How challenging RADseq data turned out to favor coalescent-based species tree inference. A case study in Aichryson (Crassulaceae)

Hühn, Philipp; Dillenberger, Markus S.; Gerschwitz-Eidt, Michael A.; Hörandl, Elvira; Los, Jessica A.; Messerschmid, Thibaud F E; Paetzold, Claudia; Rieger, Benjamin; Kadereit, Gudrun

doi:10.1016/j.ympev.2021.107342

Cited by 17 publications

(17 citation statements)

References 139 publications

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“…Variable SNP loci from all samples were filtered and clustered de novo in ipyrad v0.9.82 [ 62 ] using default options for diploids except for the parameter clust_threshold (i.e., the level of sequence similarity at which two sequences are identified as being homologous, and thus cluster together). Clustering threshold (ct) selection approaches aim at determining appropriate ct values to establish homology while avoiding clustering of paralogous RAD-seq loci [ 63 ]. Application of such a strategy is highly popular to reduce the risk of introducing assembly error to the dataset e.g., [ 63 , 64 , 65 , 66 , 67 ], ensuring the assembly of homologous loci and maximizing sequence variation.…”

Section: Methodsmentioning

confidence: 99%

“…Clustering threshold (ct) selection approaches aim at determining appropriate ct values to establish homology while avoiding clustering of paralogous RAD-seq loci [ 63 ]. Application of such a strategy is highly popular to reduce the risk of introducing assembly error to the dataset e.g., [ 63 , 64 , 65 , 66 , 67 ], ensuring the assembly of homologous loci and maximizing sequence variation. To do so, a ct range of 0.85–0.99 (in 0.01 increments) was tested and assembly results were plotted ( Figure S2 ).…”

Section: Methodsmentioning

confidence: 99%

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Geographical Patterns of Genetic Variation in Locoto Chile (Capsicum pubescens) in the Americas Inferred by Genome-Wide Data Analysis

Palombo

García

2022

Plants

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The locoto chile (Capsicum pubescens) is a regionally important food crop grown and marketed throughout the mid-highlands of South andCentral America, but little is known about its evolution and the diversity it harbours. An initial scan of genetic diversity and structure across its cultivation range was conducted, the first one using a genomic approach. The RAD-sequencing methodology was applied to a sampling of C. pubescens germplasm consisting of 67 accessions from different American countries, covering its range of distribution/cultivation on the continent. The RAD-seq SNP data obtained clustered the accessions into three major groups, with a high degree of admixture/reticulation among them. Moderate but significant differentiation and geographic structuration were found, depicting a south–north pattern in the distribution of genetic variation. The highest levels of diversity were found among central-western Bolivian individuals, while the lowest was found across Central America-Mexican germplasm. This study provides new genome-wide supported insights into the diversity and differentiation of C. pubescens, as well as a starting point for more efficient use of its genetic variation and germplasm conservation efforts. The findings also contribute to understanding the evolutionary history of C. pubescens, but further investigation is needed to disentangle its origin and diversification under domestication.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Geographical Patterns of Genetic Variation in Locoto Chile (Capsicum pubescens) in the Americas Inferred by Genome-Wide Data Analysis

Palombo

García

2022

Plants

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“…Different analytical approaches of the RADseq data resulted in partly incongruent patterns outlined in the sections “Results” and “Discussion” above, which is often the case in phylogenetic analyses of such data ( Wagner et al, 2020 ; Cai et al, 2021 ; Rose et al, 2021 ; Hühn et al, 2022 ). Both biological as well as methodological factors can be responsible for the observed incongruences.…”

Section: Discussionmentioning

confidence: 99%

From Western Asia to the Mediterranean Basin: Diversification of the Widespread Euphorbia nicaeensis Alliance (Euphorbiaceae)

2022

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The Mediterranean Basin is an important biodiversity hotspot and one of the richest areas in the world in terms of plant diversity. Its flora parallels in several aspects that of the Eurasian steppes and the adjacent Irano-Turanian floristic region. The Euphorbia nicaeensis alliance spans this immense area from the western Mediterranean to Central Asia. Using an array of complementary methods, ranging from phylogenomic and phylogenetic data through relative genome size (RGS) estimation to morphometry, we explored relationships and biogeographic connections among taxa of this group. We identified the main evolutionary lineages, which mostly correspond to described taxa. However, despite the use of highly resolving Restriction Site Associated DNA (RAD) sequencing data, relationships among the main lineages remain ambiguous. This is likely due to hybridisation, lineage sorting triggered by rapid range expansion, and polyploidisation. The phylogenomic data identified cryptic diversity in the Mediterranean, which is also correlated with RGS and, partly, also, morphological divergence, rendering the description of a new species necessary. Biogeographic analyses suggest that Western Asia is the source area for the colonisation of the Mediterranean by this plant group and highlight the important contribution of the Irano-Turanian region to the high diversity in the Mediterranean Basin. The diversification of the E. nicaeensis alliance in the Mediterranean was triggered by vicariance in isolated Pleistocene refugia, morphological adaptation to divergent ecological conditions, and, to a lesser extent, by polyploidisation.

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“…The disadvantages of restriction-enzyme based methods are locus dropout and hence, many missing data which requires many bioinformatic filtering and optimization steps. For polyploids, filtering paralogs and correct assembly of heterozygous loci can be a challenge, but estimates of heterozygosity are possible given sufficient sequencing depth and quality as well as appropriate clustering tresholds of loci [211,212]. Finally, RAD-data are usually re-usable only within a genus, but not across more divergent taxa [199].…”

Section: Recognition Of Existing Lineages: Methodical Advances In The...mentioning

confidence: 99%

Novel Approaches for Species Concepts and Delimitation in Polyploids and Hybrids

Hörandl

2022

Plants

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Hybridization and polyploidization are important processes for plant evolution. However, classification of hybrid or polyploid species has been notoriously difficult because of the complexity of processes and different evolutionary scenarios that do not fit with classical species concepts. Polyploid complexes are formed via combinations of allopolyploidy, autopolyploidy and homoploid hybridization with persisting sexual reproduction, resulting in many discrete lineages that have been classified as species. Polyploid complexes with facultative apomixis result in complicated net-work like clusters, or rarely in agamospecies. Various case studies illustrate the problems that apply to traditional species concepts to hybrids and polyploids. Conceptual progress can be made if lineage formation is accepted as an inevitable consequence of meiotic sex, which is established already in the first eukaryotes as a DNA restoration tool. The turnaround of the viewpoint that sex forms species as lineages helps to overcome traditional thinking of species as “units”. Lineage formation and self-sustainability is the prerequisite for speciation and can also be applied to hybrids and polyploids. Species delimitation is aided by the improved recognition of lineages via various novel -omics methods, by understanding meiosis functions, and by recognizing functional phenotypes by considering morphological-physiological-ecological adaptations.

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How challenging RADseq data turned out to favor coalescent-based species tree inference. A case study in Aichryson (Crassulaceae)

Cited by 17 publications

References 139 publications

Geographical Patterns of Genetic Variation in Locoto Chile (Capsicum pubescens) in the Americas Inferred by Genome-Wide Data Analysis

Geographical Patterns of Genetic Variation in Locoto Chile (Capsicum pubescens) in the Americas Inferred by Genome-Wide Data Analysis

From Western Asia to the Mediterranean Basin: Diversification of the Widespread Euphorbia nicaeensis Alliance (Euphorbiaceae)

Novel Approaches for Species Concepts and Delimitation in Polyploids and Hybrids

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