Adaptive diversification of vomeronasal receptor 1 genes in rodents

The vomeronasal receptor 1 (V1R) are believed to be pheromone receptors in rodents. Here we used computational methods to identify 95 and 62 new putative V1R genes from the draft rat and mouse genome sequence, respectively. The rat V1R repertoire consists of 11 subfamilies, 10 of which are shared with the mouse, while rat appears to lack the H and I subfamilies found in mouse and possesses one unique subfamily (M). The estimations of the relative divergence times suggest that many subfamilies originated after the split of rodents and primates. The analysis also reveals that these clusters underwent an expansion very close to the split of mouse and rat. In addition, maximum likelihood analysis showed that the nonsynonymous and synonymous rate ratio for most of these clusters was much higher than one, suggesting the role of positive selection in the diversification of these duplicated V1R genes. Because V1R are thought to mediate the process of signal transduction in response to pheromone detection, we speculate that the V1R genes have evolved under positive Darwinian selection to maintain the ability to discriminate between large and complex pheromonal mixtures.

Stepwise loss of motilin and its specific receptor genes in rodents

Specific interactions among biomolecules drive virtually all cellular functions and underlie phenotypic complexity and diversity. Biomolecules are not isolated particles, but are elements of integrated interaction networks, and play their roles through specific interactions. Simultaneous emergence or loss of multiple interacting partners is unlikely. If one of the interacting partners is lost, then what are the evolutionary consequences for the retained partner? Taking advantages of the availability of the large number of mammalian genome sequences and knowledge of phylogenetic relationships of the species, we examined the evolutionary fate of the motilin (MLN) hormone gene, after the pseudogenization of its specific receptor, MLN receptor (MLNR), on the rodent lineage. We speculate that the MLNR gene became a pseudogene before the divergence of the squirrel and other rodents about 75 mya. The evolutionary consequences for the MLN gene were diverse. While an intact open reading frame for the MLN gene, which appears functional, was preserved in the kangaroo rat, the MLN gene became inactivated independently on the lineages leading to the guinea pig and the common ancestor of the mouse and rat. Gain and loss of specific interactions among biomolecules through the birth and death of genes for biomolecules point to a general evolutionary dynamic: gene birth and death are widespread phenomena in genome evolution, at the genetic level; thus, once mutations arise, a stepwise process of elaboration and optimization ensues, which gradually integrates and orders mutations into a coherent pattern.

Origin and evolution of new exons in rodents

Gene number difference among organisms demonstrates that new gene origination is a fundamental biological process in evolution. Exon shuffling has been universally observed in the formation of new genes. Yet to be learned are the ways new exons originate and evolve, and how often new exons appear. To address these questions, we identified 2695 newly evolved exons in the mouse and rat by comparing the expressed sequences of 12,419 orthologous genes between human and mouse, using 743,856 pig ESTs as the outgroup. The new exon origination rate is about 2.71 x 10(-3) per gene per million years. These new exons have markedly accelerated rates both of nonsynonymous substitutions and of insertions/ deletions (indels). A much higher proportion of new exons have Kappa(a)/Kappa(s) ratios > 1 (where K-a is the nonsynonymous substitution rate and K-s is the synonymous substitution rate) than K do the old exons shared by human and mouse, implying a role of positive selection in the rapid evolution. The majority of these new exons have sequences unique in the genome, suggesting that most new exons might originate through "exonization" of intronic sequences. Most of the new exons appear to be alternative exons that are expressed at low levels.

Burrowing rodents as ecosystem engineers: the ecology and management of plateau zokors Myospalax fontanierii in alpine meadow ecosystems on the Tibetan Plateau

1. Plateau zokors, Myospalax fontanierii, are the only subterranean herbivores on the Tibetan plateau of China. Although the population biology of plateau zokors has been studied for many years, the interactions between zokors and plants, especially for the maintenance and structure of ecological communities, have been poorly recognized. In the past, plateau zokors have been traditionally viewed as pests, competitors with cattle, and agents of soil erosion, thus eradication programmes have been carried out by local governments and farmers. Zokors are also widely and heavily exploited for their use in traditional Chinese medicine.2. Like other fossorial animals, such as pocket gophers Geomys spp. and prairie dogs Cynomys spp. in similar ecosystems, zokors may act to increase local environmental heterogeneity at the landscape level, aid in the formation, aeration and mixing of soil, and enhance infiltration of water into the soil thus curtailing erosion. The changes that zokors cause in the physical environment, vegetation and soil clearly affect the herbivore food web. Equally, plateau zokors also provide a significant food source for many avian and mammalian predators on the plateau. Zokor control leading to depletion of prey and secondary poisoning may therefore present problems for populations of numerous other animals.3. We highlight the important role plateau zokors play in the Tibetan plateau ecosystem. Plateau zokors should be managed in concert with other comprehensive rangeland treatments to ensure the ecological equilibrium and preservation of native biodiversity, as well as the long-term sustainable use of pastureland by domestic livestock.

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.

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.

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.

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.

Origin and evolution of new exons in the rodent zinc finger protein 39 gene

The origin of new structures and functions is an important process in evolution. In the past decades, we have obtained some preliminary knowledge of the origin and evolution of new genes. However, as the basic unit of genes, the origin and evolution of exons remain unclear. Because young exons retain the footprints of origination, they can be good materials for studying origin and evolution of new exons. In this paper, we report two young exons in a zinc finger protein gene of rodents. Since they are unique sequences in mouse and rat genome and no homologous sequences were found in the orthologous genes of human and pig, the young exons might originate after the divergence of primates and rodents through exonization of intronic sequences. Strong positive selection was detected in the new exons between mouse and rat, suggesting that these exons have undergone significant functional divergence after the separation of the two species. On the other hand, population genetics data of mouse demonstrate that the new exons have been subject to functional constraint, indicating an important function of the new exons in mouse. Functional analyses suggest that these new exons encode a nuclear localization signal peptide, which may mediate new ways of nuclear protein transport. To our knowledge, this is the first example of the origin and evolution of young exons.

Effects of extremely low-frequency electromagnetic fields on morphine-induced conditioned place preferences in rats

In the present study, we examined the effects of extremely low-frequency (ELF) electromagnetic fields on morphine-induced conditioned place preferences in rats. During the conditioning phase (12 days), three groups of rats were placed in a sensory cue-defined environment paired with morphine (10 mg/kg, i.p.) following exposure to either 20 Hz (1.80 mT) or 50 Hz (2.20 mT) or sham electromagnetic fields for 60 min/day, respectively, and were placed in another sensory cue-defined environment paired with physiological saline (1 ml/kg, i.p.) without exposure to electromagnetic fields. After finishing 12 days of conditioning, preference tests for the morphine-paired place were performed during a 10-day withdrawal period. The exposure to electromagnetic fields substantially potentiated morphine-induced place preferences in rodents, suggesting that ELF electromagnetic fields can increase the propensity for morphine-induced conditioned behaviors. (C) 2005 Elsevier Ireland Ltd. All rights reserved.

Improved spatial recognition memory in mice lacking adenosine A(2A) receptors

Adenosine receptors play an important role in learning and memory as their antagonists have been found to facilitate learning and memory in various tasks in rodents. However, few studies have examined the effect of adenosine A(2A) receptor deficiency on c

Long-term exposure to extremely low-frequency magnetic fields impairs spatial recognition memory in mice

1. In the present study, we investigated the short- and long-term effects of extremely low-frequency (ELF) magnetic fields on spatial recognition memory in mice by using a two-trial recognition Y-maze that is based on the innate tendency of rodents to exp