Roe deer population structure in a highly fragmented landscape

Northern Belgium (Flanders) is one of the most densely populated and urbanized regions in Europe. Many species are therefore likely to suffer from anthropogenic pressure and habitat destruction and fragmentation. Although many large mammals are recolonizing in parts of Europe, including Belgium, due to adaptation, a relaxation of persecution and habitat restoration, we have little actual data concerning the effects of landscape features on their population structure. We analysed the genetic structure of discrete roe deer (Capreolus capreolus) populations in the Eastern part of Flanders, with special emphasis on the impact of habitat fragmentation and anthropogenic barriers. The sampled populations were clearly genetically differentiated. Genetic structure could be explained by purely distance-based landscape modelling, but a simpler model focusing solely on barrier effects of large transportation infrastructure explained nearly as much genetic variance. In contrast, analyses based on least-cost landscape modelling failed to yield a significant effect. Overall, the results suggest considerable landscape-level effects of transportation infrastructure.     

Modelling tree diversity in a highly fragmented tropical montane landscape

Aim There is an urgent need for conservation in threatened tropical forest regions. We explain and predict the spatial variation of α (i.e. within plot) and β (i.e. between plot) tree diversity in a tropical montane landscape subjected to a high deforestation rate. A major aim is to demonstrate the potential of a method that combines data from multiple sources (field data, remote sensing imagery and GIS) to evaluate and monitor forest diversity on a broad scale over large unexplored areas. Location The study covered an area of c. 3500 km² in the Highlands of Chiapas, southern Mexico. Methods We identified all of the tree species within 204 field plots (1000 m² each) and measured different environmental, human disturbance‐related, and spatial variables using remote sensing and GIS data. To obtain a predictive model of α tree diversity (Fisher's alpha) based on selected explanatory variables, we used a generalized linear model with a gamma error distribution. Mantel tests of matrix correspondence were used to determine whether similarities in floristic composition were correlated with similarities in the explanatory variables. Finally, we used a method that combines α and β tree diversity to define priority areas for conservation. Results The model for α tree diversity explained 44% of the overall variability, of which most was mainly related to precipitation, temperature, NDVI, and canopy (all relationships were positive, and quadratic for temperature and NDVI). There were no spatially structured regional factors that were ignored. Similarity in tree composition was correlated positively with climate and NDVI. Main conclusions The results were used to: (1) identify and assign conservation priority of unexplored areas that have high tree diversity, and (2) demonstrate the importance of several vegetation formations in the region's biodiversity. The method we present can be particularly useful in assessing regional needs and in developing local conservation strategies in poorly surveyed (and often at risk) tropical areas worldwide, where accessibility is usually limited.     

Effect of highly fragmented DNA on PCR.

We characterized the behavior of polymerase chain reactions (PCR) using degraded DNA as a template. We first demonstrated that fragments larger than the initial template fragments can be amplified if overlapping fragments are allowed to anneal and extend prior to routine PCR. Amplification products increase when degraded genomic DNA is pretreated by polymerization in the absence of specific primers. Secondly, we measured nucleotide uptake as a function of template DNA degradation. dNTP incorporation initially increases with increasing DNA fragmentation and then declines when the DNA becomes highly degraded. We demonstrated that dNTP uptake continues for >10 polymerization cycles and is affected by the quality and quantity of template DNA and by the amount of substrate dNTP. These results suggest that although reconstruction of degraded DNA may allow amplification of large fragments, reconstructive polymerization and amplification polymerization may compete. This was confirmed in PCR where the addition of degraded DNA reduced the resultant product. Because terminal deoxynucleotidyl transferase activity of Taq polymerase may inhibit 3' annealing and restrict the length of template reconstruction, we suggest modified PCR techniques which separate reconstructive and amplification polymerization reactions.     

Effect of spatial connectivity on host resistance in a highly fragmented natural pathosystem

Both theory and experimental evolution studies predict migration to influence the outcome of antagonistic coevolution between hosts and their parasites, with higher migration rates leading to increased diversity and evolutionary potential. Migration rates are expected to vary in spatially structured natural pathosystems, yet how spatial structure generates variation in coevolutionary trajectories across populations occupying the same landscape has not been tested. Here, we studied the effect of spatial connectivity on host evolutionary potential in a natural pathosystem characterized by a stable Plantago lanceolata host network and a highly dynamic Podosphaera plantaginis parasite metapopulation. We designed a large inoculation experiment to test resistance of five isolated and five well‐connected host populations against sympatric and allopatric pathogen strains, over 4 years. Contrary to our expectations, we did not find consistently higher resistance against sympatric pathogen strains in the well‐connected populations. Instead, host local adaptation varied considerably among populations and through time with greater fluctuations observed in the well‐connected populations. Jointly, our results suggest that in populations where pathogens have successfully established, they have the upper hand in the coevolutionary arms race, but hosts may be better able to respond to pathogen‐imposed selection in the well‐connected than in the isolated populations. Hence, the ongoing and extensive fragmentation of natural habitats may increase vulnerability to diseases.     

DNA metabarcoding uncovers dispersal-constrained arthropods in a highly fragmented restoration setting

Degraded areas are often restored through active revegetation; however, recolonization by animals is rarely engineered. Recolonization may be rapid for species with strong dispersal abilities. However, poor dispersers, such as many flightless arthropods, may struggle to recolonize newly restored sites. Actively reintroducing or “rewilding” arthropods may therefore be necessary to facilitate recolonization and restoration of arthropod communities and the ecological functions they perform. However, active interventions are rare. The purpose of this study was twofold. First, we asked whether potential source remnant arthropod communities were dispersal-constrained and struggling to recolonize restoration sites. Second, we tested whether reintroducing entire arthropod communities from remnant populations would help dispersal-constrained species establish during farmland ecological restoration in southern Australia. Rewilding was conducted in summer 2018 by transplanting leaf litter, soil, and entire communities contained within it from remnant source populations into geographically isolated restoration sites, which were paired with untreated controls (n = 6 remnant, rewilding transplant, and control sites). We collected leaf litter and extracted arthropod communities 19 months after the initial rewilding event, then sequenced mite, springtail, and insect communities using a metabarcoding approach. Within all groups, community similarity decreased with spatial distance between sites, suggesting significant dispersal barriers. However, only mite communities showed a strong response to rewilding, which was expressed as increased compositional similarity toward remnant sites and greater species richness relative to controls. Our results demonstrate that many arthropod species may struggle to recolonize geographically isolated restoration sites and that full community restoration requires active interventions via rewilding.     

Employing a highly fragmented,weedy coral species in reef restoration

A major determinant in reef restoration programs is the choice of species employed. In this paper, we concentrate on the potential use of Montipora digitata (Dana, 1846), a highly fragmented and weedy coral species, for reef restoration and for recreation of reef physiognomy in Bolinao, The Philippines, under the ‘gardening concept’. Coral ramets (n = 1960) were reared in a shallow lagoon nursery for 1 year and then, the resulting nursery-grown colonies were transplanted onto denuded reef knolls at two different sites and according to three transplantation designs (grid design with high or low density and patch design). The nursery grown ramets, which had initially exhibited a 99% survivorship, were reduced to 87% by a super typhoon. Low detachment rates, low mortality (<1% both) and low bleaching (<3% over most months), have been indicating good nursery conditions for corals. Monitoring transplanted colonies for over 15 months showed no significant differences between the sites or among the three different transplantation designs. The major events of mortality and detachment were documented during the first 3 months post-transplantation and in the wake of a bleaching event. M. digitata transplants exhibited rapid growth (a 384% increase in ecological volume) and frequent fragmentation. Some fragments remained by their colonies of origin entangled in the attached branches, while other fragments fell onto the surrounding sandy substrate, forming M. digitata ‘beds’ around the knolls. In both, nursery and transplanted corals, creation of complex 3D structures was followed by recruitment of juvenile fishes into aggregations. Above results reveal that employing fast growing, weedy and easily fragmenting branching species, which are also considered as ‘modifier species’, in reef restoration may result in a fast regeneration of reef physiognomy. Instead of ‘copying’ natural processes, reef managers should therefore concentrate on recovering the reef's ability for self-maintenance.     

Genome rearrangement distances and gene order phylogeny in gamma-Proteobacteria

Genome rearrangements have been studied in 30 gamma-proteobacterial complete genomes by comparing the order of a reduced set of genes on the chromosome. This set included those genes fulfilling several characteristics, the main ones being that an ortholog was present in every genome and that none of them had been acquired by horizontal gene transfer. Genome rearrangement distances were estimated based on either the number of breakpoints or the minimal number of inversions separating two genomes. Breakpoint and inversion distances were highly correlated, indicating that inversions were the main type of rearrangement event in gamma-Proteobacteria. In general, the progressive increase in sequence-based distances between genome pairs was associated with the increase in their rearrangement-based distances but with several groups of distances not following this pattern. Compared with free-living enteric bacteria, the lineages of Pasteurellaceae were evolving, on average, to relatively higher rates of between 2.02 and 1.64, while the endosymbiotic bacterial lineages of Buchnera aphidicola and Wigglesworthia glossinidia were evolving at moderately higher rates of 1.38 and 1.35, respectively. Because we know that the rearrangement rate in the Bu. aphidicola lineage was close to zero during the last 100-150 Myr of evolution, we deduced that a much higher rate took place in the first period of lineage evolution after the divergence of the Escherichia coli lineage. On the other hand, the lineage of the endosymbiont Blochmannia floridanus did present an almost identical rate to free-living enteric bacteria, indicating that the increase in the genome rearrangement rate is not a general change associated with bacterial endosymbiosis. Phylogenetic reconstruction based on rearrangement distances showed a different topology from the one inferred by sequence information. This topology broke the proposed monophyly of the three endosymbiotic lineages and placed Bl. floridanus as a closer relative to E. coli than Yersinia pestis. These results indicate that the phylogeny of these insect endosymbionts is still an open question that will require the development of specific phylogenetic methods to confirm whether the sisterhood of the three endosymbiotic lineages is real or a consequence of a long-branch attraction phenomenon.     

Population genetics of Mioscirtus wagneri,a grasshopper showing a highly fragmented distribution

The genetic consequences of population fragmentation and isolation are major issues in conservation biology. In this study we analyse the genetic variability and structure of the Iberian populations of Mioscirtus wagneri, a specialized grasshopper exclusively inhabiting highly fragmented hypersaline low grounds. For this purpose we have used seven species‐specific microsatellite markers to type 478 individuals from 24 localities and obtain accurate estimates of their genetic variability. Genetic diversity was relatively low and we detected genetic signatures suggesting that certain populations of M. wagneri have probably passed through severe demographic bottlenecks. We have found that the populations of this grasshopper show a strong genetic structure even at small geographical scales, indicating that they mostly behave as isolated populations with low levels of gene flow among them. Thus, several populations can be regarded as independent and genetically differentiated units which require adequate conservation strategies to avoid eventual extinctions that in highly isolated localities are not likely to be compensated for with the arrival of immigrants from neighbouring populations. Overall, our results show that these populations probably represent the ‘fragments’ of a formerly more widespread population and highlight the importance of protecting Iberian hypersaline environments due to the high number of rare and endangered species they sustain.     

Importance of riparian remnants for frog species diversity in a highly fragmented rainforest

Tropical forests undergo continuous transformation to other land uses, resulting in landscapes typified by forest fragments surrounded by anthropogenic habitats. Small forest fragments, specifically strip-shaped remnants flanking streams (referred to as riparian remnants), can be particularly important for the maintenance and conservation of biodiversity within highly fragmented forests. We compared frog species diversity between riparian remnants, other forest fragments and cattle pastures in a tropical landscape in Los Tuxtlas, Mexico. We found similar species richness in the three habitats studied and a similar assemblage structure between riparian remnants and forest fragments, although species composition differed by 50 per cent. Frog abundance was halved in riparian remnants compared with forest fragments, but was twice that found in pastures. Our results suggest that riparian remnants play an important role in maintaining a portion of frog species diversity in a highly fragmented forest, particularly during environmentally stressful (hot and dry) periods. In this regard, however, the role of riparian remnants is complementary, rather than substitutive, with respect to the function of other forest fragments within the fragmented forest.     

Nestedness-resultant community disassembly process of extinction debt in a highly fragmented semi-natural grassland

There are two major processes of species disassembly after landscape changes: non-random loss of species resulting in nested assemblages and species replacement resulting in spatial species turnover. Although time-lagged responses of species to landscape change have been widely recognized, few studies have empirically evaluated which of these two processes is more closely related to extinction debt (i.e., postponed species extinction following habitat loss). This study aimed to understand the underlying processes of extinction debt by partitioning β-diversity into components of species nestedness and species turnover. We measured grassland species richness at three spatial extents in a highly fragmented semi-natural grassland landscape in Japan. Dissimilarity-based β-diversity was partitioned into two components (i.e., nestedness-resultant dissimilarity [β_sne] and turnover-resultant dissimilarity [β_sim]), which were further analyzed using principal coordinates analyses (PCoA). The relationships between the variability of PCoA axis 1 scores and the current and past habitat proportions were evaluated. A significant positive relationship between current grassland species richness and past (i.e., the 1910s) grassland proportion was found at the largest spatial extent. The first axis of PCoA based on β_sne showed significant correlation with past habitat proportions, whereas the PCoA axis based on β_sim showed no significant correlation with either the current or past habitat proportions. A non-random loss of grassland species represented by nestedness underlay the extinction debt found at the landscape level. There is a chance of predicting the loss of species from the nested ranks of species which likely reflects the gradient of species vulnerability to historical landscape changes.     

Reduced dispersal propensity in the wingless waterstrider Aquarius najas in a highly fragmented landscape

Dispersal behaviour of animals in fragmented habitats has generated intensive theoretical attention but empirical data on the evolution of dispersal are still relatively scarce. Theory predicts reduced dispersal propensity in small and isolated habitat patches. We tested these predictions in the waterstrider Aquarius najas, a wingless species with special habitat demands. Flightlessness constrains insect dispersal and as a stream specialist A. najas cannot survive on still water. Lakes therefore represent a dispersal barrier for this species. We measured dispersal propensity of the waterstrider A. najas which originated from ten fragmented populations. In the experiment, we transplanted laboratory-grown individuals to the field. We did not find differences between sex in dispersal propensity. However, we found that waterstriders that originated from small and isolated patches moved less than individuals from large and more continuous habitats. This suggests that the cost of dispersal over hostile surrounding habitats may be high. We conclude that a low likelihood of dispersal in A. najas is an adaptation to small and isolated stream habitats.     

Isolation determines patterns of species presence in highly fragmented landscapes

In fragmented landscapes, changes in habitat availability, patch size, shape and isolation may affect survival of local populations. Proposing efficient conservation strategies for such species relies initially on distinguishing the particular effects of those factors. To address these issues, we investigated the occurrence of 3 bird species in fragmented Brazilian Atlantic Forest landscapes. Playback techniques were used to collect presence/absence data of these species inside 80 forest patches, and incidence models were used to infer their occupancy pattern from landscape spatial structure. The relative importance of patch size, shape and surrounding forest cover and isolation was assessed using a model selection approach based on maximum likelihood estimation. The presence of all species was in general positively affected by the amount of surrounding habitat and negatively affected by inter‐patch distances. The joint effects of patch size and the surrounding landscape characteristics were important determinants of occupancy for two species. The third species was affected only by forest cover and mean patch isolation. Our results suggest that local species presence is in general more influenced by the isolation from surrounding forests than by patch size alone. We found evidence that, in highly fragmented landscapes, birds that can not find patches large enough to settle may be able to overcome short distances through the matrix and include several nearby patches within their home‐ranges to complement their resource needs. In these cases, patches must be defined as functionally connected habitat networks rather than mere continuous forest segments. Bird conservation strategies in the Atlantic forest should focus on increasing patch density and connectivity, in order to implement forest networks that reduce the functional isolation between large remnants with remaining core habitat.     

Molecular phylogeny and rearrangement of rRNA genes in Rickettsia species.

It has previously been observed that Rickettsia prowazekii has an unusual arrangement of the rRNA genes. In this species, the three rRNA genes, 16S (rrs), 23S (rrl), and 5S (rrf), are not linked in the typical arrangements for bacteria. Rather, the 16S rRNA gene has been separated from the 23S and 5S rRNA gene cluster, and the 23S rRNA gene is preceded by a gene which codes for methionyl-tRNAf(Met) formyltransferase (fmt). In this study, we screened the genus Rickettsia for the fmt-rrl motif in order to examine the phylogenetic depth of this unusual rRNA gene organization. A rearranged operon structure was observed in Rickettsia conorii, Rickettsia parkeri, Rickettsia sibirica, Rickettsia rickettsii, Rickettsia amblyomii, Rickettsia montana, Rickettsia rhipicephali, Rickettsia australis, Rickettsia akari, Rickettsia felis, Rickettsia canada, and Rickettsia typhi. There is also evidence for a divided operon in Rickettsia belli, but in this species, the fmt gene could not be identified upstream of the 23S rRNA gene. In order to place the rearrangement event in the evolutionary history of the Rickettsia, phylogenetic analyses were performed based on the fmt-rrl spacer regions and the 23S rRNA genes. Based on these phylogenies, we suggest that the genomic rearrangement of the rRNA genes preceded the divergence of the typhus group and the spotted fever group Rickettsia. The unique organization of the 23S rRNA genes provides a simple diagnostic tool for identification of Rickettsia species.     

On the evolutionary descent of organisms and organelles: a global phylogeny based on a highly conserved structural core in small subunit ribosomal RNA

To probe the earliest evolutionary events attending the origin of the five known genome types (archaebacterial, eubacterial, nuclear, mitochondrial and plastid), we have analyzed sequences corresponding to a ubiquitous, highly conserved core of secondary structure in small subunit rRNA. Our results support (i) the existence of three primary lineages (archaebacterial, eubacterial, and nuclear), (ii) a specific eubacterial ancestry for plastids and mitochondria (plant, animal, fungal), and (iii) an endosymbiotic, evolutionary origin of the two types of organelle from within distinct groups of eubacteria (blue-green algae (cyanobacteria) in the case of plastids, nonphotosynthetic aerobic bacteria in the case of mitochondria). In addition, our analysis suggests (iv) a biphyletic origin of mitochondria, with animal and fungal mitochondria branching together but separately from plant mitochondria, and (v) a monophyletic origin of plastids. The method described here provides a powerful and generally applicable molecular taxonomic approach towards a global phylogeny encompassing all organisms and organelles.