Population size and major valleys explain microsatellite variation better than taxonomic units for caribou in western Canada

Identifying conservation units below the species level is becoming increasingly important, particularly when limited resources necessitate prioritization for conservation among such units. This problem is exemplified with caribou, a mammal with a circum-Arctic distribution that is exposed to a broad spectrum of ecological conditions, but is also declining in many parts of its range. We used microsatellite markers to evaluate the suitability of existing intra-specific taxonomic designations to act as population units for conservation and contrasted this with landscape features that were independent of taxonomy. We also quantified the relationship between genetic differentiation and subpopulation size, a factor that has been under-represented in landscape genetic research. Our data set included three subspecies and three ecotypes of caribou that varied in population size by five orders of magnitude. Our results indicated that genetic structure did not correspond to existing taxonomic designation, particularly at the level of ecotype. Instead, we found that major valleys and population size were the strongest factors associated with substructure. There was a negative exponential relationship between population size and F(ST) between pairs of adjacent subpopulations, suggesting that genetic drift was the mechanism causing the structure among the smallest subpopulations. A genetic assignment test revealed that movement among subpopulations was a fraction of the level needed to stabilize smaller subpopulations, indicating little chance for demographic rescue. Such results may be broadly applicable to landscape genetic studies, because population size and corresponding rates of drift have the potential to confound interpretations of landscape effects on population structure.     

Repeated trans-watershed hybridization among haplochromine cichlids (Cichlidae) was triggered by Neogene landscape evolution

The megadiverse haplochromine cichlid radiations of the East African lakes, famous examples of explosive speciation and adaptive radiation, are according to recent studies, introgressed by different riverine lineages. This study is based on the first comprehensive mitochondrial and nuclear DNA dataset from extensive sampling of riverine haplochromine cichlids. It includes species from the lower River Congo and Angolan (River Kwanza) drainages. Reconstruction of phylogenetic hypotheses revealed the paradox of clearly discordant phylogenetic signals. Closely related mtDNA haplotypes are distributed thousands of kilometres apart and across major African watersheds, whereas some neighbouring species carry drastically divergent mtDNA haplotypes. At shallow and deep phylogenetic layers, strong signals of hybridization are attributed to the complex Late Miocene/Early Pliocene palaeohistory of African rivers. Hybridization of multiple lineages across changing watersheds shaped each of the major haplochromine radiations in lakes Tanganyika, Victoria, Malawi and the Kalahari Palaeolakes, as well as a miniature species flock in the Congo basin (River Fwa). On the basis of our results, introgression occurred not only on a spatially restricted scale, but massively over almost the whole range of the haplochromine distribution. This provides an alternative view on the origin and exceptional high diversity of this enigmatic vertebrate group.     

Mosaic cycles in agricultural landscapes of Northwest Europe

Mosaic cycles were originally understood as cyclical regeneration phases in forests. In this review, we shall examine how far the concept can be extended towards cyclical mosaics of habitat quality in patterned landscapes as a special case of ‘dynamic landscapes’. We will concentrate on habitats and plants in European temperate agricultural landscapes and grasslands in particular. Mosaic cycles of habitat quality are characterised by spatiotemporal shifts between disturbance and secondary succession. We found evidence for mosaic cycles in traditional agricultural systems, modern crop farming, and in recent conservation management. The relevant disturbance parameters to describe land-use drivers of mosaic cycles are spatial extent, frequency, and magnitude (biomass loss). Land-use-related drivers are usually regular and deterministic in space and time, with the exception of year-round grazing by free-ranging large herbivores. Fluctuating soil resources such as water and nutrients in interaction with climate variability add a stochastic component to these (land-use-related) drivers. The proportion of deterministic and stochastic components and their autocorrelation in time and space divides purely deterministic mosaic cycles from purely stochastic dynamic landscapes. In a second part, we briefly review plant life-history traits that may facilitate survival of plants in mosaic cycles of habitat quality. Theoretical studies emphasise (i) dispersal functions for extinction and recolonisation processes of metapopulations, (ii) storage effects as a component of buffered population growth in response to temporal fluctuations of habitat quality, and (iii) competitive ability in metacommunities. We propose a simple scheme relating these functions to the temporal and spatial correlation of patterned landscapes. There are only a very limited number of field studies available that give some support for the proposed scheme. We provide perspectives for further research in this field.     

Horizontal gene transfer in microbial genome evolution

Horizontal gene transfer is the collective name for processes that permit the exchange of DNA among organisms of different species. Only recently has it been recognized as a significant contribution to inter-organismal gene exchange. Traditionally, it was thought that microorganisms evolved clonally, passing genes from mother to daughter cells with little or no exchange of DNA among diverse species. Studies of microbial genomes, however, have shown that genomes contain genes that are closely related to a number of different prokaryotes, sometimes to phylogenetically very distantly related ones. (Doolittle et al., 1990, J. Mol. Evol. 31, 383-388; Karlin et al., 1997, J. Bacteriol. 179, 3899-3913; Karlin et al., 1998, Annu. Rev. Genet. 32, 185-225; Lawrence and Ochman, 1998, Proc. Natl. Acad. Sci. USA 95, 9413-9417; Rivera et al., 1998, Proc. Natl. Acad. Sci. USA 95, 6239-6244; Campbell, 2000, Theor. Popul. Biol. 57 71-77; Doolittle, 2000, Sci. Am. 282, 90-95; Ochman and Jones, 2000, Embo. J. 19, 6637-6643; Boucher et al. 2001, Curr. Opin., Microbiol. 4, 285-289; Wang et al., 2001, Mol. Biol. Evol. 18, 792-800). Whereas prokaryotic and eukaryotic evolution was once reconstructed from a single 16S ribosomal RNA (rRNA) gene, the analysis of complete genomes is beginning to yield a different picture of microbial evolution, one that is wrought with the lateral movement of genes across vast phylogenetic distances. (Lane et al., 1988, Methods Enzymol. 167, 138-144; Lake and Rivera, 1996, Proc. Natl. Acad. Sci. USA 91, 2880-2881; Lake et al., 1999, Science 283, 2027-2028).     

Mammal diversity and environment evolution during the Plio-Pleistocene in East Africa

Human evolution began in East Africa four million years ago, with a transition from an arboreal state to a more terrestrial one. This evolution seems to be correlated with a large environmental change in East Africa around 2.5 m.y. due to a major climatic change leading to drier and cooler conditions. Cenogram analysis (a graphical representation of community structure) can be used to reconstruct the vegetation cover at a regional scale, and to infer the changing climatic conditions. Using cenogram sequences of different sites along the Rift Valley, we were able to determine the regional ecological context in which mammals and hominids have evolved in East Africa during the last 3 million years. Between 3.5 and 2 m.y., during a general climatic change, successive faunas of South Tanzania reflect the progressive opening of their environment. In contrast around Lake Turkana a mosaic of isolated dry and wet habitats were present throughout this period. At this time, the Rift seems to have been spatially structured in several basins isolated from one other, and isolated faunas experienced separate speciation events (particularly with the appearance ofHomo genus). After 2 m.y., the disappearance of the isolating barriers on one hand, and a regional increase in aridity, on the other hand, led to more homogenous faunas arising throughout the region. Replacements of mammal species occurred (especiallyHomo erectus replacingHomo habilis) and several others mammal species, including australopithecines, disappeared during this same period.     

1930—2010年额济纳三角洲土地利用景观格局变化

干旱区内陆河流域下游的土地利用、景观格局对水资源调配具有重要意义.本文基于1930、1961、1990、2000、2010年土地利用数据,分析黑河流域下游额济纳三角洲土地利用和景观格局的变化.结果表明: 2010年,研究区沙漠化土地面积占总面积的73.4%,其次是草地,占20.8%.1930—2010年,土地利用变化最明显的特征是草地、农田和建设用地增加;各土地类型间转化突出表现为农田和建设用地的转入;土地利用景观破碎度和多样性增加,优势度降低,且具有明显水源依赖性和地域性差异;土地利用变化使景观趋于均匀、多样、破碎.基于其驱动因素及生态环境效应的探讨,针对人-水-生态协调问题,提出“有计划生态移民、限制农田面积、发展集约式精准农业、增加生态用水比例”的建议.     

Landscape genetics of the blotched tiger salamander (Ambystoma tigrinum melanostictum)

The field of landscape genetics has great potential to identify habitat features that influence population genetic structure. To identify landscape correlates of genetic differentiation in a quantitative fashion, we developed a novel approach using geographical information systems analysis. We present data on blotched tiger salamanders (Ambystoma tigrinum melanostictum) from 10 sites across the northern range of Yellowstone National Park in Montana and Wyoming, USA. We used eight microsatellite loci to analyse population genetic structure. We tested whether landscape variables, including topographical distance, elevation, wetland likelihood, cover type and number of river and stream crossings, were correlated with genetic subdivision (F(ST)). We then compared five hypothetical dispersal routes with a straight-line distance model using two approaches: (i) partial Mantel tests using Akaike's information criterion scores to evaluate model robustness and (ii) the BIOENV procedure, which uses a Spearman rank correlation to determine the combination of environmental variables that best fits the genetic data. Overall, gene flow appears highly restricted among sites, with a global F(ST) of 0.24. While there is a significant isolation-by-distance pattern, incorporating landscape variables substantially improved the fit of the model (from an r2 of 0.3 to 0.8) explaining genetic differentiation. It appears that gene flow follows a straight-line topographic route, with river crossings and open shrub habitat correlated with lower F(ST) and thus, decreased differentiation, while distance and elevation difference appear to increase differentiation. This study demonstrates a general approach that can be used to determine the influence of landscape variables on population genetic structure.     

Critical threshold effects of benthiscape structure on stream herbivore movement

In landscape ecology, substantial theoretical progress has been made in understanding how critical threshold levels of habitat loss may result in sudden changes in landscape connectivity to animal movement. Empirical evidence for such thresholds in real systems, however, remains scarce. Streambed landscapes provide a strong testing ground for studying critical thresholds because organisms are faced with substantial environmental heterogeneity while attempting to overcome the physical force of water. In this study, I report on the results from a series of experiments investigating the influence of habitat abundance and current velocity on the movement dynamics of two stream herbivores (caddisfly larva Agapetus boulderensis and snail Physa sp.) that differ substantially in how they perceive landscape structure. Specifically, I ask whether critical thresholds to herbivore movement exist in streambed landscapes. By exploiting the pattern recognition capabilities of artificial neural networks, I found that the rate, sinuosity and directionality of movement by Agapetus and Physa varied nonlinearly according to the abundance of habitat patches, current velocity and habitat-current interaction. Both the study organisms exhibited threshold responses to habitat abundance, yet the location and slope of these thresholds differed between species and with respect to different current velocities. These results suggest that a critical threshold in functional connectivity (i.e. the connection of habitat patches by dispersal) is not an inherent property of the landscape, but in fact emerges from the interplay of species' interactions with landscape structure. Moreover, current velocity interacted with habitat abundance to elicit strong upstream-oriented movement for both the species. This suggests that dispersing individuals may be polarized in the upstream direction and therefore functional connectivity is not equal in all directions. Such results highlight the need for future research addressing the sources of variability of critical threshold effects in ecological phenomena.     

Large-scale spatial and temporal dynamics of the vulnerable and highly mobile superb parrot

Aim To investigate the spatial and temporal dynamics of the vulnerable and highly mobile superb parrot (Polytelis swainsonii) across its range in south‐eastern mainland Australia. Location South‐eastern Australia (27°–37° S latitude and 141°–151° E longitude). Methods We used generalized additive models (GAMs) to model time‐specific bird atlas occurrence data against time‐specific plant productivity data, plus a range of environmental predictor variables. We then examined the effects of environmental variables on the temporal and spatial patterns of predicted abundance and distribution of the superb parrot using a correlative mapping approach. Results Key findings from GAM analysis were: (1) there was a strong positive relationship between abundance and plant productivity in all regions, but (2) the response of abundance to other predictor variables often differed between regions. Correlative mapping predictions of the abundance and distribution of the superb parrot also indicated that: (1) predicted abundance varied through time and space, (2) predicted abundance sometimes decreased in all regions, but at other times some regions had high abundance when others had low, and (3) changes in plant productivity (and therefore climate) were associated with this variation. Main conclusion The superb parrot favours productive landscapes that are also favoured for agriculture. Movements appear to be associated with seasonal and year to year climate variability. Thus, variation in the recorded abundance of the superb parrot may mask population trends, suggesting that existing population estimates are unreliable. Also, high abundances in some areas, and at some times, may reflect deteriorating habitat conditions elsewhere rather than species recovery. Temporal variability in the distribution of the superb parrot makes it difficult to identify specific drought refugia. Consequently, through time, as key habitat continues to deteriorate, the species will become increasingly vulnerable and threatened. Whole‐landscape habitat conservation and restoration strategies are therefore needed to sustain superb parrot populations in the long‐term.     

Anuran abundance and persistence in agricultural landscapes during a climatic extreme

Climate change in concert with habitat loss and degradation are major threats to global biodiversity. As part of climate change, the occurrence of extreme climatic events is expected to increase. Agricultural intensification has led to the increased homogeneity of agricultural habitats and declines in farmland species diversity. We investigated the abundance of common frog Rana temporaria populations in boreal farmlands in relation to multiple scales of landscape structure during years 2002–2003, and the effect of habitat structure on R. temporaria population persistence during a severe drought. On average, 113 and 24 egg clutches were observed per site in years 2002 and 2003, respectively. This dramatic decline was synchronized over the entire study area (ca. 320 km²), with some local variations. Population persistence was higher in sites where ground water levels decreased less but it was also positively correlated with the heterogeneity of the adjacent landscape. Under normal weather conditions, local habitat characteristics had a dominating role on R. temporaria population abundance, as it was positively correlated with the amount of ditches and ponds within the study sites. After the drought, however, population abundance was related to landscape and regional level factors. The results indicate that landscape homogenization can have negative effects on population persistence during climate change. They also show that the scale at which landscape characteristics affect populations can be strongly dependent of processes functioning at large scales, such as weather. In summary, heterogeneous landscapes may lower the risk of regional amphibian population declines under extreme weather perturbations and serve as sources of recovery in postdisturbance recovery phases. Thus, maintaining such areas should be promoted in long-term biodiversity conservation.