Average Pairwise Distance Research Articles

Genetic characterization of small ruminant lentiviruses circulating in naturally infected sheep and goats in Ontario, Canada

Maedi–visna virus (MVV) and caprine arthritis encephalitis virus (CAEV) are related members of a group of small ruminant lentiviruses (SRLVs) that infect sheep and goats. SRLVs are endemic in many countries, including Canada. However, very little is known about the genetic characteristics of Canadian SRLVs, particularly in the province of Ontario. Given the importance of surveillance and eradication programs for the control of SRLVs, it is imperative that the diagnostic tests used to identify infected animals are sensitive to local strains of SRLVs. The aim of this work was to characterize SRLV strains circulating in Ontario and to evaluate the variability of the immunodominant regions of the Gag protein. In this study, the nearly complete gag sequence of 164 SRLVs, from 130 naturally infected sheep and 32 naturally infected goats from Ontario, was sequenced. Animals belonged to distantly located single and mixed species (sheep and goats) farms. Ovine lentiviruses from the same farm tended to cluster more closely together than did caprine lentiviruses from the same farm. Sequence analysis revealed a higher degree of heterogeneity among the caprine lentivirus sequences with an average inter-farm pairwise DNA distance of 10% and only 5% in the ovine lentivirus group. Interestingly, amplification of SRLVs from ELISA positive sheep was successful in 81% of cases, whereas amplification of SRLV proviral DNA was only possible in 55% of the ELISA positive goat samples; suggesting that a significant portion of caprine lentiviruses circulating in Ontario possess heterogeneity at the primer binding sites used in this study. Sequences of sheep and goat SRLVs from Ontario were assembled into phylogenetic trees with other known SRLVs and were found to belong to sequence groups A2 and B1, respectively, as defined by Shah et al. (2004a). A novel caprine lentivirus with a pairwise genetic difference of 15.6–25.4% relative to other group B subtypes was identified. Thus we suggest the designation of a novel subtype, B4, within the caprine lentivirus-like cluster. Lastly, we demonstrate evidence of recombination between ovine lentiviruses. These results emphasize the broad genetic diversity of SRLV strains circulating in the province of Ontario and show that the gag region is suitable for phylogenetic studies and may be applied to monitor SRLV eradication programs.

Error-estimation-guided rebuilding ofde novomodels increases the success rate ofab initiophasing

Recent advancements in computational methods for protein-structure prediction have made it possible to generate the high-quality de novo models required for ab initio phasing of crystallographic diffraction data using molecular replacement. Despite those encouraging achievements in ab initio phasing using de novo models, its success is limited only to those targets for which high-quality de novo models can be generated. In order to increase the scope of targets to which ab initio phasing with de novo models can be successfully applied, it is necessary to reduce the errors in the de novo models that are used as templates for molecular replacement. Here, an approach is introduced that can identify and rebuild the residues with larger errors, which subsequently reduces the overall C(α) root-mean-square deviation (CA-RMSD) from the native protein structure. The error in a predicted model is estimated from the average pairwise geometric distance per residue computed among selected lowest energy coarse-grained models. This score is subsequently employed to guide a rebuilding process that focuses on more error-prone residues in the coarse-grained models. This rebuilding methodology has been tested on ten protein targets that were unsuccessful using previous methods. The average CA-RMSD of the coarse-grained models was improved from 4.93 to 4.06 Å. For those models with CA-RMSD less than 3.0 Å, the average CA-RMSD was improved from 3.38 to 2.60 Å. These rebuilt coarse-grained models were then converted into all-atom models and refined to produce improved de novo models for molecular replacement. Seven diffraction data sets were successfully phased using rebuilt de novo models, indicating the improved quality of these rebuilt de novo models and the effectiveness of the rebuilding process. Software implementing this method, called MORPHEUS, can be downloaded from http://www.riken.jp/zhangiru/software.html.

Higher HIV-1 genetic diversity is associated with AIDS and neuropsychological impairment

Standard methods used to estimate HIV-1 population diversity are often resource intensive (e.g., single genome amplification, clonal amplification and pyrosequencing) and not well suited for large study cohorts. Additional approaches are needed to address the relationships between intraindividual HIV-1 genetic diversity and 2 disease. With a small cohort of individuals, we validated three methods for measuring diversity: Shannon entropy and average pairwise distance (APD) using single genome sequences, and counts of mixed bases (i.e. ambiguous nucleotides) from population based sequences. In a large cohort, we then used the mixed base approach to determine associations between measure HIV-1 diversity and HIV associated disease. Normalized counts of mixed bases correlated with Shannon Entropy at both the nucleotide (rho=0.72, p=0.002) and amino acid level (rho=0.59, p=0.015), and APD (rho=0.75, p=0.001). Among participants who underwent neuropsychological and clinical assessments (n=187), increased HIV-1 population diversity was associated with both a diagnosis of AIDS and neuropsychological impairment.

Influence of environment on the luminosity function of galaxies

The luminosity function (LF) of galaxies in different environments is studied. A method proposed by the author is used to determine the LF of galaxies. It is found that the luminosity functions of galaxies of different morphological types in single galaxies and small groups do not differ greatly. The luminosity functions of galactic clusters differ greatly from the analogous functions for other systems. A relatively large number of faint galaxies is observed in clusters. Groups with low dispersions in their radial velocities and with small average pairwise distances between the members contain relatively many faint galaxies and relatively few bright galaxies compared to groups with large dispersions in their radial velocities and large average pairwise distances between members. This applies to elliptical and lenticular galaxies, as well as to spiral and irregular galaxies.

Morphological Plasticity in the Reef ZoanthidPalythoa caribaeorumas an Adaptive Strategy

We compared morphology of Palythoa caribaeorum (number of polyps, area, diameter and height) occupying three sites located at different distances from a harbor area and with different environmental conditions, such as sedimentation. Seasonality was also considered by comparing morphology during the wet and dry seasons. GLM analyses showed significant main and first-order interaction effects between sites and seasons for each of the four morphological variables measured. Only at the site directly in front of the harbor area there was no seasonal variation. At the other two sites, no significant differences were found when the average pairwise distance of each morphological character was compared between seasons for each site. This indicates that these characters vary in a similar way and suggests growth conditions intrinsic to the species. Environmental homogeneity at the harbor area seems to promote homogeneous morphometry, which indicates different biological strategies and suggests that this species ada...

Molecular and morphological evidence for short range endemism in the Kinnecaris solitaria complex (Copepoda: Parastenocarididae), with descriptions of seven new species

Recent investigation of one of the larger calcretes in the uppermost reaches of the Carey palaeochannel in the Yilgarn region of Western Australia revealed an unprecedented diversity of copepod crustaceans. Twenty-two different species and subspecies, from six copepod families, represent 70% of the previously recorded copepod α-diversity in the whole region, although the area investigated is less than 3% of its surface. The aims of this study were to explore the diversity of the harpacticoid genus Kinnecaris Jakobi, 1972 using both molecular and morphological methods, establish precise species boundaries, find their accurate area of distribution, reconstruct phylogenetic relationships, and explore colonisation pathways. To achieve this we sampled very intensively in the area, as well as in two neighbouring palaeochannels, analysing more than 700 samples from 230 different localities, half of which contained copepods. Seven species are described here as new, five of them from the Yeelirrie palaeochannel (K. esbe sp. nov., K. lined sp. nov., K. linel sp. nov., K. linesae sp. nov., and K. uranusi sp. nov.) and one each from two neighbouring palaeochannels (K. barrambie sp. nov. and K. lakewayi sp. nov.). Parastenocaris jane Karanovic, 2006 from the Pilbara region, along with a newly described third Australian parastenocaridid genus from the Yilgarn, were used as outgroups in our molecular analysis. The COI fragment was successfully PCR-amplified from 12 parastenocaridid specimens using a nested combination of primers. All analyses supported the presence of at least seven genetically divergent lineages, most supported with very high bootstrap values. Three genera formed three separate clades, and the average pairwise distances between Kinnecaris morpho-taxa were found to be very high (8.2-16.8 %), while the highest divergences within morpho-taxa were 0.3%. Some conflict between molecular phylogenies and morphological data was observed when it came to recognizing different groups of species. While morphology indicates that K. esbe, K. linel, and K. uranusi represent a group of very closely related species, supported by a number of synapomorphies, molecular analyses suggest that K. linel and K. uranusi are only remotely related. We argue in favor of morphological data, until more markers can be studied to try to resolve these differences. In Yeelirrie, morphological evidence would suggest a downstream colonisation history in the genus Kinnecaris, where the most plesiomorphic form (K. linesae) lives in the uppermost reaches of the palaeochannel, and the trend in the caudal rami elongation and denser somite ornamentation is obvious downstream the palaeochannel (K. uranusi, K. linel, and then K. esbe), with the only exception being K. lined, which probably represents an independent colonisation event. Parastenocarids are copepods of freshwater origin, and we argure that they can probably disperse downstream during periods of increased rainfall, evolving into separate species in isolated calcrete pockets during periods of increased aridity. Although some of the questions remained unanswered in this study, detailed morphological and molecular observations indicate that we are not dealing with one widely distributed and variable species in the Yilgarn region, but rather with a complex of short range endemics. Areas of distribution for different species range from 30 km to less than 5 km in diameter. Very strong seasonal dynamics in this subterranean community was observed, and this is a novel concept for these ecosystems globally. A key to nine Australian species of Kinnecaris is also included.

Mitochondrial genome sequences illuminate maternal lineages of conservation concern in a rare carnivore

BackgroundScience-based wildlife management relies on genetic information to infer population connectivity and identify conservation units. The most commonly used genetic marker for characterizing animal biodiversity and identifying maternal lineages is the mitochondrial genome. Mitochondrial genotyping figures prominently in conservation and management plans, with much of the attention focused on the non-coding displacement ("D") loop. We used massively parallel multiplexed sequencing to sequence complete mitochondrial genomes from 40 fishers, a threatened carnivore that possesses low mitogenomic diversity. This allowed us to test a key assumption of conservation genetics, specifically, that the D-loop accurately reflects genealogical relationships and variation of the larger mitochondrial genome.ResultsOverall mitogenomic divergence in fishers is exceedingly low, with 66 segregating sites and an average pairwise distance between genomes of 0.00088 across their aligned length (16,290 bp). Estimates of variation and genealogical relationships from the displacement (D) loop region (299 bp) are contradicted by the complete mitochondrial genome, as well as the protein coding fraction of the mitochondrial genome. The sources of this contradiction trace primarily to the near-absence of mutations marking the D-loop region of one of the most divergent lineages, and secondarily to independent (recurrent) mutations at two nucleotide position in the D-loop amplicon.ConclusionsOur study has two important implications. First, inferred genealogical reconstructions based on the fisher D-loop region contradict inferences based on the entire mitogenome to the point that the populations of greatest conservation concern cannot be accurately resolved. Whole-genome analysis identifies Californian haplotypes from the northern-most populations as highly distinctive, with a significant excess of amino acid changes that may be indicative of molecular adaptation; D-loop sequences fail to identify this unique mitochondrial lineage. Second, the impact of recurrent mutation appears most acute in closely related haplotypes, due to the low level of evolutionary signal (unique mutations that mark lineages) relative to evolutionary noise (recurrent, shared mutation in unrelated haplotypes). For wildlife managers, this means that the populations of greatest conservation concern may be at the highest risk of being misidentified by D-loop haplotyping. This message is timely because it highlights the new opportunities for basing conservation decisions on more accurate genetic information.

High genetic diversity in a single population of Triatoma sanguisuga (LeConte, 1855) inferred from two mitochondrial markers: Cytochrome b and 16S ribosomal DNA

Chagas disease remains endemic across much of Latin America, but is largely enzootic – restricted to wild mammals and triatomine vectors in the United States. Within the United States, there are ten recognized species of triatomines and 18 mammals reported naturally infected with Trypanosoma cruzi, the causative agent of Chagas disease. However, only six cases of autochthonous vector-borne transmission of T. cruzi to humans have been reported in the United States. As a follow-up to the sixth reported case, triatomine insects were collected from the index case site, in a rural area of New Orleans, LA, USA. During the summer months of 2006 and 2007, 344 Triatoma sanguisuga were collected and showed a T. cruzi infection prevalence of 56%. A subset of these insects was analyzed to infer intraspecific genetic variation from a 606bp fragment of cytochrome b (n=54) and a 340bp fragment of 16S ribosomal DNA (n=17). From the 54 samples, 37 cytb haplotypes (Hd=0.978) were observed and 14.7% of positions were polymorphic. Phylogenetic analysis divides the population into two distinct groups with an average pairwise genetic distance of ∼5%. The 16S rDNA sequences revealed 6 haplotypes among 17 specimens (Hd=0.713) with 1.2% of the positions exhibiting polymorphisms. 16S polymorphism data support the concept of two groups within this single population. The genetic distance of Group 1 from Group 2 suggests that Group1 could represent a sub-species as this level of divergence is similar to that observed among other triatomine subspecies.

The divergence of two independent lineages of an endemic Chinese gecko, Gekko swinhonis, launched by the Qinling orogenic belt

The genetic structure and demographic history of an endemic Chinese gecko, Gekko swinhonis, were investigated by analysing the mitochondrial cytochrome b gene and 10 microsatellite loci for samples collected from 27 localities. Mitochondrial DNA data provided a detailed distribution of two highly divergent evolutionary lineages, between which the average pairwise distance achieved was 0.14. The geographic division of the two lineages coincided with a plate boundary consisting of the Qinling and Taihang Mts, suggesting a historical vicariant pattern. The orogeny of the Qinling Mts, a dispersal and major climatic barrier of the region, may have launched the independent lineage divergence. Both lineages have experienced recent expansion, and the current sympatric localities comprised the region of contact between the lineages. Individual-based phylogenetic analyses of nucDNA and Bayesian-clustering approaches revealed a deep genetic structure analogous to mtDNA. Incongruence between nucDNA and mtDNA at the individual level at localities outside of the contact region can be explained by the different inheritance patterns and male-biased dispersal in this species. High genetic divergence, long-term isolation and ecological adaptation, as well as the morphological differences, suggest the presence of a cryptic species.

16S–23S rRNA Intergenic Spacer Region Variability in the Genus Frankia

16S-23S rRNA internally transcribed spacer (ITS) sequences from 53 Frankia strains were sequenced and sized from polymerase chain reaction amplification products and compiled with 14 selected 16S-23S ITS sequences from public database. Frankia genomes included two to three ITS copies lacking length polymorphism except for nine strains. No tRNA gene was encountered in this region. Frankia strains exhibited various lengths (369 to 452nt) and a wide range of sequence similarity (35-100%) in the ITS region. The average pairwise distance varied from 0.368 (clusters 1 and 2) to 0.964 (clusters 3 and 4) and was 0.397, 0.138, 0.129, and 0.016, respectively, for cluster 4 (saprophytic non-infective/non-effective), clusters 1 and 3 (facultative symbiotic), and cluster 2 (obligate symbiotic). This suggests a gradual erosion of Frankia diversity concomitantly with a shift from saprophytic non-infective/non-effective to facultative and symbiotic lifestyle. Comparative sequence analyses of the 16S-23S rRNA intergenic spacer region of Frankia strains are not useful to assign them to their respective cluster or host infection group. Accurate assignment required the inclusion of the adjacent 16S and 23S rRNA gene fragments.

Fixed-parameter algorithms for Kemeny rankings

The computation of Kemeny rankings is central to many applications in the context of rank aggregation. Given a set of permutations (votes) over a set of candidates, one searches for a “consensus permutation” that is “closest” to the given set of permutations. Unfortunately, the problem is NP-hard. We provide a broad study of the parameterized complexity for computing optimal Kemeny rankings. Besides the three obvious parameters “number of votes”, “number of candidates”, and solution size (called Kemeny score), we consider further structural parameterizations. More specifically, we show that the Kemeny score (and a corresponding Kemeny ranking) of an election can be computed efficiently whenever the average pairwise distance between two input votes is not too large. In other words, Kemeny Score is fixed-parameter tractable with respect to the parameter “average pairwise Kendall–Tau distance d a ”. We describe a fixed-parameter algorithm with running time 1 6 ⌈ d a ⌉ ⋅ poly . Moreover, we extend our studies to the parameters “maximum range” and “average range” of positions a candidate takes in the input votes. Whereas Kemeny Score remains fixed-parameter tractable with respect to the parameter “maximum range”, it becomes NP-complete in the case of an average range of two. This excludes fixed-parameter tractability with respect to the parameter “average range” unless P=NP. Finally, we extend some of our results to votes with ties and incomplete votes, where in both cases one no longer has permutations as input.

Identification of descendants of an extinct bovine population from the Algarve region of Portugal using numerical taxonomy analysis of morphological traits

The morphology of a sample of four bulls and 43 cows, presumed to be descendants of the extinct cattle breed 'Algarvia' (AG), was used to assign their relationship with animals from other Portuguese autochthonous breeds - Arouquesa (AR), Barrosã (BA), Cachena (CA), Marinhoa (MA), Maronesa (MO), Minhota (MN), Mirandesa (MI), (only bulls), Alentejana (AL), Garvonesa (GA), Mertolenga (ME) and Preta (PR). Standard numerical taxonomic methods were applied to a set of 183 (cows) and 170 (bulls) traits, to derive average pairwise taxonomic distances among the sample of 257 cows and 76 bulls. Distance coefficients (morphological index of distance) ranged from 0.22 to 2.62 (cows) and from 0.49 to 2.13 (bulls). Unweighted pair group method using arithmetic averages (UPGMA)-based phenograms and a principal coordinate analysis showed that bulls were highly clustered and cows showed a tendency to cluster according to their geographical and breed origin. The AG population grouped together with GA, AL, ME and MN breeds in the Red Convex group. The average taxonomic distance among breeds was 1.02, the highest being 1.39 (ME versus BA) and the lowest being 0.64 (MA versus AR). The approach allowed for the identification of a phenotypically differentiated set of animals, comprising 19 cows and four bulls representative of the AG breed, and which can be targeted in further studies aiming at the recovery of this extinct breed.

Structure génétique et variabilité des formes phénologiques du hêtre (Fagus sylvatica L.)

(Received 28 March 2008; accepted 25 November 2008) Abstract • Microsatellite markers were used to describe the genetic structure and variability of early, interme- diate and late phenological forms of European beech (Fagus sylvatica L.). Two hundred and seventy individuals from three populations located in southern Poland were divided into three forms according to the phenological criterion - bud burst, and analyzed for allelic variation at five highly polymorphic microsatellite loci. • Population differentiation was moderate and differed significantly among phenological forms. Av- erage values of FST and RST decreased across phenological forms and amounted to FST values of 0.135, 0.110 and 0.108 and RST values of 0.365, 0.231 and 0.098 for early, intermediate and late forms of beech, respectively. • Analysis of Molecular Variance (AMOVA) revealed different genetic structures characteristic of respective phenological forms of beech. The amount of within-population variability increased with the delay of the beginning of vegetation and amounted to 64%, 77% and 90% of total variability, depending on phenological form. A similar trend was found in average pairwise genetic distance be- tween individuals belonging to a given phenological form (11.78, 11.85 and 12.22, from early to late forms). • Our results demonstrate the importance of late spring frosts as a factor influencing the genetic struc- ture of beech, and as a cause of the decrease in genetic variability as well as the increase in population differentiation proportional to the degree of phenological earliness.

The effect of habitat fragmentation on finescale population structure of wood frogs (Rana sylvatica)

We examined the impact of recent anthropogenic habitat fragmentation on the genetic structure of wood frog (Rana sylvatica) breeding sites in Wellington County of Ontario, Canada. In addition to geographic distance (average pairwise distance ~22 km, greatest distance ~50.22 km), four landscape features hypothesized to contribute to genetic differentiation between breeding sites were considered: road density, a major highway (highway 401), canopy cover, and watershed discontinuity. Analysis of data from 396 samples across nine breeding sites using eight microsatellite DNA loci, revealed a small degree of significant genetic structure between breeding sites. The presence of highway 401 and road density were correlated with small but statistically significant structure observed between several groups of sites. One outlier breeding site outside of Wellington County located within the city of Toronto, had significantly lower allelic richness and much larger population differentiation with the Wellington sites. Our data suggest that recent fragmentation has had an effect on wood frog population structure and also demonstrate the importance of dispersal for this species in maintaining levels of genetic diversity.

Molecular phylogeny and distribution of threeApodemusspecies (Muridae, Rodentia) in Serbia

Phylogenetic relationships among three species of the genus Apodemus (A. flavicollis,A. sylvaticus and A. agrarius) from seven different localities in Serbia were estimated using arbitrarily primed PCR (AP-PCR) profiling, which allowed clear distinction between the sibling species A. flavicollis and A. sylvaticus. Eight oligonucleotide primers out of the 22 screened, gained a total of 397 amplified bands. The average pairwise genetic distances within Apodemus species ranged from 0.51 between A. flavicollis and A. sylvaticus, to 0.74 between A. sylvaticus and A. agrarius. The large genetic distances obtained among populations of A. flavicollis (0.13) indicate that this part of the Balkan Peninsula was probably a refuge during the last glaciation. Furthermore, differences obtained between populations south and north from the river Danube suggest that this species survived the Last Glacial Maximum in at least two separate refuges. Although our data for molecular markers are from a limited number of localities, extended analyses of C-band distribution on chromosomes from previously studied localities south of the rivers Danube and Sava, indicate that distribution of A. sylvaticus is limited to northern Serbia. Therefore, it is possible that this part of the Balkan Peninsula was not a refuge for this species during the last glaciation.

The complete plastid genome sequence of Welwitschia mirabilis: an unusually compact plastome with accelerated divergence rates

BackgroundWelwitschia mirabilis is the only extant member of the family Welwitschiaceae, one of three lineages of gnetophytes, an enigmatic group of gymnosperms variously allied with flowering plants or conifers. Limited sequence data and rapid divergence rates have precluded consensus on the evolutionary placement of gnetophytes based on molecular characters. Here we report on the first complete gnetophyte chloroplast genome sequence, from Welwitschia mirabilis, as well as analyses on divergence rates of protein-coding genes, comparisons of gene content and order, and phylogenetic implications.ResultsThe chloroplast genome of Welwitschia mirabilis [GenBank: EU342371] is comprised of 119,726 base pairs and exhibits large and small single copy regions and two copies of the large inverted repeat (IR). Only 101 unique gene species are encoded. The Welwitschia plastome is the most compact photosynthetic land plant plastome sequenced to date; 66% of the sequence codes for product. The genome also exhibits a slightly expanded IR, a minimum of 9 inversions that modify gene order, and 19 genes that are lost or present as pseudogenes. Phylogenetic analyses, including one representative of each extant seed plant lineage and based on 57 concatenated protein-coding sequences, place Welwitschia at the base of all seed plants (distance, maximum parsimony) or as the sister to Pinus (the only conifer representative) in a monophyletic gymnosperm clade (maximum likelihood, bayesian). Relative rate tests on these gene sequences show the Welwitschia sequences to be evolving at faster rates than other seed plants. For these genes individually, a comparison of average pairwise distances indicates that relative divergence in Welwitschia ranges from amounts about equal to other seed plants to amounts almost three times greater than the average for non-gnetophyte seed plants.ConclusionAlthough the basic organization of the Welwitschia plastome is typical, its compactness, gene content and high nucleotide divergence rates are atypical. The current lack of additional conifer plastome sequences precludes any discrimination between the gnetifer and gnepine hypotheses of seed plant relationships. However, both phylogenetic analyses and shared genome features identified here are consistent with either of the hypotheses that link gnetophytes with conifers, but are inconsistent with the anthophyte hypothesis.

Development of an HIV-1 Reference Panel of Subtype B Envelope Clones Isolated From the Plasma of Recently Infected Individuals

We have developed an HIV-1 reference panel of 20 subtype B envelope clones isolated from the plasma of recently infected individuals. It is widely accepted that a prophylactic vaccine against HIV-1 requires the development of novel immunogens that are capable of eliciting broadly protective neutralizing antibody responses. Historically, patient serum has been screened for such antibodies by assaying against laboratory strains, but these viruses typically have increased neutralization sensitivity compared with primary isolates. To create a more standardized and relevant assay system for vaccine evaluation, we have developed a panel of primary envelopes derived from the plasma of individuals with documented acute/early subtype B HIV-1 infection occurring between 2000 and 2004. The HIV-1 envelopes from this panel vary in mode of transmission, coreceptor tropism, fusogenicity, and overall sensitivity to neutralization. These envelope sequences represent a broad spectrum of subtype B genetic diversity with an average pairwise genetic distance of 12% and a range from 10% to 19%. This well-characterized HIV-1 envelope panel should be a valuable resource for optimizing and standardizing vaccine assessment and improving vaccine design.

The effects of Pleistocene glaciations on the phylogeography of Melitaea cinxia (Lepidoptera: Nymphalidae)

Partial (600 bp) sequences of mitochondrial cytochrome oxidase I (COI) gene were used to infer the phylogeography of Melitaea cinxia (Lepidoptera: Nymphalidae) across the entire distributional range of the species, encompassing north Africa and Eurasia. Cladistic analysis of 49 distinct haplotypes (haplotype and nucleotide diversity were 0.95 and 0.027, respectively) revealed strong phylogeographic structure in M. cinxia, characterised by four major clades: Morocco; Western (Iberia, France, Italy); Central (central and northern Western Europe, Balkans, Greece, Anatolia, Levant); and Eastern (eastern Baltic, Urals, Iran, Siberia, China); separated by average pairwise distances of beween 2 and 6 percent. This pattern is consistent with the location of southern glacial refugia in the Iberian, Italian and Balkan peninsulas, as well as multiple eastern refugia. The Western clade is further structured into south-central Iberian, northern Iberian (and French) and southern Italian sub-clades; and the Eastern clade into Near Eastern and Far Eastern sub-clades; with weaker phylogeographical concordance within the Central clade, except for a large area in central and northern Western Europe which is monomorphic for COI haplotype. The Baltic and eastern Europe have been primarily colonized by the Far Eastern sub-clade, rather than the Central (Balkan) clade, highlighting the importance of including Near and Far Eastern populations in phylogeographic studies of Palearctic species. Maps showing the extent of clades and sub-clades suggest several regions of secondary contact and possible hybridization. Interspecific comparison of representative M. cinxia haplotypes supports a monophyletic origin of all M. cinxia.

Genetic diversity analysis in sorghum germplasm as estimated by AFLP, SSR and morpho-agronomical markers

A comparison of the different methods of the estimation of genetic diversity is important to evaluate their utility as a tool in germplasm conservation and plant breeding. Amplified fragment length polymorphism (AFLP), microsatellites or SSR and morphological traits markers were used to evaluate 45 sorghum germplasm for genetic diversity assessment and discrimination power. The mean polymorphism information content (PIC) values were 0.65 (AFLPs) and 0.46 (SSRs). The average pairwise genetic distance estimates were 0.57 (morphological traits), 0.62 (AFLPs) and 0.60 (SSRs) markers data sets. The Shannon diversity index was higher for morphological traits (0.678) than AFLP (0.487) and SSR (0.539). The correlation coefficients obtained by the Mantel matrix correspondence test, which was used to compare the cophenetic matrices for the different markers, showed that estimated values of genetic relationship given for AFLP and SSR markers, as well as for morphological and SSR markers were significantly related (p 0.05). Both data sets from AFLP and SSR allowed all accessions to be uniquely identified; two accessions could not be distinguished by the morphological data. In summary, AFLP and SSR markers proved to be efficient tools in assessing the genetic variability among sorghum genotypes. The patterns of variation appeared to be consistent for the three marker systems, and they can be used for designing breeding programmes, conservation of germplasm and management of sorghum genetic resources.

GENETIC VARIATION AND RELATIONSHIPS BETWEEN ISOLATES AND SPECIES OF THE ENTOMOPATHOGENIC NEMATODE GENUS HETERORHABDITIS DECIPHERED THROUGH ISOZYME PROFILES

We studied variation in isozyme patterns of 8 metabolic enzymes in 5 species of Heterorhabditis (H. bacteriophora, H. indica, H. marelata, H. megidis, and H. zealandica) comprising 18 isolates. Isozyme banding patterns of all the 8 enzymes were species specific; however, 3 enzymes, i.e., arginine kinase, fumarate hydratase, and malate dehydrogenase, displayed distinct patterns among all the 18 isolates. Phylogenetic analysis of the isozyme patterns produced dendrograms depicting a high degree of genetic variation among Heterorhabditis species, with the average pairwise distance of 0.2000. Trees constructed using different phylogenetic methods showed a relatively close genetic relationship between H. megidis and H. zealandica and between H. bacteriophora and H. indica. Also, H. bacteriophora HP88 was the most distant species from H. megidis (UK isolate), H. marelatus (Oregon isolate), and H. zealandica (X1 isolate) with pairwise distance of 0.1957, 0.2228, and 0.2120, respectively. Phylogenetic analysis also revealed genetic variation among H. bacteriophora isolates with the average pairwise distance of 0.1507. GPS2 and GPS3 were the most closely related isolates with the average distance of only 0.0870, followed by GPS1 and GPS2 with average distance of 0.1087. In contrast, KMD19 and HP88, OH25, and HP88, and OH25 and Acows isolates were the most divergent populations with a pairwise distance of 0.2011 and 37 character differences. Pairwise distance analysis also revealed that genetic divergence among populations of H. bacteriophora is relatively independent of geographic distance. Overall, these results demonstrate strong subspecies structuring in H. bacteriophora.