Molecular phylogeny and morphological homoplasy in fruitbats.

The present study evaluates the evolutionary framework of the Old World fruitbats based on the cytochrome b and 16S rRNA mitochondrial gene sequences from a wide range of taxa. Phylogenetic analyses indicated that morphology-based subfamilies and most suprageneric groups are nonnatural assemblages. They also support the existence of an endemic African clade of fruitbats. The discrepancy between the evolutionary relationships yielded by molecular and morphological data sets may be, at least in part, explained by the recurrent retention of primitive morphology (Rousettus-like) across different lineages. The maintenance of primitive characters in different groups of flying foxes, as well as morphological convergence in nectar-feeding bats and possibly also in short-muzzle bats, may have led to high levels of homoplasy, resulting in misleading taxonomic arrangements. This may be particularly so with respect to high taxonomic levels based on morphological characters.     

New universal mitochondrial PCR markers reveal new information on maternal citrus phylogeny

The aim of this work was to provide a set of mitochondrial markers to reveal polymorphism and to study the maternal phylogeny in citrus. We first used 44 universal markers previously described in the literature: nine of these markers produced amplification products but only one revealed polymorphism in citrus. We then designed six conserved pairs of primers using the complete mitochondrial DNA sequences of Arabidopsis thaliana and Beta vulgaris to amplify polymorphic intergenic and intronic regions. From these six pairs of primers, three from introns of genes coding for NADH dehydrogenase subunits 2, 5, and 7, revealed polymorphism in citrus. First, we confirmed that citrus have a maternal mitochondrial inheritance in two populations of 250 and 120 individuals. We then conducted a phylogenic study using four polymorphic primers on 77 genotypes representing the diversity of Citrus and two related genera. Seven mitotypes were identified. Six mitotypes (Poncirus, Fortunella, Citrus medica, Citrus micrantha, Citrus reticulata, and Citrus maxima) were congruent with previous taxonomic investigations. The seventh mitotype enabled us to distinguish an acidic mandarin group (‘Cleopatra’, ‘Sunki’ and ‘Shekwasha’) from other mandarins and revealed a maternal relationship with Citrus limonia (‘Rangpur’ lime, ‘Volkamer’ lemon) and Citrus jambhiri (‘Rough’ lemon). This mitotype contained only cultivated species used as rootstocks due to their good tolerances to abiotic stress. Our results also suggest that two species classified by Swingle and Reece, Citrus limon, and Citrus aurantifolia, have multiple maternal cytoplasmic origins.     

Pitfalls in determining size homoplasy of microsatellite loci

Size homoplasy of microsatellite loci can be detected by single‐strand conformation polymorphism analysis (SSCP) or sequence analysis. The present note demonstrates pitfalls of sequencing microsatellite loci. A complex chloroplast microsatellite locus was polymerase chain reaction (PCR) amplified from 33 Abies alba individuals, and the products cloned and sequenced. After 2–7 clones per individual had been sequenced and aligned, differences in repeat numbers occurred among clones of the same individual. It was concluded that the DNA polymerase slippage during PCR most probably caused this variation. A solution specific to the analysed complex locus was found by splitting it into two new loci.     

DNA analyses reveal abundant homoplasy in taxonomically important morphological characters of Eusiroidea (Crustacea,Amphipoda)

Eusiroidea is one of the 20 amphipod superfamilies that were erected to subdivide the very large and controversial suborder Gammaridea. Yet, the definition of the superfamily is not based on synapomorphies, but on a combination of diagnostic phenetic similarities that hold more or less consistently across families. Moreover, many of the characters used to define eusiroid families are suspected to show convergent evolution. The current classification of the Eusiroidea may therefore not reflect evolutionary relationships accurately. Here, we present a molecular phylogenetic re‐analysis of the Eusiroidea based on a comparison of 18S and 28S rDNA sequences of 73 species, representing 47 genera and 16 families that potentially belong to the superfamily. The results suggest that at least species belonging to 14 of these traditional families would be part of a eusiroid clade, increasing by more than twofold the species and generic richness of the group. However, most of the eusiroid families surveyed do not appear monophyletic. Finally, the analyses show that several important morphological characteristics, traditionally used in eusiroid taxonomy, are homoplastic.     

The 'evolutionary signal' of homoplasy in protein-coding gene sequences and its consequences for a priori weighting in phylogeny

To analyse independently homoplasy for the six possible types of substitution (i.e., A-G, C-T, A-C, A-T, C-G and G-T) at each of the three codon-positions of the cytochrome b gene, two approaches were used: the first is based on the consistency index which measures the amount of homoplasy, and the second is based on the saturation analysis which describes graphically the distribution of homoplasy within the taxonomic sampling. The results obtained from a data set of 32 sequences of Artiodactyla indicate that evolution of the cytochrome b is governed by differential constraints: 1) between the six substitutions-types, 2) between the three codon-positions, and 3) between the two mtDNA strands. Moreover, we find that non-synonymous sites can be more homoplastic than synonymous sites when the possibilities of substitutions are severely restricted because of the functional requirements of hydrophobicity. Most weighting schemes applied to protein-coding genes are elaborated from unjustified assumptions. We propose to weight each substitution-type at each codon-position according to its homoplasy content evaluated either with the consistency index or with an index representing the level of mutational saturation.     

微卫星标记中的无效等位基因

微卫星标记以其独有的优点广泛应用于遗传学研究,但无效等位基因(null alleles)的存在与潜在影响是其最大缺陷之一,在研究工作中并未得到足够重视.本文在综述国内外相关文献的基础上,明确了微卫星无效等位基因的概念与特点,对其可能的产生原因、频率估算方法、相关分析软件及其对群体遗传学、亲本分析等研究结果的影响进行述评,以期对无效等位基因有较为全面、深入的了解.微卫星无效等位基因的产生与SSR侧翼序列的变异(点突变、插入或缺失)及引物结合位点有关,其与同工酶标记中的无效等位基因有本质区别,并非基因本身的自然属性.虽然微卫星无效等位基因具有普遍性、复杂性和隐匿性等特点,但完全可以通过Hardy-Weinberg平衡检验、亲子代基因型分析和重新设计引物等方法认识、检测并估算其频率.无效等位基因会对遗传学相关研究结果造成显著影响,如降低群体遗传多样性,加大群体间遗传分化;降低亲本分析排除率,甚至可能造成亲本分析结果的错误与混乱.今后研究工作中,我们应对无效等位基因予以足够重视并谨慎对待,从标记位点选择、无效等位基因数据调整及重新设计引物分析等多个方面尽可能减少和避免其影响,以获得最真实的分析结果.     

Complex mutational patterns and size homoplasy at maize microsatellite loci

Microsatellite markers have become one of the most popular tools for germplasm characterization, population genetics and evolutionary studies. To investigate the mutational mechanisms of maize microsatellites, nucleotide sequence information was obtained for ten loci. In addition, Single-Strand Conformation Polymorphism (SSCP) analysis was conducted to assess the occurrence of size homoplasy. Sequence analysis of 54 alleles revealed a complex pattern of mutation at 8/10 loci, with only 2 loci showing allele variation strictly consistent with stepwise mutations. The overall allelic diversity resulted from changes in the number of repeat units, base substitutions, and indels within repetitive and non-repetitive segments. Thirty-one electromorphs sampled from six maize landraces were considered for SSCP analysis. The number of conformers per electromorph ranged from 1 to 7, with 74.2% of the electromorphs showing more than one conformer. Size homoplasy was apparent within landraces and populations. Variation in the amount of size homoplasy was observed within and between loci, although no differences were detected among populations. The results of the present study provide useful information on the interpretation of genetic data derived from microsatellite markers. Further efforts are still needed to determine the impact of these findings on the estimation of population parameters and on the inference of phylogenetic relationships in maize investigations. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Molecular phylogeny and morphometric analyses reveal deep divergence between Amazonia and Atlantic Forest species of Dendrophryniscus

Dendrophryniscus is an early diverging clade of bufonids represented by few small-bodied species distributed in Amazonia and the Atlantic Forest. We used mitochondrial (414 bp of 12S, 575 bp of 16S genes) and nuclear DNA (785 bp of RAG-1) to investigate phylogenetic relationships and the timing of diversification within the genus. These molecular data were gathered from 23 specimens from 19 populations, including eight out of the 10 nominal species of the genus as well as Rhinella boulengeri. Analyses also included sequences of representatives of 18 other bufonid genera that were publically available. We also examined morphological characters to analyze differences within Dendrophryniscus. We found deep genetic divergence between an Amazonian and an Atlantic Forest clade, dating back to Eocene. Morphological data corroborate this distinction. We thus propose to assign the Amazonian species to a new genus, Amazonella. The species currently named R. boulengeri, which has been previously assigned to the genus Rhamphophryne, is shown to be closely related to Dendrophryniscus species. Our findings illustrate cryptic trends in bufonid morphological evolution, and point to a deep history of persistence and diversification within the Amazonian and Atlantic rainforests. We discuss our results in light of available paleoecological data and the biogeographic patterns observed in other similarly distributed groups.     

Nine porcine microsatellite loci tested for size homoplasy in genetically diverse breeds

Kind and probability of homoplasy across allelic microsatellite fragments can be investigated using DNA of genetically diverse pig breeds. In this study, nine microsatellite loci (SW1897, SW2427, SW489, SW957, TNFB, IFNG, SW2410, SW2019 and S0215) were analysed using DNA samples of pigs from Vietnam (Indigenous breeds Co, Meo, Muong Khuong, Tap Na) and Germany (European Wild Boar, Pietrain). In a total of 39 sequences, 20 differences within isomorphic alleles were observed in comparison with the respective reference sequences. They affected five of the nine tested microsatellite loci. The majority (18) of SNPs occurred in the 5'-flanking regions of the microsatellite repeats, 10 were found in the 3'-flanking regions and only one SNP occurred within the repeat of the Wild Boar sequence of SW2427. The compound microsatellites IFNG and S0215 were unaffected by size homoplasy (SH) within our material. We conclude that the fragment length analysis of microsatellites is a reliable tool for intraspecific phylogenetic studies because SH rates within a species were low.     

What body parts reveal about the organization of the brain

In this issue of Neuron, Orlov et?al. show that the human occipitotemporal cortex contains regions responding preferentially to body part categories, such as upper limbs (hand, elbow), torsos, or lower faces (mouth, chin). This organization may reflect differences in the connectivity of these regions with other brain regions, to support the efficient processing of the different types of information different body parts provide.     

猕猴桃属植物的cpSSR遗传多样性及其同域分布物种的杂交渐渗与同塑

同域分布的近缘物种常常发生杂交而导致种间基因渐渗, 从而对相关物种的自然居群遗传结构产生重要影响, 近缘种间的杂交渐渗已成为进化生物学和保护生物学关注的热点。本研究采用8对cpSSR引物对我国西部高原台地向中东部丘陵平原过渡地带同域重叠分布的猕猴桃属(Actinidia)7个物种的自然居群遗传多样性、居群遗传结构和同域分布种间遗传分化进行了检测。结果表明: (1)在6个多态性位点检测到18个等位基因形成的42个单倍型, 尽管各单倍型间显示了复杂的网状进化关系, 但还是具有明显的物种特异性; (2)各物种有丰富的cpSSR遗传多样性, 但种间存在较大差异, 绵毛猕猴桃(Actinidia fulvicoma var. lanata)的遗传多样性水平最高(P = 62.50%, h_T = 0.173, H_T = 0.897), 美味猕猴桃(A. deliciosa)的最低(P = 37.5％, h_T = 0.041, H_T = 0.516); (3)尽管不同物种的居群分化程度存在较大差异, 但种内居群间存在明显分化(G_ST为0.319–0.780, F_ST为0.401–0.695), 居群间的基因流不足(N_m为0.219–0.747<1); 其中以美味猕猴桃的居群遗传分化度最高(G_ST = 0.780, F_ST = 0.695); (4)遗传分化系数G_ST(unordered alleles)与N_ST(ordered alleles)无显著差异, 揭示本研究的大多数猕猴桃属物种不存在系统地理结构, 与用Mantel检验得出的居群遗传距离和地理距离不存在显著性相关的结果一致; (5)除了中华/美味猕猴桃复合体(A. chinensis / A. deliciosa complex)的湖北五峰(HW)和广西资源(GZ)两个同域复合居群外, 同域分布的物种间遗传分化强烈(F_ST为0.476–0.990), 与UPGMA聚类时多数居群按各自物种聚类的结果一致。进一步分析表明, 中华/美味猕猴桃复合体近缘种间存在明显的共祖多态性和杂交渐渗现象, 近缘种植株分布的交错程度以及是否存在亚居群结构对杂交渐渗存在着重要影响。亲缘关系较远的物种间杂交渐渗事件稀少, 但存在个别同塑事件。本研究结果有助于进一步了解猕猴桃属植物自然居群cpDNA的遗传特性和渐渗杂交进化模式, 为我国猕猴桃野生种质资源保育及可持续开发利用提供基础数据和科学依据。     

Microarray and real-time PCR analyses reveal mating type-dependent gene expression in a homothallic fungus

Sordaria macrospora is a homothallic ascomycete which is able to form fertile fruiting bodies without a mating partner. To analyze the molecular basis of homothallism and the role of mating products during fruiting body development, we have deleted the mating type gene Smta-1 encoding a high-mobility group domain (HMG) protein. The ΔSmta-1 deletion strain is morphologically wild type during vegetative growth, but it is unable to produce perithecia or ascospores. To identify genes expressed under control of Smta-1, we performed a cross-species microarray analysis using Neurospora crassa cDNA microarrays hybridized with S. macrospora targets. We identified 107 genes that are more than twofold up- or down-regulated in the mutant. Functional classification revealed that 81 genes have homologues with known or putative functions. Comparison of array data from ΔSmta-1 with those from three phenotypically similar mutants revealed that only a limited set of ten genes is deregulated in all mutants. Remarkably, the ppg2 gene encoding a putative lipopeptide pheromone is 500-fold down-regulated in the ΔSmta-1 mutant while in all other sterile mutants this gene is up-regulated. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Extensive size homoplasy at a microsatellite locus in the Japanese bumblebee, Bombus diversus

An extensive size homoplasy was found at microsatellite locus B11 of the bumblebee, Bombus diversus, in northern to central Honshu, Japan. A total of 16 alleles of different nucleotide sequences in five length morphs was obtained at B11 for this species. Of these alleles, five were 141 base pairs (bp) in length, five were 137 bp and four were 133 bp. Allele diversity in each length morph was high compared with previous studies. It is noteworthy that this extensive size homoplasy was found in a relatively small geographic area, in contrast to results from previous studies. Reconstruction of a median‐joining network revealed the complicated evolutionary process of the locus, involving insertion/deletion and point mutations. Preliminary estimation of the mutation rate of the B11 locus in B. diversus gives a value comparable to those estimated from experimental Drosophila populations. Effects of the extensive size homoplasy in population genetic studies is discussed.     

What invasive species reveal about the rate and form of contemporary phenotypic change in nature

Biological invasions are opportunities to gain insight into fundamental evolutionary questions, because reproductive isolation and sudden alterations in selection pressures are likely to lead to rapid evolutionary change. Here I investigate the role played by invasive species in revealing the rate and form of contemporary phenotypic change in wild populations by expanding a database of more than 5,500 rates of phenotypic change from 90 species of plants and animals. Invasive species are frequently used as model organisms and thus contribute disproportionately to available rates of phenotypic change. However, the preponderance of these rates is the consequence of extensive study in a small number of species. I found mixed evidence to support the hypothesis that phenotypic change is associated with time depending on the metric of choice (i.e., darwins or haldanes). Insights from both invasive and native species provide evidence for abrupt phenotypic change and suggest that the environment plays a potentially important role in driving trait change in wild populations, although the environmental influence on the observed trajectories remains unclear. Thus, future work should continue to seek an understanding of the mechanistic underpinnings--both genetic and environmental--of how phenotypic variation allows populations to adapt to rapidly changing global environments.     

Orangutan fetal globin genes. Nucleotide sequence reveal multiple gene conversions during hominid phylogeny

We have determined the nucleotide sequences of the linked gamma 1- and gamma 2- fetal globin genes from a single orangutan (Pongo pygmaeus) chromosome and compared them with the corresponding genes of other simian primates (gamma 1- and gamma 2-genes of human, chimpanzee, gorilla, and the single gamma-gene of the spider monkey). Previous studies have indicated that the two gamma-gene loci in catarrhine primates resulted from a duplication about 25-35 million years ago. However, comparisons of aligned gamma-gene sequences show that these genes contain three regions with distinct histories of which only the 3' third clearly reflects the ancestral nature expected of the gamma-gene duplication. To explain these different evolutionary histories and also hominid relationships we provide evidence for the occurrence of sequence conversions which affect region 1 (120 base pairs 5'-flanking through exon 2) in all hominid species and extend to varying degrees into region 2 (intron 2 through exon 3). Close examinations of the proposed conversions further suggest that 12 of the 13 conversions identified involved gamma 1 converting gamma 2. Polarity of these conversions may be a result of differential survival between these genes because during human fetal development the gamma 1-gene is preferentially expressed over the gamma 2-gene and it may be subjected to greater selection pressure to remain unaltered.     

Phylogenetic analyses of diplomonad genes reveal frequent lateral gene transfers affecting eukaryotes

BACKGROUND: Lateral gene transfer (LGT) is an important evolutionary mechanism among prokaryotes. The situation in eukaryotes is less clear; the human genome sequence failed to give strong support for any recent transfers from prokaryotes to vertebrates, yet a number of LGTs from prokaryotes to protists (unicellular eukaryotes) have been documented. Here, we perform a systematic analysis to investigate the impact of LGT on the evolution of diplomonads, a group of anaerobic protists.RESULTS: Phylogenetic analyses of 15 genes present in the genome of the Atlantic Salmon parasite Spironucleus barkhanus and/or the intestinal parasite Giardia lamblia show that most of these genes originated via LGT. Half of the genes are putatively involved in processes related to an anaerobic lifestyle, and this finding suggests that a common ancestor, which most probably was aerobic, of Spironucleus and Giardia adapted to an anaerobic environment in part by acquiring genes via LGT from prokaryotes. The sources of the transferred diplomonad genes are found among all three domains of life, including other eukaryotes. Many of the phylogenetic reconstructions show eukaryotes emerging in several distinct regions of the tree, strongly suggesting that LGT not only involved diplomonads, but also involved other eukaryotic groups.CONCLUSIONS: Our study shows that LGT is a significant evolutionary mechanism among diplomonads in particular and protists in general. These findings provide insights into the evolution of biochemical pathways in early eukaryote evolution and have important implications for studies of eukaryotic genome evolution and organismal relationships. Furthermore, "fusion" hypotheses for the origin of eukaryotes need to be rigorously reexamined in the light of these results.