Effects of a recent founding event and intrinsic population dynamics on genetic diversity in an ungulate population

Maintenance of genetic diversity has recently become a management goal for a number of species, due to its importance for present and future population viability. Genetic drift, primarily through differential reproductive success and inbreeding, can accelerate the loss of genetic diversity in recently recovered populations. We attempt to quantify the consequences of these factors on the genetic diversity contained in a small, recently founded wood bison (Bison bison athabascae) population by examining the genetic variation in this conservation herd, the calves born therein, and its large source population. The Hook Lake Wood Bison Recovery Project was initiated to found a disease-free herd of wood bison containing a representative amount of the genetic diversity present in the Wood Buffalo National Park metapopulation. Levels of diversity in the Hook Lake Wood Bison Recovery Project founders are higher than in previous salvage attempts. To examine the effects of differential reproductive success on this population, we monitored parentage of the calves born in the Hook Lake Wood Bison Recovery Project for 3 years since the founders reached sexual maturity. Two of the male founders sired over 90% of the offspring born in this population, which has led to a reduction in diversity in their calves. Monitoring of reproductive success, and incorporation of selective breeding strategies will be required to reduce the rate at which genetic diversity is lost from this small, isolated population. These steps should occur in other recovery projects, particularly when a small number of individuals are capable of dominating reproduction.     

Genetic structure of the whitefly Bemisia tabaci populations in Colombia following a recent invasion

The whitefly Bemisia tabaci (Gennadius) is one of the most important pests causing economic losses in a variety of cropping systems around the world. This species was recently found in a coastal region of Colombia and has now spread inland. To investigate this invasive process, the genetic structure of B. tabaci was examined in 8 sampling locations from 2 infested regions (coastal, inland) using 9 microsatellite markers and the mitochondrial COI gene. The mitochondrial analysis indicated that only the invasive species of the B. tabaci complex Middle East–Asia Minor 1 (MEAM 1 known previously as biotype B) was present. The microsatellite data pointed to genetic differences among the regions and no isolation by distance within regions. The coastal region in the Caribbean appears to have been the initial point of invasion, while the inland region in the Southwest showed genetic variation among populations most likely reflecting founder events and ongoing changes associated with climatic and topographical heterogeneity. These findings have implications for tracking and managing B. tabaci.     

Sex and boldness explain individual differences in spatial learning in a lizard

Understanding individual differences in cognitive performance is a major challenge to animal behaviour and cognition studies. We used the Eastern water skink (Eulamprus quoyii) to examine associations between exploration, boldness and individual variability in spatial learning, a dimension of lizard cognition with important bearing on fitness. We show that males perform better than females in a biologically relevant spatial learning task. This is the first evidence for sex differences in learning in a reptile, and we argue that it is probably owing to sex-specific selective pressures that may be widespread in lizards. Across the sexes, we found a clear association between boldness after a simulated predatory attack and the probability of learning the spatial task. In contrast to previous studies, we found a nonlinear association between boldness and learning: both ‘bold’ and ‘shy’ behavioural types were more successful learners than intermediate males. Our results do not fit with recent predictions suggesting that individual differences in learning may be linked with behavioural types via high–low-risk/reward trade-offs. We suggest the possibility that differences in spatial cognitive performance may arise in lizards as a consequence of the distinct environmental variability and complexity experienced by individuals as a result of their sex and social tactics.     

Genetic structure,diversity and distribution of a threatened lizard affected by widespread habitat fragmentation

Understanding the demographic consequences of habitat loss on populations is essential for the conservation of threatened species. The threatened swamp skink (Lissolepis coventryi) is restricted to fragmented wetland habitats in Victoria and southeast South Australia. It has experienced significant habitat loss in the last 150 years, particularly around the Melbourne metropolitan area, where several small and isolated populations remain. Using mtDNA and nuDNA SNPs, we examined distribution patterns and population structure to infer evolutionary history and genetic distinctiveness of populations throughout the species’ range. For populations in the Melbourne metropolitan area, we examined genetic diversity. We found the species to be highly divergent, separating into two distinct lineages to the east and west of Melbourne, likely due to geological and climate influences causing isolation of populations. Species’ detectability was low, particularly in the far east despite relatively intact habitat and presumed higher abundance. Melbourne populations showed signs of limited genetic diversity. We suggest that translocations to promote gene diversity amongst these populations, together with habitat restoration and protection, present an important management strategy for L. coventryi.

     

Soil microbial community structure across a thermal gradient following a geothermal heating event

In this study microbial species diversity was assessed across a landscape in Yellowstone National Park, where an abrupt increase in soil temperature had occurred due to recent geothermal activity. Soil temperatures were measured, and samples were taken across a temperature gradient (35 to 65 degrees C at a 15-cm depth) that spanned geothermally disturbed and unimpacted soils; thermally perturbed soils were visually apparent by the occurrence of dead or dying lodgepole pine trees. Changes in soil microbial diversity across the temperature gradient were qualitatively assessed based on 16S rRNA sequence variation as detected by denaturing gradient gel electrophoresis (DGGE) using both ribosomal DNA (rDNA) and rRNA as PCR templates and primers specific for the Bacteria or Archaea domain. The impact of the major heating disturbance was apparent in that DGGE profiles from heated soils appeared less complex than those from the unaffected soils. Phylogenetic analysis of a bacterial 16S rDNA PCR clone library from a recently heated soil showed that a majority of the clones belonged to the Acidobacterium (51%) and Planctomyces (18%) divisions. Agar plate counts of soil suspensions cultured on dilute yeast extract and R2A agar media incubated at 25 or 50 degrees C revealed that thermophile populations were two to three orders of magnitude greater in the recently heated soil. A soil microcosm laboratory experiment simulated the geothermal heating event. As determined by both RNA- and DNA-based PCR coupled with DGGE, changes in community structure (marked change in the DGGE profile) of soils incubated at 50 degrees C occurred within 1 week and appeared to stabilize after 3 weeks. The results of our molecular and culture data suggest that thermophiles or thermotolerant species are randomly distributed in this area within Yellowstone National Park and that localized thermal activity selects for them.     

Genetic and morphological evolution following a founder event in the dark-eyed junco, Junco hyemalis thurberi

An isolated population of dark-eyed juncos, Junco hyemalis, became established on the campus of the University of California at San Diego (UCSD), probably in the early 1980s. It now numbers about 70 breeding pairs. Populations across the entire natural range of the subspecies J. h. thurberi are weakly differentiated from each other at five microsatellite loci (FST = 0.01). The UCSD population is significantly different from these populations, the closest of which is 70 km away. It has 88% of the genetic heterozygosity and 63% of the allelic richness of populations in the montane range of the subspecies, consistent with a harmonic mean effective population size of 32 (but with 95% confidence limits from four to > 70) over the eight generations since founding. Results suggest a moderate bottleneck in the early establishment phase but with more than seven effective founders. Individuals in the UCSD population have shorter wings and tails than those in the nearby mountains and a common garden experiment indicates that the morphological differences are genetically based. The moderate effective population size is not sufficient for the observed morphological differences to have evolved as a consequence of genetic drift, indicating a major role for selection subsequent to the founding of the UCSD population.     

Genetic evidence for a family structure in stable social aggregations of the Australian lizard Egernia stokesii

In this study we used data from six unlinked microsatellite loci to examine stable aggregations of Egernia stokesii, from a population in the southern Flinders Ranges of South Australia. We show that these aggregations are comprised of breeding partners, their offspring from two or more cohorts, and related adults, providing the first genetic evidence of a family structure in any lizard species. Despite this high level of relatedness within aggregations, most breeding pairs were unrelated and partners were less closely related to each other than they were to other potential within-group partners. Where individuals dispersed, both sexes usually moved to social groups close to their natal group. Although both sexes showed natal philopatry, there was some evidence that females in groups were more related than males in groups. These data suggest that an active choice of unrelated partners and male-biased dispersal may be the mechanisms used by E. stokesii to avoid inbreeding within groups.     

Genetic structure of a recent climate change‐driven range extension

The life‐history strategies of some species make them strong candidates for rapid exploitation of novel habitat under new climate regimes. Some early‐responding species may be considered invasive, and negatively impact on ‘naïve’ ecosystems. The barrens‐forming sea urchin Centrostephanus rodgersii is one such species, having a high dispersal capability and a high‐latitude range margin limited only by a developmental temperature threshold. Within this species’ range in eastern Australian waters, sea temperatures have increased at greater than double the global average rate. The coinciding poleward range extension of C. rodgersii has caused major ecological changes, threatening reef biodiversity and fisheries productivity. We investigated microsatellite diversity and population structure associated with range expansion by this species. Generalized linear model analyses revealed no reduction in genetic diversity in the newly colonized region. A ‘seascape genetics’ analysis of genetic distances found no spatial genetic structure associated with the range extension. The distinctive genetic characteristic of the extension zone populations was reduced population‐specific F_ST, consistent with very rapid population expansion. Demographic and genetic simulations support our inference of high connectivity between pre‐ and post‐extension zones. Thus, the range shift appears to be a poleward extension of the highly‐connected rangewide population of C. rodgersii. This is consistent with advection of larvae by the intensified warm water East Australian current, which has also increased Tasmanian Sea temperatures above the species’ lower developmental threshold. Thus, ocean circulation changes have improved the climatic suitability of novel habitat for C. rodgersii and provided the supply of recruits necessary for colonization.     

Divergent character clines across a recent secondary contact zone in a Hispaniolan lizard

Studies of genetic contact zones provide valuable information regarding the processes of population divergence, adaptation and speciation. In this paper, I examine transitions in morphology, mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) haplotypes across a recent secondary contact zone in a Hispaniolan lizard Ameiva chrysolaema . Maximum likelihood cline fitting analyses suggest non-coincidence of cline centers and that the mtDNA cline is significantly displaced to the west of the remaining clines. nDNA and morphological clines are coincident and tend to be associated with the prevailing environmental gradient. The lack of cytonuclear disequilibrium near the center of the contact zone and the non-coincidence of character clines suggest that this zone does not conform to a tension zone model of hybridization; thus, gene flow across the zone does not seem to be impeded. The extremely narrow width of the dorsal scale size cline and the close association of this cline with the steepness of the environmental (precipitation) gradient suggest that this character may be under environmental selection. Taken together, this contact zone appears to be structured by a combination of mtDNA introgression, possibly associated with eastward movement of the zone, and environmental selection on some characters.     

Genetic structure of an endangered raptor at individual and population levels

The Finnish population of White-tailed Eagle (Haliaeetus albicilla) has gone through two major demographic bottlenecks during the last two centuries. Strong conservation measures have allowed the population to recover, but despite the rapid population growth during recent years the species is still classified as endangered. We studied the genetic population structure at both individual and population levels in an attempt to recognize the processes shaping it. We used 9 microsatellite loci and 473 base pair fragment of the mitochondrial DNA control region on samples collected between the years 2003 and 2007 (N = 489). We found a clear isolation by distance pattern at fine scale (i.e. individual level) which is most likely a result of species’ philopatric behaviour. Although we did not find signs of the recent bottlenecks, we did find evidence of an ancient bottleneck that has occurred most likely over 21,000 years ago, long before the genetic divergence of the two present Finnish subpopulations (one along the Baltic Sea coast line and another in Lapland and easternmost Finland). We conclude that the present population structure is mainly a consequence of the species philopatric behaviour over a long time period instead of recent population bottlenecks. Based on our results, the Finnish population seems to have ongoing immigration from neighbouring populations. Hence, even though the population has recovered mainly through local growth, our results suggest that gene flow from genetically differentiated populations have had an impact as well.     

Genetic variation and its evolutionary implications in a Mediterranean island endemic lizard

The peculiar bioclimatic and geographic features of Corso–Sardinian islands may provide an ideal scenario for investigating microevolutionary processes, given their large heterogeneity of environments, which could affect dispersal and gene flow among populations, as well as processes of local adaptation. The genetic variation and differentiation among populations of the endemic lizard Archaeolacerta bedriagae were studied by allozyme electrophoresis at 20 presumptive loci. The genetic structure of this species is characterized by relatively high levels of polymorphism and low differentiation among populations. The pattern of genetic differentiation cannot be explained by genetic drift as a function of geographic distance. Genetic distance data show that genetic variation is distributed into three geographically coherent population groups and suggest a recent (Late Pleistocene) origin for the observed geographic fragmentation. The analysis of environmental correlates of allozymic variation indicates a strong correlation of the Idh-1 locus with climatic variables. The frequency of the Idh-1¹⁰⁶ allele is negatively correlated with annual temperature, and positively correlated with annual precipitation. In addition, the observed heterozygosity at this locus decreases towards more arid climatic regimes. The results obtained support the assumption of differential selection acting on Idh-1 allozymes under diverse climates. An association between Idh-1 allozymes and local bioclimatic regimes was also observed for the sympatric lizard Podarcis tiliguerta , suggesting a key role for such selective agents on Idh-1 polymorphism in these two Corso–Sardinian lacertids.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 98 , 661–676.     

Genetic diversity across the range of a temperate lizard

Aim  To examine range-wide patterns of genetic diversity in association with range limits in a broadly distributed temperate lizard, and to identify the contributions of a series of environmental, geographical and historical variables to the observed patterns. Reduced genetic diversity may limit local adaptation in peripheral populations, thereby limiting their ability to adapt to marginal environmental conditions, possibly explaining the existence of temporally stable range limits.
Location  Various sampling locales throughout eastern and central USA and southern Ontario, Canada.
Methods  Genetic diversity of nuclear DNA microsatellites was estimated for each of 38 populations from across the range of eastern North America's most broadly distributed lizard, the five-lined skink, Plestiodon fasciatus (Linnaeus, 1758).
Results  Local climatic conditions and an interaction between distance from range border and glaciation history best predicted a population's present-day genetic diversity. Overall, peripheral populations had reduced genetic diversity relative to that of central populations, but this difference was attributable to the reduced genetic diversity in peripheral populations to the north and west that are not bordered by any obvious physical boundaries.
Main conclusions  Some, but not all, peripheral populations had reduced genetic diversity relative to that of more central populations, which probably arose through an interaction of ecological and historical factors. Peripheral populations that were bordered by an obvious boundary (e.g. an ocean) had higher diversity than peripheral populations that were not bordered by an obvious physical barrier to range expansion, suggesting that reduced intrapopulation genetic diversity is associated with range limits in the five-lined skink.     

Genetic structure of the wild boar population in Portugal: Evidence of a recent bottleneck

The present study assesses the degree of genetic structure and the presence of recent genetic bottlenecks in the wild boar population in Portugal. One hundred and ten individuals were sampled after capture during organised legal drive hunts, conducted in 58 municipalities across the continental territory, during the game seasons of 2002/2003 and 2003/2004. Individuals were genetically typed at six microsatellite loci using multiplex PCR amplification. Significant deviations from Hardy–Weinberg equilibrium were found for the total population of wild boar in Portugal. Wild boar population genetic structure was assessed using Bayesian methods, suggesting the existence of three subpopulations (North, Centre and South). Tests were conducted to detect the presence of potential migrants and hybrids between subpopulations. After exclusion of these individuals, three sets of wild boars representative of respective subpopulations were distinguished and tested for the effects of recent bottlenecks. Genetic distances between pairs of subpopulations were quantified using F_ST and R_ST estimators, revealing a variation of 0.138–0.178 and 0.107–0.198, respectively. On the basis of genetic and distribution data for Portuguese wild boar from the beginning of the 20th century, a model of strong demographic decline and contraction to isolated refuge areas at the national level, followed by a recovery and expansion towards former distribution limits is suggested. Some evidence points to present admixture among subpopulations in contact areas.     

Genetic structure and dispersal in a small South African rodent. Is dispersal female-biased?

Dispersal greatly determines genetic structure of populations, although it is influenced by landscape heterogeneity, quality of the matrix, resource distribution and local population densities and dynamics. To get insights into some of those processes we analysed the genetic structure of the hairy-footed gerbil Gerbillurus paeba (Rodentia, Murinae, Gerbillinae) in the southern Kalahari (South Africa). Samples were taken from 20 populations covering an area of about 2200 km². Genetic data were related to landscape characters and population dynamics. We used newly developed microsatellites and found at all loci some indication for the presence of null alleles. However, null alleles seem to have little influence on the general results of our analyses. Altogether we found even nearby populations of G. paeba to be significantly differentiated, although assignment tests revealed 24% of individuals as immigrants. Genetic structure was independent of landscape heterogeneities at all spatial scales. Autocorrelation analyses (range 50–90 km) revealed significant genetic structure within populations on distances <3 km. We found some indication for female-biased dispersal. Our study suggests that dispersing individuals have little influence on the long-term genetic structure and that drift is the major cause of genetic diversity. The observed genetic pattern likely derives from strong population fluctuations of G. paeba. The landscape structure has little influence on the genetic differentiation between populations.     

Genetic evidence for co-occurrence of chromosomal and thermal sex-determining systems in a lizard

An individual's sex depends upon its genes (genotypic sex determination or GSD) in birds and mammals, but reptiles are more complex: some species have GSD whereas in others, nest temperatures determine offspring sex (temperature-dependent sex determination). Previous studies suggested that montane scincid lizards (Bassiana duperreyi, Scincidae) possess both of these systems simultaneously: offspring sex is determined by heteromorphic sex chromosomes (XX-XY system) in most natural nests, but sex ratio shifts suggest that temperatures override chromosomal sex in cool nests to generate phenotypically male offspring even from XX eggs. We now provide direct evidence that incubation temperatures can sex-reverse genotypically female offspring, using a DNA sex marker. Application of exogenous hormone to eggs also can sex-reverse offspring (oestradiol application produces XY as well as XX females). In conjunction with recent work on a distantly related lizard taxon, our study challenges the notion of a fundamental dichotomy between genetic and thermally determined sex determination, and hence the validity of current classification schemes for sex-determining systems in reptiles.     

Experimentally replicated disruptive selection on performance traits in a Caribbean lizard

A central theme underlying studies of adaptive radiation is that ecologically mediated selection drives diversification. However, demonstrating the ecological basis of natural selection and linking this process to patterns of morphological diversity represents a formidable challenge. This is because selection experiments that test correlations between an organism's phenotype and its ecology are difficult to perform in the wild. Previous studies of Anolis lizards have shown that divergent morphologies are correlated with habitat use and have evolved repeatedly on islands throughout the Greater Antilles. Here, we show that the forms of selection acting within a species support an ecological mechanism for diversification. In natural populations, performance-related traits such as limb length are subject to correlational and disruptive selection driven by differences in habitat use. Experimental manipulations in the wild verify the same pattern of selection and indicate that both the targets and forms of selection are consistent through time. Elsewhere, we have demonstrated that these traits are heritable and should therefore evolve in response to selection. Our results provide evidence for the short-term repeatability of selection and its potency in the diversification of anoles.     

E-cadherin-mediated adhesion is not the founding event of epithelial cell polarity in Drosophila

Formation of a polarized epithelial layer is a fundamental step during the development of multicellular animals. This process involves the coordinated action of adhesion molecules, actin remodeling and spatial organization of membrane traffic. A recent article describes a new hierarchy for the development of epithelial polarity in the early Drosophila embryo. Bazooka, a Par-3 homolog, is properly localized in the absence of adherens junctions, indicating that the formation of epithelial junctions is not the founding event of epithelial polarization.