Acoustic differentiation of Shiho- and Naisa-type short-finned pilot whales in the Pacific Ocean

Author Posting. © Acoustical Society of America, 2017. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 114 (2017): 737–748, doi: 10.1121/1.4974858.Divergence in acoustic signals used by different populations of marine mammals can be caused by a variety of environmental, hereditary, or social factors, and can indicate isolation between those populations. Two types of genetically and morphologically distinct short-finned pilot whales, called the Naisa- and Shiho-types when first described off Japan, have been identified in the Pacific Ocean. Acoustic differentiation between these types would support their designation as sub-species or species, and improve the understanding of their distribution in areas where genetic samples are difficult to obtain. Calls from two regions representing the two types were analyzed using 24 recordings from Hawai‘i (Naisa-type) and 12 recordings from the eastern Pacific Ocean (Shiho-type). Calls from the two types were significantly differentiated in median start frequency, frequency range, and duration, and were significantly differentiated in the cumulative distribution of start frequency, frequency range, and duration. Gaussian mixture models were used to classify calls from the two different regions with 74% accuracy, which was significantly greater than chance. The results of these analyses indicate that the two types are acoustically distinct, which supports the hypothesis that the two types may be separate sub-species.Funding for Hawaiian data collection was provided by grants from the Pacific Islands Fisheries Science Center and Office of Naval Research, as well as Commander, Pacific Fleet. The SoundTrap was purchased with funding from the Scripps Institution of Oceanography/National Science Foundation Interdisciplinary Graduate Education in Research Techniques fellowship program. DMON data collection and portions of the analysis were funded by the Office of Naval Research [Grant Nos. N000141110612 (T.A.M. and R.W.B.) and N00014-15-1-2299 (M.A.R.); Program Manager Michael J. Weise], and WHOI Marine Mammal Center and the Sawyer and Penzance Endowed Funds to T.A.M

A collection of best practices for the collection and analysis of bioacoustic data

The field of bioacoustics is rapidly developing and characterized by diverse methodologies, approaches and aims. For instance, bioacoustics encompasses studies on the perception of pure tones in meticulously controlled laboratory settings, documentation of species’ presence and activities using recordings from the field, and analyses of circadian calling patterns in animal choruses. Newcomers to the field are confronted with a vast and fragmented literature, and a lack of accessible reference papers or textbooks. In this paper we contribute towards filling this gap. Instead of a classical list of “dos” and “don’ts”, we review some key papers which, we believe, embody best practices in several bioacoustic subfields. In the first three case studies, we discuss how bioacoustics can help identify the ‘who’, ‘where’ and ‘how many’ of animals within a given ecosystem. Specifically, we review cases in which bioacoustic methods have been applied with success to draw inferences regarding species identification, population structure, and biodiversity. In fourth and fifth case studies, we highlight how structural properties in signal evolution can emerge via ecological constraints or cultural transmission. Finally, in a sixth example, we discuss acoustic methods that have been used to infer predator–prey dynamics in cases where direct observation was not feasible. Across all these examples, we emphasize the importance of appropriate recording parameters and experimental design. We conclude by highlighting common best practices across studies as well as caveats about our own overview. We hope our efforts spur a more general effort in standardizing best practices across the subareas we’ve highlighted in order to increase compatibility among bioacoustic studies and inspire cross-pollination across the discipline.Publisher PDFPeer reviewe

Marine mammal skin microbiotas are influenced by host phylogeny

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Apprill, A., Miller, C. A., Van Cise, A. M., U'Ren, J. M., Leslie, M. S., Weber, L., Baird, R. W., Robbins, J., Landry, S., Bogomolni, A., & Waring, G. Marine mammal skin microbiotas are influenced by host phylogeny. Royal Society Open Science, 7(5), (2020): 192046, doi:10.1098/rsos.192046.Skin-associated microorganisms have been shown to play a role in immune function and disease of humans, but are understudied in marine mammals, a diverse animal group that serve as sentinels of ocean health. We examined the microbiota associated with 75 epidermal samples opportunistically collected from nine species within four marine mammal families, including: Balaenopteridae (sei and fin whales), Phocidae (harbour seal), Physeteridae (sperm whales) and Delphinidae (bottlenose dolphins, pantropical spotted dolphins, rough-toothed dolphins, short-finned pilot whales and melon-headed whales). The skin was sampled from free-ranging animals in Hawai‘i (Pacific Ocean) and off the east coast of the United States (Atlantic Ocean), and the composition of the bacterial community was examined using the sequencing of partial small subunit (SSU) ribosomal RNA genes. Skin microbiotas were significantly different among host species and taxonomic families, and microbial community distance was positively correlated with mitochondrial-based host genetic divergence. The oceanic location could play a role in skin microbiota variation, but skin from species sampled in both locations is necessary to determine this influence. These data suggest that a phylosymbiotic relationship may exist between microbiota and their marine mammal hosts, potentially providing specific health and immune-related functions that contribute to the success of these animals in diverse ocean ecosystems.Funding provided by the Earth Microbiome Project, WHOI Marine Mammal Center, WHOI Ocean Life Institute and WHOI's Andrew W. Mellon Foundation Endowed Fund for Innovative Research to A.A. Hawai‘i sampling was undertaken during field projects funded by grants from ONR (N000141310648 to R.W.B, N000141110612 to T.A. Mooney and N00014101686 to R.D. Andrews) and NMFS (NA13OAR4540212 to R.W.B)

Gene-culture coevolution in a social cetacean: integrating acoustic and genetic data to understand population structure in the short-finned pilot whale (Globicephala macrorhynchus)

The evolutionary ecology of a species is driven by a combination of random events, ecological and environmental mechanisms, and social behavior. Gene-culture coevolutionary theory attempts to understand the evolutionary trajectory of a species by examining the interactions between these potential drivers. Further, our choice of data type will affect the patterns we observe, therefore by integrating several types of data we achieve a holistic understanding of the various aspects of evolutionary ecology within a species.In order to understand population structure in short-finned pilot whales, I use a combination of genetic and acoustic data to examine structure on evolutionary (genetic) and cultural (acoustic) timescales. I first examine structure among geographic populationsin the Pacific Ocean. Using genetic sequences from the mitochondrial control region, I show that two genetically and morphologically distinct types of short-finned pilot whale, described off the coast of Japan, have non-overlapping distributions throughout their rangein the Pacific Ocean. Analysis of the acoustic features of their social calls indicates that they are acoustically differentiated, possibly due to limited communication between the two types. This evidence supports the hypothesis that the two types may be separate species orsubspecies.Next, I examine structure among island communities and social groups within the Hawaiian Island population of short-finned pilot whales. Using a combination of mitochondrial and nuclear DNA, I showed that the hierarchical social structure in Hawaiianpilot whales is driven by genetic relatedness; individuals remain in groups with their immediate family members, and preferentially associate with relatives. Similarly, social structure affects genetic differentiation, likely by restricting access to mates. Acousticdifferentiation among social groups indicates that social structure may also restrict the flow of cultural information, such as vocal repertoire or dialect. The qualitative correlation between social structure, cultural information transfer, and genetic structure suggest that gene-culture coevolution may be an important mechanism to the evolutionary ecology of short-finned pilot whales. Further research may reveal asimilar structure in the transmission of ecological behaviors, such as diet preference, habitat use, or movements. The results of this research underscore the applicability of gene-culture coevolutionary theory to non-human taxa

Gene-culture coevolution in a social cetacean: integrating acoustic and genetic data to understand population structure in the short-finned pilot whale (Globicephala macrorhynchus)

The evolutionary ecology of a species is driven by a combination of random events, ecological and environmental mechanisms, and social behavior. Gene-culture coevolutionary theory attempts to understand the evolutionary trajectory of a species by examining the interactions between these potential drivers. Further, our choice of data type will affect the patterns we observe, therefore by integrating several types of data we achieve a holistic understanding of the various aspects of evolutionary ecology within a species.In order to understand population structure in short-finned pilot whales, I use a combination of genetic and acoustic data to examine structure on evolutionary (genetic) and cultural (acoustic) timescales. I first examine structure among geographic populationsin the Pacific Ocean. Using genetic sequences from the mitochondrial control region, I show that two genetically and morphologically distinct types of short-finned pilot whale, described off the coast of Japan, have non-overlapping distributions throughout their rangein the Pacific Ocean. Analysis of the acoustic features of their social calls indicates that they are acoustically differentiated, possibly due to limited communication between the two types. This evidence supports the hypothesis that the two types may be separate species orsubspecies.Next, I examine structure among island communities and social groups within the Hawaiian Island population of short-finned pilot whales. Using a combination of mitochondrial and nuclear DNA, I showed that the hierarchical social structure in Hawaiianpilot whales is driven by genetic relatedness; individuals remain in groups with their immediate family members, and preferentially associate with relatives. Similarly, social structure affects genetic differentiation, likely by restricting access to mates. Acousticdifferentiation among social groups indicates that social structure may also restrict the flow of cultural information, such as vocal repertoire or dialect. The qualitative correlation between social structure, cultural information transfer, and genetic structure suggest that gene-culture coevolution may be an important mechanism to the evolutionary ecology of short-finned pilot whales. Further research may reveal asimilar structure in the transmission of ecological behaviors, such as diet preference, habitat use, or movements. The results of this research underscore the applicability of gene-culture coevolutionary theory to non-human taxa

Data from: Familial social structure and socially-driven genetic differentiation in Hawaiian short-finned pilot whales

Social structure can have a significant impact on divergence and evolution within species, especially in the marine environment, which has few environmental boundaries to dispersal. On the other hand, genetic structure can affect social structure in many species, through an individual preference toward associating with relatives. One social species, the short-finned pilot whale (Globicephala macrorhynchus), has been shown to live in stable social groups for periods of at least a decade. Using mitochondrial control sequences from 242 individuals and SNPs from 106 individuals, we examine population structure among geographic and social groups of short-finned pilot whales in the Hawaiian Islands, and test for links between social and genetic structure. Our results show that there are at least two geographic populations in the Hawaiian Islands: a Main Hawaiian Islands (MHI) population and a Northwestern Hawaiian Islands/Pelagic population (FST and ΦST P < 0.001), as well as an eastern MHI community and a western MHI community (FST P = 0.009). We find genetically-driven social structure, or high relatedness among social units and clusters (P < 0.001), and a positive relationship between relatedness and association between individuals (P < 0.0001). Further, socially-organized clusters are genetically distinct, indicating that social structure drives genetic divergence within the population, likely through restricted mate selection (FST P = 0.05). This genetic divergence among social groups can make the species less resilient to anthropogenic or ecological disturbance. Conservation of this species therefore depends on understanding links among social structure, genetic structure, and ecological variability within the species

Genomic Methods Take the Plunge: Recent Advances in High-Throughput Sequencing of Marine Mammals

Cammen KM, Andrews KR, Carroll EL, et al. Genomic Methods Take the Plunge: Recent Advances in High-Throughput Sequencing of Marine Mammals. Journal of Heredity. 2016;107(6):481-495

Genomic Methods Take the Plunge: Recent Advances in High-Throughput Sequencing of Marine Mammals

The dramatic increase in the application of genomic techniques to non-model organisms (NMOs) over the past decade has yielded numerous valuable contributions to evolutionary biology and ecology, many of which would not have been possible with traditional genetic markers. We review this recent progression with a particular focus on genomic studies of marine mammals, a group of taxa that represent key macroevolutionary transitions from terrestrial to marine environments and for which available genomic resources have recently undergone notable rapid growth. Genomic studies of NMOs utilize an expanding range of approaches, including whole genome sequencing, restriction site-associated DNA sequencing, array-based sequencing of single nucleotide polymorphisms and target sequence probes (e.g., exomes), and transcriptome sequencing. These approaches generate different types and quantities of data, and many can be applied with limited or no prior genomic resources, thus overcoming one traditional limitation of research on NMOs. Within marine mammals, such studies have thus far yielded significant contributions to the fields of phylogenomics and comparative genomics, as well as enabled investigations of fitness, demography, and population structure. Here we review the primary options for generating genomic data, introduce several emerging techniques, and discuss the suitability of each approach for different applications in the study of NMOs