Phylogeography of a Holarctic nematode, Soboliphyme baturini, among mustelids: climate change, episodic colonization, and diversification in a complex host–parasite system

Phylogeography of Soboliphyme baturini , a nematode parasite in mustelids, is explored across Beringia. Sequences of the mitochondrial cytochrome c oxidase subunit I and nicotinamide adenine dinucleotide dehydrogenase subunit 4 genes were evaluated from 37 S. baturini , representing 19 localities throughout Alaska, Canada, and Siberia. A total of 30 haplotypes was recovered and maximum parsimony and Bayesian phylogenetic analyses support the recognition of a single species with a distribution extending from the Palearctic to the Nearctic. Within S. baturini , a host-specific partition in North America between Martes caurina and Martes americana was not identified. Instead, substantial geographic structure within S. baturini relates to the dynamic geological history of this northern region and especially the North Pacific Coast. Beringia and other coastal refugia along the western margin of North America played a large role during stadial maxima in the persistence and divergence of the parasite. Repeated events for biotic expansion and geographic colonization across the Bering Land Bridge and the Holarctic during glacial maxima in the Pleistocene appear to have facilitated at least two episodes of host-switching of this nematode among mustelids in populations now distributed in eastern Beringia.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 96 , 651–663.     

A macroevolutionary mosaic: episodic host-switching, geographical colonization and diversification in complex host–parasite systems

Aim  To integrate ecological fitting, the oscillation hypothesis and the taxon pulse hypothesis into a coherent null model for the evolution of complex host–parasite associations.
Location  Global.
Methods  This paper reviews and synthesizes literature that focuses on phylogenetic analyses and reciprocal mapping of a model system of hosts and their parasites to determine patterns of host–parasite associations and geographical distributions through time.
Results  Host-switching and geographical dispersal of parasites are common phenomena, occurring on many temporal and spatial scales. Diversification involving both co-evolution and colonization explains complex host–parasite associations. Across the expanse of Earth history, the major radiations in host–parasite assemblages have been preceded by ecological disruption, ecological breakdown and host-switching in a context that can be defined by the concept of ecological fitting. This cyclical process sets the stage for co-diversification during periods of relative stability, punctuated by host-switching during episodes of regional to global environmental disruption and climatological change.
Main conclusions  Most observed host–parasite associations can be explained by an historical interaction between ecological fitting, oscillation (episodes of increasing host range alternating with isolation on particular hosts) and taxon pulses (cyclical episodes of expansion and isolation in geographical range). Major episodes of environmental change appear to be the main drivers for both the persistence and diversification of host–parasite systems, creating opportunities for host-switching during periods of geographical expansion and allowing for co-evolution and co-speciation during periods of geographical isolation.     

When parasites persist: tapeworms survive host extinction and reveal waves of dispersal across Beringia

Investigations of intercontinental dispersal between Asia and North America reveal complex patterns of geographic expansion, retraction and isolation, yet historical reconstructions are largely limited by the depth of the record that is retained in patterns of extant diversity. Parasites offer a tool for recovering deep historical insights about the biosphere, improving the resolution of past community-level interactions. We explored biogeographic hypotheses regarding the history of dispersal across Beringia, the region intermittently linking Asia and North America, through large-scale multi-locus phylogenetic analyses of the genus Schizorchis, an assemblage of host-specific cestodes in pikas (Lagomorpha: Ochotonidae). Our genetic data support palaeontological evidence for two separate geographic expansions into North America by Ochotona in the late Tertiary, a history that genomic evidence from extant pikas does not record. Pikas descending from the first colonization of Miocene age persisted into the Pliocene, subsequently coming into contact with a second wave of Nearctic colonists from Eurasia before going extinct. Spatial and temporal overlap of historically independent pika populations provided a window for host colonization, allowing persistence of an early parasite lineage in the contemporary fauna following the extinction of its ancestral hosts. Empirical evidence for ancient ‘ghost assemblages'' of hosts and parasites demonstrates how complex mosaic faunas are assembled in the biosphere through episodes of faunal mixing encompassing parasite lineages across deep and shallow time.     

Persistence and diversification of the Holarctic shrew,Sorex tundrensis (Family Soricidae), in response to climate change

Environmental processes govern demography, species movements, community turnover and diversification and yet in many respects these dynamics are still poorly understood at high latitudes. We investigate the combined effects of climate change and geography through time for a widespread Holarctic shrew, Sorex tundrensis. We include a comprehensive suite of closely related outgroup taxa and three independent loci to explore phylogeographic structure and historical demography. We then explore the implications of these findings for other members of boreal communities. The tundra shrew and its sister species, the Tien Shan shrew (Sorex asper), exhibit strong geographic population structure across Siberia and into Beringia illustrating local centres of endemism that correspond to Late Pleistocene refugia. Ecological niche predictions for both current and historical distributions indicate a model of persistence through time despite dramatic climate change. Species tree estimation under a coalescent process suggests that isolation between populations has been maintained across timeframes deeper than the periodicity of Pleistocene glacial cycling. That some species such as the tundra shrew have a history of persistence largely independent of changing climate, whereas other boreal species shifted their ranges in response to climate change, highlights the dynamic processes of community assembly at high latitudes.     

Dynamic colonization exchanges between continents and islands drive diversification in paradise‐flycatchers (Terpsiphone,Monarchidae)

Aim We use parametric biogeographical reconstruction based on an extensive DNA sequence dataset to characterize the spatio‐temporal pattern of colonization of the Old World monarch flycatchers (Monarchidae). We then use this framework to examine the role of dispersal and colonization in their evolutionary diversification and to compare plumages between island and continental Terpsiphone species. Location Africa, Asia and the Indian Ocean. Methods We generate a DNA sequence dataset of 2300 bp comprising one nuclear and three mitochondrial markers for 89% (17/19) of the Old World Monarchidae species and 70% of the Terpsiphone subspecies. By applying maximum likelihood and Bayesian phylogenetic methods and implementing a Bayesian molecular clock to provide a temporal framework, we reveal the evolutionary history of the group. Furthermore, we employ both Lagrange and Bayes‐ Lagrange analyses to assess ancestral areas at each node of the phylogeny. By combining the ancestral area reconstruction with information on plumage traits we are able to compare patterns of plumage evolution on islands and continents. Results We provide the first comprehensive molecular phylogenetic reconstruction for the Old World Monarchidae. Our phylogenetic results reveal a relatively recent diversification associated with several dispersal events within this group. Moreover, ancestral area analyses reveal an Asian origin of the Indian Ocean and African clades. Ancestral state reconstruction analyses of plumage characters provide an interpretation of the plumage differentiation on islands and continents. Ancestral plumage traits are inferred to be close to those of the Asian paradise‐flycatcher (Terpsiphone paradisi), and island species display a high degree of plumage autapomorphy compared with continental species. Main conclusions Terpsiphone paradisi is polyphyletic and comprises populations that have retained the ancestral plumage of the widespread Terpsiphone genus. The genus appears to have colonized south‐west Asia, the Indian Ocean and Africa from eastern Asia. The phylogeny and divergence time estimates indicate multiple simultaneous colonizations of the western Old World by Terpsiphone. These results reinforce a hypothesis of range expansions of a Terpsiphone paradisi‐like ancestor into eastern Asia and the western Old World.     

Crossing to safety: dispersal,colonization and mate choice in evolutionarily distinct populations of Steller sea lions,Eumetopias jubatus

Population growth typically involves range expansion and establishment of new breeding sites, while the opposite occurs during declines. Although density dependence is widely invoked in theoretical studies of emigration and colonization in expanding populations, few empirical studies have documented the mechanisms. Still fewer have documented the direction and mechanisms of individual transfer in declining populations. Here, we screen large numbers of pups sampled on their natal rookeries for variation in mtDNA (n = 1106) and 16 microsatellite loci (n = 588) and show that new Steller sea lion breeding sites did not follow the typical paradigm and were instead colonized by sea lions from both a declining (Endangered) population and an increasing population. Dispersing individuals colonized rookeries in the distributional hiatus between two evolutionarily distinct ( = 0.222,  = 0.053, K = 2) metapopulations recently described as separate subspecies. Hardy–Weinberg, mixed‐stock and relatedness analysis revealed levels of interbreeding on the new rookeries that exclude (i) assortative mating among eastern and western forms, and (ii) inbreeding avoidance as primary motivations for dispersal. Positive and negative density dependence is implicated in both cases of individual transfer. Migration distance limits, and conspecific attraction and performance likely influenced the sequence of rookery colonizations. This study demonstrates that resource limitation may trigger an exodus of breeding animals from declining populations, with substantial impacts on distribution and patterns of genetic variation. It also revealed that this event is rare because colonists dispersed across an evolutionary boundary, suggesting that the causative factors behind recent declines are unusual or of larger magnitude than normally occur.     

The distribution of eggs per host in a herbivorous insect--intersection of oviposition, dispersal and population dynamics

1. The dynamics of parasitic organisms depend critically upon the frequency distribution of parasite individuals per host. However, the processes giving rise to this frequency distribution have rarely been modelled and tested for organisms with complex host selection behaviour. 2. In this study Microrhopala vittata, a chrysomelid beetle, was used to investigate how oviposition behaviour, movement and density of host plants interact in shaping the frequency distribution of egg clusters per host in the field. 3. Enclosures were stocked with two different host species and different beetle densities and various stochastic process models were fitted to egg cluster count data obtained from these enclosures. The different models were derived considering different scenarios, in particular whether or not plant density limits oviposition rate, whether or not ovipositing females actively seek out the most attractive plant within their perception radius and whether a female's oviposition rate is determined by plant intrinsic factors, the plant's egg cluster load or the surrounding beetle density. 4. The model parameters fitted to cage data were used to describe the frequency distribution of egg cluster counts obtained in a release experiment in the field. A total of 220 beetle pairs were released at five locations in a field where this beetle was not observed previously. Each release point was at a border between the two host species. 5. One model predicted for the preferred host species the egg cluster count frequencies in the field from parameters estimated in the cages. This model assumed that egg clusters present on a plant increased subsequent oviposition on this plant. All other models could not describe the distribution of egg cluster counts for either of the two host species. 6. The results suggest that females seek out attractive hosts actively and the attractiveness of a plant increases with its egg cluster load. This behaviour creates a frequency distribution of egg clusters per host that depends only on beetle density but not on plant density. This conclusion has important implications for modelling insect-plant interactions.     

一株番茄青枯病生防菌的鉴定与防病、定殖能力初探

摘要：【目的】采用根系分泌物培养基筛选到一株番茄根际优势细菌YPP-9。本文分析测定该菌株对植物青枯病菌茄科雷尔氏菌的拮抗作用和控病能力,及其在番茄根际的定殖能力,并系统分析该菌株的分类学地位。【方法】以平板双重培养法和温室盆栽试验分别测定菌株对病原菌的拮抗能力和对番茄青枯病的控病能力;利用变性梯度凝胶电泳技术分析菌株在番茄根际的定殖能力;以形态学和生理生化特性以及16S rRNA基因序列分析确定菌株的分类地位。【结果】菌株YPP-9对茄科雷尔氏菌SSF-4的平板抑菌带宽为5 mm,其盆栽控制番茄青枯病的效果达63.7%。菌株YPP-9在番茄根际具有较好的定殖能力。该菌株培养24 h后菌落呈奶酪色,革兰氏染色阳性,菌体杆状、大小1.8-4.1 μm×0.9-1.1 μm,形成芽孢,芽孢中生或偏端生且为近似柱形,孢囊不膨大,无伴孢晶体,侧生鞭毛。菌株生长pH范围为pH 5.5-8.5且最适生长pH为6.0,生长温度范围为20℃-45℃且最适生长温度为30℃。The BIOLOG GP2结果显示该菌为芽孢杆菌属。16S rRNA基因序列分析显示该菌株与Bacillus fumarioli的亲缘关系最近且序列相似性为97%,且其序列号为FJ231500。该菌株的G+C含量为41.9%,甲基萘醌主要类型为MK-7,细胞壁脂肪酸的主要种类为C14:0 iso、C15:0 iso 和C16:0 iso以及C16 : 1ω7c alcohol且含量分别为28.27%、19.59%、12.93%和10.88%。【结论】菌株YPP-9对茄科雷尔氏菌具有良好的拮抗作用和盆栽控病能力,且能良好的定殖于番茄根际。分类学上,该菌株归入芽胞杆菌属（Bacillus）,并可能是一个新的种。     

Drivers of population genetic differentiation in the wild: isolation by dispersal limitation,isolation by adaptation and isolation by colonization

Empirical population genetic studies have been dominated by a neutralist view, according to which gene flow and drift are the main forces driving population genetic structure in nature. The neutralist view in essence describes a process of isolation by dispersal limitation (IBDL) that generally leads to a pattern of isolation by distance (IBD). Recently, however, conceptual frameworks have been put forward that view local genetic adaptation as an important driver of population genetic structure. Isolation by adaptation (IBA) and monopolization (M) posit that gene flow among natural populations is reduced as a consequence of local genetic adaptation. IBA stresses that effective gene flow is reduced among habitats that show dissimilar ecological characteristics, leading to a pattern of isolation by environment. In monopolization, local genetic adaptation of initial colonizing genotypes results in a reduction in gene flow that fosters the persistence of founder effects. Here, we relate these different processes driving landscape genetic structure to patterns of IBD and isolation by environment (IBE). We propose a method to detect whether IBDL, IBA and M shape genetic differentiation in natural landscapes by studying patterns of variation at neutral and non‐neutral markers as well as at ecologically relevant traits. Finally, we reinterpret a representative number of studies from the recent literature by associating patterns to processes and identify patterns associated with local genetic adaptation to be as common as IBDL in structuring regional genetic variation of populations in the wild. Our results point to the importance of quantifying environmental gradients and incorporating ecology in the analysis of population genetics.     

An interaction between host and microbe genotypes determines colonization success of a key bumble bee gut microbiota member

There has been a proliferation of studies demonstrating an organism's health is influenced by its microbiota. However, factors influencing beneficial microbe colonization and the evolution of these relationships remain understudied relative to host–pathogen interactions. Vertically transmitted beneficial microbes are predicted to show high levels of specificity in colonization, including genotype matching, which may transpire through coevolution. We investigate how host and bacterial genotypes influence colonization of a core coevolved microbiota member in bumble bees. The hindgut colonizing Snodgrassella alvi confers direct benefits, but, as an early colonizer, also facilitates the further development of a healthy microbiota. Due to predominantly vertical transmission promoting tight evolution between colonization factors of bacteria and host lineages, we predict that genotype‐by‐genotype interactions will determine successful colonization. Germ‐free adult bees from seven bumble bee colonies (host genotypic units) were inoculated with one of six genetically distinct strains of S. alvi. Subsequent colonization within host and microbe genotypes combinations ranged from 0 to 100%, and an interaction between host and microbe genotypes determined colonization success. This novel finding of a genotype‐by‐genotype interaction determining colonization in an animal host‐beneficial microbe system has implications for the ecological and evolutionary dynamics of host and microbe, including associated host‐fitness benefits.     

Algal biomass dynamics during colonization of artificial islands: experimental results and a model

Algal biomass during colonization of polyurethane foam islands (5.1 cm × 7.6 cm × 7.6 cm) was approximated by measuring chlorophyll a levels on islands after exposure periods of 1, 2, 3, 4, and 6 weeks at six locations in a small lake in central Tennessee, USA. Chlorophyll, ash-free dry weight, and concurrent environmental data were collected for two colonization periods: one in late winter and spring (Set 1), a second in summer (Set 2).During Set 1 algal biomass levels, as indicated by chlorophyll a, showed a sharp rise initially, but Set 2 islands exhibited a lag period of 7 to 12 days before a rapid increase in algal biomass was noted. Equilibrium chlorophyll a values were similar for both sets. High levels of phaeopigments were found at Stations 2, 3, and 4 during Set 2 resulting in large corrections in chlorophyll a readings. Ash-free dry weight values increased steadily through each colonization period.A model of biomass accumulation during colonization was constructed postulating three major processes — photosynthesis, respiration, and passive accumulation — which were modulated by three environmental factors — light, temperature, and plankton chlorophyll a levels. For simulations parameter values were taken from the literature where possible. Additional parameter values were set and literature values adjusted when the model was tuned to Set 2 data. A simulation with the tuned model using Set 1 environmental input resulted in a good prediction of equilibrium values, but a misinterpretation of initial values. The discrepancy between model predictions and data was alleviated when the passive accumulation rate was increased demonstrating the dependence of biomass values early in colonization on passive accumulation from the plankton.     

Murine model of colonization with fungal pathogen Candida auris to explore skin tropism,host risk factors and therapeutic strategies

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Patterns of diversification of Afrotropical Otiteselline fig wasps: phylogenetic study reveals a double radiation across host figs and conservatism of host association

We studied the phylogenetic relationships of Otiteselline fig waSPS associated with Ficus in the Afrotropical region using rDNA sequences. African fig species usually host two species of Otiteselline fig waSPS. Phylogenetic analyses reveal that this pattern of association results from the radiation of two clades of waSPS superimposed on the fig system. Within each clade, wasp species generally cluster according to their host classification. The phylogenies of the two clades are also generally more congruent than expected by chance. Together these results suggest that Otiteselline wasp speciation is largely constrained by the diversification of their hosts. Finally, we show a difference in ovipositor length between the two Otiteselline species coexisting in the same Ficus species, which probably corresponds to ecological differences. The diversification of ecological niches within the fig is probably, with cospeciation, one of the key factors explaining the diversification and maintenance of species of parasites of the fig/pollinator system.     

EspP, a Type V-secreted serine protease of enterohaemorrhagic Escherichia coli O157:H7, influences intestinal colonization of calves and adherence to bovine primary intestinal epithelial cells

Enterohaemorrhagic Escherichia coli (EHEC) comprise a group of zoonotic diarrhoeal pathogens of worldwide importance. Cattle are a key reservoir; however the molecular mechanisms that promote persistent colonization of the bovine intestines by EHEC are ill-defined. The large plasmid of EHEC O157:H7 encodes several putative virulence factors. Here, it is reported that the pO157-encoded Type V-secreted serine protease EspP influences the intestinal colonization of calves. To dissect the basis of attenuation, a bovine primary rectal epithelial cell line was developed. Adherence of E. coli O157:H7 to such cells was significantly impaired by espP mutation but restored upon addition of highly purified exogenous EspP. Data of this study add to the growing body of evidence that cytotoxins facilitate intestinal colonization by EHEC.