Genetic divergence between cave and surface populations of Astyanax in Mexico (Characidae,Teleostei)

A study of genetic diversity at microsatellite loci and the mitochondrial DNA (mtDNA) cytochrome b gene was carried out to assess genetic relationships among four Mexican cave (Pachon, Sabinos, Tinaja, Chica) and four surface populations of Astyanax fasciatus (Characidae) from northeast Mexico and the Yucatan. With the exception of Chica, the cave populations were all characterized by extremely low microsatellite variability, which most likely resulted from bottleneck events. Population analyses of the microsatellite data indicated no measurable levels of gene flow between all cave and surface populations (F(ST) > 0.0707). Phylogenetic analyses of mtDNA data showed that only two cave populations - Sabinos and Tinaja - group together to the exclusion of surface populations. From the microsatellite data these cave populations cluster with the Pachon cave fish population. The mtDNA thus appears to have been replaced in Pachon because of introgressive hybridization. It is likely that these three cave populations have descended from a surface ancestor in common with current surface populations, rather than evolving recently from one of the extant surface populations. Like Pachon, the Chica population clustered with the surface populations according to mtDNA data, but was not clearly associated with either the surface or the other cave populations according to the microsatellite data. Our data indicate that the Chica population evolved recently from a surface population, and subsequently hybridized with a phylogenetically older cave population. In conclusion, both the microsatellite and mtDNA data suggest multiple origins of cave populations and the Chica and Sabinos/Tinaja/Pachon were founded after at least two independent invasions from surface populations.     

Divergence in trophic ecology characterizes colonization of extreme habitats

Extreme habitats are characterized by the presence of physio‐chemical stressors, but also differ in aspects of the biotic environment, such as resource availability or the presence of competitors. The present study quantifies variation in trophic ecology of a small livebearing fish (Poecilia mexicana, Poeciliidae) across four different habitats that included nonsulphidic and sulphidic surface waters, as well as a nonsulphidic and a sulphidic cave. Resource use in different habitat types was investigated using gut content analysis. Populations diverged in resource use from a diet dominated by algae and detritus in nonsulfidic surface habitats to a diet including invertebrate food items in the other habitats. Poecilia mexicana in cave habitats further exhibited a higher dietary niche width than conspecifics from surface habitats. The condition of P. mexicana was analysed using storage lipid extractions. Fish from sulphidic and cave habitats exhibited a very poor condition, suggesting resource limitation and/or high costs of coping with extreme conditions. Finally, divergence in resource use was correlated with variation in viscerocranial morphology. A common garden experiment indicated both a genetic and plastic basis to the morphological variation observed among field populations. It is suggested that the morphological diversification is an adaptation to the differential use of resources among populations. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 517–528.     

Standing genetic variation as a potential mechanism of novel cave phenotype evolution in the freshwater isopod,Asellus aquaticus

Novel phenotypes can come about through a variety of mechanisms including standing genetic variation from a founding population. Cave animals are an excellent system in which to study the evolution of novel phenotypes such as loss of pigmentation and eyes. Asellus aquaticus is a freshwater isopod crustacean found in Europe and has both a surface and a cave ecomorph which vary in multiple phenotypic traits. An orange eye phenotype was previously revealed by F₂ crosses and backcrosses to the cave parent within two examined Slovenian cave populations. Complete loss of pigmentation, both in eye and body, is epistatic to the orange eye phenotype and therefore the orange eye phenotype is hidden within the cave populations. Our goal was to investigate the origin of the orange eye alleles within the Slovenian cave populations by examining A. aquaticus individuals from Slovenian and Romanian surface populations and Asellus aquaticus infernus individuals from a Romanian cave population. We found orange eye individuals present in lab raised surface populations of A. aquaticus from both Slovenia and Romania. Using a mapping approach with crosses between individuals of two surface populations, we found that the region known to be responsible for the orange eye phenotype within the two previously examined Slovenian cave populations was also responsible within both the Slovenian and the Romanian surface populations. Complementation crosses between orange eye Slovenian and orange eye Romanian surface individuals suggest that the same gene is responsible for the orange eye phenotype in both surface populations. Additionally, we observed a low frequency phenotype of eye loss in crosses generated between the two surface populations and also in the Romanian surface population. Finally, in a cave population from Romania, A. aquaticus infernus, we found that the same region is also responsible for the orange eye phenotype as the Slovenian cave populations and the Slovenian and Romanian surface populations. Therefore, we present evidence that variation present in the cave populations could originate from standing variation present in the surface populations and/or transgressive hybridization of different surface phylogenetic lineages rather than de novo mutations.     

Molecular genetics of peripheral populations of Nova Scotian Unionidae (Mollusca: Bivalvia)

Peripheral populations of eight species of freshwater bivalves (Unionidae.) extending their geographic ranges into Nova Scotia, Canada, were examined electrophoretically to determine both the extent of genetic variability within such populations, and whether the hypothesized pathway of colonization across the Isthmus of Chignecto is reflected in patterns of genetic resemblance among these populations. The Nova Scotian species examined could be separated into two groups based on levels of observed heterozygosity and levels of variability in allele frequencies. The first group is characterized by low levels of heterozygosity and polymorphism compared with north-eastern American populations, and in the case of one species, Elliptio complanala, considerable variability in allele frequencies among populations occurring in similar habitats in different drainages. Populations of E. complanata from Nova Scotia can be differentiated from conspecific populations on the southern Atlantic Slope by possession of fast alleles at two loci. Multivariate analyses define subgroups within populations of E. complanata consistent with hypothesis that the species invaded Nova Scotia by way of the Isthmus of Chignecto, and then split into two groups, one of which colonized Cape Breton to the north and the other of which colonized southern areas of the Province. The second group of Nova Scotian species is characterized by little reduction in heterozygosity and polymorphism compared with values observed among north-eastern American conspecifics or congeners, little variability in allele frequencies from population to population, and little evidence to suggest that these species were dependent on the land bridge to invade the Province. The type of dispersal is hypothesized to be responsible, in part, for these differences: larvae of species in the first group rely on a parasitic attachment to fish with territorial habits limited to fresh water, and are thus likely to invade new drainages separated by salt water by chance, in small numbers, and in stepping-stone fashion. Species in the second group parasitize anadromous or saltwater tolerant hosts, are likely to be introduced into new habitats in greater numbers and/or receive greater amounts of gene flow subsequent to colonization, and seem less dependent on land-bridges to colonize new habitats.     

Random Amplified Polymorphic DNA Diversity among Surface and Subterranean Populations of Asellus aquaticus (Crustacea: Isopoda)

The ecological and evolutionary processes leading to isolation and adaptation of cave animals compared to their surface ancestors are not yet unequivocally understood. In this study the genetic relations of four cave and three surface population of the freshwater crustacean Asellus aquaticus in the Karst region of SW Slovenia and NE Italy were assessed using RAPDs as genetic markers. The results suggest that specialized populations from two caves invaded their subterranean habitat independently, and that their morphological similarity is a result of convergent evolution. Another, less specialized cave population seems to originate from a later colonization of a cave system already inhabited by a more specialized population, but the two populations do not interbreed. This series of temporally and spatially independent invasions has generated a diversity hotspot of non-interbreeding populations of a ubiquitous freshwatercrustacean, which is uniform over most of its range. Genetic variability estimated by the percentage of polymorphic RAPD fragments was similar (86–91%) in most cave and surface populations. Substantially lower values (as low as 49%) were found in two cave populations affected by heavy pollution. Two a priori groupings of populations, traditional subspecies and hydrologically connected groups, were rejected as not significant by means of nested analysis of molecular variance (AMOVA). On the other hand, groupings revealed by UPGMA clustering displayed a significant component of among-group variance. An analysis of gene flow between populations using estimated migration rates confirmed these findings.     

Genetic diversity in populations of a freshwater ciliate

RAPD fingerprinting with nine different primers revealed that all of 18 E. aediculatus isolates from nine ponds and streams in western Germany, France and the U.S.A. were genetically different. The extent of genetic similarity between genotypes from different waters did not show a significant relationship with the geographical distance among habitats, although genotypes isolated from the same habitat showed a higher genetic similarity than genotypes isolated from different habitats. Phylogenetic analyses of RAPD patterns indicate a separation of E. aediculatus strains into subgroups within one species, but all strains were genetically more similar to one another than to strains from two other Euplotes species. Crossings of the different E. aediculatus strains revealed they belonged to seven mating types of one gene pool. The high genetic diversity observed is explained by a frequent occurrence of conjugation in the studied populations.     

Phenotypic plasticity in the greater mouse-eared bat in extremely different roost conditions

Bats use various roost types with a wide spectrum of ecological features. The greater mouse-eared bat Myotis myotis (Borkhausen, 1797), creates nurseries in attics and caves in Central Europe. The stable low temperature and high humidity cave microclimate contrasts that of attics, which may alter species adaptations and life strategies. We analysed population characteristics (composition, body condition, parasite load, and immune response) and genetic relatedness of two proximal M. myotis populations. Age, sexual and parasite species composition were similar between the cave and attic sites. However, a significantly higher parasite load and body condition was detected in the post-partum females and juveniles of the cave colony (n = 263 bats from the cave, 231 from the attic), with the cave colony females having a significantly stronger immune response (n = 2 caves and 2 attics, 20 females per site). There was no evidence for genetic divergence between cave and attic populations (n = 3 caves and 3 attics, 24 females per site), indicating that different population characteristics are not genetically based and that M. myotis is an example of a species with rather unique phenotypic plasticity.     

PLEIOTROPY CAUSES LONG-TERM GENETIC CONSTRAINTS ON LIFE-HISTORY EVOLUTION IN BRASSICA RAPA

Fundamental, long-term genetic trade-offs constrain life-history evolution in wild crucifer populations. I studied patterns of genetic constraint in Brassica rapa by estimating genetic correlations among life-history components by quantitative genetic analyses among ten wild populations, and within four populations. Genetic correlations between age and size at first reproduction were always greater than +0.8 within and among all populations studied. Although quantitative genetics might provide insight about genetic constraints if genetic parameters remain approximately constant, little evidence has been available to determine the constancy of genetic correlations. I found strong and consistent estimates of genetic correlations between life-history components, which were very similar within four natural populations. Population differentiation also showed these same trade-offs, resulting from long-term genetic constraint. For some traits, evolutionary changes among populations were incompatible with a model of genetic drift. Historical patterns of natural selection were inferred from population differentiation, suggesting that correlated response to selection has caused some traits to evolve opposite to the direct forces of natural selection. Comparison with Arabidopsis suggests that these life-history trade-offs are caused by genes that regulate patterns of resource allocation to different components of fitness. Ecological and energetic models may correctly predict these trade-offs because there is little additive genetic variation for rates of resource acquisition, but resource allocation is genetically variable.     

Diverging Cave- and River-Dwelling Newts Exert the Same Mate Preference in their Native Light Conditions

When colonizing a new habitat, populations must adapt their sexual behaviour to new ecological constraints. Because caves display drastically different conditions from surface habitats and cave animals are deprived from visual information, hypogean populations are expected to have modified their mate preference and signalling behaviour after cave colonization. Here, we experimentally examined the female preference and the sexual behaviour of brook newts Calotriton asper from different cave and river populations, either in light or in darkness. Our results suggest that females prefer large individuals in both hypogean and epigean populations, but that this preference is only expressed in the light conditions of their native habitat. Hence, some mate choice criteria would be maintained across genetically divergent populations and throughout dissimilar habitats. However, this sexual behaviour is likely to be expressed via a different sensory pathway in the different habitats, suggesting that a sensory shift has occurred in cave populations, enabling animals to communicate through a non-visual channel.     

Molecular data indicate multiple independent colonizations of former lignite mining areas in Eastern Germany by <Emphasis Type="Italic">Epipactis palustris</Emphasis> (Orchidaceae)

Former lignite mining areas in Eastern Germany are valuable secondary habitats for many plant and animal species endangered in the natural landscape. Here, we present a study on genetic structure and diversity of 16 populations of the threatened orchid Epipactis palustris (Orchidaceae) from five mining pits and 11 natural habitats, which we carried out in order to ascertain how many times this species immigrated into former lignite mining areas, and where the source populations are located. We used two different anonymous genetic marker methods, random amplified polymorphic DNA (RAPD) and microRNA-primed genomic fingerprinting (miRPF) to analyze patterns of genetic variation. Results of a multivariate analysis based on asymmetric Soerensen similarity, principal coordinate analysis and a neighbor-joining cluster analysis indicate high within population-variability and a moderate genetic differentiation among E. palustris populations. We found no differences between genetic diversity values of populations from former mining areas and those of natural habitats. Thus, we could not find evidences for genetic bottlenecks in the mining populations due to founder events. Source populations are predominantly close surrounding populations as geographic distance and genetic dissimilarity were correlated. However, exchanges may reach beyond 125 km and repeated independent colonization events are highly likely.     

不同干扰生境下河口莲座蕨遗传多样性分析

该研究利用 ISSR 分子标记,对不同生境下的6个河口莲座蕨种群进行遗传多样性分析。结果表明：从44条ISSR引物中筛选出8条能够扩增出清晰、稳定条带的引物,对6个河口莲座蕨种群进行基因组 DNA扩增,共扩增出144条带,其中多态性条带119个,多态性条带比率为93.7％,Nei’s遗传多样性指数(H)为0.296,Shannon多样性指数(I)为0.457,遗传分化指数(Gst)为0.1520,种群遗传一致度和遗传距离分别为0.9138~0.9548和0.0584~0.0901;UPGMA聚类分析表明,种群间遗传距离与空间距离和生境类型有关。河口莲座蕨在不同干扰程度的生境中,种群具有高水平的遗传多样性,一定强度或频率的干扰生境中,种群遗传多样性较高,与海拔、坡度和坡向无相关性。     

Genetic structure of <Emphasis Type="Italic">Saxifraga tridactylites</Emphasis> (Saxifragaceae) from natural and man-made habitats

In contrast to many declining plant species Saxifraga tridactylites extended its distribution range in the man-made landscape of central Europe. The species naturally colonizes rocks and calcareous grasslands, but has also spread enormously in anthropogenic habitats such as railway constructions during the last decades. To analyze the genetic structure of the species 216 individuals from 8 populations in natural and 5 populations in man-made habitats were studied using AFLPs. The molecular analysis resulted in 250 scorable fragments. Population variability, measured as Nei’s gene diversity, Shannon’s Information Index and percentage of polymorphic bands, was slightly but not significantly higher in populations from natural habitats and was not correlated with population size. Mantel test indicated no significant correlation between pairwise genetic (Φ_PT) and geographic distances. An analysis of molecular variance revealed significant differentiation between the two habitat types. About 9% variability were observed between natural and man-made habitats, 21% among populations within these two habitats and 70% within populations. In a neighbour joining cluster analysis populations from natural and man-made habitats were clearly separated from each other. Populations of S. tridactylites from man-made habitats do, therefore, not suffer from reduced genetic diversity. The observed genetic differentiation between populations from man-made and natural habitats could be due to reduced gene flow and/or habitat specific selection. However, the results of the study clearly demonstrate human impact on the genetic structure of plant populations in man-made landscapes.     

Identification and conservation of remnant genetic resources of brown trout in relict populations from Western Mediterranean streams

Brown trout is a cold-adapted freshwater species with restricted distribution to headwater streams in rivers of the South European peninsulas, where populations are highly vulnerable because Mediterranean regions are highly sensitive to the global climatic warming. Moreover, these populations are endangered due to the introgressive hybridization with cultured stocks. Individuals from six remnant populations in Western Mediterranean rivers were sequenced for the complete mitochondrial DNA control region and genotyped for 11 nuclear markers. Three different brown trout lineages were present in the studied region. Significant genetic divergence was observed among locations and a strong effect of genetic drift was suggested. An important stocking impact (close to 25%) was detected in the zone. Significant correlations between mitochondrial-based rates of hatchery introgression and water flow variation suggested a higher impact of stocked females in unstable habitats. In spite of hatchery introgression, all populations remained highly differentiated, suggesting that native genetic resources are still abundant. However, climatic predictions indicated that suitable habitats for the species in these rivers will be reduced and hence trout populations are highly endangered and vulnerable. Thus, management policies should take into account these predictions to design upstream refuge areas to protect remnant native trout in the region.     

Inference of domestication history and differentiation between early‐ and late‐flowering varieties in pearl millet

Pearl millet (Pennisetum glaucum) is a staple crop in Sahelian Africa. Farmers usually grow varieties with different cycle lengths and complementary functions in Sahelian agrosystems. Both the level of genetic differentiation of these varieties and the domestication history of pearl millet have been poorly studied. We investigated the neutral genetic diversity and population genetic structure of early‐ and late‐flowering domesticated and wild pearl millet populations using 18 microsatellite loci and 8 nucleotide sequences. Strikingly, early‐ and late‐flowering domesticated varieties were not differentiated over their whole distribution area, despite a clear difference in their isolation‐by‐distance pattern. Conversely, our data brought evidence for two well‐differentiated genetic pools in wild pearl millet, allowing us to test scenarios with different numbers and origins of domestication using approximate Bayesian computation (ABC). The ABC analysis showed the likely existence of asymmetric migration between wild and domesticated populations. The model choice procedure indicated that a single domestication from the eastern wild populations was the more likely scenario to explain the polymorphism patterns observed in cultivated pearl millet.     

Matrotrophy in the cave molly: an unexpected provisioning strategy in an extreme environment

Maternal provisioning of animal embryos may be entirely through yolk deposited in the unfertilized egg (lecithotrophy) or may include post-fertilization nutrient transfer (matrotrophy) in varying degrees. Current theory suggests that the extent of post-fertilization provisioning is resource-dependent, with higher levels of matrotrophy being advantageous in more productive environments. In this study, we investigated post-fertilization embryo provisioning in a livebearing fish, Poecilia mexicana, from two different habitats (a toxic cave and a non-toxic surface habitat) that impose different energetic demands and therefore differ in resources available for reproduction. We predicted that fish in the benign habitat would be more matrotrophic than those from the toxic cave. We used two different techniques for this assay: (1) the matrotrophy-index analysis (MI) for field-collected fish and (2) both MI and radio-tracer assay for laboratory-reared females. According to the interpretation of the matrotrophy index, both populations are purely lecithotrophic, while the radio-tracer assay found females from both populations to actively transfer nutrients to developing embryos at approximately the same rate. Our results suggest that P. mexicana, which was traditionally classified as lecithotrophic, is capable of incipient matrotrophy, and that matrotrophy can contribute to embryo provisioning even in populations from resource-limited environments. Furthermore, the analysis of laboratory-reared animals provides evidence for a genetic component to the large offspring size in cave mollies, which had so far only been described from the field. Specifically, our results suggest matrotrophy occurs in species interpreted as lecithotrophic using the MI approach. Hence, to avoid misclassification, both techniques should ideally be employed in concert, rather than individually. Finally, our results provide further insights into the possible evolutionary pathway from lecithotrophic oviparity to matrotrophic viviparity.     

The population genomic signature of environmental association and gene flow in an ecologically divergent tree species Metrosideros polymorpha (Myrtaceae)

Genomewide markers enable us to study genetic differentiation within a species and the factors underlying it at a much higher resolution than before, which advances our understanding of adaptation in organisms. We investigated genomic divergence in Metrosideros polymorpha, a woody species that occupies a wide range of ecological habitats across the Hawaiian Islands and shows remarkable phenotypic variation. Using 1659 single nucleotide polymorphism (SNP) markers annotated with the genome assembly, we examined the population genetic structure and demographic history of nine populations across five elevations and two ages of substrates on Mauna Loa, the island of Hawaii. The nine populations were differentiated into two genetic clusters distributed on the lower and higher elevations and were largely admixed on the middle elevation. Demographic modelling revealed that the two genetic clusters have been maintained in the face of gene flow, and the effective population size of the high‐altitude cluster was much smaller. A F_ST‐based outlier search among the 1659 SNPs revealed that 34 SNPs (2.05%) were likely to be under divergent selection and the allele frequencies of 21 of them were associated with environmental changes along elevations, such as temperature and precipitation. This study shows a genomic mosaic of M. polymorpha, in which contrasting divergence patterns were found. While most genomic polymorphisms were shared among populations, a small fraction of the genome was significantly differentiated between populations in diverse environments and could be responsible for the dramatic adaptation to a wide range of environments.     

Population differentiation in floral and life history traits ofOxalis corniculata L. (Oxalidaceae) with style length polymorphism

A quantitative genetic analysis was conducted on the amounts and distribution of variation of 20 floral, reproductive and life history traits of a self-compatible perennial,Oxalis cornlculata L. (Oxalidaceae). This species comprises two floral morphs, homostyled and long-styled, with different breeding systems. The hierarchical design of the experiments on three homostyled and three long-styled populations allowed partitioning of variation into four levels of organization using nested ANOVAs. Seven of the 20 traits examined were differentiated between homostyled and long-styled populations. Significant genetic variance components were detected in the major traits (114 of the 120 traits) examined for six populations. Average values of variance components among families within a population across 20 traits for homostyled populations were higher than those of long-styled populations. These responses likely reflect the consequences of different levels of selfing and/or mixed mating on genetic variation in the two floral morphs ofO. corniculata. Pearson product-moment correlations for family means of seven traits selected were also calculated. Two groups of trait combinations (i.e., between floral traits, and between reproductive and life history traits) showed significant family mean correlation coefficients. The origins of these varlation patterns found in different populations ofO. corniculata are discussed in terms of the underlying selective regimes operating in each population.     

Offspring number in a livebearing fish (<Emphasis Type="Italic">Poecilia mexicana</Emphasis>, Poeciliidae): reduced fecundity and reduced plasticity in a population of cave mollies

Life history traits within species often vary among different habitats. We measured female fecundity in mollies (Poecilia mexicana) from a H₂S-rich cave and from a neighbouring surface habitat, as well as in laboratory-reared individuals of both populations raised in either light or continuous darkness. Compared to conspecifics from surface habitats, cave-dwelling P. mexicana had reduced fecundity (adjusted for size) in the field. In the laboratory, the fecundity of surface mollies was higher in light than in darkness, whereas fecundity in the cave mollies was almost unaffected by the ambient light conditions. Our results suggest a heritable component to the reduction in fecundity in female cave mollies. Moreover, the reduced plasticity in fecundity of cave mollies in response to light conditions might be an example of genetic assimilation or channelling of a life history trait in a population invading a new environment.     

MOLECULAR EVOLUTIONARY DIVERGENCE AMONG NORTH AMERICAN CAVE CRICKETS. I. ALLOZYME VARIATION

Forty-nine populations of nine species of North American cave crickets (genera Euhadenoecus and Hadenoecus) have been studied for genetic variation at 41 loci by electrophoresis. Wright's F_ST, Slatkin's Nm^* gene-flow estimator, and Nei's genetic distances (D) have been used to compare closely related species that have different ecological requirements (cave vs. forest species), distribution patterns, and/or different degrees of geographic isolation among populations. Cave and epigean (noncave) species differ greatly in their levels of genetic differentiation. Cave species have lower rates of gene exchange (low Nm, high D, and F_ST) than epigean species. Within cave species the degree of genetic differentiation among populations is correlated with the limestone structure of the area where the species occur. Species or groups of populations inhabiting areas where the limestone is continuous and highly fissured (e.g., H. subterraneus populations in the Mammoth Cave region) are genetically less differentiated than are populations occurring in regions where the limestone distribution is more fragmented, such as the Appalachian Ridge where E. fragilis occurs; this effect is more extreme in Central Tennessee where genetically differentiated E. insolitus populations occur only a few kilometers apart. This suggests that epigean dispersal through forest habitat in cave-dwelling species is negligable. For forest species, the data indicate relatively recent radiation with ongoing gene exchange among populations. For cave species, the distribution of protein polymorphisms is apparently more a function of historical patterns of gene exchange rather than current gene exchange. Phylogenetic relationships were studied using cluster analyses (UPGMA and Wagner algorithms) of Nei's and Edwards' genetic distances and multivariate analysis (correspondence analysis) of the raw allele frequencies. Different algorithms result in branching patterns that are similar but not entirely concordant with one another or with the phylogeny based on morphology.