Lars Opgenoorth

Tree endurance on the Tibetan Plateau marks the world’s highest known tree line of the Last Glacial Maximum

Because of heterogeneous topographies, high-mountain areas could harbor a significant pool of cryptic forest refugia (glacial microrefugia unrecognized by palaeodata), which, as a result of poor accessibility, have been largely overlooked. The juniper forests of the southern Tibetan Plateau, with one of the highest tree lines worldwide, are ideal for assessing the potential of high-mountain areas to harbor glacial refugia. Genetic evidence for Last Glacial Maximum (LGM) endurance of these microrefugia is presented using paternally inherited chloroplast markers. Five-hundred and ninety individuals from 102 populations of the Juniperus tibetica complex were sequenced at three polymorphic chloroplast regions. Significant interpopulation differentiation and phylogeographic structure were detected (G(ST) = 0.49, N(ST) = 0.72, N(ST) > G(ST), P < 0.01), indicating limited among-population gene flow. Of 62 haplotypes recovered, 40 were restricted to single populations. These private haplotypes and overall degrees of diversity were evenly spread among plateau and edge populations, strongly supporting the existence of LGM microrefugia throughout the present distribution range, partly well above 3500 m. These results mark the highest LGM tree lines known, illustrating the potential significance of high-mountain areas for glacial refugia. Furthermore, as the close vicinity of orographic rear-edge and leading-edge populations potentially allows gene flow, surviving populations could preserve the complete spectrum of rear-edge and leading-edge adaptations.

Ecological plant epigenetics: Evidence from model and non-model species, and the way forward

Growing evidence shows that epigenetic mechanisms contribute to complex traits, with implications across many fields of biology. In plant ecology, recent studies have attempted to merge ecological experiments with epigenetic analyses to elucidate the contribution of epigenetics to plant phenotypes, stress responses, adaptation to habitat, and range distributions. While there has been some progress in revealing the role of epigenetics in ecological processes, studies with non-model species have so far been limited to describing broad patterns based on anonymous markers of DNA methylation. In contrast, studies with model species have benefited from powerful genomic resources, which contribute to a more mechanistic understanding but have limited ecological realism. Understanding the significance of epigenetics for plant ecology requires increased transfer of knowledge and methods from model species research to genomes of evolutionarily divergent species, and examination of responses to complex natural environments at a more mechanistic level. This requires transforming genomics tools specifically for studying non-model species, which is challenging given the large and often polyploid genomes of plants. Collaboration among molecular geneticists, ecologists and bioinformaticians promises to enhance our understanding of the mutual links between genome function and ecological processes.

Molecular phylogeography and evolutionary history of Picea likiangensis in the Qinghai-Tibetan Plateau inferred from mitochondrial and chloroplast DNA sequence variation

Abstract  The aim of the present study was to examine the phylogeographic and evolutionary history of Picea likiangensis, a dominant species of the conifer forests in the eastern declivity of the Qinghai–Tibetan Plateau. We collected 422 individuals from 42 natural populations of three major varieties classified under this species. In conifers, mitochondrial (mt) DNA and chloroplast (cp) DNA dispersed by seeds or pollen experience very different levels of gene flow. To this end, we examined the sequence variation of two mtDNA fragments (nad5 intron 1 and nad1 intron b/c) and three cpDNA fragments (trnL–trnF, trnS–trnG and nadhK/C). We found that cpDNA probably introgressed from P. purpurea into remote populations of P. likiangensis through long‐distance dispersal. Multiple refugia seem to have been maintained for P. likiangensis during the Last Glacial Maximum because the cpDNA and mtDNA haplotypes recovered were fixed in the different regions. Postglacial expansions were only detected at the distributional edges of this species where a single cpDNA or mtDNA haplotype was fixed in adjacent populations. However, genetic imprints of postglacial expansions from these two sets of markers were different in the western and southeastern regions, which may result from the long‐distance dispersal of the cpDNA, as well as its fast lineage sorting during intraspecific divergences. Analysis of molecular variance further suggested that genetic differentiation between the three varieties is higher at cpDNA markers than at mtDNA markers, which supports the previous viewpoint that cpDNA markers with a high rate of gene flow may be more effective in delimitating closely related taxa. Together, the results of the present study highlight the evolutionary complexity of a widely distributed species owing to interactions among local and edge expansion, long‐distance dispersal, and intraspecific divergences at two sets of DNA genomes with different rates of gene flow.

Into the Himalayan Exile: The Phylogeography of the Ground Beetle Ethira clade Supports the Tibetan Origin of Forest-Dwelling Himalayan Species Groups

The Himalayan mountain arc is one of the hotspots of biodiversity on earth, and species diversity is expected to be especially high among insects in this region. Little is known about the origin of the Himalayan insect fauna. With respect to the fauna of high altitude cloud forests, it has generally been accepted that Himalayan lineages are derived from ancestors that immigrated from Western Asia and from adjacent mountainous regions of East and Southeast Asia (immigration hypothesis). In this study, we sought to test a Tibetan Origin as an alternative hypothesis for groups with a poor dispersal ability through a phylogeographic analysis of the Ethira clade of the genus Pterostichus. We sequenced COI mtDNA and the 18S and 28S rDNA genes in 168 Pterostichini specimens, including 46 species and subspecies of the Ethira clade. In our analysis, we were able to show that the Ethira clade is monophyletic and, thus, represents a Himalayan endemic clade, supporting endemism of two of the basal lineages to the Central Himalaya and documenting large distributional gaps within the phylogeographic structure of the Ethira clade. Furthermore, the molecular data strongly indicate very limited dispersal abilities of species and subspecies of these primary wingless ground beetles. These results are consistent with the hypothesis of a Tibetan Origin, which explains the evolution, diversity and distribution of the Himalayan ground beetle Ethira clade much more parsimoniously than the original immigration hypothesis.

Genetic support for perglacial survival of Juniperus communis L. in Central Europe

In contrast to many plant species, which had not survived in Central Europe during the last glacial maximum (LGM) and therefore recolonized from various southern or eastern refugia, we put forward the hypothesis that Juniperus communis L., a species with large ecological amplitude, could have survived in a cold steppe-like biome of the LGM throughout Central Europe. Fossils from locations above the 50th latitude dating back to 15 000—11 000 BP lead to this assumption. However, there is an absolute lack of records for the LGM. We used DNA markers to obtain genetic support for our hypothesis. If common juniper had survived in Central Europe and had not recolonized this area from diverse outside refugia, we would expect the gene pool of J. communis being imprinted in a different way than what is common for classic Holocene ‘recolonizers’. The latter tend to exhibit profound large-scale isolation-by-distance effects where genetic distances are positively correlated with geographic distances. Using AFLP (Amplified Fragment Length Polymorphism) markers in 23 modern common juniper populations sampled throughout Europe, we found a high level of genetic differentiation. However, there are no underlying phylogeographic signals or any other meaningful geographic genetic structures. Consistent with a scenario of perglacial survival there is no correlation between genetic and geographic distances as a result from Mantel tests.The present study again demonstrates the power of genetic tools when fossil records are not available. It contributes to an increasing knowledge about species distribution during unfavourable climatic conditions.

Identification and characterization of microsatellite marker in the tetraploid Juniperus tibetica Kom. using next generation sequencing

Juniperus tibetica Kom. is a tetraploid endemic tree species of the southern Tibetan Plateau. For this species ten microsatellite markers were developed using next generation sequencing. To characterize these loci a sample of 14 juniper individuals from seven populations covering large parts of the species’ distribution range was analyzed. All loci were polymorphic, ranging from two to 15 alleles per locus. Expected heterozygosity was estimated using the program TETRASAT, and ranged from 0.20 to 0.90 across loci. These markers will be used in ongoing population genetic studies to evaluate the potential genetic depauperation of the highly fragmented forest remains on the southern Tibetan Plateau and to propose strategies for conservation management.

Molecular bases for parallel evolution of translucent bracts in an alpine “glasshouse” plant Rheum alexandrae (Polygonaceae)

Parallel evolution provides an excellent framework to infer the genetic bases of adaptive traits and understand the importance of natural selection in shaping current biodiversity. The upper leaves of the “glasshouse plants” transform into translucent bracts that show numerous adaptions in alpine habitats. It remains unknown whether similar molecular changes occur under the parallel bract evolution of different “glasshouse” species. In this study, we compared the results on phenotypic and physiological differences and presented the results of cDNA‐AFLP analyses of transcriptional changes between translucent bracts and normal leaves in Rheum alexandrae. We also examined the homologous candidate genes with the same expression changes between this species and another “glasshouse” species, R. nobile. We found that bracts of R. alexandrae are similar to those of R. nobile in anatomical features: chloroplasts have degenerated and chlorophyll contents are greatly reduced, which suggests that foliar photosynthetic functions in bracts of both species have been reduced or totally altered. Among the 6000 transcript‐derived fragments (TDFs) in bracts and leaves of R. alexandrae, 420 (7%) were differentially expressed (up‐ or downregulated) between bracts and normal leaves. There were a total of 13 homologous TDFs with the same expression changes between R. alexandrae and the previously studied R. nobile. Except for the two that were not functionally annotated, eight of the homologous TDFs were found to be involved in stress and defense responses whereas the other three were related to photosynthesis. The up‐ or downregulation of these candidate genes was highly congruent with anatomical characteristics and adaptive functions of the bracts found for “glasshouse” plants. These findings suggested that the “glasshouse” phenotypes may have common molecular bases underlying their parallel evolution of similar adaptive functions and highlighted the importance of the natural selection in producing such phenotypes.

The Quaternary evolutionary history, potential distribution dynamics, and conservation implications for a Qinghai–Tibet Plateau endemic herbaceous perennial, Anisodus tanguticus (Solanaceae)

Abstract Various hypotheses have been proposed about the Quaternary evolutionary history of plant species on the Qinghai–Tibet Plateau (QTP), yet only a handful of studies have considered both population genetics and ecological niche context. In this study, we proposed and compared climate refugia hypotheses based on the phylogeographic pattern of Anisodus tanguticus (three plastid DNA fragments and nuclear internal transcribed spacer regions from 32 populations) and present and past species distribution models (SDMs). We detected six plastid haplotypes in two well‐differentiated lineages. Although all haplotypes could be found in its western (sampling) area, only haplotypes from one lineage occurred in its eastern area. Meanwhile, most genetic variations existed between populations (FST = 0.822). The SDMs during the last glacial maximum and last interglacial periods showed range fragmentation in the western area and significant range contraction in the eastern area, respectively, in comparison with current potential distribution. This species may have undergone intraspecific divergence during the early Quaternary, which may have been caused by survival in different refugia during the earliest known glacial in the QTP, rather than geological isolation due to orogenesis events. Subsequently, climate oscillations during the Quaternary resulted in a dynamic distribution range for this species as well as the distribution pattern of its plastid haplotypes and nuclear genotypes. The interglacial periods may have had a greater effect on A. tanguticus than the glacial periods. Most importantly, neither genetic data nor SDM alone can fully reveal the climate refugia history of this species. We also discuss the conservation implications for this important Tibetan folk medicine plant in light of these findings and SDMs under future climate models. Together, our results underline the necessity to combine phylogeographic and SDM approaches in future investigations of the Quaternary evolutionary history of species in topographically complex areas, such as the QTP.

Isolated Mountain Forests in Central Asian Deserts: A Case Study from the Govi Altay, Mongolia

The role of isolated mountain forests in Central Asian drylands has been the subject of a number of recent studies. The present paper examines islands of birch and willow forest in the Mongolian Govi Altay Mountains. Using vegetation surveys, dendrochronological studies and charcoal findings, it is attempted to assess the present-day ecological state of the vegetation as well as the environmental history and ecological trends. One of the three forests studied seems to be expanding rapidly due to declining levels of utilization under climatically favourable conditions. The other forests however, situated about 350 km to the south-east of the former, are threatened by consistently high levels of anthropogenic pressure. Based on ecological evidence, the forest islands’ role as witnesses of a once coherent forest belt that may have been retreating since the mid-Holocene is discussed.

Linking dendroecology and association genetics in natural populations: stress responses archived in tree rings associate with SNP genotypes in silver fir ( Abies alba Mill.)

Genetic association studies in forest trees would greatly benefit from information on the response of trees to environmental stressors over time, which can be provided by dendroecological analysis. Here, we jointly analysed dendroecological and genetic data of surviving silver fir trees to explore the genetic basis of their response to the iconic stress episode of the 1970s and 1980s that led to large‐scale forest dieback in Central Europe and has been attributed to air pollution. Specifically, we derived dendrophenotypic measures from 190 trees in the Bavarian Forest that characterize the resistance, resilience and recovery during this growth depression, and in the drought year in 1976. By focusing on relative growth changes of trees and by standardizing the dendrophenotypes within stands, we accounted for variation introduced by micro‐ and macroscale environmental differences. We associated the dendrophenotypes with single nucleotide polymorphisms (SNPs) in candidate genes using general linear models (GLMs) and the machine learning algorithm random forest with subsequent feature selection. Most trees at our study sites experienced a severe growth decline from 1974 until the mid‐1980s with minimum values during the drought year. Fifteen genes were associated with the dendrophenotypes, including genes linked to photosynthesis and drought stress. With our study, we show that dendrophenotypes can be a powerful resource for genetic association studies that permit to account for micro‐ and macroenvironmental variation when data are derived from natural populations. We call for a wider collaboration of dendroecologists and forest geneticists to integrate individual tree‐level dendrophenotypes in genetic association studies.