More than 230,000 known species representing 31 metazoan phyla populate the world’s oceans. Perhaps another 1,000,000 or more species remain to be discovered. There is reason for concern that species extinctions may outpace discovery, especially in diverse and endangered marine habitats such as coral reefs. DNA barcodes (i.e., short DNA sequences for species recognition and discrimination) are useful tools to accelerate species-level analysis of marine biodiversity and to facilitate conservation efforts. This review focuses on the usual barcode region for metazoans: a ∼648 base-pair region of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Barcodes have also been used for population genetic and phylogeographic analysis, identification of prey in gut contents, detection of invasive species, forensics, and seafood safety. More controversially, barcodes have been used to delimit species boundaries, reveal cryptic species, and discover new species. Emerging frontiers are the use of barcodes for rapid and increasingly automated biodiversity assessment by high-throughput sequencing, including environmental barcoding and the use of barcodes to detect species for which formal identification or scientific naming may never be possible.

DNA Barcoding of Marine Metazoa

The evolution of cetaceans, from their early transition to an aquatic lifestyle to their subsequent diversification, has been the subject of numerous studies. However, although the higher-level relationships among cetacean families have been largely settled, several aspects of the systematics within these groups remain unresolved. Problematic clades include the oceanic dolphins (37 spp.), which have experienced a recent rapid radiation, and the beaked whales (22 spp.), which have not been investigated in detail using nuclear loci. The combined application of high-throughput sequencing with techniques that target specific genomic sequences provide a powerful means of rapidly generating large volumes of orthologous sequence data for use in phylogenomic studies. To elucidate the phylogenetic relationships within the Cetacea, we combined sequence capture with Illumina sequencing to generate data for $\sim $3200 protein-coding genes for 68 cetacean species and their close relatives including the pygmy hippopotamus. By combining data from $>$38,000 exons with existing sequences from 11 cetaceans and seven outgroup taxa, we produced the first comprehensive comparative genomic data set for cetaceans, spanning 6,527,596 aligned base pairs (bp) and 89 taxa. Phylogenetic trees reconstructed with maximum likelihood and Bayesian inference of concatenated loci, as well as with coalescence analyses of individual gene trees, produced mostly concordant and well-supported trees. Our results completely resolve the relationships among beaked whales as well as the contentious relationships among oceanic dolphins, especially the problematic subfamily Delphinidae. We carried out Bayesian estimation of species divergence times using MCMCTree and compared our complete data set to a subset of clocklike genes. Analyses using the complete data set consistently showed less variance in divergence times than the reduced data set. In addition, integration of new fossils (e.g., Mystacodon selenensis) indicates that the diversification of Crown Cetacea began before the Late Eocene and the divergence of Crown Delphinidae as early as the Middle Miocene. [Cetaceans; phylogenomics; Delphinidae; Ziphiidae; dolphins; whales.].

/pdf/phylogenomic-resolution-of-the-cetacean-tree-of-life-using-3wjnijxz9e.pdf

Phylogenomic Resolution of the Cetacean Tree of Life Using Target Sequence Capture

Beaked whale echolocation signals are mostly frequency-modulated (FM) upsweep pulses and appear to be species specific. Evolutionary processes of niche separation may have driven differentiation of beaked whale signals used for spatial orientation and foraging. FM pulses of eight species of beaked whales were identified, as well as five distinct pulse types of unknown species, but presumed to be from beaked whales. Current evidence suggests these five distinct but unidentified FM pulse types are also species-specific and are each produced by a separate species. There may be a relationship between adult body length and center frequency with smaller whales producing higher frequency signals. This could be due to anatomical and physiological restraints or it could be an evolutionary adaption for detection of smaller prey for smaller whales with higher resolution using higher frequencies. The disadvantage of higher frequencies is a shorter detection range. Whales echolocating with the highest frequencies, or broadband, likely lower source level signals also use a higher repetition rate, which might compensate for the shorter detection range. Habitat modeling with acoustic detections should give further insights into how niches and prey may have shaped species-specific FM pulse types.

/pdf/species-specific-beaked-whale-echolocation-signals-xjtv91ya6q.pdf

Species-specific beaked whale echolocation signals

At least ten species of beaked whales inhabit the North Pacific, but little is known about their abundance, ecology, and behavior, as they are elusive and difficult to distinguish visually at sea. Six of these species produce known species-specific frequency modulated (FM) echolocation pulses: Baird’s, Blainville’s, Cuvier’s, Deraniyagala’s, Longman’s, and Stejneger’s beaked whales. Additionally, one described FM pulse (BWC) from Cross Seamount, Hawai’i, and three unknown FM pulse types (BW40, BW43, BW70) have been identified from almost 11 cumulative years of autonomous recordings at 24 sites throughout the North Pacific. Most sites had a dominant FM pulse type with other types being either absent or limited. There was not a strong seasonal influence on the occurrence of these signals at any site, but longer time series may reveal smaller, consistent fluctuations. Only the species producing BWC signals, detected throughout the Pacific Islands region, consistently showed a diel cycle with nocturnal foraging. By comparing stranding and sighting information with acoustic findings, we hypothesize that BWC signals are produced by ginkgo-toothed beaked whales. BW43 signal encounters were restricted to Southern California and may be produced by Perrin’s beaked whale, known only from Californian waters. BW70 signals were detected in the southern Gulf of California, which is prime habitat for Pygmy beaked whales. Hubb’s beaked whale may have produced the BW40 signals encountered off central and southern California; however, these signals were also recorded off Pearl and Hermes Reef and Wake Atoll, which are well south of their known range.

/pdf/spatio-temporal-patterns-of-beaked-whale-echolocation-3g4lo34f93.pdf

Spatio-Temporal Patterns of Beaked Whale Echolocation Signals in the North Pacific

Seamounts may influence the distribution of marine mammals through a combination of increased ocean mixing, enhanced local productivity and greater prey availability. To study the effects of seamounts on the presence and acoustic behaviour of cetaceans, we deployed a high-frequency acoustic recording package on the summit of Cross Seamount during April through October 2005. The most frequently detected cetacean vocalizations were echolocation sounds similar to those produced by ziphiid and mesoplodont beaked whales together with buzz-type signals consistent with prey-capture attempts. Beaked whale signals occurred almost entirely at night throughout the six-month deployment. Measurements of prey presence with a Simrad EK-60 fisheries acoustics echo sounder indicate that Cross Seamount may enhance local productivity in near-surface waters. Concentrations of micronekton were aggregated over the seamount in near-surface waters at night, and dense concentrations of nekton were detected across the surface of the summit. Our results suggest that seamounts may provide enhanced foraging opportunities for beaked whales during the night through a combination of increased productivity, vertical migrations by micronekton and local retention of prey. Furthermore, the summit of the seamount may act as a barrier against which whales concentrate prey.

Temporal patterns in the acoustic signals of beaked whales at Cross Seamount.

DNA sequence data enable not only the inference of evolutionary relationships and population histories but also represent a powerful tool for uncovering hidden biodiversity, an approach that has become known as \"DNA taxonomy\" (Dalebout eta/. 2002, Meegasku.mhura.eta/. 2002, Hebert eta/. 2004). The application of DNA taxonomy to beaked whales (Ziphiidae), the least known of all cetacean families, has led to some significant discoveries in recent years. These include the description of a new species from the North Pacific {Mesop/odon perrini; Dalebout et a/. 2002), the

A DIVERGENT mtDNA LINEAGE AMONG MESOPLODON BEAKED WHALES: MOLECULAR EVIDENCE FOR A NEW SPECIES IN THE TROPICAL PACIFIC?

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A DIVERGENT mtDNA LINEAGE AMONG MESOPLODON BEAKED WHALES: MOLECULAR EVIDENCE FOR A NEW SPECIES IN THE TROPICAL PACIFIC?