An introduction to plant phylogenomics with a focus on palms

Barrett, Craig F.; Bacon, Christine D.; Antonelli, Alexandre; Cano, Ángela; Hofmann, Tobias

doi:10.1111/boj.12399

Cited by 42 publications

(40 citation statements)

References 163 publications

(189 reference statements)

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“…The impact of the next‐generation sequencing revolution (Pyron, ) is now being felt in palm phylogenetics (Comer et al ., , ; Barrett et al ., , in press; Heyduk et al ., ). Two of these studies (Comer et al ., ; Barrett et al ., ), focusing on the whole family and Arecoideae, respectively, have already included complete or near‐complete plastid genome data for 62 genera of palms.…”

Section: Palm Phylogeneticsmentioning

confidence: 99%

BeyondGenera Palmarum: progress and prospects in palm systematics

2016

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The systematic biology of the palm family (Arecaceae) is probably better known than that of any other tropical plant family of comparable size. As a result, the palms are now regarded as a model group for tropical rain forest research. Ten years ago, the first phylogenetic classification of palms was established as a foundation for the second edition of the palm systematic synthesis, Genera Palmarum (GP2), which was published in 2008. Here, we review progress in palm systematics since GP2, summarizing the latest developments in an updated palm classification and schematic phylogenetic tree. To date, the palms comprise 181 genera and c. 2600 species. In just 8 years, six new genera and 200 new species have been described, whereas eight genera have been sunk into synonymy. This reflects the highly dynamic nature of systematic discovery of palms at both forest and phylogenetic frontiers. Palm phylogenetics is a vibrant field, with new trees being generated and utilized in increasingly innovative and ambitious ways. Existing understanding of relationships among the five subfamilies has been confirmed and deep nodes in the subfamilies are crystallizing, especially in subfamilies Arecoideae and Coryphoideae. We conclude that palm systematic knowledge is far from complete and that tools, such as GP2, only stimulate further scientific research and discovery. Despite recent advances, however, many aspects of the palm Tree of Life still remain scarcely known. The vast datasets that the phylogenomic revolution is now bringing to bear on palms promise to elucidate many of these unknowns. The ultimate goal, a species-level phylogenetic tree for palms, is now coming within reach.

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Section: Palm Phylogeneticsmentioning

confidence: 99%

BeyondGenera Palmarum: progress and prospects in palm systematics

2016

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“…Palm systematics has been a challenge due to a combination of morphological homoplasy and extremely slow plastid DNA substitution rates (Uhl and Dransfield, 1987; Uhl et al , 1995; Gaut et al , 1992; Barrett et al , 2016a). Because of this, palm systematists have turned to genome-scale datasets, as these greatly increase the number of informative characters available for phylogenetic analyses (Barrett et al , 2016a; Comer et al , 2015; 2016; Barrett et al , 2016b; Heyduk et al, 2016). Here we have sequenced over 400 kb of DNA from all three plant genomes, largely resolving and providing support for relationships among currently known species of Brahea.…”

Section: Discussionmentioning

confidence: 99%

“…Genome-scale datasets provide a solution, having become feasible to obtain with the widespread availability of high-throughput sequencing methods. Not surprisingly, palm systematists have begun to embrace phylogenomic approaches (Comer et al , 2015; Barrett et al , 2016a; Comer et al , 2016; Barrett et al , 2016b; Heyduk et al , 2016; Bacon et al in review).…”

Section: Introductionmentioning

confidence: 99%

Phylogenomics, biogeography, and evolution in the American palm genusBrahea

Barrett

Sinn

King

et al. 2018

Preprint

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0• Background and Aims: Slow rates of molecular evolution at low taxonomic levels 2 1 hamper studies of relationships among species, and subsequent biogeographic and 2 2 evolutionary analyses. An example is the genus Brahea, which is among the most poorly 2 3 understood lineages of American palms and is characterized by a wide variety of growth 2 4 forms and intermediate morphological features.2 5 • Methods: We generated approximately 400 kb of genome-scale data from all three 2 6 genomes for the 11 currently described species of Brahea to infer phylogenetic 2 7 relationships, reconstruct ancestral growth form, estimate ancestral geographic ranges, 2 8and test for niche equivalency among closely related species with geographic overlap. 2 9 • Key Results: Relationships receive strong support, and conform to previous subgeneric 3 0 assignments, except for placement of the dwarf species B. moorei within subgenus 3 1 Erythea. Our robust phylogenetic hypothesis reveals trends in growth form including an 3 2 overall increase in height in the B. armata clade, and independent evolution of dwarf 3 3 forms from taller ancestors in the B. pimo and B. dulcis clades. Ancestral range 3 4 estimation reveals roles of dispersal (e.g. B. edulis on Guadalupe Island) and sympatric 3 5 speciation in some cases (e.g. in the B. armata clade), but is equivocal in others (e.g. in 3 6 the B. pimo clade). We find evidence of niche non-equivalency among species within the 3 7 B. armata clade in northwestern Mexico, and some evidence of niche non-equivalency 3 8 between B. berlandieri and B. dulcis, the former of which is synonymized under B. 3 9 dulcis. 4 0 • Conclusions: Our findings have implications for the complex biogeographic history in 4 1 Central America and Mexico, suggesting that sympatric speciation and dispersal are the 4 2

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“…Targeted enrichment followed by high throughput sequencing of hundreds or even thousands of loci for phylogenetic reconstruction is becoming a golden standard in plant evolutionary biology (Cronn et al, 2012;Mariac et al, 2014;Barrett et al, 2016;Xi et al, 2013). Targeted capture is a genome reduction approach whereby selected regions of the genome are "captured" or hybridized in solution using site-specific baits (also called probes).…”

Section: Introductionmentioning

confidence: 99%

Phylogenomics of the major tropical plant family Annonaceae using targeted enrichment of nuclear genes

Couvreur

Helmstetter

Koenen

et al. 2018

Preprint

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Targeted enrichment and sequencing of hundreds of nuclear loci for phylogenetic reconstruction is becoming an important tool for plant systematics and evolution. Annonaceae is a major pantropical plant family with 109 genera and ca. 2450 species, occurring across all major and minor tropical forests of the world. Baits were designed by sequencing the transcriptomes of five species from two of the largest Annonaceae subfamilies. Orthologous loci were identified. The resulting baiting kit was used to reconstruct phylogenetic relationships at two different levels using concatenated and gene tree approaches: a family wide Annonaceae analysis sampling 65 genera and a species level analysis of tribe Piptostigmateae sampling 29 species with multiple individuals per species. DNA extraction was undertaken mainly on silicagel dried leaves, with two samples from herbarium dried leaves. Our kit targets 469 exons (364 653 bp of sequence data), successfully capturing sequences from across Annonaceae. Silicagel dried and herbarium DNA worked eaually well. We present for the first time a nuclear gene-based phylogenetic tree at the generic level based on 317 supercontigs. Results mainly confirm previous chloroplast based studies. However, several new relationships are found and discussed. We show significant differences in branch lengths between the two large subfamilies Annonoideae and Malmeoideae. A new tribe, Annickieae, is erected containing a single African genus Annickia. We also reconstructed a well resolved species-level phylogenetic tree of the Piptostigmteae tribe. Our baiting kit is useful for reconstructing well supported phylogenetic relationships within Annonaceae at different taxonomic levels. The nuclear genome is mainly concordant with plastome information with a few exceptions. Moreover, we find that substitution rate heterogeneity between the two subfamilies is also found within the nuclear compartment, and not just plastomes and ribosomal DNA as previously shown. Our results have implications for understanding the biogeography, molecular dating and evolution of Annonaceae.

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An introduction to plant phylogenomics with a focus on palms

Cited by 42 publications

References 163 publications

BeyondGenera Palmarum: progress and prospects in palm systematics

BeyondGenera Palmarum: progress and prospects in palm systematics

Phylogenomics, biogeography, and evolution in the American palm genusBrahea

Phylogenomics of the major tropical plant family Annonaceae using targeted enrichment of nuclear genes

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