Variations of molar morphology in the Spalax ehrenbergi superspecies: adaptive and phylogenetic significance

This study compares and contrasts variations of enamel fold pattern on the crowns of the molars of subterranean mole rats ( Spalax ) belonging to two superspecies, S. ehrenbergi and S. leucodon , and involving about 20 chromosomal species, distributed parapatrically and ranging on different soil types. The sample studied involved 397 skulls, subdivided as follows: 280 of S. ehrenbergi from Israel, representing the four chromosomal species 2n = 52, 54, 58 and 60; 59 of S. ehrenbergi from Egypt, Lebanon, Syria, Jordan and Turkey; 58 of S. leucodon from Turkey.
In making the comparisons it was necessary to take into account the marked changes of molar pattern that take place as a result of wear.
There is a reasonably good agreement between differences of molar pattern and genetic and immunological distances. The species in Israel and Egypt form a compact group, clearly differentiated from Turkish leucodon; ehrenbergi from Turkey and Syria are intermediate, in accordance with their geographical distribution.
In Israel, differences associated with soil type are at about the same level as differences between species. Local populations show a higher level of diversity, and in a number of cases neighbouring populations differed significantly, sometimes over very short distances. Population differences within species are generally associated with differences of soil and vegetation, indicating the influence of natural selection. There are also differences across species boundaries, implying a phylogenetic (heritage) effect. The nature of the adaptive link between molar pattern and soil is unknown: possible factors are contamination of the food by soil, and toughness of the food which necessitates changes of enamel fold length to improve grinding efficiency.     

Mitochondrial DNA polymorphisms in subterranean mole-rats of the Spalax ehrenbergi superspecies in Israel, and its peripheral isolates

Patterns of mitochondrial DNA (mtDNA) variation were examined in 133 mole-rats constituting all four chromosomal species (2n = 52, 2n = 54, 2n = 58, and 2n = 60) of the Spalax ehrenbergi superspecies in Israel, as well as the peripheral isolates of 2n = 60. In the main range of the complex, a total of 28 mtDNA haplotypes were found in 64 mole-rats, with most haplotypes being unique to either a single chromosomal species or population. mtDNA divergence increased from low to high diploid number in a north-to-south direction in Israel. Overall levels of mtDNA diversity were unexpectedly the highest in the 2n = 60, the youngest species of the complex. The mtDNA haplotypes can be separated into two major groups, 2n = 52-54 and 2n = 58-60, and a phylogenetic analysis for each group revealed evidence of a few haplotypes not sorted by diploid number. The overall patterns of mtDNA divergence seen within and among the four chromosomal species are consistent with the parapatric mode of speciation as suggested from previous studies of allozyme and DNA hybridization. In a separate data set the patterns of mtDNA variation were examined across the main geographic range and across peripheral semi-isolates and isolates of the 2n = 60 chromosomal species. Fifteen haplotypes were found in 69 mole-rats. High levels of mtDNA diversity characterized the main range, semi-isolated, and even some desert isolated populations. The peripheral isolates contain much mtDNA diversity, including novel haplotypes.      

Recognition of phylogenetic relationships from polypeptide chain fold similarities

Summary Structural similarities between proteins with no amino acid sequence homology either indicate a phylogenetic relationship, or they are merely the expression of a physically preferred way of folding a polypeptide chain. It is shown that one can distinguish between these alternatives by evaluating the significance of the similarity. Such significances have been derived for comparison between chain folds containing-pleated sheets (Schulz and Schirmer, 1974; Richardson et al., 1976; Sternberg and Thornton, 1976). An extension of this method to comparisons between any two chain folds is outlined here.     

Total body water and adaptive water turnover rate in four chromosomal species of subterranean mole rats of the Spalax ehrenbergi superspecies in Israel

Total body water (TBW) and water turnover rate (WTR) were measured in 24 subterranean mole rats comprising four populations, each belonging to a different chromosomal species of the Spalax ehrenbergi superspecies in Israel. The four species range in different climates: humid-cool (2n = 52); semiarid-cool (2n = 54); humid-warm (2n = 58) and arid-warm (2n = 60). TBW, as a percentage of body weight, measured by tritiated water (HTO), was 72.4%±4–7 in 2n = 52, significantly ( P < 005) higher than the similar estimates 61.7%± 7.2, and 59.4%± 5–3, for 2n = 60 and 58, respectively. A comparison of HTO space, as a percentage of TBW, closely approximated TBW, ranging from 97% to 108%. WTR was high, 218.1 and 230.9 ml/kg^0-75/day in the mesic populations of 2n = 58 and 52, respectively. By contrast, WTR estimates were significantly lower , ( P < 0.001), 150.2 and 148.9 ml/kg^0-75/day in the xeric populations of 2n = 54 and 60, respectively. The biological half-life time, T_1/2, was similar and faster, 32.7 and 27.9 hours in the mesic populations of 2n = 52 and 58, as compared with slower, 47.9 and 40.8 hours in the xeric populations of 2n = 54 and 60, respectively. Urine osmolarity in the most xeric northern Negev steppic population of 2n = 60 (737 ± 45 mmol/kg) was significantly ( P < 0.001) higher than in the other species.
We conclude that adaptive radiation in the Spalax ehrenbergi superspecies involves speciation in semiarid (2n = 54) and arid (2n = 60) climates by physiological adaptations of kidney water conservation, along with multiple morphological, physiological and behavioural syndromes of climatic adaptations to increasing aridity (Nevo, 1986).     

Molecular phylogenetic relationships among seven Japanese species of Cercopithifilaria

DNA sequences from a portion of the mitochondrial COI gene were used to clarify phylogenetic relationships among Japanese species in the genus Cercopithifilaria. Sequences were determined from seven Japanese species, five (C. shohoi, C. multicauda, C. minuta, C. tumidicervicata and C. bulboidea) from the serow (Capricornis crispus F. Bovidae) and two (C. longa and C. crassa) from the sika deer (Cervus nippon nippon F. Cervidae). No base substitutions were observed between C. bulboidea and C. longa, suggesting that recent host switching of a lineage of C. bulboidea between bovid and cervid hosts gave rise to C. longa. In phylogenetic trees inferred using a variety of methods, the morphologically ancestral type, C. bulboidea, appeared as a derived species. C. multicauda was found to be basal in the analyses. It seems therefore that C. multicauda is the most primitive out of the seven species.     

Hydra of Hawaii: phylogenetic relationships with continental species

The presence of freshwater hydra in the Hawaiian Islands, over 3,700 km from the nearest continental margin, provokes the question of how these animals could reach the islands. We examined three islands for hydra and found two species (the brown hydra, Hydra vulgaris Pallas 1766, and green hydra, H. viridissima Pallas 1766) present at multiple locations on Oahu and Kauai, and at a single site on Hawaii. Phylogenetic analysis based on the internal transcribed spacer (ITS1 and ITS2) regions of ribosomal DNA indicates that all collected strains of brown hydra were closely related to each other—consistent with a single introduced origin. The analysis also shows that all sampled Hawaiian brown hydra fall within a specific clade of H. vulgaris. This clade is sister to a North American clade and nested within a deeper North/Central America clade. The clade with all the Hawaiian brown hydra includes also individuals from Southern California, suggesting a Californian origin for the brown Hawaiian hydra. Hawaiian hydra were probably transported to the islands by man.     

基于16S rDNA部分序列探讨中国近海30种石斑鱼类的分子系统进化关系

石斑鱼因其种类繁多、分布广泛及缺乏显著的形体特征,使其系统分类的研究颇为困难。为探讨中国近海石斑鱼类的系统进化关系,通过PCR扩增获得了石斑鱼亚科(Epinephelinae)6属30个种类的线粒体16SrDNA基因片段序列。采用多个生物软件对序列变异和碱基组成进行分析,计算了Kimura2parameter遗传距离、转换/颠换比等遗传信息指数,并结合GenBank石斑鱼属的同源序列,以多纹长尾(Pronotogrammusmultifasciatus)和皮氏叫姑鱼(Johniusbelengerii)为外群构建NJ、MP和ML系统树。根据所得分子依据并结合形态学特征,推论如下:1)在本研究的30种石斑鱼中,鳃棘鲈属(Plectropomus)最先分化,并呈明显单系性;九棘鲈属(Cephalopholis)是一个单系群,并且较石斑鱼属(Epinephelus)原始;侧牙鲈属(Variola)的进化地位介于鳃棘鲈属与九棘鲈属之间;2)宽额鲈(Promicropslanceolatus)可以归入石斑鱼属,而驼背鲈(Cromileptesaltivelis)也与石斑鱼属有很近的亲缘关系,甚至可能是石斑鱼属内的特化类群;3)石斑鱼属内部存在两个平行进化的姐妹分支,分支内部的种类组成与地理分布无关,暗示了石斑鱼属早期的分化模式。     

DNA sequence variation in the mitochondrial control region of subterranean mole rats,Spalax ehrenbergi superspecies,in Israel

The complete mitochondrial control region was sequenced for 60 individuals representing different populations for each of the four species of the subterranean mole rat Spalax ehrenbergi superspecies in Israel: Spalax galili (2n = 52), S. golani (2n = 54), S. carmeli (2n = 58), and S. judaei (2n = 60). The control region of all species and populations is very similar both in length (979 to 983 bp) and in base composition. As in agreement with previous surveys on mitochondrial control regions on mammals, the mole rat control region can be divided into a central domain and two flanking domains, ETAS (extended termination associated sequences) and CSB (conserved sequence blocks). Along with the common conserved blocks found in these domains (ETAS1, ETAS2, CSB1, CSB2, and CSB3), we have also detected in all individuals an ETAS1-like and a CSB1-like element, both in the ETAS domain. The most conserved region was the central domain, followed by the CSB and ETAS domains, showing important differences in the four species analyzed. Phylogenetic analysis supported the existence of two clades. One clade contained individuals belonging to Spalax galili (2n = 52) and S. golani (2n = 54), separated in two different branches depending on the species. The other clade contained individuals belonging to S. carmeli (2n = 58) and S. judaei (2n = 60) mixed together, suggesting a more recent event of speciation. Within species we have observed a southward trend of increasing variability. These results have been explained as a consequence of the adaptation of the species to ecological factors such as aridity and temperature stresses.     

Chromosomal analysis and phylogenetic relationships in the Drosophila nasuta subgroup I. Phylogenetic relationships within the Drosophila sulfurigaster species complex

Phylogenetic relationships within the Drosophila sulfurigaster species-complex, which belongs to the D. nasuta subgroup, were investigated on the basis of chromosomal constitution and morphology. D. pulaua is thought to be the most ancestral species, from which D. s. sulfurigaster and D. s. bilimbata derived in one branch and D. s. albostrigata and D. s. neonasuta in another branch.     

Molecular classification and phylogenetic relationships of selected edible Basidiomycetes species

Morphological identification of edible mushrooms can sometimes prove troublesome, because phenotypic variation in fungi can be affected by substrate and environmental factors. One of the most important problems for mushroom breeders is the lack of a systematic consensus tool to distinguish different species, which are sometimes morphologically identical. Basidiomycetes as one of the largest groups of edible mushrooms have become more important in recent times for their medicinal and nutritional properties. Partial rDNA sequences, including the Internal Transcribed Spacer I-5.8SrDNA-Internal Transcribed Spacer II, were used in this study for molecular identification and assessment of phylogenetic relationships between selected edible species of the Basidiomycetes. Phylogenetic trees showed five distinct clades; each clade belonging to a separate family group. The first clade included all the species belonging to the Pleurotaceae (Pleurotus spp.) family; similarly, the second, third, fourth, and fifth clades consist of species from the Agaricaceae (Agaricus sp.), Lyophllaceae (Hypsigygus sp.), Marasmiaceae (Lentinula edodes sp.) and Physalacriaceae (Flammulina velutipes sp.) families, respectively. Moreover, different species of each family were clearly placed in a distinct sub-cluster and a total of 13 species were taken for analysis. Species differentiation was re-confirmed by AMOVA analysis (among the populations: 99.67%; within: 0.33%), nucleotide divergence, haplotyping and P value. Polymorphism occurred throughout the ITS regions due to insertion-deletion and point mutations, and can be clearly differentiated within the families as well as genera. Moreover, this study proves that the sequence of the ITS region is a superior molecular DNA barcode for taxonomic identification of Basidiomycetes.     

Human phylogenetic relationships according to the D1S80 locus

By analyzing the allelic frequencies at the D1S80 locus in 43 human populations, we show that the locus is polymorphic globally and that it can be used to discriminate between major racial groups and subpopulations through phylogenetic analysis. Although the use of informative multiple loci generally provides more accurate phylogenetic relationships, in instances where time and/or target DNA availability is limited, D1S80 could provide useful data to discriminate between human groups. Also, knowledge of which loci independently provide accurate phylogenetic relationships, such as the D1S80, can be used to design more accurate multi-locus combinations. In addition, allele frequencies at the locus are reported, for the first time, for Bahamian individuals of African origin and for Chimila, Bari, and Navajo (Cañoncito Valley) native Americans. Allelic data was obtained using standard polymerase chain reaction (PCR) techniques. In the four new populations, 65 genotypes and 20 segregating alleles were observed. All populations conformed to Hardy-Weinberg expectations except the Chimila.     

Estimating phylogenetic relationships despite discordant gene trees across loci: the species tree of a diverse species group of feather mites (Acari: Proctophyllodidae)

With the increased availability of multilocus sequence data, the lack of concordance of gene trees estimated for independent loci has focused attention on both the biological processes producing the discord and the methodologies used to estimate phylogenetic relationships. What has emerged is a suite of new analytical tools for phylogenetic inference--species tree approaches. In contrast to traditional phylogenetic methods that are stymied by the idiosyncrasies of gene trees, approaches for estimating species trees explicitly take into account the cause of discord among loci and, in the process, provides a direct estimate of phylogenetic history (i.e. the history of species divergence, not divergence of specific loci). We illustrate the utility of species tree estimates with an analysis of a diverse group of feather mites, the pinnatus species group (genus Proctophyllodes). Discord among four sequenced nuclear loci is consistent with theoretical expectations, given the short time separating speciation events (as evident by short internodes relative to terminal branch lengths in the trees). Nevertheless, many of the relationships are well resolved in a Bayesian estimate of the species tree; the analysis also highlights ambiguous aspects of the phylogeny that require additional loci. The broad utility of species tree approaches is discussed, and specifically, their application to groups with high speciation rates--a history of diversification with particular prevalence in host/parasite systems where species interactions can drive rapid diversification.     

Seismic communication in the blind subterranean mole-rat: patterns of head thumping and of their detection in the Spalax ehrenbergi superspecies in Israel

Patterns of seismic communication and somatosensory responses were studied in four chromosomal species (2n= 52, 54, 58, 60) of blind subterranean mole-rats, belonging to the Spalax ehrenbergi superspecies in Israel. The patterns involved head thumping signals and surface-recorded cerebral potentials evoked by vibrational signals. The patterns correspond to the differences in territory size and population density which characterize the four species. It is suggested that this correspondence is related to the adaptive significance of the seismic communication.     

基于Adhl基因分析高粱属的系统进化关系

高粱属中有重要的粮食作物和优良牧草,也有农业生产上的重要杂草.文章旨在进一步从分子水平阐明高粱属种间的系统进化关系,为有效利用种质资源进行分子育种改良作物品质提供理论依据,并明确检疫性杂草的分类地位.根据二色高粱(Sorghum bicolor)的Adhl全基因序列(GenBank登录号:AF050456)设计引物,扩增并测定黑高粱(S.almum),假高粱(S.halepense)、丝克高粱(S.silk)和苏丹草(S.sudanense)共计8个植物材料约2 000 bp的Adhl基因部分序列,结合GenBank中其他24个Sorghum属的同源序列.以Cleistachne sorghoides的对应序列为外群,进行了高粱属的亲缘关系分析,用MP、ML和NJ法分别构建了分子进化树,得到了基本相同的拓扑结构.结果显示:(1)高粱属可明显分为三大支,一支是蒴柄高粱(Chaetosorghum)和异高粱(Heterosorghum)个亚属,一支是优高粱亚属(Eusorghum),这两个分支包含2n=20、40,染色体较小的种类,另一分支包括拟高粱(Parasorghum)和有柄高粱(Stiposorghum)两个亚属,包含2n=10的种类和它们的多倍体近缘种,染色体相对较大;(2)S.almum的Adhl基因表现出明显的地理分化;(3)Parasorghum亚属的S.pur-pureosericeum和多色高粱(S.versicolor)、光高粱(S.nitidum)和S.leiocladum聚在一起,而该亚属中的S.mata-rankense、S.grande、S.timorense却与亚属Stiposorghum的种聚在一起,表现出更近的亲缘关系;(4)S.mac-rospermum和S.laxiflorum之间具有比其他高粱属种更近的亲缘关系.     

Taxonomy and phylogenetic relationships of two species of Hypocrea with Trichoderma anamorphs

Hypocrea patella is reevaluated. Its Trichoderma anamorph is described and the phylogenetic position of the species is determined through sequences of the ITS regions of rDNA. It is sister to a clade that includes Trichoderma longibrachiatum/H. schweinitzii. Hypocrea patella f. tropica is accepted for a Costa Rican collection. Hypocrea neorufa and its Trichoderma anamorph are described. Its phylogenetic position is determined by sequences of the ITS region of rDNA and the protein-coding translation-elongation factor (EF-1α). It is derived from within a clade that includes T. viride/H. rufa, T. atroviride/H. atroviridis, T. koningii/H. koningii and T. asperellum. Deceased August 2002.     

Molecular analysis of the phylogenetic relationships among the diploid aegilops species of the section Sitopsis

RAPD analysis was used to study the intraspecific variation and phylogenetic relationships of S-genome diploid Aegilops species regarded as potential donors of the B genome of cultivated wheat. In total, 21 DNA specimens from six S-genome diploid species were examined. On a dendrogram, Ae. speltoides and Ae. aucheri formed the most isolated cluster. Among the other species, Ae. searsii was the most distant while Ae. longissima and Ae. sharonensis were the closest species. The maximum difference between individual accessions within one species was approximately the same (0.18-0.22) in Ae. bicornis, Ae. longissima. Ae. sharonensis, and Ae. searsii. The difference between the clusters of questionable species Ae. speltoides and Ae. aucheri corresponded to the intraspecific level; the difference between closely related Ae. longissima and Ae. sharonensis corresponded to the interspecific level. The section Sitopsis of the genus Aegilops includes six diploid species containing the S genome, which is regarded as an ancestor of the B genome of cultivated wheat. The species of the section are thought to be closest to the genus Triticum. Note that the taxonomic status of some forms of the section Sitopsis is questionable. For instance, Ae. speltoides and Ae. aucheri are variously considered as individual species or as a single species, Ae. speltoides. The situation with Ae. longissima and Ae. sharonensis is similar. Thus, although the group includes only diploid species and is well studied morphologically, its phylogeny and taxonomy are still questionable.     

Matrix representation in reconstructing phylogenetic relationships among the eukaryotes.

The application of the method of matrix representation (MRP) addresses several problems associated with reconstructing phylogenetic relationships among composite organisms such as the eukaryotes. By allowing multiple molecular-sequence and non-molecular data sets to be combined into a single, relatively compact matrix for joint analysis, MRP addresses problems associated with the depth, diversification and specialization of eukaryotic lineages. Characters whose distributions may have been affected by endosymbiotic lateral transfer can be identified by compatibility analysis of MRP-generated hybrid matrices. In conjunction with variant-filtering techniques, MRP can be used to map patterns of lateral transfer in a given phylogenetic tree. These applications are illustrated with molecular-sequence and non-molecular data sets for eukaryotes.