Permanent Genetic Resources added to Molecular Ecology Resources Database 1 June 2012–31 July 2012

This article documents the addition of 96 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Clarias batrachus, Marmota himalayana, Schizothorax richardsonii, Sitophilus zeamais and Syagrus romanzoffiana. These loci were cross‐tested on the following species: Clarias dussumeri, Clarias gariepinus, Heteropneustus fossilis, Sitophilus granarius and Sitophilus oryzae.     

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 August 2012 – 30 September 2012

This article documents the addition of 83 microsatellite marker loci and 96 pairs of single‐nucleotide polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Bembidion lampros, Inimicus japonicus, Lymnaea stagnalis, Panopea abbreviata, Pentadesma butyracea, Sycoscapter hirticola and Thanatephorus cucumeris (anamorph: Rhizoctonia solani). These loci were cross‐tested on the following species: Pentadesma grandifolia and Pentadesma reyndersii. This article also documents the addition of 96 sequencing primer pairs and 88 allele‐specific primers or probes for Plutella xylostella.     

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 August 2009-30 September 2009

This article documents the addition of 238 microsatellite marker loci and 72 pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Adelges tsugae, Artemisia tridentata, Astroides calycularis, Azorella selago, Botryllus schlosseri, Botrylloides violaceus, Cardiocrinum cordatum var. glehnii, Campylopterus curvipennis, Colocasia esculenta, Cynomys ludovicianus, Cynomys leucurus, Cynomys gunnisoni, Epinephelus coioides, Eunicella singularis, Gammarus pulex, Homoeosoma nebulella, Hyla squirella, Lateolabrax japonicus, Mastomys erythroleucus, Pararge aegeria, Pardosa sierra, Phoenicopterus ruber ruber and Silene latifolia. These loci were cross-tested on the following species: Adelges abietis, Adelges cooleyi, Adelges piceae, Pineus pini, Pineus strobi, Tubastrea micrantha, three other Tubastrea species, Botrylloides fuscus, Botrylloides simodensis, Campylopterus hemileucurus, Campylopterus rufus, Campylopterus largipennis, Campylopterus villaviscensio, Phaethornis longuemareus, Florisuga mellivora, Lampornis amethystinus, Amazilia cyanocephala, Archilochus colubris, Epinephelus lanceolatus, Epinephelus fuscoguttatus, Symbiodinium temperate-A clade, Gammarus fossarum, Gammarus roeselii, Dikerogammarus villosus and Limnomysis benedeni. This article also documents the addition of 72 sequencing primer pairs and 52 allele specific primers for Neophocaena phocaenoides.     

Genomic Resources Notes accepted 1 October 2013 – 30 November 2013

This article documents the public availability of (i) genomic sequence data and 43 microsatellite loci for the bat species, Lasiurus borealis and Lasiurus cinereus, and (ii) complete mitochondrial and partial nuclear genomes for two jack species, Caranx ignobilis, Caranx melampygus.     

Biogeography, geographic variation and habitat preference in the Amazilia Hummingbird,Amazilia amazilia Lesson (Aves: Trochilidae), with notes on the status ofAmazilia alticola Gould

Summary This paper reviews the biogeography, geographic variation, and habitat characteristics of the Amazilia Hummingbird (Amazilia amazilia). Based on morphological features, habitat preferences, and bioacoustics, I propose that the currently recognized subspeciesA. a. alticola should be regarded as a species distinct fromA. amazilia. Synapomorphic characters found in both taxa indicate membership of the same superspecies, together with the Colombian speciesA. castaneiventris. Considering the distributional focus ofA. alticola in the Andes of southern Ecuador, the English species name Loja Hummingbird is suggested.

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Biogeographie, geographische Variation und Habitatwahl der Lesson-Amazilie (Amazilia amazilia Lesson; Aves: Trochilidae), mit Anmerkungen zum Status vonAmazilia alticola Gould

Zusammenfassung Die vorliegende Studie stellt die Ergebnisse von Untersuchungen zur Biogeographie, geographischen Variation, Habitatwahl und Taxonomie der Lesson-Amazilie (Amazilia amazilia) vor. Das Taxon umfaßt gegenwärtig fünf Unterarten, die von W-Ecuador bis SW-Peru verbreitet sind und überwiegend submontane Lebensräume besiedeln. Die Ventralfärbung unterliegt klinaler Variation; weiße Gefiederanteile nehmen von nördlichen zu südlichen Populationen ab, rotbraune Partien dagegen zu. Eigenständige morphologisch-morphometrische Kennzeichen sowie Unterschiede in den Habitatpräferenzen und in der Gesangsstruktur rechtfertigen es, die bisherige UnterartA. a. alticola als Paraspezies (A. alticola, Loja-Amazilie) anzuerkennen. Der Vulgärname weist auf den rezenten Verbreitungsschwerpunkt in den südecuadorianischen Anden hin. Aufgrund der engen Verwandtschaft bildenA. amazilia undA. alticola sowie die in Kolumbien endemische ArtA. castaneiventris eine Superspezies.

     

Permanent genetic resources added to Molecular Ecology Resources Database 1 October 2011-30 November 2011

This article documents the addition of 139 microsatellite marker loci and 90 pairs of single‐nucleotide polymorphism sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Aglaoctenus lagotis, Costus pulverulentus, Costus scaber, Culex pipiens, Dascyllus marginatus, Lupinus nanus Benth, Phloeomyzus passerini, Podarcis muralis, Rhododendron rubropilosum Hayata var. taiwanalpinum and Zoarces viviparus. These loci were cross‐tested on the following species: Culex quinquefasciatus, Rhododendron pseudochrysanthum Hay. ssp. morii (Hay.) Yamazaki and R. pseudochrysanthum Hayata. This article also documents the addition of 48 sequencing primer pairs and 90 allele‐specific primers for Engraulis encrasicolus.     

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.     

Characterization of microsatellite loci for five members of the minnow family Cyprinidae found in the Sacramento–San Joaquin Delta and its tributaries

Two microsatellite‐enriched libraries [(CAGA)_n, (TAGA)_n] were constructed using pooled DNA from three cyprinid species native to the Sacramento–San Joaquin Delta of California: Sacramento splittail (Pogonichthys macrolepidotus); Sacramento pikeminnow (Ptychocheilus grandis); and tui chub (Siphateles bicolor). Primers were designed for 105 loci and tested for levels of polymorphism in five cyprinid species found in the Delta: Sacramento splittail, Sacramento pikeminnow, tui chub, hitch (Lavinia exilicauda), and Sacramento blackfish (Orthodon microlepidotus). Fifty‐one loci were polymorphic for at least one species and 31 loci were polymorphic for multiple species. The number of polymorphic loci per species ranged from 16 to 26.     

Allozymatic diagnosis of four economically important Liriomyza species (Diptera, Agromyzidae)

Liriomyza bryoniae, L. huidobrensis, L. sativae and L. trifolii are leafminers of great economic importance; morphologically they are difficult to separate, many being inseparable at the pre-adult stages. Horizontal starch gel electrophoresis of larvae, pupae and adults was carried out in order to search for diagnostic allozymic characters. Analysis of the variation patterns at 15 genetic loci reveals that each species can be identified at all three stages of the life cycle. A biochemical key is presented.     

Primer design for identifying economically important Liriomyza species (Diptera: Agromyzidae) by multiplex PCR

Leafminer flies, especially, Liriomyza huidobrensis, Liriomyza sativae and Liriomyza trifolii, are quarantine species in many countries. Their morphological similarity makes identification difficult. To develop a rapid, reliable, sensitive and simple molecular identification method using multiplex PCR, we newly sequenced the mitochondrial cytochrome oxidase I (COI) genes of Liriomyza bryoniae, Liriomyza chinensis, L. huidobrensis, L. sativae, L. trifolii, Chromatomyia horticola and four parasitoid species. We aligned them with all the COI sequences of the leafminer flies found in the international DNA nucleotide sequence databases (DDBJ/EMBL/GenBank). We then designed species‐specific primers to allow us to differentiate between L. bryoniae, L. chinensis, L. huidobrensis, L. sativae, and L. trifolii.     

Proteomic evaluation of gymnosperm pollination drop proteins indicates highly conserved and complex biological functions

The pollination droplet is a highly conservative pollination mechanism that is observed in all major gymnosperm taxa. Proteomics analysis of the pollination drops was carried out on four gymnosperm species: Juniperus communis (common juniper), Juniperus oxycedrus (prickly juniper), Chamaecyparis lawsoniana (Port Orford cedar), and Welwitschia mirabilis. Pollination drop proteins were purified by SDS-PAGE, and the most abundant proteins were analyzed by mass spectrometry and sequenced. Based on BLAST searching of combined amino acid sequences, the following proteins were identified in the following species: an 83-kDa subtilisin-like proteinase, a 62-kDa glycosyl hydrolase, a 47.5-kDa glucan 1,3-β-glucosidase precursor, a 30-kDa chitinase, and a 25-kDa thaumatin-like protein were identified in J. communis; a 30-kDa chitinase, a 25-kDa thaumatin-like protein, and a 32.5-kDa glucanase-like protein were identified in J. oxycedrus; an 83-kDa subtilisin-like proteinase, a 62-kDa β-d-glucan exohydrolase, a 47.5-kDa glucan 1,3-β-glucosidase, and two 25-kDa thaumatin-like proteins were identified in C. lawsoniana, and a 25-kDa chitinase was identified in W. mirabilis. Based on protein identifications, there is strong evidence that the pollination drop functions in both pathogen defense and pollen development. The discovery of similarities in terms of peptide sequence and protein identifications indicates that ovular secretions are functionally conservative, and that they are essential to reproductive success.     

The Pleistocene demography of an alpine juniper of the Qinghai‐Tibetan Plateau: tabula rasa,cryptic refugia or something else?

Aim Numerous palaeoecological and genetic studies have shown that different tree species responded in very different ways to Pleistocene climatic oscillations. Some were forced into small refugia far from their current range, while others were able to survive in small refugia close to, or even within, their current natural range. In this study we examine the Pleistocene demography of a juniper species (Juniperus przewalskii, Cupressaceae) from the Qinghai‐Tibetan Plateau. Location The Qinghai‐Tibetan Plateau (QTP). Methods Eight nuclear loci were sequenced in 141 individuals from 20 natural populations distributed across the entire natural range of J. przewalskii, and coalescent analysis was used to test demographic hypotheses. Results The overall nucleotide diversity in the sample was low (π_sil = 0.0029), with few rare alleles and pronounced population genetic structure (F_ST = 0.181). We detected a division previously found using chloroplast DNA markers: all segregating sites in populations from the central part of the QTP appear to be a subset of those found around the edge of the plateau, confirming the relatively young age of the former. In contrast to the middle Pleistocene bottlenecks detected in boreal tree species, the coalescent‐based analyses failed to reject the standard neutral model for the juniper species considered here. Main conclusions Juniperus przewalskii did not undergo marked changes in population sizes during the Pleistocene, although this species seems to have experienced recent, post‐glacial expansion. This finding is largely consistent with the limited number of previous studies on conifer species of the QTP, but contradicts findings of studies on boreal species. These findings have wide implications for understanding plant species’ responses to past climatic oscillations on the high‐elevation QTP.     

Effects of landslides on the mountain vegetation of Flores Island,Azores

Question: What are the consequences of frequently occurring landslides on vegetation dynamics, floristic and structural diversity? Location: 39°27′N; 31°13′W – Morro Alto, Flores Island, Azores, Portugal. Methods: Six comparable landslides were selected. Plots were placed at the top, slope and toe of landslides. Data on floristic composition and biovolume, demography and size structure of the dominant tree species (Juniperus brevifolia) were collected. Hierarchical agglomerative clustering and Principal Component Analysis were used in order to identify succession stages and compare succession pathways and vegetation recovery in different parts of the landslides. Results: Four stages of primary succession on substrates formed by landslides were identified: pioneer (Festuca‐Sphagnum grassland), assembly (Juniperus‐Festuca‐Sphagnum open scrub), building (Juniperus‐Sphagnum scrub) and mature (Juniperus‐Sphagnum woodland). Concerning J. brevifolia populations, the succession pathways are independent of location on the landslide. However, at the floristic level, there are some differences, mainly in the pioneer stage at the toes of landslides. Better abiotic conditions, resulting in a higher succession rate, are probably responsible for a faster vegetation recovery on landslide toes. Conclusion: Landslides trigger succession processes that enable a massive regeneration of the dominant tree species and existence of species not present in mature forests. They are also responsible for the simultaneous occurrence of vegetation of different structures. Overall, landslides increase the floristic and structural diversity of the vegetation, consequently increasing landscape heterogeneity.     

Characterization of polymorphic microsatellite markers for a coniferous shrub Juniperus sabina (Cupressaceae)

Juniperus sabina L. is an evergreen coniferous shrub, with a widespread distribution in Asia and Europe. It is one of the key species for restoration of the ecosystem in desertification areas. In the present study, we isolated and characterized eight microsatellite loci of this species. The number of alleles per locus ranged from two to 27, with observed heterozygosity values ranging from 0.256 to 0.744 and expected heterozygosity from 0.276 to 0.939. The markers developed in this study could be useful for population genetics studies of J. sabina.     

Genomic Resources Notes accepted 1 April 2013–31 May 2013

This article documents the public availability of approximately 15 000 polymorphic SNP loci for the bighorn sheep Ovis canadensis.     

Genetic Diversity and Population Structure of Juniperus rigida (Cupressaceae) and Juniperus coreana

Enzyme electrophoresis was used to estimate genetic diversity and population structure of Juniperus rigida (Cupressaceae) and Juniperus coreana in Korea. In J. rigida, 16 of the 22 loci (72.7%) showed detectable polymorphism. Genetic diversity (0.224) was higher than average values for species with similar life history traits. The endemic species (J. coreana) was found to have fewer alleles per locus (1.39 vs. 1.61), fewer alleles per polymorphic locus (2.42 vs. 2.63), lower percent polymorphic locus (54.6 vs. 72.7%), and lower diversity (0.199 vs. 0.224) than J. rigida. These genetic diversity parameters indicated that J. coreana was genetically depauperate relative to its presumptive progenitor, J. rigida. Analysis of fixation indices showed a substantial deficiency of heterozygotes relative to Hardy–Weinberg expectations suggesting inbreeding in J. coreana. The G _ST values of J. rigida and J. coreana were 0.173 and 0.118 respectively. The indirect estimate of gene flow based on mean G _ST was moderate (Nm = 1.19 for J. rigida and 1.86 for J. coreana). This revised version was published online in July 2006 with corrections to the Cover Date.     

Identifying factors determining the altitudinal distribution of the invasive pest leafminers Liriomyza huidobrensis and Liriomyza sativae

Abiotic and biotic factors that change with altitude can influence the distribution of herbivorous insects. We examined factors influencing the distribution of the generalist leafminers Liriomyza sativae Blanchard and Liriomyza huidobrensis Blanchard (Diptera: Agromyzidae), two pests of agricultural crops, in the tropical Dieng mountainous area of Central Java, Indonesia. Liriomyza huidobrensis predominated at altitudes above 700 m a.s.l. and was the only species collected above 1 400 m a.s.l. In contrast, L. sativae predominated below 600 m a.s.l. and was not found above 1 200 m where the average temperature was 20.7 °C. Parasitoid diversity decreased with altitude, but parasitism did not change. The distribution of neither species was affected by parasitoids; L. huidobrensis predominant at high altitudes was preferred by Opius parasitoids common at these altitudes. Intra‐ and interspecific competition was detected in laboratory experiments where larval density was high, but led to coexistence rather than species displacement. No competition was detected in a field experiment when larval density was low. However, L. sativae failed to reproduce at the highest altitude, whereas L. huidobrensis established at all altitudes. Host composition varied with altitude and one host (faba beans) preferred by L. huidobrensis was common at high altitudes. By relating published data on the performance of the leafminer species to altitudinal temperature changes, we were partly successful in predicting the altitude at which the dominant species switched. Temperature plays an overriding influence on the altitudinal distribution of leafminers.     

Isolation and characterization of microsatellite DNA primers in Juniperus przewalskii Kom (Cupressaceae)

Juniperus przewalskii (Cupressaceae) is a dominant tree species endemic to the northeast Qinghai-Tibetan Plateau. This species plays an important role in maintaining the arid ecosystem in this region. However, natural distributions of this species have been declined. In order to develop effective conservation methods, it is important to know the distribution of the genetic diversity within and among populations. In this study, we developed nine new microsatellite loci for this species. We used the combining biotin capture method to enrich AG/CT/AC/GGT microsatellites. The polymorphisms of each locus were further assessed in 12 individuals from four geographically distant populations. The number of alleles per locus varied from three to six and expected heterozygosity ranged from 0.58 to 0.70. These loci together provide a useful tool to investigate the genetic diversity of this species. In addition, all markers have been crossly checked in the other four congeneric species.     

Development of high transferability cpSSR markers for individual identification and genetic investigation in Cupressaceae species

Given the low substitution rate in plastomes, the polymorphic and codominant nature of chloroplast SSRs (cpSSRs) makes them ideal markers, complementing their nuclear counterpart. In Cupressaceae, cpSSRs are mostly paternally inherited, thus, they are useful in mating systems and pollen flow studies. Using e‐PCR, 92 SSR loci were identified across six Cupressaceae plastomes, and primers were designed for 26 loci with potential interspecific transferability. The 26 developed cpSSRs were polymorphic in four genera, Platycladus, Sabina, Juniperus, and Cupressus and are suitable for Cupressaceae molecular genetic studies and utilization. We genotyped 192 Platycladus orientalis samples from a core breeding population using 10 of the developed cpSSRs and 10 nuclear SSRs, and these individuals were identified with high confidence. The developed cpSSRs can be used in (1) a marker‐assisted breeding scheme, specifically when paternity identification is required, (2) population genetics investigations, and (3) biogeography of Cupressaceae and unraveling the genetic relationships between related species.