P. A. Butcher

University of Western Australia, Perth City, Western Australia, Australia

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Publications (20)44.03 Total impact

  • P. A. Butcher, S. A. McNee, S. L. Krauss
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    ABSTRACT: Expansion of mining in the banded ironstone ranges of southern Western Australia has focussed attention on the genetic impacts of habitat loss on rare endemic taxa. One example is Tetratheca paynterae subsp. paynterae (Elaeocarpaceae), an insect-pollinated, perennial shrub confined to 4ha of banded ironstone outcrops in the Windarling Range. Mining removed 1,900 of the 7,700 recorded plants in 2004. Further reductions could occur if it can be demonstrated that the viability of the remaining population is not threatened. To investigate the potential impact of reductions in population size due to mining we first used Bayesian clustering and principal coordinate analysis to define population boundaries based on differentiated gene pools. The level of genetic diversity and spatial genetic structuring was then compared among populations that ranged in size from 46 to 4400 individuals. Analysis with 11 microsatellite loci revealed lower genetic diversity in small populations (A R=4.5–4.8) than a large population (A R=6.3) together with significant pair-wise differences among populations separated by distances of 80m or more. Spatial autocorrelation analysis showed the extent of spatial genetic structure differed among populations of different size, consistent with near-neighbour mating and limited dispersal. Fine scale spatial structure was consistent with historically low gene flow. Analysis of the impact of possible expansions in mining revealed small, isolated populations of T.paynterae subsp. paynterae were of high conservation value. While their removal would reduce plant numbers and genetic diversity by less than 5%, unique genotypes will be lost resulting in a 30% decline in genetic differentiation.
    Conservation Genetics 01/2009; 10(6):1735-1746. · 2.18 Impact Factor
  • P A Butcher, S L Krauss
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    ABSTRACT: Nineteen microsatellite markers were developed from Tetratheca paynterae ssp. paynterae, a rare and endangered, leafless, perennial shrub. Twelve loci were polymorphic in T. paynterae ssp. paynterae with two to 14 alleles per locus and mean expected heterozygosity of 0.62. Primer pairs were tested on four other Tetratheca species from ironstone ranges in southern Western Australia. Ten loci were polymorphic in T. paynterae ssp. cremnobata and T. aphylla ssp. aphylla, three in T. harperi and four in T. erubescens. The level of polymorphism was adequate for studies of genetic structure and mating systems in three of the five taxa.
    Molecular Ecology Resources 01/2009; 9(1):386-9. · 7.43 Impact Factor
  • P. A. Butcher, M. W. McDonald, J. C. Bell
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    ABSTRACT: Eucalyptus camaldulensis is one of the most widely utilised eucalypts. It is also the only eucalypt that occurs across the Australian continent, playing a key ecological role as fauna habitat and in riverbank stabilisation. Despite its ecological and economic importance, uncertainty remains regarding the delineation of genetic and morphological variants. Nine hundred and ninety trees from 97 populations, representing the species’ geographic range were genotyped using 15 microsatellite loci and patterns of diversity compared with restriction fragment length polymorphisms in 29 of these populations. Both markers showed that despite having a riverine distribution, downstream seed dispersal has had less influence than geographic distance on dispersal patterns. Spatial patterns in the distribution of microsatellite genotypes were compared with environmental parameters and boundaries defined by river systems, drainage basins and proposed subspecies. Significant genetic differences among populations within river systems indicated that rivers should not be treated as a single genetic entity in conservation or breeding programmes. Strong geographic trends were evident with 40% of variation in genetic diversity explained by latitude and moisture index. Isolation by distance and significant correlations between genetic distance and environmental parameters for most loci suggest historical factors have had more influence than selection on current patterns of distribution of genetic diversity. Geographic structuring of molecular variation, together with congruence between genetic and morphological variation indicate that E. camaldulensis should be treated as a number of subspecies rather than a single variable taxon. High levels of genetic diversity and geographic trends in the distribution of variation provide a firm basis for further exploration of the species’ genetic resources.
    Tree Genetics & Genomes 01/2009; 5(1):189-210. · 2.40 Impact Factor
  • Australian Systematic Botany - AUST SYSTEMATIC BOTANY. 01/2009; 22(4).
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    P. A. Butcher, A. K. Skinner, C. A. Gardiner
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    ABSTRACT: Eucalyptus benthamii Maiden & Cambage is a forest tree of interest for conservation and plantation forestry. It is vulnerable to extinction, occurring on the alluvial floodplains of the Nepean River and its tributaries, south-west of Sydney, Australia. These floodplains were largely cleared of native vegetation for agriculture by the mid-1800s. Flooding of the Cox Valley for Sydneys water supply further decreased the species distribution. The species is now confined to one population of approximately 6500 trees in the Kedumba valley and three remnant populations on the Nepean River at Bents Basin (about 300 trees), Wallacia (nine trees) and Camden (about 30 trees). Genetic analysis of the four populations using microsatellite markers revealed significant divergence among all populations, despite the Bents Basin, Wallacia and Camden remnants being separated by distances of only a few kilometres. Trees in these populations have been estimated to range from 35 to 200 years old, suggesting genetic divergence among populations occurred prior to land clearing. To investigate the impact of fragmentation on the next generation, outcrossing rates were estimated from 41 families. While no direct relationship was found between population size and outcrossing rates, fragmentation and the isolation of trees appears to have resulted in higher levels of selfing and biparental inbreeding in seed collected from the Camden and Wallacia remnants. There was also evidence from seedling morphology that inter-species gene flow increased with fragmentation since 20% of the progeny from Camden and 30% of the progeny from Wallacia were hybrids. Seed viability and germination rates were significantly lower in the remnant populations, reducing their value as seed sources for regeneration and plantation forestry. To maintain the genetic integrity of the remnant populations, germplasm should be sourced from the local area. Outcrossed, non-hybrid seed could be produced by controlled pollination in ex-situ conservation stands or by using seedling morphology and microsatellites to screen seedlings from the remnant populations.
    Conservation Genetics 02/2005; 6(2):213-226. · 2.18 Impact Factor
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    ABSTRACT: The distribution of genetic variation within and among species inCorymbia section‘Politaria’ was examined using allozymes.This section consists of four species,Corymbia citriodora (Hook.) K.D.Hill & L.A.S.Johnson, C. maculata (Hook.) K.D.Hill & L.A.S.Johnson, C. henryi (Blake) K.D.Hill & L.A.S.Johnson and C. variegata (F.Muell.) K.D.Hill & L.A.S.Johnson, which are of commercial interest for plantation and farmforestry. Thirty populations representing the species’ range-widedistributions were studied, extending from upland tropical regions of northQueensland, south to eastern Victoria. Despite relatively low allozymedivergence between species, there was a relationship between geographicdistribution patterns of populations and allozyme variation. The section wasshown to comprise very closely related species with only 15% of thetotal genetic diversity attributed to differences between species. Twodistinct genetic alliances were evident:C. maculata–C. henryi andC. citriodora–C. variegata.Corymbia citriodora andC. variegata, however, could not be distinguished bytheir allozyme profiles. The lack of genetic differentiation between thesetaxa suggests that they represent one species composed of two chemical races.Corymbia maculata and C. henryiwere shown to be closely allied but genetically distinct.Corymbia henryi had the highest genetic diversity in thegroup and lowest differentiation among populations, whileC. maculata had the lowest diversity but the highestgenetic differentiation among populations. There was evidence ofisolation-by-distance among populations ofC. citriodora, C. maculata andC. variegata but not in C. henryi,which has a smaller geographic range. The inclusion in the study ofC. torelliana (F.Muell.) K.D.Hill & L.A.S.Johnson asan outgroup accentuated the small genetic differences between species in thegroup. The patterns of genetic diversity are discussed in relation to thespecies’ taxonomic relationships, breeding systems and utilisation.
    Australian Systematic Botany - AUST SYSTEMATIC BOTANY. 01/2003; 16(5).
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    ABSTRACT: Eucalyptus cladocalyx F.Muell. is a widely cultivated tree in dryland southern Australia. It is grown for firewood, timber production and as a windbreak and ornamental species. Natural populations of E. cladocalyx are endemic to South Australia where they occur in three disjunct regions. This study assessed the mating system and patterns of genetic diversity in natural populations of E. cladocalyx by using allozymes. Populations had relatively low levels of genetic diversity (HE = 0.148) and high levels of genetic divergence (θ = 0.26) among populations, similar to other regionally distributed eucalypts. Populations clustered into three distinct groups, which corresponded to its disjunct natural distribution. Genetic differentiation among populations and between regions was highly significant. Relatively high levels of inbreeding (tm = 0.57) were detected in natural populations of E. cladocalyx. Outcrossing rates were highly variable among families, ranging from 0 to 100%. One-third of families from four populations had outcrossing rates that were not significantly different from zero. The origins of three commercially significant, cultivated stands of E. cladocalyx were also assessed. Allozyme profiles of cultivated stands from Wail and Lismore in western Victoria suggested origins in the Wirrabara region of the southern Flinders Ranges, while a cultivated stand of E. cladocalyx var. nana Hort. ex Yates had an allozyme profile consistent with origins in the Eyre Peninsula region. The results are discussed in relation to the species' morphological variation, biogeography and the implications for its domestication and conservation.
    Australian Journal of Botany 01/2003; 51(4). · 1.20 Impact Factor
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    ABSTRACT: Acacia tumida F.Muell ex. Benth. is a morphologically variable species from north-western Australia. Variants range from low, multi-stemmed shrubs to single-stemmed trees. Acacia tumida is cultivated for firewood, windbreaks and sand stabilisation. To examine patterns of genetic variation that could be utilised in domestication programs, 22 populations representing its natural distribution were surveyed by using allozymes. Estimates of genetic diversity (HE = 0.149) were within the range of other tropical, widespread woody plants, but varied widely among populations (HE = 0.064–0.203). There were strong clinal trends in diversity estimates; A, P, HO, HE were correlated with longitude and declined from west to east. HE decreased as mean monthly maximum temperatures increased and allelic richness (A) increased with mean minimum monthly temperatures. There were also significant correlations between allele frequencies at certain loci and geographic and climatic parameters. Significant isolation-by-distance and relatively high levels of differentiation (θ = 0.176) were detected among populations. Populations of the narrow-phylloded form (Pilbara region) were the most genetically divergent, despite their geographic proximity to other populations. The low-shrub and tall-tree forms could not be distinguished by allozyme profiles. Slight genetic differences were detected between the non-pruinose and pruinose forms from within one population. Phylogenetic analysis supported morphological evidence of hybridisation between A. tumida and A. difficilis Maiden in their zone of overlap. The results are discussed in relation to the taxonomy and domestication of A. tumida.
    Australian Systematic Botany 01/2003; 16(1). · 1.47 Impact Factor
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    P A Butcher, A Otero, M W McDonald, G F Moran
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    ABSTRACT: Eucalyptus camaldulensis Dehnh. is the most widely planted eucalypt in the tropics. Natural populations are riparian and sampling strategies for breeding programmes have assumed that gene flow among drainage basins is limited. RFLP variation, within and among 31 populations from river systems across northern Australia, was analysed to test this hypothesis. To allow comparisons within and between river systems, trees were sampled from up to three populations per river system. Allele frequencies were correlated with longitude for more than half the 33 RFLP loci surveyed. Genetic identity was greatest between populations in closest geographic proximity, irrespective of river system, suggesting that sampling strategies for breeding programmes should be based on geographic distance rather than river system. The level of genetic variation was similar throughout the geographic range examined (mean H(E) = 0.49). However, there was evidence of a barrier to gene flow between populations in the east and west of the species range. The RFLP data support morphological evidence of hybridisation between E. camaldulensis and E. tereticornis Sm. in several populations in northeast Queensland and the genetic divergence of E. camaldulensis subsp. simulata Brooker and Kleinig.
    Heredity 06/2002; 88(5):402-12. · 4.11 Impact Factor
  • P. A. Butcher, S. Decroocq, Y. Gray, G. F. Moran
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    ABSTRACT: Microsatellite markers were developed in Acacia mangium Willd. to provide highly variable co-dominant markers for linkage mapping and studies of the breeding system. After an enrichment procedure 40% of colonies contained microsatellites in contrast with less than 1% from a non-enriched library. The majority of microsatellite sequences were AC repeats. Co-dominant segregation of alleles in two full-sib crosses of A. mangium was demonstrated at 33 microsatellite loci. The markers were highly variable relative to restriction fragment lengths polymorphisms (RFLPs). In the two pedigrees 53% of microsatellite loci were fully informative compared with 15% of RFLPs. Based on alleles detected among four parental genotypes, the microsatellites consisting of dinucleotide repeats were more polymorphic than those with tri- and tetra-nucleotide repeats. The microsatellite markers were not as transferable across species in the genus Acacia as RFLPs. Two thirds of the primers developed in A. mangium (subgenus Phyllodineae, section Juliflorae) amplified DNA from other species within the same section but failed to amplify in species from the subgenus Acacia. The availability of multiallelic, PCR-based, co-dominant microsatellite loci makes possible efficient studies of gene flow and breeding systems in A. mangium, a species with low allozyme variation.
    Theoretical and Applied Genetics 11/2000; 101(8):1282-1290. · 3.66 Impact Factor
  • P. A. Butcher, G. F. Moran
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    ABSTRACT: An integrated genetic linkage map, comprised of 219 RFLP and 33 microsatellite loci in 13 linkage groups, was constructed using two outbred pedigrees of Acacia mangium Willd. The linkage groups ranged in size from 23 to 103 cM and the total map length was 966 cM. Individual maps were made for each pedigree and the ordering of loci was consistent with the integrated map. The use of two independent pedigrees allowed a comparison of recombination rates between linked loci in male and female meioses as well as between parents. Differences were confined to specific regions and were not uniform across the male and female genomes or between genotypes. The heterogeneity in recombination frequencies did not result in major differences in the ordering of loci between pedigrees; hence, the integrated map provides a sound basis for QTL detection, leading to marker-assisted selection in A. mangium. It also provides a reference map for comparative genome analysis in acacias. The co-dominant markers used for mapping provide a useful resource in population studies and for quality control in acacia breeding programs. Detection of a relatively high proportion of selfs in pods derived from flowers which were not emasculated (30%), compared with emasculated flowers (0.01%), indicates that emasculation is desirable for efficient delivery of control-crossed seed in acacia breeding programs.
    Theoretical and Applied Genetics 08/2000; 101(4):594-605. · 3.66 Impact Factor
  • G. F. Moran, P. A. Butcher, J. C. Glaubitz
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    ABSTRACT: Domestication programs are currently being developed for a number of Australasian tropical tree species for plantations largely outside Australia. An assessment of the genetic resources of several species has been made on the basis of levels and patterns of genetic diversity at molecular marker loci. On the basis of growth performance and other quantitatively inherited commercial traits, populations from only limited regions of the geographic range were included in baseline selections of breeding programs for species such as Acacia mangium, A. auriculiformis, A. aulacocarpa and Eucalyptus pellita. For A. mangium, this domestication strategy resulted in a high proportion of the genetic resources of the species being included in breeding programs, but for other species such as A. aulacocarpa a significant fraction of the genetic resources were not incorporated into the baseline populations. The same molecular marker data sets enabled the formulation of conservation strategies both in situ and ex situ for these important commercial species. Within Australia many tree species are utilised directly from native forests in the absence of domestication efforts. Preliminary results from a study on genetic impacts of silvicultural regeneration practices in native forests indicate that there is very limited loss in genetic diversity in E. sieberi, a locally abundant species, under either clearfelling with aerial resowing or the seed tree system. Questions remain concerning the impact of silvicultural regeneration practices on species that are more locally rare.
    Australian Journal of Botany 06/2000; 48(3):313-320. · 1.20 Impact Factor
  • P. A. Butcher, G. F. Moran, R. Bell
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    ABSTRACT: Random genomic probes were used to assess levels of restriction fragment length polymorphism (RFLP) in two 2-generation outbred pedigrees of Acacia mangium Willd. Probes were evaluated for their ability to detect polymorphic loci in each pedigree and to determine the relative efficiency of different restriction enzymes in revealing polymorphisms. Sixty two percent of the probes which detected single- or low-copy number sequences revealed polymorphisms with at least one restriction enyzme. HpaII was the most efficient in detecting polymorphism among first-generation individuals. The recognition sequence of HpaII contains a CpG dimer, suggesting that cytosines in the CpG sequence may be hotspots for mutation in plant genomes, as previously reported in bacterial and mammalian genomes. Mendelian inheritance of 230 loci was demonstrated based on single-locus segregation in second-generation individuals. Less than 5% of loci showed evidence of segregation distortion. The proportion of fully informative loci (15%) was lower than previously reported in eucalypts reflecting the lower level of genetic diversity in A. mangium. The RFLP probes are suitable for the construction of a high-density genetic linkage map in A. mangium. Cross-hybridisation of the A.mangium RFLPs to DNA from species representing the three subgenera of the genus Acacia indicates that these markers could be used in breeding programs of other diploid acacias, for comparative studies of genome organisation, and for phylogenetic studies.
    Theoretical and Applied Genetics 02/2000; 100(3):576-583. · 3.66 Impact Factor
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    P A Butcher, G F Moran, H D Perkins
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    ABSTRACT: Genetic diversity in the nuclear genome of Acacia mangium was estimated using 57 anonymous RFLP loci for 10 individuals from each of 10 natural populations representing the geographical range of the species. The level of genetic diversity varied significantly among the populations, ranging from HE=0.01 on the island of Ceram to HE=0.21 in Muting, New Guinea. The small, geographically isolated populations of Daintree, Townsville, Ceram and Sidei had low levels of diversity (HE=0.01–0.09) whereas the large New Guinea and the Cape York Peninsula populations had higher levels of diversity (HE=0.16–0.21). There was evidence of genetic differentiation between populations (=0.35), 75% of which was attributable to differences between four geographical regions of Cape York and Daintree–Townsville in Australia, New Guinea and Ceram–Sidei. This may reflect restrictions to gene flow associated with past expansions and contractions of rainforests which occurred with climate and sea level changes. The level of variation detected with RFLPs was higher than previously detected with allozymes, supporting speculation that allozyme coding regions are more likely to be constrained by selection than noncoding regions. The distribution of variation within and among populations was consistent for the two marker types.Keywords: Acacia, inbreeding, population genetics, RFLP
    Heredity 07/1998; 81(2):205-213. · 4.11 Impact Factor
  • P. A. Butcher, A. C. Matheson, M. U. Slee
    New Forests 01/1996; 11:31-51. · 1.64 Impact Factor
  • P. A. Butcher, A. C. Matheson, M. U. Slee
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    ABSTRACT: Variation in oil yields from plantations and natural stands of Melaleuca alternifolia (Maiden and Betche) Cheel indicates considerable potential for improving plantation production through breeding. Some populations of the more widely distributed species, M. linariifolia Sm., produce a similar leaf oil and may provide opportunities to expand the genetic base of plantations. Growth and oil traits were assessed for 60 half-sib families, representing three chemical forms of Melaleuca alternifolia, and 10 half-sib families of the terpinen-4-ol rich chemical form of M. linariifolia, in a provenance/progeny trial in northern New South Wales, Australia. Differences in oil composition and coppicing between the terpinen-4-ol rich forms of the two species were significant (P < 0.05),="" while="" differences="" in="" growth="" traits="" and="" leaf="" oil="" yield="" were="" not="" significant.="" the="" difference="" in="" oil="" composition="" between="" northern="" and="" southern="" populations="" of="">M. linariifolia was as great as differences between the two species, suggesting the two regions should be considered distinct races for breeding purposes.Narrow-sense heritabilities in M. alternifolia of 0.67 for oil yield, 0.25 for plant dry weight, and 0.27 for coppice indicate substantial improvement would follow selection for single traits. However, negative genetic correlations between oil yield and plant dry weight indicate it is not possible to simultaneously achieve major gains in the two traits. Using combined index selection with a restriction on plant dry weight, expected gains of 17% in oil yield and 14% in coppicing are predicted from one generation of selection at an intensity of one tree in ten.
    New Forests 12/1995; 11(1):31-51. · 1.64 Impact Factor
  • P. A. Butcher, M. Byrne, G. F. Moran
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    ABSTRACT: Melaleuca alternifolia andM. linariifolia are commercially important Australian species harvested for their essential oils. Both species have relatively narrow and disjunct distributions on the central coast of eastern Australia. Variation in the chloroplast genome was assessed for eight individuals from each of twelve populations, representing the species'' geographic range. Low nucleotide diversity withinM. alternifolia contrasted with high nucleotide diversity inM. linariifolia. CpDNA data are consistent with the southern population ofM. alternifolia being a hybrid population withM. linariifolia. The two species are sympatric in this region. Variation inM. linariifolia was geographically structured, with northern populations differing from southern populations by seven restriction site mutations, five length mutations and an inversion. There was no evidence of hybridisation of the cp genome of northernM. linariifolia with the partially sympatric speciesM. trichostachya. Intra- and interspecific variation in the chloroplast genomes ofM. alternifolia, M. linariifolia, andM. trichostachya indicate considerable potential for the use of intraspecific cpDNA studies in examining phylogenetic relationships in melaleucas.
    Plant Systematics and Evolution 02/1995; 194(1):69-81. · 1.31 Impact Factor
  • Penelope A. Butcher, John C. Doran, Michael U. Slee
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    ABSTRACT: Leaves from 109 trees in 11 populations spanning the geographic range of Melaleuca alternifolia were analyzed for qualitative and quantitative variation in essential oils. Significant differences in oil yield were recorded between populations indicating the potential for improvement from a breeding program. Considerable variation in oil composition was found, both among and within populations, Trees from the northwestern populations produced a terpinolene-rich oil while eastern populations produced an oil with either terpinen-4-ol or 1,8-cineole as the major component. Differences in terpene composition among populations support data from allozyme analyses suggesting genetic differentiation of populations in the northwestern extremity of the species range. The study confirms three previously identified chemical forms in eastern populations and proposes recognition of two chemical forms in northwestern populations. Populations were identified with individuals suitable for inclusion in a breeding program.
    Biochemical Systematics and Ecology. 01/1994;
  • PA Butcher, JC Bell, GF Moran
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    ABSTRACT: Melaleuca alternifolia (Maiden & Betche) Cheel is harvested from natural stands and plantations for production of Australian tea-tree oil. Genetic variation was examined and outcrossing rates estimated to provide baseline information for breeding and selection programs. The overall genetic diversity (HT = 0.186) is comparable to other regionally distributed Australian tree species. There was a general trend for more isolated populations to have less genetic variation than populations from the centre of the species distribution. The level of differentiation among populations was low (12%), associated with a high outcrossing rate (93%) and high levels of gene flow. Geographic separation of Queensland and New South Wales populations corresponds with genetic distance measures.
    Australian Journal of Botany - AUST J BOT. 01/1992; 40(3).
  • P. A. Butcher, D. Bradbury, S. L. Krauss
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    ABSTRACT: Patterns of mating and dispersal are key factors affecting the dynamics, viability and evolution of plant populations. Changes in mating system parameters can provide evidence of anthropogenic impacts on populations of rare plants. Tetratheca paynterae subsp. paynterae is a critically endangered perennial shrub confined to a single ironstone range in Western Australia. Mining of the range removed 25% of plants in 2004 and further plants may be removed if the viability of the remaining populations is not compromised. To provide baseline genetic data for monitoring mining impacts, we characterised the mating system and pollen dispersal over two seasons in T. paynterae subsp. paynterae and compared mating system parameters with two other ironstone endemics, T. paynterae subsp. cremnobata and T. aphylla subsp. aphylla that were not impacted by mining. T. paynterae subsp. paynterae was the only taxon showing evidence of inbreeding (t m = 0.89), although hand pollination revealed pre-zygotic self-incompatibility limits the production of seed from self-pollen. In a year of lower fruit set (2005), the estimate of correlated paternity increased from 20 to 35%. Direct estimates of realised pollen dispersal, made by paternity assignment in two small populations where all adult plants were genotyped, revealed a leptokurtic distribution with 30% of pollen dispersed less than 3 m and 90% less than 15 m. Restricted pollen dispersal maintains the strong genetic structuring of the adult populations in succeeding generations. As a consequence of preferential outcrossing, any reduction in effective population size, flowering plant density and/or the abundance and activity of pollinators may impact negatively on population viability through reduced seed set, increased inbreeding and increased correlated paternity.
    Conservation Genetics · 2.18 Impact Factor

Publication Stats

279 Citations
44.03 Total Impact Points

Institutions

  • 2009
    • University of Western Australia
      Perth City, Western Australia, Australia
  • 2000–2002
    • The Commonwealth Scientific and Industrial Research Organisation
      Canberra, Australian Capital Territory, Australia
  • 1994–1995
    • Australian National University
      Canberra, Australian Capital Territory, Australia