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The roles of different gene expression regulators in acoustic variation in the intermediate horseshoe bat revealed by long-read and short-read RNA sequencing data 长读和短读RNA测序数据揭示了不同基因表达调控因子在中间马蹄蝠声学变异中的作用
2区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2023-09-30 DOI: 10.1093/cz/zoad045
Qianqian Li, Jianyu Wu, Xiuguang Mao
Abstract Gene expression changes contribute greatly to phenotypic variations in nature. Studying patterns of regulators of gene expression is important to fully understand the molecular mechanism underlying phenotypic variations. In horseshoe bats, the cochleae are finely tuned to echoes of call frequency. Here, using 2 recently diverged subspecies of the intermediate horseshoe bat (Rhinolophus affinis hainanus and R. a. himalayanus) with great acoustic variations as the system, we aim to explore relative roles of different regulators of gene expression (differential gene expression, alternative splicing (AS) and long non-coding RNAs (lncRNAs)) in phenotypic variation with a combination of Illumina short-read and Nanopore long-read RNA-seq data from the cochlea. Compared to R. a. hainanus, R. a. himalayanus exhibited much more upregulated differentially expressed genes (DEGs) and multiple of them may play important roles in the maintenance and damage repair of auditory hair cells. We identified 411 differentially expressed lncRNAs and their target DEGs upregulated in R. a. himalayanus were also mainly involved in a protective mechanism for auditory hair cells. Using 3 different methods of AS analysis, we identified several candidate alternatively spliced genes (ASGs) that expressed different isoforms which may be associated with acoustic divergence of the 2 subspecies. We observed significantly less overlap than expected between DEGs and ASGs, supporting complementary roles of differential gene expression and AS in generating phenotypic variations. Overall, our study highlights the importance of a combination of short-read and long-read RNA-seq data in examining the regulation of gene expression changes responsible for phenotypic variations.
基因表达的变化是自然界表型变异的重要因素。研究基因表达调控模式对于充分了解表型变异的分子机制非常重要。在马蹄铁蝙蝠中,耳蜗能很好地适应叫声频率的回声。本文以声音差异较大的2个新近分化的中间马蹄蝠亚种(Rhinolophus affinis hainanus和R. a.喜马拉雅)为研究对象,结合来自耳蜗的Illumina短读和Nanopore长读RNA-seq数据,探讨不同基因表达调控因子(差异基因表达、选择性剪接(as)和长链非编码rna (lncRNAs))在表型变异中的相对作用。r . a . hainanus相比,r . a . himalayanus表现出更多的调节差异表达基因(度),其中多个可能扮演了一个重要的角色在维护和听觉毛细胞损伤修复。我们确定了411个差异表达lncRNAs及其目标度调节r . a . himalayanus还主要参与听觉毛细胞的保护机制。使用3种不同的AS分析方法,我们确定了几个候选的选择性剪接基因(ASGs),这些基因表达不同的亚型,可能与两个亚种的声学分化有关。我们观察到DEGs和ASGs之间的重叠明显少于预期,支持差异基因表达和AS在产生表型变异中的互补作用。总的来说,我们的研究强调了短读和长读RNA-seq数据结合在检查导致表型变异的基因表达变化调控中的重要性。
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引用次数: 0
Balancing selection shapes population differentiation of MHC genes in wild golden snub-nosed monkeys 平衡选择决定了野生金丝猴MHC基因的种群分化
2区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2023-09-24 DOI: 10.1093/cz/zoad043
Shixuan Dong, Bingyi Zhang, Kang Huang, Meijing Ying, Jibing Yan, Fei Niu, Hanyu Hu, Derek W Dunn, Yi Ren, Baoguo Li, Pei Zhang
Abstract Small and isolated populations face several intrinsic risks, such as genetic drift, inbreeding depression, and reduced gene flow. Thus, patterns of genetic diversity and differentiation have become an important focus of conservation genetics research. The golden snub-nosed monkey Rhinopithecus roxellana, an endangered species endemic to China, has experienced rapid reduction in population size and severe population fragmentation over the past few decades. We measured the patterns of genetic diversity and population differentiation using both neutral microsatellites and adaptive major histocompatibility complex (MHC) genes in 2 R. roxellana populations (DPY and GNG) distributed on the northern and southern slopes of the Qinling Mountains, respectively. Eight MHC-linked haplotypes formed by 5 DQA1 alleles, 5 DQB1 alleles, 5 DRB1 alleles, and 4 DRB2 alleles were detected in the 2 populations. The larger GNG population showed higher genetic variation for both MHC and microsatellites than the smaller DPY population, suggesting an effect of genetic drift on genetic variation. Genetic differentiation index (FST) outlier analyses, principal coordinate analysis (PCoA), and inferred population genetic structure showed lower genetic differentiation in the MHC variations than microsatellites, suggesting that pathogen-mediated balancing selection, rather than local adaptation, homogenized the MHC genes of both populations. This study indicates that both balancing selection and genetic drift may shape genetic variation and differentiation in small and fragmented populations.
小而孤立的种群面临着遗传漂变、近交抑制和基因流减少等内在风险。因此,遗传多样性和分化模式已成为保护遗传学研究的重要焦点。金金丝猴是中国特有的濒危物种,在过去的几十年里,其种群规模迅速减少,种群破碎化严重。利用中性微卫星和适应性主要组织相容性复合体(MHC)基因,对分布在秦岭南、北坡的2个黄颡鱼居群(DPY和GNG)的遗传多样性和群体分化模式进行了研究。在2个群体中检测到5个DQA1等位基因、5个DQB1等位基因、5个DRB1等位基因和4个DRB2等位基因组成的8个mhc连锁单倍型。大GNG群体MHC和微卫星的遗传变异高于小DPY群体,表明遗传漂变对遗传变异有影响。遗传分化指数(FST)异常值分析、主坐标分析(PCoA)和推断的群体遗传结构表明,MHC变异的遗传分化程度低于微卫星,这表明病原体介导的平衡选择,而不是局部适应,使两个群体的MHC基因均质化。该研究表明,平衡选择和遗传漂变都可能在小而分散的种群中形成遗传变异和分化。
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引用次数: 0
Correction to: Altitudinal variation in life-history features of a Qinghai-Tibetan Plateau lizard 更正:青藏高原蜥蜴生活史特征的海拔变化
2区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2023-09-16 DOI: 10.1093/cz/zoad041
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引用次数: 0
Odour cues rather than personality affect tadpole deposition in a Neotropical poison frog 气味线索而不是个性影响新热带毒蛙蝌蚪沉积
2区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2023-09-15 DOI: 10.1093/cz/zoad042
Mélissa Peignier, Max Ringler, Eva Ringler
Abstract Animals constantly need to evaluate available external and internal information to make appropriate decisions. Identifying, assessing, and acting on relevant cues in contexts such as mate choice, intra-sexual competition, and parental care is particularly important for optimizing individual reproductive success. Several factors can influence decision-making, such as external environmental cues and the animal’s own internal state, yet, we have limited knowledge on how animals integrate available information. Here, we used an entire island population (57 males, 53 females, and 1,109 tadpoles) of the neotropical brilliant-thighed poison frog Allobates femoralis to investigate how 2 factors (olfactory cues and personality traits) influence the ability of males to find and use new resources for tadpole deposition. We experimentally manipulated the location of tadpole deposition sites and their associated olfactory cues, and repeatedly measured exploration and boldness in adult males. We further reconstructed tadpole deposition choices via inferred parent–offspring relationships of adult frogs and tadpoles deposited in our experimental pools using molecular parentage analysis. We found that the discovery and use of new rearing sites were heavily influenced by olfactory cues; however, we did not find an effect of the measured behavioral traits on resource discovery and use. We conclude that in highly dynamic environments such as tropical rainforests, reliable external cues likely take priority over personality traits, helping individuals to discover and make use of reproductive resources.
动物需要不断地评估可用的外部和内部信息,以做出适当的决定。在配偶选择、性内竞争和亲代抚育等环境中,识别、评估并根据相关线索采取行动,对于优化个体的生殖成功尤为重要。有几个因素可以影响决策,比如外部环境线索和动物自己的内部状态,然而,我们对动物如何整合可用信息的了解有限。在这里,我们使用整个岛屿种群(57只雄性,53只雌性和1109只蝌蚪)的新热带耀腿毒蛙Allobates femoralis来研究嗅觉线索和人格特征如何影响雄性寻找和使用蝌蚪沉积新资源的能力。我们通过实验操纵蝌蚪沉积地点的位置及其相关的嗅觉线索,并反复测量成年雄性蝌蚪的探索和大胆程度。利用分子亲代分析方法,通过推断实验池中成年青蛙和蝌蚪的亲代关系,进一步重构了蝌蚪的沉积选择。我们发现新的饲养地点的发现和使用在很大程度上受到嗅觉线索的影响;然而,我们没有发现被测量的行为特征对资源发现和使用的影响。我们的结论是,在高度动态的环境中,如热带雨林,可靠的外部线索可能优先于人格特征,帮助个体发现和利用生殖资源。
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引用次数: 1
Changes in call properties of Boana pulchella (Anura, Hylidae) in response to different noise conditions. Boana pulchella(Anura,Hylidae)在不同噪声条件下叫声特性的变化
IF 1.6 2区 生物学 Q2 ZOOLOGY Pub Date : 2023-08-25 eCollection Date: 2024-08-01 DOI: 10.1093/cz/zoad040
Pablo Grenat, María Ferrero, Mariana Baraquet, Favio Pollo, Manuel Otero, Zulma Salinas, Nancy Salas, Adolfo Martino

The increasing expansion of urban areas leads to the emergence of new noisy environments that can affect animal communication. Calls play a crucial role in the mating displays of anurans, and the negative impact of anthropogenic noise-induced auditory masking has been reported in several species. We investigated the acoustic variation in 96 males (n = 971 calls) of the treefrog Boana pulchella across acoustically undisturbed sites and different noise conditions, associated with urban areas (URBAN) and roads (ROAD), in Central Argentina. We analyzed the effect of anthropogenic noise conditions on 6 temporal (call duration [CD], intercall interval, first and second note duration, internote interval, and call rate) and 3 spectral (dominant frequency of first and second note, frequency difference between them) call properties. The effects of temperature and size on acoustical variables were controlled. We observed differences in all call attributes among the noise conditions, except for intercall interval. Males exposed to URBAN and ROAD exhibited significant changes in CD, dominant frequency of the second note, and frequency difference between them. URBAN males had longest internote interval, while ROAD individuals displayed increased first and second note duration and call rates. Interestingly, ROAD males exhibited immediate changes in call rate in direct response to passing heavy vehicles. Our study emphasizes the impact of anthropogenic noise on the acoustic characteristics of B. pulchella calls. Understanding how animals adapt to noisy environments is crucial in mitigating the adverse effects of urbanization on their communication systems. Future investigations should explore whether the observed call adjustments are effective in avoiding or mitigating the negative consequences of anthropogenic noise on reproductive success.

城市地区的不断扩大导致新的嘈杂环境的出现,这可能会影响动物的交流。叫声在无尾动物的交配展示中起着至关重要的作用,并且在一些物种中已经报道了人为噪声诱导的听觉掩蔽的负面影响。本文研究了阿根廷中部96只雄性Boana pulchella树蛙(n = 971)在声学未受干扰的地点(AUS)和与城市地区(urban)和道路(ROAD)相关的不同噪声条件下的声学变化。我们分析了人为噪声条件对6个时间(呼叫时长、呼叫间隔、第一和第二音符持续时间、呼叫间隔、呼叫率)和3个频谱(第一和第二音符的主导频率、它们之间的频率差)呼叫特性的影响。控制了温度和尺寸对声学变量的影响。我们观察到除呼叫间隔外,噪声条件下所有呼叫属性的差异。URBAN和ROAD暴露的雄性在叫声持续时间、第二音符的主导频率和它们之间的频率差异上表现出显著的变化。URBAN雄性的间隔时间最长,而ROAD个体的第一、第二音符持续时间和呼叫率均有所增加。有趣的是,ROAD男性对过往重型车辆的直接反应显示出呼叫率的立即变化。我们的研究强调了人为噪声对白腹小蠊叫声声学特性的影响。了解动物如何适应嘈杂的环境对于减轻城市化对其通信系统的不利影响至关重要。未来的研究应探讨观察到的叫声调整是否有效地避免或减轻人为噪音对繁殖成功的负面影响。
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引用次数: 0
Expanding through the Emerald Isle: Exploration and spatial orientation of non-native bank voles in Ireland 通过翡翠岛扩张:爱尔兰非本地银行田鼠的探索和空间定位
2区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2023-08-23 DOI: 10.1093/cz/zoad038
Valeria Mazza, Jana A Eccard
Abstract Whether introduced into a completely novel habitat or slowly expanding their current range, the degree to which animals can efficiently explore and navigate new environments can be key to survival, ultimately determining population establishment and colonization success. We tested whether spatial orientation and exploratory behavior are associated with non-native spread in free-living bank voles (Myodes glareolus, N = 43) from a population accidentally introduced to Ireland a century ago. We measured spatial orientation and navigation in a radial arm maze, and behaviors associated to exploratory tendencies and risk-taking in repeated open-field tests, at the expansion edge and in the source population. Bank voles at the expansion edge re-visited unrewarded arms of the maze more, waited longer before leaving it, took longer to start exploring both the radial arm maze and the open field, and were more risk-averse compared to conspecifics in the source population. Taken together, results suggest that for this small mammal under heavy predation pressure, a careful and thorough exploration strategy might be favored when expanding into novel environments.
无论是被引入到一个全新的栖息地,还是慢慢扩大其现有的活动范围,动物能够有效地探索和导航新环境的程度是生存的关键,最终决定了种群的建立和殖民的成功。我们测试了自由生活的田鼠(Myodes glareolus, N = 43)的空间取向和探索行为是否与非本地传播有关,这些田鼠来自一个世纪前偶然引入爱尔兰的种群。我们在一个径向臂迷宫中测量了空间定向和导航,并在重复的开放场地测试中,在扩展边缘和源种群中测量了与探索倾向和冒险相关的行为。在扩张边缘的银行田鼠会更多地重新访问迷宫中没有奖励的部分,在离开之前等待更长的时间,花更长的时间开始探索放射形臂迷宫和开放区域,与源种群中的同类相比,它们更倾向于规避风险。综上所述,研究结果表明,对于这种处于严重捕食压力下的小型哺乳动物来说,在向新环境扩张时,谨慎而彻底的探索策略可能更有利。
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引用次数: 0
Alien lesser bandicoot rats have established wild populations in China 外来小地鼠已在中国建立野生种群
2区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2023-08-19 DOI: 10.1093/cz/zoad039
Ming-Yu Zhang, Zhi-Ming Li, Rui-Dong Cao, Jin-Hua Zhang, Qing Liu, Xi-Chao Zhu, Quan-Sheng Liu, Yao-Hua Zhang, Jian-Xu Zhang
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引用次数: 0
Coping with drought? The hidden microhabitat selection and underground movements of amphisbaenians under summer drought conditions. 应对干旱?夏季干旱条件下两栖类隐蔽微生境选择与地下活动
IF 1.6 2区 生物学 Q2 ZOOLOGY Pub Date : 2023-08-16 eCollection Date: 2024-10-01 DOI: 10.1093/cz/zoad034
José Martín, Gonzalo Rodríguez-Ruiz, José Javier Cuervo

Habitat selection is a dynamic process that depends on many environmental variables that can vary with weather conditions. This is important because, within a context of global change, extreme weather events, such as severe droughts, are predicted to become more frequent. We examined the patterns of microhabitat selection and underground movements (using PIT-tag telemetry) of a strictly fossorial reptile, the North African checkboard amphisbaenian Trogonophis wiegmanni, during the summer drought period. We aimed to test whether changes in strategies of habitat use and movements could allow this amphisbaenian to cope with unfavorable weather. We found that during the summer drought period, T. wiegmanni did not use the microhabitats in relationship to their availability, but particularly selected sites with high abundance of rocks but also areas under a high cover of bushes, where environmental conditions were more favorable. We also found, using PIT-tag telemetry, that the numbers of T. wiegmanni individuals located under rocks and their activity (number of days with movements) decreased largely in summer. However, the animals were not entirely inactive, but, especially males were active below the ground under bushes and made some relatively long underground hidden movements between favorable areas.

栖息地选择是一个动态过程,取决于许多环境变量,而这些变量可能随天气条件而变化。这一点很重要,因为在全球变化的背景下,极端天气事件,如严重干旱,预计将变得更加频繁。在夏季干旱期间,我们研究了一种严格的化石爬行动物——北非方格板两栖爬行动物Trogonophis wiegmanni的微栖息地选择和地下运动模式(使用PIT标签遥测)。我们的目的是测试栖息地使用和移动策略的变化是否能让这种两栖动物应对不利的天气。我们发现,在夏季干旱期间,T.wiegmanni没有使用与其可用性相关的微栖息地,而是特别选择了岩石丰度高的地点,但也选择了环境条件更有利的灌木覆盖率高的地区。我们还发现,使用PIT标签遥测,位于岩石下的威格曼尼T.wiegmanni个体的数量及其活动(活动天数)在夏季大幅减少。然而,这些动物并不是完全不活跃的,但尤其是雄性,它们在灌木丛下的地下活动,并在有利区域之间进行一些相对较长的地下隐蔽运动。
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引用次数: 0
Differential transport of a guild of mutualistic root aphids by the ant Lasius flavus. 一群共生的根蚜虫在黄蚁中的差异运输。
IF 2.2 2区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2023-08-01 DOI: 10.1093/cz/zoac060
Thomas Parmentier

Mutually beneficial associations are widespread in ecological networks. They are typically assembled as multispecies guilds of symbionts that compete for one or more host species. The ant Lasius flavus engages in an intriguing and obligate mutualistic association with a community of aphids that are cultivated on plant roots in its nests. The ant displays a repertoire of amicable behaviors toward the aphids, including their transport. I examined whether L. flavus preferentially carried some of the root aphids. Using a no-choice and a choice experiment, I comparatively analyzed the transport rate of 5 obligate and one loosely associated species back to the ant nest and used the transport rate of the ant larvae as a reference. All associated root aphids were carried back to the nest, but in a clear preferential hierarchy. Geoica utricularia, Forda Formicaria, and Trama rara were rapidly transported, but slower than the own larvae. Tetraneura ulmi and Geoica setulosa were collected at a moderate rate and the loosely associated Aploneura lentisci was slowly retrieved. In contrast, different species of unassociated aphids were not transported and even provoked aggressive behavior in L. flavus. This study revealed that co-occurring symbionts may induce different degrees of host attraction, which ultimately may affect the coexistence and assembly of ant-symbiont communities.

互利的联系在生态网络中广泛存在。它们通常组成多物种共生体协会,竞争一个或多个寄主物种。蚂蚁Lasius flavus与一群蚜虫有一种有趣的互惠关系,这些蚜虫是在蚁巢的植物根上培养的。蚂蚁对蚜虫表现出一系列友好的行为,包括它们的运输。我检查了黄乳杆菌是否优先携带一些根蚜虫。采用无选择实验和选择实验,对比分析了5种专性蚁种和1种松散关联蚁种返回蚁巢的运输速率,并以蚁幼虫的运输速率为参照。所有相关的根蚜虫都被带回巢穴,但有明显的优先等级。土蜱、formica Forda Formicaria和Trama rara的运输速度较快,但比其幼虫的运输速度慢。收集尺蠖和白地蝗的速度一般,收集松散的扁桃蝗的速度较慢。与此相反,不同种类的非亲缘蚜虫在黄乳杆菌中不被运输,甚至引起攻击行为。本研究揭示共生体可以诱导不同程度的寄主吸引力,最终影响抗共生体群落的共存和聚集。
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引用次数: 0
Interspecific differences and ecological correlations between scale number and skin structure in freshwater fishes. 淡水鱼鳞数与表皮结构的种间差异及生态相关性。
IF 2.2 2区 生物学 Q1 Agricultural and Biological Sciences Pub Date : 2023-08-01 DOI: 10.1093/cz/zoac059
Haoran Gu, Haoyu Wang, Shudang Zhu, Dengyue Yuan, Xiangyan Dai, Zhijian Wang

Fish skin is mainly composed of the epidermis, dermis, and its derivative scales. There is a wide diversity in scale number in fishes, but the diversity of skin structure lacks systematic histological comparison. This research aimed to improve our understanding of the functional relationship between the scale number and the skin structure in freshwater fishes and to determine which ecological factors affect the scale number and skin structure. First, we presented a method to quantify skin structure in fish and histologically quantified the skin structure of 54 freshwater fishes. Second, we collected the scale number and habitat information of 509 Cyprinidae fishes in China and explored which ecological factors were related to their scale number. Third, common carp and scaleless carp were used as models to study the effects of scale loss on swimming. We found a strong negative correlation between scale thickness and scale number. The main factor affecting the skin structure of fishes was the species' water column position, and the skin of benthic fishes was the most well-developed (thicker skin layers (dermis, epidermis) or more/larger goblet cells and club cells). The scale number was related to two factors, namely, temperature and water column position, and cold, benthic and pelagic adaptation may have contributed to increased scale numbers. Only in benthic fishes, the more well-developed their skin, the more scales. In common carp, scale loss did not affect its swimming performance. In summary, we suggest that there is a rich diversity of skin structure in freshwater fishes, and the scales of fish with well-developed skin tend to degenerate (greater number/smaller size/thinner, or even disappear), but the skin of fish with degenerated scales is not necessarily well developed.

鱼皮主要由表皮、真皮层及其衍生鳞片组成。鱼类鳞片数量的多样性很大,但皮肤结构的多样性缺乏系统的组织学比较。本研究旨在提高我们对淡水鱼鳞数与皮肤结构之间的功能关系的认识,并确定哪些生态因子影响鳞数和皮肤结构。首先,我们提出了一种定量鱼类皮肤结构的方法,并对54种淡水鱼的皮肤结构进行了组织学定量。其次,收集了中国509种鲤科鱼类的鳞数和生境信息,探讨了与鳞数相关的生态因子。第三,以普通鲤鱼和无鳞鲤鱼为模型,研究了鳞损失对游泳的影响。我们发现鳞片厚度和鳞片数量之间存在很强的负相关关系。影响鱼类皮肤结构的主要因素是物种的水柱位置,底栖鱼类的皮肤最发达(真皮、表皮层较厚或杯状细胞和棒状细胞较多/较大)。水垢数量的增加与温度和水柱位置两个因素有关,冷、底栖和远洋适应可能是水垢数量增加的原因。只有底栖鱼类的皮肤越发达,鳞片越多。在普通鲤鱼中,鳞片的脱落对其游泳性能没有影响。综上所述,我们认为淡水鱼的皮肤结构具有丰富的多样性,皮肤发育良好的鱼的鳞片往往会退化(数量更多/尺寸更小/更薄,甚至消失),但鳞片退化的鱼的皮肤并不一定发育良好。
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引用次数: 2
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Current Zoology
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