Can the use of zooplankton dormant stages from natural wetlands contribute to restoration of mined wetlands?

Wetlands are among the most diverse environments on the planet and are strongly threatened by human activities. Their restoration and/or mitigation of human impacts, therefore, relies on information that can aid to the management of impacted wetlands so that they return to a (semi-) natural state. We investigate in this study the relationship between dormant stages of zooplankton and clay removal in areas subjected to mining. We evaluate whether a gradual increase in topsoil addition from donor natural wetlands to the sediment of mined wetlands influenced the zooplankton community. Eight wetlands were sampled in the Sinos River floodplain, four natural and four mined. In the laboratory, four field sediment samples were incubated for zooplankton hatching in five treatments comprising sediments from: mined wetlands, natural wetlands, and three treatments containing mined sediments added with low (5%), medium (20%) and high (40%) quantities of sediment from natural wetlands. Hatching consisted of 61 individuals distributed across eight zooplankton taxa. Copepod nauplii were the most abundant (31.1%) followed by Epiphanes sp. (29.5%) and Ovalona glabra (16.4%). While natural wetlands provided 42.6% of the hatched zooplankton, mined wetlands had just 6.5%. Zooplankton richness and abundance were higher in natural wetland sediments compared with mined and added sediment wetlands. To some degree, the sediment soil donation from natural to mined wetlands was considered viable. As long as prior studies are performed to test the size and quality of the dormant banks present in the sediment of candidate donor wetlands, sediment from donor wetlands may aid in the establishment of a more diverse community in disturbed systems.

     

Effective gene flow in a historically fragmented area at the southern edge of silver fir (<Emphasis Type="Italic">Abies alba</Emphasis> Mill.) distribution

Fragmented populations at the edges of a species’ distribution can be highly exposed to the loss of genetic variation, unless sufficient gene flow maintains their genetic connectivity. Gene movements leading to successful establishment of external gametes (i.e. effective gene flow) into fragmented populations can solely be assessed by investigating the origin of natural regeneration. This study is focused on studying gene flow patterns in two silver fir stands in Central Apennines, where the species has a highly fragmented distribution. By using nuclear and chloroplast microsatellite markers, we investigated genetic variation, fine-scale spatial genetic structure, effective gene flow rates and large-scale connectivity characterizing both stands. Similar levels of genetic variation and low genetic differentiation between stands (F _ST = 0.005) and across generations were found, coupled with low inbreeding and weak to absent SGS in the adult cohort (Sp < 0.003). On the other hand, substantial differences between the two stands in terms of gene flow rates were observed. Irrespective of the parentage approach used, higher gene flow rates were found in the stand located at the upper silver fir altitudinal limit, especially for seed-mediated gene flow (0.79 in the upper stand vs. 0.48 in the lower stand). Conversely, the lower stand was characterized by a higher reproductive dominance of local adults. Our findings suggest that, despite similar levels of genetic variation and generally high gene flow rates, different processes may be acting on the two stands, reflecting varying ecological conditions.     

Aspects of Marker/Reporter Stability and Selectivity in Soil Microbiology

Based on several experiences of microbial release using genetically modified Rhizobium leguminosarum, we have highlighted a number of aspects related to the suitability of introduced markers such as resistance to mercury and β-galactosidase activity, the latter serving the function of high-expression level reporter gene obtained by the introduction of a synthetic promoter conferring strong inducible expression in Gram-negative bacteria. In vitro expression and in vivo performances of the chosen examples have been followed in model strains comparing gene dosage and expression levels. The technical possibility of unambiguously monitoring the marked GMM has been evaluated in medium- and long-term experiments carried out both in microcosms and soil, also including the presence of the plant symbiotic host. Marker stability, regardless the nature of the gene, was shown to be dependent on the location of the genetic modification and on its degree of gene expression regulation. Reporter strength was found to be an advantage allowing the distinction of marker-bearing bacterial while negatively affecting their genetic stability. Plasmid-borne regulated reporters were found to be stable up to the stages of rhizosphere colonization, but were more critically selected against upon symbiotic host invasion.     

Chloroplast DNA polymorphism reveals little geographical structure in Castanea sativa Mill. (Fagaceae) throughout southern European countries

The distribution of haplotypic diversity of 38 European chestnut (Castanea sativa Mill.) populations was investigated by PCR/RFLP analysis of regions of the chloroplast and mitochondrial genomes in order to shed light on the history of this heavily managed species. The rapid expansion of chestnut starting from 3000 years ago is strongly related to human activities such as agricultural practice. This demonstrates the importance of human impact, which lasted some thousands of years, on the present-day distribution of the species. No polymorphism was detected for the single mitochondrial analysed region, while a total of 11 different chloroplast (cp) haplotypes were scored. The distribution of the cpDNA haplotypes revealed low geographical structure of the genetic diversity. The value of population subdivision, as measured by GSTc, is strikingly lower than in the other species of the family Fagaceae investigated. The actual distribution of haplotypic diversity may be explained by the strong human impact on this species, particularly during the Roman civilization of the continent, and to the long period of cultivation experienced during the last thousand years.     

Genetic diversity and phylogeographic analysis of Pinus leiophylla: a post-glacial range expansion

Aim Mexico is a centre of diversity for species of the genus Pinus, most of which have restricted geographical distributions. An exception is Pinus leiophylla Schiede and Deppe, which is widely distributed throughout most of Mexico’s mountainous regions. We attempt to reconstruct the phylogeographic history of this species, in order to determine if its current broad distribution is associated with major events of environmental change that occurred during the Quaternary. Location Coniferous forests in Sierra Madre Occidental, Eje Volcánico Transversal and Sierra Montañosa del Norte de Oaxaca, Mexico. Methods A total of 323 individuals of both P. leiophylla var. leiophylla and P. leiophylla var. chihuahuana sampled from 22 populations were screened for variation at six paternally inherited chloroplast DNA microsatellite markers (cpSSR). In addition to haplotypic diversity estimates and neutrality tests, the following clustering methods were employed: principal components analysis (PCA), analysis of molecular variance (AMOVA), spatial analysis of molecular variance (SAMOVA), haplotype network and a technique similar to Croizat’s panbiogeographical method of individual and generalized tracks. Results The combination of mutations at the six microsatellites yielded a total of 92 different haplotypes. The percentage of shared haplotypes between varieties (P. leiophylla var. leiophylla and P. leiophylla var. chihuahuana) was only 2.2%. The average haplotypic diversity for the species was H = 0.760. PCA and SAMOVA indicate the presence of four main genetic clusters. The estimated divergence time between the two most frequent haplotypes was between 75,000 and 110,000 years. Significantly large negative F_s values suggest that most of the sampled populations are currently expanding. Individual and generalized tracks identified three potential zones that may have harboured ancestral populations of P. leiophylla and from which the expansion of this species started, as well as two secondary contact zones between the two varieties. Main conclusions The results indicate that one of the three potential areas hypothesized to have harboured ancestral populations of P. leiophylla may be related to the origin of P. leiophylla var. chihuahuana, while the other two may be related to the origin of P. leiophylla var. leiophylla. The current broad distribution of P. leiophylla is probably associated with its strong colonization ability.     

Can population genetic structure be predicted from life-history traits?

Population genetic structure is a key parameter in evolutionary biology. Earlier comparative studies have shown that genetic structure depends on species ecological attributes and life-history traits, but species phylogenetic relatedness had not been accounted for. Here we reevaluate the relationships between genetic structure and species traits in seed plants. Each species is characterized by a set of life-history and ecological features as well as by its geographic range size, its heterozygote deficit, and its genetic structure at nuclear and organelle markers to distinguish between pollen- and seed-mediated gene flow. We use both a conventional regression approach and a method that controls for phylogenetic relationships. Once phylogenetic conservatism and covariation among traits are taken into account, genetic structure is shown to be related with only a few synthetic traits, such as mating system for nuclear markers and seed dispersal mode or geographic range size for organelle markers. Along with other studies on invasiveness or rarity, our work illustrates the fact that predicting the fate of species across a broad taxonomic assemblage on the basis of simple traits is rarely possible, a testimony of the highly contingent nature of evolution.     

Range-wide phylogeography and gene zones in Pinus pinaster Ait. revealed by chloroplast microsatellite markers

Some 1339 trees from 48 Pinus pinaster stands were characterized by five chloroplast microsatellites, detecting a total of 103 distinct haplotypes. Frequencies for the 16 most abundant haplotypes (p(k) > 0.01) were spatially interpolated over a lattice made by 430 grid points. Fitting of spatially interpolated values on raw haplotype frequencies at the same geographical location was tested by regression analysis. A range-wide 'diversity map' based on interpolated haplotype frequencies allowed the identification of one 'hotspot' of diversity in central and southeastern Spain, and two areas of low haplotypic diversity located in the western Iberian peninsula and Morocco. Principal component analysis (PCA) carried out on haplotypes frequency surfaces allowed the construction of a colour-based 'synthetic' map of the first three PC components, enabling the detection of the main range-scale genetic trends and the identification of three main 'gene pools' for the species: (i) a 'southeastern' gene pool, including southeastern France, Italy, Corsica, Sardinia, Pantelleria and northern Africa; (ii) an 'Atlantic' gene pool, including all the western areas of the Iberian peninsula; and (iii) a 'central' gene pool, located in southeastern Spain. Multivariate and AMOVA analyses carried out on interpolated grid point frequency values revealed the existence of eight major clusters ('gene zones'), whose genetic relationships were related with the history of the species. In addition, demographic models showed more ancient expansions in the eastern and southern ranges of maritime pine probably associated to early postglacial recolonization. The delineation of the gene zones provides a baseline for designing conservation areas in this key Mediterranean pine.     

Genetic structure in the Genista ephedroides complex (Fabaceae) and implications for its present distribution

The present investigation investigated the genetic structure of a monophyletic group of endemic species belonging to the Genista ephedroides species group: G. bocchierii, G. cilentina, G. demarcoi, G. dorycnifolia, G. ephedroides, G. gasparrinii, G. insularis, G. numidica, G. tyrrhena subsp. tyrrhena, G. tyrrhena subsp. pontiana and G. valsecchiae, all distributed in the western Mediterranean. Using seven plastid microsatellites, 16 populations (288 individuals) were screened. Haplotype fixation was observed in particular for most of the Tyrrhenian taxa (i.e. G. bocchierii, G. cilentina, G. demarcoi, G. ephedroides, G. gasparrinii, G. insularis, G. tyrrhena subsp. tyrrhena and G. valsecchiae). However, although genetic diversity within populations was low [(h_S = 0.132 (± 0.056)], a high level of total plastid DNA diversity [h_T = 0.866 (± 0.042)] was detected, and analysis of molecular variance indicated that variation is almost exclusively expressed among populations (95.25%). The plastid microsatellites identify two groups of taxa, one including Sardinian taxa and populations of G. tyrrhena subsp. pontiana and the other including two subgroups, one of which includes Sicilian/Aeolian elements and the other with G. numidica/G. cilentina and G. dorycnifolia. Results allow us to consider G. cilentina as originating by recent anthropogenic dispersal and G. tyrrhena subsp. pontiana as a possible stabilized hybrid between local plants and members of the Sardinian group contributing the maternal lineage. The evolutionary history of the group possibly results from the effects of ancient events fostering geodispersal and range contraction, followed by more recent long‐range dispersal or geodispersion over Pleistocenic land bridges. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 177 , 607–618.     

A new scenario for the quaternary history of European beech populations: palaeobotanical evidence and genetic consequences

Here, palaeobotanical and genetic data for common beech (Fagus sylvatica) in Europe are used to evaluate the genetic consequences of long-term survival in refuge areas and postglacial spread. Four large datasets are presented, including over 400 fossil-pollen sites, 80 plant-macrofossil sites, and 450 and 600 modern beech populations for chloroplast and nuclear markers, respectively. The largely complementary palaeobotanical and genetic data indicate that: (i) beech survived the last glacial period in multiple refuge areas; (ii) the central European refugia were separated from the Mediterranean refugia; (iii) the Mediterranean refuges did not contribute to the colonization of central and northern Europe; (iv) some populations expanded considerably during the postglacial period, while others experienced only a limited expansion; (v) the mountain chains were not geographical barriers for beech but rather facilitated its diffusion; and (vi) the modern genetic diversity was shaped over multiple glacial-interglacial cycles. This scenario differs from many recent treatments of tree phylogeography in Europe that largely focus on the last ice age and the postglacial period to interpret genetic structure and argue that the southern peninsulas (Iberian, Italian and Balkan) were the main source areas for trees in central and northern Europe.