix , Myocastor and a clade with extant dactylomyines and echimyines and associated fossil taxa. Based on this phylogenetic hypothesis, patterns of tooth evolution in Echimyidae are discussed, and minimum ages for the divergence events within the family are estimated.  © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society , 2004, 142 , 445–477.     

Phylogeny of the Cocculinoidea (Mollusca, Gastropoda)

Abstract. The superfamily Cocculinoidea is a group of marine, deep-water, limpet-like gastropods. Recent speculation surrounding their affinities has concentrated on their placement within the Gastropoda. However, phylogenetic relationships within the Cocculinoidea, especially the monophyly of families and genera within the group, remain poorly understood. Phylogenetic analysis of 31 morphological characters for 15 cocculinoidean taxa and 2 outgroups resulted in a single most parsimonious tree, length=70, CI=0.62, and RI=0.71. Monophyly of the Cocculinoidea, Cocculinidae, and the genera Cocculina and Coccopigya was supported; Paracocculina and Coccocrater were found to be paraphyletic. Character optimization demonstrates that many characters often cited as diagnostic of various taxa, are often homoplastic and/or synapomorphies at different hierarchical levels.     

Morphology‐based phylogenetic analysis and classification of the family Rhinocryptidae (Aves: Passeriformes)

The family Rhinocryptidae comprises an assemblage of 12 genera and 55 species confined to the Neotropical region. Here we present the first morphology‐based phylogenetic study of the Rhinocryptidae, using 90 anatomical characters (62 osteological, 28 syringeal) scored for all genera of the family and representatives of all families of the infraorder Furnariides. Parsimony analysis of this dataset recovered 7428 equally most‐parsimonious trees. The strict consensus of those trees was completely resolved at the genus level, with the topology (Liosceles (Psilorhamphus ((Eleoscytalopus + Merulaxis) (Acropternis ((Teledromas + Rhinocrypta) ((Pteroptochos + Scelorchilus) (Eugralla (Myornis + Scytalopus)))))))). The monophyly of the Rhinocryptidae as presently understood was recovered with strong support [eight synapomorphies and Bremer support (BS) = 6). Strongly supported internal arrangements included the basal position of the Amazonian genus Liosceles relative to the rest of the family (four synapomorphies, BS = 4), a clade containing Acropternis through Scytalopus (six synapomorphies, BS = 4), and other less inclusive nodes. The main points of congruence between the present morphological phylogeny and previous molecular phylogenetic work on the family were clades supported by six or more synapomorphies and Bremer values of 6–7: Eleoscytalopus + Merulaxis (eight synapomorphies, BS = 6), Scelorchilus + Pteroptochos (seven synapomorphies, BS = 7), Rhinocrypta + Teledromas (seven synapomorphies, BS = 7), and Eugralla + Myornis + Scytalopus (six synapomorphies, BS = 6). A classification derived from the morphological phylogeny is proposed, with new suprageneric taxa being named and diagnosed. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 166 , 377–432.     

Phylogeny of the spider genus Ixchela Huber, 2000 (Araneae: Pholcidae) based on morphological and molecular evidence (CO1 and 16S), with a hypothesized diversification in the Pleistocene

The genus Ixchela Huber is composed of 20 species distributed from north‐eastern Mexico to Central America, including the five new species described here from Mexico: I xchela azteca sp. nov. , I xchela jalisco sp. nov. , I xchela mendozai sp. nov. , I xchela purepecha sp. nov. and I xchela tlayuda sp. nov. We test the monophyly and investigate the phylogenetic relationships among species of the genus Ixchela using morphological and molecular data. Parsimony (PA) analysis of 24 taxa and 40 morphological characters with equal and implied weights supported the monophyly of Ixchela with eight morphological synapomorphies. The PA analyses with equal and implied weights, and separate Bayesian inference (BI) analyses for the CO1 gene (506 characters), concatenated gene fragments CO1 + 16S (885 characters), morphology + CO1 (546 characters) and the combined evidence data set (morphology + CO1 + 16S) (925 characters) support the monophyly of Ixchela. Our preferred topology shows two large clades; clade 1 has a natural distribution in the Mesoamerican biotic component, whereas clade 2 predominates in the Mexican Montane biotic component. The genus Ixchela diverged in the late Miocene, and the divergence between the internal clades in the genus occurred in the late Pliocene; by contrast, most of the speciation events seem to have occurred mainly during the Pleistocene, where climatic changes brought on by repeated glaciations played an important role in the diversification of the genus. © 2015 The Linnean Society of London     

Sauropod dinosaur phylogeny: critique and cladistic analysis

Sauropoda is among the most diverse and widespread dinosaurlineages, having attained a near‐global distribution by the MiddleJurassic that was built on throughout the Cretaceous. These giganticherbivores are characterized by numerous skeletal specializationsthat accrued over a 140 million‐year history. This fascinating evolutionaryhistory has fuelled interest for more than a century, yet aspectsof sauropod interrelationships remain unresolved. This paper presentsa lower‐level phylogenetic analysis of Sauropoda in two parts. First,the two most comprehensive analyses of Sauropoda are critiqued toidentify points of agreement and difference and to create a coreof character data for subsequent analyses. Second, a generic‐levelphylogenetic analysis of 234 characters in 27 sauropod taxa is presentedthat identifies well supported nodes as well as areas of poorerresolution. The analysis resolves six sauropod outgroups to Neosauropoda,which comprises the large‐nostrilled clade Macronaria and the peg‐toothedclade Diplodocoidea. Diplodocoidea includes Rebbachisauridae, Dicraeosauridae,and Diplodocidae, whose monophyly and interrelationships are supportedlargely by cranial and vertebral synapomorphies. In contrast, thearrangement of macronarians, particularly those of titanosaurs,are based on a preponderance of appendicular synapomorphies. The purportedChinese clade ‘Euhelopodidae’ is shown to comprisea polyphyletic array of basal sauropods and neosauropods. The synapomorphiessupporting this topology allow more specific determination for themore than 50 fragmentary sauropod taxa not included in this analysis.Their distribution and phylogenetic affinities underscore the diversityof Titanosauria and the paucity of Late Triassic and Early Jurassicgenera. The diversification of Titanosauria during the Cretaceousand origin of the sauropod body plan duringthe Late Triassic remain frontiers for future studies. © 2002The Linnean Society of London, Zoological Journal of the LinneanSociety, 2002, 136 , 217?276.     

Suprageneric relationships of galliform birds (Aves, Galliformes): a cladistic analysis of morphological characters

Of the basal clades of extant birds (Neornithes) the 'landfowl' or galliforms (Aves, Galliformes) are the most speciose. Cladistic analysis of more than 100 morphological characters coded at the generic level for most putative galliform genera confirms that the megapodes ('mound builders'; Megapodiidae) are the most basal clade within the order. They are followed successively by the curassows, guans and chachalacas (Cracidae), which comprise the sister-group to all other extant Galliformes (i.e. Phasianoidea). Within this large 'phasianoid' clade, analyses suggest that the guineafowl (Numididae) are the most basal taxon, although monophyly of this 'family' is not strictly supported on the basis of the morphological characters employed. An additional major clade within the phasianoid Galliformes is recovered by this analysis, comprising the traditional groupings of New World quails (Odontophoridae) and Old World quails ('Perdicini'), yet only monophyly of the former is supported unambiguously by morphological characters. Relationships within the remainder of the phasianoid taxa, including the grouse (Tetraonidae), turkeys (i.e. Meleagris / Agriocharus spp.) as well as other 'pavonine' galliforms (i.e. peafowl; Pavo , Afropavo , Rheinardia , Argusianus and Polyplectron spp.) remain largely unresolved on the basis of morphological characters, yet monophyly of the major subdivisions is supported here. Although there are a number of important differences, especially with regard to relationships within the nonquail phasianoids, the results of this morphological phylogenetic (cladistic) analysis are broadly congruent both with traditional classifications and existing molecular hypotheses of galliform phylogenetic relationships.     

Monophyletic groups within 'higher land birds'– comparison of morphological and molecular data

The relationships within the ‘higher land birds’ and putatively related taxa are analysed in a study using 89 morphological characters and DNA sequences of three nuclear, protein‐coding genes, c‐myc, RAG‐1, and myoglobin intron II. Separate analyses of the different data sets and a ‘total evidence’ analysis in which the data sets of the morphological and molecular analyses were combined are compared. All three analyses support the hitherto disputed sister group relationship between Pici (Ramphastidae, Indicatoridae and Picidae) and Galbulae (Galbulidae and Bucconidae). Previously unrecognized osteological synapomorphies of this clade are presented. All analyses further resulted in monophyly of the taxon [Aegothelidae + (Apodidae/Hemiprocnidae + Trochilidae)]. Analysis of the morphological data and of the combined data set also supported monophyly of the taxon [Strigiformes + (Falconidae + Accipitridae)]. The morphological data further support monophyly of the taxon (Upupidae + Bucerotidae). Other placements in the three analyses received either no or only weak bootstrap support.     

Morphological character evolution and molecular trees in sepiids (Mollusca: Cephalopoda): is the cuttlebone a robust phylogenetic marker?

The sepiids are characterized by their cuttlebone or sepion, an internal shell resulting from secondary mineralization of a chitinous 'gladius'. The various species are identified using a combination of shell criteria and 'soft-part' characters. Using mitochondrial genes, we established phylogenetic relationships of sepiids including the three accepted genera ( Sepia , Sepiella , Metasepia ) and a species complex of uncertain status ( Doratosepion ). We showed the Sepia genus to be paraphyletic and found no direct correlation between geographical distribution and systematics. We mapped, on the molecular tree, shell characteristics commonly used as reliable diagnostic criteria for taxonomy. Due to the plasticity of the shell, these characters did not appear phylogenetically informative. In an attempt to define systematic categories related to phylogenetic relationships, new clear synapomorphies need to be established for each genus, necessitating a revision of the genus Sepia .  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 139–150.     

Evolutionary relationships of euthyneuran gastropods (Mollusca): a cladistic re-evaluation of morphological characters

Morphological characters of the Euthyneura available from the literature were re-evaluated in terms of terminology and primary homology. A total of 77 characters and 75 taxa were retained in a data matrix. Several assumptions on character weights and types were tested. In the cladistic analyses, it appeared that the data matrix was highly homoplastic, and only robust nodes (those which were little modified by variations in weight and coding of characters) were retained in a concensus tree. The evolutionary histories of all characters and monophylies of higher euthyneuran taxa were discussed. The following interrelationships of the taxa were obtained in a consensus tree: the clade Heterobranchia includes paraphyletic allogastropod taxa which emerge basally, and the clade Euthyneura. The latter includes the clade Pulmonata and at least 10 opisthobranch clades of unresolved relationship (Thecosomata, Gymnosomata, Acochlidioidea, Pyramidelloidea, Runcinoidea, Cephalaspidea, Sacoglossa, Umbraculoidea, Pleurobranchoidea, Nudibranchia). The Pulmonata include basommatophoran paraphyletic taxa and the clade Geophila (Onchidiidae, Soleolifera, Stylommatophora). The position of the Sacoglossa and the monophyly of the Notaspidea are also discussed.  © 2002 The Linnean Society of London, Zoological Journal of the Linnean Society , 2002, 135 , 403–470.     

Molecular data place Hydnoraceae with Aristolochiaceae

Utilization of molecular phylogenetic information over the past decade has resulted in clarification of the position of most angiosperms. In contrast, the position of the holoparasitic family Hydnoraceae has remained controversial. To address the question of phylogenetic position of Hydnoraceae among angiosperms, nuclear SSU and LSU rDNA and mitochondrial atp1 and matR sequences were obtained for Hydnora and Prosopanche. These sequences were used in combined analyses that included the above four genes as well as chloroplast rbcL and atpB (these plastid genes are missing in Hydnoraceae and were hence coded as missing). Three data sets were analyzed using maximum parsimony: (1) three genes with 461 taxa; (2) five genes with 77 taxa; and (3) six genes with 38 taxa. Analyses of separate and combined data partitions support the monophyly of Hydnoraceae and the association of that clade with Aristolochiaceae sensu lato (s.l.) (including Lactoridaceae). The latter clade is sister to Piperaceae and Saururaceae. Despite over 11 kilobases (kb) of sequence data, relationships within Aristolochiaceae s.l. remain unresolved, thus it cannot yet be determined whether Aristolochiaceae, Hydnoraceae, and Lactoridaceae should be classified as distinct families. In contrast to most traditional classifications, molecular phylogenetic analyses do not suggest a close relationship between Hydnoraceae and Rafflesiaceae. A number of morphological features is shared by Hydnoraceae and Aristolochiaceae; however, a more resolved phylogeny is required to determine whether these represent synapomorphies or independent acquisitions.     

Phylogenetic relationships among the Lorisoidea as indicated by craniodental morphology and mitochondrial sequence data

The phylogeny of the Afro-Asian Lorisoidea is controversial. While postcranial data attest strongly to the monophyly of the Lorisidae, most molecular analyses portray them as paraphyletic and group the Galagidae alternately with the Asian or African lorisids. One of the problems that has bedevilled phylogenetic analysis of the group in the past is the limited number of taxa sampled for both ingroup families. We present the results of a series of phylogenetic analyses based on 635 base pairs (bp) from two mitochondrial genes (12S and 16S rRNA) with and without 36 craniodental characters, for 11 galagid and five lorisid taxa. The outgroup was the gray mouse lemur (Microcebus murinus). Analyses of the molecular data included maximum parsimony (MP), neighbor joining (NJ), maximum likelihood (ML), and Bayesian methods. The model-based analyses and the combined "molecules+morphology" analyses supported monophyly of the Lorisidae and Galagidae. The lorisids form two geographically defined clades. We find no support for the taxonomy of Galagidae as proposed recently by Groves [Primate Taxonomy, Washington, DC: Smithsonian Institution Press. 350 p, 2001]. The taxonomy of Nash et al. [International Journal of Primatology 10:57-80, 1989] is supported by the combined "molecules+morphology" analysis; however, the model-based analyses suggest that Galagoides may be an assemblage of species united by plesiomorphic craniodental characters.     

Comparative morphology,phylogeny, and classification of West African callopanchacine killifishes (Teleostei: Cyprinodontiformes: Nothobranchiidae)

A phylogenetic analysis combining 63 morphological characters and DNA sequences (3296 bp), comprising segments of the mitochondrial genes 16S and ND2, and the nuclear gene 28S, for 19 taxa of the West African killifish tribe Callopanchacini and 11 out‐group taxa, highly supported the monophyly of the tribe, and made it possible to provide the first unambiguous diagnoses for the included genera (Archiaphyosemion, Callopanchax, Nimbapanchax, and Scriptaphyosemion). The monophyly of the Callopanchacini is supported by six morphological synapomorphies: posterior portion of the mandibular channel consisting of a single open groove; basihyal pentagonal, as a result of a nearly rectangular basihyal cartilage and a triangular bony support; dorsal process of the urohyal usually absent, sometimes rudimentary; presence of a wide bony flap adjacent to the proximal portion of the fourth ceratobranchial; a broad bony flap adjacent to the proximal portion of the fifth ceratobranchial; and haemal prezygapophysis of the pre‐ural vertebra 2 ventrally directed. The analysis indicates that the medially continuous rostral neuromast channel, commonly used to diagnose the tribe, is plesiomorphic. This study also indicates that, among African aplocheiloids, the annual life cycle style developed once in Callopanchax, and then again independently in the clade containing Fundulopanchax and Nothobranchius. © 2015 The Linnean Society of London     

The systematic relationships of glucosinolate-producing plants and related families: a cladistic investigation based on morphological and molecular characters

A cladistic analysis is performed using 94 morphological and biochemical characters for 42 genera to compare a phylogeny based on morphological data with those obtained using different genes ( rbc L, atp B, 18S RNA, mat K) or their combination with morphological data, and to understand the floral evolution within the expanded Brassicales (Capparales) relative to Sapindales and Malvales. The tree produced with morphological data is congruent with those obtained from macromolecular studies in obtaining a well-supported glucosinolate-producing clade and an expanded Sapindales. The combined analysis of the morphological and molecular characters is generally well resolved with support for many of the relationships. The inclusion of the fossil taxon Dressiantha demonstrates the value of inserting fossil evidence in phylogenetic analyses. However, the fossil appears to be related to the Anacardiaceae and not to the Brassicales. The core Brassicales are well supported by a number of synapomorphies, although the internal position of Tovariaceae and Pentadiplandraceae is not well resolved. Emblingiaceae appears to be related to Bataceae and Salvadoraceae. Several significant morphological characters are mapped on the combined trees and their evolutionary significance is discussed. Within Brassicales and Sapindales several well supported clades can be recognized which merit ordinal or subordinal status, putting the present orders at a higher level; these include: Tropaeolales, Setchellanthales, Batidales, Brassicales (Brassiciflorae), Burserales, Sapindales and Rutales (Sapindiflorae). The present scheme of affinities within the Brassicales corresponds well with a gradual morphological evolution in the order.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 151 , 453–494.