BACKGROUND & AIMS: BACKGROUND:The colubrid snakes of the genus Rhynchocalamus are seldom studied and knowledge of their ecology and life history is scarce. Three species of Rhynchocalamus are currently recognized, R. satunini (from Turkey eastwards to Iran), R. arabicus (Yemen and Oman), and R. melanocephalus (from the Sinai Peninsula northwards to Turkey). All are slender, secretive, mainly nocturnal and rare fossorial snakes. This comprehensive study is the first to sample all known Rhynchocalamus species in order to review the intra-generic phylogenetic relationships and historical biogeography of the genus. METHODS:We revised the systematics of Rhynchocalamus using an integrative approach and evaluated its phylogeography. The phylogenetic position within the Colubridae and the phylogenetic relationships within the genus were inferred using 29 individuals belonging to the three known species, with additional sampling of two other closely-related genera, Muhtarophis and Lytorhynchus. We analysed three mitochondrial (12S, 16S, cytb) and one nuclear (c-mos) gene fragments. Phylogenetic trees were reconstructed using maximum likelihood and Bayesian inference methods; the latter method also used to provide the first time-calibrated molecular phylogeny of the genus. We generated a nuclear network and carried out a topology test and species delimitation analysis. Morphological comparisons were used to differentiate among species and to describe a new species from Israel. The studied material was comprised of 108 alcohol-preserved specimens, 15 photographs, and data from the literature for the examination of 17 mensural, 14 meristic, and two categorical characters. RESULTS:The molecular results support Rhynchocalamus as monophyletic, and as having split from its sister genus Lytorhynchus during the Late Oligocene. The three recognized species of Rhynchocalamus comprise four independently evolving groups. The molecular results reveal that the genus began to diverge during the Middle Miocene. We revealed that the best-studied species, R. melanocephalus, is paraphyletic. A population, formally ascribed to this species, from the Negev Mountain area in southern Israel is phylogenetically closer to R. arabicus from Oman than to the northern populations of the species from Israel, Syria and Turkey. Herein we describe this population as a new species: Rhynchocalamus dayanaesp. nov. DISCUSSION:We identify four species within Rhynchocalamus: R. satunini, R. arabicus, R. melanocephalus, and R. dayanaesp. nov., the latter, to the best of our knowledge, is endemic to southern Israel. The onset of Rhynchocalamus diversification is very old and estimated to have occurred during the Middle Miocene, possibly originating in the Levant region. Radiation probably resulted from vicariance and dispersal events caused by continuous geological instability, sea-level fluctuations and climatic changes within the Levant region.

背景与目标： 背景：很少对Rhynchocalamus属的蛇蝎蛇进行研究，并且对其生态学和生活史的知识很少。目前已识别出三种Rhynchocalamus，即R. satunini（从土耳其向东至伊朗），R。arabicus（也门和阿曼）和R. melanocephalus（从西奈半岛向北至土耳其）。所有这些都是细长的，隐秘的，主要是夜行性的和罕见的软体蛇。这项全面的研究是第一个对所有已知的Rhynchocalamus物种进行采样的方法，以回顾该属的种内系统发育关系和历史生物地理学。
方法：我们采用了综合方法修订了菱角龙的系统，并对其系统地理学进行了评估。通过使用属于三个已知物种的29个个体，以及另外两个紧密相关的属Muhtarophis和Lytorhynchus的样本，推断出Colubridae中的系统发育位置和属内的系统发育关系。我们分析了三个线粒体（12S，16S，cytb）和一个核（c-mos）基因片段。使用最大似然和贝叶斯推断方法重建系统发育树。后一种方法还用于提供该属的第一个经过时间校准的分子系统发育。我们生成了一个核网络，并进行了拓扑测试和物种定界分析。形态学比较用于区分物种并描述来自以色列的新物种。研究的材料包括108个保存酒精的标本，15张照片，以及来自文献的数据，用于检查17个经期，14个分类和两个分类特征。
结果：分子结果支持菱角单眼单变，并在渐新世晚期从其姊妹属Lytorhynchus分裂而来。 Rhynchocalamus的三个公认物种包括四个独立进化的群体。分子结果表明该属在中新世中期开始分化。我们发现，研究最好的物种R. melanocephalus是共生的。以色列南部内盖夫山区的一个正式归因于该物种的种群在系统发育上比来自以色列，叙利亚和土耳其的该物种的北部种群更接近来自阿曼的R. arabicus。在此，我们将该种群描述为一种新物种：Rhynchocalamus dayanaesp。十一月
讨论：我们确定了横纹兰内的四个物种：沙爹R. satunini，R。arabicus，R。melanocephalus和R. dayanaesp。据我们所知，后者是以色列南部的地方病。 Rhynchocalamus多样化的起源非常古老，据估计发生在中新世中期，可能起源于黎凡特地区。辐射可能是由于黎凡特地区内持续的地质不稳定，海平面涨落和气候变化引起的疏忽和扩散事件所致。

BACKGROUND & AIMS: Background and Aims:The breadfruit genus ( Artocarpus , Moraceae) includes valuable underutilized fruit tree crops with a centre of diversity in Southeast Asia. It belongs to the monophyletic tribe Artocarpeae, whose only other members include two small neotropical genera. This study aimed to reconstruct the phylogeny, estimate divergence dates and infer ancestral ranges of Artocarpeae, especially Artocarpus , to better understand spatial and temporal evolutionary relationships and dispersal patterns in a geologically complex region. Methods:To investigate the phylogeny and biogeography of Artocarpeae, this study used Bayesian and maximum likelihood approaches to analyze DNA sequences from six plastid and two nuclear regions from 75% of Artocarpus species, both neotropical Artocarpeae genera, and members of all other Moraceae tribes. Six fossil-based calibrations within the Moraceae family were used to infer divergence times. Ancestral areas and estimated dispersal events were also inferred. Key Results:Artocarpeae, Artocarpus and four monophyletic Artocarpus subgenera were well supported. A late Cretaceous origin of the Artocarpeae tribe in the Americas is inferred, followed by Eocene radiation of Artocarpus in Asia, with the greatest diversification occurring during the Miocene. Borneo is reconstructed as the ancestral range of Artocarpus , with dozens of independent in situ diversification events inferred there, as well as dispersal events to other regions of Southeast Asia. Dispersal pathways of Artocarpus and its ancestors are proposed. Conclusions:Borneo was central in the diversification of the genus Artocarpus and probably served as the centre from which species dispersed and diversified in several directions. The greatest amount of diversification is inferred to have occurred during the Miocene, when sea levels fluctuated and land connections frequently existed between Borneo, mainland Asia, Sumatra and Java. Many species found in these areas have extant overlapping ranges, suggesting that sympatric speciation may have occurred. By contrast, Artocarpus diversity east of Borneo (where many of the islands have no historical connections to the landmasses of the Sunda and Sahul shelves) is unique and probably the product of over water long-distance dispersal events and subsequent diversification in allopatry. This work represents the most comprehensive Artocarpus phylogeny and biogeography study to date and supports Borneo as an evolutionary biodiversity hotspot.

背景与目标： 背景和目的：面包果属（面包果，桑科）包括有价值的未充分利用的果树作物，其在东南亚具有多样性的中心。它属于单亲部落Artocarpeae，其唯一的其他成员包括两个小的新热带属。这项研究旨在重建系统的系统发育，估计面包果，特别是面包果的发散日期和推断祖先范围，以更好地了解地质复杂区域中的时空演化关系和扩散模式。
方法：为了研究面包car的系统发育和生物地理学，本研究使用贝叶斯和最大似然方法分析了7％的面包果物种的6个质体和2个核区域的DNA序列，这两个都是新热带的腕足动物属以及所有其他桑科部落的成员。桑科中的六种基于化石的标定用于推断发散时间。还推断出祖先区域和估计的传播事件。
关键结果：面包果，面包果和四个单生的面包果亚属得到了良好的支持。据推测，美洲白垩纪部落起源于白垩纪晚期，其次是亚洲的面包果始新世辐射，在中新世发生的变化最大。婆罗洲被重建为面包果的祖传范围，在那里推断出数十个独立的原位多样化事件，以及向东南亚其他地区的传播事件。提出了面包果及其祖先的传播途径。
结论：婆罗洲（Borneo）在面包果（Artocarpus）种类的多样化中处于中心地位，并且可能是物种在多个方向上分散和多样化的中心。推测最大程度的多样化发生在中新世时期，当时海平面波动，婆罗洲，亚洲大陆，苏门答腊和爪哇岛之间经常存在陆地联系。在这些地区发现的许多物种都存在广泛的重叠范围，这表明可能发生了同族物种形成。相比之下，婆罗洲以东（许多岛屿与Sun他河和萨胡尔大陆架的陆架之间没有历史联系）的面包果树多样性是独特的，可能是水上远距离扩散事件和随后的异相生物多样性的产物。这项工作代表了迄今为止最全面的面包果树系统发育和生物地理学研究，并支持婆罗洲成为进化性生物多样性热点。

BACKGROUND & AIMS: :Detecting range shifts and contractions is critical for determining the conservation priority of rare and declining taxa. However, data on rare species occurrences frequently lack precise information on locations and habitats and may present a biased picture of biogeographic distributions and presumed habitat preferences. Herbarium or museum specimen data, which otherwise could be useful proxies for detecting temporal trends and spatial patterns in species distributions, pose particular challenges. Using data from herbaria and Natural Heritage Programs on numbers of occurrences within individual municipalities (towns, cities, or townships), we quantified temporal changes in the estimated distributions of 110 rare plant species in the six New England (USA) states. We used the partial Solow equation and a nonparametric test to estimate the probability of observing multiple absences (gaps in the collection record) if a given population was actually still extant. Bayes' Theorem was used to estimate the probability that occurrences were misclassified as extinct. Using the probabilities obtained from these three methods, we eliminated taxa with high probabilities of pseudo-absence (that would yield an inaccurate profile of species distributions), narrowing the set for final analysis to 71 taxa. We then expressed occurrences as centroids of town polygons and estimated current and historical range areas (extents of occurrence as defined by alpha-hulls inscribing occurrences), mean distances between occurrences, and latitudinal and longitudinal range boundaries. Using a geographic information system, we modeled first, second, and third circular standard deviational polygons around the mean center of the historical range. Examining the distribution of current occurrences within each standard deviational polygon, we asked whether ranges were collapsing to a center, expanding, fragmenting, or contracting to a margin of the former range. Extant ranges of the species were, on average, almost 67% smaller than their historical ranges, and distances among occurrences decreased. Five New England hotspots were observed to contain >35% of rare plant populations. Extant occurrences were more frequently marginalized at the periphery of the historical range than would be expected by chance. Coarse-grained data on current and historical occurrences can be used to examine large suites of species to prioritize taxa and sites for conservation.

背景与目标： ：检测范围的变化和收缩对于确定稀有和下降的类群的保护优先级至关重要。但是，关于稀有物种发生的数据通常缺乏有关位置和栖息地的精确信息，并且可能呈现出生物地理分布和假定的栖息地偏好的偏见。植物标本室或博物馆的标本数据，否则可能是检测物种分布的时间趋势和空间格局的有用代理，这带来了特殊的挑战。使用来自草本植物和自然遗产计划的数据，了解各个城市（城镇，城市或乡镇）内的发生次数，我们量化了六个新英格兰州（美国）中110种稀有植物物种的估计分布的时间变化。如果给定的人口实际上仍然存在，我们使用偏Solow方程和非参数检验来估计观察到多个缺勤（收集记录中存在缺口）的可能性。贝叶斯定理用于估计发生错误归类为灭绝的可能性。使用从这三种方法获得的概率，我们消除了具有高度伪缺失概率的分类单元（这将导致物种分布的轮廓不准确），从而将最终分析的范围缩小到71个分类单元。然后，我们将事件表示为城镇多边形的质心，并估计当前和历史范围区域（由Alc外壳定义的出现范围来定义出现的程度），出现之间的平均距离以及纬度和纵向范围边界。使用地理信息系统，我们围绕历史范围的平均中心对第一，第二和第三圆形标准偏差多边形进行了建模。检查每个标准偏差多边形中当前事件的分布，我们询问范围是否塌陷到中心，正在扩展，碎片化或收缩到前一个范围的边缘。该物种的现存范围平均比其历史范围小了近67％，并且出现次数之间的距离减小了。观察到五个新英格兰热点地区占稀有植物种群的> 35％。在历史范围的外围，现存的事件比被偶然预期的更经常地被边缘化。可以使用有关当前和历史事件的粗粒度数据来检查大型物种，从而优先考虑分类单元和保护地点。

BACKGROUND & AIMS: :Specialists studying the genus Viola have consistently allied the Hawaiian violets comprising section Nosphinium--most of which are subshrubs or treelets--with putatively primitive subshrubs in certain South American violet groups. Hawaiian violets also possess inflorescences, a floral disposition otherwise found only in other genera of the Violaceae, thus strengthening the hypothesis of a very ancient origin for the Hawaiian species. A survey of phylogenetic relationships among infrageneric groups of Viola worldwide using nuclear rDNA internal transcribed spacer (ITS) sequences revealed a dramatically different biogeographic origin for the Hawaiian violets: A monophyletic Hawaiian clade was placed in a close sister relationship with the amphi-Beringian tundra violet, V. langsdorffii s. 1., in a highly derived position. This remarkable and unforeseen relationship received strong clade support values across analyses, and monophyly of the Hawaiian lineage was further indicated by a unique 26-base-pair deletion in section Nosphinium. The high polyploid base chromosome number (n approximately equal to 40) in the Hawaiian violets relates them to Alaskan and eastern Siberian populations in the polyploid V. langsdorffii complex. More than 50 species of the 260 allochthonous birds wintering in the Hawaiian Islands are found to breed in the Arctic, occupying habitats in which individual birds might have encountered ancestral V. langsdorffii populations and served as dispersers to the central Pacific region. Acquisition of derived morphological traits (e.g., arborescence and inflorescences), significance of a confirmed Arctic origin for a component of the Hawaiian flora, and the likelihood of other "cryptic" Arctic elements in the Hawaiian flora deserving independent molecular phylogenetic corroboration are discussed.

背景与目标： ：研究中提琴属的专家一直将组成Nosphinium的夏威夷紫罗兰（大部分是亚灌木或小乔木）与某些南美紫罗兰组中的原始亚灌木联系在一起。夏威夷紫罗兰还具有花序，否则只能在紫堇科的其他属中发现花序，因此加强了夏威夷物种起源很久的假设。使用核内rDNA内部转录间隔区（ITS）序列对世界各地中提琴中下属群体之间的系统发生关系进行的调查显示，夏威夷紫罗兰的生物地理起源存在显着不同：单系夏威夷进化枝与两栖类-柏林苔原紫罗兰有着密切的姐妹关系。 ，V. langsdorffii s。 1.处于高度派生的位置。这种惊人的，不可预见的关系在整个分析中都得到了强有力的进化支支持价值，夏威夷血统的单亲性在Nosphinium部分中独特的26个碱基对的缺失进一步表明了这一点。夏威夷紫罗兰中较高的多倍体基本染色体数目（n约等于40）使它们与多倍体郎氏多菌复合体中的阿拉斯加和西伯利亚东部种群有关。在夏威夷群岛越冬的260只异形鸟类中，有50多种在北极繁殖，它们栖息的栖息地中个别鸟类可能曾遇到过郎氏多氏菌祖先种群，并成为中太平洋地区的传播者。讨论了衍生形态特征的获取（例如乔木和花序），确定的夏威夷起源对于夏威夷植物区系组成部分的意义以及夏威夷植物区系中其他“隐秘”北极元素是否值得独立分子系统发育确证的可能性。

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。

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。

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。

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。

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。

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。

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。

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。

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。

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。

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。