Parasitic plants Twyford, Alex D.
Current biology,
08/2018, Letnik:
28, Številka:
16
Journal Article
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In this quick guide, Twyford introduces the reader to parasitic plants, explaining how they steal nutrients from host plants and how this lifestyle has evolved multiple times in plants.
Organisms exhibit an incredible diversity of life history strategies as adaptive responses to environmental variation. The establishment of novel life history strategies involves multilocus ...polymorphisms, which will be challenging to establish in the face of gene flow and recombination. Theory predicts that adaptive allelic combinations may be maintained and spread if they occur in genomic regions of reduced recombination, such as chromosomal inversion polymorphisms, yet empirical support for this prediction is lacking. Here, we use genomic data to investigate the evolution of divergent adaptive ecotypes of the yellow monkey flower Mimulus guttatus. We show that a large chromosomal inversion polymorphism is the major region of divergence between geographically widespread annual and perennial ecotypes. In contrast, ∼40,000 single nucleotide polymorphisms in collinear regions of the genome show no signal of life history, revealing genomic patterns of diversity have been shaped by localized homogenizing gene flow and large-scale Pleistocene range expansion. Our results provide evidence for an inversion capturing and protecting loci involved in local adaptation, while also explaining how adaptive divergence can occur with gene flow.
Plastid sequencing is an essential tool in the study of plant evolution. This high‐copy organelle is one of the most technically accessible regions of the genome, and its sequence conservation makes ...it a valuable region for comparative genome evolution, phylogenetic analysis and population studies. Here, we discuss recent innovations and approaches for de novo plastid assembly that harness genomic tools. We focus on technical developments including low‐cost sequence library preparation approaches for genome skimming, enrichment via hybrid baits and methylation‐sensitive capture, sequence platforms with higher read outputs and longer read lengths, and automated tools for assembly. These developments allow for a much more streamlined assembly than via conventional short‐range PCR. Although newer methods make complete plastid sequencing possible for any land plant or green alga, there are still challenges for producing finished plastomes particularly from herbarium material or from structurally divergent plastids such as those of parasitic plants.
Telling plant species apart with DNA: from barcodes to genomes Hollingsworth, Peter M.; Li, De-Zhu; van der Bank, Michelle ...
Philosophical transactions of the Royal Society of London. Series B. Biological sciences,
09/2016, Letnik:
371, Številka:
1702
Journal Article
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Land plants underpin a multitude of ecosystem functions, support human livelihoods and represent a critically important component of terrestrial biodiversity—yet many tens of thousands of species ...await discovery, and plant identification remains a substantial challenge, especially where material is juvenile, fragmented or processed. In this opinion article, we tackle two main topics. Firstly, we provide a short summary of the strengths and limitations of plant DNA barcoding for addressing these issues. Secondly, we discuss options for enhancing current plant barcodes, focusing on increasing discriminatory power via either gene capture of nuclear markers or genome skimming. The former has the advantage of establishing a defined set of target loci maximizing efficiency of sequencing effort, data storage and analysis. The challenge is developing a probe set for large numbers of nuclear markers that works over sufficient phylogenetic breadth. Genome skimming has the advantage of using existing protocols and being backward compatible with existing barcodes; and the depth of sequence coverage can be increased as sequencing costs fall. Its non-targeted nature does, however, present a major informatics challenge for upscaling to large sample sets.
This article is part of the themed issue ‘From DNA barcodes to biomes’.
Parasitic plants demonstrate a diversity of growth strategies, life histories, and developmental and physiological characteristics. Most research to date has focused on a narrow range of parasitic ...taxa, particularly in the Orobanchaceae, while the other independent origins of parasitism have largely gone unstudied. One type of parasite that has received relatively little attention are the endophytic parasites, which have a fascinating growth strategy where the parasite is embedded within the host tissue, with the flower the only externally visibly plant part. Endophytic growth makes it challenging to understand basic aspects of species biology, such as the size of a given parasite, the number of parasites per host, and the genetic diversity of populations. Recent studies by Barkman et al. (2017) and Pelser et al. (2017) have used microsatellite genotyping to investigate the population biology of endoparasitic Rafflesiaceae species in Asia. They show the potential for extensive parasite spread within a host vine and the strong partitioning of genetic diversity by host. These species are also shown to have an outcrossing mating system. However, these studies suggest different reproductive strategies, one supporting monoecy and one suggesting dioecy. Overall, these studies partly “lift the lid” on the cryptic biology of Rafflesia and the Rafflesiaceae and open the door for future comparative studies between endophytic and free-living parasitic plants.
We investigate patterns of historical assembly of tree communities across Amazonia using a newly developed phylogeny for the species-rich neotropical tree genus Inga. We compare our results with ...those for three other ecologically important, diverse, and abundant Amazonian tree lineages, Swartzia, Protieae, and Guatteria. Our analyses using phylogenetic diversity metrics demonstrate a clear lack of geographic phylogenetic structure, and show that local communities of Inga and regional communities of all four lineages are assembled by dispersal across Amazonia. The importance of dispersal in the biogeography of Inga and other tree genera in Amazonian and Guianan rain forests suggests that speciation is not driven by vicariance, and that allopatric isolation following dispersal may be involved in the speciation process. A clear implication of these results is that over evolutionary timescales, the metacommunity for any local or regional tree community in the Amazon is the entire Amazon basin.
Natural hybridisation is now recognised as pervasive in its occurrence across the Tree of Life. Resurgent interest in natural hybridisation fuelled by developments in genomics has led to an improved ...understanding of the genetic factors that promote or prevent species cross‐mating. Despite this body of work overturning many widely held assumptions about the genetic barriers to hybridisation, it is still widely thought that ploidy differences between species will be an absolute barrier to hybridisation and introgression. Here, we revisit this assumption, reviewing findings from surveys of polyploidy and hybridisation in the wild. In a case study in the British flora, 203 hybrids representing 35% of hybrids with suitable data have formed via cross‐ploidy matings, while a wider literature search revealed 59 studies (56 in plants and 3 in animals) in which cross‐ploidy hybridisation has been confirmed with genetic data. These results show cross‐ploidy hybridisation is readily overlooked, and potentially common in some groups. General findings from these studies include strong directionality of hybridisation, with introgression usually towards the higher ploidy parent, and cross‐ploidy hybridisation being more likely to involve allopolyploids than autopolyploids. Evidence for adaptive introgression across a ploidy barrier and cases of cross‐ploidy hybrid speciation shows the potential for important evolutionary outcomes.
Premise
Strong postzygotic reproductive isolating barriers are usually expected to limit the extent of natural hybridization between species with contrasting ploidy. However, genomic sequencing has ...revealed previously overlooked examples of natural cross‐ploidy hybridization in some flowering plant genera, suggesting that the phenomenon may be more common than once thought. We investigated potential cross‐ploidy hybridization in British eyebrights (Euphrasia, Orobanchaceae), a group from which 13 putative cross‐ploidy hybrid combinations have been reported based on morphology.
Methods
We analyzed a contact zone between diploid Euphrasia rostkoviana and tetraploid E. arctica in Wales. We sequenced part of the internal transcribed spacer (ITS) of nuclear ribosomal DNA and used genotyping by sequencing (GBS) to look for evidence of cross‐ploidy hybridization and introgression.
Results
Common variant sites in the ITS region were fixed between diploids and tetraploids, indicating a strong barrier to hybridization. Clustering analyses of 356 single‐nucleotide polymorphisms (SNPs) generated using GBS clearly separated samples by ploidy and revealed strong genetic structure (FST = 0.44). However, the FST distribution across all SNPs was bimodal, indicating potential differential selection on loci between diploids and tetraploids. Demographic inference suggested potential gene flow, limited to around one or fewer migrants per generation.
Conclusions
Our results suggest that recent cross‐ploidy hybridization is rare or absent in a site of secondary contact in Euphrasia. While a strong ploidy barrier prevents hybridization over ecological timescales, such hybrids may form in stable populations over evolutionary timescales, potentially allowing cross‐ploidy introgression to take place.
Summary
Parallel evolution of similar morphologies in closely related lineages provides insight into the repeatability and predictability of evolution. In the genus Antirrhinum (snapdragons), as in ...other plants, a suite of morphological characters are associated with adaptation to alpine environments.
We tested for parallel trait evolution in Antirrhinum by investigating phylogenetic relationships using restriction‐site associated DNA (RAD) sequencing. We then associated phenotypic information to our phylogeny to reconstruct the patterns of morphological evolution and related this to evidence for hybridisation between emergent lineages.
Phylogenetic analyses showed that the alpine character syndrome is present in multiple groups, suggesting that Antirrhinum has repeatedly colonised alpine habitats. Dispersal to novel environments happened in the presence of intraspecific and interspecific gene flow.
We found support for a model of parallel evolution in Antirrhinum. Hybridisation in natural populations, and a complex genetic architecture underlying the alpine morphology syndrome, support an important role of natural selection in maintaining species divergence in the face of gene flow.
The goals of the Earth Biogenome Project-to sequence the genomes of all eukaryotic life on earth-are as daunting as they are ambitious. The Darwin Tree of Life Project was founded to demonstrate the ...credibility of these goals and to deliver at-scale genome sequences of unprecedented quality for a biogeographic region: the archipelago of islands that constitute Britain and Ireland. The Darwin Tree of Life Project is a collaboration between biodiversity organizations (museums, botanical gardens, and biodiversity institutes) and genomics institutes. Together, we have built a workflow that collects specimens from the field, robustly identifies them, performs sequencing, generates high-quality, curated assemblies, and releases these openly for the global community to use to build future science and conservation efforts.
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