242 CHAPTER 9of mating behavior showed that partial sexual isolation has evolved in at least one
of these species [34]. The level of genetic differentiation between the populations
on white sands compared with those on normal soils is lowest in the whiptail liz-
ard (Aspidoscelis inornata), the species that is most active and shows the highest
level of gene flow among populations.The Genomics of Speciation
As in all other fields in biology, the genomics revolution has opened up new per-
spectives on speciation. Genomics can help us determine the number, identities,
and genomic locations of speciation genes, the loci that contributed to the evolu-
tion of reproductive isolation [64, 65].
When two populations or species are partly isolated but continue to hybrid-
ize, alleles introgress between them. The introgression, however, is expected to be
uneven across the genome. In parts of the genome that are evolving neutrally, gene
flow between the populations will tend to make them more similar. In addition, if
a mutation appears in one species that is beneficial to both species, it will sweep
though both and homogenize that region of the genome between the species. Ear-
lier in this chapter, we saw that genes for warning colors in Heliconius butterflies
have spread among species this way (see Figure 9.5) [35].
A contrasting picture is expected in genomic regions that carry loci that isolate
hybridizing species. Those regions, sometimes called “genomic islands of specia-
tion,” are expected to show greater genetic divergence than the rest of the genome.
The group of mosquitoes that transmit malaria in Africa (genus Anopheles) includes
six species that diverged recently and that continue to hybridize [26]. Comparisons
of the genomes reveal some regions (particularly inversions) that are similar in
some species pairs because they have introgressed following hybridization, like
the color pattern genes in Heliconius butterflies. But other regions of the Anopheles
genome show unusually high divergence among species—the signature of specia-
tion genes. In particular, the X chromosome is more genetically different than the
autosomes. It has deep gene trees (see Chapter 7), which strongly suggests that
genes on the X chromosome were among the first to contribute to reproductive
isolation during the speciation process (see Figure 16.11). That pattern is consistent
with the observation that sex chromosomes often play a disproportionately large
role in the evolution of reproductive isolation [15].
Genomic islands of speciation might provide evidence about the geography of
speciation, but this is still uncertain. Genomic islands are predicted to develop
during speciation with gene flow. They will also appear when two populations that
speciated in allopatry come back into contact and then hybridize [19]. Allopatric
populations will show different genomic “islands” at sites where divergent natural
selection fixed different alleles that may or may not make a potential contribu-
tion to reproductive isolation. If these populations expand and hybridize, divergent
selection will maintain the adaptive differences between the hybridizing popu-
lations, while neutral regions introgress and become homogenized between the
populations. Distinguishing speciation with gene flow from secondary contact
presents the same difficulty as determining whether sympatric species originated
sympatrically or became sympatric by secondary contact after speciation happened
allopatrically. Deciding between those possibilities requires additional evidence.
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