Molecular systematics of sciurognathi (rodentia): the mitochondrial cytochrome b and 12S rRNA genes support the Anomaluroidea (Pedetidae and Anomaluridae)

Springhares, flying and flightless scaly-tailed squirrels (Anomaluromorpha, Rodentia) are the squirrely mouse: comparative anatomy of the masticatory musculature and its implications on the evolution of hystricomorphy in rodents

Anomaluromorpha is a particularly puzzling suborder of Rodentia. Endemic to Africa, this clade includes the extant genera Idiurus, Anomalurus, Zenkerella, and Pedetes. These rodents present an hystricomorphous condition of the skull, characterized by a large infraorbital foramen, which evolved independently within the mouse-related clade over a span of approximately 57 million years. They exhibit a high disparity in craniomandibular and dental morphology that has kept their phylogenetic affinities disputed for a long time. Given the past significance of masticatory morphotypes in establishing the classification of Rodentia, we propose to explore variations in the masticatory apparatus of Anomaluromorpha in order to evaluate whether its related features can offer additional data for systematics and contribute to our understanding of the complexity of hystricomorphy. In order to do so, we used traditional dissection and diffusible iodine-based contrast-enhanced computed tomography (diceCT) to accurately describe and compare the anatomy of the specimens. We found that the muscle morphology displays clear differentiation among each anomaluromorph taxonomic unit. Specifically, the masseteric complex of Anomaluromorpha exhibits distinctive synapomorphies such as the infraorbital part of the zygomaticomandibularis muscle being separated into a rostral and orbital part and an absence of a posterior part of the zygomaticomandibularis. Additionally, the orbital portion of the infraorbital part originates from a well-marked ridge and fossa at the level of its area of origin on the anteromedial wall of the orbital cavity, a feature that is absent in other members of the mouse-related clade. This evident bony feature, among others, is strongly associated with muscular anatomy and can contribute to ascertaining the taxonomic status of extinct representatives of the clade. Finally, we showed that the hystricomorphy of Anomaluromorpha largely differs from those of Ctenohystrica and Dipodoidea and that the definition of this morphotype is complex and cannot be reduced simply to the size of the opening of the infraorbital foramen.

Molecular Phylogeny of the Subgenus Karstomys Reveals Genetic Signature of Post-Glacial Colonization of Apodemus mystacinus (Rodentia: Muridae) in the Zagros Mountains from Different Refugia

Eastern broad-toothed field mouse, Apodemus mystacinus, is a rocky habitat dwelling rodent distributed in Asia Minor, the Levant, the Caucasus, and the Zagros Mountains. In this study, we investigated the phylogenetic relationship between different populations of A. mystacinus throughout its range, based on the mitochondrial cytb marker. Phylogenetic analyses revealed the existence of five separately evolving lineages within A. mystacinus, of which two previously unrecognized lineages were identified in the Zagros Mountains and the Levant. Divergence between two major clades of the subgenus Karstomys, corresponding to A. mystacinus and Apodemus epimelas, is inferred to coincide with the Messinian Salinity Crisis (Late Miocene), whereas the splits between major lineages of A. mystacinus are inferred to have occurred during the Pleistocene. Colonization of the Zagros may have occurred from different refugia via eastward migration of the Turkish population and then again by a more recent colonization from the Caucasus, after reopening of the land corridor between the Caucasus and the Zagros Mountains during the Holocene drought.

Oldest skeleton of a fossil flying squirrel casts new light on the phylogeny of the group

Flying squirrels are the only group of gliding mammals with a remarkable diversity and wide geographical range. However, their evolutionary story is not well known. Thus far, identification of extinct flying squirrels has been exclusively based on dental features, which, contrary to certain postcranial characters, are not unique to them. Therefore, fossils attributed to this clade may indeed belong to other squirrel groups. Here we report the oldest fossil skeleton of a flying squirrel (11.6 Ma) that displays the gliding-related diagnostic features shared by extant forms and allows for a recalibration of the divergence time between tree and flying squirrels. Our phylogenetic analyses combining morphological and molecular data generally support older dates than previous molecular estimates (~23 Ma), being congruent with the inclusion of some of the earliest fossils (~36 Ma) into this clade. They also show that flying squirrels experienced little morphological change for almost 12 million years.

Mammals can walk, hop, swim and fly; a few, like marsupial sugar gliders or colugos, can even glide. With 52 species scattered across the Northern hemisphere, flying squirrels are by far the most successful group that adopted this way of going airborne. To drift from tree to tree, these small animals pack their own ‘parachute’: a membrane draping between their lower limbs and the long cartilage rods that extend from their wrists. Tiny specialized wrist bones, which are unique to flying squirrels, help to support the cartilaginous extensions.

The origin of flying squirrels is a point of contention: while most genetic studies point towards the group splitting from tree squirrels about 23 million years ago, the oldest remains – mostly cheek teeth – suggest the animals were already soaring through forests 36 million years ago. However, recent studies show that the dental features used to distinguish between gliding and non-gliding squirrels may actually be shared by the two groups.

In 2002, the digging of a dump site in Barcelona unearthed a peculiar skeleton: first a tail and two thigh bones, big enough that the researchers thought it could be the fossil of a small primate. In fact, and much to the disappointment of paleoprimatologists, further excavating revealed that it was a rodent. As the specimen – nearly an entire skeleton – was being prepared, paleontologists insisted that all the ‘dirt’ attached to the bones had to be carefully screen-washed. From the mud emerged the minuscule specialized wrist bones: the primate-turned-rodent was in fact Miopetaurista neogrivensis, an extinct flying squirrel.

Here, Casanovas-Vilar et al. describe the 11.6 million years old fossil, the oldest ever found. The wrist bones reveal that the animal belongs to the group of flying squirrels that have large sizes. Evolutionary analyses that combined molecular and paleontological data demonstrated that flying squirrels evolved from tree squirrels as far back as 31 to 25 million years ago, and possibly even earlier. In addition, the results show that Miopetaurista is closely related to Petaurista, a modern group of giant flying squirrels. In fact, their skeletons are so similar that the large species that currently inhabit the tropical and subtropical forests of Asia could be considered living fossils.

Molecular and paleontological data are often at odds, but this fossil shows that they can be reconciled and combined to retrace history. Discovering older fossils, or even transitional forms, could help to retrace how flying squirrels took a leap from the rest of their evolutionary tree.

Morphology of an Early Oligocene beaver Propalaeocastor irtyshensis and the status of the genus Propalaeocastor

The Early to Late Oligocene Propalaeocastor is the earliest known beaver genus from Eurasia. Although many species of this genus have been described, these species are defined based on very fragmentary specimens. Propalaeocastor irtyshensis from the Early Oligocene Irtysh River Formation in northwestern Xinjiang, China is one of the earliest-known members of Propalaeocastor. This species is defined on a single maxillary fragment. We revise the diagnosis of P. irtyshensis and the genus Propalaeocastor, based on newly discovered specimens from the Irtysh River Formation. The dental morphology of P. irtyshensis is very similar to other early castorids. The caudal palatine foramen of P. irtyshensis is situated in the maxillary-palatine suture. This is a feature generally accept as diagnostic character for the castorids. On the other hand, P. irtyshensis has two upper premolars, a rudimentarily developed sciuromorph-like zygomatic plate, and a relatively large protrogomorph-like infraorbital foramen. Some previous researchers suggested that Propalaeocastor is a junior synonym of Steneofiber, while other took it as a valid genus. Our morphological comparison and phylogenetic analysis suggest that Propalaeocastor differs from Steneofiber and is a valid genus. We also suggest that Agnotocastor aubekerovi, A. coloradensis, A. galushai, A. readingi, Oligotheriomys primus, and "Steneofiber aff. dehmi" should be referred to Propalaeocastor. Propalaeocastor is the earliest and most basal beaver. The origin place of Propalaeocastor and castorids is uncertain. The Early Oligocene radiation of castorids probably is propelled by the global climate change during the Eocene-Oligocene transition.

The Beaver's Phylogenetic Lineage Illuminated by Retroposon Reads

Solving problematic phylogenetic relationships often requires high quality genome data. However, for many organisms such data are still not available. Among rodents, the phylogenetic position of the beaver has always attracted special interest. The arrangement of the beaver's masseter (jaw-closer) muscle once suggested a strong affinity to some sciurid rodents (e.g., squirrels), placing them in the Sciuromorpha suborder. Modern molecular data, however, suggested a closer relationship of beaver to the representatives of the mouse-related clade, but significant data from virtually homoplasy-free markers (for example retroposon insertions) for the exact position of the beaver have not been available. We derived a gross genome assembly from deposited genomic Illumina paired-end reads and extracted thousands of potential phylogenetically informative retroposon markers using the new bioinformatics coordinate extractor fastCOEX, enabling us to evaluate different hypotheses for the phylogenetic position of the beaver. Comparative results provided significant support for a clear relationship between beavers (Castoridae) and kangaroo rat-related species (Geomyoidea) (p < 0.0015, six markers, no conflicting data) within a significantly supported mouse-related clade (including Myodonta, Anomaluromorpha, and Castorimorpha) (p < 0.0015, six markers, no conflicting data).

New insight into the cradle of the grey voles (subgenus Microtus) inferred from mitochondrial cytochrome b sequences

Our aim in this study was to further the understanding of the taxonomic relationships and the evolutionary history of grey voles (subgenus

A critical survey of vestigial structures in the postcranial skeletons of extant mammals

In the Mammalia, vestigial skeletal structures abound but have not previously been the focus of study, with a few exceptions (e.g., whale pelves). Here we use a phylogenetic bracketing approach to identify vestigial structures in mammalian postcranial skeletons and present a descriptive survey of such structures in the Mammalia. We also correct previous misidentifications, including the previous misidentification of vestigial caviid metatarsals as sesamoids. We also examine the phylogenetic distribution of vestigiality and loss. This distribution indicates multiple vestigialization and loss events in mammalian skeletal structures, especially in the hand and foot, and reveals no correlation in such events between mammalian fore and hind limbs.

Organisation and tyrosine hydroxylase and calretinin immunoreactivity in the main olfactory bulb of paca (Cuniculus paca): a large caviomorph rodent

The majority of neuroanatomical and chemical studies of the olfactory bulb have been performed in small rodents, such as rats and mice. Thus, this study aimed to describe the organisation and the chemical neuroanatomy of the main olfactory bulb (MOB) in paca, a large rodent belonging to the Hystricomorpha suborder and Caviomorpha infraorder. For this purpose, histological and immunohistochemical procedures were used to characterise the tyrosine hydroxylase (TH) and calretinin (CR) neuronal populations and their distribution. The paca MOB has eight layers: the olfactory nerve layer (ONL), the glomerular layer (GL), the external plexiform layer (EPL; subdivided into the inner and outer sublayers), the mitral cell layer (MCL), the internal plexiform layer (IPL), the granule cell layer (GCL), the periventricular layer and the ependymal layer. TH-ir neurons were found mostly in the GL, and moderate numbers of TH-ir neurons were scattered in the EPL. Numerous varicose fibres were distributed in the IPL and in the GCL. CR-ir neurons concentrated in the GL, around the base of the olfactory glomeruli. Most of the CR-ir neurons were located in the MCL, IPL and GCL. Some of the granule cells had an apical dendrite with a growth cone. The CR immunoreactivity was also observed in the ONL with olfactory nerves strongly immunostained. This study has shown that the MOB organisation in paca is consistent with the description in other mammals. The characterisation and distribution of the population of TH and CR in the MOB is not exclusively to this species. This large rodent shares common patterns to other caviomorph rodent, as guinea pig, and to the myomorph rodents, as mice, rats and hamsters.

A phylogeographic survey of the pygmy mouse Mus minutoides in South Africa: taxonomic and karyotypic inference from cytochrome b sequences of museum specimens

The African pygmy mice (Mus, subgenus Nannomys) are a group of small-sized rodents that occur widely throughout sub-Saharan Africa. Chromosomal diversity within this group is extensive and numerous studies have shown the karyotype to be a useful taxonomic marker. This is pertinent to Mus minutoides populations in South Africa where two different cytotypes (2n = 34, 2n = 18) and a modification of the sex determination system (due to the presence of a Y chromosome in some females) have been recorded. This chromosomal diversity is mirrored by mitochondrial DNA sequences that unambiguously discriminate among the various pygmy mouse species and, importantly, the different M. minutoides cytotypes. However, the geographic delimitation and taxonomy of pygmy mice populations in South Africa is poorly understood. To address this, tissue samples of M. minutoides were taken and analysed from specimens housed in six South African museum collections. Partial cytochrome b sequences (400 pb) were successfully amplified from 44% of the 154 samples processed. Two species were identified: M. indutus and M. minutoides. The sequences of the M. indutus samples provided two unexpected features: i) nuclear copies of the cytochrome b gene were detected in many specimens, and ii) the range of this species was found to extend considerably further south than is presently understood. The phylogenetic analysis of the M. minutoides samples revealed two well-supported clades: a Southern clade which included the two chromosomal groups previously identified in South Africa, and an Eastern clade that extended from Eastern Africa into South Africa. Congruent molecular phylogenetic and chromosomal datasets permitted the tentative chromosomal assignments of museum specimens within the different clades as well as the correction of misidentified museum specimens.

High prevalence of Rickettsia typhi and Bartonella species in rats and fleas, Kisangani, Democratic Republic of the Congo

The prevalence and identity of Rickettsia and Bartonella in urban rat and flea populations were evaluated in Kisangani, Democratic Republic of the Congo (DRC) by molecular tools. An overall prevalence of 17% Bartonella species and 13% Rickettsia typhi, the agent of murine typhus, was found in the cosmopolitan rat species, Rattus rattus and Rattus norvegicus that were infested by a majority of Xenopsylla cheopis fleas. Bartonella queenslandensis, Bartonella elizabethae, and three Bartonella genotypes were identified by sequencing in rat specimens, mostly in R. rattus. Rickettsia typhi was detected in 72% of X. cheopis pools, the main vector and reservoir of this zoonotic pathogen. Co-infections were observed in rodents, suggesting a common mammalian host shared by R. typhi and Bartonella spp. Thus, both infections are endemic in DRC and the medical staffs need to be aware knowing the high prevalence of impoverished populations or immunocompromised inhabitants in this area.

Jumping and gliding rodents: mitogenomic affinities of Pedetidae and Anomaluridae deduced from an RNA-Seq approach

An RNA-Seq strategy was used to obtain the complete set of protein-coding mitochondrial genes from two rodent taxa. Thanks to the next generation sequencing (NGS) 454 approach, we determined the complete mitochondrial DNA genome from Graphiurus kelleni (Mammalia: Rodentia: Gliridae) and partial mitogenome from Pedetes capensis (Pedetidae), and compared them with published rodent and outgroup mitogenomes. We finished the mitogenome sequencing by a series of amplicons using conserved PCR primers to fill the gaps corresponding to tRNA, rRNA and control regions. Phylogenetic analyses of the mitogenomes suggest a well-supported rodent phylogeny in agreement with nuclear gene trees. Pedetes groups with Anomalurus into the clade Anomaluromorpha, while Graphiurus branches within the squirrel-related clade. Moreover, Pedetes+Anomalurus branch with Castor into the mouse-related clade. Our study demonstrates the utility of NGS for obtaining new mitochondrial genomes as well as the importance of choosing adequate models of sequence evolution to infer the phylogeny of rodents.

Phylogenetic relationships of extant zokors (Myospalacinae) (Rodentia, Spalacidae) inferred from mitochondrial DNA sequences

In this study, we use three mitochondrial markers, cytochrome b gene (Cyt b), NADH dehydrogenase subunit 4 (ND4) and control region (D-loop) to investigate the phylogenetic relationships of extant zokor species in Mysopalacinae. The phylogenetic tree constructed based on Cyt b strongly supports the monophyly genera Eospalax and Myospalax with E. fontanierii being the most ancient species in Eospalax. Further phylogenetic analyses of four species of Eospalax based on ND4 and D-loop sequences revealed two clades that correspond to two geographical distributions. The basal clade includes E. cansus which is mainly found on Loess Plateau (LP) and another clade including E. baileyi, E. smithii and E. rufescens that inhabits areas above 2000 m on Qinghai-Tibetan Plateau (QTP) and Qinling Mountains. Geographical events of QTP and LP may have played a major role in the diversification and evolution of Mysopalacinae.

Trichuris spp. (Nematoda: Trichuridae) from two rodents, Mastomys natalensis and Gerbilliscus vicinus in Tanzania

During a survey of the helminth community of several rodent species in the Morogoro region (Tanzania), Trichuris whipworms (Nematoda: Trichuridae) were found in the ceca of the Natal multimammate mouse, Mastomys natalensis and a gerbil, Gerbilliscus vicinus (both Rodentia: Muridae). The taxonomic literature regarding Trichuris from African native rodents describes 10 species, but includes few metric and morphologic characters that discriminate between some of the pairs. The whipworms we sampled in Tanzanian Natal multimammate mice and gerbils were morphologically identified, respectively, as Trichuris mastomysi Verster, 1960 and Trichuris carlieri Gedoelst, 1916 sensu lato, but with characters that overlap or partially overlap with the cosmopolitan Murinae whipworm, Trichuris muris , already reported from several rodents in Africa. To clarify our identification, we sequenced the ITS-1, 5.8S, and ITS-2 ribosomal DNA region of the worms' nuclear genome. The genetic analyses clearly distinguish the whipworms we found in M. natalensis from those found in the gerbil, and both of these from T. muris whipworm reference sequences. The overlap of morphological characters between rodent whipworms suggests that reports of T. muris from rodent species not closely related to Murinae in other parts of Africa should be treated with caution.

Bartonella prevalence and genetic diversity in small mammals from Ethiopia

More than 500 small mammals were trapped at 3 localities in northern Ethiopia to investigate Bartonella infection prevalence and the genetic diversity of the Bartonella spp. We extracted total DNA from liver samples and performed PCR using the primers 1400F and 2300R targeting 852 bp of the Bartonella RNA polymerase beta subunit (rpoB) gene. We used a generalized linear mixed model to relate the probability of Bartonella infection to species, season, locality, habitat, sex, sexual condition, weight, and ectoparasite infestation. Overall, Bartonella infection prevalence among the small mammals was 34.0%. The probability of Bartonella infection varied significantly with species, sex, sexual condition, and some locality, but not with season, elevation, habitat type, animal weight, and ectoparasite infestation. In total, we found 18 unique Bartonella genotypes clustered into 5 clades, 1 clade exclusively Ethiopian, 2 clades clustered with genotypes from central and eastern Africa, and the remaining 2 clades clustered with genotypes and species from Africa and Asia. The close relatedness of several of our Bartonella genotypes obtained from the 3 dominant rodent species in Tigray with the pathogenic Bartonella elizabethae from Rattus spp. in Asia indicates a potential public health threat.

Complete mitochondrial genome of the Eurasian flying squirrel Pteromys volans (Sciuromorpha, Sciuridae) and revision of rodent phylogeny

In this study, the complete mitochondrial genome of the Eurasian flying squirrel Pteromys volans (Rodentia, Sciuromorpha, Sciuridae) was sequenced and characterized in detail. The entire mitochondrial genome of P. volans consisted of 16,513 bp and contained 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and two non-coding regions. Its gene arrangement pattern was consistent with the mammalian ground pattern. The overall base composition and AT contents were similar to those of other rodent mitochondrial genomes. The light-strand origin generally identified between tRNA ( Asn ) and tRNA ( Cys ) consisted of a secondary structure with an 11-bp stem and an 11-bp loop. The large control region was constructed of three characteristic domains, ETAS, CD, and CSB without any repeat sequences. Each domain contained ETAS1, subsequences A, B, and C, and CSB1, respectively. In order to examine phylogenetic contentious issues of the monophyly of rodents and phylogenetic relationships among five rodent suborders, here, phylogenetic analyses based on nucleotide sequence data of the 35 rodent and 3 lagomorph mitochondrial genomes were performed using the Bayesian inference and maximum likelihood method. The result strongly supported the rodent monophyly with high node confidence values (BP 100 % in ML and BPP 1.00 in BI) and also monophylies of four rodent suborders (BP 85-100 % in ML and BPP 1.00 in BI), except for Anomalumorpha in which only one species was examined here. Also, phylogenetic relationships among the five rodent suborders were suggested and discussed in detail.

Low, complex and probably reticulated chromosome evolution of Sciuromorpha (Rodentia) and Lagomorpha

Lagomorpha (rabbits and pikas) and Sciuromorpha (squirrels) are grouped in the Glires superorder. Their chromosome diversification, since their separation from the eutherian mammalian common ancestor, was characterized by a low rate of chromosome rearrangements. Consequently, the structure of some chromosomes was either conserved or only slightly modified, making their comparison easy at the genus, family and even order level. Interspecific in situ hybridization (Zoo-FISH) largely corroborates classical cytogenetic data but provides much more reliability in comparisons, especially for distant species. We reconstructed common ancestral karyotypes for Glires, Lagomorpha, Sciuromorpha, and Sciuridae species, and then, determined the chromosome changes separating these ancestors from their common eutherian ancestor. We propose that reticulated evolution occurred during the diversification of Glires, which implies that several pericentric inversions and Robertsonian translocations were conserved in the heterozygous status for an extensive period. Finally, among Lagomorpha and Sciuromorpha, we focused on Leporidae and Sciuridae chromosome evolution. In the various attempts to establish dichotomic evolutionary schemes, it was necessary to admit that multiple homoplasies (convergent and reverse rearrangements) occurred in Sciuridae and in a lesser degree, in Leporidae. In Leporidae, additional rearrangements were sufficient to propose a resolved phylogeny. However, a resolved phylogeny was not possible for Sciuridae because most of the rearrangements occurred in terminal branches. We conclude that a reticulated evolution took place early during the evolution of both families and lasted longer in Sciuridae than in Leporidae. In Sciuridae, most chromosome rearrangements were pericentric inversions involving short fragments. Such rearrangements have only mild meiotic consequences, which may explain the long persistence of the heterozygous status characterizing reticulated evolution.

A glimpse on the pattern of rodent diversification: a phylogenetic approach

Background

Development of phylogenetic methods that do not rely on fossils for the study of evolutionary processes through time have revolutionized the field of evolutionary biology and resulted in an unprecedented expansion of our knowledge about the tree of life. These methods have helped to shed light on the macroevolution of many taxonomic groups such as the placentals (Mammalia). However, despite the increase of studies addressing the diversification patterns of organisms, no synthesis has addressed the case of the most diversified mammalian clade: the Rodentia.

Results

Here we present a rodent maximum likelihood phylogeny inferred from a molecular supermatrix. It is based on 11 mitochondrial and nuclear genes that covers 1,265 species, i.e., respectively 56% and 81% of the known specific and generic rodent diversity. The inferred topology recovered all Rodentia clades proposed by recent molecular works. A relaxed molecular clock dating approach provided a time framework for speciation events. We found that the Myomorpha clade shows a greater degree of variation in diversification rates than Sciuroidea, Caviomorpha, Castorimorpha and Anomaluromorpha. We identified a number of shifts in diversification rates within the major clades: two in Castorimorpha, three in Ctenohystrica, 6 within the squirrel-related clade and 24 in the Myomorpha clade. The majority of these shifts occurred within the most recent familial rodent radiations: the Cricetidae and Muridae clades. Using the topological imbalances and the time line we discuss the potential role of different diversification factors that might have shaped the rodents radiation.

Conclusions

The present glimpse on the diversification pattern of rodents can be used for further comparative meta-analyses. Muroid lineages have a greater degree of variation in their diversification rates than any other rodent group. Different topological signatures suggest distinct diversification processes among rodent lineages. In particular, Muroidea and Sciuroidea display widespread distribution and have undergone evolutionary and adaptive radiation on most of the continents. Our results show that rodents experienced shifts in diversification rate regularly through the Tertiary, but at different periods for each clade. A comparison between the rodent fossil record and our results suggest that extinction led to the loss of diversification signal for most of the Paleogene nodes.

Are ribosomal DNA clusters rearrangement hotspots?: a case study in the genus Mus (Rodentia, Muridae)

Background

Recent advances in comparative genomics have considerably improved our knowledge of the evolution of mammalian karyotype architecture. One of the breakthroughs was the preferential localization of evolutionary breakpoints in regions enriched in repetitive sequences (segmental duplications, telomeres and centromeres). In this context, we investigated the contribution of ribosomal genes to genome reshuffling since they are generally located in pericentromeric or subtelomeric regions, and form repeat clusters on different chromosomes. The target model was the genus Mus which exhibits a high rate of karyotypic change, a large fraction of which involves centromeres.

Results

The chromosomal distribution of rDNA clusters was determined by in situ hybridization of mouse probes in 19 species. Using a molecular-based reference tree, the phylogenetic distribution of clusters within the genus was reconstructed, and the temporal association between rDNA clusters, breakpoints and centromeres was tested by maximum likelihood analyses. Our results highlighted the following features of rDNA cluster dynamics in the genus Mus: i) rDNA clusters showed extensive diversity in number between species and an almost exclusive pericentromeric location, ii) a strong association between rDNA sites and centromeres was retrieved which may be related to their shared constraint of concerted evolution, iii) 24% of the observed breakpoints mapped near an rDNA cluster, and iv) a substantial rate of rDNA cluster change (insertion, deletion) also occurred in the absence of chromosomal rearrangements.

Conclusions

This study on the dynamics of rDNA clusters within the genus Mus has revealed a strong evolutionary relationship between rDNA clusters and centromeres. Both of these genomic structures coincide with breakpoints in the genus Mus, suggesting that the accumulation of a large number of repeats in the centromeric region may contribute to the high level of chromosome repatterning observed in this group. However, the elevated rate of rDNA change observed in the chromosomally invariant clade indicates that the presence of these sequences is insufficient to lead to genome instability. In agreement with recent studies, these results suggest that additional factors such as modifications of the epigenetic state of DNA may be required to trigger evolutionary plasticity.