On homology

Homology in cladistics is reviewed. The definition of important terms is explicated in historical context. Homology is not synonymous with synapomorphy: it includes symplesiomorphy, and Hennig clearly included both plesiomorphy and synapomorphy as types of homology. Homoplasy is error, in coding, and is analogous to residual error in simple regression. If parallelism and convergence are to be distinguished, homoplasy would be evidence of the former and analogy evidence of the latter. We discuss whether there is a difference between molecular homology and morphological homology, character state homology, nested homology (additive characters), and serial homology. We conclude by proposing a global definition of homology. ©The Will Henning Society 2011.     

Deep homology: A view from systematics

Over the past decade, it has been discovered that disparate aspects of morphology – often of distantly related groups of organisms – are regulated by the same genetic regulatory mechanisms. Those discoveries provide a new perspective on morphological evolutionary change. A conceptual framework for exploring these research findings is termed ‘deep homology’. A comparative framework for morphological relations of homology is provided that distinguishes analogy, homoplasy, plesiomorphy and synapomorphy. Four examples – three from plants and one from animals – demonstrate that homologous developmental mechanisms can regulate a range of morphological relations including analogy, homoplasy and examples of uncertain homology. Deep homology is part of a much wider range of phenomena in which biological (genes, regulatory mechanisms, morphological traits) and phylogenetic levels of homology can both be disassociated. Therefore, to understand homology, precise, comparative, independent statements of both biological and phylogenetic levels of homology are necessary.     

Phylogenetic analysis of paraneopteran orders (Insecta: Neoptera) based on forewing base structure, with comments on monophyly of Auchenorrhyncha (Hemiptera)

Phylogenetic relationships among three paraneopteran clades (Psocodea, Hemiptera and Thysanoptera) were analysed based on the morphology of forewing base structure. Monophyly of Paraneoptera was supported by nine autapomorphies, monophyly of Condylognatha (= Thysanoptera + Hemiptera) by two autapo‐ morphies, monophyly of Thysanoptera by five autapomorphies and monophyly of Hemiptera by one autapomorphy. Thus, (Psocodea + (Thysanoptera + Hemiptera)) were proposed to be the phylogenetic relationships within Paraneoptera. A homoplastic similarity of the third axillary sclerite was observed between Thysanoptera and Heteroptera, and a possible evolutionary factor providing this homoplasy was discussed. The present analysis also suggested a monophyletic Auchenorrhyncha, and reduction of the proximal median plate was considered as an autapomorphy of this clade.     

A novel family of tRNA-derived SINEs in the colugo and two new retrotransposable markers separating dermopterans from primates

Short interspersed nuclear elements (SINEs) provide a near homoplasy free and copious source of molecular evolutionary markers with precisely defined character polarity. Used as molecular cladistic markers in presence/absence analyses, they represent a powerful complement to phylogenetic reconstructions that are based on sequence comparisons on the level of nucleotide substitutions. Recent sequence comparisons of large data sets incorporating a broad eutherian taxonomic sample have led to considerations of the different primate infraorders to constitute a paraphyletic group. Statistically significant support against the monophyly of primates has been obtained by clustering the flying lemur-also termed colugo-(Cynocephalus, Dermoptera) amidst the primates as the sister group to anthropoid primates (New World monkeys, Old World monkeys, and hominoids). We discovered retrotransposed markers that clearly favor the monophyly of primates, with the markers specific to all extant primates but definitively absent at the orthologous loci in the flying lemur and other non-primates. By screening the colugo genome for phylogenetic informative SINEs, we also recovered a novel family of dermopteran specific SINE elements that we call CYN. This element is probably derived from the isoleucine tRNA and appears in monomeric, dimeric, and trimeric forms. It has no long tRNA unrelated region and no poly(A) linker between the monomeric subunits. The characteristics of the novel CYN-SINE family indicate a relatively recent history. Therefore, this SINE family is not suitable to solve the phylogenetic affiliation between dermopterans and primates. Nevertheless it is a valuable device to reconstruct the evolutionary steps from a functional tRNA to an interspersed SINE element.     

Phylogeny of nereidids (Polychaeta, Nereididae) with paragnaths

A phylogenetic analysis was conducted of the Nereidinae — those members of the Nereididae (Polychaeta) with pharyngeal paragnaths. We had two objectives: to test the monophyly of currently accepted genera, subgenera and informal subgeneric groupings within the Nereidinae, and, if warranted, to propose a more natural classification of the Nereidinae. Parsimony analyses were undertaken, including 52 terminal taxa from all genera and informal groupings from the large heterogeneous genera Nereis , Ceratonereis , Neanthes and Perinereis . Analyses of a character set of 52 informative characters yielded more than 10 000 equally parsimonious trees with a length of 176 steps (consistency index [CI] = 0.34, retention index [RI] = 0.66). Reweighting three times resulted in 445 most parsimonious trees with length 54.62 (CI = 0.59, RI = 0.79). Many characters widely used in nereidid systematics were found to exhibit high levels of homoplasy. The most parsimonious trees could not be rooted such that the selected ingroup, 'Nereididae with paragnaths', was monophyletic, causing us to reject the monophyly of the Nereidinae as currently defined. The following genera were well supported by the parsimony analyses and are newly diagnosed: Alitta , Ceratonereis , Pseudonereis , Simplisetia , Solomononereis and Unanereis . Alitta succinea , Pseudonereis cortezi , Pseudonereis noodti and Pseudonereis pseudonoodti are proposed as new combinations. The parsimony analysis supported the monophyly of neither Composetia , Neanthes , Nereis and Perinereis nor of any new groupings of remaining species presently placed in those genera. It is these poorly supported genera that comprise most species of Nereididae.     

Phylogenetic relationships in the genus mus,based on paternally,maternally, and biparentally inherited characters

Several species in the rodent genus Mus are used as model research organisms, but comparative studies of these mice have been hampered by the lack of a well-supported phylogeny. We used DNA sequences from six genes representing paternally, maternally, and biparentally inherited regions of the genome to infer phylogenetic relationships among 10 species of Mus commonly used in laboratory research. Our sample included seven species from the subgenus Mus; one species each from the subgenera Pyromys, Coelomys, and Nannomys; and representatives from three additional murine genera, which served as outgroups in the phylogenetic analyses. Although each of the six genes yielded a unique phylogeny, several clades were supported by four or more gene trees. Nodes that conflicted between trees were generally characterized by weak support for one or both of the alternative topologies, thus providing no compelling evidence that any individual gene, or part of the genome, was misleading with respect to the evolutionary history of these mice. Analysis of the combined data resulted in a fully resolved tree that strongly supports monophyly of the genus Mus, monophyly of the subgenus Mus, division of the subgenus Mus into Palearctic (M. musculus, M. macedonicus, M. spicilegus, and M. spretus) and Asian (M. cervicolor, M. cookii, and M. caroli) clades, monophyly of the house mice (M. m. musculus, "M. m. molossinus," M. m. castaneus, and M. m. domesticus), and a sister-group relationship between M. macedonicus and M. spicilegus. Other clades that were strongly supported by one or more gene partitions were not strongly supported by the combined data. This appears to reflect a localized homoplasy in one partition obscuring the phylogenetic signal from another, rather than differences in gene or genome histories.     

Comparative detailed morphology of the Heteroderinae Filip'ev & Schuurmans Stekhoven, 1941, sensu Luc et al. (1988): phylogenetic systematics and revised classification

Taxonomic schemes for the Heteroderinae Filip'ev & Schuurmans Stekhoven, 1941, sensu Luc et al., (1988) have been unstable due to the large number of genera and the paucity of known reliable characters. Reliable characters are essential when using phylogenetic inference in developing a natural classification. Morphological and developmental studies using light, scanning and transmission electron microscopy have revealed the new characters of host response, en face patterns, phasmid structure and female cuticular layers. These techniques also gave us insight into the homoplasy and polarity of many characters, revealed previously undetected character states and clarified misinterpreted character states. A matrix with the 19 most reliable characters is proposed for 20 operational taxonomic units (OTUs) and we employ this matrix for comparing computer generated phylogenetic analyses of the PHYLIP and PAUP packages. PAUP was deemed the more reliable parsimony algorithm for phylogenetic analysis of the Heteroderinae (Fink, 1986; Platnick, 1987). Monophyly of Atalodera + Sherodera + Thecavermiculatus (tribe Ataloderini), and Cactodera + Heterodera + Afenestrata, as well as Punctodera + Globodera + Dolichodera is supported by both programs. Most importantly, analyses strongly support monophyly of all cyst-forming genera (tribe Heteroderini) contrary to previous hypotheses of repeated evolution of the cyst (Wouts, 1985). In addition, monophyly of the Heteroderini with the Ataloderini is demonstrated. PAUP indicates monophyly of Sarisodera + Rhizonema + Bellodera + Hylonema and Ekphymatodera (tribe Sarisoderini new rank). Monophyly of the Sarisoderini was at first only weakly supported, but, subsequently, the reduced width of the submedial lips of second stage juveniles and males was recognized as a synapomorphy which strengthened subsequent PAUP trees and monophyly of the tribe. The present study rejects as paraphyletic or polyphyletic several previously proposed combinations, including Thecavermiculatus sequoiae (versus Rhizonema sequoiae), Sarisodera africana (versus Afenestrata africana), Dolichodera andinus (versus Thecavermiculatus andinus). The question whether T. andinus is a distinct genus, was not resolved due to insufficient data. PAUP supports our previous observations that Cactodera betulae is intermediate in a transformation series between other Cactodera and Heterodera: it also indicates these species as bring monophyletic with Heterodera + Afenestrata, but not with other Cactodera. Although these phylogenetic analyses strongly support some relationships, they indicate unresolved alternative hypotheses for others. Meloidodera (tribe Meloidoderini) and Cryphodera (tribe Cryphoderini) must be investigated for consideration of a possible synapomorphy not included in the present data matrix. Future studies are proposed to more clearly define the monophyly of the Heteroderini, as well as the Sarisoderini. Tests are also proposed to clarify questions of the monophyly of Verutus (tribe Verutini new rank) with the Heteroderinae versus other Tylenchida.     

Variation of Microsatellite Size Homoplasy Across Electromorphs, Loci, and Populations in Three Invertebrate Species

Size homoplasy was analyzed at microsatellite loci by sequencing electromorphs, that is, variants of the same size (base pairs). This study was conducted using five interrupted and/or compound loci in three invertebrate species, the honey bee Apis mellifera, the bumble bee Bombus terrestris, and the freshwater snail Bulinus truncatus. The 15 electromorphs sequenced turned out to hide 31 alleles (i.e., variants identical in sequence). Variation in the amount of size homoplasy was detected among electromorphs and loci. From one to seven alleles were detected per electromorph, and one locus did not show any size homoplasy in both bee species. The amount of size homoplasy was related to the sequencing effort, since the number of alleles was correlated with the number of copies of electromorphs sequenced, but also with the molecular structure of the core sequence at each locus. Size homoplasy within populations was detected only three times, meaning that size homoplasy was detected mostly among populations. We analyzed population structure, estimating F _st and a genetic distance, based on either electromorphs or alleles. Whereas little difference was found in A. mellifera, uncovering size homoplasy led to a more marked population structure in B. terrestris and B. truncatus. We also showed in A. mellifera that the detection of size homoplasy may alter phylogenetic reconstructions. Received: 21 July 1997 / Accepted: 29 January 1998     

Phylogeny of Cephalobina (Nematoda): molecular evidence for recurrent evolution of probolae and incongruence with traditional classifications

Nematodes of the suborder Cephalobina include an ecologically and morphologically diverse array of species that range from soil-dwelling microbivores to parasites of vertebrates and invertebrates. Despite a long history of study, certain of these microbivores (Cephaloboidea) present some of the most intractable problems in nematode systematics; the lack of an evolutionary framework for these taxa has prevented the identification of natural groups and inhibited understanding of soil biodiversity and nematode ecology. Phylogenetic analyses of ribosomal (LSU) sequence data from 53 taxa revealed strong support for monophyly of taxa representing the Cephaloboidea, but do not support the monophyly of most genera within this superfamily. Historically these genera have primarily been recognized based on variation in labial morphology, but molecular phylogenies show the same general labial (probolae) morphotype often results from recurrent similarity, a result consistent with the phenotypic plasticity of probolae previously observed for some species in ecological time. Phylogenetic analyses of LSU rDNA also recovered strong support for some other groups of cephalobs, including taxa representing most (but not all) Panagrolaimoidea. In addition to revealing homoplasy of probolae, molecular trees also imply other unexpected patterns of character evolution or polarity, including recurrent similarity of offset spermatheca presence, and representation of complex probolae as the ancestral condition within Cephaloboidea. For Cephalobidae, molecular trees do not support traditional genera as natural groups, but it remains untested if deconstructing probolae morphotypes or other structural features into finer component characters may reveal homologies that help delimit evolutionary lineages.     

The use of structural reduction in phylogenetic reconstruction of decapods and a phylogenetic hypothesis for 15 genera of Majidae: testing previous larval hypotheses and assumptions

Summary

Using larval data of zoeae from selected genera of majids, we determined tree topologies, levels of homoplasy, and frequencies of reduction under three different assumptions of character argumentation: ordered reduction events, unordered reduction events, and outgroup comparison. Under each assumption we provided a phylogenetic hypothesis for some majid genera and evaluated the assumption that structural reduction can be assumed a priori as a criterion to infer character transformation polarity in phylogenetic reconstruction of decapods. The results indicate that the a priori assumption of “reduction” as the derived condition is not justified because under this assumption, reduction is not always maintained throughout the resulting phylogenetic hypothesis. Furthermore, we also found that this criterion fails to provide the most parsimonious explanation of the data set. Therefore, we reject the use a “reduction=derived” criterion to infer polarity in phylogenetic reconstruction. Phylogenetic analysis using outgroup comparison provided a phylogenetic hypothesis with a better fit and a lower frequency of reduction events. However, we found that statements of homology may be problematic when the number of larval stages in the outgroup differ from those of the ingroup. To overcome this problem, we suggest that, in the absence of evidence for developmental homology, all larval stages should be considered as potential homologues. Using this approach to homology of larval stages, we provide a new phylogenetic hypothesis for 15 genera of majids based on larval morphology. Within Majidae, representative members of Majinae formed a highly nested monophyletic group with the following topology: ((Jacquinotia+Notomithrax) (Leptomithrax+Maja)). In contrast, the Oregoniinae (Hyas+Chionoecetes) formed a basal monophyletic group. Contrary to established ideas for the monophyly of Inachinae, Macrocheira is basal to the Oregoniinae. Other taxa did not form monophyletic groupings based on classical assignment to subfamilies.     

Phylogenetic Relationships Between the Orders Artiodactyla and Cetacea: A Combined Assessment of Morphological and Molecular Evidence

A character analysis of selected conservative morphological traits from extant and fossil artiodactyls and cetaceans was combined with a similar analysis of conservative nucleotide positions from the complete mitochondrial cytochrome b sequences of available extant artiodactyls, cetaceans, sirenians, perissodactyls, and other mammals. This combined analysis focuses on the evidence that supports conflicting hypotheses of artiodactyl monophyly, including the affinities of hippopotamids and the monophyly or paraphyly of odontocete cetaceans. Highly conserved morphological traits of the astragalus and deciduous dentition provide strong corroboration of artiodactyl monophyly, including extant and fossil hippopotamids. In contrast, cytochrome b gene sequences are incapable of confirming this monophyly, due to excessive homoplasy of nucleotide and amino acid traits within extant Eutheria. In like manner, highly conserved and uniquely derived morphological features of the skull and auditory regions provide robust corroboration of Odontoceti monophyly, including extant and fossil physeteroids. Several nucleotide similarities do exist between physeteroids and mysticetes; however, most are either silent third-position transversions or occur also in two or more odontocete families. We suggest that increased taxon sampling, combined with functional considerations of amino acids and their secondary structure in protein-coding genes, are essential requirements for the phylogenetic interpretations of molecules at higher taxonomic levels, especially when they conflict with well-supported hypotheses of mammalian phylogeny, corroborated by uniquely derived morphological traits from extant and fossil taxa.     

Cladogenesis and anagenesis: a confusion of synapomorphies

Much cladistic theory is flawed because it confuses two temporal sequences: 1. cladogenetic (branching) chronology; 2. anagenetic (primitive-advanced) polarity. The first is largely inherent and exposed by a straigram; the second requires an independent polarisation of the changes subsequent to cladogenetic branchings. Failure to consistently distinguish between these always causes confusion, but destroys cladistic theory, because plesiomorphy and apomorphy refer to anagenesis, and autapomorphy and synapomorphy refer to cladogenetis. They cannot, however, be identified wholly independently, because cladogenetic chronology establishes anagenetic polarity by out-grouping, under limited conditions; and anagenetic polarity establishes cladogenetic chronology in multiple cladistic events. The principle ‘common characters are primitive’ is more accurately expressed as ‘characters of greater s read are cladogenetically earlier', and establishes cladogenetic relationships, never anagenetic polarity as usually thought. The full temporal analysis of biological patterns, therefore, involves eight stages: 1. Homologue identification; 2. Homolostrata delimitation and definition; 3. Stratigram formation; 4. Cladogenetic sequencing; 5. Anagenetic polarity determination (chronogramy); 6. Cladogenetic and anagenetic co-analysis; 7. Cladogram construction; 8. Phylogenetic interpretation.     

Sequence evolution in mitochondrial ribosomal and ND-1 genes in lepidoptera: implications for phylogenetic analyses.

A 2,256-bp sequence of the mitochondrial genome of a lepidopteran (Spodoptera frugiperda) contains tRNAs for valine and leucine, the 16S rRNA, and three-quarters of the ND-1 presumptive protein-coding gene. A 64-bp stretch of unknown function was located between the rRNA and leucine tRNA. Sequence divergence in the 16S rRNA obtained from alignment with published insect sequences is consistent with phylogenetic hypotheses, in that Diptera and Lepidoptera are more closely related to each other (24% sequence divergence) than either is to Hymenoptera (31%). Within the ND-1 gene, sequences for four additional Lepidoptera were generated for a 314-bp region and contrasted with published sequences for the locust and Drosophila. Sequence divergence in this region was consistent with accepted phylogenetic relationships, but results of parsimony analyses were not. Cladograms consistently recovered accepted higher level relationships (monophyly of Lepidoptera), despite high homoplasy, but were unable to resolve superfamily and family relationships within Lepidoptera, regardless of the outgroup or character subset analyzed. Character analysis indicated that homoplasy was decreased at higher levels when first- and second-codon sites were used exclusively. At the lowest level (families), resolution was enhanced by inclusion of third-codon sites. Inability of molecular data to recover a well-established phylogeny may be rectified by additional characters or taxa, but it is clear that homoplasy is sufficiently high to caution against the acceptance of relationships generated with this molecular region that are not extremely robust.     

Subterranean axes in tribe Diurideae (Orchidaceae): Morphology,anatomy, and SYSTEMATIC SIGNIFICANCE

The morphological and anatomical nature of perennating storage organs of the predominantly Australasian orchid tribe Diurideae (Orchidoideae: Orchidaceae) as well as anatomical concepts in tribes Orchideae and Diseae of Orchidoideae have been problematic for 150 yr, reflected in conflicting or vague terminology and questions about polystely and even monophyly of Orchidoideae. From a representative survey of underground organs of 145 species in 37 ingroup genera (Diurideae) and two outgroup genera (Spiranthes and Disa), the so-called “root-stem tuberoids” are here interpreted as root tubers (except for the stem tubers of Rhizanthella) borne on either droppers or stolonoid roots. All root tubers examined are bounded by a 1–4 layered velamen and exodermis, whereas droppers and stolonoid roots may have velamen-exodermis or a simple epidermis depending on the taxon and often bear multiseriate or uniseriate trichomes associated with mycorrhiza (as do roots of some taxa). The “polystely” reported in tubers of many Orchideae also occurs in tubers of many Diurideae but represents only dissection of the siphonostele into 2–13 traces. Cladistic analyses of data show extraordinarily high levels of homoplasy in characters related to root, dropper/stolonoid root, and tuber, so that these characters alone are of limited usefulness.     

Improving the analysis of dinoflagellate phylogeny based on rDNA

Phylogenetic studies of dinoflagellates are often conducted using rDNA sequences. In analyses to date, the monophyly of some of the major lineages of dinoflagellates remain to be demonstrated. There are several reasons for this uncertainty, one of which may be the use of models of evolution that may not closely fit the data. We constructed and examined alignments of SSU and partial LSU rRNA along with a concatenated alignment of the two molecules. The alignments showed several characteristics that may confound phylogeny reconstruction: paired helix (stem) regions that contain non-independently evolving sites, high levels of compositional heterogeneity among some of the sequences, high levels of incompatibility (homoplasy), and rate heterogeneity among sites. Taking into account these confounding factors, we analysed the data and found that the Gonyaulacales, a well-supported clade, may be the most recently diverged order. Other supported orders were, in the analysis based on SSU, the Suessiales and the Dinophysiales; however, the Gymnodiniales and Prorocentrales appeared to be polyphyletic. The Peridiniales without Heterocapsa species appeared as a monophyletic group in the analysis based on LSU; however, the support was low. The concatenated alignment did not provide a better phylogenetic resolution than the single gene alignments.     

Morphology and systematics in mesopsammic nemerteans of the genus Ototyphlonemertes (Nemertea,Hoplonemertea, Ototyphlonemertidae)

Interstitial nemerteans of the genus Ototyphlonemertes are difficult to organize into traditional morphospecies. They occur in a multitude of slightly different local varieties that form a seemingly continuous morphological cline. In this paper, we summarize most published morphological data on the group, plus 73 new records of geographic varieties from the Mediterranean Sea in the East to the Sea of Japan in the West. We summarize morphological variation, partition traits into character and character states, propose a standardized protocol for examination of live specimens and discuss the phylogenetic structure of the group. The phylogenetic discussion leads to a hypothesis that partitions all varieties (including the established species) into six groups. These are the smallest morphologically homogenous sets of varieties (corresponding to traditional morphospecies) we can diagnose on phylogenetically reliable traits. Variation within the groups appears to be unreliable phylogenetic markers that may distinguish ecological forms rather than relatedness. However, we distinguish four of the groups by combinations of two traits, one apomorphy for a more inclusive group and one plesiomorphy, and the remaining two by one trait each that may be either a unique plesiomorphy or an apomorphy depending on the rooting, and most of them may thus join paraphyletic groups of cryptic monophyletic units. We call this kind of group phylomorph and name them the Duplex-, Pallida-, Cirrula-, Fila-, Lactea- and Macintoshi-morph (referring to the first established species within each group, i.e. Ototyphlonemertes duplex, O. pallida, O. cirrula, O. fila, O. lactea and O. macintoshi respectively). The phylogenetic scheme provides a simple tool to allocate geographical varieties to a group of possible `species' and a phylogenetic null-hypothesis for further tests with genetic data.     

Type I STS markers are more informative than cytochrome B in phylogenetic reconstruction of the Mustelidae (Mammalia: Carnivora)

We compared the utility of five nuclear gene segments amplified with type I sequence-tagged site (STS) primers versus the complete mitochondrial cytochrome b (cyt b) gene in resolving phylogenetic relationships within the Mustelidae, a large and ecomorphologically diverse family of mammalian carnivores. Maximum parsimony and likelihood analyses of separate and combined data sets were used to address questions regarding the levels of homoplasy, incongruence, and information content within and among loci. All loci showed limited resolution in the separate analyses because of either a low amount of informative variation (nuclear genes) or high levels of homoplasy (cyt b). Individually or combined, the nuclear gene sequences had less homoplasy, retained more signal, and were more decisive, even though cyt b contained more potentially informative variation than all the nuclear sequences combined. We obtained a well-resolved and supported phylogeny when the nuclear sequences were combined. Maximum likelihood and Bayesian phylogenetic analyses of the total combined data (nuclear and mitochondrial DNA sequences) were able to better accommodate the high levels of homoplasy in the cyt b data than was an equally weighted maximum parsimony analysis. Furthermore, partition Bremer support analyses of the total combined tree showed that the relative support of the nuclear and mitochondrial genes differed according to whether or not the homoplasy in the cyt b gene was downweighted. Although the cyt b gene contributed phylogenetic signal for most major groupings, the nuclear gene sequences were more effective in reconstructing the deeper nodes of the combined tree in the equally weighted parsimony analysis, as judged by the variable-length bootstrap method. The total combined data supported the monophyly of the Lutrinae (otters), whereas the Melinae (badgers) and Mustelinae (weasels, martens) were both paraphyletic. The American badger, Taxidea taxus (Taxidiinae), was the most basal taxon. Because hundreds of type I STS primer sets spanning the complete genomes of the human and mouse have been published and thus represent many independently segregating loci, the potential utility of these markers for molecular systematics of mammals and other groups is enormous.     

A phylogenetic analysis of cordyliformes (Reptilia: Squamata): comparison of molecular and karyological data

A karyological study and the analysis of two mitochondrial genes were conducted in several species of cordyliformes from Madagascar. Both studies confirmed the monophyly of cordyliformes. The karyological conservatism and small genetic distance among mitochondrial genes observed in these species are in line with the hypothesis that all cordyliformes should be included in a single family. The two studies yielded contrasting results with regard to the relationships between the Malagasy species and the Cordylidae and Gerrhosauridae. Nonetheless, the consistency between the data from mitochondrial gene analysis and those of taxonomic studies based on morphological characters is more in favor of an affinity between Malagasy Zonosaurinae and Gerrhosauridae and suggests that the karyological similarities between the former and the Cordylidae may be due to plesiomorphy. Interesting, though not conclusive, data were also obtained on interspecific relationships among Zono-