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Abstract Detail



Phylogenomics

Folk, Ryan [1], Mandel, Jennifer [2], Freudenstein, John [3].

Phylogenomic Approaches in the Genus Heuchera (Saxifragaceae) Elucidate Deep Reticulation and Simultaneous Mitochondrial and Chloroplast Capture.

The importance of the contribution of hybridization to evolution remains a contentious question even 99 years after the topic was broached by Lotsy. Published study cases strongly over-represent currently forming or very recently formed lineages, at the expense of historical examples of diploid hybridization. Evolution operates both on short- and long-term scales; therefore, failure to incorporate clear case studies of long-term hybrid entities (i.e. ancient hybrid phylogenetic lineages) leaves in the dark basic questions about the long-term fate of hybrids. To address the lack of critical work on ancient hybridization, we undertook a case study in Heuchera. Study of the historical-mosaic genome of a hybrid requires the use of numerous putatively unlinked phylogenetic loci in order to capture and resolve all underlying phylogenetic histories. We used a targeted enrichment methodology to capture 277 long loci, consisting primarily of intronic data, in order to infer resolved gene trees. Additionally, we developed genomic resources in Heuchera using genome skimming approaches in order to process off-target reads and build hundreds of kilobases of organellar data; the mitochondrial phylogeny in Heuchera has never been examined despite strong support for chloroplast capture. Sequence assemblies used an indel-tolerant reference-based method to assemble short read data. A new phylogenomic estimate of the species tree is consistent with previous Sanger work but with far greater support for relationships. Concatenation (maximum likelihood) and three different coalescent methods show broad agreement, although some tip relationships are unstable between the two coalescent methods. Mitochondrial and chloroplast trees show remarkably strong disagreement with the topology suggested by nuclear data. Some nuclear gene trees similarly show strong incongruence. The pattern of topological conflict is inconsistent with incomplete lineage sorting, suggesting a frequent and ancient background of reticulation that sometimes involves the ancestors of entire clades as well as extant species. In several cases the molecular data were able to validate hypotheses of hybrid taxa that had been proposed on the basis of morphology. Remarkably, some of these cases of hybridization involve taxa that are no longer sympatric, indicating the possibility of Pleistocene range shifts for these sky island taxa. Additionally, we report the first known instances of simultaneous chloroplast and mitochondrial capture, demonstrating the untapped potential of mitochondrial phylogenetics in confidently resolving hybridization in plants.


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1 - The Ohio State University, 1315 Kinnear Road, Columbus, OH, 43220, USA
2 - University Of Memphis, 3744 Walker Ave, Memphis, TN, 38152, USA
3 - Ohio State University, Museum Of Biological Diversity, 1315 Kinnear Rd, Columbus, OH, 43212-1157, USA

Keywords:
phylogenomics
heuchera
saxifragaceae
hybridization
ancient reticulation
gene tree discord
phylogenomic discord
coalescent
concatenation.

Presentation Type: Oral Paper:Papers for Topics
Session: 32
Location: Salon 11/The Shaw Conference Centre
Date: Tuesday, July 28th, 2015
Time: 8:45 AM
Number: 32004
Abstract ID:265
Candidate for Awards:Margaret Menzel Award


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