Molecular evolution of satellite DNA CLsat in lizards of the Darevskia species (Sauria: Lacertidae): correlation with species diversity

The structure and evolution of a satellite DNA family was examined in lizards from the genus Darevskia (family Lacertidae). Comparison of tandem units of repeated DNA (satDNA), CLsat, in all species from the genus Darevskia has shown that their variability is largely based on single-nucleotide substitutions, which constitute about 50 diagnostic positions underlying classification of the family into three subfamilies. Maximum differences between the subfamilies reached 25%. At this level of tandem unit divergence between the subfamilies, no cross-hybridization between them was observed (at 65 degrees C). The individual variability of one subfamily within the species was on average 5% while the variability between species consensuses within a subfamily was 10%. The presence of highly conserved regions in all monomers and some features of their organization show that satellites of all Darevskia species belong to one satDNA family. The organization of unit sequences of satellites CLsat and Agi also detected by us in another lizard genus, Lacerts s. str. was compared. Similarity that was found between these satellites suggests their relatedness and common origin. A possible pathway of evolution of these two satDNA families is proposed. The distribution and content of CLsat repeat subfamilies in all species of the genus was examined by Southern blotting hybridization. Seven species had mainly CLsatI (83 to 96%); three species, approximately equal amounts of CLsatI and CLsatIII (the admixture of CLsatII was 2-3%); and five species, a combination of all three subfamilies in highly varying proportions. Based on these results as well as on zoogeographic views on phylogeny and taxonomy of the Darevskia species, hypotheses on the evolution of molecular-genetic relationships within this genus are advanced.     

Molecular Evolution of Satellite DNA CLsat in Lizards from the Genus Darevskia (Sauria: Lacertidae): Correlation with Species Diversity

The structure and evolution of a satellite DNA family was examined in lizards from the genus Darevskia(family Lacertidae). Comparison of tandem units of repeated DNA (satDNA), CLsat, in all species from the genus Darevskiahas shown that their variability is largely explained by single-nucleotide substitutions, which form about 50 diagnostic positions underlying classification of the family into three subfamilies. Maximum differences between the subfamilies reached 25%. At this level of tandem unit divergence in the subfamilies, no cross-hybridization between them was observed (at 65°C). The individual variability within one subfamily within the species was on average 5% while the variability between species consensuses within a subfamily was 10%. The presence of highly conserved regions in all monomers and some features of their organization show that satellites of all Darevskia species belong to one satDNA family. The organization of unit sequences of satellites CLsat and Agi160 also detected by us in another lizard genus, Lacerta s. str. was compared. Similarity that was found between these satellites suggests their relatedness and common origin. A possible pathway of evolution of these two satDNA families is proposed. The distribution and content of CLsat repeat subfamilies in all species of the genus was examined by Southern hybridization. Seven species had mainly CLsatI (83 to 96%); three species, approximately equal amounts of CLsatI and CLsatIII (the admixture of CLsatII was 2–5%); and five species, a combination of all three subfamilies in highly varying proportions. Based on these results as well as on zoogeographic views on the taxonomy and phylogeny of theDarevskia species, hypotheses on the evolution of molecular-genetic relationships within this genus are advanced.     

Toward the phylogeny of Caucasian rock lizards: implications from mitochondrial DNA gene sequences (Reptilia: Lacertidae)

A maximum parsimony phylogeny of 14 Caucasian species of rock lizards, genus Ijicerta , subgenus Archaeolacerta , was constructed from mitochondrial cytochrome b and ATPase 6 partial gene sequences. Congruence analyses were carried out between the two genes. A synthesis of the data sets reveals three well supported monophyletic groups: (1) the caucasica group including ( Lacerta derjugini (( Lalpina, L. clarkorum ) ( L. caucasica, L. daghestanica ))); (2) the rudis group including ( L. parvula ( L. portschinskii ( L. vakntini, L. rudis ))); and (3) the saxicola group including ( L. mixta ( L. nairensis ( L. saxicola, L. raddeijj ). Despite the diagnosis of three groups, the placement of L. praticola as a basal taxon is uncertain, as are the relationships among the three groups. The mitochondrial DNA sequence data suggested prior hybridization between L. mixta and L. alpina and possibly between L. saxicola and L. nairensis. Lacerta raddei was resolved as a paraphyletic species on the mtDNA tree; this may result from either hybridization or random gene sorting.     

A fine line between sex and unisexuality: the phylogenetic constraints on parthenogenesis in lacertid lizards

A phylogeny of Caucasian rock lizards (genus Darevskia , formerly Lacerta ) was reconstructed using mitochondrial DNA sequence and allozyme data. All 15 bisexual species grouped into three major clades: the caucasica, saxicola and rudis clades. Unisexual Darevskia originate from inter-clade hybridization, never from within clades. Only two clades, the caucasica clade and the rudis clade, were involved in forming unisexuals; the saxicola clade was never involved. Furthermore, the hybridization is directional in that the caucasica clade contributed only maternal parents and the rudis clade only paternal parents. The formation of unisexual species is best explained by sexually directional phylogenetic constraints. We hypothesize that the causative agents are likely to be genes linked with the sex chromosomes within the parental sexual species.     

Reticulate evolution of parthenogenetic species of the Lacertidae rock lizards: inheritance of CLsat tandem repeats and anonymous RAPD markers

The genetic relatedness of several bisexual and of four unisexual "Lacerta saxicola complex" lizards was studied, using monomer sequences of the complex-specific CLsat tandem repeats and anonymous RAPD markers. Genomes of parthenospecies were shown to include different satellite monomers. The structure of each such monomer is specific for a certain pair of bisexual species. This fact might be interpreted in favor of co-dominant inheritance of these markers in bisexual species hybridogenesis. This idea is supported by the results obtained with RAPD markers; i.e., unisexual species genomes include only the loci characteristic of certain bisexual species. At the same time, in neither case parthenospecies possess specific, autoapomorphic loci that were not present in this or that bisexual species.     

Molecular-genetic diversification of lizard complex D. raddei (Sauria: Lacertidae): early stages of speciation

A number of populations of genus Darevskia lizards were studied using inter-SINE-PCR (IS-PCR). The number and size of PCR-amplified spacers of genomic DNA flanked by SINE-type repeats were compared in 17 populations of the D. raddei species complex along with several other species from the same genus. Nei and Li's (D(NL)) genetic distances between populations were unequivocal. Individual differences among D. r. nairensis sample specimens and between the samples fall into a range of less than 0.1. Individual variability intra each of the D. r. raddei samples--into a range of 0.1-0.2, but the inter samples differences in this subspecies depends on its geographic localizations. Thus the differences between 10 samples from Armenia and Karabach fall into a range of 0.2-0.3, but between all these and two samples from Talysh (Azerbajdzhan)--of 0.3-0.4. At the same time, the variability between both known subspecies (D. r. raddei and D. r. nairensis) reaches the same values. The differences between "good" species D. raddei and D. rudis were about 0.60-0.7. It may be supposed that D. r. raddei is currently undergoing the speciation process. The population of lizards from Turkey which is considered to be close to D. raddei by some researchers and to D. rudis by others is, according to our molecular data, more closely related to the latter species. The difference of homogeneity between other populations was revealed by comparison of the DNL values. Possible phylogeographic pathways of Darevskia species distribution based on the molecular data were proposed.     

New satellite DNA in Lacerta s. str. lizards (Sauria: Lacertidae): evolutionary pathways and phylogenetic impact

A new tandemly repeated (satellite) DNA family namely Agi160, from Lacerta agilis and Lacerta strigata (Lacerta sensu stricto (s. str.), Linnaeus 1758) have been cloned and sequenced. Agi160 is found in the above two species, as well as two other representatives of the same genus, L. viridis and L. media. DNA hybridization did not reveal it in Darevskia, Podarcis, Zootoca, Eremias, Ophisops, and Gallotia - the other genera of the family Lacertidae. The results suggest that Agi160 is a Lacerta s. str. specific family of tandem DNA repeats. However, a comparison between sequences of Agi160 and CLsat repeat units revealed 60 bp regions 62-74% identical. The latter is a satellite DNA family typical for Darevskia (syn. "L. saxicola complex") (Grechko et al., Molecular-genetic classification and phylogenetic relatedness of some species of Lacertidae lizards by taxonoprint data. Mol Biol 32:172-183, 1988.). Both Agi160 and CLsat tandem repeats share several common features (e.g., the same AT content and distribution of multiple short A-T runs, internal structure of repeated units, the presence of conservative regions). These data are indicative of their common origin and a possibly strong selective pressure upon conserving both satellites. A comparative analysis of structure, organization, and abundance of these two families of satDNA reveals evolutionary pathways that led to their formation and divergence. The data are consistent with the hypotheses of the concerted evolution of satellite DNA families. The possibility of use of Agi160 as a phylogenetic tool, defining relationships within Lacerta s. str., as well as within the whole family of Lacertidae is discussed.     

Molecular genetic relationships and some issues of systematics of rock lizards of the genus Darevskia (Squamata: Lacertidae) based on locus analysis of SINE-type repeats (Squam1)

To study the molecular genetic relationships and correlate them with the taxonomy within the complex of lacertid lizards of the genus Darevskia, the locus analysis of the copies of the SINE-type repeat (Squam1) specific for the order Squamata was used. It was demonstrated that one of the loci (No. 34) contained the Squam1 copy insert in all species and subspecies of the examined genus. SINE allelic copies in some of the loci contained large indels and specific sets of mutations. The allelic variant M (medium, about 340 bp) was found most frequently; it was detected in all subspecies of D. saxicola (saxicola, darevskii, szczerbaki, lindholmi) and in most of the other species of the genus. Two species, D. derjugini and D. praticola, differed from the other species in the presence of long (L) and short (S) alleles. The longest allele was characteristic of the D. derjugini population from the Northern Caucasus (L, 379 bp, ssp. silvatica), while the shortest allele (97 bp) united the derjugini and barani subspecies. The second allele S (279 bp) characterizes the subspecies D. praticola praticola, some individuals of which also carry allele M. The second subspecies, D. p. pontica, contains allele L2, which differs from all other medium alleles in the presence of strictly specific short indel. In addition to apomorphic indels, the specificity and mutation distribution patterns among the Squam1 alleles were also examined. An analysis of the NJ tree indicated the concordance between morphological and molecular genetic characters of the species derjugini, praticola, and saxicola. Furthermore, four subspecies of D. saxicola were much closer to each other than the subspecies within the first two species; D. d. silvatica and the group of D. d. derjugini + barani were clearly separated. It cannot be excluded that populations from Azerbaijan and Serbia can be treated as the independent subspecies of D. praticola.     

The evolutionary history of Eryngium (Apiaceae, Saniculoideae): rapid radiations, long distance dispersals, and hybridizations

Eryngium is the largest and arguably the most taxonomically complex genus in the family Apiaceae. Infrageneric relationships within Eryngium were inferred using sequence data from the chloroplast DNA trnQ-trnK 5'-exon and nuclear ribosomal DNA ITS regions to test previous hypotheses of subgeneric relationships, explain distribution patterns, reconstruct ancestral morphological features, and elucidate the evolutionary processes that gave rise to this speciose genus. In total, 157 accessions representing 118 species of Eryngium, 15 species of Sanicula (including the genus Hacquetia that was recently reduced to synonymy) and the monotypic Petagnaea were analyzed using maximum parsimony and Bayesian methods. Both separate and simultaneous analyses of plastid and nuclear data sets were carried out because of the prevalence of polyploids and hybrids within the genus. Eryngium is confirmed as monophyletic and is divided into two redefined subgenera: Eryngium subgenus Eryngium and E. subgenus Monocotyloidea. The first subgenus includes all examined species from the Old World (Africa, Europe, and Asia), except Eryngium tenue, E. viviparum, E. galioides, and E. corniculatum. Eryngium subgenus Monocotyloidea includes all examined species from the New World (North, Central and South America, and Australia; herein called the "New World sensu stricto" clade) plus the aforementioned Old World species that fall at the base of this clade. Most sectional and subgeneric divisions previously erected on the basis of morphology are not monophyletic. Within the "New World sensu stricto" group, six clades are well supported in analyses of plastid and combined plastid and nuclear data sets; the relationships among these clades, however, are unresolved. These clades are designated as "Mexican", "Eastern USA", "South American", "North American monocotyledonous", "South American monocotyledonous", and "Pacific". Members of each clade share similar geographical distributions and/or morphological or ecological traits. Evidence from branch lengths and low sequence divergence estimates suggests a rapid radiation at the base of each of these lineages. Conflict between chloroplast and nuclear data sets is weak, but the disagreements found are suggestive that hybrid speciation in Eryngium might have been a cause, but also a consequence, of the different rapid radiations observed. Dispersal-vicariance analysis indicates that Eryngium and its two subgenera originated from western Mediterranean ancestors and that the present-day distribution of the genus is explained by several dispersal events, including one trans-Atlantic dispersal. In general, these dispersals coincide with the polytomies observed, suggesting that they played key roles in the diversification of the genus. The evolution of Eryngium combines a history of long distance dispersals, rapid radiations, and hybridization, culminating in the taxonomic complexity observed today in the genus.     

The taxonomy of the Pollenia rudis species-group in the Holarctic Region (Diptera: Calliphoridae)

Abstract. A rudis species-group is defined within Pollenia Robineau-Desvoidy, and new characters found useful in the taxonomy of this genus are presented. P.rudis (Fabricius), P.angustigena Wainwright, stat.rev. and P.pseudorudis Rognes are redescribed. P.hungarica sp.n., P.longitheca sp.n. and P.luteovillosa sp.n. are described as new to science. A key is provided, and the terminalia of both sexes are illustrated for all the species. Some features of the puparia are figured for the species where these are known. A neotype is designated for Musca rudis , and a lectotype for P.angustigena. P.angustigena, P.pseudorudis and P.rudis are Holarctic species, and the latter two have also been found in New Zealand. The remaining species are confined to the western Palaearctic. P.hungarica is known from central Europe, including southern parts of Scandinavia, P.longitheca from the eastern Mediterranean, and P.luteovillosa from Algeria and Morocco in North Africa. In the larval stages P. rudis group members are parasites of or predators on earthworms. The species have several generations each year, and normally overwinter as adults. Eisenia rosea (Savigny) serves as a host for P.hungarica, P.pseudorudis and P.rudis according to the reared material available. A previous detailed account of the immature stages and life-cycle of lsquo;rudis' from North America is tentatively assigned to pseudorudis. Keilin's (1909,1915) often cited accounts of the immature stages and life-cycle of a species called 'rudis' are rejected as a source of information for any member of the rudis group.     

Agra, arboreal beetles of Neotropical forests: mixta group, virgata group, and ohausi group systematics (Carabidae)

Abstract. This paper is the fifth in a series designed to cover taxono-mically all species-groups of the lebiine genus Agra , whose cumulative ranges extend from southernmost Texas to northernmost Argentina. The mixta, virgata, feisthameli and ohausi groups constitute Section Feisthameli of the genus, and a key to these groups is provided. The mixta group consists of two species which have a composite range extending from southeastern Brazil to middle Mexico; the virgata group consists of nine species which have a composite range extending from southeastern Brazil to Guatemala; and the ohausi group consists of four species which have a composite range restricted to southeastern Brazil. The speciose feisthameli group is covered in a separate paper.
Among the three groups in the present paper, eleven new species are described from the following type localities: perkinsorum (MEXICO, Nayarit, 17.6 km southwest of Compostela), vate (MEXICO, Veracruz, Los Tuxtlas, La Playa Escondida), nola (REPUBLIC OF PANAMA, Panama, Cerro Campana), cadabra (EQUADOR, Pichincha, 47 km south of Santo Domingo de los Colorados, Rio Palenque Station), chocha (WEST INDIES, Trinidad, Arima Valley), phainops (FRENCH GUIANA, Pariacabo), imaginis (BRAZIL, Goias, Jatahy), inca (PERU, Madre de Dios, Rio Tambopata Reserve, 30 km (air) southwest of Puerto Maldonado), itatiaya (BRAZIL, Rio de Janeiro, Parque Nacional Itatiaya), calamitas (BRAZIL, Bahia, Itamaraju), anthrax (BRAZIL, Espirito Santo, Parque Socretama). A dot map illustrates the range of each taxon.
Distribution and relationships are discussed in general, but detailed cladistic and biogeographic analysis is deferred until taxonomy of the four groups of Section Feisthameli is completed. Species distribution correspond to Pleistocene refuges suggested by other authors based on other groups and classes of organisms.     

The role of vertical and horizontal transfer in the evolution of Paris-like elements in drosophilid species

The transposable element (TE) Paris was described in a Drosophila virilis strain (virilis species group) as causing a hybrid dysgenesis with other mobile genetic elements. Since then, the element Paris has only been found in D. buzzatii, a species from the repleta group. In this study, we performed a search for Paris-like elements in 56 species of drosophilids to improve the knowledge about the distribution and evolution of this element. Paris-like elements were found in 30 species from the Drosophila genus, 15 species from the Drosophila subgenus and 15 species from the Sophophora subgenus. Analysis of the complete sequences obtained from the complete available Drosophila genomes has shown that there are putative active elements in five species (D. elegans, D. kikkawai, D. ananassae, D. pseudoobscura and D. mojavensis). The Paris-like elements showed an approximately 242-bp-long terminal inverted repeats in the 5' and 3' boundaries (called LIR: long inverted repeat), with two 28-bp-long direct repeats in each LIR. All potentially active elements presented degeneration in the internal region of terminal inverted repeat. Despite the degeneration of the LIR, the distance of 185?bp between the direct repeats was always maintained. This conservation suggests that the spacing between direct repeats is important for transposase binding. The distribution analysis showed that these elements are widely distributed in other Drosophila groups beyond the virilis and repleta groups. The evolutionary analysis of Paris-like elements suggests that they were present as two subfamilies with the common ancestor of the Drosophila genus. Since then, these TEs have been primarily maintained by vertical transmission with some events of stochastic loss and horizontal transfer.     

Population structure and environmental relationships of the tropical tree Nectandra rudis (Lauraceae), a rare species in western Mexico

Population structure and environmental relationships of the tropical tree Nectandra rudis (Lauraceae), a rare species in western Mexico. The tree N. rudis is a rare species from western Mexico of which community and population features are unknown. We studied a population in an altitudinal gradient, from 550-1,850 m above sea level in the Sierra de Manantlan, Jalisco, Mexico. We established four 60x48 m sample sites at vertical distances of 100 m along this altitudinal gradient. Within each plot, ten 100 m2 circular sub-sampling units were randomly located. At each unit, we recorded diameter at breast height (dbh) and tree height for all woody vegetation > or =2.5 cm dbh. Basal area, tree density, frequency, species richness and importance values per species and plot. We estimated the vertical structure (total tree height) and diameter( as M=5log(10)N) for all N. rudis individuals. A direct ordination through Canonical Correspondence Analysis was done, involving amongst other species, edaphic and environmental data matrices. The record of 44 N. rudis individuals, in seven out the 56 plots sampled, represents the most septentrional record for the species and the first in Western Mexico. Its density and basal area represented 4.5 % and 8.7 % respectively of the total estimated for the community. The greatest importance values were observed at 1 650 m above sea level. The population structure of N. rudis is structured into five diameter categories in an inverse "J" shaped distribution. This is a typical behavior observed to occur in the Lauraceae, which produces big seeds of short viability that germinate when there is high soil moisture content. The species tend to form dense seedling banks although only a reduced number of them are able to survive. Species richness varies from 27 to 39 at plot level; the greatest importance values for the plots on which N. rudis was found, corresponds to Urera verrucosa (Liebm.) V.W. Steinm., N. rudis, Ficus sp., Beilschmiedia manantlanensis Cuevas y Cochrane, amongst others. Canonical Correspondence Analysis suggests that environmental variables such as rooted trees, crown cover, litter depth and soluble magnesium are the more significant explanatory variables for the distribution and abundance of N. rudis.     

The library model for satellite DNA evolution: a case study with the rodents of the genus Ctenomys (Octodontidae) from the Iberá marsh, Argentina

On the basement of the library model of satellite DNA evolution is the differential amplification of subfamilies through lineages diversification. However, this idea has rarely been explored from an experimental point of view. In the present work, we analyzed copy number and sequence variability of RPCS (repetitive PvuII Ctenomys sequence), the major satellite DNA present in the genomes of the rodents of the genus Ctenomys, in a closely related group of species and forms inhabiting the Iberá marsh in Argentina. We studied the dependence of these two parameters at the intrapopulation level because in the case of interbreeding genomes, differences in RPCS copy number are due to recent amplification/contraction events. We found an inverse relationship among RPCS copy number and sequence variability: amplifications lead to a decrease in sequence variability, by means of biased homogenization of the overall satellite DNA, prevailing few variants. On the contrary, the contraction events that involve tandems of homogeneous monomers contribute-by default-minor variants to become "evident", which otherwise were undetectable. On the other hand, all the RPCS sequence variants are totally or partially shared by all the studied populations. As a whole, these results are comprehensible if these RPCS variants preexisted in the common ancestor of this Ctenomys group.     

South African populations of Littorina rudis

Littorina rudis was collected from stands of Spartina capensis in saltmarsh habitats within Langebaan and knysna lagoon, Cape Province. It was absent from rocky sores and from saltmarshes east of Knysna. The shell, radular and penial morphology are described. L. rudis from both localities bore tessellated colour patterns similar to those of British saltmarsh ecotypes. The Knysna population contained individuals with a unique amber background colour. The shells from Knysna and Langebaan were very thin in accordance with the sheltered habitats. The number of embryos carried in the brood puch was similar in both countries. Sexual maturity was attained at about 4 mm shell length; the male and female modal sizes were 4.9 mm and 5.1 mm respectively at Langebaan. No. published records were found for L. rudis in South West Africa. Some possible origins of the South African L. rudis populations are discussed.     

A large 28S rDNA-based phylogeny confirms the limitations of established morphological characters for classification of proteocephalidean tapeworms (Platyhelminthes,Cestoda)

Proteocephalidean tapeworms form a diverse group of parasites currently known from 315 valid species. Most of the diversity of adult proteocephalideans can be found in freshwater fishes (predominantly catfishes), a large proportion infects reptiles, but only a few infect amphibians, and a single species has been found to parasitize possums. Although they have a cosmopolitan distribution, a large proportion of taxa are exclusively found in South America. We analyzed the largest proteocephalidean cestode molecular dataset to date comprising more than 100 species (30 new), including representatives from 54 genera (80%) and all subfamilies, thus significantly improving upon previous works to develop a molecular phylogeny for the group. The Old World origin of proteocephalideans is confirmed, with their more recent expansion in South America. The earliest diverging lineages are composed of Acanthotaeniinae and Gangesiinae but most of the presently recognized subfamilies (and genera) appear not to be monophyletic; a deep systematic reorganization of the order is thus needed and the present subfamilial system should be abandoned. The main characters on which the classical systematics of the group has been built, such as scolex morphology or relative position of genital organs in relation to the longitudinal musculature, are of limited value, as demonstrated by the very weak support for morphologically-defined subfamilies. However, new characters, such as the pattern of uterus development, relative ovary size, and egg structure have been identified, which may be useful in defining phylogenetically well-supported subgroups. A strongly supported lineage infecting various snakes from a wide geographical distribution was found. Although several improvements over previous works regarding phylogenetic resolution and taxon coverage were achieved in this study, the major polytomy in our tree, composed largely of siluriform parasites from the Neotropics, remained unresolved and possibly reflects a rapid radiation. The genus Spasskyellina Freze, 1965 is resurrected for three species of Monticellia bearing spinitriches on the margins of their suckers.