• 【深海喷口和渗水无脊椎动物的演化和生物地理学。】 复制标题 收藏 收藏
    DOI:10.1126/science.1067361 复制DOI
    作者列表:Van Dover CL,German CR,Speer KG,Parson LM,Vrijenhoek RC
    BACKGROUND & AIMS: Deep-sea hydrothermal vents and cold seeps are submarine springs where nutrient-rich fluids emanate from the sea floor. Vent and seep ecosystems occur in a variety of geological settings throughout the global ocean and support food webs based on chemoautotrophic primary production. Most vent and seep invertebrates arrive at suitable habitats as larvae dispersed by deep-ocean currents. The recent evolution of many vent and seep invertebrate species (<100 million years ago) suggests that Cenozoic tectonic history and oceanic circulation patterns have been important in defining contemporary biogeographic patterns.

    背景与目标: 深海热液喷口和冷渗漏是海底温泉,海底散发出营养丰富的流体。通风和渗漏的生态系统遍布全球海洋的各种地质​​环境中,并基于化学自养初级生产来支持食物网。大多数发泄和渗入的无脊椎动物以幼虫被深海洋流分散而到达合适的栖息地。许多发泄和渗入无脊椎动物的近代进化(<1亿年前)表明,新生代的构造历史和海洋环流模式对于定义当代生物地理模式非常重要。

  • 【复杂的复合体研究:Caridina属(十足目:Caridea:Atyidae)内的两个物种复合体的第一个得到充分支持的系统发育学为进化,生物地理学和栖息地提供了启示。】 复制标题 收藏 收藏
    DOI:10.1016/j.ympev.2018.11.002 复制DOI
    作者列表:de Mazancourt V,Klotz W,Marquet G,Mos B,Rogers DC,Keith P
    BACKGROUND & AIMS: :Atyid shrimps, a key component of tropical freshwater ecosystems, face multiple anthropogenic threats and thus need special attention. With more than 300 described species, the genus Caridina is the most speciose of all the Caridea infra-order. Caridina spp. occupy diverse habitats in tropical freshwaters of the Indo-West Pacific region. Several species complexes have been recognized, based on common morphological features, but little is known about how well these morphological characteristics align with phylogenetic characteristics. Furthermore, no phylogeny of the genus Caridina published so far has provided well-resolved and supported relationships among different species, thus impeding the possibility of proposing evolutionary hypotheses. In this study we used next generation sequencing (NGS) to provide new insights into the phylogenetic relationships among the genus Caridina, focusing on two complexes: 'Caridina nilotica' and 'Caridina weberi'. We collected 92 specimens belonging to these two groups from most of their known geographical range, representing 50 species, for which we sequenced seven mitochondrial genes and two nuclear markers using ion torrent NGS. We performed a phylogenetic analysis, which yielded the first well-supported tree for the genus Caridina. On this tree were mapped the geographic ranges and the habitats used by the different species, and a time calibration was tested. We found the driving factors that most likely account for separation of clades are differences in habitat and to a lesser extent geography. This work provides new insights into the taxonomy of this group and identifies opportunities for further studies in order to fill knowledge gaps that currently impede the management and conservation of atyid species.
    背景与目标: :虾是热带淡水生态系统的重要组成部分,面临多种人为威胁,因此需要特别注意。 Caridina属有300多个描述的物种,是所有Caridea红外物种中最特殊的物种。 Caridina spp。在印度洋-西太平洋地区的热带淡水中占据着不同的栖息地。基于常见的形态特征,已经认识到几种物种复合物,但是对于这些形态特征与系统发育特征的匹配程度知之甚少。此外,到目前为止,尚未发表Caridina属的系统发育史,已经提供了不同物种之间的良好解析和支持的关系,因此阻碍了提出进化假设的可能性。在这项研究中,我们使用了下一代测序(NGS)来提供对Caridina属之间系统发育关系的新见解,重点是两个复合体:'Caridina nilotica'和'Caridina weberi'。我们从其已知地理范围的大部分中收集了代表这两组的92个标本,它们代表50个物种,为此,我们使用离子洪流NGS对7个线粒体基因和2个核标记物进行了测序。我们进行了系统发育分析,得出了Caridina属的第一棵得到良好支持的树。在这棵树上绘制了不同物种所使用的地理范围和栖息地,并进行了时间校准测试。我们发现,最有可能导致进化枝分离的驱动因素是栖息地的差异,以及地理范围较小的差异。这项工作为该群体的分类学提供了新的见解,并确定了进一步研究的机会,以填补目前阻碍非典种管理和保护的知识空白。
  • 【树懒的系统发育,宏观进化趋势和历史生物地理学:贝叶斯形态时钟分析的见解。】 复制标题 收藏 收藏
    DOI:10.1093/sysbio/syy058 复制DOI
    作者列表:Varela L,Tambusso PS,McDonald HG,Fariña RA
    BACKGROUND & AIMS: :Sloths, like other xenarthrans, are an extremely interesting group of mammals that, after a long history of evolution and diversification in South America, became established on islands in the Caribbean and later reached North America during the Great American Biotic Interchange. In all three regions, they were part of the impressive Pleistocene megafauna. Most taxa became extinct and only two small, distantly related tree-dwelling genera survived. Here, we incorporate several recently described genera of sloths into an assembled morphological data supermatrix and apply Bayesian inference, using phylogenetic and morphological clock methods, to 64 sloth genera. Thus, we investigate the evolution of the group in terms of the timing of divergence of different lineages and their diversity, morphological disparity and biogeographical history. The phylogeny obtained supports the existence of the commonly recognized clades for the group. Our results provide divergence time estimates for the major clades within Folivora that could not be dated with molecular methods. Lineage diversity shows an early increase, reaching a peak in the Early Miocene followed by a major drop at the end of the Santacrucian (Early Miocene). A second peak in the Late Miocene was also followed by a major drop at the end of the Huayquerian (Late Miocene). Both events show differential impact at the family level. After that, a slight Plio-Pleistocene decline was observed before the marked drop with the extinction at the end of the Pleistocene. Phenotypic evolutionary rates were high during the early history of the clade, mainly associated with Mylodontidae, but rapidly decreased to lower values around 25 Ma, whereas Megalonychidae had lower rates at the beginning followed by a steady increase, peaking during the Late Miocene and the Pliocene. Morphological disparity showed a similar trend, with an early increase, followed by a slowly increasing phase through the Late Oligocene and Early Miocene, and ending with another increase beginning at the middle of the Miocene. Biogeographic analysis showed southern South America as the most probable area of origin of the clade and the main region in which the early diversification events took place. Both Megatheriinae and Nothrotheriinae basal nodes were strongly correlated with Andean uplift events, whereas the early history of Mylodontidae is closely associated with southern South America and also shows an early occupation of the northern regions. Within Megalonychidae, our results show Choloepus as a descendant of an island dispersing ancestor and a probable re-ingression to South America by a clade that originated in Central or North America.
    背景与目标: 象其他的雪生动物一样,懒惰是一群非常有趣的哺乳动物,在南美经历了漫长的进化和多样化历史之后,它们在加勒比海的岛屿上建立起来,并随后在“大美洲生物交换”中到达了北美。在所有三个地区,它们都是令人印象深刻的更新世大型动物群的一部分。大多数分类单元都灭绝了,只有两个遥远的,与树木有远缘亲缘关系的属幸免于难。在这里,我们将几个最近描述的树懒属植物合并到一个组装的形态学数据超级矩阵中,并使用系统发育和形态学时钟方法对64个树懒属植物应用贝叶斯推断。因此,我们根据不同谱系的发散时间及其多样性,形态差异和生物地理历史来研究该群体的演变。获得的系统发育支持该群体公认的进化枝的存在。我们的结果提供了无法用分子方法确定的主要叶片进化枝时间的估计。世袭多样性显示出早期增加,在中新世早期达到顶峰,随后在圣塔科鲁阶(中新世早期)大幅下降。中新世晚期的第二个高峰之后是Huayquerian(晚中新世)末期的大幅下降。这两个事件在家庭层面上都显示出不同的影响。在那之后,观察到轻微的上新世更新世下降,然后明显下降,而在更新世末期灭绝。在进化枝的早期,表型进化率很高,主要与Mylodontidae有关,但是在25 Ma左右迅速下降到较低的值,而Megalonychidae在开始时率较低,随后稳定增长,在中新世和上新世晚期达到顶峰。 。形态差异表现出相似的趋势,即早期增加,随后是渐新世晚期和中新世早期缓慢增加的阶段,最后在中新世中期开始增加。生物地理学分析表明,南美南部是进化枝最有可能的起源地区,也是发生早期多样化事件的主要地区。 Megatheriinaee和Nothrotheriinae基底节都与安第斯山隆升事件密切相关,而Mylodontidae的早期历史与南美南部紧密相关,也显示了北部地区的早期占领。在Megalonychidae内,我们的研究结果表明,梭罗普斯是岛屿散布祖先的后裔,并可能起源于中美洲或北美洲的进化枝重新进入南美。
  • 【系统发育,生物地理学和超多样化的水疱甲虫属Hycleus(鞘翅目:Meloidae)的系统学。】 复制标题 收藏 收藏
    DOI:10.1016/j.ympev.2019.106706 复制DOI
    作者列表:Riccieri A,Mancini E,Salvi D,Bologna MA
    BACKGROUND & AIMS: :Hycleus is a hyper-diverse genus of blister beetles including ~500 species widely distributed in the Old World, currently divided into three "sections" and into 45 "phenetic" species groups according to morphological characters. Recently the monophyly of Hycleus was questioned pointing out its paraphyly with respect to the genera Ceroctis and Paractenodia. In this study, we built a time-calibrated phylogenetic tree based on DNA sequence data from mitochondrial and nuclear genes obtained from 125 species, to understand the phylogenetic relationships among the species of this genus, to infer the biogeographic processes behind their diversification, and to assess their taxonomy and classification. Our results identified four main lineages one of which included the species belonging to Ceroctis and Paractenodia; therefore, both taxa are now referred to Hycleus as new synonyms. The three described sections of Hycleus resulted polyphyletic and are rejected, whereas several species groups represented well supported clades. Hycleus likely originated in Africa during the Early Miocene (~20 Mya), and subsequently spread in Europe and western Asia. Later, in the Late Miocene (~6 Mya) a Saharo-Sindian group branched off from the Palaearctic lineage, whereas the Oriental Region was colonized following a dispersal event through the Arabian Peninsula from the Afrotropical Region (~5 Mya).
    背景与目标: :Hycleus是一种水疱甲虫的超多样性属,包括在旧世界中广泛分布的约500种,目前根据形态特征分为三个“部分”和45个“显着”的物种组。最近,有人质疑Hycleus的单亲性,指出其对Ceroctis和Paractenodia属的副生。在这项研究中,我们基于线粒体和从125种物种获得的核基因的DNA序列数据,建立了经过时间校准的系统发育树,以了解该属物种之间的系统发生关系,以推断其多样化背后的生物地理过程,并评估其分类和分类。我们的结果确定了四个主要谱系,其中之一包括属于Ceroctis和Paractenodia的物种。因此,现在两个分类单元都被称为Hycleus,作为新的同义词。 Hycleus的三个描述的部分导致多系并被拒绝,而几个物种组代表了良好支持的进化枝。 Hycleus可能起源于中新世早期(约20 Mya),然后传播到欧洲和西亚。后来,在中新世晚期(〜6 Mya)中,一个萨哈罗-辛迪亚人集团从古北系支系分支出来,而东方地区则在从非洲地区(〜5 Mya)通过阿拉伯半岛扩散之后被殖民了。
  • 【Eutherian辐射的时间和生物地理学:化石和分子的比较。】 复制标题 收藏 收藏
    DOI:10.1016/s1055-7903(03)00034-4 复制DOI
    作者列表:David Archibald J
    BACKGROUND & AIMS: :Theria includes Eutheria and its sister taxon Metatheria. Placentalia includes extant eutherians plus their most recent common ancestor. The oldest eutherian is from 125mya (million years ago). Molecular studies place this origin at about 130-185mya. Older dates cannot be refuted based on fossil evidence as earliest eutherian remains are scarce. Earliest superordinal clades (hence Placentalia) range from 64-104mya (median 84mya) based on molecules, similar to 85-90mya based on fossils. Superordinal clades Archonta, Ferungulata, Glires, and Paenungulata based on fossils are similar to molecularly based clades, except Afrotheria was not predicted by fossils. Both fossils and molecules recognize 16 of 18 extant placental orders. Fossils place the origins of orders around 65mya as do some molecular studies, but others suggest ordinal diversification as old as 100mya. Fossil evidence supports a Laurasian origin for Eutheria (and Metatheria) and Placentalia, although some molecular studies suggest a Gondwanan origin for both taxa.
    背景与目标: :Theria包括Eutheria及其姊妹分类单元Metatheria。胎盘素包括现存的古希腊人及其最近的共同祖先。最古老的以太坊来自125mya(百万年前)。分子研究将此起源定在约130-185mya。由于化石的最早遗存稀少,因此无法根据化石证据推翻较旧的日期。最早的上等进化枝(因此称为胎盘虫)基于分子的范围为64-104mya(中位数为84mya),类似于基于化石的85-90mya。基于化石的上等进化枝Archonta,Ferungulata,Glires和Paenungulata与基于分子的进化枝相似,不同的是化石不能预测非洲菊。化石和分子都识别18个现存胎盘中的16个。化石像一些分子研究一样,将点状起源定在65mya左右,但另一些人则认为序数多样化的历史可以追溯到100mya。化石的证据支持Eutheria(和Metatheria)和Placentalia的Laurasian起源,尽管一些分子研究表明,这两个分类群都来自冈瓦纳人。
  • 【中国睾丸变形虫的多样性,分布和生物地理学:对亚洲生态学研究的意义。】 复制标题 收藏 收藏
    DOI:10.1016/j.ejop.2010.09.004 复制DOI
    作者列表:Qin Y,Xie S,Smith HG,Swindles GT,Gu Y
    BACKGROUND & AIMS: :Testate amoebae are a group of shelled protozoa that occur in high density populations in wet environments. More than 1900 testate amoebae species or subspecies have been reported in published literature over the last 200 years, from many regions of the world. Testate amoebae are classified as Lobosea or Filosea respectively, according to the presence of lobose or filiform pseudopodia. Testate amoebae have proved an interesting group of indicator organisms in palaeoenvironmental studies and have also been used as bioindicators of human impact on ecosystems. Until recently, the testate amoebae of China were unknown to most western scientists, but our knowledge has improved greatly over the past 20 years. This paper summarizes the testate amoebae research in China along with relevant data from other countries in Asia, and provides the necessary context for future research.
    背景与目标: :睾丸变形虫是带壳的原生动物,在潮湿环境中的高密度种群中生活。在过去的200年中,来自世界许多地区的公开文献中已经报道了1900多种遗嘱性变形虫物种或亚种。根据松散或丝状假足的存在,将睾丸变形虫分别分为Lobosea或Filosea。在古环境研究中,已证明的睾丸变形虫是一组有趣的指示生物,也已被用作人类对生态系统影响的生物指示剂。直到最近,大多数西方科学家还不知道中国的睾丸变形虫,但是在过去的20年中,我们的知识有了很大的进步。本文总结了中国的睾丸变形虫研究以及亚洲其他国家的相关数据,并为将来的研究提供了必要的背景。
  • 【贝劳(大洋洲帕劳共和国)居住在岩石和叶子上的陆地蜗牛的隐匿性多样性,分子系统发育和生物地理学。】 复制标题 收藏 收藏
    DOI:10.1098/rstb.2008.0110 复制DOI
    作者列表:Rundell RJ
    BACKGROUND & AIMS: :The endemic diplommatinid land snails (Caenogastropoda: Mollusca) of Belau (Republic of Palau, Micronesia) are an exceptionally diverse group of largely undescribed species distributed among rock and leaf litter habitats on most of Belau's 586 islands. Diplommatinid shell morphology (e.g. shell sculpture) reflects habitat type. In this study, I analysed a subset of the 90 diplommatinid species representing a broad geographical spread of islands in order to reveal the species' phylogenetic relationships and biogeography within the Belau archipelago. Diplommatinid species from the islands of Yap, Pohnpei, Kosrae and Guam are also included in the analysis. One nuclear (28S rRNA) and two mitochondrial (16S rRNA, COI) gene regions comprising 1906bp were used for phylogenetic reconstruction. Results show that (i) the Belau Diplommatinidae are not monophyletic, as Guam and Yap species should be included as part of the radiation, (ii) Pohnpei and Kosrae species are highly divergent from Belau diplommatinids, (iii) there is little evidence for in situ radiation within individual Belau islands, (iv) spined and heavily calcified rock-dwelling species form a well-supported clade, and (v) Belau diplommatinid genera are in need of revision.
    背景与目标: 贝洛(密克罗尼西亚的帕劳共和国)的地方性双翅类陆地蜗牛(Caenogastropoda:Mollusca)是一个非常多样化的群体,大部分未描述的物种分布在Belau的586个岛屿中的大多数岩石和树叶凋落物生境中。双壳类动物壳的形态(例如壳雕)反映了栖息地的类型。在这项研究中,我分析了代表岛屿广泛地理分布的90种双角类科动物的子集,以揭示该物种在贝劳群岛内的系统发育关系和生物地理学。分析还包括Yap,Pohnpei,Kosrae和关岛等岛屿的双角类物种。使用一个包含1906bp的核(28S rRNA)和两个线粒体(16S rRNA,COI)基因区域进行系统发育重建。结果表明(i)贝劳双亲科不是单系的,因为关岛和Yap物种应作为辐射的一部分,(ii)波纳皮和科斯雷科物种与贝劳双歧科的物种高度不同,(iii)几乎没有证据表明在各个贝劳岛内进行原位辐射,(iv)旋转且高度钙化的岩石居留物种形成了支撑良好的进化枝,并且(v)贝劳双角类属需要修改。
  • 【土壤细菌和真菌的岛屿生物地理学:相似的模式,但机制不同。】 复制标题 收藏 收藏
    DOI:10.1038/s41396-020-0657-8 复制DOI
    作者列表:Li SP,Wang P,Chen Y,Wilson MC,Yang X,Ma C,Lu J,Chen XY,Wu J,Shu WS,Jiang L
    BACKGROUND & AIMS: :Microbes, similar to plants and animals, exhibit biogeographic patterns. However, in contrast with the considerable knowledge on the island biogeography of higher organisms, we know little about the distribution of microorganisms within and among islands. Here, we explored insular soil bacterial and fungal biogeography and underlying mechanisms, using soil microbiota from a group of land-bridge islands as a model system. Similar to island species-area relationships observed for many macroorganisms, both island-scale bacterial and fungal diversity increased with island area; neither diversity, however, was affected by island isolation. By contrast, bacterial and fungal communities exhibited strikingly different assembly patterns within islands. The loss of bacterial diversity on smaller islands was driven primarily by the systematic decline of diversity within samples, whereas the loss of fungal diversity on smaller islands was driven primarily by the homogenization of community composition among samples. Lower soil moisture limited within-sample bacterial diversity, whereas smaller spatial distances among samples restricted among-sample fungal diversity, on smaller islands. These results indicate that among-island differences in habitat quality generate the bacterial island species-area relationship, whereas within-island dispersal limitation generates the fungal island species-area relationship. Together, our study suggests that different mechanisms underlie similar island biogeography patterns of soil bacteria and fungi.
    背景与目标: :与植物和动物相似的微生物表现出生物地理特征。但是,与对高等生物的岛屿生物地理学的广泛了解相反,我们对岛屿内部和岛屿之间的微生物分布知之甚少。在这里,我们使用来自一组陆桥岛的土壤微生物群作为模型系统,探索了岛状土壤细菌和真菌的生物地理学及其潜在机制。与观察到的许多大型生物的岛屿物种-面积关系相似,岛屿规模的细菌和真菌多样性均随岛屿面积的增加而增加。但是,这两种多样性都没有受到岛屿隔离的影响。相比之下,细菌和真菌群落在岛内表现出截然不同的组装模式。小岛上细菌多样性的丧失主要是由样本内物种多样性的系统性下降引起的,而小岛上真菌多样性的丧失则主要是由于样品中群落组成的均质化引起的。较低的土壤湿度限制了样品内部细菌的多样性,而在较小的岛屿上,样品之间较小的空间距离限制了样品之间的真菌多样性。这些结果表明,岛屿间生境质量的差异产生了细菌岛种与面积的关系,而岛屿内的扩散限制产生了真菌岛种与面积的关系。总之,我们的研究表明,不同的机制是土壤细菌和真菌的类似岛屿生物地理模式的基础。
  • 【早期胎盘哺乳动物辐射的分子测年和生物地理学。】 复制标题 收藏 收藏
    DOI:10.1093/jhered/92.2.212 复制DOI
    作者列表:Eizirik E,Murphy WJ,O'Brien SJ
    BACKGROUND & AIMS: :The timing and phylogenetic hierarchy of early placental mammal divergences was determined based on combined DNA sequence analysis of 18 gene segments (9779 bp) from 64 species. Using rooted and unrooted phylogenies derived from distinct theoretical approaches, strong support for the divergence of four principal clades of eutherian mammals was achieved. Minimum divergence dates of the earliest nodes in the placental mammal phylogeny were estimated with a quartet-based maximum-likelihood method that accommodates rate variation among lineages using conservative fossil calibrations from nine different nodes in the eutherian tree. These minimum estimates resolve the earliest placental mammal divergence nodes at periods between 64 and 104 million years ago, in essentially every case predating the Cretaceous-Tertiary (K-T) boundary. The pattern and timing of these divergences allow a geographic interpretation of the primary branching events in eutherian history, likely originating in the southern supercontinent Gondwanaland coincident with its breakup into Africa and South America 95-105 million years ago. We propose an integrated genomic, paleontological, and biogeographic hypothesis to account for these earliest splits on the placental mammal family tree and address current discrepancies between fossil and molecular evidence.
    背景与目标: :早期胎盘哺乳动物分歧的时间和系统发育层次是基于对来自64个物种的18个基因片段(9​​779 bp)的联合DNA序列分析来确定的。使用源自不同理论方法的有根和无根系统发育史,为对以太哺乳动物的四个主要进化枝的分化提供了有力的支持。使用基于四重奏的最大似然法估算胎盘哺乳动物系统发育中最早结点的最小分歧日期,该方法使用来自古生物学树中九个不同结点的保守化石标定来适应谱系间的速率变化。这些最低限度的估计值可以解决最早的胎盘哺乳动物发散点,发生在64到1.04亿年前之间,基本上在每种情况下都早于白垩纪-第三纪(K-T)边界。这些分歧的方式和时机允许对以太坊历史中的主要分支事件进行地理解释,这些事件可能起源于南部超大陆冈瓦纳大陆,与它在95-1.05亿年前进入非洲和南美的分裂相吻合。我们提出了一个综合的基因组学,古生物学和生物地理学假设,以解释胎盘哺乳动物家谱上的这些最早的分裂,并解决化石和分子证据之间的当前差异。
  • 【蝴蝶鱼的分子系统发育(Chaetodontidae):全球珊瑚礁鱼类家族的分类学和生物地理学。】 复制标题 收藏 收藏
    DOI:10.1016/j.ympev.2007.05.018 复制DOI
    作者列表:Fessler JL,Westneat MW
    BACKGROUND & AIMS: :Marine butterflyfishes (10 genera, 114 species) are conspicuously beautiful and abundant animals found on coral reefs worldwide, and are well studied due to their ecological importance and commercial value. Several phylogenies based on morphological and molecular data exist, yet a well-supported molecular phylogeny at the species level for a wide range of taxa remains to be resolved. Here we present a molecular phylogeny of the butterflyfishes, including representatives of all genera (except Parachaetodon) and at least one representative of all commonly cited subgenera of Chaetodon (except Roa sensuBlum, 1988). Genetic data were collected for 71 ingroup and 13 outgroup taxa, using two nuclear and three mitochondrial genes that total 3332 nucleotides. Bayesian inference, parsimony, and maximum likelihood methods produced a well-supported phylogeny with strong support for a monophyletic Chaetodontidae. The Chaetodon subgenera Exornator and Chaetodon were found to be polyphyletic, and the genus Amphichaetodon was not the basal sister group to the rest of the family as had been previously proposed. Molecular phylogenetic analysis of data from 5 genes resolved some clades in agreement with previous phylogenetic studies, however the topology of relationships among major butterflyfish groups differed significantly from previous hypotheses. The analysis recovered a clade containing Amphichaetodon, Coradion, Chelmonops, Chelmon, Forcipiger, Hemitaurichthys, Johnrandallia, and Heniochus. Prognathodes was resolved as the sister to all Chaetodon, as in previous hypotheses, although the topology of subgeneric clades differed significantly from hypotheses based on morphology. We use the species-level phylogeny for the butterflyfishes to resolve long-standing questions regarding the use of subgenera in Chaetodon, to reconstruct molecular rates and estimated dates of diversification of major butterflyfish clades, and to examine global biogeographic patterns.
    背景与目标: :蝴蝶鱼(10属114种)是在全世界的珊瑚礁上发现的美丽而丰富的动物,由于其生态重要性和商业价值而受到了充分研究。存在基于形态学和分子数据的几种系统发育,但是在物种水平上为广泛的分类单元提供良好支持的分子系统发育仍有待解决。在这里,我们介绍了蝶类鱼类的分子系统发育,包括所有属的代表(Parachaetodon除外)和Chaetodon的所有普遍引用的亚属的至少一位代表(Roa sensuBlum,1988)。使用两个核和三个线粒体基因,总计3332个核苷酸,收集了71个内群和13个外群类群的遗传数据。贝叶斯推断,简约和最大似然方法产生了系统支持的系统发育,并为单系phyl科提供了强有力的支持。 Chaetodon亚属Exornator和Chaetodon被发现是多系的,而Amphichaetodon属不是该家族其他成员的基础姐妹群体。对来自5个基因的数据进行的分子系统发育分析与先前的系统发育研究一致地解析了一些进化枝,但是主要蝴蝶鱼群之间的关系拓扑与先前的假设有显着差异。分析回收了包含两栖类、,类,切尔蒙诺普斯,切尔蒙,Forcipiger,Hemitaurichthys,Johnrandallia和Heniochus的进化枝。与以前的假设一样,Prognathodes被确定为所有Chaetodon的姐妹,尽管亚属进化枝的拓扑结构与基于形态的假设有显着差异。我们使用蝶类的种系系统发育来解决有关在Chaetodon中使用亚属的长期存在的问题,以重建主要蝶类进化枝的分子速率和多样化日期的估计,并研究全球生物地理格局。
  • 【大鼠消化道的微生物生物地理学和核心微生物区系。】 复制标题 收藏 收藏
    DOI:10.1038/srep45840 复制DOI
    作者列表:Li D,Chen H,Mao B,Yang Q,Zhao J,Gu Z,Zhang H,Chen YQ,Chen W
    BACKGROUND & AIMS: :As a long-standing biomedical model, rats have been frequently used in studies exploring the correlations between gastrointestinal (GI) bacterial biota and diseases. In the present study, luminal and mucosal samples taken along the longitudinal axis of the rat digestive tract were subjected to 16S rRNA gene sequencing-based analysis to determine the baseline microbial composition. Results showed that the community diversity increased from the upper to lower GI segments and that the stratification of microbial communities as well as shift of microbial metabolites were driven by biogeographic location. A greater proportion of lactate-producing bacteria (such as Lactobacillus, Turicibacter and Streptococcus) were found in the stomach and small intestine, while anaerobic Lachnospiraceae and Ruminococcaceae, fermenting carbohydrates and plant aromatic compounds, constituted the bulk of the large-intestinal core microbiota where topologically distinct co-occurrence networks were constructed for the adjacent luminal and mucosal compartments. When comparing the GI microbiota from different hosts, we found that the rat microbial biogeography might represent a new reference, distinct from other murine animals. Our study provides the first comprehensive characterization of the rat GI microbiota landscape for the research community, laying the foundation for better understanding and predicting the disease-related alterations in microbial communities.
    背景与目标: :作为一种长期存在的生物医学模型,大鼠经常被用于研究胃肠道(GI)细菌菌群与疾病之间关系的研究。在本研究中,沿大鼠消化道纵轴采集的腔和粘膜样品经过基于16S rRNA基因测序的分析,以确定基线微生物组成。结果表明,群落多样性从上消化道段到下消化道段增加,并且微生物群落的分层以及微生物代谢产物的移动是由生物地理学位置决定的。在胃和小肠中发现了较大比例的产乳酸细菌(如乳酸杆菌,轮状杆菌和链球菌),而厌氧的乳酸杆菌科和瘤胃菌科则发酵碳水化合物和植物芳香化合物,构成了大肠核心微生物群的大部分。为相邻的腔和粘膜区室构建了拓扑学上截然不同的共现网络。当比较来自不同宿主的胃肠道微生物群时,我们发现大鼠微生物的生物地理学可能代表了一个新的参考,不同于其他鼠类动物。我们的研究为研究界首次提供了大鼠胃肠微生物群景观的全面表征,为更好地了解和预测微生物群落中与疾病相关的变化奠定了基础。
  • 【夏威夷大岛沿海水域浮游和底栖蓝细菌的生物地理学。】 复制标题 收藏 收藏
    DOI:10.1111/1574-6941.12337 复制DOI
    作者列表:Chamberlain SD,Kaplan KA,Modanu M,Sirianni KM,Annandale S,Hewson I
    BACKGROUND & AIMS: :Cyanobacteria are biogeochemically significant constituents of coral reef ecosystems; however, little is known about biotic and abiotic factors influencing the abundance and composition of cyanobacterial communities in fringing coral reef waters. To understand the patterns of cyanobacterial biogeography in relation to coastal environmental factors, we examined the diversity of planktonic and benthic cyanobacteria at 12 sites along the west coast of Hawaii's Big Island. We found distinct cyanobacterial communities in sediments compared to the water column. In both sediments and water, community structure was strongly related to overall biomass (chlorophyll a concentration), although both these communities corresponded to different sets of biotic/abiotic variables. To examine the influence of freshwater input on planktonic cyanobacterial communities, we conducted a mesocosm experiment where seawater was amended with freshwater from two sources representing high- and low-human population influence. Planktonic cyanobacterial abundance decreased over time in mesocosms, although chlorophyll a concentration significantly increased with time, indicating cyanobacteria were likely outcompeted by other phytoplankton in incubations. Our results show that cyanobacterial community structure may be affected by runoff from terrestrial habitats, but that the composition of cyanobacterial communities inhabiting these locations is also structured by factors not measured in this study.
    背景与目标: :蓝细菌是珊瑚礁生态系统的生物地球化学重要组成部分;然而,关于在珊瑚礁边缘水域影响蓝藻群落数量和组成的生物和非生物因素知之甚少。为了了解与沿海环境因素相关的蓝细菌生物地理格局,我们检查了夏威夷大岛西海岸12个地点的浮游和底栖蓝细菌的多样性。与水柱相比,我们在沉积物中发现了独特的蓝细菌群落。在沉积物和水中,群落结构都与总生物量(叶绿素a浓度)密切相关,尽管这两个群落对应于不同的生物/非生物变量集。为了检验淡水输入对浮游蓝藻群落的影响,我们进行了中观实验,其中海水被来自代表高人口和低人口影响的两个来源的淡水修正。尽管中叶的浮游藻类蓝细菌丰度随着时间的推移而降低,但是叶绿素a的浓度随时间显着增加,这表明在孵化中蓝藻细菌的竞争能力可能超过其他浮游植物。我们的结果表明,蓝细菌群落结构可能受到陆地生境径流的影响,但是居住在这些位置的蓝细菌群落的组成也受到本研究中未测量的因素的影响。
  • 【对广泛存在的,高度流动的物种(Odocoileus hemionus)的遗传结构进行全范围分析,揭示了历史生物地理学的重要性。】 复制标题 收藏 收藏
    DOI:10.1111/mec.12803 复制DOI
    作者列表:Latch EK,Reding DM,Heffelfinger JR,Alcalá-Galván CH,Rhodes OE Jr
    BACKGROUND & AIMS: :Highly mobile species that thrive in a wide range of habitats are expected to show little genetic differentiation across their range. A limited but growing number of studies have revealed that patterns of broad-scale genetic differentiation can and do emerge in vagile, continuously distributed species. However, these patterns are complex and often shaped by both historical and ecological factors. Comprehensive surveys of genetic variation at a broad scale and at high resolution are useful for detecting cryptic spatial genetic structure and for investigating the relative roles of historical and ecological processes in structuring widespread, highly mobile species. In this study, we analysed 10 microsatellite loci from over 1900 samples collected across the full range of mule deer (Odocoileus hemionus), one of the most widely distributed and abundant of all large mammal species in North America. Through both individual- and population-based analyses, we found evidence for three main genetic lineages, one corresponding to the 'mule deer' morphological type and two to the 'black-tailed deer' type. Historical biogeographic events likely are the primary drivers of genetic divergence in this species; boundaries of the three lineages correspond well with predictions based on Pleistocene glacial cycles, and substructure within each lineage demonstrates island vicariance. However, across large geographic areas, including the entire mule deer lineage, we found that genetic variation fit an isolation-by-distance pattern rather than discrete clusters. A lack of genetic structure across wide geographic areas of the continental west indicates that ecological processes have not resulted in restrictions to gene flow sufficient for spatial genetic structure to emerge. Our results have important implications for our understanding of evolutionary mechanisms of divergence, as well as for taxonomy, conservation and management.
    背景与目标: :在各种生境中繁衍的高度活动的物种预计在其整个范围内几乎没有遗传分化。数量有限但数量不断增长的研究表明,大规模的遗传分化模式可以而且确实出现在易变的,连续分布的物种中。但是,这些模式很复杂,并且经常受历史和生态因素的影响。对大规模和高分辨率的遗传变异进行全面调查,对于检测隐秘的空间遗传结构以及调查历史和生态过程在构造广泛的,高度活动的物种中的相对作用是有用的。在这项研究中,我们分析了从整个range鹿(Odocoileus hemionus)(北美洲所有大型哺乳动物中分布最广,种类最多的一种)中收集的1900多个样本中的10个微卫星基因座。通过基于个体和群体的分析,我们发现了三个主要遗传谱系的证据,一个对应于“ m鹿”形态类型,而两个对应于“黑尾鹿”类型。历史的生物地理事件可能是该物种遗传差异的主要驱动力;这三个世系的边界与基于更新世冰川周期的预测非常吻合,并且每个世系内的亚结构都表明了岛屿的变异。但是,在包括整个m鹿世系在内的广大地理区域中,我们发现遗传变异符合按距离隔离的模式,而不是离散的群集。整个西部大陆广泛的地理区域缺乏遗传结构,这表明生态过程并未导致对足以导致空间遗传结构出现的基因流动的限制。我们的结果对我们理解差异的进化机制以及分类学,保护和管理具有重要的意义。
  • 【银色叶猴物种群(Trachypithecus cristatus)的线粒体系统发育,分类学和生物地理学。】 复制标题 收藏 收藏
    DOI:10.1016/j.ympev.2008.03.006 复制DOI
    作者列表:Roos C,Nadler T,Walter L
    BACKGROUND & AIMS: :With a distribution ranging from mainland Southeast Asia to the Sunda region, the silvered langur species group is the most widely distributed species complex of the genus Trachypithecus. However, the systematic classification of its members and the phylogenetic relationships among them are less understood, leading to different classification schemes and proposed distribution zones. To address these issues, we sequenced a 573 bp long fragment of the mitochondrial cytochrome b gene from 115 silvered langurs (68 individuals from known origin). According to our data, five monophyletic clades were detected, which refer to the five taxa auratus, cristatus, germaini, margarita and mauritius. The phylogenetic relationships among them are not well resolved, indicating a radiation-like splitting event, which was estimated to have occurred about 0.95-1.25 mya. Within T. cristatus, two major clades were detected, with one comprising specimens from Sumatra, Borneo and the Natuna archipelago, and the other solely individuals from the Malaysian peninsula. According to our findings, we propose to rank all five taxa as distinct species. While T. auratus, T. germaini, T. margarita and T. mauritius seem to be monotypic, T. cristatus should be split into two subspecies, with the Malaysian form being described as new form here. From a phylogeographic perspective, the species group most likely originated on Java. During the early Pleistocene, its range was expanded to the Malaysian peninsula and to the Southeast Asian mainland. Later on, the Malaysian form colonised further regions of the Sunda region, including Sumatra, Borneo and the Natuna archipelago.
    背景与目标: 银叶猴种群分布在东南亚大陆到the他地区,是曲枝属中分布最广泛的种群。但是,对其成员的系统分类及其之间的系统发育关系了解甚少,从而导致了不同的分类方案和建议的分布区域。为了解决这些问题,我们对来自115个银叶猴(来自已知来源的68个个体)的线粒体细胞色素b基因的573 bp长片段进行了测序。根据我们的数据,检测到五个单系进化枝,它们分别代表五个类群,金龟子,生殖器,玛格丽塔和毛里求斯。它们之间的系统发育关系尚未得到很好的解决,这表明发生了类似辐射的分裂事件,据估计该事件已发生在0.95-1.25 mya左右。在T. cristatus内,检测到两个主要进化枝,其中一个包含苏门答腊,婆罗洲和纳图纳群岛的标本,另外一个仅来自马来西亚半岛。根据我们的发现,我们建议将所有五个分类单元分类为不同的物种。尽管金黄色T.geraini,T.germaini,T.margarita和T. mauritius似乎是单型的,但应将T. cristatus分为两个亚种,这里将马来西亚形式称为新形式。从种系学的角度来看,物种群最有可能起源于Java。在更新世早期,它的范围扩展到了马来西亚半岛和东南亚大陆。后来,马来西亚人在苏打达地区进一步殖民,包括苏门答腊,婆罗洲和纳图纳群岛。
  • 【海洋环流模型有助于预测远洋黄腹海蛇的全球生物地理。】 复制标题 收藏 收藏
    DOI:10.1098/rsbl.2016.0436 复制DOI
    作者列表:Brischoux F,Cotté C,Lillywhite HB,Bailleul F,Lalire M,Gaspar P
    BACKGROUND & AIMS: :It is well recognized that most marine vertebrates, and especially tetrapods, precisely orient and actively move in apparently homogeneous oceanic environments. Here, we investigate the presumptive role of oceanic currents in biogeographic patterns observed in a secondarily marine tetrapod, the yellow-bellied sea snake (Hydrophis [Pelamis] platurus). State-of-the-art world ocean circulation models show how H. platurus, the only pelagic species of sea snake, can potentially exploit oceanic currents to disperse and maintain population mixing between localities that spread over two-thirds of the Earth's circumference. The very close association of these snakes with surface currents seems to provide a highly efficient dispersal mechanism that allowed this species to range extensively and relatively quickly well beyond the central Indo-Pacific area, the centre of origin, abundance and diversity of sea snakes. Our results further suggest that the pan-oceanic population of this species must be extraordinarily large.
    背景与目标: :众所周知,大多数海洋脊椎动物,特别是四足动物,都在明显均质的海洋环境中精确定向并活动。在这里,我们研究了洋流在次生海洋四足动物黄腹海蛇(Hydrophis [Pelamis] platurus)中观察到的生物地理模式中的推定作用。世界上最先进的海洋环流模型显示出,海蛇是唯一的远洋物种H. platurus如何潜在地利用洋流来分散并维持分布在地球周长三分之二的各地区之间的人口混合。这些蛇与地表流的密切联系似乎提供了一种高效的扩散机制,使该物种能够广泛而相对迅速地分布在印度洋-太平洋中部地区,海蛇的起源中心,丰富度和多样性之外。我们的结果进一步表明,该物种的泛洋种群必须非常大。

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