The genetic covariance among clinal environments after adaptation to an environmental gradient in Drosophila serrata

We examined the genetic basis of clinal adaptation by determining the evolutionary response of life-history traits to laboratory natural selection along a gradient of thermal stress in Drosophila serrata. A gradient of heat stress was created by exposing larvae to a heat stress of 36degrees for 4 hr for 0, 1, 2, 3, 4, or 5 days of larval development, with the remainder of development taking place at 25degrees. Replicated lines were exposed to each level of this stress every second generation for 30 generations. At the end of selection, we conducted a complete reciprocal transfer experiment where all populations were raised in all environments, to estimate the realized additive genetic covariance matrix among clinal environments in three life-history traits. Visualization of the genetic covariance functions of the life-history traits revealed that the genetic correlation between environments generally declined as environments became more different and even became negative between the most different environments in some cases. One exception to this general pattern was a life-history trait representing the classic trade-off between development time and body size, which responded to selection in a similar genetic fashion across all environments. Adaptation to clinal environments may involve a number of distinct genetic effects along the length of the cline, the complexity of which may not be fully revealed by focusing primarily on populations at the ends of the cline.

Factors supporting the non-persistence of fruit fly populations in South Australia

For purposes of interstate and international fruit trade, it is necessary to demonstrate that in areas in which fruit fly species have not previously established permanent populations, but which are subject to introductions of fruit flies from outside the area, the introduced population once detected, has not become established. In this paper, we apply methodology suggested mainly by Carey (1991, 1995) to introductions of Mediterranean fruit fly (Medfly), Ceratitis capitata Weid., and Queensland fruit fly (QFF) Bactrocera tryoni Froggatt (Diptera: Tephritidae) to South Australia, a state in which these species do not occur naturally and in which introductions, once detected, are actively treated. By analysing historical data associated with fruit fly outbreaks in South Australia, we demonstrate that: (i) fruit flies occur seasonally, as would occur in established populations, except there is no evidence of the critical spring generation of either species; (ii) there is no evidence of increasing frequency of outbreaks, trapped flies or larval occurrences over 29 years; (iii) there is no evidence of decreasing time between catches of adult flies as the years progress; (iv) there is no decrease in the mean number of years between outbreaks in the same locations; (v) there is no statistically significant recurrence of outbreaks in the same locations in successive years; (vi) there is no evidence of spread of outbreaks outwards from a central location; (vii) the likelihood of outbreaks in a city or town is related to the size of the human population; (viii) introduction pathways by road from Western Australia (for Medfly) and eastern Australia (for QFF) are shown to exist and to illegally or accidentally carry considerable amounts of fruit into South Australia; and (ix) there was no association between the numbers of either Queensland fruit fly or Medfly and the spatial pattern of either loquat or cumquat trees as sources of larval food in spring. This analysis supports the hypothesis that most fruit fly outbreaks in South Australia have been the result of separate introductions of infested fruit by vehicular traffic and that most of the resultant fly outbreaks were detected and died out within a few weeks of the application of eradication procedures. An alternative hypothesis, that populations of fruit flies are established in South Australia at below detectable levels, is impossible to disprove with conventional technology, but the likelihood of it being true is minimised by our analysis. Both hypotheses could be tested soon with newly developed genetic techniques.

Targeting genetic resource conservation in widespread species: a case study of Cedrela odorata L.

Conservation of genetic resources is a recognised necessity for the long term maintenance of evolutionary potential. Effective assessment and implementation Strategies are required to permit rapid evaluation and protection of resources. Here we use information from the chloroplast, total genome and quantitative characters assayed across wide-ranging populations to assess genetic resources in a Neotropical tree, Cedrela odorata. A major differentiation identified for organelle, total genomic and quantitative variation was found to coincide with an environmental gradient across Costa Rica. However, a major evolutionary divergence between the Yucatan region and Honduras/Nicaragua identified within the chloroplast genome was not differentiated using quantitative characters. Based on these and other results, a three-tiered conservation genetic prioritisation process is recommended. In order of importance, and where information is available, conservation units should be defined using quantitative (expressed genes), nuclear (genetic connectivity) and organellar (evolutionary) measures. Where possible, information from range wide and local scale studies should be combined and emphasis should be placed on coincidental disjunctions for two or more measures. However, if only rapid assessments of diversity are possible, then assessment of organelle variation provides the most cautious assessment of genetic resources, at least for C. odorata, and can be used to propose initial conservation units. When considering effective implementation of genetic resource management strategies a final tier should be considered, that of landuse/geopolitical divisions. (C) 2004 Elsevier B.V. All rights reserved.

Genetic effects of chronic habitat fragmentation on tree species: the case of Sorbus aucuparia in a deforested Scottish landscape

Sustainable forest restoration and management practices require a thorough understanding of the influence that habitat fragmentation has on the processes shaping genetic variation and its distribution in tree populations. We quantified genetic variation at isozyme markers and chloroplast DNA (cpDNA), analysed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) in severely fragmented populations of Sorbus aucuparia (Rosaceae) in a single catchment (Moffat) in southern Scotland. Remnants maintain surprisingly high levels of gene diversity (H-E) for isozymes (H-E = 0.195) and cpDNA markers (H-E = 0.490). Estimates are very similar to those from non-fragmented populations in continental Europe, even though the latter were sampled over a much larger spatial scale. Overall, no genetic bottleneck or departures from random mating were detected in the Moffat fragments. However, genetic differentiation among remnants was detected for both types of marker (isozymes Theta(n) = 0.043, cpDNA Theta(c) = 0.131; G-test, P-value < 0.001). In this self-incompatible, insect-pollinated, bird-dispersed tree species, the estimated ratio of pollen flow to seed flow between fragments is close to 1 (r = 1.36). Reduced pollen-mediated gene flow is a likely consequence of habitat fragmentation, but effective seed dispersal by birds is probably helping to maintain high levels of genetic diversity within remnants and reduce genetic differentiation between them.

Genetic assignment methods for the direct, real-time estimation of migration rate: a simulation-based exploration of accuracy and power

Genetic assignment methods use genotype likelihoods to draw inference about where individuals were or were not born, potentially allowing direct, real-time estimates of dispersal. We used simulated data sets to test the power and accuracy of Monte Carlo resampling methods in generating statistical thresholds for identifying F-0 immigrants in populations with ongoing gene flow, and hence for providing direct, real-time estimates of migration rates. The identification of accurate critical values required that resampling methods preserved the linkage disequilibrium deriving from recent generations of immigrants and reflected the sampling variance present in the data set being analysed. A novel Monte Carlo resampling method taking into account these aspects was proposed and its efficiency was evaluated. Power and error were relatively insensitive to the frequency assumed for missing alleles. Power to identify F-0 immigrants was improved by using large sample size (up to about 50 individuals) and by sampling all populations from which migrants may have originated. A combination of plotting genotype likelihoods and calculating mean genotype likelihood ratios (D-LR) appeared to be an effective way to predict whether F-0 immigrants could be identified for a particular pair of populations using a given set of markers.

Genetic effects of kangaroo harvesting

There is concern that the commercial harvest of kangaroos (Macropus spp.) is affecting species fitness and evolutionary potential because the harvest selects for larger individuals, particularly males. This paper reviews the likely effect of selective harvesting on specific traits associated with fitness, including size, and on adaptive genotypes through generalised loss of gene diversity. Heritability for traits associated with fitness is low generally. The intensity of selection imposed by harvesting is low for several reasons: the geographic size of genetic populations is much larger than the harvest localities, which are therefore not closed but open with immigration acting to correct any change in allele frequencies through harvesting; the harvest targets kangaroos above a threshold weight that includes all adult males, not the largest males specifically; larger, older males may not confer significant fitness benefits on offspring; fitness traits are inherited through both sexes while males are targeted predominantly; populations are not at a selective equilibrium because food availability fluctuates, and the fittest is unlikely to be the largest. Comparisons of harvested and unharvested populations do not show any loss of gene diversity as a result of harvesting. The likelihood of a long-term genetic impact of kangaroo harvesting as currently practiced is negligible.

Genetic diversity and population structure of Tasmanian devils, the largest marsupial carnivore

Genetic diversity and population structure were investigated across the core range of Tasmanian devils (Sarcophilus laniarius; Dasyuridae), a wide-ranging marsupial carnivore restricted to the island of Tasmania. Heterozygosity (0.386-0.467) and allelic diversity (2.7-3.3) were low in all subpopulations and allelic size ranges were small and almost continuous, consistent with a founder effect. Island effects and repeated periods of low population density may also have contributed to the low variation. Within continuous habitat, gene flow appears extensive up to 50 km (high assignment rates to source or close neighbour populations; nonsignificant values of pairwise F-ST), in agreement with movement data. At larger scales (150-250 km), gene flow is reduced (significant pairwise F-ST) but there is no evidence for isolation by distance. The most substantial genetic structuring was observed for comparisons spanning unsuitable habitat, implying limited dispersal of devils between the well-connected, eastern populations and a smaller northwestern population. The genetic distinctiveness of the northwestern population was reflected in all analyses: unique alleles; multivariate analyses of gene frequency (multidimensional scaling, minimum spanning tree, nearest neighbour); high self-assignment (95%); two distinct populations for Tasmania were detected in isolation by distance and in Bayesian model-based clustering analyses. Marsupial carnivores appear to have stronger population subdivisions than their placental counterparts.

Fine-scale spatial genetic correlation analyses reveal strong female philopatry within a brush-tailed rock-wallaby colony in southeast Queensland

We combine spatial data on home ranges of individuals and microsatellite markers to examine patterns of fine-scale spatial genetic structure and dispersal within a brush-tailed rock-wallaby (Petrogale penicillata) colony at Hurdle Creek Valley, Queensland. Brush-tailed rock-wallabies were once abundant and widespread throughout the rocky terrain of southeastern Australia; however, populations are nearly extinct in the south of their range and in decline elsewhere. We use pairwise relatedness measures and a recent multilocus spatial autocorrelation analysis to test the hypotheses that in this species, within-colony dispersal is male-biased and that female philopatry results in spatial clusters of related females within the colony. We provide clear evidence for strong female philopatry and male-biased dispersal within this rock-wallaby colony. There was a strong, significant negative correlation between pairwise relatedness and geographical distance of individual females along only 800 m of cliff line. Spatial genetic autocorrelation analyses showed significant positive correlation for females in close proximity to each other and revealed a genetic neighbourhood size of only 600 m for females. Our study is the first to report on the fine-scale spatial genetic structure within a rock-wallaby colony and we provide the first robust evidence for strong female philopatry and spatial clustering of related females within this taxon. We discuss the ecological and conservation implications of our findings for rock-wallabies, as well as the importance of fine-scale spatial genetic patterns in studies of dispersal behaviour.

An investigation into effects of long-distance seed dispersal on organelle population genetic structure and colonization rate: a model analysis

A simulation-based modelling approach is used to examine the effects of stratified seed dispersal (representing the distribution of the majority of dispersal around the maternal parent and also rare long-distance dispersal) on the genetic structure of maternally inherited genomes and the colonization rate of expanding plant populations. The model is parameterized to approximate postglacial oak colonization in the UK, but is relevant to plant populations that exhibit stratified seed dispersal. The modelling approach considers the colonization of individual plants over a large area (three 500 km x 10 km rolled transects are used to approximate a 500 km x 300 km area). Our approach shows how the interaction of plant population dynamics with stratified dispersal can result in a spatially patchy haplotype structure. We show that while both colonization speeds and the resulting genetic structure are influenced by the characteristics of the dispersal kernel, they are robust to changes in the periodicity of long-distance events, provided the average number of long-distance dispersal events remains constant. We also consider the effects of additional physical and environmental mechanisms on plant colonization. Results show significant changes in genetic structure when the initial colonization of different haplotypes is staggered over time and when a barrier to colonization is introduced. Environmental influences on survivorship and fecundity affect both the genetic structure and the speed of colonization. The importance of these mechanisms in relation to the postglacial spread and genetic structure of oak in the UK is discussed.

Mutation scanning analysis of Marteilia sydneyi populations from different geographical locations in eastern Australia

Marteilia sydneyi (Paramyxea) is the causative agent of QX disease in oysters. In spite of the economic impact of this disease, its origin and the precise reason(s) for its apparent spread in Australian waters are not yet known. Given such knowledge gaps, investigating the population genetic structure(s) of M. sydneyi populations could provide insights into the epidemiology and ecology of the parasite and could assist in its prevention and control. In this study, single strand conformation polymorphism (SSCP)-based analysis of a region (195 bp) of the first internal transcribed spacer (ITS-1) of ribosomal DNA was employed to investigate genetic variation within and among five populations of M. sydneyi from oysters from five different locations in eastern Australia. The analysis showed the existence of a genetic variant of M. sydneyi common to the Great Sandy Strait, and the Richmond and Georges Rivers, as distinct from variants at the Pimpama and Clarence Rivers. Together with historical and other information relating to the QX disease outbreaks in eastern Australia, the molecular findings support the proposal that the parasite originated in the Great Sandy Strait and/or Richmond River and then extended southward along the coast. From a technical perspective, the study demonstrated the usefulness of SSCP as a tool to study the population genetics and epidemiology of M. sydneyi. (C) 2003 Elsevier Ltd. All rights reserved.

Genetic analysis of resistance to root-lesion nematode (Pratylenchus thornei) in wheat

The inheritance of resistance to root-lesion nematode was investigated in five synthetic hexaploid wheat lines and two bread wheat lines using a half-diallel design of F-1 and F-2 crosses. The combining ability of resistance genes in the synthetic hexaploid wheat lines was compared with the performance of the bread wheat line 'GS50a', the source of resistance to Pratylenchus thornei used in Australian wheat breeding programmes. Replicated glasshouse trials identified P. thornei resistance as polygenic and additive in gene action. General combining ability (GCA) of the parents was more important than specific combining ability (SCA) effects in the inheritance of P. thornei resistance in both F-1 and F-2 populations. The synthetic hexaploid wheat line 'CPI133872' was identified as the best general combiner, however, all five synthetic hexaploid wheat lines possessed better GCA than 'GS50a'. The synthetic hexaploid wheat lines contain novel sources of P. thornei resistance that will provide alternative and more effective sources of resistance to be utilized in wheat breeding programmes.

Phenotypic divergence along lines of genetic variance

Natural populations inhabiting the same environment often independently evolve the same phenotype. Is this replicated evolution a result of genetic constraints imposed by patterns of genetic covariation? We looked for associations between directions of morphological divergence and the orientation of the genetic variance-covariance matrix (G) by using an experimental system of morphological evolution in two allopatric nonsister species of rainbow fish. Replicate populations of both Melanotaenia eachamensis and Melanotaenia duboulayi have independently adapted to lake versus stream hydrodynamic environments. The major axis of divergence (z) among all eight study populations was closely associated with the direction of greatest genetic variance (g(max)), suggesting directional genetic constraint on evolution. However, the direction of hydrodynamic adaptation was strongly associated with vectors of G describing relatively small proportions of the total genetic variance, and was only weakly associated with g(max). In contrast, divergence between replicate populations within each habitat was approximately proportional to the level of genetic variance, a result consistent with theoretical predictions for neutral phenotypic divergence. Divergence between the two species was also primarily along major eigenvectors of G. Our results therefore suggest that hydrodynamic adaptation in rainbow fish was not directionally constrained by the dominant eigenvector of G. Without partitioning divergence as a consequence of the adaptation of interest (here, hydrodynamic adaptation) from divergence due to other processes, empirical studies are likely to overestimate the potential for the major eigenvectors of G to directionally constrain adaptive evolution.

The effects of habitat fragmentation due to forestry plantation establishment on the demography and genetic variation of a marsupial carnivore, Antechinus agilis

We conducted a demographic and genetic study to investigate the effects of fragmentation due to the establishment of an exotic softwood plantation on populations of a small marsupial carnivore, the agile antechinus (Antechinus agilis), and the factors influencing the persistence of those populations in the fragmented habitat. The first aspect of the study was a descriptive analysis of patch occupancy and population size, in which we found a patch occupancy rate of 70% among 23 sites in the fragmented habitat compared to 100% among 48 sites with the same habitat characteristics in unfragmented habitat. Mark-recapture analyses yielded most-likely population size estimates of between 3 and 85 among the 16 occupied patches in the fragmented habitat. Hierarchical partitioning and model selection were used to identify geographic and habitat-related characteristics that influence patch occupancy and population size. Patch occupancy was primarily influenced by geographic isolation and habitat quality (vegetation basal area). The variance in population size among occupied sites was influenced primarily by forest type (dominant Eucalyptus species) and, to a lesser extent, by patch area and topographic context (gully sites had larger populations). A comparison of the sex ratios between the samples from the two habitat contexts revealed a significant deficiency of males in the fragmented habitat. We hypothesise that this is due to male-biased dispersal in an environment with increased dispersal-associated mortality. The population size and sex ratio data were incorporated into a simulation study to estimate the proportion of genetic diversity that would have been lost over the known timescale since fragmentation if the patch populations had been totally isolated. The observed difference in genetic diversity (gene diversity and allelic richness at microsatellite and mitochondrial markers) between 16 fragmented and 12 unfragmented sites was extremely low and inconsistent with the isolation of the patch populations. Our results show that although the remnant habitat patches comprise approximately 2% of the study area, they can support non-isolated populations. However, the distribution of agile antechinus populations in the fragmented system is dependent on habitat quality and patch connectivity. (C) 2004 Elsevier Ltd. All rights reserved.

Historical and contemporary mating patterns in remnant populations of the forest tree Fraxinus excelsior L.

Genetic variation at microsatellite markers was used to quantify genetic structure and mating behavior in a severely fragmented population of the wind-pollinated, wind-dispersed temperate tree Fraxinus excelsior in a deforested catchment in Scotland. Remnants maintain high levels of genetic diversity, comparable with those reported for continuous populations in southeastern Europe, and show low interpopulation differentiation (Theta = 0.080), indicating that historical gene exchange has not been limited (Nm = 3.48). We estimated from seeds collected from all trees producing fruits in three of five remnants that F. excelsior is predominantly outcrossing (t(m). = 0.971 +/- 0.028). Use of a neighborhood model approach to describe the relative contribution of local and long-distance pollen dispersal indicates that pollen gene flow into each of the three remnants is extensive (46-95%) and pollen dispersal has two components. The first is very localized and restricted to tens of meters around the mother trees. The second is a long-distance component with dispersal occurring over several kilometers. Effective dispersal distances, accounting for the distance and directionality to mother trees of sampled pollen donors, average 328 m and are greater than values reported for a continuous population. These results suggest that the opening of the landscape facilitates airborne pollen movement and may alleviate the expected detrimental genetic effects of fragmentation.

Gene-flow between populations of cotton bollworm Helicoverpa armigera (Lepidoptera: Noctuidae) is highly variable between years

Both large and small scale migrations of Helicoverpa armigera Hübner in Australia were investigated using AMOVA analysis and genetic assignment tests. Five microsatellite loci were screened across 3142 individuals from 16 localities in eight major cotton and grain growing regions within Australia, over a 38-month period (November 1999 to January 2003). From November 1999 to March 2001 relatively low levels of migration were characterized between growing regions. Substantially higher than average gene-flow rates and limited differentiation between cropping regions characterized the period from April 2001 to March 2002. A reduced migration rate in the year from April 2002 to March 2003 resulted in significant genetic structuring between cropping regions. This differentiation was established within two or three generations. Genetic drift alone is unlikely to drive genetic differentiation over such a small number of generations, unless it is accompanied by extreme bottlenecks and/or selection. Helicoverpa armigera in Australia demonstrated isolation by distance, so immigration into cropping regions is more likely to come from nearby regions than from afar. This effect was most pronounced in years with limited migration. However, there is evidence of long distance dispersal events in periods of high migration (April 2001-March 2002). The implications of highly variable migration patterns for resistance management are considered.