Genomics of invasion: diversity and selection in introduced populations of monkeyflowers (Mimulus guttatus)

Global trade and travel is irreversibly changing the distribution of species around the world. Because introduced species experience drastic demographic events during colonization and often face novel environmental challenges from their native range, introduced populations may undergo rapid evolutionary change. Genomic studies provide the opportunity to investigate the extent to which demographic, historical and selective processes shape the genomic structure of introduced populations by analysing the signature that these processes leave on genomic variation. Here, we use next‐generation sequencing to compare genome‐wide relationships and patterns of diversity in native and introduced populations of the yellow monkeyflower (Mimulus guttatus). Genome resequencing data from 10 introduced populations from the United Kingdom (UK) and 12 native M. guttatus populations in North America (NA) demonstrated reduced neutral genetic diversity in the introduced range and showed that UK populations are derived from a geographic region around the North Pacific. A selective‐sweep analysis revealed site frequency changes consistent with selection on five of 14 chromosomes, with genes in these regions showing reduced silent site diversity. While the target of selection is unknown, genes associated with flowering time and biotic and abiotic stresses were located within the swept regions. The future identification of the specific source of origin of introduced UK populations will help determining whether the observed selective sweeps can be traced to unsampled native populations or occurred since dispersal across the Atlantic. Our study demonstrates the general potential of genome‐wide analyses to uncover a range of evolutionary processes affecting invasive populations.     

Fission and fusion in island taxa – serendipity,or something to be expected?

A well‐used metaphor for oceanic islands is that they act as ‘natural laboratories’ for the study of evolution. But how can islands or archipelagos be considered analogues of laboratories for understanding the evolutionary process itself? It is not necessarily the case that just because two or more related species occur on an island or archipelago, somehow, this can help us understand more about their evolutionary history. But in some cases, it can. In this issue of Molecular Ecology, Garrick et al. ( 2014 ) use population‐level sampling within closely related taxa of Galapagos giant tortoises to reveal a complex demographic history of the species Chelonoidis becki – a species endemic to Isabela Island, and geographically restricted to Wolf Volcano. Using microsatellite genotyping and mitochondrial DNA sequencing, they provide a strong case for C. becki being derived from C. darwini from the neighbouring island of Santiago. But the interest here is that colonization did not happen only once. Garrick et al. ( 2014 ) reveal C. becki to be the product of a double colonization event, and their data reveal these two founding lineages to be now fusing back into one. Their results are compelling and add to a limited literature describing the evolutionary consequences of double colonization events. Here, we look at the broader implications of the findings of Garrick et al. ( 2014 ) and suggest genomic admixture among multiple founding populations may be a characteristic feature within insular taxa.     

Topo‐climatic microrefugia explain the persistence of a rare endemic plant in the Alps during the last 21 millennia

Ongoing rapid climate change is predicted to cause local extinction of plant species in mountain regions. However, some plant species could have persisted during Quaternary climate oscillations without shifting their range, despite the limited evidence from fossils. Here, we tested two candidate mechanisms of persistence by comparing the macrorefugia and microrefugia (MR) hypotheses. We used the rare and endemic Saxifraga florulenta as a model taxon and combined ensembles of species distribution models (SDMs) with a high‐resolution paleoclimatic and topographic dataset to reconstruct its potential current and past distribution since the last glacial maximum. To test the macrorefugia hypothesis, we verified whether the species could have persisted in or shifted to geographic areas defined by its realized niche. We then identified potential MR based on climatic and topographic properties of the landscape and applied refined scenarios of MR dynamics and functions over time. Last, we quantified the number of known occurrences that could be explained by either the macrorefugia or MR model. A consensus of two or three SDM techniques predicted absence between 14–10, 3–4 and 1 ka bp , which did not support the macrorefugia model. In contrast, we showed that S. florulenta could have contracted into MR during periods of absence predicted by the SDMs and later re‐colonized suitable areas according to the macrorefugia model. Assuming a limited and realistic seed dispersal distance for our species, we explained a large number of the current occurrences (61–96%). Additionally, we showed that MR could have facilitated range expansions or shifts of S. florulenta. Finally, we found that the most recent and the most stable MR were the ones closest to current occurrences. Hence, we propose a novel paradigm to explain plant persistence by highlighting the importance of supporting functions of MR when forecasting the fate of plant species under climate change.     

Influence of ectomycorrhizal inoculation on Pinus wallichiana and Cedrus deodara seedlings under nursery conditions

A study was undertaken to examine the extent of root colonization by four locally isolated ectomycorrhizal （ECM） fungi （Hebeloma theobrominum, Boletus dryophilus, Scleroderma citrinum and Suillus luteus） and their effects on seedling growth in Pinus wallichiana and Cedrus deodara under nursery conditions. Seedlings of the two conifers were inoculated with mycelium of ECM fungi and were grown in pots containing sterilized forest soil for six months. The percentage of ECM colonization of roots was 38%-52% in Pinus wallichiana and 33%-48~ in Cedrus deodara. ECM colonization increased shoot height, needle number, shoot and root biomass and survival of inoculated seedlings. Among the four ECM fungi Hebeloma theobrominum was more effective with Pinus wallichiana and Scleroderma citrinum with Cedrus deodara in promoting seedling survival and overall growth. All the four ECM fungi used enhanced growth of inoculated seedlings and thus can be used in afforestation and regeneration programmes in degraded forests ecosystems.     

Investigating the Effects of Probiotics on Pneumococcal Colonization Using an In Vitro Adherence Assay

Adherence of Streptococcus pneumoniae (the pneumococcus) to the epithelial lining of the nasopharynx can result in colonization and is considered a prerequisite for pneumococcal infections such as pneumonia and otitis media. In vitro adherence assays can be used to study the attachment of pneumococci to epithelial cell monolayers and to investigate potential interventions, such as the use of probiotics, to inhibit pneumococcal colonization. The protocol described here is used to investigate the effects of the probiotic Streptococcus salivarius on the adherence of pneumococci to the human epithelial cell line CCL-23 (sometimes referred to as HEp-2 cells). The assay involves three main steps: 1) preparation of epithelial and bacterial cells, 2) addition of bacteria to epithelial cell monolayers, and 3) detection of adherent pneumococci by viable counts (serial dilution and plating) or quantitative real-time PCR (qPCR). This technique is relatively straightforward and does not require specialized equipment other than a tissue culture setup. The assay can be used to test other probiotic species and/or potential inhibitors of pneumococcal colonization and can be easily modified to address other scientific questions regarding pneumococcal adherence and invasion.     

Colonization,diversity, and seasonality of fishes at pelagic fish aggregating devices

The pelagic zone of the ocean can be a challenging environment in which to conduct research and as a result we lack the robust baseline abundance and diversity data, compared to what is available in more accessible coastal habitats, to be able to track changes or stressors to the biota in this environment. Many large-scale fisheries target pelagic fish, and much of the information available on these species is based on fisheries-dependent data that may be biased towards hotspots and commercially valuable fishes. Here, a long-term video and visual fish survey was conducted on two subsurface moored fish aggregating devices (FADs) in the pelagic waters of the central Bahamas to determine the feasibility of using moored pelagic FADs as tools for collecting fish abundance and diversity data. A wide range of species was documented, including large migratory fish that are the focus of commercial and recreational fisheries, and smaller often overlooked species on which little abundance or seasonality information exists. We found that FADs colonize quickly and reach a peak stable (albeit seasonally cyclical) abundance and diversity within the first several months after deployment. Species richness was higher in video surveys, but abundance was higher in visual surveys, except for sharks. Our results highlight the need to tailor survey methods to fit the context and study objective, and provide further evidence for the importance of fisheries-independent data in monitoring pelagic species.     

Eretmoptera murphyi: pre‐adapted to survive a colder climate

During the late 1960s, larvae of the flightless midge Eretmoptera murphyi Schaeffer were accidentally transferred from the sub‐Antarctic island of South Georgia to Signy Island in the maritime Antarctic. Higher insects are rare in the Antarctic and the introduction and establishment of a new species is an unusual event. The fly has overcome the two major barriers to colonization of the Antarctic by new species: the geographical isolation of the region and its severe climate. Larvae of the flightless midge overwinter in the surface layers of soil on Signy Island where the temperature may fall to below ?10 °C, compared with as little as ?1.5 °C on South Georgia. This suggests the possession of a level of pre‐adaption to colder conditions. Summer‐collected larvae have a supercooling point (SCP or whole body freezing point) of approximately ?5.0 °C but survive experimental exposure to ?13 °C, giving them a level of freeze tolerance. After acclimation at ?4 °C for 4 days, the SCP changes little but the temperature at which 50% of the population would die decreases to lower than ?19 °C. Larvae are also resistant to dehydration. Under experimental conditions of 88% relative humidity at 5 °C, larvae lose water linearly (0.42% h^?1) over the first 30 h but resist further water loss once their water content decreases to approximately 1.4 g g^?1 dry weight. All larvae survive these conditions for the duration of the experiment (55 h). Eretmoptera murphyi is well adapted to survive on Signy Island, and these studies suggest that it has the ability to survive at more extreme locations at higher latitudes if it were to be inadvertently transferred to a suitable habitat.     

How important were stepping stones in the colonization of Krakatau?

In theory, one factor determining the rate and nature of the assembly of island biotas is the presence or absence of stepping stone islands, yet no field studies have demonstrated stepping stone function in practice. Krakatau, in Sunda Strait, is about equidistant from Java and Sumatra. Sebesi lies about half way between Krakatau and Sumatra, but no island intervenes between Krakatau and the nearest coast of Java. We assess the evidence that Sebesi has acted as an important stepping stone for Krakatau's recolonization since the devastating 1883 volcanic eruption. About a quarter of Krakatau's resident land birds, two-fifths of its reptiles, bats and land molluscs, and about two-thirds of its termites, pteridophytes, butterflies and spermatophytes are unknown on Sebesi, evidently having colonized without stepping stone involvement. Identifiable Sumatran taxa do not outnumber identifiable Javan ones on Krakatau, nor do historical distribution records indicate movement from Sebesi to Krakatau in animal groups. Krakatau's biota is not a subset of Sebesi's in predominantly anemochorous or thallassochorous plant groups, butterflies, reptiles or bats, and is only marginally so in termites. It is a subset in predominantly zoochorous spermatophyte groups, except Ficus species, and in birds and land molluscs. Comparison with a weaker stepping stone candidate, Panaitan, provides no evidence for a stepping stone role for Sebesi in butterflies or termites. We discuss the dispersal and establishment constraints on colonization by the groups involved, and conclude that, overall, Sebesi had little impact as a stepping stone. Instead, it is more probable that divergence of the environments of the two islands has led to an increasingly independent recolonization of Krakatau.  © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 77 , 275–317.