Permanent genetic resources added to Molecular Ecology Resources Database 1 December 2011-31 January 2012

This article documents the addition of 473 microsatellite marker loci and 71 pairs of single‐nucleotide polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Barteria fistulosa, Bombus morio, Galaxias platei, Hematodinium perezi, Macrocentrus cingulum Brischke (a.k.a. M. abdominalis Fab., M. grandii Goidanich or M. gifuensis Ashmead), Micropogonias furnieri, Nerita melanotragus, Nilaparvata lugens Stål, Sciaenops ocellatus, Scomber scombrus, Spodoptera frugiperda and Turdus lherminieri. These loci were cross‐tested on the following species: Barteria dewevrei, Barteria nigritana, Barteria solida, Cynoscion acoupa, Cynoscion jamaicensis, Cynoscion leiarchus, Cynoscion nebulosus, Cynoscion striatus, Cynoscion virescens, Macrodon ancylodon, Menticirrhus americanus, Nilaparvata muiri and Umbrina canosai. This article also documents the addition of 116 sequencing primer pairs for Dicentrarchus labrax.     

Potentials and limitations of the cross-species transfer of nuclear microsatellite marker in six species belonging to three sections of the genus Populus L.

The genus Populus is classified into six different sections, and depending on the declaration of hybrids, the number of species varies between 22 and 85. Species within one section, and sometimes between sections, are crossable to each other, resulting in many naturally but also artificially produced hybrids. Morphological attributes for a clone characterisation are often difficult to evaluate when different poplar species or even hybrids are crossed; thus, molecular markers are needed to characterise the different species. Taking advantage of the large microsatellite resource developed for Populus trichocarpa, however, amplification of these microsatellite markers in other Populus species either often fails, or in the case of amplification, unrelated genomic regions are amplified. To meet this obvious problem of the species transferability of microsatellite markers, in total, 305 microsatellite loci, mainly from P. trichocarpa but also few from Populus tremuloides and Populus nigra, were tested for their transferability to diverse genotypes of six species belonging to three sections of the genus Populus. Ultimately, 209 microsatellite loci could be amplified with varying sizes in the different species. The PCR products of selected loci were separated in a polyacrylamide gel and sequenced to assure that the expected loci were derived from the database genome of P. trichocarpa. The present results constitute a large study for microsatellite transferability for Populus species. The documented microsatellite loci can be applied to species-, hybrid- and clone-specific diagnostic approaches or as universal markers for comprehensive ecological studies.     

<Emphasis Type="Italic">BrRxLR11</Emphasis> – a new phylogenetic marker with high resolution in the downy mildew genus <Emphasis Type="Italic">Bremia</Emphasis> and related genera

The genus Bremia (Peronosporaceae; Oomycete) is a widespread pathogen of Eurasian Asteraceae (Compositae). In addition to several species infecting weeds, it includes the economically important species, B. lactucae, which causes downy mildew of lettuce (Lactuca sativa). A few loci have already been successfully sequenced for this genus, but the resolution of the resultant phylogenies is insufficient to resolve the evolutionary history of Bremia. Therefore, there is a need to develop additional loci that can provide high resolution in phylogenetic inference. In this study, we report a new locus, BrRxLR11, derived from genomic data, which shows high resolving power within the genus Bremia, similar to phylogenies based on three different loci. This gene encodes a protein of 204 aa with unknown function, a below-threshold secretion signal, and an RxLR-EER motif in the c-terminal half. As only one site seems to be under positive selection, it has potential for future application in phylogenetic investigations in the economically important genus Bremia and related genera.     

Evaluation of genetic structure across freshwater mussel community (genus Elliptio) in the Altamaha River basin

Using mitochondrial DNA sequence data and genotypic data from four microsatellite loci, we evaluate the population genetic structure for three common species of the freshwater mussel genus Elliptio in the Altamaha River basin in Georgia, USA. These data are intended to evaluate whether distinct management strategies should be applied to upper and lower reaches of the Altamaha, which are separated by some discontinuities in appropriate habitat and may have been differentially influenced by heavier urbanization in the upstream reaches. Our results show no significant structure of mitochondrial data for E. dariensis, E. hopetonensis, or mussels in the E. icterina–complanata group. However, microsatellite data do suggest moderate genotypic structure of mussels in the E. icterina–complanata group, consistent with (but not necessarily caused by) the noted habitat disjunction. Application of these data may prove useful in management of rare endemic congeners such as the Altamaha spinymussel, E. spinosa, in showing that management resources can be applied uniformly throughout the Altamaha basin.     

Invasive and socially parasitic ants are good bioindicators of habitat quality in Mediterranean forest remnants in northeast Spain

We surveyed ants in 16 forest remnants in the Vallès lowlands north of Barcelona, Spain: eight with invasive exotic ants (IE = Linepithema humile and/or Lasius neglectus) present, seven with native parasitic ants (P = Lasius meridionalis, Lasius carniolicus, Plagiolepis xene, Chalepoxenus muellerianus, and/or Polyergus rufescens) present, and one remnant with both invasive exotic and parasitic ants present. Forest remnants with IE ants were smaller, more isolated, had greater perimeter/area, lower ant species density, and lower ant species richness than remnants with P ants. The community composition was also significantly different, with greater dissimilarity within remnants with alien, invasive species. The presence of some species is bio-indicator of low disturbance, whereas others are indicative of high disturbance. Our findings underscore the value of different types of ants as bio-indicators of fragmentation and habitat quality.     

The dynamics of ant mosaics in tropical rainforests characterized using the Self‐Organizing Map algorithm

Ants, the most abundant taxa among canopy‐dwelling animals in tropical rainforests, are mostly represented by territorially dominant arboreal ants (TDAs) whose territories are distributed in a mosaic pattern (arboreal ant mosaics). Large TDA colonies regulate insect herbivores, with implications for forestry and agronomy. What generates these mosaics in vegetal formations, which are dynamic, still needs to be better understood. So, from empirical research based on 3 Cameroonian tree species (Lophira alata, Ochnaceae; Anthocleista vogelii, Gentianaceae; and Barteria fistulosa, Passifloraceae), we used the Self‐Organizing Map (SOM, neural network) to illustrate the succession of TDAs as their host trees grow and age. The SOM separated the trees by species and by size for L. alata, which can reach 60 m in height and live several centuries. An ontogenic succession of TDAs from sapling to mature trees is shown, and some ecological traits are highlighted for certain TDAs. Also, because the SOM permits the analysis of data with many zeroes with no effect of outliers on the overall scatterplot distributions, we obtained ecological information on rare species. Finally, the SOM permitted us to show that functional groups cannot be selected at the genus level as congeneric species can have very different ecological niches, something particularly true for Crematogaster spp., which include a species specifically associated with B. fistulosa, nondominant species and TDAs. Therefore, the SOM permitted the complex relationships between TDAs and their growing host trees to be analyzed, while also providing new information on the ecological traits of the ant species involved.     

Parasites may help stabilize cooperative relationships

Background  

The persistence of cooperative relationships is an evolutionary paradox; selection should favor those individuals that exploit their partners (cheating), resulting in the breakdown of cooperation over evolutionary time. Our current understanding of the evolutionary stability of mutualisms (cooperation between species) is strongly shaped by the view that they are often maintained by partners having mechanisms to avoid or retaliate against exploitation by cheaters. In contrast, we empirically and theoretically examine how additional symbionts, specifically specialized parasites, potentially influence the stability of bipartite mutualistic associations. In our empirical work we focus on the obligate mutualism between fungus-growing ants and the fungi they cultivate for food. This mutualism is exploited by specialized microfungal parasites (genus Escovopsis) that infect the ant's fungal gardens. Using sub-colonies of fungus-growing ants, we investigate the interactions between the fungus garden parasite and cooperative and experimentally-enforced uncooperative ("cheating") pairs of ants and fungi. To further examine if parasites have the potential to help stabilize some mutualisms we conduct Iterative Prisoner's Dilemma (IPD) simulations, a common framework for predicting the outcomes of cooperative/non-cooperative interactions, which incorporate parasitism as an additional factor.     

Isolation of polymorphic microsatellite loci in the genus Clusia (Clusiaceae)

Microsatellite flanking region sequences may provide phylogenetically useful information. We isolated 13 polymorphic microsatellite loci from two species, Clusia minor (five loci) and Clusia nemorosa (eight loci), to aid in the determination of phylogenetic relationships within the genus Clusia. Eleven loci amplified across all 17 Clusia species tested, while two loci amplified in 10 out of 17 species. The extensive cross‐species amplification suggests that these loci may be useful for an examination of phylogenetic relationships in this genus.     

Fire triggers the activity of extrafloral nectaries,but ants fail to protect the plant against herbivores in a neotropical savanna

Herbivores are attracted to young shoots and leaves because of their tender tissues. However, in extrafloral nectaried plants, young leaves also attract patrolling ants, which may chase or prey on herbivores. We examined this scenario in extrafloral nectaried shrubs of Banisteriopsis malifolia resprouting after fire, which promoted both the aseasonal production of leaves and the activity of extrafloral nectaries (EFNs). Results were compared between resprouting (burned) and unburned control plants. The aggressive ant species Camponotus crassus and the herbivorous thrips Pseudophilothrips obscuricornis were respectively rapidly attracted to resprouting plants because of the active EFNs and their less sclerophyllous leaves. The abundance of these insects was almost negligible in the control (unburned) shrubs. Ants failed to protect B. malifolia, as no thrips were preyed upon or injured by ants in resprouting plants. Consequently, on average, 37 % of leaves from resprouting shrubs had necrosis marks. Upon contact with ants, thrips released small liquid droplets from their abdomen, which rapidly displaced ants from the surroundings. This study shows that P. obscuricornis disrupted the facultative mutualism between C. crassus and B. malifolia, since ants received extrafloral nectar from plants, but were unable to deter herbivore thrips.     

Extreme Reproduction and Survival of a True Cliffhanger: The Endangered Plant Borderea chouardii (Dioscoreaceae)

Cliff sides are extreme habitats, often sheltering a rich and unique flora. One example is the dioecious herb Borderea chouardii (Dioscoreaceae), which is a Tertiary, tropical relict, occurring only on two adjacent vertical cliffs in the world. We studied its reproductive biology, which in some aspects is extreme, especially the unusual double mutualistic role of ants as both pollinators and dispersers. We made a 2-year pollination census and four years of seed-dispersal experiments, recording flower visitors and dispersal rates. Fruit and seed set, self-sowing of seeds, seedling recruitment, and fate of seedlings from seeds sowed by different agents were scored over a period of 17 years. The ants Lasius grandis and L. cinereus were the main pollinators, whereas another ant Pheidole pallidula dispersed seeds. Thus ants functioned as double mutualists. Two thirds of all new seedlings came from self-sown seeds, and 1/3 was dispersed by ants, which gathered the seeds with their oil-rich elaiosome. Gravity played a minor role to dispersal. Both ant dispersal and self-sowing resulted in the same survival rate of seedlings. A double mutualism is a risky reproductive strategy, but B. chouardii buffers that by an unusual long–term demographic stability (some individuals exceed 300 years in lifespan) and its presence in a climatically very stable habitat, inaccessible to large herbivores. Such a combination of traits and habitat properties may explain the persistence of this relict species.     

Isolation and Characterization of Microsatellite Markers for <Emphasis Type="Italic">Viola websteri</Emphasis> (Violaceae) and Cross-Species Amplification within the Genus <Emphasis Type="Italic">Viola</Emphasis>

We isolated and characterized microsatellite loci in Viola websteri (Violaceae), an endangered species from Korea and endemic to Northeast Asia. A total of 27 microsatellite loci were developed and tested in Korean and Chinese populations. The number of alleles per locus varied from two to eight. The observed and expected heterozygosities within two populations were 0.000 to 1.000 and 0.080 to 0.816, respectively. Korean and Chinese populations were clearly distinguished by the private alleles from 16 loci. A total of 21 loci out of the 27 developed loci were successfully cross-amplified in 39 other Viola species. We believe that these microsatellite loci will be useful for future studies on genetic diversity and population structure of V. websteri, as well as other Viola species.     

Evolutionary and Biogeographic Insights on the Macaronesian Beta-Patellifolia Species (Amaranthaceae) from a Time-Scaled Molecular Phylogeny

The Western Mediterranean Region and Macaronesian Islands are one of the top biodiversity hotspots of Europe, containing a significant native genetic diversity of global value among the Crop Wild Relatives (CWR). Sugar beet is the primary crop of the genus Beta (subfamily Betoideae, Amaranthaceae) and despite the great economic importance of this genus, and of the close relative Patellifolia species, a reconstruction of their evolutionary history is still lacking. We analyzed nrDNA (ITS) and cpDNA gene (matK, trnH-psbA, trnL intron, rbcL) sequences to: (i) investigate the phylogenetic relationships within the Betoideae subfamily, and (ii) elucidate the historical biogeography of wild beet species in the Western Mediterranean Region, including the Macaronesian Islands. The results support the Betoideae as a monophyletic group (excluding the Acroglochin genus) and provide a detailed inference of relationships within this subfamily, revealing: (i) a deep genetic differentiation between Beta and Patellifolia species, which may have occurred in Late Oligocene; and (ii) the occurrence of a West-East genetic divergence within Beta, indicating that the Mediterranean species probably differentiated by the end of the Miocene. This was interpreted as a signature of species radiation induced by dramatic habitat changes during the Messinian Salinity Crisis (MSC, 5.96–5.33 Mya). Moreover, colonization events during the Pleistocene also played a role in shaping the current diversity patterns among and within the Macaronesian Islands. The origin and number of these events could not be revealed due to insufficient phylogenetic resolution, suggesting that the diversification was quite recent in these archipelagos, and unravelling potential complex biogeographic patterns with hybridization and gene flow playing an important role. Finally, three evolutionary lineages were identified corresponding to major gene pools of sugar beet wild relatives, which provide useful information for establishing in situ and ex situ conservation priorities in the hotspot area of the Macaronesian Islands.     

Highly polymorphic microsatellite markers for the highly polymorphic strawberry poison-dart frog and some of its congeners

Members of the poison-dart frog genus Oophaga, including the strawberry poison-dart frog (O. pumilio) display among the most striking examples of color polymorphism of any amphibians. We developed twelve novel microsatellite markers with di-, tri-, and tetra-nucleotide repeats for this genus. These loci are highly polymorphic with between 2 and 29 alleles (average = 14.7) and high heterozygosity (H _O = 0.704). These highly polymorphic markers should be useful for resolving fine-scale genetic differences between the different color morphs of these highly variable species, for investigations into the ecological importance of this variation, and for determining the effects of habitat loss and fragmentation on population persistence in these species.     

Intra- and interspecific polymorphism of (AAT) n in microsatellite locus Du47D in parthenogenetic species of the genus Darevskia

The molecular structure of the allelic variants of (AAT) _n of the Du47D microsatellite locus was determined in parthenogenetic lizards Darevskia dahli, D. armeniaca, and D. rostombekovi. Comparative analysis of these alleles showed that they were characterized by perfect structure of microsatellite cluster, and were different in the number of (AAT) monomeric units, as well as in the combinations of species-specific substitutions and deletions in the microsatellite flanking regions. Molecular structure of microsatellite cluster, species-specific single nucleotide polymorphism (SNP), and different representation of alleles Du47 in the samples of parthenogenetic species examined point to the origin of the alleles from different bisexual species, which is consistent with the hybrid nature of unisexual species of the genus Darevskia. In addition, these data reflect different combination patterns of interspecific hybridization events with the participation of the same bisexual species upon the formation of hybrid genomes of parthenogenetic species. Possible application of the allelic variants of microsatellite loci of parthenogenetic lizards as the genetic markers for the analysis of the genomes of parthenogenetic species in the light of evolution, ecology, and parthenogenetic type of reproduction in vertebrates is discussed.     

Genetic Divergence among Regions Containing the Vulnerable Great Desert Skink (Liopholis kintorei) in the Australian Arid Zone

Knowledge of genetic structure and patterns of connectivity is valuable for implementation of effective conservation management. The arid zone of Australia contains a rich biodiversity, however this has come under threat due to activities such as altered fire regimes, grazing and the introduction of feral herbivores and predators. Suitable habitats for many species can be separated by vast distances, and despite an apparent lack of current geographical barriers to dispersal, habitat specialisation, which is exhibited by many desert species, may limit connectivity throughout this expansive region. We characterised the genetic structure and differentiation of the great desert skink (Liopholis kintorei), which has a patchy, but widespread distribution in the western region of the Australian arid zone. As a species of cultural importance to local Aboriginal groups and nationally listed as Vulnerable, it is a conservation priority for numerous land managers in central Australia. Analysis of mitochondrial ND4 sequence data and ten nuclear microsatellite loci across six sampling localities through the distribution of L. kintorei revealed considerable differentiation among sites, with mitochondrial F_ST and microsatellite F′_ST ranging from 0.047-0.938 and 0.257-0.440, respectively. The extent of differentiation suggests three main regions that should be managed separately, in particular the southeastern locality of Uluru. Current genetic delineation of these regions should be maintained if future intervention such as translocation or captive breeding is to be undertaken.     

Comparative cytogenetic analysis of the genomes of the model grass Brachypodium distachyon and its close relatives

Background and Aims

Brachypodium is a small genus of temperate grasses that comprises 12–15 species. Brachypodium distachyon is now well established as a model species for temperate cereals and forage grasses. In contrast to B. distachyon, other members of the genus have been poorly investigated at the chromosome level or not at all.

Methods

Twenty accessions comprising six species and two subspecies of Brachypodium were analysed cytogenetically. Measurements of nuclear genome size were made by flow cytometry. Chromosomal localization of 18–5·8–25S rDNA and 5S rDNA loci was performed by dual-colour fluorescence in situ hybridization (FISH) on enzymatically digested root-tip meristematic cells. For comparative phylogenetic analyses genomic in situ hybridization (GISH) applied to somatic chromosome preparations was used.

Key Results

All Brachypodium species examined have rather small genomes and chromosomes. Their chromosome numbers and genome sizes vary from 2n = 10 and 0·631 pg/2C in B. distachyon to 2n = 38 and 2·57 pg/2C in B. retusum, respectively. Genotypes with 18 and 28 chromosomes were found among B. pinnatum accessions. GISH analysis revealed that B. pinnatum with 28 chromosomes is most likely an interspecific hybrid between B. distachyon (2n = 10) and B. pinnatum (2n = 18). Two other species, B. phoenicoides and B. retusum, are also allopolyploids and B. distachyon or a close relative seems to be one of their putative ancestral species. In chromosomes of all species examined the 45S rDNA loci are distally distributed whereas loci for 5S rDNA are pericentromeric.

Conclusions

The increasing significance of B. distachyon as a model grass emphasizes the need to understand the evolutionary relationships in the genus Brachypodium and to ensure consistency in the biological nomenclature of its species. Modern molecular cytogenetic techniques such as FISH and GISH are suitable for comparative phylogenetic analyses and may provide informative chromosome- and/or genome-specific landmarks.     

Microsatellite primers for fungus‐growing ants

We isolated five polymorphic microsatellite loci from a library of two thousand recombinant clones of two fungus‐growing ant species, Cyphomyrmex longiscapus and Trachymyrmex cf. zeteki. Amplification and heterozygosity were tested in five species of higher attine ants using both the newly developed primers and earlier published primers that were developed for fungus‐growing ants. A total of 20 variable microsatellite loci, developed for six different species of fungus‐growing ants, are now available for studying the population genetics and colony kin‐structure of these ants.     

Strong correlation between cross-amplification success and genetic distance across all members of 'True Salamanders' (Amphibia: Salamandridae) revealed by Salamandra salamandra-specific microsatellite loci

The unpredictable and low cross-amplification success of microsatellite loci tested for congeneric amphibian species has mainly been explained by the size and complexity of amphibian genomes, but also by taxonomy that is inconsistent with phylogenetic relationships among taxa. Here, we tested whether the cross-amplification success of nine new and 11 published microsatellite loci cloned for an amphibian source species, the fire salamander (Salamandra salamandra), correlated with the genetic distance across all members of True Salamanders (genera Chioglossa, Lyciasalamandra, Mertensiella and Salamandra that form a monophyletic clade within the family of Salamandridae) serving as target species. Cross-amplification success varied strongly among the species and showed a highly significant negative relationship with genetic distance and amplification success. Even though lineages of S. salamandra and Lyciasalamndra have separated more than 30 Ma, a within genus amplification success rate of 65% was achieved for species of Lyciasalamandra thus demonstrating that an efficient cross-species amplification of microsatellite loci in amphibians is feasible even across large evolutionary distances. A decrease in genome size, on the other hand, paralleled also a decrease in amplified loci and therefore contradicted previous results and expectations that amplification success should increase with a decrease in genome size. However, in line with other studies, our comprehensive dataset clearly shows that cross-amplification success of microsatellite loci is well explained by phylogenetic divergence between species. As taxonomic classifications on the species and genus level do not necessarily mirror phylogenetic divergence between species, the pure belonging of species to the same taxonomic units (i.e. species or genus) might be less useful to predict cross-amplification success of microsatellite loci between such species.