Progress 10/01/03 to 09/30/06
Outputs
During the funding period we achieved success in the central goal of the awarded funding, which opens the way to the general goal of our laboratory: tracing the genetic origins of hybrid species. Over the past year we have been working to clinch the development of a system to profile the component genomes of polyploids in the genus Polystichum; in September of this year we did it. We now have a single-copy nuclear gene sequence (in the area of exon 15 of the gene phosphoglucoisomerase - PGI) that we can use to provide clues to the identity of ancestral genomes in our hybrids and polyploids. A senior thesis in the lab will take advantage of his developing this tool to work on a suite of three to four polyploids for whom we would like to profile and possibly identify ancestors. Currently, we are exploring a second sequence from the same gene, to provide us with additional characters for identifying ancestors. A related accomplishment was the demonstration of chloroplast
DNA contributions from each of the two progenitors of our test hybrid. Using a sample of hybrids and their progenitors from the field in tropical America, we were able to demonstrate uniparental chloroplast sequence contributions to different hybrid individuals - from each of the two parents hypothesized from previous studies on traditional grounds. At the same time, we have used Hatch funding to continue to expand our sample of Polystichum species from throughout the world with the goal of creating a three-sequence molecular phylogeny for the genus for the whole world. The goal is an evolutionary portrait for this extraordinarily diverse and successful genus - as a context for understanding the evolution of the polyploids. It is this goal, the ecology and geography of origin of polyploids, that is most relevant to the agricultural mission that justified the Hatch funding. Our work on the origin of the Hawaiian Polystichum species is now complete and in press. Like most other Hawaiian
fern groups, has resulted from multiple migrations: two migrations yielded the three species. This pattern reinforces the idea that propagule vagility is a key determinant of colonization history and evolutionary divergence on the species-rich, remote oceanic islands of the Hawaiian archipelago. Work on the number of origins as well as the geographic provenances of the Hawaiian polystichums was based on improved resolution of global phylogenetic relationships within Polystichum from combined Combining coding (rbcL) and non-coding (trnL-F) chloroplast sequences. The phylogeny based on the combined cpDNA data set supports a monophyletic Polystichum s.l. and corroborates recent hypotheses as to membership and sequence of origin of the major groups within the genus. The phylogeny suggests that the two Hawaiian lineages appear to have originated from remotely related high-elevation species of Polystichum in the Old World. Taken together, these insights demonstrate the power of modern
phylogenetic analysis, as informed by geography, to provide insight into the sources and patterns of evolutionary diversity on oceanic islands.
Impacts
Our work on the structure of genomes contributed to polyploids continues to be productive. We have now been able to retrieve the two component genomes from our test hybrid, the well-documented hybrid that we have in hand from our previous research activities. This process of retrieving component genomes from hybrids and hybrid species (allopolyploid) species is still in its infancy, and we believe that our research is contributing to understanding of this sort of study, the analysis of genomes contributed to established polyploid species. This work is significant because critical agricultural crops such as potatoes and tomatoes are polyploids that originated in nature in the region where our study plants also originated, the Andes of Latin America.
Publications
- No publications reported this period
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Progress 10/01/04 to 09/30/05
Outputs
During the past year we have been working on identifying a nuclear gene sequence that will allow us to fingerprint individual hybrid progenitor species for our work on wild polyploids. In this endeavor we have had limited success. In the last annual report we reported our work on a partial sequence from the nuclear gene LEAFY. Because of problems with consistent retrieval of equivalent sequences from different species and lack of sufficient variation to allow resolution of all the species involved, we have started to explore alternative nuclear genes. This year we have been working with a partial sequence of the phosphoglucoseisomerase gene that is active in the cytoplasm (PGIc), for which primers were available from Japanese colleagues working on ferns in the same family. This work has gone better than for LEAFY, in that we have been able to consistently retrieve a single, alignable sequence. Variation is sufficient to allow us to distinguish different individuals of
the same species. However, the genetic variation in the sequences does not appear to be of the sort needed to reconstruct evolutionary history based on the sequence. The problem we now face is that our sequence cannot be used to assess the genetic relatednesse of PGIc sequences retrieved from polyploids, though it is likely that we could identify genomes of still-extant species from these data. Our plan is to continue to work on PGIc with the idea that it would provide an adequate tool for identifying the constitution of hybrids and species, but to explore alternate sequences that provide us more information about the affinities of a particular nuclear sequence. Our current intent is to explore amplified fragment-length polymorphisms (AFLPs) for this purpose.
Impacts
We expect to make a substantial contribution to understanding the origin or polyploid species in their original, wild situations with our work. Knowing this will contribute substantively to the potential to develop new polyploid crops, since almost all current critical crops are polyploids of wild origin. This year's work has moved us to the point where we are able to identify molecular profiles for diploid progenitors of polyploid species. However, we are still unable to assess the origin of genomes encountered in polyploids that are not those of known non-hybrid species in the study groupOnce, we solve this problem, we can move on to our study of the geography and ecology of the origin of these polyploids -- which is at the heart of providing insight into the origin of polyploid species in nature.
Publications
- Barrington, D. S. 2005. Helechos de los paramos de Costa Rica. In M. Kappelle and S. P. Horn [eds.] Paramos de Costa Rica, 375-395. InBio Press, San Jose, Costa Rica.
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Progress 10/01/03 to 09/30/04
Outputs
The phylogeny of Polystichum and allied genera that we have developed using rbcL and morphological has served as a starting point for the current work in our lab. In this work, we showed that the fern Polystichum is a monophyletic genus with the segregation of one group of Asian species as Cyrtomidictyum, and that the sister genus to this monophyletic Polystichum is the well-known greenhouse plant Cyrtomium known from Asia and Hawaii. The genus Phanerophlebia is sister to all of these lineages. This analysis, which included 41 species from throughout the world distribution of the genus, first revealed a monophyletic Neotropical group, from a sample of seven species. Our recent activity has been to expand the sample size and add new sequences to improve resolution. We have a working phylogeny for a set of 18 species (45% of the diversity in continental tropical America) based on an analysis of the trnL-F spacer data. This phylogeny (available at
http://www.uvm.edu/dbarring/polystichum/) corroborates our preliminary hypotheses: 1) Neotropical Polystichum constitutes a monophyletic group: 2) Its sister taxon is the circumboreal once-pinnate limestone dweller P. lonchitis (the type species of the genus). 3) The first event in the history of the Neotropical clade was the divergence of the West-Indian once-pinnate polystichums, also growing on limestone, from the continental Neotropical alliance. An analysis of rbcL with an expanded set of Neotropical species based on both rbcL and trnL-F spacer data reveals the same features. In our pilot study for the polyploidy analysis, we chose to address the inheritance of molecular characters in the hybrid Polystichum concinnum X P. speciosissimum. This morphologically distinctive primary hybrid combines the disparate morphologies of the Costa Rican endemic P. concinnum, common in the oak forests from 2800 to 3200 m, with the paramo species P. speciosissimum, disjunct between high
elevations (3000-3500 m) in southeastern most Mexico and Costa Rica. We used the P. concinnum X P. speciosissimum hybrid as a probe to analyze inheritance of cpDNA sequences in the hybrid. We found that different accessions of the hybrid incorporated the cpDNA sequences of P. concinnum and P. speciosissimum, corroborating earlier evidence of the proposed hybrid progenitors. In addition, since P. concinnum is variable for the trnL-F spacer, we were able to identify which of the two P. concinnum haplotypes was involved in the origin of the hybrid. During this fiscal year, we were able to sequence the second intron of the nuclear gene LEAFY. An analysis of these sequences from 10 species revealed insufficient variation to pursue characterization of ancestral genomes as planned in our proposal. Our current activity is focused on identifying a nuclear sequence for this purpose. We have amplified the nuclear ribosomal ITS sequence successfully, and are hopeful that it will be variable
enough to allow us to distinguish ancestral genomes in Polystichum.
Impacts
As we noted in our proposal, we expect to make a substantial contribution to understanding the origin or polyploid species in their original, wild situations with our work. Knowing this will contribute substantively to the potential to develop new polyploid crops, since almost all current critical crops are poyploids of wild origin. This year's work has moved us to the point where we are hopeful of identifying molecular profiles for diploid progenitors of polyploid species. Once these profiles are in place we can move on to our study of the geography and ecology of the origin of these polyploids -- which is at the heart of providing insight into the origin of polyploid species in nature.
Publications
- Driscoll, H,E,, D.S. Barrington, and A.V. Gilman. 2003. A re-examination of the apogamous tetraploid Phegopteris (Thelypteridaceae) from northeastern North America. Rhodora 105: 309-321.
- Barrington, D.S. 2003. Polystichum lilianae sp. nov. (Dryopteridaceae) and its relationships to P. fournieri and P. turrialbae. Brittonia 55: 317-325.
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