Genetic and morphological studies of Nothobranchius (Cyprinodontiformes) from Malawi with description of Nothobranchius wattersi sp. nov.

Molecular and morphological data were used to explore evolutionary differentiation among populations of Nothobranchius in the Lake Malawi–upper Shire River and the Lakes Chilwa–Chiuta drainage systems in Malawi. The aim of the study was to test the hypothesis that Nothobranchius of the Malawi–Shire system constitute a separate evolutionary group from Nothobranchius kirki. Mitochondrial and nuclear sequence data show a strongly supported phylogenetic split into two monophyletic groups separating the Lake Malawi basin fish from N. kirki. Unlike N. kirki, Lake Malawi–Shire fish do not deviate from neutrality and express an excess of rare haplotypes and mutations in terminal branches, characteristic of recently expanded populations. Further, the two groups significantly differ in morphology. Two body characters (dorsal‐fin base length and pre‐pelvic–pre‐anal distance) are significantly different between the two species in both sexes. Several other characters are significantly different in either male or female comparisons with respect to both standard and head lengths, and robust morphological differentiation is detected by multivariate analysis. The two groups are readily distinguished on the basis of male colouration, especially in scale centres and the caudal fin. On the basis of this differentiation at the molecular and morphological levels, in addition to colouration, the Lake Malawi–Shire fish are hereby formally recognized as constituting a new species, Nothobranchius wattersi. This distinction is in agreement with the geomorphologic and recent climatic history in the region.     

Estimating divergence times from DNA sequences

The patterns of genetic variation within and among individuals and populations can be used to make inferences about the evolutionary forces that generated those patterns. Numerous population genetic approaches have been developed in order to infer evolutionary history. Here, we present the “Two-Two (TT)” and the “Two-Two-outgroup (TTo)” methods; two closely related approaches for estimating divergence time based in coalescent theory. They rely on sequence data from two haploid genomes (or a single diploid individual) from each of two populations. Under a simple population-divergence model, we derive the probabilities of the possible sample configurations. These probabilities form a set of equations that can be solved to obtain estimates of the model parameters, including population split times, directly from the sequence data. This transparent and computationally efficient approach to infer population divergence time makes it possible to estimate time scaled in generations (assuming a mutation rate), and not as a compound parameter of genetic drift. Using simulations under a range of demographic scenarios, we show that the method is relatively robust to migration and that the TTo method can alleviate biases that can appear from drastic ancestral population size changes. We illustrate the utility of the approaches with some examples, including estimating split times for pairs of human populations as well as providing further evidence for the complex relationship among Neandertals and Denisovans and their ancestors.     

Parallels,nonparallels, and plasticity in population differentiation of threespine stickleback within a lake

The frequent occurrence of parallel phenotypic divergence in similar habitats is often evoked when emphasizing the role of ecology in adaptive radiation and speciation. However, because phenotypic plasticity can contribute to the observed pattern of divergence, confirmation of divergence at loci underlying phenotypic traits is important for confirming adaptive divergence. In the present study, we examine parallel morphological, neutral, and potentially adaptive genetic divergence of threespine stickleback inhabiting different habitats within a lake. Three genetic clusters best explained the neutral genetic structure within the lake; however, morphological differences were only weakly connected to genetic clusters and there was considerable phenotypic variation within clusters. Among the factors that could contribute to the observed pattern of morphological and genetic divergence are phenotypic plasticity, selective mortality of hybrids, and habitat choice based on morphology. Several loci are identified as outliers indicating divergent selection between the morphs and some parallels in morphological and adaptive genetic divergence are found in stickleback spawning at two lava sites. However, neutral genetic structure indicates considerable genetic connectivity among the two lava sites, and the parallels in morphology may therefore represent selective distribution of phenotypes rather than parallel divergence. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98 , 803–813.     

寻找水稻DNA编码与非编码区边界方法的比较研究

在分析DNA序列复杂度、预测基因编码区和非编码的DNA边界识别等问题中,以熵为基础构造的离散量度量提供了一种强有力的工具。为改进寻找水稻基因编码与非编码区边界的效率,本文提出了两个新的离散量度量（α-KL离散量与α-Jensen-Shannon 离散量）,根据密码子的GC含量对氨基酸对应密码子构建了粗粒化向量。 比较了融合Jensen-Shannon 离散量、Jensen-Renyi 离散量、α-KL离散量和α-Jensen-Shannon 离散量等不同向量所获得的精度,结果表明,在对水稻基因编码区‘终止子’的识别效率上,构建的密码子粗粒化向量融合新引进的度量方法比Bernaola等人的方法(2000)提高了4~5倍。     

Spatial phenotypic and genetic structure of threespine stickleback (Gasterosteus aculeatus) in a heterogeneous natural system,Lake Mývatn,Iceland

Eco‐evolutionary responses of natural populations to spatial environmental variation strongly depend on the relative strength of environmental differences/natural selection and dispersal/gene flow. In absence of geographic barriers, as often is the case in lake ecosystems, gene flow is expected to constrain adaptive divergence between environments – favoring phenotypic plasticity or high trait variability. However, if divergent natural selection is sufficiently strong, adaptive divergence can occur in face of gene flow. The extent of divergence is most often studied between two contrasting environments, whereas potential for multimodal divergence is little explored. We investigated phenotypic (body size, defensive structures, and feeding morphology) and genetic (microsatellites) structure in threespine stickleback (Gasterosteus aculeatus) across five habitat types and two basins (North and South) within the geologically young and highly heterogeneous Lake Mývatn, North East Iceland. We found that (1) North basin stickleback were, on average, larger and had relatively longer spines than South basin stickleback, whereas (2) feeding morphology (gill raker number and gill raker gap width) differed among three of five habitat types, and (3) there was only subtle genetic differentiation across the lake. Overall, our results indicate predator and prey mediated phenotypic divergence across multiple habitats in the lake, in face of gene flow.     

Contrasting patterns of morphological and neutral genetic divergence among geographically proximate populations of sockeye salmon Oncorhynchus nerka in Lake Aleknagik,Alaska

Levels of differentiation in morphological traits (age at maturity, body length at age, egg mass and body depth) and spawning time were examined in sockeye salmon Oncorhynchus nerka from three geographically proximate but physically distinct creeks in Lake Aleknagik, Alaska. Happy Creek fish had significantly greater values for most measured morphological traits, and Eagle Creek fish spawned significantly later than fish in the other creeks. Phenotypic differentiation between creeks, measured as P_ST, was then compared with microsatellite marker differentiation between creeks, measured as F_ST. No correlations were apparent between P_ST and F_ST values, and P_ST values were generally significantly larger than zero (P_ST= 0·0018–0·31) whereas F_ST values were not (F_ST=?0·0004 to 0·0016). The insignificant pair‐wise F_ST values between creek samples indicated that gene flow occurs between creeks, assuming the creek populations have reached migration–drift equilibrium. However, the strong homing behaviour of sockeye salmon precludes a scenario in which fish from the three creeks constitute a single population that segregates by body size. Rather, significant phenotypic differentiation suggests that strong divergent selection occurs on the phenotypic traits despite the homogenizing effects of gene flow.     

Environmental factors associated with genetic and phenotypic divergence among sympatric populations of Arctic charr (Salvelinus alpinus)

The mechanisms by which phenotypic and genetic divergence may occur among sympatric, conspecific populations have been widely discussed but are still not well understood. Possible mechanisms include assortative mating based on morphology or variation in the reproductive behaviour of phenotypes, and both have been suggested to be relevant to the differentiation of salmonid populations in post-glacial lakes. Here, we studied Arctic charr (Salvelinus alpinus) in Windermere, where putative populations are defined by spatial and temporal variation in spawning. Genetic differentiation was assessed based on nine microsatellite loci, and phenotypic variation was assessed from morphometric characters. We test hypotheses about the relative role of morphology, spawning season and spawning habitat in the evolution of genetic divergence among these populations. Distinct from other lake systems, we find that both morphological and genetic differentiation are restricted primarily to one of two interconnecting basins, that genetic and morphological differentiation are decoupled in this lake and that both phenotype and environment have changed over the last 20 years. The implication is that breeding habitat plays a primary role in isolating populations that differentiate by drift and that phenotypically plastic changes, potentially related to foraging specializations, have either become secondarily decoupled from the genetically defined populations or were never fundamental in driving the evolution of genetic diversity in the Windermere system.     

Sex‐biased transcriptome divergence along a latitudinal gradient

Sex‐dependent gene expression is likely an important genomic mechanism that allows sex‐specific adaptation to environmental changes. Among Drosophila species, sex‐biased genes display remarkably consistent evolutionary patterns; male‐biased genes evolve faster than unbiased genes in both coding sequence and expression level, suggesting sex differences in selection through time. However, comparatively little is known of the evolutionary process shaping sex‐biased expression within species. Latitudinal clines offer an opportunity to examine how changes in key ecological parameters also influence sex‐specific selection and the evolution of sex‐biased gene expression. We assayed male and female gene expression in Drosophila serrata along a latitudinal gradient in eastern Australia spanning most of its endemic distribution. Analysis of 11 631 genes across eight populations revealed strong sex differences in the frequency, mode and strength of divergence. Divergence was far stronger in males than females and while latitudinal clines were evident in both sexes, male divergence was often population specific, suggesting responses to localized selection pressures that do not covary predictably with latitude. While divergence was enriched for male‐biased genes, there was no overrepresentation of X‐linked genes in males. By contrast, X‐linked divergence was elevated in females, especially for female‐biased genes. Many genes that diverged in D. serrata have homologs also showing latitudinal divergence in Drosophila simulans and Drosophila melanogaster on other continents, likely indicating parallel adaptation in these distantly related species. Our results suggest that sex differences in selection play an important role in shaping the evolution of gene expression over macro‐ and micro‐ecological spatial scales.     

Correlated asymmetry of sequence and functional divergence between duplicate proteins of Saccharomyces cerevisiae

The role of sequence divergence in functional divergence of duplicate genes is a topic of great interest. In this study, we compare the numbers of amino acid substitutions in each sequence since two yeast duplicates diverged, using a preduplication ancestral outgroup. Using this strategy, we explored the relationship between sequence divergence and functional divergence between duplicate partners. We show that the degree of relative functional asymmetry between duplicate proteins is proportional to the relative sequence divergence between them. Furthermore, of the two duplicates, the copy closer to their ancestral sequence (fewer number of amino acid substitutions) interacts with more proteins and affects fitness more severely when deleted. Therefore, asymmetric sequence divergence between duplicates is correlated with asymmetric functional divergence and may underlie the duplicate's role in genetic robustness against mutations. Among the functional traits considered, protein abundance appears to have the strongest correlation with the nonsynonymous divergence between duplicates. Taken together with the results from whole-genome analyses, our results indicate that within-species duplicates are subject to the same evolutionary force that acts on interspecific sequence and functional divergence. In particular, we detect signs of purifying selection on the more slowly evolving duplicate.     

GENETIC AND MORPHOLOGICAL DIVERGENCE AMONG MORPHOTYPES OF THE ISOPOD EXCIROLANA ON THE TWO SIDES OF THE ISTHMUS OF PANAMA

Excirolana braziliensis is a dioecious marine isopod that lives in the high intertidal zone of sandy beaches on both sides of Central and South America. It possesses no larval stage and has only limited means of adult dispersal. Indirect estimates of gene flow have indicated that populations from each beach exchange less than one propagule per generation. Multivariate morphometrics have discovered three morphs of this species in Panama, two of them closely related and found on opposite sides of Central America (“C morph” in the Caribbean and “C′ morph” in the eastern Pacific), the third found predominantly in the eastern Pacific (“P morph”). Though the P and C′ morphs are seldom found on the same beach, they have overlapping latitudinal ranges in the eastern Pacific. A related species, Excirolana chamensis, has been described from the Pacific coast of Panama. Each beach contains populations that remain morphologically and genetically stable, but a single drastic change in both isozymes and morphology has been documented. We studied isozymes and multivariate morphology of 10 populations of E. braziliensis and of one population of E. chamensis. Our objective was to assess the degree of genetic and morphological variation, the correlation of divergence on these two levels of integration, the phylogenetic relationships between morphs, and the possible contributions of low vagility, low gene flow, and occasional extinction and recolonization to the genetic structuring of populations. Genetic distance between the P morph, on one hand, and the other two morphotypes of E. braziliensis, on the other, was as high as the distance between E. braziliensis and E. chamensis. Several lines of evidence agree that E. chamensis and the P morph had diverged from other morphs of E. braziliensis before the rise of the Panama Isthmus separated the C and C′ forms, and that the P morph constitutes a different species. A high degree of genetic differentiation also exists between populations of the same morph. On the isozyme level, every population can be differentiated from every other on the basis of at least one diagnostically different locus, regardless of geographical distance or morphological affiliation. Morphological and genetic distances between populations are highly correlated. However, despite the high degree of local variation, evolution of E. braziliensis as a whole has not been particularly rapid; divergence between the C and C′ morphs isolated for 3 million yr by the Isthmus of Panama is not high by the standard of within-morph differentiation or by comparison with other organisms similarly separated. Alleles that are common in one population may be absent from another of the same morph, yet they appear in a different morph in a separate ocean. The high degree of local differentiation, the exclusive occupation of a beach by one genotype with rare arrival of foreign individuals that cannot interbreed freely with the residents, the genetic stability of populations with infrequent complete replacement by another genetic population, and the sharing by morphs of polymorphisms that are not shared by local populations, all suggest a mode of evolution concentrated in rare episodes of extinction and recolonization, possibly coupled with exceptional events of gene flow that help preserve ancestral variability in both oceans.     

Reproductive isolation of sympatric morphs in a population of Darwin's finches

Recent research on speciation has identified a central role for ecological divergence, which can initiate speciation when (i) subsets of a species or population evolve to specialize on different ecological resources and (ii) the resulting phenotypic modes become reproductively isolated. Empirical evidence for these two processes working in conjunction, particularly during the early stages of divergence, has been limited. We recently described a population of the medium ground finch, Geospiza fortis, that features large and small beak morphs with relatively few intermediates. As in other Darwin's finches of the Galápagos Islands, these morphs presumably diverged in response to variation in local food availability and inter- or intraspecific competition. We here demonstrate that the two morphs show strong positive assortative pairing, a pattern that holds over three breeding seasons and during both dry and wet conditions. We also document restrictions on gene flow between the morphs, as revealed by genetic variation at 10 microsatellite loci. Our results provide strong support for the central role of ecology during the early stages of adaptive radiation.     

The devil's in the details: genetic and phenotypic divergence between artificial and native populations of the endangered pupfish (Cyprinodon diabolis)

Propagation of threatened or endangered species in artificial habitats is a common strategy for reducing the probability of extinction by demographic or stochastic forces. Differential selection, founder effects and genetic drift can conspire to cause artificial populations to differ irreversibly from native populations for characters important for fitness, thereby compromising conservation efforts. Here we show that artificial propagation of the endangered Devil's Hole pupfish Cyprinodon diabolis resulted in rapid divergence for phenotypic and genetic characteristics despite attempts to replicate key characteristics of the species' native habitat when designing the artificial environments. Although differences in behavior and morphology between the native pool population and the two artificial pools may reflect phenotypic plasticity, the results underscore the need to monitor and control (to the extent possible) closely the evolutionary process when propagating native species in artificial pools for multiple generations.     

Divergence of mate recognition systems among conspecific populations of the plethodontid salamander Desmognathus santeetlah (Amphibia: Plethodontidae)

The disjunct geographic distribution of plethodontid salamanders of the genus Desmognathus provides excellent opportunities to test whether populations diverge in mate recognition systems so as to result in sexual incompatibility. Previous work has shown that sexual incompatibility may exist both among conspecific populations and between different species in this genus. Populations of the Santeetlah dusky salamander, Desmognathus santeetlah , are found at higher elevations in three mountain ranges in the southern Appalachian Mountains of eastern North America, where they are sympatric with congeneric species of similar body size. We report that statistically significant levels of sexual incompatibility exist among populations of D. santeetlah collected from across the species' range. Contrary to popular belief, but in accord with a growing body of empirical literature, aspects of mate recognition systems can diverge among conspecific populations of salamanders, resulting in incidental sexual incompatibility.     

A Collection of Amino Acid Replacement Matrices Derived from Clusters of Orthologs

Sequence divergence among orthologous proteins was characterized with 34 amino acid replacement matrices, sequence context analysis, and a phylogenetic tree. The model was trained on very large datasets of aligned protein sequences drawn from 15 organisms including protists, plants, Dictyostelium, fungi, and animals. Comparative tests with models currently used in phylogeny, i.e., with JTT+Γ±F and WAG+Γ±F, made on a test dataset of 380 multiple alignments containing protein sequences from all five of the major taxonomic groups mentioned, indicate that our model should be preferred over the JTT+Γ±F and WAG+Γ±F models on datasets similar to the test dataset. The strong performance of our model of orthologous protein sequence divergence can be attributed to its ability to better approximate amino acid equilibrium frequencies to compositions found in alignment columns. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editor : Dr. Martin Kreitman]     

Habitat-dependent song divergence at subspecies level in the grey-breasted wood-wren

Song divergence among populations can theoretically lead to reproductive divergence and speciation. Despite many studies, this theory is still controversial. Habitat differences have been shown to shape songs, but few studies have looked for a link between ecologically driven acoustic and genetic divergence. We tested whether environmental selection has driven song divergence in two genetically distinct, but hybridizing, subspecies of the grey-breasted wood-wren (Henicorhina leucophrys) in Ecuador. Several acoustic features showed significant divergence between the subspecies. Spectral song divergence correlated with ambient noise profiles which differed significantly between the habitats of both subspecies. Temporal song divergence also corresponded as expected to vegetation density. However, in terms of quantified levels of reverberations, we found no significant differences in habitat-dependent sound transmission properties. We conclude that ecological niche segregation may explain acoustic divergence among the two wren subspecies. The resulting habitat-dependent song divergence may have contributed to reproductive divergence by guiding assortative mating in parapatric conditions or just currently contribute to maintenance of reproductive isolation upon secondary contact.     

The Isthmus of Panama: a major physical barrier to gene flow in a highly mobile pantropical seabird

To further test the hypothesis that the Isthmus of Panama is a major barrier to gene flow in pantropical seabirds, we applied phylogeographic methods to mitochondrial control sequence variation in masked booby (Sula dactylatra) populations on either side of the Isthmus of Panama and the southern tip of Africa. In accord with Steeves et al. (2003), we found that all Caribbean masked boobies with the 'secondary contact' cytochrome b haplotype (m-B) shared a control region haplotype (Sd_100), which grouped with Indian-Pacific haplotypes and not Caribbean-Atlantic haplotypes. In addition, Sd_100 was more closely related to control region haplotypes in the Indian Ocean than in the Pacific. We also found that the 'secondary contact' birds diverged more recently from extant populations in the Indian Ocean than in the Pacific. Thus, it appears that these masked boobies did not breach the Isthmus of Panama. Rather, birds likely dispersed around the southern tip of Africa during favourable oceanographic conditions in the Pleistocene.     

小熊猫种内遗传及亚种分化研究(食肉目:浣熊科)

到目前为止,多数学者认为小熊猫种内已分指名亚种A.f.fulgens和川西亚种A.f.styani。然而,由于其个体毛色变异较大,一些学者对其亚种分化问题提出质疑。本文采用DNA指纹方法,对小熊猫的种内遗传和亚种分化进行了研究。结果表明,川西亚种所有个体在分子量约为8.4kb处均有一条指名亚种不具有的共有谱带,指名亚种所有个体则在分子量约为1.8kb处具有另外一条川西亚种不具有的共有谱带,且这两条谱带可通过双亲遗传给子代,说明此共有谱带可分别作为区分小熊猫川西亚种和指名亚种的特征带。另外,种内的遗传分化研究表明,川西亚种基因组的多态性强于指名亚种,且川西亚种内各个体之间的遗传变异高于指各亚种,说明小熊猫种内已形成遗传分化。因此,笔者认为以上研究结果为基因水平上进一步证明小熊猫种内已产生遗传分化,并形成两独立亚种,目前的亚种地位成立。     

Divergent selection as revealed by P(ST) and QTL-based F(ST) in three-spined stickleback (Gasterosteus aculeatus) populations along a coastal-inland gradient

Three measures of divergence, estimated at nine putatively neutral microsatellite markers, 14 quantitative traits, and seven quantitative trait loci (QTL) were compared in eight populations of the three-spined stickleback (Gasterosteus aculeatus L.) living in the Scheldt river basin (Belgium). Lowland estuarine and polder populations were polymorphic for the number of lateral plates, whereas upland freshwater populations were low-plated. The number of short gill rakers and the length of dorsal and pelvic spines gradually declined along a coastal-inland gradient. Plate number, short gill rakers and spine length showed moderate to strong signals of divergent selection between lowland and upland populations in comparison between P(ST) (a phenotypic alternative for Q(ST)) and neutral F(ST). However, such comparisons rely on the unrealistic assumption that phenotypic variance equals additive genetic variance, and that nonadditive genetic effects and environmental effects can be minimized. In order to verify this assumption and to confirm the phenotypic signals of divergence, we tested for divergent selection at the underlying QTL. For plate number, strong genetic evidence for divergent selection between lowland and upland populations was obtained based on an intron marker of the Eda gene, of which the genotype was highly congruent with plate morph. Genetic evidence for divergent selection on short gill rakers was limited to some population pairs where F(ST) at only one of two QTL was detected as an outlier, although F(ST) at both loci correlated significantly with P(ST). No genetic confirmation was obtained for divergent selection on dorsal spine length, as no outlier F(ST)s were detected at dorsal spine QTL, and no significant correlations with P(ST) were observed.     

Species richness in plant genera disjunct between temperate eastern Asia and North America

The species richness of 109 amphi-Pacific disjunct genera was examined in eastern Asia and North America. Although the entire flora of eastern Asia contains approximately one-third more species than that of North America, the difference in species richness among disjunct taxa is less. When woody and herbaceous genera are considered separately, the former exhibit a strong diversity bias favouring eastern Asia whereas there is no significant difference in diversity between continents among herbaceous genera. This result is not due to habitat differences between woody and herbaceous genera, because the disjunct herbs inhabit primarily moist forests and woodlands. This result is also not related to relative phylogenetic advancement, even though older major lineages of plants tend to have a predominance of woody taxa. Woody genera are distributed in lower latitudes than herbaceous genera on both continents, and both woody and herbaceous genera are distributed in lower latitudes in eastern Asia than in North America. The North American temperate flora is primarily a relict of a flora form 7 more widespread throughout the Northern Hemisphere. Contemporary patterns of diversity suggest that the effects of climate changes in the late Tertiary were less severe in eastern Asia and promoted diversification, but were more severe in North America and may have caused widespread extinction. The difference in the effect of climate change on diversity in herbaceous and woody lineages reflects the different ecological relationships of species having these contrasting life forms. Clearly, the contemporary floras of eastern Asia and North America bear the imprint of history and emphasize the important interface between ecological relationships and evolutionary responses.     

Non-equilibrium gene frequency divergence: persistent founder effects in natural populations

The estimation of gene flow using gene frequency divergence information has become increasingly popular because of the difficulty involved in the direct determination of gene flow among populations. The present study examined allozyme gene frequencies in populations of eighteen aquatic invertebrate taxa at two sites in northern Canada. Gene frequencies at polymorpic loci were significantly different among 8–31 localized populations of all species at Igloolik and among 10–36 populations at Churchill confirming the generality of gene pool fragmentation in pond-dwelling organisms. Measures of gene flow estimated from gene frequency divergence, which assume that gene frequency distributions are at equilibrium, were inconsistent with the probable dispersal capacities of taxa. This provoked an examination of historical events as alternative explanations. Both theory and computer simulations demonstrated that when populations grow rapidly in size after founding from few individuals, the gene frequency divergence established during colonization is resistant to decay by gene exchange. Our work suggests that gene frequency distributions are often not in equilibrium and that caution should be employed in attempts to infer gene flow from them in natural populations.