Species Delimitation in Tetraploid, Apomictic <i>Amelanchier</i> (Rosaceae)

Cushman, Kevin R.; Burgess, Michael B.; Doucette, Eric T.; Nelson, Gretchen A.; Campbell, Christopher S.

doi:10.1600/036364417x695529

Cited by 9 publications

(7 citation statements)

References 67 publications

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“…Most apomictic complexes show the greatest variability at the tetraploid level. Cushman & al. (2017) classified morphological clusters of 4x Amelanchier populations and clones under species names, but rejected classification of local microspecies.…”

Section: From Theory To Practice: Species Delimitationmentioning

confidence: 99%

The classification of asexual organisms: Old myths, new facts, and a novel pluralistic approach

Hörandl

2018

TAXON

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Organisms reproducing via asexuality harbor a great diversity of lineages, morphotypes and ecotypes. However, classification of asexual taxa does not fit into contemporary species concepts, and hence the diversity of apomictic plant complexes is not well reflected in taxonomy. Plants reproducing via apomixis (i.e., asexual seed formation = agamospermy) exemplify the theoretical and practical problems of classification. Obligately asexual organisms do not form reproductive communities, but they do constitute ancestor-descendant lineages. From the conceptual side, evolutionary lineage concepts would fit best for species delimitation. Recent research showed that these lineages are not necessarily threatened by rapid extinction and do have persistence in time and space. Facultative sexuality and low levels of residual recombination counteract the accumulation of deleterious mutations due to the lack of recombination (Muller's ratchet). Apomictic lineages do have adaptive potential, which is demonstrated by the ability to occupy large distribution areas and to experience ecological niche shifts. The challenge for classification of asexual lineages, however, is to find operational criteria for species delimitation. Current practices of species delimitation can be grouped into four main principles: (1) the sexuals-first principle means that obligate sexual progenitor species are classified separately from their apomictic derivatives.(2) The all-in-one principle merges sexual progenitors and highly facultative apomictic derivatives into one species, whereby the apomicts often represent autopolyploids without differentiated phenotypes. (3) The cluster concept applies to allopolyploid complexes with facultative apomixis and a huge diversity of genotypes and morphotypes; here the main genetic clusters are treated as species. (4) Almost obligate apomictic lineages are being classified as agamospecies. The four principles reflect quite well evolutionary traits and diversity of lineages. Finally, a recommendation for a workflow is given, following this gradient from obligate sexuality to obligate apomixis.

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Section: From Theory To Practice: Species Delimitationmentioning

confidence: 99%

The classification of asexual organisms: Old myths, new facts, and a novel pluralistic approach

Hörandl

2018

TAXON

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“…Concerning apomictic polyploid complexes, [ 38 ] reviewed four alternative approaches for a case-by-case classification: (i) classify the obligate sexual progenitors as species; (ii) merge them and highly facultative apomictic lineages into a single species; (iii) treat the main hybrid clusters of the facultative apomicts as species. If the parentage of allopolyploid apomicts can be reconstructed, then designating apomicts as nothotaxa [ 63 ] can be a useful approach to formally separate from sexual species [ 51 , 64 , 65 , 66 ]; and (iv), classify obligate apomictic lineages as agamospecies. While options (i) and (ii) have been applied in several genera (reviewed by [ 38 ]), the challenge remains for (iii) polyploid complexes comprising hundreds and thousands of described taxa with uncertain taxonomic circumscriptions.…”

Section: Introductionmentioning

confidence: 99%

Geometric Morphometric Versus Genomic Patterns in a Large Polyploid Plant Species Complex

Hodač

Karbstein

Tomasello

et al. 2023

Biology

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Plant species complexes represent a particularly interesting example of taxonomically complex groups (TCGs), linking hybridization, apomixis, and polyploidy with complex morphological patterns. In such TCGs, mosaic-like character combinations and conflicts of morphological data with molecular phylogenies present a major problem for species classification. Here, we used the large polyploid apomictic European Ranunculus auricomus complex to study relationships among five diploid sexual progenitor species and 75 polyploid apomictic derivate taxa, based on geometric morphometrics using 11,690 landmarked objects (basal and stem leaves, receptacles), genomic data (97,312 RAD-Seq loci, 48 phased target enrichment genes, 71 plastid regions) from 220 populations. We showed that (1) observed genomic clusters correspond to morphological groupings based on basal leaves and concatenated traits, and morphological groups were best resolved with RAD-Seq data; (2) described apomictic taxa usually overlap within trait morphospace except for those taxa at the space edges; (3) apomictic phenotypes are highly influenced by parental subgenome composition and to a lesser extent by climatic factors; and (4) allopolyploid apomictic taxa, compared to their sexual progenitor, resemble a mosaic of ecological and morphological intermediate to transgressive biotypes. The joint evaluation of phylogenomic, phenotypic, reproductive, and ecological data supports a revision of purely descriptive, subjective traditional morphological classifications.

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“…The relative importance of hybridization in the evolution of Crataegus L. (and in some other Rosaceae) has been contentious in the past, and is reviewed elsewhere ( Dickinson, 2018 ); it suffices for now to note that just within subtribe Malinae (fleshy fruits derived from hypanthial, or inferior, ovaries; Rosaceae subfamily Amygdaloideae) there are molecular data to document hybridization in several large genera ( Burgess et al, 2015 ; Cushman et al, 2017 ; Hamston et al, 2018 ; Li et al, 2014 ; Li et al, 2017 ; Liu et al, 2020 ; Németh et al, 2020 ), including Crataegus . This genus of approximately 200 or more species ( Phipps, 2015 ) is found in a small clade of five genera and ca.…”

Section: Introductionmentioning

confidence: 99%

Phylogeny ofCrataegus(Rosaceae) based on 257 nuclear loci and chloroplast genomes: evaluating the impact of hybridization

Liston

Weitemier

Letelier

et al. 2021

PeerJ

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Background Hawthorn species (Crataegus L.; Rosaceae tribe Maleae) form a well-defined clade comprising five subgeneric groups readily distinguished using either molecular or morphological data. While multiple subsidiary groups (taxonomic sections, series) are recognized within some subgenera, the number of and relationships among species in these groups are subject to disagreement. Gametophytic apomixis and polyploidy are prevalent in the genus, and disagreement concerns whether and how apomictic genotypes should be recognized taxonomically. Recent studies suggest that many polyploids arise from hybridization between members of different infrageneric groups. Methods We used target capture and high throughput sequencing to obtain nucleotide sequences for 257 nuclear loci and nearly complete chloroplast genomes from a sample of hawthorns representing all five currently recognized subgenera. Our sample is structured to include two examples of intersubgeneric hybrids and their putative diploid and tetraploid parents. We queried the alignment of nuclear loci directly for evidence of hybridization, and compared individual gene trees with each other, and with both the maximum likelihood plastome tree and the nuclear concatenated and multilocus coalescent-based trees. Tree comparisons provided a promising, if challenging (because of the number of comparisons involved) method for visualizing variation in tree topology. We found it useful to deploy comparisons based not only on tree-tree distances but also on a metric of tree-tree concordance that uses extrinsic information about the relatedness of the terminals in comparing tree topologies. Results We obtained well-supported phylogenies from plastome sequences and from a minimum of 244 low copy-number nuclear loci. These are consistent with a previous morphology-based subgeneric classification of the genus. Despite the high heterogeneity of individual gene trees, we corroborate earlier evidence for the importance of hybridization in the evolution of Crataegus. Hybridization between subgenus Americanae and subgenus Sanguineae was documented for the origin of Sanguineae tetraploids, but not for a tetraploid Americanae species. This is also the first application of target capture probes designed with apple genome sequence. We successfully assembled 95% of 257 loci in Crataegus, indicating their potential utility across the genera of the apple tribe.

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Species Delimitation in Tetraploid, Apomictic Amelanchier (Rosaceae)

Cited by 9 publications

References 67 publications

The classification of asexual organisms: Old myths, new facts, and a novel pluralistic approach

The classification of asexual organisms: Old myths, new facts, and a novel pluralistic approach

Geometric Morphometric Versus Genomic Patterns in a Large Polyploid Plant Species Complex

Phylogeny ofCrataegus(Rosaceae) based on 257 nuclear loci and chloroplast genomes: evaluating the impact of hybridization

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