Comparative analysis of genetic diversity in Norway spruce (Picea abies) clonal seed orchards and seed stands

Norway spruce, Picea abies (L.) Karst. is the most important conifer species in Romania and the most planted tree species in the Carpathian Mountains. Here we compare the genetic diversity of four Norway spruce clonal seed orchards and two seed stands located in the Eastern Carpathians. A set of highly polymorphic nuclear microsatellite markers was used. The analysis of genotypic identity of ramets for each Norway spruce clone in all seed orchards indicated that nearly all sampled ramets (97%) were genetically identical. The genetic diversity in seed orchards (He=0.700) was slightly smaller compared to the seed stands (He=0.718). Allelic richness was higher in seed stands (10.874), compared to clonal seed orchards (8.941). The Bayesian analysis indicated a genetic structure with two clusters, one corresponding to the clonal seed orchards and a second one consisting of the two seed stands. Our results provide valuable information for the management of Norway spruce seed orchards in Romania.

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.

Historical Dynamics of Semi-Humid Evergreen Forests in the Southeast Himalaya Biodiversity Hotspot: A Case Study of the Quercus franchetii Complex (Fagaceae)

The Oligocene and Miocene are key periods in the formation of the modern topography and flora of East Asian and Indo-China. However, it is unclear how geological and climatic factors contributed to the high endemism and species richness of this region. The Quercus franchetii complex is widespread in the southeast Himalaya fringe and northern Indo-China with a long evolutionary history. It provides a unique proxy for studying the diversity pattern of evergreen woody lineages in this region since the Oligocene. In this study, we combined chloroplast (cpDNA) sequences, nuclear microsatellite loci (nSSRs), and species distribution modeling (SDM) to investigate the impacts of geological events on genetic diversity of the Q. franchetii complex. The results showed that the initial cpDNA haplotype divergence was estimated to occur during the middle Oligocene (30.7 Ma), which might have been raised by the tectonic activity at this episode to the Miocene. The nSSR results revealed two major groups of populations, the central Yunnan-Guizhou plateau (YGP) group and the peripheral distribution group when K = 2, in responding to the rapid YGP uplift during the late Miocene, which restricted gene flow between the populations in core and marginal areas. SDM analysis indicated that the distribution ranges of the Q. franchetii complex expanded northwards after the last glacial maximum, but the core distribution range in YGP was stable. Our results showed that the divergence of Q. franchetii complex is rooted in the mid-Oligocene. The early geological events during the Oligocene, and the late Miocene may play key roles to restrict seed-mediated gene flow among regions, but the pollen-mediated gene flow was less impacted. The uplifts of the YGP and the climate since LGM subsequently boosted the divergence of the populations in core and marginal areas.

Red foxes harbor two genetically distinct, spatially separated Echinococcus multilocularis clusters in Brandenburg, Germany

Background Alveolar echinococcosis (AE) is a clinically serious zoonosis caused by the fox tapeworm Echinococcus multilocularis. We studied the diversity and the distribution of genotypes of E. multilocularis isolated from foxes in Brandenburg, Germany, and in comparison to a hunting ground in North Rhine-Westphalia. Methods Echinococcus multilocularis specimens from 101 foxes, 91 derived from Brandenburg and 10 derived from North Rhine-Westphalia, were examined. To detect potential mixed infections with different genotypes of E. multilocularis, five worms per fox were analyzed. For genotyping, three mitochondrial markers, namely cytochrome c oxidase subunit 1 (Cox1), NADH dehydrogenase subunit 1 (Nad1), and ATP synthase subunit 6 (ATP6), and the nuclear microsatellite marker EmsB were used. To identify nucleotide polymorphisms, the mitochondrial markers were sequenced and the data were compared, including with published sequences from other regions. EmsB fragment length profiles were determined and confirmed by Kohonen network analysis and grouping of Sammon’s nonlinear mapping with k-means clustering. The spatial distribution of genotypes was analyzed by SaTScan for the EmsB profiles found in Brandenburg. Results With both the mitochondrial makers and the EmsB microsatellite fragment length profile analyses, mixed infections with different E. multilocularis genotypes were detected in foxes from Brandenburg and North Rhine-Westphalia. Genotyping using the mitochondrial markers showed that the examined parasite specimens belong to the European haplotype of E. multilocularis, but a detailed spatial analysis was not possible due to the limited heterogeneity of these markers in the parasite population. Four (D, E, G, and H) out of the five EmsB profiles described in Europe so far were detected in the samples from Brandenburg and North Rhine-Westphalia. The EmsB profile G was the most common. A spatial cluster of the E. multilocularis genotype with the EmsB profile G was found in northeastern Brandenburg, and a cluster of profile D was found in southern parts of this state. Conclusions Genotyping of E. multilocularis showed that individual foxes may harbor different genotypes of the parasite. EmsB profiles allowed the identification of spatial clusters, which may help in understanding the distribution and spread of the infection in wildlife, and in relatively small endemic areas. Graphical Abstract

Unrestricted gene flow between two subspecies of translocated brushtail possums (Trichosurus vulpecula) in Aotearoa New Zealand

Two lineages of brushtail possums (Trichosurus vulpecula) were historically introduced to Aotearoa New Zealand, and these two subspecies have different phenotypic forms. Despite over 100 years of potential interbreeding, they appear to retain morphological differences, which may indicate reproductive isolation. We examined this using population samples from a confined landscape and scored each specimen for phenotype using a number of fur colour traits. This resulted in a bimodal trait distribution expected for segregated grey and black lineages. We also sought evidence for genetic partitioning based on spatial and temporal effects. Genetic structure and rates of genetic mixing were determined using seven neutral, species-specific nuclear microsatellite markers and mitochondrial DNA control region sequence. Genotype analyses indicated high levels of variation and mtDNA sequences formed two major haplogroups. Pairwise tests for population differentiation of these markers found no evidence of subdivision, indicating that these brushtail possums behave as a single randomly mating unit. Despite maintenance of two main colour phenotypes with relatively few intermediates, previous inference of assortative mating and anecdotes of distinct races, our data indicate that New Zealand brushtail possums can freely interbreed, and that in some locations they have formed completely mixed populations where neutral genetic markers are unrelated to phenotype. This has implications for effective pest management towards eradication.

Population genetic structure of raccoons as a consequence of multiple introductions and range expansion in the Boso Peninsula, Japan

The raccoon (Procyon lotor) is an invasive carnivore that invaded various areas of the world. Although controlling feral raccoon populations is important to reduce serious threats to local ecosystems, raccoons are not under rigid population control in Europe and Japan. We examined the D-loop and nuclear microsatellite regions to identify spatially explicit and feasible management units for effective population control and further range expansion retardation. Through the identification of five mitochondrial DNA haplotypes and three nuclear genetic groups, we identified at least three independent introductions, range expansion, and subsequent genetic admixture in the Boso Peninsula. The management unit considered that two were appropriate because two populations have already genetic exchange. Furthermore, when taking management, we think that it is important to monitor DNA at the same time as capture measures for feasible management. This makes it possible to determine whether there is a invasion that has a significant impact on population growth from out of the unit, and enables adaptive management.

Genetic polymorphism of mountain-taiga populations of siberian stone pine in Kusnetsky Alatau

Aim. Study of DNA polymorphism of 7 coenopopulations of Siberian stone pine (Pinus sibirica) growing in theKuznetsk Alatau. Methods. Nuclear microsatellite loci developed for P. sibirica were used as genetic markers. Results. 44 allelic variants were identified from 11 nuclear microsatellite loci, which significantly differ in the composition and frequency of occurrence of the studied P. sibirica coenopopulations. The highest level of allelic diversity is found in loci Ps_80612 and Ps_1502048, where 8 and 7 alleles were identified, respectively. The calculation of the main parameters of genetic diversity showed a relatively low level of polymorphism in the studied samples (NA = 3.078; NE = 1.877; HE = 0.445; HO = 0.401). The assessment of the degree of genetic differences between populations using the Nei genetic distance (DN) showed that, despite the low genetic differentiation (DN varies from 0.019 to 0.061), the differences between them can be traced quite clearly. Conclusions. Differences in the level of genetic polymorphism of P. sibirica is defined by the presence of orographic and phytocoenotic barriers between coenopopulations, as well as a high degree of ecological and anthropogenic extremity of individual growth sites. Keywords: Pinus sibirica, Kuznetsk Alatau, microsatellites, genetic diversity, heterozygosity.

Origins, Diversity and Naturalization of Eucalyptus globulus (Myrtaceae) in California

Eucalyptus globulus is native to southeastern Australia, including the island of Tasmania, but is one of the most widely grown hardwood forestry species in the world and is naturalized on several continents. We studied its naturalization in California, where the species has been planted for over 150 years. We sampled 70 E. globulus trees from 53 locations spanning the entire range of the species in California to quantify the genetic variation present and test whether particular genotypes or native origin affect variation in naturalization among locations. Diversity and native affinities were determined based on six nuclear microsatellite markers and sequences from a highly variable chloroplast DNA region (JLA+). The likely native origin was determined by DNA-based comparison with a range-wide native stand collection. Most of California’s E. globulus originated from eastern Tasmania. Genetic diversity in California is greatly reduced compared with that of the native Australian population, with a single chloroplast haplotype occurring in 66% of the Californian samples. Throughout California, the degree of E. globulus naturalization varies widely but was not associated with genotype or native origin of the trees, arguing that factors such as local climate and disturbance are more important than pre-introduction evolutionary history.

Phylogeography of high Andean killifishes Orestias (Teleostei: Cyprinodontidae) in Caquena and Lauca sub-basins of the Altiplano (Chile): mitochondrial and nuclear analysis of an endangered fish

From the early Miocene, the uplift of the Andes Mountains, intense volcanic activity and the occurrence of successive periods of dryness and humidity would have differentially influenced the modification of Altiplano watersheds, and consequently the evolutionary history of the taxa that live there. We analyzed Orestias populations from the Caquena and Lauca Altiplanic sub-basins of northern Chile to determine their genetic differentiation and relationship to their geographical distribution using mitochondrial (D-loop) and nuclear (microsatellite) molecular markers and to reconstruct its biogeographic history on these sub-basins. The results allowed reconstructing and reevaluating the evolutionary history of the genus in the area; genic diversity and differentiation together with different founding genetic groups suggest that Orestias have been spread homogeneously in the study area and would have experienced local disturbances that promoted isolation and diversification in restricted zones of their distribution.

Assessment of the Structure and Diversity of Latvian Acer platanoides Populations Using Cross-Species Nuclear Microsatellite Markers

Acer platanoides L. (Norway maple) is the most widespread native maple species in Europe, with a distribution from south and central Europe to northern Europe and Scandinavia. Acer platanoides is widespread throughout the territory of Latvia, and is mainly found in mixed broadleaf and conifer stands. The genetic diversity and differentiation of Latvian A. platanoides populations was analysed. Sampled populations were located throughout the territory of Latvia, and were selected to represent a range of ecological conditions, with differing levels of anthropogenic impact. A total of 496 individuals from 21 populations were analysed with eight microsatellite markers, which were developed from related Acer species. The obtained molecular data revealed a moderate level of polymorphism, and the analysed Latvian A. platanoides populations were moderately differentiated. This study provides an initial assessment of the genetic diversity and differentiation of Latvian A. platanoides populations, and is also one of the first reports of the analysis of A. platanoides populations using microsatellite markers. The results can be utilised to define A. platanoides genetic resource stands to ensure conservation of a wide range of germplasm.