New World Monkeys and Color

The visual worlds of most primates are rich with potential color signals, and many representatives of the order have evolved the biological mechanisms that allow them to exploit these sources of information. Unlike the catarrhines, platyrrhines typically have sex-linked polymorphic color vision that provides individuals with any of several distinct types of color vision, including both trichromatic and dichromatic variants. In recent years, this polymorphism has been the target of an expanding range of research efforts. As a result, researchers now reasonably understand the proximate biology underlying the polymorphisms, and a number of ideas have emerged as to their evolution. Progress has also been made in illuminating how color vision capacities may be related to the particular visual tasks that New World monkeys face.     

Color Vision Variation as Evidenced by Hybrid L/M Opsin Genes in Wild Populations of Trichromatic Alouatta New World Monkeys

Platyrrhine (New World) monkeys possess highly polymorphic color vision owing to allelic variation of the single-locus L/M opsin gene on the X chromosome. Most species consist of female trichromats and female and male dichromats. Howlers (genus Alouatta) are an exception; they are considered to be routinely trichromatic with L and M opsin genes juxtaposed on the X chromosome, as seen in catarrhine primates (Old World monkeys, apes, and humans). Yet it is not known whether trichromacy is invariable in howlers. We examined L/M opsin variation in wild howler populations in Costa Rica and Nicaragua (Alouatta palliata) and Belize (A. pigra), using fecal DNA. We surveyed exon 5 sequences (containing the diagnostic 277th and 285th residues for λ_max) for 8 and 18 X chromosomes from Alouatta palliata and A. pigra, respectively. The wavelengths of maximal absorption (λ_max) of the reconstituted L and M opsin photopigments were 564 nm and 532 nm, respectively, in both species. We found one M–L hybrid sequence with a recombinant 277/285 haplotype in Alouatta palliata and two L–M hybrid sequences in A. pigra. The λ_max values of the reconstituted hybrid photopigments were in the range of 546~554 nm, which should result in trichromat phenotypes comparable to those found in other New World monkey species. Our finding of color vision variation due to high frequencies of L/M hybrid opsin genes in howlers challenges the current view that howlers are routine and uniform trichromats. These results deepen our understanding of the evolutionary significance of color vision polymorphisms and routine trichromacy and emphasize the need for further assessment of opsin gene variation as well as behavioral differences among subtypes of trichromacy.     

Biomechanical scaling of mandibular dimensions in New World Monkeys

Previous studies show that folivorous Old World monkeys have shorter, deeper mandibles and shorter, wider condyles than frugivorous ones. These morphologies have been related to leaf mastication in colobines and ingestion of large, tough fruits in cercopithecines. This study examines New World monkeys in order to determine whether they exhibit similar adaptations to diet. New World monkeys have relatively long, transversely thin mandibles and somewhat deep mandibles and narrow condyles. Except for their deep mandibles, folivorous New World monkeys (i.e., Alouatta) do not exhibit the mandibular and condylar specializations typical of cercopithecid folivores. Reliance on comparatively nonfibrous foods plus alterations in masticatory muscle ratios among New World monkeys partially accounts for observed differences between folivorous New and Old World monkeys. In addition, adaptations for howling in Alouatta appear to have a significant effect on mandibular morphology. A biomechanical interpretation of craniofacial scaling patterns suggests that the mandibles of New World monkeys are subjected to lower condylar loads and considerably less twisting of the mandibular corpus than those of comparable Old World monkeys.     

Genetic Diversity in Oxytocin Ligands and Receptors in New World Monkeys

Oxytocin (OXT) is an important neurohypophyseal hormone that influences wide spectrum of reproductive and social processes. Eutherian mammals possess a highly conserved sequence of OXT (Cys-Tyr-Ile-Gln-Asn-Cys-Pro-Leu-Gly). However, in this study, we sequenced the coding region for OXT in 22 species covering all New World monkeys (NWM) genera and clades, and characterize five OXT variants, including consensus mammalian Leu⁸-OXT, major variant Pro⁸-OXT, and three previously unreported variants: Ala⁸-OXT, Thr⁸-OXT, and Phe²-OXT. Pro⁸-OXT shows clear structural and physicochemical differences from Leu⁸-OXT. We report multiple predicted amino acid substitutions in the G protein-coupled OXT receptor (OXTR), especially in the critical N-terminus, which is crucial for OXT recognition and binding. Genera with same Pro⁸-OXT tend to cluster together on a phylogenetic tree based on OXTR sequence, and we demonstrate significant coevolution between OXT and OXTR. NWM species are characterized by high incidence of social monogamy, and we document an association between OXTR phylogeny and social monogamy. Our results demonstrate remarkable genetic diversity in the NWM OXT/OXTR system, which can provide a foundation for molecular, pharmacological, and behavioral studies of the role of OXT signaling in regulating complex social phenotypes.     

Monomorphic Region of the Serotonin Transporter Promoter Gene in New World Monkeys

Genetic variation in the human serotonin system has long been studied because of its functional consequences and links to various neuropsychiatric and behavior‐related disorders. Among non‐human primates, the common marmosets (Callithrix jacchus) and tufted capuchins monkeys (Cebus apella) are becoming increasingly used as models to study the effects of genes, environments, and their interaction on physiology and complex behavior. In order to investigate the independent functions of and potential interactions between serotonin‐related genes, anxiety and neuropsychiatric disorders, we analyzed the presence and variability of the serotonin transporter gene‐linked polymorphic region (5‐HTTLPR) in marmoset and capuchin monkeys. By PCR and using heterologous primers from the human sequence, we amplified and then sequenced the corresponding 5‐HTT region in marmosets and capuchins. The resulting data revealed the presence of a tandem repeat sequence similar to that described in humans, but unlike humans and other Old World primates, no variable length alleles were detected in these New World monkeys, suggesting that if serotonin transporter is involved in modulating behavior in these animals it does so through different molecular mechanisms. Am. J. Primatol. 74:1028‐1034, 2012. © 2012 Wiley Periodicals, Inc.     

Climatic Niche Evolution in New World Monkeys (Platyrrhini)

Despite considerable interest in recent years on species distribution modeling and phylogenetic niche conservatism, little is known about the way in which climatic niches change over evolutionary time. This knowledge is of major importance to understand the mechanisms underlying limits of species distributions, as well as to infer how different lineages might be affected by anthropogenic climate change. In this study we investigate the tempo and mode climatic niche evolution in New World monkeys (Platyrrhini). Climatic conditions found throughout the distribution of 140 primate species were investigated using a principal component analysis, which indicated that mean temperature (particularly during the winter) is the most important climatic correlate of platyrrhine geographical distributions, accounting for nearly half of the interspecific variation in climatic niches. The effects of precipitation were associated with the second principal component, particularly with respect to the dry season. When models of trait evolution were fit to scores on each of the principal component axes, significant phylogenetic signal was detected for PC1 scores, but not for PC2 scores. Interestingly, although all platyrrhine families occupied comparable regions of climatic space, some aotid species such as Aotus lemurinus, A. jorgehernandezi, and A. miconax show highly distinctive climatic niches associated with drier conditions (high PC2 scores). This shift might have been made possible by their nocturnal habits, which could serve as an exaptation that allow them to be less constrained by humidity during the night. These results underscore the usefulness of investigating explicitly the tempo and mode of climatic niche evolution and its role in determining species distributions.     

Developmental Processes, Evolvability, and Dental Diversification of New World Monkeys

The developmental processes that contribute to variation of morphological traits are the subject of considerable interest when attempting to understand phenotypic evolution. It is well demonstrated that most characteristics of tooth pattern can be modified by tinkering conserved signal pathways involved in dental development. This effect can be evaluated by comparing developmental models with naturally occurring variation within explicit phylogenetic contexts. Here, we assess whether evolutionary changes in lower molar (M) ratios among platyrrhines were channelled by alterations in the balance of activators and inhibitors as predicted by the inhibitory cascade (IC) model (Kavanagh et al. in Nature 449:427–432, 2007). Ordinary linear regression adjusted to M2/M1 versus M3/M1 ratios of 38 species of platyrrhines indicated that the slope and intercept were significantly different from the IC model. Conversely, when the phylogeny was incorporated into the regression analyses (PGLS), variation in molar ratios did not differ from the developmental model. PGLS also showed that changes in molar proportions are not an allometric effect associated with body size. Discrepancies between phylogenetically corrected and non-corrected analyses are mainly due to the departure of Callitrichines from the predicted values. This subfamily displays agenesis of M3 with higher than expected M2/M1 ratios, indicating that M3 fails to develop even when the inhibition by M1 on the subsequent molars is not increased. Our results show that evolution in molar ratios is concordant with slight changes in the proportion of activators and inhibitors that regulate molar development; however, other processes are required to account for variation in the number of teeth.     

Growth hormone locus expands and diverges after the separation of New and Old World Monkeys

While most mammals including the prosimians have a single copy of the growth hormone (GH) gene, anthropoids possess a cluster of GH-related genes. Throughout the evolution of the main anthropoid groups [New World Monkeys (NWM), Old World Monkeys (OWM), and apes], two features stand out of the GH loci. The first is the appearance of chorionic somatommamotropin hormone (CSH) genes within the OWM lineage and the second is the expansion of the loci intergenic regions in the OWM and apes. In relation with this loci expansion, the NWM possess intergenic regions of homogeneous lengths (3.5 kb). In contrast, heterogeneous lengths (6 and 13 kb) have been reported for species of the OWM. At the present, none of the OWM genomic GH loci organizations have been described. Here, we report the genomic organization of the GH locus in the rhesus monkey, this locus has six GH-related genes separated by five intergenic regions. The 5' end gene (GH-1) encodes for the pituitary GH and is followed by CSH-1, GH-2, CSH-2, CSH-3 and CSH-4 genes. The five intergenic regions have heterogeneous lengths and also present more or less the same Alu distribution as the human GH locus. To analyze the events that contributed to the extension of the intergenic regions of the GH locus and the emergence of the regulatory elements, the five GH locus intergenic regions of the spider monkey (NWM) were sequenced. The results of comparing the loci from both species suggest that the long intergenic regions (13 kb) of the rhesus GH locus share a common ancestor with the 3.5 kb intergenic regions of the spider monkey. However, the observed increased length of the former is due to an insertion (approximately 8.7 kb) at their 3' end. Interestingly in this insert, we discovered a DNA element resembling the enhancer of the CSH genes of the human GH locus. On the other hand, we observed that the short intergenic regions (6 kb) increased by a different recombination event.     

New specimens of the early Oligocene Old World hummingbird Eurotrochilus inexpectatus

New specimens of the early Oligocene (32 million years ago) stem group hummingbird Eurotrochilus inexpectatus Mayr, 2004, are described from the type locality Frauenweiler in Southern Germany. One of these is the second slab of the holotype, whose existence has been hitherto unknown. The new fossils add significantly to our knowledge of the morphology of E. inexpectatus and allow more detailed comparisons with other stem and crown group Trochilidae. A new apomorphy of the clade (Eurotrochilus + crown group Trochilidae) is described. With species successively more closely related to the crown group, the temporal sequence of stem group hummingbirds in Europe indicates an Old World origin of Pan-Trochilidae. E. inexpectatus is the earliest long-beaked stem group hummingbird with hovering capabilities, and absence of modern-type hummingbirds before the early Oligocene may provide a maximum age for the origin of hummingbird-pollinated plants and the colonization of the New World by modern-type stem group hummingbirds.     

百合黄烷酮3-羟化酶基因LhSorF3H的克隆与表达

为了探究百合花色的调控机制,以东方百合品种‘索邦’(Sorbonne)的花蕾为试验材料,根据前期转录组测序结果,成功克隆出黄烷酮3-羟化酶(flavanone 3-hydroxylase,F3H)基因的编码序列和基因组序列,其中,编码序列全长1 110bp,可编码369个氨基酸;基因组序列全长1 438bp,包含3个外显子和2个内含子,命名该基因为LhSorF3 H(GenBank登录号为MF614135)。生物信息学分析结果显示,黄烷酮3-羟化酶在进化上具有较高的保守性。LhSorF3 H编码的蛋白与郁金香(Tulipafosteriana)最为相似。半定量RT-PCR结果显示,LhSorF3H在花被、柱头以及花柱中表达明显,在花丝、子房、嫩茎、茎生根及上部叶片中表达较弱,而在花药和中下部叶片中基本不表达。LhSorF3 H在不同发育阶段的花被片中均有表达(S2和S6阶段除外);黑暗处理使LhSorF3 H表达降低,黑暗处理2h的LhSorF3 H表达量降到最低,之后表达量开始上升;转入光照条件后,LhSorF3H的表达水平持续增加。研究表明,LhSorF3 H基因对昼夜节律和光照具有双重响应的特性。     

文心兰COL基因的分离及其表达分析

CONSTANS(CO)及CONSTANS-like(COL)基因在光周期调控植物开花中起到重要的作用。该研究以文心兰(Oncidium)品种‘金辉’为材料,分离了CO同源基因OnCOL2及另外2个COL基因(OnCOL8和OnCOL9),它们分别编码326、411和291个氨基酸;生物信息分析预测它们均定位于细胞核;OnCOL2、OnCOL8有2个锌指B-box结构域和1个CCT结构域,而OnCOL9缺少B-box结构域。多序列比对及进化树分析结果表明,所有COL蛋白可划分为3组,OnCOL2与OnCOL8、OnCOL9分到了2个不同组中。OnCOL2与建兰(Cymbidium ensifolium)CeCOL(90.77%)高度相似;OnCOL8与OnCOL9在进化关系上更为接近,分别与拟南芥(Arabidopsis thaliana)AtCOL9和AtCOL10关系最近,它们在B-box和CCT结构域都极为保守。表达分析结果表明OnCOL2、OnCOL8与OnCOL9分别在花、根和假鳞茎中表达量最高,在叶片中的表达呈周期性变化趋势,且在长、短日照条件下表达的峰值及时间均存在差异,在花芽分化时期的叶片中表达量均显著上调。研究表明,OnCOL2、OnCOL8与OnCOL9基因均受到生物钟和日长调节,在光周期途径中,可能通过上调它们的表达以促进文心兰花芽的形成。该研究结果为进一步研究基因功能及光周期调控文心兰开花机制奠定了基础。     

Evolutionary Significance of the Entepicondylar Foramen of the Humerus in New World Monkeys (Platyrrhini)

Although consistently absent in extant catarrhine monkeys, the presence and absence of the entepicondylar foramen of the humerus (EEF) vary greatly among living and fossil platyrrhines. Aiming to test the mode of evolution of this character in platyrrhine phylogeny, we performed stochastic character mapping of the presence and absence of the EEF based on museum material and literature research. We also tested for phylogenetic signal of the EEF and its correlation with semi-brachation, vertical clinging, and manipulative foraging in New World monkeys. We found more losses than gains of the EEF in the Haplorhini and Platyrrhini phylogenies. The EEF showed a strong phylogenetic signal congruent with a Brownian model of evolution. All models that assumed a dependence between foraging and locomotion behaviors showed a better fit to the data, but the differences from an independent model were not statistically significant. Thus, we assume that the observed pattern could have originated from genetic drift, except in Leontopithecus where the EEF appears to have been lost due to the narrowing of the distal humerus. Although not functionally relevant, the presence and absence of EEF is taxonomically useful for discriminating between the Aotus and Callicebus species groups, and diagnoses large platyrrhine clades such as marmosets and Atelidae. Thus, it should be considered when inferring systematic relationships among living and extinct platyrrhines.     

油茶DELLA基因的克隆和表达分析

为了解油茶(Camellia oleifera)中DELLA基因功能及其表达特性,采用PCR技术从‘长林4号’油茶中克隆了5个DELLA基因,命名为CoDELLA1~CoDELLA5,对其编码的5个CoDELLA蛋白进行生物信息学分析,并对5个DELLA基因的表达模式以及激素响应活性进行了分析。结果表明,5个CoDELLA基因的编码区长度分别为1 791、1 875、1 848、1 593和1 581 bp,分别编码597、625、616、531和527个氨基酸。5个CoDELLA蛋白的氨基酸序列相似度较高,丝氨酸残基为主要的潜在磷酸化位点,CoDELLA蛋白N端均含有典型的DELLA结构域。不同物种中DELLA蛋白的系统发育存在差异,CoDELLA与茶树的CsDELLA同源性最高。CoDELLA基因在油茶不同组织中的表达也存在差异,且赤霉素和独脚金内酯等多种激素和非生物胁迫对其表达具有调控作用。CoDELLA基因可能在油茶的生长发育和非生物胁迫响应中发挥重要作用。     

鹅掌楸属GST家族基因的克隆与表达分析

该研究以鹅掌楸属植物为试验材料,在北美鹅掌楸和鹅掌楸转录组数据库中筛选出54条GST基因家族的EST序列,通过比对将其归为Tau、Zeta、Theta和Phi等4个亚类。在这4个亚类中各选取1条EST序列设计引物,通过反转录PCR(RT-PCR)与cDNA末端快速扩增(RACE)技术,从鹅掌楸属植物中克隆出4条全长分别为1 150、932、1 022和1 067bp的基因,并分别命名为LtGSTparCb、LtGSTZ-like、LtGSTF13a和LcGSTT1。对LtGSTparCb、LtGSTZ-like、LtGSTF13a和LcGSTT1这4个基因编码蛋白质的结构预测发现,其蛋白质的分子质量分别为25.17、25.34、24.49和28.09kD;理论等电点分别是5.60、6.53、6.66和9.20,即LtGSTparCb、LtGSTZlike、LtGSTF13a蛋白质属于酸性蛋白,LcGSTT1属于碱性蛋白;不稳定系数分别是33.01、36.97、43.19和47.96,即LtGSTparCb、LtGSTZ-like为稳定蛋白,LtGSTF13a、LcGSTT1为不稳定蛋白;α-螺旋(alpha helix)是这4个蛋白质二级结构的主要成分。利用在线软件TargetP并结合GST蛋白质在其他植物中亚细胞定位的结果,推测这4种蛋白质极有可能位于鹅掌楸属植物的细胞质内。实时荧光定量PCR分析结果表明,这4个基因在北美鹅掌楸各个组织中均有表达,其中LtGSTparCb和LtGSTF13a在叶中的表达量最高,在其他组织中的表达量均较低;LtGSTZ-like在花器官中的表达量最高,在叶中的表达量最低,在其他组织中的表达量居于两者之间;LcGSTT1在叶中表达量最高,花器官中表达量其次,在茎和叶芽中的表达量偏低。该研究结果可为鹅掌楸属GST家族基因的功能研究奠定基础。     

ASPM and the Evolution of Cerebral Cortical Size in a Community of New World Monkeys

The ASPM (abnormal spindle-like microcephaly associated) gene has been proposed as a major determinant of cerebral cortical size among primates, including humans. Yet the specific functions of ASPM and its connection to human intelligence remain controversial. This debate is limited in part by a taxonomic focus on Old World monkeys and apes. Here we expand the comparative context of ASPM sequence analyses with a study of New World monkeys, a radiation of primates in which enlarged brain size has evolved in parallel in spider monkeys (genus Ateles) and capuchins (genus Cebus). The primate community of Costa Rica is perhaps a model system because it allows for independent pairwise comparisons of smaller- and larger-brained species within two taxonomic families. Accordingly, we analyzed the complete sequence of exon 18 of ASPM in Ateles geoffroyi, Alouatta palliata, Cebus capucinus, and Saimiri oerstedii. As the analysis of multiple species in a genus improves phylogenetic reconstruction, we also analyzed eleven published sequences from other New World monkeys. Our exon-wide, lineage-specific analysis of eleven genera and the ratio of rates of nonsynonymous to synonymous substitutions (d_N/d_S) on ASPM revealed no detectable evidence for positive selection in the lineages leading to Ateles or Cebus, as indicated by d_N/d_S ratios of <1.0 (0.6502 and 0.4268, respectively). Our results suggest that a multitude of interacting genes have driven the evolution of larger brains among primates, with different genes involved in this process in different encephalized lineages, or at least with evidence for positive selection not readily apparent for the same genes in all lineages. The primate community of Costa Rica may serve as a model system for future studies that aim to elucidate the molecular mechanisms underlying cognitive capacity and cortical size.     

白菜型油菜RbohC和RbohF基因克隆与表达分析

该研究以白菜型油菜（Brassica rapa L.）‘陇油6号’为实验材料,采用RT PCR方法克隆油菜RbohC和RbohF基因,并采用实时荧光定量PCR技术对RbohC、RbohF基因在不同组织及非生物胁迫下的表达进行分析,为深入研究油菜RbohC、RbohF基因的生物学功能提供依据。结果显示：(1) 成功克隆得到2个全长分别为3 050 bp和2 995 bp的油菜RbohC (GenBank登录号：XM_009134386) 和RbohF (GenBank登录号：XM_009114548) 基因序列。(2) 生物信息学分析显示,油菜RbohC和RbohF基因开放阅读框（ORF）分别为2 733 bp和2 847 bp,编码910和948个氨基酸,推测二者的蛋白质分子量分别为103 kDa和108 kDa,理论等电点分别为9.47和9.21; 油菜RbohC、RbohF编码的氨基酸序列与萝卜等多种植物相应蛋白氨基酸序列具有较高的同源性,且这些序列高度保守并含有NADPH氧化酶的典型保守结构域,包括2个可以与Ca²⁺结合的EF手性模体结构、6个跨膜结构域、黄素腺嘌呤二核苷酸结合结构域、NAD焦磷酸结合结构域和C末端区域中的NADP核糖保守结合位点。(3) 油菜RbohC和RbohF基因在根、茎、叶和下胚轴中均表达,无组织特异性,但RbohC基因在根中表达量最高, RbohF基因在下胚轴中表达量最高。(4) 低温、干旱、盐、ABA、H₂O₂处理都能够诱导油菜RbohC和RbohF基因的表达,但抗寒性强的 ‘陇油6号’的RbohC和RbohF基因对胁迫的响应更敏感,且RbohC基因的表达量均高于RbohF基因。(5) 用H₂O₂清除剂DMTU、NADPH氧化酶抑制剂DPI和IMD、MAPKK抑制剂U0126处理后,油菜RbohC和RbohF基因的表达均较对照下降,说明U0126和DMTU对油菜RbohC和RbohF基因的表达有抑制作用。研究认为,油菜RbohC和RbohF基因在油菜适应逆境胁迫中具有重要作用,两基因的表达均受MAPK激酶信号途径的调节,并受到H₂O₂的反馈调节,而且抗寒性强的‘陇油6号’品种中RbohC和RbohF基因对H2O2和MAPK激酶信号途径的响应更敏感。     

木奈WRKY同源基因的分离与表达分析

以木奈（Prunus salicina Lindli.var cordata J.Y.Zhang et al.）为试验材料,采用稀释池PCR法,筛选木奈叶片全长均一化cDNA文库,获得了木奈WRKY同源基因的12个全长cDNA分别命名为PsWRKY7、PsWRKY14、PsWRKY20、PsWRKY21、PsWRKY22、PsWRKY29、PsWRKY31、PsWRKY32、PsWRKY33、PsWRKY40、PsWRKY46和PsWRKY75,长度分别为1 517、1 798、2 098、1 177、1 242、1 396、2 135、1 760、2 113、1 047、1 258和700 bp,ORF长度分别为1 095、1 572、1 764、1 068、1 071、1 002、1 944、1 602、1 770、963、1 077和672 bp,分别编码364、523、587、355、357、333、647、533、589、320、358、223个氨基酸。荧光定量结果显示,12个WRKY同源基因在1.0 mmol/L水杨酸处理后,所获得的PsWRKY表达量均显著上调,表明木奈WRKY基因可能是水杨酸诱导防御反应的重要调控因子。