Phylogeography of chamois (Rupicapra spp.) inferred from microsatellites

Evolutionary relationships among populations of chamois (Rupicapra spp.) across their current range from the Caucasus to the Cantabrian Mountains were investigated. The allelic variation in 23 microsatellite loci was assessed in eight geographical populations, recognised as subspecies of the two closely related species R. pyrenaica and R. rupicapra. Analysis of variance in allele frequencies (Fst, statistics) and in repeat numbers (Rst, statistics) showed these data to be highly structured. Two genetic distances between pairs of populations, Ds and (deltamu)(2), were computed and phylogenetic trees were constructed. Similar patterns were produced by the different statistics. All trees indicate a deep divergence between the two recognised species, which is compatible with archaeological data that place their split in the Riss-Würm interglacial period. Genetic distances between pairs of populations are highly correlated with geographical distance. This suggests that the history of the genus during Pleistocene glacial-interglacial periods was dominated by expansions and contractions within limited geographic regions, leading to alternate contact and isolation of contiguous populations. In addition, the alpine barrier has played a substantial role in West-East differentiation.     

基于叶绿体DNA的黄土高原特有植物蕤核的谱系地理学

该文利用母系遗传的叶绿体DNA片段(psbA-trnH,psbI-psbK和psbJ-petA)对黄土高原地区的特有植物蕤核(Prinsepia uniflora)进行谱系地理学研究,以揭示其现有的遗传结构和群体历史动态.结果表明:(1)蕤核自然种群总的遗传多样性较高(HT=0.796),而种群内的遗传多样性较低(HS...     

Nitrate removal and DO levels in batch wetland mesocosms: Cattail (Typha spp.) versus bulrush (Scirpus spp.)

Nitrate removal rates and dissolved oxygen (DO) levels were evaluated in small batch-mode wetland mesocosms with two different plant species, cattail (Typha spp.) and bulrush (Scirpus spp.), and associated mineral-dominated sediment collected from a mature treatment wetland. Nitrate loss in both cattail and bulrush mesocosms was first-order in nature. First-order volumetric rate constants (k_V) were 0.30 d⁻¹ for cattail and 0.21 d⁻¹ for bulrush and rates of nitrate loss were significantly different between plant treatments (p < 0.005). On an areal basis, maximum rates of nitrate removal were around 500 mg N/(m² d) early in the experiment when nitrate levels were high (> 15 mg N/L). Areal removal rates were on average 25% higher in cattail versus bulrush mesocosms. DO in mesocosm water was significantly higher in bulrush versus cattail (p < 0.001). DO in bulrush generally ranged between 0.5 and 2 mg/L, while DO in cattail mesocosms was consistently below 0.3 mg/L. Based on cumulative frequency analysis, DO exceeded 1 mg/L around 50% of the time in bulrush, but only 2% of the time in cattail. DO in bulrush exhibited a statistically significant diel cycle with DO peaks in the late afternoon and DO minimums in the early morning hours. Difference in nitrate removal rates between wetland plant treatments may have been due to differing plant carbon quality. Cattail litter, which has been shown in other studies to exhibit superior biodegradability, may have enhanced biological denitrification by fueling heterotrophic microbial activity, which in turn may have depressed DO levels, a prerequisite for denitrification. Our results show that the cattail is more effective than bulrush for treating nitrate-dominant wastewaters.     

Seasonal utilization of saltgrass (Distichlis spp.) by cattle

Published information on utilization of saltgrass (Distichlis spicata and D. scoparia) by cattle in the Pampa Deprimida region of Argentina is contradictory. The contribution of saltgrass to grassland and cattle diets from trials carried out in the region was analyzed using a preference index. Under different grazing conditions, saltgrass comprised from 8 to 24% of diet dry weight in summer months. Results indicate that saltgrass is a valuable seasonal forage for cattle during summer, when it has a medium to high relative quality, in native communities developed on saline and alkaline soils.     

Gelling properties of water-soluble polysaccharides from proliferating marine green seaweeds (Ulva spp.)

Water-soluble polysaccharides (12·2% of the algal dry weight) were extracted from marine green seaweed (Ulva spp.) which proliferate along the Brittany shores of France. They were composed of 18·4% rhamnose, 4·4% glucose, 1·9% xylose, 0·9% mannose, 0·9% galactose, 15·2% uronic acid, 15·8% sulphate and 23·7% ash based on the extract dry weight. These polysaccharides, formed a weak gel (about 3 Pa) at a concentration of 1·6% (w/v) in deionized water. The elastic modulus increased to about 160 Pa when boric acid (15–33 m ) was added and reached 250 Pa when both boric acid (7 m ) and calcium chloride (7 m ) were present. Adjusting the pH to 7·5 or higher by sodium tetraborate, phosphate or Tris-HCl buffers was detrimental to the gel. These results demonstrate that the poorly exploited biomass of Ulva spp. is a source of gelling polysaccharides of potential economical value. Mechanisms for gel formation which unusually involve both boron and calcium ions are proposed and will be studied further.     

Pleistocene diversification of living squirrel monkeys (Saimiri spp.) inferred from complete mitochondrial genome sequences

In order to enhance our understanding of the evolutionary history of squirrel monkeys (Saimiri spp.), we newly sequenced and analyzed data from seven complete mitochondrial genomes representing six squirrel monkey taxa. While previous studies have lent insights into the taxonomy and phylogeny of the genus, phylogenetic relationships and divergence date estimates among major squirrel monkey clades remain unclear. Using maximum likelihood and Bayesian procedures, we inferred a highly resolved phylogenetic tree with strong support for a sister relationship between Saimiri boliviensis and all other Saimiri, for monophyly of Saimiri oerstedii and Saimiri sciureus sciureus, and for Saimiri sciureus macrodon as the sister lineage to the S. oerstedii/S. s. sciureus clade. We inferred that crown lineages for extant squirrel monkeys diverged around 1.5 million years ago (MYA) in the Pleistocene Epoch, with other major clades diverging between 0.9 and 1.1 MYA. Our results suggest a relatively recent timeline of squirrel monkey evolution and challenge previous conceptions about the diversification of the genus and its expansion into Central America.     

Phylogeography of the Northern Atlantic species Chondrus crispus (Gigartinales, Rhodophyta) inferred from nuclear rDNA internal transcribed spacer sequences

Eighteen isolates of the red algae Chondrus crispus were collected from Northern Atlantic sites, together with C. ocellatus, C. yendoi and C. pinnulatus from the North Pacific. The nuclear rDNA internal transcribed spacer (ITS) was sequenced and compared, spanning both the ITS regions and the 5.8S rRNA gene. Percentage of nucleotide variation for C. crispus ranged from 0.3% to 4.0%. Phylogenetic analyses were performed using maximum parsimony (MP), neighbor-joining (NJ) and minimum evolution methods. They showed that two main clades existed within the C. crispus samples examined and that suggested C. crispus had a single Atlantic origin. The clustering however did not follow the geographic origin. We hypothesized that the current distribution of C. crispus populations might be a result of three main factors: temperature boundaries, paleoclimate and paleoceanography. ITS data exhibited abundant molecular information not only for phylogeographical investigation but also for systematics studies. Handling editor: C. Sturmbauer     

Phylogeography of two hybridizing southern beeches (Nothofagus spp.) with different adaptive abilities

In phylogenetically related plant species, hybridization can influence their current genetic structure. Long-lasting hybridization may be related to persistence in shared glacial refugia, where the differential abilities of each species to survive could have provided adaptations to changing environmental conditions. In temperate South American forests at the Patagonia region, the pattern of Quaternary glaciations offered several opportunities for refuge. At mid-latitudes (42° to 44° S), particular topographic characteristics determined different glaciation patterns, defining the existence of a transitional zone. We studied two widespread Nothofagus species (Nothofagus pumilio, Nothofagus antarctica) characterized by contrasting plasticity. We screened 40 coupled populations with three cpDNA markers and found 14 different haplotypes. Both species presented significant phylogeographic structure (N _ST????G _ST, p?>?0.001), with two geographically segregated lineages (north?Csouth). A latitudinal cline in the distribution of genetic diversity was determined, with most variable populations in the north (35°?C41°?S). Population diversity diminished to southern latitudes, but a particular situation occurs between 42°S and 44°S. The transition zone, a putative refuge area, presented unique haplotypes. The more plastic species, N. antarctica, probably persisted in more refuge areas, which could be reflected in its higher levels of diversity. In these species, sympatric distribution explains introgression (IG?>?IG _e), but the differential levels of haplotype sharing between N. pumilio and N. antarctica at population level are relevant to the understanding of phylogeographic patterns. Hybridization may have facilitated recruitment in the onset of postglacial colonization by middle to long-distance pollen dispersal. In the current scenario of climate change, the presence of hybrids with different plastic responses is of remarkable importance.     

Isolation and characterization of microsatellites in Echinochloa (L.) Beauv. spp.

Five primer pairs were developed that amplify microsatellite loci in three agronomically important Echinochloa (L.) Beauv. species: E. colona (L.) Link, E. crus‐galli (L.) Beauv. and E. crus‐pavonis (Kunth) Schultes. The microsatellites were tested on 24 individuals representing three species collected in rice fields from different geographical regions and revealed 3–7 alleles per microsatellite. Gene diversity [1 ? Σp_ij²] for four polymorphic loci within E. crus‐galli ranged from 0.12 to 0.61. Alleles at a fifth locus were useful in discriminating the species. The microsatellites should provide useful markers for intraspecific diversity studies and aid classification of species within this complex genus.     

Phylogeny and diversity of Japanese truffles (Tuber spp.) inferred from sequences of four nuclear loci

The genus Tuber, which includes some highly valued truffles, comprises ascomycetous ectomycorrhizal fungi associated with ecologically important tree species. Although the genus is distributed over northern temperate regions, we know little about the phylogeny and diversity of Tuber species in Japan. We have collected 186 new Tuber ascoma samples in Japan over a 10 y period. The identities and phylogenies of the samples were analyzed with sequences of four nuclear loci (i.e. internal transcribed spacer [ITS] and large subunit [LSU] regions of rDNA, elongation factor 1 alpha [EF1-α], and RNA polymerase II large subunit [rpb2] genes). Based on the species delimitation of 95% sequence matches in the ITS region, which is a suitable region for species-level identification of higher fungi, we identified 20 Tuber species. The number of observed species did not reach an asymptote with our maximum sampling localities in a species accumulation curve. The Chao2 species richness estimator indicated that at least 40 Tuber species should be present in Japan. Molecular phylogenetic analyses revealed that Japanese Tuber species belong to five major phylogroups, including Macrosporum, which had not been reported previously in Asia. Two Japanese species were morphologically and phylogenetically distinct from other known phylogroups, and here we propose a new Tuber phylogroup, Japonicum. In addition most of the other Japanese species formed separate clades within individual major phylogroups and deserve to be proposed as new species. Detailed molecular phylogeny within individual phylogroups revealed the existence of phylogeographic structures at both continental and within-Asia scales, indicating that migration and allopatric speciation have occurred even between the mainland and islands in Asia. Although our findings substantially advance current understanding of Tuber diversity and phylogeny, comparable richness estimation and multilocus phylogeny in other geographic regions are necessary to unequivocally address global patterns of Tuber diversity and biogeography.     

Phylogeography of white-spotted Charr (Salvelinus leucomaenis) inferred from mitochondrial DNA sequences

The white-spotted charr (Salvelinus leucomaenis) is a coldwater-adapted fish distributed in far-eastern Asia. To assess phylogeographic patterns of this species over most of its range in the Japanese archipelago and Sakhalin Island, Russia, we examined nucleotide sequences of the mitochondrial DNA (mtDNA) cytochrome b region (557 bp) in 141 individuals from 50 populations. A total of 33 (5.5%) nucleotide positions were polymorphic and defined 29 haplotypes. Phylogenetic analysis assigned the observed haplotypes to four main clades, which were characterized by the idiosyncrasies and discontinuity of geographic distributions. The nested clade analyses revealed that the geographical distribution patterns of some haplotypes and clades were explained by historical event such as past fragmentation. Although substantial genetic differentiation was found among the four main clades, their geographic distributions overlapped extensively in several regions. Since white-spotted charr can potentially use both freshwater and marine environments, coexistence among different lineages can be attributed to secondary contact through range expansion by migratory individuals during multiple glacial periods after interglacial isolation. Finally, our data demonstrate that the current subspecies designation does not reflect the phylogeography of this species based on mtDNA analysis. Hierarchical analysis (AMOVA) also showed that genetic variation was far more pronounced within subspecies than among subspecies (i.e., among discrete regions). These results suggest that each population, rather than each subspecies, must be treated as an evolutionarily significant unit.     

Global phylogeography of the ridley sea turtles (Lepidochelys spp.) as inferred from mitochondrial DNA sequences

The Kemp's ridley sea turtle (Lepidochelys kempi) is restricted to the warm temperate zone of the North Atlantic Ocean, whereas the olive ridley turtle (L. olivacea) is globally distributed in warm-temperate and tropical seas, including nesting colonies in the North Atlantic that nearly overlap the range of L. kempi. To explain this lopsided distribution, Pritchard (1969) proposed a scenario in which an ancestral taxon was divided into Atlantic and Pacific forms (L. kempi and L. olivacea, respectively) by the Central American land bridge. According to this model, the olive ridley subsequently occupied the Pacific and Indian Oceans and recently colonized the Atlantic Ocean via southern Africa. To assess this biogeographic model, a 470 bp sequence of the mtDNA control region was compared among 89 ridley turtles, including the sole L. kempi nesting population and 7 nesting locations across the range of L. olivacea. These data confirm a fundamental partition between L. olivacea and L. kempi (p=0.052-0.069), shallow separations within L. olivacea (p=0.002-0.031), and strong geographic partitioning of mtDNA lineages. The most divergent L. olivacea haplotype is observed in the Indo-West Pacific region, as are the central haplotypes in a parsimony network, implicating this region as the source of the most recent radiation of olive ridley lineages. The most common olive ridley haplotype in Atlantic samples is distinguished from an Indo-West Pacific haplotype by a single nucleotide substitution, and East Pacific samples are distingushed from the same haplotype by two nucleotide substitutions. These shallow separations are consistent with the recent invasion of the Atlantic postulated by Pritchard (1969), and indicate that the East Pacific nesting colonies were also recently colonized from the Indo-West Pacific region. Molecular clock estimates place these invasions within the last 300,000 years. This revised version was published online in July 2006 with corrections to the Cover Date.     

A set of 21 polymorphic microsatellites in Alpine chamois (Rupicapra rupicapra)

A cross‐species amplification test of 39 bovid microsatellite markers was carried out on chamois (Rupicapra rupicapra), a species with a high economic and tourist value, for which a number of life‐history traits remain to be quantified. Of 39 primer pairs tested, 26 gave a specific amplification product and 21 were polymorphic. Locus‐specific allelic richness ranged from two to six. Our results suggest that these loci will be useful for investigating basic population genetics as well as life‐history traits, such as dispersal.     

Characterization of microsatellites and gene contents from genome shotgun sequences of mungbean (Vigna radiata (L.) Wilczek)

Background  

Mungbean is an important economical crop in Asia. However, genomic research has lagged behind other crop species due to the lack of polymorphic DNA markers found in this crop. The objective of this work is to develop and characterize microsatellite or simple sequence repeat (SSR) markers from genome shotgun sequencing of mungbean.     

Open field host selection and behavior by tamarisk beetles (Diorhabda spp.) (Coleoptera: Chrysomelidae) in biological control of exotic saltcedars (Tamarix spp.) and risks to non-target athel (T. aphylla) and native Frankenia spp.

Biological control of invasive saltcedars (Tamarix spp.) in the western U.S. by exotic tamarisk leaf beetles, Diorhabda spp., first released in 2001 after 15 years of development, has been successful. In Texas, beetles from Crete, Greece were first released in 2004 and are providing control. However, adults alight, feed and oviposit on athel (Tamarix aphylla), an evergreen tree used for shade and as a windbreak in the southwestern U.S. and México, and occasionally feed on native Frankenia spp. plants. The ability of tamarisk beetles to establish on these potential field hosts was investigated in the field. In no-choice tests in bagged branches, beetle species from Crete and Sfax, Tunisia produced 30–45% as many egg masses and 40–60% as many larvae on athel as on saltcedar. In uncaged choice tests in south Texas, adult, egg mass and larval densities were 10-fold higher on saltcedar than on adjacent athel trees after 2 weeks, and damage by the beetles was 2- to 10-fold greater on saltcedar. At a site near Big Spring, in west-central Texas, adults, egg masses and 1st and 2nd instar larvae were 2- to 8-fold more abundant on saltcedar than on athel planted within a mature saltcedar stand being defoliated by Crete beetles, and beetles were 200-fold or less abundant or not found at all on Frankenia. At a site near Lovelock, Nevada, damage by beetles of a species collected from Fukang, China was 12–78% higher on saltcedar than on athel planted among mature saltcedar trees undergoing defoliation. The results demonstrate that 50–90% reduced oviposition on athel and beetle dispersal patterns within resident saltcedar limit the ability of Diorhabda spp. to establish populations and have impact on athel in the field.     

Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross transferable to erianthus and sorghum

Analysis of a sugarcane (Saccharum spp.) EST (expressed sequence tag) library of 8678 sequences revealed approximately 250 microsatellite or simple sequence repeats (SSRs) sequences. A diversity of dinucleotide and trinucleotide SSR repeat motifs were present although most were of the (CGG)_n trinucleotide motif. Primer sets were designed for 35 sequences and tested on five sugarcane genotypes. Twenty-one primer pairs produced a PCR product and 17 pairs were polymorphic. Primer pairs that produced polymorphisms were mainly located in the coding sequence with only a single pair located within the 5′ untranslated region. No primer pairs producing a polymorphic product were found in the 3′ untranslated region. The level of polymorphism (PIC value) in cultivars detected by these SSRs was low in sugarcane (0.23). However, a subset of these markers showed a significantly higher level of polymorphism when applied to progenitor and related genera (Erianthus sp. and Sorghum sp.). By contrast, SSRs isolated from sugarcane genomic libraries amplify more readily, show high levels of polymorphism within sugarcane with a higher PIC value (0.72) but do not transfer to related species or genera well.     

Effect of aggregations of aphids (Periphyllus spp.) on their size

In autumn, aphids reared on the opposite side of a sycamore leaf from an aggregation ofPeriphyllus acericola nymphs are heavier than aphids reared on uninfested leaves. Groups ofP. testudinaceus nymphs do not enhance the growth of aphids reared opposite.     

Vocal types in crossbill populations (Loxia spp.) of Southwest Europe

The evolution of crossbills is one of the most fascinating topics in evolutionary ecology. Recent studies have shown an astonishing divergence in terms of vocalisation between morphologically quite similar crossbill populations in the Red/Common Crossbill complex (Loxia curvirostra) of North America and Europe. Some evidence even indicates the existence of “cryptic” species with different vocal types and bill sizes, which are adapted to different conifer species. However, there is so far no strong genetic evidence for the existence of separate species, although assortative mating occurs with respect to bill size. To understand the role of vocalisation in the speciation process of crossbill taxa, basic studies that assess the distribution of vocal types of crossbills and the use of different habitats and resources are needed. In our study, we investigated the occurrence of crossbill vocal types in Southwest Europe. In addition to the well-known vocal types described first by Robb (Dutch Birding 22:61–107, 2000) for the Benelux and Great Britain, we discovered at least six more vocal types in the Mediterranean area. Some vocal types were found exclusively in rather small areas, e.g. in the Pyrenees, the Sierra de Cazorla, Sierra de Javalambre and on Corsica, and appeared to be tightly linked to certain habitat types and pine species. Overall, vocal types in the Mediterranean had a more local occurrence than vocal types from northern populations, which were more widely distributed. This might reflect the nomadic behaviour of northern European crossbills, which feed, in contrast to Mediterranean crossbills, mostly on rather unstable food sources, especially spruce seeds. Furthermore, the vocal types of Mediterranean crossbills show at least some similarities to the vocal types of the rather sedentary crossbills of North Europe (L. pytyopsittacus, L. scotica), which are as well adapted to pine seeds. This might reflect a common ancestry of crossbills adapted for pines. We therefore suggest the existence of two main groups of crossbills in Europe: one group that is rather sedentary and feeds mainly on pine seeds (L. pytyopsittacus, L. scotica and the Mediterranean forms), and another group in Central, Northern and Eastern Europe that is highly nomadic and mostly feeds on spruce seeds (L. curvirostra). Further studies are needed to unravel the consistency of vocal types and the genetic relationship between the different forms, and to provide more evidence for the degree of assortative mating of crossbills with distinct vocalisation breeding in sympatry.     

Phylogeography and genetic structure of the Canarian common chaffinch (Fringilla coelebs) inferred with mtDNA and microsatellite loci

The widespread common chaffinch (Fringilla coelebs) inhabits five of the seven Canary Islands. Sequences of the mitochondrial cytochrome b gene (1002 bp) revealed new insights into the systematics and phylogeography of this taxon. Additionally, a set of microsatellite loci were analyzed to examine the structure of these populations. Our results suggest that a new species of the genus Fringilla is present in the Canary Islands, which comprises at least three subspecies, but with a different distribution to that which has been morphologically accepted. The specimens from Gran Canaria are genetically distinct from those of La Gomera and Tenerife (F. c. canariensis), which suggests the existence of an undescribed taxon. Furthermore, nuclear microsatellite data suggest an ongoing incipient speciation process in this population. This study provides both important conservationist implications and a basis for re-evaluating the taxonomic status of the Canarian Fringilla coelebs populations.