Population genomics as a new tool for wildlife management

Admixture and introgression have varied effects on population viability and fitness. Admixture might be an important source of new alleles, particularly for small, geographically isolated populations. However, admixture might also cause outbreeding depression if populations are adapted to different ecological or climatic conditions. Because of the emerging use of translocation and admixture as a conservation and wildlife management strategy to reduce genetic load (termed genetic rescue), the possible effects of admixture have practical consequences ( Bouzat et al. 2009 ; Hedrick & Fredrickson 2010 ). Importantly, genetic load and local adaptation are properties of individual loci and epistatic interactions among loci rather than properties of genomes. Likewise, the outcome and consequences of genetic rescue depend on the fitness effects of individual introduced alleles. In this issue of Molecular Ecology, Miller et al. (2012) use model‐based, population genomic analyses to document locus‐specific effects of a recent genetic rescue in the bighorn sheep population within the National Bison Range wildlife refuge (NBR; Montana, USA). They find a subset of introduced alleles associated with increased fitness in NBR bighorn sheep, some of which experienced accelerated introgression following their introduction. These loci mark regions of the genome that could constitute the genetic basis of the successful NBR bighorn sheep genetic rescue. Although population genomic analyses are frequently used to study local adaptation and selection (e.g. Hohenlohe et al. 2010 ; Lawniczak et al. 2010 ), this study constitutes a novel application of this analytical framework for wildlife management. Moreover, the detailed demographic data available for the NBR bighorn sheep population provide a rare and powerful source of information and allow more robust population genomic inference than is often possible.     

Beyond splitting hares and rabbiting on about major histocompatibility complex complexity

The genes of the major histocompatibility complex (MHC) have become the target of choice for studies wishing to examine adaptively important genetic diversity in natural populations. Within Molecular Ecology alone, there have been 71 papers on aspects of MHC evolution over the past few years, with an increasing year on year trend. This focus on the MHC is partly driven by the hypothesized links between MHC gene dynamics and ecologically interesting and relevant traits, such as mate choice and host–parasite interactions. However, an ability to pin down the evolutionary causes and ecological consequences of MHC variation in natural populations has proven challenging and has been hampered by the very issue that is attractive about MHC genes – their high levels of diversity. Linking high levels of MHC diversity to ecological factors in inherently complex natural populations requires a level of experimental design and analytical rigour that is extremely difficult to achieve owing to a plethora of potentially confounding and interacting variables. In this issue of Molecular Ecology, Smith et al. (2010) elegantly overcome the challenge of detecting complex interactions in complex systems by using an intricate analytical approach to demonstrate a role for MHC in the reproductive ability of a natural population of the European hare Lepus europaeus ( Fig. 1 ). Also in this issue, Oppelt et al. (2010) demonstrate a role for MHC variation in determining levels of hepatic coccidian infection in the European rabbit Oryctolagus cuniculus ( Fig. 2 ).

Figure 1 Open in figure viewer PowerPoint The European hare (Lepus europaeus).     

Mutants with aberrant numbers of gametic cells shed new light on old questions

In contrast to animals, plant gametes form in distinct haploid generations, termed gametophytes. The female gametophyte of Arabidopsis consists of two gametic cells, the egg and central cell, which are flanked by accessory cells. The gametic cells differ with respect to morphology, molecular attributes and, importantly, their fate: whereas the egg cell, upon fertilisation, gives rise to the embryo, the central cell forms the endosperm. To ensure correct endosperm formation, not only the egg cell but also the central cell has to fuse with a sperm cell. The respective sperm cell pair is delivered by a single pollen tube. In some plant species, the two male gametes appear to express a different bias towards the female gametes. Such a preference consequently determines their respective contribution to either embryo or endosperm development. In Arabidopsis and many other species the sperm cells are indistinguishable and it has been discussed whether they possess an inherent preference for either of the female gametes. The recent isolation of mutants that form an aberrant number of either male or female gametes stimulates discussion, albeit with different results. Furthermore, some data indicate that the central cell is competent to initiate endosperm formation without a paternal contribution. These data support the theory that the endosperm is of gametophytic rather than sporophytic origin.     

Using isolation‐by‐distance‐based approaches to assess the barrier effect of linear landscape elements on badger (Meles meles) dispersal

As the European badger (Meles meles) can be of conservation or management concern, it is important to have a good understanding of the species’ dispersal ability. In particular, knowledge of landscape elements that affect dispersal can contribute to devising effective management strategies. However, the standard approach of using Bayesian clustering methods to correlate genetic discontinuities with landscape elements cannot easily be applied to this problem, as badger populations are often characterized by a strong confounding isolation‐by‐distance (IBD) pattern. We therefore developed a two‐step method that compares the location of pairs of related badgers relative to a putative barrier and utilizes the expected spatial genetic structure characterized by IBD as a null model to test for the presence of a barrier. If a linear feature disrupts dispersal, the IBD pattern characterising pairs of individuals located on different sides of a putative barrier should differ significantly from the pattern obtained with pairs of individuals located on the same side. We used our new approach to assess the impact of rivers and roads of different sizes on badger dispersal in western England. We show that a large, wide river represented a barrier to badger dispersal and found evidence that a motorway may also restrict badger movement. Conversely, we did not find any evidence for small rivers and roads interfering with badger movement. One of the advantages of our approach is that potentially it can detect features that disrupt gene flow locally, without necessarily creating distinct identifiable genetic units.     

Monitoring the effective population size of a brown bear (Ursus arctos) population using new single-sample approaches

The effective population size (N(e) ) could be the ideal parameter for monitoring populations of conservation concern as it conveniently summarizes both the evolutionary potential of the population and its sensitivity to genetic stochasticity. However, tracing its change through time is difficult in natural populations. We applied four new methods for estimating N(e) from a single sample of genotypes to trace temporal change in N(e) for bears in the Northern Dinaric Mountains. We genotyped 510 bears using 20 microsatellite loci and determined their age. The samples were organized into cohorts with regard to the year when the animals were born and yearly samples with age categories for every year when they were alive. We used the Estimator by Parentage Assignment (EPA) to directly estimate both N(e) and generation interval for each yearly sample. For cohorts, we estimated the effective number of breeders (N(b) ) using linkage disequilibrium, sibship assignment and approximate Bayesian computation methods and extrapolated these estimates to N(e) using the generation interval. The N(e) estimate by EPA is 276 (183-350 95% CI), meeting the inbreeding-avoidance criterion of N(e) > 50 but short of the long-term minimum viable population goal of N(e) > 500. The results obtained by the other methods are highly consistent with this result, and all indicate a rapid increase in N(e) probably in the late 1990s and early 2000s. The new single-sample approaches to the estimation of N(e) provide efficient means for including N(e) in monitoring frameworks and will be of great importance for future management and conservation.     

Population genetic structure and conservation of marbled murrelets (<Emphasis Type="Italic">Brachyramphus marmoratus</Emphasis>)

Marbled murrelets (Brachyramphus marmoratus) are coastal seabirds that nest from California to the Aleutian Islands. They are declining and considered threatened in several regions. We compared variation in the mitochondrial control region, four nuclear introns and three microsatellite loci among194 murrelets from throughout their range except Washington and Oregon. Significant population genetic structure was found: nine private control region haplotypes and three private intron alleles occurred at high frequency in the Aleutians and California; global estimates of F _ST or Φ_ST and most pairwise estimates involving the Aleutians and/or California were significant; and marked isolation-by-distance was found. Given the available samples, murrelets appear to comprise five genetic management units: (1) western Aleutian Islands, (2) central Aleutian Islands, (3) mainland Alaska and British Columbia, (4) northern California, and (5) central California.     

The oldest ionoscopiform from China sheds new light on the early evolution of halecomorph fishes

The Halecomorphi are a major subdivision of the ray-finned fishes. Although living halecomorphs are represented solely by the freshwater bowfin, Amia calva, this clade has a rich fossil history, and the resolution of interrelationships among extinct members is central to the problem of understanding the origin of the Teleostei, the largest clade of extant vertebrates. The Ionoscopiformes are extinct marine halecomorphs that were inferred to have originated in the Late Jurassic of Europe, and subsequently dispersed to the Early Cretaceous of the New World. Here, we report the discovery of a new ionoscopiform, Robustichthys luopingensis gen. et sp. nov., based on eight well-preserved specimens from the Anisian (242–247 Ma), Middle Triassic marine deposits of Luoping, eastern Yunnan Province, China. The new species documents the oldest known ionoscopiform, extending the stratigraphic range of this group by approximately 90 Ma, and the geographical distribution of this group into the Middle Triassic of South China, a part of eastern Palaeotethys Ocean. These new data provide a minimum estimate for the split of Ionoscopiformes from its sister clade Amiiformes and shed new light on the origin of ionoscopiform fishes.     

Skipper genome sheds light on unique phenotypic traits and phylogeny

Background

Butterflies and moths are emerging as model organisms in genetics and evolutionary studies. The family Hesperiidae (skippers) was traditionally viewed as a sister to other butterflies based on its moth-like morphology and darting flight habits with fast wing beats. However, DNA studies suggest that the family Papilionidae (swallowtails) may be the sister to other butterflies including skippers. The moth-like features and the controversial position of skippers in Lepidoptera phylogeny make them valuable targets for comparative genomics.

Results

We obtained the 310 Mb draft genome of the Clouded Skipper (Lerema accius) from a wild-caught specimen using a cost-effective strategy that overcomes the high (1.6 %) heterozygosity problem. Comparative analysis of Lerema accius and the highly heterozygous genome of Papilio glaucus revealed differences in patterns of SNP distribution, but similarities in functions of genes that are enriched in non-synonymous SNPs. Comparison of Lepidoptera genomes revealed possible molecular bases for unique traits of skippers: a duplication of electron transport chain components could result in efficient energy supply for their rapid flight; a diversified family of predicted cellulases might allow them to feed on cellulose-enriched grasses; an expansion of pheromone-binding proteins and enzymes for pheromone synthesis implies a more efficient mate-recognition system, which compensates for the lack of clear visual cues due to the similarities in wing colors and patterns of many species of skippers. Phylogenetic analysis of several Lepidoptera genomes suggested that the position of Hesperiidae remains uncertain as the tree topology varied depending on the evolutionary model.

Conclusion

Completion of the first genome from the family Hesperiidae allowed comparative analyses with other Lepidoptera that revealed potential genetic bases for the unique phenotypic traits of skippers. This work lays the foundation for future experimental studies of skippers and provides a rich dataset for comparative genomics and phylogenetic studies of Lepidoptera.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1846-0) contains supplementary material, which is available to authorized users.     

Hunting Primates and Managing Forests: The Case of Iban Forest Farmers in Indonesian Borneo

Hunting by Iban forest farmers in West Kalimantan, Indonesia, is an important part of their subsistence economy, and as such became a focus of study as part of a conservation project in the Danau Sentarum Wildlife Reserve. In this paper, we examine Iban hunting of nonhuman primates with comparison to other large mammals. We analyze rates of encounter and capture, comparing encounters, hunting trips, and animal numbers. Information on habitats hunted shows the importance of secondary and old growth forest. Also examined are Iban attitudes, game preferences, and taboos. The significance of these findings is discussed with regard to the threats to wildlife from increases in the use of shotguns, human population, and habitat destruction, showing that conservation may be aided by promoting or enhancing certain aspects of the traditional Iban agroforestry system.     

A new approach to an old conundrum--DNA barcoding sheds new light on phenotypic plasticity and morphological stasis in microsnails (Gastropoda, Pulmonata, Carychiidae)

The identification of microsnail taxa based on morphological characters is often a time-consuming and inconclusive process. Aspects such as morphological stasis and phenotypic plasticity further complicate their taxonomic designation. In this study, we demonstrate that the application of DNA barcoding can alleviate these problems within the Carychiidae (Gastropoda, Pulmonata). These microsnails are a taxon of the pulmonate lineage and most likely migrated onto land independently of the Stylommatophora clade. Their taxonomical classification is currently based on conchological and anatomical characters only. Despite much confusion about historic species assignments, the Carychiidae can be unambiguously subdivided into two taxa: (i) Zospeum species, which are restricted to karst caves, and (ii) Carychium species, which occur in a broad range of environmental conditions. The implementation of discrete molecular data (COI marker) enabled us to correctly designate 90% of the carychiid microsnails. The remaining cases were probably cryptic Zospeum and Carychium taxa and incipient species, which require further investigation into their species status. Because conventional reliance upon mostly continuous (i.e. nondiscrete) conchological characters is subject to fallibility for many gastropod species assignments, we highly recommend the use of DNA barcoding as a taxonomic, cutting-edge method for delimiting microsnail taxa.     

Population size and habitat quality affect genetic diversity and fitness in the clonal herb <Emphasis Type=Italic>Cirsium dissectum</Emphasis>

Remaining populations of plant species in fragmented landscapes are threatened by declining habitat quality and reduced genetic diversity, but the interactions of these major factors are rarely studied together for species conservation. In this study, the interactions between population size, habitat quality, genetic diversity and fitness were investigated in 22 populations of the clonal herb Cirsium dissectum throughout the British Isles. Regression analysis was used to identify significant factors, and a structural equation model was developed to illustrate and integrate these interactions. It was found that smaller populations (measured as the total number of plants) had lower genetic diversity (proportion of polymorphic loci), and that reduced genetic diversity (allelic richness) had a negative impact on the survival of seedlings grown under standard conditions. Habitat quality also had a large effect on C. dissectum. Unmanaged sites with tall vegetation, no bare soil and higher nutrient levels had smaller populations of C. dissectum, but flowering was promoted. Flowering was suppressed in heavily grazed sites with short vegetation. Higher levels of bare soil and phosphorus both had a positive relationship with genetic diversity, but probably for distinctly different reasons: bare soil provides safe sites for establishment, whilst phosphorus may promote flowering and improve seed germination. In order to conserve C. dissectum, management needs to maintain site heterogeneity so that C. dissectum can flower and establishment gaps are still available for seedlings; when either component is reduced, negative feedbacks through reduced genetic diversity and individual fitness can be expected. This study therefore highlights the importance of considering both conservation genetics and habitat quality in the conservation of plant species.     

The mitochondrial genome of the moss Physcomitrella patens sheds new light on mitochondrial evolution in land plants

The phylogenetic positions of bryophytes and charophytes, together with their genome features, are important for understanding early land plant evolution. Here we report the complete nucleotide sequence (105,340 bp) of the circular-mapping mitochondrial DNA of the moss Physcomitrella patens. Available evidence suggests that the multipartite structure of the mitochondrial genome in flowering plants does not occur in Physcomitrella. It contains genes for 3 rRNAs (rnl, rns, and rrn5), 24 tRNAs, and 42 conserved mitochondrial proteins (14 ribosomal proteins, 4 ccm proteins, 9 nicotinamide adenine dinucleotide dehydrogenase subunits, 5 ATPase subunits, 2 succinate dehydrogenase subunits, apocytochrome b, 3 cytochrome oxidase subunits, and 4 other proteins). We estimate that 5 tRNA genes are missing that might be encoded by the nuclear genome. The overall mitochondrial genome structure is similar in Physcomitrella, Chara vulgaris, Chaetosphaeridium globosum, and Marchantia polymorpha, with easily identifiable inversions and translocations. Significant synteny with angiosperm and chlorophyte mitochondrial genomes was not detected. Phylogenetic analysis of 18 conserved proteins suggests that the moss-liverwort clade is sister to angiosperms, which is consistent with a previous analysis of chloroplast genes but is not consistent with some analyses using mitochondrial sequences. In Physcomitrella, 27 introns are present within 16 genes. Nine of its intron positions are shared with angiosperms and 4 with Marchantia, which in turn shares only one intron position with angiosperms. The phylogenetic analysis as well as the syntenic structure suggest that the mitochondrial genomes of Physcomitrella and Marchantia retain prototype features among land plant mitochondrial genomes.     

The ecological advantage of sexual reproduction in multicellular long-lived organisms

We present a model for the advantage of sexual reproduction in multicellular long-lived species in a world of structured resources in short supply. The model combines features of the Tangled Bank and the Red Queen hypothesis of sexual reproduction and is of broad applicability. The model is ecologically explicit with the dynamics of resources and consumers being modelled by differential equations. The life history of consumers is shaped by body mass-dependent rates as implemented in the metabolic theory of ecology. We find that over a broad range of parameters, sexual reproduction wins despite the two-fold cost of producing males, due to the advantage of producing offspring that can exploit underutilized resources. The advantage is largest when maturation and production of offspring set in before the resources of the parents become depleted, but not too early, due to the cost of producing males. The model thus leads to the dominance of sexual reproduction in multicellular animals living in complex environments, with resource availability being the most important factor affecting survival and reproduction.     

Polyploidy and its effect on evolutionary success: old questions revisited with new tools

Polyploidy, the condition of possessing more than two complete genomes in a cell, has intrigued biologists for almost a century. Polyploidy is found in many plants and some animal species and today we know that polyploidy has had a role in the evolution of all angiosperms. Despite its widespread occurrence, the direct effect of polyploidy on evolutionary success of a species is still largely unknown. Over the years many attractive hypotheses have been proposed in an attempt to assign functionality to the increased content of a duplicated genome. Among these hypotheses are the proposal that genome doubling confers distinct advantages to a polyploid and that these advantages allow polyploids to thrive in environments that pose challenges to the polyploid''s diploid progenitors. This article revisits these long-standing questions and explores how the integration of recent genomic developments with ecological, physiological and evolutionary perspectives has contributed to addressing unresolved problems about the role of polyploidy. Although unsatisfactory, the current conclusion has to be that despite significant progress, there still isn''t enough information to unequivocally answer many unresolved questions about cause and effect of polyploidy on evolutionary success of a species. There is, however, reason to believe that the increasingly integrative approaches discussed here should allow us in the future to make more direct connections between the effects of polyploidy on the genome and the responses this condition elicits from the organism living in its natural environment.     

Host–pathogen relationship between Salix and Melampsora sheds light on the parentage of some biomass willows

The association between willow ( Salix ) and rust ( Melampsora ) is highly specific. Willows named Salix burjatica , S. dasyclados ( S. × dasyclados ) and S. × calodendron are important in renewable-energy plantations in the UK and western Europe. There has been much controversy over their origin, species status and nomenclature. It has been suggested that they have originated from hybridization between. S. caprea , S. viminalis and S. cinerea . In the present work, 59 willow clones were investigated through morphological examination and detached leaf inoculation using willow differentials, for their association, in southwest England, with M. capraearum and three pathotypes of Melampsora epitea (Me-A, B and C). M. capraearum was found on all clones of S. caprea and its hybrids with S. aurita ; Me-A on all S. viminalis clones; Me-B on wild S. cinerea , S. × calodendron , S. × dasyclados 'De Biardii 445' and S . 'Spaethii'; Me-C on all S. burjatica clones and most S. × dasyclados clones. Both M. caprearum and Me-A infected all S. × sericans ( S. caprea × viminalis ) clones and S. × dasyclados 'LA041/03'. We suggest that S. × dasyclados 'LA041/03' should be treated as S. × sericans ( S. caprea × S. viminalis ); S. burjatica , S. dasyclados and S. × dasyclados as synonyms; S. × dasyclados 'De Biardii 445' as S. × calodendron 'De Biardii 445'; and S . 'Spaethii' as S. × calodendron 'Spaethii'.