卫星细胞中敲除磷脂酰丝氨酸翻转酶β亚基Tmem30a延迟骨骼肌再生
真核细胞质膜中的磷脂酰丝氨酸（PS）是不对称分布的。磷脂酰丝氨酸翻转酶（flippase）能将PS从质膜双分子层的外叶转移到膜的内叶，维持PS的不对称分布。Flippase的β亚基TMEM30A决定其正确的细胞定位及细胞功能。先前研究报道ATP11A和TMEM30A复合物是控制肌管形成的分子开关，然而Tmem30a在骨骼肌再生过程中的作用尚不明确。在该研究中，我们发现Tmem30a在肌肉营养不良小鼠和BaCl2诱导骨骼肌损伤模型小鼠的胫骨前肌中都有高表达。进一步我们构建了在卫星细胞中特异性敲除Tmem30a的小鼠模型来研究Tmem30a在骨骼肌再生过程中的作用。通过H&E和天狼星红染色，分析BaCl2损伤骨骼肌后再生卫星细胞的数量和直径，发现敲除小鼠的骨骼肌再生被延迟。紧接着通过免疫组织化学实验发现，条件性敲除小鼠的再生骨骼肌区域中Pax7阳性和MYH3阳性的卫星细胞数量减少，表明卫星细胞增殖受到一定的影响。随后发现在敲除小鼠的再生骨骼肌区域中肌肉调节因子(MYOD和MYOG)表达也减少，表明骨骼肌再生中成肌细胞的增殖受损。综上所述，这些结果证明Tmem30a在骨骼肌再生过程中发挥着重要作用。
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基于全基因组重测序的少鳞鱚（Sillago japonica）地理群体本地适应进化研究
西北太平洋地区海洋生物对不同环境的适应进化研究尚未系统开展。种群之间的基因组差异能够反映环境选择作用。开展海洋生物群体对温度适应进化研究对于理解生物对气候变化的适应机制以及预测生物对全球变暖的未来适应潜力非常重要。我们采集了少鳞鱚（Sillago japonica）中国和日本近海不同纬度的地理群体样品，利用全基因组重测序检测研究温度适应机制。我们对5个群体基因组重测序，获得548万个单核苷酸多态位点（SNPs），可以将中国和日本群体完全区分开。这种遗传结局形成主要是归因于地理隔离和本地适应性。两个隔离的种群（舟山和伊势湾/东京湾）之间共享大量受选择基因，这表明两种群间存在温度驱动的平行进化现象。这也表明温度对不同种群的选择过程可能是可重复的。此外，我们观察到冷适应的受选择基因在功能上主要跟细胞膜的流动性相关。物种分布预测模型表明，少鳞鱚中国和日本群体可能对未来的气候变化有不同的响应，在未来前者分布区将扩大，后者分布区将收缩。该研究的结果促进了对鱼类群体本地温度适应的遗传机制的理解，扩大了我们对群体遗传分化和群体如何适应温度变化的新认知。
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两个食蚁兽属（Tamandua和Myrmecophaga）比较线粒体组的系统地理学研究：来自不同进化特征的证据
贫齿目Xenarthra（树懒sloths，食蚁兽anteaters和犰狳armadillos）是典型的南美洲哺乳动物。在这三个类群中，蠕舌亚目Vermilingua（食蚁兽anteaters；食蚁兽科Myrmecophagidae）是现存最少的古生物种。该研究对来自中美洲和南美洲的两种小食蚁兽（Tamandua tetradactyla和T. mexicana）(n=74)，以及来自南美洲的大食蚁兽Myrmecophaga tridactyla (n=41)进行采样和全线粒体组测序。在小食蚁兽Tamandua中，检测出了三种不同的单倍群。最古老的单倍群（THI）包含了许多T. tetradactyla的形态型（也包含一些T. mexicana的形态型），该单倍群起源于南美洲东南部（现在的乌拉圭），后来迁往南美洲北部，后者是THII单倍群的起源地。单倍群THII包含T. mexicana的形态型（也包含一些T. tetradactyla的形态型），主要分布于中美洲，哥伦比亚和厄瓜多尔。单倍群THI和THII之间的遗传距离达到4%。THII起源于南美洲北部或中美洲“原生”的单倍群THIII（由50%的T. mexicana和50%的T. tetradactyla组成）。THIII与THII大致分布在同一地区，如中美洲、厄瓜多尔和哥伦比亚，尽管以后者THII为主。由于三个单倍群在哥伦比亚和厄瓜多尔有重叠区，且T. tetradactyla和T. mexicana没有互为单系，所以该研究认为在小食蚁兽属Tamandua内存在一个独特的新种，即T. tetradactyla。与Tamandua相比，尽管检测出两种遗传分化很大（遗传距离约为10%）的两个单倍群（MHI和MHII），但M. tridactyla在新热带地区范围内没有表现出不同的形态。基部的单倍群（MHI）起源于南美洲西北部，而地理衍生出的单倍群（MHII），虽然与MHI有重叠区，但却扩张到了南美洲中部和南部。因此，小食蚁兽属Tamandua是从北向南迁移，而大食蚁兽属Myrmecophaga从南向北迁移。该研究还发现，当前的线粒体多样性开始于晚上新世和上更新世。此外，两个类群均表现出较高的线粒体遗传多样性水平。Tamandua比Myrmecophaga表现出更多的雌性种群扩张的证据。Tamandua在约0.6–0.17百万年前经历了种群扩张，Myrmecophaga在约0.3–0.2百万年前发生种群扩张。然而这两个类群在近期1–2 万年中均经历了明显的雌性数量的下降，并且它们的空间遗传结构很低。因此，Tamandua和 Myrmecophaga在形成它们的遗传结构过程中可能没有受到生物地理、地质或气候事件的影响。
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东喜马拉雅一种被忽视鼯鼠的系统发育和形态学显著性暨一新属描记
鼯鼠（啮齿目松鼠科鼯鼠族）是分化最高、分布最广的滑翔性哺乳动物，其物种间界限区分及其相互关系一直是兽类学研究的活跃方向。李氏小飞鼠Pteromys (Hylopetes) leonardi Thomas, 1921一度被大多数学者认为是黑白飞鼠Hylopetes alboniger的亚种或同物异名。该研究基于在云南省西北部新采集到的李氏小飞鼠标本对该分类单元进行了形态学和遗传学的分析。系统发育重建使用了两个线粒体（12S rDNA和16S rDNA）和一个核（interphotoreceptor retinoid-binding protein）基因片段。形态学分析包括检视、比较博物馆标本皮张、头骨和阴茎特征，并对颅骨的测量数据进行主成分分析（PCA）。综合形态学和遗传学的证据，该研究认为李氏小飞鼠不仅是一个独立的物种，还应该作为一个新属，该文描记为喜山大耳飞鼠属（Priapomys）。
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基因组层面揭示藏野驴和藏家驴在高海拔适应方面的选择性清除现象
在过去的几百年里，生活在青藏高原的家驴已经适应了高海拔的环境。有趣的是，同属于马科的近缘物种藏野驴也居住在这一地区。以往的研究阐述了不同谱系中特定基因的适应性渐渗对青藏高原低氧环境适应有重要的作用。在这项研究中，我们对藏家驴和藏野驴是否通过相同或不同的生物途径适应高原环境，以及是否发生了适应性渐渗现象展开了研究。我们从头组装了一个藏野驴的基因组，结合5个藏野驴和93个家驴(包括24个藏家驴)的基因组重测序数据展开了分析研究。分析表明，藏野驴EPAS1基因存在强的选择性清除信号；然而，藏家驴的高原适应，则是另一与高原适应相关的基因EGLN1，参与它们适应高海拔环境。此外，针对基因流的分析，我们未发现藏野驴和藏家驴中与高原适应相关的基因流动。我们的研究结果表明，尽管家驴在青藏高原的进化时间较短，且存在一个已经适应高原低氧环境的近缘物种，但藏家驴并没有通过与藏野驴的适应性渐渗来获得对高原的适应性，藏野驴与藏家驴这两个物种通过不同的生物途径进化出了对高原的适应能力。
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并联共生小鼠模型的建立方案、应用和展望
并联共生（parabiosis）是通过手术方法将两只实验动物进行外科连接的一种历史悠久的动物模型。在过去的二十年里，该模型被广泛应用于生物医学研究，特别是在衰老、干细胞、神经科学和免疫等领域。虽然并联共生模型已经得到了不断改进和完善，但从手术操作到围术期管理，仍有诸多细节值得研究者们关注，以降低死亡率和提高并联共生的稳定性。尽管存在着自身的局限性，但作为一种不可替代的研究手段，并联共生动物模型在生物医学研究领域仍有广阔的应用前景。
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动物分泌型内吞溶酶体通道的发现
分泌型孔道形成蛋白（pore-forming proteins, PFPs）广泛分布于自然界的各种生物物种中。我们以两栖动物大蹼铃蟾（Bombina maxima）为模型开展的研究发现：细菌孔道形成毒素家族（aerolysin family）蛋白（af-PFPs）和三叶因子（trefoil factors, TFFs）在大蹼铃蟾中广泛分布，而且它们之间存在相互作用网络。首先，大蹼铃蟾af-PFP蛋白BmALP1可被其同源蛋白BmALP3进行氧浓度依赖的负调控，造成 BmALP1蛋白可在其活性（单体）和非活性形式（同源二聚体或多聚体）之间进行可逆性的转变。其次，活性形式的BmALP1可与BmTFF3相互作用以形成具有细胞活性的复合物βγ-CAT。该孔道形成蛋白复合物的特性在于通过受体介导的内吞（endocytosis）进入细胞并在内吞溶酶体上（endolysosomes）形成物质通道调控内吞溶酶体的生化特性，包括刺激和参与细胞巨胞饮（macropinocytosis）的作用。βγ-CAT复合物还同时具有诱导和调节细胞胞吐（exocytosis）的作用。取决于细胞类型和状态以及细胞外环境，βγ-CAT的细胞作用和效应可促进大蹼铃蟾的物质（例如水、营养成分、代谢物和外来抗原等）吸收和囊泡化运输以及胞内物质交换与外排，同时维持粘膜屏障和免疫防御的功能。基于已有的实验证据，我们提出了分泌型内吞溶酶体通道（secretory endolysosome channel, SELC）的创新性慨念并提出了SELC细胞通路的特征框架，两栖动物大蹼铃蟾βγ-CAT是第一个被实验验证了的SELC蛋白实例。鉴于新发现的SELC蛋白以及相应细胞作用通路在细胞与环境相互作用和环境适应中发挥的基础作用，它们在生物体，特别是脊椎动物物种中，应该具有进化上的保守性。
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下呼吸道标本核酸检测是SARS-CoV-2感染诊断和研究的可靠依据
新型冠状病毒（SARS-CoV-2）及其造成的肺炎（COVID-19）持续严重影响世界各国。稳定可靠的诊断方法和评价系统的欠缺严重阻碍了有效预防和治疗策略的实施和发展。该研究通过横向和纵向研究，比较分析来源于COVID-19患者和SARS-CoV-2感染猴的不同类型样本中SARS-CoV-2的核酸检出率，分析COVID-19患者和SARS-CoV-2感染猴血清中抗SARS-CoV-2抗体的阳性率，以评估SARS-CoV-2感染诊断方法的可靠性。结果显示无论感染者的临床症状如何，痰液和气管刷样品中病毒核酸检出率较高，感染确诊率高，诊断结果稳定。而6.90% COVID-19患者血清中未检测到抗SARS-CoV-2免疫球蛋白M和G。此外，同时采集不同类型样本并结合其核酸检测的结果并不能提高诊断率。另外，与鼻拭子和咽拭子相比，痰和气管刷中SARS-CoV-2病毒载量持续时间较长，动态变化较明显。因此，痰和气管刷中SARS-CoV-2核酸检测受感染途径、疾病进展和个体差异的影响较小，用下呼吸道标本进行SARS-CoV-2核酸检测是SARS-CoV-2感染诊断和研究的可靠依据。
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刺突蛋白的突变和血管紧张素转化酶2的等位基因变异对SARS-CoV-2靶向治疗策略的影响
新型冠状病毒肺炎(COVID-19)是由严重急性呼吸系统综合征冠状病毒2 (SARS-CoV-2)引起的一种大流行疾病，目前正在全球范围内迅速蔓延，其传播速度快，死亡人数高。迄今为止，尚无针对COVID-19的有效治疗或疫苗。血管紧张素转化酶2 (ACE2)和刺突蛋白（spike）在COVID-19治疗中的作用是当前的研究重点。在本研究中，我们探索了ACE2和spike作为靶点开发抗SARS-CoV-2病毒药物的潜力。我们分析了临床数据、测序数据和受体结合能力。其中，临床资料显示，COVID-19合并肾素-血管紧张素系统异常的患者早期症状多，预后差。然而，ACE2表达水平与COVID-19进展之间的关系尚不清楚。因此，ACE2可能不是一个很好的靶标适用于治疗不同人群的COVID-19。根据序列分析，与ACE2相互作用的spike-S1受体结合区域有许多氨基酸突变。通过受体-配体对接和ELISA试验，我们鉴定了两个spike-S1点突变体(V354F和V470A)。这些变异增强了spike蛋白与ACE2受体的结合，可能与突变体传染性增加有关。更重要的是，随着SARS-CoV-2的流行，感染V354F或V470A突变体的患者数量正在增加。这些结果表明，ACE2和spike-S1可能不适用设计广泛用于治疗不同人群COVID-19的药物理想靶点。
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古颚类鸟类转座元件、种群历史和基因的动态演化
古颚类鸟类包括平胸目和䳍形目，对它们的研究有助于我们对鸟类早期演化的了解。我们通过对古颚类15个物种全基因组序列的分析来重构其种群演化历史。除了分布在澳大利亚，新西兰和南美洲最南端的物种，我们发现，自上个冰川期开始以来，大多数古鄂类物种的种群数量都减少了。基因组转座元件不同程度的收缩和扩增塑造了古颚类的基因组结构，相对于平胸目，䳍形目的转座子有更高的丢失速率。大约3000万年前，AviRTE重复序列可能发生了从热带寄生虫向小穴䳍和波斑穴䳍祖先的水平转移。我们对基因家族的分析确定了与免疫和繁殖相关基因的快速变化，但是没有发现平胸目飞行趋同退化的基因家族变化。我们还发现线粒体基因在䳍形目中的进化速率高于平胸目，前者的W染色体退化地更严重。该结果可以通过W染色体和线粒体因为遗传连锁受到希尔·罗伯森干涉效应的影响来解释。综上，我们重建了古颚类种群，基因和转座元件的演化历史。线粒体和W染色体共同演化的发现突出了ZW性染色体物种与XY性染色体物种之间基因组进化的关键差异。
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多基因位点系统发育揭示熊猴(Macaca assamensis)尼泊尔种群的独立物种地位及其对进化和保护的启示
长期以来，基于形态、行为和分子特征的猕猴属(Macaca)斯里兰卡猴种组(sinica group)系统发育关系一直饱受争议。熊猴(M. assamensis)尼泊尔种群生活在该物种分布范围的最西部，形态特征独特，但其系统发育关系仍未有相关研究。本研究利用多个线粒体和Y染色体基因位点检验熊猴尼泊尔种群与其他猕猴间的系统发育关系，估算其分化时间与遗传距离。结果显示，斯里兰卡猴种组分化为两个主要分支：第一个分支包括藏酋猴（M. thibetana）、斯里兰卡猴（M. sinica）和熊猴指名亚种(M. assamensis assamensis)，第二个分支包括帽猴（M. radiata）、喜马拉雅山脉东部和中部的白颊猕猴（M. leucogenys）、达旺猴（M. munzala）和熊猴尼泊尔种群。在第二分支当中，熊猴尼泊尔种群大约于1.9百万年前最先与该分支其他成员分开。研究结果揭示熊猴尼泊尔种群与东部的熊猴指名亚种显著分化，而与白颊猕猴和达旺猴更接近，说明熊猴尼泊尔种群可能是一个独立的物种。由于其系统发育关系特殊、分布区隔离且种群数量少，斯里兰卡猴种组尼泊尔种群亟需详细的分类修订并采取相应优先保护措施。
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Journal Scope
Primates and Animal Models Conservation and Utilization of Animal ResourcesAnimal Diversity and Evolution
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SARS-CoV-2感染老年中国猕猴呈现迟发且严重的细胞因子风暴和免疫细胞浸润
截至2020年6月，全球新型冠状病毒感染者死亡人数已增至44万人，死亡患者中年龄大于65岁的老年人约占74％。因此，高龄是目前公认的新型冠状病毒感染死亡最重要风险因素。本研究通过构建老年及青年中国猕猴新型冠状病毒感染疾病模型，分析年龄对新型冠状病毒感染疾病进程的影响。结果表明，青年猕猴在感染后第1周表现为呼吸功能受损、肺部病毒活跃复制、肺部严重病理损伤以及肺组织中CD11b+ 细胞和CD8+ T细胞浸润，但在感染第2周疾病特征迅速恢复。与之相比，老年猕猴在感染第2周表现出明显的免疫反应和严重的细胞因子风暴，肺部CD11b+ 细胞浸润增加并伴有CD8+ T细胞持续浸润。同时，老年猕猴外周血T细胞显示出比年轻猕猴更明显的趋化性，但其抗病毒功能较弱。因此，延迟但更严重的细胞因子风暴和免疫细胞浸润可能是老年新型冠状病毒感染者预后不良的原因。
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乳腺癌动物模型及应用
乳腺癌是女性最常见的恶性肿瘤。乳腺癌基础和转化研究依赖于实验动物模型。理想的乳腺癌模型应与人类乳腺癌在肿瘤病因，生物学行为，病理学和对治疗的反应而言最好具有共性。根据构建模型的方法以及实验目的的不同，目前乳腺癌动物模型分为自发型、诱发型、移植型、基因工程型等，该篇综述介绍了不同乳腺癌实验动物模型研究的最新进展，并分析了它们的特征，优缺点和潜在应用。最后，我们指出了乳腺癌动物模型的未来研究方向。
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SARS-CoV-2感染中国树鼩呈现COVID-19样症状
2019冠状病毒病（COVID-19）大流行对全球公共卫生安全构成了巨大威胁。找到易感染新型冠状病毒（SARS-CoV-2/HCoV-19）的实验动物对于控制疫情、筛选有效的预防或治疗方法都是至关重要的。在本研究中，我们对灵长动物近亲——树鼩进行了新型冠状病毒感染模型创建研究。我们选择了不同年龄段的树鼩，包括1岁左右的成年树鼩和5-6岁的老年树鼩，感染SARS-CoV-2。在树鼩接种病毒后的不同天数进行肺部影像学、病毒载量、血常规和生化以及组织病理学等分析。结果表明，树鼩可以感染SARS-CoV-2病毒。X射线检查可以在大多数感染树鼩看到肺部浸润。在感染后3、5和7天，感染树鼩肺组织中可检测到病毒RNA，血常规和血清生化相关参数也发生变化，包括天冬氨酸转氨酶（AST）和尿素氮（BUN）水平升高。感染后3天成年组和7天老年组树鼩肺组织病理学染色显示肺泡间隔增厚，间质出血。在病毒排出高峰方面，两个不同的年龄组中存在一些差异。我们的研究结果表明，中国树鼩有可能成为COVID-19机制研究、药物和疫苗评价的模型动物。
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磁性纳米氧化铁药物介导的脑磁刺激新策略可快速改善小鼠抑郁样行为
磁刺激极大地促进了神经科学的进步，其中高频（10 Hz）重复经颅磁刺激（rTMS）刺激左背外侧前额叶皮层（DLPFC）已于2008年获得美国食品药品监督管理局（FDA）的批准，用于治疗成人难治性抑郁。但目前rTMS仍然存在技术局限性，包括穿透力差，磁刺激聚焦精度不足，刺激深度有限等。特别是在小动物精神疾病模型中，即使最小的通用线圈也会刺激整个半球甚至整个大脑，无法做到精准定位，难以研究rTMS的神经调控机制等脑科学相关的重大科学问题。针对此问题，我们提出了利用获得中国FDA批准的超顺磁性纳米氧化铁（SPIO）药物，结合轻度磁脉冲序列，以提高局部皮层敏感性的磁性脑刺激的新策略，即联合磁性刺激系统（c-MSS）。小鼠左前额叶皮层中与人类DLPFC同源的脑区为PrL，磁共振成像证明SPIO可稳定存在于PrL脑区至少11天。从细胞、动物和体外模型多方面证明了c-MSS的安全性和物理性特征。建立慢性不可预测的轻度应激（CUMS）抑郁模型小鼠，使用0.1T c-MSS（每次5分钟，每天两次）进行磁干预，结果表明10 Hz磁刺激5天可快速改善CUMS小鼠的抑郁样症状，这可能与增加脑源性神经营养因子（BDNF）和改善下丘脑-垂体-肾上腺（HPA）轴有密切关系。c-MSS是一种可精准刺激小动物任意皮层靶标的新方法，这一项研究成果将极大地丰富磁刺激的潜在应用领域，促进基于磁性纳米药物的磁刺激技术临床转化。
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印支灰叶猴 (Trachypithecus crepusculus) 林层利用及森林覆盖率对乌叶猴属 (Trachypithecus) 地栖性的影响
研究动物在不同栖息地条件下表现出的行为弹性对于濒危物种保护来说至关重要。乌叶猴属动物生活在多样的栖息地中，表现出不同的林层利用模式；然而栖息地结构对于林层利用的影响尚未得到深入研究。本研究于2012年6月至2016年1月调查了印支灰叶猴 (Trachypithecus crepusculus) 在无量山原始常绿林中的林层利用模式，并且比较了印支灰叶猴和其它5个乌叶猴属物种在林层利用和地栖行为上的异同。不同于生活在喀斯特石山的叶猴，印支灰叶猴研究群体表现出高度的树栖性，在地面活动的时间只占总活动时间的2.9%。研究群体倾向于在较高的林层休息，在较低的林层 (<20m) 移动；在地面的时间主要用于食土，极少用于取食其它食物。这些林层利用模式与石山叶猴 (黑叶猴，T. francoisi) 在连续性较好的森林中的行为相似。本研究还发现乌叶猴属地栖程度与栖息地森林覆盖率之间存在显著的负相关关系，这种关系在石山叶猴内部也具有显著性，暗示石山叶猴因森林覆盖率的下降而提高了地栖性。本研究结果揭示了乌叶猴属物种在林层利用方面的行为弹性，强调了连续程度高的森林对于叶猴保护的重要性。
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2019年人类冠状病毒(HCoV-19)引起人畜共患病溯源研究的重要性
2019年人类冠状病毒（HCoV-19/SARS-CoV-2/2019-nCoV）感染引起2019年肺炎爆发，造成对人类全球性威胁。作者参考两种引起人类严重肺炎的新型冠状病毒SARS-CoV和MERS-CoV的流行病学数据，总结了HCoV-19人畜共患病起源的现有数据。作者建议今后应加紧HCoV-19的溯源研究，为控制和预防该病提供重要的科学依据。
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基于全基因组数据解析新型冠状病毒演化和传播
2019年12月中旬新型肺炎疫情(COVID-19)在湖北武汉爆发，截至2020年2月29日，新冠病毒SARS-CoV-2（2019-nCoV/HCoV-19）已感染全球85 000多人。在本研究中，我们使用了GISAID EpiFluTM数据库中的93个完整新冠病毒基因组来解析新冠病毒在疫情爆发前两个月的演化，以及人际传播情况。我们采用系统发育网状分析方法，构建了SARS-CoV-2基因组的单倍型的演化关系，并进一步对病毒的潜在种群大小变化进行估算。利用公式t =τ/ 2u，基于扩展参数tau（τ）推算了病毒可能发生扩张（即大量人传人）日期。在新冠病毒基因组的八个编码区中共发现120个的变异位点，关联119个密码子有79个非同义和40个同义替换。我们猜测40个改变氨基酸属性的非同义替换可能与病毒适应性有关。另外，我们分析中没有检测到病毒重组事件。从93个病毒基因组中鉴定出58种单倍型，将其划分为五组用于传播和扩散分析。通过蝙蝠冠状病毒基因组（bat-RaTG13-CoV）作为外群，我们发现单倍型H13和H38可能是古老的单倍型，单倍型H1是从单倍型H3演化而来。种群扩张时间估算发现在2020年1月6日和2019年12月8日可能发生大量人传人。此外，我们利用谱系流行病学方法回溯了一些人际传播事件。同时，这种方法可以用于寻找感染病例的病毒感染源。
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短腿蟾属（无尾目：角蟾科）复查并恢复平头短腿蟾的有效性及描述一新种
最近，关于广义角蟾属有诸多分类争论，其中也包括单系群短腿蟾。短腿蟾具有明显的可识别的形态特征，且最近所有分子系统学研究都表明其为一个稳定的单系群，因此将其作为一个独立属是合理的。本研究对该属做了全面复查，并基于形态学差异和系统发育关系提出了两个种组，同时认为平头短腿蟾是一个有效种，其与宽头短腿蟾有较大遗传分化和显著形态差异。此外，基于采自中国东南部的一系列标本，描述了一新种——东方短腿蟾。至此，短腿蟾属成员增加到7个，其多样性显然被低估了。另外，基于分类便利性、单系性和紧凑性原则，本研究还讨论了角蟾亚科其他单系群的属级分类地位问题。
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利用两种携带不同荧光蛋白的逆行感染的腺相关病毒证明小鼠副嗅球的向心投射具有弥散特征
脊椎动物拥有主嗅和副嗅两套嗅觉系统，共同感知和处理挥发性和非挥发性的社会性化学信息，进而调控不同的性行为和社会行为。副嗅球是副嗅系统进行信息传递和处理的第一级中枢，位于主嗅球的背后侧。由于其特殊的解剖位置和缺乏特异性分子细胞标记，我们对副嗅球的内部和外部神经网络了解得非常有限。本文中，我们利用可以在轴突末端吸收并逆行传递和感染神经元胞体的腺相关病毒（retro-rAAV），在小鼠副嗅皮层（终纹床核、皮层杏仁核前侧、中央杏仁核和皮层杏仁核后内侧）注射retro-rAAV，成功实现了对小鼠副嗅球内投射神经元的荧光标记，证明了该方法的有效性。在此基础上，我们利用携带不同荧光蛋白的retro-rAAV分别注射在上述不同的副嗅皮层，发现了副嗅球内投射神经元被共标，证明了小鼠副嗅球内投射神经元向心投射具有弥散的特征（1对多），与主嗅球的投射神经元类似。此外，我们还发现投射到不同皮层的副嗅球投射神经元被感染的数量有所不同，表明单个投射神经元的信息在向心传递过程中，可能会传递到不同皮层内不同数量的皮层神经元。这些结果为我们理解脊椎动物副嗅系统对外周环境中的气味信息的编码和解码机制提供了一定的神经环路基础。
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2021, 42(6): 675-691.
doi: 10.24272/j.issn.2095-8137.2021.074
The highly speciose gekkonid genus Cnemaspis Strauch, 1887 is polyphyletic, with three distantly related and geographically isolated clades from Africa, South Asia (SA), and Southeast Asia. At present, there are 85 known species within SA Cnemaspis, although the number continues to increase rapidly with focused surveys and rigorous taxonomic work. Recent studies have provided valuable insights into the diversity and evolutionary history of SA Cnemaspis; however, most of these studies lack sufficient sampling in the Western Ghats (WG), where the genus has its greatest diversity. We addressed this research gap by conducting extensive sampling across the WG and re-examining museum specimens, thus providing a systematic account of various extant Cnemaspis species along with their distribution and natural history. We described 12 new species and a southern WG endemic clade of SA Cnemaspis. Ten of the newly described species are endemic to the forests of the southern WG. We also identified 10 well-supported subclades that can be separated across morphological, geographic, and phylogenetic axes. A time-calibrated phylogeny and ancestral area reconstructions confirmed the Paleocene origin of SA Cnemaspis in the WG and provide insights into its evolutionary history and biogeography. The discovery of multiple endemic and deeply divergent lineages further highlights the evolutionary significance of the WG for lizards.
2021, 42(6): 692-709.
doi: 10.24272/j.issn.2095-8137.2021.272
The Chinese tree shrew (Tupaia belangeri chinensis) is emerging as an important experimental animal in multiple fields of biomedical research. Comprehensive reference genome annotation for both mRNA and long non-coding RNA (lncRNA) is crucial for developing animal models using this species. In the current study, we collected a total of 234 high-quality RNA sequencing (RNA-seq) datasets and two long-read isoform sequencing (ISO-seq) datasets and improved the annotation of our previously assembled high-quality chromosome-level tree shrew genome. We obtained a total of 3 514 newly annotated coding genes and 50 576 lncRNA genes. We also characterized the tissue-specific expression patterns and alternative splicing patterns of mRNAs and lncRNAs and mapped the orthologous relationships among 11 mammalian species using the current annotated genome. We identified 144 tree shrew-specific gene families, including interleukin 6 (IL6) and STT3 oligosaccharyltransferase complex catalytic subunit B (STT3B), which underwent significant changes in size. Comparison of the overall expression patterns in tissues and pathways across four species (human, rhesus monkey, tree shrew, and mouse) indicated that tree shrews are more similar to primates than to mice at the tissue-transcriptome level. Notably, the newly annotated purine rich element binding protein A (PURA) gene and the STT3B gene family showed dysregulation upon viral infection. The updated version of the tree shrew genome annotation (KIZ version 3: TS_3.0) is available at http://www.treeshrewdb.org and provides an essential reference for basic and biomedical studies using tree shrew animal models.
2021, 42(6): 710-720.
doi: 10.24272/j.issn.2095-8137.2021.189
The Chantecler chicken, a unique Canadian indigenous breed, is well adapted to extremely cold environments. However, its genetic characteristics have not been well studied. Here, we analyzed the whole genomes of 10 Chantecler chickens and 121 worldwide chickens, which indicated that Chantecler chickens were derived from commercial chickens and exhibit a high level of inbreeding. Based on a genome-wide scan, we identified two vital candidate regions containing ME3 and ZNF536, which are related to fat metabolism and nervous system in cold adaptation, respectively. We also found that the genetic mechanism of cold adaptation in Chantecler chickens differed from that of chickens from other cold regions, such as northern China. Our study indicated that specialized commercial chickens in the early 20th century contained sufficient genetic diversity to adapt to extreme cold environments over a very short time. These findings enrich our understanding of the adaptive potential of commercial species.
2021, 42(6): 721-725.
doi: 10.24272/j.issn.2095-8137.2021.136
SOX9 (SRY-related HMG box gene 9) is an essential regulator of male sex determination and testis differentiation in many vertebrate species. However, the functional role of Sox9 in testis differentiation has not yet been identified in any reptilian species. Herein, Sox9 knockdown in the red-eared slider turtle (Trachemys scripta) embryos at a male-producing temperature led to complete male-to-female sex reversal, characterized by the formation of an ovary-like structure, disappearance of male marker AMH, and ectopic expression of ovarian regulator FOXL2, as well as a female distribution pattern of germ cells. Conversely, in-ovo overexpression of Sox9 at a female-producing temperature resulted in partial masculinization of putative female embryos, with the co-existence of AMH and FOXL2. Our study provides the first direct evidence that Sox9 is indispensable for testicular differentiation in a reptilian species, further confirming the conserved role of Sox9 in vertebrate sexual development.
2021, 42(6): 726-733.
doi: 10.24272/j.issn.2095-8137.2021.228
We report a new species of the genus Micryletta from the montane evergreen forest in the Bidoup-Nui Ba National Park, Lam Dong Province, Langbian Plateau, southern Vietnam, based on molecular and morphological evidence. The new species is diagnosed by a combination of the following morphological characters: body size small (snout-vent length (SVL) 22.4 mm, single female); iris uniform black; snout nearly truncate in dorsal view, slightly rounded in profile; tibiotarsal articulation of adpressed limb reaching level of eye; dorsal surface smooth; supratympanic fold present, prominent; outer metatarsal tubercle absent; tips of toes very weakly dilated into small discs; finger webbing absent, toe webbing rudimentary; dorsal surfaces of head and body orange-red with small irregularly shaped dark-brown patches; dorsal surface of limbs pale dark brown with small reddish speckles; body flanks dark brown anteriorly fading to grayish brown posteriorly with brown spots in groin area; lateral sides of head immaculate blackish brown without white patches; coloration of ventral surfaces immaculate dark gray. The new species is divergent from all other congeners in 16S rRNA gene sequences (2.6%–5.8%). Following the IUCN Red List Categories and Criteria, we propose the new species be listed as Data Deficient (DD).
2021, 42(6): 734-738.
doi: 10.24272/j.issn.2095-8137.2021.211
2021, 42(6): 739-745.
doi: 10.24272/j.issn.2095-8137.2021.199
The small-eared shrew genus Cryptotis is the third largest in the family Soricidae and occurs in North, Central, and northern South America. In Mexico and Central and South America, most species inhabit geographically isolated moist, montane habitats at middle and high elevations in a typical sky-island pattern. The 49 recognized species have been partitioned into as many as six species groups based on morphological and molecular phylogenetic studies. The relationships among these species groups are poorly resolved, and their evolutionary histories, including migration patterns and locomotor adaptations, remain unclear. Herein, we provide a new phylogeny incorporating complete mitochondrial genomes (mitogenomes) and supermatrix approach. We compared different evolutionary scenarios using approximately unbiased (AU), Kishino-Hasegawa (KH), and Shimodaira-Hasegawa (SH) statistical tests. The phylogenetic hypothesis based on mitogenomes revealed novel relationships supporting a basal position for the Cryptotis parvus-group in the genus, and a close relationship between C. gracilis and one clade of the C. thomasi-group. The former relationship is consistent with the least derived humerus morphology and northern distribution of the species. The latter relationship implies multiple migrations between Central and South America. The lack of fine resolution for the species group relationships may be due partly to the lack of taxon sampling. In contrast, multi-approach analyses suggest that the unresolved relationships may be a result of rapid diversification during the early stages of Cryptotis evolution.
2021, 42(6): 746-760.
doi: 10.24272/j.issn.2095-8137.2021.224
Oxygen is an essential molecule for animal respiration, growth, and survival. Unlike in terrestrial environments, contamination and climate change have led to the frequent occurrence of hypoxia in aquatic environments, thus impacting aquatic animal survival. However, the adaptative mechanisms underlying fish responses to environmental hypoxia remain largely unknown. Here, we used large yellow croaker (Larimichthys crocea) and large yellow croaker fry (LYCF) cells to investigate the roles of the Hif-1α/Hsf1/Hsp70 signaling pathway in the regulation of cellular redox homeostasis, and apoptosis. We confirmed that hypoxia induced the expression of Hif-1α, Hsf1, and Hsp70 in vivo and in vitro. Genetic Hsp70 knockdown/overexpression indicated that Hsp70 was required for maintaining redox homeostasis and resisting oxidative stress in LYCF cells under hypoxic stress. Hsp70 inhibited caspase-dependent intrinsic apoptosis by maintaining normal mitochondrial membrane potential, enhancing Bcl-2 mRNA and protein expression, inhibiting Bax and caspase3 mRNA expression, and suppressing caspase-3 and caspase-9 activation. Hsp70 suppressed caspase-independent intrinsic apoptosis by inhibiting nuclear translocation of apoptosis-inducing factor (AIF) and disturbed extrinsic apoptosis by inactivating caspase-8. Genetic knockdown/overexpression of Hif-1α and dual-luciferase reporter assay indicated that Hif-1α activated the Hsf1 DNA promoter and enhanced Hsf1 mRNA transcription. Hsf1 enhanced Hsp70 mRNA transcription in a similar manner. In summary, the Hif-1α/Hsf1/Hsp70 signaling pathway plays an important role in regulating redox homeostasis and anti-apoptosis in L. crocea under hypoxic stress.
2021, 42(6): 761-771.
doi: 10.24272/j.issn.2095-8137.2021.143
The pygmy marmoset, the smallest of the anthropoid primates, has a broad distribution in Western Amazonia. Recent studies using molecular and morphological data have identified two distinct species separated by the Napo and Solimões-Amazonas rivers. However, reconciling this new biological evidence with current taxonomy, i.e., two subspecies, Cebuella pygmaea pygmaea (Spix, 1823) and Cebuella pygmaea niveiventris (Lönnberg, 1940), was problematic given the uncertainty as to whether Spix’s pygmy marmoset (Cebuella pygmaea pygmaea) was collected north or south of the Napo and Solimões-Amazonas rivers, making it unclear to which of the two newly revealed species the name pygmaea would apply. Here, we present the first molecular data from Spix’s type specimen of Cebuella pygmaea, as well as novel mitochondrial genomes from modern pygmy marmosets sampled near the type locality (Tabatinga) on both sides of the river. With these data, we can confirm the correct names of the two species identified, i.e., C. pygmaea for animals north of the Napo and Solimões-Amazonas rivers and C. niveiventris for animals south of these two rivers. Phylogenetic analyses of the novel genetic data placed into the context of cytochrome b gene sequences from across the range of pygmy marmosets further led us to re-evaluate the geographical distribution for the two Cebuella species. We dated the split of these two species to 2.54 million years ago. We discuss additional, more recent, subdivisions within each lineage, as well as potential contact zones between the two species in the headwaters of these rivers.
2021, 42(6): 772-782.
doi: 10.24272/j.issn.2095-8137.2021.186
Salamanders are unique among tetrapods in their ability to regenerate the limbs throughout life. Like other poikilothermic amphibians, salamanders also show a remarkable capacity to survive long periods of starvation. Whether the physiological reserves necessary for tissue regeneration are preserved or sacrificed in starved salamanders is unknown. In the current study, we maintained Iberian ribbed newts (Pleurodeles waltl) under extreme physiological stress to assess the extent of regeneration and identify the molecular and cellular changes that may occur under such conditions. After 19 months of complete food deprivation, the animals exhibited extensive morphological and physiological adaptations but remained behaviorally active and vigilant. Autophagy was elevated in different tissues and the transformed gut microbiota indicated remodeling of the intestinal tract related to autophagy. Upon limb amputation in animals starved for 21 months, regeneration proceeded with progenitor cell proliferation and migration, leading to limb blastema formation. However, limb outgrowth and patterning were substantially attenuated. Blockage of autophagy inhibited cell proliferation and blastema formation in starved animals, but not in fed animals. Hence, tissue autophagy and the regenerative response were tightly coupled only when animals were under stress. Our results demonstrate that under adverse conditions, salamanders can exploit alternative strategies to secure blastema formation for limb regeneration.
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2021, 42(5): 525-547.
doi: 10.24272/j.issn.2095-8137.2020.365
The species within Xenarthra (sloths, anteaters, and armadillos) are quintessential South American mammals. Of the three groups, Vermilingua (anteaters) contains the fewest extant and paleontological species. Here, we sampled and sequenced the entire mitochondrial genomes (mitogenomes) of two Tamandua species (Tamandua tetradactyla and T. mexicana) (n=74) from Central and South America, as well as Myrmecophaga tridactyla (n=41) from South America. Within Tamandua, we detected three different haplogroups. The oldest (THI) contained many specimens with the T. tetradactyla morphotype (but also several with the T. mexicana morphotype) and originated in southeastern South America (currently Uruguay) before moving towards northern South America, where the THII haplogroup originated. THII primarily contained specimens with the T. mexicana morphotype (but also several with the T. tetradactyla morphotype) and was distributed in Central America, Colombia, and Ecuador. THI and THII yielded a genetic distance of 4%. THII originated in either northern South America or “in situ” in Central America with haplogroup THIII, which consisted of ~50% T. mexicana and 50% T. tetradactyla phenotypes. THIII was mostly located in the same areas as THII, i.e., Central America, Ecuador, and Colombia, though mainly in the latter. The three haplogroups overlapped in Colombia and Ecuador. Thus, T. tetradactyla and T. mexicana were not reciprocally monophyletic. For this reason, we considered that a unique species of Tamandua likely exists, i.e., T. tetradactyla. In contrast to Tamandua, M. tridactyla did not show different morphotypes throughout its geographical range in the Neotropics. However, two very divergent genetic haplogroups (MHI and MHII), with a genetic distance of ~10%, were detected. The basal haplogroup, MHI, originated in northwestern South America, whereas the more geographically derived haplogroup, MHII, overlapped with MHI, but also expanded into central and southern South America. Thus, Tamandua migrated from south to north whereas Myrmecophaga migrated from north to south. Our results also showed that temporal mitochondrial diversification for Tamandua began during the Late Pliocene and Upper Pleistocene, but for Myrmecophaga began during the Late Miocene. Furthermore, both taxa showed elevated levels of mitochondrial genetic diversity. Tamandua showed more evidence of female population expansion than Myrmecophaga. Tamandua experienced population expansion ~0.6–0.17 million years ago (Mya), whereas Myrmecophaga showed possible population expansion ~0.3–0.2 Mya. However, both taxa experienced a conspicuous female decline in the last 10 000–20 000 years. Our results also showed little spatial genetic structure for both taxa. However, several analyses revealed higher spatial structure in Tamandua than in Myrmecophaga. Therefore, Tamandua and Myrmecophaga were not subjected to the same biogeographical, geological, or climatological events in shaping their genetic structures.
2021, 42(5): 548-561.
doi: 10.24272/j.issn.2095-8137.2021.116
The genetic adaptations of various organisms to heterogeneous environments in the northwestern Pacific remain poorly understood. Heterogeneous genomic divergence among populations may reflect environmental selection. Advancing our understanding of the mechanisms by which organisms adapt to different temperatures in response to climate change and predicting the adaptive potential and ecological consequences of anthropogenic global warming are critical. We sequenced the whole genomes of Japanese whiting (Sillago japonica) specimens collected from different latitudinal locations along the coastal waters of China and Japan to detect possible thermal adaptations. Using population genomics, a total of 5.48 million single nucleotide polymorphisms (SNPs) from five populations revealed a complete genetic break between the Chinese and Japanese groups, which was attributed to both geographic distance and local adaptation. The shared natural selection genes between two isolated populations (i.e., Zhoushan and Ise Bay/Tokyo Bay) indicated possible parallel evolution at the genetic level induced by temperature. These genes also indicated that the process of temperature selection on isolated populations is repeatable. Moreover, we observed natural candidate genes related to membrane fluidity, possibly underlying adaptation to cold environmental stress. These findings advance our understanding of the genetic mechanisms underlying the rapid adaptations of fish species. Species distribution projection models suggested that the Chinese and Japanese groups may have different responses to future climate change, with the former expanding and the latter contracting. The findings of this study enhance our understanding of genetic differentiation and adaptation to changing environments.
2021, 42(5): 562-573.
doi: 10.24272/j.issn.2095-8137.2021.075
Inositol requiring mutant 80 (INO80) is a chromatin remodeler that regulates pluripotency maintenance of embryonic stem cells and reprogramming of somatic cells into pluripotent stem cells. However, the roles and mechanisms of INO80 in porcine pre-implantation embryonic development remain largely unknown. Here, we show that INO80 modulates trophectoderm epithelium permeability to promote porcine blastocyst development. The INO80 protein is highly expressed in the nuclei during morula-to-blastocyst transition. Functional studies revealed that RNA interference (RNAi)-mediated knockdown of INO80 severely blocks blastocyst formation and disrupts lineage allocation between the inner cell mass and trophectoderm. Mechanistically, single-embryo RNA sequencing revealed that INO80 regulates multiple genes, which are important for lineage specification, tight junction assembly, and fluid accumulation. Consistent with the altered expression of key genes required for tight junction assembly, a permeability assay showed that paracellular sealing is defective in the trophectoderm epithelium of INO80 knockdown blastocysts. Importantly, aggregation of 8-cell embryos from the control and INO80 knockdown groups restores blastocyst development and lineage allocation via direct complementation of the defective trophectoderm epithelium. Taken together, these results demonstrate that INO80 promotes blastocyst development by regulating the expression of key genes required for lineage specification, tight junction assembly, and fluid accumulation.
2021, 42(5): 574-591.
doi: 10.24272/j.issn.2095-8137.2021.107
Amolops chunganensis is a species complex and reported widely from eastern, southern, and southwestern China. Based on molecular data of 19 populations of A. chunganensis sensu lato from China, including the population from Mt. Wuyi (type locality), we recognize A. chunganensis sensu stricto and provide an expanded description based on the topotypic specimens. Combining morphological and molecular data, we describe a new species, Amolops chaochin sp. nov. , from southwestern China, which was previously identified as A. chunganensis. The new species is distinguished from all other species in the A. monticola group by: (1) moderate body size, SVL 35.3−39.2 mm in males (n=7), and 50.5−54.4 mm in females (n=7); (2) distinct tympanum, larger than half of eye diameter; (3) small tooth-like projection on anteromedial edge of mandible; (4) circummarginal groove on all fingers; (5) white tubercles on dorsal side of posterior body in both sexes; (6) distinct tubercles on dorsal thigh and white spinose tubercles on dorsal tibia in both sexes; (7) white tubercles on posterior region of tympanum in males; (8) toe webbing reaching disk by dermal fringe on inner side of toe II; (9) vomerine teeth present; (10) transverse bands on dorsal limbs; (11) external vocal sacs present in males. We further reviewed the assignment of Amolops groups, with an overall revision of membership and diagnosis of all species groups.
2021, 42(5): 592-605.
doi: 10.24272/j.issn.2095-8137.2021.079
The large yellow croaker (Larimichthys crocea), which is an economically important mariculture fish in China, is often exposed to environmental hypoxia. Reactive oxygen species (ROS) homeostasis is essential for the maintenance of normal physiological conditions in an organism. Direct evidence that environmental hypoxia leads to ROS overproduction is scarce in marine fish. Furthermore, the sources of ROS overproduction in marine fish under hypoxic stress are poorly known. In this study, we investigated the effects of hypoxia on redox homeostasis in L. crocea and the impact of impaired redox homeostasis on fish. We first confirmed that hypoxia drove ROS production mainly via the mitochondrial electron transport chain and NADPH oxidase complex pathways in L. crocea and its cell line (large yellow croaker fry (LYCF) cells). We subsequently detected a marked increase in the antioxidant systems of the fish. However, imbalance between the pro-oxidation and antioxidation systems ultimately led to excessive ROS and oxidative stress. Cell viability showed a remarkable decrease while oxidative indicators, such as malondialdehyde, protein carbonylation, and 8-hydroxy-2 deoxyguanosine, showed a significant increase after hypoxia, accompanied by tissue damage. N-acetylcysteine (NAC) reduced ROS levels, alleviated oxidative damage, and improved cell viability in vitro. Appropriate uptake of ROS scavengers (e.g., NAC and elamipretide Szeto-Schiller-31) and inhibitors (e.g., apocynin, diphenylene iodonium, and 5-hydroxydecanoate) may be effective at overcoming hypoxic toxicity. Our findings highlight previously unstudied strategies of hypoxic toxicity resistance in marine fish.
2021, 42(5): 606-613.
doi: 10.24272/j.issn.2095-8137.2020.363
The genus Tropidophorus consists of small semi-aquatic lizards that dwell in lowland forest steams (Barbour, 1921 ; Bauer & Jackman, 2008 ). Here, we designate the neotype and re-describe T. guangxiensis Wen, 1992 based on newly collected topotypic specimens. We also describe a new subspecies from Xuefeng Mountain, Hongjiang County, Hunan Province, central South China. Based on two mitochondrial genes (12S rRNA and 16S rRNA), the phylogenetic position of T. guangxiensis is allocated for the first time. Additionally, our data strongly support that the new subspecies is phylogenetically closely related to T. g. guangxiensis. We also present a morphological identification key for known species and subspecies of Tropidophorus in China.
2021, 42(5): 614-619.
doi: 10.24272/j.issn.2095-8137.2021.117
Butterflies are diverse in virtually all aspects of their ontogeny, including morphology, life history, and behavior. However, the developmental regulatory mechanisms underlying the important phenotypic traits of butterflies at different developmental stages remain unknown. Here, we investigated the developmental regulatory profiles of butterflies based on transposase accessible chromatin sequencing (ATAC-seq) at three developmental stages in two representative species (Papilio xuthus and Kallima inachus). Results indicated that 15%–47% of open chromatin peaks appeared in associated genes located 3 kb upstream (i.e., promoter region) of their transcription start site (TSS). Comparative analysis of the different developmental stages indicated that chromatin accessibility is a dynamic process and associated genes with differentially accessible (DA) peaks show functions corresponding to their phenotypic traits. Interestingly, the black color pattern in P. xuthus 4th instar larvae may be attributed to promoter peak-related genes involved in the melanogenesis pathway. Furthermore, many longevity genes in 5th instar larvae and pupae showed open peaks 3 kb upstream of their TSS, which may contribute to the overwintering diapause observed in K. inachus adults. Combined with RNA-seq analysis, our data demonstrated that several genes enriched in the melanogenesis and longevity pathways also exhibit higher expression, confirming that the expression of genes may be closely related to their phenotypic traits. This study offers new insights into larval cuticle color and adult longevity in butterflies and provides a resource for investigating the developmental regulatory mechanisms underlying butterfly ontogeny.
2021, 42(5): 620-625.
doi: 10.24272/j.issn.2095-8137.2021.093
We describe a new species of the genus Hebius and provide evidence for the validity of H. septemlineatus comb. nov. . Morphological and molecular analyses of Hebius specimens collected in Yunnan Province, China, revealed three distinct lineages, namely the newly described Hebius weixiensis sp. nov. , as well as H. octolineatus (Boulenger, 1904), and H. septemlineatus comb. nov. (Schmidt 1925), which is removed from synonymy with H. octolineatus. Based on mitochondrial genealogy, Hebius weixiensis sp. nov. is sister to H. septemlineatus comb. nov. , while H. octolineatus is sister to H. bitaeniatus. The new species and H. septemlineatus comb. nov. showed considerable genetic divergence from their recognized congeners (uncorrected P-distance ≥3.9%). Furthermore, the new species and H. septemlineatus comb. nov. can be diagnosed from closely related congeners by a combination of pholidosis characters.
2021, 42(5): 626-632.
doi: 10.24272/j.issn.2095-8137.2021.080
Viruses can be transmitted from animals to humans (and vice versa) and across animal species. As such, host-virus interactions and transmission have attracted considerable attention. Non-human primates (NHPs), our closest evolutionary relatives, are susceptible to human viruses and certain pathogens are known to circulate between humans and NHPs. Here, we generated global statistics on virus infections in NHPs (VI-NHPs) based on a literature search and public data mining. In total, 140 NHP species from 12 families are reported to be infected by 186 DNA and RNA virus species, 68.8% of which are also found in humans, indicating high potential for crossing species boundaries. The top 10 NHP species with high centrality in the NHP-virus network include two great apes (Pan troglodytes, Pongo pygmaeus) and eight Old World monkeys (Macaca mulatta, M. fascicularis, M. leonina, Papio cynocephalus, Cercopithecus ascanius, C. erythrotis, Chlorocebus aethiops, and Allochrocebus lhoesti). Given the wide distribution of Old World monkeys and their frequent contact with humans, there is a high risk of virus circulation between humans and such species. Thus, we suggest recurring epidemiological surveillance of NHPs, specifically Old World monkeys that are in frequent contact with humans, and other effective measures to prevent potential circulation and transmission of viruses. Avoidance of false positives and sampling bias should also be a focus in future work.
2021, 42(5): 633-636.
doi: 10.24272/j.issn.2095-8137.2021.206
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent responsible for the global coronavirus disease 2019 (COVID-19) pandemic. Numerous studies have demonstrated that cardiovascular disease may affect COVID-19 progression. In the present study, we investigated the effect of hypertension on viral replication and COVID-19 progression using a hypertensive mouse model infected with SARS-CoV-2. Results revealed that SARS-CoV-2 replication was delayed in hypertensive mouse lungs. In contrast, SARS-CoV-2 replication in hypertensive mice treated with the antihypertensive drug captopril demonstrated similar virus replication as SARS-CoV-2-infected normotensive mice. Furthermore, antihypertensive treatment alleviated lung inflammation induced by SARS-CoV-2 replication (interleukin (IL)-1β up-regulation and increased immune cell infiltration). No differences in lung inflammation were observed between the SARS-CoV-2-infected normotensive mice and hypertensive mice. Our findings suggest that captopril treatment may alleviate COVID-19 progression but not affect viral replication.
2021, 42(5): 637-649.
doi: 10.24272/j.issn.2095-8137.2021.126
The insect brain is the central part of the neurosecretory system, which controls morphology, physiology, and behavior during the insect’s lifecycle. Lepidoptera are holometabolous insects, and their brains develop during the larval period and metamorphosis into the adult form. As the only fully domesticated insect, the Lepidoptera silkworm Bombyx mori experienced changes in larval brain morphology and certain behaviors during the domestication process. Hormonal regulation in insects is a key factor in multiple processes. However, how juvenile hormone (JH) signals regulate brain development in Lepidoptera species, especially in the larval stage, remains elusive. We recently identified the JH receptor Methoprene tolerant 1 (Met1) as a putative domestication gene. How artificial selection on Met1 impacts brain and behavioral domestication is another important issue addressing Darwin’s theory on domestication. Here, CRISPR/Cas9-mediated knockout of Bombyx Met1 caused developmental retardation in the brain, unlike precocious pupation of the cuticle. At the whole transcriptome level, the ecdysteroid (20-hydroxyecdysone, 20E) signaling and downstream pathways were overactivated in the mutant cuticle but not in the brain. Pathways related to cell proliferation and specialization processes, such as extracellular matrix (ECM)-receptor interaction and tyrosine metabolism pathways, were suppressed in the brain. Molecular evolutionary analysis and in vitro assay identified an amino acid replacement located in a novel motif under positive selection in B. mori, which decreased transcriptional binding activity. The B. mori MET1 protein showed a changed structure and dynamic features, as well as a weakened co-expression gene network, compared with B. mandarina. Based on comparative transcriptomic analyses, we proposed a pathway downstream of JH signaling (i.e., tyrosine metabolism pathway) that likely contributed to silkworm larval brain development and domestication and highlighted the importance of the biogenic amine system in larval evolution during silkworm domestication.
2021, 42(5): 650-659.
doi: 10.24272/j.issn.2095-8137.2021.195
Phosphatidylserine (PS) is distributed asymmetrically in the plasma membrane of eukaryotic cells. Phosphatidylserine flippase (P4-ATPase) transports PS from the outer leaflet of the lipid bilayer to the inner leaflet of the membrane to maintain PS asymmetry. The β subunit TMEM30A is indispensable for transport and proper function of P4-ATPase. Previous studies have shown that the ATP11A and TMEM30A complex is the molecular switch for myotube formation. However, the role of Tmem30a in skeletal muscle regeneration remains elusive. In the current study, Tmem30a was highly expressed in the tibialis anterior (TA) muscles of dystrophin-null (mdx) mice and BaCl2-induced muscle injury model mice. We generated a satellite cell (SC)-specific Tmem30a conditional knockout (cKO) mouse model to investigate the role of Tmem30a in skeletal muscle regeneration. The regenerative ability of cKO mice was evaluated by analyzing the number and diameter of regenerated SCs after the TA muscles were injured by BaCl2-injection. Compared to the control mice, the cKO mice showed decreased Pax7+ and MYH3+ SCs, indicating diminished SC proliferation, and decreased expression of muscular regulatory factors (MYOD and MYOG), suggesting impaired myoblast proliferation in skeletal muscle regeneration. Taken together, these results demonstrate the essential role of Tmem30a in skeletal muscle regeneration.
2021, 42(5): 660-665.
doi: 10.24272/j.issn.2095-8137.2021.236
2021, 42(5): 666-670.
doi: 10.24272/j.issn.2095-8137.2021.156
In a precautionary response to the current coronavirus (COVID-19) pandemic, China’s Ministries permanently banned eating and trading in terrestrial wild (non-livestock) animals on 24 February 2020, and extensively updated the list of Fauna under Special State Protection (LFSSP) in 2020 and 2021, in which pangolins (Manidae spp.) were upgraded to the highest protection level. Examining 509 pangolin prosecution records from China Judgements online prior to these changes (01/01/14–31/12/19), we identified that Guangdong, Guangxi and Yunnan Provinces were hotspots for trade in whole pangolins and their scales. Interrupting trade in these three principal southern provinces would substantially fragment the pangolin trade network and reduce supply of imports from other south-east Asian countries. In the context of the revised legislation and strategies intended to prevent wildlife trade, we conclude that targeting interventions at key trade nodes could significantly reduce illegal trade in pangolins, and that this approach could also be effective with other taxa.
2021, 42(5): 671-674.
doi: 10.24272/j.issn.2095-8137.2021.240
All extant species in the rodent family Spalacidae are subterranean and have evolved various traits for underground life. However, the phylogenomic relationships among its three subfamilies (Myospalacinae, Spalacinae, and Rhizomyinae) and the molecular basis underlying their adaptations to underground life remain poorly understood. Here, we inferred the phylogenomic relationships among these subfamilies based on de novo sequencing the genome of the hoary bamboo rat (Rhizomys pruinosus). Analyses showed that ~50% of the identified 11 028 one-to-one orthologous protein-coding genes and the concatenated sequences of these orthologous genes strongly supported a sister relationship between Myospalacinae and Rhizomyinae. The three subfamilies diversified from each other within ~2 million years. Compared with the non-subterranean controls with similar divergence dates, the spalacids shared more convergent genes with the African subterranean mole-rats at the genomic scale due to more rapid protein sequence evolution. Furthermore, these convergent genes were enriched in the functional categories of carboxylic acid transport, vascular morphogenesis, and response to oxidative stress, which are closely associated with adaptations to the hypoxic-hypercapnic underground environment. Our study presents a well-supported phylogenomic relationship among the three subfamilies of Spalacidae and offers new insights into the molecular adaptations of spalacids living underground.
The highly speciose gekkonid genus Cnemaspis Strauch, 1887 is polyphyletic, with three distantly related and geographically isolated clades from Africa, South Asia (SA), and Southeast Asia. At present, there are 85 known species within SA Cnemaspis, although the number continues to increase rapidly with focused surveys and rigorous taxonomic work. Recent studies have provided valuable insights into the diversity and evolutionary history of SA Cnemaspis; however, most of these studies lack sufficient sampling in the Western Ghats (WG), where the genus has its greatest diversity. We addressed this research gap by conducting extensive sampling across the WG and re-examining museum specimens, thus providing a systematic account of various extant Cnemaspis species along with their distribution and natural history. We described 12 new species and a southern WG endemic clade of SA Cnemaspis. Ten of the newly described species are endemic to the forests of the southern WG. We also identified 10 well-supported subclades that can be separated across morphological, geographic, and phylogenetic axes. A time-calibrated phylogeny and ancestral area reconstructions confirmed the Paleocene origin of SA Cnemaspis in the WG and provide insights into its evolutionary history and biogeography. The discovery of multiple endemic and deeply divergent lineages further highlights the evolutionary significance of the WG for lizards.
The Chinese tree shrew (Tupaia belangeri chinensis) is emerging as an important experimental animal in multiple fields of biomedical research. Comprehensive reference genome annotation for both mRNA and long non-coding RNA (lncRNA) is crucial for developing animal models using this species. In the current study, we collected a total of 234 high-quality RNA sequencing (RNA-seq) datasets and two long-read isoform sequencing (ISO-seq) datasets and improved the annotation of our previously assembled high-quality chromosome-level tree shrew genome. We obtained a total of 3 514 newly annotated coding genes and 50 576 lncRNA genes. We also characterized the tissue-specific expression patterns and alternative splicing patterns of mRNAs and lncRNAs and mapped the orthologous relationships among 11 mammalian species using the current annotated genome. We identified 144 tree shrew-specific gene families, including interleukin 6 (IL6) and STT3 oligosaccharyltransferase complex catalytic subunit B (STT3B), which underwent significant changes in size. Comparison of the overall expression patterns in tissues and pathways across four species (human, rhesus monkey, tree shrew, and mouse) indicated that tree shrews are more similar to primates than to mice at the tissue-transcriptome level. Notably, the newly annotated purine rich element binding protein A (PURA) gene and the STT3B gene family showed dysregulation upon viral infection. The updated version of the tree shrew genome annotation (KIZ version 3: TS_3.0) is available at http://www.treeshrewdb.org and provides an essential reference for basic and biomedical studies using tree shrew animal models.
The Chantecler chicken, a unique Canadian indigenous breed, is well adapted to extremely cold environments. However, its genetic characteristics have not been well studied. Here, we analyzed the whole genomes of 10 Chantecler chickens and 121 worldwide chickens, which indicated that Chantecler chickens were derived from commercial chickens and exhibit a high level of inbreeding. Based on a genome-wide scan, we identified two vital candidate regions containing ME3 and ZNF536, which are related to fat metabolism and nervous system in cold adaptation, respectively. We also found that the genetic mechanism of cold adaptation in Chantecler chickens differed from that of chickens from other cold regions, such as northern China. Our study indicated that specialized commercial chickens in the early 20th century contained sufficient genetic diversity to adapt to extreme cold environments over a very short time. These findings enrich our understanding of the adaptive potential of commercial species.
SOX9 (SRY-related HMG box gene 9) is an essential regulator of male sex determination and testis differentiation in many vertebrate species. However, the functional role of Sox9 in testis differentiation has not yet been identified in any reptilian species. Herein, Sox9 knockdown in the red-eared slider turtle (Trachemys scripta) embryos at a male-producing temperature led to complete male-to-female sex reversal, characterized by the formation of an ovary-like structure, disappearance of male marker AMH, and ectopic expression of ovarian regulator FOXL2, as well as a female distribution pattern of germ cells. Conversely, in-ovo overexpression of Sox9 at a female-producing temperature resulted in partial masculinization of putative female embryos, with the co-existence of AMH and FOXL2. Our study provides the first direct evidence that Sox9 is indispensable for testicular differentiation in a reptilian species, further confirming the conserved role of Sox9 in vertebrate sexual development.
We report a new species of the genus Micryletta from the montane evergreen forest in the Bidoup-Nui Ba National Park, Lam Dong Province, Langbian Plateau, southern Vietnam, based on molecular and morphological evidence. The new species is diagnosed by a combination of the following morphological characters: body size small (snout-vent length (SVL) 22.4 mm, single female); iris uniform black; snout nearly truncate in dorsal view, slightly rounded in profile; tibiotarsal articulation of adpressed limb reaching level of eye; dorsal surface smooth; supratympanic fold present, prominent; outer metatarsal tubercle absent; tips of toes very weakly dilated into small discs; finger webbing absent, toe webbing rudimentary; dorsal surfaces of head and body orange-red with small irregularly shaped dark-brown patches; dorsal surface of limbs pale dark brown with small reddish speckles; body flanks dark brown anteriorly fading to grayish brown posteriorly with brown spots in groin area; lateral sides of head immaculate blackish brown without white patches; coloration of ventral surfaces immaculate dark gray. The new species is divergent from all other congeners in 16S rRNA gene sequences (2.6%–5.8%). Following the IUCN Red List Categories and Criteria, we propose the new species be listed as Data Deficient (DD).
The small-eared shrew genus Cryptotis is the third largest in the family Soricidae and occurs in North, Central, and northern South America. In Mexico and Central and South America, most species inhabit geographically isolated moist, montane habitats at middle and high elevations in a typical sky-island pattern. The 49 recognized species have been partitioned into as many as six species groups based on morphological and molecular phylogenetic studies. The relationships among these species groups are poorly resolved, and their evolutionary histories, including migration patterns and locomotor adaptations, remain unclear. Herein, we provide a new phylogeny incorporating complete mitochondrial genomes (mitogenomes) and supermatrix approach. We compared different evolutionary scenarios using approximately unbiased (AU), Kishino-Hasegawa (KH), and Shimodaira-Hasegawa (SH) statistical tests. The phylogenetic hypothesis based on mitogenomes revealed novel relationships supporting a basal position for the Cryptotis parvus-group in the genus, and a close relationship between C. gracilis and one clade of the C. thomasi-group. The former relationship is consistent with the least derived humerus morphology and northern distribution of the species. The latter relationship implies multiple migrations between Central and South America. The lack of fine resolution for the species group relationships may be due partly to the lack of taxon sampling. In contrast, multi-approach analyses suggest that the unresolved relationships may be a result of rapid diversification during the early stages of Cryptotis evolution.
Oxygen is an essential molecule for animal respiration, growth, and survival. Unlike in terrestrial environments, contamination and climate change have led to the frequent occurrence of hypoxia in aquatic environments, thus impacting aquatic animal survival. However, the adaptative mechanisms underlying fish responses to environmental hypoxia remain largely unknown. Here, we used large yellow croaker (Larimichthys crocea) and large yellow croaker fry (LYCF) cells to investigate the roles of the Hif-1α/Hsf1/Hsp70 signaling pathway in the regulation of cellular redox homeostasis, and apoptosis. We confirmed that hypoxia induced the expression of Hif-1α, Hsf1, and Hsp70 in vivo and in vitro. Genetic Hsp70 knockdown/overexpression indicated that Hsp70 was required for maintaining redox homeostasis and resisting oxidative stress in LYCF cells under hypoxic stress. Hsp70 inhibited caspase-dependent intrinsic apoptosis by maintaining normal mitochondrial membrane potential, enhancing Bcl-2 mRNA and protein expression, inhibiting Bax and caspase3 mRNA expression, and suppressing caspase-3 and caspase-9 activation. Hsp70 suppressed caspase-independent intrinsic apoptosis by inhibiting nuclear translocation of apoptosis-inducing factor (AIF) and disturbed extrinsic apoptosis by inactivating caspase-8. Genetic knockdown/overexpression of Hif-1α and dual-luciferase reporter assay indicated that Hif-1α activated the Hsf1 DNA promoter and enhanced Hsf1 mRNA transcription. Hsf1 enhanced Hsp70 mRNA transcription in a similar manner. In summary, the Hif-1α/Hsf1/Hsp70 signaling pathway plays an important role in regulating redox homeostasis and anti-apoptosis in L. crocea under hypoxic stress.
The pygmy marmoset, the smallest of the anthropoid primates, has a broad distribution in Western Amazonia. Recent studies using molecular and morphological data have identified two distinct species separated by the Napo and Solimões-Amazonas rivers. However, reconciling this new biological evidence with current taxonomy, i.e., two subspecies, Cebuella pygmaea pygmaea (Spix, 1823) and Cebuella pygmaea niveiventris (Lönnberg, 1940), was problematic given the uncertainty as to whether Spix’s pygmy marmoset (Cebuella pygmaea pygmaea) was collected north or south of the Napo and Solimões-Amazonas rivers, making it unclear to which of the two newly revealed species the name pygmaea would apply. Here, we present the first molecular data from Spix’s type specimen of Cebuella pygmaea, as well as novel mitochondrial genomes from modern pygmy marmosets sampled near the type locality (Tabatinga) on both sides of the river. With these data, we can confirm the correct names of the two species identified, i.e., C. pygmaea for animals north of the Napo and Solimões-Amazonas rivers and C. niveiventris for animals south of these two rivers. Phylogenetic analyses of the novel genetic data placed into the context of cytochrome b gene sequences from across the range of pygmy marmosets further led us to re-evaluate the geographical distribution for the two Cebuella species. We dated the split of these two species to 2.54 million years ago. We discuss additional, more recent, subdivisions within each lineage, as well as potential contact zones between the two species in the headwaters of these rivers.
Salamanders are unique among tetrapods in their ability to regenerate the limbs throughout life. Like other poikilothermic amphibians, salamanders also show a remarkable capacity to survive long periods of starvation. Whether the physiological reserves necessary for tissue regeneration are preserved or sacrificed in starved salamanders is unknown. In the current study, we maintained Iberian ribbed newts (Pleurodeles waltl) under extreme physiological stress to assess the extent of regeneration and identify the molecular and cellular changes that may occur under such conditions. After 19 months of complete food deprivation, the animals exhibited extensive morphological and physiological adaptations but remained behaviorally active and vigilant. Autophagy was elevated in different tissues and the transformed gut microbiota indicated remodeling of the intestinal tract related to autophagy. Upon limb amputation in animals starved for 21 months, regeneration proceeded with progenitor cell proliferation and migration, leading to limb blastema formation. However, limb outgrowth and patterning were substantially attenuated. Blockage of autophagy inhibited cell proliferation and blastema formation in starved animals, but not in fed animals. Hence, tissue autophagy and the regenerative response were tightly coupled only when animals were under stress. Our results demonstrate that under adverse conditions, salamanders can exploit alternative strategies to secure blastema formation for limb regeneration.
Vol 42, No 5 (18 September 2021)
Indexed by SCI-E
2020 影响因子 4.56
5/175 Zoology (Q1)
2021 Journal Citation Reports®
双月刊, 始于 1980
主编: Yong-Gang Yao
ISSN 2095-8137
CN 53-1229/Q
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