Differences in heritable trait variation among populations of varying size in the perennial herb Phyteuma spicatum

Habitat fragmentation may affect trait evolution in plants through changes in the environment. Evolutionary change, however, may be limited when fragmented populations suffer from genetic or environmental deterioration. In this study, we examined the potential of plants in fragmented populations to respond to altered selective pressures by estimating the amount of heritable variation in several phenotypic traits, using Phyteuma spicatum as study species. We grew offspring of plants of ten natural populations of varying size under common environmental conditions and assessed if population trait means or heritability estimates were related to the size and abiotic environmental conditions of the populations of origin. All traits differed significantly among populations and maternal families, suggesting that genetic effects were responsible for the observed trait variation. Narrow-sense heritabilities (h ² ) ranged between 0 and 1.13, depending on trait and population of origin. Size and/or environmental conditions of the populations of origin affected means and h ² -estimates of some of the measured traits. Heritabilities for flowering duration and mean seed mass decreased with decreasing population size, suggesting that plants in small populations may have a reduced capacity to respond and adapt to changes in the environment which alter selective pressures on these traits. Still, mean h ² -estimates were in some cases low, and patterns were generally quite variable. Further studies are therefore needed to gain more conclusive insights into the adaptive potential of small plant populations. Such knowledge is important if we want to understand how habitat fragmentation and associated changes in the environment affect trait evolution.     

Low genetic diversity in pygmy blue whales is due to climate-induced diversification rather than anthropogenic impacts

Unusually low genetic diversity can be a warning of an urgent need to mitigate causative anthropogenic activities. However, current low levels of genetic diversity in a population could also be due to natural historical events, including recent evolutionary divergence, or long-term persistence at a small population size. Here, we determine whether the relatively low genetic diversity of pygmy blue whales (Balaenoptera musculus brevicauda) in Australia is due to natural causes or overexploitation. We apply recently developed analytical approaches in the largest genetic dataset ever compiled to study blue whales (297 samples collected after whaling and representing lineages from Australia, Antarctica and Chile). We find that low levels of genetic diversity in Australia are due to a natural founder event from Antarctic blue whales (Balaenoptera musculus intermedia) that occurred around the Last Glacial Maximum, followed by evolutionary divergence. Historical climate change has therefore driven the evolution of blue whales into genetically, phenotypically and behaviourally distinct lineages that will likely be influenced by future climate change.     

Population Structure Limits Parallel Evolution in Sticklebacks

Population genetic theory predicts that small effective population sizes (N_e) and restricted gene flow limit the potential for local adaptation. In particular, the probability of evolving similar phenotypes based on shared genetic mechanisms (i.e., parallel evolution), is expected to be reduced. We tested these predictions in a comparative genomic study of two ecologically similar and geographically codistributed stickleback species (viz. Gasterosteus aculeatus and Pungitius pungitius). We found that P. pungitius harbors less genetic diversity and exhibits higher levels of genetic differentiation and isolation-by-distance than G. aculeatus. Conversely, G. aculeatus exhibits a stronger degree of genetic parallelism across freshwater populations than P. pungitius: 2,996 versus 379 single nucleotide polymorphisms located within 26 versus 9 genomic regions show evidence of selection in multiple freshwater populations of G. aculeatus and P. pungitius, respectively. Most regions involved in parallel evolution in G. aculeatus showed increased levels of divergence, suggestive of selection on ancient haplotypes. In contrast, haplotypes involved in freshwater adaptation in P. pungitius were younger. In accordance with theory, the results suggest that connectivity and genetic drift play crucial roles in determining the levels and geographic distribution of standing genetic variation, providing evidence that population subdivision limits local adaptation and therefore also the likelihood of parallel evolution.     

Molecular phylogeography and population evolution analysis of <Emphasis Type="Italic">Citrus ichangensis</Emphasis> (Rutaceae)

Ichang papeda (Citrus ichangensis), a wild and endemic perennial plant in Rutaceae, is characterized by the existence of wild and natural populations in southwestern and middle-west China. We analyzed a total of 231 individuals across 16 natural populations using chloroplast SSR markers, nuclear SSR markers, and single-copy nuclear genes. Standard population genetic analyses as well as Bayesian and maximum likelihood models were used to clarify the genetic diversity, population differentiation, barriers to gene flow, bottleneck events, isolation by distance, history migration, demographic history among populations, and phylogeny evolution. The chloroplast and nuclear genome analyses revealed a low level of genetic diversity in C. ichangensis. Clear signals of recent bottlenecks and strong patterns of isolation by distance were detected among different subpopulations, indicating a low extent of historical gene flow for this species and that genetic drift would occur after population differentiation. Bayesian clustering analyses revealed a clear pattern of genetic structure, with one cluster spanning the potential refugia in Wuling Mountains and Ta-pa Mountains, and other two clusters covering a more limited distribution range. The demographic history also supported the scenario that two isolated clusters originated in parallel from the genetic diversity center. Taxonomically, Ichang papeda may be a member of subgenus Citrus. Owing to the complicated topography, the mountainous regions and the Yangtze River have provided long-term stable habitats for C. ichangensis and acted as main barriers for its expansion, which might facilitate the process of speciation. Statistical population models and genetic data indicated strong genetic structure in C. ichangensis, which might result from the restricted gene flow, genetic drift, and population bottlenecks.     

Low mtDNA Cytb diversity and shallow population structure of Eleutheronema tetradactylum in the East China Sea and the South China Sea

Eleutheronema tetradactylum is an economically important fish species in China water. To investigate the genetic diversity and describe population structure of it, an 1151 base pair (bp) fragment of the mitochondrial DNA Cytb sequence was analyzed in 120 individuals from four populations in the East China Sea and the South China Sea. A total of 16 haplotypes were defined by 24 variable nucleotide sites. High level of haplotype diversity and low nucleotide diversity were observed in all populations. The results of AMOVA detected that 89.44% of the genetic variation occurred within populations. Significant genetic differentiations were detected among populations (0.05097, P < 0.05), but no large-scale regional differences were detected. Analysis of neutral evolution and mismatch distribution suggested no recent population expansion happened. The present results provided new information for genetic assessment, fishery management and conservation of this species.     

Clonal Evolution of Enterocytozoon bieneusi Populations in Swine and Genetic Differentiation in Subpopulations between Isolates from Swine and Humans

Enterocytozoon bieneusi is a widespread parasite with high genetic diversity among hosts. Its natural reservoir remains elusive and data on population structure are available only in isolates from primates. Here we describe a population genetic study of 101 E. bieneusi isolates from pigs using sequence analysis of the ribosomal internal transcribed spacer (ITS) and four mini- and microsatellite markers. The presence of strong linkage disequilibrium (LD) and limited genetic recombination indicated a clonal structure for the population. Bayesian inference of phylogeny, structural analysis, and principal coordinates analysis separated the overall population into three subpopulations (SP3 to SP5) with genetic segregation of the isolates at some geographic level. Comparative analysis showed the differentiation of SP3 to SP5 from the two known E. bieneusi subpopulations (SP1 and SP2) from primates. The placement of a human E. bieneusi isolate in pig subpopulation SP4 supported the zoonotic potential of some E. bieneusi isolates. Network analysis showed directed evolution of SP5 to SP3/SP4 and SP1 to SP2. The high LD and low number of inferred recombination events are consistent with the possibility of host adaptation in SP2, SP3, and SP4. In contrast, the reduced LD and high genetic diversity in SP1 and SP5 might be results of broad host range and adaptation to new host environment. The data provide evidence of the potential occurrence of host adaptation in some of E. bieneusi isolates that belong to the zoonotic ITS Group 1.     

Ecological Specialization in a Spatially Structured Population of the Thermophilic Cyanobacterium Mastigocladus laminosus

Laboratory evolution experiments suggest the potential for microbial populations to contribute significant ecological variation to ecosystems, yet the functional importance of genetic diversity within natural populations of microorganisms is largely unknown. Here, we investigated the distribution of genetic and phenotypic variation for a population of the cyanobacterium Mastigocladus laminosus distributed along the temperature gradient of White Creek, Yellowstone NP. A total of 153 laboratory strains were directly isolated from five sites with mean annual temperatures ranging between 39 and 54°C. Genetic characterization at four nitrogen metabolism genes identified 15 closely related lineages in the population sample. These lineages were distributed nonrandomly along White Creek, but the observed geographic structure could not be explained by limited dispersal capabilities. Temperature performance experiments with six M. laminosus lineages that maximized their respective relative abundances at different positions along the gradient provided evidence for niche differentiation within the population. Niche differentiation included a tradeoff in performance at high and low temperatures, respectively. The physiological variation of these lineages in laboratory culture was generally well matched to the prevailing temperature conditions experienced by these organisms in situ. These results suggest that sympatric diversification along an ecological selection gradient can be a potent source of evolutionary innovation in microbial populations.     

Microsatellite polymorphism in the endangered snail kite reveals a panmictic,low diversity population

Genetic structure and genetic diversity are key population characteristics that can inform conservation decisions, such as delineating management units or assessing potential risks for inbreeding depression. Evidence of genetic structuring or low genetic diversity in the critically endangered snail kite (Rostrhamus sociabilis plumbeus) would have implications for monitoring and planning decisions. Recent work on understanding connectivity across the snail kite range indicated that there is less dispersal between northern and southern parts of the current range, and that dispersal is shaped by individual habitat preference. We examine whether there is neutral genetic structure and the amount of genetic variation in the population by non-lethally sampling 235 nestlings from unique nests across the entire breeding range between 2013 and 2014. Data on 15 microsatellite revealed low diversity (e.g., N _a?=?2.54, H _e?=?0.37) and range-wide panmixia based on AMOVA, Bayesian clustering, spatial autocorrelation, isolation by distance, and spatially explicit ordination analyses. Our results emphasize that long-term recovery goals and management strategies should be based on viewing snail kites as a single genetic population, despite evidence for non-random dispersal between wetlands over ecological time scales. These results also highlight the need to understand potential effects of low genetic diversity on population dynamics and viability of snail kites. More broadly, these results add to the growing evidence for potential discrepancies between dispersal and genetic patterns, emphasizing that care should be taken if using one to interpret the other, particularly for widely-ranging species.     

Compensatory Evolution and the Origins of Innovations

Cryptic genetic sequences have attenuated effects on phenotypes. In the classic view, relaxed selection allows cryptic genetic diversity to build up across individuals in a population, providing alleles that may later contribute to adaptation when co-opted—e.g., following a mutation increasing expression from a low, attenuated baseline. This view is described, for example, by the metaphor of the spread of a population across a neutral network in genotype space. As an alternative view, consider the fact that most phenotypic traits are affected by multiple sequences, including cryptic ones. Even in a strictly clonal population, the co-option of cryptic sequences at different loci may have different phenotypic effects and offer the population multiple adaptive possibilities. Here, we model the evolution of quantitative phenotypic characters encoded by cryptic sequences and compare the relative contributions of genetic diversity and of variation across sites to the phenotypic potential of a population. We show that most of the phenotypic variation accessible through co-option would exist even in populations with no polymorphism. This is made possible by a history of compensatory evolution, whereby the phenotypic effect of a cryptic mutation at one site was balanced by mutations elsewhere in the genome, leading to a diversity of cryptic effect sizes across sites rather than across individuals. Cryptic sequences might accelerate adaptation and facilitate large phenotypic changes even in the absence of genetic diversity, as traditionally defined in terms of alternative alleles.     

Genetic population structure of the swimming crab, Portunus trituberculatus in the East China Sea based on mtDNA 16S rRNA sequences

Portunus trituberculatus is a commercially important fishery species. In this study, intraspecific variation was examined by using mitochondrial DNA 16S rRNA gene in 213 individual crabs sampled from six localities along the coast of the East China Sea. Twenty-two polymorphic sites defined 25 distinct haplotypes, revealing a moderately high haplotype diversity and relatively low sequence divergence among the six localities. An excess of within population unique haplotypes at most sample locations were detected, which might influence genetic structure of the swimming crab populations. Neither neighbor-joining tree nor minimum spanning network (MSN) based on the haplotype data indicated distinct patterns of phylogeographic structure among the 25 haplotypes. Analyses of molecular variance (AMOVA) and F_ST statistics supported the hypothesis that population samples from the East China Sea were genetically nonhomogenous, indicating that gene flow might be restricted across those regions, despite the high potential of dispersal. In addition, tests of neutral evolution and analysis of mismatch distribution suggested that P. trituberculatus might have undergone a population expansion, possibly within the last 127,000 and 429,000 years. Our study unraveled the extant population genetic structure of the P. trituberculatus, and addressed the related fishery management issues including artificial breeding, fishery stock identification and conservation.     

Unrestricted migration favours virulent pathogens in experimental metapopulations: evolutionary genetics of a rapacious life history

Understanding pathogen infectivity and virulence requires combining insights from epidemiology, ecology, evolution and genetics. Although theoretical work in these fields has identified population structure as important for pathogen life-history evolution, experimental tests are scarce. Here, we explore the impact of population structure on life-history evolution in phage T4, a viral pathogen of Escherichia coli. The host–pathogen system is propagated as a metapopulation in which migration between subpopulations is either spatially restricted or unrestricted. Restricted migration favours pathogens with low infectivity and low virulence. Unrestricted migration favours pathogens that enter and exit their hosts quickly, although they are less productive owing to rapid extirpation of the host population. The rise of such ‘rapacious’ phage produces a ‘tragedy of the commons’, in which better competitors lower productivity. We have now identified a genetic basis for a rapacious life history. Mutations at a single locus (rI) cause increased virulence and are sufficient to account for a negative relationship between phage competitive ability and productivity. A higher frequency of rI mutants under unrestricted migration signifies the evolution of rapaciousness in this treatment. Conversely, spatially restricted migration favours a more ‘prudent’ pathogen strategy, in which the tragedy of the commons is averted. As our results illustrate, profound epidemiological and ecological consequences of life-history evolution in a pathogen can have a simple genetic cause.     

Conservation genetics of the endangered terrestrial orchid Liparis japonica in Northeast China based on AFLP markers

Levels of genetic diversity and population genetic structure of the rare, endangered terrestrial orchid Liparis japonica were examined for eight natural populations (n = 185) in Northeast China using six AFLP primer pairs, where this species has experienced severe habitat loss and fragmentation. Based on 406 DNA bands, a high level of genetic diversity was found at the species level with the PPB of 85.47 %, while the genetic diversity at the population level was low (PPB = 47.48 %). A significantly high degree of population differentiation was found with 42.69 % variation existed among populations as measured by AMOVA, indicating potential restricted gene flow. The genetic distances between populations were independent of the corresponding geographic distances, and the genetic relationship of individuals had no significant correlation with their spatial distribution. The restricted gene flow might be impacted by reduced population size, habitat destruction and fragmentation. The results in this study suggested that habitat protection and keeping a stable environment are critical for the conservation of L. japonica species.     

Quantitative genetic analysis of brain size variation in sticklebacks: support for the mosaic model of brain evolution

The mosaic model of brain evolution postulates that different brain regions are relatively free to evolve independently from each other. Such independent evolution is possible only if genetic correlations among the different brain regions are less than unity. We estimated heritabilities, evolvabilities and genetic correlations of relative size of the brain, and its different regions in the three-spined stickleback (Gasterosteus aculeatus). We found that heritabilities were low (average h² = 0.24), suggesting a large plastic component to brain architecture. However, evolvabilities of different brain parts were moderate, suggesting the presence of additive genetic variance to sustain a response to selection in the long term. Genetic correlations among different brain regions were low (average r_G = 0.40) and significantly less than unity. These results, along with those from analyses of phenotypic and genetic integration, indicate a high degree of independence between different brain regions, suggesting that responses to selection are unlikely to be severely constrained by genetic and phenotypic correlations. Hence, the results give strong support for the mosaic model of brain evolution. However, the genetic correlation between brain and body size was high (r_G = 0.89), suggesting a constraint for independent evolution of brain and body size in sticklebacks.     

Genetic variation in a female genital trait evolved by sexual coevolution

Understanding the patterns of genetic variation of traits subject to sexual selection is fundamental for explaining its evolutionary dynamics and potential for sexual coevolution. The signa of female Lepidoptera are sclerotized structures located on the inner surface of the genital receptacle that receives the spermatophore during copulation (the corpus bursae), whose main function is tearing the spermatophore envelope. Comparative data indicate that the evolution of signa has been influenced by sexually antagonistic coevolution with spermatophore envelopes. We looked for additive genetic variation in the size and shape of signa in females of the butterfly Callophrys xami (Lycaenidae) from two localities (BG and FC) in Mexico City. We also looked for genetic variation in female body size and in the size of corpus bursae. There were significant between-population differences in female body size, signa width and three signa shape traits. We found significant extranuclear maternal effects in one component of signa shape in the BG population, and in body weight, signa length and in one uniform component of signa shape in the FC population. Extranuclear maternal contributions could permit the evolution of female adaptations even if these reduce male fitness. We found additive genetic variation in signa length and width only in one population (BG); heritability estimates were high: 0.96 and 0.8, respectively. The existence of additive genetic variation in signa size could be, at least in part, a result of relaxed sexually antagonistic selection pressures due to the low level of polyandry exhibited by this species. Our results imply that there is currently potential for further sexual coevolution in this trait.     

Population genetics of the invasive water weed Elodea canadensis in Finnish waterways

Invasions of exotic species often involve a rapid evolutionary change in the introduced populations. Elodea canadensis is an invasive aquatic weed native to North America. Our aims were to reveal the evolutionary consequences of invasion to the population genetic structure of the presumably clonal E. canadensis in Finland and to test the hypothesis that the whole Finnish population originates from the first introduction of the species. We used ten polymorphic microsatellite markers to analyze the genetic characteristics of seven introduced E. canadensis populations in Finland. Despite the species' totally asexual mode of reproduction in Finland, two to five alleles per locus were detected in Finnish populations, and the expected heterozygosities varied between 0.19 and 0.37. The majority of variation was found within populations. Except for one, all pairwise values of population differentiation (F _ST) were significant, indicating restricted gene flow among the Finnish populations. In addition, a Bayesian analysis of population structure revealed the presence of regional population structuring. Genetic analyses indicate that E. canadensis could have been introduced to Finland multiple times. However, the amount of genetic variation and regional clustering detected could also be explained by post-establishment evolution, and based on this study it is not possible to exclude one introduction event followed by rapid evolution. We also tested the usability of the microsatellite markers for native North American samples in order to compare the within-population genetic characteristics of introduced and native populations. However, in native populations only four microsatellite markers amplified reliably, indicating sequence variation within primer-binding regions and, thus, genetic differentiation among populations of E. canadensis.     

Genetic diversity and fine-scale genetic structure in Hancornia speciosa Gomes (Apocynaceae)

We studied the genetic diversity and spatial genetic structure (SGS) of adult and juvenile individuals in a population of Hancornia speciosa in Central-West Brazil. For this, we sampled and mapped 113 adults and 100 juveniles in an area of 2.5 ha. Genomic DNA was obtained from leaves and seven microsatellite loci were used to genotype all individuals. The studied population showed high genetic diversity (H_e) but with significant inbreeding (f) for both life stages most likely due to biparental inbreeding. Spatial genetic structure was weak for both life stages and the values of S_P were low and neighborhoods (Nb) was high for both generations showing a potential long-distance gene dispersal.     

Natural Genetic Transformation Generates a Population of Merodiploids in Streptococcus pneumoniae

Partial duplication of genetic material is prevalent in eukaryotes and provides potential for evolution of new traits. Prokaryotes, which are generally haploid in nature, can evolve new genes by partial chromosome duplication, known as merodiploidy. Little is known about merodiploid formation during genetic exchange processes, although merodiploids have been serendipitously observed in early studies of bacterial transformation. Natural bacterial transformation involves internalization of exogenous donor DNA and its subsequent integration into the recipient genome by homology. It contributes to the remarkable plasticity of the human pathogen Streptococcus pneumoniae through intra and interspecies genetic exchange. We report that lethal cassette transformation produced merodiploids possessing both intact and cassette-inactivated copies of the essential target gene, bordered by repeats (R) corresponding to incomplete copies of IS861. We show that merodiploidy is transiently stimulated by transformation, and only requires uptake of a ∼3-kb DNA fragment partly repeated in the chromosome. We propose and validate a model for merodiploid formation, providing evidence that tandem-duplication (TD) formation involves unequal crossing-over resulting from alternative pairing and interchromatid integration of R. This unequal crossing-over produces a chromosome dimer, resolution of which generates a chromosome with the TD and an abortive chromosome lacking the duplicated region. We document occurrence of TDs ranging from ∼100 to ∼900 kb in size at various chromosomal locations, including by self-transformation (transformation with recipient chromosomal DNA). We show that self-transformation produces a population containing many different merodiploid cells. Merodiploidy provides opportunities for evolution of new genetic traits via alteration of duplicated genes, unrestricted by functional selective pressure. Transient stimulation of a varied population of merodiploids by transformation, which can be triggered by stresses such as antibiotic treatment in S. pneumoniae, reinforces the plasticity potential of this bacterium and transformable species generally.     

Genetic drift and natural selection in an isolated Zapotec-speaking community in the Valley of Oaxaca, southern Mexico

Genetic drift and natural selection were analyzed in a genetically isolated Zapotec-speaking community in the Valley of Oaxaca, southern Mexico. Moderately intense genetic drift and selection potentials were found. Potential for drift was related to (1) the small effective size of the population, and (2) the exceptionally low number of migrants into the population. Potential for selection was due to (1) an unusually high variance in fertility, and (2) a high contribution of prereproductive mortality. Significant potential for genetic evolution was found due to genetic drift and natural selection.