Using inter-SINE-PCR to study mammalian phylogeny

Results of the use of the fingerprinting method related to short interspersed elements (SINEs), inter-SINE-PCR, in the study of phylogenetic and taxonomic relationship in mammals from orders Chiroptera (family Vespertilionidae) and Lipotyphla (family Erinaceidae) are reported. The inter-SINE-PCR method is based on the amplification of fragments situated between copies of SINEs, which are short retroposons spaced 100 to 1000 bp apart. Specifically selected primers were used, which are complementary to consensus sequences of two short retroposons: the mammalian interspersed repeat (MIR), which is typical of all mammals and some other vertebrates, was used in the cases of bats and Erinaceidae, and the ERI-1 element recently isolated from the genome of the Daurian hedgehog was used in the case of Erinaceidae. The results support the current view on phylogenetic relationship between hedgehogs belonging to genera Erinaceus, Hemiechinus, and Paraechinus (but not the genus Atelerix). In bats, the phylogenetic reconstruction revealed a statistically valid topology only at lower taxonomic levels, whereas the topology for the genus and supragenus ranks was unresolved and fan-shaped. The benefits and limitations of the inter-SINE-PCR method are discussed.     

Forelimb anatomy of New World monkeys: myology and the interpretation of primitive anthropoid models

The forelimbs of 12 genera of New World monkeys, two genera of Old World monkeys, and a gibbon were dissected. Of the 54 muscles examined, 19 exhibited significant intergeneric variation. We present arguments for which morphologies are primitive and which are derived within platyrrhines and within anthropoids. We conclude that the forelimbs of Cebus apella and Callicebus moloch represent good models of the ancestral anthropoid morphology. Thus among living anthropoids they are most appropriate for comparisons with early fossil anthropoids. They are also useful for determining whether myological anomalies of human aneuploids are atavistic. Wagner tree analyses were conducted to assess the value of these myological characters in phylogenetic studies of platyrrhines. In most respects the Wagner trees were consonant with phylogenies previously proposed, although some hypothesized trees are less parsimonious than others in explaining our data. There is an unexpected number of derived features shared by Aotus and the Atelines. There are marked dissimilarities in forelimb musculature between Aotus and Callicebus.     

Description of Brachylecithum mackoi n. sp. (Digenea: Dicrocoeliidae) from the European hedgehog, Erinaceus europaeus (Insectivora: Erinaceidae)

A new hepatic dicrocoeliid species, Brachylecithum mackoi n. sp. (Digenea, Dicrocoeliidae), is described from the European hedgehog, Erinaceus europaeus (L.) (Insectivora, Erinaceidae). An infected host was found in the Mediterranean island of Elba (Italy), and more than 60 individuals were isolated from the biliary ducts. The holotype and 55 paratypes were examined. Brachylecithum mackoi n. sp. differs from congeneric species found in mammal hosts by having well-developed lappets in the ventral sucker, a sloping uterus between anterior testis and acetabulum, no overlap between vitellaria, and metrical features in the body size, sucker diameters, cirrus sac, and size of eggs. The only other Brachylecithum species of erinaceids in Europe and Africa, Brachylecithum aetechini Dollfus, 1951, differs from the new species in the above-mentioned morphological characters, greater dimensions of the body, and oral sucker, pharynx, cirrus sac, and egg dimensions. The presence of B. mackoi n. sp. in Elba Island is discussed in the light of apparent host specificity of erinaceid dicrocoeliids and geographical distribution of Palearctic and Ethiopian Erinaceidae.     

Evidence for a phylogenetic position of button quails (Turnicidae: Aves) among the Gruiformes

The phylogenetic position of the Turnicidae (Aves) was unresolved. Historically, they were classified as members of the Struthioniformes, Galliformes, Charadriiformes, Columbiformes or the Gruiformes. In these classifications they had taxonomic rank of order 'Turniciformes' or family 'Turnicidae'. However, most of these studies followed phenetic methodology and used morphological similarity of taxa and plesiomorphic characters to classify Turnix . Recent phylogenetic studies on the basis of morphological character analyses or phenetic comparisons based on DNA-DNA hybridization experiments failed to clarify the phylogenetic realtionship of Turnix and suggested a position as 'incerte sedis', either among the Gruiformes or as the parvclass 'Turnicac'as a sistergroup to the 'Neoaves'.
We studied skeletal and myological material of Turnix to resolve its phylogenetic position. Further, we considered all characters that were previously discussed in literature to classify Turnix and tested them for their potential use in phylogenetic analysis. We added several yet unemployed morphological characters of phylogenetic significance to the analysis. The Struthioniformes, 'Galloanseres', and Columbiformes are each characterized by a clear set of autapomorpies. Only one autapomorphy in known for the Gruiformes but this character is of satisfying consistency and can be found in all families of the Gruiformes (Gruidae, Psophiidae, Aramidae. Rallidae) and Turnix. Turnix and the Rallidae share four complex morphological characters implying a close phylogenetic relationship. The data presented in this paper support the hypothesis that Turnix is a member of the Gruiformes with close relationships to the Rallidae. No evidence was found that would support a parvclass 'Turnicae'as sistergroup to the 'Neoaves'.     

Evolutionary morphology of the Tenrecoidea (Mammalia) carpal complex

The mammalian carpus can be difficult to interpret both phylogenetically and functionally. It is evolutionarily constrained in terms of functional morphology, yet there is considerable variation among many eutherian and metatherian lower and higher level taxa. The ecologically diverse Tenrecoidea (Mammalia) is a useful model for morphological interpretation of the interplay between function and phylogenetic constraint. Elements from the wrist and hand of 13 tenrecoid species, and one species each from Macroscelididae, Solenodontidae, and Erinaceidae, were compared to test form–function hypotheses of specific carpal, metacarpal, and phalangeal characters. Qualitative comparisons illustrate that several aspects of the tenrecoid carpus can be correlated with positional behaviour. Convergences within Tenrecoidea, and between tenrecoids and nontenrecoids with similar locomotor regimes, confirm a small number of carpal characters and a larger number of distal forearm, metacarpal, and phalangeal characters that reliably correspond with functional expectations. In addition, several features of the carpus appear to be phylogenetically constrained and indicate specific affinities within Tenrecoidea. Finally, there are a significant number of carpal features that vary among the studied taxa and remain ambiguous in terms of phylogenetic and/or functional significance.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 267–288.     

Monophyly of the Citharidae (Pleuronectoidei: Pleuronectiformes: Teleostei) with considerations of pleuronectoid phylogeny

The monophyly of Citharidae, the pleuronectoid family thought to be a transitional group between the Psettodoidei and other typical pleuronectoids, has been in question mainly because of the lack of recognized synapomorphies for the family. In this study, the citharid skeleton is described, and the monophyly of the family and its phylogenetic position within the Pleuronectoidei are reassessed following a phylogenetic analysis based on 45 osteological, myological, and external characters. The Citharidae was found to represent a monophyletic group, supported by six synapomorphies (e.g., first dorsal proximal radials firmly wedged into notch of blind side lateral ethmoid; anterior dorsal proximal radials tightly mutually attached; blind side posterior nostril considerably enlarged). Two previously recognized subfamilies, sinistral Citharinae and dextral Brachypleurinae, are invalid because of their nonmonophylies. Interrelationships of the pleuronectoids shown herein are discussed. Received: February 19, 2001 / Revised: July 10, 2001 / Accepted: July 23, 2001     

Chromosome evolution in eulipotyphla

We integrated chromosome painting information on 5 core-insectivora species available in the literature with new Zoo-FISH data for Iberian shrew (Sorex granarius) and Altai mole (Talpa altaica). Our analysis of these 7 species allowed us to determine the chromosomal features of Eulipotyphla genomes and to update the previously proposed ancestral karyotype for 2 main groups of the Sorex genus. The chromosome painting evidence with human painting probes (HSA) reveals the presence of the 2 unique associations HSA4/5 and 1/10p/12/22b, which support Eulipotyphla. There are a series of synapomorphies both for Erinaceidae (HSA3/1/5, 3/17, 11/15 and 10/20) and for Soricinae (HSA5/9, 6/7/16, 8/3/21 and 11/12/22). We found associations that link Talpidae/Erinaceidae (HSA7/8, 1/5 and 1/19p), Talpidae/Soricidae (HSA1/8/4) and Erinaceidae/Soricidae (HSA4/20 and 2/13). Genome conservation in Eulipotyphla was estimated on the basis of the number of evolutionary breaks in the ancestral mammalian chromosomes. In total, 7 chromosomes of the boreo-eutherian ancestor (BEA8 or 10, 9, 17, 18, 20-22) were retained in all eulipotyphlans studied; among them moles show the highest level of chromosome conservation. The integration of sequence data into the chromosome painting information allowed us to further examine the chromosomal syntenies within a phylogenetic perspective. Based on our analysis we offer the most parsimonious reconstruction of phylogenetic relationships in Eulipotyphla. The cytogenetic reconstructions based on these data do not conflict with molecular phylogenies supporting basal position of Talpidae in the order.     

Using Inter-SINE–PCR to Study Mammalian Phylogeny

Results of the use of the fingerprinting method related to short interspersed elements (SINEs), inter-SINE–PCR, in the study of phylogenetic and taxonomic relationship in mammals from orders Chiroptera (family Vespertilionidae) and Lipotyphla (family Erinaceidae) are reported. The inter-SINE–PCR method is based on the amplification of fragments situated between copies of SINEs, which are short retroposons spaced 100 to 1000 bp apart. Specifically selected primers were used, which are complementary to consensus sequences of two short retroposons: the mammalian interspersed repeat (MIR), which is typical of all mammals and some other vertebrates, was used in the cases of bats and Erinaceidae, and the ERI-1 element recently isolated from the genome of the Daurian hedgehog was used in the case of Erinaceidae. The results support the current view on phylogenetic relationship between hedgehogs belonging to genera Erinaceus, Hemiechinus, and Paraechinus (but not the genus Atelerix). In bats, the phylogenetic reconstruction revealed a statistically valid topology only at lower taxonomic levels, whereas the topology for the genus and supragenus ranks was unresolved and fan-shaped. The benefits and limitations of the inter-SINE–PCR method are discussed.     

Comparative myology of the forelimb of Liolaemus sand lizards (Liolaemidae)

The lizard genus Liolaemus includes numerous constituent clusters of putatively related taxa, one of which is the Liolaemus boulengeri group, which in turn includes the sand lizards (of the Liolaemus wiegmannii subgroup). Members of the sand lizard group exhibit three different modes of burying into sand. The general morphology of the forelimb muscles of those Liolaemus species is analysed. Herein, we present a study of the forelimb musculature of all species considered by Halloy et al. (1998). This study has three principal goals. First, we are seeking myological characters that will be useful in formulating phylogenetic hypothesis about the species of Liolaemus. With these characters, we also wish to compile morphological data that represent the morphological space implied in the diverse locomotor behaviours of these animals. Second, we are looking for derived features that reflect functional changes in the use of forelimb. Third, we wish to provide a cladistic analysis that can be used to test phylogenetic hypothesis derived from other sources of data. We present 48 characters in a data set and analyse it cladistically. We obtained a hypothesis of relationships of the Liolaemus species and compared this with previous hypotheses based on other characters. The trees obtained are not congruent with previously proposed phylogenies. We were unable to identify in our trees nodes that are based on structures reflecting functional changes in the use of the forelimb. The morphological similarities in the forelimb musculature of all species analysed seems to conform a very conservative general anatomical pattern with which Liolaemus sand lizards perform most of their locomotor behaviours.     

Anatomical description of the genus Perryena, and proposal to erect a new family for it based on its phylogenetic relationships with related taxa (Scorpaeniformes)

Osteological and myological characters of the genus Perryena are described and the phylogenetic position of the genus is inferred cladistically on the basis of 89 character transformation series, with Perryena representing a branch off a clade comprising the Tetrarogidae, Synanceiidae, Aploactinidae, Congiopodidae, Gnathanacanthidae and Pataecidae, following an initial divergence of the family Apistidae. Perryena is not closely related to Congiopodidae, despite its historical referral to that family. In keeping with the familial rankings given to successive branches of the remaining ingroup, the new family name Perryenidae is proposed for Perryena, here designated as the type genus of the family.     

Higher Taxonomic Relationships among Extant Mammals Based on Morphology, with Selected Comparisons of Results from Molecular Data

Until a few decades ago, phylogenetic relationships among placental orders were ambiguous and usually depicted to radiate as an unresolved “bush.” Resolution of this bush by various workers has been progressing slowly, but with promising results corroborated by nondental, dental, and molecular characters. In this study we continue to seek resolution. A total of 258 nondental and 2 dental characters was analyzed by PAUP and MacClade on 39 vertebrate taxa (3 reptiles, 1 nonmammalian therapsid, and 35 mammals; 20 of the mammals are extant and 15 are extinct) to study higher taxonomic relationships with emphasis on Placentalia (Eutheria). About two-thirds of the characters are osteological, the rest concern soft tissues, including myological but excluding molecular characters (most are our data, the rest are from the literature). Cladistic analysis included all 39 taxa (fossil taxa help to evaluate polarities of characters) and all characters were given equal weight. Extant Mammalia are divided into Prototheria and Theria, the latter into Marsupialia and Placentalia. Placentalia comprises Xenarthra and Epitheria. Within Epitheria, Lipotyphla and Preptotheria (emended) are sister-taxa. Preptotherian taxa group into: ungulate-related taxa and various nonungulates. The former include Carnivora, Pholidota, Tubulidentata, Artiodactyla, Cetacea, Perissodactyla, Hyracoidea, Proboscidea, and Sirenia. A possible association to embrace Lagomorpha, Rodentia, Macroscelidea, Scandentia, Primates, Chiroptera, and Dermoptera is suggested. Significant differences between our findings and those of recent investigators include the dissociation of Pholidota from Xenarthra and the plesiomorphous position of Lipotyphla within Epitheria. Congruence between morphological and molecular results is closer than previously reported.     

水螨群总科阶元系统发育的支序分析 (蜱螨亚纲：水螨群)

对水螨群9总科进行了系统发育分析,支序分析选用了23个形态学特征和3个生物学特征。据分析结果所揭示的9总科间的系统发育关系和姐妹群关系,将水螨群9总科划分为5类：拟水螨类,含冥绒螨总科;始水螨类,含溪螨总科;真水螨类,含古水螨类和新水螨类;古水螨类,含水螨总科、盾水螨总科和皱喙螨总科;新水螨类,含刺触螨总科、腺水螨总科、湿螨总科和雄尾螨总科。类间姐妹群关系为：拟水螨类与始水螨类+真水螨类为姐妹群,始水螨类与真水螨类(古水螨类+新水螨类)为姐妹群,古水螨类与新水螨类为姐妹群。该文还就所提出的水螨群5类9总科的阶元排列建议与已有的观点进行了比较。     

The broader evolutionary lessons to be learned from a comparative and phylogenetic analysis of primate muscle morphology

The present publication reviews the broader evolutionary implications of our long‐term study of primate musculature. It summarizes the implications of the study for our understanding of the use of myological characters for phylogenetic reconstruction, for assessing the importance of homoplasy and reversions in evolution, and for our understanding of Dollo's law, the notion of ‘direction’ in evolution, the common myth of human complexity, the tempo and mode of primate and human evolutionary history, adaptive radiations, the notion that ‘common’ equals ‘primitive’ and the influence of morphogenesis on the variability of head, neck, pectoral and upper limb muscles. Among other results our study shows that myological characters are useful for phylogenetic reconstruction. The results also stress the importance of homoplasy and of evolutionary reversions in morphological evolution, and they provide examples of reversions that violate Dollo's law due to the retention of ancestral developmental pathways. They also show that contrary to the idea of a ‘general molecular slow‐down of hominoids’ the rates of muscle evolution at the nodes leading to and within the hominoid clade are higher than those in most other primate clades. However, there is no evidence of a general trend or ‘directionality’ towards an increasing complexity during the evolutionary history of hominoids and of modern humans in particular, at least regarding the number of muscles or of muscle bundles. The rates of muscle evolution at the major euarchontan and primate nodes are different, but within each major primate clade (Strepsirrhini, Platyrrhini, Cercopithecidae and Hominoidea) the rates at the various nodes, and particularly at the nodes leading to the higher groups (i.e. those including more than one genus) are strikingly similar. Our results also support, in general terms, the assumption that ‘common is primitive’ and they lend some support for the ‘vertebrate‐specific model’ in the sense that during the divergent events that resulted in these four major primate clades there was more emphasis on postcranial changes than on cranial changes. Our study of primates does not, however, support suggestions that the distal structures of the upper limb are more prone to variation than the proximal ones, or that the topological origins of the upper limb muscles are more prone to evolutionary change than their insertions.     

Phylogenetic interrelationships of living and extinct Tinamidae,volant palaeognathous birds from the New World

Tinamous, one of the earliest diverging living avian lineages, consists of a Neotropical clade of palaeognathous birds with a fossil record limited to the early Miocene–Quaternary of southern South America. Here, we conduct a comprehensive, morphology‐based phylogenetic study of the interrelationships among extinct and living species of tinamous. Morphological data of fossil species are included in a matrix of 157 osteological and myological characters of 56 terminal taxa. The monophyly of most recognized genera is supported by the results of the analysis. The cladistic analysis also recovers the traditional subdivision between those tinamous specialized for open areas (Nothurinae) and those inhabiting forested environments (Tinaminae). Temporal calibration of the resultant phylogeny indicates that such a basal divergence had already taken place in the early Miocene, some 17 million years ago. The placement of the fossil species within the open‐area (Nothurinae) and the forest‐dwelling (Tinaminae) tinamous is also consistent with the palaeoenvironmental conditions inferred from the associated fauna. © 2014 The Linnean Society of London     

The adductor mandibulae muscle complex in lower teleostean fishes (Osteichthyes: Actinopterygii): comparative anatomy,synonymy, and phylogenetic implications

Bony fishes of the morphologically diverse infraclass Teleostei include more than 31 000 species, encompassing almost one‐half of all extant vertebrates. A remarkable anatomical complex in teleosts is the adductor mandibulae, the primary muscle in mouth closure and whose subdivisions vary in number and complexity. Difficulties in recognizing homologies amongst adductor mandibulae subdivisions across the Teleostei have hampered the understanding of the evolution of this system and consequently its application in phylogenetic analyses. The adductor mandibulae in representatives of all lower teleost orders is described, illustrated, and compared based on broad taxonomic sampling complemented by extensive literature information. Muscle division homologies are clarified via the application of a standardized homology‐driven anatomical terminology with synonymies provided to the myological terminologies of previous studies. Phylogenetic implications of the observed variations in the adductor mandibulae are discussed and new possible synapomorphies are proposed for the Notacanthiformes, Ostariophysi, Cypriniformes, Siluriphysi, Gymnotiformes, and Alepocephaloidei. New characters corroborate the putative monophyly of the clades Albuliformes plus Notacanthiformes (Elopomorpha), Argentinoidei plus Esocoidei plus Salmonoidei (Protacanthopterygii) and Hemiodontidae plus Parodontidae (Characiformes). We further confirm the validity of characters from the adductor mandibulae previously proposed to support the monophyly of the Esocoidei and the gonorynchiform clade Gonorynchoidei plus Knerioidei. © 2014 The Linnean Society of London     

Molecular Evidence on the Evolutionary and Biogeographical Patterns of European Cyprinids

The phylogenetic relationships of 106 European cyprinid taxa were determined based on the complete nucleotide sequence (1140 bp) of the mitochondrial cytochrome b gene. The molecular phylogeny was used (1) to revise the current systematics of European cyprinids, (2) to establish the phylogenetic utility of traditional morphological characters that are widely used in Cyprinidae systematics, and (3) to discuss alternative hypotheses on the biogeography of the family in Europe. The age of the major lineages within European cyprinids was tentatively estimated with a molecular clock and showed full agreement with the fossil record of the group. Moreover, the results provided unambiguous evidence for a close phylogenetic affinity of some Caucasian and Greek endemic cyprinid taxa (e.g., B. capito and B. brachycephalus and Leuciscus keadicus, Barbus graecus, and B. albanicus, respectively) to Iberian and North African, but not Central European, cyprinids. The existence of such unexpected phylogenetic relationships refutes the classical hypothesis on the biogeography of European cyprinids, which assumes a dispersal of the cyprinid fauna from central Europe to southern Europe and northern Africa during the Miocene (and, hence, predicts a close phylogenetic relationship of all Caucasian, Greek, Iberian, and North African cyprinids to central European taxa). Instead, the existence of a Mediterranean realm independent of the central European route seems plausible based on the molecular evidence. It is likely that the new biogeographical scenario proposed here might apply to other primary freshwater European animals with low dispersal abilities, including fish, amphibians, and invertebrates. Received: 2 February 1999 / Accepted: 16 March 1999     

Suitability of cuticular pores and sensilla for harpacticoid copepod species delineation and phylogenetic reconstruction

Cuticular organs have not been described systematically in harpacticoids until recently, and they have never been used as characters for reconstructing phylogenetic relationships in any crustacean group. We survey cuticular pores and sensilla on somites in ten Miraciidae species, belonging to six genera, from Korea, Australia, and Russia. Nine species belong to the subfamily Stenheliinae, while the outgroup belongs to the subfamily Diosaccinae. We aim to compare phylogenetic trees reconstructed for these harpactioids based on: 1) cuticular organs (with 76 characters scored, 71% of them phylogenetically informative); 2) traditionally used macro-morphological characters (66 scored, 77% of them informative); and 3) mtCOI DNA data. All analyses suggest that cuticular organs are useful characters for harpacticoid species delineation, although not as sensitive as some fast-evolving molecular markers. Reconstructed cladograms based on all three datasets show very high bootstrap values for clades representing distinct genera, suggesting that cuticular organs are suitable characters for studying phylogenetic relationships. Bootstrap values for the more basal nodes differ among the different cladograms, as do the sister-group relationships they suggest, indicating that cuticular organs probably have different evolutionary constraints from macro-morphological characters. Cuticular organs could be quite useful in the study of old museum specimens and fossil crustaceans.     

Phylogenetic relationship of street rabies virus strains and their antigenic reactivity with antibodies induced by vaccine strains. I. Analysis of phylogenetic relationship of street rabies virus strains isolated in Poland

The aims of these studies were: genetic characteristic of street rabies virus strains isolated from different animal species in Poland and determination of phylogenetic relationships to reference laboratory strains of the street rabies viruses belonging to genotype 1 and 5. The variability of rabies isolates and their phylogenetic relationship were studied by comparing the nucleotide sequence of the virus genome fragment. The Polish strains of genotype 1 belong to four phylogenetic groups (NE, CE, NEE, EE) corresponding to four variants: fox-racoon dog (F-RD); European fox 1 (F1); European fox 2 (F2) and European fox 3 (F3). On the Polish territories there are no rabies strains representing the variant dog-wolf and typical for arctic fox variant. The similarity of nucleotide and amino acid sequences of street rabies strains belonging to genotype 1 and laboratory strain CVS is very high. It is about 91% similarity at nucleotide level and 95% at amino acid level. Rabies strain CVS is similar to genotype 5 bat strains (EBL 1) only in about 69% and 74% at nucleotide and amino acid level, respectively. The genetic divergence of rabies strains circulating in Poland raised the need of permanent epidemiological and virological surveillance. The genotype and variant of isolated strains should be determined (using PCR and RLFP methods).