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Mesoplodon eueu sp. nov. Holotype NMNZ MM003000, a pregnant, 5.06 m long adult female named Nihongore by Te Rūnanga o Makaawhio. Collected by Ramari Stewart, Nathaniel Scott and Don Neale after beachcast on 27 November 2011. The complete skeletons of the female and fetus are held by Museum of New Zealand Te Papa Tongarewa (NMNZ, Wellington, Aotearoa New Zealand; specimen MM003000), and a tissue sample is held in the New Zealand Cetacean Tissue Archive (NZCeTA, Universityof Auckland, Auckland, Aotearoa New Zealand; all institutional abbreviations in electronic supplementary material, S1). Type locality Waiatoto Spit, South Westland, Aotearoa New Zealand. Paratypes Adult females (PEM N0136 and PEM N3438) and adult male (PEM N1114) held at Port Elizabeth Museum (Gqeberha, South Africa) and adult males (SAM-ZM-041596 and SAM- ZM-039840) held at Iziko South African Museum (Cape Town, South Africa). Full description of paratypes is found in electronic supplementary material S2. Etymology The scientific and common names acknowledge links with Indigenous communities in South Africa and Aotearoa New Zealand, respectively, and were chosen in consultation with these peoples. Most of the South African strandings come from territory inhabited by the Khoisan peoples. Guided by the Khoisan Council, we chose the name //eu//’eu (simplified to eueu to fit nomenclature standards; correct pronunciation available in associated audio clip a 1 in the electronic supplementary material), which means ‘big fish’ in Khwedam (from the Khoe language family). In Aotearoa New Zealand, Māori cultural expert Brad Haami developed a shortlist of potential names meaningful in the Māori language, whichwasthen sent for comment to Te Rūnanga o Ngāi Tahu. The selected common name, Ramari’ s beaked whale, pays homage to Māoritohunga (expert) Ramari Stewart, who has kept traditional knowledge alive, contributed extensively to scientific research on marine mammals, and helped prepare the skeleton of the holotype. The word ‘Ramari’ means a rare event in the Māori language, reflecting the elusive nature of most beaked whales. Diagnosis Molecular characteristics M. eueu differs from M. mirus based on nuclear DNA markers, and from M. mirus and its closest relatives M. europaeus, M. ginkgodens and M. bidens using mtDNA markers (figure 2). M. mirus is distinct from all other mesoplodont species based on previous mitochondrial and nuclear DNA trees [7,20,24]. Mitochondrial DNA: analysis of mitochondrial data includes sequences from the holotypes of both M. mirus and M. eueu at all sequence lengths. Over the 304 bp mitochondrial control region segment, M. eueu is distinguished by seven fixed differences from M. mirus, with F ST = 0.85 (p dA = 0.04 between the two species. At the full mitochondrial genome lengths, M. eueu is distinguished by 579 fixed differences from M. mirus with F ST = 0.96 (p dA = 0.04 (electronic supplementary material, table S2). Nuclear DNA: reduced representation sequencing with ddRAD showed M. eueu had a distinct admixture pattern to M. mirus (figure 2), and an F ST = 0.64 (p M. mirus and M. eueu weredistinguished by 1909 fixed differences (12%, per SNP allele error rate = 0.002), across a dataset of 15671 SNPs found between or within both species. Comparison of one whole nuclear genome each from M. mirus and M. eueu showed a level of nucleotide divergence of 0.28%. Morphological characters M. eueu is a larger (5.3 m) species of Mesoplodon differing from all other members of the genus except M. mirus, M. hectori and M. perrini in having tusks positioned at the tip of the mandible. It also differs from M. hectori and M. perrini in having smaller, less triangular tusks and from M. mirus in having a relatively shorter rostrum with a wider base, a shorter mandibular symphysis, wider premaxillary sac fossae and crests, and a taller cranium. External appearance The external appearances of M. eueu and M. mirus are not known to be consistently distinguishable. Both species are rotund mesoplodonts with bodies that taper towards the tail and rostrum, with somewhat bulbous and well-defined melons, a mostly straight beak and short, straight gape. Colouration is generally grey with a dark eye patch in both species, but there may be specific colouration patterns linked to M. eueu; for example, a female that stranded in South Africa showed a whitish dorsal colouration from the fin to caudal peduncle [14]. However, Aguilar et al. [6] reported M. mirus with varying dorsal and ventral white colouration in the Canary and Azores Islands, so colouration patterns linked to species cannot yet be conclusively defined. Distribution M. eueu probably occurs throughout temperate SH waters, with reports from several locations. Genetic methods have confirmed at least some of these records in South Africa ([20], this study), Australia [20] and Aotearoa New Zealand [11]. Nomenclatural acts This published work and the nomenclatural acts it contains are registered in ZooBank (http://zoobank.org/), the online registration system for the International Commission on Zoological Nomenclature (ICZN). The ZooBank Life Science Identifier is urn:lsid:zoobank.org:pub: C61A1A33-B234-476E- AA24-86C6ED130C10, and for the new species is urn:lsid:zoo bank.org:act: C56121C4-1E15-4A07-A270-D92AF43AE74A., Published as part of Carroll, Emma L., McGowen, Michael R., McCarthy, Morgan L., Marx, Felix G., Aguilar, Natacha, Dalebout, Merel L., Dreyer, Sascha, Gaggiotti, Oscar E., Hansen, Sabine S., Helden, Anton van, Onoufriou, Aubrie B., Baird, Robin W., Baker, C. Scott, Berrow, Simon, Cholewiak, Danielle, Claridge, Diane, Constantine, Rochelle, Davison, Nicholas J., Eira, Catarina, Fordyce, R. Ewan, Gatesy, John, Greg Hofmeyr, G. J., Martín, Vidal, Mead, James G., Mignucci-Giannoni, Antonio A., Morin, Phillip A., Reyes, Cristel, Rogan, Emer, Rosso, Massimiliano, Silva, Mónica A., Springer, Mark S., Steel, Debbie & Olsen, Morten Tange, 2021, Speciation in the deep: genomics and morphology reveal a new species of beaked whale Mesoplodon eueu., pp. 1-10 in Proceedings of the Royal Society B 288 (1961) on pages 5-6, DOI: 10.1098/rspb.2021.1213

Funding: E.L.C. is supported by a Rutherford Discovery Fellow from the Royal Society of New Zealand Te Apārangi. Stable isotope analyses were supported by a Marie Curie fellowship to E.L.C. (Brazilian samples) and an Australian Marine Mammal Centre grant to G.D., S.C., M.H. (New Zealand samples). P.H.O. was supported by the Brazilian National Research Council (CNPq proc. n° 144064/98-7) and World Wildlife Fund (WWF-Brazil). The New Zealand biopsy samples were collected under New Zealand Department of Conservation Marine Mammal Research permit and University of Auckland Animal Ethics Committee approved protocol AEC/02/2005/R334 to CSB. The New Zealand field work was funded by a Winifred Violet Scott Estate Research Grant Fund, Australian Antarctic Division, Marine Conservation Action Fund, Blue Planet Marine NZ Ltd, Holsworth Wildlife Research Endowment, New Zealand Ministry of Foreign Affairs, DOC, South Pacific Whale Research Consortium, National Geographic, and Brian Skerry Photography. Southern right whales (SRW) are capital breeders that use stored energy reserves to sustain themselves and their calves on nursery areas. With successful calving events declining in some SRW populations, it has been hypothesized that nutritional stress in adult females causes reproductive failure or death of calves shortly after birth. Here we compared offsets in carbon and nitrogen isotope values of mothers and their offspring (Δ13Ccalf-cow and Δ15Ncalf-cow) among three SRW populations. SRW from Aotearoa New Zealand, with high population growth rates and body conditions scores, have negative Δ13Ccalf-cow suggesting calves are utilizing 13C-depleted lipid carbon in milk to fuel the synthesis of nonessential amino acids used to build new tissues and rapidly grow. In contrast, a significantly positive Δ13Ccalf-cow offset previously reported for SRW from Argentina during a mass die-off event was hypothesized to be due to calves consuming milk with low lipid content. Patterns in Δ15Ncalf-cow were more difficult to interpret and highlight the complexity in nitrogen transfer between mother and offspring. When combined with similar data collected from Brazil and during a low mortality year in Argentina, we hypothesize this approach provides a way to retrospectively compare nutritional condition of breeding adult female SRW across nursery areas. Postprint

This document contains Supplementary material text, tables S1-S4, and figures S1-S8.

Includes Supplementary text, Figure S1, Tables S1 to S7 and associated References

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This work was supported by a combined NERC and St Andrews 600th Anniversary PhD Studentship [grant NE/L501852/1] to RAWW and also supported by a NERC grant [grant NE/I027800/1] to MGR and Rhonda R. Snook. MBM was supported by The Royal Society. OEG was supported by MASTS (Marine Alliance for Science and Technology for Scotland). Computational analyses were supported by the University of St Andrews Bioinformatics Unit which is funded by a Wellcome Trust ISSF award [grant 105621/Z/14/Z]. 1. With increasing application of pooled-sequencing approaches to population genomics robust methods are needed to accurately quantify allele frequency differences between populations. Identifying consistent differences across stratified populations can allow us to detect genomic regions under selection and that differ between populations with different histories or attributes. Current popular statistical tests are easily implemented in widely available software tools which make them simple for researchers to apply. However, there are potential problems with the way such tests are used,which means that underlying assumptions about the data are frequently violated. 2. These problems are highlighted by simulation of simple but realistic population genetic models of neutral evolution and the performance of different tests are assessed. We present alternative tests (including GLMs with quasibinomial error structure) with attractive properties for the analysis of allele frequency differences and re-analyse a published dataset. 3. The simulations show that common statistical tests for consistent allele frequency differences perform poorly, with high false positive rates. Applying tests that do not confound heterogeneity and main effects significantly improves inference. Variation in sequencing coverage likely produces many false positives and re-scaling allele frequencies to counts out of a common value or an effective sample size reduces this effect. 4. Many researchers are interested in identifying allele frequencies that vary consistently across replicates to identify loci underlying phenotypic responses to selection or natural variation in phenotypes. Popular methods that have been suggested for this task perform poorly in simulations. Overall, quasibinomial GLMs perform better and also have the attractive feature of allowing correction for multiple testing by standard procedures and are easily extended to other designs. Publisher PDF

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