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Baleen Whale Genomes Point to Evolution With Gene Flow

Blue whale

NEW YORK (GenomeWeb) – Large baleen whales in the Balaenopteridae family (commonly known as rorqual whales) have undergone sympatric speciation — speciation without clear geographic barriers between them — despite ongoing hybridization, according to new research from investigators in Sweden and Germany.

"Speciation under gene flow is rare," co-first author Fritjof Lammers, a researcher affiliated with the Senckenberg Biodiversity and Climate Research Centre, Goethe University Frankfurt, and the LOEWE Centre for Translational Biodiversity Genomics, said in a statement.

"Usually, species are assumed to be reproductively isolated because geographical or genetic barriers inhibits genetic exchange," Lammers explained. "Apparently, however, this does not apply to whales."

In an effort to get a better look at whales' evolutionary history, Lammers and his colleagues used new and available genome sequences for half a dozen baleen whale representatives, including the blue whale (Balaenoptera musculus), humpback whale (Megaptera novaeangliae), and gray whale (Eschrichtius robustus). Based on patterns at nearly 34,200 sequence fragments in the whale genomes, they retraced whale relationships, radiation events, and population histories.

The analyses suggested the gray whale belongs to the rorqual family, for example, and pointed to rapid rorqual radiation events occurring between 7.5 million and 10.5 million years ago. The comparison also highlighted high levels of heterozygosity in the genome of the most massive living animal, the blue whale. The team published its findings online this week in Science Advances.

For their study, the researchers used Illumina instruments to sequence six baleen whales, mapping the reads to an available genome sequence for the bowhead whale, which falls in a distinct whale lineage with the North Atlantic right whale. The newly generated reads covered the bowhead genome to depths ranging from around sixfold to more than twenty-sevenfold.

For comparative purposes, the team did paired-end and mate-pair sequencing on a hippopotamus (H. amphibius) using Illumina HiSeq instruments and genomic DNA extracted from a muscle sample from an animal that died naturally at Copenhagen Zoo. The hippo belongs to a lineage that diverged from the cetacean lineage containing whales and dolphins roughly 54 million years ago. That genome was sequenced to fifty-fivefold coverage, on average.

The researchers tracked down 25 million fixed SNP differences, on average, between the baleen whale genomes and the baleen whale reference sequence. Along with gene flow and population analyses, they used a multi-species coalescent model to tease out rorqual whale speciation patterns based on 34,192 genome fragments.

Based on the data available, the authors concluded that rorqual evolution "appears to be a process of gradual divergences that likely gave rise to three lineages almost simultaneously: (i) blue plus sei whales, (ii) gray whale, and (iii) fin plus humpback whales."

"The early rorqual radiation is therefore best understood as a phylogenetic network because different fragments of the rorqual genomes support three different evolutionary histories," they wrote.