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

A comparison of Northeast Atlantic killer whale (Orcinus orca) stereotyped call repertoires

Funding for data collection was provided by the BBC Natural History Unit, Fundação para a Ciência e a Tecnologia (grant number SFRH/BD/30303/2006), the Icelandic Research Fund (i. Rannsóknasjóður) through a START Postdoctoral Fellowship (grant number 120248042) and a Project Grant (grant number 163060‐051), the National Geographic Global Exploration Fund (grant number GEFNE65‐12), a Marie Curie International Incoming Fellowship (project number 297116), the Office of Naval Research (grant number N00014‐08‐1‐0984), and a Russell Trust Award from the University of St. Andrews.Killer whale call repertoires can provide information on social connections among groups and populations. Killer whales in Iceland and Norway exhibit similar ecology and behavior, are genetically related, and are presumed to have been in contact before the collapse of the Atlanto-Scandian herring stock in the 1960s. However, photo-identification suggests no recent movements between Iceland and Norway but regular movement between Iceland and Shetland. Acoustic recordings collected between 2005 and 2016 in Iceland, Norway, and Shetland were used to undertake a comprehensive comparison of call repertoires of Northeast Atlantic killer whales. Measurements of time and frequency parameters of calls from Iceland (n = 4,037) and Norway (n = 1,715) largely overlapped in distribution, and a discriminant function analysis had low correct classification rate. No call type matches were confirmed between Iceland and Norway or Shetland and Norway. Three call types matched between Iceland and Shetland. Therefore, this study suggests overall similarities in time and frequency parameters but some divergence in call type repertoires. This argues against presumed past contact between Icelandic and Norwegian killer whales and suggests that they may not have been one completely mixed population.PostprintPeer 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)

Oceanographic barriers, divergence, and admixture : phylogeography and taxonomy of two putative subspecies of short-finned pilot whale

Funding:Commander, U.S. Pacific Fleet Environmental Readiness Division and NMFS Pacific Islands Fisheries Science Center; NMFS West Coast Region; Scripps Institution of Oceanography Edna Bailey Sussman Research Fellowship; and Woods Hole Oceanographic Institution.Genomic phylogeography plays an important role in describing evolutionary processes and their geographic, ecological, or cultural drivers. These drivers are often poorly understood in marine environments, which have fewer obvious barriers to mixing than terrestrial environments. Taxonomic uncertainty of some taxa (e.g., cetaceans), due to the difficulty in obtaining morphological data, can hamper our understanding of these processes. One such taxon, the short‐finned pilot whale, is recognized as a single global species but includes at least two distinct morphological forms described from stranding and drive hunting in Japan, the “Naisa” and “Shiho” forms. Using samples (n = 735) collected throughout their global range, we examine phylogeographic patterns of divergence by comparing mitogenomes and nuclear SNP loci. Our results suggest three types within the species: an Atlantic Ocean type, a western/central Pacific and Indian Ocean (Naisa) type, and an eastern Pacific Ocean and northern Japan (Shiho) type. mtDNA control region differentiation indicates these three types form two subspecies, separated by the East Pacific Barrier: Shiho short‐finned pilot whale, in the eastern Pacific Ocean and northern Japan, and Naisa short‐finned pilot whale, throughout the remainder of the species' distribution. Our data further indicate two diverging populations within the Naisa subspecies, in the Atlantic Ocean and western/central Pacific and Indian Oceans, separated by the Benguela Barrier off South Africa. This study reveals a process of divergence and speciation within a globally‐distributed, mobile marine predator, and indicates the importance of the East Pacific Barrier to this evolutionary process.PostprintPeer reviewe

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

Protocol for the Cultural Translation and Adaptation of the World Endometriosis Research Foundation Endometriosis Phenome and Biobanking Harmonization Project Endometriosis Participant Questionnaire (EPHect)

Endometriosis affects 10% of women worldwide and is one of the most common causes of chronic pelvic pain and infertility. However, causal mechanisms of this disease remain unknown due to its heterogeneous presentation. In order to successfully study its phenotypic variation, large sample sizes are needed. Pooling of data across sites is not always feasible given the large variation in the complexity and quality of the data collected. The World Endometriosis Research Foundation (WERF) Endometriosis Phenome and Biobanking Harmonization Project (EPHect) have developed an endometriosis participant questionnaire (EPQ) to harmonize non-surgical clinical participant characteristic data relevant to endometriosis research, allowing for large-scale collaborations in English-speaking populations. Although the WERF EPHect EPQs have been translated into different languages, no study has examined the cross-cultural translation and adaptation for content and face validity. In order to investigate this, we followed the standard guidelines for cross-cultural adaptation and translation of the minimum version of the EPQ (EPQ-M) using 40 patients who underwent laparoscopic surgery in Turkey and 40 women in Northern Cyprus, aged between 18 and 55. We assessed the consistency by using cognitive testing and found the EPHect EPQ-M to be comprehensive, informative, and feasible in these two Turkish-speaking populations. The translated and adapted questionnaire was found to be epidemiologically robust, taking around 30–60 min to complete; furthermore, participants reported a similar understanding of the questions, showing that common perspectives were explored. Results from the cognitive testing process led to minor additions to some items such as further descriptive and/or visuals in order to clarify medical terminology. This paper illustrates the first successful cross-cultural translation and adaptation of the EPHect EPQ-M and should act as a tool to allow for further studies that wish to use this questionnaire in different languages. Standardized tools like this should be adopted by researchers worldwide to facilitate collaboration and aid in the design and conduction of global studies to ultimately help those affected by endometriosis and its associated symptoms

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

Ttru reference sequence: Reference sequence for nuclear genome assembly from Tursiops truncatus. SNP genotypes: Location and variation data for nuclear SNPs used in this study