Comparison of multivariate methods for the analysis of genetic resources and adaptation in Phytolacca dodecandra using RAPD

The extent of genetic differentiation among 17 Ethiopian populations (249 individuals) of Phytolacca dodecandra (Endod) sampled along altitudinal gradients that varied from 1600 to 3000 m was investigated using random amplified polymorphic DNA (RAPD). The populations were classified into three altitude groups: lowland (1600–2100 m), central-highland (2101–2500 m) and highland (2500–3000 m). Seventy polymorphic loci scored from 12 RAPD primers, singly or in combination with ecogeographical variables (altitude, longitude, latitude, temperature and rainfall), were used for principal component, discriminant, correlation, and stepwise multiple regression analyses. Principal component analysis (PCA) clearly differentiated lowland and the central-highland populations from those of the highlands independent of their geographical regions. Canonical discriminant analysis separated the lowland plants from those of the highlands with the central-highland plants being intermediate. Classificatory discriminant analysis corrected classification of 92.8% of the 249 plants into their respective three altitude groups. Multiple regression analysis identified a strong association between some RAPDs and altitude, temperature and rainfall, while the variation in most RAPDs was explained by combinations of the different ecogeographical variables. It is hypothesised that the different altitude groups may be (1) chemical and/or physiological ecotypes produced as a result of complex interactions of altitude with climatic and/or edaphic factors, or (2) different in ploidy levels. The significant correlations obtained between population means from some RAPDs and altitude and temperature as well as the strong association of some RAPDs with the ecogeographical variables in the multiple regression analysis suggest that part of the RAPD polymorphism could be adaptive, and responsive to environmental selection. Received: 15 December 1999 / Accepted: 12 February 2000     

The impact of elevated UV-B (280–320 nm) radiation levels on the reproduction biology of a highland and a lowland population of Silene vulgaris

A highland (altitude 1600 m) and a lowland (altitude –2 m) population of the perennial herb Silene vulgaris were tested on the effects of elevated levels of UV-B radiation on their reproductivity. Highland populations receive higher natural UV-B doses than lowland populations. Therefore adaptation to high UV-B levels of the highland population is to be expected. The lowland population showed a decrease in the number of seed producing flowers and the number of seeds produced per plant under elevated UV-B levels. The highland population increased the number of seeds per plant under elevated UV-B levels. In both populations individual seed mass as well as seed germination percentages were unaffected by the UV-B flux received by the parental plant. Possible effects of UV-B induced alterations in reproductivity on the geographical distribution of the different populations are discussed.     

Sex-specific migration patterns in Central Asian populations, revealed by analysis of Y-chromosome short tandem repeats and mtDNA.

Eight Y-linked short-tandem-repeat polymorphisms (DYS19, DYS388, DYS389I, DYS389II, DYS390, DYS391, DYS392, and DYS393) were analyzed in four populations of Central Asia, comprising two lowland samples-Uighurs and lowland Kirghiz-and two highland samples-namely, the Kazakhs (altitude 2,500 m above sea level) and highland Kirghiz (altitude 3,200 m above sea level). The results were compared with mtDNA sequence data on the same individuals, to study possible differences in male versus female genetic-variation patterns in these Central Asian populations. Analysis of molecular variance (AMOVA) showed a very high degree of genetic differentiation among the populations tested, in discordance with the results obtained with mtDNA sequences, which showed high homogeneity. Moreover, a dramatic reduction of the haplotype genetic diversity was observed in the villages at high altitude, especially in the highland Kirghiz, when compared with the villages at low altitude, which suggests a male founder effect in the settlement of high-altitude lands. Nonetheless, mtDNA genetic diversity in these highland populations is equivalent to that in the lowland populations. The present results suggest a very different migration pattern in males versus females, in an extended historical frame, with a higher migration rate for females.     

Genetic diversity within and among populations of Diprion pini (Hym., Diprionidae) determined by random amplified polymorphic DNA-polymerase chain reaction of haploid males

Abstract: Based on haploid males, random amplified polymorphic DNA (RAPD) markers were used to study genetic variation within and among four French populations and one Finnish outgroup population of the common pine sawfly, Diprion pini (L.), representing a severe European forest pest associated with mass outbreaks. Taking into account that all multilocus haplotypes were detected, a total of 140 individuals were completely discriminated by means of 17 polymorphic markers (present or absent), which were amplified from nine selected random-decamer primers. All populations shared the same genetic types, but pronounced population-specific frequency distributions were found, indicating that on average 84% of the present genetic variation exists within populations and the remaining smaller part counts for interpopulational variation. The haplotype differentiation registered was able to distinguish between the class of lowland populations and the class of highland populations. Reproductive isolation and therefore limited altitudinal gene flow, indicated in case of a French highland population by an enlarged number of fixed markers, and hitchhiking effects with respect to selective processes at certain loci following local adaptation and speciation are discussed to explain the population structures found. A possible selection is indicated by five markers, showing significantly different frequency distributions between the class of highland populations and the class of lowland populations.     

Variations in body melanisation,ovariole number and fecundity in highland and lowland populations of Drosophila melanogaster from the Indian subcontinent

We investigated geographical variations in three fitness‐related traits (body melanisation, ovariole number and fecundity) in laboratory‐reared offspring of 10 populations of Drosophila melanogaster. The populations were collected from adjacent lowland and highland localities (～80–100 km apart) in the tropical as well as subtropical regions (11.15–31.06 °N) covering a linear distance about 3 000 kilometers from south to north on the Indian subcontinent. Persistence of within‐as well as between‐population differences at 21 °C suggest that observed variations in fitness‐related traits have a genetic basis. Populations from higher altitudes showed consistently higher trait values (1.4‐fold increase) as compared with their corresponding lowland populations. By contrast, latitudinal variations were about two‐fold higher across the entire continent. Along latitude as well as altitude, population means showed higher correlation values (r > 0.98) between all the three fitness traits. However, on the basis of within‐population analysis (assorted darker and lighter flies), changes in body melanisation were significantly correlated with fecundity but not with ovariole number. Thus, analysis of within‐population trait variability should be preferred as compared with data on population means for adaptive significance of fitness‐related traits. In the present study, the role of climatic selection is evident from regression analysis with changes in annual average temperature of the sites of origin of populations along latitude as well as altitude.     

Genetic and biochemical differentiation in Vitis vinifera (Kabarcik) populations grown at different altitudes in Coruh Valley

We examined genetic differences of four Vitis vinifera populations (A, B, C, D) including local Kabarcik cultivar grown along an altitude gradient of 800, 900, 1000, and 1150 m above sea level in the Coruh Valley (800 m: A population; 900 m: B population; 1000 m: C population; 1150 m: D population). Leaf samples were used for both RAPD and fatty acid analysis. A total of 60 individuals with 15 individuals per population were included in this study. RAPD analyses showed various band sizes, which ranged from 250 to 3000 bp. Mean polymorphic locus ratios were determined as 96.29% considering four populations. The highest percentage of polymorphic loci (97.8%) was produced by the highest altitude. Thirty-two different fatty acids were found; linoleic acid was the most common in all four populations. According to the dendograms obtained from statistical analyses of RAPD and fatty acid profiles the populations that were close to each other in terms of geographical distance also were similar genetically.     

Developmental time,body size and wing loading in Drosophila buzzatii from lowland and highland populations in Argentina

Genotype-by-temperature interaction is a necessary condition for adaptive evolution of fitness traits as a response to temperature. Several fitness-related traits (developmental time, pre-adult survival, thorax and wing lengths, and wing loading) were measured in laboratory-reared D. buzzatii from four populations sampled at different altitudes in north-western Argentina: a lowland population (407 m a.s.l.), two populations from intermediate altitude (780 to 950 m a.s.l.), and a highland population (2380 m a.s.l.). Temperature is the main climatic difference between the collection sites: lowland but not highland populations are exposed to physiologically high temperatures during both spring and summer in nature. Three growth temperatures (20, 25 and 30 degrees C) were used to test for population-by-temperature interactions. Both developmental time and pre-adult survival exhibit highly significant population-by-temperature interaction. Pre-adult survival at 30 degrees C is significantly higher in lowland than in highland populations, but not so at lower growth temperatures (20 and 25 degrees C). Both wing length and wing loading show no population-by-temperature interaction, indicating that these traits are not the direct targets of thermal adaptation in nature. Wing loading is higher in highland than in lowland populations, suggesting that flight performance is subject to stronger selection in the highland population. This hypothesis is consistent with ecological observations in both types of populations. There is no obvious among-population relationship between developmental time and body size, even though both traits are related within populations in a well-known trade-off. Overall, thermal adaptation is evident for developmental time and pre-adult survival but not for size-related traits.     

浙江产车前(Plantago asiatica)种群遗传分化的主坐标分析

运用18个有效的10mer-寡核苷酸引物对浙江产车前（Plantago asiatica)的8个种群基因组DNA进行了PCR扩增,共检测到186个位点,其中多态位点125个,占68.70%,应用Jaccard公式计算了8个种群在125个位点上的相似性,以此为基础,应用主坐标排序,作出了8个种群遗传分化的三维排序图,结果表明,8个种群的遗传分化与地理位置、海拔高度有联系。     

Genetic variation in wild sorghum (Sorghum bicolor ssp. verticilliflorum (L.) Moench) germplasm from Ethiopia assessed by random amplified polymorphic DNA (RAPD)

The extent and distribution of genetic variation in wild sorghum (Sorghum bicolor ssp. verticilliflorum (L.) Moench) collected from five different geographical regions in Ethiopia were analyzed using random amplified polymorphic DNA (RAPD) markers for 93 individuals representing 11 populations. Nine decamer primers generated a total of 83 polymorphic bands with 8-12 bands per primer and a mean of 9 bands across the 93 individuals. The amount of genetic variation among the populations (H = 0.37) and among the geographical region (H = 0.44) was low to moderate, despite the high degree of polymorphic bands per primer. Similarly, the mean genetic distance (0.08) among populations as well as among regions of origin (0.04) of the population was found to be low. The low genetic variation may be due to the reduced population size of the wild sorghum in Ethiopia because of habitat change. Partitioning of the genetic variation into between and within the population as well as between and within the regions of origin revealed that 75% and 88% of the variation was found within the populations and within the regions, respectively. Cluster analysis of genetic distance estimates further confirmed low level of differentiation of wild sorghum populations both on population and regional bases. The implications of the results for genetic conservation purposes are discussed.     

Genetic diversity and differentiation of cultivated amochi (Arisaema schimperianum Schott) in Ethiopia as revealed by AFLP markers

Amochi (Arisaema schimperianum Schott) is an off-season crop plant in southern Ethiopia, grown during the dry season on residual moisture, for its edible tubers. It has gained importance as a "security crop" especially during the years of moisture stress and food shortage. Amochi is irritating in contact to the skin. Removal of this effect is an important question for breeding. As the first step, however we attempt to establish base line information of its breeding system and genetic variability using AFLPs. The extent of genetic differentiation among 11 populations (96 individuals) of amochi sampled along altitudinal gradients that varied from 1700 to 3200 m a.s.l. was investigated. The populations were classified in to three altitudinal groups: lowland (1700 to 2200 m a.s.l.), central-highland (2201 to 2600 m a.s.l.) and highland (2601 to 3200 m a.s.l.). Polymorphic loci (167) scored from four primer pair combinations, were used for principal component analysis (PCA), and analysis of molecular variance (AMOVA). Both PCA and unweighed pair group with arithmetic mean (UPGMA) clearly differentiated populations into their respective altitude groups, with large genetic distances. AMOVA analysis revealed 70.5%, 16.7% and 12.8% variability between altitude groups, between populations and within populations respectively. Average diversity indices within populations were also low. Since the largest proportion of variation is located between altitude groups, rather than within populations, we suggest future studies on the chemical composition, low irritation, and other desirable traits should consider populations from different altitude ranges.     

Analysis of genetic diversity in common loon Gavia immer using RAPD and mitochondrial RFLP techniques

We used random amplified polymorphic DNA (RAPD) and restriction fragment length polymorphisms (RFLP) of mitochondrial cytochrome b (cyt b ) gene to evaluate the genetic diversity in common loon Gavia immer populations from two regions in the United States: New England (NE) and Michigan (MI). RAPD analysis with 18 primers showed 74% polymorphism in NE and 50% in MI loons (similarity coefficient F = 0.92). Although no population-specific markers were found, the frequencies of some RAPD bands varied between the two populations suggesting geographical differences. RFLP analyses with Bam HI enzyme and a 307-bp mitochondrial cyt b gene showed four haplotypes in the NE loon samples and two in the MI samples. The mtDNA haplotype diversity was 0.74 for NE and 0.51 for MI loons, supporting the RAPD data that NE loons have greater genetic diversity than MI loons.     

Randomly Amplified Polymorphic DNA Variation in Populations of Eastern Australian Koalas, Phascolarctos cinereus

Randomly amplified polymorphic DNA (RAPD) variation in populations of the koala, Phascolarctos cinereus, was investigated, revealing significant differences in the level of diversity between southern and northern regions of eastern Australia. Of the 20 polymorphic RAPD markers identified in koalas, 4-7 were polymorphic in southern populations, while 12-17 were polymorphic in northern populations. Analysis of molecular variance revealed a significant difference in the estimated variance between koalas from northern and those from southern regions (P < 0.001), where populations from the north were greater than twice as variable as their southern cousins. The total genetic diversity observed was attributed to regional differences (30.91%), population differences within a region (11.77%), and differences among individuals within a population (57.32%). For the within-region analyses, a large proportion of the genetic diversity was attributable to individual differences within a population, 80.34% for the north and 91.23% for the south. These results demonstrate that RAPD markers are useful for determining population structure among koalas.     

BEHAVIORAL DIFFERENTIATION IN OVIPOSITION ACTIVITY IN DROSOPHILA BUZZATII FROM HIGHLAND AND LOWLAND POPULATIONS IN ARGENTINA: PLASTICITY OR THERMAL ADAPTATION?

Highland populations of several Drosophila species in Argentina were active early in the afternoon in the field as opposed to populations from a much warmer lowland site, where flies were mainly active in the early evening prior to sunset. For one of these species, Drosophila buzzatii, we tested for a genetic component of activity differences by carrying out crosses within and between populations and measuring oviposition activity of the progeny in the laboratory. We found that activity in the highland population exceeded that in the lowland one during the midafternoon, whereas activity in the lowland population exceeded that in the highland one prior to the beginning of the dark period. Oviposition activity for the period corresponding to the field observations was regressed on the proportion of the genome derived from the highland population. This variable significantly predicted oviposition activity between 1400 and 1600 and between 2000 and 2200 h. Activity of both reciprocal crosses was intermediate and not significantly different from each other, suggesting that nuclear genetic, rather than cytoplasmic factors contribute to differences in oviposition activity between the populations. Two morphological, one genetic, and one stress resistance trait were also scored to examine whether temperature differences between environments were associated with other differences between populations. Wing length of wild-caught and laboratory-reared flies from the highland population significantly exceeded that in the lowland. Thorax length of laboratory-reared flies from the highland population also significantly exceeded that from the lowland. Chromosomal inversion frequencies differed significantly between the two populations with a fivefold reduction in the frequency of arrangement 2st in the highland as compared to the lowland population. This arrangement is known for its negative dose effect on size, and thus, the highland population has experienced a genetic change, perhaps as a result of adaptation to the colder environment, where body size and the frequency of arrangement 2st have changed in concert. Finally, a heat knockdown test revealed that the lowland population was significantly more resistant to high temperature than the highland one. In conclusion, we suggest that temperature has been an important selective agent causing adaptive differentiation between these two populations. We also suggest that the activity rhythms of the two populations have diverged as a consequence of behavioral evolution, that is, through avoidance of stressful temperatures as a mean of thermal adaptation.     

Geographic patterns of genetic diversity in Poulsenia armata (Moraceae): implications for the theory of Pleistocene refugia and the importance of riparian forest

Abstract. Tropical forests are species-diverse communities, but we know very little about the geographical distribution of genetic diversity within a species. During the late Pleistocene, lower temperatures and rainfall reduced the distribution of tropical wet forests, and in Central America lowland species may have been limited to riparian habitats. Approximately 12,000 years bp , temperature and rainfall increased in Central America, the distribution of wet forest species expanded, and today the distribution of some species extends into southern Mexico. The distribution of genetic diversity, based on RAPD markers, among ten populations of Poulsenia armata (Miq.) Standl. (Moraceae) suggests that these populations did not originate from a single refugium or region in the late Pleistocene. The Central American populations had high genetic diversity and unique bands giving support to the hypothesis that populations of P. armata occurred in Central American during the late Pleistocene. The majority of genetic diversity was partitioned among populations and there was no geographical relationship among populations, suggesting that these populations were isolated for a long period and there has been little gene flow. Populations of P. armata may have persisted in riparian zones along the Caribbean coast during the late Pleistocene. Given that riparian forest can support high levels of biodiversity in ecological time, and they have played an important role during periods of climate change over geological time, their conservation is of utmost importance particularly with the threat of a rapid shift in climatic patterns.     

Analysis of genetic diversity and relationships in East African banana germplasm

The genetic diversity and phylogenetic relationships of 29 East African highland banana (Musa spp.) cultivars and two outgroup taxa, M. acuminata Calcutta 4 and Agbagba were surveyed by RAPD analysis. A genetic similarity matrix was established based on the presence or absence of polymorphic amplified fragments. Phylogenetic relationships were determined by UPGMA cluster analysis. RAPDs showed that the highland bananas are closely related with a narrow genetic base. Nevertheless, there were sufficient RAPD polymorphisms that were collectively useful in distinguishing the cultivars. The dendrogram was divisible into a major cluster composed of all the AAA highland banana cultivars and Agbagba (AAB) and a minor cluster consisting of Kisubi (AB), Kamaramasenge (AB) and Calcutta 4 (AA). Several subgroups are recognized within the major cluster. RAPD data did not separate beer and cooking banana cultivars. Our study showed that RAPD markers can readily dissect genetic differences between the closely related highland bananas and provide a basis for the selection of parents for improvement of this germplasm. Received: 28 June 2000 / Accepted: 1 August 2000     

Promiscuity in populations of the cushion plant Saxifraga oppositifolia in the Swiss Alps as inferred from random amplified polymorphic DNA (RAPD)

Overviews on patterns of genetic variation within and among plant populations show that widespread, outcrossing species should have a high proportion of the total genetic variation within populations and a low proportion among populations, which results in little population differentiation. However, in Alpine areas, large–scale distribution barriers as well as small-scale habitat heterogeneity could lead to geographical and temporal isolation, respectively. We investigated the genetic variation of Saxifraga oppositifolia from 10 populations of the Alps in southeastern Switzerland using random amplified polymorphic DNA (RAPD). Based on the banding patterns of four RAPD primers, 84 polymorphic markers identified all 189 sampled individuals as being genetically different. The genetic variation was mainly found within populations (95%), whereas less than 5% was found among populations and among regions. Analyses of molecular variance ( AMOVA ) suggested that population differentiation was highly significant. However, grouping populations differently into regions did not appear to result in a clear correspondence of genetic and geographical relatedness. Genetic variation did not significantly differ between populations of two elevational levels. This coincides with results of former pollination experiments that revealed a breeding system of S. oppositifolia which remains the same irrespective of the elevation. We assume that the high outcrossing rate, rare clonal reproduction, and some long-distance dispersal even among topographically separated populations are the crucial determinants for the pattern of genetic variation found in the investigated area.     

Changes in body melanisation and desiccation resistance in highland vs. lowland populations of D. melanogaster

Wild caught samples of Drosophila melanogaster from five highland localities showed parallel changes in melanisation and desiccation resistance in darker versus lighter phenotypes, i.e. darker flies (>45% melanisation) showed significantly higher desiccation resistance than lighter flies (<30% melanisation). In order to find an association between body melanisation and desiccation resistance, highland and lowland populations from tropical and subtropical regions (11.15-31.06 degrees N) of the Indian subcontinent were raised and investigated at 21 degrees C for four physiological traits, i.e. per cent body melanisation, desiccation resistance, rate of water loss and rate of water absorption. On the basis of mother-offspring regression, body melanisation and desiccation resistance showed higher heritability (0.58-0.68) and thus these traits are suitable for laboratory analyses. Significantly higher melanisation as well as desiccation resistance were observed in highland populations as compared with lowland populations. The rates of water loss as well as absorption were negatively correlated with body melanisation, i.e. darker flies from highlands showed a reduced rate of water loss as well as a lower rate of water absorption while the reverse trend was observed in lighter flies from lowlands. On the basis of multiple regressions, significant effects due to combined altitude and latitude were observed for all the four physiological traits. Local climatic conditions (i.e. annual average temperature and relative humidity) helped in explaining parallel changes in body melanisation and desiccation resistance in D. melanogaster.     

Immunoglobulin allotypes among Taiwan aborigines: evidence of malarial selection could affect studies of population affinity

The aborigines of Taiwan represent the indigenous inhabitants of the island at the time of the arrival of the Chinese from the mainland. Linguistically, the aboriginal Taiwanese are related to the Malayo-Polynesian-speaking inhabitants of Indonesia and the Philippines. Three tribes occupied lowland areas while six tribes occupied highland areas. Previous studies indicate that genetic markers associated with malaria occur in lowland populations. Though the GM haplotypes are demonstrated to be very useful in the measure of population affinities, the possibility of malarial selection on this locus could affect studies of population affinity. The present work is a case study to see whether a subdivided insular population under a possible selective load will provide divergent clustering analysis depending on the population sampled. Immunoglobulin allotype (GM and KM) profiles were generated on 230 lowland and 407 highland Taiwan Aborigines from the nine tribes. A highly significant difference in GM haplotype distribution was detected between lowland and highland populations (adjusted G = 69.408, 2 df [degrees of freedom], p < 0.00001). There were no significant differences in KM*1 frequency by altitude. The Taiwan Aboriginal GM and KM frequencies were compared to data from Indonesians, Vietnamese, Thai, Malay, Chinese from Taiwan, and Ryukyu Islanders from Okinawa using cluster analysis. The lowland populations plot among the Thai (N, NC) and Malayan Aborigines. In contrast, the highland and total Taiwan Aborigine samples plot with the Indonesian, Vietnamese, and Malayan Negrito samples. Thus, depending on the populations of Taiwan Aborigines used, different conclusions could be reached. The highland population supports the published linguistic ties; however, the lowland population does not support the linguistic relationship with Indonesian populations but is more closely related to Thai and Malays, or reflects a similar selection history.     

冬小麦对不同海拔气候条件的反应 Ⅲ.植株光合作用特征

我们在原地测量了840米和2150米两地种植的冬小麦“凤麦13”苗期、拔节期、抽穗期和灌浆初期的光合作用速率的日变化,光合作用速率对光量子通量密度的反应和CO_2补偿点。结果表明生育前期(苗期和拔节期)和后期(抽穗期和灌浆初期)光合作用速率的一日内变化形式相反,而且低地种植的冬小麦其光合速率在前期高于高地种植的,后期高地种植的冬小麦有比低地高的光合速率。光饱和点基本相同。光补偿点在生育前期高地小麦比低地小麦低,而后期低地小麦的的光补偿点减低,并低于高地小麦的。高地小麦的光补偿点比较稳定。CO_2补偿点高地小麦比低地的较低。并就两地气候条件讨论了上述差异。     

Molecular Genetic Variation in a Clonal Plant Population of Leymus chinensis (Trin.) Tzvel.

Randomly amplified polymorphic DNA (RAPD) analysis was used to investigate the genetic variation among populations, between populations, and within populations, relationships between genetic distance and geographic distance, and the molecular variation and population size. The effects of geographic and genetic distances, as well as of genetic differentiation and population size, on genetic variations of Leymus chinensis (Trin.) Tzvel. are discussed. The present study showed that there was significant RAPD variation between the Baicheng region population and the Daqing region population, with a molecular variance of 6.35% (P ＜ 0.04), and for differentiation among area populations of the Daqing region, with a molecular variance of 8.78% (P ＜ 0.002). A 21.06% RAPD variation among all 16 populations among two regions was found (P ＜ 0.001), as well as 72.59% variation within populations (P ＜ 0.001). Molecular variation within populations was significantly different among 16 populations.