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.

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)”.

Adaptive Evolution and Addressing the Relevance for Genetic Improvement of Sago Palm Commodity

Adaptive evolution implies evolutionary shifts within an organism which make it suitable and adaptable for its environment. Genetic resources of sago palm (Metroxylon sagu Rottb.) populations in Indonesia were explicated as follows: (1) Characters of sago palm in Indonesia were shown varied based on cpDNA markers and large variation based on RAPD markers. (2) Variation of starch production of sago palm correlated with Wx genes variation, (3) Distances barrier and geographies isolation in line of sago palm dispersions in Indonesia (4) Characteristics of genetic were observed does not related with vernacular names those were given by local people (5) Papua islands, Indonesia territorial is proposed the center of sago palm diversities, (6) Papua islands, Sulawesi islands and Kalimantan islands will be the provenance of the diversities (7) Genetic improvement of sago palm might enhanced using molecular marker that link to interesting genes by developing marker-assisted breeding.

Notholirion campanulatum is co-specific with N. bulbuliferum (Liliaceae) based on morphology and molecular data

Notholirion campanulatum and N. bulbuliferum are parapatrically distributed in the Qinghai-Tibetan Plateau and adjacent regions, however, their relationship has been controversial for a long time. In this study, six morphological characters including colour of corolla/ovary/bulblet, corolla shape, tepal size, and pollen form, together with nuclear ITS and four cpDNA markers (matK, ndhA, ndhG-I, and petL-G) were selected to perform a comprehensive analysis on 23 populations. Our results indicate that morphological characters of N. campanulatum and N. bulbuliferum are congruent with each other, and the phylogenetic analysis revealed that N. campanulatum closely nested with N. bulbuliferum. Therefore, we propose that these two species should be regarded as synonyms.

Complete Chloroplast Genome of Japanese Larch (Larix kaempferi): Insights into Intraspecific Variation with an Isolated Northern Limit Population

Research Highlights: The complete chloroplast genome for eight individuals of Japanese larch, including from the isolated population at the northern limit of the range (Manokami larch), revealed that Japanese larch forms a monophyletic group, within which Manokami larch can be phylogenetically placed in Japanese larch. We detected intraspecific variation for possible candidate cpDNA markers in Japanese larch. Background and Objectives: The natural distribution of Japanese larch is limited to the mountainous range in the central part of Honshu Island, Japan, with an isolated northern limit population (Manokami larch). In this study, we determined the phylogenetic position of Manokami larch within Japanese larch, characterized the chloroplast genome of Japanese larch, detected intraspecific variation, and determined candidate cpDNA markers. Materials and Methods: The complete genome sequence was determined for eight individuals, including Manokami larch, in this study. The genetic position of the northern limit population was evaluated using phylogenetic analysis. The chloroplast genome of Japanese larch was characterized by comparison with eight individuals. Furthermore, intraspecific variations were extracted to find candidate cpDNA markers. Results: The phylogenetic tree showed that Japanese larch forms a monophyletic group, within which Manokami larch can be phylogenetically placed, based on the complete chloroplast genome, with a bootstrap value of 100%. The value of nucleotide diversity (π) was calculated at 0.00004, based on SNP sites for Japanese larch, suggesting that sequences had low variation. However, we found three hyper-polymorphic regions within the cpDNA. Finally, we detected 31 intraspecific variations, including 19 single nucleotide polymorphisms, 8 simple sequence repeats, and 4 insertions or deletions. Conclusions: Using a distant genotype in a northern limit population (Manokami larch), we detected sufficient intraspecific variation for the possible candidates of cpDNA markers in Japanese larch.

Analyses of Hybrid Viability across a Hybrid Zone between Two Alnus Species Using Microsatellites and cpDNA Markers

Diploid Alnus glutinosa s. str. and autotetraploid A. rohlenae form a narrow hybrid zone in a study area in southern Serbia, which results in triploid hybrid formation. The vast majority of previous studies have been focused on studies of maternal plants, but the offspring resulting from their crossing have not been much studied. Here, we use the variability of microsatellites and chloroplast DNA between these species and their putative hybrids to create an overall picture of the development of the hybrid zone and its predicted type. To elucidate the gene transfer within both species, the origins of individual ploidies and especially the role of triploid hybrids, a germination experiment was carried out linked with a flow cytometry study of the resulting seedlings. The tension zone model seems to offer the most adequate explanation of our observations, with selection against triploid hybrids and the spatial positioning of the hybrid zone. Despite selection against them, the triploid hybrids play an important role in the exchange of genes between the two species and therefore serve as a bridge for introgression. The presence of fertile triploids is essential for enriching the haplotype diversity between these species and for the development of new genetic lineages.

Biosystematic study of the genus Lallemantia (Lamiaceae): species delimitation and relationship

Lallemantia (Lamiaceae) is a small genus with 5 species. In general, little biosystematics and molecular study has been performed on the genus Lallemantia. Moreover, the studies used only some of the species; none of them has considered all 5 species as a whole in one specific approach. Therefore, the species inter-relationship or nexus in the genus is not thoroughly probed. The present study investigated the molecular phylogeny and species relationship of all five species in the genus Lallemantia, using ribosomal protein L16 and the multilocus ISSR markers. It also compared their morphometric, anatomical and seed results. The species were efficaciously delimited by the morphological, anatomical and seed characters, as well as by ISSR and cpDNA markers. The PCA (Principal components analysis) plot of the species based upon the morphological characters, the MDS (Multidimensional Scaling) plot of the species based on the nutlet and anatomical characters, the NJ (neighbor joining) tree plot of ISSR dataand the ML tree of cpDNA revealed closer affinity between L. iberica and L. canescens and L. peltata was placed at some distance from these species. The phylogenetic trees displayed monophyly of the genus Lallemantia. The Bayesian Evolutionary Analysis by Sampling Trees (BEAST) analysis unveiled that the studied Lallemantia species started to diverge about 25 million years ago.

High Genetic Diversity and Low Differentiation in Michelia shiluensis, an Endangered Magnolia Species in South China

Research Highlights: This study is the first to examine the genetic diversity of Michelia shiluensis (Magnoliaceae). High genetic diversity and low differentiation were detected in this species. Based on these results, we discuss feasible protection measures to provide a basis for the conservation and utilization of M. shiluensis. Background and Objectives: Michelia shiluensis is distributed in Hainan and Guangdong province, China. Due to human disturbance, the population has decreased sharply, and there is thus an urgent need to evaluate genetic variation within this species in order to identify an optimal conservation strategy. Materials and Methods: In this study, we used eight nuclear single sequence repeat (nSSR) markers and two chloroplast DNA (cpDNA) markers to assess the genetic diversity, population structure, and dynamics of 78 samples collected from six populations. Results: The results showed that the average observed heterozygosity (Ho), expected heterozygosity (He), and percentage of polymorphic loci (PPL) from nSSR markers in each population of M. shiluensis were 0.686, 0.718, and 97.92%, respectively. For cpDNA markers, the overall haplotype diversity (Hd) was 0.674, and the nucleotide diversity was 0.220. Analysis of markers showed that the genetic variation between populations was much lower based on nSSR than on cpDNA (10.18% and 77.56%, respectively, based on an analysis of molecular variance (AMOVA)). Analysis of the population structure based on the two markers shows that one of the populations (DL) is very different from the other five. Conclusions: High genetic diversity and low population differentiation of M. shiluensis might be the result of rich ancestral genetic variation. The current decline in population may therefore be due to human disturbance rather than to inbreeding or genetic drift. Management and conservation strategies should focus on maintaining the genetic diversity in situ, and on the cultivation of seedlings ex-situ for transplanting back to their original habitat.

Development of novel Quercus rubra chloroplast genome CAPS markers for haplotype identification

Our main objective was to generate cost-effective chloroplast (cp) DNA markers that are easy to apply and to score. In combination with already published cpSSR markers they should increase haplotype resolution in populations. To discover new cpDNA markers, we sequenced 87-97 % of the entire chloroplast genome (except the second inverted repeat) of 8 trees representing different regions of the Quercus rubra L. natural range with 4,030X-6,297X coverage and assembled the genome sequences using the publicly available chloroplast genome of Quercus rubra L. as a reference. In total, 118 single nucleotide polymorphisms (SNPs) and 107 insertions or deletions (indels) were detected, and 15 cleaved amplified polymorphic sequence (CAPS) markers were developed for Q. rubra. Using these new markers together with five chloroplast microsatellite or simple sequence repeat (cpSSR) markers, we identified 10 haplotypes in our diversity panel of 19 Q. rubra populations. Specifically, two haplotypes based only on the cpSSR markers could now be separated in five haplotypes. These markers are useful to assess haplotype diversity with high resolution and are also transferable to a closely related species, Quercus ellipsoidalis E. J. Hill.