Showing papers in "Molecular Ecology in 2003"
TL;DR: It is shown that although challenges still exist, the above‐mentioned obstacles are now being removed, and recent advances in technology and increases in statistical power provide the prospect of nuclear DNA analyses becoming routine practice, allowing allele‐discriminating characterization of scnp loci and microsatellite loci.
Abstract: Population-genetic studies have been remarkably productive and successful in the last decade following the invention of PCR technology and the introduction of mitochondrial and microsatellite DNA markers. While mitochondrial DNA has proven powerful for genealogical and evolutionary studies of animal populations, and microsatellite sequences are the most revealing DNA markers available so far for inferring population structure and dynamics, they both have important and unavoidable limitations. To obtain a fuller picture of the history and evolutionary potential of populations, genealogical data from nuclear loci are essential, and the inclusion of other nuclear markers, i.e. single copy nuclear polymorphic (scnp) sequences, is clearly needed. Four major uncertainties for nuclear DNA analyses of populations have been facing us, i.e. the availability of scnp markers for carrying out such analysis, technical laboratory hurdles for resolving haplotypes, difficulty in data analysis because of recombination, low divergence levels and intraspecific multifurcation evolution, and the utility of scnp markers for addressing population-genetic questions. In this review, we discuss the availability of highly polymorphic single copy DNA in the nuclear genome, describe patterns and rate of evolution of nuclear sequences, summarize past empirical and theoretical efforts to recover and analyse data from scnp markers, and examine the difficulties, challenges and opportunities faced in such studies. We show that although challenges still exist, the above-mentioned obstacles are now being removed. Recent advances in technology and increases in statistical power provide the prospect of nuclear DNA analyses becoming routine practice, allowing allele-discriminating characterization of scnp loci and microsatellite loci. This certainly will increase our ability to address more complex questions, and thereby the sophistication of genetic analyses of populations.
725 citations
TL;DR: This review of the leading techniques in parentage analysis, with a particular emphasis on those that have been implemented in readily useable software packages, should serve as a useful guide to anyone who wishes to embark on the study of parentage.
Abstract: The recent proliferation of hypervariable molecular markers has ushered in a surge of techniques for the analysis of parentage in natural and experimental populations. Consequently, the potential for meaningful studies of paternity and maternity is at an all-time high. However, the details and implementation of the multifarious techniques often differ in subtle ways that can influence the results of parentage analyses. Now is a good time to reflect on the available techniques and to consider their strengths and weaknesses. Here, we review the leading techniques in parentage analysis, with a particular emphasis on those that have been implemented in readily useable software packages. Our survey leads to some important insights with respect to the utility of the different approaches. This review should serve as a useful guide to anyone who wishes to embark on the study of parentage.
631 citations
TL;DR: There is now excellent fossil, molecular and phytogeographical evidence to support Hultén's proposal that Beringia was a major northern refugium for arctic plants throughout the Quaternary, but most molecular evidence fails to support his proposal that contemporary east and west Atlantic populations of circumarctic and amphi‐Atlantic species have been separated throughout the quaternary.
Abstract: A major contribution to our initial understanding of the origin, history and biogeography of the present-day arctic flora was made by Eric Hulten in his landmark book Outline of the History of Arctic and Boreal Biota during the Quarternary Period, published in 1937. Here we review recent molecular and fossil evidence that has tested some of Hulten's proposals. There is now excellent fossil, molecular and phytogeographical evidence to support Hulten's proposal that Beringia was a major northern refugium for arctic plants throughout the Quaternary. In contrast, most molecular evidence fails to support his proposal that contemporary east and west Atlantic populations of circumarctic and amphi-Atlantic species have been separated throughout the Quaternary. In fact, populations of these species from opposite sides of the Atlantic are normally genetically very similar, thus the North Atlantic does not appear to have been a strong barrier to their dispersal during the Quaternary. Hulten made no detailed proposals on mechanisms of speciation in the Arctic; however, molecular studies have confirmed that many arctic plants are allopolyploid, and some of them most probably originated during the Holocene. Recurrent formation of polyploids from differentiated diploid or more low-ploid populations provides one explanation for the intriguing taxonomic complexity of the arctic flora, also noted by Hulten. In addition, population fragmentation during glacial periods may have lead to the formation of new sibling species at the diploid level. Despite the progress made since Hulten wrote his book, there remain large gaps in our knowledge of the history of the arctic flora, especially about the origins of the founding stocks of this flora which first appeared in the Arctic at the end of the Pliocene (approximately 3 Ma). Comprehensive analyses of the molecular phylogeography of arctic taxa and their relatives together with detailed fossil studies are required to fill these gaps.
551 citations
TL;DR: In this article, the authors used the terminal restriction fragment length polymorphism (T-RFLP) strategy to assess the diversity of arbuscular mycorrhizal (AM) fungi in 89 roots of three grass species.
Abstract: Arbuscular mycorrhizal (AM) fungi are biotrophic symbionts colonizing the majority of land plants, and are of major importance in plant nutrient supply. Their diversity is suggested to be an important determinant of plant community structure, but the influence of host-plant and environmental factors on AM fungal community in plant roots is poorly documented. Using the terminal restriction fragment length polymorphism (T-RFLP) strategy, the diversity of AM fungi was assessed in 89 roots of three grass species (Agrostis capillaris, Festuca rubra, Poa pratensis) that co-occurred in the same plots of a field experiment. The impact of different soil amendments (nitrogen, lime, nitrogen and lime) and insecticide application on AM fungal community was also studied. The level of diversity found in AM fungal communities using the T-RFLP strategy was consistent with previous studies based on clone libraries. Our results clearly confirm that an AM fungal host-plant preference exists, even between different grass species. AM communities colonizing A. capillaris were statistically different from the others (P < 0.05). Although grass species evenness changed in amended soils, AM fungal community composition in roots of a given grass species remained stable. Conversely, in plots where insecticide was applied, we found higher AM fungal diversity and, in F. rubra roots, a statistically different AM fungal community.
432 citations
TL;DR: Data is presented from 21 population inventory studies that relied on the noninvasive collection of hair, and the methods that were used to prevent genetic errors in these studies are reviewed.
Abstract: I present data from 21 population inventory studies - 20 of them on bears - that relied on the noninvasive collection of hair, and review the methods that were used to prevent genetic errors in these studies. These methods were designed to simultaneously minimize errors (which can bias estimates of abundance) and per-sample analysis effort (which can reduce the precision of estimates by limiting sample size). A variety of approaches were used to probe the reliability of the empirical data, producing a mean, per-study estimate of no more than one undetected error in either direction (too few or too many individuals identified in the laboratory). For the type of samples considered here (plucked hair samples), the gain or loss of individuals in the laboratory can be reduced to a level that is inconsequential relative to the more universal sources of bias and imprecision that can affect mark-recapture studies, assuming that marker systems are selected according to stated guidelines, marginal samples are excluded at an early stage, similar pairs of genotypes are scrutinized, and laboratory work is performed with skill and care.
431 citations
TL;DR: Findings lend support to the notion that low levels of differentiation are due to passive transport of eggs or larvae by the ocean currents rather than to adult dispersal, the latter being strongly dependent on distance.
Abstract: Compared with many terrestrial and freshwater environments, dispersal and interbreeding is generally much less restricted in the marine environment. We studied the tendency for a marine species, the Atlantic cod, to be sub-structured into genetically differentiated populations on a fine geographical scale. We selected a coastal area free of any obvious physical barriers and restricted sampling to a 300-km region, well within the dispersal ability of this species. Screening 10 polymorphic microsatellite loci in 6 samples we detected a weak, but consistent, differentiation at all 10 loci. The average FST over loci was small (0.0023) but highly significant statistically, demonstrating that genetically differentiated populations can arise and persist in the absence of physical barriers or great distance. We found no geographical pattern in the genetic differentiation and there was no apparent trend of isolation by distance along the coastline. These findings lend support to the notion that low levels of differentiation are due to passive transport of eggs or larvae by the ocean currents rather than to adult dispersal, the latter being strongly dependent on distance.
385 citations
TL;DR: Strong evidence for pleiotropy is found using near‐isogenic lines of FRIGIDA and FLOWERING LOCUS C, cloned loci known to be responsible for natural variation in flowering time, to suggest the correlated evolution of δ13C and flowering time is explained in part by the fixation of pleiotropic alleles that alter both δ 13C and time to flowering.
Abstract: We examined patterns of genetic variance and covariance in two traits (i) carbon stable isotope ratio delta13C (dehydration avoidance) and (ii) time to flowering (drought escape), both of which are putative adaptations to local water availability. Greenhouse screening of 39 genotypes of Arabidopsis thaliana native to habitats spanning a wide range of climatic conditions, revealed a highly significant positive genetic correlation between delta13C and flowering time. Studies in a range of C3 annuals have also reported large positive correlations, suggesting the presence of a genetically based trade-off between mechanisms of dehydration avoidance (delta13C) and drought escape (early flowering). We examined the contribution of pleiotropy by using a combination of mutant and near-isogenic lines to test for positive mutational covariance between delta13C and flowering time. Ecophysiological mutants generally showed variation in delta13C but not flowering time. However, flowering time mutants generally demonstrated pleiotropic effects consistent with natural variation. Mutations that caused later flowering also typically resulted in less negative delta13C and thus probably higher water use efficiency. We found strong evidence for pleiotropy using near-isogenic lines of Frigida and Flowering locus C, cloned loci known to be responsible for natural variation in flowering time. These data suggest the correlated evolution of delta13C and flowering time is explained in part by the fixation of pleiotropic alleles that alter both delta13C and time to flowering.
376 citations
TL;DR: The results suggest that in highly disturbed habitats Apis mellifera may expand genetic neighbourhood areas, thereby linking fragmented and continuous forest populations, and that large areas of rainforest must be preserved to maintain minimum viable populations.
Abstract: Tropical rainforest trees typically occur in low population densities and rely on animals for cross-pollination. It is of conservation interest therefore to understand how rainforest fragmentation may alter the pollination and breeding structure of remnant trees. Previous studies of the Amazonian tree Dinizia excelsa (Fabaceae) found African honeybees (Apis mellifera scutellata) as the predominant pollinators of trees in highly disturbed habitats, transporting pollen up to 3.2 km between pasture trees. Here, using microsatellite genotypes of seed arrays, we compare outcrossing rates and pollen dispersal distances of (i) remnant D. excelsa in three large ranches, and (ii) a population in undisturbed forest in which African honeybees were absent. Self-fertilization was more frequent in the disturbed habitats (14%, n = 277 seeds from 12 mothers) than in undisturbed forest (10%, n = 295 seeds from 13 mothers). Pollen dispersal was extensive in all three ranches compared to undisturbed forest, however. Using a twogener analysis, we estimated a mean pollen dispersal distance of 1509 m in Colosso ranch, assuming an exponential dispersal function, and 212 m in undisturbed forest. The low effective density of D. excelsa in undisturbed forest (approximately 0.1 trees/ha) indicates that large areas of rainforest must be preserved to maintain minimum viable populations. Our results also suggest, however, that in highly disturbed habitats Apis mellifera may expand genetic neighbourhood areas, thereby linking fragmented and continuous forest populations.
364 citations
TL;DR: A ‘matching approach’ is proposed to eliminate overestimation of population size in wolves in Yellowstone National Park by counting distinct microsatellite genotypes from noninvasive samples, which is essential for conservation.
Abstract: Determining population sizes can be difficult, but is essential for conservation. By counting distinct microsatellite genotypes, DNA from noninvasive samples (hair, faeces) allows estimation of population size. Problems arise because genotypes from noninvasive samples are error-prone, but genotyping errors can be reduced by multiple polymerase chain reaction (PCR). For faecal genotypes from wolves in Yellowstone National Park, error rates varied substantially among samples, often above the 'worst-case threshold' suggested by simulation. Consequently, a substantial proportion of multilocus genotypes held one or more errors, despite multiple PCR. These genotyping errors created several genotypes per individual and caused overestimation (up to 5.5-fold) of population size. We propose a 'matching approach' to eliminate this overestimation bias.
321 citations
TL;DR: The workload involved in isolating nuclear microsatellites from plants is reviewed to quantify the attrition of loci at each stage in the process, and the average effort required to obtain 10 working microsatellite primer pairs.
Abstract: The attributes of codominance, reproducibility and high resolution have all contributed towards the current popularity of nuclear microsatellites as genetic markers in molecular ecological studies. One of their major drawbacks, however, is the development phase required to obtain working primers for a given study species. To facilitate project planning, we have reviewed the literature to quantify the workload involved in isolating nuclear microsatellites from plants. We highlight the attrition of loci at each stage in the process, and the average effort required to obtain 10 working microsatellite primer pairs.
319 citations
TL;DR: Findings on the prevalence of these symbionts within many aphid taxa, along with published observations concerning their effects on host fitness, imply a significant role of facultative symbiosis in aphid ecology and evolution.
Abstract: To elucidate the co-evolutionary relationships between phloem-feeding insects and their secondary, or facultative, bacterial symbionts, we explore the distributions of three such microbes--provisionally named the R-type (or PASS, or S-sym), T-type (or PABS), and U-type--across a number of aphid and psyllid hosts through the use of diagnostic molecular screening techniques and DNA sequencing. Although typically maternally transmitted, phylogenetic and pairwise divergence analyses reveal that these bacteria have been independently acquired by a variety of unrelated insect hosts, indicating that horizontal transfer has helped to shape their distributions. Based on the high genetic similarity between symbionts in different hosts, we argue that transfer events have occurred recently on an evolutionary timescale. In several instances, however, closely related symbionts associate with related hosts, suggesting that horizontal transfer between distant relatives may be rarer than transmission between close relatives. Our findings on the prevalence of these symbionts within many aphid taxa, along with published observations concerning their effects on host fitness, imply a significant role of facultative symbiosis in aphid ecology and evolution.
TL;DR: It is argued that the estimators developed should find major applications, notably for conservation biology, and that this new relatedness estimator can be used to characterize isolation by distance within populations, leading to essentially unbiased estimates of the neighbourhood size.
Abstract: A new estimator of the pairwise relatedness coefficient between individuals adapted to dominant genetic markers is developed. This estimator does not assume genotypes to be in Hardy-Weinberg proportions but requires a knowledge of the departure from these proportions (i.e. the inbreeding coefficient). Simulations show that the estimator provides accurate estimates, except for some particular types of individual pairs such as full-sibs, and performs better than a previously developed estimator. When comparing marker-based relatedness estimates with pedigree expectations, a new approach to account for the change of the reference population is developed and shown to perform satisfactorily. Simulations also illustrate that this new relatedness estimator can be used to characterize isolation by distance within populations, leading to essentially unbiased estimates of the neighbourhood size. In this context, the estimator appears fairly robust to moderate errors made on the assumed inbreeding coefficient. The analysis of real data sets suggests that dominant markers (random amplified polymorphic DNA, amplified fragment length polymorphism) may be as valuable as co-dominant markers (microsatellites) in studying microgeographic isolation-by-distance processes. It is argued that the estimators developed should find major applications, notably for conservation biology.
University of California, Berkeley1, Celera Corporation2, Hoffmann-La Roche3, University of São Paulo4, Federal University of Rio de Janeiro5, Peking Union Medical College6, University of Sydney7, Chiba University8, University of Tokyo9, National Autonomous University of Mexico10, National Institutes of Health11
TL;DR: Combining DNA substitution rates of protein‐coding genes with the phylogeny suggests that the radiation of Histoplasma started between 3 and 13 million years ago in Latin America.
Abstract: Until recently, Histoplasma capsulatum was believed to harbour three varieties, var. capsulatum (chiefly a New World human pathogen), var. duboisii (an African human pathogen) and var. farciminosum (an Old World horse pathogen), which varied in clinical manifestations and geographical distribution. We analysed the phylogenetic relationships of 137 individuals representing the three varieties from six continents using DNA sequence variation in four independent protein-coding genes. At least eight clades were identified: (i) North American class 1 clade; (ii) North American class 2 clade; (iii) Latin American group A clade; (iv) Latin American group B clade; (v) Australian clade; (vi) Netherlands (Indonesian?) clade; (vii) Eurasian clade and (viii) African clade. Seven of eight clades represented genetically isolated groups that may be recognized as phylogenetic species. The sole exception was the Eurasian clade which originated from within the Latin American group A clade. The phylogenetic relationships among the clades made a star phylogeny. Histoplasma capsulatum var. capsulatum individuals were found in all eight clades. The African clade included all of the H. capsulatum var. duboisii individuals as well as individuals of the other two varieties. The 13 individuals of var. farciminosum were distributed among three phylogenetic species. These findings suggest that the three varieties of Histoplasma are phylogenetically meaningless. Instead we have to recognize the existence of genetically distinct geographical populations or phylogenetic species. Combining DNA substitution rates of protein-coding genes with the phylogeny suggests that the radiation of Histoplasma started between 3 and 13 million years ago in Latin America.
TL;DR: Only five variable nucleotide positions were detected among 10 loci, consistent with the description of B. dendrobatidis as a recently emerged disease agent, and electrophoretic karyotyping of multiple strains demonstrated a number of chromosome length polymorphisms.
Abstract: Chytridiomycosis is a recently identified fungal disease associated with global population declines of frogs. Although the fungus, Batrachochytrium dendrobatidis , is considered an emerging pathogen, little is known about its population genetics, including the origin of the current epidemic and how this relates to the dispersal ability of the fungus. In this study, we use multilocus sequence typing to examine genetic diversity and relationships among 35 fungal strains from North America, Africa and Australia. Only five variable nucleotide positions were detected among 10 loci (5918 bp). This low level of genetic variation is consistent with the description of B. dendrobatidis as a recently emerged disease agent. Fixed (i.e. 100%) or nearly fixed frequencies of heterozygous genotypes at two loci suggested that B. dendrobatidis is diploid and primarily reproduces clonally. In contrast to the lack of nucleotide polymorphism, electrophoretic karyotyping of multiple strains demonstrated a number of chromosome length polymorphisms.
TL;DR: It is reported the first use of DNA‐based techniques to detect predation by arthropods on natural populations of prey in the field and it was possible to demonstrate that the spiders were exercising prey choice.
Abstract: Collembola comprise a major source of alternative prey to linyphiid spiders in arable fields, helping to sustain and retain these predators as aphid control agents within the crop. Polymerase chain reaction primers were developed for the amplification, from spider gut samples, of DNA from three of the most abundant species of Collembola in wheat crops in Europe, namely Isotoma anglicana, Lepidocyrtus cyaneus and Entomobrya multifasciata. The primers amplified fragments of the mitochondrial cytochrome oxidase subunit I (COI) gene and were designed following alignment of comparable sequences for a range of predator and prey species. Each of the primer pairs proved to be species-specific to a Collembola species, amplifying DNA fragments from 211 to 276 base pairs in length. Following consumption of a single collembolan, prey DNA was detectable in 100% of spiders after 24 h of digestion. We report the first use of DNA-based techniques to detect predation by arthropods on natural populations of prey in the field. All three species of Collembola were consumed by the spiders. By comparing the ratios of the Collembola species in the field with the numbers of spiders that gave positive results for each of those species, it was possible to demonstrate that the spiders were exercising prey choice. Overall, a single target species of Collembola was eaten by 48% of spiders while a further 16% of spiders contained DNA from two different species of Collembola. Preference was particularly evident for I. anglicana, the species most frequently found in spider guts yet the least numerous of the three target species in the field.
TL;DR: In a study of 53 faeces sampled from three social groups over 10 days, it is found that direct enumeration could not be used to estimate population size, but that the application of mark–recapture models has the potential to provide more accurate results.
Abstract: The potential link between badgers and bovine tuberculosis has made it vital to develop accurate techniques to census badgers. Here we investigate the potential of using genetic profiles obtained from faecal DNA as a basis for population size estimation. After trialling several methods we obtained a high amplification success rate (89%) by storing faeces in 70% ethanol and using the guanidine thiocyanate/silica method for extraction. Using 70% ethanol as a storage agent had the advantage of it being an antiseptic. In order to obtain reliable genotypes with fewer amplification reactions than the standard multiple-tubes approach, we devised a comparative approach in which genetic profiles were compared and replication directed at similar, but not identical, genotypes. This modified method achieved a reduction in polymerase chain reactions comparable with the maximum-likelihood model when just using reliability criteria, and was slightly better when using reliability criteria with the additional proviso that alleles must be observed twice to be considered reliable. Our comparative approach would be best suited for studies that include multiple faeces from each individual. We utilized our approach in a well-studied population of badgers from which individuals had been sampled and reliable genotypes obtained. In a study of 53 faeces sampled from three social groups over 10 days, we found that direct enumeration could not be used to estimate population size, but that the application of mark-recapture models has the potential to provide more accurate results.
TL;DR: A genetic survey of the forest elephant population at Kakum National Park, Ghana was performed using multilocus genotyping of noninvasively collected samples, and the population size, sex ratio and genetic variability was very close to that obtained using dung counts.
Abstract: African forest elephants are difficult to observe in the dense vegetation, and previous studies have relied upon indirect methods to estimate population sizes. Using multilocus genotyping of noninvasively collected samples, we performed a genetic survey of the forest elephant population at Kakum National Park, Ghana. We estimated population size, sex ratio and genetic variability from our data, then combined this information with field observations to divide the population into age groups. Our population size estimate was very close to that obtained using dung counts, the most commonly used indirect method of estimating the population sizes of forest elephant populations. As their habitat is fragmented by expanding human populations, management will be increasingly important to the persistence of forest elephant populations. The data that can be obtained from noninvasively collected samples will help managers plan for the conservation of this keystone species.
TL;DR: The results suggest that extended pre‐ and post‐commercial monitoring are necessary to assess the long‐term impact of Bt toxin in transgenic plant residues on soil organisms.
Abstract: Large quantities of Bacillus thuringiensis (Bt) corn plant residue are left in the field after harvest, which may have implications for the soil ecosystem Potential impacts on soil organisms will also depend on the persistence of the Bt toxin in plant residues Therefore, it is important to know how long the toxin persists in plant residues In two field studies in the temperate corn-growing region of Switzerland we investigated degradation of the Cry1Ab toxin in transgenic Bt corn leaves during autumn, winter and spring using an enzyme-linked immunosorbent assay (ELISA) In the first field trial, representing a tillage system, no degradation of the Cry1Ab toxin was observed during the first month During the second month, Cry1Ab toxin concentrations decreased to ∪ 20% of their initial values During winter, there was no further degradation When temperatures again increased in spring, the toxin continued to degrade slowly, but could still be detected in June In the second field trial, representing a no-tillage system, Cry1Ab toxin concentrations decreased without initial delay as for soil-incorporated Bt plants, to 38% of the initial concentration during the first 40 days They then continued to decrease until the end of the trial after 200 days in June, when 03% of the initial amount of Cry1Ab toxin was detected Our results suggest that extended pre- and post-commercial monitoring are necessary to assess the long-term impact of Bt toxin in transgenic plant residues on soil organisms
TL;DR: The study of hybrid zones is central to the understanding of the genetic basis of reproductive isolation and speciation, and using a model‐based clustering method for individual admixture analysis, the existence of intermediate genotypes in all samples from the transition area is demonstrated.
Abstract: The study of hybrid zones is central to our understanding of the genetic basis of reproductive isolation and speciation, yet very little is known about the extent and significance of hybrid zones in marine fishes. We examined the population structure of cod in the transition area between the North Sea and the Baltic Sea employing nine microsatellite loci. Genetic differentiation between the North Sea sample and the rest increased along a transect to the Baltic proper, with a large increase in level of differentiation occurring in the Western Baltic area. Our objective was to determine whether this pattern was caused purely by varying degrees of mechanical mixing of North Sea and Baltic Sea cod or by interbreeding and formation of a hybrid swarm. Simulation studies revealed that traditional Hardy-Weinberg analysis did not have sufficient power for detection of a Wahlund effect. However, using a model-based clustering method for individual admixture analysis, we were able to demonstrate the existence of intermediate genotypes in all samples from the transition area. Accordingly, our data were explained best by a model of a hybrid swarm flanked by pure nonadmixed populations in the North Sea and the Baltic Sea proper. Significant correlation of gene identities across loci (gametic phase disequilibrium) was found only in a sample from the Western Baltic, suggesting this area as the centre of the apparent hybrid zone. A hybrid zone for cod in the ecotone between the high-saline North Sea and the low-saline Baltic Sea is discussed in relation to its possible origin and maintenance, and in relation to a classical study of haemoglobin variation in cod from the Baltic Sea/Danish Belt Sea, suggesting mixing of two divergent populations without interbreeding.
TL;DR: The genetic structure of the mosaic hybrid zone between the marine mussels Mytilus edulis and M. galloprovincialis is analysed using three length‐polymorphic PCR loci as neutral and diagnostic markers along the Atlantic coast of Europe, indicating a strong genetic barrier within all transition zones.
Abstract: Hybrid zones are fascinating systems to investigate the structure of genetic barriers. Marine hybrid zones deserve more investigation because of the generally high dispersion potential of planktonic larvae which allows migration on scales unrivalled by terrestrial species. Here we analyse the genetic structure of the mosaic hybrid zone between the marine mussels Mytilus edulis and M. galloprovincialis , using three length-polymorphic PCR loci as neutral and diagnostic markers on 32 samples along the Atlantic coast of Europe. Instead of a single genetic gradient from M. galloprovincialis on the Iberian Peninsula to M. edulis populations in the North Sea, three successive transitions were observed in France. From South to North, the frequency of alleles typical of M. galloprovincialis first decreases in the southern Bay of Biscay, remains low in Charente, then increases in South Brittany, remains high in most of Brittany, and finally decreases again in South Normandy. The two enclosed patches observed in the midst of the mosaic hybrid zone in Charente and Brittany, although predominantly M. edulis -like and M. galloprovincialis -like, respectively, are genetically original in two respects. First, considering only the various alleles typical of one species, the patches show differentiated frequencies compared to the reference external populations. Second, each patch is partly introgressed by alleles of the other species. When introgression is taken into account, linkage disequilibria appear close to their maximum possible values, indicating a strong genetic barrier within all transition zones. Some pre- or postzygotic isolation mechanisms (habitat specialization, spawning asynchrony, assortative fertilization and hybrid depression) have been documented in previous studies, although their relative importance remains to be evaluated. We also provided evidence for a recent migratory ‘shortcut’ connecting M. edulis -like populations of the Charente patch to an external M. edulis population in Normandy and thought to reflect artificial transfer of spat for aquaculture.
TL;DR: The root vole (Microtus oeconomus) is divided into four main mtDNA phylogenetic lineages that seem to have largely allopatric distributions as discussed by the authors.
Abstract: A species-wide phylogeographical study of the root vole (Microtus oeconomus) was performed using the whole 1140 base pair mitochondrial (mt) cytochrome b gene. We examined 83 specimens from 52 localities resulting in 65 unique haplotypes. Our results demonstrate that the root vole is divided into four main mtDNA phylogenetic lineages that seem to have largely allopatric distributions. Net divergence estimates (2.0-3.5%) between phylogroups, as well as relatively high nucleotide diversity estimates within phylogroups, indicate that the distinct phylogeographical structure was initiated by historical events that predated the latest glaciation. European root voles are divided into a Northern and a Central mtDNA phylogroup. The mtDNA data in concert with fossil records imply that root voles remained north of the classical refugial areas in southern Europe during the last glacial period. The currently fragmented populations in central Europe belong to a single mtDNA phylogroup. The Central Asian and the North European lineages are separated by the Ural Mountains, a phylogeographical split also found in collared lemmings (Dicrostonyx) and the common vole (M. arvalis). The Beringian lineage occurs from eastern Russia through Alaska to northwestern Canada. This distribution is congruent with the traditional boundaries of the Beringian refugium and with phylogeographical work on other organisms. In conclusion, similarities between the phylogeographical patterns in the root vole and other rodents, such as Arctic and subarctic lemmings, as well as more temperate vole species, indicate that late Quaternary geological and climatic events played a strong role in structuring northern biotic communities.
TL;DR: Fungi and oomycetes are important in the nutrient cycles of the world and their interactions with plants sometimes benefit and sometimes act to the detriment of humans as discussed by the authors.
Abstract: Fungi (kingdom Mycota) and oomycetes (kingdom Stramenopila, phylum Oomycota) are crucially important in the nutrient cycles of the world. Their interactions with plants sometimes benefit and sometimes act to the detriment of humans. Many fungi establish ecologically vital mutualisms, such as in mycorrhizal fungi that enhance nutrient acquisition, and endophytes that combat insects and other herbivores. Other fungi and many oomycetes are plant pathogens that devastate natural and agricultural populations of plant species. Studies of fungal and oomycete evolution were extraordinarily difficult until the advent of molecular phylogenetics. Over the past decade, researchers applying these new tools to fungi and oomycetes have made astounding new discoveries, among which is the potential for interspecific hybridization. Consequences of hybridization among pathogens include adaptation to new niches such as new host species, and increased or decreased virulence. Hybrid mutualists may also be better adapted to new hosts and can provide greater or more diverse benefits to host plants.
TL;DR: It is shown that diversification and establishment of spatial genetic structure across six taxonomic groups coincide with the putative age of California's mountain ranges and aridification in the region, demonstrating the importance of geographical barriers and climatological events to species diversifying and the overall geographical structure of biodiversity.
Abstract: The California Floristic Province harbours more endemic plant and animal taxa and more identifiable subspecies than any other area of comparable size in North America. We present evidence that physical historical processes have resulted in congruent patterns of genetic diversity over the past 2-10 million years. Using a molecular clock approach we show that diversification and establishment of spatial genetic structure across six taxonomic groups coincide with the putative age of California's mountain ranges and aridification in the region. Our results demonstrate the importance of geographical barriers and climatological events to species diversification and the overall geographical structure of biodiversity. These results should facilitate conservation efforts in this biodiversity hotspot for taxa whose population genetic structure is still unknown and may suggest the potential utility of this approach in regional conservation planning efforts.
TL;DR: The overall pattern of genetic variation within and between subpopulations suggested a ‘classical’ metapopulation structure of the species suggested by the ecological surveys, and relative high amounts of linkage disequilibrium at subpopulation level indicated recent population bottlenecks or admixture.
Abstract: We investigated the distribution of genetic variation within and between seven subpopulations in a riparian population of Silene tatarica in northern Finland by using amplified fragment length polymorphism (AFLP) markers. A Bayesian approach-based clustering program indicated that the marker data contained not only one panmictic population, but consisted of seven clusters, and that each original sample site seems to consist of a distinct subpopulation. A coalescent-based simulation approach shows recurrent gene flow between subpopulations. Relative high FST values indicated a clear subpopulation differentiation. However, amova analysis and UPGMA-dendrogram did not suggest any hierarchical regional structuring among the subpopulations. There was no correlation between geographical and genetic distances among the subpopulations, nor any correlation between the subpopulation census size and amount of genetic variation. Estimates of gene flow suggested a low level of gene flow between the subpopulations, and the assignment tests proposed a few long-distance bidirectional dispersal events between the subpopulations. No apparent difference was found in within-subpopulation genetic diversity among upper, middle and lower regions along the river. Relative high amounts of linkage disequilibrium at subpopulation level indicated recent population bottlenecks or admixture, and at metapopulation levels a high subpopulation turnover rate. The overall pattern of genetic variation within and between subpopulations also suggested a 'classical' metapopulation structure of the species suggested by the ecological surveys.
TL;DR: The results show that the distribution of genetically distinct zooxanthellae is correlated with light regime and possibly temperature in some (but not all) colonies of A. tenuis and A. valida and at some reef locations, which is interpreted as acclimation to local environmental conditions.
Abstract: Intra- and intercolony diversity and distribution of zooxanthellae in acroporid corals is largely uncharted. In this study, two molecular methods were applied to determine the distribution of zooxanthellae in the branching corals Acropora tenuis and A. valida at several reef locations in the central section of the Great Barrier Reef. Sun-exposed and shaded parts of all colonies were examined. Single-stranded conformational polymorphism analysis showed that individual colonies of A. tenuis at two locations harbour two strains of Symbiodinium belonging to clade C (C1 and C2), whereas conspecific colonies at two other reefs harboured a single zooxanthella strain. A. valida was found to simultaneously harbour strains belonging to two distinct phylogenetic clades (C and D) at all locations sampled. A novel method with improved sensitivity (quantitative polymerase chain reaction using Taqman™ fluorogenic probes) was used to map the relative abundance distribution of the two zooxanthella clades. At two of the five sampling locations both coral species were collected. At these two locations, composition of the zooxanthella communities showed the same pattern in both coral species, i.e. correlation with ambient light in Pioneer Bay and an absence thereof in Nelly Bay. The results show that the distribution of genetically distinct zooxanthellae is correlated with light regime and possibly temperature in some (but not all) colonies of A. tenuis and A. valida and at some reef locations, which we interpret as acclimation to local environmental conditions.
TL;DR: The results suggest a very high degree of genetic subdivision both in neutral marker genes and genes coding quantitative traits across a relatively recently colonized environmental gradient and give evidence for natural selection being the primary agent behind the observed latitudinal differentiation in quantitative traits.
Abstract: 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.
TL;DR: In this paper, a bias-corrected estimator of the effective number of types (mates or alleles) was proposed, and compared to previous methods for estimating true and effective numbers of types using Monte Carlo simulations.
Abstract: Estimating paternity and genetic relatedness is central to many empirical and theoretical studies of social insects. The two important measures of a queen's mating number are her actual number of mates and her effective number of mates. Estimating the effective number of mates is mathematically identical to the problem of estimating the effective number of alleles in population genetics, a common measure of genetic variability introduced by Kimura & Crow (1964). We derive a new bias-corrected estimator of effective number of types (mates or alleles) and compare this new method to previous methods for estimating true and effective numbers of types using Monte Carlo simulations. Our simulation results suggest that the examined estimators of the true number of types have very similar statistical properties, whereas the estimators of effective number of types have quite different statistical properties. Moreover, our new proposed estimator of effective number of types is approximately unbiased, and has considerably lower variance than the original estimator. Our new method will help researchers more accurately estimate intracolony genetic relatedness of social insects, which is an important measure in understanding their ecology and social behaviour. It should also be of use in population genetic studies in which the effective number of alleles is of interest.
TL;DR: The case study showed that given a comparable analytical effort in the laboratory, AFLP were much more efficient than the microsatellites in discriminating the source of an individual among putative populations, especially in systems characterized by weak population structuring.
Abstract: Individual-based population assignment tests have thus far mainly relied on the use of microsatellite loci. However, the logistic difficulty of screening large numbers of loci required to reach sufficient statistical power hampers the usefulness of microsatellites in situations of weak population structuring. Amplified fragment length polymorphisms (AFLP) represents an alternative for overcoming this logistical issue as the technique allows the user to characterize a much larger number of loci with a comparable analytical effort. In this study, an assignment test based on maximum likelihood for dominant markers was used to investigate the potential usefulness of AFLP for population assignment. We also compared assignment success achieved with AFLP with that obtained using microsatellites in a case study of low population differentiation involving whitefish (Coregonus clupeaformis) sympatric ecotypes. The analytical investigation showed that the minimum number of AFLP loci required to reach an assignment success of 95% stood within values that are easily achievable in many situations. This also showed how assignment success varied according to the number of AFLP loci used, their absolute frequency and their frequency differential and sampling errors, as well as the number of putative source populations. The case study showed that given a comparable analytical effort in the laboratory, AFLP were much more efficient than the microsatellite loci in discriminating the source of an individual among putative populations. AFLP resulted in higher assignment success at all levels of stringency and the log-likelihood differences between populations obtained with AFLP for each individual were much larger than those obtained with microsatellites. These results indicate that research involving individual-based population assignment methods should benefit importantly from the use of AFLP markers, especially in systems characterized by weak population structuring.
TL;DR: Patterns of differentiation in 10 microsatellite loci among North American and European Phragmites individuals are compared with results obtained from sequencing of noncoding chloroplast DNA, emphasizing that native, introduced and Gulf Coast North American PhragMites lineages are genetically distinct.
Abstract: Over the past century, the spread of the common reed (Phragmites australis) has had a dramatic impact on wetland communities across North America. Although native populations of Phragmites persist, introduced invasive populations have dominated many sites and it is not clear if the two types can interbreed. This study compares patterns of differentiation in 10 microsatellite loci among North American and European Phragmites individuals with results obtained from sequencing of noncoding chloroplast DNA. Three population lineages (native, introduced and Gulf Coast) were previously identified in North America from chloroplast DNA and similar structuring was found in the nuclear genome. Each lineage was distinguished by unique alleles and allele combinations and the introduced lineage was closely related to its hypothesized source population in Europe. Size homoplasy and diagnostic base substitutions distinguishing lineages were evident at several loci, further emphasizing that native, introduced and Gulf Coast North American Phragmites lineages are genetically distinct. Gene flow between lineages was low and invasive introduced populations do not represent a hybrid population type.
TL;DR: Comparisons with published distribution patterns of unrelated fish groups indicate that several of the reconstructed and dated hydrogeological–cladogenetic events may have acted at a large scale on the diversification of Neotropical freshwater fish fauna during late Tertiary.
Abstract: Tropical South America possesses the largest ichthyofauna of any continental region. To test whether palaeohydrological changes may have been the causes of such diversification, the 'hydrogeological' hypothesis, the phylogenetic relationships of 51 representatives of the catfish genus Hypostomus (Siluriformes: Loricariidae) were inferred using mitochondrial D-loop haplotype sequences. Specimens were collected in all main tropical South American rivers systems east to the Andes. The major interrelationships found with the D-loop data were confirmed with a subset of 21 species using complete internal transcribed spacer (ITS) region sequences. The phylogenetic analysis indicate that the genus Hypostomus can be divided into four monophyletic clades. The historical biogeographical analysis of each of these clades allows the identification of seven major cladogenetic events. Using calibrated D-loop and ITS molecular clocks, date estimations were attributed to each of these cladogenetic events allowing a linkage between four of them with documented hydrogeological changes. Comparisons with published distribution patterns of unrelated fish groups indicate that several of the reconstructed and dated hydrogeological-cladogenetic events may have acted at a large scale on the diversification of Neotropical freshwater fish fauna during late Tertiary.