Eco‐evolutionary evidence for the global diversity pattern of <i>Cycas</i> (Cycadaceae)

Liu, Jian; Lindstrom, Anders J.; Gong, Yiqing; Dong, Shanshan; Liu, Yusheng (Chris); Zhang, Shouzhou; Gong, Xun

doi:10.1111/jipb.13638

Cited by 5 publications

(1 citation statement)

References 125 publications

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“…RNA sequencing has been shown to be highly efficient for phylogenetic reconstruction at the species level, even for taxa that have undergone a rapid radiation (36,(45)(46)(47)(48)(49). This is certainly the case with Isodon, for which we have reconstructed a well-resolved phylogeny which includes nearly 90% of extant species and is based on transcriptome sequences with complementary data from genome resequencing (Fig.…”

Section: Rapid Evolutionary Radiation Of Isodon In the Dry Valleysmentioning

confidence: 99%

Rapid radiation of a plant lineage sheds light on the assembly of dry valley biomes

Chen,

Sunojkumar,

Spicer

et al. 2024

Preprint

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Southwest China is characterized by high plateaus, large mountain systems, and deeply incised dry valleys formed by major rivers and their tributaries. Despite the considerable attention given to alpine plant radiations in this region, the timing and mode of the diversification of the numerous plant lineages in the dry valley habitat remains unknown. To address this knowledge gap, we investigate the macroevolution of Isodon (Lamiaceae), a lineage commonly distributed in the dry valleys in southwest China and wetter areas of Asia and Africa. We reconstructed a robust phylogeny encompassing nearly 90% of the approximately 140 extant Isodon species using transcriptome and genome-resequencing data. Our results suggest a rapid radiation of Isodon during the Pliocene that coincided with a habit shift from herbs to shrubs and a habitat shift from humid areas to dry valleys. The shrubby growth form likely acted as a preadaptation allowing for the movement of Isodon species into these valleys. Ecological analysis highlighted aridity and precipitation as key factors influencing the niche preferences of different growth forms and species richness of Isodon. Integrating our results with insights from tectonic movements in the Tibetan Plateau and adjacent regions, we infer that the interplay between topography and the evolution of the East Asian monsoon since the middle Miocene likely contributed to the formation of the dry valley biome in southwest China. This study enhances our understanding of evolutionary dynamics and ecological drivers shaping the distinctive flora of this region.

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Section: Rapid Evolutionary Radiation Of Isodon In the Dry Valleysmentioning

confidence: 99%

Rapid radiation of a plant lineage sheds light on the assembly of dry valley biomes

Chen,

Sunojkumar,

Spicer

et al. 2024

Preprint

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Transcriptome sequencing data provide a solid base to understand the phylogenetic relationships, biogeography and reticulated evolution of the genus Zamia L. (Cycadales: Zamiaceae)

Lindstrom,

Habib,

Dong

et al. 2024

Annals of Botany

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Background and Aims Cycad is a key lineage to understand the early evolution of seed plants and their response to past environmental changes. However, tracing the evolutionary trajectory of cycad species is challenging when the robust relationships at inter- or infrageneric level are not well resolved. Methods Here, using 2,901 single-copy nuclear genes, we explored the species relationships and gene flow within the second largest genus of cycads, i.e., Zamia, based on phylotranscriptomic analyses of 90% extant Zamia species. Based on a well-resolved phylogenetic framework, we performed gene flow analyses, molecular dating, and biogeographical reconstruction to examine the spatiotemporal evolution of Zamia. We also performed ancestral state reconstruction (ASR) of a total of 62 traits of the genus to comprehensively investigate its morphological evolution. Key Results Zamia is comprised of seven major clades corresponding to seven distinct distribution areas in the Americas, with at least three reticulation nodes revealed in this genus. Extant lineages of Zamia initially diversified around 18.4-32.6 (29.14) million years ago (MA) in the Mega-Mexico, and then expanded eastward into the Caribbean and southward into Central and South America. ASR revealed homoplasy in most of the morphological characters. Conclusions This study revealed congruent phylogenetic relationships from comparative methods/datasets, with some conflicts being the result of incomplete lineage sorting and ancient/recent hybridization events. The strong association between the clades and the biogeographic areas suggested that ancient dispersal events shaped the modern distribution pattern, and regional climatic factors may have resulted in the following in-situ diversification. Climate cooling starting during the mid Miocene is associated with the global expansion of Zamia to the tropical South America that have dramatically driven lineage diversification in the New World flora, as well as the extinction of cycad species in the nowadays cooler regions of both hemispheres as indicated by the fossil records.

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Unraveling the Web of Life: Incomplete lineage sorting and hybridization as primary mechanisms over polyploidization in the evolutionary dynamics of pear species

Jin,

Lin,

et al. 2024

Preprint

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In contrast to the traditional Tree of Life (ToL) paradigm, the Web of Life (WoL) model provides a more nuanced and precise depiction of organismal phylogeny, particularly considering the prevalent incongruence observed among gene/species trees. The lack of a generalized pipeline for teasing apart potential evolutionary mechanisms-such as Incomplete Lineage Sorting (ILS), hybridization, introgression, polyploidization, and Whole-Genome Duplication-poses significant challenges to the delineation of the WoL. The pear genus Pyrus, characterized by extensive hybridization events, serves as an excellent model for investigating the WoL. This study introduces a novel Step-by-Step Exclusion (SSE) approach to deciphering the complexities inherent in the WoL. Our findings indicate: 1) ILS, rather than polyploidization, is identified as the primary driver behind the origin of Pyrus from the arid regions of the Himalayas-Central Asia; 2) the two subgenera of Pyrus have independent evolutionary trajectories, facilitated by the geographical barriers that arose via the uplift of the Tibetan Plateau and increased aridity in Central Asia; 3) ILS and hybridization have facilitated the diversification of Oriental pears, while hybridization alone has driven the reticulate evolution of Occidental pears; 4) the establishment of the Silk Road during the Han Dynasty acted as a conduit for genetic exchange between Occidental and Oriental pears. The novel SSE approach provides a universally applicable framework for investigating evolutionary mechanisms defining the WoL paradigm.

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Eco‐evolutionary evidence for the global diversity pattern of Cycas (Cycadaceae)

Cited by 5 publications

References 125 publications

Rapid radiation of a plant lineage sheds light on the assembly of dry valley biomes

Rapid radiation of a plant lineage sheds light on the assembly of dry valley biomes

Transcriptome sequencing data provide a solid base to understand the phylogenetic relationships, biogeography and reticulated evolution of the genus Zamia L. (Cycadales: Zamiaceae)

Unraveling the Web of Life: Incomplete lineage sorting and hybridization as primary mechanisms over polyploidization in the evolutionary dynamics of pear species

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