Molecular Phylogeny and Historical Biogeography of Goodyera R. Br. (Orchidaceae): A Case of the Vicariance Between East Asia and North America

Abstract

Understanding of intercontinental distribution in the Northern Hemisphere has attracted a lot of attention from botanists. However, although Orchidaceae is the largest group of angiosperms, biogeographical studies on the disjunctive pattern have not been sufficient for this family. Goodyera R. Br. (tribe Cranichideae, subfamily Orchidoideae, family Orchidaceae) is widely distributed in temperate and tropical regions. Although the phylogenetic relationship of Goodyera inferred from both morphological and molecular data has been conducted, the sampled taxa were mainly distributed in Asia regions that resulted in non-monophyly of this genus. In this study, the complete plastid genomes of Goodyera, generated by next-generation sequencing (NGS) technique and sampled in East Asia and North America, were used to reconstruct phylogeny and explore the historical biogeography. A total of 18 Goodyera species including seven newly sequenced species were analyzed. Based on 79 protein-coding genes, the phylogenetic analysis revealed that Goodyera could be subdivided into four subclades with high support values. The polyphyletic relationships among Goodyera taxa were confirmed, and the unclear position of G. foliosa was also resolved. The datasets that are composed of the 14 coding sequences (CDS) (matK, atpF, ndhK, accD, cemA, clpP, rpoA, rpl22, ndhF, ccsA, ndhD, ndhI, ndhA, and ycf 1) showed the same topology derived from 79 protein-coding genes. Molecular dating analyses revealed the origin of Goodyera in the mid-Miocene (15.75 Mya). Nearctic clade of Goodyera was diverged at 10.88 Mya from their most recent common ancestor (MRCA). The biogeographical reconstruction suggests that subtropical or tropical Asia is the origin of Goodyera and it has subsequently spread to temperate Asia during the Miocene. In addition, Nearctic clade is derived from East Asian species through Bering Land Bridge (BLB) during the Miocene. The speciation of Goodyera is most likely to have occurred during Miocene, and climatic and geological changes are thought to have had a part in this diversification. Our findings propose both origin and vicariance events of Goodyera for the first time and add an example for the biogeographical history of the Northern Hemisphere.

Out of the Qinghai-Tibetan plateau: Origin, evolution and historical biogeography of Morchella (both Elata and Esculenta clades)

“…we used BEAST v.2.6.6 ( Chen et al, 2015 ; Zhu et al, 2019 ; Kim and Kim, 2022 ) to estimate the divergence times of Morchella phylospecies in the QTPs. In this study, we used Floccularia luteovirens , which is the endemic basidiomycete fungus in the QTPs, instead of P. devonicus as the calibration point 1 in Basidiomycota and Ascomycota ( Taylor et al, 2004 ; Chen et al, 2015 ; Zhu et al, 2019 ; Guo et al, 2022 ).…”

“…In addition, the world-widely distribution of 8 Morchella species ( Supplementary Table S2 ), M. spongiola , M. esculenta , M. crassipes , M. eohespera , M. eximia , M. costata , Mel -13, Mel -14, were downloaded in NCBI to estimate the differentiation time and reconstruction ancestral area using BEAST v2.6.6 and RASP v3.1, respectively. ArcGIS v10.7 was used to visualize the geographic distribution and possible dispersal routes of Morchella ( Yu et al, 2015 ; Kim et al, 2019 ; Kim and Kim, 2022 ).…”

“…ArcGIS v10.7 was used to visualize the 10.3389/fmicb. 2022.1078663 Frontiers in Microbiology 05 frontiersin.org geographic distribution and possible dispersal routes of Morchella (Yu et al, 2015;Kim et al, 2019;Kim and Kim, 2022).…”

First Record of Comparative Plastid Genome Analysis and Phylogenetic Relationships among Corylopsis Siebold & Zucc. (Hamamelidaceae)

“…The GC content of the IR regions is relatively higher than that of the SC regions, implying that fewer AT contents have relatively weak hydrogen bonds. Consequently, evidence exists that IR regions are better preserved than SC regions ( Figure 2 and Figure 6 , Table 1 ) [ 20 , 42 , 43 , 44 , 45 ]. The IR region is commonly found duplicated in most plastid genomes.…”

“…Due to the high conservation of plastid protein-coding gene composition, reconstructing phylogenetic relationships among taxa is essential [ 16 , 17 , 18 ]. Furthermore, it is useful for inferring biogeography, molecular evolution, and age estimation [ 19 , 20 ]. With the development of next-generation sequencing (NGS), genomic data can be obtained quickly and easily.…”