Chromosomal and molecular divergence in the Indian pygmy field mice Mus booduga-terricolor lineage of the subgenus Mus

C-value paradox: Genesis in misconception that natural selection follows anthropocentric parameters of 'economy' and 'optimum'

C-value paradox refers to the lack of correlation between biological complexity and the intuitively expected protein-coding genomic information or DNA content. Here I discuss five questions about this paradox: i) Do biologically complex organisms carry more protein-coding genes? ii) Does variable accumulation of selfish/ junk/ parasitic DNA underlie the c-value paradox? iii) Can nucleoskeletal or nucleotypic function of DNA explain the enigma of orders of magnitude high levels of DNA in some 'lower' taxa or in taxonomically related species? iv) Can the newly understood noncoding but functional DNA explain the c-value paradox? and, v) Does natural selection uniformly apply the anthropocentric parameters for 'optimum' and 'economy'? Answers to Q.1-5 are largely negative. Biology presents numerous 'anomalous' examples where the same end function/ phenotype is attained in different organisms through astoundingly diverse ways that appear 'illogical' in our perceptions. Such evolutionary oddities exist because natural selection, unlike a designer, exploits random and stochastic events to modulate the existing system. Consequently, persistence of the new-found 'solution/s' often appear bizarre, uneconomic, and therefore, paradoxical to human logic. The unexpectedly high c-values in diverse organisms are irreversible evolutionary accidents that persisted, and the additional DNA often got repurposed over the evolutionary time scale. Therefore, the c-value paradox is a redundant issue. Future integrative biological studies should address evolutionary mechanisms and processes underlying sporadic DNA expansions/ contractions, and how the newly acquired DNA content has been repurposed in diverse groups.

Phylogenetic relationship and time of divergence of Mus terricolor with reference to other Mus species

Mitochondrial DNA control region of Mus terricolor, three aboriginal species M. spretus, M. macedonicus, M. spicilegus; the Asian lineage M. caroli, M. cervicolor, M. cookii; and the two house mice, M. musculus domesticus and M. m. castaneus were analysed to estimate the substitution rate, phylogenetic relationship and the probable time of divergence. Results showed that M. spretus, M. caroli and M. terricolor are highly diverged from each other (caroli/terricolor = 0.146, caroli/spretus = 0.147 and terricolor/spretus = 0.122), whereas M. spretus showed less divergence with two house mice species (0.070 and 0.071). Sequence divergence between M. terricolor and the Palearctic group were found to be ranging from 0.121 to 0.134. Phylogenetic analysis by minimum evolution, neighbour-joining, unweighed pair group method with arithmetic mean and maximum parsimony showed almost similar topology. Two major clusters were found, one included the Asian lineage, M. caroli, M. cookii and M. cervicolor and the other included the house mice M. m. domesticus, M. m. castaneus and the aboriginal mice M. macedonicus and M. spicilegus along with M. spretus, forming the Palearctic clade. M. terricolor was positioned between the Palearctic and Asian clades. Results showed that Palearctic-terricolor and the Asian lineages diverged 5.47 million years ago (Mya), while M. terricolor had split around 4.63 Mya from their ancestor. M. cervicolor, M. cookii and M. caroli diverged between 4.70 and 3.36 Mya, which indicates that M. terricolor and the Asian lineages evolved simultaneously. M. spretus is expected to have diverged nearly 2.9 Mya from their most recent common ancestor.

Heterochromatin variation among the populations of Mus terricolor Blyth, 1851 (Rodentia, Muridae) chromosome type I

Twenty five to thirty specimens each from ten populations of Mus terricolor of the Terai and the Dooars regions of the Darjeeling foothills of West Bengal were cytogenetically analyzed using C-banding. Results showed intra- and inter- population variation of C-band positive heterochromatin ranging from very large blocks to minute amounts or even complete absence of heterochromatin. Large blocks of centromeric C-bands were found in Bidhan Nagar, Garidhura, Malbazar, Nagrakata and Maynaguri populations in most of the autosomes, while the rest of the populations had large blocks of C-bands on a few autosomes only. Such intra- and inter- population variation may be due to accumulation of C-positive heterochromatin, which has not got fixed homogeneously in all autosome pairs. X-chromosomes invariably possess a C-banded short arm a telomeric C-band at the distal end of the long arm in all populations. The entire Y-chromosome was C-band positive with slight population differences in staining intensity. The results suggest quantitative as well as qualitative variation of C-positive heterochromatin.

Burrow characteristics of the co-existing sibling species Mus booduga and Mus terricolor and the genetic basis of adaptation to hypoxic/hypercapnic stress

BACKGROUND

The co-existing, sibling species Mus booduga and Mus terricolor show a difference in site-preference for burrows. The former build them in flat portion of the fields while the latter make burrows in earthen mounds raised for holding water in cultivated fields. In northern India which experiences great variation in climatic condition between summer and winter, M. booduga burrows have an average depth of 41 cm, as against 30 cm in southern India with less climatic fluctuation.M. terricolor burrows are about 20 cm deep everywhere. The three chromosomal species M. terricolor I, II and III have identical burrows, including location of the nest which is situated at the highest position. In contrast, in M. booduga burrows, the nest is at the lowest position.

RESULTS

The nest chamber of M. booduga is located at greater depth than the nest chamber of M. terricolor. Also, in the burrows of M. booduga the exchange of air takes place only from one side (top surface) in contrast to the burrows of M. terricolor where air exchange is through three sides. Hence, M. booduga lives in relatively more hypoxic and hypercapnic conditions than M. terricolor.We observed the fixation of alternative alleles in M. booduga and M. terricolor at Superoxide dismutase-1 (Sod-1), Transferrin (Trf) and Hemoglobin beta chain (Hbb) loci. All the three are directly or indirectly dependent on oxygen concentration for function. In addition to these, there are differences in burrow patterns and site-preference for burrows suggesting difference in probable adaptive strategy in these co-existing sibling species.

CONCLUSION

The burrow structure and depth of nest of the chromosomal species M. terricolor I, II and III are same everywhere probably due to the recency of their evolutionary divergence. Moreover, there is lack of competition for the well-adapted 'microhabitats' since they are non-overlapping in distribution. However, the co-existing sibling species M. booduga and M. terricolor exhibit mutual "exclusion" of the 'microhabitats' for burrow construction. Thus, location, structure and depth of the burrows might have been the contributory factors for selection of alternative alleles at three loci Sod-1, Trf and Hbb, which reflect difference in probable adaptive strategy in M. booduga and M. terricolor.

Temporal, spatial, and ecological modes of evolution of Eurasian Mus based on mitochondrial and nuclear gene sequences

We sequenced mitochondrial (cytochrome b, 12S rRNA) and nuclear (IRBP, RAG1) genes for 17 species of the Old World murine genus Mus, drawn primarily from the Eurasian subgenus Mus. Phylogenetic analysis of the newly and previously available sequences support recognition of four subgenera within Mus (Mus, Coelomys, Nannomys, and Pyromys), with an unresolved basal polytomy. Our data further indicate that the subgenus Mus contains three distinct 'species groups': (1) a Mus booduga Species Group, also including Mus terricolor and Mus fragilicauda (probably also Mus famulus); (2) a Mus cervicolor Species Group, also including Mus caroli and Mus cookii; and (3) a Mus musculus Species Group, also including Mus macedonicus, Mus spicilegus, and Mus spretus. Species diversity in Eurasian Mus is probably explicable in terms of several phases of range expansion and vicariance, and by a propensity within the group to undergo biotope transitions. IRBP and RAG1 molecular clocks for Mus date the origin of subgenera to around 5-6 mya and the origin of Species Groups within subgenus Mus to around 2-3 mya. The temporal pattern of evolution among Eurasian Mus is more complex than that within the Eurasian temperate genus Apodemus.

Reduced meiotic fitness in hybrids with heterozygosity for heterochromatin in the speciating Mus terricolor complex

Mus terricolor I, II and III are the three chromosomal species which differ in stable autosomal short-arm heterochromatin variations established in homozygous condition. Analysis of meiosis in the laboratory-generated F1 male hybrids from crosses (both ways) between M. terricolor I and II and between M. terricolor I and III shows high frequencies of pairing abnormalities at pachytene. The backcross (N3 generation) male hybrids between M. terricolor I and II have meiotic abnormalities as in the F1 male hybrids, though to a lesser extent. They show difference in pairing abnormalities in the different karyotypic forms; the backcross hybrids heterozygous for the heterochromatic short arms have more anomalies compared to the homokaryotypic hybrids. This suggests a negative influence of the heterochromatin heterozygosity in meiotic pairing. The results indicate a role for heterochromatin variations in the development of a reproductive barrier in the speciating M. terricolor complex.

Wild mice: an ever-increasing contribution to a popular mammalian model

Classical laboratory inbred strains of mice have been extremely helpful for research in immunology and oncology, and more generally, for the analysis of complex traits. Unfortunately, because they all derive from a relatively small pool of ancestors, their genetic polymorphism is rather limited. However, recently strains belonging to different species of Mus have been established from wild progenitors. These are an interesting addition to the arsenal of mouse geneticists, because they can be crossed with classical laboratory strains to produce viable and fertile offspring with a large number of polymorphisms of natural origin. These strains are helpful for making genome annotations because they permit highly refined genotype-phenotype correlations. They also allow the interpretation of molecular variation within a clear evolutionary framework. In this article, we provide examples with the aim of promoting the use of these new strains.

Sequential meiotic prophase development in the pubertal Indian pygmy field mouse: synaptic progression of the XY chromosomes, autosomal heterochromatin, and pericentric inversions

Sequential meiotic prophase development has been followed in the pubertal male pygmy mouse Mus terricolor, with the objective to identify early meiotic prophase stages. The pygmy mouse differs from the common mouse by having large heterochromatic blocks in the X and Y chromosomes. These mice also show various chromosomal mutations; for example, fixed variations of autosomal short arms heterochromatin among different chromosomal species and pericentric inversion polymorphism. Identification of prophase stages was crucial to analyzing effects of heterozygosity for these chromosomal changes on the process of homologous synapsis. Here we describe identification of the prophase stages in M. terricolor, especially the pachytene substages, on the basis of morphology of the XY bivalent. Based on this substaging, we show delayed pairing of the heterochromatic short arms, which may be the reason for their lack of chiasmata. The identification of precise pachytene substages also reveals an early occurrence of "synaptic adjustment" in the pericentric inversion heterobivalents, a mechanism that would prevent chiasma formation in the inverted segment and thereby would abate adverse effects of such heterozygosity. The identification of pachytene substages would serve as the basis to analyze the nature of synaptic anomalies met in M. terricolor hybrids (which will be the basis of a subsequent paper).