Geographic differentiation of genomic DNA of <Emphasis Type="Italic">Chironomus plumosus</Emphasis> (Diptera,Chironomidae) in natural holarctic populations

Using RAPD markers, polymorphism and differentiation of genomic DNA was examined in seven natural populations of Chironomus plumosus from Europe, Siberia, and North America. All these populations showed high polymorphism of genomic DNA. The Palearctic and Nearctic populations of this species were not statistically significantly different in the genomic DNA polymorphism level. The genetic distance (GD), which characterizes the extent of intraspecific differentiation of population genetic structure, was determined among the natural populations of C. plumosus. The genetic distance was on average 0.245. It was demonstrated that genetic structures of the Palearctic and Nearctic populations of C. plumosus was differentiated to a higher extent than in Palearctic. However, the genetic distances between the populations from different zoogeographical zones (0.313) did not exceed the level characteristic of the among-population differences, which do not disturb the species genetic integrity.     

The role of chromosomal polymorphism in divergence of populations and species of the genus Chironomus (Diptera)

The data on the structure and level of chromosomal polymorphism in natural populations of species of the genus Chironomus are summarized. A very high level of chromosomal polymorphism was noted for most species. Paracentric inversions prevailed among the chromosomal rearrangements found in natural populations. Changes in the set and frequency of inversion sequences are the most important factor of cytogenetic divergence of populations. Several cytogenetic types of populations were distinguished. The Palaearctic and Nearctic populations of Holarctic species diverged to a greater extent due to the formation of endemic Palearctic and Nearctic inversion sequences. The sequences common for both regions indicated a common ancestry of the populations. The cytogenetic distances between the Palearctic and Nearctic populations are greater by an order of magnitude than those between populations within each zoogeographic region. Divergence of species karyotypes was found to result from fixation of different inversion sequences in the course of evolution. The karyotypes of Palearctic and Nearctic species mainly differ by the presence of endemic Palearctic and Nearctic banding sequences. Several basic sequences common for some species allow the cytogenetic history of their origin to be revealed. A NJ phylogenetic tree was built for the genus Chironomus, demonstrating chromosomal evolution of its species.     

Intercontinental karyotypic differentiation of Chironomus entis Shobanov, a Holarctic member of the C. plumosus group (Diptera, Chironomidae).

Analysis of banding sequences of polytene chromosomes in Palearctic (Russian) and Nearctic (North American) Chironomus entis shows strong karyotype divergence between populations on the two continents. Four out of seven chromosomal arms in the North American C. entis karyotype are characterized by sequences found only in the Nearctic. In total, 44 banding sequences are now known for this species across the Holarctic, including 22 exclusively Palearctic, 6 Holarctic, and 16 exclusively Nearctic sequences. The degree of cytogenetic differentiation between Palearctic and Nearctic C. entis populations is an order of magnitude greater than differentiation among populations within either continent, but is only one third as great as the cytogenetic distance between the sibling species C. entis and C. plumosus. C. entis is the only sibling species of C. plumosus uncovered during cytological identification of Chironomus species from more than 50 North American lakes, indicating that the plumosus sibling-species group is much smaller in the Nearctic than in the Palearctic, where a dozen sibling species are known. Cytogenetic distance values calculated between Nearctic and Palearctic representatives of both C. entis and its sibling species C. plumosus are similar, but result from different patterns of karyotype divergence. New World C. entis is distinguished from Old World populations by the 16 uniquely Nearctic sequences, four of which occur in the homozygous state. In contrast, North American C. plumosus has fewer uniquely Nearctic sequences, and only one that occurs as a homozygote. However, four chromosomal arms in C. plumosus that are polymorphic in the Palearctic show fixation, or near fixation, of Holarctic sequences in the Nearctic C. plumosus karyotype. Thus, both the fixation of Holarctic sequences, and the occurrence or fixation of distinctly Nearctic sequences, contribute significantly to karyotype divergence. Patterns of karyotype divergence in Palearctic and Nearctic populations of different Holarctic chironomid species are discussed relative to intercontinental cytogenetic differentiation in other dipterans.     

Cytogenetic differentiation of natural populations of <Emphasis Type="Italic">Chironomus obtusidens</Emphasis> (Diptera,Chironomidae)

The cytogenetic structure of Siberian and European populations of Chironomus obtusidens Goetgh. was studied. The clear differentiation of these populations was revealed using quantitative analysis of sets and frequencies of inversion banding sequences. The Siberian populations were found to have six new inversion sequences, and the alternative obtG2 sequence dominated instead of the main obtG1 sequence typical of European populations. In general, chromosomal polymorphism was 3–4 times higher in the Siberian populations. Therefore, the cytogenetic distances (Dcg) between the Siberian and European populations were higher (Dcg 0.059–0.097) than Dcg between the populations in each of the geographic zones investigated (Dcg 0–0.015). The NJ phylogenetic tree constructed for the chromosomal evolution of the genus Chironomus demonstrates that Chironomus obtusidens is the most divergent member among Palaearctic species of the obtusidens group. In addition, it is closer related to the Nearctic Ch. decorus group.     

Genetic diversity and differentiation between Palearctic and Nearctic populations of Aedimorphus (=Aedes) vexans (Meigen, 1830) (Diptera,Culicidae)

Genetic diversity was studied at allozyme loci in two Palearctic and one Nearctic population of Aedimorphus (=Aedes) vexans, a species of public health and veterinary importance. The population from Serbia was the most polymorphic (P= 35%) with the highest observed heterozygosity (H_o= 0.027). The lowest observed heterozygosity (H_o= 0.010) was obtained for the Nearctic population. All analyses based on individual (STRUCTURE analysis) and population level (pairwise F_ST,Nm values, AMOVA, Nei's D value) revealed significant structuring between Nearctic and Palearctic populations, indicating a lack of gene flow and thus, the presence of independent gene pools. Taxon‐specific alleles at the diagnostic Ao, Hk‐2, Hk‐3, Hk‐4, Idh‐1, and Idh‐2 loci were used for identification and separation of Nearctic and Palearctic populations. Population genetics study provided valuable information on the correct distinction of Am. vexans populations and their adaptive potential that could find a future use in the studies of vector competence and development of vector‐control strategies.     

Evolutionary implications of morphological variation in the lower carnassial of red fox<Emphasis Type="Italic">Vulpes vulpes</Emphasis>

Research on the morphological variability of the occlusal surface of M₁ talonid in the red foxVulpes vulpes (Linnaeus, 1758) in the Holarctic has been carried out on 2271 specimens originating from 42 populations. The Nearctic was represented by 666 specimens belonging to 13 populations, whereas Palearctic was represented by 1605 specimens from 29 populations. Analyses of the developmental level and formation of cristids between the hypoconid and entoconid allowed the differentiation of 34 shape variants of the occlusal surface of the talonid in the red fox. Because of the complicated variation of cristids, 34 variants were assigned to 5 morphotypes of group P. In the Palearctic and Nearctic a significant geographic variation occurred of P morphotypes and their variants. Primitive variants of the talonid structure on M₁ are predominant in populations from the south of the Asian range of the red fox, while more progressive characters of the occlusal surface of the lower carnassial are typical of the northern and centrally located red fox populations in the Palearctic and Nearctic. The geographic differentiation is probably connected with different Pleistocene histories of particular populations.     

DNA barcode libraries provide insight into continental patterns of avian diversification

Background

The causes for the higher biodiversity in the Neotropics as compared to the Nearctic and the factors promoting species diversification in each region have been much debated. The refuge hypothesis posits that high tropical diversity reflects high speciation rates during the Pleistocene, but this conclusion has been challenged. The present study investigates this matter by examining continental patterns of avian diversification through the analysis of large-scale DNA barcode libraries.

Methodology and Principal Findings

Standardized COI datasets from the avifaunas of Argentina, the Nearctic, and the Palearctic were analyzed. Average genetic distances between closest congeners and sister species were higher in Argentina than in North America reflecting a much higher percentage of recently diverged species in the latter region. In the Palearctic genetic distances between closely related species appeared to be more similar to those of the southern Neotropics. Average intraspecific variation was similar in Argentina and North America, while the Palearctic fauna had a higher value due to a higher percentage of variable species. Geographic patterning of intraspecific structure was more complex in the southern Neotropics than in the Nearctic, while the Palearctic showed an intermediate level of complexity.

Conclusions and Significance

DNA barcodes can reveal continental patterns of diversification. Our analysis suggests that avian species are older in Argentina than in the Nearctic, supporting the idea that the greater diversity of the Neotropical avifauna is not caused by higher recent speciation rates. Species in the Palearctic also appear to be older than those in the Nearctic. These results, combined with the patterns of geographic structuring found in each region, suggest a major impact of Pleistocene glaciations in the Nearctic, a lesser effect in the Palearctic and a mild effect in the southern Neotropics.     

Evaluation of soybean RFLP marker diversity in adapted germ plasm

Summary Soybean RFLP markers have been primarily developed and genetically mapped using wide crosses between exotic and adapted genotypes. We have screened 38 soybean lines at 128 RFLP marker loci primarily to characterize germ plasm structure but also to evaluate the utility of RFLP markers identified in unadapted populations. Of these DNA probes 70% detected RFLPs in this set of soybean lines with an average polymorphism index of 0.30. This means that only 1 out of 5 marker loci was informative between any particular pair of adapted soybean lines. The variance associated with the estimation of RFLP genetic distance (GD_R) was determined, and the value obtained suggested that the use of more than 65–90 marker loci for germ plasm surveys will add little precision. Cluster analysis and principal coordinate analysis of the GD_R matrix revealed the relative lack of diversity in adapted germ plasm. Within the cultivated lines, several lines adapted to Southern US maturity zones also appeared as a separate group. GD_R data was compared to the genetic distance estimates obtained from pedigree analysis (GD_P). These two measures were correlated with r = 0.54 for all 38 lines, but the correlation increased to r = 0.73 when only adapted lines were analyzed.     

Evolutionary and climatic factors affecting tooth size in the red foxVulpes vulpes in the Holarctic

Research into the geographical pattern of tooth size in the red fox,Vulpes vulpes (Linnaeus, 1758) in the Holarctic was conducted on a sample of 3806 skulls belonging to 41 fox populations. The Nearctic was represented by 948 specimens (249 females, 359 males, 340 specimens of unknown sex) belonging to 13 populations, whereas the Palearctic was represented by 2858 red foxes (1034 females, 1256 males, 568 specimens of unknown sex) from 32 populations. In the Nearctic, the largest foxes live on Kodiak Island (V. v. harrimani) and the Kenai Peninsula (V. v. kenaiensis), while the smallest ones live in California (V. v. necator) and Georgia (V. v. fulvus). In the Palearctic, the largest foxes come from the Far East (V. v. jakutensis, V. v. beringiana, V. v. tobolica), while the smallest are from the southern borders of the Eurasian range (V. v. pusilla, V. v. barbara, V. v. arabica). In both the Palearctic and Nearctic, tooth size in the fox varies depending on the geo-climatic factors. The fox’s tooth size confirms the general basis of Bergmann’s rule. In the Palearctic, specimens with larger teeth occur in cooler habitats with greater seasonality. These are first and foremost Northern and Far Eastern populations. In the Nearctic, tooth size in red foxes depends on the temperature and humidity of their habitat. Competition within the species and between species has important impact on the variation and dimorphism of tooth size in the red fox. Both in the Nearctic and Palearctic, red foxes from regions of sympatric co-occurrence with other closely relatedVulpes species, are more sexually dimorphic in terms of tooth size than red foxes from allopatric regions. Analysis of morphological distance on the basis of the size of dental characteristics shows, that in the Palearctic, the foxes from India (V. v. pusilla), while in the Nearctic, the population from Kodiak Island (V. v. harrimani) are most distant from the remaining populations. Geographic barriers such as the Bering Strait, Parry Channel, Mackenzie River, Kolyma and Omolon River systems have had a critical impact on red fox evolution. The most likely place for the evolution and diversification of the phyletic lineVulpes vulpes seems to be the Middle East region.     

Genomic content and new insights on the origin of the B chromosome of the cichlid fish <Emphasis Type="Italic">Astatotilapia latifasciata</Emphasis>

B chromosomes are additional chromosomes widely studied in a diversity of eukaryotic groups, including fungi, plants and animals, but their origin, evolution and possible functions are not clearly understood. To further understand the genomic content and the evolutionary history of B chromosomes, classical and molecular cytogenetic analyses were conducted in the cichlid fish Astatotilapia latifasciata, which harbor 1–2 B chromosomes. Through cytogenetic mapping of several probes, including transposable elements, rRNA genes, a repeated DNA genomic fraction (C ₀ t − 1 DNA), whole genome probes (comparative genomic hybridization), and BAC clones from Oreochromis niloticus, we found similarities between the B chromosome and the 1st chromosome pair and chromosomes harboring rRNA genes. Based on the cytogenetic mapping data, we suggest the B chromosome may have evolved from a small chromosomal fragment followed by the invasion of the proto-B chromosome by several repeated DNA families.     

An integrated map of Oryza sativa L. chromosome 5

The developments of molecular marker-based genetic linkage maps are now routine. Physical maps based on contigs of large insert genomic clones have been established in several plant species. However, integration of genetic, physical, and cytological maps is still a challenge for most plant species. Here we present an integrated map of rice (Oryza sativa L.) chromosome 5, developed by fluorescence in situ hybridization mapping of 18 bacterial artificial chromosome (BAC) clones or PI-derived artificial chromosome (PAC) clones on meiotic pachytene chromosomes. Each BAC/PAC clone was anchored by a restriction fragment length polymorphism marker mapped to the rice genetic linkage map. This molecular cytogenetic map shows the genetic recombination and sequence information of a physical map, correlated to the cytological features of rice chromosome 5. Detailed comparisons of the distances between markers on genetic, cytological, and physical maps, revealed the distributions of recombination events and molecular organization of the chromosomal features of rice chromosome 5 at the pachytene stage. Discordance of distances between the markers was found among the different maps. Our results revealed that neither the recombination events nor the degree of chromatin condensation were evenly distributed along the entire length of chromosome 5. Detailed comparisons of the correlative positions of markers on the genetic, cytological, and physical maps of rice chromosome 5 provide insight into the molecular architecture of rice chromosome 5, in relation to its cytological features and recombination events on the genetic map. The prospective applications of such an integrated cytogenetic map are discussed.     

Chromosome arm‐specific patterns of polymorphism associated with chromosomal inversions in the major African malaria vector,Anopheles funestus

Chromosomal inversions facilitate local adaptation of beneficial mutations and modulate genetic polymorphism, but the extent of their effects within the genome is still insufficiently understood. The genome of Anopheles funestus, a malaria mosquito endemic to sub‐Saharan Africa, contains an impressive number of paracentric polymorphic inversions, which are unevenly distributed among chromosomes and provide an excellent framework for investigating the genomic impacts of chromosomal rearrangements. Here, we present results of a fine‐scale analysis of genetic variation within the genome of two weakly differentiated populations of Anopheles funestus inhabiting contrasting moisture conditions in Cameroon. Using population genomic analyses, we found that genetic divergence between the two populations is centred on regions of the genome corresponding to three inversions, which are characterized by high values of F_ST, absolute sequence divergence and fixed differences. Importantly, in contrast to the 2L chromosome arm, which is collinear, nucleotide diversity is significantly reduced along the entire length of three autosome arms bearing multiple overlapping chromosomal rearrangements. These findings support the idea that interactions between reduced recombination and natural selection within inversions contribute to sculpt nucleotide polymorphism across chromosomes in An. funestus.     

Assessment of Genetic Diversity in <Emphasis Type="Italic">Trigonella foenum-graecum</Emphasis> Based on Nuclear Ribosomal DNA,Internal Transcribed Spacer and RAPD Analysis

Fenugreek (Trigonella foenum-graecum) is receiving global attention due to rare medicinal properties of significance to human health. Gene banks possess scanty germplasm and very little background information regarding its genetic variability that has hampered its improvement. We investigated the extent of variability among 17 Indian varieties of fenugreek using phenotypic and genetic markers. Multilocus genotyping by ten random amplified polymorphic DNA (RAPD) primers detected an average of intraspecific variations amounting to 64.7% polymorphism in banding patterns. Analysis of molecular variance indicated that a greater proportion of total genetic variation exists within population (91%) rather than among populations. Higher values of Nei’s gene diversity (h) and Shannon Information Index (i) and genetic distance analysis validate higher genetic diversity among Indian fenugreek varieties. SNPs at 14 sites of rDNA region revealed further lineages of distinct varieties with main RAPD clusters. The representative sequences of each subgroup and all distinct varieties have been submitted to NCBI database and assigned Gen Accession numbers HM 176640–176649. The measures of relative genetic distances among varieties of fenugreek did not completely correlate with the geographical distances of places of their development. The homogeneous phenotypic markers proved insufficient in exhibiting genetic divergence among fenugreek varieties studied. Eventually, the knowledge of their genetic relationships, DNA bar coding and phylogenies might contribute for the designing of intraspecific crosses between cultivars of this fenugreek collection with potential interest in seed spices breeding programme.     

Early stages of sex chromosome differentiation in fish as analysed by simple repetitive DNA sequences

Animal sex chromosome evolution has started on different occasions with a homologous pair of autosomes leading to morphologically differentiated gonosomes. In contrast to other vertebrate classes, among fishes cytologically demonstrable sex chromosomes are rare. In reptiles, certain motifs of simple tandemly repeated DNA sequences like (gata)_n/(gaca)_m are associated with the constitutive heterochromatin of sex chromosomes. In this study a panel of simple repetitive sequence probes was hybridized to restriction enzyme digested genomic DNA of poeciliid fishes. Apparent male heterogamety previously established by genetic experiments in Poecilia reticulata (guppy) was correlated with male-specific hybridization using the (GACA)₄ probe. The (GATA)₄ oligonucleotide identifies certain male guppies by a Y chromosomal polymorphism in the outbred population. In contrast none of the genetically defined heterogametic situations in Xiphophorus could be verified consistently using the collection of simple repetitive sequence probes. Only individuals from particular populations produced sex-specific patterns of hybridization with (GATA)₄. Additional poeciliid species (P. sphenops, P. velifera) harbour different sex-specifically organized simple repeat motifs. The observed sex-specific hybridization patterns were substantiated by banding analyses of the karyotypes and by in situ hybridization using the (GACA)₄ probe.by E.R. SchmidtDedicated to Professor Karl Sperling on the occasion of his 50th birthday     

Insertional polymorphism of a non-LTR mobile element (NLRCth1) in European populations of Chironomus riparius (Diptera, Chironomidae) as detected by transposon insertion display.

The midge Chironomus riparius is distributed all over the Palearctic region and is well characterized both at the morphological and cytogenetic levels. Here we describe a population study based on the insertional polymorphism of the retroposon NLRCth1, by means of a S-SAP (sequence-specific amplification polymorphism) derived technique (transposon insertion display; TID). While a previous study of allozyme polymorphism in Russian samples showed little variability, all the amplicons we identified are polymorphic. Genetic distances between 6 natural populations were calculated according to Nei and did not show a positive correlation with geographic distances. The genetic diversity detected among individuals of a given population was one order of magnitude higher than that among populations. However, the value of phi(ST) was significant (p < 0.001) and indicates that natural populations are more genetically differentiated than random samples of individuals.     

Chromosome Differentiated Populations of Cruzii: Evidence for a Third Sibling Species

Anopheles cruziiis the most common species of mosquito in Southeast Brazil and a vector of human and monkey malaria. The banding pattern of the ovarian polytene chromosomes and the frequencies of paracentric inversions of individuals from two populations were studied. A new sequence of bands on the sex chromosome, defined as form C, was disclosed. In both populations where forms A (considered as standard) and C are sympatric no heterozygotes were detected. A sequence of events that could account for the observed changes in the banding sequences of the X chromosome forms was proposed. The frequencies of 22 paracentric inversions were used to assess panmixia and the results indicated the presence of two distinct genetic pools in each population. We consider these results as evidence of another sibling species in the taxon cruzii, characterized by a distinctive form of the X chromosome and provisionally designated Anopheles cruziispecies C.     

Karyotypic features of Chironomus entis and Chironomus borokensis (Diptera, Chironomidae) from Lake Kotokel (Lake Baikal Basin)

Karyotypes and chromosomal polymorphism of sympatric sibling species Chironomus entis and Chironomus borokensis from Lake Kotokel were studied. Five inversion banding sequences were found in C. entis, including p’entA16, p’entB9, and p’entF6 that are new for the species; in C. borokensis, four inversion banding sequences were revealed, borA4 being new for the species. The level of chromosome polymorphism in C. entis and C. borokensis can be considered similar: 54.2 and 53.8% heterozygosity, 0.67 and 0.73 inversions per individual, respectively. The new data are compared with those on C. entis population from Lake Kotokel obtained in 1981 and those of C. borokensis from Lake Dukhovoe (Lake Baikal basin) obtained in 1983.     

Use of single-primer DNA amplifications in genetic studies of peanut (Arachis hypogaea L.)

A recent approach to detecting genetic polymorphism involves the amplification of genomic DNA using single primers of arbitrary sequence. When separated electrophoretically in agarose gels, the amplification products give banding patterns that can be scored for genetic variation. The objective of this research was to apply these techniques to cultivated peanut (Arachis hypogaea L.) and related wild species to determine whether such an approach would be feasible for the construction of a genetic linkage map in peanut or for systematic studies of the genus. Two peanut cultivars, 25 unadapted germplasm lines of A. hypogaea, the wild allotetraploid progenitor of cultivated peanut (A. monticola), A. glabrata (a tetraploid species from section Rhizomatosae), and 29 diploid wild species of Arachis were evaluated for variability using primers of arbitrary sequence to amplify segments of genomic DNA. No variation in banding pattern was observed among the cultivars and germplasm lines of A. hypogaea, whereas the wild Arachis species were uniquely identified with most primers tested. Bands were scored (+/–) in the wild species and the PAUP computer program for phylogenetic analysis and the HyperRFLP program for genetic distance analysis were used to generate dendrograms showing genetic relationships among the diploid Arachis species evaluated. The two analyses produced nearly identical dendrograms of species relationships. In addition, approximately 100 F₂ progeny from each of two interspecific crosses were evaluated for segregation of banding patterns. Although normal segregation was observed among the F₂ progeny from both crosses, banding patterns were quite complex and undesirable for use in genetic mapping. The dominant behavior of the markers prevented the differentiation of heterozygotes from homozygotes with certainty, limiting the usefulness of arbitrary primer amplification products as markers in the construction of a genetic linkage map in peanut.     

Polymorphism of STR Loci of the Y Chromosome in Three Populations of Eastern Slavs from Belarus,Russia, and Ukraine

Allelic polymorphism of five microsatellite loci of the human Y chromosome (DYS19, DYS390, DYS391, DYS392, and DYS393) was analyzed in samples of male populations from Ukraine, Russia, and Belarus (152 subjects in total). The allelic diversity indices (D _g) were determined for all loci; they varied from 0.23 to 0.72. The mean values of this parameter in the Ukrainian, Russian, and Belarussian populations were 0.45, 0.47, and 0.52, respectively. A total of 53 different haplotypes were found in 152 subjects from three populations. The most frequent haplotype was found in 14.5% of the subjects, whereas 35 haplotypes (23%) were each found in only one person. The haplotypic diversity index (D _hp) was 0.94. The genetic distances between the populations studied and some populations of Western and Central Europe were estimated. These data were used to construct a phylogram (tree) of genetic similarity between the populations, which demonstrated that the three Eastern Slavic populations are genetically close to one another and remote from Western European populations.     

Insertional variability of four transposable elements and population structure of the midge Chironomus riparius (Diptera)

The dipteran Chironomus riparius is found across the entire Palearctic region; its larvae are among the most abundant macroinvertebrates inhabiting inland waterbodies. Chironomid larvae have been extensively used in ecotoxicological and cytogenetic research, but relatively little is known on the population structure of this species. Transposable elements (TEs) are DNA sequences that are capable of autonomous replication; the number and genomic location of TE insertions varies across individuals; this variability is increasingly being used in population studies. Several TEs had been characterized in Chironomids; this enabled the analysis of insertional variability of four different TEs in six natural populations of C. riparius from Italy, Bulgaria and Russia using a PCR-based method, transposon insertion display (TID). The method allows to obtain dominant markers, similar to AFLP. In all populations, TE insertions showed high individual polymorphism, while median copy numbers of the same TEs did not vary between populations. Analysis of molecular variance (AMOVA) detected significant differentiation between populations for three of the TEs; although no correlation between genetic and geographic distances was found, the corresponding population structures were found to be significantly correlated and indicate a degree of isolation by distance. TEs belonging to different classes have different mechanisms of replication, resulting in different transposition rates of mobilization; the finding of mostly concordant population structuring for three of the TEs indicates that population dynamics contributed significantly in shaping the detected insertional polymorphism.