Stalking the wild Tetrahymena

We live on a microbial planet. Microorganisms dominate in terms of numbers of lineages, numbers of organisms, biomass and evolutionary innovations. Yet much remains to be learned about our microbial neighbours. We have gotten to know a few species that have been transformed into ‘laboratory rats’ (i.e. model organisms), but even here our understanding of the natural history of these lineages remains inadequate as there are few data from populations living in natural habitats. Zufall et al. (2013) move beyond this trend by providing insights into the natural history of Tetrahymena thermophila, a ciliate that has been used in many studies of cellular and molecular biology. Characterization of T. thermophila sampled from numerous ponds across this ciliate's range in Eastern North America reveals the following: (i) considerable differentiation among isolates, with the greatest diversity among lineages in New England, and (ii) a relatively small effective population size for this model ciliate. Such population data are fundamental for inferences about the origins of the numerous remarkable features of T. thermophila.     

The “<Emphasis Type="Italic">Tetrahymena pyriformis</Emphasis>” complex of cryptic species

Cryptic species are common among protists and have long been known in ciliates. The ciliate genus Tetrahymena contains a large group of morphologically indistinguishable species referred to as the ‘T. pyriformis’ complex. These species include those reproductively isolated by mating type as well as asexual species characterized by the absence of the germinal micronucleus. This paper examines the molecular diversity of the species and describes the biogeography of ‘T. pyriformis’ species. Most species are globally distributed, though the best studied species, T. thermophila, is confined to North America and gives evidence of population structure in local populations. Selfers and asexual species are common and arise from sexual species, a possible exploitation of nuclear dimorphism. It is argued that the cryptic species likely have different ecological roles and that the biodiversity of Tetrahymena in particular, and ciliates in general, is underestimated. Special Issue: Protist diversity and geographic distribution. Guest editor: W. Foissner.     

Vicariance patterns in the Mediterranean Sea: east–west cleavage and low dispersal in the endemic seagrass Posidonia oceanica

Aim The seagrass, Posidonia oceanica is a clonal angiosperm endemic to the Mediterranean Sea. Previous studies have suggested that clonal growth is far greater than sexual recruitment and thus leads to low clonal diversity within meadows. However, recently developed microsatellite markers indicate that there are many different genotypes, and therefore many distinct clones present. The low resolution of markers used in the past limited our ability to estimate clonality and assess the individual level. New high‐resolution dinucleotide microsatellites now allow genetically distinct individuals to be identified, enabling more reliable estimation of population genetic parameters across the Mediterranean Basin. We investigated the biogeography and dispersal of P. oceanica at various spatial scales in order to assess the influence of different evolutionary factors shaping the distribution of genetic diversity in this species. Location The Mediterranean. Methods We used seven hypervariable microsatellite markers, in addition to the five previously existing markers, to describe the spatial distribution of genetic variability in 34 meadows spread throughout the Mediterranean, on the basis of an average of 35.6 (± 6.3) ramets sampled. Results At the scale of the Mediterranean Sea as a whole, a strong east–west cleavage was detected (amova) . These results are in line with those obtained using previous markers. The new results showed the presence of a putative secondary contact zone at the Siculo‐Tunisian Strait, which exhibited high allelic richness and shared alleles absent from the eastern and western basins. F statistics (pairwise θ ranges between 0.09 and 0.71) revealed high genetic structure between meadows, both at a small scale (about 2 to 200 km) and at a medium scale within the eastern and western basins, independent of geographical distance. At the intrameadow scale, significant spatial autocorrelation in six out of 15 locations revealed that dispersal can be restricted to the scale of a few metres. Main conclusions A stochastic pattern of effective migration due to low population size, turnover and seed survival is the most likely explanation for this pattern of highly restricted gene flow, despite the importance of an a priori seed dispersal potential. The east–west cleavage probably represents the outline of vicariance caused by the last Pleistocene ice age and maintained to this day by low gene flow. These results emphasize the diversity of evolutionary processes shaping the genetic structure at different spatial scales.     

Distance,elevation and environment as drivers of diversity and divergence in bumble bees across latitude and altitude

Identifying drivers of dispersal limitation and genetic differentiation is a key goal in biogeography. We examine patterns of population connectivity and genetic diversity using restriction site‐associated DNA sequencing (RADseq) in two bumble bee species, Bombus vosnesenskii and Bombus bifarius, across latitude and altitude in mountain ranges from California, Oregon and Washington, U.S.A. Bombus vosnesenskii, which occurs across a broader elevational range at most latitudes, exhibits little population structure while B. bifarius, which occupies a relatively narrow higher elevation niche across most latitudes, exhibits much stronger population differentiation, although gene flow in both species is best explained by isolation with environmental niche resistance. A relationship between elevational habitat breadth and genetic diversity is also apparent, with B. vosnesenskii exhibiting relatively consistent levels of genetic diversity across its range, while B. bifarius has reduced genetic diversity at low latitudes, where it is restricted to high‐elevation habitat. The results of this study highlight the importance of the intersect between elevational range and habitat suitability in influencing population connectivity and suggest that future climate warming will have a fragmenting effect even on populations that are presently well connected, as they track their thermal niches upward in montane systems.     

Increasing temperature weakens the positive effect of genetic diversity on population growth

Genetic diversity and temperature increases associated with global climate change are known to independently influence population growth and extinction risk. Whether increasing temperature may influence the effect of genetic diversity on population growth, however, is not known. We address this issue in the model protist system Tetrahymena thermophila. We test the hypothesis that at temperatures closer to the species’ thermal optimum (i.e., the temperature at which population growth is maximal, or T _opt), genetic diversity should have a weaker effect on population growth compared to temperatures away from the thermal optimum. To do so, we grew populations of T. thermophila with varying levels of genetic diversity at increasingly warmer temperatures and quantified their intrinsic population growth rate, r. We found that genetic diversity increases population growth at cooler temperatures, but that as temperature increases, this effect weakens. We also show that a combination of changes in the amount of expressed genetic diversity (G) in r, plastic changes in population growth across temperatures (E), and strong G × E interactions underlie this temperature effect. Our results uncover important but largely overlooked temperature effects that have implications for the management of small populations with depauperate genetic stocks in an increasingly warming world.     

Genetic structure of Partamona helleri (Apidae, Meliponini) from Neotropical Atlantic rainforest

Stingless bees of the genus Partamona are distributed from southern Mexico to southern Brazil. This genus has been subject to different approaches to solve questions concerning general biology, taxonomy, systematics and biogeography, but population studies applying molecular techniques are inexistent. We analyzed the genetic structure of P. helleri across its geographic distribution along the coastal Atlantic tropical rainforest in Brazil. Ten mtDNA haplotypes were observed in 47 colonies of P. helleri of which some were exclusive and others shared among geographic sub-groups. Statistical analysis showed high genetic differentiation between geographic areas sampled. Fragmentation of the Atlantic forest during Pleistocene glaciations is discussed as a possible cause of the present haplotype distribution and frequency.     

Inferred global connectivity of whale shark Rhincodon typus populations

Ten years have passed since the last synopsis of whale shark Rhincodon typus biogeography. While a recent review of the species' biology and ecology summarized the vast data collected since then, it is clear that information on population geographic connectivity, migration and demography of R. typus is still limited and scattered. Understanding R. typus migratory behaviour is central to its conservation management considering the genetic evidence suggesting local aggregations are connected at the generational scale over entire ocean basins. By collating available data on sightings, tracked movements and distribution information, this review provides evidence for the hypothesis of broad‐scale connectivity among populations, and generates a model describing how the world's R. typus are part of a single, global meta‐population. Rhincodon typus occurrence timings and distribution patterns make possible a connection between several aggregation sites in the Indian Ocean. The present conceptual model and validating data lend support to the hypothesis that R. typus are able to move among the three largest ocean basins with a minimum total travelling time of around 2–4 years. The model provides a worldwide perspective of possible R. typus migration routes, and suggests a modified focus for additional research to test its predictions. The framework can be used to trim the hypotheses for R. typus movements and aggregation timings, thereby isolating possible mating and breeding areas that are currently unknown. This will assist endeavours to predict the longer‐term response of the species to ocean warming and changing patterns of human‐induced mortality.     

Vicariance and marine migration in continental island populations of a frog endemic to the Atlantic Coastal forest

The theory of island biogeography is most often studied in the context of oceanic islands where all island inhabitants are descendants from founding events involving migration from mainland source populations. Far fewer studies have considered predictions of island biogeography in the case of continental islands, where island formation typically splits continuous populations and thus vicariance also contributes to the diversity of island populations. We examined one such case on continental islands in southeastern Brazil, to determine how classic island biogeography predictions and past vicariance explain the population genetic diversity of Thoropa taophora, a frog endemic to the Atlantic Coastal Forest. We used nuclear microsatellite markers to examine the genetic diversity of coastal and island populations of this species. We found that island isolation has a role in shaping the genetic diversity of continental island species, with island populations being significantly less diverse than coastal populations. However, area of the island and distance from coast had no significant effect on genetic diversity. We also found no significant differences between migration among coastal populations and migration to and from islands. We discuss how vicariance and the effects of continued migration between coastal and island populations interact to shape evolutionary patterns on continental islands.     

Global mapping of Jatropha curcas yield based on response of fitness to present and future climate

Although acclaimed as a biofuel crop with high potential to sustainably replace fossil fuels, Jatropha curcas L. remains a poorly studied plant. Reliable yield assessments with conventional methods require agroclimatic and physiological knowledge, which is not yet available for Jatropha. To fill this gap, we tested a novel two‐step approach integrating knowledge from biogeography and population biology with available Jatropha field data. In the first step, using MaxEnt, a widely implemented model in biogeography, we predicted Jatropha fitness in response to climate by relating natural occurrence recorded in herbaria with bioclimatic geodatasets. In the second step, we relied on population biology principles supported by seed mass addition experiments to relate fitness to reproductive potential, hence seed yield. Jatropha seed yield in response to climate was mapped worldwide for actual (1950–2000 average) and future (2020) climate conditions. The modelled Jatropha seed yield was validated against a set of on‐field yield assessments (R²=0.67, P<0.001). The discrepancies between estimated and measured yields were partially explained by model uncertainties, as quantified by the sensitivity analysis of our modelling (R²=0.57, P=0.001). Jatropha has a pan‐tropical distribution, plus specific adaptability to hot temperate areas. Climate variables most significantly affecting modelled yield response were annual average temperature, minimum temperature, annual precipitation and precipitation seasonality.     

Comparative phylogeography of two closely related <Emphasis Type="Italic">Viola</Emphasis> species occurring in contrasting habitats in the Japanese archipelago

Similar distribution ranges shared by closely related plant species may have been shaped through different migration histories if those species have differing habitat preference. To test this hypothesis, phylogeographical patterns and population genetic structures were compared between two sister Viola species: Viola eizanensis preferring woodland and V. chaerophylloides var. sieboldiana preferring grassland, both being native to the Japanese Archipelago. Amplified fragment length polymorphism (AFLP) was used for phylogenetic reconstruction, together with Bayesian ancestry analysis, AMOVA, analysis of genetic diversity statistics, and analysis of the relative contribution of each population to total diversity. The results indicated that V. eizanensis had two distinct lineages occurring in the western and eastern part of Japan, but such lineages are not distinct in V. chaerophylloides var. sieboldiana. Both species exhibited the low genetic diversity and high between-population differentiation typical of selfing plants. In V. chaerophylloides var. sieboldiana, one particular population made a significantly higher contribution to the total heterozygosity (H _T), whereas in V. eizanensis, no population was identified as making a particularly higher contribution to H _T. These findings suggest that V. eizanensis had been isolated in two large glacial refugia, whereas populations of V. chaerophylloides var. sieboldiana were restricted to a single small refuge. Different light requirements between these two closely related species probably caused these differing responses to climatic change during the last ice age. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

ALLOZYME VARIATION,GENECOLOGY, AND PHYTOGEOGRAPHY OF ANTENNARIA ARCUATA (ASTERACEAE), A RARE SPECIES FROM THE GREAT BASIN AND RED DESERT WITH SMALL DISJUNCT POPULATIONS

Antennaria arcuata (Asteraceae: Inuleae) is a rare sexual diploid species that occurs in three disjunct regions of Idaho, Nevada, and Wyoming. Isozyme diversity in six populations of the species from the three regions utilized 26 putative loci to provide clues to its population genetic structure. Results show that, in general, the amount of genetic diversity in A. arcuata is very low in comparison to other sexual species of Antennaria. The values of several genetic statistics such as mean number of alleles per locus, proportion of loci polymorphic, and observed heterozygosity, are significantly lower than populations of any of 17 other sexual species of Antennaria that have been studied previously. It is likely that the unusual disjunct and restricted distribution of A. arcuata is partially the result of its unusual ecology, as it occurs in moist basins having high concentrations of salts that are frequently disturbed by large grazing animals. Canonical correspondence analysis shows strong relationships between several edaphic, environmental, and geographic features and the genetic variation in the populations. The migration of A. arcuata to other regions since the end of the Wisconsinan might have been inhibited by the fact that suitable habitats occur as small isolated islands in a sea of inhospitable terrain, the dry sagebrush steppe.     

Landscape genetics of a recent population extirpation in a burnet moth species

The intensification of agricultural land use over wide parts of Europe has led to the decline of semi-natural habitats, such as extensively used meadows, with those that remain often being small and isolated. These rapid changes in land use during recent decades have strongly affected populations inhabiting these ecosystems. Increasing habitat deterioration and declining permeability of the surrounding landscape matrix disrupt the gene flow within metapopulations. The burnet moth species Zygaena loti has suffered strongly from recent habitat fragmentation, as reflected by its declining abundance. We have studied its population genetic structure and found a high level of genetic diversity in some of the populations analysed, while others display low genetic diversity and a lack of heterozygosity. Zygaena loti was formerly highly abundant in meadows and along the skirts of forests. However, the species is currently restricted to isolated habitat remnants, which is reflected by the high genetic divergence among populations (F _ST: 0.136). Species distribution modelling as well as the spatial examination of panmictic clusters within the study area strongly support a scattered population structure for this species. We suggest that populations with a high level of genetic diversity still represent the former genetic structure of interconnected populations, while populations with low numbers of alleles, high F _IS values, and a lack of heterozygosity display the negative effects of reduced interconnectivity. A continuous exchange of individuals is necessary to maintain high genetic variability. Based on these results, we draw the general conclusion that more common taxa with originally large population networks and high genetic diversity suffer stronger from sudden habitat fragmentation than highly specialised species with lower genetic diversity which have persisted in isolated patches for long periods of time.     

Flies on the move: an inherited virus mirrors Drosophila melanogaster's elusive ecology and demography

Vertically transmitted parasites rely on their host's reproduction for their transmission, leading to the evolutionary histories of both parties being intimately entwined. Parasites can thus serve as a population genetic magnifying glass for their host's demographic history. Here, we study the fruitfly Drosophila melanogaster's vertically transmitted sigma virus DMelSV. The virus has a high mutation rate and low effective population size, allowing us to reconstruct at a fine scale how the combined forces of the movement of flies and selection on the virus have shaped its migration patterns. We found that the virus is likely to have spread to Europe from Africa, mirroring the colonization route of Drosophila. The North American DMelSV population appears to be the result of a recent single immigration from Europe, invading together with its host in the late 19th century. Across Europe, DMelSV migration rates are low and populations are highly genetically structured, likely reflecting limited fly movement. Despite being intolerant of extreme cold, viral diversity suggests that fly populations can persist in harsh continental climates and that recolonization from the warmer south plays a minor role. In conclusion, studying DMelSV can provide insights into the poorly understood ecology of D. melanogaster, one of the best‐studied organisms in biology.     

Modelling differential extinctions to understand big cat distribution on Indonesian islands

Aims To model differential extinction rates for island populations of tigers Panthera tigris and leopards P. pardus. Location Indonesia. Methods We built VORTEX population models of tiger and leopard populations on an island the size of Bali (3632 km²), using data from the literature. Results The tiger populations were less extinction prone than the leopard populations. This was unexpected as tigers had the smaller population sizes and, as such, might be assumed to be more extinction prone. We identified several aspects of tiger breeding biology that explain the result. Main conclusions Sea level reconstructions suggest that both tiger and leopard would have been present in Java, Sumatra and Bali at the end of the last glacial. Our model provides a plausible mechanism based on population ecology to explain why these leopard populations were more extinction prone than the tiger populations. In addition it illustrates the potential utility of population ecology models in understanding historical patterns in biogeography.     

Not as Ubiquitous as We Thought: Taxonomic Crypsis,Hidden Diversity and Cryptic Speciation in the Cosmopolitan Fungus Thelonectria discophora (Nectriaceae,Hypocreales, Ascomycota)

The distribution of microbial species, including fungi, has long been considered cosmopolitan. Recently, this perception has been challenged by molecular studies in historical biogeography, phylogeny and population genetics. Here we explore this issue using the fungal morphological species Thelonectria discophora, one of the most common species of fungi in the family Nectriaceae, encountered in almost all geographic regions and considered as a cosmopolitan taxon. In order to determine if T. discophora is a single cosmopolitan species or an assemblage of sibling species, we conducted various phylogenetic analyses, including standard gene concatenation, Bayesian concordance methods, and coalescent-based species tree reconstruction on isolates collected from a wide geographic range. Results show that diversity among isolates referred as T. discophora is greatly underestimated and that it represents a species complex. Within this complex, sixteen distinct highly supported lineages were recovered, each of which has a restricted geographic distribution and ecology. The taxonomic status of isolates regarded as T. discophora is reconsidered, and the assumed cosmopolitan distribution of this species is rejected. We discuss how assumptions about geographically widespread species have implications regarding their taxonomy, true diversity, biological diversity conservation, and ecological functions.     

Spatial differences in genetic diversity and northward migration suggest genetic erosion along the boreal caribou southern range limit and continued range retraction

With increasing human activities and associated landscape changes, distributions of terrestrial mammals become fragmented. These changes in distribution are often associated with reduced population sizes and loss of genetic connectivity and diversity (i.e., genetic erosion) which may further diminish a species' ability to respond to changing environmental conditions and lead to local population extinctions. We studied threatened boreal caribou (Rangifer tarandus caribou) populations across their distribution in Ontario/Manitoba (Canada) to assess changes in genetic diversity and connectivity in areas of high and low anthropogenic activity. Using data from >1,000 caribou and nine microsatellite loci, we assessed population genetic structure, genetic diversity, and recent migration rates using a combination of network and population genetic analyses. We used Bayesian clustering analyses to identify population genetic structure and explored spatial and temporal variation in those patterns by assembling networks based on R_ST and F_ST as historical and contemporary genetic edge distances, respectively. The Bayesian clustering analyses identified broad‐scale patterns of genetic structure and closely aligned with the R_ST network. The F_ST network revealed substantial contemporary genetic differentiation, particularly in areas presenting contemporary anthropogenic disturbances and habitat fragmentation. In general, relatively lower genetic diversity and greater genetic differentiation were detected along the southern range limit, differing from areas in the northern parts of the distribution. Moreover, estimation of migration rates suggested a northward movement of animals away from the southern range limit. The patterns of genetic erosion revealed in our study suggest ongoing range retraction of boreal caribou in central Canada.     

Microbial macroecology: highly structured prokaryotic soil assemblages in a tropical deciduous forest

Aim To assess the hypothesis that free‐living prokaryotes show a pattern of ‘no biogeography’ by examining the scaling of soil prokaryotic diversity and by comparing it with other groups’ biogeographical patterns. Location Two sites in the tropical deciduous forest of Chamela, Jalisco, on the western coast of Mexico. Methods We examined the diversity and distribution of soil prokaryotes in two 8 × 8 m quadrats divided in such manner that we could sample at four spatial scales. Restriction fragment length polymorphisms of 16S rRNA genes were used to define operational taxonomic units (OTUs) that we used in lieu of species to assess diversity. Results We found highly structured species assemblages that allowed us to reject multiple predictions of the hypothesis that soil bacteria show ‘no biogeography’. The frequency distribution of range size (measured as the occupancy of quadrats) of OTUs followed a hollow curve similar to that of vertebrates on continents. Assemblages showed high levels of beta diversity and a non‐random nested pattern of diversity. OTU diversity scaled with area followed a power function with slopes z = 0.42 and 0.47. Main conclusions We demonstrate a non‐ubiquitous dispersal for soil prokaryotes, which suggests a complex biogeography similar to that found for terrestrial vertebrates.     

Genetic footprints of habitat fragmentation in the extant populations of Sinojackia (Styracaceae): implications for conservation

Sinojackia, a member of the family Styracaceae, is an endangered genus endemic to China. The number of populations and population size of Sinojackia have decreased sharply because of habitat fragmentation and destruction. We studied the genetic diversity of extant populations in two different cohorts (adult and seedling) using eight microsatellite markers to investigate the genetic footprints of habitat fragmentation in four recognized Sinojackia spp. and to develop appropriate conservation measures. Data on intrapopulational genetic diversity suggest that Sinojackia populations have maintained relatively high levels of genetic diversity and low levels of genetic differentiation despite severe fragmentation. The high genetic diversity may be explained by the outcrossing mating system and high longevity of Sinojackia spp. The amount of genetic variation is not associated with population size, which was also supported by bottleneck analysis. In the species studied, there was no significant difference in the genetic diversity between the two cohorts analysed. However, inbreeding increased from adult trees to seedling populations, suggesting that the higher proportion of biparental inbreeding in the recent generations of seedlings is the result of restricted current genetic flow caused by habitat fragmentation. Average seed set per population was not significantly correlated with either population size or genetic diversity. Conservation management should aim to monitor inbreeding and outbreeding depression carefully to ensure the in situ and ex situ conservation of Sinojackia spp. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, ?? , ??–??.     

Genetic diversity and ecological niche modelling of the restricted Recordia reitzii (Verbenaceae) from southern Brazilian Atlantic forest

Genetic diversity analyses, coupled with ecological niche modelling (ENM) of species with a restricted distribution, may provide valuable information for understanding diversification patterns in endangered areas. We analyzed the genetic diversity of Recordia reitzii, a tree restricted to the threatened and highly fragmented Brazilian Atlantic forest, using three intergenic cpDNA spacers and ten microsatellite (SSR) loci. To assess the historical processes that may have influenced the distribution of extant R. reitzii populations, the current potential distributions of R. reitzii and Recordia boliviana, a closely related species, were modelled and projected onto the Last Glacial Maximum (LGM) and Last Interglacial (LIG) periods. Niche divergence was quantified between these two. The cpDNA and SSR data showed a north–south pattern of the diversity distribution and structured populations, suggesting that gene flow is probably limited. According to our data, R. reitzii exhibits low genetic diversity, which may be a result of a founder or distribution‐reduction effect, narrow distribution or small population size. The ecological niche models showed a wider palaeodistribution during the LIG and a retraction during the LGM for both species. Tests of niche divergence and conservatism indicated that bioclimatic factors might have influenced the diversification of these Recordia species. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176 , 332–348.     

Populations genetically rifting within a complex geological system: The case of strong structure and low genetic diversity in the migratory freshwater catfish,Bagrus docmak,in East Africa

The complex geological history of East Africa has been a driving factor in the rapid evolution of teleost biodiversity. While there is some understanding of how macroevolutionary drivers have shaped teleost speciation in East Africa, there is a paucity of research into how the same biogeographical factors have affected microevolutionary processes within lakes and rivers. To address this deficiency, population genetic diversity, demography, and structure were investigated in a widely distributed and migratory (potamodromous) African teleost species, Ssemutundu (Bagrus docmak ). Samples were acquired from five geographical locations in East Africa within two major drainage basins; the Albertine Rift and Lake Victoria Basin. Individuals (N  = 175) were genotyped at 12 microsatellite loci and 93 individuals sequenced at the mitochondrial DNA control region. Results suggested populations from Lakes Edward and Victoria had undergone a severe historic bottleneck resulting in very low nucleotide diversity (π = 0.004 and 0.006, respectively) and negatively significant Fu values (?3.769 and ?5.049; p  < .05). Heterozygosity deficiencies and restricted effective population size (N _eLD) suggested contemporary exposure of these populations to stress, consistent with reports of the species decline in the East African Region. High genetic structuring between drainages was detected at both historical (?_ST = 0.62 for mtDNA; p  < .001) and contemporary (microsatellite F _ST = 0.460; p  < .001) levels. Patterns of low genetic diversity and strong population structure revealed are consistent with speciation patterns that have been linked to the complex biogeography of East Africa, suggesting that these biogeographical features have operated as both macro‐ and micro‐evolutionary forces in the formation of the East African teleost fauna.