Patristic Distances Research Articles

Molecular characterization and phylogenetics of Fennoscandian cowpox virus isolates based on the p4c and atip genes.

BackgroundCowpox virus (CPXV), a rodent-borne Orthopoxvirus (OPV) that is indigenous to Eurasia can infect humans, cattle, felidae and other animals. Molecular characterization of CPXVs isolated from different geographic locations is important for the understanding of their biology, geographic distribution, classification and evolution. Our aim was to characterize CPXVs isolated from Fennoscandia on the basis of A-type inclusion (ATI) phenotype, restriction fragment length polymorphism (RFLP) profiles of atip gene fragment amplicon, and phylogenetic tree topology in conjunction with the patristic and genetic distances based on full length DNA sequence of the atip and p4c genes.MethodsATI phenotypes were determined by transmission electron microcopy and RFLP profiles were obtained by restriction enzyme digestion of the atip gene fragment PCR product. A 6.2 kbp region spanning the entire atip and p4c genes of Fennoscandian CPXV isolates was amplified and sequenced. The phylogenetic affinity of Fennoscandian CPXV isolates to OPVs isolated from other geographic regions was determined on the basis of the atip and p4c genes.ResultsFennoscandian CPXV isolates encoded full length atip and p4c genes. They produce wild type V+ ATI except for CPXV-No-H2. CPXVs were resolved into six and seven species clusters based on the phylogeny of the atip and p4c genes respectively. The CPXVs isolated from Fennoscandia were grouped into three distinct clusters that corresponded to isolates from Norway, Sweden and Finland.ConclusionCPXV is a polyphyletic assemblage of six or seven distinct clusters and the current classification in which CPXVs are united as one single species should be re-considered. Our results are of significance to the classification and evolution of OPVs.

Geometric morphometric study of the skull shape diversification in Sciuridae (Mammalia, Rodentia).

It is generally accepted that the high phenotypic diversity of mammals is a combined result of developmental constraint and ecological adaptation, although the influence of these endogenous and exogenous factors varies in different mammal groups. The rodent family Sciuridae represents an ideal candidate for examining phenotypic diversity in relation to phylogeny and ecological adaptations. In the present study, we investigate the effects of phylogeny and lifestyle on the skull shape in different species of Sciuridae by applying geometric morphometric methods. In addition, we investigate the importance of allometry on sciurid skull shape, because results from geometric morphometrics sometimes dispute those of traditional morphometry. Here, we identify significant associations between patristic distances obtained from molecular phylogeny and shape distances in all 3 views of the cranium and the lateral view of the mandible. Multivariate regression demonstrates that shape differences among lifestyle categories are substantial, especially in the dorsal and ventral structures after the influence of phylogeny is taken into account. Allometry plays an important role in the shape variation, although its importance on different skull structures varies. Our results indicate that complex structures of this highly diverse mammal group, which occupies different niches, are affected by ecological factors and developmental constraint.

TreSpEx–-Detection of Misleading Signal in Phylogenetic Reconstructions Based on Tree Information

Phylogenies of species or genes are commonplace nowadays in many areas of comparative biological studies. However, for phylogenetic reconstructions one must refer to artificial signals such as paralogy, long-branch attraction, saturation, or conflict between different datasets. These signals might eventually mislead the reconstruction even in phylogenomic studies employing hundreds of genes. Unfortunately, there has been no program allowing the detection of such effects in combination with an implementation into automatic process pipelines. TreSpEx (Tree Space Explorer) now combines different approaches (including statistical tests), which utilize tree-based information like nodal support or patristic distances (PDs) to identify misleading signals. The program enables the parallel analysis of hundreds of trees and/or predefined gene partitions, and being command-line driven, it can be integrated into automatic process pipelines. TreSpEx is implemented in Perl and supported on Linux, Mac OS X, and MS Windows. Source code, binaries, and additional material are freely available at http://www.annelida.de/research/bioinformatics/software.html.

Can Environment Predict Cryptic Diversity? The Case of Niphargus Inhabiting Western Carpathian Groundwater

In the last decade, several studies have shown that subterranean aquatic habitats harbor cryptic species with restricted geographic ranges, frequently occurring as isolated populations. Previous studies on aquatic subterranean species have implied that habitat heterogeneity can promote speciation and that speciation events can be predicted from species’ distributions. We tested the prediction that species distributed across different drainage systems and karst sectors comprise sets of distinct species. Amphipods from the genus Niphargus from 11 caves distributed along the Western Carpathians (Romania) were investigated using three independent molecular markers (COI, H3 and 28S). The results showed that: 1) the studied populations belong to eight different species that derive from two phylogenetically unrelated Niphargus clades; 2) narrow endemic species in fact comprise complexes of morphologically similar species that are indistinguishable without using a molecular approach. The concept of monophyly, concordance between mitochondrial and nuclear DNA, and the value of patristic distances were used as species delimitation criteria. The concept of cryptic species is discussed within the framework of the present work and the contribution of these species to regional biodiversity is also addressed.

Molecular diversity of freshwater crabs from Sulawesi and the sequential colonization of ancient lakes

Ancient lakes represent one of the most stable freshwater environments on Earth, with a species richness clearly exceeding that of younger and more short-lived limnic habitats. In most cases, the biological colonization of old lake systems must have occurred via the surrounding rivers. Two ancient lake systems of Sulawesi (Malili lake system and Lake Poso) have been studied in terms of the taxonomy and phylogeny of freshwater crabs (Decapoda: Brachyura: Gecarcinucidae: Parathelphusinae). Both systems have been colonized twice independently, and in both systems we can find three trophic niches which are always occupied by different crab species: molluskivores, omnivores, and detritivores. In the present study, we reconstruct phylogenies of freshwater crabs from more than 20 river systems of Sulawesi. We thereby confirm two independent colonization events for both ancient lake systems, with subsequent radiations. The phylogenies imply that the lineages which evolved into the molluskivore forms were the first ones to colonize, whereas omnivores and detritivores are derived from later colonization events and, based on their monophyletic relationship, resulted from minor lacustrine radiations. Most of the diversity of freshwater crabs from Sulawesi remains taxonomically undescribed. This study uncovers several undocumented phylogenetic units, with long independent evolutionary histories according to patristic distances.

Limited, episodic diversification and contrasting phylogeography in a New Zealand cicada radiation.

BackgroundThe New Zealand (NZ) cicada fauna contains two co-distributed lineages that independently colonized the isolated continental fragment in the Miocene. One extensively studied lineage includes 90% of the extant species (Kikihia + Maoricicada + Rhodopsalta; ca 51 spp.), while the other contains just four extant species (Amphipsalta – 3 spp. + Notopsalta – 1 sp.) and has been little studied. We examined mitochondrial and nuclear-gene phylogenies and phylogeography, Bayesian relaxed-clock divergence timing (incorporating literature-based uncertainty of molecular clock estimates) and ecological niche models of the species from the smaller radiation.ResultsMitochondrial and nuclear-gene trees supported the monophyly of Amphipsalta. Most interspecific diversification within Amphipsalta-Notopsalta occurred from the mid-Miocene to the Pliocene. However, interspecific divergence time estimates had large confidence intervals and were highly dependent on the assumed tree prior, and comparisons of uncorrected and patristic distances suggested difficulty in estimation of branch lengths. In contrast, intraspecific divergence times varied little across analyses, and all appear to have occurred during the Pleistocene. Two large-bodied forest taxa (A. cingulata, A. zelandica) showed minimal phylogeographic structure, with intraspecific diversification dating to ca. 0.16 and 0.37 Ma, respectively. Mid-Pleistocene-age phylogeographic structure was found within two smaller-bodied species (A. strepitans – 1.16 Ma, N. sericea – 1.36 Ma] inhabiting dry open habitats. Branches separating independently evolving species were long compared to intraspecific branches. Ecological niche models hindcast to the Last Glacial Maximum (LGM) matched expectations from the genetic datasets for A. zelandica and A. strepitans, suggesting that the range of A. zelandica was greatly reduced while A. strepitans refugia were more extensive. However, no LGM habitat could be reconstructed for A. cingulata and N. sericea, suggesting survival in microhabitats not detectable with our downscaled climate data.ConclusionsUnlike the large and continuous diversification exhibited by the Kikihia-Maoricicada-Rhodopsalta clade, the contemporaneous Amphipsalta-Notopsalta lineage contains four comparatively old (early branching) species that show only recent diversification. This indicates either a long period of stasis with no speciation, or one or more bouts of extinction that have pruned the radiation. Within Amphipsalta-Notopsalta, greater population structure is found in dry-open-habitat species versus forest specialists. We attribute this difference to the fact that NZ lowland forests were repeatedly reduced in extent during glacial periods, while steep, open habitats likely became more available during late Pleistocene uplift.

Sequence diversity and novelty of natural assemblages of picoeukaryotes from the Indian Ocean

Despite the ecological importance of marine pico-size eukaryotes, the study of their in situ diversity using molecular tools started just a few years ago. These studies have revealed that marine picoeukaryotes are very diverse and include many novel taxa. However, the amount and structure of their phylogenetic diversity and the extent of their sequence novelty still remains poorly known, as a systematic analysis has been seldom attempted. In this study, we use a coherent and carefully curated data set of 500 published 18S ribosomal DNA sequences to quantify the diversity and novelty patterns of picoeukaryotes in the Indian Ocean. Our phylogenetic tree showed many distant lineages. We grouped sequences in OTUs (operational taxonomic units) at discrete values delineated by pair-wise Jukes-Cantor (JC) distances and tree patristic distances. At a distance of 0.01, the number of OTUs observed (237/242; using JC or patristic distances, respectively) was half the number of sequences analyzed, indicating the existence of microdiverse clusters of highly related sequences. At this distance level, we estimated 600-800 OTUs using several statistical methods. The number of OTUs observed was still substantial at higher distances (39/82 at 0.20 distance) suggesting a large diversity at high-taxonomic ranks. Most sequences were related to marine clones from other sites and many were distant to cultured organisms, highlighting the huge culturing gap within protists. The novelty analysis indicated the putative presence of pseudogenes and of truly novel high-rank phylogenetic lineages. The identified diversity and novelty patterns among marine picoeukaryotes are of great importance for understanding and interpreting their ecology and evolution.

Similarity in ectoparasite faunas of Palaearctic rodents as a function of host phylogenetic, geographic or environmental distances: Which matters the most?

Different host species harbour parasite faunas that are anywhere from very similar to very different in species composition. A priori, the similarity in the parasite faunas of any two host species should decrease with increases in either the phylogenetic distance, the distinctness of the environments occupied or the geographical distance between these hosts. We tested these predictions using extensive data on the faunas of fleas (Insecta: Siphonaptera) and gamasid mites (Acari: Parasitiformes) parasitic on rodents across the Palaearctic. For each pair of host species, we computed the similarity in parasite faunas based on both species composition as well as the phylogenetic and/or taxonomic distinctness of parasite species. Phylogenetic distances between hosts were based on patristic distances through a rodent phylogeny, geographic distances were computed from geographic range data, and environmental dissimilarity was measured from the average climatic and vegetation scores of each host range. Using multiple regressions on distance matrices to assess the separate explanatory power of each of the three dependent variables, environmental dissimilarity between the ranges of host species emerged as the best predictor of dissimilarity between parasite faunas, especially for fleas; in the case of mites, phylogenetic distance between host species was also important. A closer look at the data indicates that the flea and mite faunas of two hosts inhabiting different environments are always different, whilst hosts living in similar environments can have either very similar or dissimilar parasite faunas. Additional tests showed that dissimilarity in flea or mite faunas between host geographic ranges was best explained by dissimilarity in vegetation, followed by dissimilarity in climatic conditions. Thus, external environmental factors may play greater roles than commonly thought in the evolution of host–parasite associations.

Inferring speciation modes in a clade of Iberian chafers from rates of morphological evolution in different character systems.

BackgroundStudies of speciation mode based on phylogenies usually test the predicted effect on diversification patterns or on geographical distribution of closely related species. Here we outline an approach to infer the prevalent speciation mode in Iberian Hymenoplia chafers through the comparison of the evolutionary rates of morphological character systems likely to be related to sexual or ecological selection. Assuming that mitochondrial evolution is neutral and not related to measured phenotypic differences among the species, we contrast hypothetic outcomes of three speciation modes: 1) geographic isolation with subsequent random morphological divergence, resulting in overall change proportional to the mtDNA rate; 2) sexual selection on size and shape of the male intromittent organs, resulting in an evolutionary rate decoupled to that of the mtDNA; and 3) ecological segregation, reflected in character systems presumably related to ecological or biological adaptations, with rates decoupled from that of the mtDNA.ResultsThe evolutionary rate of qualitative external body characters was significantly correlated to that of the mtDNA both for the overall root-to-tip patristic distances and the individual inter-node branches, as measured with standard statistics and the randomization of a global comparison metric (the z-score). The rate of the body morphospace was significantly correlated to that of the mtDNA only for the individual branches, but not for the patristic distances, while that of the paramere outline was significantly correlated with mtDNA rates only for the patristic distances but not for the individual branches.ConclusionStructural morphological characters, often used for species recognition, have evolved at a rate proportional to that of the mtDNA, with no evidence of directional or stabilising selection according to our measures. The change in body morphospace seems to have evolved randomly at short term, but the overall change is different from that expected under a pure random drift or randomly fluctuating selection, reflecting either directional or stabilising selection or developmental constraints. Short term changes in paramere shape possibly reflect sexual selection, but their overall amount of change was unconstrained, possibly reflecting their lack of functionality. Our approach may be useful to provide indirect insights into the prevalence of different speciation modes in entire lineages when direct evidence is lacking.

Phylogenetic diversity: a quantitative framework for measurement of priority and achievement in biodiversity conservation

The value of biodiversity lies in its option value for the future, the greater the complement of contemporary biodiversity conserved today, the greater the possibilities for future biodiversity because of the diverse genetic resource needed to ensure continued evolution in a changing and uncertain world. From this perspective, biodiversity option value can be equated with richness in the different features expressed by species. An individual species of greater value is one contributing more novel features to a given subset. The feature diversity of species and communities is difficult to estimate directly, but can be predicted by the phylogenetic relationships among the species. The ‘Phylogenetic Diversity’ measure (PD) (Faith, 1992a) estimates the relative feature diversity of any nominated set of species by the sum of the lengths of all those branches spanned by the set. These branch lengths reflect patristic or path-length distances. This study first reviews and expands on some of the properties of PD, and develops simple modifications of the measure (δnPD and enPD) to enable capture of both the phylogenetic relatedness of species and their abundances in each sample. Then the application of PD, δnPD and enPD to a wide range of conservation and resource management issues is demonstrated using avian case studies. Supertree construction procedures (matrix representation using parsimony analysis; average consensus) were used to combine the extensive DNA-DNA hybridization tree of Sibley & Ahlquist (1990) with numerous, recently published phylogenetic reconstructions to derive a phylogenetic tree for the global avian fauna. Using this supertree as a systematic framework, the utility of PD was demonstrated in four case studies: (i) state of the environment reporting, with changes in avian faunas resulting from extinctions quantified as indicators of the state of biodiversity at Global, New Zealand and Waikato region scales, and changes in available habitat quantified as indicators of pressures on biodiversity in the Waikato region; (ii) setting priorities for threatened species management, with PD as a measure of option value integrated with information on survivorship expectations to develop a ranking among threatened New Zealand forest bird species; (iii) monitoring biotic response to management, with data from 5-minute counts used to analyse changes in forest bird communities under three management regimes in New Zealand; and (iv) selection of indicator species, with PD used to objectively identify subsets of species in the Global, New Zealand and Waikato avian faunas that comprise a high proportion of the option value in those faunas.

Topology testing of phylogenies using least squares methods

BackgroundThe least squares (LS) method for constructing confidence sets of trees is closely related to LS tree building methods, in which the goodness of fit of the distances measured on the tree (patristic distances) to the observed distances between taxa is the criterion used for selecting the best topology. The generalized LS (GLS) method for topology testing is often frustrated by the computational difficulties in calculating the covariance matrix and its inverse, which in practice requires approximations. The weighted LS (WLS) allows for a more efficient albeit approximate calculation of the test statistic by ignoring the covariances between the distances.ResultsThe goal of this paper is to assess the applicability of the LS approach for constructing confidence sets of trees. We show that the approximations inherent to the WLS method did not affect negatively the accuracy and reliability of the test both in the analysis of biological sequences and DNA-DNA hybridization data (for which character-based testing methods cannot be used). On the other hand, we report several problems for the GLS method, at least for the available implementation. For many data sets of biological sequences, the GLS statistic could not be calculated. For some data sets for which it could, the GLS method included all the possible trees in the confidence set despite a strong phylogenetic signal in the data. Finally, contrary to WLS, for simulated sequences GLS showed undercoverage (frequent non-inclusion of the true tree in the confidence set).ConclusionThe WLS method provides a computationally efficient approximation to the GLS useful especially in exploratory analyses of confidence sets of trees, when assessing the phylogenetic signal in the data, and when other methods are not available.

PATRISTIC: a program for calculating patristic distances and graphically comparing the components of genetic change

BackgroundPhylogenies are commonly used to analyse the differences between genes, genomes and species. Patristic distances calculated from tree branch lengths describe the amount of genetic change represented by a tree and are commonly compared with other measures of mutation to investigate the substitutional processes or the goodness of fit of a tree to the raw data. Up until now no universal tool has been available for calculating patristic distances and correlating them with other genetic distance measures.ResultsPATRISTICv1.0 is a java program that calculates patristic distances from large trees in a range of file formats and allows graphical and statistical interpretation of distance matrices calculated by other programs.ConclusionThe software overcomes some logistic barriers to analysing signals in sequences. In additional to calculating patristic distances, it provides plots for any combination of matrices, calculates commonly used statistics, allows data such as isolation dates to be entered and reorders matrices with matching species or gene labels. It will be used to analyse rates of mutation and substitutional saturation and the evolution of viruses. It is available at and requires the Java runtime environment.

Yamaceratops Dorngobiensis, a New Primitive Ceratopsian (Dinosauria: Ornithischia) from the Cretaceous of Mongolia

A new basal neoceratopsian taxon from the eastern Gobi Desert is described. Yamaceratops dorngobiensis, tax. nov., is probably of late Early Cretaceous age, and occupies a phylogenetic position intermediate between Liaoceratops and Archaeoceratops. It is the most basal taxon to display a number of traditional neoceratopsian synapomorphies concentrated in the cheek region and mandible. These include presence of an epijugal, lateral displacement of the coronoid process, a lateral ridge on the surangular for insertion of the jaw adductors, and a lateral wall to the mandibular glenoid. Yamaceratops shares two synapomorphies (tubercles on the ventral edge of the angular and shape of the jugal) with Liaoceratops, indicating that the transient presence of derived characters may be prevalent in the early evolutionary history of Ceratopsia. Yamaceratops shares aspects of frill morphology with Liaoceratops and Leptoceratops that suggest a function unrelated to display for this anatomical structure in basal neoceratopsians, and hints at a more complex evolutionary history for ceratopsian frills. Considerations of patristic distances and mosaic evolution among basal neoceratopsian taxa indicate that a greater diversity of these animals remains undiscovered.

Population differentiation and nuclear gene flow in the Dominican anole (Anolis oculatus)

Allele frequency data from nuclear microsatellite loci were used to investigate patterns of nuclear gene flow and population structure in the morphologically variable Dominican anole (Anolis oculatus). All six loci used proved to be highly polymorphic, with an average of 18.8 alleles per locus. Test for Hardy-Weinberg equilibrium revealed small numbers of heterozygote deficiencies at single loci in single populations and consistent patterns of increasingly significant heterozygote deficiency in global tests across populations and loci. No significant relationship between FST and patristic distances estimated from mitochondrial DNA sequences was detected and estimates of FIS were significantly higher in females than in males, indicating that gene flow may be sex-biased and mediated mainly by male migration. A highly significant correlation between linearized FST and loge (geographical distance) indicates that geographical proximity is a significant factor in the genetic structure of A. oculatus populations. However, levels of gene flow between morphologically differentiated parapatric populations are frequently seen to be relatively high. This supports the hypothesis of natural selection being the driving force behind the development and maintenance of morphological variation and shows that adaptive differentiation may be maintained despite the homogenizing influence of gene flow. Generally, the morphologically variable populations of A. oculatus are seen to be poor candidates for in situ speciation, but an exceptional case on the west coast of Dominica indicates that isolation resulting from vicariant events may lead to rapid differentiation at both mitochondrial and nuclear loci. This provides a possible mechanism for anole speciation on other Caribbean islands.

Phylogenetic diversity: a quantitative framework for measurement of priority and achievement in biodiversity conservation

The value of biodiversity lies in its option value for the future, the greater the complement of contemporary biodiversity conserved today, the greater the possibilities for future biodiversity because of the diverse genetic resource needed to ensure continued evolution in a changing and uncertain world. From this perspective, biodiversity option value can be equated with richness in the different features expressed by species. An individual species of greater value is one contributing more novel features to a given subset. The feature diversity of species and communities is difficult to estimate directly, but can be predicted by the phylogenetic relationships among the species. The ‘Phylogenetic Diversity’ measure (PD) (Faith, 1992a) estimates the relative feature diversity of any nominated set of species by the sum of the lengths of all those branches spanned by the set. These branch lengths reflect patristic or path-length distances. This study first reviews and expands on some of the properties of PD, and develops simple modifications of the measure (δnPD and enPD) to enable capture of both the phylogenetic relatedness of species and their abundances in each sample. Then the application of PD, δnPD and enPD to a wide range of conservation and resource management issues is demonstrated using avian case studies. Supertree construction procedures (matrix representation using parsimony analysis; average consensus) were used to combine the extensive DNA-DNA hybridization tree of Sibley & Ahlquist (1990) with numerous, recently published phylogenetic reconstructions to derive a phylogenetic tree for the global avian fauna. Using this supertree as a systematic framework, the utility of PD was demonstrated in four case studies: (i) state of the environment reporting, with changes in avian faunas resulting from extinctions quantified as indicators of the state of biodiversity at Global, New Zealand and Waikato region scales, and changes in available habitat quantified as indicators of pressures on biodiversity in the Waikato region; (ii) setting priorities for threatened species management, with PD as a measure of option value integrated with information on survivorship expectations to develop a ranking among threatened New Zealand forest bird species; (iii) monitoring biotic response to management, with data from 5-minute counts used to analyse changes in forest bird communities under three management regimes in New Zealand; and (iv) selection of indicator species, with PD used to objectively identify subsets of species in the Global, New Zealand and Waikato avian faunas that comprise a high proportion of the option value in those faunas.

THE USE OF DNA DIVERGENCE TO HELP DETERMINE THE CORRELATES OF EVOLUTION OF MORPHOLOGICAL CHARACTERS.

Even though, from Darwin onwards, interisland evolution has been a cornerstone of evolutionary theory it has not been possible to determine to what extent this geographic variation reflects the phylogeny (e.g., pattern of island colonization) or ecogenetic adaptation to different ecological conditions on each island. Using the morphology of western Canary Island lacertids (Gallotia galloti) as an example, a procedure is explored that gives a preliminary answer to this problem when there are a limited number of islands. The phylogenetic component (represented by patristic distances derived from 1005 mitochondrial DNA [mtDNA] base pairs) can be separated from two potential ecogenetic factors (environmental richness and climate) by partial Mantel tests. This reveals that, although these components interact, some characters are correlated primarily to biodiversity/paucity (e.g., size), others are correlated to wet and lush environments (e.g., dorsal pattern), and others are correlated primarily to the phylogeny (e.g., sexual leg markings). The former two correlations may be due to ecogenetic adaptation to current ecological conditions, wheras the latter reflects historical processes.

Congruence among Character Sets in Phylogenetic Studies of the Frog Genus Leptodactylus

Miyamoto, M. M. (Department of Biological Sciences, Allan Hancock Foundation, University of Southern California, University Park, Los Angeles, California 90007) 1981. Congruence among character sets in phylogenetic studies of the frog genus Leptodactylus. Syst. Zool., 30:281-290.-Four species groups of the neotropical frog genus Leptodactylus are currently recognized on the bases of morphological arnd life history characteristics. The fuscus and pentadactylus groups are related as a monophyletic cluster, whereas the phylogenetic relationships of the melanonotus and ocellatus groups remain unknown. Five species representing all four species groups occur in Costa Rica. This study examined protein variability among four Costa Rican species as ascertained by electrophoretic and histochemical techniques. The presumptive genetic data were analyzed cladistically with the Wagner method. This procedure constructed a cladogram for the Costa Rican species which was congruent with the phylogenetic relationships proposed for their species groups from morphological and life history characteristics. This congruence among phylogenetic inferences based on different character sets argues for the continued recognition of species group relationships as currently viewed within the genus. [Leptodactylus; Costa Rica; phylogenetic relationships; electrophoresis, Wagner analysis; congruence.] The genus Leptodactylus (Leptodactylidae) contains approximately 30 nominal species of primarily neotropical frogs (Heyer, 1969a). Four species groups (fuscus, melanonotus, ocellatus, and pentadactylus) are currently recognized within the genus on the bases of morphological and life history characteristics (Heyer, 1969b, 1970a, 1974, 1978, 1979). Phylogenetic relationships among the species groups are represented in Figure 1 as ascertained by Heyer (1969c) from cladistic analysis of the morphological and life history data. The fuscus and pentadactylus groups are related as a monophyletic cluster, whereas the relationships of the melanonotus and ocellatus groups remain in question as reflected by the unresolved trichotomy at the base of the phylogeny. His patristic distances suggest that the melanonotus and ocellatus groups are relatively primitive and that the fuscus and pentadactylus groups are intermediate and derived, respectively, with respect to morphological and life history characteristics. Five species representing all four species groups of Leptodactylus occur in Costa Rica (Taylor, 1952; Heyer, 1970b; Savage, 1980). Leptodactylus bolivianus, L. melanonotus, and L. pentadactylus are the sole Costa Rican representatives of the ocellatus, melanonotus, and pentadactylus groups, respectively. The fuscus group is represented in Costa Rica by two species, L. fragilis and L. poecilochilus. The occurrence of taxonomically diverse species in Costa Rica provides an opportunity to test the phylogenetic relationships among the species groups of Leptodactylus. Phylogenetic relationships among the Costa Rican species must be congruent with the phylogeny recognized for their species groups if the latter are to be considered a stable and useful representation of evolutionary history within the genus. This study examines protein variability among the Costa Rican Leptodactylus (excluding L. fragilis) as ascertained by electrophoretic and histochemical techniques (Case et al., 1975; Case, 1978a, 1978b). Presumptive genetic data are analyzed with cladistic methods and these results are compared against the

An electrophoretic investigation of six species of darters in the subgenus Catonotus

The electrophoretic patterns of lactate dehydrogenase, phosphoglucomutase and total muscle proteins distinguished the species Etheostoma flabellare, E. kennicotti and E. squamiceps from each other and from three species of the E. virgatum group ( E. virgatum, E. obeyense and E. barbouri), which all possessed identical patterns. Etheostoma flabellare, the species with the widest geographic range, possessed the greatest amount of genetic variation in all three protein systems studied. Patristic distances were calculated via an unrooted Wagner network. Using this method it was shown that E. flabellare was the most divergent species, E. kennicotti and E. squamiceps were less divergent, and the members of the E. virgatum group clustered closely.

Phylogeny of Tetraploid Catostomid Fishes Based on the Loss of Duplicate Gene Expression

Ferris, S. D. and G. S. Whitt (Department of Genetics and Development, University of Illinois, Urbana, Illinois 61801) 1978. Phylogeny of tetraploid catostomidfishes based on the of duplicate gene expression. Syst. Zool. 27:189-206.-A distinctive property of polyploids, the of duplicate gene expression over time, allows phylogenetic inferences to be drawn from multilocus isozyme data. Once the loss of a duplicate gene expression has begun, soon after polyploidization, primitive and derived character states are clearly defined, though not immune to errors in coding. Even with a relatively small number of characters, cladistic, and phenetic trees may be constructed which are similar to each other and to those based on morphology. The Wagner method is shown to be a particularly appropriate method of analysis for handling gene duplication data. Comparison of patristic and phenetic distances has revealed little homoplasy for species in closely related genera of catostomid fishes, but increasing homoplasy for comparisons between more divergent taxa. With increasing employment of isozyme technology, and the concomitant increase in the number of characters it should be possible to analyze many other polyploid taxa with this cladistic technique. [Duplicate gene expression; cladistic analysis; catostomid fishes.] A continuing challenge in the use of the cladistic method in systematics is the identification of primitive and derived character states (Mayr, 1976). This problem becomes particularly acute when allelic isozyme (allozyme) data are employed in the analysis. For example, Avise (1974) has suggested primarily phenetic means of analyzing such data, whereas Farris (1972) has derived several statistical approaches for determining ancestral positions in Wagner networks (Lundberg, 1972) so that phylogenies may be inferred. The present report describes the analysis of a biological system in which multilocus isozyme data may be readily coded into primitive and derived character states. This method of analysis should be useful for assessing the relationships of species whose ancestors have undergone substantial gene duplications. Specifically, we report the results of phenetic and cladistic analyses based on the of duplicate gene 1 Send reprint requests to G. S. Whitt. 2 Present address: Department of Biochemistry, University of California, Berkeley, California 94720. expression in tetraploid catostomid fishes (Teleostomi, Cypriniformes). The Catostomidae are a coherent family of predominantly North American freshwater fishes. Their coherence arises in part from their presumed descent from a single tetraploid ancestor 50 million years ago (Uyeno and Smith, 1972). Uyeno and Smith have demonstrated that species of catostomids have twice the number of chromosomes and cellular DNA content of related families of Cypriniformes, e.g., the diploid species of cyprinids. Ferris and Whitt (1977a) have investigated the expression of duplicate genes in representatives of most of the catostomid genera by employing starch gel electrophoresis of enzymes encoded in 20 loci (the diploid number). The average catostomid species expressed 47% of its genes in duplicate (range 35-65%), an observation consistent with tetraploidy followed by a partial functional diploidization. As a consequence of our observation of substantial differences in the extent of duplicate gene expression among species we decided to test the postulate that these differences in gene expression would reflect their evolution-