Papers by Siegfried Krauss
Molecular Ecology Notes, 2007
We developed 11 polymorphic microsatellite DNA markers for an Australian native shrub Banksia att... more We developed 11 polymorphic microsatellite DNA markers for an Australian native shrub Banksia attenuata. The number of alleles per locus in 50 individuals varied from five to 18, observed and expected heterozygosities ranged from 0.300 to 0.740 and from 0.537 to 0.918, respectively. Six loci showed no significant deviation from Hardy–Weinberg equilibrium (P > 0.05), and null alleles appear to exist at locus BA-B1. All loci showed independent inheritance.
Molecular Ecology, 2006
Spatial genetic variation within species is influenced by both contemporary and historical factor... more Spatial genetic variation within species is influenced by both contemporary and historical factors. We attempted to assess the impact of increased aridity and lower temperatures associated with the last glacial maximum on possible refugia and the structuring of genetic variation in Banksia hookeriana, a shrub species restricted to deep sands on the Eneabba sandplain and adjacent Gingin Scarp/Dandaragan Plateau, centred 300 km north of Perth, Western Australia. We used optically stimulated luminescence (OSL) dating to estimate the last time these sands were mobile, as well as amplified fragment length polymorphisms (AFLP) to infer spatial patterns and the phylogeographical history of genetic variation among 15 populations of B. hookeriana. While genetic variation at the species level was high, with 96.6% of 238 AFLP markers polymorphic, average within population gene diversity was low (Hpop = 0.16). Of the total genetic variation, an analysis of molecular variance (amova) partitioned 70% within populations, 24% among populations within substrate and 6% between substrates. There was an isolation-by-distance effect among populations within the same substrate, but not across substrates, and ordination highlighted genetic differentiation between the sandplain and scarp/plateau populations. A neighbour-joining tree identified the sandplain populations as a distinct clade, with the exception of the most northern sandplain population, which clustered with two northern and eastern plateau populations. The most southern plateau populations formed a clade sister to the sandplain clade. OSL dating of sand at six extant populations suggested that dunes were last mobile 15 000–35 000 years ago, with no clear difference in the ages of sandplain and plateau dunes. These data are consistent with a historical scenario of (re)colonization from isolated refugia of smaller populations either within the patchily vegetated sandplain and/or refugia at the northern, eastern and southern sandplain/scarp margins following postglacial climate amelioration and dune stabilization. Historic interpretations were confounded by the possible effects of long-distance dispersal, natural selection by substrate, and weak and/or ancient introgression with the sister species, Banksia prionotes.
Ecography, 2009
Long-distance dispersal (LDD) of seeds enables alleles, individuals and species of plants to (re)... more Long-distance dispersal (LDD) of seeds enables alleles, individuals and species of plants to (re)colonize suitable but remote habitats. Banksia attenuata is a long-lived resprouting shrub restricted to dune crests in fire-prone sclerophyll shrublands of the Eneabba sandplain, southwestern Australia. Highly polymorphic microsatellite DNA genetic markers and population assignment tests were employed to identify LDD immigrants among 788 individuals from 27 stands of B. attenuata comprising a metapopulation. Of the 487 (61.8% of the total) individuals unambiguously assigned to a unique source population, 27 (5.5%) were identified as immigrants by assignment to a known population other than that from which they were sampled, while the remaining 460 were assigned to the population from which they were sampled. The distance between source and sink populations for these immigrants ranged from 0.2 to 2.6 km, averaging 1.4 km, and broadly trending in the direction of seasonal winds. These results suggest that B. attenuata has similar long-distance seed dispersal properties as its co-occurring shorter-lived and fire-sensitive congener, B. hookeriana, despite fewer, larger and less mobile seeds. The frequency and distance of LDD for seeds observed in both species (5.5–6.8%) helps explain the persistence of populations on these geographically isolated dunes, where they are subject to local extinction from recurrent fire and severe summer drought, and will remain important under predicted climate change conditions. Analysis also revealed that species richness of the functional group to which B. attenuata belongs was positively correlated with the number of immigrants identified per dune, and such correlation was likely driven by environmental properties of the dunes, particularly water availability.
Physical Geography, 2003
Spatial genetic variation within species is influenced by both contemporary and historical factor... more Spatial genetic variation within species is influenced by both contemporary and historical factors. We attempted to assess the impact of increased aridity and lower temperatures associated with the last glacial maximum on possible refugia and the structuring of genetic variation in Banksia hookeriana , a shrub species restricted to deep sands on the Eneabba sandplain and adjacent Gingin Scarp/Dandaragan Plateau, centred 300 km north of Perth, Western Australia. We used optically stimulated luminescence (OSL) dating to estimate the last time these sands were mobile, as well as amplified fragment length polymorphisms (AFLP) to infer spatial patterns and the phylogeographical history of genetic variation among 15 populations of B. hookeriana . While genetic variation at the species level was high, with 96.6% of 238 AFLP markers polymorphic, average within population gene diversity was low ( H pop = 0.16). Of the total genetic variation, an analysis of molecular variance ( AMOVA ) partitioned 70% within populations, 24% among populations within substrate and 6% between substrates. There was an isolation-by-distance effect among populations within the same substrate, but not across substrates, and ordination highlighted genetic differentiation between the sandplain and scarp/plateau populations. A neighbour-joining tree identified the sandplain populations as a distinct clade, with the exception of the most northern sandplain population, which clustered with two northern and eastern plateau populations. The most southern plateau populations formed a clade sister to the sandplain clade. OSL dating of sand at six extant populations suggested that dunes were last mobile 15 000 -35 000 years ago, with no clear difference in the ages of sandplain and plateau dunes. These data are consistent with a historical scenario of (re)colonization from isolated refugia of smaller populations either within the patchily vegetated sandplain and/or refugia at the northern, eastern and southern sandplain/scarp margins following postglacial climate amelioration and dune stabilization. Historic interpretations were confounded by the possible effects of long-distance dispersal, natural selection by substrate, and weak and/or ancient introgression with the sister species, Banksia prionotes .
Molecular Ecology, 2004
There is currently a poor understanding of the nature and extent of long-distance seed dispersal,... more There is currently a poor understanding of the nature and extent of long-distance seed dispersal, largely due to the inherent difficulty of detection. New statistical approaches and molecular markers offer the potential to accurately address this issue. A log-likelihood population allocation test (aflpop) was applied to a plant metapopulation to characterize interpopulation seed dispersal. Banksia hookeriana is a fire-killed shrub, restricted to sandy dune crests in fire-prone shrublands of the Eneabba sandplain, southwest Australia. Population genetic variation was assessed for 221 individuals sampled from 21 adjacent dune-crest populations of B. hookeriana using amplified fragment length polymorphism. Genetic diversity was high, with 175 of 183 (96%) amplified fragment length polymorphism markers polymorphic. Of the total genetic diversity, 8% was partitioned among populations by amova and FST. There was no relationship between genetic diversity within populations and population demographic parameters such as population size and sample size. A population allocation test on these data unambiguously assigned 177 of 221 (80.1%) individuals to a single population. Of these, 171 (77.4% of total) were assigned to the population from which they were sampled and 6 (2.7% of total) were assigned to a known population other than the one from which they were sampled. A further 9 (4.1% of total) were assigned to outside the sampled metapopulation area, and 35 individuals (15.8%) could not be assigned unambiguously to any particular population. These results suggest that both the extent [15 of 221 (6.8%) individuals originating from a population other than the one in which they occur] and distance (1.6 to > 2.5 km), of seed dispersal between dune-crest populations is greater than expected from previous studies. The extent of long-distance interpopulation seed dispersal observed provides a basis for explaining the survival of populations of the fire-killed B. hookeriana in a landscape experiencing frequent fire, where local extinctions and recolonizations may be a regular occurrence.
Molecular Ecology Resources, 2008
We developed 11 polymorphic microsatellite DNA markers for an Australian native plant, Daviesia t... more We developed 11 polymorphic microsatellite DNA markers for an Australian native plant, Daviesia triflora. The number of alleles per locus in 40 individuals varied from four to 19, and observed and expected heterozygosities ranged from 0.450 to 0.925 and from 0.497 to 0.899, respectively. Nine loci showed no significant deviation from Hardy–Weinberg equilibrium (P > 0.05), and null alleles appear to exist at loci DT-A102 and DT-B103. All loci showed independent inheritance.
Molecular Ecology, 2005
The pattern of accumulation of genetic variation over time in seed banks is poorly understood. We... more The pattern of accumulation of genetic variation over time in seed banks is poorly understood. We examined the genetic structure of the aerial seed bank of Banksia hookeriana within a single 15-year-old population in fire-prone southwestern Australia, and compared genetic variation between adults and each year of a 9-year-old seed bank using amplified fragment length polymorphism (AFLP). B. hookeriana is well suited to the study of seed bank dynamics due to the canopy storage of its seeds, and because each annual crop can be identified. A total of 304 seeds from nine crop years and five maternal plants were genotyped, along with 113 plants from the adult population. Genetic variation, as assessed by the proportion of polymorphic markers (Pp) and Shannon's index (I), increased slightly within the seed bank over time, while gene diversity (Hj), did not change. Pp, I, and Hj all indicated that genetic variation within the seed bank quickly approached the maximal level detected. Analysis of molecular variance revealed that less than 4% of variation could be accounted for by variation among seeds produced in different years, whereas there was greater differentiation among maternal plants (12.7%), and among individual seeds produced by different maternal plants (83.4%). With increasing population age, offspring generated each year were slightly more outbred, as indicated by an increase in the mean number of nonmaternal markers per offspring. There were no significant differences for Hj or I between adults and the seed bank. Viability of seeds decreased with age, such that the viability of 9-year-old seeds was half that of 2-year-old seeds. These results suggest that variable fire frequencies have only limited potential to influence the amount of genetic variation stored within the seed bank of B. hookeriana.
Journal of Ecology, 2008
1Species diversity and genetic diversity are fundamental components of biodiversity. A primary go... more 1Species diversity and genetic diversity are fundamental components of biodiversity. A primary goal of biodiversity studies is to explain the distribution of species and alleles in space and time. A new challenge is to cross discipline boundaries and explore the relationship between these two scales of diversity.2In the biodiverse northern sandplain shrublands of south-western Australia, the woody shrub Banksia attenuata occurs on patchily distributed sand dunes, and coexists with B. hookeriana, B. menziesii, and two small tree species, Eucalyptus todtiana and Xylomelum angustifolium, which together comprise a plant functional group of large shrubs/small trees.3Genetic variation (alleles per locus and heterozygosity) between 736 B. attenuata individuals on 27 discrete dunes was assessed using 11 polymorphic microsatellite markers. For each dune, the physical properties of area and height, and species diversity (richness and evenness) of the functional group, were measured.4Synthesis. Genetic diversity of B. attenuata covaried positively with species diversity, which in turn covaried strongly with dune height rather than dune area. The positive relationship between species and genetic diversity demonstrated here supports the theory of common environmental, rather than neutral, processes acting directly or indirectly on both scales of diversity, and suggests the possibility of predicting one component of diversity on the basis of the other.Species diversity and genetic diversity are fundamental components of biodiversity. A primary goal of biodiversity studies is to explain the distribution of species and alleles in space and time. A new challenge is to cross discipline boundaries and explore the relationship between these two scales of diversity.In the biodiverse northern sandplain shrublands of south-western Australia, the woody shrub Banksia attenuata occurs on patchily distributed sand dunes, and coexists with B. hookeriana, B. menziesii, and two small tree species, Eucalyptus todtiana and Xylomelum angustifolium, which together comprise a plant functional group of large shrubs/small trees.Genetic variation (alleles per locus and heterozygosity) between 736 B. attenuata individuals on 27 discrete dunes was assessed using 11 polymorphic microsatellite markers. For each dune, the physical properties of area and height, and species diversity (richness and evenness) of the functional group, were measured.Synthesis. Genetic diversity of B. attenuata covaried positively with species diversity, which in turn covaried strongly with dune height rather than dune area. The positive relationship between species and genetic diversity demonstrated here supports the theory of common environmental, rather than neutral, processes acting directly or indirectly on both scales of diversity, and suggests the possibility of predicting one component of diversity on the basis of the other.
Journal of Evolutionary Biology, 2003
Putative hybrids between Banksia hookeriana and B. prionotes were identified among 12 of 106 popu... more Putative hybrids between Banksia hookeriana and B. prionotes were identified among 12 of 106 populations of B. hookeriana located at or near anthropogenically disturbed sites, mainly roadways, but none in 156 undisturbed populations. Morphometrics and AFLP markers confirmed that a hybrid swarm existed in a selected disturbed habitat, whereas no intermediates were present where the two species co-occurred in undisturbed vegetation. Individuals of both species in disturbed habitats at 12 sites were more vigorous, with greater size and more flower heads than their counterparts in undisturbed vegetation. These more fecund plants also showed a shift in season and duration of flowering. By promoting earlier flowering of B. hookeriana plants and prolonging flowering of B. prionotes, anthropogenic disturbance broke the phenological barrier between these two species. We conclude that anthropogenic disturbance promotes hybridization through increasing opportunities for gene flow by reducing interpopulation separation, increasing gamete production and, especially, promoting coflowering.
Molecular Ecology, 2000
Three procedures for the estimation of null allele frequencies and gene diversity from dominant m... more Three procedures for the estimation of null allele frequencies and gene diversity from dominant multilocus data were empirically tested in natural populations of the outcrossing angiosperm Persoonia mollis (Proteaceae). The three procedures were the square root transform of the null homozygote frequency, the Lynch & Milligan procedure, and the Bayesian method. Genotypes for each of 116 polymorphic loci generated by amplified fragment length polymorphism (AFLP) were inferred from segregation patterns in progeny arrays. Therefore, for the plus phenotype (band present), heterozygotes were distinguished from homozygotes. In contrast to previous studies, all three procedures produced very similar mean estimates of heterozygosity, which were in turn accurate estimators of the direct value (HO = 0.28). A second population of P. mollis displayed markedly lower levels of heterozygosity (HO = 0.20) but approximately twice as many polymorphic loci (284). These AFLP results show that biases in estimates of average null allele frequency and heterozygosity are largely eliminated in highly polymorphic dominant marker data sets displaying a J-shaped beta distribution with a high percentage of loci containing more than three null homozygotes and relatively few loci with no null homozygotes. This distribution may be typical of outcrossing angiosperms.
Molecular Ecology, 1999
The utility of the new polymerase chain reaction (PCR)-based multilocus DNA fingerprinting techni... more The utility of the new polymerase chain reaction (PCR)-based multilocus DNA fingerprinting technique amplified fragment length polymorphism (AFLP) for paternity analysis in natural plant populations was assessed. In a natural population of 25 plants of Persoonia mollis (Proteaceae), three AFLP primer pairs generated 147 dominant loci. Of these, 125 (85%) were polymorphic, with a mean recessive allele frequency of 0.735. The theoretical expected percentage of offspring for which all males except the true father can be excluded (PET) was 99.9% for this population. The estimates of PET drop marginally to 99.6% and 97.6% for larger populations of 100 and 1000 individuals, respectively. A preliminary investigation confirmed the power of AFLP for paternity analysis by assigning paternity, or excluding all known potential sires, for 242 of 252 (96.0%) naturally pollinated seeds. Ambiguous paternity for the remaining 10 seeds was quickly resolved by utilizing two further AFLP primer pairs, ultimately generating over 200 polymorphic loci and resulting in the exclusion of all nonsires for all 252 (100%) seeds. This study highlights the utility of AFLP for paternity analysis because: (i) it generates sufficiently large numbers of highly reproducible polymorphic loci, that are (ii) quickly and accurately scored using an automated DNA sequencer and dedicated software, and (iii) unlike microsatellites, requires no sequence knowledge so it is more easily applied to new study species.
Journal for Nature Conservation, 2006
ABSTRACT The ecological restoration of native plant communities requires the collection of large ... more ABSTRACT The ecological restoration of native plant communities requires the collection of large amounts of seed. Use of non-local provenance seed can have detrimental consequences for the success of restoration if there is a home-site advantage, and for nature conservation through the erosion of natural patterns of population genetic structuring and/or genetic swamping (and extirpation) of locally significant genotypes. As part of an ongoing project to genetically delineate local provenance seed collection zones for species within a large urban bushland remnant of high conservation value, we assessed population genetic differentiation in two widespread coastal leguminous species, Acacia rostellifera and A. cochlearis (Fabaceae), commonly used in restoration programmes in SW Australia. Using amplified fragment length polymorphism (AFLP), we found very high levels of genetic differentiation among populations, with an analysis of molecular variance (AMOVA) showing more than 50% of the total genetic variance to be partitioned among populations (ΦST=0.58 and 0.51 for A. rostellifera and A. cochlearis, respectively), and marked non-overlap of almost all potential seed source populations from the local population in ordinations. Our results suggest extremely restricted natural dispersal among populations, possibly due to a combination of low seed set, seed dispersal by ants, clonality, a linear distribution of naturally fragmented populations and possibly low outcrossing rates. We suggest a narrow seed collection zone should be applied to these species for the conservation of genetic diversity and natural patterns of population genetic structure, and we highlight the value and importance of provenance evaluation to ecological restoration.
Australian Journal of Botany, 2008
Ecological restoration benefits from information on population genetic structure and variation wi... more Ecological restoration benefits from information on population genetic structure and variation within a species to make informed decisions on where to source material of the local genetic provenance. Conospermum triplinervium is extremely rare in Bold Park, a large bushland remnant currently undergoing restoration in Perth, Western Australia. We sampled plants from Bold Park and six other native populations across the northern half of the species' range to assess patterns of morphological and genetic variation. There was considerable variation across six leaf measures with significant differentiation among some populations. The molecular data showed a high level of population structure (Q B = 0.4974), with varying degrees of spatial overlap among populations in an ordination plot. Significant differentiation was observed among all pairs of populations, except for Bold Park and its geographically closest populations at Kings Park and Neerabup. These two populations had greater genetic variation (50.9% and 54.5% polymorphic markers, respectively) than did that at Bold Park (20.2%). The small Bold Park population would benefit from augmentation (via cuttings) from local plants. However, in the longer term, should the Bold Park population show evidence of declining viability, then material should be sourced from the genetically similar Kings Park population to increase genetic variation whilst also maintaining genetic integrity.
Conservation Biology, 2002
Grevillea scapigera is one of the world's rarest plant species, currently known from only five pl... more Grevillea scapigera is one of the world's rarest plant species, currently known from only five plants in the wild. In 1995, 10 plants were selected from the 47 plants known at the time to act as genetically representative founders for translocation into secure sites. Ramets were micropropagated and introduced into one of these secure sites (Corrigin) in 1996. By late 1998 plants had been successfully translocated and were producing large numbers of seeds. With the development of an artificial seed-germination technique and because of an absence of seed germination in situ, seed was collected from these plants and germinated ex situ, and 161 seedlings were returned to the field site in winter 1999. We used the DNA fingerprinting technique of amplified fragment-length polymorphism (AFLP) to (1) assess the genetic fidelity of the clones through the propagation process, (2) contrast genetic variation and average genetic similarities of the F1s to their parents to assess genetic decline, and (3) assign paternity to the reintroduced seeds to assess the reproductive success of each clone. We found that 8 clones, not 10, were present in the translocated population, 54% of all plants were a single clone, and the F1s were on average 22% more inbred and 20% less heterozygous than their parents, largely because 85% of all seeds were the product of only 4 clones. Ultimately, effective population size ( N e ) of the founding population was approximately two. Our results highlight the difficulty of maintaining genetic fidelity through a large translocation program. More generally, rapid genetic decline may be a feature of many translocated populations when N e is small, which may ultimately threaten their long-term survival. Strategies to reverse this genetic decline include equalizing founder numbers, adding new genotypes when discovered, optimizing genetic structure and plant density to promote multiple siring and reduce kinship, promoting natural seed germination in situ rather than artificially germinating seeds ex situ, and creating a metapopulation of numerous translocated populations to restore historical distribution patterns and processes.
6. Facchini, P. J. and Bird, D. A., Developmental regulation of benzylisoquinoline alkaloid biosy... more 6. Facchini, P. J. and Bird, D. A., Developmental regulation of benzylisoquinoline alkaloid biosynthesis in opium poppy plants and tissue cultures. In Vitro Cell 34,[69][70][71][72][73][74][75][76][77][78][79]. Facchini, P. J. and De Luca, V., Differential and tissue-specific expression of a gene family for tyrosine/dopa decarboxylases in opium poppy. J. Biol. Chem., 1994, 269, 26684−26690. 8. Park, S. and Facchini, P. J., Agrobacterium-mediated transformation of opium poppy, Papaver somniferum, via shoot organogenesis. J. Plant Physiol., 2000, 157, 207−214. 9. Park, S. and Facchini, P. J., Agrobacterium rhizogenes-mediated transformation of opium poppy, Papaver somniferum L., and California poppy, Eschscholzia californica Cham., root cultures.
Austral Ecology, 2006
Abstract The rehabilitation of native plant communities in urban bushland remnants is an increas... more Abstract The rehabilitation of native plant communities in urban bushland remnants is an increasingly important activity requiring the collection of large amounts of seed. Best practice generally identifies that local seed are best, but how far does the local provenance extend? Using the DNA fingerprinting technique amplified fragment length polymorphism, we assessed genetic differentiation between potential seed source populations and the target population, Bold Park, a large and significant bushland remnant in Perth, Western Australia. For each of 15 species, analysis of molecular variance was used to partition genetic variation within and among populations. Genetic differentiation between Bold Park and potential seed source populations was assessed by non-metric multidimensional scaling ordination, and statistically by Fisher’s exact tests. The partitioning of variation among populations (ΦST) varied from 0.66 for Santalum acuminatum to 0.04 for Mesomelaena pseudostygia. For eight of 15 species, Bold Park plants were completely or largely non-overlapping with other populations in ordinations, suggesting genetic differentiation and a narrow provenance. Five species showed overlap between Bold Park and some other, but not all, populations sampled, with geographically closest populations generally undifferentiated. Only two species, Acanthocarpus preissii and Mesomeleana pseudostygia, showed little genetic differentiation between Bold Park and all other populations, suggesting a regional genetic provenance. These species can be classified into three broad provenance classes – narrow, local and regional – to help guide decisions about appropriate seed-collection zones for the rehabilitation of urban bushland remnants.
Conservation Genetics, 2009
The Orchidaceae is characterised by a diverse range of life histories, reproductive strategies an... more The Orchidaceae is characterised by a diverse range of life histories, reproductive strategies and geographic distribution, reflected in a variety of patterns in the population genetic structure of different species. In this study, the genetic diversity and structure was assessed within and among remnant populations of the critically endangered sexually deceptive orchid, Caladenia huegelii. This species has experienced severe recent habitat loss in a landscape marked by ancient patterns of population fragmentation within the Southwest Australian Floristic Region, a global biodiversity hotspot. Using seven polymorphic microsatellite loci, high levels of within-population diversity (mean alleles/locus = 6.73; mean H E = 0.690), weak genetic structuring among 13 remnant populations (F ST = 0.047) and a consistent deficit of heterozygotes from Hardy–Weinberg expectation were found across all populations (mean F IS = 0.22). Positive inbreeding coefficients are most likely due to Wahlund effects and/or inbreeding effects from highly correlated paternity and typically low fruit set. Indirect estimates of gene flow (Nm = 5.09 using F ST; Nm = 3.12 using the private alleles method) among populations reflects a historical capacity for gene flow through long distance pollen dispersal by sexually deceived wasp pollinators and/or long range dispersal of dust-like orchid seed. However, current levels of gene flow may be impacted by habitat destruction, fragmentation and reduced population size. A genetically divergent population was identified, which should be a high priority for conservation managers. Very weak genetic differentiation indicates that the movement and mixing of seeds from different populations for reintroduction programs should result in minimal negative genetic effects.
Ecological Management and Restoration, 2006
Australian Journal of Botany, 2006
... Conservation biology of the rare species Conospermum undulatum and Macarthuria keigheryi in a... more ... Conservation biology of the rare species Conospermum undulatum and Macarthuria keigheryi in an urban bushland remnant Dugald C. CloseA,B,E, Giuseppe MessinaA,C, Siegfried L. KraussA,B, Deanna P. RokichA,B, Jennifer StritzkeD and Kingsley W. DixonA,B ...
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Papers by Siegfried Krauss