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Julie A Hawkins - One of the best experts on this subject based on the ideXlab platform.
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Interfamilial relationships in order Fabales: new insights from the nuclear regions sqd1 and 26S rDNA
Plant Systematics and Evolution, 2020Co-Authors: Deniz Aygoren Uluer, Julie A Hawkins, Fe Lix ForestAbstract:Leguminosae, Polygalaceae, Quillajaceae and Surianaceae together comprise the order Fabales. Phylogenetic relationships within Fabales remain an unsolved problem even though interfamilial relationships have been examined in a number of studies using different sampling approaches and both molecular and morphological data. In this study, we gather information from the nuclear 26S rDNA region as well as previously published data from the sqd 1 , mat K and rbc L regions. Phylogenetic analyses were performed by maximum parsimony, maximum likelihood and Bayesian inference. Overall, the best-supported topology for the relationships among families within the order places the pair of Leguminosae and Polygalaceae as sister to the pair of Quillajaceae and Surianaceae. However, our approximately unbiased (AU) test of the combined data results has shown that none of the seven different topologies rejected. Furthermore, three topologies were not significantly different from each other. Therefore, similar to the previous studies, this study did not find well-supported dichotomous relationships among the four Fabales families. The Fabales topology was very sensitive to both data choice and the phylogenetic methods used, which may indicate a rapid-near-simultaneous evolution of the four Fabales families. Our results also show that while nuclear sqd 1 can be helpful as a complementary region, both the nuclear sqd 1 and rDNA 26S regions could be problematic when analyzed individually.
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supermatrix analyses and molecular clock rooting of Fabales exploring the effects of outgroup choice and long branch attraction on topology
Botany, 2020Co-Authors: Deniz Aygoren Uluer, Fe Lix Forest, Julie A HawkinsAbstract:Fabales is a cosmopolitan angiosperm order that consists of four families: Leguminosae (Fabaceae), Polygalaceae, Surianaceae, and Quillajaceae. Despite the great interest in this group, a convincin...
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Combined phylogenetic analyses reveal interfamilial relationships and patterns of floral evolution in the eudicot order Fabales
Cladistics, 2012Co-Authors: M. Angélica Bello, Julie A HawkinsAbstract:Relationships between the four families placed in the angiosperm order Fabales (Leguminosae, Polygalaceae, Quillajaceae, Surianaceae) were hitherto poorly resolved. We combine published molecular data for the chloroplast regions matK and rbcL with 66 morphological characters surveyed for 73 ingroup and two outgroup species, and use Parsimony and Bayesian approaches to explore matrices with different missing data. All combined analyses using Parsimony recovered the topology Polygalaceae (Leguminosae (Quillajaceae + Surianaceae)). Bayesian analyses with matched morphological and molecular sampling recover the same topology, but analyses based on other data recover a different Bayesian topology: ((Polygalaceae + Leguminosae) (Quillajaceae + Surianaceae)). We explore the evolution of floral characters in the context of the more consistent topology: Polygalaceae (Leguminosae (Quillajaceae + Surianaceae)). This reveals synapomorphies for (Leguminosae (Quillajaceae + Surianaceae)) as the presence of free filaments and marginal ⁄ ventral placentation, for (Quillajaceae + Surianaceae) as pentamery and apocarpy, and for Leguminosae the presence of an abaxial median sepal and unicarpellate gynoecium. An octamerous androecium is synapomorphic for Polygalaceae. The development of papilionate flowers, and the evolutionary context in which these phenotypes appeared in Leguminosae and Polygalaceae, shows that the morphologies are convergent rather than synapomorphic within Fabales.
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Elusive relationships within order Fabales: phylogenetic analyses using matK and rbcL sequence data.
Systematic Botany, 2009Co-Authors: María Angélica Bello, Fe Lix Forest, Anne Bruneau, Julie A HawkinsAbstract:Abstract The order Fabales, including Leguminosae, Polygalaceae, Quillajaceae and Surianaceae, represents a novel hypothesis emerging from angiosperm molecular phylogenies. Despite good support for the order, molecular studies to date have suggested contradictory poorly supported interfamilial relationships. Our reappraisal of relationships within Fabales addresses past taxon sampling deficiencies, and employs parsimony and Bayesian approaches using sequences from the plastid regions rbcL (166 spp.) and matK (78 spp.). Five alternative hypotheses for interfamilial relationships within Fabales were recovered. The Shimodaira-Hasegawa test found the likelihood of a resolved topology significantly higher than the one calculated for a polytomy but did not favour any of the alternative hypotheses of relationship within Fabales. In the light of the morphological evidence available and the comparative behavior of rbcL and matK, the topology recovering Polygalaceae as sister to the rest of the order Fabales with L...
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the role of biotic and abiotic factors in evolution of ant dispersal in the milkwort family polygalaceae
Evolution, 2007Co-Authors: Fe Lix Forest, Peter R Crane, Claes Persson, Mark W Chase, Julie A HawkinsAbstract:A phylogenetic approach was taken to investigate the evolutionary history of seed appendages in the plant family Polygalaceae (Fabales) and determine which factors might be associated with evolution of elaiosomes through comparisons to abiotic (climate) and biotic (ant species number and abundance) timelines. Molecular datasets from three plastid regions representing 160 species were used to reconstruct a phylogenetic tree of the order Fabales, focusing on Polygalaceae. Bayesian dating methods were used to estimate the age of the appearance of ant-dispersed elaiosomes in Polygalaceae, shown by likelihood optimizations to have a single origin in the family. Topology-based tests indicated a diversification rate shift associated with appearance of caruncular elaiosomes. We show that evolution of the caruncular elaiosome type currently associated with ant dispersal occurred 54.0-50.5 million year ago. This is long after an estimated increase in ant lineages in the Late Cretaceous based on molecular studies, but broadly concomitant with increasing global temperatures culminating in the Late Paleocene-Early Eocene thermal maxima. These results suggest that although most major ant clades were present when elaiosomes appeared, the environmental significance of elaiosomes may have been an important factor in success of elaiosome-bearing lineages. Ecological abundance of ants is perhaps more important than lineage numbers in determining significance of ant dispersal. Thus, our observation that elaiosomes predate increased ecological abundance of ants inferred from amber deposits could be indicative of an initial abiotic environmental function.
Rui Faria - One of the best experts on this subject based on the ideXlab platform.
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phylogeographic history of flat periwinkles littorina fabalis and l obtusata
BMC Evolutionary Biology, 2020Co-Authors: Graciela Sotelo, Marten Duvetorp, Diana Soares Da Costa, Marina Panova, Kerstin Johannesson, Rui FariaAbstract:The flat periwinkles, Littorina fabalis and L. obtusata, are two sister species widely distributed throughout the Northern Atlantic shores with high potential to inform us about the process of ecological speciation in the intertidal. However, whether gene flow has occurred during their divergence is still a matter of debate. A comprehensive assessment of the genetic diversity of these species is also lacking and their main glacial refugia and dispersal barriers remain largely unknown. In order to fill these gaps, we sequenced two mitochondrial genes and two nuclear fragments to perform a phylogeographic analysis of flat periwinkles across their distribution range. We identified two main clades largely composed by species-specific haplotypes corresponding to L. obtusata and L. fabalis, with moderate to strong support, respectively. Importantly, a model of divergence with gene flow between the two species (from L. obtusata to L. fabalis) was better supported, both in Iberia and in northern-central Europe. Three mitochondrial clades were detected within L. fabalis and two within L. obtusata, with strong divergence between Iberia and the remaining populations. The largest component of the genetic variance within each species was explained by differences between geographic regions associated with these clades. Our data suggests that overall intraspecific genetic diversity is similar between the two flat periwinkle species and that populations from Iberia tend to be less diverse than populations from northern-central Europe. The phylogeographic analysis of this sister-species pair supports divergence with gene flow. This system thus provides us with the opportunity to study the contribution of gene flow and natural selection during diversification. The distribution of the different clades suggests the existence of glacial refugia in Iberia and northern-central Europe for both species, with a main phylogeographic break between these regions. Although the genetic diversity results are not fully conclusive, the lower diversity observed in Iberia could reflect marginal conditions at the southern limit of their distribution range during the current interglacial period.
Chengxin Fu - One of the best experts on this subject based on the ideXlab platform.
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the complete chloroplast genome of chinese bayberry morella rubra myricaceae implications for understanding the evolution of fagales
Frontiers in Plant Science, 2017Co-Authors: Rui Li, James R P Worth, Xian Li, Pan Li, Kenneth M Cameron, Chengxin FuAbstract:Morella rubra (Myricaceae), also known as Chinese bayberry, is an economically important, subtropical, evergreen fruit tree. The phylogenetic placement of Myricaceae within Fagales and the origin of Chinese bayberry’s domestication are still unresolved. In this study, we report the chloroplast (cp) genome of M. rubra and take advantage of several previously reported chloroplast genomes from related taxa to examine patterns of evolution in Fagales. The cp genomes of three M. rubra individuals were 159,478 bp, 159,568 bp and 159.586 bp in length, respectively, comprising a pair of inverted repeat (IR) regions (26,014–26,069 bp) separated by a large single-copy (LSC) region (88,683–88,809 bp) and a small single-copy (SSC) region (18,676–18,767 bp). Each cp genome encodes the same 111 unique genes, consisting of 77 different protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes, with 18 duplicated in the inverted repeats. Comparative analysis of chloroplast genomes from four representative Fagales families revealed the loss of infA and the pseudogenization of ycf15 in all analyzed species, and rpl22 has been pseudogenized in M. rubra and Castanea mollissima, but not in Juglans regia or Ostrya rehderiana. The genome size variations are detected mainly due to the length of intergenic spacers rather than gene loss, gene pseudogenization, IR expansion or contraction. The phylogenetic relationships yielded by the complete genome sequences strongly support the placement of Myricaceae as sister to Juglandaceae. Furthermore, seven cpDNA markers (trnH-psbA, psbA-trnK, rps2-rpoC2, ycf4-cemA, petD-rpoA, ndhE-ndhG and ndhA intron) with relatively high levels of variation and variable cpSSR loci were identified within M. rubra, which will be useful in future researches characterizing the population genetics of M. rubra and investigating the origin of domesticated Chinese bayberry.
Fe Lix Forest - One of the best experts on this subject based on the ideXlab platform.
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Interfamilial relationships in order Fabales: new insights from the nuclear regions sqd1 and 26S rDNA
Plant Systematics and Evolution, 2020Co-Authors: Deniz Aygoren Uluer, Julie A Hawkins, Fe Lix ForestAbstract:Leguminosae, Polygalaceae, Quillajaceae and Surianaceae together comprise the order Fabales. Phylogenetic relationships within Fabales remain an unsolved problem even though interfamilial relationships have been examined in a number of studies using different sampling approaches and both molecular and morphological data. In this study, we gather information from the nuclear 26S rDNA region as well as previously published data from the sqd 1 , mat K and rbc L regions. Phylogenetic analyses were performed by maximum parsimony, maximum likelihood and Bayesian inference. Overall, the best-supported topology for the relationships among families within the order places the pair of Leguminosae and Polygalaceae as sister to the pair of Quillajaceae and Surianaceae. However, our approximately unbiased (AU) test of the combined data results has shown that none of the seven different topologies rejected. Furthermore, three topologies were not significantly different from each other. Therefore, similar to the previous studies, this study did not find well-supported dichotomous relationships among the four Fabales families. The Fabales topology was very sensitive to both data choice and the phylogenetic methods used, which may indicate a rapid-near-simultaneous evolution of the four Fabales families. Our results also show that while nuclear sqd 1 can be helpful as a complementary region, both the nuclear sqd 1 and rDNA 26S regions could be problematic when analyzed individually.
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supermatrix analyses and molecular clock rooting of Fabales exploring the effects of outgroup choice and long branch attraction on topology
Botany, 2020Co-Authors: Deniz Aygoren Uluer, Fe Lix Forest, Julie A HawkinsAbstract:Fabales is a cosmopolitan angiosperm order that consists of four families: Leguminosae (Fabaceae), Polygalaceae, Surianaceae, and Quillajaceae. Despite the great interest in this group, a convincin...
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Elusive relationships within order Fabales: phylogenetic analyses using matK and rbcL sequence data.
Systematic Botany, 2009Co-Authors: María Angélica Bello, Fe Lix Forest, Anne Bruneau, Julie A HawkinsAbstract:Abstract The order Fabales, including Leguminosae, Polygalaceae, Quillajaceae and Surianaceae, represents a novel hypothesis emerging from angiosperm molecular phylogenies. Despite good support for the order, molecular studies to date have suggested contradictory poorly supported interfamilial relationships. Our reappraisal of relationships within Fabales addresses past taxon sampling deficiencies, and employs parsimony and Bayesian approaches using sequences from the plastid regions rbcL (166 spp.) and matK (78 spp.). Five alternative hypotheses for interfamilial relationships within Fabales were recovered. The Shimodaira-Hasegawa test found the likelihood of a resolved topology significantly higher than the one calculated for a polytomy but did not favour any of the alternative hypotheses of relationship within Fabales. In the light of the morphological evidence available and the comparative behavior of rbcL and matK, the topology recovering Polygalaceae as sister to the rest of the order Fabales with L...
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pollen morphology of the family polygalaceae Fabales
Botanical Journal of the Linnean Society, 2008Co-Authors: Hannah Banks, Fe Lix Forest, Bente B Klitgaard, Frances Claxton, Peter R CraneAbstract:An overview of pollen morphology from all genera in the family Polygalaceae is presented to assist systematic studies of the Fabales clade. The pollen of 72 species, representing 18 genera, in Polygalaceae was examined using light microscopy and scanning electron microscopy. In addition, the pollen of eight species, representing seven genera, was examined using transmission electron microscopy. Pollen is described and illustrated for each genus, and the first pollen descriptions and publication of photomicrographs are presented for seven genera: Balgoya, Barnhartia, Comesperma, Diclidanthera, Eriandra, Moutabea, plus Polygala subgenus Badiera, and species previously included in Nylandtia (now in Muraltia). Pollen morphological similarities and differences broadly correspond with relationships suggested by recent molecular phylogenies. The aperture number was also found to correlate with trees generated using molecular data; early branching taxa have lower aperture numbers than later branching ones. The overall range of ectoaperture numbers seen in Polygalaceae, excluding Balgoya, is between five and 33. The pollen of Balgoya is tricolporate; all other genera have pollen with a range of ectoaperture numbers within each sample. The degree of endoaperture fusion to form endocingula is variable at a subgeneric level. All pollen is isopolar, except for that of Heterosamara and Polygala wattersii. © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society, 2008, 156, 253–289.
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the role of biotic and abiotic factors in evolution of ant dispersal in the milkwort family polygalaceae
Evolution, 2007Co-Authors: Fe Lix Forest, Peter R Crane, Claes Persson, Mark W Chase, Julie A HawkinsAbstract:A phylogenetic approach was taken to investigate the evolutionary history of seed appendages in the plant family Polygalaceae (Fabales) and determine which factors might be associated with evolution of elaiosomes through comparisons to abiotic (climate) and biotic (ant species number and abundance) timelines. Molecular datasets from three plastid regions representing 160 species were used to reconstruct a phylogenetic tree of the order Fabales, focusing on Polygalaceae. Bayesian dating methods were used to estimate the age of the appearance of ant-dispersed elaiosomes in Polygalaceae, shown by likelihood optimizations to have a single origin in the family. Topology-based tests indicated a diversification rate shift associated with appearance of caruncular elaiosomes. We show that evolution of the caruncular elaiosome type currently associated with ant dispersal occurred 54.0-50.5 million year ago. This is long after an estimated increase in ant lineages in the Late Cretaceous based on molecular studies, but broadly concomitant with increasing global temperatures culminating in the Late Paleocene-Early Eocene thermal maxima. These results suggest that although most major ant clades were present when elaiosomes appeared, the environmental significance of elaiosomes may have been an important factor in success of elaiosome-bearing lineages. Ecological abundance of ants is perhaps more important than lineage numbers in determining significance of ant dispersal. Thus, our observation that elaiosomes predate increased ecological abundance of ants inferred from amber deposits could be indicative of an initial abiotic environmental function.
Kenneth M Cameron - One of the best experts on this subject based on the ideXlab platform.
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the complete chloroplast genome of chinese bayberry morella rubra myricaceae implications for understanding the evolution of fagales
Frontiers in Plant Science, 2017Co-Authors: Rui Li, James R P Worth, Xian Li, Pan Li, Kenneth M Cameron, Chengxin FuAbstract:Morella rubra (Myricaceae), also known as Chinese bayberry, is an economically important, subtropical, evergreen fruit tree. The phylogenetic placement of Myricaceae within Fagales and the origin of Chinese bayberry’s domestication are still unresolved. In this study, we report the chloroplast (cp) genome of M. rubra and take advantage of several previously reported chloroplast genomes from related taxa to examine patterns of evolution in Fagales. The cp genomes of three M. rubra individuals were 159,478 bp, 159,568 bp and 159.586 bp in length, respectively, comprising a pair of inverted repeat (IR) regions (26,014–26,069 bp) separated by a large single-copy (LSC) region (88,683–88,809 bp) and a small single-copy (SSC) region (18,676–18,767 bp). Each cp genome encodes the same 111 unique genes, consisting of 77 different protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes, with 18 duplicated in the inverted repeats. Comparative analysis of chloroplast genomes from four representative Fagales families revealed the loss of infA and the pseudogenization of ycf15 in all analyzed species, and rpl22 has been pseudogenized in M. rubra and Castanea mollissima, but not in Juglans regia or Ostrya rehderiana. The genome size variations are detected mainly due to the length of intergenic spacers rather than gene loss, gene pseudogenization, IR expansion or contraction. The phylogenetic relationships yielded by the complete genome sequences strongly support the placement of Myricaceae as sister to Juglandaceae. Furthermore, seven cpDNA markers (trnH-psbA, psbA-trnK, rps2-rpoC2, ycf4-cemA, petD-rpoA, ndhE-ndhG and ndhA intron) with relatively high levels of variation and variable cpSSR loci were identified within M. rubra, which will be useful in future researches characterizing the population genetics of M. rubra and investigating the origin of domesticated Chinese bayberry.
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The Complete Chloroplast Genome of Chinese Bayberry (Morella rubra, Myricaceae): Implications for Understanding the Evolution of Fagales
Frontiers Media S.A., 2017Co-Authors: James R P Worth, Lu-xian Liu, Kenneth M CameronAbstract:Morella rubra (Myricaceae), also known as Chinese bayberry, is an economically important, subtropical, evergreen fruit tree. The phylogenetic placement of Myricaceae within Fagales and the origin of Chinese bayberry’s domestication are still unresolved. In this study, we report the chloroplast (cp) genome of M. rubra and take advantage of several previously reported chloroplast genomes from related taxa to examine patterns of evolution in Fagales. The cp genomes of three M. rubra individuals were 159,478, 159,568, and 159.586 bp in length, respectively, comprising a pair of inverted repeat (IR) regions (26,014–26,069 bp) separated by a large single-copy (LSC) region (88,683–88,809 bp) and a small single-copy (SSC) region (18,676–18,767 bp). Each cp genome encodes the same 111 unique genes, consisting of 77 different protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes, with 18 duplicated in the IRs. Comparative analysis of chloroplast genomes from four representative Fagales families revealed the loss of infA and the pseudogenization of ycf15 in all analyzed species, and rpl22 has been pseudogenized in M. rubra and Castanea mollissima, but not in Juglans regia or Ostrya rehderiana. The genome size variations are detected mainly due to the length of intergenic spacers rather than gene loss, gene pseudogenization, IR expansion or contraction. The phylogenetic relationships yielded by the complete genome sequences strongly support the placement of Myricaceae as sister to Juglandaceae. Furthermore, seven cpDNA markers (trnH-psbA, psbA-trnK, rps2-rpoC2, ycf4-cemA, petD-rpoA, ndhE-ndhG, and ndhA intron) with relatively high levels of variation and variable cpSSR loci were identified within M. rubra, which will be useful in future research characterizing the population genetics of M. rubra and investigating the origin of domesticated Chinese bayberry
