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Impact of cucurbit crop management techniques on the foraging behavior of honeybees and hoverflies in Morogoro, Tanzania 葫芦科作物管理技术对坦桑尼亚莫罗戈罗蜜蜂和食蚜蝇觅食行为的影响
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2024-01-17 DOI: 10.1186/s12862-024-02202-9
Elvillah William Rweyemamu, Maulid Walad Mwatawala, George Muhamba Tryphone, Marc De Meyer, Sija Kabota, Patroba Masatu Bwire
Poor agricultural practices have drastically threatened insect pollinators’ biodiversity. Little is known in Tanzania about how different agricultural practices affect pollinators’ foraging behavior. This study investigated the effects of the agroecological zone, season, cucurbit species and management practices on visitation frequency, visitation rate and time spent on cucurbit flowers by five pollinator species viz. Apis mellifera, Eristalinus megacephalus, Mesembrius caffer, Paragus borbonicus and Toxomerus floralis. The experiment was designed as a 5 × 3 × 3 × 2 × 2 factorial arrangement in a Randomized Complete Block Design (RCBD) with four replications. GAMOUR-Agroecology was tested against conventional practices and untreated control. This study revealed significant effects of agroecological zone × season × cucurbit species × management practice on pollinators’ visitation frequency (p = 0.007) and time spent on flowers (p = 0.005). Also, agroecological zone × season × cucurbit species × pollinator species significantly (p < 0.0001) affected pollinators’ visitation frequency. Agroecological zones × season × cucurbit species × cucurbits management practices × pollinators significantly (p = 0.001) affected pollinators’ visitation rate. Apis mellifera was the most frequent visitor in Cucurbita moschata plots treated with GAMOUR- Agroecology in the plateau zone, also, visited higher number of Cucumis sativus plots under GAMOUR-Agroecology practices in the mountainous zone during the October–November season. Furthermore, it has been found that pollinators spent much in cucurbit flowers on plots with GAMOUR-Agroecology practices and control. Pollinators’ foraging behavior were enhanced by GAMOUR-Agroecology practices. Therefore, this study recommended that cucurbit growers should consider management practices that positively influence pollinator foraging activities for sustainable cucurbit production.
不良的农业生产方式严重威胁了昆虫授粉者的生物多样性。在坦桑尼亚,人们对不同的农业生产方式如何影响传粉昆虫的觅食行为知之甚少。本研究调查了农业生态区、季节、葫芦物种和管理方法对五种授粉昆虫(即蜜蜂、巨型蚜虫、中蚜虫、花叶蚜虫和花叶病毒)的访问频率、访问率和在葫芦花上花费的时间的影响。实验采用 5 × 3 × 3 × 2 × 2 的因子排列,随机完全区组设计(RCBD),四次重复。GAMOUR 生态农业与传统做法和未处理对照进行了对比试验。该研究表明,农业生态区×季节×葫芦科植物种类×管理方法对传粉昆虫的访问频率(p = 0.007)和在花朵上花费的时间(p = 0.005)有明显影响。此外,农业生态区×季节×葫芦科植物种类×传粉昆虫种类对传粉昆虫的访问频率也有显著影响(p < 0.0001)。农业生态区×季节×葫芦科植物物种×葫芦科植物管理方法×传粉昆虫对传粉昆虫的访问率有显著影响(p = 0.001)。在高原区采用 GAMOUR- Agroecology 方法的 Cucurbita moschata 地块中,Apis mellifera 是最常光顾的传粉昆虫;在山区采用 GAMOUR- Agroecology 方法的 Cucumis sativus 地块中,Apis mellifera 在 10-11 月份光顾的次数也较多。此外,研究还发现,传粉昆虫在采用 GAMOUR 生态农业措施的地块和对照地块的葫芦科植物花朵上逗留的时间更长。GAMOUR 生态农业措施增强了传粉昆虫的觅食行为。因此,本研究建议葫芦种植者应考虑采取能积极影响传粉昆虫觅食活动的管理措施,以实现葫芦的可持续生产。
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引用次数: 0
Expectations of duplicate gene retention under the gene duplicability hypothesis 基因重复性假说下对重复基因保留的预期
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2023-12-14 DOI: 10.1186/s12862-023-02174-2
Amanda E. Wilson, David A. Liberles
Gene duplication is an important process in evolution. What causes some genes to be retained after duplication and others to be lost is a process not well understood. The most prevalent theory is the gene duplicability hypothesis, that something about the function and number of interacting partners (number of subunits of protein complex, etc.), determines whether copies have more opportunity to be retained for long evolutionary periods. Some genes are also more susceptible to dosage balance effects following WGD events, making them more likely to be retained for longer periods of time. One would expect these processes that affect the retention of duplicate copies to affect the conditional probability ratio after consecutive whole genome duplication events. The probability that a gene will be retained after a second whole genome duplication event (WGD2), given that it was retained after the first whole genome duplication event (WGD1) versus the probability a gene will be retained after WGD2, given it was lost after WGD1 defines the probability ratio that is calculated. Since duplicate gene retention is a time heterogeneous process, the time between the events (t1) and the time since the most recent event (t2) are relevant factors in calculating the expectation for observation in any genome. Here, we use a survival analysis framework to predict the probability ratio for genomes with different values of t1 and t2 under the gene duplicability hypothesis, that some genes are more susceptible to selectable functional shifts, some more susceptible to dosage compensation, and others only drifting. We also predict the probability ratio with different values of t1 and t2 under the mutational opportunity hypothesis, that probability of retention for certain genes changes in subsequent events depending upon how they were previously retained. These models are nested such that the mutational opportunity model encompasses the gene duplicability model with shifting duplicability over time. Here we present a formalization of the gene duplicability and mutational opportunity hypotheses to characterize evolutionary dynamics and explanatory power in a recently developed statistical framework. This work presents expectations of the gene duplicability and mutational opportunity hypotheses over time under different sets of assumptions. This expectation will enable formal testing of processes leading to duplicate gene retention.
基因复制是进化过程中的一个重要过程。导致一些基因在复制后保留而另一些基因丢失的原因是一个尚不清楚的过程。最流行的理论是基因可复制性假说,即有关相互作用伙伴的功能和数量(蛋白质复合体的亚基数量等)的某些东西,决定了拷贝是否有更多的机会在长进化时期内保留下来。一些基因也更容易受到WGD事件后的剂量平衡效应的影响,使它们更有可能保留更长时间。人们会期望这些影响重复副本保留的过程会影响连续全基因组复制事件后的条件概率比。在第一次全基因组复制事件(WGD1)后保留的基因在第二次全基因组复制事件(WGD2)后保留的概率与在WGD1后丢失的基因在WGD2后保留的概率定义了计算的概率比。由于重复基因保留是一个时间异质性过程,事件之间的时间(t1)和距离最近事件的时间(t2)是计算任何基因组中观察期望的相关因素。在此,我们使用生存分析框架来预测基因可复制假设下不同t1和t2值的基因组的概率比,其中一些基因更容易受到选择性功能转移的影响,一些基因更容易受到剂量补偿的影响,而另一些基因只会漂移。在突变机会假设下,我们还预测了t1和t2不同值的概率比,即某些基因的保留概率在随后的事件中发生变化,这取决于它们先前的保留方式。这些模型是嵌套的,这样突变机会模型就包含了随时间变化的基因可复制性模型。在这里,我们提出了基因可复制性和突变机会假说的形式化,以表征进化动力学和解释力在最近发展的统计框架。这项工作提出了期望的基因可复制性和突变机会假设随时间在不同的假设集。这一期望将使导致重复基因保留过程的正式测试成为可能。
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引用次数: 0
Microsatellites reveal divergence in population genetic diversity, and structure of osyris lanceolata (santalaceae) in Uganda and Kenya 微卫星揭示了乌干达和肯尼亚osyris lanceolata(山茶科)种群遗传多样性和结构的差异
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2023-12-08 DOI: 10.1186/s12862-023-02182-2
Ben Belden Mugula, S. F. Omondi, Manuel Curto, Samuel Kuria Kiboi, James Ireri Kanya, Anthony Egeru, Paul Okullo, Harald Meimberg
Osyris lanceolata (Hochst. & Steud.) (Santalaceae) is a multipurpose plant highly valued culturally and economically in Africa. However, O. lanceolata populations have rapidly dwindled in East Africa due to overexploitation and this is believed to cause further consequences on the species’ genetic diversity and structure within the region. Information regarding a species’ genetic diversity and structure is necessary for conservation but this is currently lacking for O. lanceolata in Uganda and Kenya. Lack of adequate scientific data hinders conservation efforts hence threatening the species survival and livelihoods. This study investigated patterns in genetic diversity and structure of O. lanceolata in Uganda and Kenya. Ten polymorphic microsatellite loci were used to genotype 210 individuals: 96 from Ugandan and 114 from Kenyan populations. All populations were highly polymorphic (80–100% polymorphism). A genetic differentiation was found between Kenyan and Ugandan populations. The highest genetic differentiation was among individuals and the least among populations. The Kenyan populations showed higher genetic diversity than Ugandan populations. The Ugandan populations showed more marker deviations from Hardy-Weinberg equilibrium and inbreeding coefficient. Two populations showed evidence of going through a recent bottleneck. There was significant genetic differentiation and structuring at higher K values into larger clusters and observed admixture between populations. The populations were significantly isolated by altitude as opposed to distance and climatic variables. Main barriers were associated with altitude differences. The data supports the idea of long-distance gene-flow between high altitude populations in both countries. The divergence in genetic structure suggests unrecognised taxonomic units within O. lanceolata which are characteristic to lower altitudes and higher altitudes including most Kenyan populations with divergent evolutionary patterns. Geographical barriers and environmental gradients could have influenced this genetic divergence, and such patterns may escalate the species microevolutionary processes into full allopatric speciation. Further investigations into the species’ genetic admixture and emerging taxonomic units are necessary to guide conservation strategies in the region.
Osyris lanceolata (Hochst. & Steud.)(山檀科)是一种多用途植物,在非洲具有很高的文化和经济价值。然而,由于过度开发,O. lanceolata 在东非的数量迅速减少,据信这将进一步影响该物种在该地区的遗传多样性和结构。有关物种遗传多样性和结构的信息是保护物种所必需的,但目前乌干达和肯尼亚的 O. lanceolata 还缺乏这方面的信息。缺乏足够的科学数据阻碍了保护工作,从而威胁到物种的生存和生计。本研究调查了乌干达和肯尼亚长尾杉的遗传多样性和结构模式。研究利用 10 个多态微卫星位点对 210 个个体进行了基因分型:其中 96 个来自乌干达种群,114 个来自肯尼亚种群。所有种群都具有高度多态性(80-100% 的多态性)。肯尼亚种群和乌干达种群之间存在遗传分化。个体间的遗传差异最大,种群间的差异最小。肯尼亚种群的遗传多样性高于乌干达种群。乌干达种群在哈代-温伯格平衡和近交系数方面表现出更多的标记偏离。有两个种群显示出近期出现瓶颈的迹象。遗传分化明显,K 值越高,结构越大,种群间的混杂现象也越明显。与距离和气候变量相比,海拔对这些种群有明显的隔离作用。主要障碍与海拔差异有关。这些数据支持了两国高海拔种群之间存在长距离基因流动的观点。遗传结构的差异表明,在 O. lanceolata 中存在未被认可的分类单元,这些单元具有低海拔和高海拔的特征,其中包括大多数具有不同进化模式的肯尼亚种群。地理障碍和环境梯度可能会影响这种遗传分化,这种模式可能会使物种的微进化过程升级为完全的同域物种分化。有必要进一步调查该物种的遗传混合情况和新出现的分类单元,以指导该地区的保护策略。
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引用次数: 0
Age, growth, and energy storage of the subterranean fish Triplophysa rosa (Cypriniformes: Nemacheilidae) from Chongqing, China 中国重庆地下鱼类胭脂鱼(鲤形目:胭脂鱼科)的年龄、生长和能量储存情况
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2023-12-07 DOI: 10.1186/s12862-023-02186-y
Yuan Xu, Yangyang Jing, Jing Zhou, Rui Long, Juanzhu Meng, Ya Yang, Yiping Luo
This study explores the age, growth, and energy storage of Triplophysa rosa, a troglobitic cavefish. A total of 102 wild T. rosa specimens were collected in Wulong County, Chongqing, China, between 2018 and 2022, with otoliths used for age determination. The earliest mature individuals were determined to be 4.8 years old, while the maximum ages for females and males were estimated at 15.8 years and 12.2 years, respectively. The length (L, cm)-weight (W, g) relationship was found to be the same for both sexes, following the eq. W = 0.0046 L3.03. Von Bertalanffy growth models were applied to the total length-at-age data, resulting in an asymptotic length of 23.4 cm and a K-parameter of 0.060 year−1. The body content of protein, ash, and glycogen did not show a significant correlation with the total length of T. rosa. However, both lipid and energy content exhibited a significant increase with total length. The lipid content ranged from 40.5 to 167.1 mg g−1, while the energy content ranged from 4.50 to 11.39 kJ g−1, indicating high storage features of T. rosa. The results affirm that T. rosa exhibits life traits conducive to its population dynamics in cave conditions, characterized by slow growth, small size, and high lipid energy storage.
本研究探讨了蛙穴鱼Triplophysa rosa的年龄、生长和能量储存。2018年至2022年期间,本研究在中国重庆市武隆县共采集了102个野生蛙穴鱼标本,并利用耳石进行了年龄测定。经测定,最早成熟个体的年龄为4.8岁,雌性和雄性的最大年龄分别为15.8岁和12.2岁。发现雌雄个体的体长(L,厘米)-体重(W,克)关系相同,公式为W = 0.0046 L3.03。冯-贝塔朗菲生长模型适用于总长度-年龄数据,得出渐近长度为 23.4 厘米,K 参数为 0.060 年-1。体内的蛋白质、灰分和糖原含量与蔷薇总长度没有明显的相关性。但是,脂质和能量含量随着总长度的增加而显著增加。脂质含量在 40.5 至 167.1 mg g-1 之间,能量含量在 4.50 至 11.39 kJ g-1 之间,这表明玫瑰茄具有较高的储藏特性。研究结果表明,玫瑰蛙具有生长缓慢、体型小、脂质能量储存高的特点,有利于其在洞穴条件下的种群动态发展。
{"title":"Age, growth, and energy storage of the subterranean fish Triplophysa rosa (Cypriniformes: Nemacheilidae) from Chongqing, China","authors":"Yuan Xu, Yangyang Jing, Jing Zhou, Rui Long, Juanzhu Meng, Ya Yang, Yiping Luo","doi":"10.1186/s12862-023-02186-y","DOIUrl":"https://doi.org/10.1186/s12862-023-02186-y","url":null,"abstract":"This study explores the age, growth, and energy storage of Triplophysa rosa, a troglobitic cavefish. A total of 102 wild T. rosa specimens were collected in Wulong County, Chongqing, China, between 2018 and 2022, with otoliths used for age determination. The earliest mature individuals were determined to be 4.8 years old, while the maximum ages for females and males were estimated at 15.8 years and 12.2 years, respectively. The length (L, cm)-weight (W, g) relationship was found to be the same for both sexes, following the eq. W = 0.0046 L3.03. Von Bertalanffy growth models were applied to the total length-at-age data, resulting in an asymptotic length of 23.4 cm and a K-parameter of 0.060 year−1. The body content of protein, ash, and glycogen did not show a significant correlation with the total length of T. rosa. However, both lipid and energy content exhibited a significant increase with total length. The lipid content ranged from 40.5 to 167.1 mg g−1, while the energy content ranged from 4.50 to 11.39 kJ g−1, indicating high storage features of T. rosa. The results affirm that T. rosa exhibits life traits conducive to its population dynamics in cave conditions, characterized by slow growth, small size, and high lipid energy storage.","PeriodicalId":9111,"journal":{"name":"BMC Evolutionary Biology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2023-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138554686","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Globins in the marine annelid Platynereis dumerilii shed new light on hemoglobin evolution in bilaterians. 海洋无脊椎动物钝鳃鳗的球蛋白为两栖动物血红蛋白的进化提供了新的线索。
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2020-12-29 DOI: 10.1186/s12862-020-01714-4
Solène Song, Viktor Starunov, Xavier Bailly, Christine Ruta, Pierre Kerner, Annemiek J M Cornelissen, Guillaume Balavoine

Background: How vascular systems and their respiratory pigments evolved is still debated. While many animals present a vascular system, hemoglobin exists as a blood pigment only in a few groups (vertebrates, annelids, a few arthropod and mollusk species). Hemoglobins are formed of globin sub-units, belonging to multigene families, in various multimeric assemblages. It was so far unclear whether hemoglobin families from different bilaterian groups had a common origin.

Results: To unravel globin evolution in bilaterians, we studied the marine annelid Platynereis dumerilii, a species with a slow evolving genome. Platynereis exhibits a closed vascular system filled with extracellular hemoglobin. Platynereis genome and transcriptomes reveal a family of 19 globins, nine of which are predicted to be extracellular. Extracellular globins are produced by specialized cells lining the vessels of the segmental appendages of the worm, serving as gills, and thus likely participate in the assembly of a previously characterized annelid-specific giant hemoglobin. Extracellular globin mRNAs are absent in smaller juveniles, accumulate considerably in growing and more active worms and peak in swarming adults, as the need for O2 culminates. Next, we conducted a metazoan-wide phylogenetic analysis of globins using data from complete genomes. We establish that five globin genes (stem globins) were present in the last common ancestor of bilaterians. Based on these results, we propose a new nomenclature of globins, with five clades. All five ancestral stem-globin clades are retained in some spiralians, while some clades disappeared early in deuterostome and ecdysozoan evolution. All known bilaterian blood globin families are grouped in a single clade (clade I) together with intracellular globins of bilaterians devoid of red blood.

Conclusions: We uncover a complex "pre-blood" evolution of globins, with an early gene radiation in ancestral bilaterians. Circulating hemoglobins in various bilaterian groups evolved convergently, presumably in correlation with animal size and activity. However, all hemoglobins derive from a clade I globin, or cytoglobin, probably involved in intracellular O2 transit and regulation. The annelid Platynereis is remarkable in having a large family of extracellular blood globins, while retaining all clades of ancestral bilaterian globins.

背景:血管系统及其呼吸色素是如何进化而来的,目前仍存在争议。虽然许多动物都有血管系统,但血红蛋白作为一种血色素只存在于少数类群中(脊椎动物、无脊椎动物、少数节肢动物和软体动物)。血红蛋白由属于多基因家族的球蛋白亚单位组成,具有不同的多聚体组合。迄今为止,人们还不清楚不同两栖类的血红蛋白家族是否有共同的起源:为了揭示双翼类动物的球蛋白进化过程,我们研究了基因组进化缓慢的海洋无脊椎类动物Platynereis dumerilii。Platynereis有一个充满细胞外血红蛋白的封闭血管系统。Platynereis 的基因组和转录组揭示了一个由 19 个球蛋白组成的家族,其中 9 个被预测为细胞外球蛋白。细胞外球蛋白是由蠕虫节肢附属器血管内壁的特化细胞产生的,起到鳃的作用,因此很可能参与了先前表征的环带动物特异性巨型血红蛋白的组装。细胞外球蛋白 mRNA 在较小的幼虫体内缺失,在生长和活跃的蠕虫体内大量积累,并在成虫对氧气的需求达到高潮时达到顶峰。接下来,我们利用完整基因组的数据,对整个后生动物的球蛋白进行了系统进化分析。我们确定,双翼类最后的共同祖先中有五个球蛋白基因(茎球蛋白)。基于这些结果,我们提出了一个新的球蛋白命名法,其中包括五个支系。所有五个祖先茎球蛋白支系都保留在一些旋毛虫类中,而一些支系则在去壳类和低等动物进化的早期就消失了。所有已知的双足类血球蛋白家族都被归入一个支系(支系I),同时还包括没有红血的双足类细胞内球蛋白:我们发现了球蛋白复杂的 "前血液 "进化过程,以及祖先双翼类的早期基因辐射。不同双叶类群的循环血红蛋白是趋同进化的,这可能与动物的体型和活动有关。然而,所有的血红蛋白都来源于 I 族球蛋白或细胞血红蛋白,可能参与细胞内氧气的转运和调节。有孔虫类动物 Platynereis 的显著特点是拥有一个庞大的细胞外血球蛋白家族,同时保留了所有两栖类祖先的球蛋白支系。
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引用次数: 0
Is there any intron sliding in mammals? 哺乳动物中有内含子滑动吗?
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2020-12-11 DOI: 10.1186/s12862-020-01726-0
Irina V Poverennaya, Nadezhda A Potapova, Sergey A Spirin

Background: Eukaryotic protein-coding genes consist of exons and introns. Exon-intron borders are conserved between species and thus their changes might be observed only on quite long evolutionary distances. One of the rarest types of change, in which intron relocates over a short distance, is called "intron sliding", but the reality of this event has been debated for a long time. The main idea of a search for intron sliding is to use the most accurate genome annotation and genome sequence, as well as high-quality transcriptome data. We applied them in a search for sliding introns in mammals in order to widen knowledge about the presence or absence of such phenomena in this group.

Results: We didn't find any significant evidence of intron sliding in the primate group (human, chimpanzee, rhesus macaque, crab-eating macaque, green monkey, marmoset). Only one possible intron sliding event supported by a set of high quality transcriptomes was observed between EIF1AX human and sheep gene orthologs. Also, we checked a list of previously observed intron sliding events in mammals and showed that most likely they are artifacts of genome annotations and are not shown in subsequent annotation versions as well as are not supported by transcriptomic data.

Conclusions: We assume that intron sliding is indeed a very rare evolutionary event if it exists at all. Every case of intron sliding needs a lot of supportive data for detection and confirmation.

背景:真核生物的蛋白质编码基因由外显子和内含子组成。外显子-内含子边界在物种之间是保守的,因此只有在相当长的进化距离上才能观察到它们的变化。内含子在短距离内移动是最罕见的变化类型之一,被称为“内含子滑动”,但这一事件的真实性已经争论了很长时间。搜索内含子滑动的主要思路是使用最准确的基因组注释和基因组序列,以及高质量的转录组数据。我们将其应用于哺乳动物中滑动内含子的搜索,以扩大对该群体中存在或不存在此类现象的认识。结果:在灵长类动物(人类、黑猩猩、恒河猴、食蟹猴、绿猴、狨猴)中未发现内含子滑动的明显证据。在EIF1AX人类和绵羊基因同源物之间只观察到一组高质量转录组支持的内含子滑动事件。此外,我们检查了先前在哺乳动物中观察到的内含子滑动事件列表,并表明它们很可能是基因组注释的产物,并且在随后的注释版本中没有显示出来,也没有转录组学数据支持。结论:我们假设内含子滑动确实是一个非常罕见的进化事件,如果它存在的话。每一例内含子滑动都需要大量的支持性数据进行检测和确认。
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引用次数: 4
You don't have the guts: a diverse set of fungi survive passage through Macrotermes bellicosus termite guts. 你没有肠道:一种不同种类的真菌通过巨白蚁的肠道存活下来。
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2020-12-09 DOI: 10.1186/s12862-020-01727-z
Nick Bos, Leandro Guimaraes, Romen Palenzuela, Justinn Renelies-Hamilton, Lorrie Maccario, Simon Kolotchèlèma Silue, N 'golo Abdoulaye Koné, Michael Poulsen

Background: Monoculture farming poses significant disease challenges, but fungus-farming termites are able to successfully keep their monoculture crop free from contamination by other fungi. It has been hypothesised that obligate gut passage of all plant substrate used to manure the fungal symbiont is key to accomplish this. Here we refute this hypothesis in the fungus-farming termite species Macrotermes bellicosus.

Results: We first used ITS amplicon sequencing to show that plant substrate foraged on by termite workers harbour diverse fungal communities, which potentially could challenge the farming symbiosis. Subsequently, we cultivated fungi from dissected sections of termite guts to show that fungal diversity does not decrease during gut passage. Therefore, we investigated if healthy combs harboured these undesirable fungal genera, and whether the presence of workers affected fungal diversity within combs. Removal of workers led to a surge in fungal diversity in combs, implying that termite defences must be responsible for the near-complete absence of other fungi in functioning termite gardens.

Conclusions: The rapid proliferation of some of these fungi when colonies are compromised indicates that some antagonists successfully employ a sit-and-wait strategy that allows them to remain dormant until conditions are favourable. Although this strategy requires potentially many years of waiting, it prevents these fungi from engaging in an evolutionary arms race with the termite host, which employs a series of complementary behavioural and chemical defences that may prove insurmountable.

背景:单一栽培带来了重大的疾病挑战,但真菌栽培白蚁能够成功地使其单一栽培作物免受其他真菌的污染。据推测,所有用于给真菌共生体施肥的植物基质的专性肠道通道是实现这一目标的关键。在这里,我们以养殖真菌的白蚁Macrotermes bellicosus为例反驳了这一假设。结果:我们首先利用ITS扩增子测序表明,白蚁工蚁觅食的植物基质中含有多种真菌群落,这可能会挑战农业共生关系。随后,我们从白蚁内脏的解剖部分培养真菌,以证明真菌多样性在肠道通道中不会减少。因此,我们调查了健康的梳子是否含有这些不受欢迎的真菌属,以及工人的存在是否影响了梳子内真菌的多样性。工蚁的移除导致了蜂巢中真菌多样性的激增,这意味着白蚁的防御一定是白蚁花园中几乎完全没有其他真菌的原因。结论:当菌落受到损害时,一些真菌的快速增殖表明,一些拮抗剂成功地采用了坐等策略,使它们保持休眠状态,直到条件有利。尽管这一策略可能需要多年的等待,但它可以防止这些真菌与白蚁宿主进行进化军备竞赛,白蚁宿主采用了一系列互补的行为和化学防御,这些防御可能被证明是不可克服的。
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引用次数: 8
The evolution of the huntingtin-associated protein 40 (HAP40) in conjunction with huntingtin. 亨廷相关蛋白 40 (HAP40) 与亨廷蛋白的进化。
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2020-12-09 DOI: 10.1186/s12862-020-01705-5
Manuel Seefelder, Vikram Alva, Bin Huang, Tatjana Engler, Wolfgang Baumeister, Qiang Guo, Rubén Fernández-Busnadiego, Andrei N Lupas, Stefan Kochanek

Background: The huntingtin-associated protein 40 (HAP40) abundantly interacts with huntingtin (HTT), the protein that is altered in Huntington's disease (HD). Therefore, we analysed the evolution of HAP40 and its interaction with HTT.

Results: We found that in amniotes HAP40 is encoded by a single-exon gene, whereas in all other organisms it is expressed from multi-exon genes. HAP40 co-occurs with HTT in unikonts, including filastereans such as Capsaspora owczarzaki and the amoebozoan Dictyostelium discoideum, but both proteins are absent from fungi. Outside unikonts, a few species, such as the free-living amoeboflagellate Naegleria gruberi, contain putative HTT and HAP40 orthologs. Biochemically we show that the interaction between HTT and HAP40 extends to fish, and bioinformatic analyses provide evidence for evolutionary conservation of this interaction. The closest homologue of HAP40 in current protein databases is the family of soluble N-ethylmaleimide-sensitive factor attachment proteins (SNAPs).

Conclusion: Our results indicate that the transition from a multi-exon to a single-exon gene appears to have taken place by retroposition during the divergence of amphibians and amniotes, followed by the loss of the parental multi-exon gene. Furthermore, it appears that the two proteins probably originated at the root of eukaryotes. Conservation of the interaction between HAP40 and HTT and their likely coevolution strongly indicate functional importance of this interaction.

背景:亨廷顿相关蛋白40(huntingtin-associated protein 40,HAP40)与亨廷顿病(Huntington's disease,HD)中发生改变的亨廷顿蛋白(huntingtin,HTT)有大量相互作用。因此,我们分析了HAP40的进化及其与HTT的相互作用:结果:我们发现,在羊膜动物中,HAP40由单外显子基因编码,而在所有其他生物中,它由多外显子基因表达。HAP40与HTT共存于单子叶动物中,包括丝虫(如Capsaspora owczarzaki)和变形虫(Dictyostelium discoideum),但真菌中不存在这两种蛋白质。在单孔菌之外,少数物种,如自由生活的变形虫Naegleria gruberi,含有推测的HTT和HAP40直向同源物。我们的生物化学研究表明,HTT 和 HAP40 之间的相互作用延伸到了鱼类,生物信息学分析为这种相互作用的进化保护提供了证据。在目前的蛋白质数据库中,与HAP40最接近的同源物是可溶性N-乙基马来酰亚胺敏感因子附着蛋白(SNAPs)家族:我们的研究结果表明,从多外显子基因到单外显子基因的转变似乎是在两栖类和羊膜类的分化过程中通过逆位发生的,随后亲代多外显子基因丢失。此外,这两种蛋白质似乎可能起源于真核生物的根部。HAP40和HTT之间相互作用的保守性及其可能的共同进化有力地表明了这种相互作用在功能上的重要性。
{"title":"The evolution of the huntingtin-associated protein 40 (HAP40) in conjunction with huntingtin.","authors":"Manuel Seefelder, Vikram Alva, Bin Huang, Tatjana Engler, Wolfgang Baumeister, Qiang Guo, Rubén Fernández-Busnadiego, Andrei N Lupas, Stefan Kochanek","doi":"10.1186/s12862-020-01705-5","DOIUrl":"10.1186/s12862-020-01705-5","url":null,"abstract":"<p><strong>Background: </strong>The huntingtin-associated protein 40 (HAP40) abundantly interacts with huntingtin (HTT), the protein that is altered in Huntington's disease (HD). Therefore, we analysed the evolution of HAP40 and its interaction with HTT.</p><p><strong>Results: </strong>We found that in amniotes HAP40 is encoded by a single-exon gene, whereas in all other organisms it is expressed from multi-exon genes. HAP40 co-occurs with HTT in unikonts, including filastereans such as Capsaspora owczarzaki and the amoebozoan Dictyostelium discoideum, but both proteins are absent from fungi. Outside unikonts, a few species, such as the free-living amoeboflagellate Naegleria gruberi, contain putative HTT and HAP40 orthologs. Biochemically we show that the interaction between HTT and HAP40 extends to fish, and bioinformatic analyses provide evidence for evolutionary conservation of this interaction. The closest homologue of HAP40 in current protein databases is the family of soluble N-ethylmaleimide-sensitive factor attachment proteins (SNAPs).</p><p><strong>Conclusion: </strong>Our results indicate that the transition from a multi-exon to a single-exon gene appears to have taken place by retroposition during the divergence of amphibians and amniotes, followed by the loss of the parental multi-exon gene. Furthermore, it appears that the two proteins probably originated at the root of eukaryotes. Conservation of the interaction between HAP40 and HTT and their likely coevolution strongly indicate functional importance of this interaction.</p>","PeriodicalId":9111,"journal":{"name":"BMC Evolutionary Biology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2020-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7725122/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38704246","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Mitochondrial DNAs provide insight into trypanosome phylogeny and molecular evolution. 线粒体dna提供了对锥虫系统发育和分子进化的深入了解。
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2020-12-09 DOI: 10.1186/s12862-020-01701-9
C Kay, T A Williams, W Gibson

Background: Trypanosomes are single-celled eukaryotic parasites characterised by the unique biology of their mitochondrial DNA. African livestock trypanosomes impose a major burden on agriculture across sub-Saharan Africa, but are poorly understood compared to those that cause sleeping sickness and Chagas disease in humans. Here we explore the potential of the maxicircle, a component of trypanosome mitochondrial DNA to study the evolutionary history of trypanosomes.

Results: We used long-read sequencing to completely assemble maxicircle mitochondrial DNA from four previously uncharacterized African trypanosomes, and leveraged these assemblies to scaffold and assemble a further 103 trypanosome maxicircle gene coding regions from published short-read data. While synteny was largely conserved, there were repeated, independent losses of Complex I genes. Comparison of pre-edited and non-edited genes revealed the impact of RNA editing on nucleotide composition, with non-edited genes approaching the limits of GC loss. African tsetse-transmitted trypanosomes showed high levels of RNA editing compared to other trypanosomes. The gene coding regions of maxicircle mitochondrial DNAs were used to construct time-resolved phylogenetic trees, revealing deep divergence events among isolates of the pathogens Trypanosoma brucei and T. congolense.

Conclusions: Our data represents a new resource for experimental and evolutionary analyses of trypanosome phylogeny, molecular evolution and function. Molecular clock analyses yielded a timescale for trypanosome evolution congruent with major biogeographical events in Africa and revealed the recent emergence of Trypanosoma brucei gambiense and T. equiperdum, major human and animal pathogens.

背景:锥虫是单细胞真核寄生虫,其线粒体DNA具有独特的生物学特征。非洲牲畜锥虫对撒哈拉以南非洲的农业造成了重大负担,但与导致人类昏睡病和恰加斯病的锥虫相比,人们对其了解甚少。在这里,我们探讨了锥虫线粒体DNA的一个组成部分——最大环的潜力,以研究锥虫的进化史。结果:我们使用长读测序技术完全组装了来自4个以前未被鉴定的非洲锥虫的maxicycle线粒体DNA,并利用这些组装来支架和组装来自已发表的短读数据的另外103个锥虫maxicycle基因编码区。虽然synteny在很大程度上是保守的,但Complex I基因存在重复的、独立的损失。对预编辑和未编辑基因的比较揭示了RNA编辑对核苷酸组成的影响,未编辑基因接近GC损失的极限。与其他锥虫相比,非洲采采虫传播的锥虫表现出高水平的RNA编辑。利用大圆环线粒体dna基因编码区构建时间分辨系统进化树,揭示了布鲁氏锥虫和刚果锥虫分离株之间的深度分化事件。结论:我们的数据为锥虫的系统发育、分子进化和功能的实验和进化分析提供了新的资源。分子钟分析得出了与非洲主要生物地理事件一致的锥虫进化时间表,并揭示了最近出现的布氏冈比亚锥虫和装备锥虫这两种主要的人类和动物病原体。
{"title":"Mitochondrial DNAs provide insight into trypanosome phylogeny and molecular evolution.","authors":"C Kay,&nbsp;T A Williams,&nbsp;W Gibson","doi":"10.1186/s12862-020-01701-9","DOIUrl":"https://doi.org/10.1186/s12862-020-01701-9","url":null,"abstract":"<p><strong>Background: </strong>Trypanosomes are single-celled eukaryotic parasites characterised by the unique biology of their mitochondrial DNA. African livestock trypanosomes impose a major burden on agriculture across sub-Saharan Africa, but are poorly understood compared to those that cause sleeping sickness and Chagas disease in humans. Here we explore the potential of the maxicircle, a component of trypanosome mitochondrial DNA to study the evolutionary history of trypanosomes.</p><p><strong>Results: </strong>We used long-read sequencing to completely assemble maxicircle mitochondrial DNA from four previously uncharacterized African trypanosomes, and leveraged these assemblies to scaffold and assemble a further 103 trypanosome maxicircle gene coding regions from published short-read data. While synteny was largely conserved, there were repeated, independent losses of Complex I genes. Comparison of pre-edited and non-edited genes revealed the impact of RNA editing on nucleotide composition, with non-edited genes approaching the limits of GC loss. African tsetse-transmitted trypanosomes showed high levels of RNA editing compared to other trypanosomes. The gene coding regions of maxicircle mitochondrial DNAs were used to construct time-resolved phylogenetic trees, revealing deep divergence events among isolates of the pathogens Trypanosoma brucei and T. congolense.</p><p><strong>Conclusions: </strong>Our data represents a new resource for experimental and evolutionary analyses of trypanosome phylogeny, molecular evolution and function. Molecular clock analyses yielded a timescale for trypanosome evolution congruent with major biogeographical events in Africa and revealed the recent emergence of Trypanosoma brucei gambiense and T. equiperdum, major human and animal pathogens.</p>","PeriodicalId":9111,"journal":{"name":"BMC Evolutionary Biology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2020-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12862-020-01701-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38355580","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 11
Stress-related changes in leukocyte profiles and telomere shortening in the shortest-lived tetrapod, Furcifer labordi. 在寿命最短的四足动物中,白细胞谱和端粒缩短的应激相关变化。
IF 3.4 Q1 Agricultural and Biological Sciences Pub Date : 2020-12-01 DOI: 10.1186/s12862-020-01724-2
Falk Eckhardt, Angela Pauliny, Nicky Rollings, Frank Mutschmann, Mats Olsson, Cornelia Kraus, Peter M Kappeler

Background: Life history theory predicts that during the lifespan of an organism, resources are allocated to either growth, somatic maintenance or reproduction. Resource allocation trade-offs determine the evolution and ecology of different life history strategies and define an organisms' position along a fast-slow continuum in interspecific comparisons. Labord's chameleon (Furcifer labordi) from the seasonal dry forests of Madagascar is the tetrapod species with the shortest reported lifespan (4-9 months). Previous investigations revealed that their lifespan is to some degree dependent on environmental factors, such as the amount of rainfall and the length of the vegetation period. However, the intrinsic mechanisms shaping such a fast life history remain unknown. Environmental stressors are known to increase the secretion of glucocorticoids in other vertebrates, which, in turn, can shorten telomeres via oxidative stress. To investigate to what extent age-related changes in these molecular and cellular mechanisms contribute to the relatively short lifetime of F. labordi, we assessed the effects of stressors indirectly via leukocyte profiles (H/L ratio) and quantified relative telomere length from blood samples in a wild population in Kirindy Forest. We compared our findings with the sympatric, but longer-lived sister species F. cf. nicosiai, which exhibit the same annual timing of reproductive events, and with wild-caught F. labordi that were singly housed under ambient conditions.

Results: We found that H/L ratios were consistently higher in wild F. labordi compared to F. cf. nicosiai. Moreover, F. labordi already exhibited relatively short telomeres during the mating season when they were 3-4 months old, and telomeres further shortened during their post-reproductive lives. At the beginning of their active season, telomere length was relatively longer in F. cf. nicosiai, but undergoing rapid shortening towards the southern winter, when both species gradually die off. Captive F. labordi showed comparatively longer lifespans and lower H/L ratios than their wild counterparts.

Conclusion: We suggest that environmental stress and the corresponding accelerated telomere attrition have profound effects on the lifespan of F. labordi in the wild, and identify physiological mechanisms potentially driving their relatively early senescence and mortality.

背景:生命史理论预测,在生物体的生命周期中,资源被分配到生长、体细胞维持或繁殖。资源分配权衡决定了不同生活史策略的进化和生态,并确定了生物在种间比较中沿快-慢连续体的位置。来自马达加斯加季节性干旱森林的拉伯德变色龙(Furcifer labordi)是四足动物中寿命最短的物种(4-9个月)。以往的研究表明,它们的寿命在一定程度上取决于环境因素,如降雨量和植被期的长短。然而,形成如此快速生命史的内在机制仍然未知。众所周知,环境压力会增加其他脊椎动物体内糖皮质激素的分泌,而糖皮质激素反过来又会通过氧化应激缩短端粒。为了研究这些与年龄相关的分子和细胞机制的变化在多大程度上导致了F. labordi相对较短的寿命,我们通过白细胞谱(H/L比)间接评估了应激源的影响,并量化了Kirindy森林野生种群血液样本的相对端粒长度。我们将我们的发现与同域的,但寿命较长的姐妹物种F. cf. nicosiai进行了比较,它们表现出相同的年度繁殖时间,以及在环境条件下单独饲养的野生捕获的F. labordi。结果:我们发现,野生白曲螺旋藻的H/L比值始终高于白曲螺旋藻。此外,F. labordi在3-4个月大的交配季节已经表现出相对较短的端粒,并且在其生殖后的生活中端粒进一步缩短。在活动季节开始时,nicosiai的端粒长度相对较长,但在进入南方冬季时,端粒长度迅速缩短,两种物种逐渐死亡。圈养的蓝藻比野生的蓝藻寿命更长,H/L比更低。结论:我们认为环境胁迫和相应的端粒加速磨损对野生labordi的寿命有深远的影响,并确定了导致其相对早衰老和死亡的生理机制。
{"title":"Stress-related changes in leukocyte profiles and telomere shortening in the shortest-lived tetrapod, Furcifer labordi.","authors":"Falk Eckhardt,&nbsp;Angela Pauliny,&nbsp;Nicky Rollings,&nbsp;Frank Mutschmann,&nbsp;Mats Olsson,&nbsp;Cornelia Kraus,&nbsp;Peter M Kappeler","doi":"10.1186/s12862-020-01724-2","DOIUrl":"https://doi.org/10.1186/s12862-020-01724-2","url":null,"abstract":"<p><strong>Background: </strong>Life history theory predicts that during the lifespan of an organism, resources are allocated to either growth, somatic maintenance or reproduction. Resource allocation trade-offs determine the evolution and ecology of different life history strategies and define an organisms' position along a fast-slow continuum in interspecific comparisons. Labord's chameleon (Furcifer labordi) from the seasonal dry forests of Madagascar is the tetrapod species with the shortest reported lifespan (4-9 months). Previous investigations revealed that their lifespan is to some degree dependent on environmental factors, such as the amount of rainfall and the length of the vegetation period. However, the intrinsic mechanisms shaping such a fast life history remain unknown. Environmental stressors are known to increase the secretion of glucocorticoids in other vertebrates, which, in turn, can shorten telomeres via oxidative stress. To investigate to what extent age-related changes in these molecular and cellular mechanisms contribute to the relatively short lifetime of F. labordi, we assessed the effects of stressors indirectly via leukocyte profiles (H/L ratio) and quantified relative telomere length from blood samples in a wild population in Kirindy Forest. We compared our findings with the sympatric, but longer-lived sister species F. cf. nicosiai, which exhibit the same annual timing of reproductive events, and with wild-caught F. labordi that were singly housed under ambient conditions.</p><p><strong>Results: </strong>We found that H/L ratios were consistently higher in wild F. labordi compared to F. cf. nicosiai. Moreover, F. labordi already exhibited relatively short telomeres during the mating season when they were 3-4 months old, and telomeres further shortened during their post-reproductive lives. At the beginning of their active season, telomere length was relatively longer in F. cf. nicosiai, but undergoing rapid shortening towards the southern winter, when both species gradually die off. Captive F. labordi showed comparatively longer lifespans and lower H/L ratios than their wild counterparts.</p><p><strong>Conclusion: </strong>We suggest that environmental stress and the corresponding accelerated telomere attrition have profound effects on the lifespan of F. labordi in the wild, and identify physiological mechanisms potentially driving their relatively early senescence and mortality.</p>","PeriodicalId":9111,"journal":{"name":"BMC Evolutionary Biology","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2020-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12862-020-01724-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38665010","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
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BMC Evolutionary Biology
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