Molecular markers for phylogenetic applications derived from comparative plastome analysis of Prunus species

Interspecific and intergeneric relationships of Prunus s.l. are still unclear due to low levels of genetic variation among species, and resulting partially unresolved phylogenetic inferences. Here we sequenced and compared six complete plastomes from two subgenera of Prunus in order to choose molecular markers to increase the amount of genetic variation suitable for inference of Prunus phylogeny. The plastomes range between 157 817 and 158 995 bp in length, and we found different levels of inverted repeat (IR) contraction among the three sampled subgenera of Prunus s.l. Most regions in Prunus plastomes considered individually provide low phylogenetic resolution at the subgenus or species level compared to a tree constructed using all 78 coding regions combined. We compared levels of variation among 206 coding regions and noncoding (intergenic and intron) plastid regions and inferred phylogenies from each region considered individually. We then chose using two regions together for future studies of relationships in Prunus, ycf1 and trnT-L, that display high to moderate levels of variation among coding and intergenic regions, respectively, and that individually permit inference of resolved species-level trees in Prunus with moderate to strong branch support. Considered together, these two regions allow inference of the same topology of Prunus inferred using all coding plastid regions combined, with comparable levels of tree support to the full plastome set. These two loci should therefore be useful as a plastid phylogenetic marker set for further inference of relationships within Prunus s.l.     

Plastome phylogenomic analysis of Torreya (Taxaceae)

Torreya Arn., a small genus of Taxaceae, consists of six species occurring in North America and eastern Asia. Several phylogenetic studies have previously been undertaken to reveal relationships within this genus, although only a few DNA segments or species were used. In the present study, we sequenced five Torreya plastomes and combined these with two existing plastomes from the genus to investigate plastome evolution and phylogenetic relationships within Torreya. All sequenced Torreya plastomes shared the same complement of 82 protein‐coding genes, 4 ribosomal RNA genes, and 31 transfer RNA genes. Phylogenetic inference using a maximum likelihood framework consisted of an 82‐gene, 17‐taxon dataset, including all species of Torreya, resolved Torreya as a monophyletic clade. Strongly supported relationships within the genus include the position of the early diverging T. jackii Chun, the two sister pairs T. fargesii Franch.–T. nucifera (L.) Siebold & Zucc. and T. grandis Fortune ex Lindl.–T. californica Torr., and the monophyly of the clade including T. fargesii var. yunnanensis, T. fargesii, and T. nucifera. In addition to the inference of species relationships, divergence time estimation and biogeographical analysis were carried out. The diversification of Torreya was estimated to be approximately 8.9 Ma. Ancestral state reconstruction of the geographical area suggested China/eastern North America as the most likely ancestral region for the six extant Torreya species.     

Systematics of Mukdenia and Oresitrophe (Saxifragaceae): Insights from genome skimming data

Oresitrophe and Mukdenia (Saxifragaceae) are epilithic sister genera used in traditional Chinese medicine. The taxonomy of Mukdenia, especially of M. acanthifolia, has been controversial. To address this, we produced plastid and mitochondrial data using genome skimming for Mukdenia acanthifolia and Mukdenia rossii, including three individuals of each species. We assembled complete plastomes, mitochondrial CDS and nuclear ribosomal ETS/ITS sequences using these data. Comparative analysis shows that the plastomes of Mukdenia and Oresitrophe are relatively conservative in terms of genome size, structure, gene content, RNA editing sites and codon usage. Five plastid regions that represent hotspots of change (trnH-psbA, psbC-trnS, trnM-atpE, petA-psbJ and ccsA-ndhD) are identified within Mukdenia, and six regions (trnH-psbA, petN-psbM, trnM-atpE, rps16-trnQ, ycf1 and ndhF) contain a higher number of species-specific parsimony-informative sites that may serve as potential DNA barcodes for species identification. To infer phylogenetic relationships between Mukdenia and Oresitrophe, we combined our data with published data based on three different datasets. The monophyly of each species (Oresitrophe rupifraga, M. acanthifolia and M. rossii) and the inferred topology ((M. rossii, M. acanthifolia), O. rupifraga) are well supported in trees reconstructed using the complete plastome sequences, but M. acanthifolia and M. rossii did not form a separate clade in the trees based on ETS + ITS data, while the mitochondrial CDS trees are not well-resolved. We found low recovery of genes in the Angiosperms353 target enrichment panel from our unenriched genome skimming data. Hybridization or incomplete lineage sorting may be the cause of discordance between trees reconstructed from organellar and nuclear data. Considering its morphological distinctiveness and our molecular phylogenetic results, we strongly recommend that M. acanthifolia be treated as a distinct species.     

The complete plastome of Panax stipuleanatus: Comparative and phylogenetic analyses of the genus Panax (Araliaceae)

Panax stipuleanatus (Araliaceae) is an endangered and medicinally important plant endemic to China. However, phylogenetic relationships within the genus Panax have remained unclear. In this study, we sequenced the complete plastome of P. stipuleanatus and included previously reported Panax plastomes to better understand the relationships between species and plastome evolution within the genus Panax. The plastome of P. stipuleanatus is 156,069 base pairs (bp) in length, consisting of a pair of inverted repeats (IRs, each 25,887 bp) that divide the plastome into a large single copy region (LSC, 86,126 bp) and a small single copy region (SSC, 8169 bp). The plastome contains 114 unigenes (80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes). Comparative analyses indicated that the plastome gene content and order, as well as the expansion/contraction of the IR regions, are all highly conserved within Panax. No significant positive selection in the plastid protein-coding genes was observed across the eight Panax species, suggesting the Panax plastomes may have undergone a strong purifying selection. Our phylogenomic analyses resulted in a phylogeny with high resolution and supports for Panax. Nine proteincoding genes and 10 non-coding regions presented high sequence divergence, which could be useful for identifying different Panax species.     

Genetic markers in Andean Puya species (Bromeliaceae) with implications on plastome evolution and phylogeny

The Andean plant endemic Puya is a striking example of recent and rapid diversification from central Chile to the northern Andes, tracking mountain uplift. This study generated 12 complete plastomes representing nine Puya species and compared them to five published plastomes for their features, genomic evolution, and phylogeny. The total size of the Puya plastomes ranged from 159,542 to 159,839 bp with 37.3%–37.4% GC content. The Puya plastomes were highly conserved in organization and structure with a typical quadripartite genome structure. Each of the 17 consensus plastomes harbored 133 genes, including 87 protein‐coding genes, 38 tRNA (transfer RNA) genes, and eight rRNA (ribosomal RNA) genes; we found 69–78 tandem repeats, 45–60 SSRs (simple sequence repeats), and 8–22 repeat structures among 13 species. Four protein‐coding genes were identified under positive site‐specific selection in Puya. The complete plastomes and hypervariable regions collectively provided pronounced species discrimination in Puya and a practical tool for future phylogenetic studies. The reconstructed phylogeny and estimated divergence time for the lineage suggest that the diversification of Puya is related to Andean orogeny and Pleistocene climatic oscillations. This study provides plastome resources for species delimitation and novel phylogenetic and biogeographic studies.     

Geographical vs. ecological diversification in Carex section Phacocystis (Cyperaceae): Patterns hidden behind a twisted taxonomy

Carex section Phacocystis (Cyperaceae) is one of the most diverse and taxonomically complex groups of sedges (between 116 and 147 species), with a worldwide distribution in a wide array of biomes. It has a very complicated taxonomic history, with numerous disagreements among different treatments. We studied the biogeography and niche evolution in a phylogenetic framework to unveil the relative contribution of geographical and ecological drivers to diversification of the group. We used a large species sampling of the section (82% of extant species) to build a phylogeny based on four DNA regions, constrained with a phylogenomic HybSeq tree and dated with six fossil calibrations. Our phylogenetic results recovered section Phacocystis s.s. (core Phacocystis) as sister to section Praelongae. Ancestral area reconstruction points toward the N Pacific as the cradle for the crown diversification of section Phacocystis during the Middle Miocene. Wide distributions were recurrently inferred across deep nodes. Large Northern Hemisphere lineages with geographical congruence were retrieved, pointing toward the importance of allopatric divergence at deep phylogenetic levels, whereas within-area speciation emerges as the predominant pattern at shallow phylogenetic level. The Southern Hemisphere (Neotropics, SW Pacific) was colonized several times from the Northern Hemisphere. The global expansion of Carex section Phacocystis did not entail major ecological changes along the inner branches of the phylogeny. Nevertheless, ecological differentiation seems to gain importance toward recent times.     

Passiflora plastome sequencing reveals widespread genomic rearrangements

Although past studies have included Passiflora among angiosperm lineages with highly rearranged plastid genomes (plastomes), knowledge about plastome organization in the genus is limited. So far only one draft and one complete plastome have been published. Expanded sampling of Passiflora plastomes is needed to understand the extent of the genomic rearrangement in the genus, which is also unusual in having biparental plastid inheritance and plastome‐genome incompatibility. We sequenced 15 Passiflora plastomes using either Illumina paired‐end or shotgun cloning and Sanger sequencing approaches. Assembled plastomes were annotated using Dual Organellar GenoMe Annotator (DOGMA) and tRNAscan‐SE. The Populus trichocarpa plastome was used as a reference to estimate genomic rearrangements in Passiflora by performing whole genome alignment in progressiveMauve. The phylogenetic distribution of rearrangements was plotted on the maximum likelihood tree generated from 64 plastid encoded protein genes. Inverted repeat (IR) expansion/contraction and loss of the two largest hypothetical open reading frames, ycf1 and ycf2, account for most plastome size variation, which ranges from 139 262 base pairs (bp) in P. biflora to 161 494 bp in P. pittieri. Passiflora plastomes have experienced numerous inversions, gene and intron losses along with multiple independent IR expansions and contractions resulting in a distinct organization in each of the three subgenera examined. Each Passiflora subgenus has a unique plastome structure in terms of gene content, order and size. The phylogenetic distribution of rearrangements shows that Passiflora has experienced widespread genomic changes, suggesting that such events may not be reliable phylogenetic markers.     

Plastome characteristics of Cannabaceae

Cannabaceae is an economically important family that includes ten genera and ca.117 accepted species. To explore the structure and size variation of their plastomes,we sequenced ten plastomes representing all ten genera of Cannabaceae.Each plastome possessed the typical angiosperm quadripartite structure and contained a total of 128 genes.The Inverted Repeat (IR) regions in five plastomes had experienced small expansions (330-983 bp) into the Large Single-Copy (LSC) region.The plastome of Chaetachme aristata has experienced a 942-bp IR contraction and lost rpl22 and rps19 in its IRs.The substitution rates of rps19 and rpl22 decreased after they shifted from the LSC to IR.A 270-bp inversion was detected in the Parasponia rugosa plastome,which might have been mediated by 18-bp inverted repeats.Repeat sequences,simple sequence repeats,and nucleotide substitution rates varied among these plastomes. Molecular markers with more than 13% variable sites and 5% parsimony-informative sites were identified,which may be useful for further phylogenetic analysis and species identification.Our results show strong support for a sister relationship between Gironniera and Lozanell (BS=100).Celtis,Cannabis-Humulus,Chaetachme-Pteroceltis,and Trema-Parasponia formed a strongly supported clade,and their relationships were well resolved with strong support (BS=100).The availability of these ten plastomes provides valuable genetic information for accurately identifying species,clarifying taxonomy and reconstructing the intergeneric phylogeny of Cannabaceae.     

Plastome phylogenomics and phylogenetic diversity of endangered and threatened grassland species (Poaceae) in a North American tallgrass prairie

Native grasslands are one of the most endangered ecosystems in North America. In this study, we examined the ecological and evolutionary roles of endangered and threatened (e/t) grasses by establishing robust evolutionary relationships with other nonthreatened native and introduced grass species of the community. We hypothesized that the phylogenomic distribution of e/t species of grasses in Illinois would be phylogenetically clustered because closely related species would be vulnerable to the same threats and have similar requirements for survival. This study presents the first time a phylogeny based on complete plastome DNA of Poaceae was analyzed by phylogenetic diversity analysis. To avoid the disturbance of e/t populations, DNA was extracted from herbarium specimens. Next‐generation sequencing (NGS) techniques were used to sequence DNA of plastid genomes (plastomes). The resulting phylogenomic tree was analyzed by phylogenetic diversity metrics. The extracted DNA successfully produced complete plastomes demonstrating that herbarium material is a practical source of DNA for genomic studies. The phylogenomic tree was strongly supported and defined Dichanthelium as a separate clade from Panicum. The phylogenetic metrics revealed phylogenetic clustering of e/t species, confirming our hypothesis.     

Comparative analysis of plastomes in Oxalidaceae: Phylogenetic relationships and potential molecular markers

The wood sorrel family, Oxalidaceae, is mainly composed of annual or perennial herbs, a few shrubs, and trees distributed from temperate to tropical zones. Members of Oxalidaceae are of high medicinal, ornamental, and economic value. Despite the rich diversity and value of Oxalidaceae, few molecular markers or plastomes are available for phylogenetic analysis of the family. Here, we reported four new whole plastomes of Oxalidaceae and compared them with plastomes of three species in the family, as well as the plastome of Rourea microphylla in the closely related family Connaraceae. The eight plastomes ranged in length from 150,673 bp (Biophytum sensitivum) to 156,609 bp (R. microphylla). Genome annotations revealed a total of 129–131 genes, including 83–84 protein-coding genes, eight rRNA genes, 37 tRNA genes, and two to three pseudogenes. Comparative analyses showed that the plastomes of these species have minor variations at the gene level. The smaller plastomes of herbs B. sensitivum and three Oxalis species are associated with variations in IR region sizes, intergenic region variation, and gene or intron loss. We identified sequences with high variation that may serve as molecular markers in taxonomic studies of Oxalidaceae. The phylogenetic trees of selected superrosid representatives based on 76 protein-coding genes corroborated the Oxalidaceae position in Oxalidales and supported it as a sister to Connaraceae. Our research also supported the monophyly of the COM (Celastrales, Oxalidales, and Malpighiales) clade.     

Phylogenomic relationships and species identification of the olive genus Olea (Oleaceae)

The olive genus Olea includes c. 30–40 taxa in three subgenera (Olea, Tetrapilus, and Paniculatae) within the family Oleaceae. Historically, the Olea genus was classified into four groups that were overall well supported by reconstructed phylogenies, despite incomplete sampling of subgenus Tetrapilus and poor resolution within clades. These analyses also showed that the genus was not monophyletic. Reliable identification of Olea species is important for both their conservation and utilization of this economically important genus. In this study, we used phylogenomic data from genome skimming to resolve relationships within Olea and to identify molecular markers for species identification. We assembled the complete plastomes, and nrDNA of 26 individuals representing 13 species using next-generation sequencing and added 18 publicly available accessions of Olea. We also developed nuclear SNPs using the genome skimming data to infer the phylogenetic relationships of Olea. Large-scale phylogenomic analyses of 138 samples of tribe Oleeae supported the polyphyly of Olea, with Olea caudatilimba and Olea subgenus Tetrapilus not sharing their most recent common ancestor with the main Olea clade (subgenus Paniculatae and subgenus Olea). The interspecific phylogenetic resolution was poor owing to a possible rapid radiation. By comparing with the plastome data, we identified the markers ycf1b and psbE-petL as the best Olea-specific chloroplast DNA barcodes. Compared with universal barcodes, specific DNA barcodes and super-barcode exhibited higher discriminatory power. Our results demonstrated the power of phylogenomics to improve phylogenetic relationships of intricate groups and provided new insights into barcodes that allow for accurate identification of Olea species.     

Prospects on the evolutionary mitogenomics of plants: A case study on the olive family (Oleaceae)

The mitogenome is rarely used to reconstruct the evolutionary history of plants, contrary to nuclear and plastid markers. Here, we evaluate the usefulness of mitochondrial DNA for molecular evolutionary studies in Oleaceae, in which cases of cytoplasmic male sterility (CMS) and of potentially contrasted organelle inheritance are known. We compare the diversity and the evolution of mitochondrial and chloroplast genomes by focusing on the olive complex and related genera. Using high‐throughput techniques, we reconstructed complete mitogenomes (ca. 0.7 Mb) and plastomes (ca. 156 kb) for six olive accessions and one Chionanthus. A highly variable organization of mitogenomes was observed at the species level. In olive, two specific chimeric genes were identified in the mitogenome of lineage E3 and may be involved in CMS. Plastid‐derived regions (mtpt) were observed in all reconstructed mitogenomes. Through phylogenetic reconstruction, we demonstrate that multiple integrations of mtpt regions have occurred in Oleaceae, but mtpt regions shared by all members of the olive complex derive from a common ancestor. We then assembled 52 conserved mitochondrial gene regions and complete plastomes of ten additional accessions belonging to tribes Oleeae, Fontanesieae and Forsythieae. Phylogenetic congruence between topologies based on mitochondrial regions and plastomes suggests a strong disequilibrium linkage between both organellar genomes. Finally, while phylogenetic reconstruction based on plastomes fails to resolve the evolutionary history of maternal olive lineages in the Mediterranean area, their phylogenetic relationships were successfully resolved with complete mitogenomes. Overall, our study demonstrates the great potential of using mitochondrial DNA in plant phylogeographic and metagenomic studies.     

Phylogenomics and biogeography of Wisteria: Implications on plastome evolution among inverted repeat-lacking clade (IRLC) legumes

The genus Wisteria (Fabaceae) is disjunctly distributed in eastern Asian and eastern North American temperate deciduous forests, and it is widely cultivated around the world as spectacular garden plants. It is a member of inverted repeat-lacking clade (IRLC). The IRLC Species are characterized by the loss of an IR region in their plastomes, which has long been of great interest. In this research, we report whole plastome sequences from all four Wisteria species and a Wisteriopsis japonica, combining these with existing data to explore phylogenetic relationships and biogeography of Wisteria, as well as plastome evolution of IRLC species. Phylogenetic analyses recognized a clade containing Glycyrrhiza–Wisteriopsis–Wisteria as sister to the remaining genera of IRLC. North American Wisteria frutescens and the three Asian species formed reciprocal clades, and Wisteria brachybotrys was sister to Wisteria floribunda and Wisteria sinensis. Wisteria may have originated in Japan near the boundary of the Oligocene and Miocene. The disappearance of Bering Land Bridge in the late Miocene might lead to the Eastern Asian–Eastern North American disjunction of Wisteria. Allopatric speciation of Wisteria between the Japanese archipelago and the Asian continent in the Quaternary increased the species richness of eastern Asia in comparison with eastern North America. Synonymous substitution rates (d_S) of protein-coding genes in the IRLC species were around 2-fold (SC genes) or 11-fold (IR genes) higher than those of non-IRLC species. For both SC and IR genes, herbaceous legumes have around 3-fold higher d_S than woody ones. Both loss of one IR region and herbaceous habit elevated substitution rates of the plastomes.     

Plastomes of Betulaceae and phylogenetic implications

Betulaceae is a well‐defined family of Fagales, including six living genera and more than 160 modern species. Species of the family have high ecological and economic value for the abundant production of wood. However, phylogenetic relationships within Betulaceae have remained partly unresolved, likely due to the lack of a sufficient number of informative sites used in previous studies. Here, we re‐investigate the Betulaceae phylogeny with whole chloroplast genomes from 24 species (17 newly assembled), representing all genera of the family. All the 24 plastomes are relatively conserved with four regions, and each genome is ∼158–161 kb long, with 111 genes. The six genera are all monophyletic in the plastome tree, whereas Ostrya Scop. is nested in the Carpinus clade in the internal transcribed spacer tree. Further incongruencies are also detected within some genera between species. Incomplete lineage sorting and/or hybrid introgression during the diversification of the family could account for such incongruencies. Our dating analysis, based on four fossils, suggests that the most recent common ancestors of the extant genera date back to the mid‐ to late Miocene, and confirms that Betulaceae started to diversify in the upper Cretaceous/early Paleocene. Our results highlight the significance of using more informative sites in resolving phylogenetic relationships. Plastome data and increased taxon sampling will help to better understand the evolutionary history of Betulaceae in the future.     

柴达木野生黑果枸杞的空间遗传结构

基于cpDNA序列, 研究柴达木野生黑果枸杞(Lycium ruthenicum)的遗传多样性、遗传结构和单倍型进化关系, 可为其种群的遗传保护提供理论依据。该研究基于3个筛选的叶绿体多态引物: psbA-trnH、psbK-psbI和trnV, 利用群体遗传分析方法研究柴达木盆地野生黑果枸杞的遗传变异格局: 利用软件DnaSP 6.0和Permut 2.0计算分子多样性指标, 利用分子方差分析研究组间和种群间的遗传变异来源, 利用单倍型网络分析和主坐标分析研究单倍型的聚类关系; 利用最大似然树和贝叶斯系统树分析单倍型的谱系进化关系。结果显示: 叶绿体序列psbA-trnH、psbK-psbI和trnV拼接后的总长度为1 454 bp, 鉴别出14个核苷酸变异位点, 共定义了7个单倍型。种群间总的遗传多样(h_T)和种群内遗传多样性(h_S)分别为0.916和0.512。AMOVA分析结果表明, 80%以上的遗传变异来源于组间和种群间。叶绿体单倍型的贝叶斯系统树和最大似然树均表明柴达木盆地黑果枸杞种群聚为2支: 德令哈和格尔木为一支, 诺木洪为另一支。单倍型网络和主坐标分析结果揭示的拓扑结构和聚类关系与系统树一致。Mantel检验结果表明柴达木黑果枸杞种群间的遗传距离与地理距离存在显著的弱相关关系(r = 0.591 1, p = 0.000 9)。柴达木盆地黑果枸杞种群具有较高的遗传多样性, 种群间遗传分化显著。从遗传多样性保护的角度而言, 具有较高遗传多样性的诺木洪林业站和格尔木新乐村种群可划分为保护管理单元。     

Herbarium phylogenomics: Resolving the generic status of the enigmatic Pseudobartsia (Orobanchaceae)

The millions of herbarium specimens in collections around the world provide historical resources for phylogenomics and evolutionary studies. Many rare and endangered species exist only as historical specimens. Here, we report a case study of the monotypic Pseudobartsia yunnanensis D. Y. Hong (=Pseudobartsia glandulosa[Bentham] W. B. Yu & D. Z. Li: Orobanchaceae) known from a single Chinese collection taken in 1940. We obtained genomic data of Pseudobartsia glandulosa using high-throughput short-read sequencing, and then assembled a complete chloroplast genome and nuclear ribosome DNA region in this study. We found that the newly assembled three plastid DNA regions (atpB-rbcL, rpl16, and trnS-G) and nuclear ribosomal internal transcribed spacer (nrITS) of Pseudobartsia glandulosa were more than 99.98% similar to published sequences obtained by target sequencing. Phylogenies of Orobanchaceae using 30 plastomes (including 10 new plastomes), using both supermatrix and multispecies coalescent approaches following a novel plastid phylogenomic workflow, recovered seven recognized tribes and two unranked groups, both of which were proposed as new tribes, that is, Brandisieae and Pterygielleae. Within Pterygielleae, all analyses strongly supported Xizangia D. Y. Hong as the first diverging genus, with Pseudobartsia D. Y. Hong as sister to Pterygiella Oliver + Phtheirospermum Bunge (excluding Phtheirospermum japonicum [Thunberg] Kanitz); this supports reinstatement of Pseudobartsia and Xizangia. Although elements of Buchnereae-Cymbarieae-Orobancheae and Brandisieae-Pterygielleae-Rhinantheae showed incongruence among gene trees, the topology of the supermatrix tree was congruent with the majority of gene trees and functional-group trees. Therefore, most plastid genes are evolving as a linkage group, allowing the supermatrix tree approach to yield internally consistent phylogenies for Orobanchaceae.     

Incongruence of mitochondrial and nuclear gene trees in the Carabid beetles Ohomopterus

We studied the molecular phylogeny of the carabid subgenus Ohomopterus (genus Carabus), using two mitochondrial (mt) DNA regions (16SrRNA and NADH dehydrogenase subunit 5) and three nuclear DNA regions (wingless, phosphoenolpyruvate carboxykinase, and an anonymous locus). We revisited the previously reported incongruence between the distribution of mtDNA markers and morphologically defined species (Su et al., 1996; J. Mol. Evol. 43:662-671), which those authors attributed to "type switching", a concerted change in many morphological characters that results in the repeated evolution of a particular morphological type. Our mtDNA gene tree obtained from 44 individuals representing all 15 currently recognized species of Ohomopterus revealed that haplotypes isolated from individuals of a single "species" were frequently separated into distant clades, confirming the previous report. The three nuclear markers generally conformed better-with the morphologically defined species than did the mitochondrial markers. The phylogenetic signal in mtDNA and nuclear DNA data differed strongly, and these two partitions were significantly incongruent with each other according to the incongruence length difference test of Farris et al. (1994; Cladistics 10:315-320), although the three nuclear partitions were not homogeneous either. Our results did not support the type-switching hypothesis that had been proposed to fit the morphological data to the mitochondrial gene tree: The incongruence of the mtDNA tree with other nuclear markers indicates that the mtDNA-based tree does not reflect species history any better than the morphological data do. Incongruence of gene trees in Ohomopterus may have been promoted by the complex processes of geographic isolation and hybridization in the Japanese Archipelago that have led to occasional gene flow and recombination between separated entities. The occurrence of reticulate patterns in this group is intriguing, because species of Ohomopterus exhibit extremely divergent genitalic structures that represent a highly efficient reproductive isolation mechanism.     

Spatial genetic structure of Lycium ruthenicum in the Qaidam Basin

基于cpDNA序列, 研究柴达木野生黑果枸杞(Lycium ruthenicum)的遗传多样性、遗传结构和单倍型进化关系, 可为其种群的遗传保护提供理论依据。该研究基于3个筛选的叶绿体多态引物: psbA-trnH、psbK-psbI和trnV, 利用群体遗传分析方法研究柴达木盆地野生黑果枸杞的遗传变异格局: 利用软件DnaSP 6.0和Permut 2.0计算分子多样性指标, 利用分子方差分析研究组间和种群间的遗传变异来源, 利用单倍型网络分析和主坐标分析研究单倍型的聚类关系; 利用最大似然树和贝叶斯系统树分析单倍型的谱系进化关系。结果显示: 叶绿体序列psbA-trnH、psbK-psbI和trnV拼接后的总长度为1 454 bp, 鉴别出14个核苷酸变异位点, 共定义了7个单倍型。种群间总的遗传多样(h_T)和种群内遗传多样性(h_S)分别为0.916和0.512。AMOVA分析结果表明, 80%以上的遗传变异来源于组间和种群间。叶绿体单倍型的贝叶斯系统树和最大似然树均表明柴达木盆地黑果枸杞种群聚为2支: 德令哈和格尔木为一支, 诺木洪为另一支。单倍型网络和主坐标分析结果揭示的拓扑结构和聚类关系与系统树一致。Mantel检验结果表明柴达木黑果枸杞种群间的遗传距离与地理距离存在显著的弱相关关系(r = 0.591 1, p = 0.000 9)。柴达木盆地黑果枸杞种群具有较高的遗传多样性, 种群间遗传分化显著。从遗传多样性保护的角度而言, 具有较高遗传多样性的诺木洪林业站和格尔木新乐村种群可划分为保护管理单元。     

A comparative plastomics approach reveals available molecular markers for the phylogeographic study of Dendrobium huoshanense,an endangered orchid with extremely small populations

Comparative plastomics approaches have been used to identify available molecular markers for different taxonomic level studies of orchid species. However, the adoption of such methods has been largely limited in phylogeographic studies. Therefore, in this study, Dendrobium huoshanense, an endangered species with extremely small populations, was used as a model system to test whether the comparative plastomic approaches could screen available molecular markers for the phylogeographic study. We sequenced two more plastomes of D. huoshanense and compared them with our previously published one. A total of 27 mutational hotspot regions and six polymorphic cpSSRs have been screened for the phylogeographic studies of D. huoshanense. The cpDNA haplotype data revealed that the existence of haplotype distribution center was located in Dabieshan Mts. (Huoshan). The genetic diversity and phylogenetic analyses showed that the populations of D. huoshanense have been isolated and evolved independently for long period. On the contrary, based on cpSSR data, the genetic structure analysis revealed a mixed structure among the populations in Anhui and Jiangxi province, which suggested that the hybridization or introgression events have occurred among the populations of D. huoshanense. These results indicated that human activities have played key roles in shaping the genetic diversity and distributional patterns of D. huoshanense. According to our results, both two markers showed a high resolution for the phylogeographic studies of D. huoshanense. Therefore, we put forth that comparative plastomic approaches could revealed available molecular markers for phylogeographic study, especially for the species with extremely small populations.