Molecular phylogeny and phylogeography of genus Pseudois (Bovidae,Cetartiodactyla): New insights into the contrasting phylogeographic structure

Blue sheep, Pseudois nayaur, is endemic to the Tibetan Plateau and the surrounding mountains, which are the highest‐elevation areas in the world. Classical morphological taxonomy suggests that there are two subspecies in genus Pseudois (Bovidae, Artiodactyla), namely Pseudois nayaur nayaur and Pseudois nayaur szechuanensis. However, the validity and geographic characteristics of these subspecies have never been carefully discussed and analyzed. This may be partially because previous studies have mainly focused on the vague taxonomic status of Pseudois schaeferi (dwarf blue sheep). Thus, there is an urgent need to investigate the evolutionary relationship and taxonomy system of this genus. This study enriches a previous dataset by providing a large number of new samples, based on a total of 225 samples covering almost the entire distribution of blue sheep. Molecular data from cytochrome b and the mitochondrial control region sequences were used to reconstruct the phylogeny of this species. The phylogenetic inferences show that vicariance plays an important role in diversification within this genus. In terms of molecular dating results and biogeographic analyses, the striking biogeographic pattern coincides significantly with major geophysical events. Although the results raise doubt about the present recognized distribution range of blue sheep, they have corroborated the validity of the identified subspecies in genus Pseudois. Meanwhile, these results demonstrate that the two geographically distinct populations, the Helan Mountains and Pamir Plateau populations, have been significantly differentiated from the identified subspecies, a finding that challenges the conventional taxonomy of blue sheep.     

Molecular insights into the evolution of the family Bovidae: a nuclear DNA perspective.

The evolutionary history of the family Bovidae remains controversial despite past comprehensive morphological and genetic investigations. In an effort to resolve some of the systematic uncertainties within the group, a combined molecular phylogeny was constructed based on four independent nuclear DNA markers (2,573 characters) and three mitochondrial DNA genes (1,690 characters) for 34 bovid taxa representing all seven of the currently recognized bovid subfamilies. The nuclear DNA fragments were analyzed separately and in combination after partition homogeneity tests were performed. There was no significant rate heterogeneity among lineages, and retention index values indicated the general absence of homoplasy in the nuclear DNA data. The conservative nuclear DNA data were remarkably effective in resolving associations among bovid subfamilies, which had a rapid radiation dating back to approximately 23 MYA. All analyses supported the monophyly of the Bovinae (cow, nilgai, and kudu clade) as a sister lineage to the remaining bovid subfamilies, and the data convincingly suggest that the subfamilies Alcelaphinae (hartebeest, tsessebe, and wildebeest group) and Hippotraginae (roan, sable, and gemsbok clade) share a close evolutionary relationship and together form a sister clade to the more primitive Caprinae (represented by sheep, goat, and muskox). The problematic Reduncinae (waterbuck, reedbuck) seem to be the earliest-diverging group of the Caprinae/Alcelaphinae/Hippotraginae clade, whereas the Antilopinae (gazelle and dwarf antelope clade) were always polyphyletic. The sequence data suggest that the initial diversification of the Bovidae took place in Eurasia and that lineages such as the Cephalophinae and other enigmatic taxa (impala, suni, and klipspringer) most likely originated, more or less contemporaneously, in Africa.     

Molecular insights into mechanisms regulating faithful chromosome separation in female meiosis

The faithful segregation of chromosomes into daughter cells in meiosis is crucial to produce healthy progeny. In gametogenesis, two consecutive rounds of chromosome separation occur with only one round of DNA replication, and the chromosome number is reduced to half to produce haploid gametes. Here, we discuss the molecular mechanisms underlying faithful chromosome separation in meiosis from three aspects: Spindle checkpoint, two-step releases of cohesion, and the specific space-time protection of cohesin.     

Molecular insights into ion channel function (Review)

Water is probably the most important molecule in biology. It solvates molecules, all biochemical reactions occur in it and it is a major driving force in protein folding. Phospholipid membranes separate different water environments, but connections do exist between the different compartments. The integral membrane proteins (IMPs) form these connections. In the case of ions, IMPs form the passageways that regulate ion movement across the membrane. Structural information from three ion distinct channels are examined to see how these channels first select for and then control the movement of their target ions. This review focuses on how these channels select for target ions and control their movement while taking into account and using different properties of water. This includes the use of hydrophobic gates, mimicking the water environment, and controlling ions indirectly by controlling water.     

Molecular insights into ion channel function (Review)

Water is probably the most important molecule in biology. It solvates molecules, all biochemical reactions occur in it and it is a major driving force in protein folding. Phospholipid membranes separate different water environments, but connections do exist between the different compartments. The integral membrane proteins (IMPs) form these connections. In the case of ions, IMPs form the passageways that regulate ion movement across the membrane. Structural information from three ion distinct channels are examined to see how these channels first select for and then control the movement of their target ions. This review focuses on how these channels select for target ions and control their movement while taking into account and using different properties of water. This includes the use of hydrophobic gates, mimicking the water environment, and controlling ions indirectly by controlling water.     

Molecular phylogeny of the tribe Bovini (Bovidae, Bovinae) and the taxonomic status of the Kouprey, Bos sauveli Urbain 1937

The kouprey is a very rare bovid species of the Indochinese peninsula, and no living specimen has been described for a long time, suggesting that it is possibly extinct. Its systematic position within the tribe Bovini remains confused since the analyses of morphological characters have led to several conflicting hypotheses. Some authors have also suggested that it could be a hybrid species produced by the crossing of the banteng with gaur, zebu, or water buffalo. Here we performed a molecular phylogeny of the tribe Bovini to determine the taxonomic status of the kouprey. DNA was extracted from the holotype specimen preserved in the MNHN collections. Phylogenetic analyses were carried out on a matrix including all the taxonomic diversity described in the tribe Bovini, and 2065 nucleotide characters, representing three different markers, i.e., the promotor of the lactoferrin and two mitochondrial genes (cytochrome b and subunit II of the cytochrome c oxidase). The results show that the kouprey belongs to the subtribe Bovina, and that three different clades can be evidenced into this group: the first includes the domestic ox, zebu, and European bison; the second incorporates the yak and American bison; and the third contains the kouprey, banteng and gaur. All hypotheses involving hybridization for the origin of the kouprey can be rejected, confirming that it is a real wild species. Molecular datings and biogeographic inferences suggest that the kouprey diverged from banteng and gaur during the Plio-Pleistocene of Asia. In addition, several molecular signatures were detected in the cytochrome b gene, permitting a molecular identification of the kouprey. We propose a conservation project based on a molecular taxonomy approach for tracking the kouprey in Indochina in order to determine whether some populations still survive in the wild.     

Molecular phylogeny of the neotropical genus Christensonella (Orchidaceae, Maxillariinae): species delimitation and insights into chromosome evolution

Background and Aims

Species'' boundaries applied within Christensonella have varied due to the continuous pattern of variation and mosaic distribution of diagnostic characters. The main goals of this study were to revise the species'' delimitation and propose a more stable classification for this genus. In order to achieve these aims phylogenetic relationships were inferred using DNA sequence data and cytological diversity within Christensonella was examined based on chromosome counts and heterochromatin patterns. The results presented describe sets of diagnostic morphological characters that can be used for species'' identification.

Methods

Phylogenetic studies were based on sequence data of nuclear and plastid regions, analysed using maximum parsimony and maximum likelihood criteria. Cytogenetic observations of mitotic cells were conducted using CMA and DAPI fluorochromes.

Key Results

Six of 21 currently accepted species were recovered. The results also support recognition of the ‘C. pumila’ clade as a single species. Molecular phylogenetic relationships within the ‘C. acicularis–C. madida’ and ‘C. ferdinandiana–C. neowiedii’ species'' complexes were not resolved and require further study. Deeper relationships were incongruent between plastid and nuclear trees, but with no strong bootstrap support for either, except for the position of C. vernicosa. Cytogenetic data indicated chromosome numbers of 2n = 36, 38 and 76, and with substantial variation in the presence and location of CMA/DAPI heterochromatin bands.

Conclusions

The recognition of ten species of Christensonella is proposed according to the molecular and cytogenetic patterns observed. In addition, diagnostic morphological characters are presented for each recognized species. Banding patterns and chromosome counts suggest the occurrence of centric fusion/fission events, especially for C. ferdinandiana. The results suggest that 2n = 36 karyotypes evolved from 2n = 38 through descendent dysploidy. Patterns of heterochromatin distribution and other karyotypic data proved to be a valuable source of information to understand evolutionary patterns within Maxillariinae orchids.Key words: Chromosome number, Christensonella, Cymbidieae, cytotaxonomy, fluorochrome staining, Maxillaria, Maxillariinae, molecular phylogenetics, species delimitation     

Molecular cytogenetic insights into the ageing syndrome Hutchinson-Gilford Progeria (HGPS)

Hutchinson-Gilford Progeria Syndrome (HGPS) is an extremely rare genetic disorder characterized by premature ageing in childhood and serves as a valuable model for the human ageing process in general. Most recently, point mutations in the lamin A (LMNA) gene on chromosome 1q have been associated with the disease, however how these mutations relate to the complex phenotype of HGPS remains to be established. It has been shown that fibroblasts from HGPS patients are frequently resistant to immortalization with telomerase (hTERT), consistent with the idea that the loss of a dominant acting HGPS gene is a pre-requisite for immortalization. In this study we report the first detailed cytogenetic analysis of hTERT-immortalised HGPS cell lines from three patients and one corresponding primary fibroblast culture. Our results provide evidence for a cytogenetic mosaicism in HGPS with a distinctive pattern of chromosome aberrations in all the HGP clones. Chromosome 11 alterations were observed at a high frequency in each immortalised HGPS cell line but were also present at a lower frequency in the corresponding primary cells. Moreover, we were able to identify the 11q13-->q23 region as a potential site of breakage. Our results are therefore consistent with a role of chromosome 11 alterations in the escape from senescence observed in HGPS cells. In addition to this defined rearrangement, we consistently observed complex chromosomal rearrangements, suggesting that HGPS displays features of chromosomal instability.     

Molecular phylogenetics of tribe Poranthereae (Phyllanthaceae; Euphorbiaceae sensu lato)

Novel insights into the evolutionary history of a taxonomically complex tropical plant group were gained in this study using DNA sequence data. A molecular phylogenetic analysis of the newly circumscribed and expanded tribe Poranthereae (Phyllanthaceae) is presented. Sampling included 97 accessions for 63 of c. 120 species. Largely congruent results have been obtained from nuclear ribosomal ITS and plastid matK sequences. These analyses support the recognition of Andrachne and Leptopus as distinct genera. The deceptively similar Andrachne section Phyllanthopsis, Andrachne ovalis, and Leptopus decaisnei are separate lineages to be segregated. Zimmermannia and Zimmermanniopsis are embedded in Meineckia; Oreoporanthera is embedded in Poranthera; and Archileptopus is embedded in Leptopus. Andrachne section Pseudophyllanthus is polyphyletic, the two Madagascan endemics emerging as a sister clade to Meineckia. The noncontiguous distributions of Andrachne sensu lato and Leptopus sensu lato were found to be the result of separate evolutionary histories of morphologically similar clades, whereas Andrachne sensu stricto and Meineckia remain geographically disjunct. Actephila and Leptopus are sisters with a sympatric distribution in humid Asia. Presence of petals appears to be plesiomorphic for the tribe. Petals are reduced in Actephila and Oreoporanthera and lost in the Meineckia clade.     

Molecular insights into Cumacean family relationships (Crustacea, Cumacea)

Cumaceans are a diverse order of small, benthic marine crustaceans. Phylogenetic hypotheses for the eight currently recognized cumacean families have not been formally proposed. However, based on external morphological traits and Linnean classification, a few conflicting hypotheses of relatedness have been proposed. Family definitions rely on morphological characters that often overlap and diagnoses are based on a combination of non-unique characters. Morphological analysis does not provide a well-resolved phylogeny. In the present study, we use amino acid sequences from the mitochondrial cytochrome oxidase I gene to produce a molecular phylogenetic hypothesis for the families of Cumacea. Phylogenetic analyses at the amino acid level were performed under Bayesian, likelihood, and parsimony methods. Results strongly suggest that families lacking an articulated telson form a monophyletic group. This pleotelson clade, composed of the families Bodotriidae, Leuconidae, and Nannastacidae, is the most derived within the Cumacea. Within this group, the Bodotriidae resolve paraphyletically, with Leuconidae and Nannastacidae embedded within it. Comparison of the molecular phylogeny with that based on morphology suggests that many "diagnostic" characters are homoplasious.     

New insights into sex chromosome evolution in anole lizards (Reptilia,Dactyloidae)

Anoles are a clade of iguanian lizards that underwent an extensive radiation between 125 and 65 million years ago. Their karyotypes show wide variation in diploid number spanning from 26 (Anolis evermanni) to 44 (A. insolitus). This chromosomal variation involves their sex chromosomes, ranging from simple systems (XX/XY), with heterochromosomes represented by either micro- or macrochromosomes, to multiple systems (X₁X₁X₂X₂/X₁X₂Y). Here, for the first time, the homology relationships of sex chromosomes have been investigated in nine anole lizards at the whole chromosome level. Cross-species chromosome painting using sex chromosome paints from A. carolinensis, Ctenonotus pogus and Norops sagrei and gene mapping of X-linked genes demonstrated that the anole ancestral sex chromosome system constituted by microchromosomes is retained in all the species with the ancestral karyotype (2n?=?36, 12 macro- and 24 microchromosomes). On the contrary, species with a derived karyotype, namely those belonging to genera Ctenonotus and Norops, show a series of rearrangements (fusions/fissions) involving autosomes/microchromosomes that led to the formation of their current sex chromosome systems. These results demonstrate that different autosomes were involved in translocations with sex chromosomes in closely related lineages of anole lizards and that several sequential microautosome/sex chromosome fusions lead to a remarkable increase in size of Norops sagrei sex chromosomes.     

Phylogenetic relationships and the primitive X chromosome inferred from chromosomal and satellite DNA analysis in Bovidae

The early phylogeny of the 137 species in the Bovidae family is difficult to resolve; knowledge of the evolution and relationships of the tribes would facilitate comparative mapping, understanding chromosomal evolution patterns and perhaps assist breeding and domestication strategies. We found that the study of the presence and organization of two repetitive DNA satellite sequences (the clone pOaKB9 from sheep, a member of the 1.714 satellite I family and the pBtKB5, a 1.715 satellite I clone from cattle) on the X and autosomal chromosomes by in situ hybridization to chromosomes from 15 species of seven tribes, was informative. The results support a consistent phylogeny, suggesting that the primitive form of the X chromosome is acrocentric, and has satellite I sequences at its centromere. Because of the distribution of the ancient satellite I sequence, the X chromosome from the extant Tragelaphini (e.g. oryx), rather than Caprini (sheep), line is most primitive. The Bovini (cow) and Tragelaphini tribes lack the 1.714 satellite present in the other tribes, and this satellite is evolutionarily younger than the 1.715 sequence, with absence of the 1.714 sequence being a marker for the Bovini and Tragelaphini tribes (the Bovinae subfamily). In the other tribes, three (Reduncini, Hippotragini and Aepycerotini) have both 1.714 and 1.715 satellite sequences present on both autosomes and the X chromosome. We suggest a parallel event in two lineages, leading to X chromosomes with the loss of 1.715 satellite from the Bovini, and the loss of both 1.714 and 1.715 satellites in a monophyletic Caprini and Alcelaphini lineage. The presence and X chromosome distribution of these satellite sequences allow the seven tribes to be distributed to four groups, which are consistent with current diversity estimates, and support one model to resolve points of separation of the tribes.     

FISH-microdissection (FISH-MD) analysis of complex chromosome rearrangements

We combined the techniques of fluorescence in situ hybridization (FISH) and chromosomal microdissection in one experiment (FISH-MD). This novel method permits rapid identification of the composition, origin, and breakpoints of rearranged chromosomes. Rearranged chromosomes are first identified by multicolor-FISH, then the fluorophore-labeled derivative chromosomes are directly isolated by microdissection and reverse painted to identify the breakpoints.     

Molecular phylogeny and systematics of the tribe Chorisporeae (Brassicaceae)

Sequence data from nuclear (ITS) and chloroplast (trnL-F) regions for 89 accessions representing 56 out of 64 species from all five genera of the tribe Chorisporeae (plus Dontostemon tibeticus) have been studied to test the monophyly of the tribe and its component genera, clarify its boundaries, and elucidate its phylogenetic position in the family. Both data sets showed strong support for the monophyly of the Chorisporeae as currently delimited, though the position of its tentative member D. tibeticus was not resolved by ITS. Parrya and Pseudoclausia are poly- and paraphyletic with regard to each other, and Chorispora is either polyphyletic or at least paraphyletic (comprising Diptychocarpus) within a weakly supported monophyletic clade. The incongruence in branching pattern among the markers was most likely caused by hybridization and possibly influenced by incomplete lineage sorting. The present results suggest uniting Pseudoclausia, Clausia podlechii, and Achoriphragma with Parrya and transferring P. beketovii and P. saposhnikovii to Leiospora (Euclidieae). We also obtained support for splitting Chorispora into two geographically defined groups, one of which is closer to Diptychocarpus. Both data sets revealed a close relationship of the Chorisporeae to Dontostemoneae, while ITS also indicated affinity to Hesperideae. Therefore, the position of Chorisporeae needs further verification.     

Molecular insights into the taxonomy of Glyceria (Poaceae: Meliceae) in North America

Eighteen Glyceria species grow in the United States and Canada, with 16 being native to the region. We used data from morphology and three chloroplast DNA intergenic regions to address taxonomic questions concerning Glyceria in North America, particularly the status of G. declinata, G. occidentalis, G. fluitans, G. striata, and G. elata in western North America. The chloroplast data confirmed the presence of two European species, G. declinata and G. fluitans, in western North America. Glyceria occidentalis was exceptional among the taxa studied in having chloroplast genotypes that fell into two different clades, one of which contained G. fluitans and the other the North American species G. leptostachya. The morphological data showed G. occidentalis to be intermediate between G. fluitans and G. leptostachya with respect to their distinguishing characters. Based on these results, we hypothesize that G. occidentalis consists of hybrids between G. fluitans and G. leptostachya. Glyceria elata and G. striata, which have sometimes been treated as a single species, had different chloroplast genotypes, supporting their recognition as distinct taxa. DNA data from all three intergenic regions would be needed for unequivocal identification of the non-hybrid species examined.     

New insights into the evolution of chromosome 1

A complex low-repetitive human DNA probe (BAC RP11-35B4) together with two microdissection-derived region-specific probes of the multicolor banding (MCB) probe-set for chromosome 1 were used to re-analyze the evolution of human chromosome 1 in comparison to four ape species. BAC RP11-35B4 derives from 1q21 and contains 143 kb of non-repetitive DNA; however, it produces three specific FISH signals in 1q21, 1p12 and 1p36.1 of Homo sapiens (HSA). Human chromosome 1 was studied in comparison to its homologues in Hylobates lar (HLA), Pongo pygmaeus (PPY), Gorilla gorilla (GGO) and Pan troglodytes (PTR). A duplication of sequences homologous to human 1p36.1 could be detected in PPY plus an additional signal on PPY 16q. The region homologous to HSA 1p36.1 is also duplicated in HLA, and split onto chromosomes 7q and 9p; the region homologous to HSA 1q21/1p12 is present as one region on 5q. Additionally, the breakpoint of a small pericentric inversion in the evolution of human chromosome 1 compared to other great ape species could be refined. In summary, the results obtained here are in concordance with previous reports; however, there is evidence for a deletion of regions homologous to human 1p34.2-->p34.1 during evolution in the Pongidae branch after separation of PPY.     

Chromosomal rearrangements and the first indication of an ♀X1X1X2X2/♂X1X2Y sex chromosome system in Rineloricaria fishes (Teleostei: Siluriformes)

Rineloricaria is the most diverse genus within the freshwater fish subfamily Loricariinae, and it is widely distributed in the Neotropical region. Despite limited cytogenetic data, records from southern and south-eastern Brazil suggest a high rate of chromosomal rearrangements in this genus, mirrored in remarkable inter- and intraspecific karyotype variability. In the present work, we investigated the karyotype features of Rineloricaria teffeana, an endemic representative from northern Brazil, using both conventional and molecular cytogenetic techniques. We revealed different diploid chromosome numbers (2n) between sexes (33♂/34♀), which suggests the presence of an ♀X₁X₁X₂X₂/♂X₁X₂Y multiple sex chromosome system. The male-limited Y chromosome was the largest and the only biarmed element in the karyotype, implying Y-autosome fusion as the most probable mechanism behind its origination. C-banding revealed low amounts of constitutive heterochromatin, mostly confined to the (peri)centromeric regions of most chromosomes (including the X₂ and the Y) but also occupying the distal regions of a few chromosomal pairs. The chromosomal localization of the 18S ribosomal DNA (rDNA) clusters revealed a single site on chromosome pair 4, which was adjacent to the 5S rDNA cluster. Additional 5S rDNA loci were present on the autosome pair 8, X₁ chromosome, and in the presumed fusion point on the Y chromosome. The probe for telomeric repeat motif (TTAGGG)_n revealed signals of variable intensities at the ends of all chromosomes except for the Y chromosome, where no detectable signals were evidenced. Male-to-female comparative genomic hybridization revealed no sex-specific or sex-biased repetitive DNA accumulations, suggesting a presumably low level of neo-Y chromosome differentiation. We provide evidence that rDNA sites might have played a role in the formation of this putative multiple sex chromosome system and that chromosome fusions originate through different mechanisms among different Rineloricaria species.     

Molecular insights into the phylogeny of Blapstinina (Coleoptera: Tenebrionidae: Opatrini)

The monophyly of the North and South American endemic subtribe Blapstinina (Tenebrionidae: Opatrini) is tested through phylogenetic analyses using five molecular markers [nuclear ribosomal 28S (28S), cytochrome oxidase subunit II (COII), arginine kinase (ArgK), carbamoyl-phosphate synthetase domain of rudimentary (CAD), wingless (wg)]. Representatives of several opatrinoid subtribes were taken into consideration, including other geographically overlapping endemic genera, namely Ammodonus, Ephalus and Pseudephalus (all previously considered representatives of Ammobiina). A comparative study of morphology was performed to assess resulting phylogenetic hypotheses. Analyses support the monophyly of Blapstinina; however, they also strongly indicate that Ammodonus should be included within the subtribe. Mecysmus is nested within Blapstinus and therefore, a new synonymy, Blapstinus (= Mecysmus syn.n. ), and the following combinations are introduced: Blapstinus advena comb.n. , B. angustus comb.r. , B. laticollis comb.n. , B. parvulus comb.n. , B. tenuis comb.n. Morphological analysis showed a close affiliation between Ephalus and Pseudephalus. Based on these results, Pseudephalus is synonymized with Ephalus [Ephalus (= Pseudephalus syn.n. )], and the following combination is introduced: Ephalus brevicornis comb.n. Recovered topologies also strongly support transferring Ephalus stat.n. into Opatrina, making the distribution of Opatrina amphi-Atlantic.     

Molecular evidence for the polyphyly of the genus Hemitragus (Mammalia, Bovidae)

The genus Hemitragus includes three species of tahr distributed in distant geographical areas: the Himalayan tahr, H. jemlahicus, occupies the southern flanks of the Himalaya Mountains; the Nilgiri tahr, H. hylocrius, is endemic to southern India; and the Arabian tahr, H. jayakari, is unique to the mountains of south-east Arabia. All previous investigations were based on morphology, and these three species together have never been included in a molecular phylogenetic study. In this study, we constructed a molecular phylogeny of the tribe Caprini sensu lato to determine the taxonomic status of the three species of tahr. Phylogenetic analyses were carried out on a matrix including most extant species currently described in the tribe Caprini sensu lato, and 3165 nucleotide characters, coming from four different markers, i.e., an intron of the nuclear gene coding for the protein kinase C iota, and three mitochondrial genes (subunit II of the cytochrome c oxidase, cytochrome b, and 12S rRNA). The results show that the genus Hemitragus is polyphyletic, as H. jemlahicus is associated with Capra (goats), H. hylocrius is the sister-group of Ovis (sheep), and H. jayakari is allied with Ammotragus lervia (aoudad). In the light of these unexpected results, we revaluate the validity of the morphological characters originally used for defining the genus Hemitragus. At least, we propose a new taxonomy, where the three species of tahr are ranged into three monospecific genera: the genus Hemitragus is restricted to the Himalayan tahr, and two new genera are created: Arabitragus for the Arabian tahr and Nilgiritragus for the Nilgiri tahr.