cpDNA Markers Research Articles

Species Differentiation of Prunus serrulata and Prunus xueluoensis Based on Combined Analysis of SSR and cpDNA Markers

Species Differentiation of Prunus serrulata and Prunus xueluoensis Based on Combined Analysis of SSR and cpDNA Markers

Phylogenetic Analysis of Rare and Endangered Tulipa Species (Liliaceae) of Kazakhstan Based on Universal Barcoding Markers.

In Kazakhstan, the genus Tulipa is represented by 35 species, 18 of which are listed in the Red Data Book of Kazakhstan and protected by the state. Recent studies of tulip specimens from regions bordering Kazakhstan emphasize the significance of species inventory and report the discovery of several hybrids. In this study, eight tulip species were identified based on morphological characteristics and using DNA barcoding methods. Molecular genetic markers, including nrDNA (ITS) and cpDNA markers (rbcL, matK), of the studied species were sequenced and analyzed using the Bayesian inference and maximum likelihood phylogenetic analysis methods. Our work demonstrates that DNA barcodes based on the ITS, rbcL, and matK marker regions have successful practical applicability, with ITS being the most informative at the intragenic level. However, for distinguishing closely related taxa, the most effective approach would be to use a combined dataset of sequences from multiple DNA markers. The results showed discrepancies in the placement of several taxa (T. kaufmanniana, T. patens), likely due to introgression and natural spontaneous hybridization. The molecular phylogenetic analysis suggests the existence of a previously undescribed hybrid between T. patens and T. alberti. Further detailed population studies are needed to validate this hypothesis.

Re-establishment of Aechmea laxiflora (Bromeliaceae, Bromelioideae) based on morphological and phylogenetic evidence, with notes on its geographical distribution

Background: Previous phylogenetic analyses suggested that Aechmea bracteata is not a monophyletic species, being each variety an individual lineage within the Aechmea bracteata complex.
 Hypothesis: A phylogenetic analysis based on molecular data and a morphological analysis will provide evidence to support the taxonomic recognition of A. bracteata var. pacifica as a distinct species.
 Studies species: A. bracteata var. bracteata, A. bracteata var. pacifica and related species.
 Study site and dates: Mexico to Northern South America; 17 populations from Southeastern and Western Mexico. Analyses were performed between 2021 and 2023.
 Methods: A linear morphometric analysis was conducted with 85 herbarium specimens testing 28 quantitative and three qualitative variables. Potential diagnostic traits were reviewed in living specimens. A phylogenetic analysis was performed with two nDNA markers (ETS and g3pdh) and one cpDNA marker (trnL-F). A total of 373 records were projected into biogeographical provinces of the Neotropics.
 Results: The morphometric analysis allowed to separate each variety into a group, also, nine of the evaluated traits resulted statistically significant through a univariate analysis. Five additional diagnostic traits from the inflorescence and leaves were recognized. According to nDNA both taxa present reciprocal monophyly, however, cpDNA groups A. bracteata var. pacifica with Central American species, showcasing a potential hybrid origin. Geographically, the Sierra Madre del Sur acts as a barrier between both taxa.
 Conclusions: Due to the gathered evidence is possible to recognize A. bracteata var. pacifica as an endemic species to Mexico, reestablishing the basionym A. laxiflora.

Morphological and molecular evidence for natural hybridization between Sorbus pohuashanensis and S. discolor (Rosaceae)

In overlapping distribution areas of Sorbus pohuashanensis and S. discolor in North China (Mount Tuoliang, Mount Xiling and Mount Baihua), Sorbus individuals were found with pink fruit, which have never been recorded for the flora of China. Fourteen morphological characters combined with four chloroplast DNA markers and internal transcribed spacer (ITS) were used to analyze the origin of the Sorbus individuals with pink fruits and their relationship to S. pohuashanensis and S. discolor. PCA, SDA and one-way (taxon) ANOVA of morphological characters provided convincing evidence of the hybrid origin of Sorbus individuals with pink fruits based on a novel morphological character and many intermediate characters. Haplotype analysis based on four cpDNA markers showed that either S. pohuashanensis or S. discolor were maternal parents of Sorbus individuals with pink fruits. Incongruence of the position of Sorbus individuals with pink fruits between cpDNA and ITS in cluster trees supported by DNA sequence comparative analysis, implying former hybridization events between S. pohuashanensis and S. discolor. Multiple hybridization events between S. pohuashanensis and S. discolor might have contributed to the generation of Sorbus individuals with pink fruits. This study has provided insights into hybridization between species of the same genus in sympatric areas, which is of great significance for the study of interspecific hybridization.

Genetic diversity of tomato (Solanum lycopersicum) accessions using chloroplast DNA and random amplified polymorphic DNA markers

Information regarding genetic diversity and genetic relationships among different genotypes is invaluable in crop improvement of which its success is largely dependent on genetic variability. As molecular markers continue to be an effective tool for localization of a gene to improvement of plant varieties, the need to establish phylogenetic relationships becomes extremely important for the process of breeding new cultivars. This study reports genetic diversity for Tomato accessions across Nigeria (Six geo-Political Zones) as revealed by chloroplast DNA (cpDNA) and Random Amplified Polymorphic DNA (RAPD) markers. cpDNA data showed a Nucleotide diversity for all accessions of Tomato at 0.302 while the number of segregated sites as well as parsimony informative sites to be 4.0. Data from five Random Amplified Polymorphic DNA (RAPD) primers showed a low Gene diversity (h) which ranged from 0.10 to 0.28, Percentage polymorphism (Pp) ranged from 20 % to 84%. The Unweighted Pair Group Method with Arithmetic Mean (UPGMA) dendrogram grouped the accessions into two groups at similarity coefficient of 72%, with a value of r = 0.98, showing an excellent correlation between the accessions and the values of the initial distances (similarity matrix). Similar results were seen with the dendrogram constructed for genetic relationships of Tomato accessions using RAPD or cpDNA (you have mentioned RAPD up) markers. Split tree analysis equally revealed a 2 structured gene pool for Tomato gene pool in Nigeria. The high homogeneity of species observed in the study signifies a low genetic diversity and limited variability in tomato species in Nigeria. Amongst the consequences of low genetic diversity is the absence of unique variants that can possibly combat disease conditions or adapt to unfavourable environmental changes. The use of both cpDNA and RAPD markers in this study has efficiently shown that continuous cycling/shuffling of species within the narrow gene pool is expected to lead to a continuous reduction in genetic variability. No addition of new variant into the gene pool and in turn leads to inbreeding depression, thus suggesting the need to breed with known wild cultivars to increase genetic variability. Key words: CpDNA, Gene pool, Genetic Diversity, Inbreeding depression, RAPD marker, Tomatoes breeding

Genetic diversity and structure of Slovenian native germplasm of plum species (P. domestica L., P. cerasifera Ehrh. and P. spinosa L.).

Slovenia has particular climatic, soil, geographic and historical conditions that lead to long tradition of plum cultivation and use. In this work, a set of 11 SSR and three universal cpDNA markers, as well as flow cytometry, were used to (1) evaluate the genetic diversity of 124 accessions of the three Prunus species (P. domestica L., P. cerasifera Ehrh., and P. spinosa L.), (2) investigate the possible involvement of P. cerasifera and P. spinosa species in P. domestica origin, (3) study the genetic relationships and variability among the most typical P. domestica accessions present in Slovenia. Ten haplotypes of cpDNA were identified and clustered into three groups according to the Neighbor-Joining analysis (NJ). All 11 SSR primer pairs were polymorphic, revealing 116 unique genotypes. A total of 328 alleles were detected with an average value of 29.82 alleles per locus, showing relatively high diversity. Bayesian analysis of genetic structure was used to identify two ancestral populations in the analyses of all three species as well as in a separate set consisting of P. domestica material only. Principal Coordinate Analysis (PCoA) showed that accessions clustered largely in agreement with Bayesian analysis. Neighbor-Joining analysis grouped 71 P. domestica accessions into three clusters with many subgroups that exhibited complex arrangement. Most accessions clustered in agreement with traditional pomological groups, such as common prunes, mirabelle plums and greengages. In this study, the analyses revealed within P. domestica pool valuable local landraces, such as traditional prunes or bluish plums, which seem to be highly interesting from a genetic point of view. Moreover, complementary approaches allowed us to distinguish between the three species and to gain insights into the origin of plum. The results will be instrumental in understanding the diversity of Slovenian plum germplasm, improving the conservation process, recovering local genotypes and enriching existing collections of plant genetic resources.

Comparative Analysis of the Characteristics, Phylogenetic Relationships of the Complete Chloroplast Genome, and Maternal Origin Track of White Poplar Interspecific Hybrid GM107

White poplars are a dominant tree species in natural ecosystems throughout China, where they are also widely planted for agroforestry and industrial uses. However, the phylogenetic relationships among poplars in section Populus have a complex genetic background influenced by frequent hybridization events and, to date, only a few studies have attempted to clarify this background. In this study, we performed de novo assembly of the whole chloroplast (cp) genome of an elite individual GM107 with the size of 156,493 bp, which consists of a large single-copy (LSR) (84,610 bp), a small single-copy (SSC) (16,567 bp), and a pair of inverted repeats (27,658 bp). It comprises 127 genes, including 85 protein-coding genes, 36 tRNAs, and 6 rRNAs. Comparative analysis of the cp genomes was conducted among 7 poplars in section Populus and 4 cp DNA markers with >1% variable sites were detected. We found that Populus alba was the most closely related species to GM107 by phylogenetic analyses. RNA sequencing detected 66 genes that participated in translation, transcription, and photosynthesis. The expression levels of almost all 66 genes were higher in leaves than in other tissues, except for PtatpF and PtatpH. In all tissues, we detected higher transcript abundances of PtndhF, PtpsbA, PtpsbB, Ptrps14, PtatpF, and PtatpH than of other genes. Both cp genome and transcriptome data help understand evolution events in section Populus and unravel the origin of Chinese white poplars, and may contribute to the molecular genetic improvement of wood properties and carbon sink capacities in the breeding of poplars in this section.

Geographic isolation and long-distance gene flow influence the genetic structure of the blue fan palm Brahea armata (Arecaceae)

The formation of the Baja California Peninsula (BCP) has impacted the microevolutionary dynamics of different species in ways that depend on biological traits such as dispersal capacity. Plants with relatively low levels of vagility have exhibited high genetic divergence between the BCP and Continental mainland. Brahea armata (Arecaceae) is a palm species inhabiting the northern part of the BCP and Sonora; its distribution occurs in isolated oases of vegetation. We aimed to evaluate the influence of the formation of the BCP on the genetic structure of B. armata using nuclear microsatellites and chloroplast markers (cpDNA) to compare patterns of genetic diversity and structure with previous published studies. Because gene flow through seeds is usually more limited compared to pollen flow, we expect to find stronger genetic structure at (cpDNA) than at nuclear markers. Moreover, larger genetic structure might also be explained by the smaller effective population size of cpDNA. We analyzed six microsatellite markers and two cpDNA regions. The main results indicated high levels of genetic differentiation among isolated populations located in the BCP, while low genetic differentiation was found between southern populations of the BCP and Sonora, suggesting long distance gene flow. In contrast, chloroplast markers indicated high levels of genetic structure between BCP and Sonora populations, suggesting asymmetrical gene flow between pollen (measured by nuclear microsatellites) and seed (cpDNA markers). This study provides valuable information on genetic diversity of B. armata that can be relevant for conservation and management; and develops microsatellites markers that can be transferred to other Brahea species.

Molecular (ISSR, cp DNA, ITS) and morphological study of the genus Tragopogon L. (Asteraceae)

Tragopogon is an Old World genus with 150 species. Mediterranean, Middle East, and Eastern Europe are the distribution centers of this genus. This genus has 26 species in Iran, of which 11 are endemic. The morphology studies of 32 species and Molecular studies (ISSR, ITS, cp DNA) of 22 species of the genus Tragopogon were investigated. Despite the anatomical and molecular studies done around the world, the exact classification of this genus is not clear due to the high number of secret species, hybridization, polyploidy, and rapid diversification. The purpose of these studies is to classify, determine interspecific relationship in this genus, and determine the important morphological characteristics in taxon differentiation. We conclude that sections of Rubriflori, Sosnowskya, Chromopappus, Majores, Angustissimi, and Krascheninnikovia introduced by the flora of Iranica are confirmed by our morphometry and molecular studies. Section of Profundisulcati in flora Iranica is confirmed based on morphometry data. The Species of T. jesdianus, T. porphyrocephalus, T. rezaiyensis, and T. Stroterocarpus in the flora of Iranica are not classified in any section which we classified in the Rubriflori section. Cp DNA dendrogram is not useful for classification in this genus and Chloroplast sequences are very similar among Tragopogon species. Therefore, the use of cp DNA markers in the classification of this genus is not recommended. The use of ISSR and ITS molecular markers are useful for classifying the genus Tragopogon.

Molecular identity of native coconut (Cocos nucifera L.) germplasm from South Kalimantan, Indonesia

Coconut (Cocos nucifera L.) is an agricultural commodity that is very prospective to be developed in Indonesia and other tropical countries, but its development is constrained by various factors. This study aimed to determine the genetic identity, as well as diversity and relationships of native coconut germplasm from South Kalimantan, Indonesia, using a cpDNA (matK) marker. The results show that this germplasm has a low-level genetic diversity, π% = 0.0258. However, the phylogenetic analysis revealed that native coconut germplasms from this region have separated into different clades, two for Maximum Likelihood and three for Neighbor-Joining, where Genjah Kuning 3 has closely related to an outgroup. Thus, this information is important as a fundamental reference in developing new high-yielding coconut in the future

Molecular phylogeography and species distribution modelling evidence of \u2018oceanic\u2019 adaptation for Actinidia eriantha with a refugium along the oceanic\u2013continental gradient in a biodiversity hotspot

BackgroundRefugia is considered to be critical for maintaining biodiversity; while discerning the type and pattern of refugia is pivotal for our understanding of evolutionary processes in the context of conservation. Interglacial and glacial refugia have been studied throughout subtropical China. However, studies on refugia along the oceanic–continental gradient have largely been ignored. We used a liana Actinidia eriantha, which occurs across the eastern moist evergreen broad-leaved forests of subtropical China, as a case study to test hypotheses of refugia along the oceanic–continental gradient and ‘oceanic’ adaptation.ResultsThe phylogeographic pattern of A. eriantha was explored using a combination of three cpDNA markers and 38 nuclear microsatellite loci, Species distribution modelling and dispersal corridors analysis. Our data showed intermediate levels of genetic diversity [haplotype diversity (hT) = 0.498; unbiased expected heterozygosity (UHE) = 0.510] both at the species and population level. Microsatellite loci revealed five clusters largely corresponding to geographic regions. Coalescent time of cpDNA lineages was dated to the middle Pliocene (ca. 4.03 Ma). Both geographic distance and climate difference have important roles for intraspecific divergence of the species. The Zhejiang-Fujian Hilly Region was demonstrated to be a refugium along the oceanic–continental gradient of the species and fit the ‘refugia in refugia’ pattern. Species distribution modelling analysis indicated that Precipitation of Coldest Quarter (importance of 44%), Temperature Seasonality (29%) and Mean Temperature of Wettest Quarter (25%) contributed the most to model development. By checking the isolines in the three climate layers, we found that A. eriantha prefer higher precipitation during the coldest quarter, lower seasonal temperature difference and lower mean temperature during the wettest quarter, which correspond to ‘oceanic’ adaptation. Actinidia eriantha expanded to its western distribution range along the dispersal corridor repeatedly during the glacial periods.ConclusionsOverall, our results provide integrated evidence demonstrating that the Zhejiang-Fujian Hilly Region is a refugium along the oceanic–continental gradient of Actinidia eriantha in subtropical China and that speciation is attributed to ‘oceanic’ adaptation. This study gives a deeper understanding of the refugia in subtropical China and will contribute to the conservation and utilization of kiwifruit wild resources in the context of climate change.

Homogenized Phylogeographic Structure across the Indo-Burma Ranges of a Large Monoecious Fig, Ficus altissima Blume

As well as bountiful natural resources, the Indo-Burma biodiversity hotspot features high rates of habitat destruction and fragmentation due to increasing human activity; however, most of the Indo-Burma species are poorly studied. The exploration of plants closely associated with human activity will further assist us to understand our influence in the context of the ongoing extinction events in the Anthropocene. This study, based on widely and intensively sampled F. altissima across Indo-Burma and the adjacent south China ranges, using both the chloroplast psbA-trnH spacer and sixteen newly developed nuclear microsatellite markers (nSSRs), aims to explore its spatial genetic structure. The results indicated low chloroplast haplotype diversity and a moderate level of nuclear genetic diversity. Although limited seed flow was revealed by psbA-trnH, no discernible phylogeographic structure was shown due to the low resolution of cpDNA markers and dominance of an ancestral haplotype. From the nSSRs data set, phylogeographic structure was homogenized, most likely due to extensive pollen flow mediated by pollinating fig wasps. Additionally, human cultivation and human-mediated transplanting further confounded the analyses of population structure. No geographic barriers are evident across the large study range, with F. altissima constituting a single population, and extensive human cultivation is likely to have had beneficial consequences for protecting the genetic diversity of F. altissima.

Genetic diversity and structure of the narrow endemic species Crepis granatensis: implications for conservation

In this study, we studied the genetic diversity and population genetic structure of the endangered endemic Crepis granatensis, using amplified fragments length polymorphism (AFLP) and plastid DNA (cpDNA). No genetic divergences were obtained using cpDNA markers. Three primers combinations selected from a total of 12 produced a total of 421 fragments, of which 418 (99.3%) were polymorphic. The total genetic diversity of C. granatensis was moderate (Ht = 0.260). Neís gene diversity ranged from 0.202 to 0.258. The fixation index (Fst) was 0.137, suggesting low to moderate genetic differentiation among populations. The AMOVA analysis revealed that genetic diversity was mainly concentrated among individuals within populations (74%), while 8% was found among populations and 18% among regions. The Bayesian analysis and PCoA identified two genetic clusters: one corresponded to La Sagra population and the other corresponded to the Mágina populations. Based on our genetic results, it is necessary to preserve the evolutionary potential of C. granatensis by protecting all extant populations. Both in situ and ex-situ conservation measures should be considered. Reinforcement, reintroduction, and translocation programmes could be performed if necessary. Finally, such conservation strategies should be considered both in the current recovery plan and management actions for the species.

Long‐term continuity of steppe grasslands in eastern Central Europe: Evidence from species distribution patterns and chloroplast haplotypes

AbstractAimThe steppe grasslands of eastern Central Europe are exceptionally species rich and valuable from a nature conservation point of view. However, their historical biogeography is still poorly understood. Here we use the regional diversity of habitat specialists and chloroplast DNA data to investigate potential long‐term refugia of steppe species in this region.LocationPannonian Basin and adjacent regions; SW Russia.TaxonVascular plants.MethodsAfter identifying habitat specialists of the three main steppe types (meadow steppes, grass steppes and rocky steppes), we compiled their regional presence–absence in grid cells of 75 km × 75 km. We analysed the dependency of habitat specialist diversity to climate, topographic heterogeneity and geographical distance to potential refugia. For genetic analysis, we sampled three or four habitat specialists of each steppe type and used cpDNA markers to investigate intraspecific diversity and geographical distribution of haplotypes. We also tested for correspondence between the number of habitat specialists and haplotype diversity.ResultsClimate and topography explained between 40% and 63% of the variance in habitat specialist diversity. Adding geographical distance to potential refugia increased the explained variance in the models for all steppe types. Chloroplast haplotypes featured a complex pattern across the study area. Several species showed a strong geographical differentiation, suggesting migration waves from multiple refugia with only limited subsequent genetic intermixture. Maximum haplotype diversity in a region showed a better correlation with the number of habitat specialists per steppe type than mean haplotype diversity.Main conclusionsWe can clearly reject the scenario of a late‐Holocene immigration of steppe species from areas outside the Pannonian Basin. Most species must have been present in the region since at least the early Holocene, highlighting the importance of the lower mountain ranges surrounding the Pannonian Basin as long‐term refugia for European steppe species. Dispersal limitation and resulting migration lags seem to have a strong influence on the distribution of steppe species in Central Europe.

Novel Post-Glacial Haplotype Evolution in Birch—A Case for Conserving Local Adaptation

Despite constituting the western-most edge of the population distributions for several native European plants, Ireland has largely been left out of key Europe-wide phylogeographic studies. This is true for birch (Betula pubescens Ehrh. and Betula pendula Roth), for which the genetic diversity has yet to be mapped for Ireland. Here we used eight cpDNA markers (two Restriction Fragment Length Polymorphism (RFLP) and six Simple Sequence Repeat (SSR)) to map the genetic diversity of B. pubescens, B. pendula, and putative hybrid individuals sampled from 19 populations spread cross most of the island of Ireland. Within Ireland, 11 distinct haplotypes were detected, the most common of which (H1) was also detected in England, Scotland, France, and Norway. A moderate level of population structuring (GST = 0.282) was found across Ireland and the genetic diversity of its northern populations was twice that of its southern populations. This indicates that, unlike other native Irish trees, such as oak and alder, post-glacial recolonization by birch did not begin in the south (i.e., from Iberia). Rather, and in agreement with palynological data, birch most likely migrated in from eastern populations in Britain. Finally, we highlight Irish populations with comparatively unique genetic structure which may be included as part of European genetic conservation networks.

Genetic differentiation of indigenous (Quercus robur L.) and late flushing oak stands (Q. robur L. subsp. slavonica (G\xe1yer) M\xe1ty\xe1s) in western Germany (North Rhine-Westphalia)

Slavonian oaks (Quercus robur subsp. slavonica (Gáyer) Mátyás) originating from Croatia have been cultivated in Germany mainly in the Münsterland region of North Rhine-Westphalia since the second half of the nineteenth century. Compared to indigenous pedunculate oak stands in Germany, they are characterised by their late bud burst, but also by their excellent bole shape and faster height growth. Previously, Slavonian pedunculate oaks (= late flushing oaks) were mainly studied at chloroplast (cp) DNA markers in order to determine their geographical origin. The origin of the material is probably the Sava lowland between Zagreb and Belgrade. In the present study, the aim was to genetically differentiate between indigenous Quercus robur and Slavonian oak stands using nuclear DNA markers. For this purpose, we used 20 nuclear Simple Sequence Repeats (nSSRs). A total of 37 pedunculate oak stands (mean: 18.6 samples per population with an age of 95 to 210 years) were examined, of which 21 were characterized as Slavonian late flushing oaks and three stands for which the Slavonian origin was not clear. Maternally inherited chloroplast markers were analysed earlier in all 37 stands to validate their geographic origin. We found that the stands of native pedunculate oaks and Slavonian pedunculate oaks are represented by two genetic clusters which are weakly differentiated. Slavonian oaks (Na = 9.85, Ar = 8.689, Ho = 0.490, He = 0.540) showed similar levels of genetic variation as native oak stands (Na = 7.850, Ar = 7.846, Ho = 0.484, He = 0.526). Differences in growth and phenology and low but consistent genetic differentiation between groups suggest that both taxa represent different ecotypes with specific local adaptations, which are perhaps separated by less overlapping flowering phenologies. The nuclear microsatellite markers in combination with the cpDNA markers are suitable to differentiate between Slavonian and local oak stands.

The Complete Chloroplast Genome of Plukenetia volubilis Provides Insights Into the Organelle Inheritance.

Plukenetia volubilis L. (Malpighiales: Euphorbiaceae), also known as Sacha inchi, is considered a promising crop due to its high seed content of unsaturated fatty acids (UFAs), all of them highly valuable for food and cosmetic industries, but the genetic basis of oil biosynthesis of this non-model plant is still insufficient. Here, we sequenced the total DNA of Sacha inchi by using Illumina and Nanopore technologies and approached a de novo reconstruction of the whole nucleotide sequence and the organization of its 164,111 bp length of the chloroplast genome, displaying two copies of an inverted repeat sequence [inverted repeat A (IRA) and inverted repeat B (IRB)] of 28,209 bp, each one separating a small single copy (SSC) region of 17,860 bp and a large single copy (LSC) region of 89,833 bp. We detected two large inversions on the chloroplast genome that were not presented in the previously reported sequence and studied a promising cpDNA marker, useful in phylogenetic approaches. This chloroplast DNA (cpDNA) marker was used on a set of five distinct Colombian cultivars of P. volubilis from different geographical locations to reveal their phylogenetic relationships. Thus, we evaluated if it has enough resolution to genotype cultivars, intending to crossbreed parents and following marker’s trace down to the F1 generation. We finally elucidated, by using molecular and cytological methods on cut flower buds, that the inheritance mode of P. volubilis cpDNA is maternally transmitted and proposed that it occurs as long as it is physically excluded during pollen development. This de novo chloroplast genome will provide a valuable resource for studying this promising crop, allowing the determination of the organellar inheritance mechanism of some critical phenotypic traits and enabling the use of genetic engineering in breeding programs to develop new varieties.

Population genetics under the Massenerhebung effect: The influence of topography on the demography of Acer morrisonense

AbstractAimThe Massenerhebung effect (Mass elevation effect) refers to heat‐ or wind‐driven altitudinal distribution patterns of temperature‐dependent parameters among massifs with narrower range and lower elevation around peripheral and isolated mountains compared to core and continuous ones. Although common in ecology, this effect is rarely discussed in population genetics. Here, we use genetic markers to reveal population genetic patterns and also test the mountain‐ and sky‐barrier hypotheses relevant to the Massenerhebung distribution pattern of Acer morrisonense in Taiwan's rugged topography and varied local climates.LocationThe alpine and cloud forest of Taiwan.TaxonAcer morrisonense Hayata.MethodsTwo chloroplast DNA (cpDNA) fragments and 17 expressed sequence tag‐simple sequence repeat (EST‐SSR) loci, respectively, from 200 to 286 individuals were used to elucidate the phylogeographic pattern of pollen and seed dispersal of A. morrisonense. These data were combined with ecological niche modeling (ENM) to infer distribution range shifts and refugia. We also correlated the genetic‐divergence indices with spatial factors to clarify latitudinal and altitudinal effects on genetic diversity.ResultsThe incongruent phylogeographic patterns of genetic distributions between nuclear and cpDNA markers indicate unhindered pollen flow but spatially constrained seed dispersal. Taken together with ENM, the genetic pattern further reflects historical colonization from central‐mountain refugia to edges since the Holocene. The Massenerhebung reduces the gene flow by the surrounding mountains and also causes lower genetic diversity compared to central alpine populations.Main conclusionsThis study is the first to reveal the influence of Massenerhebung effect on cpDNA genetic structure of montane trees and reflect the spatial trends of seed dispersal. This population genetic pattern can also be attributed to the demography‐related range shifts with paleoclimate fluctuations under complex mountain topography, supporting the mountain‐barrier hypothesis. The results have important implications for conserving the genetic diversity of species with a wide altitudinal distribution range.

Rediscovery of Pogostemon dielsianus (Lamiaceae, Lamioideae), a rare endemic species from southwestern China, after one century.

Pogostemon dielsianus (Lamiaceae) was described in 1913 based on a single gathering from northwestern Yunnan of China collected in 1905, and thereafter no further collections were observed until 2019. We rediscovered the rare endemic species in Lushui County, Yunnan. Molecular phylogenetic analyses based on four cpDNA markers (rbcL, rps16, psbA-trnH, and trnL-trnF) and the nuclear ribosomal internal transcribed spacer (ITS) region confirmed its infrageneric placement within subg. Pogostemon. Based on observations of the rediscovered population of P. dielsianus, we updated its morphological description, provided an illustration, and discussed its distribution. Under IUCN criteria, the species was categorized as “Critically Endangered (CR)”.

Comparative study on the chloroplast genomes of five Larix species from the Qinghai-Tibet Plateau and the screening of candidate DNA markers

Five Larix species (L. griffithii, L. speciose, L. himalaica, L. kongboensis, and L. potaninii var. australis), have survived on the Qinghai-Tibet Plateau (QTP) under specific climate conditions for decades. The lack of genomic information seriously hinders research on the evolution, conservation and ecology of these Larix resources. In this study, complete chloroplast (cp) genomes of the 5 species were assembled and compared based on next generation sequencing technology combined with polymerase chain reaction validation. The results show that the 5 cp genomes are relatively conservative in size, gene content and arrangement, and border variation. Phylogenetic analysis showed that the species are closely related as well as to seven other species of the same genus. In addition, the 5 cp genomes contained few simple sequence repeats and relatively low nucleotide variability; thus, 12 candidate polymorphic cp DNA markers will be helpful for further research on relevant population genetics. These results will provide valuable genetic information for the conservation, evolution and ecology of these species and their relatives.