Holocene chloroplast genetic variation of shrubs (Alnus alnobetula, Betula nana, Salix sp.) at the siberian tundra‐taiga ecotone inferred from modern chloroplast genome assembly and sedimentary ancient DNA analyses

Abstract

Climate warming alters plant composition and population dynamics of arctic ecosystems. In particular, an increase in relative abundance and cover of deciduous shrub species (shrubification) has been recorded. We inferred genetic variation of common shrub species (Alnus alnobetula, Betula nana, Salix sp.) through time. Chloroplast genomes were assembled from modern plants (n = 15) from the Siberian forest‐tundra ecotone. Sedimentary ancient DNA (sedaDNA; n = 4) was retrieved from a lake on the southern Taymyr Peninsula and analyzed by metagenomics shotgun sequencing and a hybridization capture approach. For A. alnobetula, analyses of modern DNA showed low intraspecies genetic variability and a clear geographical structure in haplotype distribution. In contrast, B. nana showed high intraspecies genetic diversity and weak geographical structure. Analyses of sedaDNA revealed a decreasing relative abundance of Alnus since 5,400 cal yr BP, whereas Betula and Salix increased. A comparison between genetic variations identified in modern DNA and sedaDNA showed that Alnus variants were maintained over the last 6,700 years in the Taymyr region. In accordance with modern individuals, the variants retrieved from Betula and Salix sedaDNA showed higher genetic diversity. The success of the hybridization capture in retrieving diverged sequences demonstrates the high potential for future studies of plant biodiversity as well as specific genetic variation on ancient DNA from lake sediments. Overall, our results suggest that shrubification has species‐specific trajectories. The low genetic diversity in A. alnobetula suggests a local population recruitment and growth response of the already present communities, whereas the higher genetic variability and lack of geographical structure in B. nana may indicate a recruitment from different populations due to more efficient seed dispersal, increasing the genetic connectivity over long distances.

The chloroplast genome of Salix floderusii and characterization of chloroplast regulatory elements

“…The phylogenetic tree showed that most species from the same Section could not cluster into a branch. The main reasons for this phenomenon are as follows: (1) due to the selection of different datasets, the interspecific relationships presented by the phylogenetic tree constructed in this study are slightly inconsistent compared with the results of previous studies; (2) other studies have also shown that Salix is not monophyletic, mainly due to its widespread hybridization, which leading to multiple evolving networks and an unstable morphological classification based on the difference of reproductive organs (Wu et al, 2015); (3) warmer climates were shown to alter the increasing relative abundance of Salix, which showed higher genetic diversity in arctic ecosystems, highlighting the significant role of environmental factors in the evolution of species (Meucci et al, 2021). Therefore, further studies are needed to clarify the classification and phylogeny of Salix.…”

“…To date, the cp genome of Salix has been reported (Chen et al, 2019;Guo et al, 2021;Li et al, 2021;Gulyaev et al, 2022;Wang et al, 2022). The published cp genomic data of these species offer important references for related research (Lauron-Moreau et al, 2015;Zong et al, 2019;Meucci et al, 2021).…”

Structure and Phylogeny of the Curly Birch Chloroplast Genome

“…They can be used to study the direction of introgressive hybridization, which is very common in birch species, by comparing phylogeny based on maternally inherited chloroplast markers with phylogeny based on the bi-parentally inherited nuclear markers. The chloroplast genomes are much more abandoned than nuclear ones and are better preserved in the ancient and environmental DNA that is widely used now for different analyses such as sedimentary analyses that allow inferring the flora structure and related climate in the past ( Meucci et al, 2021 ).…”

The untapped potential of macrofossils in ancient plant DNA research

“…Plant genomes are generally complex, containing 10–80% noncoding repeated elements (Metcalfe & Casane, 2013), and can thus be very large, such as in conifers (Nystedt et al ., 2013; Mosca et al ., 2019). Libraries can be enriched for chloroplast genomes (Meucci et al ., 2021; Schulte et al ., 2021) or exome (protein‐coding) sequences, using probes generated from messenger RNA (Schmid et al ., 2017; Toussaint et al ., 2021), which may significantly reduce sequencing costs. Last but not least, bioinformatic suites have made it possible to apply the whole set of post‐sequencing analytical steps in a glance (Schubert et al ., 2014; Fellows Yates et al ., 2021), including corrections for postmortem damage (Jónsson et al ., 2013) and incorporating uncertainty in the genotype calling for low‐coverage sequence data (Nielsen et al ., 2011).…”