Target Capture Sequencing Unravels Rubus Evolution

Carter, Katherine A.; Liston, Aaron; Bassil, Nahla V.; Alice, Lawrence A.; Bushakra, Jill M.; Sutherland, Brittany L.; Mockler, Todd C.; Bryant, Douglas W.; Hummer, Kim E.

doi:10.3389/fpls.2019.01615

Cited by 64 publications

(131 citation statements)

References 83 publications

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“…Genomic data are increasingly called upon to elucidate evolutionary and taxonomic challenges posed by several cryptic or ambiguously related organisms, which could not be resolved using traditional approaches, such as morphometrics or standard molecular methods (Harrison and Kidner, 2011;Straub et al, 2012;Carter et al, 2020;Larridon et al, 2020). The advent of the high-throughput sequencing (HTS) methods have outpaced classical molecular barcoding and phylogenetic procedures based on few molecular markers that have served to build phylogenies with constrained resolution limits (Diaz-Perez et al, 2018;Sancho et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Museomics Unveil the Phylogeny and Biogeography of the Neglected Juan Fernandez Archipelago Megalachne and Podophorus Endemic Grasses and Their Connection With Relict Pampean-Ventanian Fescues

et al. 2020

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Biogeography of Juan-Fernandez Endemic Grasses resolved as sister to Megalachne. Bayesian divergence dating and dispersal-extinctioncladogenesis range evolution analyses estimated the split of the Fernandezian clade from its ancestral southern American Pampas-Ventanian Loliinae lineage in the Miocene-Pliocene transition, following a long distance dispersal from the continent to the uplifted volcanic palaeo-island of Santa Clara-Masatierra. Consecutive Pliocene-Pleistocene splits and a Masatierra-to-Masafuera dispersal paved the way for in situ speciation of Podophorus and Megalachne taxa.

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Section: Introductionmentioning

confidence: 99%

Museomics Unveil the Phylogeny and Biogeography of the Neglected Juan Fernandez Archipelago Megalachne and Podophorus Endemic Grasses and Their Connection With Relict Pampean-Ventanian Fescues

et al. 2020

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“…Despite this progress, several relationships within the Andean tetraploid clade were unresolved or weakly supported in these previous studies. Sequence capture using anchored hybrid enrichment, also known as Hyb-Seq (Cronn et al, 2012;Lemmon et al, 2012;Lemmon and Lemmon, 2013;Weitemier et al, 2014) has been informative at various taxonomic levels in plants (Fragoso-Martínez et al, 2017;Wanke et al, 2017;Carter et al, 2019;Granados Mendoza et al, 2020;Larridon et al, 2020;Murphy et al, 2020). The methodology yields sequences of hundreds of single or low copy nuclear loci.…”

Section: Introductionmentioning

confidence: 99%

Phylogenomics of the Andean Tetraploid Clade of the American Amaryllidaceae (Subfamily Amaryllidoideae): Unlocking a Polyploid Generic Radiation Abetted by Continental Geodynamics

2020

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One of the two major clades of the endemic American Amaryllidaceae subfam. Amaryllidoideae constitutes the tetraploid-derived (n = 23) Andean-centered tribes, most of which have 46 chromosomes. Despite progress in resolving phylogenetic relationships of the group with plastid and nrDNA, certain subclades were poorly resolved or weakly supported in those previous studies. Sequence capture using anchored hybrid enrichment was employed across 95 species of the clade along with five outgroups and generated sequences of 524 nuclear genes and a partial plastome. Maximum likelihood phylogenetic analyses were conducted on concatenated supermatrices, and coalescent-based species tree analyses were run on the gene trees, followed by hybridization network, age diversification and biogeographic analyses. The four tribes Clinantheae, Eucharideae, Eustephieae, and Hymenocallideae (sister to Clinantheae) are resolved in all analyses with > 90 and mostly 100% support, as are almost all genera within them. Nuclear gene supermatrix and species tree results were largely in concordance; however, some instances of cytonuclear discordance were evident. Hybridization network analysis identified significant reticulation in Clinanthus, Hymenocallis, Stenomesson and the subclade of Eucharideae comprising Eucharis, Caliphruria, and Urceolina. Our data support a previous treatment of the latter as a single genus, Urceolina, with the addition of Eucrosia dodsonii. Biogeographic analysis and penalized likelihood age estimation suggests an origin in the Cauca, Desert and Puna Neotropical bioprovinces for the complex in the mid-Oligocene, with more dispersals than vicariances in its history, but no extinctions. Hymenocallis represents the only instance of long-distance vicariance from the tropical Andean origin of its tribe Hymenocallideae. The absence of extinctions correlates with the lack of diversification rate shifts within the clade. The Eucharideae experienced a sudden lineage radiation ca. 10 Mya. We tie much of the divergences in the Andean-centered lineages to the rise of

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“…Microsatellites are efficient, high-resolution genetic markers for both population-and species-level studies (Hodel et al, 2016;Li et al, 2017), and have also been used with success when addressing hybridization events and polyploid evolution (e.g., Sampson and Byrne, 2012;Zozomová-Lihová et al, 2014aFeulner et al, 2019;Hu et al, 2019). The Hyb-Seq approach, which captures target exons with flanking intronic and intergenic regions (Weitemier et al, 2014), allows to resolve relationships at various evolutionary levels from the population level up (Villaverde et al, 2018;Tomasello et al, 2020), including polyploids (e.g., Carter et al, 2019). Our specific aims were to (1) resolve the cytotypic and genetic structure of the species under study, (2) identify intraspecific genetic lineages, potentially reflecting descendants from distinct glacial refugia and postglacial colonization routes, (3) explore if and to what extent the lineages correlate with the cytotypic variation and display different environmental niches, (4) resolve single or polytopic polyploid origins, (5) explore the patterns and extent of hybridization between species and lineages, and, finally, (6) to determine how the structure resolved corresponds with previous taxonomic treatments.…”

Section: Introductionmentioning

confidence: 99%

So Closely Related and Yet So Different: Strong Contrasts Between the Evolutionary Histories of Species of the Cardamine pratensis Polyploid Complex in Central Europe

et al. 2020

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Recurrent polyploid formation and weak reproductive barriers between independent polyploid lineages generate intricate species complexes with high diversity and reticulate evolutionary history. Uncovering the evolutionary processes that formed their present-day cytotypic and genetic structure is a challenging task. We studied the species complex of Cardamine pratensis, composed of diploid endemics in the European Mediterranean and diploid-polyploid lineages more widely distributed across Europe, focusing on the poorly understood variation in Central Europe. To elucidate the evolution of Central European populations we analyzed ploidy level and genome size variation, genetic patterns inferred from microsatellite markers and target enrichment of low-copy nuclear genes (Hyb-Seq), and environmental niche differentiation. We observed almost continuous variation in chromosome numbers and genome size in C. pratensis s.str., which is caused by the co-occurrence of euploid and dysploid cytotypes, along with aneuploids, and is likely accompanied by inter-cytotype mating. We inferred that the polyploid cytotypes of C. pratensis s.str. are both of single and multiple, spatially and temporally recurrent origins. The tetraploid Cardamine majovskyi evolved at least twice in different regions by autopolyploidy from diploid Cardamine matthioli. The extensive genome size and genetic variation of Cardamine rivularis reflects differentiation induced by the geographic isolation of disjunct populations, establishment of triploids of different origins, and hybridization with sympatric C. matthioli. Geographically structured genetic lineages identified in the species under study, which are also ecologically divergent, are interpreted as descendants from different source populations in multiple glacial refugia. The postglacial range expansion was accompanied by substantial genetic admixture between the lineages of C. pratensis s.str., which is reflected by diffuse borders in their contact zones. In conclusion, we identified an interplay of diverse processes that have driven the evolution of the species studied, including allopatric and ecological divergence, hybridization, multiple polyploid origins, and genetic reshuffling caused by Pleistocene climate-induced range dynamics.

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Target Capture Sequencing Unravels Rubus Evolution

Abstract: the importance of using multiple phylogenetic methods when examining complex groups and the utility of software programs that estimate signal conflict within datasets.

Cited by 64 publications

References 83 publications

Museomics Unveil the Phylogeny and Biogeography of the Neglected Juan Fernandez Archipelago Megalachne and Podophorus Endemic Grasses and Their Connection With Relict Pampean-Ventanian Fescues

Museomics Unveil the Phylogeny and Biogeography of the Neglected Juan Fernandez Archipelago Megalachne and Podophorus Endemic Grasses and Their Connection With Relict Pampean-Ventanian Fescues

Phylogenomics of the Andean Tetraploid Clade of the American Amaryllidaceae (Subfamily Amaryllidoideae): Unlocking a Polyploid Generic Radiation Abetted by Continental Geodynamics

So Closely Related and Yet So Different: Strong Contrasts Between the Evolutionary Histories of Species of the Cardamine pratensis Polyploid Complex in Central Europe

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