河北中新世球果和果实及云南、浙江上新世化石木研究

本研究以河北围场县广发永化石点早中新世地层中的球果和果实、浙江宁海县杜岙化石点早上新世地层中的半矿化化石木、云南寻甸县金所和先锋化石点晚上新世地层中的丝炭和褐煤化木材为研究对象，对这三个化石点数百个植物大化石的形态或解剖结构进行了详细研究，鉴定出6个新的化石种，4个新记录种，7个未定种;其中2个化石属为我国新记录。根据其结构特征探讨这些化石类群与相关化石和现代植物的系统关系。并依据其现代亲缘种生长的生态和气候范围，对化石点沉积时期的植被和气候类型进行了推测。 果实中含有多种有价值的分类和系统发育的信息，对于种子植物的演化和系统发育研究具有重要的意义。在河北围场县发现大量保存较好的松科球果和姜科化石，为我们进一步研究松科植物和姜科植物解剖结构，以及探讨其系统演化提供难得的机会和直接的证据，同时为该化石地的植被演替和地层对比研究提供更多的植物学证据。对河北围场县广发永化石点球果和果实的形态研究，鉴定出三种松科球果化石种和一种姜科植物。分别为围场松（Pinus weichangensis sp. nov.）、围场云杉（Picea weichangensis sp. nov.）、围场铁杉（Tsuga weichangensis sp. nov.）以及化石Spirematospermum属未定种。其中围场云杉、围场铁杉球果在形态上与相应现代类群具有明显的差异，可能代表已灭绝的种类。Spirematospermum属未定种为一绝灭类型，是该属在我国的首次记录。这四种化石类群发现，反映早中新世化石该化石点气候与现代完全不同，为湿润的暖温带和亚热带气候。 浙江省在地质结构上位于东亚大陆边缘，是环太平洋岩浆活动带的重要组成部分。宁海县属于浙东南区属华南地层区，其第三纪地层嵊县群在该区分布广泛，其古植物研究仅限于孢粉和叶化石。本报告中首次对该层铜岭祝组的木化石进行了报道。对浙江宁海杜岙化石点早上新世地层中化石木样品的解剖研究，鉴定出三种木材类型，为史马库栎型木Quercus shimakurae、Liqumdambar cf. hisauchi和蔷薇科未定种。前者与现代栎属槲栎类、后者与枫香树属分别具有密切的亲缘关系，是我国首次报道栎属和枫香树属化石木。 云南现今复杂的地势地貌，独特的气候，丰富的植物种类和多样的植被类型是经历了长达数百万年的地质构造运动和自然环境演变的结果。第三纪时期由于大陆板块运动导致印度板块与亚洲板块的对接和碰撞，其地壳构造运动异常活跃。其第三系陆相地层广泛分布于古生代褶皱区的200多个互不相连的中、小型盆地及中、新生代断陷和拗陷型山间盆地中，并蕴涵了丰富的植物化石，为我们研究植被和植物演化提供了众多的证据。本次研究基于云南中部寻甸县金所煤矿和先锋煤矿的大量褐煤化和丝炭化材料，为进一步恢复云南晚第三纪气候和植被提供更多的依据，尤其是丝炭材料保存了木材精细而真实的结构，为木材准确鉴定和演化提供了可靠的依据。根据对云南金所和先锋化石点晚上新世沉积中褐煤化材料和丝炭样品解剖结构的研究，鉴定出8种化石木，包括2种裸子植物，5种双子叶植物和1种单子叶植物;分属5科7属。化石类群包括松属（Pinus）五针松组未定种Section Cembra sp.、云杉属未定种Picea sp、寻甸含笑Michelia xundianensis sp. nov.、多角含笑 Michelia angulata sp. nov.、Lithocarpoxylon cf. radiporosum、Castanoradix sp.、寻甸珍珠花Lyonia xundianensis sp. nov.、竹亚科未定种Bambusoideae sp。根据现今这些化石对应类群的生长和分布的气候区域，沉积时期的气候与现代气候较为接近。

杉科植物的表皮结构研究及古环境重建

全球古近纪和新近纪气候波动明显，很多科学家对古近纪和新近纪生物演化和气候演变规律的定量研究给予了相当的重视。杉科植物有长期发展的历史、少数的现存种和丰富的化石记录，成为指示古环境的理想植物之一。利用杉科植物重建古环境，首先要对化石植物进行正确的分类鉴定。杉科各属枝叶形态特征变异幅度较大，且枝叶排列和形态特征近似，有时各属之间存在交叉特征。杉科化石标本通常仅保存枝叶形式，且多个属的化石标本经常发现于同一地层，因而分类鉴定比较困难。植物的叶表皮结构是压型植物化石细胞信息的重要来源，是属种分类鉴定重要依据之一。本文在以往研究的基础上，完整分析了杉科9属现生植物的表皮特征，建立了杉科化石植物分类鉴定的现生植物的表皮特征参照系。 杉科植物的叶多为条形、钻形、鳞形或披针形，同种植物有1种、2种甚至3种叶型。其中水杉属的叶交互对生，其它属的叶螺旋状互生。水杉属的多数表皮细胞垂周壁明显弯曲，落羽杉属和杉木属有时微呈波状，其他属的表皮细胞垂周壁直。多数植物的叶片近轴面和远轴面的气孔数量和分布不同。一般来说，条形叶和披针形叶的远轴面气孔分布状况和气孔数量稳定，远轴面的中部最稳定。条形叶远轴面的气孔分布于中脉两侧，形成纵向的气孔带。条形叶近轴面气孔分布状况和气孔数量变化大，近轴面的气孔数量有时与远轴面近似，但多数情况下比远轴面少，有时整个叶片的近轴面仅少数几个气孔或没有气孔分布。钻形叶的近轴面和远轴面的气孔数量近似，或叶片近轴面的气孔数量比远轴面的气孔数量多，气孔分布范围也比远轴面气孔分布范围广。气孔椭圆形，落羽杉属植物和水松鳞形叶的气孔长轴方向与叶片长轴垂直或斜向排列，柳杉属植物的气孔多斜向排列，水松的条形叶和条状钻形叶的气孔多平行向排列。落羽杉属和柳杉属以外的杉科植物的气孔长轴多数与叶片长轴平行。在扫描电子显微镜下的密叶杉属植物叶片角质层的内表面，副卫细胞和表皮细胞的垂周壁与叶表面的角度一致，且副卫细胞的形态与表皮细胞类似，这种特殊气孔器被称为A-型气孔器。杉科植物中水杉属、落羽杉属和杉木属的气孔器近似密叶杉的这种A-型气孔器。台湾杉属、柳杉属、水松属、红杉属和巨杉属植物的气孔器与这种A-型气孔器不同，这几属的副卫细胞垂周壁表皮细胞的垂周壁方向不同，且副卫细胞的形态与表皮细胞的形态明显不同。因而气孔所有副卫细胞组成呈明显的圆盘状，保卫细胞在盘子的中央。综合分析植物的枝叶形态和表皮特征可以区分杉科各属。 本文研究了采自抚顺始新世的杉科植物标本，经枝叶特征、表皮结构和球果鳞片等特征分析为水松属的欧洲水松。论文分析了中国东北地区古温度定量研究结果与杉科植物的相关性。抚顺植物群发现有化石水杉M. occidentalis、中华红杉和欧洲水松，根据这三种化石植物的年均温度和年降水量，通过共存分析，推测抚顺始新世的年均温为12.1-17℃，年降水量为1199.6-2231mm。

买麻藤目的化石记录及其与 被子植物起源关系的探讨

二十世纪初，前人在中国的东北地区发现了大量保存完好的动物化石，其中以狼鳍鱼最具代表性，科学家将在该地区发现的化石生物群命名为“热河生物群”。“热河”这一名称得名于该化石群的经典产地，即当时的热河省东部地区。建国后，热河省被撤消，其西部划归河北省，东部划归辽宁省。原热河生物群的经典产地因此落在了今天辽宁省的西部，即辽西地区。但是，“热河生物群”这一在地质古生物学界具有深刻影响的名称仍然保留着，而且近几年来在该地区又有大量的鸟类以及恐龙的化石被发现。该地区现在已经成为世界级的古生物宝库。通过不同的方法对该地区进行时代测定的结果认为该地区的时代为白垩纪早期。 与发现众多、研究深入的动物群相比，在该地区开展的植物学研究起步较晚，但在最近几年取得了很大的进展。目前为止，已经发现的植物类群就有苔藓、蕨类、银杏、苏铁、松柏类和被子植物。其中，银杏、苏铁、松柏类尤为丰富。理论上，被子植物也正是从该生物群所代表的白垩纪早期开始出现并逐步走向繁荣的。近年来在热河生物群中就有不少关于被子植物早期类群的报道，如古果属A rchaefructus和里海果属Hyrcantha等。传统上认为，买麻藤目植物与被子植物起源的关系非常密切，但是最近的分子系统学研究却将该类群推离了被子植物，而作为裸子植物高等类群松柏类的姐妹群对待。但是，在热河生物群中的一些新买麻藤目植物的化石标本与被子植物早期类型化石标本的发现却提供了新的思路或证据。如近年来，我国学者已经在该生物群中报道的麻黄科下的2属4种。这些发现的类群都与买麻藤植物的基部类群麻黄属密切相关。这种新发现带来的证据或许可以为被子植物起源这一世界难题的解决提供新的思路。 在对前人关于买麻藤目植物化石标本的研究进行整理的时候，我们发现我们的部分化石与前人发表的一个种Ephedrites chenii在标本的形态学特征方面完全相同。但是在对该类群及其所在的属与麻黄的现代类群作对比研究后发现，该种植物的繁殖器官的特征完全符合麻黄属的特征，因此将该类群转移到麻黄属中作为新组合对待。另外，根据前人对该种在种加词的命名上的修改，我们将该新组合命名为Ephedra cheniae。 在调查该生物群中的买麻藤植物时，我们发现在部分化石类群中出现了前人没有记载过的新性状，比如在麻黄科类植物中发现了互生的分枝方式，并据此命名一个新的单种属Alloephedra xingxuei。为了探讨互生分枝这一性状对于麻黄科的分类意义，我们调查了国内外不少标本馆中的标本，并在野外做了取样统计。结果发现，在不少现代麻黄的枝条上都出现了不同程度的分枝发育不均衡，表现为在同一节上对生的两个分枝中一侧分枝能够正常发育而另一侧发育迟缓甚至不发育，这种不均衡的发育造成了在现代麻黄中出现了类似互生的分枝状况。在整理前人对麻黄分枝方式研究的基础上，结合我们对野外类群形态学性状的调查，我们认为由于在同一节上对生的两个分枝中一侧延迟或不发育而引起的类似互生的性状是较为广泛存在的，它不应该成为属一级的分类依据，而只能作为种一级的分类依据对待。因此我们将AHoephedra xingxuei转移到麻黄属中作为新组合Ephedra xingxuei处理。 除此之外，我们也发现了不少其他的买麻藤目化石标本，在对买麻藤目以往的化石记录了解以及对这些标本形态学性状把握的基础上，我们将这些新发现的化石标本放置在麻黄科麻黄属中作为新种对待，并根据其叶片以及苞片的特征分别将他们命名为披针叶麻黄（Ephedra lanceoleta）、裂叶麻黄（Ephedra divisa），卵叶麻黄（Ephedra ovata）以及双苞麻黄（Ephedra bibracta）。 与此同时，我们也发现了保存完好的被子植物的化石标本。该标本中具有5个离生的心皮、分枝方式兼具侧生和二叉分枝两种、并具有多裂的叶片。在辽西地区同时代发现的被子植物早期类型共有两个，分别是Archaefructus和Hyrcantha。其中前者具有许多个离生的螺旋状排列在可育枝的顶端1cm内的子房／心皮，而后者只有2-4个子房／心皮。在对我们新发现的化石标本与这两个被子植物的早期类型在叶片形态、分枝式样、果实大小、果实构成、果实排布、心 皮数目等形态学特征对比的基础上，我们认为新的化石标本描述了一个被子植物早期类群的新形态，并根据其具有五个心皮以及多裂的叶片的特征，命名为裂叶文采果Wentsaia divisa gen.＆sp. nov。 由于我们有幸能在辽西同时发现了买麻藤植物的化石标本和被子植物早期类型的标本，这就给了我们一个讨论二者在起源关系方面的机会。在对二者的营养器官特征、繁殖器官结构组成、繁殖器官性别构成以及对二者生活环境理解进行对比的基础上，我们认为，买麻藤目植物的早期类型与被子植物的早期类型之间存在相关性。但是就目前的证据而言，尚无法推测二者之间是否存在性状上的演化关系，而该问题的解决需要更多的化石证据的积累。

岷江中上游植被生态恢复过程中若干问题的探讨

　1．对四川省岷江上游地区（茂县）的锐齿槲栎（Quercus aliena var. acuteserrata）天然次生林进行研究，发现：(1) 坚果完好比例约在14% ~26%之间，完好坚果的发芽率和发芽势都比较高，但在天然状况下能够留存到翌年5月的坚果几乎没有。因此，实生幼苗的天然补充就受到了严重的限制。(2) 林缘的幼苗密度低于所有其它生境的 (P<0.05)，林中的幼苗密度最高，和林窗的比较有显著差异(P<0.05), 而和灌丛的比较则差异不显著（P>0.05）。在灌丛幼苗密度和林中以及林窗的比较都没有差异。动物对坚果的取食速度则是林中的最慢 (10.0%)，林窗和林缘的基本相同(分别为61.1%和66.5%)，取食速度都明显快于林中(P<0.01)。(3) 林中的幼苗在小于100 cm的各高度内都有大量分布，说明在林中树冠下幼苗是可以长期存在的，暗示在幼苗阶段的锐齿槲栎可能是耐荫的。(4) 在林中缺失幼树，在林缘则有包括幼树在内的完整的更新大小系列，表明林缘是更新的关键地点。(5) 在栎林的每一个大小级别上，萌生个体和实生个体都按各种比例伴生，说明导致萌生的干扰一直在发生，并可能在森林的更新中扮演重要角色;也说明该地区的锐齿槲栎林由萌生和实生起源的个体混合组成。 2．栎林是北半球温带森林的重要组成部分，因此栎林更新是全球森林更新研究的热点之一，而啮齿动物对栎林更新的影响则是关注的焦点。在2002~2003年，通过坚果标记研究了未被取食和遗弃坚果（即咬开后只有少部分被捕食后丢弃在林中的坚果）的健康比例，并定量测定了坚果的捕食、搬运、遗弃、丢弃、贮藏和留存等各种命运的比例和特点;对坚果也进行了各种人为的处理，以观测其命运和动物取食速度，发现：(1) 遗弃坚果中不健康坚果的比例比动物未取食的天然坚果中的比例有极显著的增加 (P>0.05)，暗示啮齿动物一般是通过咬开坚果来识别坚果健康与否并决定是否捕食。(2) 根据坚果命运和对照相比改变与否以及如何改变，各种人工处理坚果的命运可以分为 4 类：① 坚果命运没有任何显著改变;② 坚果被就地捕食的速度降低，搬运的速度不变，最终搬运坚果的比例增加而就地捕食坚果的比例降低，留存坚果的比例偶尔能增加至0.2%;③ 坚果就地捕食的速度几乎降至0，搬运的速度则在下降一段时间后又上升，并且搬运作用持续了相对长的时间，最终搬运坚果的比例大大增加，就地捕食坚果的比例很低，留存率为0;④ 坚果被搬运和就地捕食的速度和比例都降低，留存坚果的比例相应的大大增加，甚至可以达到50%。(3) 命运得到显著改变的②、③、④类坚果所承受的人工处理按照作用方式又可以分为主要作用于坚果化学状态（即气味浓度）的处理、主要作用于坚果物理状态（颜色、形态、有无附属物等）的处理以及使坚果处于不同颜色背景的处理;其中主要作用于坚果化学状态的处理对坚果命运具有最重大的改变，如胶带包裹处理和烧焦处理;其它各种主要作用于坚果的物理状态和所处背景的处理对其命运则也具有相对轻微的改变。这一试验结果可能证明：啮齿动物在对坚果进行识别和取食选择等活动时主要依赖于嗅觉来感知坚果的可食性，但是能感觉物理状态和所处背景的视觉也起一定程度的作用。(4) 啮齿动物对栎树坚果进行就地捕食、遗弃、搬运、异地捕食、丢弃、贮藏等作用，使各种命运的坚果都具有一定的数量比例和特点，也提供了动物影响栎林更新的多种可能途径。 3．人工干扰是任何退化生态系统中都始终存在的重大问题。除了明显的砍伐或者采摘外，人工践踏也是一种重要的干扰，特别是在茂县的山林普遍被牛马不断的放牧的情况下，这个干扰的后果就更加显著。为此研究了人脚踩踏的路上的白车轴草和未踩踏草坪上白车轴草在最大叶长、株高、芽高、构件数量、构件平均鲜重、死叶数量、根长等构型指标，根、茎、叶三者的生物量（干重）及比例等生物量指标，平均花序数量、花平均数量等繁殖指标方面的不同，发现踩踏使白车轴草植株：(1) 株高降低，芽高降低，最大叶长变小，平均每厘米的构件数量增加，构件平均鲜重降低，根长度减小，死叶数量增加。(2) 平均花序数量下降，每花序的花平均数量下降。(3) 但是在生物量的分配上，根和茎的生物量没有显著的下降，但是叶的生物量显著减低。因为白车轴草的茎可以不断克隆繁殖，所以踩踏对其存活可能没有太大的影响，只是造成了植株的矮化和密集化，根也变短;但是对种子繁殖有重大影响，反映在平均花序数量和每花序平均花数的显著下降上。在生物量的分配中，作为主要的同化器官，叶的生物量显著下降，而根茎比没有变化。这可能说明这样的克隆植物其物质流动是呈现网络化的特征，具有比较强的抗干扰能力。 4．连香树、油松、日本落叶松、华山松油松混合林是茂县地区的几种主要的已经营造的林型或者树种。为了了解其20年来的营林效果，运用样方调查的方法测量了这几种树种或者林型的胸径、持水量、凋落物现存量、密度等，评价了它们在生长、营业循环和水土保持等方面的差异。结果表明：日本落叶松具有生长缓慢，凋落物现存量大，涵养水分能力良好的树种，值得推广;油松生长迅速，凋落物现存量巨大，涵养水分能力一般的树种，也可以大力栽植;油松和华山松的混交林具有比较大的蓄积量和较好的涵养水分的能力，可以推广;而连香树则做为生长速度中等，成材率低，凋落物现存量小，涵养水分能力差的树种，不应该进一步推广。

Chromosome painting in the long-tailed field mouse provides insights into the ancestral murid karyotype

We report on the hybridization of mouse chromosomal paints to Apodemus sylvaticus, the long-tailed field mouse. The mouse paints detected 38 conserved segments in the Apodemus karyotype. Together with the species reported here there are now six species of rodents mapped with Mus musculus painting probes. A parsimony analysis indicated that the syntenies of nine M. musculus chromosomes were most likely already formed in the muroid ancestor: 3, 4, 7, 9, 14, 18, 19, X and Y. The widespread occurrence of syntenic segment associations of mouse chromosomes 1/17, 2/13, 7/19, 10/17, 11/16, 12/17 and 13/15 suggests that these associations were ancestral syntenies for muroid rodents. The muroid ancestral karyotype probably had a diploid number of about 2n = 54. It would be desirable to have a richer phylogenetic array of species before any final conclusions are drawn about the Muridae ancestral karyotype. The ancestral karyotype presented here should be considered as a working hypothesis. Copyright (C) 2004 S. Karger AG, Basel.

MULTIPLE GENOTYPES OF MITOCHONDRIAL-DNA WITHIN A HORSE POPULATION FROM A SMALL REGION IN YUNNAN PROVINCE OF CHINA

mtDNA genotypes of six domestic horses (three adult short horses whose heights are under 1 m and three common domestic horses) from a small region of 15 km(2) in Malipo county of Yunnan province of China were investigated by the technique of restriction fragment length polymorphism (RFLP) with restriction endonucleases which recognize 6-bp sequences. An average of fragments for an individual was obtained. Unlike other domestic animals, this population of horses exhibits high mtDNA genetic diversity. Each of the six horses has a specific mtDNA genotype showing a pattern of multiple maternal origins, as suggested by fossil and literature records. We think the population of horses is an amazing seed-resource pool of horses and hence deserves to be paid more attention from the view of conservation genetics. However it is also remarkable that we did not find any typical mtDNA genetic markers which would discriminate between short horses and common domestic horses.

Y-chromosome evidence of southern origin of the East Asian - Specific haplogroup O3-M122

The prehistoric peopling of East Asia by modern humans remains controversial with respect to early population migrations. Here, we present a systematic sampling and genetic screening of an East Asian-specific Y-chromosome haplogroup (O3-M122) in 2,332 individuals from diverse East Asian populations. Our results indicate that the O3-M122 lineage is dominant in East Asian populations, with an average frequency of 44.3%. The microsatellite data show that the O3-M122 haplotypes in southern East Asia are more diverse than those in northern East Asia, suggesting a southern origin of the O3-M122 mutation. It was estimated that the early northward migration of the O3-M122 lineages in East Asia occurred similar to 25,000-30,000 years ago, consistent with the fossil records of modern humans in East Asia.

Phylogenetic study of complete cytochrome b genes in musk deer (genus Moschus) using museum samples

As an endangered animal group, musk deer (genus Moschus) are not only a great concern of wildlife conservation, but also of special interest to evolutionary studies due to long-standing arguments on the taxonomic and phylogenetic associations in this group. Using museum samples, we sequenced complete mitochondrial cytochrome b genes (1140 bp) of all suggested species of musk deer in order to reconstruct their phylogenetic history through molecular information. Our results showed that the cytochrome b gene tree is rather robust and concurred for all the algorithms employed (parsimony, maximum likelihood, and distance methods). Further, the relative rate test indicated a constant sequence substitution rate among all the species, permitting the dating of divergence events by molecular clock. According to the molecular topology, M. moschiferus branched off the earliest from a common ancestor of musk deer (about 700,000 years ago); then followed the bifurcation forming the M. berezouskii lineage and the lineage clustering M. fuscus, M. chrysogaster, and M. leucogaster (around 370,000 years before present), interestingly the most recent speciation event in musk deer happened rather recently (140,000 years ago), which might have resulted from the diversified habitats and geographic barriers in southwest China caused by gigantic movements of the Qinghai-Tibetan Plateau in history. Combining the data of current distributions, fossil records, and molecular data of this study, we suggest that the historical dispersion of musk deer might be from north to south in China. Additionally, in our further analyses involving other pecora species, musk deer was strongly supported as a monophyletic group and a valid family in Artiodactyla, closely related to Cervidae. (C) 1999 Academic Press.

啮齿目泌乳刺激素基因家族的分子进化研究

在大鼠基因组数据库中搜索得到两个泌乳刺激素基因家族的新成员.进一步分析显示该基因家族起源于啮齿目和其他哺乳动物分歧之后,而且大部分基因座位的重排在大、小鼠分歧之前已经完成.但PL-Ⅰ和PL-Ⅱ基因簇却是例外,它们在基因树上以物种特异的方式聚类.结合基因转换的检验、染色体上相对位置比较和基因重复时间估计的结果,认为啮齿目PL-Ⅰ和PL-Ⅱ基因是物种特异的,它们由一系列在大、小鼠分歧之后发生的基因重复事件形成.结果还揭示了在啮齿目泌乳刺激素基因家族进化过程中持续不断的发生了基因重复和基因分化事件.

Phylogenetic relationships of five pika species (genus Ochotona) based on mitochondrial DNA restriction maps

Restriction site mapping of mitochondrial DNA (mtDNA) with 16 restriction endonucleases was used to examine the phylogenetic relationships of Ochotona cansus, O. huangensis, O. thibetana, O. curzoniae and O. erythrotis. A 1-kb length variation between O. erythrotis of subgenus Pika and other four species of subgenus Ochotona was observed, which may be a useful genetic marker for identifying the two subgenera. The phylogenetic tree constructed using PAUP based on 61 phylogenetically informative sites suggests that O. erythrotis diverged first, followed by O. cansus, while O. curzoniae and O. huangensis are sister taxa related to O. thibetana, The results indicate that both O. cansus and O. huangensis should be treated as independent species. If the base substitution rate of pikas mtDNA was 2% per million years, then the divergence time of the two subgenera, Pika and Ochotana, is about 8.8 Ma ago of late Miocence, middle Bao-dian of Chinese mammalian age, and the divergence of the four species in subgenus Ochotona would have occurred about 2.5 - 4.2 Ma ago, Yushean of Chinese mammalian age. This calculation appears to be substantiated by the fossil record.

Sequence evolution of the CCR5 chemokine receptor gene in primates

The chemokine receptor CCR5 can serve as a coreceptor for M-tropic HIV-1 infection and both M-tropic and T-tropic SIV infection. We sequenced the entire CCR5 gene from 10 nonhuman primates: Pongo pygmaeus, Hylobates leucogenys, Trachypithecus francoisi, Trachypithecus phayrei, Pygathrix nemaeus, Rhinopithecus roxellanae, Rhinopithecus bieti, Rhinopithecus avunculus, Macaca assamensis, and Macaca arctoides. When compared with CCR5 sequences from humans and other primates, our results demonstrate that:(1) nucleotide and amino acid sequences of CCR5 among primates are highly homologous, with variations slightly concentrated on the amino and carboxyl termini; and (2) site Asp13, which is critical for CD4-independent binding of SIV gp120 to Macaca mulatta CCR5, was also present in all other nonhuman primates tested here, suggesting that those nonhuman primate CCR5s might also bind SIV gp120 without the presence of CD4. The topologies of CCR5 gene trees constructed here conflict with the putative opinion that the snub-nosed langurs compose a monophyletic group, suggesting that the CCR5 gene may not be a good genetic marker for low-level phylogenetic analysis. The evolutionary rate of CCR5 was calculated, and our results suggest a slowdown in primates after they diverged from rodents. The synonymous mutation rate of CCR5 in primates is constant, about 1.1 x 10(-9) synonymous mutations per site per year. Comparisons of K-a and K-s suggest that the CCR5 genes have undergone negative or purifying selection. K-a/K-s ratios from cercopithecines and colobines are significantly different, implying that selective pressures have played different roles in the two lineages.

Evolutionary trends of the mitochondrial lineage differentiation in species of genera Martes and Mustela

We compared partial sequences (402 bp) of the mitochondrial cytochrome b gene in 68 individuals of martens (Martes), weasels (Mustela) and their relatives from the Northern Hemisphere to identify the modes of geographic differentiation in each species. We then compared complete sequences (1140 bp) of the gene in 17 species of the family Mustelidae to know the spatial and temporal modes of speciation, constructing linearized trees with transversional substitutions for deeper lineage divergences and with transversions and transitions for younger lineages. Our data suggested that these lineages of Martes and Mustela differentiated in a stepwise fashion with five radiation stages from the generic divergences (stage I) to the intraspecific divergences (stage V), during the last 10 or 20 million years as the fossil evidence suggests. In the lineage of Martes, the first offshoots are of Martes flavigula, M. pennanti, and Gulo gulo (stage II), the second is M. foina (stage III), and the third are M. americana, M. martes, M. melampus, and M. zibellina (stage IV). The divergence of the lineages of Mustela is likely to have taken place concurrently with the radiations of the Martes. These divergence processes are attributable in part to the geographic allocation along the two continents, North America and Eurasia, as well as among peripheral insular domains, such as Taiwan and the Japanese Islands. In addition, the Eurasian continent itself was shown to have been involved in the species diversification in the martens and weasels.

Episodic evolution of prolactin receptor gene in mammals: coevolution with its ligand

Divergence of proteins in signaling pathways requires ligand and receptor coevolution to maintain or improve binding affinity and/or specificity. In this paper we show a clear case of coevolution between the prolactin (PRL) gene and its receptor (prolactin receptor, PRLR) in mammals. First we observed episodic evolution of the extracellular and intracellular domains of the PRLR, which is closely consistent with that seen in PRL. Correlated evolution was demonstrated both between PRL and its receptor and between the two domains of the PRLR using Pearson's correlation coefficient. On comparing the ratio of the nonsynonymous substitution rate to synonymous substitution rate (omega=d(N)/d(S)) for each branch of the star phylogeny of mammalian PRLRs, separately for the extracellular domain (ECD) and the transmembrane domain/intracellular domain (TMD/ICD), we observed a lower omega ratio for ECD than TMD/ICD along those branches leading to pig, dog and rabbit but a higher ratio for ECD than TMD/ICD on the branches leading to primates, rodents and ruminants, on which bursts of rapid evolution were observed. These observations can be best explained by coevolution between PRL and its receptor and between the two domains of the PRLR.

Evolutionary implications of multiple SINE insertions in an intronic region from diverse mammals

An analysis of the nuclear beta-fibrinogen intron 7 locus from 30 taxa representing 12 placental orders of mammals reveals the enriched occurrences of short interspersed clement (SINE) insertion events. Mammalian-wide interspersed repeats (MIRs) are present at orthologous sites of all examined species except those in the order Rodentia. The higher substitution rate in mouse and a rare MIR deletion from rat account for the absence of MIR in the rodents. A minimum of five lineage-specific SINE sequences are also found to have independently inserted into this intron in Carnivora, Artiodactyla and Lagomorpha. In the case of Carnivora, the unique amplification pattern of order-specific CAN SINE provides important evidence for the "pan-carnivore" hypothesis of this repeat element and reveals that the CAN SINE family may still be active today. Particularly interesting is the finding that all identified lineage-specific SINE elements show a strong tendency to insert within or in very close proximity to the preexisting MIRs for their efficient integrations, suggesting that the MIR clement is a hot spot for successive insertions of other SINEs. The unexpected MIR excision as a result of a random deletion in the rat intron locus and the non-random site targeting detected by this study indicate that SINEs actually have a greater insertional flexibility and regional specificity than had previously been recognized. Implications for SINE sequence evolution upon and following integration, as well as the fascinating interactions between retroposons and the host genomes are discussed.

A multi-locus phylogeny of Nectogalini shrews and influences of the paleoclimate on speciation and evolution

Nectogaline shrews are a major component of the small mammalian fauna of Europe and Asia, and are notable for their diverse ecology, including utilization of aquatic habitats. So far, molecular phylogenetic analyses including nectogaline species have been unable to infer a well-resolved, well-supported phylogeny, thus limiting the power of comparative evolutionary and ecological analyses of the group. Here, we employ Bayesian phylogenetic analyses of eight mitochondrial and three nuclear genes to infer the phylogenetic relationships of nectogaline shrews. We subsequently use this phylogeny to assess the genetic diversity within the genus Episoriculus, and determine whether adaptation to aquatic habitats evolved independently multiple times. Moreover, we both analyze the fossil record and employ Bayesian relaxed clock divergence dating analyses of DNA to assess the impact of historical global climate change on the biogeography of Nectogalini. We infer strong support for the polyphyly of the genus Episoriculus. We also find strong evidence that the ability to heavily utilize aquatic habitats evolved independently in both Neomys and Chimarrogale + Nectogale lineages. Our Bayesian molecular divergence analysis suggests that the early history of Nectogalini is characterized by a rapid radiation at the Miocene/Pliocene boundary, thus potentially explaining the lack of resolution at the base of the tree. Finally, we find evidence that nectogalines once inhabited northern latitudes, but the global cooling and desiccating events at the Miocene/Pliocene and Pliocene/Pleistocene boundaries and Pleistocene glaciation resulted in the migration of most Nectogalini lineages to their present day southern distribution. (C) 2010 Elsevier Inc. All rights reserved.