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The field of phylogenetics is entering a new era in which trees of historical relationships
between species are increasingly inferred from multilocus and genomic data. A major
challenge for incorporating such large amounts of data into inference of species trees
is that conflicting genealogical histories often exist in different genes throughout
the genome. Recent advances in genealogical modeling suggest that resolving close
species relationships is not quite as simple as applying more data to the problem.
Here we discuss the complexities of genealogical discordance and review the issues
that new methods for multilocus species tree inference will need to address to account
successfully for naturally occurring genomic variability in evolutionary histories.