Intra-strain biological and epidemiological characterization of plum pox virus

Plum pox virus (PPV) is one of the most important plant viruses causing serious economic losses. Thus far, strain typing based on the definition of 10 monophyletic strains with partially differentiable biological properties has been the sole approach used for epidemiological characterization of PPV. However, elucidating the genetic determinants underlying intra-strain biological variation among populations or isolates remains a relevant but unexamined aspect of the epidemiology of the virus. In this study, based on complete nucleotide sequence information of 210 Japanese and 47 non-Japanese isolates of the PPV-Dideron (D) strain, we identified five positively selected sites in the PPV-D genome. Among them, molecular studies showed that amino acid substitutions at position 2,635 in viral replicase correlate with viral titre and competitiveness at the systemic level, suggesting that amino acid position 2,635 is involved in aphid transmission efficiency and symptom severity. Estimation of ancestral genome sequences indicated that substitutions at amino acid position 2,635 were reversible and peculiar to one of two genetically distinct PPV-D populations in Japan. The reversible amino acid evolution probably contributes to the dissemination of the virus population. This study provides the first genomic insight into the evolutionary epidemiology of PPV based on intra-strain biological variation ascribed to positive selection.     

Parthenogenesis and developmental constraints

The absence of a paternal contribution in an unfertilized ovum presents two developmental constraints against the evolution of parthenogenesis. We discuss the constraint caused by the absence of a centrosome and the one caused by the missing set of chromosomes and how they have been broken in specific taxa. They are examples of only a few well‐underpinned examples of developmental constraints acting at macro‐evolutionary scales in animals. Breaking of the constraint of the missing chromosomes is the best understood and generally involves rare occasions of drastic changes of meiosis. These drastic changes can be best explained by having been induced, or at least facilitated, by sudden cytological events (e.g., repeated rounds of hybridization, endosymbiont infections, and contagious infections). Once the genetic and developmental machinery is in place for regular or obligate parthenogenesis, shifts to other types of parthenogenesis can apparently rather easily evolve, for example, from facultative to obligate parthenogenesis, or from pseudoarrhenotoky to haplodiploidy. We argue that the combination of the two developmental constraints forms a near‐absolute barrier against the gradual evolution from sporadic to obligate or regular facultative parthenogenesis, which can probably explain why the occurrence of the highly advantageous mode of regular facultative parthenogenesis is so rare and entirely absent in vertebrates.     

Historical and philosophical perspectives on the study of developmental bias

Throughout the recent history of research at the intersection of evolution and development, notions such as developmental constraint, evolutionary novelty, and evolvability have been prominent, but the term “developmental bias” has scarcely been used. And one may even doubt whether a unique and principled definition of bias is possible. I argue that the concept of developmental bias can still play a vital scientific role by means of setting an explanatory agenda that motivates investigation and guides the formulation of integrative explanatory frameworks. Less crucial is a definition that would classify patterns of phenotypic variation and unify variational patterns involving different traits and taxa as all being “bias.” Instead, what we should want is a concept that generates intellectual identity across various researchers, and that unites the diverse fields and approaches relevant to the study of developmental bias, from paleontology to behavioral biology. I point to some advantages of conducting research specifically under the label of “developmental bias,” compared with employing other, more common terms such as “evolvability.”     

分子标记在濒危物种保护中的应用

分子标记可揭示种群遗传和进化信息, 为制定濒危物种保护措施、指导恢复实践提供重要依据。本文主要介绍了分子标记在濒危物种保护过程不同环节中的应用, 包括: (1)正确识别保护单元, 如排除隐存种和杂交种的影响; (2)确定优先保护单元, 包括优先保护区域、优先保护物种、优先保护种群等; (3)指导迁地保护; (4)对保护工作的动态监测和评估。文章最后探讨了分子标记应用于保护的发展方向, 如开展长期的种群遗传组成监测、切实应用于保护管理实践、将基因组学等遗传信息用于全球变化背景下保护策略的制定等, 期望为分子标记技术在生物多样性保护的研究和实践中提供参考。     

Evolutionary trajectory of fish Piscine novirhabdovirus (=Viral Hemorrhagic Septicemia Virus) across its Laurentian Great Lakes history: Spatial and temporal diversification

Piscine novirhabdovirus = Viral Hemorrhagic Septicemia Virus (VHSV) first appeared in the Laurentian Great Lakes with large outbreaks from 2005 to 2006, as a new and novel RNA rhabdovirus subgenogroup (IVb) that killed >30 fish species. Interlude periods punctuated smaller more localized outbreaks in 2007, 2010, and 2017, although some fishes tested positive in the intervals. There have not been reports of outbreaks or positives from 2018, 2019, or 2020. Here, we employ a combined population genetics and phylogenetic approach to evaluate spatial and temporal evolutionary trajectory on its G‐gene sequence variation, in comparison with whole‐genome sequences (11,083 bp) from a subset of 44 individual isolates (including 40 newly sequenced ones). Our results show that IVb (N = 184 individual fish isolates) diversified into 36 G‐gene haplotypes from 2003 to 2017, stemming from two originals (“a” and “b”). G‐gene haplotypes “a” and “b” differed by just one synonymous single‐nucleotide polymorphism (SNP) substitution, remained the most abundant until 2011, then disappeared. Group “a” descendants (14 haplotypes) remained most prevalent in the Upper and Central Great Lakes, with eight (51%) having nonsynonymous substitutions. Group “b” descendants primarily have occurred in the Lower Great Lakes, including 22 haplotypes, of which 15 (68%) contained nonsynonymous changes. Evolutionary patterns of the whole‐genome sequences (which had 34 haplotypes among 44 isolates) appear congruent with those from the G‐gene. Virus populations significantly diverged among the Upper, Central, and Lower Great Lakes, diversifying over time. Spatial divergence was apparent in the overall patterns of nucleotide substitutions, while amino acid changes increased temporally. VHSV‐IVb thus significantly differentiated across its less than two decades in the Great Lakes, accompanied by declining outbreaks and virulence. Continuing diversification likely allowed the virus to persist at low levels in resident fish populations, and may facilitate its potential for further and future spread to new habitats and nonacclimated hosts.     

Exploring context dependency in eco‐evolutionary patterns with the stick insect Timema cristinae

Rapid evolution can influence the ecology of populations, communities, and ecosystems, but the importance of evolution for ecological dynamics remains unclear, largely because the contexts in which evolution is powerful are poorly resolved. Here, we carry out a large observational study to test hypotheses about context dependency of eco‐evolutionary patterns previously identified on the stick insect Timema cristinae. Experiments and observations conducted in 2011 and 2012 documented predator‐mediated negative effects of camouflage maladaptation (i.e., evolutionary dynamics) on: (a) T. cristinae abundance and, (b) species richness and abundance of other arthropods. Here we show that camouflage maladaptation does not correlate with T. cristinae abundance and, instead, is associated with increased abundance and species richness of cohabitating arthropods. We furthermore find that plants with high levels of Timema maladaptation tend to have higher foliar nitrogen, that is, higher nutritional value, and more positive mass‐abundance slopes in the coexisting arthropod communities. We propose explanations for the observed contrasting results, such as negative density‐ and frequency‐dependent selection, feedbacks between herbivore abundance and plant nutritional quality, and common effects of predation pressure on selection and prey abundance. Our results demonstrate the utility of observational studies to assess the context dependency of eco‐evolutionary dynamics patterns and provide testable hypotheses for future work.     

Species diversity and phylogeography of Cornus kousa (Asian dogwood) captured by genomic and genic microsatellites

Cornus kousa (Asian dogwood), an East Asia native tree, is the most economically important species of the dogwood genus, owing to its desirable horticultural traits and ability to hybridize with North America‐native dogwoods. To assess the species genetic diversity and to better inform the ongoing and future breeding efforts, we assembled an herbarium and arboretum collection of 131 noncultivated C. kousa specimens. Genotyping and capillary electrophoresis analyses of our C. kousa collection with the newly developed genic and published nuclear genomic microsatellites permitted assessment of genetic diversity and evolutionary history of the species. Regardless of the microsatellite type used, the study yielded generally similar insights into the C. kousa diversity with subtle differences deriving from and underlining the marker used. The accrued evidence pointed to the species distinct genetic pools related to the plant country of origin. This can be helpful in the development of the commercial cultivars for this important ornamental crop with increased pyramided utility traits. Analyses of the C. kousa evolutionary history using the accrued genotyping datasets pointed to an unsampled ancestor population, possibly now extinct, as per the phylogeography of the region. To our knowledge, there are few studies utilizing the same gDNA collection to compare performance of genomic and genic microsatellites. This is the first detailed report on C. kousa species diversity and evolutionary history inference.     

基于线粒体基因组的华蝉族系统发育地位研究(半翅目: 蝉科)(英文)

【目的】本研究旨在明确无鼓膜发音器的华蝉族(Sinosenini)昆虫在蝉总科(Cicadoidea)的系统发育地位。【方法】依据在陕西宁陕采集的合哑蝉Karenia caelatata成虫标本,对华蝉族的合哑蝉K. caelatata线粒体基因组进行测序、注释和生物信息学分析;并与蝉总科其他类群的线粒体基因组进行了比较,然后利用最大似然法(ML)和贝叶斯法(BI)分别构建了蝉总科分子系统发育树。【结果】合哑蝉线粒体基因组长14 960 bp (GenBank登录号: MN922304),其基因组成、蛋白编码基因的核苷酸组成和密码子使用等,与蝉总科其他类群具相似特征。核苷酸多样性分析表明,atp8, nad6和nad2为易变基因,而cox1比较保守。非同义替换率和同义替换率比表明,蝉总科昆虫线粒体基因组进化处于高水平的纯化选择下。系统发育分析结果支持蝉次目(Cicadomorpha)的单系性,该次目3个总科的关系为：角蝉总科Membraciodea+(蝉总科Cicadoidea+沫蝉总科Cercopodidea)。无鼓膜发音器的哑蝉属与蝉亚科(Cicadinae)的蜩蝉族(Dundubiini)相关类群聚在一起,且与寒蝉属Meimuna关系最近;黑蝉族(Cicadatrini)的草蝉属Mogannia和音蝉属Vagitanus则与姬蝉亚科(Cicadettinae)相关类群聚在一起;日宁蝉属Yezoterpnosia并非一个单系群。【结论】华蝉族应从姬蝉亚科转移至蝉亚科并与蜩蝉族(Dundubiini)合并,而黑蝉族应从蝉亚科转移至姬蝉亚科。研究结果为进一步解析具有不同发声机制的蝉科昆虫系统演化提供了新信息。     

Mitonuclear Coevolution,but not Nuclear Compensation,Drives Evolution of OXPHOS Complexes in Bivalves

In Metazoa, four out of five complexes involved in oxidative phosphorylation (OXPHOS) are formed by subunits encoded by both the mitochondrial (mtDNA) and nuclear (nuDNA) genomes, leading to the expectation of mitonuclear coevolution. Previous studies have supported coadaptation of mitochondria-encoded (mtOXPHOS) and nuclear-encoded OXPHOS (nuOXPHOS) subunits, often specifically interpreted with regard to the “nuclear compensation hypothesis,” a specific form of mitonuclear coevolution where nuclear genes compensate for deleterious mitochondrial mutations due to less efficient mitochondrial selection. In this study, we analyzed patterns of sequence evolution of 79 OXPHOS subunits in 31 bivalve species, a taxon showing extraordinary mtDNA variability and including species with “doubly uniparental” mtDNA inheritance. Our data showed strong and clear signals of mitonuclear coevolution. NuOXPHOS subunits had concordant topologies with mtOXPHOS subunits, contrary to previous phylogenies based on nuclear genes lacking mt interactions. Evolutionary rates between mt and nuOXPHOS subunits were also highly correlated compared with non-OXPHO-interacting nuclear genes. Nuclear subunits of chimeric OXPHOS complexes (I, III, IV, and V) also had higher dN/dS ratios than Complex II, which is formed exclusively by nuDNA-encoded subunits. However, we did not find evidence of nuclear compensation: mitochondria-encoded subunits showed similar dN/dS ratios compared with nuclear-encoded subunits, contrary to most previously studied bilaterian animals. Moreover, no site-specific signals of compensatory positive selection were detected in nuOXPHOS genes. Our analyses extend the evidence for mitonuclear coevolution to a new taxonomic group, but we propose a reconsideration of the nuclear compensation hypothesis.