**1. Introduction**

Minke whales are members of the Order Cetacea. They are the smallest species within the suborder Mysticeti (baleen whales), usually not exceeding the 10 m in body length. They are characterized by a sharply pointed head that looks V-shaped when see from above, and they present a sharp longitudinal ridge that runs along the top of the rostrum [1]. Minke whales are the most abundant of the baleen whales and they are hunted in limited numbers by some countries for commercial (Japan and Norway) or aboriginal subsistence (Greenland) purposes.

Until relatively recently, only one species of minke whale was thought to exist: *Balaenoptera acutorostrata*. This even though historical morphological [2–6] and genetics [7–9] data collected from extant populations pointed out to substantial differentiation within the minke whales.

#### **Figure 1.**

*External morphology of minke whales. From top to bottom: Antarctic minke whale, North Pacific common minke whale, North Atlantic common minke whale and Southern Hemisphere common minke whale (dwarf minke whale).*

*Phylogeny and Population Genetic Structure of Minke Whales Worldwide: A Review of Recent… DOI: http://dx.doi.org/10.5772/intechopen.102675*

In 1998, based on a review of both morphological and genetic data, two species of minke whales were recognized, the Antarctic minke whale (*Balaenoptera bonaerensis*), which is restricted to the Southern Hemisphere, and the cosmopolitan common minke whale (*B. acutorostrata*) [10]. Furthermore, three sub-species of the common minke whale were recognized, North Atlantic (*B. a. acutorostrata*), North Pacific (*B. a. scammoni*) and Southern Hemisphere (*B. a. subsp*.) [10]. The common minke whale in the Southern Hemisphere is commonly referred to as the 'dwarf' minke whale [6]. **Figure 1** shows the external morphology of minke whale species and sub-species. As seen in **Figure 1**, the main external morphological character that most readily distinguished the two species is a white flipper patch that is only present in the common minke whale.

Several genetic studies of minke whales have been conducted since the 1998 review. Some studies have focused on phylogenetic issues while others have focused on elucidating population genetic structure in each oceanic basin. This chapter aims to provide a short review of recent genetic studies, outlining the main new findings and implications. After introducing the genetic markers in Section 2, in Section 3, we review the studies that focus primarily on phylogeny and other matters that are relevant to taxonomy and then, in Section 4, we concentrate on the studies on the population genetic structure of each species and sub-species by oceanic basin (Southern Hemisphere, North Atlantic and North Pacific).

Both information on taxonomy and population identification and structure of minke whales are important and necessary for effective decision-making about conservation and sustainable use of the species.

### **2. Genetic markers**

Two main genetic markers have been used in recent genetic analyses of minke whales, mitochondrial DNA (mtDNA) control region sequences and microsatellite DNA (msDNA, a nuclear marker) genotypes, which are briefly explained here based on [11].

The mitochondrial genome is a circular, double-stranded molecule ranging in size from 16,500 to 17,600 base-pairs (bp) in cetaceans. The main features of mtDNA are (a) maternal inheritance, (b) no recombination during reproduction and (c) it is haploid. Features (a) and (c) mean that the effective population size for the mtDNA genome is ¼ of that for nuclear markers. Sequence changes in animal mitochondrial genomes are of four types: sequence arrangements; additions; deletions; and nucleotide substitutions. The substitution rate is not constant across the mitochondrial genome. The most variable part is where replication begins (the 'control region'). The control region is the only major non-coding region in the mitochondrial genome. In whales, its length is approximately 1000 bp. In most studies on minke whales, the sequence of the first 300-500 bp in the control region is determined, which is the most variable part.

MsDNA or simple tandem repeats (STRs) are segments of non-coding nuclear DNA containing a varying number (different alleles) of tandem repeats of short sequences of less than six nucleotides. As a nuclear marker, they are diploid with recombination during reproduction. They are abundant and widely distributed throughout the mammalian genome. MsDNA is highly variable, presenting a large number of alleles at each locus, selectively neutral, inherited in standard Mendelian fashion and allelically codominant. MsDNA generally evolves by changes in the number of repeats, i.e., in the length of the repetitive region. MsDNA alleles can be distinguished by differences in the length of the repetitive region. They predominantly

mutate by insertion or deletion of repeats. In most studies on minke whales, a set of approximately 12–16 msDNA loci are used.

Most of the recent genetic studies on minke whales have made combined use of these two genetic markers, which presents several advantages. Some of the genetic criteria for taxonomic definition require results of both markers (see below). Different species of large whales can produce hybrid whales and such cases can be detected by the combined use of mtDNA and msDNA. In studies on population identification and structure, parallel analyses of Mendelian and maternally inherited loci are particularly important. Some species may display maternally directed phylopatry. In such cases, genetic differences can be found for the mtDNA but not for msDNA. The use of msDNA in addition to mtDNA allows for an investigation of kinship, which is important information for the interpretation of population structure.

Details of laboratory procedures for mtDNA and msDNA in minke whales can be found in [12].
