COMPARATIVE KARYOLOGICAL ANALYSIS OF FIVE SPECIES OF VIVIPARUS (GASTROPODA: PROSOBRANCHIA)

Karyological analysis was performed on Viviparus ater (Cristofori& Jan, 1832), V. acerosus Bourguignat, 1862, V. mamillatus (Kuster),V. viviparus (Linnaeus, 1758) and V. contectus (Millet, 1813),collected from different freshwater bodies of Switzerland, Hungary,Albania, Italy and Lithuania. The karyotypes of V. acerosusand V. mamillatus are described for the first time. The diploidnumber of chromosomes in V. contectus equals 14, whereas indiploid sets of other studied species, 18 chromosomes are present.The karyotype formula is in V. contectus (5m + 2sm, NF = 28,in V. ater, 7m + 1sm-m + 1 sm, in V. acerosus and V. viviparus,8m + 1sm, NF = 36, in V. mamillatus, 6m + 1m-sm + 1sm-m + 1sm,NF = 36. In females of V. ater, V. mamillatus and V. acerosus,the heteromorphism of chromosome pair no. 8 was observed, witha sex-determining mechanism — ZW female /ZZ male. Although,Z and W chromosomes are metacentric, significant differences(P > 0.05, or P > 0.001) in their size were determined.The interspecific significant differences (P > 0.05) in karyotypesof V. ater, V. mamillatus, V. acerosus and V. viviparus weredetected by using one-way ANOVA and Bonferronis Multiple Comparisontests. Only chromosomes of the pair no. 5 were of similar shapein all of these species. The smallest interspecific differencewas between V. viviparus and V. acerosus. The intraspecifickaryological differences in relative chromosome length and centromericindex of V. contectus from lakes Garda (Italy), Olauka andAsveja (Lithuania) were observed in the chromosome pair no.5. (Received 29 March 1999; accepted 19 October 1999)     

An alternating least squares approach to inferring phylogenies from pairwise distances

A computational method is presented for minimizing the weighted sum of squares of the differences between observed and expected pairwise distances between species, where the expectations are generated by an additive tree model. The criteria of Fitch and Margoliash (1967, Science 155:279-284) and Cavalli-Sforza and Edwards (1967, Evolution 21:550-570) are both weighted least squares, with different weights. The method presented iterates lengths of adjacent branches in the tree three at a time. The weighted sum of squares never increases during the process of iteration, and the iterates approach a stationary point on the surface of the sum of squares. This iterative approach makes it particularly easy to maintain the constraint that branch lengths never become negative, although negative branch lengths can also be allowed. The method is implemented in a computer program, FITCH, which has been distributed since 1982 as part of the PHYLIP package of programs for inferring phylogenies, and is also implemented in PAUP*. The present method is compared, using some simulated data sets, with an implementation of the method of De Soete (1983, Psychometrika 48:621-626); it is slower than De Soete's method but more effective at finding the least squares tree. The relationship of this method to the neighbor-joining method is also discussed.     

Evolutionary divergence in Dolichopoda cave crickets: A comparison of single copy DNA hybridization data with allozymes and morphometric distances

In this paper we attempt to investigate relationships between the amount of genetic divergence in nuclear genes and the degree of morphological differentiation for different sets of characters in Dolichopoda cave crickets. Six populations representing five Dolichopoda species from Central and Southern Italy have been studied. The overall genetic divergence at nuclear genes was estimated both by single copy DNA-DNA hybridization and allozyme frequencies at 26 loci. Euclidean distances for two multivariate sets of morphometric variables: one describing body and appendage morphology, the other male epiphallus shape. Results showed a close agreement between the branching patterns of ΔTm values from DNA hybridization and Nei's allozyme distance values. On the other hand, patterns of morphological divergence revealed independent trends, although the branching pattern based on epiphallus morphology matched to some extent the phylogenies inferred from molecular data. The relative value of molecular and morphological characters as reliable phylogenetic tracers was evaluated in relation to their dependence on evolutionary factors. Implications of these findings on the calibration of molecular clocks are also discussed. The absolute rate of molecular change based on scDNA was estimated to be at least 0.98% divergence/my/lineage. This result is in agreement with calibrations attempted on other insects. Estimates of time of divergence based on allozymes (Nei's D) were highly consistent with the estimate from geological data.     

PATTERNS OF ALLOZYME RELATIONSHIPS COMPARED WITH MORPHOLOGY,HYBRIDIZATION, AND GEOLOGIC HISTORY IN ALLOPATRIC ISLAND-DWELLING MOSQUITOES

Allozyme relationships were compared with morphology, interspecific hybridization, and geologic history in 14 closely-related species in the Aedes (Stegomyia) scutellaris subgroup. The phylogeny generated by the electrophoretic data was generally in agreement with morphological classifications except that one morphologically distinct species pair (A. alcasidi and A. malayensis) showed only populational differentiation and several nearly identical morphological pairs in Polynesia (e.g., A. pseudoscutellaris and A. polynesiensis) were very distant genetically. A molecular clock, based on the ratio between genetic distance and divergence time (one unit of Nei's distance = 11 million years) inferred from a dated geologic event, was used to compare zoogeography, morphology, and biochemical relationships. Genetic distances between species from the Solomon Islands and the Vanuatu-Polynesia area correspond to an early Pliocene separation of these areas. An invasion of Micronesia occurred approximately 5 million years ago. Most remaining speciation occurred during the mid-Pliocene as islands moved into their present-day positions. The close relationship between southeast Asian and Philippine species could have resulted from the recent onset of isolation in the Pleistocene. Interspecific hybridization potential was not significantly correlated with Nei's genetic distance. Many quite distantly related species readily hybridize, while some closely related pairs show only unidirectional compatibility. Slight interspecific morphological divergence and the independence of hybridization capabilities from phylogeny are not unexpected in a group in which species are allopatric and occupy similar habitats.     

Molecular phylogeny in 3-D

Molecular phylogenetic trees are constructed in three dimensions relative to the distribution of MW and pl classes and immunocrossreactivity against polyclonal antibodies to lens crystallins, as well as multiple sequence alignment between amino acid sequences, coding nucleotide sequences and the gene nucleotide sequences for beta-globin. Euclidian distances are estimated to position species in x, y, z space by multidimensional scaling and merged with bootstrap-tested branching pattern of Fitch & Margoliash plots to obtain 3-D phylogenetic tree. Compared to single attributes, phylogenetic trees based on multiple parameters allow significant repositioning of rodents, chiroptera and primates.     

Construction of phylogenetic trees for proteins and nucleic acids: Empirical evaluation of alternative matrix methods

Summary The methods of Fitch and Margoliash and of Farris for the construction of phylogenetic trees were compared. A phenetic clustering technique - the UPGMA method — was also considered.The three methods were applied to difference matrices obtained from comparison of macromolecules by immunological, DNA hybridization, electrophoretic, and amino acid sequencing techniques. To evaluate the results, we used the goodness-of-fit criterion. In some instances, the F-M and Farris methods gave a comparably good fit of the output to the input data, though in most cases the F-M procedure gave a much better fit. By the fit criterion, the UPGMA procedure was on the average better than the Farris method but not as good as the F-M procedure.On the basis of the results given in this report and the goodness-of-fit criterion, it is suggested that where input data are likely to include overestimates as well as true estimates and underestimates of the actual distances between taxonomic units, the F-M method is the most reasonable to use for constructing phylogenies from distance matrices. Immunological, DNA hybridization, and electrophoretic data fall into this category. By contrast, where it is known that each input datum is indeed either a true estimate or an underestimate of the actual distance between 2 taxonomic units, the Farris procedure appears, on theoretical grounds, to be the matrix method of choice. Amino acid and nucleotide sequence data are in this category.The following abbreviations are used in this work F-M Fitch-Margoliash - UPGMA unweighted pair-group method using arithmetic averages - SD percent standard deviation     

Different thermal conditions of lakes affect host–parasite systems: A case study of Viviparus contectus (Millet, 1813) and digenean trematodes

1. Thermal disturbance of aquatic ecosystems directly and/or indirectly affects interspecific interactions, including parasitism. Both hosts and parasites respond differently to environmental changes, thus, predicting how host–parasite systems behave under the influence of disturbance remains a challenge. The aim of the study was to check how the differences in thermal conditions of lakes affect life-history traits of hosts and the level of parasitism, using a Viviparus contectus–digenean trematodes model.
2. Overall, we examined 480 individuals of V. contectus collected from a thermally polluted lake (TPL) and a natural lake (NL). Host features, including body size and fecundity, as well as the prevalence and species richness of digenean trematodes in snail populations were investigated.
3. We found that V. contectus from the TPL were significantly larger, heavier, and females were more fertile than snails collected from the NL. A total of 20.4% of the collected snails were infected with digenean larvae. The species richness of parasites was twice as high in the NL compared to the TPL (six and three species, respectively). A significant difference in the percentage of snails infected with parasites was identified between both types of lakes, with a higher prevalence of V. contectus in the NL (31.3%) compared to the TPL (7.3%).
4. These results indicate that host–parasite systems follow the environmental changes in lakes due to thermal pollution by increasing fertility and metabolism rate of viviparid hosts and by decreasing the prevalence and diversity of digenean trematodes.

     

A Comparative Statistical Analysis of Genetic Distances. I - Estimation of Distances and of their Variances: Distribution of the Estimators

We present a Monte-Carlo simulation analysis of the statistical properties of absolute genetic distance and of Nei's minimum and standard genetic distances. The estimation of distances (bias) and of their variances is analysed as well as the distributions of distance and variance estimators, taking into account both gamete and locus samplings. Both of Nei's statistics are non-linear when distances are small and consequently the distributions of their estimators are extremely asymmetrical. It is difficult to find theoretical laws that fit such asymmetrical distributions. Absolute genetic distance is linear and its distributions are better fit by a normal distribution. When distances are medium or large, minimum distance and absolute distance distributions are close to a normal distribution, but those of the standard distance can never be considered as normal. For large distances the jack-knife estimator of the standard distance variance is bad; another standard distance estimator is suggested. Absolute distance, which has the best mathematical properties, is particularly interesting for small distances if the gamete sample size is large, even when the number of loci is small. When both distance and gamete sample size are small, this statistic is biased.     

Computer comparison of new and existing criteria for constructing evolutionary trees from sequence data

Summary Three new methods for constructing evolutionary trees from molecular sequence data are presented. These methods are based on a theory for correcting for non-constant evolutionary rates (Klotz et al. 1979; Klotz and Blanken 1981). Extensive computer simulations were run to compare these new methods to the commonly used criteria of Dayhoff (1978) and Fitch and Margoliash (1967). The results of these simulations showed that two of the new methods performed as well as Dayhoff's criterion, significantly better than that of Fitch and Margoliash, and as well as a simple variation of the latter (Prager and Wilson 1978) where any topology containing negative branch mutations is discarded. However, no method yielded the correct topology all of the time, which demonstrated the need to determine confidence estimates in a particular result when evolutionary trees are determined from sequence data.     

Linking seed dispersal and genetic structure of trees: a biogeographical approach

Aim Natural and human‐induced differences in frugivore assemblages can influence the seed dispersal distances of trees. An important issue in seed dispersal systems is to understand whether differences in seed dispersal distances also affect the genetic structure of mature trees. One possible approach to test for a relationship between seed dispersal and the genetic structure of mature trees is to compare the genetic structure of two closely related tree species between two biogeographical regions that differ in frugivore assemblages and seed dispersal distances. Previous studies on two Commiphora species revealed that Commiphora guillauminii in Madagascar has a much lower seed dispersal distance than Commiphora harveyi in South Africa. We tested whether the lower seed dispersal distance might have caused decreased gene flow, resulting in a stronger genetic structure in Madagascar than in South Africa. Location Madagascar and South Africa. Methods Using amplified fragment length polymorphism markers we investigated the genetic structure of 134 trees in Madagascar and 158 trees in South Africa at a local and a regional spatial scale. Results In concordance with our hypothesis, kinship analysis suggests that gene flow was restricted mostly to 3 km in Madagascar and to 30 km in South Africa. At the local spatial scale, the genetic differentiation among groups of trees within sample sites was marginally significantly higher in Madagascar (F_ST = 0.069) than in South Africa (F_ST = 0.021). However, at a regional spatial scale genetic differentiation was lower in Madagascar (F_ST = 0.053) than in South Africa (F_ST = 0.163). Main conclusions Our results show that lower seed dispersal distances of trees were linked to higher genetic differentiation of trees only at a local spatial scale. This suggests that seed dispersal affects the genetic population structure of trees at a local, but not at a regional, spatial scale.     

Genetic relationships among some new cat populations sampled in Europe: A spatial autocorrelation analysis

The allelic frequencies of nine Mendelizing genetic characteristics that control coat colour, tabby and length and some skeletal abnormalities have been studied in four feral domestic cat populations, two in the north of Catalonia (Girona and Roses & L’Estartit, northeastern Spain) and two Adriatic Italian populations (Rimini and Venice). Using different genetic and multivariate analyses (Nei’s and Cavalli-Sforza and Edwards’s genetic distances, phenograms and cladograms using different algorithms, strict consensus trees, canonical population, principal coordinates and nonmetric multidimensional scaling analyses), I show the genetic relationships between these populations and other Western European cat populations previously studied. In the Western European area comprising Catalonia, Italy, France and Great Britain, I found significant spatial structure for thet ^b, l andW alleles and for the average correlogram for the seven alleles studied as a whole using a spatial autocorrelation analysis. The genetic distance matrices between these European cat populations also showed a significant correlation with the geographical distance between these populations using Mantel’s test. These analyses showed that in each of these countries, local cat populations have characteristic genetic profiles which were different to neighbouring populations in nearby countries. At least in this area of Western Europe, the geographical distances between cat populations (although the gene flow can be relatively high) is an important factor which can explain differences in allele frequencies between these populations.     

Life on the edge: survival and behavioural responses of freshwater gill‐breathing snails to declining water level and substratum drying

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How useful are microsatellite loci in recovering short-term evolutionary history?

Because microsatellite loci are abundant in the human genome and are highly polymorphic in most global populations, such loci have become very popular in studies on reconstructing evolutionary relationships among contemporary human populations. We have made an assessment of the efficiency of recovery of true evolutionary relationships using simulated data of microsatellite loci and a variety of distance measures. We find that allele frequency data on about 30 microsatellite loci and the use ofD _A (Neiet al. 1983) orD _c (Cavalli-Sforza and Edwards 1967) distance measures with UPGMA clustering algorithm can recover true short-term evolutionary relationships with a high degree of accuracy, unless the effective sizes of the populations or mutation rates or both are very small.     

Allozymic differentiation in the land snail Arianta arbustorum (Stylommatophora, Helicidae): historical inferences

The intraspecific genetic differentiation depends to a large part on historical factors. The mode of dispersal is an important determinant of the genetic diversity especially of newly founded populations. Fast long-distance colonization of formerly unsuitable habitats results in reduced genetic diversity and lineages originating from different glacial refugia form well-defined hybrid zones, where they meet. Slow dispersers, on the other hand, preserve their refugial genetic diversity. Paleontological findings and a previous analysis of mtDNA suggest that the land snail Arianta arbustorum, which today is widely spread across Europe, has survived the Pleistocene glaciations within the boundaries of permafrost. In the present paper, we asked, whether the differentiation of nuclear markers, i.e. allozymes, supports these results. We investigated the allozymic differentiation at 15 polymorphic loci in 14 Alpine and one English populations of the land snail A. arbustorum. Various tests of genetic population differentiation yielded ambiguous results. Allele frequencies differed significantly across populations and all but five pairwise F_ST values were significant. Genetic distances between populations were comparatively high. On the other hand, an exact test of population differentiation found no differences and the assignment of individuals to their populations of origin was poor. This indicates that allozymic differentiation is constrained. Whether these constraints are of natural or methodological nature remains open. Matrices of genetic and geographical distances were correlated only after removal of the English population from the analysis. Similarly, with one exception F_ST values increased as the number of regions included in the calculations increased. Thus, on a regional scale, we largely observed a pattern of isolation by distance, which does no longer hold on a larger scale. This is well in accordance with the previous findings based on mtDNA. Mitochondrial lineages were widely distributed across Europe and overlapped extensively. Considering the low potential for dispersal of a land snail, the patchy distribution of lineages, and the high genetic diversity also found in the present study suggests that A. arbustorum has survived the Pleistocene within the boundaries of permafrost.     

Fast computation of distance estimators

Background  

Some distance methods are among the most commonly used methods for reconstructing phylogenetic trees from sequence data. The input to a distance method is a distance matrix, containing estimated pairwise distances between all pairs of taxa. Distance methods themselves are often fast, e.g., the famous and popular Neighbor Joining (NJ) algorithm reconstructs a phylogeny of n taxa in time O(n ³). Unfortunately, the fastest practical algorithms known for Computing the distance matrix, from n sequences of length l, takes time proportional to l·n ². Since the sequence length typically is much larger than the number of taxa, the distance estimation is the bottleneck in phylogeny reconstruction. This bottleneck is especially apparent in reconstruction of large phylogenies or in applications where many trees have to be reconstructed, e.g., bootstrapping and genome wide applications.     

Phylogenetic relationships among laboratory and wild-origin Mus musculus strains on the basis of genomic DNA RFLPs

Genetic distance measures between the laboratory mouse strains C57BL/6J and RF/J and the wild-origin Mus musculus mouse strains CAST/Ei, MOLF/Ei, POSCH I, and CZECH II were estimated by allelic patterns revealed by RFLP analysis. These results suggest phylogenetic relationships indicating that the mouse strains related to the subspecies M.m. domesticus (RF/J, POSCH I and C57BL/6J) are more closely related to the CAST/Ei strain (derived from M.m. castaneus) than to the strains CZECH II (M.m. musculus) and MOLF/Ei (M.m. molossinus). Furthermore, the hybrid strain C57BL/6J is more closely related to POSCH I (M.m. poschiavinus) than to RF/J as calculated by the method distance measures of Cavalli-Sforza and Edwards (Evolution 21,550, 1967), Nei's minimum (Am. Natural. 106,283, 1972) and unbiased minimum (Genetics 89,583, 1978), Edwards (Biometrics 27,873, 1971; Genetic Distance, p. 41, 1974) and Rogers modified (1986).     

Developing a DNA barcode library for perciform fishes in the South China Sea: Species identification,accuracy and cryptic diversity

DNA barcodes were studied for 1,353 specimens representing 272 morphological species belonging to 149 genera and 55 families of Perciformes from the South China Sea (SCS). The average Kimura 2‐parameter (K2P) distances within species, genera and families were 0.31%, 8.71% and 14.52%, respectively. A neighbour‐joining (NJ) tree, Bayesian inference (BI) and maximum‐likelihood (ML) trees and Automatic Barcode Gap Discovery (ABGD) revealed 260, 253 and 259 single‐species‐representing clusters, respectively. Barcoding gap analysis (BGA) demonstrated that barcode gaps were present for 178 of 187 species analysed with multiple specimens (95.2%), with the minimum interspecific distance to the nearest neighbour larger than the maximum intraspecific distance. A group of three Thunnus species (T. albacares, T. obesus and T. tonggol), a pair of Gerres species (G. oyena and G. japonicus), a pair of Istiblennius species (I. edentulous and I. lineatus) and a pair of Uranoscopus species (U. oligolepis and U. kaianus) were observed with low interspecific distances and overlaps between intra‐ and interspecific genetic distances. Three species (Apogon ellioti, Naucrates ductor and Psenopsis anomala) showed deep intraspecific divergences and generated two lineages each, suggesting the possibility of cryptic species. Our results demonstrated that DNA barcodes are highly reliable for delineating species of Perciformes in the SCS. The DNA barcode library established in this study will shed light on further research on the diversity of Perciformes in the SCS.     

Morphological stasis in the Eurytemora affinis species complex (Copepoda: Temoridae)

Morphological stasis has long been regarded as one of the most challenging problems in evolutionary biology. This study focused on the copepod species complex, Eurytemora affinis, as a model system to determine pattern and degree of morphological stasis. This study revealed discordant rates of morphological differentiation, molecular evolution, and reproductive isolation, where speciation was accompanied by lack of morphological differentiation in secondary sex characters. Comparisons were made among phylogenies based on morphometrics, nuclear (allozyme) loci, and mitochondrial DNA (mtDNA) sequences from cytochrome oxidase I, for a total of 43 populations within the complex. These systematic relationships were also compared to patterns of reproductive isolation. In addition, genetic subdivision of nuclear molecular (allozyme) markers (G _ST) and quantitative (morphological) characters (Q _ST) were determined to infer evolutionary forces driving morphological differentiation. The morphometric phylogeny revealed that all clades, excluding the European clade, were morphologically undifferentiated and formed a polytomy (multifurcation). Morphometric distances were not correlated with mtDNA distances, or with patterns of reproductive isolation. In contrast, nuclear and mtDNA phylogenies were mostly congruent. Reproductive isolation proved to be the most sensitive indicator of speciation, given that two genetically and morphologically proximate populations showed evidence of hybrid breakdown. Quantitative genetic (morphological) subdivision (Q _ST = 0.162) was lower than nuclear genetic subdivision (G _ST = 0.617) for four laboratory-reared North American populations, indicating retarded evolution of morphological characters. This result contrasts with most other species, where Q _ST typically exceeds G _ST as a result of directional selection. Thus, in all but the European populations, evolution of the secondary sex characters was marked by morphological stasis, even between reproductively-isolated populations.     

Allozymic and morphometric variation inLemna minor (Lemnaceae)

Allozymic and morphometric variation was studied in 28 clones ofLemna minor. This variation was compared with the corresponding variation in four clones ofLemna gibba and four clones ofSpirodela polyrrhiza. A high level of allozymic variation was observed among the clones, despite having been grown under uniform laboratory conditions for several years and despite its quasi-exclusive clonal means of propagation. Based on degree of allozymic similarity,Spirodela polyrrhiza was distinguished from the twoLemna species but the latter species were genetically indistinguishable. Allozymic similarity among clones ofLemna minor was not related to morphometric similarity, nor was it related to the degree of geographic separation or climatic similarity of their sites of origin. The results suggest that allozymic variation among these clones ofLemna minor may be largely neutral and not a consequence of differential selection.     

GENETIC VARIATION,DIFFERENTIATION, AND EVOLUTION IN A SPECIES COMPLEX OF TROPICAL SHRUBS BASED ON ISOZYMIC DATA

An isozyme investigation of the Lisianthius skinneri (Gentianaceae) species complex in central Panama assayed levels of genetic variation within and among isolated populations and was used to reconstruct phylogenetic relationships within the complex. The widespread and low elevation L. skinneri and one derived cloud forest endemic species, L. habuensis, are depauperate in genetic variation. Three other endemic cloud forest species exhibiting larger population sizes and apparently more outcrossed breeding systems have higher levels of heterozygosity but retain low levels of allelic diversity. More than 90% of the genetic variation in the species complex is confined to among-population differentiation rather than witnin-population variation. Isozyme-based relationships within the species complex using both genetic divergence values (Fitch and Margoliash algorithm) and shared allelic states (Nelson and Van Horn algorithm) are identical. This network is not entirely congruent with a previous DNA-based network. Geographical isolation, small population size, low allelic diversity, and high levels of among-population differentiation suggest that repeated instances of founder events and genetic drift have been important in the evolution of this tropical shrub complex.