Randy Linder - Academia.edu (original) (raw)
Papers by Randy Linder
Pacific Symposium on Biocomputing, Dec 1, 2008
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2004
Phylogenetic networks model the evolutionary history of sets of organisms when events such as hyb... more Phylogenetic networks model the evolutionary history of sets of organisms when events such as hybrid speciation and horizontal gene transfer occur. In spite of their widely acknowledged importance in evolutionary biology, phylogenetic networks have so far been studied mostly for specific data sets. We present a general definition of phylogenetic networks in terms of directed acyclic graphs (DAGs) and a set of conditions. Further, we distinguish between model networks and reconstructible ones and characterize the effect of extinction and taxon sampling on the reconstructibility of the network. Simulation studies are a standard technique for assessing the performance of phylogenetic methods. A main step in such studies entails quantifying the topological error between the model and inferred phylogenies. While many measures of tree topological accuracy have been proposed, none exist for phylogenetic networks. Previously, we proposed the first such measure, which applied only to a restricted class of networks. In this paper, we extend that measure to apply to all networks, and prove that it is a metric on the space of phylogenetic networks. Our results allow for the systematic study of existing network methods, and for the design of new accurate ones.
Genetics, 1995
The sexual transfer of genes between taxa possessing different structural karyotypes must involve... more The sexual transfer of genes between taxa possessing different structural karyotypes must involve the passage of genes through a chromosomal sterility barrier. Yet little is known about the effects of structural differences on gene introgression within or adjacent to the rearranged chromosomal fragments or about the patterns of introgression in collinear regions. Here, we employ 197 mapped molecular markers to study the effects of chromosomal structural differences on introgression in backcrossed progeny of the domesticated sunflower, Helianthus annuus, and its karyotypically divergent wild relative, H. petiolaris. Forty percent of the genome from the seven collinear linkages introgressed, whereas only 2.4% of the genome from the 10 rearranged linkages was transferred. Thus, chromosomal rearrangements appear to provide an effective mechanism for reducing or eliminating introgression in rearranged chromosomal segments. On the other hand, observations that 60% of the markers from with...
Note: Tutorial available at textttcompbio.unm,edu/papers.html Reference LCBB-REPORT-2004-001 Reco... more Note: Tutorial available at textttcompbio.unm,edu/papers.html Reference LCBB-REPORT-2004-001 Record created on 2006-12-12, modified on 2017-05-12
Biocomputing 2008, 2007
Many multiple sequence alignment methods (MSAs) use guide trees in conjunction with a progressive... more Many multiple sequence alignment methods (MSAs) use guide trees in conjunction with a progressive alignment technique to generate a multiple sequence alignment but use differing techniques to produce the guide tree and to perform the progressive alignment. In this paper we explore the consequences of changing the guide tree used for the alignment routine. We evaluate four leading MSA methods (ProbCons, MAFFT, Muscle, and ClustalW) as well as a new MSA method (FTA, for "Fixed Tree Alignment") which we have developed, on a wide range of simulated datasets. Although improvements in alignment accuracy can be obtained by providing better guide trees, in general there is little effect on the "accuracy" (measured using the SP-score) of the alignment by improving the guide tree. However, RAxML-based phylogenetic analyses of alignments based upon better guide trees tend to be much more accurate. This impact is particularly significant for ProbCons, one of the best MSA methods currently available, and our method, FTA. Finally, for very good guide trees, phylogenies based upon FTA alignments are more accurate than phylogenies based upon ProbCons alignments, suggesting that further improvements in phylogenetic accuracy may be obtained through algorithms of this type.
Science, 2009
Rapid Tree Building Phylogenetic reconstruction is used to determine the relationships between or... more Rapid Tree Building Phylogenetic reconstruction is used to determine the relationships between organisms and requires an accurate alignment and analysis of multiple sequences. Iterative rounds of alignment and tree building are often necessary to prevent errors in the phylogeny estimate. One such way to address this problem is to assess alignment and trees in a single step. However, efficient algorithms to analyze data sets of reasonable size have been lacking. Liu et al. (p. 1561 ; see the Perspective by Löytynoja and Goldman ) describe an iterative approach that simultaneously incorporates both alignment and phylogeny and applies a fast maximum likelihood algorithm to the tree-building part. By assembling the components of the methods in this way, accurate results were obtained for up to 1000 sequences. Thus, it is possible to produce coestimation of sequence alignment and phylogeny that is both rapid and accurate.
Proceedings of the National Academy of Sciences, 1999
Belowground vertical community composition and maximum rooting depth of the Edwards Plateau of ce... more Belowground vertical community composition and maximum rooting depth of the Edwards Plateau of central Texas were determined by using DNA sequence variation to identify roots from caves 5–65 m deep. Roots from caves were identified by comparing their DNA sequences for the internal transcribed spacer (ITS) region of the 18S–26S ribosomal DNA repeat against a reference ITS database developed for woody plants of the region. Sequencing the ITS provides, to our knowledge, the first universal method for identifying plant roots. At least six tree species in the system grew roots deeper than 5 m, but only the evergreen oak, Quercus fusiformis , was found below 10 m. The maximum rooting depth for the ecosystem was ≈25 m. 18 O isotopic signatures for stem water of Q. fusiformis confirmed water uptake from 18 m underground. The availability of resources at depth, coupled with small surface pools of water and nutrients, may explain the occurrence of deep roots in this and other systems.
Molecular Ecology, 2008
One potential eff ect of transgenes escaped from cultivation, either in crop plank themselves or ... more One potential eff ect of transgenes escaped from cultivation, either in crop plank themselves or introgressed into wild relatives, is release of the plants from ecological constraints that currently limit or control their distribution and abundance. Release may occur only within the community that the species presently occupies, or it may allow range expansion into new communities. Experience with ecological range expansions of invading plant species suggests that when ecological release occurs, the consequences can be severe. To assess properly the likelihood of ecological release, the factors that currently limit species'distributionsand abundances must be determined by manipulative experiments. The effect of transgenes on these factors must then be investigated throughout the life cycle of the species and on a case-by-case basis. For ruderal annual species, seed survival and seedling establishment phases may be particularly important.
Molecular Ecology, 2008
Transgenes introduced into crops can escape in time, as well as space, via the seed bank. For ann... more Transgenes introduced into crops can escape in time, as well as space, via the seed bank. For annual plants, especially ruderals, seed bank behaviour may be the most important factor determining population persistence. Crop seeds may exhibit some dormancy and germination cueing in the soil but are expected to be less able to persist than their wild relatives, which often have considerable dormancy and longevity, as well as effective germination cueing responses. Cropwild hybrids may have seed bank characteristics more suited to persistence, and maternal effects may favour persistence of hybrids having wild plants for their female parent. Escape of transgenes via crop-wild hybrids presents unique concerns not present for crops. Hybrids can undergo natural selection and may back-cross with wild plants. We suggest methods that can be used in conjunction with evaluation of the relative fitness of crop-wild hybrids that will determine the likelihood of back-crossing. Accurate assessment of escape in time and transgene persistence via crop-wild hybrids requires proper plant materials. We emphasize the use of null segregants as controls for transgenic crops and for generating crop-wild hybrid controls for transgenic hybrids. Since good empirical and theoretical understanding of how individual genes influence the fate of plants in different environments is lacking, evaluation of escape in time and the persistence of transgenes via crop-wild hybrids should be on a case-by-case basis.
Functional Ecology, 1993
Seeds of two wild populations, a crop type (canola) and reciprocal crop-wild hybrids of Brassica ... more Seeds of two wild populations, a crop type (canola) and reciprocal crop-wild hybrids of Brassica rapa were exposed to a factorial combination of light, nutrient and stratification treatments in a growth chamber study to test differences in germination responses to environmental cues. The effects of seed density and nutrient treatment on germination were tested in a separate study. Germination of each type differed in response to treatment combinations. Canola had higher levels of germination than the wild populations. Hybrid germination more closely resembled that of the maternal parent than that of the reciprocal hybrid or paternal parent. Seeds from agricultural and non-agricultural wild populations differed in germination responses to treatments (...)
Bioinformatics, 2012
Motivation: While phylogenetic analyses of datasets containing 1000-5000 sequences are challengin... more Motivation: While phylogenetic analyses of datasets containing 1000-5000 sequences are challenging for existing methods, the estimation of substantially larger phylogenies poses a problem of much greater complexity and scale. Methods: We present DACTAL, a method for phylogeny estimation that produces trees from unaligned sequence datasets without ever needing to estimate an alignment on the entire dataset. DACTAL combines iteration with a novel divide-and-conquer approach, so that each iteration begins with a tree produced in the prior iteration, decomposes the taxon set into overlapping subsets, estimates trees on each subset, and then combines the smaller trees into a tree on the full taxon set using a new supertree method. We prove that DACTAL is guaranteed to produce the true tree under certain conditions. We compare DACTAL to SATé and maximum likelihood trees on estimated alignments using simulated and real datasets with 1000-27 643 taxa. Results: Our studies show that on average DACTAL yields more accurate trees than the two-phase methods we studied on very large datasets that are difficult to align, and has approximately the same accuracy on the easier datasets. The comparison to SATé shows that both have the same accuracy, but that DACTAL achieves this accuracy in a fraction of the time. Furthermore, DACTAL can analyze larger datasets than SATé, including a dataset with almost 28 000 sequences.
American Potato Journal, 1990
... Berries from open pollination, in the other four plots, were placed in mesh bags as each infl... more ... Berries from open pollination, in the other four plots, were placed in mesh bags as each inflorescence matured. ... The diagnostic loci were Mdh-1, Prx-2, Got-1 and Got-2, which were homozy-gous for different allozymes in the plants sampled from both species. ...
Adaptive Behavior, 2005
This paper elaborates on the possibilities for self-adjustment of a biological neural network use... more This paper elaborates on the possibilities for self-adjustment of a biological neural network used as feedback controller in the motor control system of a six-legged walker. As biological systems, in contrast to technical systems, show an impressive capability of self-adaptation, this is meant as a proof of principle. Complementing an intensity encoded system (Linder, 2002), where scalar values are represented as the activity of a given neuron, this mechanism is based on spatial encoding, where a scalar value is represented as the location of the most active neuron in a chain of neurons. This encoding scheme can often be observed in biological systems. While the intensity encoded system requires linear input characteristics and symmetrical distribution of the input values over the whole range for both target angles and actual angles, the spatially encoded system presented here is completely self-organizing for evenly distributed target angles and actual angles. By employing an inter...
Theoretical and Applied Genetics, 1996
Population genetic theory suggests that mating designs employing one or more generations of sib-c... more Population genetic theory suggests that mating designs employing one or more generations of sib-crossing or selfing prior to backcrossing are more effective than backcrossing alone for moving alleles across linkage groups where effective recombination rates are low (e.g., chromosomally divergent linkages). To test this hypothesis, we analyzed the effects of chromosomal structural differences and mating designs on the frequency and genomic distribution of introgressed markers using the domesticated sunflower, Helianthus annuus, and one of its wild relatives, H. petiolaris, as the experimental system. We surveyed 170 progeny, representing the end products of three different mating designs (design I, P-F1-BC1-BC2-F 2-F3, design II, P-F1-F2-BCI-BCz-F3; and design III, P-FI-F 2_ F3-BC1-BC2), for 197 parental RAPD markers of known genomic location. Comparison of observed patterns of introgression with expectations based on simulations of unrestricted introgression revealed that much of the genome was protected from introgression regardless of mating design or chromosomal structural differences. Although the simulations indicated that all markers should introgress into multiple individuals in each of the three mating designs, 20 of 58 (34%) markers from collinear linkage groups, and 112 of 139 (81%) markers from rearranged linkage groups did not introgress. In addition, the average size of introgressed fragments (12.2 cM) was less than half that predicted by theoretical models (26-33 cM). Both of these observations are consistent with strong selection against introgressed linkage blocks, particularly in chromosomally divergent linkages. Nonetheless, mating designs II and III, which employed one and two generations of sib-mating, respectively, prior to backcrossing, were sig-Communicated by B. S. Gill
Molecular Phylogenetics and Evolution, 2000
For molecular phylogenetic reconstruction of some intrageneric groups of plants, a DNA region is ... more For molecular phylogenetic reconstruction of some intrageneric groups of plants, a DNA region is needed that evolves more rapidly than the internal transcribed spacer (ITS) of the 18S-26S nuclear ribosomal DNA (nrDNA) repeat. If the region identified is nuclear, it would also be desirable for it to undergo rapid concerted evolution to eliminate problems with coalescence. The external transcribed spacer (ETS) of the nrDNA repeat has shown promise for intrageneric phylogenetic reconstruction, but only the 3' end of the region has been utilized for phylogenetic reconstruction and "universal" primers for PCR amplification have been elusive. We present a method for reliably amplifying and sequencing the entire ETS throughout Asteraceae and some closely allied families. We also show that the ETS is more variable and phylogenetically informative than the ITS in three disparate genera of Asteraceae-Argyranthemum (tribe Anthemideae), Asteriscus (tribe Inuleae), and Helianthus (tribe Heliantheae). The full ETS was amplified using a primer (ETS1f) within the intergenic spacer in combination with a primer (18S-2L) in the 5' end of the highly conserved 18S gene. ETS1f was designed to correspond to a highly conserved region found in Helianthus and Crepis, which are in separate subfamilies of Asteraceae. ETS1f/18S-2L primed in all of the tribes of Asteraceae as well as exemplar taxa from Campanulaceae, Goodeniaceae, and Calyceraceae. For both Argyranthemum and Asteriscus, we were able to directly sequence the ETS PCR products when a single band was produced. When multiple bands were produced, we gel-purified and occasionally cloned the band of interest before sequencing. Although PCR produced single bands for Helianthus species, it was necessary to clone Helianthus amplifications prior to sequencing due to multiple intragenomic ETS repeat types. Alignment of ETS sequences for Argyranthemum and Asteriscus was straightforward and unambiguous despite some subrepeat structure in the 5' end. For Helianthus, different numbers of large tandem subrepeats in different species required analysis of the orthology of the subrepeats prior to alignment. In all three genera, the ETS provided more informative variation for phylogenetic reconstruction and allowed better resolution of relationships than the ITS. Although cloned sequences from Helianthus differed, intragenomic clones consistently formed clades. This result indicated that concerted evolution was proceeding rapidly enough in ETS that species-specific phylogenetic signal was retained. It should be now be possible to use the entire ETS for phylogenetic reconstruction of recently diverged lineages in Asteraceae and at least three other families (approximately 26,000 species or about 8% of all…
American Journal of Botany, 2007
The sunflower genus, Helianthus, is recognized widely for the cultivated sunflower H. annuus and ... more The sunflower genus, Helianthus, is recognized widely for the cultivated sunflower H. annuus and scientifically as a model organism for studying diploid and polyploid hybrid speciation, introgression, and genetic architecture. A resolved phylogeny for the genus is essential for the advancement of these scientific areas. In the past, phylogenetic relationships of the perennial species and polyploid hybrids have been particularly difficult to resolve. Using the external transcribed spacer region of the nuclear 18S-26S rDNA region, we reveal for the first time a highly resolved gene tree for Helianthus. Phylogenetic analysis allowed the determination of a monophyletic annual H. sect. Helianthus, a two-lineage polyphyletic H. sect. Ciliares, and the monotypic H. sect. Agrestis, all of which were nested within a large perennial and polyphyletic H. sect. Divaricati. The distribution of perennial polyploids and known annual diploid hybrids on this phylogeny suggested multiple independent hybrid speciation events that gave rise to at least four polyploids and three diploid hybrids. Also provided by this phylogeny was evidence for homoploid hybrid speciation outside H. sect. Helianthus. Finally, previous hypotheses about the secondary chemistry in the genus were tested in a phylogenetic framework to obtain a better understanding of the evolution of these compounds in Helianthus.
Biocomputing 2008 - Proceedings of the Pacific Symposium, 2007
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Theoretical and Applied Genetics, 1998
Hybrids between cultivated and wild sunflowers (Helianthus annuus) are frequently reported. As mu... more Hybrids between cultivated and wild sunflowers (Helianthus annuus) are frequently reported. As much as 42% of progeny from wild plants near cultivar fields are hybrids, and cultivar genes have been shown to persist in wild populations at least five generations. We report the effects of up to 40 years of persistent cultivar gene flow on the genetic structure of three wild H. annuus populations that are adjacent to cultivated fields. Eighteen cultivar-specific markers were surveyed in a total of 115 individuals. We also developed cultivar-based genetic maps for the markers and used them to see if marker patterns in the wild populations were consistent with introgression and if selection was acting jointly on unlinked loci. High levels of crop specific markers were detected in all three wild populations, ranging from 0.315 to 0.382, on average. All 115 plants had at least 1 cultivar marker. Introgression is the most likely explanation for the presence of cropspecific markers in the sympatric populations because (1) the markers were either not present or found at much lower levels in four allopatric populations, (2) markers that were genetically linked in the cultivar invariably showed linkage disequilibrium patterns in the sympatric populations consistent with introgres-Communicated by B. S. Gill
Pacific Symposium on Biocomputing, Dec 1, 2008
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2004
Phylogenetic networks model the evolutionary history of sets of organisms when events such as hyb... more Phylogenetic networks model the evolutionary history of sets of organisms when events such as hybrid speciation and horizontal gene transfer occur. In spite of their widely acknowledged importance in evolutionary biology, phylogenetic networks have so far been studied mostly for specific data sets. We present a general definition of phylogenetic networks in terms of directed acyclic graphs (DAGs) and a set of conditions. Further, we distinguish between model networks and reconstructible ones and characterize the effect of extinction and taxon sampling on the reconstructibility of the network. Simulation studies are a standard technique for assessing the performance of phylogenetic methods. A main step in such studies entails quantifying the topological error between the model and inferred phylogenies. While many measures of tree topological accuracy have been proposed, none exist for phylogenetic networks. Previously, we proposed the first such measure, which applied only to a restricted class of networks. In this paper, we extend that measure to apply to all networks, and prove that it is a metric on the space of phylogenetic networks. Our results allow for the systematic study of existing network methods, and for the design of new accurate ones.
Genetics, 1995
The sexual transfer of genes between taxa possessing different structural karyotypes must involve... more The sexual transfer of genes between taxa possessing different structural karyotypes must involve the passage of genes through a chromosomal sterility barrier. Yet little is known about the effects of structural differences on gene introgression within or adjacent to the rearranged chromosomal fragments or about the patterns of introgression in collinear regions. Here, we employ 197 mapped molecular markers to study the effects of chromosomal structural differences on introgression in backcrossed progeny of the domesticated sunflower, Helianthus annuus, and its karyotypically divergent wild relative, H. petiolaris. Forty percent of the genome from the seven collinear linkages introgressed, whereas only 2.4% of the genome from the 10 rearranged linkages was transferred. Thus, chromosomal rearrangements appear to provide an effective mechanism for reducing or eliminating introgression in rearranged chromosomal segments. On the other hand, observations that 60% of the markers from with...
Note: Tutorial available at textttcompbio.unm,edu/papers.html Reference LCBB-REPORT-2004-001 Reco... more Note: Tutorial available at textttcompbio.unm,edu/papers.html Reference LCBB-REPORT-2004-001 Record created on 2006-12-12, modified on 2017-05-12
Biocomputing 2008, 2007
Many multiple sequence alignment methods (MSAs) use guide trees in conjunction with a progressive... more Many multiple sequence alignment methods (MSAs) use guide trees in conjunction with a progressive alignment technique to generate a multiple sequence alignment but use differing techniques to produce the guide tree and to perform the progressive alignment. In this paper we explore the consequences of changing the guide tree used for the alignment routine. We evaluate four leading MSA methods (ProbCons, MAFFT, Muscle, and ClustalW) as well as a new MSA method (FTA, for "Fixed Tree Alignment") which we have developed, on a wide range of simulated datasets. Although improvements in alignment accuracy can be obtained by providing better guide trees, in general there is little effect on the "accuracy" (measured using the SP-score) of the alignment by improving the guide tree. However, RAxML-based phylogenetic analyses of alignments based upon better guide trees tend to be much more accurate. This impact is particularly significant for ProbCons, one of the best MSA methods currently available, and our method, FTA. Finally, for very good guide trees, phylogenies based upon FTA alignments are more accurate than phylogenies based upon ProbCons alignments, suggesting that further improvements in phylogenetic accuracy may be obtained through algorithms of this type.
Science, 2009
Rapid Tree Building Phylogenetic reconstruction is used to determine the relationships between or... more Rapid Tree Building Phylogenetic reconstruction is used to determine the relationships between organisms and requires an accurate alignment and analysis of multiple sequences. Iterative rounds of alignment and tree building are often necessary to prevent errors in the phylogeny estimate. One such way to address this problem is to assess alignment and trees in a single step. However, efficient algorithms to analyze data sets of reasonable size have been lacking. Liu et al. (p. 1561 ; see the Perspective by Löytynoja and Goldman ) describe an iterative approach that simultaneously incorporates both alignment and phylogeny and applies a fast maximum likelihood algorithm to the tree-building part. By assembling the components of the methods in this way, accurate results were obtained for up to 1000 sequences. Thus, it is possible to produce coestimation of sequence alignment and phylogeny that is both rapid and accurate.
Proceedings of the National Academy of Sciences, 1999
Belowground vertical community composition and maximum rooting depth of the Edwards Plateau of ce... more Belowground vertical community composition and maximum rooting depth of the Edwards Plateau of central Texas were determined by using DNA sequence variation to identify roots from caves 5–65 m deep. Roots from caves were identified by comparing their DNA sequences for the internal transcribed spacer (ITS) region of the 18S–26S ribosomal DNA repeat against a reference ITS database developed for woody plants of the region. Sequencing the ITS provides, to our knowledge, the first universal method for identifying plant roots. At least six tree species in the system grew roots deeper than 5 m, but only the evergreen oak, Quercus fusiformis , was found below 10 m. The maximum rooting depth for the ecosystem was ≈25 m. 18 O isotopic signatures for stem water of Q. fusiformis confirmed water uptake from 18 m underground. The availability of resources at depth, coupled with small surface pools of water and nutrients, may explain the occurrence of deep roots in this and other systems.
Molecular Ecology, 2008
One potential eff ect of transgenes escaped from cultivation, either in crop plank themselves or ... more One potential eff ect of transgenes escaped from cultivation, either in crop plank themselves or introgressed into wild relatives, is release of the plants from ecological constraints that currently limit or control their distribution and abundance. Release may occur only within the community that the species presently occupies, or it may allow range expansion into new communities. Experience with ecological range expansions of invading plant species suggests that when ecological release occurs, the consequences can be severe. To assess properly the likelihood of ecological release, the factors that currently limit species'distributionsand abundances must be determined by manipulative experiments. The effect of transgenes on these factors must then be investigated throughout the life cycle of the species and on a case-by-case basis. For ruderal annual species, seed survival and seedling establishment phases may be particularly important.
Molecular Ecology, 2008
Transgenes introduced into crops can escape in time, as well as space, via the seed bank. For ann... more Transgenes introduced into crops can escape in time, as well as space, via the seed bank. For annual plants, especially ruderals, seed bank behaviour may be the most important factor determining population persistence. Crop seeds may exhibit some dormancy and germination cueing in the soil but are expected to be less able to persist than their wild relatives, which often have considerable dormancy and longevity, as well as effective germination cueing responses. Cropwild hybrids may have seed bank characteristics more suited to persistence, and maternal effects may favour persistence of hybrids having wild plants for their female parent. Escape of transgenes via crop-wild hybrids presents unique concerns not present for crops. Hybrids can undergo natural selection and may back-cross with wild plants. We suggest methods that can be used in conjunction with evaluation of the relative fitness of crop-wild hybrids that will determine the likelihood of back-crossing. Accurate assessment of escape in time and transgene persistence via crop-wild hybrids requires proper plant materials. We emphasize the use of null segregants as controls for transgenic crops and for generating crop-wild hybrid controls for transgenic hybrids. Since good empirical and theoretical understanding of how individual genes influence the fate of plants in different environments is lacking, evaluation of escape in time and the persistence of transgenes via crop-wild hybrids should be on a case-by-case basis.
Functional Ecology, 1993
Seeds of two wild populations, a crop type (canola) and reciprocal crop-wild hybrids of Brassica ... more Seeds of two wild populations, a crop type (canola) and reciprocal crop-wild hybrids of Brassica rapa were exposed to a factorial combination of light, nutrient and stratification treatments in a growth chamber study to test differences in germination responses to environmental cues. The effects of seed density and nutrient treatment on germination were tested in a separate study. Germination of each type differed in response to treatment combinations. Canola had higher levels of germination than the wild populations. Hybrid germination more closely resembled that of the maternal parent than that of the reciprocal hybrid or paternal parent. Seeds from agricultural and non-agricultural wild populations differed in germination responses to treatments (...)
Bioinformatics, 2012
Motivation: While phylogenetic analyses of datasets containing 1000-5000 sequences are challengin... more Motivation: While phylogenetic analyses of datasets containing 1000-5000 sequences are challenging for existing methods, the estimation of substantially larger phylogenies poses a problem of much greater complexity and scale. Methods: We present DACTAL, a method for phylogeny estimation that produces trees from unaligned sequence datasets without ever needing to estimate an alignment on the entire dataset. DACTAL combines iteration with a novel divide-and-conquer approach, so that each iteration begins with a tree produced in the prior iteration, decomposes the taxon set into overlapping subsets, estimates trees on each subset, and then combines the smaller trees into a tree on the full taxon set using a new supertree method. We prove that DACTAL is guaranteed to produce the true tree under certain conditions. We compare DACTAL to SATé and maximum likelihood trees on estimated alignments using simulated and real datasets with 1000-27 643 taxa. Results: Our studies show that on average DACTAL yields more accurate trees than the two-phase methods we studied on very large datasets that are difficult to align, and has approximately the same accuracy on the easier datasets. The comparison to SATé shows that both have the same accuracy, but that DACTAL achieves this accuracy in a fraction of the time. Furthermore, DACTAL can analyze larger datasets than SATé, including a dataset with almost 28 000 sequences.
American Potato Journal, 1990
... Berries from open pollination, in the other four plots, were placed in mesh bags as each infl... more ... Berries from open pollination, in the other four plots, were placed in mesh bags as each inflorescence matured. ... The diagnostic loci were Mdh-1, Prx-2, Got-1 and Got-2, which were homozy-gous for different allozymes in the plants sampled from both species. ...
Adaptive Behavior, 2005
This paper elaborates on the possibilities for self-adjustment of a biological neural network use... more This paper elaborates on the possibilities for self-adjustment of a biological neural network used as feedback controller in the motor control system of a six-legged walker. As biological systems, in contrast to technical systems, show an impressive capability of self-adaptation, this is meant as a proof of principle. Complementing an intensity encoded system (Linder, 2002), where scalar values are represented as the activity of a given neuron, this mechanism is based on spatial encoding, where a scalar value is represented as the location of the most active neuron in a chain of neurons. This encoding scheme can often be observed in biological systems. While the intensity encoded system requires linear input characteristics and symmetrical distribution of the input values over the whole range for both target angles and actual angles, the spatially encoded system presented here is completely self-organizing for evenly distributed target angles and actual angles. By employing an inter...
Theoretical and Applied Genetics, 1996
Population genetic theory suggests that mating designs employing one or more generations of sib-c... more Population genetic theory suggests that mating designs employing one or more generations of sib-crossing or selfing prior to backcrossing are more effective than backcrossing alone for moving alleles across linkage groups where effective recombination rates are low (e.g., chromosomally divergent linkages). To test this hypothesis, we analyzed the effects of chromosomal structural differences and mating designs on the frequency and genomic distribution of introgressed markers using the domesticated sunflower, Helianthus annuus, and one of its wild relatives, H. petiolaris, as the experimental system. We surveyed 170 progeny, representing the end products of three different mating designs (design I, P-F1-BC1-BC2-F 2-F3, design II, P-F1-F2-BCI-BCz-F3; and design III, P-FI-F 2_ F3-BC1-BC2), for 197 parental RAPD markers of known genomic location. Comparison of observed patterns of introgression with expectations based on simulations of unrestricted introgression revealed that much of the genome was protected from introgression regardless of mating design or chromosomal structural differences. Although the simulations indicated that all markers should introgress into multiple individuals in each of the three mating designs, 20 of 58 (34%) markers from collinear linkage groups, and 112 of 139 (81%) markers from rearranged linkage groups did not introgress. In addition, the average size of introgressed fragments (12.2 cM) was less than half that predicted by theoretical models (26-33 cM). Both of these observations are consistent with strong selection against introgressed linkage blocks, particularly in chromosomally divergent linkages. Nonetheless, mating designs II and III, which employed one and two generations of sib-mating, respectively, prior to backcrossing, were sig-Communicated by B. S. Gill
Molecular Phylogenetics and Evolution, 2000
For molecular phylogenetic reconstruction of some intrageneric groups of plants, a DNA region is ... more For molecular phylogenetic reconstruction of some intrageneric groups of plants, a DNA region is needed that evolves more rapidly than the internal transcribed spacer (ITS) of the 18S-26S nuclear ribosomal DNA (nrDNA) repeat. If the region identified is nuclear, it would also be desirable for it to undergo rapid concerted evolution to eliminate problems with coalescence. The external transcribed spacer (ETS) of the nrDNA repeat has shown promise for intrageneric phylogenetic reconstruction, but only the 3' end of the region has been utilized for phylogenetic reconstruction and "universal" primers for PCR amplification have been elusive. We present a method for reliably amplifying and sequencing the entire ETS throughout Asteraceae and some closely allied families. We also show that the ETS is more variable and phylogenetically informative than the ITS in three disparate genera of Asteraceae-Argyranthemum (tribe Anthemideae), Asteriscus (tribe Inuleae), and Helianthus (tribe Heliantheae). The full ETS was amplified using a primer (ETS1f) within the intergenic spacer in combination with a primer (18S-2L) in the 5' end of the highly conserved 18S gene. ETS1f was designed to correspond to a highly conserved region found in Helianthus and Crepis, which are in separate subfamilies of Asteraceae. ETS1f/18S-2L primed in all of the tribes of Asteraceae as well as exemplar taxa from Campanulaceae, Goodeniaceae, and Calyceraceae. For both Argyranthemum and Asteriscus, we were able to directly sequence the ETS PCR products when a single band was produced. When multiple bands were produced, we gel-purified and occasionally cloned the band of interest before sequencing. Although PCR produced single bands for Helianthus species, it was necessary to clone Helianthus amplifications prior to sequencing due to multiple intragenomic ETS repeat types. Alignment of ETS sequences for Argyranthemum and Asteriscus was straightforward and unambiguous despite some subrepeat structure in the 5' end. For Helianthus, different numbers of large tandem subrepeats in different species required analysis of the orthology of the subrepeats prior to alignment. In all three genera, the ETS provided more informative variation for phylogenetic reconstruction and allowed better resolution of relationships than the ITS. Although cloned sequences from Helianthus differed, intragenomic clones consistently formed clades. This result indicated that concerted evolution was proceeding rapidly enough in ETS that species-specific phylogenetic signal was retained. It should be now be possible to use the entire ETS for phylogenetic reconstruction of recently diverged lineages in Asteraceae and at least three other families (approximately 26,000 species or about 8% of all…
American Journal of Botany, 2007
The sunflower genus, Helianthus, is recognized widely for the cultivated sunflower H. annuus and ... more The sunflower genus, Helianthus, is recognized widely for the cultivated sunflower H. annuus and scientifically as a model organism for studying diploid and polyploid hybrid speciation, introgression, and genetic architecture. A resolved phylogeny for the genus is essential for the advancement of these scientific areas. In the past, phylogenetic relationships of the perennial species and polyploid hybrids have been particularly difficult to resolve. Using the external transcribed spacer region of the nuclear 18S-26S rDNA region, we reveal for the first time a highly resolved gene tree for Helianthus. Phylogenetic analysis allowed the determination of a monophyletic annual H. sect. Helianthus, a two-lineage polyphyletic H. sect. Ciliares, and the monotypic H. sect. Agrestis, all of which were nested within a large perennial and polyphyletic H. sect. Divaricati. The distribution of perennial polyploids and known annual diploid hybrids on this phylogeny suggested multiple independent hybrid speciation events that gave rise to at least four polyploids and three diploid hybrids. Also provided by this phylogeny was evidence for homoploid hybrid speciation outside H. sect. Helianthus. Finally, previous hypotheses about the secondary chemistry in the genus were tested in a phylogenetic framework to obtain a better understanding of the evolution of these compounds in Helianthus.
Biocomputing 2008 - Proceedings of the Pacific Symposium, 2007
Theoretical and Applied Genetics, 1998
Hybrids between cultivated and wild sunflowers (Helianthus annuus) are frequently reported. As mu... more Hybrids between cultivated and wild sunflowers (Helianthus annuus) are frequently reported. As much as 42% of progeny from wild plants near cultivar fields are hybrids, and cultivar genes have been shown to persist in wild populations at least five generations. We report the effects of up to 40 years of persistent cultivar gene flow on the genetic structure of three wild H. annuus populations that are adjacent to cultivated fields. Eighteen cultivar-specific markers were surveyed in a total of 115 individuals. We also developed cultivar-based genetic maps for the markers and used them to see if marker patterns in the wild populations were consistent with introgression and if selection was acting jointly on unlinked loci. High levels of crop specific markers were detected in all three wild populations, ranging from 0.315 to 0.382, on average. All 115 plants had at least 1 cultivar marker. Introgression is the most likely explanation for the presence of cropspecific markers in the sympatric populations because (1) the markers were either not present or found at much lower levels in four allopatric populations, (2) markers that were genetically linked in the cultivar invariably showed linkage disequilibrium patterns in the sympatric populations consistent with introgres-Communicated by B. S. Gill