Horseshoe bats (genus Rhinolophus, family Rhinolophidae) represent an important group within chiropteran phylogeny due to their distinctive traits, including constant high-frequency echolocation, rapid karyotype evolution, and unique immune system. Advances in evolutionary biology, supported by high-quality reference genomes and comprehensive whole-genome data, have significantly enhanced our understanding of species origins, speciation mechanisms, adaptive evolutionary processes, and phenotypic diversity. However, genomic research and understanding of the evolutionary patterns of Rhinolophus are severely constrained by limited data, with only a single published genome of R. ferrumequinum currently available. In this study, we constructed a high-quality chromosome-level reference genome for the intermediate horseshoe bat ( R. affinis). Comparative genomic analyses revealed potential genetic characteristics associated with virus tolerance in Rhinolophidae. Notably, we observed expansions in several immune-related gene families and identified various genes functionally associated with the SARS-CoV-2 signaling pathway, DNA repair, and apoptosis, which displayed signs of rapid evolution. In addition, we observed an expansion of the major histocompatibility complex class II (MHC-II) region and a higher copy number of the HLA- DQB2 gene in horseshoe bats compared to other chiropteran species. Based on whole-genome resequencing and population genomic analyses, we identified multiple candidate loci (e.g., GLI3) associated with variations in echolocation call frequency across R. affinis subspecies. This research not only expands our understanding of the genetic characteristics of the Rhinolophus genus but also establishes a valuable foundation for future research.
菊头蝠物种（菊头蝠属，菊头蝠科）是蝙蝠众多科中的一个重要类群，它们具有多个显著区别于其他蝙蝠的特征，例如特化的高恒定频率回声定位信号、快速的核型进化以及独特的免疫系统。利用高质量参考基因组和全基因组数据进行的进化研究，使我们对物种起源、物种形成、适应性进化和表型变异有了更深入的见解。然而，目前有限的基因组数据（仅有一种菊头蝠物种（马铁菊头蝠， Rhinolophus ferrumequinum）的基因组已发表）限制了我们对菊头蝠进化模式的深入理解。在该研究中，我们构建了高质量染色体水平的中菊头蝠（ R. affinis）参考基因组。通过比较基因组分析，我们揭示了与菊头蝠物种病毒耐受性相关的潜在遗传特征，包括多个与免疫反应相关的基因家族发生了显著扩张，以及多个与SARS-CoV-2信号通路、DNA修复和细胞凋亡功能相关的基因，发生了快速进化。此外，与其他蝙蝠相比，我们发现菊头蝠基因组中的MHC-2区域有所扩张，尤其是 HLA-DQB2基因呈现更高的拷贝数。最后，通过对中菊头蝠种群进行全基因组重测序分析，我们鉴定到了多个与中菊头蝠亚种回声定位频率变异相关的候选基因（例如基因 GLI3）。我们的工作不仅加深了对菊头蝠类群遗传特征的理解，还为将来蝙蝠比较基因组学研究提供了重要的数据基础。.

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Understanding how the environment mediates an organism\'s ability to meet basic survival requirements is a fundamental goal of ecology. Vessel noise is a global threat to marine ecosystems and is increasing in intensity and spatiotemporal extent due to growth in shipping coupled with physical changes to ocean soundscapes from ocean warming and acidification. Odontocetes rely on biosonar to forage, yet determining the consequences of vessel noise on foraging has been limited by the challenges of observing underwater foraging outcomes and measuring noise levels received by individuals. To address these challenges, we leveraged a unique acoustic and movement dataset from 25 animal-borne biologging tags temporarily attached to individuals from two populations of fish-eating killer whales (Orcinus orca) in highly transited coastal waters to (1) test for the effects of vessel noise on foraging behaviors-searching (slow-click echolocation), pursuit (buzzes), and capture and (2) investigate the mechanism of interference. For every 1 dB increase in maximum noise level, there was a 4% increase in the odds of searching for prey by both sexes, a 58% decrease in the odds of pursuit by females and a 12.5% decrease in the odds of prey capture by both sexes. Moreover, all but one deep (≥75 m) foraging attempt with noise ≥110 dB re 1 μPa (15-45 kHz band; n = 6 dives by n = 4 whales) resulted in failed prey capture. These responses are consistent with an auditory masking mechanism. Our findings demonstrate the effects of vessel noise across multiple phases of odontocete foraging, underscoring the importance of managing anthropogenic inputs into soundscapes to achieve conservation objectives for acoustically sensitive species. While the timescales for recovering depleted prey species may span decades, these findings suggest that complementary actions to reduce ocean noise in the short term offer a critical pathway for recovering odontocete foraging opportunities.

Behaviors and auditory physiological responses of some species of echolocating bats remain unaffected after exposure to intense noise, but information on the underlying mechanisms remains limited. Here, we studied whether the vocalization-induced middle ear muscle (MEM) contractions (MEM reflex) and auditory fovea contributed to the unimpaired auditory sensitivity of constant frequency-frequency modulation (CF-FM) bats after exposure to broad-band intense noise. The vocalizations of the CF-FM bat, Hipposideros pratti, were inhibited through anesthesia to eliminate the vocalization-induced MEM reflex. First, the anesthetized bats were exposed to intense broad-band noise, and the findings showed that the bats could still maintain their auditory sensitivities. However, auditory sensitivities were seriously impaired in CBA/Ca mice exposed to intense noise under anesthesia. This indicated that the unimpaired auditory sensitivity in H. pratti after exposure to intense noise under anesthesia was not due to anesthetization. The bats were further exposed to low-frequency band-limited noise, whose passband did not overlap with echolocation call frequencies. The results showed that the auditory responses to sound frequencies within the noise spectrum and one-half octave higher than the spectrum were also unimpaired. Taken together, the results indicate that both vocalization-induced MEM reflex and auditory fovea do not contribute to the unimpaired auditory sensitivity in H. pratti after exposure to intense noise. The possible mechanisms underlying the unimpaired auditory sensitivity after echolocating bats were exposed to intense noise are discussed.

Like other odontocetes, Risso\'s dolphins actively emit clicks and passively listen to the echoes during echolocation. However, the head anatomy of Risso\'s dolphins differs from that of other odontocetes by a unique vertical cleft along the anterior surface of the forehead and a differently-shaped lower jaw. In this study, 3D finite-element sound reception and production models were constructed based on computed tomography (CT) data of a deceased Risso\'s dolphin. Our results were verified by finding good agreement with experimental measurements of hearing sensitivity. Moreover, the acoustic pathway for sounds to travel from the seawater into the dolphin\'s tympanoperiotic complexes (TPCs) was computed. The gular reception mechanism, previously discovered inDelphinus delphisandZiphius cavirostris, was also found in this species. The received sound pressure levels and relative displacement at TPC surfaces were compared between the cases with and without the mandibular fats or mandible. The results demonstrate a pronounced wave-guiding role of the mandibular fats and a limited bone-conductor role of the mandible. For sound production modelling, we digitally filled the cleft with neighbouring soft tissues, creating a hypothetical \'cleftless\' head. Comparison between sound travelling through a \'cleftless\' head vs. an original head indicates that the distinctive cleft plays a limited role in biosonar sound propagation.

Oceans are increasingly crowded by anthropogenic activities yet the impact on Outer Continental Shelf (OCS) marine life remains largely unquantified. The MAPS (Marine Mammal Acoustic and Spatial Ecology) study of 2019 included passive acoustic and visual vessel surveys over the Mid-Atlantic OCS of the USA to address data gaps in winter/spring for deep-diving cetaceans, including sperm whales. Echolocation clicks were used to derive slant ranges to sperm whales for design- and model-based density estimates. Although more survey effort was realised in the spring, high densities of whales were identified in both winter and spring (10.46 and 8.89 per 1000 km2 respectively). The spring model-based abundance estimate of 1587 whales (CI 946-2663) was considered the most representative figure, in part due to lower coefficients of variation. Modelling suggested that high densities of whales were associated with warm core rings, eddies and edges. As OCS waters provide an important foraging habitat for North Atlantic sperm whales, appropriate mitigation is required to ensure commercial pressures to develop offshore energy do not negatively affect this endangered species.

Quantification of bat communities and habitat heavily rely on non-invasive acoustic bat surveys the scope of which has greatly amplified with advances in remote monitoring technologies. Despite the unprecedented amount of acoustic data being collected, analysis of these data is often limited to simple species classification which provides little information on habitat function. Feeding buzzes, the rapid sequences of echolocation pulses emitted by bats during the terminal phase of prey capture, have historically been used to evaluate foraging habitat quality. Automated identification of feeding buzzes in recordings could benefit conservation by helping identify critical foraging habitat. I tested if detection of feeding buzzes in recordings could be automated with bat recordings from Ontario, Canada. Data were obtained using three different recording devices. The signal detection method involved sequentially scanning narrow frequency bands with the \"Bioacoustics\" R package signal detection algorithm, and extracting temporal and signal strength parameters from detections. Buzzes were best characterized by the standard deviation of the time between consecutive pulses, the average pulse duration, and the average pulse signal-to-noise ratio. Classification accuracy was highest with artificial neural networks and random forest algorithms. I compared each model\'s receiver operating characteristic curves and random forest provided better control over the false-positive rate so it was retained as the final model. When tested on a new dataset, buzzfindr\'s overall accuracy was 93.4% (95% CI: 91.5%- 94.9%). Overall accuracy was not affected by recording device type or species frequency group. Automated detection of feeding buzzes will facilitate their integration in the analytical workflow of acoustic bat studies to improve inferences on habitat use and quality.

Sperm whales (Physeter macrocephalus) have been studied for decades, but the development of their clicks during the animal growth is not yet well known. The click they emit during socialization and echolocation contains information about the length of their acoustic organs and, therefore the length of the body through the interpulse interval (IPI). This paper provides the first IPI/age relationship for juvenile male and female sperm whales (Physeter macrocephalus) based on field recordings of individuals whose age is largely known. Across 9 years, audiovisual recordings of a Mauritian sperm whale social unit were carried out. Adult female and juvenile sperm whales were identified and aged. The dataset made from those recordings is publicly available. The interpulse interval was measured for individuals whose ages ranged from 7 days to around 38 years. The growth of the acoustic organ of juveniles showed an early inter-individual variability as well as sexual dimorphism. Usual growth models were also fitted, predicting a mean I P I ∞ of 3.5 ms for adults and a physical maturity reached at around 30 years old. The use of passive acoustic monitoring (PAM) is one of the main tools used to study sperm whales. This IPI-age relationship may aid demographic studies on sperm whales by enabling PAM to assess the ages of recorded sperm whales.

Echolocating bats rely on precise auditory temporal processing to detect echoes generated by calls that may be emitted at rates reaching 150-200 Hz. High call rates can introduce forward masking perceptual effects that interfere with echo detection; however, bats may have evolved specializations to prevent repetition suppression of auditory responses and facilitate detection of sounds separated by brief intervals. Recovery of the auditory brainstem response (ABR) was assessed in two species that differ in the temporal characteristics of their echolocation behaviors: Eptesicus fuscus, which uses high call rates to capture prey, and Carollia perspicillata, which uses lower call rates to avoid obstacles and forage for fruit. We observed significant species differences in the effects of forward masking on ABR wave 1, in which E. fuscus maintained comparable ABR wave 1 amplitudes when stimulated at intervals of <3 ms, whereas post-stimulus recovery in C. perspicillata required 12 ms. When the intensity of the second stimulus was reduced by 20-30 dB relative to the first, however, C. perspicillata showed greater recovery of wave 1 amplitudes. The results demonstrate that species differences in temporal resolution are established at early levels of the auditory pathway and that these differences reflect auditory processing requirements of species-specific echolocation behaviors.

Analyses of the cetacean (whale and dolphin) inner ear provide glimpses into the ecology and evolution of extinct and extant groups. The paleoecology of the long-snouted odontocete (toothed whale) group, Parapontoporia, is primarily marine with its depositional context also suggesting freshwater tolerance. As an extinct relative of the exclusively riverine Lipotes vexillifer, Parapontoporia provides insight into a transition from marine to freshwater environments. High-resolution X-ray CT scans (~3 microns or less) of three individual specimens from two species, P. sternbergi and P. pacifica, were acquired. Digital endocasts of the inner ear labyrinths were extracted non-destructively. Nine measurements of the inner ear were compared with an existing dataset covering 125 terrestrial and aquatic artiodactyls. These measurements were then subjected to a principal component analysis to interpret hearing sensitivities among other artiodactyls. Based on our analyses, Parapontoporia was likely to have been able to hear within narrow-band high frequency (NBHF) ranges. This finding indicates another convergence of NBHF-style hearing, or, more intriguingly, suggests that it may be an ancestral characteristic present among the longirostrine dolphins that dominated in the Miocene prior to the evolution of more modern lineages.