Molecular Ecology

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.

Symbiosis plays a fundamental role in nature. Lichens are among the best known, globally distributed symbiotic systems whose ecology is shaped by the requirements of all symbionts forming the holobiont. The widespread lichen‐forming fungal genusStereocaulonprovides a suitable model to study the ecology of microscopic green algal symbionts (i.e., phycobionts) within the lichen symbiosis. We analysed 282Stereocaulonspecimens, collected in diverse habitats worldwide, using the algalITS rDNAand actin gene sequences and fungalITS rDNAsequences. Phylogenetic analyses revealed a great diversity among the predominant phycobionts. The algal genusAsterochloris(Trebouxiophyceae) was recovered in most sampled thalli, but two additional genera,VulcanochlorisandChloroidium, were also found. We used variation‐partitioning analyses to investigate the effects of climatic conditions, substrate/habitat characteristic, spatial distribution and mycobionts on phycobiont distribution. Based on an analogy, we examined the effects of climate, substrate/habitat, spatial distribution and phycobionts on mycobiont distribution. According to our analyses, the distribution of phycobionts is primarily driven by mycobionts andvice versa. Specificity and selectivity of both partners, as well as their ecological requirements and the width of their niches, vary significantly among the species‐level lineages. We demonstrated that species‐level lineages, which accept more symbiotic partners, have wider climatic niches, overlapping with the niches of their partners. Furthermore, the survival of lichens on substrates with high concentrations of heavy metals appears to be supported by their association with toxicity‐tolerant phycobionts. In general, low specificity towards phycobionts allows the host to associate with ecologically diversified algae, thereby broadening its ecological amplitude.

Microbial symbionts are instrumental to the ecological and long‐term evolutionary success of their hosts, and the central role of symbiotic interactions is increasingly recognized across the vast majority of life. Lichens provide an iconic group for investigating patterns in species interactions; however, relationships among lichen symbionts are often masked by uncertain species boundaries or an inability to reliably identify symbionts. The species‐rich lichen‐forming fungal family Parmeliaceae provides a diverse group for assessing patterns of interactions of algal symbionts, and our study addresses patterns of lichen symbiont interactions at the largest geographic and taxonomic scales attempted to date. We analysed a total of 2356 algal internal transcribed spacer (ITS) region sequences collected from lichens representing ten mycobiont genera in Parmeliaceae, two genera in Lecanoraceae and 26 cultured Trebouxia strains. Algal ITS sequences were grouped into operational taxonomic units (OTUs); we attempted to validate the evolutionary independence of a subset of the inferred OTUs using chloroplast and mitochondrial loci. We explored the patterns of symbiont interactions in these lichens based on ecogeographic distributions and mycobiont taxonomy. We found high levels of undescribed diversity in Trebouxia, broad distributions across distinct ecoregions for many photobiont OTUs and varying levels of mycobiont selectivity and specificity towards the photobiont. Based on these results, we conclude that fungal specificity and selectivity for algal partners play a major role in determining lichen partnerships, potentially superseding ecology, at least at the ecogeographic scale investigated here. To facilitate effective communication and consistency across future studies, we propose a provisional naming system for Trebouxia photobionts and provide representative sequences for each OTU circumscribed in this study.

Lichens are symbioses between fungi (mycobionts) and photoautotrophic green algae or cyanobacteria (photobionts). Many lichens occupy large distributional ranges covering several climatic zones. So far, little is known about the large‐scale phylogeography of lichen photobionts and their role in shaping the distributional ranges of lichens. We studied south polar, temperate and north polar populations of the widely distributed fruticose lichen Cetraria aculeata. Based on the DNA sequences from three loci for each symbiont, we compared the genetic structure of mycobionts and photobionts. Phylogenetic reconstructions and Bayesian clustering methods divided the mycobiont and photobiont data sets into three groups. An amova shows that the genetic variance of the photobiont is best explained by differentiation between temperate and polar regions and that of the mycobiont by an interaction of climatic and geographical factors. By partialling out the relative contribution of climate, geography and codispersal, we found that the most relevant factors shaping the genetic structure of the photobiont are climate and a history of codispersal. Mycobionts in the temperate region are consistently associated with a specific photobiont lineage. We therefore conclude that a photobiont switch in the past enabled C. aculeata to colonize temperate as well as polar habitats. Rare photobiont switches may increase the geographical range and ecological niche of lichen mycobionts by associating them with locally adapted photobionts in climatically different regions and, together with isolation by distance, may lead to genetic isolation between populations and thus drive the evolution of lichens.

The distribution patterns of symbiotic algae are thought to be conferred mainly by their hosts, however, they may originate in algal environmental requirements as well. In lichens, predominantly terrestrial associations of fungi with algae or cyanobacteria, the ecological preferences of photobionts have not been directly studied so far. Here, we examine the putative environmental requirements in lichenized alga Asterochloris, and search for the existence of ecological guilds in Asterochloris‐associating lichens. Therefore, the presence of phylogenetic signal in several environmental traits was tested. Phylogenetic analysis based on the concatenated set of internal transcribed spacer rDNA and actin type I intron sequences from photobionts associated with lichens of the genera Lepraria and Stereocaulon (Stereocaulaceae, Ascomycota) revealed 13 moderately to well‐resolved clades. Photobionts from particular algal clades were found to be associated with taxonomically different, but ecologically similar lichens. The rain and sun exposure were the most significant environmental factor, clearly distinguishing the Asterochloris lineages. The photobionts from ombrophobic and ombrophilic lichens were clustered in completely distinct clades. Moreover, two photobiont taxa were obviously differentiated based on their substrate and climatic preferences. Our study, thus reveals that the photobiont, generally the subsidiary member of the symbiotic lichen association, could exhibit clear preferences for environmental factors. These algal preferences may limit the ecological niches available to lichens and lead to the existence of specific lichen guilds.

Wolbachia are a group of intracellular bacteria that cause reproductive alterations in their arthropod hosts. Widely discordant host and Wolbachia phylogenies indicate that horizontal transmission of these bacteria among species sometimes occurs. A likely means of horizontal transfer is through the feeding relations of organisms within communities. Feeding interactions among insects within the rice‐field insect community have been well documented in the past. Here, we present the results of a polymerase chain reaction‐based survey and phylogenetic analysis of Wolbachia strains in the rice‐field insect community of Thailand. Our field survey indicated that 49 of 209 (23.4%) rice‐field insect species were infected with Wolbachia. Of the 49 infected species, 27 were members of two feeding complexes: (i) a group of 13 hoppers preyed on by 2 mirid species and parasitized by a fly species, and (ii) 2 lepidopteran pests parasitized by 9 wasp species. Wolbachia strains found in three hoppers, Recilia dorsalis, Nephotettix malayanus and Nisia nervosa, the two mirid predators, Cyrtorhinus lividipennis and Tytthus chinensis, and the fly parasitoid, Tomosvaryella subvirescens, were all in the same Wolbachia clade. In the second complex, the two lepidopteran pests, Cnaphalocrocis medinalis and Scirpophaga incertulas, were both infected with Wolbachia from the same clade, as was the parasitoid Tropobracon schoenobii. However, none of the other infected parasitoid species in this feeding complex was infected by Wolbachia from this clade. Mean (± SD) genetic distance of Wolbachia wsp sequences among interacting species pairs of the hopper feeding complex (0.118 ± 0.091 nucleotide sequence differences), but not for the other two complexes, was significantly smaller than that between noninteracting species pairs (0.162 ± 0.079 nucleotide sequence differences). Our results suggest that some feeding complexes, such as the hopper complex described here, could be an important means by which Wolbachia spreads among species within arthropod communities.

The seagrassPosidonia oceanicais a key engineering species structuring coastal marine systems throughout much of theMediterranean basin. Its decline is of concern, leading to the search for short‐ and long‐term indicators of seagrass health. UsingArcGISmaps from a recent, high‐resolution (1–4 km) modelling study of 18 disturbance factors affecting coastal marine systems across theMediterranean (Micheliet al. 2013,http://globalmarine.nceas.ucsb.edu/mediterranean/), we tested for correlations with genetic diversity metrics (allelic diversity, genotypic/clonal diversity and heterozygosity) in a meta‐analysis of 56 meadows. Contrary to initial predictions, weak but significantlypositivecorrelations were found for commercial shipping, organic pollution (pesticides) and cumulative impact. This counterintuitive finding suggests greater resistance and resilience of individuals with higher genetic and genotypic diversity under disturbance (at least for a time) and/or increased sexual reproduction under an intermediate disturbance model. We interpret the absence of low and medium levels of genetic variation at impacted locations as probable local extinctions of individuals that already exceeded their resistance capacity. Alternatively, high diversity at high‐impact sites is likely a temporal artefact, reflecting the mismatch with pre‐environmental impact conditions, especially because flowering and sexual recruitment are seldom observed. While genetic diversity metrics are a valuable tool for restoration and mitigation, caution must be exercised in the interpretation of correlative patterns as found in this study, because the exceptional longevity of individuals creates a temporal mismatch that may falsely suggest good meadow health status, while gradual deterioration of allelic diversity might go unnoticed.

Mycobacterium tuberculosis (M.tb) is a globally distributed, obligate pathogen of humans that can be divided into seven clearly defined lineages. An emerging consensus places the origin and global dispersal of M.tb within the past 6,000 years: identifying how the ancestral clone of M.tb spread and differentiated within this timeframe is important for identifying the ecological drivers of the current pandemic. We used Bayesian phylogeographic inference to reconstruct the migratory history of M.tb in Africa and Eurasia and to investigate lineage specific patterns of spread from a geographically diverse sample of 552 M.tb genomes. Applying evolutionary rates inferred with ancient M.tb genome calibration, we estimated the timing of major events in the migratory history of the pathogen. Inferred timings contextualize M.tb dispersal within historical phenomena that altered patterns of connectivity throughout Africa and Eurasia: trans‐Indian Ocean trade in spices and other goods, the Silk Road and its predecessors, the expansion of the Roman Empire, and the European Age of Exploration. We found that Eastern Africa and Southeast Asia have been critical in the dispersal of M.tb. Our results further reveal that M.tb populations have grown through range expansion, as well as in situ, and delineate the independent evolutionary trajectories of bacterial subpopulations underlying the current pandemic.