Blurred boundaries: lifestyle lessons from ectomycorrhizal fungal genomes

Soils contain a multitude of fungi with vastly divergent lifestyles ranging from saprotrophic to mutualistic and pathogenic. The recent release of many fungal genomes has led to comparative studies that consider the extent to which these lifestyles are encoded in the genome. The genomes of the symbiotic fungi Laccaria bicolor and Tuber melanosporum are proving especially useful in characterizing the genetic foundation of mutualistic symbiosis. New insights gleaned from these genomes, as compared to their saprotrophic and pathogenic cousins, have helped to redefine and shape our understanding of the nature of the symbiotic lifestyle. Here we detail the current state of research into this complex relationship and discuss avenues for future exploration.     

Implications of flexible foraging for interspecific interactions: lessons from simple models

1.  Some types of flexible foraging behaviours were incorporated into ecological thought in the 1960s, but the population dynamical consequences of such behaviours are still poorly understood.
2.  Flexible foraging-related traits can be classified as shifts in general and specific foraging effort, and shifts in general and specific defense.
3.  Many flexible foraging behaviours suggested by theory have received very little empirical attention, and empirical techniques used to compare the magnitudes of behavioural and non-behavioural responses to predation are likely to have overestimated the behavioural components.
4.  Adaptively flexible foraging in theory causes significant changes in the forms of consumer functional responses and generates a variety of indirect interactions. These can alter fundamental ecological processes, such as co-existence of competitors, and top-down or bottom-up effects in food webs.
5.  Many aspects of flexible foraging are still largely unknown, including the issues of how to represent the dynamics of such phenotypically plastic traits, how flexible traits in multiple species interact, what types of adaptive movements occur in metacommunities, and how adaptive behaviours influence evolutionary change.
6.  Population dynamics in large food webs may be less dependent on behavioural flexibility than in small webs because species replacement may preempt some potential types of behavioural change within species.     

Cryptic species complexes,widespread species and conservation: lessons from Amazonian frogs of the Leptodactylus marmoratus group (Anura: Leptodactylidae)

Morphologically cryptic species act as a wild card when it comes to biodiversity assessments and conservation, with the capacity to dramatically alter our understanding of the biological landscape at the taxonomic, ecological, biogeographic, evolutionary, and conservation levels. We discuss the potential effects that cryptic species may have on biodiversity assessments and conservation, as well as some of the current issues involving the treatment of cryptic species both at taxonomic and conservation levels. In addition, using a combination of advertisement call and morphological data, we describe a new species of the Leptodactylus marmoratus group from the upper Amazon basin, and we assess how cryptic species can affect conservation assessments of species in the Leptodactylus marmoratus group by examining how recent findings affect our understanding of the distribution of what is assumed to be a widespread Amazonian species, Leptodactylus andreae.     

The butterfly fauna of Wisconsin bogs: lessons for conservation

During 2002–2009, we surveyed butterflies at 73 bogs, 20 adjacent lowland roadsides, and 5 nearby upland roadsides in northern Wisconsin and three bogs in central Wisconsin, with additional observations from 1986 to 2001. Especially in northern Wisconsin, bogs are relatively unaffected by humans, but naturally comprise <1% of the landscape. Bog specialist species composition varied by bog type (muskeg, kettlehole, coastal peatland). Specialist abundance also varied significantly both among bog types and within type among sites. A number of bog specialists frequently occurred in numerous examples of bogs, including all three types. But virtually no specialist individuals occurred in nearby upland roadsides. Northern Wisconsin bogs had similar specialist species richness compared to large barrens and heaths in the same region. Specialist species comprised a small proportion (10%) of all butterfly species recorded in bogs, similar to proportions reported for specialists in tallgrass prairie and barrens. However, specialists accounted for nearly half the total individuals recorded in bogs, comparable to proportions of specialists found in less fragmented vegetation (barrens) and larger patches of favorably managed prairie, but far exceeding proportions observed in other highly fragmented prairie patches. A fundamental lesson may be that aiming to conserve typical ecosystems, even if native, and their average processes, leads to average (generalist) butterflies. Bogs have different vegetation types superimposed on each other, including bog, heath, forest, sedge meadow, and wet meadow associates in the same spots. Conservation management needs to avoid simplifying the vegetation to one layer, reducing specialist fauna. Long-term vegetative consistency, as in bogs, is advised for conservation management of specialist butterflies in other fragmented vegetations.     

Landscape-scale conservation in practice: lessons from northern England, UK

Landscape-scale conservation projects are now Butterfly Conservation??s main delivery mechanism to conserve the UK??s threatened Lepidoptera. Butterfly Conservation currently works or has recently worked in 79 different landscapes targeted at key areas for threatened species, all of which involve partnerships with government agencies, other conservation organisations and landowners. Broadly we utilise two approaches firstly by providing advice to landowners and encouraging or assisting with the uptake of agri-environment or woodland grant schemes and secondly by securing external funding to directly undertake habitat management under the guidance of Butterfly Conservation project officers. These are not mutually exclusive with most projects having elements of both approaches. We describe two projects from northern England which utilise the direct funding approach and provide evidence for some of the lessons learnt by Butterfly Conservation??s 10 years experience of landscape-scale conservation delivery. From County Durham we demonstrate that for the Small Pearl-bordered Fritillary Boloria selene Denis & Schiff. it is possible to restore even very small fragmented landscapes. On the North York Moors we show that a non-equilibrium declining Duke of Burgundy Hamearis lucina L. metapopulation can be stabilised by carefully targeting restoration management, demonstrating the cost benefits of early intervention.     

Six endemic plant species from central Argentina: an evaluation of their conservation status

The purpose of this study is to determine the conservation status of six vascular plant species with a restricted distribution or endemic to the mountainous areas in the province of Córdoba, central Argentina, by using the IUCN 1994 Red List Categories. The population number was estimated using a statistical method based on field data. The predicted decrease in the population number on a 10 yr projection was estimated taking into account the area to be used for future afforestation programs. To determine the area of occupancy and the extent of occurrence, an exhaustive bibliographical survey was carried out and herbarium specimens deposited in several institutions were revised. Aa achalensis, Adesmia cordobensis, Buddleja cordobensis, Croton argentinus and Oenothera cordobensis were considered as Vulnerable, whereas Solanum restrictum was assigned to the Endangered category. The categories assigned to Aa achalensis and Solanum restrictum are considered at the global level, whereas those assigned to Croton argentinus, Oenothera cordobensis, Adesmia cordobensis and Buddleja cordobensis should be considered at the local level. In all six cases the risk of extinction is high and suitable conservation strategies should be developed for each species. The most important threat factor is the planned afforestation in the area using exotic timber species; under these conditions the creation of a reserve in the studied area would be desirable in order to conserve five of the plants studied and, considering that 95% of its species are indigenous, the local flora as a whole.     

Tasmanian devil facial tumour disease: lessons for conservation biology

Tasmanian devil facial tumour disease is an infectious cancer that threatens the largest surviving marsupial carnivore with extinction. After emerging in 1996, it has spread across most of the range of the species, leading to a population decline of more than 60%. This bizarre disease, in which the cancer cells themselves are the infective agent, illustrates some important general principles about disease and conservation biology, including the threat posed by loss of genetic diversity and the potential of pathogens with frequency-dependent transmission to cause extinction.     

Ancient DNA and conservation: lessons from the endangered kiwi of New Zealand

Conservation genetics typically seeks to map the distribution of contemporary genetic variation across space, and to use the resulting genetic parameters to infer any likely short-term evolutionary consequences for rare and endangered species. Recent developments in the study of ancient DNA now enable the extension of genetic variation studies backwards in time and provide a context by which to interpret contemporary levels of genetic variation, in addition to any patterns of genetic change over time. Ancient DNA research can also help to determine past levels of genetic diversity, identify species' boundaries and reveal former ranges among morphologically cryptic taxa. Ancient DNA sequence data for the New Zealand kiwi (Apteryx spp.) are presented and we show that most ancient populations of rowi and tokoeka exhibited private mitochondrial DNA haplotypes. Moreover, we illustrate that the extinction of these populations has led to the loss of considerable genetic variation. We also use ancient DNA methodology to determine past species distributions for brown kiwi and great spotted kiwi whose bones are morphologically indistinguishable.     

Ecology of Salix variegata seed germination: Implications for species distribution and conservation in the Three Gorges region

The Three Gorges Project in China has brought significant changes to the region's riparian environment, posing serious challenges to biodiversity conservation. Salix variegata is a native shrub distributed on riverbanks in the Three Gorges reservoir region, and has important ecological function in the community. In this study, we studied the ecology of seed germination of S. variegata as efforts to understand its spatial distribution and develop conservation strategies. We found that soil type, soil moisture content and temperature all had significant effects on seed germination in S. variegata. Germination rate increased with the increasing soil moisture, while decreased in over-saturated soil. The germination rate in riverbank sand was higher than in sandy soil and clay loam. The optimal temperature for seed germination was 24 °C, under which 100% of germination was reached in 7 days. Seed viability and germination declined significantly with time after being released from fruits. The results suggest that soil moisture is the determining factor on seed germination, and influenced distribution of S. variegata. The tributary riverbanks above 175 m in the Three Gorges reservoir region can be used for the conservation of the species, as their fluvial patterns should have not been disturbed by the hydropower project.     

Coordinating conservation: global networking for species survival

The Species Survival Commission (SSC) of IUCN—the World Conservation Union is the largest, most comprehensive and diverse professional conservation network in existence today. It brings together over 6000 volunteers from more than 160 countries to contribute to the conservation of biological diversity by developing and executing programmes to study, save, restore, and manage wisely species and their habitats. The SSC is organized primarily along taxonomic lines, with members distributed in 96 Specialist Groups focusing on distinct groups of species. These groups are a source of the most current and expert information on the conservation status and priorities for action for species in the wild. As such, they provide an invaluable resource in setting priorities for captive propagation and in linking ex situ actions. In addition, the SSC has five disciplinary Specialist Groups that provide expertise to both the zoo community and field conservationists in areas such as reintroductions, veterinary medicine, captive breeding as a conservation tool, and the impact of invasive species on native flora and fauna. The effectiveness of the SSC is greatly enhanced by the close connections within its network between zoo professionals, academic scientists, field conservationists, and managers of natural resources. Challenges to the SSC currently include better information management, organization at the national level, and extending coverage in areas such as marine biodiversity.     

Thermophilic lifestyle for an uncultured archaeon from hydrothermal vents: evidence from environmental genomics

We present a comparative analysis of two genome fragments isolated from a diverse and widely distributed group of uncultured euryarchaea from deep-sea hydrothermal vents. The optimal activity and thermostability of a DNA polymerase predicted in one fragment were close to that of the thermophilic archaeon Thermoplasma acidophilum, providing evidence for a thermophilic way of life of this group of uncultured archaea.     

Prioritizing species for conservation planning

The efforts to protect biological diversity must be prioritized because resources for nature conservation are limited. Conservation prioritization can be based on numerous criteria, from ecological integrity to species representation, but in this review I address only species-level prioritization. Criteria used for species prioritization range from aesthetical to evolutionary considerations, but I focus on the aspects that are biologically relevant. I distinguish between two main aspects of diversity that are used as objectives: Maintenance of biodiversity pattern, and maintenance of biodiversity process. I identify two additional criteria typically used in species prioritization that serve for achieving the objectives: The species’ need of protection, and cost and effectiveness of conservation actions. I discuss how these criteria could be combined with either of the objectives in a complementarity-based benefit function framework for conservation prioritization. But preserving evolutionary process versus current diversity pattern may turn out to be conflicting objectives that have to be traded-off with each other, if pursued simultaneously. Although many reasonable criteria and methods exist, species prioritization is hampered by uncertainties, most of which stem from the poor quality of data on what species exist, where they occur, and what are the costs and benefits of protecting them. Surrogate measures would be extremely useful but their performance is still largely unknown. Future challenges in species prioritization lie in finding ways to compensate for missing information.     

Implications of the variance effective population size on the genetic conservation of monoecious species

The concept of variance effective population size [Ne_(v)] and other expressions are reviewed and described for specific sampling steps in germplasm collection and regeneration of monoecious species. Special attention is given to procedures for computing the variance of the number of contributed gametes [V(k)] to the next generation. Drift, as it occurs between generations, was considered to contain a component due to the sampling of parents and a subsequent component due to the sampling of gametes. This demonstrates that drift, caused by reduction of seed viability, damages the genetic integrity of accessions stored in germplasm banks. The study shows how mating designs, such as plant-to-plant or chain crossings with additional female gametic control, can partially alleviate this problem. Optimal procedures for increasing Ne_(v) when collecting germplasm in the field are also discussed. The effect of different female and male gametic control strategies on Ne_(v) is considered under several situations. Practical examples illustrating the use of V(k) and Ne_(v) expressions are given.     

The hemibiotrophic lifestyle of Colletotrichum species

Colletotrichum species infect several economically important crop plants. To establish a compatible parasitic interaction, a specialized infection cell, the melanized appressorium, is differentiated on the cuticle of the host. After penetration, an infection vesicle and primary hyphae are formed. These structures do not kill the host cell and show some similarities with haustoria formed by powdery mildews and rust fungi. Therefore, this stage of infection is called biotrophic. Later in the infection process, necrotrophic secondary hyphae spread within and kill the host tissue. The lifestyle of Colletotrichum species is called hemibiotrophic, as biotrophic and necrotrophic developmental stages are sequentially established. As most Colletotrichum species are accessible to molecular techniques, genes can be identified and functionally characterized. Here we demonstrate that Agrobacterium tumefaciens-mediated transformation is a well-suited method for tagging of genes mediating compatibility in the Colletotrichum graminicola-maize interaction.