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Many large-seeded Neotropical trees depend on a limited guild of animals for seed dispersal. Fragmented landscapes reduce animal abundance and movement, limiting seed dispersal between distant forest remnants. In 2006, experimental plantings were established in pasture to determine whether plantings enhance seed dispersal and, ultimately, seedling recruitment. We examined patterns of naturally recruited seedlings of Ocotea uxpanapana, a large-seeded bird-dispersed tree endemic to southern Mexico that occurs in the surrounding landscape. We used GIS and least-cost path analysis to ask: (1) Do restoration efforts alter recruitment patterns? (2) What is the importance of canopy cover and likely dispersal pathways to establishment? Patterns of seedling establishment indicated that dispersal agents crossed open pastures to wooded plots. Recruitment was greatest under woody canopies. Also, by reducing movement cost or risk for seed dispersers, wooded canopies increased influx of large, animal-dispersed seeds, thereby restoring a degree of functional connectivity to the landscape. Together, canopy openness and path distance from potential parent trees in the surrounding landscape explained 73% of the variance in O. uxpanapana seedling distribution. Preliminary results suggest that strategic fenced plantings in pastures increase dispersal and establishment of large-seeded trees, thereby accelerating forest succession in restorations and contributing to greater connectivity among forest fragments.

Assessing the geographic structure of populations has relied heavily on Sewell Wright's F‐statistics and their numerous analogues for many decades. However, it is well appreciated that, due to their nonlinear relationship with gene flow, F‐statistics frequently fail to reject the null model of panmixia in species with relatively high levels of gene flow and large population sizes. Coalescent genealogy samplers instead allow a model‐selection approach to the characterization of population structure, thereby providing the opportunity for stronger inference. Here, we validate the use of coalescent samplers in a high gene flow context using simulations of a stepping‐stone model. In an example case study, we then re‐analyze genetic datasets from 41 marine species sampled from throughout the Hawaiian archipelago using coalescent model selection. Due to the archipelago's linear nature, it is expected that most species will conform to some sort of stepping‐stone model (leading to an expected pattern of isolation by distance), but F‐statistics have only supported this inference in ~10% of these datasets. Our simulation analysis shows that a coalescent sampler can make a correct inference of stepping‐stone gene flow in nearly 100% of cases where gene flow is ≤100 migrants per generation (equivalent to FST = 0.002), while F‐statistics had mixed results. Our re‐analysis of empirical datasets found that nearly 70% of datasets with an unambiguous result fit a stepping‐stone model with varying population sizes and rates of gene flow, although 37% of datasets yielded ambiguous results. Together, our results demonstrate that coalescent samplers hold great promise for detecting weak but meaningful population structure, and defining appropriate management units.

Aim The maintenance of broad‐scale connectivity patterns is suggested as a sustainable strategy for biodiversity preservation. However, explicit approaches for quantifying the functional role of different areas in biogeographic connectivity have been elusive. Freshwaters are spatially structured ecosystems critically endangered because of human activities and global change, demanding connectivity‐based approaches for their conservation. Mass effects—the increase in local diversity by immigration—and corridor effects—the connections with distant communities—are basic and relevant mechanisms connecting diversity with landscape configuration. Here, we identified freshwater hotspots areas for mass and corridor effects across Europe. Location Europe. Methods Using satellite images, we quantified the areas of ephemeral, temporal and permanent freshwaters. The landscape structure of the freshwater ecoregions was represented as a directed‐graph, and the link weights were determined by the distance between cells and the water cover. Three centrality metrics were used to rank freshwater areas with respect to their potential role in dispersal‐mediated mechanisms. Out‐degree represents the potential of an area to operate as a diversity source to other regions. In‐degree reflects the importance that incoming dispersal may have in local diversity. Betweenness refers to the importance of local areas for connecting other distant areas. Results We detected great concentrations of source hotspots on the northern regions associated to lentic ecosystems, main European rivers acting as ecological corridors for all freshwaters, and a mixed distribution of connectivity hotspots in southern and Mediterranean ecoregions, associated with lentic and/or lotic systems. Main Conclusions We showed an explicit connection between landscape structure and dispersal process at large geographic scales, highlighting hotspots of connectivity for the European waterscape. The spatial distribution of hotspots points to differences in landscape configurations potentially accounting for biogeographic diversity patterns and for mechanisms that have to be considered in conservation planning.

1. Because host–parasite interactions are so ubiquitous, it is of primary interest for ecologists to understand the factors that generate, maintain and constrain these associations. Phylogenetic comparative studies have found abundant evidence for host-switching to relatively unrelated hosts, sometimes related to diversification events, in a variety of host–parasite systems. For Monogenoidea (Platyhelminthes) parasites, it has been suggested that the co-speciation model alone cannot explain host occurrences, hence host-switching and/or non-vicariant modes of speciation should be associated with the origins and diversification of several monogenoid taxa. 2. The factors that shape broad patterns of parasite sharing were investigated using path analysis as a way to generate hypotheses about the origins of host–parasite interactions between monogenoid gill parasites and Neotropical freshwater fishes. 3. Parasite sharing was assessed from an interaction matrix, and explanatory variables included phylogenetic relationships, environmental preferences, biological traits and geographic distribution for each host species. 4. Although geographic distribution of hosts and host ecology are important factors to understand host–parasite interactions, especially within host lineages that share a relatively recent evolutionary history, phylogeny had the strongest overall direct effect on parasite sharing. 5. Phylogenetic contiguity of host communities may allow a 'stepping-stone' mode of host-switching, which increases parasite sharing. Our results reinforce the importance of including evolutionary history in the study of ecological associations, including emerging infectious diseases risk assessment.

Aim: We investigated the spatial and temporal patterns of diversification among colourful and flightless weevils, the Pachyrhynchus orbifer complex, to test the stepping-stone hypothesis of colonization across the Taiwan–Luzon volcanic belt. Location: Southeast Asia. Methods: The phylogeny of the P. orbifer complex was reconstructed from a multi-locus data set of mitochondrial and nuclear genes using maximum likelihood in RAxML and Bayesian inference in MRBAYES. Likelihood-based tests in CONSEL were used to evaluate alternative tree topologies. Divergence times were estimated in BEAST based on a range of mutation rates. Ancestral range and biogeographical history were reconstructed using Bayesian binary MCMC (BBM) methods in RASP and in BioGeoBEARS. Demographic histories were inferred using the extended Bayesian skyline plot (EBSP). Species boundaries were tested using BPP. Results: The phylogeny of the P. orbifer complex indicated strong support for seven reciprocally monophyletic lineages grouped by current island boundaries (Camiguin, Fuga, Dalupiri, Calayan, Babuyan, Orchid and Yaeyama Islands), except for a sister Green + Itbayat lineage. Complex and stochastic colonization of P. orbifer was inferred to have involved both northward and southward directions with short- and long-distance dispersal events, which are strongly inconsistent with the strict stepping-stone hypothesis. Divergence time estimates for all extant island lineages (<1 Myr of Middle Pleistocene) are much more recent than the geological ages (22.4–1.7 Myr) and subaerial existence (c. 3 Myr) of the islands. The statistically delimited seven cryptic species imply that the diversity of Pachyrhynchus from small peripheral islands continues to be largely under-estimated. Main conclusions: The non-linear, more complex spatial and temporal settings of the archipelago and stochastic dispersal were probable key factors shaping the colonization history of the P. orbifer complex. Speciation of the P. orbifer complex may have occurred only between islands, indicating that peripatric speciation through the founders of stochastic dispersals was the major evolutionary driver.

To understand empirical patterns of phenotypic plasticity, we need to explore the complexities of environmental heterogeneity and how it interacts with cue reliability. I consider both temporal and spatial variation separately and in combination, the timing of temporal variation relative to development, the timing of movement relative to selection, and two different patterns of movement: stepping‐stone and island. Among‐generation temporal heterogeneity favors plasticity, while within‐generation heterogeneity can result in cue unreliability. In general, spatial variation more strongly favors plasticity than temporal variation, and island migration more strongly favors plasticity than stepping‐stone migration. Negative correlations among environments between the time of development and selection can result in seemingly maladaptive reaction norms. The effects of higher dispersal rates depend on the life history stage when dispersal occurs and the pattern of environmental heterogeneity. Thus, patterns of environmental heterogeneity can be complex and can interact in unforeseen ways to affect cue reliability. Proper interpretation of patterns of trait plasticity requires consideration of the ecology and biology of the organism. More information on actual cue reliability and the ecological and developmental context of trait plasticity is needed. To understand why adaptive plasticity is less common than we would expect, we need to explore the complexities of environmental heterogeneity and how it interacts with cue reliability. I consider both temporal and spatial variation separately and in combination, the timing of temporal variation relative to development, the timing of movement relative to selection, and two different patterns of movement: stepping‐stone and island. In general, spatial variation more strongly selects for plasticity than temporal variation, and island migration more strongly selects for plasticity than stepping‐stone migration.

Aim The impact of Pleistocene climatic oscillations on tropical biomes is associated with changes in the extent of forest cover. Fruit bats have played a role in woodland dynamics via pollination and seed dispersal. We hypothesized that phylogeographic patterns of Rousettus on continental Africa and adjacent islands should show a signature of pluvial‐drought cycles, involving demographic expansions and contractions. Location Afrotropical, Malagasy and Saharo‐Arabian biogeographic realms. Taxon Genus Rousettus (Pteropodidae). Methods Phylogeographic and population genetic approaches using mitochondrial and microsatellite data were integrated with species distribution modelling of currently suitable habitats and those of the Last Glacial Maximum using climate simulations. Results Phylogenetic reconstruction yielded an Asian outgroup followed by pectinate branching of the Indian Ocean taxa and Rousettus aegyptiacus. While nuclear microsatellites were homogeneous across the African mainland, two mitochondrial haplogroups were found. Haplogroup I is widespread in regions with extensive tree cover, including tropical rain forests, and has close relationships to isolated lineages in the Middle East and islands in the Gulf of Guinea. Haplogroup II is sister to the rest of the R. aegyptiacus radiation and is found in eastern and southern Africa and the Sudanian savanna in habitats with semi‐open land cover. Main Conclusion Palaeodistributional modelling ascertained that the Indian Ocean islands provided more extensive areas of suitable habitat in the past relative to conditions today, suggesting stepping stone connectivity between Asia and Africa during Pleistocene interpluvial sea‐level lowstands. Inverse pluvial‐drought demography was detected in lineages ancestral to recent haplogroups, providing evidence of past forest refugia and complex ecogeographic scenarios of haplogroup origins involving allopatry and parapatry connected with the eastern Afromontane biodiversity hotspot, and subsequent admixture of nuclear gene pools. The Middle Eastern lineage probably originated during pluvial green Sahara periods, possibly in co‐evolution with ancestors of tree crop species domesticated later during the Neolithic revolution. The keystone role of rousettine bats for forest regeneration and their ability to pioneer dry and distant habitats emphasize their role in conservation biology and restoration ecology.

Aim Dispersal explains the disjunct distributions of many austral plant lineages. However, the role of Antarctica is largely uncertain and the routes of dispersal have remained speculative. Based on niche conservatism we can make predictions about the timing of disjunction establishment, as well as the availability of direct transoceanic, Antarctic stepping-stone, and out-of-Antarctica dispersal routes over time. We evaluate these predictions using molecular divergence time estimates for the establishment of disjunct distributions across multiple plant lineages.Location Southern Hemisphere.Methods We estimated the timing of disjunction establishment and determined habitat affinities for 72 austral plant groups. We used Wilcoxon rank sum tests to compare the timing of disjunction establishment between cold and temperate climate lineages for the full data set, as well as within several subsets. We compared our results with those from a literature survey. Results As niche conservatism predicts, the timing of disjunction establishment in cold and temperate climate austral lineages is consistent with the availability of the corresponding habitats over time. Our results also suggest that disjunction establishment has involved a combination of Antarctic and direct dispersal routes. For cold climate lineages, both out-of-Antarctica and direct dispersal routes are required to explain the observed estimates, while stepping stone routes cannot be ruled out. It appears that for these lineages the importance of the three dispersal routes differs with environmental, geographical and temporal context.Main conclusions Both direct and Antarctic dispersal routes are necessary to explain the establishment of contemporary austral distributions. Evidence that some taxa were, until recently, restricted to Antarctica changes how we view the evolutionary histories of austral floras and the lineages they contain. Moreover, that we detect differences in the importance of alternative dispersal routes suggests that long-distance plant dispersal processes can be explicitly incorporated into models of climate change response.

Genetic connectivity is expected to be lower in species with limited dispersal ability and a high degree of habitat specialization (intrinsic factors). Also, gene flow is predicted to be limited by habitat conditions such as physical barriers and geographic distance (extrinsic factors). We investigated the effects of distance, intervening pools, and rapids on gene flow in a species, the Tuxedo Darter (Etheostoma lemniscatum), a habitat specialist that is presumed to be dispersal‐limited. We predicted that the interplay between these intrinsic and extrinsic factors would limit dispersal and lead to genetic structure even at the small spatial scale of the species range (a 38.6 km river reach). The simple linear distribution of E. lemniscatum allowed for an ideal test of how these factors acted on gene flow and allowed us to test expectations (e.g., isolation‐by‐distance) of linearly distributed species. Using 20 microsatellites from 163 individuals collected from 18 habitat patches, we observed low levels of genetic structure that were related to geographic distance and rapids, though these factors were not barriers to gene flow. Pools separating habitat patches did not contribute to any observed genetic structure. Overall, E. lemniscatum maintains gene flow across its range and is comprised of a single population. Due to the linear distribution of the species, a stepping‐stone model of dispersal best explains the maintenance of gene flow across its small range. In general, our observation of higher‐than‐expected connectivity likely stems from an adaptation to disperse due to temporally unstable and patchy habitat. We examine whether physical obstacles and geographic distance influence genetic structure in a presumably dispersal‐limited, habitat specialist riverine fish. We found minimal levels of genetic structure associated with rapids and distance. So, we conclude that there are minimal filters to gene flow in this endangered species and that higher‐than‐expected connectivity likely stems from an adaptation to disperse due to temporally unstable and patchy habitats.

The biogeographical patterns and drivers of diversity on oceanic islands in the tropical South Pacific (TSP) are synthesized. We use published studies to determine present patterns of diversity on TSP islands, the likely sources of the biota on these islands and how the islands were colonized. We also investigate the effect of extinctions. We focus on oceanic islands in the TSP. We review available literature and published molecular studies. Examples of typical island features (e.g. gigantism, flightlessness, gender dimorphism) are common, as are adaptive radiations. Diversity decreases with increasing isolation from mainland sources and with decreasing size and age of archipelagos, corresponding well with island biogeographical expectations. Molecular studies support New Guinea/Malesia, New Caledonia and Australia as major source areas for the Pacific biota. Numerous studies support dispersal-based scenarios, either over several 100 km (long-distance dispersal) or over shorter distances by island-hopping (stepping stones) and transport by human means (hitch-hiking). Only one vicariance explanation, the eastward drift of continental fragments (shuttles) that may have contributed biota to Fiji from New Caledonia, is supported by some geological evidence, although there is no evidence for the transport of taxa on shuttle fragments. Another vicariance explanation, the existence of a major continental landmass in the Pacific within the last 100 Myr (Atlantis theory), receives little support and appears unlikely. Extinction of lineages in source areas and persistence in the TSP has probably occurred many times and has resulted in misinterpretation of biogeographical data. Malesia has long been considered the major source region for the biota of oceanic islands in the TSP because of shared taxa and high species diversity. However, recent molecular studies have produced compelling support for New Caledonia and Australia as alternative important source areas. They also show dispersal events, and not vicariance, to have been the major contributors to the current biota of the TSP. Past extinction events can obscure interpretations of diversity patterns.