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Introduction to the AMS Symposium “Phylogenomics of Mollusks,” 82nd Annual Meeting of the American Malacological Society AMS研讨会“软体动物系统基因组学”介绍,美国马六甲学会第82届年会
IF 0.5 4区 生物学 Q4 MARINE & FRESHWATER BIOLOGY Pub Date : 2017-05-22 DOI: 10.4003/006.035.0110
K. Kocot
70 If you search the NCBI nucleotide database for “Mollusca” and sort the entries by date modifi ed, the fi rst sequence to appear in the list is a 119 bp sequence from the 5.8S rRNA gene from the snail Helix pomatia Linnaeus, 1758, which was published by Fang and colleagues in 1982. Since then there has been, to put it lightly, signifi cant growth in the amount of available molecular sequence data from molluscs (3,371,221 sequences in the NCBI nucleotide database alone at the time of writing this manuscript). This growth has been punctuated by advances in DNA sequencing technology. I was born around the time that 5.8S sequence was uploaded and I’ve only ever seen discarded relics of the labor-intensive denaturing polyacrylamide-urea gel and autoradiography equipment that were used to generate it. When I began my Ph.D. dissertation research in 2007, my fi rst chapter was aimed at amplifying nuclear protein-coding genes via PCR from cDNA and sequencing them using Sanger sequencing on a capillary sequencer. We performed our own capillary sequencing and, although I imagine it was a breeze compared to running sequencing gels, every successful reaction felt like a personal victory. About a year after starting my dissertation research and before I was able to collect enough data using this approach to have anything remotely worthy of a publication, Roche 454 pyrosequencing came out and it became clear that it would be faster to start all over using this “cutting-edge” technology. In less than ten years, we have watched Roche 454 pyrosequencing rise and fall, Illumina sequencing soar in popularity and capability, and the cost of sequencing a human genome drop two orders of magnitude (Muir et al. 2016). Today, there are instruments that can generate about one billion sequences slightly longer than the aforementioned 5.8S rRNA sequence in 3 days for about USD $1,000 (Illumina 2016). Recent leaps forward in high-throughput DNA sequencing technology have made it feasible for single laboratories working on non-model organisms to conduct whole genome sequencing, sequence numerous transcriptomes, conduct targetcapture approaches to sequence pools of DNA enriched for genes of interest, etc. These exciting advances in highthroughput sequencing have led to a number of high profi le papers dealing with diverse aspects molluscan biology (e.g., Kocot et al. 2011, Smith et al. 2011, 2013, Zhang et al. 2012, Introduction to the AMS symposium “Phylogenomics of Mollusks,” 82 annual meeting of the American Malacological Society
70如果你在NCBI核苷酸数据库中搜索“Mollusca”,并根据修改的日期对条目进行排序,那么列表中出现的第一个序列是一个119 bp的序列,来自1758年由Fang及其同事发表的蜗牛Helix pomatia Linnaeus的5.8S rRNA基因。从那时起,简单地说,软体动物的可用分子序列数据数量显著增加(在撰写本文时,仅NCBI核苷酸数据库中就有3371221个序列)。这种增长被DNA测序技术的进步所打断。我出生在5.8S序列上传的时候,我只见过劳动密集型变性聚丙烯酰胺尿素凝胶和用于生成它的放射自显影设备的废弃遗迹。2007年,当我开始博士论文研究时,我的第一章旨在通过PCR从cDNA中扩增核蛋白编码基因,并在毛细管测序仪上使用Sanger测序对其进行测序。我们进行了自己的毛细管测序,尽管我认为与运行测序凝胶相比,这是一件轻而易举的事,但每一次成功的反应都感觉像是个人的胜利。在我开始论文研究大约一年后,在我能够使用这种方法收集足够的数据来发表任何有价值的论文之前,Roche 454焦磷酸测序问世了,很明显,全面使用这种“尖端”技术会更快。在不到十年的时间里,我们目睹了罗氏454焦磷酸测序的兴衰,Illumina测序的普及率和能力飙升,人类基因组测序的成本下降了两个数量级(Muir等人,2016)。如今,有一些仪器可以在3天内产生比上述5.8S rRNA序列略长的约10亿个序列,价格约为1000美元(Illumina 2016)。最近高通量DNA测序技术的飞跃使研究非模式生物的单个实验室能够进行全基因组测序、对大量转录组进行测序、对富含感兴趣基因的DNA序列库进行靶向捕获方法等。高通量测序的这些令人兴奋的进展导致了许多涉及软体动物生物学各个方面的高收益论文(例如,Kocot等人2011,Smith等人20112013,Zhang等人2012,AMS研讨会“软体动物的系统基因组学”简介,82美国马六甲学会年会
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引用次数: 0
Description of Pyropelta elongata sp. nov. (Gastropoda, Pyropeltidae) from a Methane Seep Area in the South China Sea. 南海甲烷渗漏区长叶火螺(腹足目,火螺科)描述。
IF 0.5 4区 生物学 Q4 MARINE & FRESHWATER BIOLOGY Pub Date : 2017-05-22 DOI: 10.4003/006.035.0106
Shuqian Zhang, Suping Zhang
Abstract: The genus Pyropelta McLean & Haszprunar, 1987 is exclusively restricted to deep-sea chemosynthesis-based environments, that range from the Western and Eastern Pacific to West Africa. In the present study, a new species, Pyropelta elongata sp. nov., collected from a methane seep area in South China Sea is described and illustrated. The generic assignation is mainly based on shell and radula characters. Pyropelta elongata sp. nov. is characterized by relatively large, elongate shell with a low profile and has a radula formula of (ca. 20)+5+1+5+(ca. 20). These features can distinguish the new species from other congeners.
摘要/ Abstract摘要:Pyropelta McLean & Haszprunar, 1987属仅局限于以化学合成为基础的深海环境,范围从西太平洋和东太平洋到西非。本文报道了在南海甲烷渗漏区发现的一种新种——长形焦蕨(Pyropelta elongata sp. nov.)。通用赋值主要是基于壳字符和radula字符。长叶火椒(Pyropelta elongata sp. 11 .)的特征是相对较大的、细长的、低轮廓的壳,其半径公式为(约20)+5+1+5+(约20)。20)。这些特征可以将新物种与其他同类区分开来。
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引用次数: 5
Terrestrial Gastropods of South Fox Island, Leelanau Co., Michigan, U.S.A. 美国密歇根州利拉瑙公司南福克斯岛陆生腹足类动物
IF 0.5 4区 生物学 Q4 MARINE & FRESHWATER BIOLOGY Pub Date : 2017-05-22 DOI: 10.4003/006.035.0105
T. Pearce, Christen M. Drescher
Abstract: Despite the existence of more than 565 islands in the upper three United States Great Lakes, land snails have been reported from only about 1% of them. This first publication about land snails of any island in eastern Lake Michigan reports on the 38 species (10,162 individuals) of land snails we found on South Fox Island. We examined leaf litter samples collected from 14 localities on South Fox Island in the years 1993 and 1997. We provide identification notes and habitat notes (beech-maple forest, cedar forest, meadow) for each of the species. The number of species, 38, on South Fox Island is about average when compared to the number of species from six other islands in the upper three Great Lakes that have had comparable sampling intensity. We report the northernmost published localities for two minute snails, Carychium nannodes G.H. Clapp, 1905 and Striatura meridionalis (Pilsbry and Ferriss, 1906), and one of the northernmost localities for the minute snail Guppya sterkii (Dall, 1888). The absence of two larger species that are present on the adjacent mainland is consistent with our hypothesis that the sequences of glacial history, island development, and northward snail colonization have influenced modern distributions of snails.
摘要/ Abstract摘要:美国五大湖区北部有超过565个岛屿,但据报道仅有约1%的岛屿有蜗牛。这是我们在南福克斯岛发现的38种(10,162只)陆地蜗牛的第一篇关于密歇根湖东部任何岛屿的陆地蜗牛的出版物。研究了1993年和1997年在南福克斯岛14个地点采集的凋落叶样。我们为每个物种提供了鉴定笔记和栖息地笔记(山毛榉枫林,雪松林,草甸)。南福克斯岛的物种数量为38种,与三大湖上游其他六个具有可比采样强度的岛屿的物种数量相比,南福克斯岛的物种数量约为平均水平。我们报道了两种微小蜗牛Carychium nannodes G.H. Clapp(1905年)和Striatura meridionalis (Pilsbry和Ferriss, 1906年)的最北端位置,以及微小蜗牛Guppya sterkii (Dall, 1888年)的最北端位置之一。邻近大陆上没有两个较大的物种,这与我们的假设是一致的,即冰川历史、岛屿发展和蜗牛向北迁移的顺序影响了蜗牛的现代分布。
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引用次数: 1
AMS 2017 Meeting Announcement AMS 2017会议公告
IF 0.5 4区 生物学 Q4 MARINE & FRESHWATER BIOLOGY Pub Date : 2017-05-22 DOI: 10.4003/006.035.0113
L. Shea
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引用次数: 0
Insights into the Systematics, Phylogeny, and Evolution of Cladobranchia (Gastropoda: Heterobranchia). 分支鳃亚门的系统学、系统发育和进化研究(腹足目:异鳃亚门)。
IF 0.5 4区 生物学 Q4 MARINE & FRESHWATER BIOLOGY Pub Date : 2017-05-22 DOI: 10.4003/006.035.0111
Jessica A. Goodheart
Abstract: Cladobranchia is a diverse clade of nudibranch gastropods, with ∼1,000 coastal (benthic) and off shore (pelagic) marine species. Their diversity may be tied to dietary specialization and the evolution of remarkable adaptations that are rare among animals, such as the sequestration of cnidarian nematocysts. Due to the deep divergences within Cladobranchia, and other higher-order taxa within Mollusca, phylogenetic analyses based on morphology or a few genes have been unable to resolve relationships within these clades with high support. The introduction of high-throughput sequencing technologies, however, has provided the opportunity to collect large genomic data sets, which have proven useful in resolving relationships within molluscs, as in other metazoan groups. As sequencing costs decrease, it has become easier to collect ever larger data sets in an attempt to resolve relationships within more recently diverged groups, such as Cladobranchia. The phyly and relationships of the three main groups within Cladobranchia (Arminida, Dendronotida, and Aeolidida) have been difficult to determine, primarily due to the rapid evolution of mtDNA and rDNA genes analyzed in traditional molecular phylogenetic studies. In this review, I discuss the systematics of Cladobranchia in regards to morphological data, molecular analyses with one or a few genes, and address the impact of genomic data. I then contend that the supported phylogenetic hypotheses provided by high-throughput sequencing data will provide a better framework for studying taxonomy and character evolution within Cladobranchia, as these data provide strong support for Cladobranchia itself, as well as the nested subclades within it. Although it is important to note that a broader taxon sampling is still needed for genomic data, it is clear that utilizing these data has provided the most-well-supported phylogenetic hypotheses of Cladobranchia to date. In doing so, these genomic data have challenged well-established relationships, including the monophyly of Facelinidae and inclusion of Tritoniidae in Dendronotida, and resolved the position of taxa that have been traditionally quite difficult to place, including Melibe Rang, 1829 and the families Proctonotidae and Dironidae. Finally, these genomic data provide a much stronger phylogenetic framework for studying character evolution within Cladobranchia, including the evolution of nematocyst sequestration, one of the quintessential characters in this clade.
摘要:枝鳃亚目是裸鳃腹足类的一个多样化分支,有约1000种沿海(底栖)和近海(远洋)海洋物种。它们的多样性可能与饮食的特殊性和动物中罕见的显著适应的进化有关,例如刺线虫的隔离。由于枝叉亚门和软体动物门内其他高阶分类群之间的深刻分歧,基于形态学或少数基因的系统发育分析无法在高支持率下解决这些分支内的关系。然而,高通量测序技术的引入为收集大型基因组数据集提供了机会,这些数据集已被证明在解决软体动物内部的关系方面很有用,就像在其他后生动物群体中一样。随着测序成本的降低,收集越来越大的数据集变得越来越容易,以试图解决最近分化的群体内的关系,如分支杆菌。分支杆菌内三个主要类群(Arminida、Dendronotida和Aeolidida)的门和关系一直很难确定,主要是由于传统分子系统发育研究中分析的mtDNA和rDNA基因的快速进化。在这篇综述中,我从形态学数据、一个或几个基因的分子分析以及基因组数据的影响等方面讨论了分支杆菌的系统学。然后,我认为,高通量测序数据提供的系统发育假说将为研究分支杆菌的分类学和特征进化提供更好的框架,因为这些数据为分支杆菌本身及其嵌套的子支提供了强有力的支持。尽管重要的是要注意,基因组数据仍然需要更广泛的分类单元采样,但很明显,利用这些数据提供了迄今为止最受支持的分支杆菌系统发育假说。在这样做的过程中,这些基因组数据挑战了已建立的关系,包括Facelinidae的单系性和Tritonidae在Dendronotida中的包含,并解决了传统上很难定位的分类群的位置,包括Melibe Rang,1829以及Proctonotidae和Dironidae科。最后,这些基因组数据为研究分支杆菌内的特征进化提供了一个更强的系统发育框架,包括该分支中的典型特征之一线虫囊隔离的进化。
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引用次数: 13
In Memoriam: William K. Emerson (1925–2016), with a List of His Publications and Taxa 《追忆似水年华》:威廉·K·爱默生(1925–2016),及其出版物和税收清单
IF 0.5 4区 生物学 Q4 MARINE & FRESHWATER BIOLOGY Pub Date : 2017-05-22 DOI: 10.4003/006.035.0112
P. Mikkelsen, N. Landman
82 On October 19, 2016, malacology lost one of its most respected senior members. William “Bill” Emerson died in New York City at the age of 91, following a 50-year career mainly spent at the American Museum of Natural History. It was there that he built a legacy of research, curation, and public service, including supervising world-class exhibitions and serving as President of most of this country’s major malacological societies. His accolades include honorary life memberships and other tributes in recognition of his career achievements. In memoriam: William K. Emerson (1925–2016), with a list of his publications and taxa
2016年10月19日,malacology失去了一位最受尊敬的资深成员。威廉·“比尔”·爱默生在纽约去世,享年91岁,他在美国自然历史博物馆工作了50年。正是在那里,他建立了研究、策展和公共服务的遗产,包括监督世界级的展览,并担任这个国家大多数主要线虫学学会的主席。他的荣誉包括终身荣誉会员和其他荣誉,以表彰他的职业成就。纪念:威廉·k·爱默生(1925-2016),以及他的出版物和分类群清单
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引用次数: 2
Urban Ecology of Invasive Giant African Snail Achatina fulica (Férussac) (Gastropoda: Achatinidae) on its First Recorded Sites in the Ecuadorian Amazon 厄瓜多尔亚马逊地区首次记录的入侵非洲大蜗牛Achatina fulica(Férussac)(腹足目:Achatidae)的城市生态学
IF 0.5 4区 生物学 Q4 MARINE & FRESHWATER BIOLOGY Pub Date : 2017-05-22 DOI: 10.4003/006.035.0108
B. Gołdyn, Ł. Kaczmarek, M. Roszkowska, Pedro Ríos Guayasamín, Z. Książkiewicz-Parulska, H. Cerda
Abstract: We are reporting the first locality of invasive giant African snail, Achatina (Lissachatina) fulica (Férussac, 1821) in the Ecuadorian Amazon. It was found present in 32 out of 50 urban sites studied. The abundance where present was relatively high when compared to literature from other parts of the world. The snails were found in aggregations, usually foraging — most often on dogs' feces. Statistical analysis suggests a preference toward this source of alimentation. This is the first report of such preference in this species, which is highly significant considering the possible implications. Besides the threat posed by an invasive species to the invaluable ecosystems of the Amazon, the pathogens transferred by A. fulica combined with a high abundance of the species in an urban environment and its food preferences may constitute an important health hazard for local human populations.
摘要:我们报道了入侵性巨型非洲蜗牛Achatina(Lissachatina)fulica(Férussac,1821)在厄瓜多尔亚马逊的第一个地方。在所研究的50个城市遗址中,有32个发现了这种病毒。与世界其他地区的文献相比,现有文献的丰度相对较高。蜗牛聚集在一起,通常觅食——最常见的是在狗的粪便上。统计分析表明,人们更喜欢这种营养来源。这是第一份关于该物种这种偏好的报告,考虑到可能的影响,这是非常重要的。除了入侵物种对亚马逊宝贵的生态系统构成的威胁外,黄曲霉转移的病原体,加上城市环境中该物种的高丰度及其食物偏好,可能对当地人口的健康构成重要危害。
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引用次数: 14
Descriptions of Nautilus pompilius Linnaeus, 1758 from the Type Area, Ambon, Molucca Islands, and from Sumbawa - Lombok Islands, Indonesia 鹦鹉螺pompilius Linnaeus的描述,1758年,来自摩鹿加群岛安汶的类型区和印度尼西亚松巴哇-龙目岛
IF 0.5 4区 生物学 Q4 MARINE & FRESHWATER BIOLOGY Pub Date : 2017-05-22 DOI: 10.4003/006.035.0102
W. Saunders, R. Mapes, M. White, L. Hastie, K. Yaqin
Abstract: The taxonomic history of Nautilus pompilius Linnaeus, 1758, the most widely distributed species of Nautilus Linnaeus, 1758, is complex, mostly owing to the antiquity of the earliest description by the naturalist Rumphius (Rumpf) in 1705. His account of its habits and illustrations of soft anatomy of specimens from Ambon, Molucca Islands, Indonesia were cited by Linnaeus in his description of N. pompilius. Nevertheless, there is almost no information on Nautilus in Indonesia. Live-caught animals (n = 44) from 150–400 m depth off Ambon provide the first morphologic and genetic details on Nautilus pompilius from the type region, including a recently proposed neotype for the type species. An additional sample (n = 62) obtained from the Sumbawa-Lombok Islands area, Indonesia, 1,500km to the southeast appears identical to those from Ambon. These populations have the largest known mature shells (mean ∼198mm diameter, ∼1,160 g shell plus body weight) of any of the numerous Indo-Pacific occurrences of Nautilus pompilius s.l. presently assigned to this species. Aside from size, few major phenotypic aspects differ from other populations of the species throughout its broad Indo-Pacific range. Data from two mitochondrial DNA gene regions identified a strongly supported clade comprising Ambon, Sumbawa, and Philippines N. pompilius s.s. These new data provide a baseline for evaluating genetic, phenotypic and geographic variation in the broadly distributed species N. pompilius s.l., as well as for establishing taxonomic relationships in populations of living Nautilus, including N. pompilius pompilius Linnaeus, 1758.
摘要:1758年林奈鹦鹉螺(Nautilus Linnaeus, 1758)是分布最广的鹦鹉螺种,其分类学历史复杂,主要是由于1705年博物学家Rumphius (Rumpf)最早对其进行描述。他对其习性的描述和印度尼西亚摩鹿加群岛安汶岛标本的软解剖插图被林奈引用在他对庞皮留斯的描述中。然而,在印度尼西亚几乎没有关于鹦鹉螺的资料。在Ambon海域150-400米深度的活捕动物(n = 44)提供了来自模式区域的鹦鹉螺的第一个形态和遗传细节,包括最近提出的模式物种的新类型。另一个样本(n = 62)来自印度尼西亚松巴瓦-龙目岛地区,位于东南部1500公里处,与安汶岛的样本相同。这些种群拥有已知最大的成熟壳(平均直径约198毫米,壳加体重约1160克),是目前属于该物种的众多印度太平洋鹦鹉螺中最大的。除了大小之外,在其广阔的印度太平洋范围内,几乎没有主要的表型方面与其他种群不同。来自两个线粒体DNA基因区域的数据确定了一个强有力支持的进化支,包括Ambon、Sumbawa和菲律宾的N. pompilius s.s。这些新数据为评估广泛分布的N. pompilius s.l的遗传、表型和地理变异提供了基线,并为建立包括N. pompilius Linnaeus, 1758在内的现存鹦鹉螺种群的分类关系提供了基线。
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引用次数: 5
Sexual Differentiation and size at First Maturity of the Mussel Choromytilus chorus (Molina, 1782) (Mollusca, Bivalvia) in Northern Chile. 智利北部贻贝Choromytilus chorus (Molina, 1782)(软体动物,Bivalvia)首次成熟时的性别分化和大小。
IF 0.5 4区 生物学 Q4 MARINE & FRESHWATER BIOLOGY Pub Date : 2017-05-22 DOI: 10.4003/006.035.0104
Maryori Ruiz-Velásquez, M. Zapata, M. T. González, Daniela Ordenes, Mauricio Escalona
Abstract: The mussel Choromytilus chorus (Molina, 1782) is a commercially and ecologically important bivalve, which is extensively distributed along the Chilean coast (20°S–54°S). However, there are no previous studies regarding the reproductive aspects of this species in the northern part of its range. Mussels were collected at Caleta Errázuriz, along the Antofagasta coast (ca. 24°S), between December 2014 and June 2015. A total of 1620 individuals were examined using histological techniques and macroscopic visual inspection. Seventeen size categories, which included individuals from 5 mm to 100 mm in length, were analyzed. The size at the onset of sexual differentiation and the size at first sexual maturity (50% mature individuals) were determined. Males comprised 49% of the total sample, and 51% were females. Mussels from 5–22 mm in valve length were undifferentiated and from 22–24 mm were sexually differentiated. The size at first sexual maturity was recorded as 38–40 mm. In vitro fertilization trials demonstrated that sexually differentiated individuals were able to produce viable gametes. The biological parameters analyzed for C. chorus were similar to those recorded for populations of this bivalve from the southern latitudes. However, the lower number of eggs per female and the smaller egg size suggests that the population parameters may be different for C. chorus between the northern and southern latitudes.
摘要:贻贝Choromytilus chorus (Molina, 1782)是一种具有重要商业价值和生态价值的双壳类动物,广泛分布于智利沿海(20°S - 54°S)。然而,在其分布范围的北部地区,尚无关于该物种生殖方面的研究。贻贝于2014年12月至2015年6月在Antofagasta海岸(约24°S)的卡莱塔Errázuriz收集。采用组织学技术和肉眼检查共对1620例个体进行了检查。分析了17个尺寸类别,包括个体从5毫米到100毫米的长度。测定了性分化开始时的大小和初次性成熟时(50%成熟个体)的大小。男性占总样本的49%,女性占51%。阀长在5 ~ 22mm的贻贝未分化,阀长在22 ~ 24mm的贻贝有性分化。初性成熟时大小为38 ~ 40 mm。体外受精试验表明,性别分化的个体能够产生可存活的配子。分析的生物参数与南纬双壳类种群的生物学参数相似。然而,每只雌鸟的卵数较低,卵的大小较小,这表明南北纬地区的种群参数可能不同。
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引用次数: 5
Shell Fouling and Behavior of the Caribbean Predatory Gastropod Cassis tuberosa 加勒比捕食性腹足类晚香菜的外壳污染和行为
IF 0.5 4区 生物学 Q4 MARINE & FRESHWATER BIOLOGY Pub Date : 2017-05-22 DOI: 10.4003/006.035.0107
Tobias B. Grun, J. Nebelsick
Abstract: The gastropod Cassis tuberosa (Linnaeus, 1758) usually lives in and on soft sediments and sea grass meadows. This carnivorous snail is primarily a semi-epifaunal and nocturnal hunter that, during daytime, rests burrowed in sediments. Around the Bahamian island of San Salvador, C. tuberosa has extended its behavior from nocturnal to metaturnal; feeding both night and day. This modification also involves further changes in behavior as an individual was observed resting epifaunally between rocks during the day even though this substrate was surrounded by soft bottoms. Epifaunal Cassis specimens are entirely encrusted primarily by coralline algae, but also by various green algae accompanied by vagile snails and crabs. The high degree of encrustation suggests that these snails do not remain burrowed for long periods of time. Cassis has thus extended its resting behavior from a semi-endofaunal to an epifaunal mode of life. The fouled shells also function as mobile benthic substrates for various organisms.
摘要:晚香菜腹足目(林奈,1758)通常生活在柔软的沉积物和海草草地上。这种食肉蜗牛主要是半表目动物和夜间猎人,白天在沉积物中休息。在巴哈马的圣萨尔瓦多岛周围,C.tuberosa已经将其行为从夜间扩展到了夜间;夜以继日地进食。这种改变还涉及行为的进一步变化,因为观察到一个人在白天在岩石之间的动物表面休息,尽管这个基底被柔软的底部包围。表动物卡西斯标本主要由珊瑚藻包裹,但也有各种绿藻伴随着迷走蜗牛和螃蟹。高度的外壳表明,这些蜗牛不会长时间呆在洞穴里。因此,卡西斯将其休息行为从半动物区系扩展到动物区系外的生活模式。被污染的贝壳也可以作为各种生物的移动海底基质。
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引用次数: 4
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American Malacological Bulletin
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