Complete mitochondrial genome of the Asian paddle crab Charybdis japonica (Crustacea: Decapoda: Portunidae): gene rearrangement of the marine brachyurans and phylogenetic considerations of the decapods

Given the commercial and ecological importance of the Asian paddle crab, Charybdis japonica, there is a clearly need for genetic and molecular research on this species. Here, we present the complete mitochondrial genome sequence of C. japonica, determined by the long-polymerase chain reaction and primer walking sequencing method. The entire genome is 15,738 bp in length, encoding a standard set of 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes, plus the putative control region, which is typical for metazoans. The total A+T content of the genome is 69.2%, lower than the other brachyuran crabs except for Callinectes sapidus. The gene order is identical to the published marine brachyurans and differs from the ancestral pancrustacean order by only the position of the tRNA (His) gene. Phylogenetic analyses using the concatenated nucleotide and amino acid sequences of 13 protein-coding genes strongly support the monophyly of Dendrobranchiata and Pleocyemata, which is consistent with the previous taxonomic classification. However, the systematic status of Charybdis within subfamily Thalamitinae of family Portunidae is not supported. C. japonica, as the first species of Charybdis with complete mitochondrial genome available, will provide important information on both genomics and molecular ecology of the group.

The complete mitochondrial genome of the mantid shrimp Oratosquilla oratoria (Crustacea: Malacostraca: Stomatopoda): Novel non-coding regions features and phylogenetic implications of the Stomatopoda

The complete mitochondrial (mt) genome sequence of Oratosquilla oratoria (Crustacea: Malacostraca: Stomatopoda) was determined; a circular molecule of 15,783 bp in length. The gene content and arrangement are consistent with the pancrustacean ground pattern. The mt control region of O. oratoria is characterized by no GA-block near the 3' end and different position of [TA(A)]n-blocks compared with other reported Stomatopoda species. The sequence of the second hairpin structure is relative conserved which suggests this region may be a synapomorphic character for the Stomatopoda. In addition, a relative large intergenic spacer (101 bp) with higher A + T content than that in control region was identified between the tRNA(Glu) and tRNA(Phe) genes. Phylogenetic analyses based on the current dataset of complete mt genomes strongly support the Stomatopoda is closely related to Euphausiacea. They in turn cluster with Penaeoidea and Caridea clades while other decapods form a separate group, which rejects the monophyly of Decapoda. This challenges the suitability of Stomatopoda as an outgroup of Decapoda in phylogenetic analyses. The basal position of Stomatopoda within Eumalacostraca according to the morphological characters is also questioned. (C) 2010 Elsevier Inc. All rights reserved.

A close phylogenetic relationship between Sipuncula and Annelida evidenced from the complete mitochondrial genome sequence of Phascolosoma esculenta

Background: There are many advantages to the application of complete mitochondrial (mt) genomes in the accurate reconstruction of phylogenetic relationships in Metazoa. Although over one thousand metazoan genomes have been sequenced, the taxonomic sampling is highly biased, left with many phyla without a single representative of complete mitochondrial genome. Sipuncula (peanut worms or star worms) is a small taxon of worm-like marine organisms with an uncertain phylogenetic position. In this report, we present the mitochondrial genome sequence of Phascolosoma esculenta, the first complete mitochondrial genome of the phylum. Results: The mitochondrial genome of P. esculenta is 15,494 bp in length. The coding strand consists of 32.1% A, 21.5% C, 13.0% G, and 33.4% T bases (AT = 65.5%; AT skew = -0.019; GC skew = -0.248). It contains thirteen protein-coding genes (PCGs) with 3,709 codons in total, twenty-two transfer RNA genes, two ribosomal RNA genes and a non-coding AT-rich region (AT = 74.2%). All of the 37 identified genes are transcribed from the same DNA strand. Compared with the typical set of metazoan mt genomes, sipunculid lacks trnR but has an additional trnM. Maximum Likelihood and Bayesian analyses of the protein sequences show that Myzostomida, Sipuncula and Annelida (including echiurans and pogonophorans) form a monophyletic group, which supports a closer relationship between Sipuncula and Annelida than with Mollusca, Brachiopoda, and some other lophotrochozoan groups. Conclusion: This is the first report of a complete mitochondrial genome as a representative within the phylum Sipuncula. It shares many more similar features with the four known annelid and one echiuran mtDNAs. Firstly, sipunculans and annelids share quite similar gene order in the mitochondrial genome, with all 37 genes located on the same strand; secondly, phylogenetic analyses based on the concatenated protein sequences also strongly support the sipunculan + annelid clade (including echiurans and pogonophorans). Hence annelid "key-characters" including segmentation may be more labile than previously assumed.

桦木科植物的系统发育和地理分布

本文对桦木科植物的研究历史作了详细的总结;在钻研文献的基础上，补充了部分系统学资料，使得花序、花、花粉、叶表皮等各类性状能够在属间进行比较，根据外类群比较、和谐性分析等原则确定了性状的演化极性，利用最大同步法和最小平行演化法对桦木科植物进行了分支分析;对各属的现代分布和地史分布作了描述，在此基础上，讨论了桦木科植物的分布中心、起源地、起源的时间和散布的途径;在第四章，作者试图回到遥远的晚白垩纪和早第三纪，从描绘桦木科植物起源和早期分化的古地理和古气候背景入手，分析了在这种背景下桦木科植物所发生的空间辐射以及植物体本身所产生的形态进化，以求得对桦木科植物起源、散布和分化作出比较合理的解释;最后对桦木科组以上的等级作了分类处理。全文包括五个部分，主要的结论如下： 1、分支分析：广泛阅读桦木科、壳斗科和南青冈科的文献，详细研究中国科学院植物研究所标本馆所藏的桦木科植物的标本。首先以壳斗科和南青冈科作为外类群对各类性状进行了分析，得到一个由22个性状组成的数值矩阵;接着又对上述的22个性状作了和谐性分析，结果有7个性状的CN>O,2，其中3个性状在调整性状状态后被保留，有4个性状在颠倒极性和调整性状状态后仍不和谐被去除．最后得到由18个性状组成的矩阵，该矩阵和谐性检验的结果是：所有性状的KN值和CN值均为O，将此矩阵用最大同步法和最小平行演化法进行分支分析，得到一个相同的分支图。分支图用了19个演化步数，与矩阵的最小步数相同，较好地反映了桦木科植物的属间关系。分支图说明：桤木属是从桦木科植物的祖先中最早分出的一个分支，几乎保留了祖先所有的原始性状;桦木属和桤木属近缘，但并非姊妹群;榛届在桦木科中占有特殊的地位，是桦木科植物的原始类群向进化类群演化的中间纽带;虎棒子属是榛属向鹅耳枥属和铁木属进化过程中分化出的一支;铁木属和鹅耳枥属为姊妹群，在桦木科植物中演化水平最高。 2、地理分布：地理分布分析是以经典分类、系统发育和古植物学三方面的资料为基础，根据生物进化的时、序、空相互统一的观点来讨论的。 根据Takhtajan (1978)对世界植物系的分区，认为：东亚区分布6属、13组、77种，占桦木科植物全部种类的59%，为第一分布中心;大西洋一一北美区分布5属。8组、20种，为第二分布中心;环北方区分布5属、8组，35种，是桦木科植物分化的重要地区。在中国，根据吴征镒(1979)对中国植物区系的分区，认为：中国一一日本森林亚区和中国一一喜马拉雅亚区在种数，组数和属数的分布上分别位居第一和第二。四川及其毗邻省区分布6属、52种，占全部中国种类的70, 3%，是中国桦木科植物的分布中心。 桦木科最早的化石记录是具多个角萌发孔并有带状加厚的桤木粉，发现于日本桑托期．随之这类花粉和另外一种花粉类型：副桤木粉（有微弱带状加厚的三孔粉）在欧亚大陆和北美的地层中便开始普遍起来;可能的桤木属植物的叶子发现于白垩纪最晚期，而可辨认的果序的记录则开始于古新世． 8孔的具带状加厚的桦粉最早见于日本的坎佩尼期，而缺少带状加厚的拟桦粉最早发现于中国内蒙古的梅斯特利克蒂期，以上两类花粉均和现代桦木属植物的花粉相似;可归于同一个化石植物Betula leopoldae的叶子、雄花序，果序和果实的化石发现于加拿大大不列颠哥伦比亚的中始新世地层中。基于果实化石的榛属植物的最早记录发生在欧洲和北美古新世;被认为和榛属有亲缘关系的绝灭属——古鹅耳枥属的叶子，果序和雄花序的化石发现于古新世和始新世;开始见于中国梅斯特利克蒂期的拟榇粉和最早发现于苏格兰古新世的米勒三孔粉也均和榛属植物有关。基于可辨认的花粉和果苞的化石，鹅耳枥属和铁木属分别在晚始新世和早渐新世有了最早的化石记录． 最后根据化石证据和现代地理分布特征提出：以四川为中心的中国中部地区是桦木科植物起源和早期分化的中心;最早的桦木科植物生活在晚白垩纪桑托期，桤木属、榇属、桦木属可能在白垩纪最晚期或古新世时就已经出现了，而最迟不晚于中始新世;鹅耳枥属和铁木属的形成均不晚于晚始新世，到渐新世时，除虎榛子属外，桦木科其它各属均广泛分布在北半球。 3、进化分析：桦木科植物起源和早期演化的晚白垩纪和早第三纪在古地理和古环境方面主要有四个特点：(1)地球板块相对稳定;(2)气候相对一致，区带环流是大气环流的基本成份; (3)恐龙绝灭，哺乳动物作为传播媒介变得重要起来; (4)风媒和虫媒植物共荣。桦木科植物就是在上述背景下起源的。桤木属蒙自桤木组和桤木组最早从祖先类群中分化出来，接着一方面较缓慢地向欧洲散布，并在古新世到达欧洲;另一方面，向中国东北地区散布，然后迅速地扩散到了北极地区，通过白令陆桥在白垩纪最晚期到达了北美。从北美西北部和从欧洲通过大西洋北极陆桥散布到北美东部的桦木科植物在始新世时汇合，形成第二个分化中心。虎榛子属、鹅耳枥属和铁木属植物的大量分化很可能是从全球气候恶化的渐新世开始的，并在分化的同时伴随着其它的桦木科植物向南迁移。桤木属在渐新世时就散布到了当时位于中国东南部的加里曼丹岛;桤木属、鹅耳枥属和铁木属中新世时散布到了墨西哥和中美洲;第四纪冰期加速了桦木科植物的南移，桤木属到达非洲北部和南美洲，桤木属和鹅耳枥属到达台湾岛均发生在更新世。 在环境的选择压力下，桦木科植物经历了一系列的形态演化，作者将这些演化归纳成34个进化趋势。为了对桦木科植物可能祖先的大概轮廓有一个认识，我们又从34个进化趋势中总结出桦木科植物的11个原始特征，并且认为这些特征中的大多数应该是它的祖先拥有的。 (1)裸芽有柄。 (2)气孔器为轮列型或无规则型。 (3)木材具管胞，导管有螺旋加厚，为梯状穿孔。 (4)雌、雄花序共生成总状花序，雄花序位于上部。 (5)花序两性。 (6)雄花序有梗、裸露过冬。 (7)小聚伞花序由多个花组成，苞片多数。 (8)花两性，有花被，子房3室。 (9)花药药室木分离，花丝也不分叉。 (10)花粉粒4-5孔;孔具孔室;孔间有带状加厚;外壁较厚，在孔处翘起并加厚。 (11)具翅坚果小型。 本文提出桦术科植物不可能起源于现存的壳斗科植物，而两者有可能共祖，它们共同的祖先和正型粉类复合群有关，可能来源于正型粉类复合群的某些成员，那么‘正型粉类复合群是否就是金缕梅目和壳斗目进行的中间链环呢?’本文仅作为一个问题提出，而未作回答。 4、系统分类：根据分支分析和表征分类的结果，桦木科是非常自然的一个类群，科内表现出从原始到高级的演化次序并具有三条主要的演化路线。因此，将桦木科划分为三个族与科内的三条演化线相一致，比较符合其属间的系统发育关系。按照各属的变异程度，进一步在桦木族和鹅耳枥族之下分别设立两个亚族。此外在桦木科植物属之下共确立了13个组。桦木科组以上的系统排列为： Betulaceae S. F. Gray Trib. 1. Betuleae Subtrib. 1. Alninae Z. D. Chen subtrib. nov. Alnus Mill. Sect. 1. Clethropsis ( Spach ) Endl. Sect. 2. Alnus Sect. 3. Cremastogyne H. Winkl, Sect. 4. Alnobetula W. D. Koch Subtrib. 2. Betulinae Betula L. Sect. 1. Betulaster ( Spach ) Regel Sect. 2. Betula Sect. 3. Costatae Regel Sect. 4. Chinenses ( Nakai ) Z. D. Chen comb. et stat.nov. Sect. 5. Humiles W.D.Koch Trib. 2. Coryleae Aacheraon Corylus L. Sect. 1, Acanthochlamys Spach Sect. 2. Corylus Trib. 3. Carpineae A. DC. Subtrib. 1. Ostryopsinae Z. D. Chen subtrib. nov.Ostryopsis Dence. Subtrib. 2. Carpininae Ostrya Scop. Carpinus L. Sect. 1. Distegocarpus ( Sieb. et Zucc. ) Sarg. Sect. 2. Carpinus

Bacillus pallidus sp nov., isolated from forest soil

A Gram-positive bacterium, designated strain CW 7(T), was isolated from forest soil in Anhui Province, south-east China. Cells were strictly aerobic, motile with peritrichous flagella and rod-shaped. The strain grew optimally at 30-37 degrees C and pH 7.0-8.0. The major fatty acids of strain CW 7(T) were anteiso-C-15:0, iso-C-15:0 and anteiso-C-17:0. The predominant menaquinone was MK-7. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The G + C content of the genomic DNA was 42.3 mol%. Phylogenetic analysis indicated that strain CW 7(T) belonged to a monophyletic cluster within the genus Bacillus and showed 16S rRNA gene sequence similarities of less than 96.5% to recognized species of the genus Bacillus. The results of the polyphasic taxonomic study, including phenotypic, chemotaxonomic and phylogenetic analyses, showed that strain CW 7(T) represents a novel species of the genus Bacillus, for which the name Bacillus pallidus sp. nov. is proposed. The type strain is CW 7(T) (=KCTC 13200(T)=CCTCC AB 207188(T)=LMG 24451(T)).

A phylogeny of Chinese leaf monkeys using mitochondrial ND3-ND4 gene sequences

The phylogeny of Chinese leaf monkeys, especially the snub-nosed monkeys (Rhinopithecus), has not been thoroughly investigated using molecular sequence data, perhaps due to their rarity in the wild and their poor representation in institutional collections. Despite several proposed classifications, systematic relationships of these species remain poorly defined and this has hindered their conservation. To clarify the phylogenetic relationships of the leaf monkey clade in China, we sequenced the mitochondrial ND3, ND4L, ND4, tRNA(Arg), tRNA(His), tRNA(Ser), and tRNA(Leu) genes for Rhinopithecus bieti, R. roxellana, Trachypithecus francoisi, T. f. leucocephalus, and T. phayrei as well as Pygathrix nemaeus and Colobus guereza. We included a rotal of 2252 characters for each individual, excluding gaps in primary sequences. Our interpretation of the results from character- and distance-based phylogenetic analyses suggest that (1) Pygathrix nemaeus is sister to Rhinopithecus rather than to Trachypithecus though it is quite divergent from the former; (2) the Yunnan snub-nosed monkey, Rhinopithecus bieti, represents a valid species; (3) the white-headed leaf monkey is not a distinct species, but instead is a subspecies of Trachypithecus francoisi (T. f. leucocephalus), though it should still be considered a separate evolutionarily significant unit (ESU); and (4) because two individuals of the Phayrei's leaf monkey, T. phayrei, are genetically distinct from one another, a more extensive revision of the taxonomy of this putative species in China is needed. These results, plus ongoing work on the molecular systematics of the entire Asian leaf monkey radiation, can provide a sound basis for identifying the appropriate units of conservation for this endangered group of primates.

Molecular phylogeny and biogeography of Oriental voles: genus Eothenomys (Muridae, Mammalia)

Oriental voles of the genus Eothenomys are predominantly distributed along the Southeastern shoulder of the Qinghai-Tibetan Plateau. Based on phylogenetic analyses of the mitochondrial cytochrome b gene (1143 bp) obtained from 23 specimens (eight species)

Mitochondrial diversity and phylogeographic structure of Chinese domestic goats

China has numerous native domestic goat breeds, but so far there has been no extensive study on genetic diversity, population demographic history, and origin of Chinese goats. Here, we examined the genetic diversity and phylogeographic structure of Chinese domestic goats by determining a 481-bp fragment of the first hypervariable region of mitochondrial DNA (mtDNA) control region from 368 individuals representing 18 indigenous breeds. Phylogenetic analyses revealed that there were four mtDNA lineages (A-D) identified in Chinese goats, in which lineage A was predominant, lineage B was moderate, and lineages C and D were at low frequency. These results further support the multiple maternal origins of domestic goats. The pattern of genetic variation in goat mtDNA sequences indicated that the two larger lineages A and B had undergone population expansion events. In a combined analysis of previously reported sequences and our sequences belonging to lineage B, we detected two subclades, in which one was unique to eastern Asia and another was shared between eastern and southern Asia. A larger genetic variation in eastern Asia than southern Asia and the pattern of phylogeographic variation in lineage B suggest that at least one subclade of lineage B originated from eastern Asia. There was no significant geographical structuring in Chinese goat populations, which suggested that there existed strong gene flow among goat populations caused by extensive transportation of goats in history. (c) 2005 Elsevier Inc. All rights reserved.

Genetic differentiation and cryptic speciation in natural populations of Drosophila lacertosa

Drosophila lacertosa, an Oriental member of the robusta species group in the virilis-repleta radiation, has a wide distribution from northern India throughout China to the Far East. Phylogenetic analyses of mitochondrial ND2 gene sequences revealed two ge

What are the closest relatives of the hot-spring snakes (Colubridae, Thermophis), the relict species endemic to the Tibetan Plateau?

We conducted phylogenetic analyses to identify the closest related living relatives of the Xizang and Sichuan hot-spring snakes (T baileyi and T. zhaoermii) endemic to the Tibetan Plateau, using mitochondrial DNA sequences (cyt b, ND4) from eight specimen

Adaptive Evolution of Digestive RNASE1 Genes in Leaf-Eating Monkeys Revisited: New Insights from Ten Additional Colobines

Pancreatic RNase genes implicated in the adaptation of the colobine monkeys to leaf eating have long intrigued evolutionary biologists since the identification of a duplicated RNASE1 gene with enhanced digestive efficiencies in Pygathrix nemaeus. The recent emergence of two contrasting hypotheses, that is, independent duplication and one-duplication event hypotheses, make it into focus again. Current understanding of Colobine RNASE1 gene evolution of colobine monkeys largely depends on the analyses of few colobine species. The present study with more intensive taxonomic and character sampling not only provides a clearer picture of Colobine RNASE1 gene evolution but also allows to have a more thorough understanding about the molecular basis underlying the adaptation of Colobinae to the unique leaf-feeding lifestyle. The present broader and detailed phylogenetic analyses yielded two important findings: 1) All trees based on the analyses of coding, noncoding, and both regions provided consistent evidence, indicating RNASE1 duplication occurred after Asian and African colobines speciation, that is, independent duplication hypothesis; 2) No obvious evidence of gene conversion in RNASE1 gene was found, favoring independent evolution of Colobine RNASE1 gene duplicates. The conclusion drawn from previous studies that gene conversion has played a significant role in the evolution of Colobine RNASE1 was not supported. Our selective constraint analyses also provided interesting insights, with significant evidence of positive selection detected on ancestor lineages leading to duplicated gene copies. The identification of a handful of new adaptive sites and amino acid changes that have not been characterized previously also provide a necessary foundation for further experimental investigations of RNASE1 functional evolution in Colobinae.

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.

Generic allocation of Indian and Sri Lankan Philautus (Anura: Rhacophoridae) inferred from 12S and 16S rRNA genes

The generic allocation of Indian and Sri Lankan Philautus needs further examination. In this study, a comprehensive understanding of the phylogeny of Indian and Sri Lankan Philautus is obtained based on 125 and 16S rRNA genes. All phylogenetic analyses indicate that Indian-Sri Lankan Philautus, Philautus menglaensis, Philautus longchuanensis, and Philautus gryllus form a well supported clade, separate from Philautus of Sunda Islands that form another well supported clade representing true Philautus. This result supports the designation of the genus Pseudophilautus to accommodate the Indian and Sri Lankan species. Pseudophilautus consists of two major lineages, one comprises the majority of Indian species, Chinese species, and Southeast Asian species, and one comprises all Sri Lankan species and a few Indian species. Pseudophilautus may have originated in South Asia and dispersed into Southeast Asia and China. Based on the results, we further suggest that Philautus cf. gryllus (MNHN1997.5460) belongs to the genus Kurixalus. (C) 2010 Published by Elsevier Ltd.

Molecular phylogeography and population structure of a mid-elevation montane frog Leptobrachium ailaonicum in a fragmented habitat of southwest China

Leptobrachium ailaonicum is a vulnerable anuran restricted to a patchy distribution associated with small mountain streams surrounded by forested slopes at mid-elevations (approximately 2000-2600 m) in the subtropical Mount Wuliang and Mount Ailao ranges in southwest China (Yunnan Province) and northern Vietnam. Given high habitat specificity and lack of suitable habitat in lower elevations between these ranges, we hypothesized limited gene flow between populations throughout its range. We used two mitochondrial genes to construct a phylogeographic pattern within this species in order to test our hypothesis. We also examined whether this phylogeographic pattern is a response to past geological events and/or climatic oscillations. A total of 1989 base pairs were obtained from 81 individuals of nine populations yielding 51 unique haplotypes. Both Bayesian and maximum parsimony phylogenetic analyses revealed four deeply divergent and reciprocally monophyletic mtDNA lineages that approximately correspond to four geographical regions separated by deep river valleys. These results suggest a long history of allopatric separation by vicariance. The distinct geographic distributions of four major clades and the estimated divergence time suggest spatial and temporal separations that coincide with climatic and paleogeographic changes following the orogeny and uplift of Mount Ailao during the late Miocene to mid Pliocene in southwest China. At the southern distribution, the presence of two sympatric yet differentiated clades in two areas are interpreted as a result of secondary contact between previously allopatric populations during cooler Pleistocene glacial cycles. Analysis of molecular variance indicates that most of the observed genetic variation occurs among the four regions implying long-term interruption of maternal gene flow, suggesting that L ailaonicum may represent more than one distinct species and should at least be separated into four management units corresponding to these four geographic lineages for conservation. (C) 2009 Elsevier Inc. All rights reserved.

Evolutionary status of Entamoeba

In addition to its medical importance as parasitic pathogen, Entamoeba has aroused people's interest in its evolutionary status for a long time. Lacking mitochondrion and other intracellular organelles common to typical eukaryotes, Entamoeba and several other amitochondrial protozoans have been recognized as ancient pre-mitochondriate eukaryotes and named "archezoa", the most primitive extant eukaryotes. It was suggested that they might be living fossils that remained in a primitive stage of evolution before acquisition of organelles, lying close to the transition between prokaryotes and eukaryotes. However, recent studies revealed that Entamoeba contained an organelle, "crypton" or "mitosome", which was regarded as specialized or reductive mitochondrion. Relative molecular phylogenetic analyses also indicated the existence or the probable existence of mitochondrion in Entamoeba. Our phylogenetic analysis based on DNA topoisomerase II strongly suggested its divergence after some mitchondriate eukaryotes. Here, all these recent researches are reviewed and the evolutionary status of Entamoeba is discussed.