383 resultados para COI


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用六个线粒体基因片段序列数据,对称猴属的分子系统发育关系进行了分析。8种称猴:台湾猴,北平顶猴,藏酋猴,熊猴,红面猴,J厦河猴,狮尾猴和食蟹猴共40个样本用于本研究。结合从GenBank里下载的雯猴的相应序列,用拂拂作为外群构建了系统发育树。由于六个目的片段均为线粒体基因片段,缺乏重组且作为单一位点遗传,因此我们将六个数据集合并为一个数据集进行分析。我们获得了比前人置信度更高的线粒体系统树。除了红面猴,我们的结果支持Delson(1980)的分组。与前人研究结果一致,红面猴与食蟹猴组成员关系较近(尤其是食蟹猴)。恒河猴(相对于台湾猴),熊猴(相对于藏酋猴)和北平顶猴(相对于狮尾猴)都形成了并系。通过线粒体控制区序列和20个微卫星位点对14个恒河猴地理群体的群体结构进行了研究。微卫星数据和线粒体控制区数据均显示恒河猴有较高的遗传多样度。线粒体数据表明各地区的恒河猴群体间的差异显著大于微卫星数据显示的结果。也就是说,基于微卫星数据所得到的群体间基因流远大于基于线粒体数据所得到的群体间基因流。两种分子标记所得到的结果差异应归因为雌性恒河猴的归家冲动和雄性恒河猴的扩散。线粒体数据显示所有恒河猴群体近期没有发生过快速扩张。微卫星数据显示大部分恒河猴群体近期没有经历过瓶颈效应。恒河猴是分布较广的非人灵长类动物,但它的地理差异研究一直颇有争论且不足以划分其亚种。我们对采自包括印度、越南、缅甸和18个中国地区在内的21个地区共35个恒河猴样品的四个线粒体基因片段(COI,Cofl,COlll和12srRNA)进行了研究。食蟹猴、红面猴、台湾猴和史猴的相应序列作为外群。大约长为100bp的序列用于构建最大似然树和贝叶斯树。与前人结果一致(彭燕章等,1993;蒋学龙等,1995;Groves,2001),西部恒河猴(印度).相当于M.m.mulatta。根据王应祥(2003)的分类,我们的东部恒河猴可分为四组:M.最早分离出来且一个来自缅甸的恒河猴位于该组基部;M.m.brachyurus和M.m.littoralis组成一个大枝,这个大枝与M.m,lasiotus构成姐妹群。

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急流牙甲族Sperchopsini属于鞘翅目Coleoptera牙甲科Hydrophilidae的水牙甲亚科Hydrophilinae,共包括五属,即水龟虫属 Hydrocassis、革牙甲属 Ametor、Sperchopsis、Anticura、Cylomissus,世界共计有25种,我国分布有2属18个种。 本文回顾了水甲虫、牙甲科以及急流牙甲族的研究简史;综述了水甲虫在分类学、保护生物学、形态学、遗传学、分子生物学等方面研究进展,总结了水甲虫与生态因子的关系以及水甲虫作为生态系统健康指示物的可行性。还简要介绍了昆虫分子系统学,以及细胞色素氧化酶亚基I(COI)和rDNA内部转录间隔区(ITS)在昆虫学研究中的应用。 通过对收集到的700余号急流牙甲族的标本观察和分类研究,发现了一新种(内蒙水龟甲Hydrocassis mongolica sp.nov.)。并且对已知全部种类重新作了描述,特别是长茎革牙甲 Ametor elongatus雄性外生殖器部分,首次对7个种类(长茎革牙甲 Ametor elongatus、粗革牙甲 Ametor scabrosus、帝水龟甲 Hydrocassis imperialis、伪舟水龟甲Hydrocassis pesudoscapha、条纹水龟甲Hydrocassis scapulata、舟水龟甲 Hydrocassi scapha、四川水龟甲Hydrocassis sichuana)的雌性个体进行了描述。编制了急流牙甲族的分属、分种检索表。 采用支序分类学的方法对中国急流牙甲族种类的系统发育关系进行探讨。结果显示革牙甲属内的A. latus、A. rudesculptus、A. rugosus 及A. scabrosus 构成单系(不包括A. elongates),支持皱革牙甲A. rugosus和A. latus属于革牙甲属。水龟虫属内H. anhuiensis、H. baoshanensis、H. lacustris、H. pseudoscapha、H. scaphoides、H. scapulata、H. sichuana、H. taiwana、H. uncinata、H. schillhammeri构成一个单系。水龟虫属包括两大类群,一类群包括H. anhuiensis、H. lacustris、H. scapulata、H. sichuana 、H. taiwana,另一类群包括H. baoshanensis、H. scaphoides、 H. schillhammeri 、H. uncinata。两类群的不同之处在于后一类群的阳基侧突上有一齿状凸起。 测序了H. scapulata、H. sichuana和H. mongolica雌雄各一个个体的COI和ITS2序列。全部的COI基因序列为828bp,编码275个氨基酸。H. scapulata的ITS2序列有446bp,H. sichuana的有456bp,H. mongolica的有455bp。用MEGA 3.1计算比对距离(pairwise distances)和构建邻近系统树。结果显示对于COI,种内的比对距离分别是0(H. scapulata)、0.008(H. mongolica)、0.004(H. sichuana),种间的比对距离在0.024-0.045之间。对于ITS2,种内的比对距离分别为0.005(H. scapulata)、0(H. mongolica)、0.007(H. sichuana),种间的比对距离在0.028-0.047之间。H. sichuana和新种间的比对距离在0.024-0.037(COI)和0.044(ITS2)。比对距离揭示出种内低于0.008,种间在0.024-1.078之间。因而,它们之间应该是种间关系而不是种内的关系。COI数据集和ITS2数据集所构建的系统树存在一定的差异,前者显示四川水龟甲和条纹水龟甲是姐妹种,后者显示新种和条纹水龟甲是姐妹种。总之,在内蒙古自治区发现的为一新的物种。

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小鲵属为亚洲特有的有尾两栖类,是小鲵科之模式属。现记载小鲵属动物有29种,占全科物种数一半以上(Frost, 2007),为小鲵科第一大属。该属分布跨越古北界和东洋界,分布于中国、朝鲜、韩国、日本等地区,其系统学研究一直以来颇为中外学者所关注。澄清该属的物种分类问题,阐明其种间的系统发育关系对整个小鲵科的系统演化与分布格局关系的研究具有关键性意义。 本论文以中国及周边地区的小鲵属物种为主要对象,主要利用分子生物学实验与生物信息学途径相结合的手段,运用支序系统学与分子进化生物学理论及分析方法,展开系统发育的研究。在此基础上诠释现存的分类问题,并探讨该属系统发育关系。 研究材料上,本研究采用野外采集与网络下载数据相结合的方法,获取了较为全面的小鲵属物种DNA序列资料。技术手段上,选取了线粒体DNA的Cytb、12S、16S、NADH 2、COI等多个基因部分片段序列,对小鲵属开展了较为全面系统的研究。分析方法上,针对小鲵属物种各类群的具体情况,运用了处于领域前沿的多种分析方法。应用PAUP、MrBayes、Modeltest、Mega等软件,采用了最大简约法(MP)、邻接法(NJ)、贝叶斯推断(BI)及K2P遗传距离分析等方法。 本研究对小鲵属进行了较为全面的系统发育研究,弥补了有关小鲵属系统发育研究的不足,并得出了以下结果: (1)关于豫南小鲵Hynobius yunanicus的有效性,基于细胞色素b序列的系统发育关系联合形态和染色体组型等证据证明了豫南小鲵是商城肥鲵的同物异名。 (2)获得了较为全面的小鲵属物种系统发育树,并以此解释了北海道滞育小鲵、东北小鲵、中国小鲵与义乌小鲵等存在的分类问题。 (3)本研究利用DNA条形码技术对小鲵属及小鲵科物种进行了鉴定,再次证明豫南小鲵为商城肥鲵的同物异名;并认为猫儿山小鲵与挂榜山小鲵为同物异名。 综上,本研究较为完整地勾勒了小鲵属的系统发育关系全貌,并对小鲵属物种的起源进行了推测。 Hynobius, the type genus of the Family Hynobiidae, is the only exclusively Asian salamander genus. This genus which contains 29 species (beyond half of total Family), is the key group in Hynobiidae. The genus distributed across Palaearctic and Oriental Realm, and was found in China, Korea, and Japan. Systematics of genus Hynobius draws attention of researchers all the times. Resolving the taxonomic and phynogenetic questions of Hynobius is very important to the evolutionary research of Family Hynobiidae. Firstly, studies on systematics of genus Hynobius based on morphology, karyotype and molecular phylogeny of Hynobius are reviewed along with existing questions of this genus. The sequential reaserch project of phylogenetics is perspectively outlined. Using molecular data, we compared Hynobius yunanicus with a sympatric species Pachyhynobius shangchengensis. Our cytb sequences associating with karyotypic and morphological data supportted that H. yunanicus is not a valid species, but a synonym of P. shangchengensis. Because of phenotypic plasticity, some morphological characters are not even suitable for identifying hynobiids. The taxonomy of hynobiids is still controversial to a certain extent (Zhao et al. 1993; Fei, 1999; Chen et al. 2001; Zeng et al. 2006) and needs to be resolved by a new method. Here we examined the utility of COI barcoding for the discrimination of hynobiids. Meantime, the taxonomy of this Family was looked-over again. Our result show that the DNA Barcoding based on COI is easier and more rapidly than classic methods. And the DNA Barcodes data supported the actual taxonomy of Hynobiidae. Based on the achievements of our research, the phylogeny of Hynobius was reconstructed including some new species (H. maoershanensis, H. guabangshanensis, etc). Besides the phylogenetics of Hynobius was outlined, some questions and the hypothesis about the origin of genus Hynobius was put out.

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近年来,胶质类浮游动物尤其是水母类在近岸高生产力的海洋生态系统中的作用越来越受到全球科学家们的关注。这种关注很大程度上是由于近年来很多海域或海湾出现水母类大量繁殖的现象而引起的,这种现象与过度捕捞、气候变化、富营养化以及生物入侵等因素有着内在的联系,给人们带来经济,社会和生态等各方面的损失。这种损失包括:当水母大量出现时,由于它们与鱼类存在食物和捕食竞争,使渔业资源和渔业生产锐减;由于它们会堵塞和撕破渔业生产网,干扰了人们的渔业生产活动;另外水母增多增加了海滨游泳爱好者被蛰伤甚至死亡事件发生的频率,对旅游者们的娱乐行为造成不便。到目前为止全球范围内报道了许多水母大量繁殖并对经济社会或海洋生态系统造成负面影响的事件。在北海水母数量爆发的频率与气候相关的事实表明了该海域将要面临一个更多的胶质类浮游动物的未来。所有这些都表明海洋中水母的生态学问题仍旧是全球的一个研究热点。到目前为止,在世界上许多海湾和海区有关水母生态学问题的研究上,均已取得方方面面有意义的进展。但在我国,由于对水母功能群的研究缺乏足够的重视,对于大型水母来讲它们被认为是渔业生产的副产品或者‘垃圾’,在渔业拖网捕获后把它们直接扔入海中并不去研究;对于小型水母来讲,因为它们为非饵料生物,并且有易碎,粘糊糊等难操作的特点,对浮游生物网同步采集到的水母的研究力度远不如对其他浮游动物类群的研究力度,因此我国对水母功能群生态学的研究基础相当薄弱。 本论文基于以上背景对黄东海大型和小型水母类的生物地理分布格局进行了研究,对其生物量或丰度等生态学指标进行了定量研究。(1)利用浮游生物网样品对黄海小型水母类的种类组成及其丰度的时空变化进行了研究,表明黄海测区内小型水母整体丰度很低,且主要分布在50 m等深线以浅海域,各水母类群以及优势种类的季节更替非常明显。比较不同海区的小型水母的丰度水平及其占浮游动物丰度的比例,发现黄海的小型水母丰度水平最低,为0.8(0.04–1.3)ind. m-3,只占浮游动物丰度的 < 0.5 %,表明小型水母在黄海海域并非占优势的功能群。(2)在中国黄东海采集的沙海蜇和在日本采集的越前水母的COI基因序列差异(0.2%)处于种内水平,从分子水平上证明两者为同一个种类,基于形态学和分子生物学的证据,我国大型水母沙海蜇的分类地位可初步订正为:Nemopilema nomurai Kishinouye, 1922(Scyphozoa:Rhizostomeae:Rhizostomatidae)。(3)利用渔业底层拖网的方法对黄东海大型水母的种类组成,总生物量及各优势种类生物量的时空分布进行了半定量研究。结果共鉴定到11个种(类),其中沙海蜇(Nemopilema nomurai),洋须水母(Ulmaridae genus sp.)以及多管水母(Aequorea spp.)为黄海的优势种(类),沙海蜇(只在东海北部)和霞水母(Cyanea spp.)为东海的优势种(类);这四个种(类)的湿重随着伞径的增大成冪增长的方式。大型水母平均总生物量的季节变化模式为:3月份水母总生物量最低,为4.6 ± 9.4 kg km–2,春夏季随着海水表层温度的升高,大型水母的生物量逐渐增加,9月初水母的总生物量达到最高值,为22891 ± 25888 kg km–2,随后随着海水的温度下降,生物量也逐渐下降。洋须水母的生物量在10月份达到最高值(2780 ind. km–2,1807 kg km–2),主要在黄海中部出现。多管水母在5月份丰度最高,为8262 kg km–2,且主要分布在30N以北海域。 聚焦大量爆发的水母种(类)沙海蜇和霞水母,基于实测的拖网资料,提供了该种可见的浮游阶段1周年的地理发生和生物量数据;结果表明,这两个种(类)表现了不同的季节出现和生物量格局:首先是黄海出现的沙海蜇(5–12月在黄海出现),5月份少量幼水母体在黄东海的交界处出现,6月它们的分布范围在南黄海扩大,到8月末及9月初沙海蜇几乎遍布黄海,其生物量和丰度以压倒其他大型水母类的优势形成“bloom”(生物量占所有大型水母的96.7%,丰度占93%,在南黄海平均生物量20446 kg km-2,平均占渔获物生物量的86.1 %),10月份至12月,沙海蜇的生物量逐渐减少甚至为零,其分布区域也向北回缩。其次为东海出现的霞水母(5月–10月):霞水母在5月初达到生物量的高值(平均生物量为380 kg km-2),其伞径随纬度的升高而变小,8月至10月其生物量骤然下降。这两个种类的生物量高值分布在温度或潮汐锋区。结合水文条件及沙海蜇和霞水母关键的生活史策略推测了黄东海该种浮游阶段的生活史模型。 最后,通过对黄海8、9月份沙海蜇生物量的最高峰或暴发时期的呼吸率,摄食率进行估算,获得其每天对浮游动物现存量及生产力的潜在摄食压力,结果表明2006年9月在对沙海蜇最大捕获率的情况下,沙海蜇的摄食率为8.37(0.12–37.83)mg C m-2d-1,假设都以浮游动物为食,这时每天对浮游动物现存量及生产力的摄食压力分别为11.2%(0.17–50.6%),134.1%(1.98–605.7%)。因此在沙海蜇暴发期间对浮游动物的潜在的消耗非常大,甚至为毁灭性的。

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为了进一步研究青蟹属系统进化的科学问题,并揭示我国东南沿海青蟹群体遗传结构和群体进化细节信息,本论文主要开展了以下两个方面的研究:(1)基于线粒体12S rRNA、16S rRNA和COI三种基因序列探讨中国东南沿海青蟹的种类归属与青蟹属的系统进化;(2)利用线粒体COI基因标记分析中国东南沿海拟穴青蟹的群体遗传结构。序列特征、遗传距离和系统进化分析结果都表明本文研究的青蟹均为S. paramamosain。NJ、BAYES和ML系统进化树显示S. paramamosain与S. tranquebarica互为姐妹种,S. olivecea应该是4种青蟹中最早分化出来的种类。10个地理群体130只拟穴青蟹的线粒体DNA(mitochondrial DNA,mtDNA)细胞色素氧化酶亚基I(COI)基因序列Mantel检验结果显示群体间的遗传分化程度与地理距离没有显著的相关性。分子进化中性检验结果表明自然选择在分子进化过程中起了重要作用,并暗示该物种在最近经历了一个快速的群体爆发及扩张事件。

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中国牡蛎种类丰富,但是由于贝壳可塑性强,表型变化大,分类学及系统发生学研究进展缓慢,存在诸多争议。本文在全国部分海区采集牡蛎样品,并通过表型和分子生物学方法进行鉴定,重点调查潮下带牡蛎的分布情况。选取江苏南通小庙洪牡蛎礁作为典型海域,研究亲缘关系接近的巨蛎属牡蛎之间在繁殖上如何维持相互之间的关系。本研究的目的在于摸索牡蛎物种鉴定的实用方法,并阐明熊本牡蛎和近江牡蛎生殖隔离是如何维持的。研究结果对牡蛎等海洋贝类的分类及系统发生学研究具有一定的借鉴作用,为牡蛎礁的生态保护提供生物学参考依据。 在辽宁营口、海洋岛,河北秦皇岛,山东西霞口、潍坊、青岛,江苏南通,浙江舟山、奉化,福建莆田,广东汕头等地区采集牡蛎样品,重点采集潮下带的牡蛎,通过地理分布、表型、DNA含量测定和COI种特异性探针鉴定对各地区的牡蛎物种组成进行分析。选取了南通小庙洪牡蛎礁作为研究牡蛎物种间相互关系的最佳地点。该地区牡蛎由主要分布在潮间带的熊本牡蛎和主要分布在潮下带的近江牡蛎组成。 对南通小庙洪牡蛎礁上两种巨蛎属牡蛎在空间上的分布进行调查;定期取样,制作性腺切片,观察两种牡蛎的性腺发育情况;同时,定期在海区挂板,采用半人工采苗的方式采集海区牡蛎幼体,通过ITS1基因鉴定采集的稚贝所属物种。通过调查发现二者的分布存在重叠区域;两种牡蛎在2007年6月中旬至9月中旬存在两个明显的繁殖高峰期,在每个繁殖期内两种牡蛎同时发生大量繁殖行为的可能性极高。结果表明,两种牡蛎不存在明显的生态隔离和季节隔离等交配前生殖隔离机制。 在室内对两种牡蛎进行2×2完全双列杂交,并通过ITS1基因的克隆测序验证杂种后代。双列杂交受精实验采用多亲本混合交配的方式(即每个物种的卵子或精子均来自多个个体),共进行7次重复。结果表明,熊本牡蛎的卵子能够被近江牡蛎的精子以较低的受精率(24.6%)受精,且形成的后代确实为两个物种杂交产生,而反方向不能受精。 幼虫和稚贝生长存活的双列杂交实验共进行3次重复。估测受精率、受精卵的孵化率,第1至29日每两天测量一次D形幼虫的壳高和密度。结果表明杂交幼虫(熊本牡蛎♀与近江牡蛎♂的杂交,SA)的受精率(12.5%)显著低于(P < 0.05)熊本牡蛎(75.4%)和近江牡蛎(84.5%)纯种对照组;而孵化率与对照组无显著差异(P > 0.05);自受精至29日龄,杂交幼虫壳高的生长速度明显低于纯种对照组(P < 0.05);但是存活率与熊本牡蛎无显著差异(P > 0.05)。杂交幼虫附着变态期间死亡率高;93日龄,熊本牡蛎有10.08%的匍匐期面盘幼虫存活至稚贝,显著大于(P < 0.05)近江牡蛎(2.18%)和杂交幼虫(0.76%);杂交稚贝壳高显著小于(P < 0.05)纯种对照组。稚贝在海区挂养3个月。与挂养前相比,杂交稚贝在潮下带的存活率为19.2%,125个稚贝仅存24个,壳高平均增加2.15 mm。熊本牡蛎在潮间带的存活率达到65%,壳高平均增加3.99 mm。近江牡蛎在潮下带的存活率达到85.7%,壳高平均增加5.22 mm,在潮间带的存活率仅10.9%,壳高平均增加3.28 mm。受精6个月后,所有杂交稚贝仅剩3枚,运回实验室暂养一段时间后全部死亡。 设置20、25、30、35共4个盐度梯度,估算双列杂交组合在不同盐度下的受精率、孵化率、7日内的存活率和壳高生长,实验共进行3个重复。结果表明,杂交组合在4个盐度下的受精率(平均为11.2%)均显著低于(P < 0.05)熊本牡蛎(75.0%)和近江牡蛎(77.5%)纯种对照组;而孵化率与对照组无显著差异(P > 0.05);杂交组合在盐度35时的孵化率(85.0%)显著大于20(49.6%)、25(51.3%)和30(55.4%)三个盐度梯度。7日龄杂交幼虫(10.5%)和近江牡蛎(11.4%)的存活率显著小于(P < 0.05)熊本牡蛎(30.3%);杂交幼虫的壳高(75.7 μm)显著小于(P < 0.05)熊本牡蛎(81.5 μm)和近江牡蛎(85.6 μm)对照组。两因素方差分析表明,杂交组合方式对受精率、孵化率、7日龄存活率和7日龄壳高均有显著影响,盐度对7日龄壳高的影响显著。 实验结果表明,江苏小庙洪牡蛎礁上的熊本牡蛎和近江牡蛎之间在分布空间上存在重叠区域,繁殖时间也存在重叠,并未产生明显的生态隔离和季节隔离。二者之间存在不对称性杂交,熊本牡蛎的卵子能够与近江牡蛎的精子以较低的受精率受精,而反方向完全不亲和。杂交幼虫在受精率上存在显著劣势;但是受精卵的孵化率与纯种受精卵无显著差异;杂交幼虫在生长上也存在显著劣势;而存活率与熊本牡蛎无显著差异;杂交幼虫附着变态期间大量死亡,存活下来的稚贝生长缓慢,死亡率高。表明熊本牡蛎和近江牡蛎之间即存在交配前的配子不亲和性隔离,又存在交配后隔离,主要表现为杂种不活。

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Oysters are commonly found on rocky shores along China's northern coast, although there is considerable confusion as to what species they are. To determine the taxonomic status of these oysters, we collected specimens from nine locations north of the Yangtze River and conducted genetic identification using DNA sequences. Fragments from three genes, mitochondrial 165 rRNA, mitochondria! cytochrome oxidase I (COI), and nuclear 285 rRNA, were sequenced in six oysters from each of the nine sites. Phylogenetic analysis of all three gene fragments clearly demonstrated that the small oysters commonly found on intertidal rocks in north China are Crassostrea gigas (Thunberg, 1793), not C. plicatula (the zhe oyster) as widely assumed. Their small size and irregular shell characteristics are reflections of the stressful intertidal environment they live in and not reliable characters for classification. Our study confirms that the oysters from Weifang, referred to as Jinjiang oysters or C. rivularis (Gould, 1861), are C. ariakensis (Wakiya, 1929). We found no evidence for the existence of C. talienwhanensis (Crosse, 1862) and other Crassostrea species in north China. Our study highlights the need for reclassifying oysters of China with molecular data.

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Genetic markers are needed for rapid and reliable identification of oysters. In this study, we developed multiplex genus- and species-specific PCR markers for the identification of oysters from China. We used the mitochondrial cytochrome oxidase I (COI) and nuclear 28S ribosomal RNA genes for marker development. DNA sequences from different species were obtained from GenBank or by direct sequencing. Sequences were aligned, and genus- and species-specific nucleotides were identified. Primers were designed for genus/species-specific amplification to generate fragments of different sizes. A multiplex set of genus- and species-specific primers from the 28S gene was able to separate C. ariakensis and C. hongkongensis from other species and assign oysters to four genera. A set of species-specific COI primers provided positive identification of all five Crassostrea species from China, C. ariakensis, C. hongkongensis, C. angulata, C. gigas, and C. sikamea in a single PCR. The multiplex PCR assays do not require fluorescence-labeling or post-PCR enzyme digestion, providing a simple, fast and reliable method for the identification of oysters from China.

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Wydział Biologii i Hodowli Zwierząt Uniwersytet Przyrodniczy we Wrocławiu

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This study was undertaken to investigate the general biology, including the reproductive cycle and health status, of two clam taxa in Irish waters, with particular reference to the Irish Sea area. Monthly samples of the soft shell clam, Mya arenaria, were collected from Bannow Bay, Co. Wexford, Ireland, for sixteen months, and of the razor clam, Ensis spp. from the Skerries region (Irish Sea) between June 2010 and September 2011. In 2010, M. arenaria in Bannow Bay matured over the summer months, with both sexes either ripe or spawning by August. The gonads of both sexes of E. siliqua developed over autumn and winter 2010, with the first spawning individuals being recorded in January 2011. Two unusually cold winters, followed by a warmer than average spring, appear to have affected M. arenaria and E. siliqua gametogenesis at these sites. It was noted that wet weight of E. siliqua dropped significantly in the summer of both 2010 and 2011, after spawning, which may impact on the economic viability of fishing during this period. Additional samples of M. arenaria were collected at Flaxfort (Ireland), and Ensis spp. at Oxwich (Wales), and the pathology of all clams was examined using both histological and molecular methods. No pathogenic conditions were observed in M. arenaria while Prokaryote inclusions, trematode parasites, Nematopsis spp. and inflammatory pathologies were observed at low incidences in razor clams from Ireland but not from Wales; the first time these conditions have been reported in Ensis spp. in northern European waters. Mya arenaria from sites in Europe and eastern and western North America were investigated for genetic variation using both mitochondrial (cytochrome oxidase I (COI) and 16S ribosomal RNA genes) and nuclear markers (10 microsatellite loci). Both mitochondrial CO1 and all nuclear markers showed reduced levels of variation in certain European samples, with significant differences in haplotype and allelic composition between most samples, particularly those from the two different continents, but with the same common haplotypes or alleles throughout the range. The appearance of certain unique rare haplotypes and microsatellite alleles in the European samples suggest a complicated origin involving North American colonization but also possible southern European Pleistocene refugia. Specimens of Ensis spp. were obtained from five coastal areas around Ireland and Wales and species-specific PCR primers were used to amplify the internal transcribed spacer region 1 (ITS1) and the mitochondrial DNA CO1 gene and all but 15 razor clams were identified as Ensis siliqua. Future investigations should focus on continued monitoring of reproductive biology and pathology of the two clam taxa (in particular, to assess the influence of environmental change), and on genetics of southern European M. arenaria and sequencing the CO1 gene in Ensis individuals to clarify species identity

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This study describes phenotypic and genotypic variations in the planktonic copepod, Centropages typicus (Copepoda: Calanoida) that indicate differentiation between geographical samples. We found consistent differences in the morphology of the chela of the sexually modified fifth pereiopod (P5) of male C. typicus between samples from the Mediterranean, western North Atlantic and eastern North Atlantic. A 560 base pairs (bp) region of the C. typicus mitochondrial cytochrome c oxidase subunit I (COI) and a 462 bp fragment of the nuclear rDNA internal transcribed spacer (ITS) tandem array were analysed to determine whether these morphological variations reflect population genetic differentiation. Mitochondrial haplotype diversity was found to be high with 100 unique COI haplotypes among 116 individuals. Analysis of mtCOI variation suggested differentiation between the Mediterranean and Atlantic populations but no separation was detected within the Atlantic. Intragenomic variation in the ITS array suggested genetic differentiation between samples from the western North Atlantic and those from the eastern North Atlantic and Mediterranean. Breeding experiments would be required to elucidate the extent of genetic isolation between C. typicus from the different population centres.

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DNA barcoding offers an efficient way to determine species identification and to measure biodiversity. For dinoflagellates, an ancient alveolate group of about 2000 described extant species, DNA barcoding studies have revealed large amounts of unrecognized species diversity, most of which is not represented in culture collections. To date, two mitochondrial gene markers, Cytochrome Oxidase I (COI) and Cytochrome b oxidase (COB), have been used to assess DNA barcoding in dinoflagellates, and both failed to amplify all taxa and suffered from low resolution. Nevertheless, both genes yielded many examples of morphospecies showing cryptic speciation and morphologically distinct named species being genetically similar, highlighting the need for a common marker. For example, a large number of cultured Symbiodinium strains have neither taxonomic identification, nor a common measure of diversity that can be used to compare this genus to other dinoflagellates.

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A new species of lamellibrachiid vestimentiferan, Lamellibrachia anaximandri n. sp., has been found in the Eastern Mediterranean, close to cold seeps of fluid carrying dissolved methane and sources of sulfide in superficial sediments. It occurs at about 1100 to 2100 m depth, on some of the mud volcanoes on the Anaximander Mountains, south of Turkey, on the Mediterranean Ridge, south of Crete, and on the Nile deep-sea fan. In addition, it has been obtained from rotting paper inside a sunken ship, torpedoed in 1915 and lying at 2800 m depth, southeast of Crete. Some frenulate pogonophores also occur on the mud volcanoes (including a species of Siboglinum resembling S. carpinei and tubes of other unidentified genera). The new Lamellibrachia is the first vestimentiferan species to be described from the Mediterranean. It differs from L. luymesi taken from the Gulf of Mexico population in the very weak development of collars on its tube and in having a smaller number of pairs of branchial lamellae in the branchial plume. Sequencing of the COI and the mt16S genes confirms a difference at the species level between the new species and L. luymesi, and a difference between these two species and four described species of Lamellibrachia from the Pacific Ocean. The largest individuals of L. anaximandri n. sp. may be many years old, but there are numerous young individuals at some sites, showing that favourable conditions are available for settlement and early growth. The development of the branchial plume in a series of young stages reveals that the sheath lamellae, which are characteristic of the genus Lamellibrachia, begin to form only after the establishment of several pairs of branchial lamellae. Examination of the adult trophosome by transmission electron microscopy shows Gram-negative bacteria without internal stacked membranes, indicating that the symbionts are most probably sulfide oxidizing.

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Morphometrics and DNA microsatellites were used to analyse the genetic structure of populations of the stingless bee M. beecheii from two extremes of its geographic range. The results showed that populations from Costa Rica and Yucatan exhibit substantial phenotypic and molecular differentiation. Bees from Yucatan were smaller and paler than those from Costa Rica. The value of multilocus F-ST = 0.280 (P <0.001) confirmed that there were significant molecular genetic differences between the two populations. Populations showed significant deviation from Hardy Weinberg equilibrium and the values of FIS (the inbreeding coefficient) were positive for Costa Rica = 0.416 and the Yucatan Peninsula = 0.193, indicating a lack of heterozygotes in both populations possibly due to inbreeding. The DNA sequence of 678 bp of the mitochondrial gene COI differed between populations by 1.2%. The results of this study should be considered in conservation programmes, particularly with regard to the movement of colonies between regions.

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Eusociality is widely considered a major evolutionary transition. The socially polymorphic sweat bee Halictus rubicundus, solitary in cooler regions of its holarctic range and eusocial in warmer parts, is an excellent model organism to address this transition, and specifically the question of whether sociality is associated with a strong barrier to gene flow between phenotypically divergent populations. Mitochondrial DNA (COI) from specimens collected across the British Isles, where both solitary and social phenotypes are represented, displayed limited variation, but placed all specimens in the same European lineage; haplotype network analysis failed to differentiate solitary and social lineages. Microsatellite genetic variability was high and enabled us to quantify genetic differentiation among populations and social phenotypes across Great Britain and Ireland. Results from conceptually different analyses consistently showed greater genetic differentiation between geographically distant populations, independently of their social phenotype, suggesting that the two social forms are not reproductively isolated. A landscape genetic approach revealed significant isolation by distance (Mantel test r = 0.622, p