The Experts below are selected from a list of 303 Experts worldwide ranked by ideXlab platform
Jim Leebens-mack - One of the best experts on this subject based on the ideXlab platform.
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Phylogenomic analyses of species relationships in the genus Sabal (Arecaceae) using targeted sequence capture
Biological Journal of the Linnean Society, 2015Co-Authors: Karolina Heyduk, Dorset W. Trapnell, Craig F. Barrett, Jim Leebens-mackAbstract:With the increasing availability of high-throughput sequencing, phylogenetic analyses are no longer constrained by the limited availability of a few loci. Here, we describe a sequence capture methodology, which we used to collect data for analyses of diversification within Sabal (Arecaceae), a palm genus native to the south-eastern USA, Caribbean, Bermuda and Central America. RNA probes were developed and used to enrich DNA samples for putatively low copy nuclear genes and the plastomes for all Sabal species and two outgroup species. Sequence data were generated on an Illumina MiSeq sequencer and target sequences were assembled using custom workflows. Both coalescence and supermatrix analyses of 133 nuclear genes were used to estimate species trees relationships. Plastid genomes were also analysed, yielding generally poor resolution with regard to species relationships. Species relationships described in both nuclear gene and plastome sequences largely reflect the biogeography of the group and, to a lesser extent, previous morphology-based hypotheses. Beyond the biological implications, this research validates a high-throughput methodology for generating a large number of genes for coalescence-based phylogenetic analyses in plant lineages.
Karolina Heyduk - One of the best experts on this subject based on the ideXlab platform.
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Phylogenomic analyses of species relationships in the genus Sabal (Arecaceae) using targeted sequence capture
Biological Journal of the Linnean Society, 2015Co-Authors: Karolina Heyduk, Dorset W. Trapnell, Craig F. Barrett, Jim Leebens-mackAbstract:With the increasing availability of high-throughput sequencing, phylogenetic analyses are no longer constrained by the limited availability of a few loci. Here, we describe a sequence capture methodology, which we used to collect data for analyses of diversification within Sabal (Arecaceae), a palm genus native to the south-eastern USA, Caribbean, Bermuda and Central America. RNA probes were developed and used to enrich DNA samples for putatively low copy nuclear genes and the plastomes for all Sabal species and two outgroup species. Sequence data were generated on an Illumina MiSeq sequencer and target sequences were assembled using custom workflows. Both coalescence and supermatrix analyses of 133 nuclear genes were used to estimate species trees relationships. Plastid genomes were also analysed, yielding generally poor resolution with regard to species relationships. Species relationships described in both nuclear gene and plastome sequences largely reflect the biogeography of the group and, to a lesser extent, previous morphology-based hypotheses. Beyond the biological implications, this research validates a high-throughput methodology for generating a large number of genes for coalescence-based phylogenetic analyses in plant lineages.
Rodolfo Dirzo - One of the best experts on this subject based on the ideXlab platform.
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Floristic diversity of Sabal palmetto woodland: an endemic and endangered vegetation type from Mexico
Biodiversity and Conservation, 2006Co-Authors: Juan Carlos López, Rodolfo DirzoAbstract:The Sabal palmetto woodland is a tropical plant formation dominated by Sabal mexicana, with restricted distribution to southeast Mexico. Sabal palms grow on poor soils but accumulate large quantities of organic substrate in their crowns, harboring a contingent of plants that use it as phorophyte. Although it is a threatened formation, basic information on its biodiversity is scant. We examined the floristic diversity of recruited (diameter at breast height, DBH, ≥1 cm) and understory (DBH ≤ 1 cm) plants, and its variation with anthropogenic disturbance. We also examined the floristic diversity of plants that use the Sabal palms as phorophytes, and assessed its variation with human impact. All plants present in transects within a conserved and an adjacent perturbed area were sampled. The list of observed taxa shows that this vegetation has a clear affinity with tropical dry and wet forests of Mexico, with a small representation of taxa from desert ecosystems. The floristic contingent included a total of 81 species in 2000 m2. Richness, composition and diversity were affected by disturbance. Recruited and understory vegetation in the disturbed site were 5- and 1.6-times less diverse than in the conserved site, and species of mature, conserved vegetation were substituted by heliophytes in the disturbed site. In contrast, abundance of palms and diversity and identity of epiphytic/hemiepiphytic plants were not affected by disturbance. We show that even monodominated tropical ecosystems growing on poor soils have a high floristic diversity and that current anthropogenic impact threatens not only species and populations but also entire plant formations.
Craig F. Barrett - One of the best experts on this subject based on the ideXlab platform.
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Phylogenomic analyses of species relationships in the genus Sabal (Arecaceae) using targeted sequence capture
Biological Journal of the Linnean Society, 2015Co-Authors: Karolina Heyduk, Dorset W. Trapnell, Craig F. Barrett, Jim Leebens-mackAbstract:With the increasing availability of high-throughput sequencing, phylogenetic analyses are no longer constrained by the limited availability of a few loci. Here, we describe a sequence capture methodology, which we used to collect data for analyses of diversification within Sabal (Arecaceae), a palm genus native to the south-eastern USA, Caribbean, Bermuda and Central America. RNA probes were developed and used to enrich DNA samples for putatively low copy nuclear genes and the plastomes for all Sabal species and two outgroup species. Sequence data were generated on an Illumina MiSeq sequencer and target sequences were assembled using custom workflows. Both coalescence and supermatrix analyses of 133 nuclear genes were used to estimate species trees relationships. Plastid genomes were also analysed, yielding generally poor resolution with regard to species relationships. Species relationships described in both nuclear gene and plastome sequences largely reflect the biogeography of the group and, to a lesser extent, previous morphology-based hypotheses. Beyond the biological implications, this research validates a high-throughput methodology for generating a large number of genes for coalescence-based phylogenetic analyses in plant lineages.
Dorset W. Trapnell - One of the best experts on this subject based on the ideXlab platform.
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Phylogenomic analyses of species relationships in the genus Sabal (Arecaceae) using targeted sequence capture
Biological Journal of the Linnean Society, 2015Co-Authors: Karolina Heyduk, Dorset W. Trapnell, Craig F. Barrett, Jim Leebens-mackAbstract:With the increasing availability of high-throughput sequencing, phylogenetic analyses are no longer constrained by the limited availability of a few loci. Here, we describe a sequence capture methodology, which we used to collect data for analyses of diversification within Sabal (Arecaceae), a palm genus native to the south-eastern USA, Caribbean, Bermuda and Central America. RNA probes were developed and used to enrich DNA samples for putatively low copy nuclear genes and the plastomes for all Sabal species and two outgroup species. Sequence data were generated on an Illumina MiSeq sequencer and target sequences were assembled using custom workflows. Both coalescence and supermatrix analyses of 133 nuclear genes were used to estimate species trees relationships. Plastid genomes were also analysed, yielding generally poor resolution with regard to species relationships. Species relationships described in both nuclear gene and plastome sequences largely reflect the biogeography of the group and, to a lesser extent, previous morphology-based hypotheses. Beyond the biological implications, this research validates a high-throughput methodology for generating a large number of genes for coalescence-based phylogenetic analyses in plant lineages.
