Molecular Phylogeny and Genetic Divergence of the Introduced Populations of Japanese Guppies, Poecilia reticulata

A phylogenetic tree of guppies from seven introduced Japanese populations was constructed using a mitochondrial gene, and the relationship between these Japanese populations and indigenous South American populations was examined. Phylogenetic trees constructed by maximum parsimony and neighbor joining methods indicated four major groups: Group A: Trinidadian populations; Group B: the northernmost Okinawa populations; Group C: the northern Okinawa populations; Group D: Shimoda populations and the remainder of Trinidadian, Venezuelan, and southern Okinawa populations. Considerable genetic differences were observed among the haplotypes within each Okinawa population similar to that found among haplotypes of different native populations, but not within the Shimoda population, because each Okinawa population included haplotypes belonging to different groups. Genetic differences between Groups B, C, and D might reflect those of the introduced lineages; however, these differences might not result from the divergence after introduction events. These results suggested that multiple introductions of different breeding lineages might cause considerable divergence within and between Okinawa populations.     

Evolutionary distances in hawaiian drosophila measured by DNA reassociation

Summary Comparisons of the sequence divergence of three species of Hawaiian Drosophila have been made by hybridization of single-copy tracer DNA of each of the species with driver DNA from each species, and measurement of the average melting temperature (Tma) in a chaotropic solvent (2.4 M tetraethylammonium chloride) which minimizes differences due to base composition. Correction was made for the length of hybrid duplex regions to obtain the reduction in thermal stability due to divergence.An accuracy of ± 0.2°C was achieved and the mean reduction in Tm for hybridization betweenD. heteroneura andD. silvestris (found only on the island of Hawaii) was 0.55°C and betweenD. picticornis, found only on the island of Kauai, and the other two species was 2.13°C. The rate of DNA change is estimated to be between 0.2 and 0.4%/My by assuming that theD. heteroneura-D. silvestris divergence occurred 0.8 My ago and the divergence between these species andD. picticornis between 4 and 6 My ago.The general single copy DNA sequence divergence appears to be very much greater than the minimal coding region sequence divergence previously estimated from allozyme studies.     

EVOLUTIONARY ADAPTATION TO TEMPERATURE II. THERMAL NICHES OF EXPERIMENTAL LINES OF ESCHERICHIA COLI

Groups of replicated lines of the bacterium Escherichia coli were propagated for 2,000 generations at constant 32, 37, or 42°C, or in an environment that alternated between 32 and 42°C. Here, we examine the performance of each group across a temperature range of 12-44°C measuring the temperatures over which each line can maintain itself in serial dilution culture (the thermal niche). Thermal niche was not affected by selection history: average lower and upper limits remained about 19 and 42°C for all groups. In addition, no significant differences among groups were observed in rate of extinction at more extreme temperatures. Within the thermal niche, we measured the mean fitness of the evolved groups relative to their common ancestor. Increases in mean fitness were temperature specific, with the largest increase for each group occurring near its selected temperature. Thus, the temperature at which mean fitness relative to the ancestor was greatest (the thermal optimum) diverged by about 10°C for the groups selected at constant 32°C versus constant 42°C. Tradeoffs in relative fitness (decrements relative to the ancestor elsewhere within the thermal niche) did not necessarily accompany fitness improvements, although tradeoffs were observed for a few of the lines. We conclude that adaptation in this system was quite temperature specific, but substantial divergence among groups in thermal optima had little effect on the limits of their thermal niches and did not necessarily involve tradeoffs in fitness at other temperatures.     

Reduction in the rate of DNA reassociation by sequence divergence

An estimate is made of the effect of imperfectly complementary sequences on the rate of reassociation of DNA. Rate measurements are reported for the reassociation of deaminated DNA and for the pairing of DNAs from related bacteria. A method is presented for separating the effect of the incubation temperature on the rate from the effect of sequence divergence. After correction to the optimum incubation temperature, the rate of DNA reassociation appears to be reduced by a factor of two for each 10 deg. C reduction in melting temperature due to sequence divergence. For most typical cases this effect is modest. However it can be quite important for measurements of the relation between the DNAs of different species.     

Morphological divergence within and between the Mexican sailfin mollies, Poecilia velifera and Poecilia petenensis

This study examined the patterns of morphological variation both between species, and between sexes and among populations within each species of the Mexican sailfin mollies, Poecilia velifera and Poecilia petenensis , using geometric morphometrics and linear measurements of morphological traits. While sexes within each species differed in characteristics that may be important in sexual selection, such as length of the dorsal fin, species differed in traits, such as body depth, that may also be influenced by natural selection due to differences in habitats. Within each species, many morphological traits were similar among populations, but important differences, including caudal peduncle depth in P. petenensis (but not in P. velifera ), suggested that habitat differences may also be important in shaping population divergence independently within each species. Indeed, the evolutionary vectors of male morphological population divergence for each species differed by an angle of 98·5°, representing nearly orthogonal vectors and suggesting independent shape divergence between these two molly species. Finally, geographic isolation did not explain the morphological differentiation seen among populations, suggesting that natural and sexual selection were strong forces promoting morphological diversification within these two species, despite the potential for a high degree of population connectivity and gene flow.     

Reproductive rates of Russian wheat aphid (Hemiptera: Aphididae) biotypes 1 and 2 on a susceptible and a resistant wheat at three temperature regimes

The reproductive rates of Russian wheat aphid, Diuraphis noxia (Kurdjumov) (Hemiptera: Aphididae), Biotype 1 (RWA 1) and Biotype 2 (RWA 2) were compared in the laboratory at three temperature regimes on a Russian wheat aphid resistant cultivar ('Prairie Red') and a susceptible cultivar ('TAM 107'). The objective of this study was to expose RWA 1 and RWA 2 to three temperature regimes and two levels of resistance to find whether there were reproductive differences that may occur within each biotype as well as differences in reproduction between biotypes. In addition, temperature effects of the Dn4 gene on biotype reproduction were noted. Differences in reproductive rates between the two biotypes seem to be driven by temperature. For both biotypes, longevity and reproductive rate parameters, except for intrinsic rate of increase, were lower at the 24-29 degree C temperature regime than the 13-18 degree C and 18-24 degree C temperature regimes. The intrinsic rate of increase was higher for both biotypes at the 18-24 degree C and 24-29 degree C temperature regimes than at the 13-18 degree C temperature regime. Reproductive rates between biotypes were similar at the two higher temperature regimes, but the fecundity for RWA 1 was less than RWA 2 at the 13-18 degree C temperature. The change in fecundity rates between RWA 1 and RWA 2 at lower temperatures could have ecological and geographical implications for RWA 2.     

Evolutionary divergence of AP-PCR (RAPD) patterns

Rates at which AP-PCR patterns diverge among isolated taxa were examined to test whether they exhibit clocklike regularity. The results showed that rates of divergence differed significantly among the groups examined (primates, antelopes, and Hawaiian Drosophila grimshawi). Therefore, AP-PCR divergence rates cannot be used as a "universal clock" with an invariant rate in all animals. Nevertheless, within each group, a strong relationship existed between degree of AP-PCR pattern divergence and time since separation of isolated taxa. Thus, AP-PCR divergence may prove useful for dating evolutionary events if calibrated within a more limited taxon.      

Detection of mutations in exon 8 of TP53 by temperature gradient 96-capillary array electrophoresis

Various capillary electrophoresis applications have increasingly been utilized in mutation detection. Separation of two species is either based on secondary structure or differences in melting of DNA due to the mutation. Detection of the mutant is based on its mobility difference in the sieving matrix. We have adapted a regular 96-capillary sequencing instrument, the MegaBACE 1000, for mutation detection based on thermodynamic stability and mobility shift during electrophoresis. Denaturation of the lower melting domain of the DNA was achieved with a gradually decreasing temperature gradient in combination with a chemical denaturant. Samples were analyzed for mutants in exon 8 of the TP53 genefrom tumor samples and controls. Genomic DNA was PCR-amplified with one fluorescein labeled primer and one GC-clamped primer, diluted in water, and analyzed by temperature gradient 96-capillary array electrophoresis. Tumor samples and PCR reconstruction experiment samples were resolved by capillary gel electrophoresis under appropriate temperature gradient denaturing conditions. Ninety-six samples were analyzed in one run, with an analysis time of 30 min and a sensitivity to detect mutated alleles in wild-type background down to 0.4%. The technique proved to be robust, in that the gradient compensatesfor temperature differences within the capillary chamber; thus, each capillary will pass through the optimal separating conditions around the theoretical melting temperature for TP53 exon 8, separating homoduplexes and heteroduplexes. This technique is applicable to any sequence previously analyzed by DNA melting gel techniques or sequences harboring iso-melting domains of 100-120 bp.     

Genetic characterization of the Psilotrema (Digenea: Psilostomatidae) genus by partial 28S ribosomal DNA sequences

In the present study, we successfully amplified the 28S ribosomal DNA of 3 species of the Psilotrema genus (Psilotrema oschmarini Besprozvannykh, 2007, P. acutirostris Oschmarin, 1963 and P. simillimum Muhling, 1989) from the Russian Far East. The genetic divergence between these species was estimated, and the phylogenetic relationships of the Psilotrema genus and the Psilostomatidae family were inferred. The resulting data support the independent taxonomical status of P. oschmarini as a valid species in the Russian Far East. In spite of the considerable morphological differences between P. simillimum and P. acutirostris, these species are genetically very close to each other. Genetic distances, calculated from the pairwise comparison of two obtained clusters using transversions, show that Psilostomatidae is the most divergent family. Phylogenetic analysis revealed two clusters, which corresponds to family Psilostomatidae (basal cluster) and other Echinostomatoidea species.     

芦鹀种群中的文化、遗传和形态进化的同时比较

我们比较了芦 (Emberizaschoeniclus)两个亚种组 ,即北部的薄喙亚种组和南部的厚喙亚种组的 10个种群中的文化、遗传和形态变异。使用了四个不同的变异标记物 ,其中两个用来测量文化分化 ,一个用来测量遗传分化 ,即微卫星等位基因的频次 ,一个用来测量种群的形态分化 ,即喙的高度。将遗传分化作为进化时间的尺度 ,我们计算了亚种组间和组内分化指标与所估计的进化率之间的相关性 ,发现只有文化定量指标和遗传分化与种群的形态分化相关 ,而两个文化分化指标之间没有关系 ,文化分化与遗传分化之间也没有关系。使用文化 -定量分化指标 ,发现亚种组间的文化进化率高于亚种内的文化进化率 ,提示鸣唱在防止杂交方面只有微弱的、也许是次要的作用。鸣唱定量特征的变异与微卫星频次相同 ,实际上在自然界中更可能是遗传决定的 ,这可以解释由于分析两个文化变异指标所得出的结果的不一致性。鸣唱的声学特性可能由于栖息地的差异或形态上的限制而发生了演变 ,而文化传播单位 (Meme)的特性可能由于学习鸣唱和文化传播而受到了影响     

Geographical variation in echolocation vocalizations of the Himalayan leaf‐nosed bat: contribution of morphological variation and cultural drift

Ecologists and evolutionary biologists have a long‐standing interest in the patterns and causes of geographical variation in animals’ acoustic signals. Nonetheless, the processes driving acoustic divergence are still poorly understood. Here, we studied the geographical variation in echolocation vocalizations (commonly referred to as echolocation ‘pulses’ given their short duration and relatively stereotypic nature, and to contrast them from the communicative vocalizations or ‘calls’) of a widespread bat species Hipposideros armiger in south China, and assessed whether the acoustic divergence was driven by either ecological selection, or cultural or genetic drift. Our results revealed that the peak frequency of echolocation pulses varied significantly across populations sampled, with the maximum variation of about 6 kHz. The peak frequency clustered into three groups: eastern and western China, Hainan and southern Yunnan. The population differences in echolocation pulses were not significantly related to the variation in climatic (mean annual temperature, mean annual relative humidity, and mean annual precipitable water) or genetic (genetic distance) factors, but significantly related to morphological (forearm length) variation which was correlated with mean annual temperature. Moreover, the acoustic differences were significantly correlated with geographical and latitudinal distance after controlling for ‘morphological distance’. Thus, neither direct ecological selection nor genetic drift contributed to the acoustic divergence observed in H. armiger. Instead, we propose that the action of both indirect ecological selection (i.e. selection on body size) as well as cultural drift promote, in part, divergence in echolocation vocalizations of individuals within geographically distributed populations.     

Geographical variation of genetic and phenotypic traits in the Mexican sailfin mollies, Poecilia velifera and P. petenensis

Comparing the patterns of population divergence using both neutral genetic and phenotypic traits provides an opportunity to examine the relative importance of evolutionary mechanisms in shaping population differences. We used microsatellite markers to examine population genetic structure in the Mexican sailfin mollies Poecilia velifera and P. petenensis. We compared patterns of genetic structure and divergence to that in two types of phenotypic traits: morphological characters and mating behaviours. Populations within each species were genetically distinct, and conformed to a model of isolation by distance, with populations within different geographical regions being more genetically similar to one another than were populations from different regions. Bayesian clustering and barrier analyses provided additional support for population separation, especially between geographical regions. In contrast, none of the phenotypic traits showed any type of geographical pattern, and population divergence in these traits was uncorrelated with that found in neutral markers. There was also a weaker pattern of regional differences among geographical regions compared to neutral genetic divergence. These results suggest that while divergence in neutral traits is likely a product of population history and genetic drift, phenotypic divergence is governed by different mechanisms, such as natural and sexual selection, and arises at spatial scales independent from those of neutral markers.     

Distinguishing Anuran species by high‐resolution melting analysis of the COI barcode (COI‐HRM)

Taxonomic identification can be difficult when two or more species appear morphologically similar. DNA barcoding based on the sequence of the mitochondrial cytochrome c oxidase 1 gene (COI) is now widely used in identifying animal species. High‐resolution melting analysis (HRM) provides an alternative method for detecting sequence variations among amplicons without having to perform DNA sequencing. The purpose of this study was to determine whether HRM of the COI barcode can be used to distinguish animal species. Using anurans as a model, we found distinct COI melting profiles among three congeners of both Lithobates spp. and Hyla spp. Sequence variations within species shifted the melting temperature of one or more melting domains slightly but do not affect the distinctness of the melting profiles for each species. An NMDS ordination plot comparing melting peak profiles among eight Anuran species showed overlapping profiles for Lithobates sphenocephala and Gastrophryne carolinensis. The COI amplicon for both species contained two melting domains with melting temperatures that were similar between the two species. The two species belong to two different families, highlighting the fact that COI melting profiles do not reveal phylogenetic relationships but simply reflect DNA sequence differences among stretches of DNA within amplicons. This study suggests that high‐resolution melting analysis of COI barcodes (COI‐HRM) may be useful as a simple and rapid method to distinguish animal species that appear morphologically similar.     

Ancient differentiation in the single-island avian radiation of endemic Hispaniolan chat-tanagers (Aves: Calyptophilus)

The simple geographic structure of island systems often makes them tractable for studies of the patterns and processes of biological diversification. The Calyptophilus chat-tanagers of Hispaniola are of general evolutionary interest because their multiple lineages might have arisen on a single island, of conservation concern because several isolated populations are nearly extinct, and taxonomically ambiguous because they have been variously lumped or split into one to four species. To explore the context of diversification of the seven extant Calyptophilus populations, we conducted a multilocus coalescent analysis based on sequences of mitochondrial ND2 and three nuclear intron loci. We then compared patterns of phylogeographic genetic variation with the morphological differences that distinguish these populations. Mitochondrial haplotypes formed two reciprocally monophyletic groups separated by a large magnitude of nucleotide divergence. Intron structure largely paralleled the geographic grouping pattern of the mitochondrial DNA (mtDNA), but these groups were only reciprocally monophyletic at one of the three introns. Also, the magnitude of between-group divergence was much lower in the introns than mtDNA genealogies. Multilocus coalescent analyses inferred a nonzero divergence time between these two major geographic groups, but suggested that they have experienced a low level of gene flow. All four markers showed substantial allele sharing within each of the two groups, demonstrating that many now separated montane populations do not have long histories of isolation. Considered in concert, our multilocus phylogeographic reconstructions support the recognition of two species within the Calyptophilus complex, and raise the possibility that these taxa differentiated prior to the fusion of the two palaeo-islands that form present-day Hispaniola.     

Evidence for adaptive divergence of thermal responses among Bemisia tabaci populations from tropical Colombia following a recent invasion

There is an increasing evidence that populations of ectotherms can diverge genetically in response to different climatic conditions, both within their native range and (in the case of invasive species) in their new range. Here, we test for such divergence in invasive whitefly Bemisia tabaci populations in tropical Colombia, by considering heritable variation within and between populations in survival and fecundity under temperature stress, and by comparing population differences with patterns established from putatively neutral microsatellite markers. We detected significant differences among populations linked to mean temperature (for survival) and temperature variation (for fecundity) in local environments. A Q_ST ? F_ST analysis indicated that phenotypic divergence was often larger than neutral expectations (Q_ST > F_ST). Particularly, for survival after a sublethal heat shock, this divergence remained linked to the local mean temperature after controlling for neutral divergence. These findings point to rapid adaptation in invasive whitefly likely to contribute to its success as a pest species. Ongoing evolutionary divergence also provides challenges in predicting the likely impact of Bemisia in invaded regions.     

Differentiation of <Emphasis Type="Italic">Harmonia axyridis</Emphasis> Pall. according to polymorphic morphological traits and variability of the mitochondrial COI gene

The geographic variability of Harmonia axyridis Pall. has been studied with regard to three morphological features. A study of the cytochrome C oxidase subunit I (COI) polymorphism was begun. Two geographically separated zones inside the Russian part of the geographic range of the species are recognized. Interpopulational differences, as judged using polymorphic traits, are very small within each zone. In contrast, the differences between the populations of the western and eastern zones reach the subspecies level of. A zone of clinal variability of morphological traits is noted in Transbaikalia. It obviously resulted from secondary contact between the western and eastern groups of populations, which were separated during the last glaciation and then rejoined.     

Minor quantitative trait loci underlie floral traits associated with mating system divergence in Mimulus

The genetic basis of species differences provides insight into the mode and tempo of phenotypic divergence. We investigate the genetic basis of floral differences between two closely related plant taxa with highly divergent mating systems, Mimulus guttatus (large-flowered outcrosser) and M. nasutus (small-flowered selfer). We had previously constructed a framework genetic linkage map of the hybrid genome containing 174 markers spanning approximately 1800 cM on 14 linkage groups. In this study, we analyze the genetics of 16 floral, reproductive, and vegetative characters measured in a large segregating M. nasutus x M. guttatus F2 population (N = 526) and in replicates of the parental lines and F1 hybrids. Phenotypic analyses reveal strong genetic correlations among floral traits and epistatic breakdown of male and female fertility traits in the F2 hybrids. We use multitrait composite interval mapping to jointly locate and characterize quantitative trait loci (QTLs) underlying interspecific differences in seven floral traits. We identified 24 floral QTLs, most of which affected multiple traits. The large number of QTLs affecting each trait (mean = 13, range = 11-15) indicates a strikingly polygenic basis for floral divergence in this system. In general, QTL effects are small relative to both interspecific differences and environmental variation within genotypes, ruling out QTLs of major effect as contributors to floral divergence between M. guttatus and M. nasutus. QTLs show no pattern of directional dominance. Floral characters associated with pollinator attraction (corolla width) and self-pollen deposition (stigma-anther distance) share several pleiotropic or linked QTLs, but unshared QTLs may have allowed selfing to evolve independently from flower size. We discuss the polygenic nature of divergence between M. nasutus and M. guttatus in light of theoretical work on the evolution of selfing, genetics of adaptation, and maintenance of variation within populations.     

Morphological differentiation within the population of Siah Mahi, Capoeta capoeta gracilis, (Cyprinidae, Teleostei) in a river of the south Caspian Sea basin: a pilot study

Siah Mahi, Capoeta capoeta gracilis, is a predominant fish in the river systems of the south Caspian Sea basin. Although there is evidence of the geographical divergence of this taxon, no information is available on morphological differences within the subspecies populations. The study was designed to evaluate this differentiation in the Shirud River system of the south Caspian Sea basin in Iran. A total of 120 fish specimens (≥ 180 mm) were collected from the Shirud River; 33 morphometric and 10 meristic characteristics were recorded for each specimen. The standardized data were subjected to a principal component analysis (PCA) and variables with eigenvector ≥ 0.74 used as input for analysis of clustering, which grouped the 120 fish specimens into five distinct clusters. The overall random assignment of individuals into their original groups was high (86.7%), indicating that these specimens are highly divergent from each other. The proportion of individuals correctly classified into their original groups was 90, 81.8, 85.7, 100 and 76% for groups 1, 2, 3, 4 and 5, respectively. There were significant differences in nine morphometic characteristics among the five multivariate groups. Pectoral-anal length was the only characteristic that, based on all possible pair combinations of the five groups, could be individually distinguishable. With regard to meristic characteristics, a Kruskal–Wallis test showed that there were no significant differences among medians of the five multivariate groups.