Haploid chromosomes

When discussing the inheritance of nuclear and organelle markers we usually refer to nuclear genes as being inherited biparentally following sexual reproduction. For the most part this is true, but sex chromosomes (chromosomes that have a role in the determination of sex) provide an exception to this rule. Not all species have sex chromosomes, for example crocodiles and many turtles and lizards follow environmental sex determination, which means that the sex of an individual is determined by the temperature that it is exposed to during early development. Many other species follow genetic sex determination, which occurs when an individual's sex is determined genetically by sex chromosomes. This can happen in a number of different ways. In most mammals, and some dioecious plants, females are homogametic ( two copies of the same sex chromosome: XX), whereas males are heterogametic (one copy of each sex chromosome: XY). The opposite is true in birds and lepidopterans, which have heterogametic females (ZW) and homo-gametic males (ZZ). In some other species such as the nematode Caenorhabditis elegans, the heterogametic (male) sex is XO, meaning that it has only a single X chromosome. Monoecious plant species typically lack discrete sex chromosomes.

In mammals, each female gives one of her X chromosomes to all of her children, male and female alike. It is the male parent's contribution that determines the sex of the offspring; if he donates an X chromosome it will be female, and if he donates a Y chromosome then the offspring will be male. The Y chromosome therefore follows a pattern of patrilineal descent because it is passed down only through the male lineage, from father to son (Table 2.1). Because there is never more than

Table 2.1 Usual mode of inheritance of different genomic regions in sexually reproducing taxa

Genomic region

Typical mode of inheritance


Autosomal chromosomes Mitochondrial DNA

Y chromosome Higher plant

Autosomal chromosomes Mitochondrial DNA

Plastid DNA (including chloroplast DNA)

Y chromosome


Maternal in most animals Biparental in some bivalves Paternal


Usually maternal

Maternal in most angiosperms

Paternal in most gymnosperms

Biparental in some plants

Paternal in some dioecious plants one copy of a Y chromosome in the same individual (barring genetic abnormalities), Y chromosomes are the only mammalian chromosomes that are effectively haploid. In addition, like mtDNA, Y chromosomes for the most part do not undergo recombination. There are two small pseudo-autosomal regions at the tips of the chromosome that recombine with the X chromosome, but in between these are approximately 60 Mb of non-recombining sequence (Figure 2.3).

The mutation rate of Y chromosomes is relatively low. One study found that the variability of three genes on the Y chromosome was approximately five times lower p arm p arm

Pseudo-autosomal region

SRY gene

Pseudo-autosomal region

SRY gene qarm

Pseudo-autosomal region

Figure 2.3 Mammalian Y chromosome. The SRY gene (sex-determining region Y) effectively converts an embryo into a male than that of the corresponding regions of autosomal genes (Shen et al., 2000). Reasons for this remain unclear, although it may be due in part to its smaller population size: the total number of Y chromosomes in any given species is a quarter of that for autosomes and a third of that for X chromosomes. This may seem initially confusing because the population size of mtDNA and Y chromosomes is essentially the same and yet mtDNA is relatively variable; however, Y chromosomes have the same repair processes that are found in other regions of nuclear DNA but are lacking in mtDNA. Despite relatively low levels of variability, the Y chromosome still has the potential to be a significant source of information because it is much larger than mtDNA and, unlike mitochondria, contains substantial amounts of non-coding DNA.

One important property of Y chromosomes is that they allow biologists to follow the transmission of paternal genotypes in animals in much the same way that chloroplast markers can be used for gymnosperms. A recent study (Zerjal et al., 2003) found that a particular Y chromosome haplotype is abundant in human populations in a large area of Asia, from the Pacific to the Caspian Sea. Approximately 8 per cent of the men in this region carry it and, because of the high population density in this part of the world, this translates into approximately 0.5 per cent of the world's total population. The researchers who conducted this study suggested that this prevalent Y chromosome haplotype can be traced back to the infamous warrior Genghis Khan. Born in the 12th century, Khan created the biggest land-based empire that the world has seen (Genghis Khan means supreme ruler). He had a vast number of descendants, many of whom were fathered following his conquests, and apparently his sons were also extremely prolific. His policy of slaughtering millions of people and then reproducing en masse is one possible explanation for the widespread occurrence of a single Y chromosome haplotype in Asia today.

Identifying hybrids

It should be apparent from the examples in the previous section that there is often an advantage to using multiple molecular markers that have contrasting modes of inheritance. These potential benefits are further illustrated by studies of hybridization. Hybrids can be identified from their genotypes because hybridization results in introgression, the flow of alleles from one species (or population) to another. As a result, hybrids typically contain a mixture of alleles from both parental species, for example a comparison of grass species in the genus Miscanthus revealed that M. giganteus was a hybrid of M. sinensis and M. sacchariflorus because it had one ITS allele from each parental species and a plastid sequence that identified the maternal lineage as M. sacchariflorus (Hodkinson et al., 2002). Identification of hybrids in the wild is often based on cytonuclear disequilibrium, which occurs in hybrids that have cytoplasmic markers (another name for mitochondria and chloroplasts) from one species or population and nuclear markers from another. Some examples of cytonuclear disequilibrium are given in Table 2.2. By using a combination of markers that have maternal, paternal or biparental inheritance, we may be able to identify which species -- or even which population -- the hybrid's mother and father came from.

Table 2.2 Some examples of cytonuclear disequilibrium in hybrids


Nuclear DNA

mtDNA or cpDNA


Freshwater crustaceans

D. pulicaria

D. pulex

Crease et al. (1997)

Daphnia pulex x D. pulicaria

Grey wolf (Canis lupus) x



Lehman et al. (1991)

coyote (C. latrans)

House mice Mus musculus x

M. musculus

M. domesticus

Gyllensten and Wilson

M. domesticus


Northern red-backed vole

Bank vole


Tegelstrom (1987)

(Clethrionomys rutilus) x


bank vole (C. glareolus)


White poplar (Populus alba) x

Black poplar

White poplar

Smith and Sytsma

black poplar (P. nigra)


Researchers used multiple markers to determine whether or not members of the declining wolf (Canis lupus) populations in Europe have been hybridizing with domestic dogs (C. familiaris), a question that has been open to debate for some time. One study that used mitochondrial markers to investigate this possibility found only a few instances of haplotype sharing between wolves and dogs and therefore concluded that hybridization between dogs and declining wolf populations was not a cause for concern (Randi et al. 2000). However, because mtDNA is inherited maternally, dog haplotypes would appear in wolf populations only if hybridization occurred between female dogs and male wolves. In a more recent study, researchers used a combination of markers from mtDNA, Y chromosome and autosomal nuclear DNA to conduct a more detailed assessment of a possible wolf--dog hybrid from Norway. The mitochondrial haplotype in this suspected hybrid came from a Scandinavian wolf. The Y chromosome data suggested that the father of the hybrid was not a Scandinavian wolf, but did not provide enough information for researchers to discriminate between dogs or migrant wolves from Finland or Russia. However, data from autosomal chromosomes suggested that the most likely father was a dog. It was therefore the combination of uniparental and biparental markers that identified this specimen as a hybrid that had resulted from a cross between a female Scandinavian wolf and a male dog (Vila et al., 2003b).

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