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1.
The phylogeny of the Family Spongodiscidae (polycystine Radiolaria), which includes Dictyocoryne profunda Ehrenberg, Dictyocoryne truncatum (Ehrenberg) and Spongaster tetras Ehrenberg, was examined using 18S ribosomal DNA (small-subunit ribosomal DNA) sequence analysis. Three types of tree construction methods, the neighbor joining (NJ), maximum parsimony (MP), and maximum likelihood (ML) methods, were used to infer the phylogenetic relationships of the polycystine and acantharian Radiolaria among eukaryotes. The obtained 18S rDNA molecular phylogenetic tree argues for the monophyly of the two groups. Furthermore, the Polycystinea is divided into at least two distinct lineages consisting of: (1) colonial and skeletonless Polycystinea, including Thalassicollidae, Collospaeridae, and Sphaerozoidae; and (2) shell-bearing solitary Polycystinea, including Spongodiscidae. The Polycystinea thus show a paraphyly among Radiolaria. Moreover, the monophyly of the clade including the acantharians and the spongodiscid polycystines was supported by bootstrap values, which were 94%, 53%, and 59% in the NJ, MP, and ML analyses, respectively. This lineage is characterized by having latticed or spongy skeletons of different chemical composition, namely SiO2 (Class Polycystinea) or SrSO4 (Class Acantharea). According to the present taxonomic scheme, the Acantharea and the Polycystinea have not been placed in different classes, but the results of our molecular study show the opposite. We therefore suggest, based on the monophyly of the two clades, that a new taxonomic group of Radiolaria can be established. Our molecular data also suggest that the currently used radiolarian taxonomic system may need serious revisions.  相似文献   

2.
苋科(Amaranthaceae sensu lato)是石竹目(Caryophyllales)第二大科, 目前被普遍接受的苋科为其广义概念, 含狭义苋科(Amaranthaceae sensu stricto)和藜科(Chenopodiaceae)。然而到目前为止, 藜科是否应作为独立的科还存在争议。此外, 广义苋科内部各亚科之间的系统关系也尚未厘清。对广义苋科所有13个亚科代表类群进行取样(共59种), 基于8个叶绿体序列片段重建其系统发育关系, 并结合分子钟估算, 对该科及其主要分支的起源与分化时间进行推测。结果表明, 广义苋科与狭义苋科都是很好的单系, 但藜科并非单系, 因此不支持藜科在科级水平的地位, 支持广义苋科的观点。除了多节草亚科(Polycnemoideae)之外, 其它亚科的系统位置均得到很好的分辨。分子钟估算结果表明, 广义苋科于白垩纪晚期约69.9 Ma分化出该科的2个主要分支, 且该科在白垩纪-古近纪边界附近时期(约66.0 Ma)可能发生过快速辐射分化事件。  相似文献   

3.
Chtoranthaceae is one of the earliest diverging angiosperm families and is comprised of approximately 75 species in four genera (Chloranthus,Sarcandra,Ascarina,and Hedyosmurn).This family has received considerable attention because of its seemingly primitive morphology,disjunct tropical distribution in Asia and America,and extensive fossil record from the Early Cretaceous.In the present study,we reconstructed the phylogeny of Chloranthaceae based on a combined dataset of three plastid DNA regions and 56 species.We then estimated divergence times in the family using two relaxed molecular clock methods (BEAST and penalized likelihood).We focused on testing the influence of fossil taxa in calibrating the molecular phylogeny,and on assessing the current taxonomy of the family in light of the phylogenetic results.Our results indicate that most intrageneric divisions within Ascarina and Hedyosmum are not monophyletic.The results from the dating analysis suggest that the Hedyosmum-like fossil Asteropollis represents a stem lineage of Hedyosmum,as has been suggested previously from morphological analyses.In contrast,our results indicate that the Chloranthus-like fossil Chloranthistemon,previously suggested on morphological grounds to be a stem relative of Chloranthus,may,instead,belong to the branch leading to the clade Chloranthus + Sarcandra.The median crown ages of Chloranthus,Sarcandra,Ascarina,and Hedyosmum estimated in the BEAST analysis were 26.3,9.5,31.0 and 45.8 million years ago (Ma),respectively,whereas the divergence between Chloranthus and Sarcandra,the splitting of Ascarina with the former two genera,and Hedyosmum separating from the three genera were estimated to 63.8,95.7 and 111.1 Ma.The present study sheds further light on the temporal evolution of Chloranthaceae and exemplifies how molecular dating analyses may be used to explore alternative phylogenetic placements of fossil taxa.  相似文献   

4.
随着分子系统发育研究的普及,真菌各分类类群逐渐被修订为单系发生类群,通常结合形态学特征为代表的表型特征(“单系+表型特征”)对不同的分类等级命名是最为普遍的方法。历史上存在的大量多系名称被逐步修订、补充和完善,各个不同等级类群的分类系统变得更加合理、客观和趋于自然,这是分类学进程中巨大的进步。然而系统发育重建所揭示的单系类群并没有相应的标准来对应于纲目科属等种上分类等级,所以并不能直接转换为分类系统,且在分类实践中,由于不同分类学家在决定各个单系类群对应的分类等级时采用的尺度不同、依据不一,严重影响分类系统的科学性和稳定性。随着分子钟分析方法的出现,实现了对现生生物类群演化时间的估算,所以在系统发育、表型特征研究的基础上,把演化时间作为真菌分类的新增指标来划分和命名种上分类等级的方法(“单系+表型特征+演化时间”)得以应用。本文回顾了首次利用这种方法重建蘑菇属分类系统的工作,目前研究所揭示的担子菌门和子囊菌门从门至科各分类等级的演化时间范围,及利用演化时间为新增指标在分类命名中的应用;分析了影响演化时间估算可靠性的关键因素及对策。我们认为在构建分类系统的研究中增加演化时间指标,使新分类系统体现类群进化过程中的时间维度,能更全面反映类群的进化历程,促进分类系统的科学性和稳定性。  相似文献   

5.
Using mitochondrial DNA cytochrome c oxidase subunit I and nuclear DNA 28S rRNA data, we explored the phylogenetic relationships of the family Pimoidae (Arachnida: Araneae) and tested the North America to Asia dispersal hypothesis. Sequence data were analysed using maximum parsimony and Bayesian inference. A phylogenetic analysis suggested that vicariance, instead of dispersal, better explained the present distribution pattern of Pimoidae. Times of divergence events were estimated using penalized likelihood method. The dating analysis suggested that the emergence time of Pimoidae was approximately 140 million years ago (Ma). The divergence time of the North American and Asian species of Pimoa was approximately 110 Ma. Our phylogenetic hypothesis supports the current morphology‐based taxonomy and suggests that the cave dwelling might have played an important role in the speciation of pimoids in arid areas.  相似文献   

6.
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 0. 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. aythrotis diverged first, followed by O. cansus, while O. atrzoniae 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 Ochotona, 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  相似文献   

7.
Understanding how environmental forcing has generated and maintained large‐scale patterns of biodiversity is a key goal of evolutionary research and critical to predicting the impacts of global climate change. We suggest that the initiation of the global thermohaline circulation provided a mechanism for the radiation of Southern Ocean fauna into the deep sea. We test this hypothesis using a relaxed phylogenetic approach to coestimate phylogeny and divergence times for a lineage of octopuses with Antarctic and deep‐sea representatives. We show that the deep‐sea lineage had their evolutionary origins in Antarctica, and estimate that this lineage diverged around 33 million years ago (Ma) and subsequently radiated at 15 Ma. Both of these dates are critical in development of the thermohaline circulation and we suggest that this has acted as an evolutionary driver enabling the Southern Ocean to become a centre of origin for deep‐sea fauna. This is the first unequivocal molecular evidence that deep‐sea fauna from other ocean basins originated from Southern Ocean taxa and this is the first evidence to be dated. © The Willi Hennig Society 2008.  相似文献   

8.
The completion of the land bridge between North and South America approximately 3.5-3.1 million years ago (Ma) initiated a tremendous biogeographic event called the Great American Biotic Interchange (GABI), described principally from the mammalian fossil record. The history of biotic interchange between continents for taxonomic groups with poor fossil records, however, is not well understood. Molecular and fossil data suggest that a number of plant and animal lineages crossed the Isthmus of Panama well before 3.5 Ma, leading biologists to speculate about trans-oceanic dispersal mechanisms. Here we present a molecular phylogenetic analysis of the frog genus Pristimantis based on 189 individuals of 137 species, including 71 individuals of 31 species from Panama and Colombia. DNA sequence data were obtained from three mitochondrial (COI, 12S, 16S) and two nuclear (RAG-1 and Tyr) genes, for a total of 4074 base pairs. The resulting phylogenetic hypothesis showed statistically significant conflict with most recognized taxonomic groups within Pristimantis, supporting only the rubicundus Species Series, and the Pristimantis myersi and Pristimantis pardalis Species Groups as monophyletic. Inference of ancestral areas based on a likelihood model of geographic range evolution via dispersal, local extinction, and cladogenesis (DEC) suggested that the colonization of Central America by South American Pristimantis involved at least 11 independent events. Relaxed-clock analyses of divergence times suggested that at least eight of these invasions into Central America took place prior to 4 Ma, mainly in the Miocene. These findings contribute to a growing list of molecular-based biogeographic studies presenting apparent temporal conflicts with the traditional GABI model.  相似文献   

9.
Rates of primary productivity by the symbiotic algae of a varietyof planktonic sarcodines (Acantharia, Radiolaria, Foraminifera)were measured at two times of the year in 1991 from surfacewaters of the Sargasso Sea near Bermuda Rates of symbiont production(expressed on a ‘per host’ basis) were not significantlydifferent for the two seasons, but measurements for individualsarcodine species varied by more than four orders of magnitudeand were roughly correlated with sarcodine size (and therebywith the biomass of the protozoan host). Overall, Acanthariahad the lowest production rates per host, while solitary andcolonial Radiolaria displayed the highest rates. Symbiont-bearingplanktonic sarcodines were always microenvironments of highlyconcentrated primary production in this oligotrophic oceanicenvironment. Rates of primary production within the volumesdefined by the extension of the cytoplasmic networks of thesarcodines generally exceeded rates of primary production inequivalent volumes of the seawater surrounding these associationsby more than four orders of magnitude and showed no clear differencesamong the sarcodine groups Total symbiont production, however,contributed a small fraction (generally <1%) of the totalprimary production in surface waters because of relatively lowsarcodine abundances (compared to other primary producers) andbecause of high total primary production in surface waters.Combining the production rates measured in this study with seasonalabundances of Acantharia and Foraminifera, however, indicatesthat these assemblages may have contributed an average of  相似文献   

10.
Although molecular studies have helped to clarify the phylogeny of the problematic family Viverridae, a recent phylogenetic investigation based on cytochrome b (cyt b) has excluded the Asiatic linsangs (genus Prionodon) from the family. To assess the phylogenetic position of the Asiatic linsangs within the Feliformia, we analysed an exhaustive taxonomic sample set with cyt b and newly produced transthyretin intron I sequences (TR-I-I). TR-I-I alone and cyt b +TR-I-I combined (maximum-likelihood analysis) highly support the position of Asiatic linsangs as sister-group of the Felidae. The estimation of minimum divergence dates from molecular data suggests a splitting event ca. 33.3 million years (Myr) ago, which lends support to historical assertions that the Asiatic linsangs are "living fossils" that share a plesiomorphic morphotype with the Oligocene feliform Paleoprionodon. The African linsang is estimated to appear more than 20 Myr later and represents the sister-group of the genus Genetta. Our phylogenetic results illustrate numerous morphological convergences of "diagnostic" characters among Feliformia that might be problematic for the identification of fossil taxa. The morphotype reappearance from the Asiatic to the African linsangs suggests that the genome of the Feliformia conserved its potential ability of expression for a peculiar adaptive phenotype throughout evolution, in this case arboreality and hypercarnivory in tropical forest.  相似文献   

11.
Analysis of the AMP-forming ACS gene was performed in 12 species of the Drosophilidae family. Systematically four introns, aligned at the same positions, were detected, but none of them showed a position similar to those known for species outside the Drosophilidae family. The average length of introns varied from 63 to 75 bp but in two species Drosophila takahashii and D. kikkawai the length of the second intron was 343 and 210 bp, respectively. In coding regions, about 80% of the third codon positions were substituted while first and second positions showed, respectively, 14% and 6% substitutions. Interestingly, the divergence observed at the protein level between species was very low. The phylogenetic tree based on the DNA sequences of the exons was mainly in agreement with taxonomic classification and previous molecular phylogenies except for D. ananassae, which appeared more closely related to D. subobscura and D. funebris than to the species of the melanogaster group.  相似文献   

12.
The serum albumin gene family is composed of four members that have arisen by a series of duplications from a common ancestor. From sequence differences between members of the gene family, we infer that a gene duplication some 580 Myr ago gave rise to the vitamin D–binding protein (DBP) gene and a second lineage, which reduplicated about 295 Myr ago to give the albumin (ALB) gene and a common precursor to α-fetoprotein (AFP) and α-albumin (ALF). This precursor itself duplicated about 250 Myr ago, giving rise to the youngest family members, AFP and ALF. It should be possible to correlate these dates with the phylogenetic distribution of members of the gene family among different species. All four genes are found in mammals, but AFP and ALF are not found in amphibia, which diverged from reptiles about 360 Myr ago, before the divergence of the AFP-ALF progenitor from albumin. Although individual family members display an approximate clock-like evolution, there are significant deviations—the rates of divergence for AFP differ by a factor of 7, the rates for ALB differ by a factor of 2.1. Since the progenitor of this gene family itself arose by triplication of a smaller gene, the rates of evolution of individual domains were also calculated and were shown to vary within and between family members. The great variation in the rates of the molecular clock raises questions concerning whether it can be used to infer evolutionary time from contemporary sequence differences. Received: 28 February 1995 / Accepted: 6 October 1997  相似文献   

13.
14.
The Capromyidae (hutias) are endemic rodents of the Caribbean and represent a model of dispersal for non-flying mammals in the Greater Antilles. This family has experienced severe extinctions during the Holocene and its phylogenetic affinities with respect to other caviomorph relatives are still debated as morphological and molecular data disagree. We used target enrichment and next-generation sequencing of mitochondrial and nuclear genes to infer the phylogenetic relationships of hutias, estimate their divergence ages, and understand their mode of dispersal in the Greater Antilles. We found that Capromyidae are nested within Echimyidae (spiny rats) and should be considered a subfamily thereof. We estimated that the split between hutias and Atlantic Forest spiny rats occurred 16.5 (14.8–18.2) million years ago (Ma), which is more recent than the GAARlandia land bridge hypothesis (34–35 Ma). This would suggest that during the Early Miocene, an echimyid-like ancestor colonized the Greater Antilles from an eastern South American source population via rafting. The basal divergence of the Hispaniolan Plagiodontia provides further support for a vicariant separation between Hispaniolan and western islands (Bahamas, Cuba, Jamaica) hutias. Recent divergences among these western hutias suggest Plio-Pleistocene dispersal waves associated with glacial cycles.  相似文献   

15.
Phyllactinia is a unique genus within the Erysiphales (Ascomycota) having a partly endo-parasitic nature of the mycelium within the host plant tissues. We constructed phylogenetic trees for the genus Phyllactinia and its allied genera based on a total of 120 nucleotide sequences of the 28S rDNA and ITS regions to discuss their phylogenetic relationships with special references to host plants, biogeography, evolutionary dating, and taxonomy. The analysis of the Erysiphales confirmed the monophyly of the endo-parasitic genera, i.e. Leveillula, Phyllactinia, and Pleochaeta. Phyllactinia specimens used in this study were divided into six distinctive groups and three subgroups. Interestingly, Leveillula, an obligately endo-parasitic genus of the Erysiphales, grouped together with Phyllactinia, although this was not significantly supported by the Kishino–Hasegawa and Shimodaira–Hasegawa tests. This suggests that the evolution within this group of fungi occurred from partial endo-parasitism to obligate endo-parasitism. The host range of Phyllactinia is mostly confined to woody plants, especially deciduous trees. Betulaceae, Fagaceae, Ulmaceae, Moraceae, and Rosaceae may have close connections to the divergence of the groups and subgroups of Phyllactinia concerned. Most of these plant families are known as major members of the boreotropical flora of the Tertiary, which suggests an early Tertiary origin of this genus. A comparison of the phylogenies of hosts and parasites revealed that host range expansion at higher taxonomic levels (higher than family level) is independent of the phylogeny of plants. Conversely, host range expansions in lower taxonomic levels (infrafamilial or infrageneric) tend to occur within a single family or genus. An estimation of the evolutionary timing using a molecular clock approach suggested that Phyllactinia split from Pleochaeta about 60 M years ago (Ma) in the early Tertiary and divergence of the six major clades of Phyllactinia occurred between 5 and 40 Ma during the Oligocene and Miocene. Divergence within the major clades and within Leveillula occurred maybe from more than 5 Ma onwards during the Pliocene and Quaternary. This is the first comprehensive phylogenetic study of Phyllactinia and other endo-parasitic genera of the Erysiphales.  相似文献   

16.
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. berezovskii 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.  相似文献   

17.
In order to characterize the phylogenetic relationship and deep-sea adaptation process of the deep-sea fish genus Coryphaenoides, the nucleotide sequences of the mitochondrial (mt) 12 S rRNA and COI gene sequences for seven Coryphaenoides species were analyzed. Our molecular phylogenetic tree shows a new arrangement of seven Coryphaenoides species, which form two distinct groups, abyssal and nonabyssal species, and differs from the results of previous taxonomic studies. Using the mutation rate of mitochondrial genes, the divergence time between abyssal and nonabyssal Coryphaenoides was found to be 3.2-7.6 million years ago. Our study suggests that hydraulic pressure plays an important role in the speciation process in the marine environment.  相似文献   

18.
Recently, molecular analyses revealed that African and Eurasian golden jackals are distinct species. This finding suggests re‐investigation of the phylogenetic relationships and taxonomy of other African members of the Canidae. Here, we provide a study on the phylogenetic relationship between populations of African jackals Lupulella mesomelas and L. adusta inferred from 962 bp of the mitochondrial cytochrome b (cytb) gene. As expected from its disjunct distribution, with one population in eastern Africa and the other one in southern Africa, we found two mitochondrial lineages within L. mesomelas, which diverged about 2.5 million years ago (Ma). In contrast, in L. adusta with its more continuous distribution in sub‐Saharan Africa, we found only a shallower genetic diversification, with the exception of the West African population, which diverged around 1.4 Ma from the Central and East African populations. Both divergence ages are older than, for example the 1.1–0.9 million years between the grey wolf Canis lupus and the African golden wolf C. lupaster. One taxonomic implication of our findings might be that the two L. mesomelas populations warrant species status. However, genome‐wide data with adequate geographical sampling are needed to substantiate our results.  相似文献   

19.
Pelagic gobies are considered of particular zoological interest because the acquisition of a pelagic lifestyle is achieved through the persistence of larval anatomical features. The Mediterranean Sea is inhabited by three goby species (Aphia minuta, Crystallogobius linearis and Pseudaphya ferreri) characterized by paedomorphic traits. Owing to the shared larval morphological features, these species have generally been considered as a monophyletic group. This study aimed at establishing the phylogenetic relationships of these paedomorphic species within the family Gobiidae to ascertain whether the pelagic lifestyle achieved through paedomorphosis is due to an event that took place in a common ancestor or not. For this purpose, we amplified by polymerase chain reaction and sequenced the mitochondrial 12S rDNA (complete sequence) and 16S rDNA (partial sequence) of 15 Mediterranean gobies. The phylogenetic analysis strongly supported the polyphyletic origin of the three paedomorphic gobies, indicating that the heterochronic change leading to the retention of larval features seems to have occurred independently in the ancestors of these species. Thus, the sharing of morphological traits can be considered homoplasious and the classification of these species in the same taxonomic group is rejected on the basis of molecular data.  相似文献   

20.
Fairy armadillos or pichiciegos (Xenarthra, Dasypodidae) are among the most elusive mammals. Due to their subterranean and nocturnal lifestyle, their basic biology and evolutionary history remain virtually unknown. Two distinct species with allopatric distributions are recognized: Chlamyphorus truncatus is restricted to central Argentina, while Calyptophractus retusus occurs in the Gran Chaco of Argentina, Paraguay, and Bolivia. To test their monophyly and resolve their phylogenetic affinities within armadillos, we obtained sequence data from modern and museum specimens for two mitochondrial genes (12S RNA [MT-RNR1] and NADH dehydrogenase 1 [MT-ND1]) and two nuclear exons (breast cancer 1 early onset exon 11 [BRCA1] and von Willebrand factor exon 28 [VWF]). Phylogenetic analyses provided a reference phylogeny and timescale for living xenarthran genera. Our results reveal monophyletic pichiciegos as members of a major armadillo subfamily (Chlamyphorinae). Their strictly fossorial lifestyle probably evolved as a response to the Oligocene aridification that occurred in South America after their divergence from Tolypeutinae around 32 million years ago (Mya). The ancient divergence date (~17Mya) for separation between the two species supports their taxonomic classification into distinct genera. The synchronicity with Middle Miocene marine incursions along the Paraná river basin suggests a vicariant origin for pichiciegos by the disruption of their ancestral range. Their phylogenetic distinctiveness and rarity in the wild argue in favor of high conservation priority.  相似文献   

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