Using target sequence capture to improve the phylogenetic resolution of a rapid radiation in New Zealand <i>Veronica</i>

Thomas, Anne; Igea, Javier; Meudt, Heidi M.; Albach, Dirk C.; Lee, William G.; Tanentzap, Andrew J.

doi:10.1002/ajb2.1678

Cited by 30 publications

(28 citation statements)

References 91 publications

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“…S2 – S7). The low number of informative genes coupled with coalescence and concordance analyses suggest that incomplete lineage sorting (likely due to rapid radiations) along the backbone of the group as indicated by short branch lengths, may have played a significant role in the group’s evolutionary history, a common theme in modern-day phylogenomic studies (Morales-Briones et al, 2021; Stubbs et al, 2020; Thomas et al, 2021). Our analyses also hint that historical hybridization may be contributing to further phylogenetic discordance within the group, particularly within a subclade of Ledebouria Clade A (Fig.…”

Section: Discussionmentioning

confidence: 99%

Peeling Back the Layers: First Phylogenomic Insights into the Ledebouriinae (Scilloideae, Asparagaceae)

Howard

Crowl

Harvey³

et al. 2020

Preprint

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The Ledebouriinae (Scilloideae, Asparagaceae) are a widespread group of bulbous geophytes found predominantly throughout seasonal climates in sub-Saharan Africa, with a handful of taxa in Madagascar, the Middle East, India and Sri Lanka. An understanding of the phylogenetic relationships within the group have been historically difficult to reconstruct, however. Here, we provide the first phylogenomic perspective into the Ledebouriinae. We use this renewed phylogenetic framework to hypothesize historical factors that have resulted in the topology recovered. Using the Angiosperms353 targeted enrichment probe set, we consistently recovered four major clades (i.e. two Ledebouria clades, Drimiopsis, and Resnova). The two Ledebouria clades closely align with geography, either consisting almost entirely of sub-Saharan African taxa (Ledebouria Clade A), or East African and non-African taxa (Ledebouria Clade B). Our results also suggest that the Ledebouriinae underwent a rapid radiation leading to rampant incomplete lineage sorting.

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Section: Discussionmentioning

confidence: 99%

Peeling Back the Layers: First Phylogenomic Insights into the Ledebouriinae (Scilloideae, Asparagaceae)

Howard

Crowl

Harvey³

et al. 2020

Preprint

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“…Larridon et al ( 2020 ) also compared results obtained with Cyperaceae‐specific baits and found that they were not better at resolving relationships than those acquired with the Angiosperms353 probe set, thus indicating that use of the Angiosperms353 probe set can be as productive a method without the time and cost associated with the development of taxon‐specific baits. Similarly, Thomas et al ( 2021a ) used both introns and exons from the Angiosperms353 probe set to better resolve phylogenetic relationships in Veronica sect. Hebe (Plantaginaceae), a radiation estimated at 5–10 million years ago.…”

Section: Discussionmentioning

confidence: 99%

Resolving species boundaries in a recent radiation with the Angiosperms353 probe set: the Lomatium packardiae/L. anomalum clade of the L. triternatum (Apiaceae) complex

Ottenlips¹,

Mansfield

Buerki³

et al. 2021

American J of Botany

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Speciation not associated with morphological shifts is challenging to detect unless molecular data are employed. Using Sanger-sequencing approaches, the Lomatium packardiae/L. anomalum subcomplex within the larger Lomatium triternatum complex could not be resolved. Therefore, we attempt to resolve these boundaries here. METHODS:The Angiosperms353 probe set was employed to resolve the ambiguity within Lomatium triternatum species complex using 48 accessions assigned to L. packardiae, L. anomalum, or L. triternatum. In addition to exon data, 54 nuclear introns were extracted and were complete for all samples. Three approaches were used to estimate evolutionary relationships and define species boundaries: STACEY, a Bayesian coalescent-based species tree analysis that takes incomplete lineage sorting into account; ASTRAL-III, another coalescent-based species tree analysis; and a concatenated approach using MrBayes. Climatic factors, morphological characters, and soil variables were measured and analyzed to provide additional support for recovered groups. RESULTS:The STACEY analysis recovered three major clades and seven subclades, all of which are geographically structured, and some correspond to previously named taxa. No other analysis had full agreement between recovered clades and other parameters. Climatic niche and leaflet width and length provide some predictive ability for the major clades. CONCLUSIONS:The results suggest that these groups are in the process of incipient speciation and incomplete lineage sorting has been a major barrier to resolving boundaries within this lineage previously. These results are hypothesized through sequencing of multiple loci and analyzing data using coalescent-based processes.

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“…While phylogenomic datasets show great promise to resolve relationships in previously intractable angiosperm lineages, the irony is that many of these groups have undergone rapid radiations ( Larson et al, 2020 ; Shee et al, 2020 ; Rose et al, 2021 ; Thomas et al, 2021 ), which increases the chance of gene tree heterogeneity due to ILS ( Pamilo and Nei, 1988 ; Maddison, 1997 ; Oliver, 2013 ). Rampant gene tree discordance need not mean that species trees are poorly supported, provided that the discordance is consistent with the underlying model used to generate the species tree.…”

Section: Discussionmentioning

confidence: 99%

Sage Insights Into the Phylogeny of Salvia: Dealing With Sources of Discordance Within and Across Genomes

et al. 2021

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Next-generation sequencing technologies have facilitated new phylogenomic approaches to help clarify previously intractable relationships while simultaneously highlighting the pervasive nature of incongruence within and among genomes that can complicate definitive taxonomic conclusions. Salvia L., with ∼1,000 species, makes up nearly 15% of the species diversity in the mint family and has attracted great interest from biologists across subdisciplines. Despite the great progress that has been achieved in discerning the placement of Salvia within Lamiaceae and in clarifying its infrageneric relationships through plastid, nuclear ribosomal, and nuclear single-copy genes, the incomplete resolution has left open major questions regarding the phylogenetic relationships among and within the subgenera, as well as to what extent the infrageneric relationships differ across genomes. We expanded a previously published anchored hybrid enrichment dataset of 35 exemplars of Salvia to 179 terminals. We also reconstructed nearly complete plastomes for these samples from off-target reads. We used these data to examine the concordance and discordance among the nuclear loci and between the nuclear and plastid genomes in detail, elucidating both broad-scale and species-level relationships within Salvia. We found that despite the widespread gene tree discordance, nuclear phylogenies reconstructed using concatenated, coalescent, and network-based approaches recover a common backbone topology. Moreover, all subgenera, except for Audibertia, are strongly supported as monophyletic in all analyses. The plastome genealogy is largely resolved and is congruent with the nuclear backbone. However, multiple analyses suggest that incomplete lineage sorting does not fully explain the gene tree discordance. Instead, horizontal gene flow has been important in both the deep and more recent history of Salvia. Our results provide a robust species tree of Salvia across phylogenetic scales and genomes. Future comparative analyses in the genus will need to account for the impacts of hybridization/introgression and incomplete lineage sorting in topology and divergence time estimation.

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Using target sequence capture to improve the phylogenetic resolution of a rapid radiation in New Zealand Veronica

Cited by 30 publications

References 91 publications

Peeling Back the Layers: First Phylogenomic Insights into the Ledebouriinae (Scilloideae, Asparagaceae)

Peeling Back the Layers: First Phylogenomic Insights into the Ledebouriinae (Scilloideae, Asparagaceae)

Resolving species boundaries in a recent radiation with the Angiosperms353 probe set: the Lomatium packardiae/L. anomalum clade of the L. triternatum (Apiaceae) complex

Sage Insights Into the Phylogeny of Salvia: Dealing With Sources of Discordance Within and Across Genomes

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