Molecular cytogenetics of tragelaphine and alcelaphine interspecies hybrids: hybridization,introgression and speciation in some African antelope

Hybridization can occur naturally among diverging lineages as part of the evolutionary process leading to complete reproductive isolation, or it can result from range shifts and habitat alteration through global warming and/or other anthropogenic influences. Here we report a molecular cytogenetic investigation of hybridization between taxonomically distinct species of the Alcelaphini (Alcelaphus buselaphus 2n = 40 × Damaliscus lunatus 2n = 36) and the Tragelaphini (Tragelaphus strepsiceros 2n = 31/32 × Tragelaphus angasii 2n = 55/56). Cross-species fluorescence in situ hybridization provides unequivocal evidence of the scale of karyotypic difference distinguishing parental species. The findings suggest that although hybrid meiosis of the former cross would necessitate the formation of a chain of seven, a ring of four and one trivalent, the progeny follow Haldane''s rule showing F₁ male sterility and female fertility. The tragelaphine F₁ hybrid, a male, was similarly sterile and, given the 11 trivalents and chain of five anticipated in its meiosis, not unexpectedly so. We discuss these findings within the context of the broader evolutionary significance of hybridization in African antelope, and reflect on what these hold for our views of antelope species and their conservation.     

An extraordinarily stable karyotype of the woody Populus species revealed by chromosome painting

The karyotype represents the basic genetic make‐up of a eukaryotic species. Comparative cytogenetic analysis of related species based on individually identified chromosomes has been conducted in only a few plant groups and not yet in woody plants. We have developed a complete set of 19 chromosome painting probes based on the reference genome of the model woody plant Populus trichocarpa. Using sequential fluorescence in situ hybridization we were able to identify all poplar chromosomes in the same metaphase cells, which led to the development of poplar karyotypes based on individually identified chromosomes. We demonstrate that five Populus species, belonging to five different sections within Populus, have maintained a remarkably conserved karyotype. No inter‐chromosomal structural rearrangements were observed on any of the 19 chromosomes among the five species. Thus, the chromosomal synteny in Populus has been remarkably maintained after nearly 14 million years of divergence. We propose that the karyotypes of woody species are more stable than those of herbaceous plants since it may take a longer period of time for woody plants to fix chromosome number or structural variants in natural populations.     

Population differentiation and speciation in the genus Characidium (Characiformes: Crenuchidae): effects of reproductive and chromosomal barriers

Both time and low gene flow are the key factors by which different biological species arise. The divergence process among lineages and the development of pre‐ or postzygotic isolation occur when gene flow events are lacking. The separation among species of the genus Characidium was analysed in relation to the geomorphological mechanisms in river courses, events of captured adjacent upland drainages in south‐eastern Brazil, and sex chromosome differences. The ZZ/ZW sex chromosomes of Characidium vary in size, morphology, degree of heterochromatinization, and presence/absence of ribosomal DNA. The goal of this study was to understand the mechanism of sex chromosome differentiation, its close association with the geological history of cladogenetic events among drainages, and reproductive isolation leading to Characidium speciation. The W‐specific probe from Characidium gomesi generated a highlighted signal on the entire W chromosome of C. gomesi, Characidium heirmostigmata, Characidium pterostictum, and Characidium sp., instead of karyotypes of three Characidium aff. zebra populations, which showed scattered signals. An evolutionary and biogeographic landscape arose by analysis of ribosomal DNA site location and differentiation of the sex chromosomes, which established mechanisms of reproductive isolation leading to meiotic barriers, keeping the biological unit distinct even if the contact among species was restored. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 541–553.     

Cytogenetic mapping of the W chromosome in the genus Leporinus (Teleostei, Anostomidae) using a highly repetitive DNA sequence

The distribution of the Leporinus elongatus LeSpeI repetitive sequence in other Leporinus species was studied in an attempt to elucidate the evolutionary history of sex chromosomes in this genus using chromosome fluorescence in situ hybridization. The presence of fluorescent signals only in species that have differentiated sex chromosomes suggests that this sequence is related to the differentiation of sex chromosomes in this genus. Thus, these data will contribute to a better understanding of chromosome evolution, especially for sex chromosomes, in the Leporinus genus.     

Chromosomal diversification of diploid number,heterochromatin and rDNAs in two species of Phanaeus beetles (Scarabaeidae,Scarabaeinae)

The genus Phanaeus is included in the tribe Phanaeini, one of the most diverse tribes within the subfamily Scarabaeinae in terms of chromosomal characteristics. However, so far the species of this genus were not studied with differential cytogenetic techniques, limiting any inference of the probable mechanisms responsible for this diversity. In this work, several techniques were applied with the aim of cytogenetically characterizing two Phanaeus species. The karyotype found for Phanaeus (Notiophanaeus) chalcomelas was 2n = 12, neo-XY, and that of P. (N.) splendidulus was 2n = 20, Xy_p, considered primitive for the family Scarabaeidae. The chromosomes of both species showed a high amount of constitutive heterochromatin (CH), with blocks rich in base pairs GC (CMA₃⁺). Moreover, in P. (N.) chalcomelas the marks revealed by C-banding and fluorochrome staining were different in size, showing CH variability. Sites of 18S ribosomal DNA (rDNA) were identified in one autosomal pair of P. (N.) chalcomelas and in five autosomal pairs of P. (N.) splendidulus. On the other hand, only one autosomal pair exhibited 5S rDNA sequences in these species. The results suggest that the karyotype differentiation of the Phanaeus species studied here involved pericentric inversions and centric fusions, as well as mechanisms related to amplification and dispersion of CH and rDNA sequences.     

Cytotaxonomy of Gallinula melanops (Gruiformes,Rallidae): Karyotype evolution and phylogenetic inference

Although Rallidae is the most diverse family within Gruiformes, there is little information concerning the karyotype of the species in this group. In fact, Gallinula melanops, a species of Rallidae found in Brazil, is among the few species studied cytogenetically, but only with conventional staining and repetitive DNA mapping, showing 2n=80. Thus, in order to understand the karyotypic evolution and phylogeny of this group, the present study aimed to analyze the karyotype of G. melanops by classical and molecular cytogenetics, comparing the results with other species of Gruiformes. The results show that G. melanops has the same chromosome rearrangements as described in Gallinula chloropus (Clade Fulica), including fission of ancestral chromosomes 4 and 5 of Gallus gallus (GGA), beyond the fusion between two of segments resultants of the GGA4/GGA5, also fusions between the chromosomes GGA6/GGA7. Thus, despite the fact that some authors have suggested the inclusion of G. melanops in genus Porphyriops, our molecular cytogenetic results confirm its place in the Gallinula genus.     

Chromosome assignment of six dog genes by FISH, and correlation with dog-human Zoo-FISH data

Cross-species chromosome painting analyses have recently demonstrated the presence of regions of conserved synteny between the human and domestic dog genomes, aiding the search for candidate genes for inherited traits. Concerted efforts to subchromosomally assign substantial numbers of dog gene sequences are now needed in order to refine these comparative data, both in terms of marker density and resolution. We have developed novel PCR markers representing three dog genes (ALB, FOS, HNRPA2B1) for which no sequence or mapping data were previously available, to our knowledge. These, in addition to three gene markers previously described (ALDOA, RPE65, VCAM1), were used to isolate and chromosomally assign corresponding large insert genomic clones by fluorescence in situ hybridization (FISH). Chromosome assignments for these six dog genes are discussed in terms of those of the human orthologues, and correlated with existing comparative mapping information, identifying one apparent exception to existing Zoo-FISH data, and aiding refinement of the boundaries of conserved chromosome segments in both genomes.     

Structural homology in the Solanaceae: analysis of genomic regions in support of synteny studies in tomato, potato and pepper

We have analysed the structural homology in euchromatin regions of tomato, potato and pepper with special attention for the long arm of chromosome 2 (2L). Molecular organization and colinear junctions were delineated using multi-color BAC FISH analysis and comparative sequence alignment. We found large-scale rearrangements including inversions and segmental translocations that were not reported in previous comparative studies. Some of the structural rearrangements are specific for the tomato clade, and differentiate tomato from potato, pepper and other Solanaceous species. Although local gene vicinity is largely preserved, there are many small-scale synteny perturbations. Gene adjacency in the aligned segments was frequently disrupted for 47% of the ortholog pairs as a result of gene and LTR retrotransposon insertions, and occasionally by single gene inversions and translocations. Our data also suggests that long distance intra-chromosomal rearrangements and local gene rearrangements have evolved frequently during speciation in the Solanum genus, and that small changes are more prevalent than large-scale differences. The occurrence of sonata and harbinger transposable elements and other repeats near or at junction breaks is considered in the light of repeat-mediated rearrangements and a reconstruction scenario for an ancestral 2L topology is discussed.     

Phylogeny and sex chromosome evolution of Palaeognathae

Many paleognaths (ratites and tinamous) have a pair of homomorphic ZW sex chromosomes in contrast to the highly differentiated sex chromosomes of most other birds. To understand the evolutionary causes for the different tempos of sex chromosome evolution, we produced female genomes of 12 paleognathous species and reconstructed the phylogeny and the evolutionary history of paleognathous sex chromosomes. We uncovered that Palaeognathae sex chromosomes had undergone stepwise recombination suppression and formed a pattern of “evolutionary strata”. Nine of the 15 studied species' sex chromosomes have maintained homologous recombination in their long pseudoautosomal regions extending more than half of the entire chromosome length. We found that in the older strata, the W chromosome suffered more serious functional gene loss. Their homologous Z-linked regions, compared with other genomic regions, have produced an excess of species-specific autosomal duplicated genes that evolved female-specific expression, in contrast to their broadly expressed progenitors. We speculate such “defeminization” of Z chromosome with underrepresentation of female-biased genes and slow divergence of sex chromosomes of paleognaths might be related to their distinctive mode of sexual selection targeting females rather than males, which evolved in their common ancestors.     

Chromosome mapping of Miller-Diecker,Smith-Magenis and RARA loci in non-human primates: implications in the evolution of human chromosome 17

Molecular cytogenetics allows to verify chromosomal homologies previously hypothesised on the base of banding pattern comparison in different species. So far only the chromosome painting technique has been extensively used in studies of chromosomal evolution. This technique allows to detect only interchromosomal rearrangements. Human and Great Apes chromosomes basically differ by intrachromosomal rearrangements, in particular inversions; with chromosome painting it has just been possible to confirm the origin by fusion of human chromosome 2 and a reciprocal translocation in Gorilla, involving the homologous of chromosome 5 and 17. In order to verify intrachromosomal rearrangements in human chromosomal evolution, chromosome mapping of human loci in non-human primates is a useful approach. We mapped Miller-Diecker, Smith-Magenis and RARA loci localised on human chromosome 17, in Gorilla gorilla, Pongo pygmaeus, Macaca fascicularis and Cercopithecus aethiops. On the base of the obtained results it was possible to verify chromosomal rearrangements previously identified by banding, to achieve new informations about the controversial evolution of human chromosome 17, and to detect the occurrence of a paracentric inversion in the homologous in Cercopithecus aethiops.     

Phylogeny and evolutionary origins of the Leporidae: a review of cytogenetics, molecular analyses and a supermatrix analysis

• 1 We review current knowledge of the evolutionary relationships among species of Leporidae drawing on molecular, cytogenetic and morphological data. We highlight problems associated with retrieving phylogenetic information under conditions of a rapid radiation and the lack of phylogenetically informative cytogenetic and mitochondrial DNA characters. Most morphological features underpinning generic distinctions are subtle and prone to reversal and convergence and as a consequence, they generally provide little basis for assessing phylogenetic affinity.
• 2 We report the results of a supermatrix analysis that combines published nucleotide sequence data, unique insertion/deletion events, morphological characters and presumed geographical centres of origin of each genus. This represents the most comprehensive intergeneric comparison of the Leporidae thus far undertaken.
• 3 The monophyly of the 11 leporid genera is unambiguously supported. There is support for an Afroasian assemblage that comprises Poelagus, Pronolagus and Nesolagus, a primitive Lepus, with the problematic Bunolagus, Oryctolagus, Caprolagus and Pentalagus as derived species in a clade that also includes the closely related Brachylagus and Sylvilagus as sister taxa.
• 4 There is no support for the Palaeolaginae, although Romerolagus is an ancient lineage within the extant Leporidae.
• 5 We hold that of the polytypic genera Lepus remains the most problematic, and provide a working hypothesis that will hopefully encourage future research on the various hare species.

     

Phylogeny and historical biogeography of ancient assassin spiders (Araneae: Archaeidae) in the Australian mesic zone: evidence for Miocene speciation within Tertiary refugia

The rainforests, wet sclerophyll forests and temperate heathlands of the Australian mesic zone are home to a diverse and highly endemic biota, including numerous old endemic lineages restricted to refugial, mesic biomes. A growing number of phylogeographic studies have attempted to explain the origins and diversification of the Australian mesic zone biota, in order to test and better understand the mode and tempo of historical speciation within Australia. Assassin spiders (family Archaeidae) are a lineage of iconic araneomorph spiders, characterised by their antiquity, remarkable morphology and relictual biogeography on the southern continents. The Australian assassin spider fauna is characterised by a high diversity of allopatric species, many of which are restricted to individual mountains or montane systems, and all of which are closely tied to mesic and/or refugial habitats in the east and extreme south-west of mainland Australia. We tested the phylogeny and vicariant biogeography of the Australian Archaeidae (genus Austrarchaea Forster & Platnick), using a multi-locus molecular approach. Fragments from six mitochondrial genes (COI, COII, tRNA-K, tRNA-D, ATP8, ATP6) and one nuclear protein-coding gene (Histone H3) were used to infer phylogenetic relationships and to explore the phylogeographic origins of the diverse Australian fauna. Bayesian analyses of the complete molecular dataset, along with differentially-partitioned Bayesian and parsimony analyses of a smaller concatenated dataset, revealed the presence of three major Australian lineages, each with non-overlapping distributions in north-eastern Queensland, mid-eastern Australia and southern Australia, respectively. Divergence date estimation using mitochondrial data and a rate-calibrated relaxed molecular clock revealed that major lineages diverged in the early Tertiary period, prior to the final rifting of Australia from East Antarctica. Subsequent speciation occurred during the Miocene (23-5.3 million years ago), with tropical and subtropical taxa diverging in the early-mid Miocene, prior to southern and temperate taxa in the mid-late Miocene. Area cladograms reconciled with Bayesian chronograms for all known Archaeidae in southern and south-eastern Australia revealed seven potentially vicariant biogeographic barriers in eastern Queensland, New South Wales and southern Australia, each proposed and discussed in relation to other mesic zone taxa. Five of these barriers were inferred as being of early Miocene age, and implicated in the initial vicariant separation of endemic regional clades. Phylogeographic results for Australian Archaeidae are congruent with a model of sequential allopatric speciation in Tertiary refugia, as driven by the contraction and fragmentation of Australia’s mesic biomes during the Miocene. Assassin spiders clearly offer great potential for further testing historical biogeographic processes in temperate and eastern Australia, and are a useful group for better understanding the biology and biogeography of the Australian mesic zone.     

Fluorescence in situ hybridization establishes homology between human and silvered leaf monkey chromosomes,reveals reciprocal translocations between chromosomes homologous to human Y/5, 1/9, and 6/16, and delineates an X1X2Y1Y2/X1X1X2X2 sex-chromosome system

We employed in situ hybridization of chromosome-specific DNA probes (“chromosome painting”) of all human chromosomes to establish homologies between the human and the silvered lead monkey karyotypes (Presbytis cristata 2n=44). The 24 human paints gave 30 signals on the haploid female chromosome set and 34 signals on the haploid male chromosome set. This difference is due to a reciprocal translocation between the Y and an autosome homologous to human chromosome 5. This Y/autosome reciprocal translocation which is unique among catarrhine primates has produced a X₁X₂Y₁Y₂/X₁X₁X₂X₂ sex-chromosome system. Although most human syntenic groups have been maintained in the silvered leaf monkey chromosomes homologous to human chromosomes 14 and 15, 21 and 22 have experienced Robertsonian fusions. Further, the multiple FISH signals provided by libraries to human chromosomes 1/9, 6/16 indicate that these chromosomes have been split by reciprocal translocations. G-banding analysis shows three different forms of chromosome 1 (X₂) which differ by a complex series of inversions in the 10 individuals karyotyped. Comparisons with the hybridization patterns in hylobatids (gibbons and siamang) demonstrate that resemblances in chromosomal morphology and banding previously taken to indicate a special phylogenetic relationship between gibbons and colobines are due to convergence. A. J. Phys. Anthropol. 102:315–327, 1997. © 1997 Wiley-Liss, Inc.     

Chromosome analysis of walking catfish,Clarias magur (Teleostei,Siluriformes, Clariidae), using staining,FISH with 18S, 5S and BAC probes

The chromosomal characteristics of Clarias magur were examined using conventional (Giemsa-staining, Ag-impregnation and CMA₃ + DAPI fluorescence) and molecular/ FISH (18S & 5S rDNA probes + one BAC DNA probe) cytogenetic tools. The diploid chromosome number was 50 and the karyotype consisted of 14 metacentric, 20 sub-metacentric, 8 sub-telocentric, 8 acrocentric chromosomes with 84 chromosome arms without any heteromorphic pair. The C-heterochromatic blocks were located on centromeric position of 13 pairs of chromosomes. The NOR sites, visualized by AgNO₃- and CMA₃- staining, were situated at p arms of chromosome pair No. 21, which also corresponded to 18S rDNA site visualized by FISH. The FISH signal of ICF_001_D19 clone probe was observed on 18th chromosome pair. The findings of the present study on C. magur provided valuable markers for the chromosome identification and locations of genes of the BAC clone on the chromosome will lead to the construction of physical map of genome of this species.     

Phylogeny and speciation of the eastern Asian cyprinid genus Sarcocheilichthys

The genus Sarcocheilichthys is a group of small cyprinid fishes comprising 10 species/sub‐species widely distributed in East Asia, which represents a valuable model for understanding the speciation of freshwater fishes in East Asia. In the present study, the molecular phylogenetic relationship of the genus Sarcocheilichthys was investigated using a 1140 bp section of the mitochondrial cytochrome b gene. Two different tree‐building methods, maximum parsimony (MP) and Bayesian methods, yielded trees with almost the same topology, yielding high bootstrap values or posterior probabilities. The results showed that the genus Sarcocheilichthys consists of two large clades, clades I and II. Clade I contains Sarcocheilichthys lacustris, Sarcocheilichthys sinensis and Sarcocheilichthys parvus, with S. parvus at a basal position. In clade II, Sarcocheilichthys variegatus microoculus is at a basal position; samples of the widespread species, Sarcocheilichthys nigripinnis, form a large subclade containing another valid species Sarcocheilichthys czerskii. Sarcocheilichthys kiangsiensis is retained at an intermediate position. Since S. czerskii is a valid species in the S. nigripinnis clade, remaining samples of S. nigripinnis form a paraphyly. This speciation process is attributed to geographical isolation and special environmental conditions experienced by S. czerskii and stable environments experienced by the other S. nigripinnis populations. This type of speciation process was suggested to be very common. Samples of Sarcocheilichthys sinensis sinensis and Sarcocheilichthys sinensis fukiensis that did not form their own monophyletic groups suggest an early stage of speciation and support their sub‐species status. Molecular clock analysis indicates that the two major lineages of the genus Sarcocheilichthys, clades I and II diverged c. 8·89 million years ago (mya). Sarcocheilichthys v. microoculus from Japan probably diverged 4·78 mya from the Chinese group. The northern–southern clades of S. nigripinnis began to diverge c. 2·12 mya, while one lineage of S. nigripinnis evolved into a new species, S. czerski, c. 0·34 mya.     

Barcodes Reveal 48 New Species of Tetrahymena,Dexiostoma, and Glaucoma: Phylogeny,Ecology, and Biogeography of New and Established Species

Tetrahymena mitochondrial cox1 barcodes and nuclear SSUrRNA sequences are particularly effective at distinguishing among its many cryptic species. In a project to learn more about Tetrahymena natural history, the majority of >1,000 Tetrahymena‐like fresh water isolates were assigned to established Tetrahymena species with the remaining assigned to 37 new species of Tetrahymena, nine new species of Dexiostoma and 12 new species of Glaucoma. Phylogenetically, all but three Tetrahymena species belong to the well‐established “australis” or “borealis” clades; the minority forms a divergent “paravorax” clade. Most Tetrahymena species are micronucleate, but others are exclusively amicronucleate. The self‐splicing intron of the LSUrRNA precursor is absent in Dexiostoma and Glaucoma and was likely acquired subsequent to the “australis/borealis” split; in some instances, its sequence is diagnostic of species. Tetrahymena americanis, T. elliotti, T. gruchyi n. sp., and T. borealis, together accounted for >50% of isolates, consistent with previous findings for established species. The biogeographic range of species found previously in Austria, China, and Pakistan was extended to the Nearctic; some species show evidence of population structure consistent with endemism. Most species were most frequently collected from ponds or lakes, while others, particularly Dexiostoma species, were collected most often from streams or rivers. The results suggest that perhaps hundreds of species remain to be discovered, particularly if collecting is global and includes hosts of parasitic forms.     

Phylogeny of Myxobolidae (Myxozoa) and the evolution of myxospore appendages in the Myxobolus clade

Genera Myxobolus Bütschli, 1882 and Henneguya Thélohan, 1892 (Myxobolidae) are specious myxozoan genera. They comprise nearly half of overall known myxozoan species diversity. A typical spore feature of Henneguya is the presence of two caudal appendages of the spore valves, which distinguishes them from species of the genus Myxobolus. Several Myxobolus spp., however, were reported to show aberrant spores with Henneguya-like caudal appendages. We found such aberrant spores in Myxobolus tsangwuensis and Myxobolus wulii. We studied the ultrastructure of M. wulii and Myxobolus oralis spores with caudal appendages by transmission electron microscopy (TEM). TEM of these aberrant spores revealed that their caudal appendages have the same ultrastructure as the appendages of Henneguya spp. Small caudal appendages of M. wulii spores observed only on TEM suggested that this character may be often overlooked and more Myxobolus species potentially have the ability to express the caudal appendages on the myxospore. In order to trace the evolution of this character, we performed broad phylogenetic analysis of all species of the family Myxobolidae which are available in GenBank including nearly 300 taxa. We found at least eight independent evolutionary origins of spores with two appendages, three origins of a single appendage and 12 apparent secondary losses of the spore projections. Therefore, genus Henneguya with typical two-tailed myxospores is polyphyletic, however a majority of its species has a common ancestor and groups in the second largest subclade of the Myxobolus clade. We also mapped the biological characteristics (host, site of infection and environment) of Myxobolidae species on the phylogenetic tree. We revealed an evident host-associated evolutionary pattern in all parts of the Myxobolus clade with a distinct and species-rich subclade containing almost exclusively species infecting species of the Order Cypriniformes.     

Phylogeny,speciation, and distribution of the Japanese dwarf bamboos of genus Sasa and allies

Development of the concept of the subfamily Bambusoideae during the past three decades is briefly reviewed. Phylogeny, putative hybrid taxa, a new, simplified key to explicit identification, and the revision of the distribution range among the Japanese dwarf bamboos of genus Sasa and its close allies are discussed. Based on analyses of the random amplified polymorphic DNA and morphological data and of FLOWERING LOCUS T (FT) homologs, parsimonious trees resolved that genus Sasa sec. Macrochlamys were the most basal and sect. Monilicladae were the next most basal, followed by the terminal sister clades of sects. Sasa and Crassinodi.