The influence of recent geography, palaeogeography and climate on the composition of the fauna of the central Aegean Islands

Partial Mantel tests and structural equation models were used to investigate the influence of recent geography, palaeogeography and climate on the composition of the fauna of the central Aegean Islands. The composition of land snail and isopod island faunas was significantly influenced by recent and by Pliocene geography. Only Pleistocene palaeogeography had a significant influence on the composition of tenebrionid beetle island faunas. The composition of butterfly island faunas was influenced by recent and by Miocene geographical distances. The composition of reptile island faunas was correlated with recent and Pliocene geography as well as with Pleistocene and/or Miocene geographical distances. Island area influenced only the composition of the island faunas of the volant butterflies, and not that of the less mobile land snails, land isopods, tenebrionid beetles and reptiles. This might indicate that butterflies are able to colonize large islands with suitable habitats even if such islands are comparatively far from source areas more frequently than can the nonvolant groups. Influence of a climatic parameter, namely annual precipitation, on faunal composition was found only for reptiles.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 84 , 785–795.     

Drivers of the beta diversity of spider assemblages in southern Brazilian temporary wetlands

1. The composition of local assemblages is assembled by an interplay of species sorting, mass effects and dispersal limitation processes. The contributions of assembly processes to metacommunity structure can change with ecosystem type and specificities of the study area. Spider composition is influenced by environmental features such as habitat structure and climate, and also by spatial distances between patches. However, little is known about the roles of assembly processes in spider metacommunity structure in wetlands. 2. The beta diversity patterns of spider assemblages were assessed in 24 temporary wetlands distributed along a latitudinal gradient in southern Brazil. The study also assessed the individual correspondence of beta diversity (and its turnover and richness components) with dissimilarities in habitat structure and climate, as well as with geographic distances, using Mantel and partial Mantel correlation tests and multivariate correlograms. 3. Turnover was the most important component of spider beta diversity. Mantel tests detected significant correlations of spider beta diversity with habitat structure. Partial Mantel tests detected significant relationships only between spider beta diversity (and the richness component) and geographic distances. Additionally, spider composition was more similar than chance on smaller scales. 4. These results evidenced a complex interplay of assembly processes explaining spider metacommunity structure in temporary wetlands. Although species-sorting processes associated with habitat structure were important in structuring local spider composition, mass effects and dispersal limitation across climatic zones played an important role on a broader scale.     

Fire frequency and species associations in perennial grasslands of south-west Ethiopia

Fires play an important role in shaping species composition and associations in East African grasslands. Grassland plains of Omo National Park (ONP), Ethiopia, which are dominated by perennial grass species, exist in a fire-prone environment. Our objective was to determine if the current pattern of plant species composition in ONP's grassland plains was correlated with the historical pattern of fire frequency. Species composition was determined at 160 plots along 30 west-trending transects, approximately 2 km apart. Fire frequency for each plot was estimated using eleven Landsat satellite images that spanned a 23-year period. The Mantel and partial Mantel tests were used to test for correlation between species composition and fire frequency.
Plots in the northern grassland plain appear to burn every other year, while plots in the southern grassland plain burn once every 4–5 years. However, no significant correlation was found between patterns in species composition and fire frequency. Likewise, a selective analysis by functional group (i.e. grass, shrubs) revealed no relationship with fire frequency. It appears that fire does play a role in dictating species composition in ONP, but only in the sense that species that can tolerate the current fire regime persist. Species distribution, however, appears to be under the influence of other factors.     

The biogeography of non-marine molluscs in the Tuscan Archipelago reveals combined effects of current eco-geographical drivers and paleogeography

We investigated the role of present (Recent) and historical (Pleistocene, i.e., Würmian Last Glacial Maximum) eco-geographical variables on the richness and diversity of non-marine molluscs in the Tuscan Archipelago, as well as inter-island faunal dissimilarity and relationships with source pools (Sardinia and Corsica, Tuscany). The association between species richness and present and historical eco-geographical variables were assessed with Spearman’s rank correlation test, while faunal dissimilarity both between islands and with their source pools was analyzed through beta-diversity partitioning (Sørensen index and its nestedness and turnover component) with UPGMA clustering tested with a multiscale bootstrap procedure. Non-metric multidimensional scaling in RGB color space was also used. Multiple regressions on distance matrices were then applied to explain assemblage composition between islands. Analyses were performed on all species and on all species except aliens. The overall framework showed the combined effects of current eco-geographical and paleogeographical imprints on non-marine malacofauna in the Tuscan Archipelago. However, excluding aliens, differences in species spatial turnover showed a clear correlation with Pleistocene inter-island distances, evidence of stronger historical biogeographical relationships between islands. This may indicate that widespread native species established their distribution during the Pleistocene, while alien species spread into the Tuscan Archipelago through stochastic and human-mediated dispersion events in recent times. Interestingly, Giglio’s relationships do not agree with the most accepted paleogeographical model, suggesting that this island might have been connected to the Tuscan mainland during the Würmian Last Glacial Maximum. An in-depth revision of the paleogeographic framework of the northern Tyrrhenian is therefore called for.     

Historical processes and environmental factors as determinants of inter-island differences in endemic faunas: the case of the Balearic Islands

Aim We describe current interisland similarities of endemic faunas, and elucidate the significance of historical factors and environmental ones in determining the pattern found. Location The six major islands of the Balearics (Western Mediterranean). Method An extensive review of all the endemic fauna ranging from platyhelminthes to mammals is made. From 568 presumed endemic species and subspecies, 230 full species with neither taxonomic nor distributional uncertainty are chosen. Inter-island similarities are determined using such a presence-absence matrix. Finally, relationships between the matrix of faunistic similarity and a number of matrices measuring environmental and historical factors are elucidated. Results Endemic fauna similarities depend clearly on historical factors. Dependence on environmental factors is unclear. Moreover, endemic fauna reveals two clear-cut clusters of islands within the Balearics: the Gymnesic Islands, in the NE, and the Pityusic Islands in the SW. Historical factors cluster the Balearic Islands in the same way. Contrasting, environmental variables show smoothed, no significant differences among the Gymnesics and the Pityusics. Main conclusions Pre-human flora (palynology) and fauna (bird and mammal fossil record) suggest that environmental differences among the Gymnesics and the Pityusics have now been reduced in comparison to the environmental differences at the Pleistocene and Holocene boundary. This environmental homogenization is likely related with human invasion. Historical effects of prehuman differences between Gymnesic and Pityusic Islands are still recognizable on endemic fauna. In contrast, there is no historical effects on interisland similarities using currently breeding birds (as an example of organisms well-dispersed and related to vegetation type). We explain the pattern of interisland similarities of endemic fauna as the result of the independent histories among the two islands groups. Contrasting, successive colonizations and extinctions would determine interisland similarities of breeding birds.     

Benthische Foraminiferen auf dem Island-Schottland Rücken: Umwelt-Anzeiger an der Grenze zweier ozeanischer Räume

Surface sediment samples taken by box corer from 32 stations on the Iceland-Scotland Ridge have been investigated for their benthic foraminiferal content. The live (Rose Bengal stained) benthic foraminiferal fauna was differentiated from empty tests comprising the foraminiferal death assemblage. Principal component analysis of both the live and dead faunal data from the Iceland-Scotland Ridge reveals eight live species assemblages and six corresponding dead assemblages. Bottom water current conditions, surface sediment characteristics, particulate organic matter supply, and to some extent also the bottom water temperatures are the main factors limiting and governing the composition and distribution of live benthic foraminiferal species assemblages on the Iceland-Scotland Ridge. On the Atlantic slope of the Iceland-Scotland Ridge the dead species assemblages differ greatly from the foraminiferal fauna living there today due to winnowing processes and redeposition of Pleistocene sediments. In this area an investigation of distribution patterns of the empty tests only would lead to wrong results concerning ecologic interrelations between benthic foraminiferal species assemblages and their environment.     

Spatial factors affecting primary succession on the Muddy River Lahar,Mount St. Helens,Washington

Primary succession is controlled by a combination of landscape and habitat factors whose actions may be stochastic or deterministic. The 1980 eruption of Mount St. Helens, Washington spawned a massive lahar that now supports a mosaic of vegetation. Our goals were to describe vegetation patterns after 28 growing seasons, determine the factors associated with these patterns, and to contrast the effects of stochastic and deterministic processes. We described species composition and explanatory factors that included location and habitat features in one hundred and fifty one 200-m² plots. We classified these plots into nine community types (CTs) that were distinguished quantitatively by variations in dominant species. We used multiple regressions, redundancy analysis (RDA), and Mantel tests to compare the vegetation relationships with explanatory factors. Plots in different CTs mingled spatially and in multivariate space. Species patterns were weakly related to explanatory variables by RDA (31.6% of the species variation). RDA indicated that vegetation was most strongly related to elevation, latitude, and isolation, which are primarily landscape factors. Mantel tests confirmed that factors associated with elevation were most closely associated with vegetation. The effects of arrival order were suggested by the dominance of different colonizers in similar environment and by plots with similar vegetation found in different habitats. We concluded that species composition cannot be predicted well from the data available, suggesting that there were no prominent deterministic assembly rules.     

Phylogeography of northern Dolly Varden Salvelinus malma (Salmoniformes: Salmonidae) from Asia and North America: An analysis based on the mitochondrial DNA genealogy

Spawning in habitats affected by Pleistocene glacial advances over most of its natural range, northern Dolly Varden Salvelinus malma malma typifies Arctic fauna distributed in northeastern Asia and northwestern North America. We reconstructed a genealogy of mtDNA haplotypes from 27 Alaskan and Asian populations to study the influence of historical events on the phylogeography and contemporary population genetic structure. Analysis of molecular variance partitioned most of the mtDNA variability to the intrapopulation component (72.5%) with much reduced differences between populations (21.1%) and regions (6.4%). Similar patterns of variation apparent from hierarchical diversity and nested clade phylogeographical analysis (NCPA) of mtDNA haplotypes identify weak spatial differentiation and low levels of divergence. These findings suggest (1) that demographic history has been influenced by historical range expansions and recent isolation by distance, (2) that present populations from Asia and North America were colonized from one main Beringian Refugium, and (3) that this taxon’s ancestral population probably experienced a bottleneck in the Beringian Refugium during the late Pleistocene (Wisconsin) glacial period. The genealogical and NCPA analyses, and mismatch distribution of S. m. malma mtDNA haplotypes do not confirm the assumptions about presence of the two refugia on the territories of the Beringian Land, in which allopatric S. m. malma ancestral populations evolved, and independent origin of the Sea of Okhotsk populations.     

Spatial Distribution of Algal Assemblages in a Temperate Lowland Peat Bog

Samples of phytobenthos were collected during three different seasons in 2005 along a linear transect of a lowland peat bog at various spatial scales (10 cm, 1 m, 10 m) to investigate the seasonal dynamics, diversity, and factors influencing the spatial patterns of microalgal communities. Non‐metric multidimensional scaling (NMDS), similarity percentage (SIMPER) analyses, ANOSIM, Mantel tests and diversity indices were used to analyze the data. Seasonal dynamics were exhibited by an increase in diversity, and a decrease in dominance from May to October, with significant differences in species composition. Mantel tests showed the significant influence of distance, microhabitat type, and conductivity on maintaining the similarity of species composition on scales of 1 m and 10 m. The small‐scale processes (colonization and niche differentiation), microhabitat type, geographic distance and conductivity were found to be the main factors influencing the distribution of algal assemblages. We conclude that these factors are related to winter disturbance, and the consequent colonization and subsequent niche differentiation. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

The role of repeated sea-level fluctuations in the generation of shrew (Soricidae: Crocidura) diversity in the Philippine Archipelago

Repeated sea-level fluctuations during and prior to the Pleistocene had a dramatic effect on the distribution of land and connection among islands between the Asian and Australian continents. These cycles of connection and isolation have long been recognized as an important factor determining the distribution and organization of biodiversity in the Philippines. However, surprisingly few studies have tested for predicted patterns of genetic diversity derived from a Pleistocene sea-level model of geography. Here, we examine evidence for fit to such a model in a widely distributed lineage of shrews (Crocidura). The topology of relationships among Crocidura from the Philippines is concordant with a Pleistocene sea-level model, but (1) AMOVAs reveal that genetic diversity is explained at least as well by modern islands as by Pleistocene islands; (2) Mantel tests reveal a significant influence of isolation by distance; and (3) the degree of genetic divergence between some populations connected by dry land during the last glacial maximum reveals isolation that almost certainly predates the most recent glacial activity. We further employ multiple strategies for inferring time-calibrated phylogenies, but these result in widely varying time estimates for the invasion of SE Asian islands by shrews. Overall, our results suggest Pleistocene sea-level fluctuations have been an important, but not dominant factor shaping shrew diversity.     

The response of amphibian communities to fish and habitat features in Mediterranean permanent ponds

Generalized linear models were used to test the effect of fish, using ponds with and without fish and habitat features as covariates, on richness and abundance of amphibian species. Five fish species and six amphibian species were recorded in 60 permanent ponds located in central Italy. The choice of covariates (macrophyte cover and pond surface area) was made after studying the correlations. The richness of amphibian species was not significantly affected by fish presence or macrophyte cover, in line with previous studies, since almost all the fish species were non-predatory. However, abundance of urodeles (newts) was negatively affected by fish and positively affected by macrophyte cover. Although fish may strongly influence the abundance and composition of amphibian communities, the results indicate that the cover of aquatic macrophytes may increase the available habitat for amphibians and therefore their abundance. Anuran species preferred ponds where fish were present, since both groups preferred larger ponds. Concordance between fish and amphibian species composition was not found by the Mantel and Partial Mantel tests. This indicates that the fish assemblages do not predict which amphibian species occur in the pond.     

The Ethiopian subregion fish fauna: an original patchwork with various origins

In this article, I analysed the biogeographical distribution and the historical origin of freshwater fish of the Ethiopian Rift Valley (ERV) region which is not a homogeneous area. The Ethiopian region, including Eritrea and part of Somalia, includes 13 basins as geographical units. A comparison was carried out with four Near East geographical units. A correspondence analysis was applied to presence–absence data for the 17 basins × 170 species’ matrix. Then, a faunistic distance (Euclidian distance) between basins was computed from the coordinates of factors retained in this new analysis. From this faunistic distance, a hierarchical cluster analysis was performed and a dendrogram produced by a UGPMA classification. The old Abyssinian ichthyo-province (sensu Roberts, Zool J Linn Soc 57:249–319, 1975) was not homogeneous in species composition. I distinguished four main groups based on the present species composition which seemed to be mainly influenced by historical events. The species composition of the ERV basins was not randomly distributed and can be classified into four main geographical units. The importance of the historical events was demonstrated and two origins can be considered. The westernmost basins are under Nilo-Sudan influence whereas the easternmost ones seem to have been colonised from the Near East. In this Eastern part it can be distinguished three different groups: the main ERV province and two derived sub-regions, Lake Tana with a Labeobarbus intermedius related species flock and the Coastal Red Sea, characterised by a very impoverished freshwater fish fauna.     

The role of historical factors and natural selection in the evolution of breeding systems of Oxalis alpina in the Sonoran desert ‘Sky Islands’

Pleistocene climatic oscillations are known to influence the patterns of genetic diversity and the distribution of traits that are the target of selection. Here, we combine phylogeographical and ecological niche modelling (ENM) approaches to explore the influence of historical factors (Pleistocene climatic shifts) and natural selection on the evolution of distyly (two floral morphs) from tristyly (three floral morphs) of Oxalis alpina in the Sky Islands of the Sonoran Desert. Molecular data and ENM indicate that historical factors have had a strong influence on the genetic structure and the geographical distribution of reproductive systems of O. alpina. Moreover, genetic results suggest the possibility that distylous populations do not represent a monophyletic group. We propose that the combined effects of natural selection and genetic drift have influenced the tristyly–distyly transition.     

Genetic signals of demographic expansion in Downy Woodpecker (Picoides pubescens) after the last North American glacial maximum

The glacial cycles of the Pleistocene have been recognized as important, large-scale historical processes that strongly influenced the demographic patterns and genetic structure of many species. Here we present evidence of a postglacial expansion for the Downy Woodpecker (Picoides pubescens), a common member of the forest bird communities in North America with a continental distribution. DNA sequences from the mitochondrial tRNA-Lys, and ATPase 6 and 8 genes, and microsatellite data from seven variable loci were combined with a species distribution model (SDM) to infer possible historical scenarios for this species after the last glacial maximum. Analyses of Downy Woodpeckers from 23 geographic areas suggested little differentiation, shallow genealogical relationships, and limited population structure across the species' range. Microsatellites, which have higher resolution and are able to detect recent differences, revealed two geographic groups where populations along the eastern edge of the Rocky Mountains (Montana, Utah, Colorado, and southern Alberta) were genetically isolated from the rest of the sampled populations. Mitochondrial DNA, an important marker to detect historical patterns, recovered only one group. However, populations in Idaho and southeast BC contained high haplotype diversity and, in general were characterized by the absence of the most common mtDNA haplotype. The SDM suggested several areas in the southern US as containing suitable Downy Woodpecker habitat during the LGM. The lack of considerable geographic structure and the starburst haplotype network, combined with several population genetic tests, suggest a scenario of demographic expansion during the last part of Pleistocene and early Holocene.     

Phylogeography of the longhorn cactus beetle Moneilema appressum LeConte (Coleoptera: Cerambycidae): was the differentiation of the Madrean sky islands driven by Pleistocene climate changes?

Although it has been suggested that Pleistocene climate changes drove population differentiation and speciation in many groups of organisms, population genetic evidence in support of this scenario has been ambiguous, and it has often been difficult to distinguish putative vicariance from simple isolation by distance. The sky island communities of the American Southwest present an ideal system in which to compare late Pleistocene range fragmentations documented by palaeoenvironmental studies with population genetic data from organisms within these communities. In order to elucidate the impact of Pleistocene climate fluctuations on these environments, biogeographic patterns in the flightless longhorn cactus beetle, Moneilema appressum were examined using mitochondrial DNA sequence data. Gene tree relationships between haplotypes were inferred using parsimony, maximum-likelihood, and Bayesian analysis. Nested clade analysis, Mantel tests, and coalescent modelling were employed to examine alternative biogeographic scenarios, and to test the hypothesis that Pleistocene climate changes drove population differentiation in this species. The program mdiv was used to estimate migration and divergence times between populations, and to measure the statistical support for isolation over ongoing migration. These analyses showed significant geographic structure in genetic relationships, and implicated topography as a key determinant of isolation. However, although the coalescent analyses suggested that a history of past habitat fragmentation underlies the observed geographic patterns, the nested clade analysis indicated that the pattern was consistent with isolation by distance. Estimated divergence times indicated that range fragmentation in M. appressum is considerably older than the end of the most recent glacial, but coincided with earlier interglacial warming events and with documented range expansions in other, desert-dwelling species of Moneilema.     

Multiple Mantel tests and isolation-by-distance, taking into account long-term historical divergence

Mantel tests of matrix correspondence have been widely used in population genetics to examine microevolutionary processes, such as isolation-by-distance (IBD). We used partial and multiple Mantel tests to simultaneously test long-term historical effects and current divergence and equilibrium processes, such as IBD. We used these procedures to calculate genetic divergence among Eugenia dysenterica (Myrtaceae) populations in Central Brazil. The Nei's genetic distances between pairs of local populations were strongly correlated with geographic distances, suggesting an IBD process, but field observations and the geographic distribution of the samples suggest that populations may have been subjected to more complex evolutionary processes of genetic divergence. Partial Mantel regression was used to partition the effects of geographic structure and long-term divergence associated with a possible historical barrier. The R(2) of the model with both effects was 73.3%, and after the partition 21.9% of the variation in the genetic distances could be attributed to long-term historical divergence alone, whereas only 1.5% of the variation in genetic distances could be attributed to IBD. As expected, there was a large overlap between these processes when explaining genetic divergence, so it was not possible to entirely partition divergence between historical and contemporary processes.     

The relative role of rivers,environmental heterogeneity and species traits in driving compositional changes in southeastern Amazonian bird assemblages

Amazonian rivers have been proposed to act as geographic barriers to species dispersal, either driving allopatric speciation or defining current distribution limits. The strength of the barrier varies according to the species’ ecological characteristics and the river's physical properties. Environmental heterogeneity may also drive compositional changes but has not been well assessed in Amazonia. Aiming to understand the contributions of riverine barriers and environmental heterogeneity in shaping compositional changes in Amazonian forest bird assemblages, we focus on the Tapajós River. We investigate how spatial variation in species composition is related to physical barriers (Tapajós and Jamanxim rivers), species’ ecological characteristics (distinct guilds), and environmental heterogeneity (canopy reflectance, soils, and elevation). We sampled birds through point-counts and mist nets on both banks of the Tapajós and Jamanxim rivers. To test for relationships between bird composition and environmental data, we used Mantel and partial Mantel tests, NMDS, and ANOVA + Tukey HSD. The Mantel tests showed that the clearest compositional changes occurred across the Tapajós River, which seems to act unequally as a significant barrier to the bird guilds. The Jamanxim River was not associated with differences in bird communities. Our results reinforce that the Tapajós River is a biogeographical boundary for birds, while environmental heterogeneity influences compositional variation within interfluves. We discuss the combined influence of geographical barriers, environmental heterogeneity, and ecological characteristics of species in shaping species distributions and community composition and the complexity of extrapolating the patterns found for birds to other Amazonian organisms. Abstract in Portuguese is available with online material.     

Species composition of local riffle beetle (Coleoptera: Elmidae) assemblages in small coastal streams of the Gulf of Mexico: the influences of local and regional factors

Using Partial Mantel tests to isolate distance and environmental effects from each other, we examined species composition of riffle beetle assemblages (Coleoptera: Elmidae) of 22 local streams from the Gulf of Mexico, as a function of dispersal and environmental constraints. In addition, we examined how different stream topologies (Euclidean, Network) influenced dispersal constraints on species composition. In general, when the influences of local and regional influences were isolation from each other (Partial Mantel test), community dissimilarity increased between sites as differences in both stream conditions and distance between sites increased. However, these trends varied over the scale of study (within and across water basins) and stream topology. For example, at the scale of the watershed, overland dispersal did not appear to be a limiting factor in the formation of local elmid assemblages. The relationship between local species composition and distance was not evident in a distance–decay regression, nor was an environmental similarity versus community similarity regression significant. At least within the limits of our study, it was clear that if local and regional influences were not isolation from each other (Partial Mantel test), their associations with local assemblages were not evident. We also argue the utility of restricting study to a single family of insects when attempting to clarify the causal mechanisms responsible for local species assemblages.     

Effects of historical legacies on soil nematode communities are mediated by contemporary environmental conditions

Both contemporary and historical factors are documented to be crucial in regulating species diversity and distribution. Soil fauna contribute substantially to global biodiversity and ecosystem functioning, while it is unclear whether and to what extent historical factors shape their diversity patterns. Here, we used soil nematodes as a model organism to test historical effects on soil fauna and to investigate the relative importance of climatic, soil, and historical factors. Based on nematode distribution data in 16 natural sites at a large scale (ranging from 22 to 40°N) in mainland China, we conducted elastic net regression model to test the effects of climatic (e.g., mean and seasonality of temperature/precipitation), soil (e.g., soil carbon, nitrogen, and pH), and historical (e.g., temperature/precipitation anomaly and the velocity of the change since the Last Glacial Maximum) variables on nematode genus richness and Shannon's diversity. Additionally, variation partitioning was used to determine the contribution of the three predictor sets to the explanation of both Jaccard and Bray–Curtis community dissimilarity. We found that climate generally explained more variations in both diversity and composition than soil and historical predictors in our samples. We also showed that although historical factors (e.g., temperature change velocity) were correlated with nematode diversity and composition, the pure effects of these historical factors were negligible. In other words, the historical effects were commonly represented by their interactions with current climatic and soil factors within our selected sites. Our results indicated that contemporary factors, especially climate, may outperform historical factors in regulating soil nematode diversity patterns at large scales.