Allele frequency covariance among cohorts and its use in estimating effective size of age-structured populations

A general expression for the covariance of allele frequencies among cohorts in age-structured populations is derived. The expression is used to extend the so-called temporal method for estimating effective population size from allele frequency shifts among samples from cohorts born any number of years apart. Computer simulations are used to check on the accuracy and precision of the method, and an application to coastal Atlantic cod is presented.     

Population structure and impact of supportive breeding inferred from mitochondrial and microsatellite DNA analyses in land-locked Atlantic salmon Salmo salar L.

Four tributaries of Lake St-Jean (Québec, Canada) are used for spawning and juvenile habitat by land-locked Atlantic salmon. Spawning runs have drastically declined since the mid-1980s, and consequently, a supportive-breeding programme was undertaken in 1990. In this study, we analysed seven microsatellite loci and mtDNA, and empirically estimated effective population sizes to test the hypotheses that (i) fish spawning in different tributaries form genetically distinct populations and (ii) the supportive breeding programme causes genetic perturbations on wild populations. Allele frequency distribution, molecular variance and genetic distance estimates all supported the hypothesis of genetic differentiation among salmon from different tributaries. Gene flow among some populations was much more restricted than previously reported for anadromous populations despite the small geographical scale (40 km) involved. Both mtDNA and microsatellites revealed a more pronounced differentiation between populations from two tributaries of a single river compared with their differentiation with a population from a neighbouring river. The comparison of wild and F₁-hatchery fish (produced from breeders originating from the same river) indicated significant changes in allele frequencies and losses of low-frequency alleles but no reduction in heterozygosity. Estimates of variance and inbreeding population size indicated that susceptibility to genetic drift and inbreeding in one population increased by twofold after only one generation of supplementation.     

Fine-scale population structure in a desert amphibian: landscape genetics of the black toad (Bufo exsul)

Environmental variables can strongly influence a variety of intra- and inter-population processes, including demography, population structure and gene flow. When environmental conditions are particularly harsh for a certain species, investigating these effects is important to understanding how populations persist under difficult conditions. Furthermore, species inhabiting challenging environments present excellent opportunities to examine the effects of complex landscapes on population processes because these effects will often be more pronounced. In this study, I use 16 microsatellite loci to examine population structure, gene flow and demographic history in the black toad, Bufo exsul , which has one of the most restricted natural ranges of any amphibian. Bufo exsul inhabits four springs in the Deep Springs Valley high desert basin and has never been observed more than several meters from any source of water. My results reveal limited gene flow and moderately high levels of population structure ( F _ST = 0.051–0.063) between all but the two closest springs. I found that the geographic distance across the arid scrub habitat between springs is significantly correlated with genetic structure when distance accounts for topography and barriers to dispersal. I also found very low effective population sizes ( N _e = 7–30) and substantial evidence for historical population bottlenecks in all four populations. Together, these results suggest that the desert landscape and B.   exsul 's high habitat specificity contribute significantly to population structure and demography in this species and emphasize the importance of considering behavioural and landscape data in conservation genetic studies of natural systems.     

Population genetic structure, gene flow and sex-biased dispersal in frillneck lizards (Chlamydosaurus kingii)

By using both mitochondrial and nuclear multiloci markers, we explored population genetic structure, gene flow and sex-specific dispersal of frillneck lizards ( Chlamydosaurus kingii ) sampled at three locations, separated by 10 to 50 km, in a homogenous savannah woodland in tropical Australia. Apart from a recombinant lizard, the mitochondrial analyses revealed two nonoverlapping haplotypes/populations, while the nuclear markers showed that the frillneck lizards represented three separate clusters/populations. Due to the small population size of the mtDNA, fixation may occur via founder effects and/or drift. We therefore suggest that either of these two processes, or a combination of the two, are the most likely causes of the discordant results obtained from the mitochondrial and the nuclear markers. In contrast to the nonoverlapping mitochondrial haplotypes, in 12 out of 74 lizards, mixed nuclear genotypes were observed, hence revealing a limited nuclear gene flow. Although gene flow should ultimately result in a blending of the populations, we propose that the distinct nuclear population structure is maintained by frequent fires resulting in local bottlenecks, and concomitant spatial separation of the frillneck lizard populations. Limited mark–recapture data and the difference in distribution of the mitochondrial and nuclear markers suggest that the mixed nuclear genotypes were caused by juvenile male-biased dispersal.     

Small effective population sizes in a widespread selfing species, Lymnaea truncatula (Gastropoda: Pulmonata)

We present here a spatial and temporal population genetic survey of a common freshwater snail, also a predominantly selfing species, Lymnaea truncatula. The rate of genetic diversity loss was quantified by estimating the effective size (Ne) of the snail populations, using two different methods. A temporal survey allowed estimation of a variance effective size of the populations, and a spatial survey allowed the estimation of an inbreeding effective size, from two-locus identity disequilibria estimates. Both methods were consistent and provided low Ne values. Drift due to (i) high amounts of selfing and (ii) fluctuations in population sizes because of temporary habitats, and also selection coupled to genome-wide linkage disequilibria, could explain such reductions in Ne. The loss of genetic diversity appears to be counterbalanced only very partially by low apparent rates of gene flow.     

Contemporary gene flow and the spatio-temporal genetic structure of subdivided newt populations (Triturus cristatus, T. marmoratus)

Gene flow and drift shape the distribution of neutral genetic diversity in metapopulations, but their local rates are difficult to quantify. To identify gene flow between demes as distinct from individual migration, we present a modified Bayesian method to genetically test for descendants between an immigrant and a resident in a nonmigratory life stage. Applied to a metapopulation of pond-breeding European newts (Triturus cristatus, T. marmoratus) in western France, the evidence for gene flow was usually asymmetric and, for demes of known census size (N), translated into maximally seven reproducing immigrants. Temporal sampling also enabled the joint estimation of the effective demic population size (Ne) and the immigration rate m (including nonreproductive individuals). Ne ranged between 4.1 and 19.3 individuals, Ne/N ranged between 0.05 and 0.65 and always decreased with N; m was estimated as 0.19-0.63, and was possibly biased upwards. We discuss how genotypic data can reveal fine-scale demographic processes with important microevolutionary implications.     

Population structure and mitochondrial DNA variation in sedentary Neotropical birds isolated by forest fragmentation

The current worldwide concern about tropical deforestation raises questions about the sustainability of avian populations in isolated forest fragments. One of the most important issues concerns the sizes of forest fragments necessary to maintain populations and the genetic variation within them. We address this by: (1) using mtDNA sequence variation to infer aspects of the population structure of four species of understory birds from four sites in southern Costa Rican rainforest; and (2) determining whether forest fragmentation that has occurred in the last 50 years has had an effect on the amount of within-population variation for the species in question. High levels of between-population differentiation (D_xy) were found over a relatively small geographic scale (<130 km) for white-breasted wood-wren (Henicorhina leucosticta), bicolored antbird (Gymnopithys leucaspis), and gray-headed tanager (Eucometis penicillata), suggesting that these species are highly sedentary and exhibit strong female philopatry. No mtDNA variation was found in Plain Antvireo (Dysithamnus mentalis). In all three of the polymorphic species there was a significant decrease in mtDNA nucleotide diversity in populations isolated by forest fragmentation as compared to populations in contiguous primary forest. Even in relatively large (250–1000 ha) forest reserves, sedentary avian species have lost roughly half (range 43–85) of the nucleotide diversity in mtDNA over a relatively short period of time. Our results indicate that sedentary avian species in forest fragments isolated by clearing have undergone severe reductions in effective population size due to population bottlenecks perpetuated by prolonged isolation and potential edge effects.     

Life histories ofNeomysis integer,and its copepod prey,Eurytemora affinis,in a eutrophic and brackish shallow lake

Data was collected on the population structure and fecundity of the mysidNeomysis integer and the calanoid copepodEurytemora affinis in Hickling Broad, a shallow and eutrophic brackish lake, over a two-year period 1988/89. Standing biomass and production rate estimates were made using estimates of size-specific dry weights and development times obtained from laboratory measurements, field observations and information found in the literature. Both mysid and copepod are capable of a rapid response to favourable conditions and have high rates of birth, growth and production.E. affinis reproduces throughout the year with an estimated annual (May 1988–May 1989) production of 20 g dry wt m⁻². Copepod standing biomass was less in 1989 compared with 1988 owing to an overall reduction in copepod body-size and a reduction of size at maturity. There was a suggestion from the data that this was caused by predation from a greater number of large (>9 mm body-length) mysids in 1989 compared with 1988.N. integer is highly seasonal in its growth with distinct peaks of recruitment in May and July. Annual (May 1988–May 1989) production of the mysid was estimated as 5.8 g dry wt m⁻². AlthoughE. affinis is the only available prey ofN. integer in the lake, the mysid population appears independent of changes in that of the copepod and probably avoids negative predator-prey feedback mechanisms owing to an ability to feed on epiphytic algae.     

Population structure of North American beluga whales (Delphinapterus leucas) based on nuclear DNA microsatellite variation and contrasted with the population structure revealed by mitochondrial DNA variation

Beluga whales ( Delphinapterus leucas ) in North American waters migrate seasonally between wintering areas in broken pack ice and summering locations in estuaries and other open water areas in the Arctic and sub-Arctic. Results from our previous investigation of beluga whale mitochondrial DNA (mtDNA) revealed genetic heterogeneity among beluga from different summering locations that was interpreted as representing a high degree of summering site philopatry. However, mtDNA is maternally inherited and does not reflect mating that may occur among beluga from different summering locations in wintering areas or during annual migrations. To test the possibility that breeding occurs among beluga from different summering locations, genetic variability at five nuclear DNA (nDNA) microsatellite loci was examined in the same animals tested in the mtDNA study. Beluga samples ( n = 640) were collected between 1984 and 1994 from 24 sites across North America, mostly during the summer. Whales from the various sites were categorized into eight summering locations as identified by mtDNA analysis, as well as four hypothesized wintering areas: Bering Sea, Hudson Strait (Hudson Strait, Labrador Sea, southwest Davis Strait), Baffin Bay (North Water, east Davis Strait), and St Lawrence River. Microsatellite allele frequencies indicated genetic homogeneity among animals from summering sites believed to winter together but differentiation among whales from some of the wintering areas. In particular, beluga from western North America (Bering Sea) were clearly distinguished from beluga from eastern North America (Hudson Strait, Baffin Bay, and St Lawrence River). Based upon the combined data set, the population of North American beluga whales was divided into two evolutionarily significant units. However, the population may be further subdivided into management units to reflect distinct groups of beluga at summering locations.     

Population structure of North American beluga whales (Delphinapterus leucas) based on nuclear DNA microsatellite variation and contrasted with the population structure revealed by mitochondrial DNA variation

Beluga whales ( Delphinapterus leucas ) in North American waters migrate seasonally between wintering areas in broken pack ice and summering locations in estuaries and other open water areas in the Arctic and sub-Arctic. Results from our previous investigation of beluga whale mitochondrial DNA (mtDNA) revealed genetic heterogeneity among beluga from different summering locations that was interpreted as representing a high degree of summering site philopatry. However, mtDNA is maternally inherited and does not reflect mating that may occur among beluga from different summering locations in wintering areas or during annual migrations. To test the possibility that breeding occurs among beluga from different summering locations, genetic variability at five nuclear DNA (nDNA) microsatellite loci was examined in the same animals tested in the mtDNA study. Beluga samples ( n = 640) were collected between 1984 and 1994 from 24 sites across North America, mostly during the summer. Whales from the various sites were categorized into eight summering locations as identified by mtDNA analysis, as well as four hypothesized wintering areas: Bering Sea, Hudson Strait (Hudson Strait, Labrador Sea, southwest Davis Strait), Baffin Bay (North Water, east Davis Strait), and St Lawrence River. Microsatellite allele frequencies indicated genetic homogeneity among animals from summering sites believed to winter together but differentiation among whales from some of the wintering areas. In particular, beluga from western North America (Bering Sea) were clearly distinguished from beluga from eastern North America (Hudson Strait, Baffin Bay, and St Lawrence River). Based upon the combined data set, the population of North American beluga whales was divided into two evolutionarily significant units. However, the population may be further subdivided into management units to reflect distinct groups of beluga at summering locations.     

Extremely low effective population sizes, genetic structuring and reduced genetic diversity in a threatened bumblebee species, Bombus sylvarum (Hymenoptera: Apidae)

Habitat fragmentation may severely affect survival of social insect populations as the number of nests per population, not the number of individuals, represents population size, hence they may be particularly prone to loss of genetic diversity. Erosion of genetic diversity may be particularly significant among social Hymenoptera such as bumblebees (Bombus spp.), as this group may be susceptible to diploid male production, a suggested direct cost of inbreeding. Here, for the first time, we assess genetic diversity and population structuring of a threatened bumblebee species (Bombus sylvarum) which exists in highly fragmented habitat (rather than oceanic) islands. Effective population sizes, estimated from identified sisterhoods, were very low (range 21-72) suggesting that isolated populations will be vulnerable to loss of genetic variation through drift. Evidence of significant genetic structuring between populations (theta = 0.084) was found, but evidence of a bottleneck was detected in only one population. Comparison across highly fragmented UK populations and a continental population (where this species is more widespread) revealed significant differences in allelic richness attributable to a high degree of genetic diversity in the continental population. While not directly related to population size, this is perhaps explained by the high degree of isolation between UK populations relative to continental populations. We suggest that populations now existing on isolated habitat islands were probably linked by stepping-stone populations prior to recent habitat loss.     

Phylogeography, geographic structure, genetic variation, and potential species boundaries in Philippine slender toads

We investigated phylogeography of Philippine slender toads (genus Ansonia) and used a temporal framework for diversification, statistical tests of alternate topologies, and Bayesian approaches to test previous hypotheses concerning dispersal to, and colonization routes within, the southern Philippine island of Mindanao. Two species of Ansonia previously have been documented, with ranges separated by an east–west split corresponding to the approximate boundaries of Mindanao’s paleoisland precursors. We present new mtDNA sequence data (1946 bp from genes encoding ND1, 16S rRNA and tRNA^Leu) for 105 Ansonia specimens sampled from 20 localities on Mindanao Island. Our data suggest that Philippine Ansonia is composed of at least eight, well-supported population lineages, structured into a minimum of four highly divergent mtDNA clades. One clade corresponds to Ansonia mcgregori, a range-restricted species apparently limited to the distal portion of the Zamboanga Peninsula of western Mindanao. Two morphologically indistinguishable, but genetically divergent, lineages possibly are undescribed cryptic species from western Mindanao. We recognize the five remaining lineages as Ansonia muelleri pending data from morphology or bioacoustics that might diagnose separate species among these lineages. Regardless of their species status, the five allopatric lineages of A. muelleri should be viewed as important genetic units for future genetic conservation planning.     

Population genetic analysis of microsatellite variation of guppies (Poecilia reticulata) in Trinidad and Tobago: evidence for a dynamic source–sink metapopulation structure,founder events and population bottlenecks

Riverine fish populations are traditionally considered to be highly structured and subject to strong genetic drift. Here, we use microsatellites to analyse the population structure of the guppy (Poecilia reticulata), focussing on the headwater floodplain area of the Caroni drainage in Trinidad. We also analyse the population genetics of guppies in the Northern Drainage in Trinidad, a habitat characterized by rivers flowing directly into the sea, and a small isolated population in Tobago. Upland Caroni populations are highly differentiated and display low levels of genetic diversity. However, we found no evidence to suggest that these upland populations experienced recent population crashes and the populations appear to approach mutation–drift equilibrium. Dominant downstream migration over both short‐ and long‐time frames has a strong impact on the population genetics of lowland Caroni populations. This drainage system could be considered a source–sink metapopulation, with the tributary furthest downstream representing a ‘super sink’, receiving immigrants from rivers upstream in the drainage. Moreover, the effective population size in the lowlands is surprisingly low in comparison with the apparently large census population sizes.     

Fasciola hepatica demonstrates high levels of genetic diversity,a lack of population structure and high gene flow: possible implications for drug resistance

Fasciola hepatica, the liver fluke, is a trematode parasite of considerable economic importance to the livestock industry and is a re-emerging zoonosis that poses a risk to human health in F. hepatica-endemic areas worldwide. Drug resistance is a substantial threat to the current and future control of F. hepatica, yet little is known about how the biology of the parasite influences the development and spread of resistance. Given that F. hepatica can self-fertilise and therefore inbreed, there is the potential for greater population differentiation and an increased likelihood of recessive alleles, such as drug resistance genes, coming together. This could be compounded by clonal expansion within the snail intermediate host and aggregation of parasites of the same genotype on pasture. Alternatively, widespread movement of animals that typically occurs in the UK could promote high levels of gene flow and prevent population differentiation. We identified clonal parasites with identical multilocus genotypes in 61% of hosts. Despite this, 84% of 1579 adult parasites had unique multilocus genotypes, which supports high levels of genotypic diversity within F. hepatica populations. Our analyses indicate a selfing rate no greater than 2%, suggesting that this diversity is in part due to the propensity for F. hepatica to cross-fertilise. Finally, although we identified high genetic diversity within a given host, there was little evidence for differentiation between populations from different hosts, indicating a single panmictic population. This implies that, once those emerge, anthelmintic resistance genes have the potential to spread rapidly through liver fluke populations.     

Regulation of water flux through trunks, branches, and leaves in trees of a lowland tropical forest

We studied regulation of whole-tree water use in individuals of five diverse canopy tree species growing in a Panamanian seasonal forest. A construction crane equipped with a gondola was used to access the upper crowns and points along the branches and trunks of the study trees for making concurrent measurements of sap flow at the whole-tree and branch levels, and vapor phase conductances and water status at the leaf level. These measurements were integrated to assess physiological regulation of water use from the whole-tree to the single-leaf scale. Whole-tree water use ranged from 379 kg day⁻¹ in a 35 m-tall Anacardium excelsum tree to 46 kg day⁻¹ in an 18 m-tall Cecropia longipes tree. The dependence of whole-tree and branch sap velocity and sap flow on sapwood area was essentially identical in the five trees studied. However, large differences in transpiration per unit leaf area (E) among individuals and among branches on the same individual were observed. These differences were substantially reduced when E was normalized by the corresponding branch leaf area:sapwood area ratio (LA/SA). Variation in stomatal conductance (g _s) and crown conductance (g _c), a total vapor phase conductance that includes stomatal and boundary layer components, was closely associated with variation in the leaf area-specific total hydraulic conductance of the soil/leaf pathway (G _t). Vapor phase conductance in all five trees responded similarly to variation in G _t. Large diurnal variations in G _t were associated with diurnal variation in exchange of water between the transpiration stream and internal stem storage compartments. Differences in stomatal regulation of transpiration on a leaf area basis appeared to be governed largely by tree size and hydraulic architectural features rather than physiological differences in the responsiveness of stomata. We suggest that reliance on measurements gathered at a single scale or inadequate range of scale may result in misleading conclusions concerning physiological differences in regulation of transpiration. Received: 1 October 1997 / Accepted: 6 March 1998     

Genetic variation and diadromy in some native New Zealand galaxiids (Teleostei: Galaxiidae)

We examined genetic variation at 13 isozyme loci in three diadromous and two non-diadromous species of galaxiid fish from streams in South and Stewart Islands of New Zealand. Analysis of allele frequency data revealed higher F_s7 and Nei's D values among conspecific populations of the non-diadromous species. We propose that the genetic structurings of these species are affected by their migratory behaviours. We suggest that the derived condition of non-diadromous behaviour may increase scope for speciation, but also the probability of extinction. This is exacerbated by population fragmentation over the last century.     

Landscape genetics and hierarchical genetic structure in Atlantic salmon: the interaction of gene flow and local adaptation

Disentangling evolutionary forces that may interact to determine the patterns of genetic differentiation within and among wild populations is a major challenge in evolutionary biology. The objective of this study was to assess the genetic structure and the potential influence of several ecological variables on the extent of genetic differentiation at multiple spatial scales in a widely distributed species, the Atlantic salmon, Salmo salar . A total of 2775 anadromous fish were sampled from 51 rivers along the North American Atlantic coast and were genotyped using 13 microsatellites. A Bayesian analysis clustered these populations into seven genetically and geographically distinct groups, characterized by different environmental and ecological factors, mainly temperature. These groups were also characterized by different extent of genetic differentiation among populations. Dispersal was relatively high and of the same magnitude within compared to among regional groups, which contrasted with the maintenance of a regional genetic structure. However, genetic differentiation was lower among populations exchanging similar rates of local as opposed to inter-regional migrants, over the same geographical scale. This raised the hypothesis that gene flow could be constrained by local adaptation at the regional scale. Both coastal distance and temperature regime were found to influence the observed genetic structure according to landscape genetic analyses. The influence of other factors such as latitude, river length and altitude, migration tactic, and stocking was not significant at any spatial scale. Overall, these results suggested that the interaction between gene flow and thermal regime adaptation mainly explained the hierarchical genetic structure observed among Atlantic salmon populations.     

Estimates of gene flow, genetic substructure and population heterogeneity in bracken (Pteridium aquilinum)

Bracken [ Pteridium aquilinum (L.) Kuhn] is a cosmopolitan species and is a noxious weed in many areas. Because of its abundance, particularly in Britain, bracken affords an ideal system for investigating various aspects of population genetics and evolution. High mobility of dispersal units (spores) suggests that rates of gene flow among distant populations should be high. Gene flow is a major evolutionary force that influences the genetic structure of populations. To examine the effects of gene flow on population heterogeneity and population substructuring in bracken, starch gel electrophoresis of enzymes was used to provide the necessary genetic database. Allele frequency data at 21 loci were obtained for seven British populations, one Majorcan and one from the eastern United States. A model was employed to estimate the amount of gene flow ( Nm ) at several levels. Gene flow among British populations was extremely high ( Nm = 36.51), one of the highest estimates reported for plants. Among eight European populations gene flow was lower (but still considered high) at Nm = 2.47. Trans-Atlantic gene flow was low ( Nm = 0.0926).
F -statistics were used to assess population heterogeneity and substructuring. The data indicate that, compared with other species, there is very little genetic differentiation among British populations of bracken. Indeed, it appears that the whole island is behaving as a single randommating population. This result is consistent with high levels of gene flow. Only one population (on the Isle of Arran) showed statistically significant genetic substructuring. Habitat heterogeneity on the island and age structure are hypothesized as possible causes of this result.
The data reported here support previous studies demonstrating that bracken is genetically polymorphic and is an outcrossing species.