Molecular Ecology

Molecular tools have now been applied for the past 5 years to dissect ectomycorrhizal (EM) community structure, and they have propelled a resurgence in interest in the field. Results from these studies have revealed that: (i) EM communities are impressively diverse and are patchily distributed at a fine scale below ground; (ii) there is a poor correspondence between fungi that appear dominant as sporocarps vs. those that appear dominant on roots; (iii) members of Russulaceae, Thelephoraceae, and/or non‐thelephoroid resupinates are among the most abundant EM taxa in ecosystems sampled to date; (iv) dissimilar plants are associated with many of the same EM species when their roots intermingle — this occurs on a small enough spatial scale that fungal individuals are likely to be shared by dissimilar plants; and (v) mycoheterotrophic plants have highly specific fungal associations. Although, these results have been impressive, they have been tempered by sampling difficulties and limited by the taxonomic resolution of restriction fragment length polymorphism methods. Minor modifications of the sampling schemes, and more use of direct sequencing, has the potential to solve these problems. Use of additional methods, such as in situ hybridization to ribosomal RNA or hybridization coupled to microarrays, are necessary to open up the analysis of the mycelial component of community structure.

Interest in the ecology of ectomycorrhizal (ECM) fungi has increased considerably, but little is known about interspecific interactions among ECM species. We examined competitive interactions between Rhizopogon occidentalis and R. salebrosus at Point Reyes National Seashore, California, USA. At three field sites, species abundances were compared in single‐ and two‐species treatments on Pinus muricata seedlings inoculated with spores. Competition for root tips was assessed using real‐time polymerase chain reaction (PCR) of internal transcribed spacer rDNA. In general, we found strong competitive exclusion of R. salebrosus by R. occidentalis, with ≥ 75% of the seedlings in the two‐species treatment colonized exclusively by R. occidentalis after 5 and 10 months. However, on the seedlings that were co‐colonized, we observed no significant difference in the abundances of R. salebrosus and R. occidentalis, suggesting that once R. salebrosus was established, it was no longer competitively inferior. There were no significant differences in survival, growth, or percentage leaf nitrogen of seedlings colonized with either Rhizopogon species, but both growth and percentage leaf nitrogen were significantly higher for ECM than non‐ECM seedlings. We also observed strong positive correlations between actual ECM root tip weight and that inferred from real‐time PCR for both species, indicating that this method provided an accurate assessment of root tip occupation and hence ECM competitive dynamics. In conjunction with a previous experiment, our results indicate that competition between these two Rhizopogon species occurs similarly in both field and laboratory settings and that when colonizing from spore, timing largely determines the outcome of initial competitive interactions.

Collembola comprise a major source of alternative prey to linyphiid spiders in arable fields, helping to sustain and retain these predators as aphid control agents within the crop. Polymerase chain reaction primers were developed for the amplification, from spider gut samples, of DNA from three of the most abundant species of Collembola in wheat crops in Europe, namelyIsotoma anglicana,Lepidocyrtus cyaneusandEntomobrya multifasciata. The primers amplified fragments of the mitochondrial cytochrome oxidase subunit I (COI) gene and were designed following alignment of comparable sequences for a range of predator and prey species. Each of the primer pairs proved to be species‐specific to a Collembola species, amplifying DNA fragments from 211 to 276 base pairs in length. Following consumption of a single collembolan, prey DNA was detectable in 100% of spiders after 24 h of digestion. We report the first use of DNA‐based techniques to detect predation by arthropods on natural populations of prey in the field. All three species of Collembola were consumed by the spiders. By comparing the ratios of the Collembola species in the field with the numbers of spiders that gave positive results for each of those species, it was possible to demonstrate that the spiders were exercising prey choice. Overall, a single target species of Collembola was eaten by 48% of spiders while a further 16% of spiders contained DNA from two different species of Collembola. Preference was particularly evident forI. anglicana, the species most frequently found in spider guts yet the least numerous of the three target species in the field.

The Brazilian Atlantic Forest is one of the world's major biodiversity hotspots and is threatened by a severe habitat loss. Yet little is known about the processes that originated its remarkable richness of endemic species. Here we present results of a large‐scale survey of the genetic variation at the mitochondrial cytochromebgene of the pitviper, jararaca lancehead (Bothrops jararaca), and two closely related insular species (Bothrops insularisandBothrops alcatraz), endemic of this region. Phylogenetic and network analyses revealed the existence of two well‐supported clades, exhibiting a southern and a northern distribution. The divergence time of these two phylogroups was estimated at 3.8 million years ago, in the Pliocene, a period of intense climatic changes and frequent fragmentation of the tropical rainforest. Our data also suggest that the two groups underwent a large size expansion between 50 000 and 100 000 years ago. However, the southern group showed a more marked signal of population size fluctuation than the northern group, corroborating evidences that southern forests may have suffered a more pronounced reduction in area in the late Pleistocene. The insular speciesB. alcatrazandB. insularispresented very low diversity, each one sharing haplotypes with mainland individuals placed in different subclades. Despite their marked morphological and behavioural uniqueness, these two insular species seem to have originated very recently and most likely from distinct costalB. jararacapopulations, possibly associated with late Pleistocene or Holocene sea level fluctuations.

A rapid procedure for the identification of fluorescent pseudomonads, based on the polymerase chain reaction (PCR) and restriction fragment analysis of 16S rDNA genes is described. Thirty‐one strains belonging to 10 different Pseudomonas species of the Pseudomonas fluorescens rRNA branch were characterized. Amplified rDNA was digested with 13 different restriction endonucleases. The combined data from restriction analysis enabled the definition of 17 different 16S rDNA genotypes. All type strains belonging to different species were differentiated. The good correlation between grouping obtained using restriction analysis with other molecular classification criteria demonstrates the value of the described method to characterize rapidly fluorescent Pseudomonas strains at the species level.

Intraspecific phylogeny and genetic variation were investigated based on nucleotide sequences of the mitochondrial cytochromebgene in six soricine shrew species,Sorex unguiculatus,S. caecutiens,S. shinto,S. gracillimus,S. minutissimusandS. hosonoi, collected primarily from northeastern Asia. Maximum likelihood trees and a phylogenetic network were generated to estimate intraspecific phylogenies.S. minutissimusshowed high congruence between phylogenetic position and geographical origin andS. gracillimusshowed low congruence. In contrast, there was no congruence between phylogeny and geography inS. unguiculatusand theS. caecutiensfrom Sakhalin‐Eurasia. Positive correlation between genetic and geographical distances was found inS. minutissimusandS. gracillimus, but not in the other species (or regional populations). The results of the phylogenetic and genetic analyses suggest thatS. minutissimusandS. gracillimushave occupied their present ranges for a longer time than the other species if we assume a stepping‐stone model of population structure. In addition, there was no contradiction between the present investigations and the hypotheses of multiple immigration byS. gracillimusand a single immigration byS. unguiculatusinto Hokkaido Island. It is proposed that these six northeastern Asian species experienced different historical processes of range expansion and dispersal despite the fact that some of them currently show similar patterns of distribution.

It is now evident that the genetic mating system can be very different to the observed mating system. However, it is less well known what makes particular individuals more (or less) successful than expected from the observed system. In this study the observed territorial structure of a field population of the agamid lizard, Ctenophorus ornatus, was compared with the mating system as evidenced by microsatellite parentage assignment. This study also investigated whether any male traits predicted reproductive success. Sixty‐five per cent of clutches were sired at least partially by a male other than the main territory‐holding male and 35% of clutches were sired by a male with no overlap of the female’s territory. Multiple paternity was moderately frequent at 25% of clutches. Male chest patch size predicted territory size and the number of females in the territory, but did not predict reproductive success. Instead, male head depth and body size were independently related to the number of offspring sired. As male head depth also predicted the number of females in a territory, these males are likely to be gaining increased reproductive success as a consequence of the higher number of females in their territories. Larger body size males, however, did not have a greater number of females in their territory and instead had more extra‐territorial copulations. Whether these extra‐territorial copulations are due to female choice or success in male competition is unknown.

Molecular ecologists increasingly require ‘universal’ genetic markers that can easily be transferred between species. The distribution of cross‐species transferability of nuclear microsatellite loci is highly uneven across taxa, being greater in animals and highly variable in flowering plants. The potential for successful cross‐species transfer appears highest in species with long generation times, mixed or outcrossing breeding systems, and where genome size in the target species is small compared to the source. We discuss the implications of these findings and close with an outlook on potential alternative sources of cross‐species transferable markers.