Pleistocene diversification in an ancient lineage: a role for glacial cycles in the evolutionary history of <i>Dioon</i> Lindl. (Zamiaceae)

Dorsey, Brian; Gregory, Timothy J.; Sass, Chodon; Specht, Chelsea D.

doi:10.1002/ajb2.1149

Cited by 19 publications

(43 citation statements)

References 90 publications

(174 reference statements)

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“…On the other hand, despite the improvements in performance in StarBEAST 2, species tree inferences often require very long runs for the MCMC to converge (Ogilvie et al 2017). Our RWTY analyses indicate that species tree topologies did indeed reach convergence, and we only noted some convergence problems with the speciation rate parameter (cySpeciationRate, with 100 < ESS < 200), an observation made previously (Dorsey et al 2018).…”

Section: Differences Among Phylogenetic Analysessupporting

confidence: 79%

Phylogeny and character evolution in the Dacrymycetes, and systematics of Unilacrymaceae and Dacryonaemataceae fam. nov.

Zamora¹,

Ekman²

2020

persoonia

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We present a multilocus phylogeny of the class Dacrymycetes, based on data from the 18S, ITS, 28S, RPB1, RPB2, TEF-1α, 12S, and ATP6 DNA regions, with c. 90 species including the types of most currently accepted genera. A variety of methodological approaches was used to infer phylogenetic relationships among the Dacrymycetes, from a supermatrix strategy using maximum likelihood and Bayesian inference on a concatenated dataset, to coalescence-based calculations, such as quartet-based summary methods of independent single-locus trees, and Bayesian integration of single-locus trees into a species tree under the multispecies coalescent. We evaluate for the first time the taxonomic usefulness of some cytological phenotypic characters, i.e., vacuolar contents (vacuolar bodies and lipid bodies), number of nuclei of recently discharged basidiospores, and pigments, with especial emphasis on carotenoids. These characters, along with several others traditionally used for the taxonomy of this group (basidium shape, presence and morphology of clamp connections, morphology of the terminal cells of cortical/marginal hyphae, presence and degree of ramification of the hyphidia), are mapped on the resulting phylogenies and their evolution through the class Dacrymycetes discussed. Our analyses reveal five lineages that putatively represent five different families, four of which are accepted and named. Three out of these four lineages correspond to previously circumscribed and published families (Cerinomycetaceae, Dacrymycetaceae, and Unilacrymaceae), and one is proposed as the new family Dacryonaemataceae. Provisionally, only a single order, Dacrymycetales, is accepted with in the class. Furthermore, the systematics of the two smallest families, Dacryonaemataceae and Unilacrymaceae, are investigated to the species level, using coalescence-based species delimitation on multilocus DNA data, and a detailed morphological study including morphometric analyses of the basidiospores. Three species are accepted in Dacryonaema, the type, Da. rufum, the newly combined Da. macnabbii (basionym Dacrymyces macnabbii), and a new species named Da. macrosporum. Two species are accepted in Unilacryma, the new U. bispora, and the type, U. unispora, the latter treated in a broad sense pending improved sampling across the Holarctic.

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Section: Differences Among Phylogenetic Analysessupporting

confidence: 79%

Phylogeny and character evolution in the Dacrymycetes, and systematics of Unilacrymaceae and Dacryonaemataceae fam. nov.

Zamora¹,

Ekman²

2020

persoonia

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“…Although the Pleistocene ice events were evident in Europe (Taberlet et al, 1998), the climate also changed in China (Harrison et al, 2001). Climate oscillations during the Pleistocene had effects on the demographic history of plants (Dorsey et al, 2018;Zhang et al, 2019). Different Cycas species had different population dynamics to respond to glacial and interglacial influences.…”

Section: Divergence Time and Demographic Dynamicsmentioning

confidence: 99%

Population Differentiation and Demographic History of the Cycas taiwaniana Complex (Cycadaceae) Endemic to South China as Indicated by DNA Sequences and Microsatellite Markers

Wang

Zhang

et al. 2019

Front. Genet.

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Historical geology, climatic oscillations, and seed dispersal capabilities are thought to influence the population dynamics and genetics of plants, especially for distribution-restricted and threatened species. Investigating the genetic resources within and among taxa is a prerequisite for conservation management. The Cycas taiwaniana complex consists of six endangered species that are endemic to South China. In this study, we investigated the relationship between phylogeographic history and the genetic structure of the C. taiwaniana complex. To estimate the phylogeographic history of the complex, we assessed the genetic structure and divergence time, and performed phylogenetic and demographic historical analyses. Two chloroplast DNA intergenic regions (cpDNA), two single-copy nuclear genes (SCNGs), and six microsatellite loci (SSR) were sequenced for 18 populations. The SCNG data indicated a high genetic diversity within populations, a low genetic diversity among populations, and significant genetic differentiation among populations. Significant phylogeographical structure was detected. Structure and phylogenetic analyses both revealed that the 18 populations of the C. taiwaniana complex have two main lineages, which were estimated to diverge in the Middle Pleistocene. We propose that Cycas fairylakea was incorporated into Cycas szechuanensis and that the other populations, which are mainly located on Hainan Island, merged into one lineage. Bayesian skyline plot analyses revealed that the C. taiwaniana complex experienced a recent decline, suggesting that the complex probably experienced a bottleneck event. We infer that the genetic structure of the C. taiwaniana complex has been affected by Pleistocene climate shifts, sea-level oscillations, and human activities. In addition to providing new insights into the evolutionary legacy of the genus, the genetic characterizations will be useful for the conservation of Cycas species.

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“…Pleistocene climatic cycles have had profound impacts on how intraspecific genetic diversity is structured across landscapes (Hewitt, 2004). Despite these events being quite recent, they coincide with speciation in a broad suite of taxa (e.g., Carstens & Knowles, 2007; Dorsey, Gregory, Sass, & Specht, 2018; Ho, Saarma, Barnett, Haile, & Shapiro, 2008). Globally, alternations between cool dry glacials and warm humid interglacials have occurred on ~100 thousand‐year (Kyr) rotations over the past ~800 Kyr (Bennett, 1990).…”

Section: Introductionmentioning

confidence: 99%

Efficient summary statistics for detecting lineage fusion from phylogeographic datasets

Garrick

Hyseni

Arantes

2020

Journal of Biogeography

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Aim: Lineage fusion (merging of two or more populations of a species resulting in a single panmictic group) is a special case of secondary contact. It has the potential to counteract diversification and speciation, or to facilitate it through creation of novel genotypes. Understanding the prevalence of lineage fusion in nature requires reliable detection of it, such that efficient summary statistics are needed. Here, we report on simulations that characterized the initial intensity and subsequent decay of signatures of past fusion for 17 summary statistics applicable to DNA sequence haplotype data. Location: Global. Taxa: Diploid out-crossing species. Methods: We considered a range of scenarios that could reveal the impacts of different combinations of read length versus number of loci (arrangement of DNA sequence data), and whether or not pre-fusion populations experienced bottlenecks coinciding with their divergence (historical context of fusion). Post-fusion gene pools were sampled along 10 successive time points representing increasing lag times following merging of sister populations, and summary statistic values were recalculated at each. Results: Many summary statistics were able to detect signatures of complete merging of populations after a sampling lag time of 1.5 N e generations, but the most informative ones included two neutrality tests and four diversity metrics, with Z nS (a linkage disequilibrium-based neutrality test) being particularly powerful. Correlation was relatively low among the two neutrality tests and two of the diversity metrics. There were clear benefits of many short (200-bp × 200) loci over a handful of long (4-kb × 10) loci. Also, only the latter genetic dataset type showed impacts of bottlenecks during divergence upon the number of informative summary statistics. Main conclusions: This work contributes to identifying cases of lineage fusion, and advances phylogeography by enabling more nuanced reconstructions of how individual species, or multiple members of an ecological community, responded to past environmental change.

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Pleistocene diversification in an ancient lineage: a role for glacial cycles in the evolutionary history of Dioon Lindl. (Zamiaceae)

Cited by 19 publications

References 90 publications

Phylogeny and character evolution in the Dacrymycetes, and systematics of Unilacrymaceae and Dacryonaemataceae fam. nov.

Phylogeny and character evolution in the Dacrymycetes, and systematics of Unilacrymaceae and Dacryonaemataceae fam. nov.

Population Differentiation and Demographic History of the Cycas taiwaniana Complex (Cycadaceae) Endemic to South China as Indicated by DNA Sequences and Microsatellite Markers

Efficient summary statistics for detecting lineage fusion from phylogeographic datasets

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