Finding unknown species in the genomes of extant species

Although many species have gone extinct, their genetic components might exist in extant species because of ancient hybridization. Via advances in genome sequencing and development of modern population genetics, one can find the legacy of unknown or extinct species in the context of available genomes from extant species. Such discovery can be used as a strategy to search for hidden species or fossils in conservation biology and archeology, gain novel insight into complex evolutionary history, and provide the new sources of genetic variation for breeding and trait improvement in agriculture.     

Phylogenetic signal in module composition and species connectivity in compartmentalized host-parasite networks

Abstract Across different taxa, networks of mutualistic or antagonistic interactions show consistent architecture. Most networks are modular, with modules being distinct species subsets connected mainly with each other and having few connections to other modules. We investigate the phylogenetic relatedness of species within modules and whether a phylogenetic signal is detectable in the within- and among-module connectivity of species using 27 mammal-flea networks from the Palaearctic. In the 24 networks that were modular, closely related hosts co-occurred in the same module more often than expected by chance; in contrast, this was rarely the case for parasites. The within- and among-module connectivity of the same host or parasite species varied geographically. However, among-module but not within-module connectivity of host and parasites was somewhat phylogenetically constrained. These findings suggest that the establishment of host-parasite networks results from the interplay between phylogenetic influences acting mostly on hosts and local factors acting on parasites, to create an asymmetrically constrained pattern of geographic variation in modular structure. Modularity in host-parasite networks seems to result from the shared evolutionary history of hosts and by trait convergence among unrelated parasites. This suggests profound differences between hosts and parasites in the establishment and functioning of bipartite antagonistic networks.     

Phylogenetic relationships among six species of Epistylis inferred from 18S-ITS1 sequences

Phylogenetic relationships among six species of Epistylis (i. e. E. plicatilis, E. urceolata, E. chrysemydis, E. hentscheli, E. wenrichi, and E. galea) were investigated using sequences of the first internal transcribed spacer region (ITS-1) of ribosomal DNA (rDNA). Amplified rDNA fragment sequences consisted of 215 or 217 bases of the flanking 18S and 5.8S regions, and the entire ITS-1 region (from 145 to 155 bases). There were more than 33 variable bases between E. galea and the other five species in both the 18S region and the ITS-1 region. The affiliation of them was assessed using Neighbor-joining (NJ), maximum parsimony (MP) and maximum likelihood (ML) analyses. In all the NJ, MP and ML analyses E. galea, whose macronucleic position and shape are distinctly different from those of the other five species, was probably diverged from the ancestor of Epistylis earlier than the other five species. The topology in which E. plicatilis and E. hentscheli formed a strongly supported sister clade to E. urceol     

Molecular phylogeny of extant equids and effects of ancestral polymorphism in resolving species-level phylogenies

Short divergence times and processes such as incomplete lineage sorting and species hybridization are known to hinder the inference of species-level phylogenies due to the lack of sufficient informative genetic variation or the presence of shared but incongruent polymorphism among taxa. Extant equids (horses, zebras, and asses) are an example of a recently evolved group of mammals with an unresolved phylogeny, despite a large number of molecular studies. Previous surveys have proposed trees with rather poorly supported nodes, and the bias caused by genetic introgression or ancestral polymorphism has not been assessed. Here we studied the phylogenetic relationships of all extant species of Equidae by analyzing 22 partial mitochondrial and nuclear genes using maximum likelihood and Bayesian inferences that account for heterogeneous gene histories. We also examined genetic signatures of lineage sorting and/or genetic introgression in zebras by evaluating patterns of intraspecific genetic variation. Our study improved the resolution and support of the Equus phylogeny and in particular the controversial positions of the African wild ass (E. asinus) and mountain zebra (E. zebra): the African wild ass is placed as a sister species of the Asiatic asses and the mountain zebra as the sister taxon of Grevy's and Burchell's zebras. A shared polymorphism (indel) detected among zebra species in the Estrogen receptor 1 gene was likely due to incomplete lineage sorting and not genetic introgression as also indicated by other mitochondrial (Cytochrome b) and nuclear (Y chromosome and microsatellites) markers. Ancestral polymorphism in equids might have contributed to the long-standing lack of clarity in the phylogeny of this highly threatened group of mammals.     

Large and small rearrangements in the evolution of prokaryotic genomes

Relative frequencies of large and small genome rearrangements (inversions and transpositions) in the evolution of prokaryotic genomes can be evaluated using the ratio between the index S (the ratio of the number of identical pairs of neighboring genes in two genomes to the total number of genes in the sample of interest) and 1 - 6 x L/n, where L is the mean difference in intergenic distances and n is the number of genes in the sample. The S value uniformly decreases with the fixation of genome rearrangements, while the decrease rate of I - 6 x L/n is determined by the rearrangement size. Specifically, large inversions and transpositions lead to a dramatic decrease in the index value, while small rearrangements result in an insignificant decrease. The ratio between these indices was computed for twenty pairs of closely related species belonging to different groups of bacteria and archaea. The pairs examined strongly differed in the relative frequency of large and small rearrangements. However, computer simulation showed that the total variation can be reproduced with the same input parameters of the model. This means that the differences observed can be stochastic and can be interpreted without assuming different mechanisms and factors of genome rearrangements for different groups of prokaryotes. Relative frequencies of large and small rearrangements displayed no noticeable correlations with taxonomic position, total rate of rearrangement fixation, habitation conditions, and the abundance of transposons and repetitive sequences. It is suggested that, in some cases, phage activity increases the frequency of large genome rearrangements.     

Large and small rearrangements in the evolution of prokaryotic genomes

Relative frequencies of large and small genome rearrangements (inversions and transpositions) in the evolution of prokaryotic genomes can be evaluated using the ratio between the index S (the ratio of the number of identical pairs of neighboring genes in two genomes to the total number of genes in the sample of interest) and 1–6L/n, where L is the mean difference in intergenic distances and n is the number of genes in the sample. The S value uniformly decreases with the fixation of genome rearrangements, while the decrease rate of 1–6L/n is determined by the rearrangement size. Specifically, large inversions and transpositions lead to a dramatic decrease in the index value, while small rearrangements result in an insignificant decrease. The ratio between these indices was computed for twenty pairs of closely related species belonging to different groups of bacteria and archaea. The pairs examined strongly differed in the relative frequency of large and small rearrangements. However, computer simulation showed that the total variation can be reproduced with the same input parameters of the model. This means that the differences observed can be stochastic and can be interpreted without assuming different mechanisms and factors of genome rearrangements for different groups of prokaryotes. Relative frequencies of large and small rearrangements displayed no noticeable correlations with taxonomic position, total rate of rearrangement fixation, habitation conditions, and the abundance of transposons and repetitive sequences. It is suggested that, in some cases, phage activity increases the frequency of large genome rearrangements.     

Phylogenetic relationships among six species of Epistylis inferred from 18S-ITS1 sequences

Phylogenetic relationships among six species of Epistylis (i. e. E. plicatilis, E. urceolata, E. chrysemydis, E. hentscheli, E. wenrichi, and E. galea) were investigated using sequences of the first internal transcribed spacer region (ITS-1) of ribosomal DNA (rDNA). Amplified rDNA fragment sequences consisted of 215 or 217 bases of the flanking 18S and 5.8S regions, and the entire ITS-1 region (from 145 to 155 bases). There were more than 33 variable bases between E. galea and the other five species in both the 18S region and the ITS-1 region. The affiliation of them was assessed using Neighbor-joining (NJ), maximum parsimony (MP) and maximum likelihood (ML) analyses. In all the NJ, MP and ML analyses E. galea, whose macronucleic position and shape are distinctly different from those of the other five species, was probably diverged from the ancestor of Epistylis earlier than the other five species. The topology in which E. plicatilis and E. hentscheli formed a strongly supported sister clade to E. urceolata, E. chrysemydis, and E. wenrichi was consistent with variations in the thickness of the peristomial lip. We concluded that the macronucleus and peristomial lip might be the important phylogenetic characteristics within the genus Epistylis.     

Multiple rearrangements in mitochondrial genomes of Isopoda and phylogenetic implications

In this study, we analyse the evolutionary dynamics and phylogenetic implications of gene order rearrangements in five newly sequenced mitochondrial (mt) genomes and four published mt genomes of isopod crustaceans. The sequence coverage is nearly complete for four of the five newly sequenced species, with only the control region and some tRNA genes missing, while in Janira maculosa only two thirds of the genome could be determined. Mitochondrial gene order in isopods seems to be more plastic than that in other crustacean lineages, making all nine known mt gene orders different. Especially the asellote Janira is characterized by many autapomorphies. The following inferred ancestral isopod mt gene order exists slightly modified in modern isopods: nad1, tnrL1, rrnS, control region, trnS1, cob, trnT, nad5, trnF. We consider the inferred gene translocation events leading to gene rearrangements as valuable characters in phylogenetic analyses. In this first study covering major isopod lineages, potential apomorphies were identified, e.g., a shared relative position of trnR in Valvifera. We also report one of the first findings of homoplasy in mitochondrial gene order, namely a shared relative position of trnV in unrelated isopod lineages. In addition to increased taxon sampling secondary structure, modification in tRNAs and GC-skew inversion may be potentially fruitful subjects for future mt genome studies in a phylogenetic context.     

Phylogenetic relationships among rodent Eimeria species determined by plastid ORF470 and nuclear 18S rDNA sequences

Phylogenetic analyses for 10 rodent Eimeria species from different host genera based on plastid ORF470 and nuclear 18S rDNA sequences were done to infer the evolutionary relationships of these rodent Eimeria species and their correlation to morphology and host specificity. The phylogenies based on both data sets clearly grouped the 10 rodent Eimeria species into two major lineages, which reflect more their morphological differences than host specificity. Species in lineage A have spheroidal to subspheroidal sporulated oocysts, are similar in size (18-29 x 17-23; xbar = 22 x 20 microm), have an oocyst residuum and one-two polar granules; these include Eimeria albigulae (Neotoma), Eimeria arizonensis (Peromyscus, Reithrodontomys), Eimeria onychomysis (Onychomys) and Eimeria reedi (Perognathus). Species in lineage B, including Eimeria falciformis (Mus), Eimeria langebarteli (Reithrodontomys), Eimeria nieschulzi (Rattus), Eimeria papillata (Mus), Eimeria separata (Rattus) and Eimeria sevilletensis (Onychomys) have different shapes (ovoid, ellipsoid, elongated ellipsoid, etc.), differ greatly in size (10-27 x 9-24; xbar = 19 x 16 microm) and all lack an oocyst residuum. Thus, The oocyst residuum was the most determinant feature that differentiated the two lineages. The accession numbers of ORF470 of E. albigulae, E. arizonensis, E. falciformis, E. nieschulzi, E. onychomysis, E. papillata, E. reedi, E. separata, E. sevilletensis, E. langebarteli are AF311630-AF311639 and 18S rDNA of E. langebarteli, E. papillata, E. reedi, E. separata, E. sevilletensis are AF311640-AF311644.     

Repetitive DNA and chromosomal rearrangements: speciation-related events in plant genomes

Chromosomal change is one of the more hotly debated potential mechanisms of speciation. It has long been argued over whether--and to what degree--changes in chromosome structure contribute to reproductive isolation and, ultimately, speciation. In this review we do not aim to completely analyze accumulated data about chromosomal speciation but wish to draw attention to several critical points of speciation-related chromosomal change, namely: (a) interrelations between chromosomal rearrangements and repetitive DNA fraction; (b) mobility of ribosomal DNA clusters; and (c) rDNA and transposable elements as perpetual generators of genome instability.     

Phylogenetic analysis of Oryza species, based on simple sequence repeats and their flanking nucleotide sequences from the mitochondrial and chloroplast genomes

Simple sequence repeats (SSR) and their flanking regions in the mitochondrial and chloroplast genomes were sequenced in order to reveal DNA sequence variation. This information was used to gain new insights into phylogenetic relationships among species in the genus Oryza. Seven mitochondrial and five chloroplast SSR loci equal to or longer than ten mononucleotide repeats were chosen from known rice mitochondrial and chloroplast genome sequences. A total of 50 accessions of Oryza that represented six different diploid genomes and three different allopolyploid genomes of Oryza species were analyzed. Many base substitutions and deletions/insertions were identified in the SSR loci as well as their flanking regions. Of mononucleotide SSR, G (or C) repeats were more variable than A (or T) repeats. Results obtained by chloroplast and mitochondrial SSR analyses showed similar phylogenetic relationships among species, although chloroplast SSR were more informative because of their higher sequence diversity. The CC genome is suggested to be the maternal parent for the two BBCC genome species (O. punctata and O. minuta) and the CCDD species O. latifolia, based on the high level of sequence conservation between the diploid CC genome species and these allotetraploid species. This is the first report of phylogenetic analysis among plant species, based on mitochondrial and chloroplast SSR and their flanking sequences.     

Phylogenetic species recognition and species concepts in fungi

The operational species concept, i.e., the one used to recognize species, is contrasted to the theoretical species concept. A phylogenetic approach to recognize fungal species based on concordance of multiple gene genealogies is compared to those based on morphology and reproductive behavior. Examples where Phylogenetic Species Recognition has been applied to fungi are reviewed and concerns regarding Phylogenetic Species Recognition are discussed.     

PCR assay for identification of Anopheles quadriannulatus species B from Ethiopia and other sibling species of the Anopheles gambiae complex

Sibling species A and B of Anopheles quadriannulatus (Theobald) are recognized as allopatric members of the Anopheles gambiae Giles complex of Afrotropical mosquitoes (Diptera: Culicidae). Species A represents An. quadriannulatus sensu stricto, widespread in southern Africa, whereas An. quadriannulatus species B occurs in Ethiopia. Because of difficulty of identification, distribution of An. quadriannulatus sensu lato remains poorly known. Cytotaxonomy and the standard DNA polymerase chain reaction (PCR) assay do not distinguish between species A and B of An. quadriannulatus. By optimizing the standard PCR assay (Scott et al., 1993) for identification of members of the An. gambiae complex, we identified two discriminant fragments of 153 bp and 900 bp from DNA of An. quadriannulatus species B, whereas only the 153 bp fragment was amplified for species A from South Africa. This modified PCR assay can therefore be used to distinguish between species A and B of An. quadriannulatus s.l. as well as other members of the An. gambiae complex.     

基于mtDNA和rDNA基因序列的中国按蚊属塞蚊亚属种类的系统发育研究（双翅目：蚊科）

【目的】应用mtDNA和rDNA基因特征重建中国按蚊属塞蚊亚属已知种类的系统发育关系, 以阐明亚属内各蚊种的亲缘关系。【方法】对采自中国的按蚊属塞蚊亚属Anopheles (Cellia) 20种蚊的mtDNA-COⅡ和 rDNA-28S-D3序列进行测定和分析, 以按蚊属按蚊亚属Anopheles (Anopheles)的中华按蚊An. (An.) sinensis和赫坎按蚊An. (An.) hyrcanus为外群, 采用COⅡ和D3单基因, 以及“COⅡ+D3”联合数据组以邻接法（NJ）、 最大简约法（MP）、 最大似然法（ML）和贝叶斯法（BI）等重建这些种类的系统发育树。【结果】 mtDNA-COⅡ和rDNA-28S-D3序列的长度范围分别为685 bp和375～410 bp, 在塞蚊亚属蚊种间的遗传距离分别为0.015～0.117和0.003～0.111。各系统树显示外群被合理分开,除在COⅡ树中新塞蚊系为并系外,各系均聚为单系群,新迈蚊系和迈蚊系亲缘关系最近。联合数据组构建的系统合意树显示中国塞蚊亚属各蚊种形成4支,除伪威氏按蚊与多斑按蚊种团未聚为单系群外,其他各种团和复合体成员种均分别聚在一起,各分支的置信值均大于50%。【结论】本研究获得的分子系统发育树清楚地显示了中国按蚊属塞蚊亚属各种类及系之间的系统发育关系, 对其分类和防治研究具有参考价值。