Cloning and genetic variability of a HindIII repetitive DNA in Acrossocheilus paradoxus (Cyprinidae)

Low satellite DNA variability in natural populations of Drosophila antonietae involved in different evolutionary events

Drosophila antonietae is a cactophilic species that is found in the mesophilic forest of the Paraná-Paraguay river basin and in the dunes of the South Atlantic coast of Brazil. Although the genetic structure of the Paraná-Paraguay river basin populations has already been established, the relationship between these populations and those on the Atlantic coast is controversial. In this study, we compared 33 repetitive units of pBuM-2 satellite DNA isolated from individuals from 8 populations of D. antonietae in these geographic regions, including some populations found within a contact zone with the closely related D. serido. The pBuM-2 sequences showed low interpopulational variability. This result was interpreted as a consequence of both gene flow among the populations and unequal crossing over promoting homogenization of the tandem arrays. The results presented here, together with those of previous studies, highlight the use of pBuM-2 for solving taxonomic conflicts within the D. buzzatii species cluster.

Conservation of pBuM-2 satellite DNA sequences among geographically isolated Drosophila gouveai populations from Brazil

In this study, we have compared 34 repetition units of pBuM-2 satellite DNA of individuals from six isolated populations of Drosophila gouveai, a cactophilic member of Drosophila buzzatii cluster (repleta group). In contrast to the results of previous morphological and molecular data, which suggest differentiation among the D. gouveai populations, the sequences and the cluster analysis of pBuM-2 monomers showed that this repetitive element is highly conserved among the six D. gouveai populations (97.8% similarity), indicating a slow rate of evolution of pBuM-2 sequences at the population level. Probably, some homogenization mechanisms of tandem sequences, such as unequal crossing or gene conversion, have maintained the sequence similarity of pBuM-2 among D. gouveai populations. Alternatively, such a result may be associated with a functional role of pBuM-2 sequences, although it is not understood at present.

On the pBuM189 satellite DNA variability among South American populations of Drosophila buzzatii

The pBuM189 satellite DNA was analysed in Drosophila buzzatii populations that cover most of the species distribution in South America. This satDNA consists of A + T-rich monomers of 189 bp and previous studies showed a fast rate of evolutionary change of this component of D. buzzatii genome. A total of 63 pBuM189 repetition units from 14 D. buzzatii populations (9 from Brazil and 5 from Argentina) were studied. The average nucleotide variability among the 63 repeats is 4.2 %. At least one repeat (Juan/4) seems to be part of another pBuM189 satDNA subfamily. The nucleotide alignment of all 63 repeats revealed no specific nucleotide substitutions, or indels, that could discriminate each population or groups of geographically close populations. Such lack of satDNA interpopulational differentiation is congruent with previous mtDNA data that indicate a high gene flow and very little population differentiation throughout most of the D. buzzatii distribution in South America. Gene flow might have been possible during glaciation events in the Pleistocene, such as the one occurred between 13,000 and 18,000 years ago, when D. buzzatii probably had a more continuous distribution than what is observed today.

Mitochondrial DNA phylogeography of Acrossocheilus paradoxus (Cyprinidae) in Taiwan

Nucleotide sequences of 3' end of the cytochrome b gene, tRNA genes, D-loop control region, and the 5' end of the 12S rRNA of mitochondrial DNA (mtDNA) were used to assess the genetic and phylogeographic structure of Acrossocheilus paradoxus populations, a Cyprinidae fish of Taiwan. A hierarchical examination of populations in 12 major streams from three geographical regions using an analysis of molecular variance (AMOVA) indicates high genetic differentiation both among populations (PhiST = 0.511, P < 0.001) and among regions (PhiCT = 0.368, P < 0.001). Limited migration largely contributed to the genetic differentiation. High nucleotide diversity (1.13%) and haplotype diversity (0.80%) were detected among populations. The degree of genetic differentiation was correlated with geographical distance between populations, a result consistent with the one-dimensional stepping stone models. A neighbour-joining tree recovered by (DAMBE) supports the pattern of isolation by distance and reveals a closer relationship between populations of the central and southern regions. A minimum spanning network based on nucleotide substitutions reflected migration routes from populations of the central region to the northern and southern regions, respectively. Postglacial colonization and expansion can explain the phylogeographical pattern. Single and ancient migration events may have allowed the northern region to attain the monophyly of mtDNA alleles. In contrast, most populations within geographical regions are either paraphyletic or polyphyletic due to the relatively shorter time period for coalescence. Both low haplotype number and genetic variability suggest a bottleneck event in the Chingmei population of northern Taiwan. Based on coalescence theory, the monophyly of the Tungkang population of the southern region may be associated with a founder event.

Molecular evolution and phylogeny of the atpB-rbcL spacer of chloroplast DNA in the true mosses

The nucleotide variation of a noncoding region between the atpB and rbcL genes of the chloroplast genome was used to estimate the phylogeny of 11 species of true mosses (subclass Bryidae). The A+T rich (82.6%) spacer sequence is conserved with 48% of bases showing no variation between the ingroup and outgroup. Rooted at liverworts, Marchantia and Bazzania, the monophyly of true mosses was supported cladistically and statistically. A nonparametric Wilcoxon Signed-Ranks test Ts statistic for testing the taxonomic congruence showed no significant differences between gene trees and organism trees as well as between parsimony trees and neighbor-joining trees. The reconstructed phylogeny based on the atpB-rbcL spacer sequences indicated the validity of the division of acrocarpous and pleurocarpous mosses. The size of the chloroplast spacer in mosses fits into an evolutionary trend of increasing spacer length from liverworts through ferns to seed plants. According to the relative rate tests, the hypothesis of a molecular clock was supported in all species except for Thuidium, which evolved relatively fast. The evolutionary rate of the chloroplast DNA spacer in mosses was estimated to be (1.12 +/- 0.019) x 10(-10) nucleotides per site per year, which is close to the nonsynonymous substitution rates of the rbcL gene in the vascular plants. The constrained molecular evolution (total nucleotide substitutions, K approximately 0.0248) of the chloroplast DNA spacer is consistent with the slow evolution in morphological traits of mosses. Based on the calibrated evolutionary rate, the time of the divergence of true mosses was estimated to have been as early as 220 million years ago.