In June of 1997 Orson Scott Card, a popular science fiction author and prominent Latter-day Saint... more In June of 1997 Orson Scott Card, a popular science fiction author and prominent Latter-day Saint, seized upon the news of the erosion of an ancient skeleton out of a riverbank along the Columbia River in eastern Washington during the previous summer. Card prematurely suggested to a Mormon audience that this Kennewick Man represented an ancient founding Caucasoid population displaced by ancestors of American Indians. Indigenous peoples called this ancestor the Ancient One and participated in a long and contentious struggle between a team of scientists and the U.S. Army Corps of Engineers over repatriation. This article critically examines the deployment and evolution of images of Kennewick Man in Latter-day Saint discourse about Native Americans, DNA, and the Book of Mormon. Despite cautionary warnings from the Church of Jesus Christ of Latter-day Saints and Latter-day Saint scientists, the latest pseudoscientific resurrection of a Latter-day settler colonial narrative about ancient America appears as David Read’s Face of a Nephite (2020) featuring a racialized and creationist distortion of the scientific analysis and facial reconstructions of Kennewick Man. Read’s book feeds into a larger discourse advocating a Heartland setting for the Book of Mormon in North America advocated by Rodney Meldrum’s misnamed Foundation for Indigenous Research and Mormonism (FIRM). These authors anachronistically racialize both scripture and human DNA, misrepresent archaeological and genetic science, draw from fraudulent and looted materials, and disregard Indigenous perspectives on the Ancient One, now firmly established as ancestral to American Indians.
Two genes cloned from Eucalyptus globulus, Eucalyptus LeaFy (ELF1 and ELF2), have sequence homolo... more Two genes cloned from Eucalyptus globulus, Eucalyptus LeaFy (ELF1 and ELF2), have sequence homology to the floral meristem identity genes LEAFY from Arabidopsis and FLORICAULA from Antirrhinum. ELF1 is expressed in the developing eucalypt floral organs in a pattern similar to LEAFY while ELF2 appears to be a pseudo gene. ELF1 is expressed strongly in the early floral primordium and then successively in the primordia of sepals, petals, stamens and carpels. It is also expressed in the leaf primordia and young leaves and adult and juvenile trees. The ELF1 promoter coupled to a GUS reporter gene directs expression in transgenic Arabidopsis in a temporal and tissue-specific pattern similar to an equivalent Arabidopsis LEAFY promoter construct. Strong expression is seen in young flower buds and then later in sepals and petals. No expression was seen in rosette leaves or roots of flowering plants or in any non-flowering plants grown under long days. Furthermore, ectopic expression of the E...
ABSTRACT Genetic research into Native American and Polynesian origins has provoked controversy wi... more ABSTRACT Genetic research into Native American and Polynesian origins has provoked controversy within the Church of Jesus Christ of Latter-day Saints. The Book of Mormon claims that the principal ancestors of the American Indians came from the ancient Middle East, an historical assertion now repudiated by mtDNA evidence. Mormon interpretations of the scripture led to the popular belief that Polynesians, likewise, descended from ancient Israelite populations. This belief is now also undermined by genetic research. Protests erupted when the LDS Church initiated and then aborted an effort to excommunicate Thomas Murphy. Protestors objected to racism within LDS Family Services and questioned practices that subverted paternal rights of Native Americans.
ABSTRACT The river red gum (Eucalyptus camaldulensis Dehnh.) inhabits riparian zones and associat... more ABSTRACT The river red gum (Eucalyptus camaldulensis Dehnh.) inhabits riparian zones and associated floodplains throughout Australia. Following changes to hydrological regime due to river regulation and prolonged drought in south-eastern Australia, river red gum populations within the Murray–Darling Basin have suffered substantial decline. To better understand the effect of drought on river red gum genetic diversity, we examined single nucleotide polymorphism (SNP) variation in 12 candidate genes among six red gum floodplain forest sites in Yanga National Park, which had experienced contrasting levels of drought and associated decline over an eight-year period. We also examined genetic diversity using these markers in five additional river red gum populations from the Murray–Darling Basin to place genetic diversity results from Yanga in a regional context. Tree condition was significantly lower and mortality higher in the most drought affected sites; however, differences in overall genetic diversity and divergence were not detected among sites. No evidence of genetic adaptation in response to drought in this set of candidate genes was detected when differentiation at individual SNP loci was examined. While the overall condition of E. camaldulensis was strongly influenced by hydrological regime, our results suggest the evolutionary potential of floodplain forests in Yanga were not immediately impacted by population decline linked with drought and changes in hydrological regime. We propose that due to low genetic structure among populations in the region, genetic diversity of river red gums within the Murray–Darling Basin might be effectively conserved during periods of extended drought by protecting representative populations.
Fasciclin-like arabinogalactan protein (FLA) families have been identified and characterised in k... more Fasciclin-like arabinogalactan protein (FLA) families have been identified and characterised in key plant species, with some members exhibiting functional specialization. Here we identify the FLA family of Eucalyptus grandis, and investigate the roles of three single-FAS domain FLAs, with particular focus on secondary cell-wall formation and wood properties. We use various in-silico approaches to identify and characterise E. grandis genome FLAs, and perform phylogenetic comparisons with other species. For three key FLAs, we perform functional testing including promoter-reporter and overexpression transgenic approaches using eucalypts, poplar and tobacco. Of the 18 eucalypt FLAs identified, several were specifically and highly expressed in stems. The specificity to stem xylem vessel and fibre development was demonstrated with EniFLA1promoter:GUS studies in several species. Testing of select eucalypt FLAs resulted in altered wood development and properties, for example 35S:EgrFLA2 led to a 3 degree reduction in cellulose microfibril angle in eucalypt xylem fibres, and 35S:EgrFLA3 to a reduction in tobacco stem flexural strength. These results indicate that the eucalypt FLA family contains diverse members, and particular members with single FAS domains that are functionally specialized for secondary cell wall growth and properties.
ABSTRACT Due to their long reproductive cycles and the time to expression of mature traits, marke... more ABSTRACT Due to their long reproductive cycles and the time to expression of mature traits, marker-assisted selection is particularly attractive for tree breeding. In this review, we discuss different approaches used for developing markers and propose a method for application of markers in low linkage disequilibrium (LD) populations. Identification of useful markers for application in tree breeding is mainly based on two approaches, quantitative trait locus (QTL) mapping and association genetic studies. While several studies have identified significant markers, effect of the individual markers is low making it difficult to utilize them in breeding programs. Recently, genomic selection (GS) was proposed for overcoming some of these difficulties. In GS, high density markers are used for predicting phenotypes from genotypes. Currently small effective populations with high LD are being tested for GS in tree breeding. For wider application, GS needs to be applied in low LD populations which are found in many tree breeding programs. Here we propose an approach in which the significant markers from association studies may be used for developing prediction models in low LD populations using the same methods as in GS. Preliminary analyses indicate that a modest numbers of markers may be sufficient for developing prediction models in low LD populations. GS based on large numbers of random markers or small numbers of associated markers is poised to make marker-assisted selection a reality in forest tree breeding.
Two cDNA clones encoding endo-b-1,4-glucanases (EGases) were isolated from a radiata pine (Pinus ... more Two cDNA clones encoding endo-b-1,4-glucanases (EGases) were isolated from a radiata pine (Pinus radiata) cDNA library prepared from immature female strobili. The cDNAs PrCel1 (P O inus r Oadiata cellulase 1 O ) and PrCel2 encode proteins 509 and 515 amino acids in length, respectively, including putative signal peptides. Both proteins contain domains conserved in plant and bacterial EGases. The
The Plant journal : for cell and molecular biology, 2010
The ancient cell adhesion fasciclin (FAS) domain is found in bacteria, fungi, algae, insects and ... more The ancient cell adhesion fasciclin (FAS) domain is found in bacteria, fungi, algae, insects and animals, and occurs in a large family of fasciclin-like arabinogalactan proteins (FLAs) in higher plants. Functional roles for FAS-containing proteins have been determined for insects, algae and vertebrates; however, the biological functions of the various higher-plant FLAs are not clear. Expression of some FLAs has been correlated with the onset of secondary-wall cellulose synthesis in Arabidopsis stems, and also with wood formation in the stems and branches of trees, suggesting a biological role in plant stems. We examined whether FLAs contribute to plant stem biomechanics. Using phylogenetic, transcript abundance and promoter-GUS fusion analyses, we identified a conserved subset of single FAS domain FLAs (group A FLAs) in Eucalyptus and Arabidopsis that have specific and high transcript abundance in stems, particularly in stem cells undergoing secondary-wall deposition, and that the p...
Eucalyptus nitens is a perennial forest tree species grown mainly for kraft pulp production in ma... more Eucalyptus nitens is a perennial forest tree species grown mainly for kraft pulp production in many parts of the world. Kraft pulp yield (KPY) is a key determinant of plantation profitability and increasing the KPY of trees grown in plantations is a major breeding objective. To speed up the breeding process, molecular markers that can predict KPY are desirable. To achieve this goal, we carried out RNA-Seq studies on trees at extremes of KPY in two different trials to identify genes and alleles whose expression correlated with KPY. KPY is positively correlated with growth measured as diameter at breast height (DBH) in both trials. In total, six RNA bulks from two treatments were sequenced on an Illumina HiSeq platform. At 5% false discovery rate level, 3953 transcripts showed differential expression in the same direction in both trials; 2551 (65%) were down-regulated and 1402 (35%) were up-regulated in low KPY samples. The genes up-regulated in low KPY trees were largely involved in ...
As an increasing number of ecosystems face departures from long standing environmental conditions... more As an increasing number of ecosystems face departures from long standing environmental conditions under climate change, our understanding of the capacity of species to adapt will become important for directing conservation and management of biodiversity. Insights into the potential for genetic adaptation might be gained by assessing genomic signatures of adaptation to historic or prevailing environmental conditions. The river red gum (Eucalyptus camaldulensis Dehnh.) is a widespread Australian eucalypt inhabiting riverine and floodplain habitats which spans strong environmental gradients. We investigated the effects of adaptation to environment on population level genetic diversity of E. camaldulensis, examining SNP variation in candidate gene loci sampled across 20 climatically diverse populations approximating the species natural distribution. Genetic differentiation among populations was high (F(ST) = 17%), exceeding previous estimates based on neutral markers. Complementary stat...
In June of 1997 Orson Scott Card, a popular science fiction author and prominent Latter-day Saint... more In June of 1997 Orson Scott Card, a popular science fiction author and prominent Latter-day Saint, seized upon the news of the erosion of an ancient skeleton out of a riverbank along the Columbia River in eastern Washington during the previous summer. Card prematurely suggested to a Mormon audience that this Kennewick Man represented an ancient founding Caucasoid population displaced by ancestors of American Indians. Indigenous peoples called this ancestor the Ancient One and participated in a long and contentious struggle between a team of scientists and the U.S. Army Corps of Engineers over repatriation. This article critically examines the deployment and evolution of images of Kennewick Man in Latter-day Saint discourse about Native Americans, DNA, and the Book of Mormon. Despite cautionary warnings from the Church of Jesus Christ of Latter-day Saints and Latter-day Saint scientists, the latest pseudoscientific resurrection of a Latter-day settler colonial narrative about ancient America appears as David Read’s Face of a Nephite (2020) featuring a racialized and creationist distortion of the scientific analysis and facial reconstructions of Kennewick Man. Read’s book feeds into a larger discourse advocating a Heartland setting for the Book of Mormon in North America advocated by Rodney Meldrum’s misnamed Foundation for Indigenous Research and Mormonism (FIRM). These authors anachronistically racialize both scripture and human DNA, misrepresent archaeological and genetic science, draw from fraudulent and looted materials, and disregard Indigenous perspectives on the Ancient One, now firmly established as ancestral to American Indians.
Two genes cloned from Eucalyptus globulus, Eucalyptus LeaFy (ELF1 and ELF2), have sequence homolo... more Two genes cloned from Eucalyptus globulus, Eucalyptus LeaFy (ELF1 and ELF2), have sequence homology to the floral meristem identity genes LEAFY from Arabidopsis and FLORICAULA from Antirrhinum. ELF1 is expressed in the developing eucalypt floral organs in a pattern similar to LEAFY while ELF2 appears to be a pseudo gene. ELF1 is expressed strongly in the early floral primordium and then successively in the primordia of sepals, petals, stamens and carpels. It is also expressed in the leaf primordia and young leaves and adult and juvenile trees. The ELF1 promoter coupled to a GUS reporter gene directs expression in transgenic Arabidopsis in a temporal and tissue-specific pattern similar to an equivalent Arabidopsis LEAFY promoter construct. Strong expression is seen in young flower buds and then later in sepals and petals. No expression was seen in rosette leaves or roots of flowering plants or in any non-flowering plants grown under long days. Furthermore, ectopic expression of the E...
ABSTRACT Genetic research into Native American and Polynesian origins has provoked controversy wi... more ABSTRACT Genetic research into Native American and Polynesian origins has provoked controversy within the Church of Jesus Christ of Latter-day Saints. The Book of Mormon claims that the principal ancestors of the American Indians came from the ancient Middle East, an historical assertion now repudiated by mtDNA evidence. Mormon interpretations of the scripture led to the popular belief that Polynesians, likewise, descended from ancient Israelite populations. This belief is now also undermined by genetic research. Protests erupted when the LDS Church initiated and then aborted an effort to excommunicate Thomas Murphy. Protestors objected to racism within LDS Family Services and questioned practices that subverted paternal rights of Native Americans.
ABSTRACT The river red gum (Eucalyptus camaldulensis Dehnh.) inhabits riparian zones and associat... more ABSTRACT The river red gum (Eucalyptus camaldulensis Dehnh.) inhabits riparian zones and associated floodplains throughout Australia. Following changes to hydrological regime due to river regulation and prolonged drought in south-eastern Australia, river red gum populations within the Murray–Darling Basin have suffered substantial decline. To better understand the effect of drought on river red gum genetic diversity, we examined single nucleotide polymorphism (SNP) variation in 12 candidate genes among six red gum floodplain forest sites in Yanga National Park, which had experienced contrasting levels of drought and associated decline over an eight-year period. We also examined genetic diversity using these markers in five additional river red gum populations from the Murray–Darling Basin to place genetic diversity results from Yanga in a regional context. Tree condition was significantly lower and mortality higher in the most drought affected sites; however, differences in overall genetic diversity and divergence were not detected among sites. No evidence of genetic adaptation in response to drought in this set of candidate genes was detected when differentiation at individual SNP loci was examined. While the overall condition of E. camaldulensis was strongly influenced by hydrological regime, our results suggest the evolutionary potential of floodplain forests in Yanga were not immediately impacted by population decline linked with drought and changes in hydrological regime. We propose that due to low genetic structure among populations in the region, genetic diversity of river red gums within the Murray–Darling Basin might be effectively conserved during periods of extended drought by protecting representative populations.
Fasciclin-like arabinogalactan protein (FLA) families have been identified and characterised in k... more Fasciclin-like arabinogalactan protein (FLA) families have been identified and characterised in key plant species, with some members exhibiting functional specialization. Here we identify the FLA family of Eucalyptus grandis, and investigate the roles of three single-FAS domain FLAs, with particular focus on secondary cell-wall formation and wood properties. We use various in-silico approaches to identify and characterise E. grandis genome FLAs, and perform phylogenetic comparisons with other species. For three key FLAs, we perform functional testing including promoter-reporter and overexpression transgenic approaches using eucalypts, poplar and tobacco. Of the 18 eucalypt FLAs identified, several were specifically and highly expressed in stems. The specificity to stem xylem vessel and fibre development was demonstrated with EniFLA1promoter:GUS studies in several species. Testing of select eucalypt FLAs resulted in altered wood development and properties, for example 35S:EgrFLA2 led to a 3 degree reduction in cellulose microfibril angle in eucalypt xylem fibres, and 35S:EgrFLA3 to a reduction in tobacco stem flexural strength. These results indicate that the eucalypt FLA family contains diverse members, and particular members with single FAS domains that are functionally specialized for secondary cell wall growth and properties.
ABSTRACT Due to their long reproductive cycles and the time to expression of mature traits, marke... more ABSTRACT Due to their long reproductive cycles and the time to expression of mature traits, marker-assisted selection is particularly attractive for tree breeding. In this review, we discuss different approaches used for developing markers and propose a method for application of markers in low linkage disequilibrium (LD) populations. Identification of useful markers for application in tree breeding is mainly based on two approaches, quantitative trait locus (QTL) mapping and association genetic studies. While several studies have identified significant markers, effect of the individual markers is low making it difficult to utilize them in breeding programs. Recently, genomic selection (GS) was proposed for overcoming some of these difficulties. In GS, high density markers are used for predicting phenotypes from genotypes. Currently small effective populations with high LD are being tested for GS in tree breeding. For wider application, GS needs to be applied in low LD populations which are found in many tree breeding programs. Here we propose an approach in which the significant markers from association studies may be used for developing prediction models in low LD populations using the same methods as in GS. Preliminary analyses indicate that a modest numbers of markers may be sufficient for developing prediction models in low LD populations. GS based on large numbers of random markers or small numbers of associated markers is poised to make marker-assisted selection a reality in forest tree breeding.
Two cDNA clones encoding endo-b-1,4-glucanases (EGases) were isolated from a radiata pine (Pinus ... more Two cDNA clones encoding endo-b-1,4-glucanases (EGases) were isolated from a radiata pine (Pinus radiata) cDNA library prepared from immature female strobili. The cDNAs PrCel1 (P O inus r Oadiata cellulase 1 O ) and PrCel2 encode proteins 509 and 515 amino acids in length, respectively, including putative signal peptides. Both proteins contain domains conserved in plant and bacterial EGases. The
The Plant journal : for cell and molecular biology, 2010
The ancient cell adhesion fasciclin (FAS) domain is found in bacteria, fungi, algae, insects and ... more The ancient cell adhesion fasciclin (FAS) domain is found in bacteria, fungi, algae, insects and animals, and occurs in a large family of fasciclin-like arabinogalactan proteins (FLAs) in higher plants. Functional roles for FAS-containing proteins have been determined for insects, algae and vertebrates; however, the biological functions of the various higher-plant FLAs are not clear. Expression of some FLAs has been correlated with the onset of secondary-wall cellulose synthesis in Arabidopsis stems, and also with wood formation in the stems and branches of trees, suggesting a biological role in plant stems. We examined whether FLAs contribute to plant stem biomechanics. Using phylogenetic, transcript abundance and promoter-GUS fusion analyses, we identified a conserved subset of single FAS domain FLAs (group A FLAs) in Eucalyptus and Arabidopsis that have specific and high transcript abundance in stems, particularly in stem cells undergoing secondary-wall deposition, and that the p...
Eucalyptus nitens is a perennial forest tree species grown mainly for kraft pulp production in ma... more Eucalyptus nitens is a perennial forest tree species grown mainly for kraft pulp production in many parts of the world. Kraft pulp yield (KPY) is a key determinant of plantation profitability and increasing the KPY of trees grown in plantations is a major breeding objective. To speed up the breeding process, molecular markers that can predict KPY are desirable. To achieve this goal, we carried out RNA-Seq studies on trees at extremes of KPY in two different trials to identify genes and alleles whose expression correlated with KPY. KPY is positively correlated with growth measured as diameter at breast height (DBH) in both trials. In total, six RNA bulks from two treatments were sequenced on an Illumina HiSeq platform. At 5% false discovery rate level, 3953 transcripts showed differential expression in the same direction in both trials; 2551 (65%) were down-regulated and 1402 (35%) were up-regulated in low KPY samples. The genes up-regulated in low KPY trees were largely involved in ...
As an increasing number of ecosystems face departures from long standing environmental conditions... more As an increasing number of ecosystems face departures from long standing environmental conditions under climate change, our understanding of the capacity of species to adapt will become important for directing conservation and management of biodiversity. Insights into the potential for genetic adaptation might be gained by assessing genomic signatures of adaptation to historic or prevailing environmental conditions. The river red gum (Eucalyptus camaldulensis Dehnh.) is a widespread Australian eucalypt inhabiting riverine and floodplain habitats which spans strong environmental gradients. We investigated the effects of adaptation to environment on population level genetic diversity of E. camaldulensis, examining SNP variation in candidate gene loci sampled across 20 climatically diverse populations approximating the species natural distribution. Genetic differentiation among populations was high (F(ST) = 17%), exceeding previous estimates based on neutral markers. Complementary stat...
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Papers by Simon Southerton