Multiple gains and losses of Wolbachia symbionts across a tribe of fungus‐growing ants

Although the intracellular bacterium Wolbachia is ubiquitous in insects, it has a unique relationship with New World ants on which particular bacterial strains have specialized. However, data are from distantly related hosts and detailed phylogenetic information which could reveal transmission dynamics are lacking. Here, we investigate host–Wolbachia relationships in the monophyletic fungus‐growing ant tribe Attini, screening 23 species and using multilocus sequence typing to reliably identify Wolbachia strains. This technique reduces the significant problem of recombination seen using traditional single gene techniques. The relationship between Wolbachia and the fungus‐growing ants appears complex and dynamic. There is evidence of co‐cladogenesis, supporting vertical transmission; however, this is incomplete, demonstrating that horizontal transmission has also occurred. Importantly, the infection prevalence is frequently different between closely related taxa, with the Acromyrmex leaf‐cutting ants appearing particularly prone to infection and there being no consistent relationship with any of the major life history transitions. We suggest that infection loss and horizontal transmission have driven epidemics or selective sweeps of Wolbachia, resulting in multiple gains and losses of infection across the fungus‐growing ants.     

Nuclear sequences reveal mid-range isolation of an imperilled deep-water coral population

The mitochondrial DNA of corals and their anthozoan kin evolves slowly, with substitution rates about two orders of magnitude lower than in typical bilateral animals. This has impeded the delineation of closely related species and isolated populations in corals, compounding problems caused by high morphological plasticity. Here we characterize rates of divergence and levels of variation for three nuclear gene regions, then use these nuclear sequences as markers to test for population structure in Oculina , a taxonomically confused genus of corals. Rates of sequence divergence (obtained by comparison to Solenastrea hyades ) were at least five (and sometimes over 10) times faster for the three nuclear markers than for a mitochondrial reference sequence. Nuclear sequence variation was also high within populations, although it tended to decline north of Cape Canaveral. Significant subdivision was evident among samples from 10 locations from between North Carolina and the Florida Panhandle, but neither nominal species designation nor population depth explained much of this variation. Instead, a single population from the unique deep (> 70 m) water reefs at the Oculina Banks off central Florida was a strong genetic outlier: all pairwise measures of subdivision involving this population were greater than those involving all other populations, and multilocus clustering recognized the Oculina Banks as distinct from other populations, despite its close proximity (≤ 36 km) to populations from shallower waters nearby and its location at the centre of the sampled range. Genetic isolation of the Oculina Banks population suggests that focused efforts will be needed to conserve the foundation species of these monotypic reefs and that depth may play a role in isolating marine populations and perhaps facilitating initial steps towards speciation.     

Species detection and individual assignment in species delimitation: can integrative data increase efficacy?

Statistical species delimitation usually relies on singular data, primarily genetic, for detecting putative species and individual assignment to putative species. Given the variety of speciation mechanisms, singular data may not adequately represent the genetic, morphological and ecological diversity relevant to species delimitation. We describe a methodological framework combining multivariate and clustering techniques that uses genetic, morphological and ecological data to detect and assign individuals to putative species. Our approach recovers a similar number of species recognized using traditional, qualitative taxonomic approaches that are not detected when using purely genetic methods. Furthermore, our approach detects groupings that traditional, qualitative taxonomic approaches do not. This empirical test suggests that our approach to detecting and assigning individuals to putative species could be useful in species delimitation despite varying levels of differentiation across genetic, phenotypic and ecological axes. This work highlights a critical, and often overlooked, aspect of the process of statistical species delimitation—species detection and individual assignment. Irrespective of the species delimitation approach used, all downstream processing relies on how individuals are initially assigned, and the practices and statistical issues surrounding individual assignment warrant careful consideration.     

Tracing horizontal Wolbachia movements among bees (Anthophila): a combined approach using multilocus sequence typing data and host phylogeny

The endosymbiotic bacterium Wolbachia enhances its spread via vertical transmission by generating reproductive effects in its hosts, most notably cytoplasmic incompatibility (CI). Additionally, frequent interspecific horizontal transfer is evident from a lack of phylogenetic congruence between Wolbachia and its hosts. The mechanisms of this lateral transfer are largely unclear. To identify potential pathways of Wolbachia movements, we performed multilocus sequence typing of Wolbachia strains from bees (Anthophila). Using a host phylogeny and ecological data, we tested various models of horizontal endosymbiont transmission. In general, Wolbachia strains seem to be randomly distributed among bee hosts. Kleptoparasite‐host associations among bees as well as other ecological links could not be supported as sole basis for the spread of Wolbachia. However, cophylogenetic analyses and divergence time estimations suggest that Wolbachia may persist within a host lineage over considerable timescales and that strictly vertical transmission and subsequent random loss of infections across lineages may have had a greater impact on Wolbachia strain distribution than previously estimated. Although general conclusions about Wolbachia movements among arthropod hosts cannot be made, we present a framework by which precise assumptions about shared evolutionary histories of Wolbachia and a host taxon can be modelled and tested.     

Transcriptome‐based target‐enrichment baits for stony corals (Cnidaria: Anthozoa: Scleractinia)

Despite the ecological and economic significance of stony corals (Scleractinia), a robust understanding of their phylogeny remains elusive due to patchy taxonomic and genetic sampling, as well as the limited availability of informative markers. To increase the number of genetic loci available for phylogenomic analyses in Scleractinia, we designed 15,919 DNA enrichment baits targeting 605 orthogroups (mean 565 ± SD 366 bp) over 1,139 exon regions. A further 236 and 62 barcoding baits were designed for COI and histone H3 genes respectively for quality and contamination checks. Hybrid capture using these baits was performed on 18 coral species spanning the presently understood scleractinian phylogeny, with two corallimorpharians as outgroup. On average, 74% of all loci targeted were successfully captured for each species. Barcoding baits were matched unambiguously to their respective samples and revealed low levels of cross‐contamination in accordance with expectation. We put the data through a series of stringent filtering steps to ensure only scleractinian and phylogenetically informative loci were retained, and the final probe set comprised 13,479 baits, targeting 452 loci (mean 531 ± SD 307 bp) across 865 exon regions. Maximum likelihood, Bayesian and species tree analyses recovered maximally supported, topologically congruent trees consistent with previous phylogenomic reconstructions. The phylogenomic method presented here allows for consistent capture of orthologous loci among divergent coral taxa, facilitating the pooling of data from different studies and increasing the phylogenetic sampling of scleractinians in the future.     

On statistical methods for estimating heritability in wild populations

Here we take a look at molecular marker-based heritability estimation suitable for non-model organisms. We address several theoretical issues involved and discuss similarities and differences between our two main approaches: the animal model approach and the shrinkage-estimation based multilocus association approach. Also computational issues and hypothetical example applications for ecologists are considered.     

天津地区气单胞菌分离株的鉴定与多位点序列分型

[目的]研究气单胞菌菌株分类情况,并分析其致病性.[方法]采集环境样品和鱼类标本,分离并鉴定气单胞菌菌株,并运用多位点序列分型(Multilocus sequence typing,MLST)方法进行分类研究,利用PCR和测序方法分析毒力基因Aera、Hly、Aha1、GCAT和Nuc的分布.[结果]通过对分离菌株的16S rRNA基因进行分析,确认属于4种不同气单胞菌的7个分离株.发现所有菌株至少有1种毒力基因阳性,其中3株具有4种毒力基因.药物敏感实验显示,6株分离株对3种或3种以上抗菌素具有多重耐药性.最后,对看家基因gyrB、groL、gltA、metG、ppsA和recA进行分析,与MLST数据库中的等位基因序列比对,发现7株分离株均为新的不同的序列型(Sequence type,ST).[结论]气单胞菌具有较高的遗传多样性.     

两株炭疽芽胞杆菌MLST 新序列型(ST)

【目的】2株炭疽芽胞杆菌(Bacillus anthracis)17003-14和17003-32的多位点序列分型(Multilocussequence typing,MLST)研究。【方法】选取B.anthracis基因组7个常见管家基因位点glpF、gmk、ilvD、pta、pur、pycA和tpi进行PCR扩增、测序,与MLST数据库中的等位基因序列进行比对,确定菌株的序列型(sequence type,ST)。【结果】B.anthracis 17003-14和17003-32的等位基因编号分别为113、31、1、43、1、53、7和113、31、1、43、1、53、37,比对结果显示这2株细菌的等位基因编号组合未见报道。【结论】17003-14和17003-32为新ST菌株,已被MLST数据库确认,注册号(pubMLST id)分别为id-1053和id-1054。