[Show abstract][Hide abstract] ABSTRACT: Threatened species often have small and isolated populations where mating among relatives can result in inbreeding depression increasing extinction risk. Effective management is hampered by a lack of syntheses summarising the magnitude of, and variation in inbreeding depression. Here we describe the nature and scope of the literature examining phenotypic/fitness consequences of inbreeding, to provide a foundation for future syntheses and management.
We searched the literature for articles documenting the impact of inbreeding in natural populations. Article titles, abstracts and full-texts were assessed against a priori defined criteria, and information relating to study design, quality and other factors that may influence inbreeding responses (e.g. population size) was extracted from relevant articles.
The searches identified 11457 articles, of which 614 were assessed as relevant and included in the systematic map (corresponding to 703 distinct studies). Most studies (663) assessed within-population inbreeding resulting from self-fertilisation or consanguineous pairings, while 118 studies assessed among-population inbreeding due to drift load. Plants were the most studied taxon (469 studies) followed by insects (52 studies) and birds (43 studies). Most studies investigated the effects of inbreeding on components of fitness (e.g. survival or fecundity; 648 studies) but measurements were typically under laboratory/greenhouse conditions (486 studies). Observations were also often restricted to the first inbred generation (607 studies) and studies frequently lacked contextual information (e.g. population size).
Our systematic map describes the scope and quality of the evidence describing the phenotypic consequences of inbreeding. The map reveals substantial evidence relating to inbreeding responses exists, but highlights information is still limited for some aspects, including the effects of multiple generations of inbreeding. The systematic map allowed us to define several conservation-relevant questions, where sufficient data exists to support systematic reviews, e.g. How do inbreeding responses vary with population size? However, we found that such syntheses are likely to be constrained by incomplete reporting of critical contextual information. Our systematic map employed the same rigorous literature assessment methods as systematic review, including a novel survey of study quality and thus provides a robust foundation to guide future research and syntheses seeking to inform conservation decision-making.
[Show abstract][Hide abstract] ABSTRACT: Obtaining accurate phylogenies and effective species discrimination using a small standardised set of plastid genes is challenging in evolutionarily young lineages. Complete plastid genome sequencing offers an increasingly easy-to-access source of characters that helps address this. The usefulness of this approach, however, depends on the extent to which plastid haplotypes track morphological species boundaries. We have tested the power of complete plastid genomes to discriminate among multiple accessions of 11 out of 13 New Caledonian Araucaria species, an evolutionary young lineage where the standard DNA barcoding approach has so far failed and phylogenetic relationships have remained elusive. Additionally, 11 nuclear gene regions were Sanger sequenced for all accessions to ascertain the success of species discrimination using a moderate number of nuclear genes. Overall, fewer than half of the New Caledonian Araucaria species with multiple accessions were monophyletic in the plastid or nuclear trees. However, the plastid data retrieved a phylogeny with a higher resolution compared to any previously published tree of this clade and supported the monophyly of about twice as many species and nodes compared to the nuclear data set. Modest gains in discrimination thus are possible, but using complete plastid genomes or a small number of nuclear genes in DNA barcoding may not substantially raise species discriminatory power in many evolutionarily young lineages. The big challenge therefore remains to develop techniques that allow routine access to large numbers of nuclear markers scaleable to thousands of individuals from phylogenetically disparate sample sets.This article is protected by copyright. All rights reserved.
[Show abstract][Hide abstract] ABSTRACT: Background: Hybridisation between locally common and rare plant species is of conservation concern as it may lead to the extinction of the rare taxon. Rumex aquaticus (2n = ca. 200, Polygonaceae) is a widespread Euro-Siberian species but rare in the British Isles. It hybridises freely with the locally abundant congener R. obtusifolius (2n = 40) producing fertile and viable hybrids.
Aims: We aimed to establish whether hybridisation poses an extinction threat to R. aquaticus in Britain.
Methods: Flow cytometry, AFLPs and morphological characters were used to assess the extent of hybridisation between R. obtusifolius and R. aquaticus.
Results: Flow cytometry was the most useful tool to distinguish between hybrids and parental species and indicated that out of 88 samples from two hybrid populations, 85% were likely to be F1s and only 15% were likely to be back-crosses to R. aquaticus. AFLP markers were only able to identify putative F1 hybrids reliably and 11 morphological traits could not distinguish unambiguously between hybrids and pure R. aquaticus.
Conclusions: Although our data suggest that genetic assimilation of pure R. aquaticus populations is unlikely to be the case in the future, there is a potential threat from demographic swamping by hybrids and targeted protection of R. aquaticus habitat is proposed as a management strategy.
[Show abstract][Hide abstract] ABSTRACT: New Caledonia is a global biodiversity hotspot. Hypotheses for its biotic richness suggest either that the island is a 'museum' for an old Gondwana biota or alternatively it has developed following relatively recent long distance dispersal and in situ radiation. The conifer genus Araucaria (Araucariaceae) comprises 19 species globally with 13 endemic to this island. With a typically Gondwanan distribution, Araucaria is particularly well suited to testing alternative biogeographic hypotheses concerning the origins of New Caledonian biota. We derived phylogenetic estimates using 11 plastid and rDNA ITS2 sequence data for a complete sampling of Araucaria (including multiple accessions of each of the 13 New Caledonian Araucaria species). In addition, we developed a dataset comprising 4 plastid regions for a wider taxon sample to facilitate fossil based molecular dating. Following statistical analyses to identify a credible and internally consistent set of fossil constraints, divergence times estimated using a Bayesian relaxed clock approach were contrasted with geological scenarios to explore the biogeographic history of Araucaria. The phylogenetic data resolve relationships within Araucariaceae and among the main lineages in Araucaria, but provide limited resolution within the monophyletic New Caledonian species group. Divergence time estimates suggest a Late Cretaceous-Cenozoic radiation of extant Araucaria and a Neogene radiation of the New Caledonian lineage. A molecular timescale for the evolution of Araucariaceae supports a relatively recent radiation, and suggests that earlier (pre-Cenozoic) fossil types assigned to Araucaria may have affinities elsewhere in Araucariaceae. While additional data will be required to adequately resolve relationships among the New Caledonian species, their recent origin is consistent with overwater dispersal following Eocene emersion of New Caledonia but is too old to support a single dispersal from Australia to Norfolk Island for the radiation of the Pacific Araucaria sect. Eutacta clade.
PLoS ONE 10/2014; 9(10). DOI:10.1371/journal.pone.0110308 · 3.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: AimTo examine the phylogeography of Ficus insipida subsp. insipida in order to investigate patterns of spatial genetic structure across the Neotropics and within Amazonia.LocationNeotropics.Methods
Plastid DNA (trnH–psbA; 410 individuals from 54 populations) and nuclear ribosomal internal transcribed spacer (ITS; 85 individuals from 27 populations) sequences were sampled from Mexico to Bolivia, representing the full extent of the taxon's distribution. Divergence of plastid lineages was dated using a Bayesian coalescent approach. Genetic diversity was assessed with indices of haplotype and nucleotide diversities, and genetic structure was examined using spatial analysis of molecular variance (SAMOVA) and haplotype networks. Population expansion within Amazonia was tested using neutrality and mismatch distribution tests.ResultstrnH–psbA sequences yielded 19 haplotypes restricted to either Mesoamerica or Amazonia; six haplotypes were found among ITS sequences. Diversification of the plastid DNA haplotypes began c. 14.6 Ma. Haplotype diversity for trnH–psbA was higher in Amazonia. Seven genetically differentiated SAMOVA groups were described for trnH–psbA, of which two were also supported by the presence of unique ITS sequences. Population expansion was suggested for both markers for the SAMOVA group that contains most Amazonian populations.Main conclusionsOur results show marked population genetic structure in F. insipida between Mesoamerica and Amazonia, implying that the Andes and seasonally dry areas of northern South America are eco-climatic barriers to its migration. This pattern is shared with other widespread pioneer species affiliated to wet habitats, indicating that the ecological characteristics of species may impact upon large-scale phylogeography. Ficus insipida also shows genetic structure in north-western Amazonia potentially related to pre-Pleistocene historical events. In contrast, evident population expansion elsewhere in Amazonia, in particular the presence of genetically uniform populations across the south-west, indicate recent colonization. Our findings are consistent with palaeoecological data that suggest recent post-glacial expansion of Amazonian forests in the south.
Journal of Biogeography 05/2014; 41(9). DOI:10.1111/jbi.12326 · 4.59 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: New Caledonia is a global biodiversity hotspot facing extreme environmental degradation. Given the urgent need for conservation prioritisation, we have made a first-pass quantitative assessment of the distribution of Narrow Endemic Species (NES) in the flora to identify species and sites that are potentially important for conservation action. We assessed the distributional status of all angiosperm and gymnosperm species using data from taxonomic descriptions and herbarium samples. We characterised species as being NES if they occurred in 3 or fewer locations. In total, 635 of the 2930 assessed species were classed as NES, of which only 150 have been subjected to the IUCN conservation assessment. As the distributional patterns of un-assessed species from one or two locations correspond well with assessed species which have been classified as Critically Endangered or Endangered respectively, we suggest that our distributional data can be used to prioritise species for IUCN assessment. We also used the distributional data to produce a map of "Hotspots of Plant Narrow Endemism" (HPNE). Combined, we used these data to evaluate the coincidence of NES with mining activities (a major source of threat on New Caledonia) and also areas of conservation protection. This is to identify species and locations in most urgent need of further conservation assessment and subsequent action. Finally, we grouped the NES based on the environments they occurred in and modelled the habitat distribution of these groups with a Maximum Entropy Species Distribution Model (MaxEnt). The NES were separable into three different groups based primarily on geological differences. The distribution of the habitat types for each group coincide partially with the HPNE described above and also indicates some areas which have high habitat suitability but few recorded NES. Some of these areas may represent under-sampled hotspots of narrow endemism and are priorities for further field work.
PLoS ONE 09/2013; 8(9):e73371. DOI:10.1371/journal.pone.0073371 · 3.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Conservation policies usually focus on in situ protection of native populations, a priority that requires accurate assessment of population status. Distinction between native and introduced status can be particularly difficult (and at the same time, is most important) for species whose natural habitat has become both rare and highly fragmented. Here, we address the status of the white elm (Ulmus laevis Pallas), a European riparian tree species whose populations have been fragmented by human activity and is protected wherever it is considered native. Small populations of this species are located in Iberia, where they are unprotected because they are considered introductions due to their rarity. However, Iberia and neighbouring regions in southwestern France have been shown to support discrete glacial refuge populations of many European trees, and the possibility remains that Iberian white elms are native relicts. We used chloroplast RFLPs and nuclear microsatellites to establish the relationship between populations in Iberia and the Central European core distribution. Bayesian approaches revealed significant spatial structure across populations. Those in Iberia and southwestern France shared alleles absent from Central Europe, and showed spatial population structure within Iberia common in recognized native taxa. Iberian populations show a demographic signature of ancient population bottlenecks, while those in Central European show a signature of recent population bottlenecks. These patterns are not consistent with historical introduction of white elm to Iberia, and instead strongly support native status, arguing for immediate implementation of conservation measures for white elm populations in Spain and contiguous areas of southern France.Heredity advance online publication, 11 September 2013; doi:10.1038/hdy.2013.81.
[Show abstract][Hide abstract] ABSTRACT: To understand the evolutionary consequences of hybridization between the outcrossing plant Geum rivale (Rosaceae) and the selfer Geum urbanum, we tested the predictions of two simple models that assume either (A) low or (B) high pollen fitness in hybrids. Model A predicts only four genotypic classes (G. rivale, G. rivale backcross [BCR ], F1, and Geum urbanum) and asymmetric introgression from inbreeding to outbreeding species. Model B predicts additional genotypic classes and potential generation of novel inbreeding lines in the hybrid swarm. Amplified fragment length polymorphism (AFLP) analysis of adults revealed only the four genotypes predicted by model A. However, microsatellite analysis of parent-progeny arrays demonstrated production of selfed offspring by F1 and BCR maternal parents and contribution of these genotypes to outcross pollen pools, as predicted by model B. Moreover, AFLP and morphological analysis showed that the offspring generation comprised genotypes and phenotypes covering the entire spectrum of variation between the two parental species, in line with model B. A common garden experiment indicated no systematic reduction in fitness of offspring derived from hybrid parents. The genetic structure of the adults in the Geum hybrid swarm cannot be explained by restricted mating patterns but may result from ecological selection acting on a diverse offspring population.
[Show abstract][Hide abstract] ABSTRACT: Scotland's mountains are home to a rare and unique liverwort community, 'the oceanic-montane liverwort-rich heath', but its component species are absent from regions where they could potentially thrive. Many biological characteristics of these species are unknown, making it impossible to explain the reasons for their rarity; however, they have not been observed to produce sporophytes within Britain. We use ex situ cultivation of whole liverworts and fragments, and in situ cultivation of fragments, to assess the growth rate and the potential for vegetative reproduction of several species. Most of the species grew from both fragments and as whole plants, indicating that the rarity of the liverwort heath is not due to poor powers of regeneration. We propose that growth rate and the potential to regenerate from fragments are important factors structuring the liverwort heath community, at least locally. Furthermore, this study demonstrates that there is potential for ex situ conservation of rare liverwort species, in situ enhancement of existing populations, and creation of new ones.
[Show abstract][Hide abstract] ABSTRACT: Premise of the study:
Microsatellite markers were developed for the hemiparasitic plant Melampyrum sylvaticum to investigate the breeding system, genetic diversity, and structure of populations in the United Kingdom, Sweden, and Norway.
Methods and results:
Microsatellites were isolated from genomic DNA using an enrichment protocol. Twenty-nine loci were characterized in two individuals from each of 15 geographically disparate populations ("global"). Seven polymorphic loci were further characterized in one population ("local"). The number of alleles per locus ranged from two to 12 in the global sample and one to seven in the local sample. The expected heterozygosity ranged from 0-0.75, the observed heterozygosity from 0-0.1, and the inbreeding coefficient from 0.84-1 in the local sample.
The results show the utility of these novel polymorphic microsatellite markers for further conservation genetic analyses. The strong deficit of heterozygosity across all loci in the local sample suggests the species may be inbreeding.
American Journal of Botany 10/2012; 99(11). DOI:10.3732/ajb.1200103 · 2.60 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: We developed ten microsatellites markers to study the population genetic structure of two ultramafic scrublands species in New Caledonia, Scaevola montana a common species used in ecological restoration of mining sites, and S. coccinea a narrow endemic species of the Tontouta valley. The markers were isolated from S. montana. Nine loci are polymorphic in S. montana; eight were polymorphic in S. coccinea. The narrow endemic species showed lower variation at these loci than S. montana. There is a significant heterozygosity deficit in S. montana at four loci, and a global significant inbreeding coefficient across all loci (F
IS = 0.159). In contrast, the tested populations of S. coccinea did not show significant deviations from Hardy–Weinberg expectations. These markers are now being used in conservation genetic studies aiming to understand the biology of these species and to provide information to guide restoration programmes.
[Show abstract][Hide abstract] ABSTRACT: DNA barcoding in the land plants presents a number of challenges compared to DNA barcoding in many animal clades. The CO1 animal DNA barcode is not effective for plants. Plant species hybridize frequently, and there are many cases of recent speciation via mechanisms, such as polyploidy and breeding system transitions. Additionally, there are many life-history trait combinations, which combine to reduce the likelihood of a small number of markers effectively tracking plant species boundaries. Recent results, however, from the two chosen core plant DNA barcode regions rbcL and matK plus two supplementary regions trnH-psbA and internal transcribed spacer (ITS) (or ITS2) have demonstrated reasonable levels of species discrimination in both floristic and taxonomically focused studies. We describe sampling techniques, extraction protocols, and PCR methods for each of these two core and two supplementary plant DNA barcode regions, with extensive notes supporting their implementation for both low- and high-throughput facilities.