Contrasting patterns of divergence in quantitative traits and neutral DNA markers: analysis of clinal variation

Clinal variation in quantitative traits is often attributed to the effects of spatially varying selection. However, identical patterns can be produced by the interplay between purely stochastic processes (i.e. drift in combination with spatially restricted gene flow). One means of distinguishing between adaptive and nonadaptive causes of geographical variation is to compare relative levels of between-population divergence in quantitative traits and neutral DNA markers. Such comparisons can be used to test whether levels of trait divergence attributable to additive genetic effects (as measured by QST) exceed null expectations based on the level of divergence at neutral marker loci (as measured by FST). The purpose of this study was to use an approach based on 'QST vs. FST' contrasts to test for evidence of diversifying selection on body size of an Indian fruit bat, Cynopterus sphinx (Chiroptera: Pteropodidae). Specifically, relative levels of between-population divergence in body size and microsatellite DNA markers were compared to assess whether the observed pattern of clinal size variation could be explained by a neutral model of isolation by distance. QST for body size was calculated using unbiased estimators of within- and between-population variance of principal component scores. The association between body size variation and geographical/environmental distance was tested using pairwise and partial matrix correspondence tests (MCTs). Independent variables (representing causal hypotheses) were constructed as between-locality distance matrices. The effects of neutral genetic divergence were assessed by including a matrix of pairwise FST as an independent variable. Partial MCTs revealed highly significant associations between phenotypic divergence (QST) and both geographical and environmental distance, even when the effects of neutral genetic divergence (FST) were partialled out. Results of the tests confirmed that migration-drift equilibrium is not a sufficient explanation for the latitudinal pattern of clinal size variation in C. sphinx. The geographical patterning of pairwise QST is most likely attributable to spatially varying selection and/or the direct influence of latitudinally ordered environmental effects.     

Molecular genetic evidence for parallel evolution in a marine gastropod,Littorina subrotundata.

Littorina subrotundata from wave-exposed rocky shores differ consistently in shell and radula morphology from those found in wave-protected salt-marshes. To determine if the two morphological forms of this gastropod represent separate species, clades, or ecotypes, DNA sequencing and single-stranded conformational polymorphism (SSCP) analysis were used to assay variation in a 480 bp fragment of the mitochondrial cytochrome-b gene. Several nested analyses of molecular variance (AMOVA) were then performed to test if grouping populations by geographical region or habitat type better explained the distribution of cytochrome-b haplotypes among some northeastern Pacific populations. The analysis by geographic region resulted in a significant variance component that explained 53% of the variance, whereas the analysis by habitat type was not significant. These results, along with previous studies showing that the differences in shell morphology among different forms have a heritable component, suggest that the two forms are ecotypes and not separate species or clades as had been previously proposed. These results also imply that each ecotype has evolved independently in each geographic area and that the morphological similarity of individuals from the same habitat type is most likely the result of parallel evolution.     

Quantitative and molecular genetic variation in sympatric populations of Medicago laciniata and M. truncatula (Fabaceae): relationships with eco-geographical factors

Medicago laciniata is restricted to south of the Mediterranean basin and it extends in Tunisia from the inferior semi-arid to Saharan stages, whereas M. truncatula is a widespread species in such areas. The genetic variability in four Tunisian sympatric populations of M. laciniata and M. truncatula was analysed using 19 quantitative traits and 20 microsatellites. We investigated the amplification transferability of 52 microsatellites developed in M. truncatula to M. laciniata. Results indicate that about 78.85% of used markers are valuable genetic markers for M. laciniata. M. laciniata displayed significantly lower quantitative differentiation among populations (QST=0.12) than did M. truncatula (QST=0.45). However, high molecular differentiations, with no significant difference, were observed in M. laciniata (FST=0.48) and M. truncatula (FST=0.47). Several quantitative traits exhibited significantly smaller QST than FST for M. laciniata, consistent with constraining selection. For M. truncatula, the majority of traits displayed no statistical difference in the level of QST and FST. Furthermore, these traits are significantly associated with eco-geographical factors, consistent with selection for local adaptation rather than genetic drift. In both species, there was no significant correlation between genetic variation at quantitative traits and molecular markers. The site-of-origin explains about 5.85% and 11.27% of total quantitative genetic variability among populations of M. laciniata and M. truncatula, respectively. Established correlations between quantitative traits and eco-geographical factors were generally more moderate for M. laciniata than for M. truncatula, suggesting that the two species exhibit different genetic bases of local adaptation to varying environmental conditions. Nevertheless, no consistent patterns of associations were found between gene diversity (He) and environmental factors in either species.     

High quantitative and no molecular differentiation of a freshwater snail (Galba truncatula) between temporary and permanent water habitats

We investigate the variation in quantitative and molecular traits in the freshwater snail Galba truncatula, from permanent and temporary water habitats. Using a common garden experiment, we measured 20 quantitative traits and molecular variation using seven microsatellites in 17 populations belonging to these two habitats. We estimated trait means in each habitat. We also estimated the distributions of overall genetic quantitative variation (QST), and of molecular variation (FST), within and between habitats. Overall, we observed a lack of association between molecular and quantitative variance. Among habitats, we found QST>FST, an indication of selection for different optima. Individuals from temporary water habitat matured older, at a larger size and were less fecund than individuals from permanent water habitat. We discuss these findings in the light of several theories for life-history traits evolution.     

小叶锦鸡儿天然居群叶形态性状变异研究

为揭示小叶锦鸡儿(Caragana microphylla)天然居群叶形态性状的变异规律及其生态适应性特征,该研究以10个小叶锦鸡儿天然居群为对象,通过多重比较、巢式方差分析、相关性分析、聚类分析和主成分分析等方法,对7个叶形态性状进行分析。结果表明：(1)小叶锦鸡儿叶形态性状在居群内和居群间均存在极显著差异(P < 0.01),平均变异系数为10.13%,不同性状的变异幅度为6.23%~12.78%;平均叶形态性状的表型分化系数为43.62%,居群内变异(30.09%)大于居群间变异(24.91%),说明居群内是其叶形态性状变异的主要来源。(2)相关性分析表明,环境因子对小叶锦鸡儿的叶形态性状变异有很大的影响,在地理空间上主要呈现出沿海拔梯度的变异模式;主成分分析的结果显示,小叶宽、叶柄宽和叶柄长对小叶锦鸡儿叶形态变异起主导作用;利用欧式距离对小叶锦鸡儿居群进行UPGMA聚类分析结果显示,基于叶形态性状和环境因子可分别将小叶锦鸡儿10个居群分为3类和2类,Mantel检验结果表明,小叶锦鸡儿的叶形态性状变异不存在地理连续性。研究结果为小叶锦鸡儿的适应性进化和开发利用提供了理论依据。     

A geometric morphometric assessment of the effects of environment and cladogenesis on the evolution of the turtle shell

In the largest group of extant turtles, the Testudinoidea, the acquisition of an aquatic or terrestrial way of life has occurred within two clades, allowing the study of homoplasy linked to environment (commonly named convergence). Here we appraise the respective importance of two sources of morphological variation: a major cladogenetic event and a major environmental shift (aquatic vs. terrestrial). The repeatability of the same evolutionary process (environmental change) allows an assessment of the weights of both natural selection and phylogenetic constraints on several morphological features of the shell. These sources of morphological variance on the complex shell structure were studied using geometric morphometrics. We depict the morphological variation of three parts of the turtle shell: epidermal carapace, bony carapace, and plastron. In the three structures, we found that both phylogeny and environment were significant sources of morphological variation, and geometric morphometrics allowed the pattern of morphological variation due to each effect to be assessed. The assessment of the homoplasy due to environment and of the pattern of morphological variability suggests that the carapace has undergone similar morphological changes between aquatic and terrestrial environments within the two clades. The radiation of the Testudinoidea is interpreted as an adaptive radiation.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 79 , 485–501.     

Associations between heterozygosity and morphological variance

Recent studies have contrasted the expression of phenotypic traits, such as variance in morphological characters, with levels of genetic variation (heterozygosity) as determined by electrophoretic analysis of protein-coding loci. The theoretical basis for interpreting significant covariation stems in part from Lerner's work on genetic homeostasis, which predicts that within populations increased heterozygosity will produce decreased morphological variance, owing to a buffering effect of heterosis during development. However, the prediction for the relationship between genic heterozygosity and the variance of morphological traits among populations is unclear. To determine if a relationship existed between heterozygosity and morphological variance, we compared estimates of heterozygosity and morphological variance across 15 population samples of the fox sparrow and 17 samples of the pocket gopher. The estimates of morphological variance included coefficients of variation for each character and the variance of individual scores about the population mean in a principal components analysis. Although several recent studies have reported a significant relationship between heterozygosity and morphological variance, we found that the two measures do not covary significantly.     

Latitudinal divergence of common frog (Rana temporaria) life history traits by natural selection: evidence from a comparison of molecular and quantitative genetic data

The relative roles of natural selection and direct environmental induction, as well as of natural selection and genetic drift, in creating clinal latitudinal variation in quantitative traits have seldom been assessed in vertebrates. To address these issues, we compared molecular and quantitative genetic differentiation between six common frog (Rana temporaria) populations along an approximately 1600 km long latitudinal gradient across Scandinavia. The degree of population differentiation (QST approximately 0.81) in three heritable quantitative traits (age and size at metamorphosis, growth rate) exceeded that in eight (neutral) microsatellite loci (FST = 0.24). Isolation by distance was clear for both neutral markers and quantitative traits, but considerably stronger for one of the three quantitative traits than for neutral markers. QST estimates obtained using animals subjected to different rearing conditions (temperature and food treatments) revealed some environmental dependency in patterns of population divergence in quantitative traits, but in general, these effects were weak in comparison to overall patterns. Pairwise comparisons of FST and QST estimates across populations and treatments revealed that the degree of quantitative trait differentiation was not generally predictable from knowledge of that in molecular markers. In fact, both positive and negative correlations were observed depending on conditions where the quantitative genetic variability had been measured. All in all, the results suggest a very high degree of genetic subdivision both in neutral marker genes and genes coding quantitative traits across a relatively recently (< 9000 years) colonized environmental gradient. In particular, they give evidence for natural selection being the primary agent behind the observed latitudinal differentiation in quantitative traits.     

新疆草兔的种群遗传结构和亚种分化

新疆草兔 (Lepus capensis) 的群体遗传结构至今无系统的研究报道,亚种水平的分类也长期存在争议.该文测定了形态分类上的新疆草兔3个亚种共87个个体的线粒体DNA (mtDNA)控制区(control region,D-Loop)592 bp的序列,经分析发现148个多态性位点,共定义了44个单倍型.新疆草兔的单倍型多样度(h,0.977 ± 0.005)和核苷酸多样度(π,0.064 ± 0.031)都较高,显示了较高的遗传多样性.分子变异分析(AMOVA)结果显示,4个地理群体间的显著分化可能是由地理隔离造成的.群体遗传结构分析显示,新疆草兔包含4个进化枝,并且每个进化枝都对应特定的分布区域,显示了明显的系统地理结构.该研究的结果支持形态分类上草兔西域亚种(L.c.lehmanni)的分类地位; 但中亚亚种(L.c.centrasiaticus)被分为两个独立的进化枝,提示可能存在两个亚种; 帕米尔亚种(L.c.pamirensis)与其他亚种间的遗传距离在13%以上,提示其可能已达到种的分化水平.     

Effect of captivity on genetic variance for five traits in the large milkweed bug (Oncopeltus fasciatus)

Understanding the changes in genetic variance which may occur as populations move from nature into captivity has been considered important when populations in captivity are used as models of wild ones. However, the inherent significance of these changes has not previously been appreciated in a conservation context: are the methods aimed at founding captive populations with gene diversity representative of natural populations likely also to capture representative quantitative genetic variation? Here, I investigate changes in heritability and a less traditional measure, evolvability, between nature and captivity for the large milkweed bug, Oncopeltus fasciatus, to address this question. Founders were collected from a 100-km transect across the north-eastern US, and five traits (wing colour, pronotum colour, wing length, early fecundity and later fecundity) were recorded for founders and for their offspring during two generations in captivity. Analyses reveal significant heritable variation for some life history and morphological traits in both environments, with comparable absolute levels of evolvability across all traits (0-30%). Randomization tests show that while changes in heritability and total phenotypic variance were highly variable, additive genetic variance and evolvability remained stable across the environmental transition in the three morphological traits (changing 1-2% or less), while they declined significantly in the two life-history traits (5-8%). Although it is unclear whether the declines were due to selection or gene-by-environment interactions (or both), such declines do not appear inevitable: captive populations with small numbers of founders may contain substantial amounts of the evolvability found in nature, at least for some traits.     

基于线粒体COI基因序列的大豆食心虫中国东北地理种群遗传多样性分析

【目的】大豆食心虫Leguminivora glycinivorella (Matsumura)是一种危害大豆的主要害虫,在中国北方地区危害较重。本研究旨在探讨大豆食心虫在中国东北不同地理种群间的遗传变异。【方法】测定了10个不同地理种群153个个体的线粒体细胞色素氧化酶亚基Ⅰ (mtCOI)基因的657 bp序列,利用DnaSP 5. 0和Arlequin 3. 5. 1. 2等软件对大豆食心虫种群间的遗传多样性、基因流水平和分子变异进行分析。【结果】结果表明：10个地理种群间的COI基因共有36个变异位点和17个单倍型,其中1个单倍型为10个种群所共享。总种群的单倍型多样性指数Hd为0.456,各地理种群单倍型多样度范围在0~0.634之间。总群体的固定系数Fst为0.12545,遗传分化系数Gst为0.06326,总基因流Nm为3.49,且各种群间的基因流均大于1,种群间基因交流的水平较高。【结论】大豆食心虫种群内遗传多样性水平处于中低等水平。总群体和各种群的Tajima’s D检验结果皆不显著,说明中国东北地区大豆食心虫在较近的历史时期内没有出现种群扩张现象。AMOVA分子变异分析结果表明,大豆食心虫的遗传分化主要来自种群内部,而种群间未发生明显的遗传分化。各地理种群的单倍型在系统发育树上和中介网络图上散布在不同的分布群中,缺乏明显的地理分布格局。各种群的遗传距离与地理距离之间没有显著线性相关性,种群间的基因交流并未受到地理距离的影响。     

Conservation units based on mitochondrial and nuclear DNA variation among European bullhead populations (Cottus gobio L., 1758) from Flanders, Belgium

In this study, we aimed to delineateevolutionarily significant units (ESUs) andmanagement units (MUs) for the Europeanbullhead in Flanders (Belgium). Therefore, wedetermined the genetic interrelationshipsbetween 11 bullhead populations, using lengthvariation at 7 polymorphic microsatellite lociand sequence variation in the d-loop of themitochondrial DNA (mtDNA). Despite therelatively small geographical scale of ourstudy, the analysis of the d-loop sequencesshows that the Flemish bullhead populationscontain 3 haplotype groups, which can beassigned to 3 previously described EuropeanmtDNA clades. Because of the importantdifferences between these clades, they may bedefined as evolutionarily significant units,which should be managed separately. Analysis ofmicrosatellite data reveals very high degreesof isolation between populations, with theexception of 3 pairwise comparisons whichinvolved adjacent populations. Our data suggestthat the 3 haplotype groups probably qualify asESUs, as they show phylogeographicdifferentiation for mtDNA variants as well assignificant divergence of allele frequencies atnuclear loci. However, one of these units,limited to a single population, may be ofCentral European origin. All populations of theScheldt basin meet the criteria for MUrecognition, since significantly differentmicrosatellite allele frequencies as well asprivate alleles are found. In contrast, geneticdifferentiation among the 3 populations of theMeuse basin is very low.     

云南4个地区高山姬鼠线粒体控制区种群遗传分化研究

对云南4个种群38个个体的线粒体控制区（D-loop）905 bp的核苷酸序列遗传变异进行分析,探讨了高山姬鼠种群遗传结构和分化。在905 bp D-loop基因的碱基序列中,共发现了57个变异位点（全变异的6.30%）,共定义了23个单倍型,其中有一个单倍型（Hap1）为横断山3个种群（中甸、丽江和剑川）所共享,其余22个单倍型均为各个种群所特有。分子变异分析（AMOVA）表明,种群间的遗传变异占33.7%,种群内的遗传变异占66.3%。FST统计结果表明,除昆明种群和横断山种群之间差异显著（P〈0.05）,其它地理种群间的差异均不显著（P〉0.05）,说明昆明种群与横断山种群之间出现了明显的遗传分化。     

Phylogeographic history of the land snail Candidula unifasciata (Helicellinae,Stylommatophora): fragmentation,corridor migration,and secondary contact

Abstract.— We studied sequence variation in 16S rDNA in 204 individuals from 37 populations of the land snail Candidula unifasciata (Poiret 1801) across the core species range in France, Switzerland, and Germany. Phylogeographic, nested clade, and coalescence analyses were used to elucidate the species evolutionary history. The study revealed the presence of two major evolutionary lineages that evolved in separate refuges in southeast France as result of previous fragmentation during the Pleistocene. Applying a recent extension of the nested clade analysis (Templeton 2001), we inferred that range expansions along river valleys in independent corridors to the north led eventually to a secondary contact zone of the major clades around the Geneva Basin. There is evidence supporting the idea that the formation of the secondary contact zone and the colonization of Germany might be postglacial events. The phylogeographic history inferred for C. unifasciata differs from general biogeographic patterns of postglacial colonization previously identified for other taxa, and it might represent a common model for species with restricted dispersal.     

中国北鳅谱系地理学分析

北鳅(Lefua costata)为冷水性鱼类,分布于淮河以北,分析遗传结构能够反映其适应环境变迁的响应.基于线粒体D-loop区211条序列分析了我国北鳅的谱系地理学和遗传多样性,样本采自9条水系共18个样点.单倍型分析显示共计55个单倍型,呈高单倍型多样性(h=0.9304)和高核苷酸多样性(π=0.0087).单...     

Population genetics of Glossina morsitans submorsitans (Diptera: Glossinidae)

Breeding structure of Glossina morsitans submorsitans Newstead was evaluated by using genetic markers in mitochondrial DNA where diversity was scored at two loci in five natural populations from The Gambia and two populations in Ethiopia (form ugandensis Vanderplank), countries separated by c. 5450 km. Twenty six haplotype combinations were found, of which 17 were shared among two or more populations. Nine haplotypes were found in The Gambia and 23 haplotypes in Ethiopia. There were 12 unique haplotypes. Only six haplotypes were shared between the two countries. Populations in The Gambia (he = 0.26 +/- 0.04) showed less than a third of the diversity of populations in Ethiopia (he = 0.84 +/- 0.03). This suggests recovery from an earlier reduction in population. In a nested analysis of molecular variance of haplotype frequencies, 65% of the variance was due to differences within populations, 34% to differences between populations grouped by country, and only 1% was due to differences among populations within countries. In terms of gene flow, the fixation index FST = 0.35, which leads to an estimate by Wright's island model of less than one reproducing migrant per generation exchanged between the eastern and western submorsitans populations. Nei's genetic similarity measure showed a deep division between Gambian and Ethiopian populations.     

Population diversity of Cistopus indicus inferred from mitochondrial DNA (Cytochrome b) variation from China and Vietnam

ABSTRACT

The octopus Cistopus indicus is an important target of cephalopod fisheries in China. It is widely distributed in the South Pacific and tropical Indian Ocean, from the South China Sea, the Philippines, Malaysia, to Indian and Pakistan seas. We collected specimens from five sites in China and Vietnam (Zhoushan, Wenzhou, Shacheng, Zhanjiang and Mangjie). A fragment of 675bp of cytochrome b (Cytb) was amplified from 95 individuals. A total of 27 haplotypes and 78 variable nucleotide sites was observed. High haplotype diversity and low nucleotide diversity were observed in all populations. The phylogenetic analysis separated these populations into two clades; one was composed of three populations (Zhoushan, Wenzhou and Shacheng), the other of two (Zhanjiang, Mangjie). AMOVA analysis detected that 4.67% of the genetic variation occurred within populations and 95.33% occurred among populations. FST values ranged from 0.014 to 0.993, highlighting the high genetic variation among the populations. Assuming a molecular clock with a rate of 2.15–2.6%/Ma for the Cytb gene, the two clades may have diverged 2.88–3.49 million years ago (Pliocene). Neutral evolution tests and mismatch distribution analysis suggested recent population expansion. The present results revealed valuable information for genetic assessment, management and conservation of this species.     

不同壳色福寿螺形态性状与体质量的关系

【背景】福寿螺因其食性杂、抗逆性和繁殖力强以及自然天敌少等不断扩散,侵害农作物,被列为我国首批外来入侵物种。国内外学者一直致力于研究对其的防治与监控。自然界中福寿螺存在2种壳色——黄色和黑色,壳色受遗传因素和环境因素的双重影响。广东省福寿螺多以黑色为主,福寿螺倾向于与不同壳色的螺交配。壳色在一定程度上影响其交配的选择性,但2种壳色的福寿螺繁殖力指标差异不显著。而关于这2种壳色的螺在形态学上的差异鲜有报道。【方法】利用生物统计软件和分析方法进行相关性分析、通径分析及多元回归分析,计算相关系数、通径系数和决定系数,研究2种壳色福寿螺形态性状与体质量的关系。【结果】2种壳色福寿螺的体质量、层高的变异系数较大,且黄色比黑色变异系数大。对黄色福寿螺体质量影响较大的依次为壳高、口宽;对黑色福寿螺体质量影响较大的依次为口宽、层高。【结论与意义】2种壳色福寿螺在形态性状方面差异显著,可以将壳色作为特征标记,为福寿螺的监测与灾害评估提供参考。     

濒危植物独花兰的形态变异及其适应意义

采用ANOVA和UPGMA等方法对濒危植物独花兰(Changnieniaamoena)分布于庐山、新宁和神农架3个地点的12个自然居群的形态变异进行了研究,探讨其形态多样性水平和地理变异式样及其可能的适应机制。结果表明,庐山居群13个性状的平均观测值均高于新宁和神农架居群。在物种水平上各个性状存在较丰富的变异,变异系数(CV值)为0.02–0.30。尽管同一性状在不同居群中的变异程度较大,但总体而言,花部器官的变异性比营养器官低。单因素方差分析显示3个地区间多个形态性状存在极显著差异(P<0.01);UPGMA聚类分析也表明这3个地区分别形成明显不同的分支。值得注意的是,神农架地区龙门河和关门山两个地点间存在明显的形态分化,而这种形态分化是以传粉者为媒介自然选择的结果。相关性分析显示,营养器官之间、花部器官之间,以及营养器官与花部器官之间均存在较高的相关性。上述结果对进一步了解独花兰的适应机制以及制定科学的保护策略提供了有益的资料。     

Pedigree-free animal models: the relatedness matrix reloaded

Animal models typically require a known genetic pedigree to estimate quantitative genetic parameters. Here we test whether animal models can alternatively be based on estimates of relatedness derived entirely from molecular marker data. Our case study is the morphology of a wild bird population, for which we report estimates of the genetic variance-covariance matrices (G) of six morphological traits using three methods: the traditional animal model; a molecular marker-based approach to estimate heritability based on Ritland's pairwise regression method; and a new approach using a molecular genealogy arranged in a relatedness matrix (R) to replace the pedigree in an animal model. Using the traditional animal model, we found significant genetic variance for all six traits and positive genetic covariance among traits. The pairwise regression method did not return reliable estimates of quantitative genetic parameters in this population, with estimates of genetic variance and covariance typically being very small or negative. In contrast, we found mixed evidence for the use of the pedigree-free animal model. Similar to the pairwise regression method, the pedigree-free approach performed poorly when the full-rank R matrix based on the molecular genealogy was employed. However, performance improved substantially when we reduced the dimensionality of the R matrix in order to maximize the signal to noise ratio. Using reduced-rank R matrices generated estimates of genetic variance that were much closer to those from the traditional model. Nevertheless, this method was less reliable at estimating covariances, which were often estimated to be negative. Taken together, these results suggest that pedigree-free animal models can recover quantitative genetic information, although the signal remains relatively weak. It remains to be determined whether this problem can be overcome by the use of a more powerful battery of molecular markers and improved methods for reconstructing genealogies.