Speciation by monobrachial centric fusions: A test of the model using nuclear DNA sequences from the bat genus Rhogeessa

Evolution of the ancestral mammalian karyotype and syntenic regions

Computational reconstruction of ancestral mammalian karyotypes revealed a comprehensive picture of the chromosome rearrangements that occurred over the evolutionary history of mammals. Ancient gene order, in some cases extending to full chromosomes, was found conserved for more than 300 My, demonstrating strong evolutionary constraint against rearrangements in some regions. Conserved segments of chromosomes are enriched for genes that control developmental processes. Therefore, Darwinian selection likely maintains ancient gene combinations while allowing for genomic innovations within or near chromosomal sites that break and rearrange over evolutionary time. The revealed relationship between the three-dimensional structure of chromosomes and the evolutionary stability of chromosome segments provides additional insights into the mechanisms of chromosome evolution and diseases associated with genome rearrangements.

Decrypting the rearrangements that drive mammalian chromosome evolution is critical to understanding the molecular bases of speciation, adaptation, and disease susceptibility. Using 8 scaffolded and 26 chromosome-scale genome assemblies representing 23/26 mammal orders, we computationally reconstructed ancestral karyotypes and syntenic relationships at 16 nodes along the mammalian phylogeny. Three different reference genomes (human, sloth, and cattle) representing phylogenetically distinct mammalian superorders were used to assess reference bias in the reconstructed ancestral karyotypes and to expand the number of clades with reconstructed genomes. The mammalian ancestor likely had 19 pairs of autosomes, with nine of the smallest chromosomes shared with the common ancestor of all amniotes (three still conserved in extant mammals), demonstrating a striking conservation of synteny for ∼320 My of vertebrate evolution. The numbers and types of chromosome rearrangements were classified for transitions between the ancestral mammalian karyotype, descendent ancestors, and extant species. For example, 94 inversions, 16 fissions, and 14 fusions that occurred over 53 My differentiated the therian from the descendent eutherian ancestor. The highest breakpoint rate was observed between the mammalian and therian ancestors (3.9 breakpoints/My). Reconstructed mammalian ancestor chromosomes were found to have distinct evolutionary histories reflected in their rates and types of rearrangements. The distributions of genes, repetitive elements, topologically associating domains, and actively transcribed regions in multispecies homologous synteny blocks and evolutionary breakpoint regions indicate that purifying selection acted over millions of years of vertebrate evolution to maintain syntenic relationships of developmentally important genes and regulatory landscapes of gene-dense chromosomes.

Chromosome Synapsis and Recombination in Male Hybrids between Two Chromosome Races of the Common Shrew (Sorex araneus L., Soricidae, Eulipotyphla)

Hybrid zones between chromosome races of the common shrew (Sorex araneus) provide exceptional models to study the potential role of chromosome rearrangements in the initial steps of speciation. The Novosibirsk and Tomsk races differ by a series of Robertsonian fusions with monobrachial homology. They form a narrow hybrid zone and generate hybrids with both simple (chain of three chromosomes) and complex (chain of eight or nine) synaptic configurations. Using immunolocalisation of the meiotic proteins, we examined chromosome pairing and recombination in males from the hybrid zone. Homozygotes and simple heterozygotes for Robertsonian fusions showed a low frequency of synaptic aberrations (<10%). The carriers of complex synaptic configurations showed multiple pairing abnormalities, which might lead to reduced fertility. The recombination frequency in the proximal regions of most chromosomes of all karyotypes was much lower than in the other regions. The strong suppression of recombination in the pericentromeric regions and co-segregation of race specific chromosomes involved in the long chains would be expected to lead to linkage disequilibrium between genes located there. Genic differentiation, together with the high frequency of pairing aberrations in male carriers of the long chains, might contribute to maintenance of the narrow hybrid zone.

Nuclear and mtDNA phylogenetic analyses clarify the evolutionary history of two species of native Hawaiian bats and the taxonomy of Lasiurini (Mammalia: Chiroptera)

Previous studies on genetics of hoary bats produced differing conclusions on the timing of their colonization of the Hawaiian Islands and whether or not North American (Aeorestes cinereus) and Hawaiian (A. semotus) hoary bats are distinct species. One study, using mtDNA COI and nuclear Rag2 and CMA1, concluded that hoary bats colonized the Hawaiian Islands no more than 10,000 years ago based on indications of population expansion at that time using Extended Bayesian Skyline Plots. The other study, using 3 mtDNA and 1 Y-chromosome locus, concluded that the Hawaiian Islands were colonized about 1 million years ago. To address the marked inconsistencies between those studies, we examined DNA sequences from 4 mitochondrial and 2 nuclear loci in lasiurine bats to investigate the timing of colonization of the Hawaiian Islands by hoary bats, test the hypothesis that Hawaiian and North American hoary bats belong to different species, and further investigate the generic level taxonomy within the tribe. Phylogenetic analysis and dating of the nodes of mtDNA haplotypes and of nuclear CMA1 alleles show that A. semotus invaded the Hawaiian Islands approximately 1.35 Ma and that multiple arrivals of A. cinereus occurred much more recently. Extended Bayesian Skyline plots show population expansion at about 20,000 years ago in the Hawaiian Islands, which we conclude does not represent the timing of colonization of the Hawaiian Islands given the high degree of genetic differentiation among A. cinereus and A. semotus (4.2% divergence at mtDNA Cytb) and the high degree of genetic diversity within A. semotus. Rather, population expansion 20,000 years ago could have resulted from colonization of additional islands, expansion after a bottleneck, or other factors. New genetic data also support the recognition of A. semotus and A. cinereus as distinct species, a finding consistent with previous morphological and behavioral studies. The phylogenetic analysis of CMA1 alleles shows the presence of 2 clades that are primarily associated with A. semotus mtDNA haplotypes, and are unique to the Hawaiian Islands. There is evidence for low levels of hybridization between A. semotus and A. cinereus on the Hawaiian Islands, but it is not extensive (<15% of individuals are of hybrid origin), and clearly each species is able to maintain its own genetic distinctiveness. Both mtDNA and nuclear DNA sequences show deep divergence between the 3 groups (genera) of lasiurine bats that correspond to the previously recognized morphological differences between them. We show that the Tribe Lasiurini contains the genera Aeorestes (hoary bats), Lasiurus (red bats), and Dasypterus (yellow bats).

Chromosomal Speciation in the Genomics Era: Disentangling Phylogenetic Evolution of Rock-wallabies

The association of chromosome rearrangements (CRs) with speciation is well established, and there is a long history of theory and evidence relating to "chromosomal speciation." Genomic sequencing has the potential to provide new insights into how reorganization of genome structure promotes divergence, and in model systems has demonstrated reduced gene flow in rearranged segments. However, there are limits to what we can understand from a small number of model systems, which each only tell us about one episode of chromosomal speciation. Progressing from patterns of association between chromosome (and genic) change, to understanding processes of speciation requires both comparative studies across diverse systems and integration of genome-scale sequence comparisons with other lines of evidence. Here, we showcase a promising example of chromosomal speciation in a non-model organism, the endemic Australian marsupial genus Petrogale. We present initial phylogenetic results from exon-capture that resolve a history of divergence associated with extensive and repeated CRs. Yet it remains challenging to disentangle gene tree heterogeneity caused by recent divergence and gene flow in this and other such recent radiations. We outline a way forward for better integration of comparative genomic sequence data with evidence from molecular cytogenetics, and analyses of shifts in the recombination landscape and potential disruption of meiotic segregation and epigenetic programming. In all likelihood, CRs impact multiple cellular processes and these effects need to be considered together, along with effects of genic divergence. Understanding the effects of CRs together with genic divergence will require development of more integrative theory and inference methods. Together, new data and analysis tools will combine to shed light on long standing questions of how chromosome and genic divergence promote speciation.

A multimarker phylogeography of crested newts (Triturus cristatus superspecies) reveals cryptic species

The crested newt Triturus cristatus superspecies is composed of five recognized species. One of these, T. karelinii sensu lato, comprises three geographically structured mitochondrial DNA lineages: 'eastern', 'central' and 'western T. karelinii'. Genetic divergence among these lineages is comparable to that of recognized crested newt species, but morphologically they are indistinguishable. Here, we conduct a multimarker phylogeographical survey to explore the evolutionary independence of these mitochondrial DNA lineages and we include representatives of the other species to guide our interpretation of the results. All markers show distinct patterns when analyzed singly (as a phylogeny or haplotype network) and none of them sort haplotypes fully in line with species or mitochondrial DNA lineage. A multilocus approach (BAPS and *BEAST) on the other hand shows that not only the recognized species, but also the three mitochondrial DNA lineages represent discrete nuclear DNA gene pools. A mismatch is found in the northwest of Asiatic Turkey, where several populations identified as 'central T. karelinii' based on nuclear DNA possesses 'western T. karelinii' mitochondrial DNA. We invoke asymmetric mitochondrial DNA introgression to explain this pattern and support this with a historical biogeographical scenario. The three spatial groups in T. karelinii sensu lato should be regarded as distinct species.

Cytogenetics meets phylogenetics: a review of karyotype evolution in diprotodontian marsupials

We have used a combined approach of phylogenetics and cytogenetics to describe karyotype evolution in Diprotodontia. Molecular relationships of diprotodontian marsupials have been clarified using a concatenation of 5 nuclear gene sequences from multiple exemplars of all extant genera. Our well-resolved phylogenetic tree has been used as a basis for understanding chromosome evolution both within this Order, as well as in marsupials in general. It is clear that the ancestral marsupial karyotype comprised 14 relatively large chromosomes of the form retained relatively unchanged in caenolestids, microbiotherians, peramelemorphians, vombatids, and pygmy possums. Four pericentric inversions occurred in the ancestral dasyuromorphian (chromosomes 1, 2, 4, and 6) and a different 4 in the ancestral didelphimorphian (chromosomes 1, 3, 5 and 6). Within Diprotodontia, although the ancestral marsupial karyotype has been retained in some families such as the extant wombats and pygmy possums, there have been major karytoypic repatternings early in the evolution of others. Chromosome rearrangements in diprotodontia include centric fissions and fusions, translocations, and centromere shifts. Karyotypic changes are discussed in the context of current hypotheses concerning centromeres, chromosomal fragile sites, and mobile elements in marsupials and the probable repeated involvement of these elements in karyotypic restructuring.

A network approach to study karyotypic evolution: the chromosomal races of the common shrew (Sorex araneus) and house mouse (Mus musculus) as model systems

The development of methods to reconstruct phylogenies from karyotypic data has lagged behind what has been achieved with molecular and morphological characters. This hampers our understanding of the role of chromosomal rearrangements in speciation, which depends on knowledge of the karyotypic relationships both among forms that have recently speciated and among forms within species that may speciate in the future. Here, we present a new approach to reconstruct chromosomal phylogenies. Our approach involves the use of networks, which we believe offer a flexible alternative to bifurcating phylogenetic trees for chromosomal phylogenetic analyses, and can incorporate a wide range of chromosomal mutations as well as allowing reticulate evolution through hybridization. In this paper, we apply our method at the within-species level to establish the phylogenetic history, in terms of minimum number of evolutionary steps, of chromosomal races within both the common shrew (Sorex araneus) and the house mouse (Mus musculus). There have been several previous attempts to reconstruct the phylogenies of chromosomal races within shrews and mice, but we describe the first computer-based analysis that considers the whole range of possible mutations generating new races (Robertsonian fusions and fissions and whole-arm reciprocal translocations [WARTs]) and other race-generating processes (zonal raciation events involving both acrocentric and recombinant peaks) postulated for these species. The analysis for common shrew chromosomal races reveals a greater importance of zonal raciation and WARTs than has been suggested hitherto.