Range-edge effects promote clonal growth in peripheral populations of the one-sided wintergreen Orthilia secunda

Existing in suboptimal conditions is a frequent occurrence for species inhabiting the cusp of their ecological range. In range-edge populations of plants, the scarcity of suitable habitat may be reflected in small population sizes which may result in increased self-pollination and/or inbreeding and an increase in the incidence of clonal reproduction. These factors may result in a decrease in levels of genetic diversity and a loss of potential adaptive variation that may compromise species' ability to cope with changes in their environment, an issue that is particularly relevant today with the current concern surrounding global climate change and its effect on species' distributional ranges. In the present study, we have compared the levels of clonal reproduction in the one-sided wintergreen Orthilia secunda (L.) House in (1) populations from its main continuous distribution range, (2) populations occurring on the limits of the continuous range, and (3) peripheral populations outwith the species' continuous distribution range. Range-edge populations in Scotland and Sweden displayed significantly lower genotypic richness and diversity than those from the main area of the species' distribution in these countries. Populations from Ireland, which occur in the temperate zone rather than the boreal conditions that are the preferred habitat for the species, and which represent relict populations left over from cooler periods in the Earth's history, displayed no within-population genetic diversity, suggesting a complete lack of sexual reproduction. Furthermore, the genetic distinctiveness of the Irish populations, which contained alleles not found in either the Scottish or the Swedish populations, highlights the value of 'trailing edge' populations and supports the concept of 'parochial conservation', namely the conservation of species that are locally rare but globally common.

Expressed sequence tag-derived microsatellites for the cool-water marine copepod Calanus finmarchicus

The copepod Calanus finmarchicus is the major contributor to zooplankton biomass in the North Atlantic and Norwegian Sea, but recent studies have shown a 70% decrease in abundance as well as a northward shift in the species' range. Insights into dispersal capabilities gained from population genetic studies will be crucial in predicting the response of C. finmarchicus communities to climate change and, consequently, we have developed a set of expressed sequence tag-derived microsatellite markers to allow fine-scale elucidation of population structuring and dispersal. Ten polymorphic markers displayed between two and 19 alleles, with levels of expected heterozygosity ranging from 0.044 to 0.924.

Cryptic species diversity in a widespread bumble bee complex revealed using mitochondrial DNA RFLPs

Cryptic species diversity is thought to be common within the class Insecta, posing problems for basic ecological and population genetic studies and conservation management. Within the temperate bumble bee (Bombus spp.) fauna, members of the subgenus Bombus sensu stricto are amongst the most abundant and widespread. However, their species diversity is controversial due to the extreme difficulty or inability morphologically to identify the majority of individuals to species. Our character-based phylogenetic analyses of partial CO1 (700 bp) from 39 individuals spread across their sympatric European ranges provided unequivocal support for five taxa (3-22 diagnostic DNA base pair sites per species). Inclusion of 20 Irish specimens to the dataset revealed >= 2.3% sequence divergence between taxa and 200 m) whilst B. cryptarum was relatively more abundant at higher altitudes. Bombus magnus was rarely encountered at urban sites. Both B. lucorum and B. terrestris are nowadays reared commercially for pollination and transported globally. Our RFLP approach to identify native fauna can underpin ecological studies of these important cryptic species as well as the impact of commercial bumble bees on them.

Morphological and molecular characters reveal differentiation in a Neotropical social bee, Melipona beecheii (Apidae : Meliponini)

Morphometrics and DNA microsatellites were used to analyse the genetic structure of populations of the stingless bee M. beecheii from two extremes of its geographic range. The results showed that populations from Costa Rica and Yucatan exhibit substantial phenotypic and molecular differentiation. Bees from Yucatan were smaller and paler than those from Costa Rica. The value of multilocus F-ST = 0.280 (P <0.001) confirmed that there were significant molecular genetic differences between the two populations. Populations showed significant deviation from Hardy Weinberg equilibrium and the values of FIS (the inbreeding coefficient) were positive for Costa Rica = 0.416 and the Yucatan Peninsula = 0.193, indicating a lack of heterozygotes in both populations possibly due to inbreeding. The DNA sequence of 678 bp of the mitochondrial gene COI differed between populations by 1.2%. The results of this study should be considered in conservation programmes, particularly with regard to the movement of colonies between regions.

Development of microsatellites for the invasive riparian plant Impatiens glandulifera (Himalayan balsam) using intersimple sequence repeat cloning

Impatiens glandulifera (Himalayan balsam) is an invasive riparian plant species that can outcompete native perennials. Population genetic data on dispersal may aid in the management of invasive species, so we have developed microsatellite markers for this significant invader using an intersimple sequence repeat (ISSR)-based cloning method. Eight polymorphic markers displayed between two and five alleles, with overall levels of observed and expected heterozygosities ranging from 0.0500 to 0.7500 and from 0.1449 to 0.7692, respectively.

Universal plastid primers for chlorophyta and rhodophyta

To date, the majority of molecular genetic studies in algae have utilized a fairly limited range of markers such as the plastid rbcL gene and spacer, the mitochondrial cox2-3 spacer or the nuclear ribosomal DNA and spacers. The lack of available markers has been particularly problematic in studies of within-species variation. Whilst microsatellites are now being developed in many algal species, there remains a need for universal markers that can be applied to a wide range of species. The increasing availability of complete plastid genome sequences for several algae has allowed us to develop two sets of universal primers, similar to those available in higher plants, for the amplification of coding and non-coding regions of the plastid genome in red and green algae. These markers are expected to be useful in a broad range of algal population genetic and phylogenetic studies.

Characterization of polymorphic microsatellites for the periwinkle gastropod, Littorina littorea (Linnaeus, 1758) and their cross-amplification in four congeners

Eight polymorphic microsatellite loci are described for Littorina littorea (Linnaeus, 1758). Data on allelic variation in Irish and Celtic Sea samples are reported. The average number of alleles per locus was 11 (range 4-29), and observed and expected heterozygosities ranged from 6.9 to 84.3% and from 9.4 to 95.2%, respectively. Loci did not deviate from Hardy-Weinberg equilibrium and no linkage disequilibrium between loci pairs was detected. Microsatellites were not highly conserved in the congeners, L. fabalis, L. saxatilis, L. compressa and L. obtusata as evidenced by a low rate of cross-amplification. These microsatellites should prove useful in population genetic studies.

Characterization of polymorphic microsatellites for the rough periwinkle gastropod, Littorina saxatilis (Olivi, 1792) and their cross-amplification in four congeners.

Eight new microsatellite loci were characterized for Littorina saxatilis (Olivi, 1792) and tested for their cross-hybridization in congeners. All loci were polymorphic in Irish and Celtic Sea samples, with an average number of alleles per locus of 15 (range, 6–31). Observed and expected locus heterozygosities ranged from 26 to 85% and from 53 to 92%, respectively. Three loci showed excess homozygosity and significant departures from Hardy–Weinberg expectations in one sample, possibly due to null alleles, population structuring or inbreeding. No linkage disequilibrium was detected among loci within samples. A high degree of cross-hybridization was observed in closely related congeners and most loci were polymorphic. These markers will be useful for investigating population genetic diversity and connectivity in coastal populations, especially for marine reserve design.

Multiple origins of European populations of giant liver fluke Fascioloides magna (Trematoda: Fasciolidae), an invasive liver parasite of ruminants

The giant liver fluke, Fascioloides magna, liver parasite of free-living and domestic ruminants of Europe and North America, was analysed in order to determine the origin of European populations and to reveal the biogeography of this originally North American parasite on the European continent. The previously selected variable fragments of the mitochondrial cytochrome c oxidase subunit I (cox1; 384 bp) and nicotinamid dehydrogenase subunit I (nad1; 405 bp) were applied as a tool. The phylogenetic trees and haplotype networks were constructed and the level of genetic structuring was evaluated using population genetic tools. In F. magna individuals originating from all European natural foci (Italy, Czech Republic, Danube floodplain forests) and from four of five major North American enzootic areas, 16 cox1 and 18 nad1 haplotypes were determined. The concatenated sequence set produced 22 distinct haplotypes. The European fluke populations were less diverse than those from North America in that they contained proportionately fewer haplotypes (8), while more substantial level of genetic diversity and higher number of haplotypes (15) were recorded in North America. Only one haplotype was shared between the European (Italy) and North American (USA/Oregon and Canada/Alberta) flukes supporting a western North American origin of the Italian F. magna population. Haplotypes found in Italy were distinct from those determined in the remaining European localities what indicates that introduction of F. magna onto the European continent is a result of more than one event. In Czech focus, a south-eastern US origin of giant liver fluke was revealed. Identical haplotypes, common for parasites from Czech Republic and from expanding focus of Danube floodplain forests, implies introduction of F. magna to the Danube region from an already established Czech focus.

The conservation of bees: a global perspective

Bees are major pollinators of Angiosperms and therefore their apparent decline is of importance for humans and biodiversity. We synthesise results of 12 recent reviews to provide a global picture of the threats they face. Habitat loss is the major threat to bee diversity, whilst invasive species, emerging diseases, pesticide use, and climate change also have the potential to impact bee populations. We suggest that future conservation strategies need to prioritise (i) minimising habitat loss, (ii) making agricultural habitats bee-friendly, (iii) training scientists and the public in bee taxonomy and identification, (iv) basic autecological and population genetic studies to underpin conservation strategies, (v) assessing the value of DNA barcoding for bee conservation, (vi) determining the impact of invasive plants, animals, parasites and pathogens, and (vii) integrating this information to understand the potential impact of climate change on current bee diversity.

Identification of genetically and oceanographically distinct blooms of jellyfish

Reports of nuisance jellyfish blooms have increased worldwide during the last half-century, but the possible causes remain unclear.Apersistent difficulty lies in identifying whether blooms occur owing to local or regional processes. This issue can be resolved, in part, by establishing the geographical scales of connectivity among locations, which may be addressed using genetic analyses and oceanographic modelling. We used landscape genetics and Lagrangian modelling of oceanographic dispersal to explore patterns of connectivity in the scyphozoan jellyfish Rhizostoma octopus, which occurs en masse at locations in the Irish Sea and northeastern Atlantic. We found significant genetic structure distinguishing three populations, with both consistencies and inconsistencies with prevailing physical oceanographic patterns. Our analyses identify locations where blooms occur in apparently geographically isolated populations, locations where blooms may be the source or result of migrants, and a location where blooms do not occur consistently and jellyfish are mostly immigrant. Our interdisciplinary approach thus provides a means to ascertain the geographical origins of jellyfish in outbreaks, which may have wide utility as increased international efforts investigate jellyfish blooms. © 2013 The Authors.

The Opportunistic Pathogen Propionibacterium acnes: Insights into Typing, Human Disease, Clonal Diversification and CAMP Factor Evolution

We previously described a Multilocus Sequence Typing (MLST) scheme based on eight genes that facilitates population genetic and evolutionary analysis of P. acnes. While MLST is a portable method for unambiguous typing of bacteria, it is expensive and labour intensive. Against this background, we now describe a refined version of this scheme based on two housekeeping (aroE; guaA) and two putative virulence (tly; camp2) genes (MLST) that correctly predicted the phylogroup (IA, IA, IB, IC, II, III), clonal complex (CC) and sequence type (ST) (novel or described) status for 91% isolates (n = 372) via cross-referencing of the four gene allelic profiles to the full eight gene versions available in the MLST database (http://pubmlst.org/pacnes/). Even in the small number of cases where specific STs were not completely resolved, the MLST method still correctly determined phylogroup and CC membership. Examination of nucleotide changes within all the MLST loci provides evidence that point mutations generate new alleles approximately 1.5 times as frequently as recombination; although the latter still plays an important role in the bacterium's evolution. The secreted/cell-associated 'virulence' factors tly and camp2 show no clear evidence of episodic or pervasive positive selection and have diversified at a rate similar to housekeeping loci. The co-evolution of these genes with the core genome might also indicate a role in commensal/normal existence constraining their diversity and preventing their loss from the P. acnes population. The possibility that members of the expanded CAMP factor protein family, including camp2, may have been lost from other propionibacteria, but not P. acnes, would further argue for a possible role in niche/host adaption leading to their retention within the genome. These evolutionary insights may prove important for discussions surrounding camp2 as an immunotherapy target for acne, and the effect such treatments may have on commensal lineages. © 2013 McDowell et al.

Chiton phylogeny (Mollusca Polyplacophora) and the placement of the enigmatic species Choriplax grayi (H. Adams & Angas)

Shallow marine chitons (Mollusca:Polyplacophora:Chitonida) are widespread and well described from established morphoanatomical characters, yet key aspects of polyplacophoran phylogeny have remained unresolved. Several species, including Hemiarthrum setulosum Carpenter in Dall, 1876, and especially the rare and enigmatic Choriplax grayi (Adams & Angas, 1864), defy systematic placement. Choriplax is known from only a handful of specimens and its morphology is a mosaic of key taxonomic features from two different clades. Here, new molecular evidence provides robust support for its correct association with a third different clade: Choriplax is placed in the superfamily Mopalioidea. Hemiarthrum is included in Cryptoplacoidea, as predicted from morphological evidence. Our multigene analysis of standard nuclear and mitochondrial markers demonstrates that the topology of the order Chitonida is divided into four clades, which have also been recovered in previous studies: Mopalioidea is sister to Cryptoplacoidea, forming a clade Acanthochitonina. The family Callochitonidae is sister to Acanthochitonina. Chitonoidea is resolved as the earliest diverging group within Chitonida. Consideration of this unexpected result for Choriplax and our well-supported phylogeny has revealed differing patterns of shell reduction separating the two superfamilies within Acanthochitonina. As in many molluscs, shell reduction as well as the de novo development of key shell features has occurred using different mechanisms, in multiple lineages of chitons.

A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding

This study examines the potential of next-generation sequencing based ‘genotyping-by-sequencing’ (GBS) of microsatellite loci for rapid and cost-effective genotyping in large-scale population genetic studies. The recovery of individual genotypes from large sequence pools was achieved by PCR-incorporated combinatorial barcoding using universal primers. Three experimental conditions were employed to explore the possibility of using this approach with existing and novel multiplex marker panels and weighted amplicon mixture. The GBS approach was validated against microsatellite data generated by capillary electrophoresis. GBS allows access to the underlying nucleotide sequences that can reveal homoplasy, even in large datasets and facilitates cross laboratory transfer. GBS of microsatellites, using individual combinatorial barcoding, is potentially faster and cheaper than current microsatellite approaches and offers better and more data.