Towards automated long-term acoustic monitoring of endangered river dolphins: a case study in the Brazilian Amazon floodplains.

Using passive acoustic monitoring (PAM) and convolutional neural networks (CNN), we monitored the movements of the two endangered Amazon River dolphin species, the boto (Inia geoffrensis) and the tucuxi (Sotalia fluviatilis) from main rivers to floodplain habitats (várzea) in the Mamirauá Reserve (Amazonas, Brazil). We detected dolphin presence in four main areas based on the classification of their echolocation clicks. Using the same method, we automatically detected boat passages to estimate a possible interaction between boat and dolphin presence. Performance of the CNN classifier was high with an average precision of 0.95 and 0.92 for echolocation clicks and boats, respectively. Peaks of acoustic activity were detected synchronously at the river entrance and channel, corresponding to dolphins seasonally entering the várzea. Additionally, the river dolphins were regularly detected inside the flooded forest, suggesting a wide dispersion of their populations inside this large area, traditionally understudied and particularly important for boto females and calves. Boats overlapped with dolphin presence 9% of the time. PAM and recent advances in classification methods bring a new insight of the river dolphins' use of várzea habitats, which will contribute to conservation strategies of these species.

Echolocation variability of franciscana dolphins (Pontoporia blainvillei) between estuarine and open-sea habitats, with insights into foraging patterns.

Environmental and ecological factors can trigger changes in the acoustic repertoire of cetaceans. This study documents the first use of a well-established passive acoustic monitoring device (C-POD) to analyze echolocation sounds and behavior of franciscana dolphins in different habitats: estuary [Babitonga Bay (BB)] and open sea [Itapirubá Beach (IB)]. A total of 10 924 click trains were recorded in BB and 6 093 in IB. An inter-click interval < 10 ms (so called "feeding buzzes") was used as a proxy for foraging activity. The main difference in the acoustic parameters between the two habitats was related to the frequency spectrum, with higher maximum and lower modal and minimum click frequencies in BB, and a train frequency range of 17 kHz, against 10 kHz in IB. Also, the click emission rate (clicks/s) was almost 20% higher in BB. Both studied habitats showed a high proportion of feeding buzzes (BB = 68%; IB = 58%), but with a higher probability of occurrence in BB (p < 0.001) and at night (p < 0.001) in both habitats. The C-PODs showed great potential to monitor occurrence, bioacoustics parameters, and echolocation behavior of franciscana dolphins. Longer-term temporal and spatial monitoring are necessary for elucidating several issues raised in this study.

Cytoarchitecture of the medial nucleus of trapezoid body of three neotropical species of bats (Noctilio leporinus, Phyllostomus hastatus, and Carollia perspicillata) with different foraging behavior / Citoarquitetura do núcleo medial do corpo trapezoidal de três espécies neotropicais de morcegos (Noctilio leporinus, Phyllostomus hastatus e Carollia perspicillata) com diferentes comportamentos de forrageamento

Abstract The present study was taken to test the hypothesis that the medial nucleus of the trapezoid body (MNTB) of echolocating neotropical bats with different foraging behavior will exhibit morphological variations in relative size, degree of complexity and spatial distribution. The brains were collected from six male adult bats of each species: Noctilio leporinus (fish-eating), Phyllostomus hastatus (carnivorous/ omnivorous) and Carollia perspicillata (fruit-eating) and were double-embedded and transverse serial sections were cut and stained with cresyl fast violet. The results showed that the MNTB is well developed in all the bats in general and the mean length of the MNTB was 1160 ± 124 µm in N. leporinus, 400 ± 59 µm in P. hastatus and 320 ± 25µm in C. perspicillata. The body and brain weight do not reflect proportionately on the size of the MNTB in the present study. The hearing frequency spectrum did not covary with the size of the MNTB among the bats studied. The MNTB is clearly demarcated from the ventral nucleus of the trapezoid body (VNTB) only in P. hastatus. The MNTB comprised mainly three types of cells in all three bats: dense-staining multipolar cells (12.5 µm and 25.0 µm diameter); light-staining multipolar cells measuring (12.5 µm and 25.0 µm diameter) and light-staining round cells (5.0 µm diameter). The large sized MNTB was observed in N. leporinus, which suggests that it relies heavily on echolocation whereas P. hastatus and C. perspicillata use echolocation as well but also rely on hearing, smell and vision.

Resumo O presente estudo foi realizado para testar a hipótese de que o núcleo medial do corpo trapezoide (MNTB) de morcegos neotropicais ecolocativos com comportamento forrageiro diferente apresenta variações morfológicas no tamanho relativo, grau de complexidade e distribuição espacial. Os cérebros foram coletados de seis morcegos machos adultos de cada espécie, Noctilio leporinus (comedor de peixe), Phyllostomus hastatus (carnívoro/onívoro) e Carollia perspicillata (comedor de frutas), e foram seccionados em série e seções seriais transversais duplas e coradas com cresil violeta. Os resultados mostraram que o MNTB é bem desenvolvido em todos os morcegos em geral e que o comprimento médio do MNTB foi de 1.160 ± 124 µm em N. leporinus, 400 ± 59 µm em P. hastatus e 320 ± 25 µm em C. perspicillata. O peso corporal e cerebral não reflete proporcionalmente o tamanho do MNTB no presente estudo. O espectro da frequência auditiva não covaria com o tamanho do MNTB entre os morcegos estudados. O MNTB é claramente demarcado do núcleo ventral do corpo trapezoidal (VNTB) apenas em P. hastatus. O MNTB compreendia principalmente três tipos de células nos três morcegos: células multipolares de coloração densa (12,5 µm e 25,0 µm de diâmetro), células multipolares de coloração clara (12,5 µm e 25,0 µm de diâmetro) e células redondas manchadas de luz (5,0 µm de diâmetro). O MNTB de grande porte foi observado em N. leporinus, o que sugere que ele depende muito da ecolocalização, enquanto P. hastatus e C. perspicillata também usam a ecolocalização, mas dependem da audição, olfato e visão.

Cytoarchitecture of the medial nucleus of trapezoid body of three neotropical species of bats (Noctilio leporinus, Phyllostomus hastatus, and Carollia perspicillata) with different foraging behavior.

The present study was taken to test the hypothesis that the medial nucleus of the trapezoid body (MNTB) of echolocating neotropical bats with different foraging behavior will exhibit morphological variations in relative size, degree of complexity and spatial distribution. The brains were collected from six male adult bats of each species: Noctilio leporinus (fish-eating), Phyllostomus hastatus (carnivorous/ omnivorous) and Carollia perspicillata (fruit-eating) and were double-embedded and transverse serial sections were cut and stained with cresyl fast violet. The results showed that the MNTB is well developed in all the bats in general and the mean length of the MNTB was 1160 ± 124 µm in N. leporinus, 400 ± 59 µm in P. hastatus and 320 ± 25µm in C. perspicillata. The body and brain weight do not reflect proportionately on the size of the MNTB in the present study. The hearing frequency spectrum did not covary with the size of the MNTB among the bats studied. The MNTB is clearly demarcated from the ventral nucleus of the trapezoid body (VNTB) only in P. hastatus. The MNTB comprised mainly three types of cells in all three bats: dense-staining multipolar cells (12.5 µm and 25.0 µm diameter); light-staining multipolar cells measuring (12.5 µm and 25.0 µm diameter) and light-staining round cells (5.0 µm diameter). The large sized MNTB was observed in N. leporinus, which suggests that it relies heavily on echolocation whereas P. hastatus and C. perspicillata use echolocation as well but also rely on hearing, smell and vision.

Head adaptation for sound production and feeding strategy in dolphins (Odontoceti: Delphinida).

Head morphology in toothed whales evolved under selective pressures on feeding strategy and sound production. The postnatal development of the skull (n = 207) and mandible (n = 219) of six Delphinida species which differ in feeding strategy but exhibit similar sound emission patterns, including two narrow-band high-frequency species, were investigated through 3D morphometrics. Morphological changes throughout ontogeny were demonstrated based on the main source of variation (i.e., prediction lines) and the common allometric component. Multivariate trajectory analysis with pairwise comparisons between all species was performed to evaluate specific differences on the postnatal development of skulls and mandibles. Changes in the rostrum formation contributed to the variation (skull: 49%; mandible: 90%) of the entire data set and might not only reflect the feeding strategy adopted by each lineage but also represents an adaptation for sound production and reception. As an important structure for directionality of sound emissions, this may increase directionality in raptorial feeders. Phylogenetic generalized least squares analyses indicated that shape of the anterior portion of the skull is strongly dependent on phylogeny and might not only reflect feeding mode, but also morphological adaptations for sound production, particularly in raptorial species. Thus, postnatal development seems to represent a crucial stage for biosonar maturation in some raptorial species such as Pontoporia blainvillei and Sousa plumbea. The ontogeny of their main tool for navigation and hunting might reflect their natural history peculiarities and thus potentially define their main vulnerabilities to anthropogenic changes in the environment.

The masked seducers: Lek courtship behavior in the wrinkle-faced bat Centurio senex (Phyllostomidae).

Centurio senex is an iconic bat characterized by a facial morphology deviating far from all other New World Leaf Nosed Bats (Phyllostomidae). The species has a bizarrely wrinkled face and lacks the characteristic nose leaf. Throughout its distribution from Mexico to Northern South America the species is most of the time rarely captured and only scarce information on its behavior and natural history is available. Centurio senex is frugivorous and one of the few bats documented to consume also hard seeds. Interestingly, the species shows a distinct sexual dimorphism: Adult males have more pronounced facial wrinkles than females and a fold of skin under the chin that can be raised in style of a face mask. We report the first observations on echolocation and mating behavior of Centurio senex, including synchronized audio and video recordings from an aggregation of males in Costa Rica. Over a period of 6 weeks we located a total of 53 perches, where during the first half of the night males were hanging with raised facial masks at a mean height of 2.35 m. Most of the time, the males moved just their wing tips, and spontaneously vocalized in the ultrasound range. Approaches of other individuals resulted in the perching male beating its wings and emitting a very loud, low frequency whistling call. Following such an encounter we recorded a copulation event. The observed aggregation of adult C. senex males is consistent with lek courtship, a behavior described from only few other bat species.

Functional organization of the primary auditory cortex of the free-tailed bat Tadarida brasiliensis.

The Mexican free-tailed bat, Tadarida brasiliensis, is a fast-flying bat that hunts by biosonar at high altitudes in open space. The auditory periphery and ascending auditory pathways have been described in great detail for this species, but nothing is yet known about its auditory cortex. Here we describe the topographical organization of response properties in the primary auditory cortex (AC) of the Mexican free-tailed bat with emphasis on the sensitivity for FM sweeps and echo-delay tuning. Responses of 716 units to pure tones and of 373 units to FM sweeps and FM-FM pairs were recorded extracellularly using multielectrode arrays in anesthetized bats. A general tonotopy was confirmed with low frequencies represented caudally and high frequencies represented rostrally. Characteristic frequencies (CF) ranged from 15 to 70 kHz, and fifty percent of CFs fell between 20 and 30 kHz, reflecting a hyper-representation of a bandwidth corresponding to search-phase echolocation pulses. Most units showed a stronger response to downward rather than upward FM sweeps and forty percent of the neurons interspersed throughout AC (150/371) showed echo-delay sensitivity to FM-FM pairs. Overall, the results illustrate that the free-tailed bat auditory cortex is organized similarly to that of other FM-type insectivorous bats.

Cytoarchitecture of the superior olivary complex of three neotropical species of bats (Noctilio leporinus, Phyllostomus hastatus and Carollia perspicillata) with different foraging behavior / Citoarquitetura do complexo olivar superior de três espécies neotropicais de morcegos (Noctilio leporinus, Phyllostomus hastatus e Carollia perspicillata) com diferentes comportamentos de forrageamento

Abstract The understanding of the echolocation by studying different auditory nuclei of echolocating bats can be an important link in elucidating questions arising in relation to their foraging behavior. The superior olivary complex (SOC) is the primary center for processing the binaural cues used in sound localization since echo locating bats rely on acoustic cues to navigate and capture prey while in flight. The present study was taken to test the hypothesis that the SOC of echolocating neotropical bats with different foraging behavior will exhibit morphological variations in relative size, degree of complexity and spatial distribution. The brains were collected from six male adult bats of each species: Noctilio leporinus (fish eating), Phyllostomus hastatus (carnivorous/omnivorous) and Carollia perspicillata (fruit eating). They were double-embedded and transverse serial sections were cut and stained with cresyl fast violet. The SOC measured as 640 ± 70 µm in the N. leporinus bat, 480 ± 50 µm in the P. hastatus and 240 ± 30 µm in the C. perspicillata bat. The principal nuclei of the SOC of in all three bats were the LSO, MSO and MNTB. The MSO and LSO were very well developed in N. leporinus bats. The MSO of N. leporinus bat subdivided into DMSO and VMSO. The main cell type of cells present in MSO and LSO are dark staining multipolar cells in all the bats studied. The well-developed MSO and LSO of N. leporinus bats indicate that these bats are highly sensitive to low frequency sounds and interaural intensity differences, which help these bats to forage over water by using various types of echolocation signals. The average size of SOC in P. hastatus and C. perspicillata bats can be attributed to the fact that these bats use vision and smell along with echolocation to forage the food.

Resumo O entendimento da ecolocalização pelo estudo de diferentes núcleos auditivos de morcegos pode ser um elo importante na elucidação das inúmeras questões que surgem em relação ao seu comportamento de forrageamento. O complexo olivar superior (SOC) é o principal centro de processamento das pistas binaurais usadas na localização do som, já que os morcegos ecolocalizadores contam com sinais acústicos para navegar e capturar as presas durante o vôo. O presente estudo foi realizado para testar a hipótese de que morcegos que usam a ecolocalização para diferentes comportamentos de forrageamento irão variar na estrutura, tamanhos relativos e grau de complexidade e distribuição espacial do grupo SOC. Os cérebros foram coletados de seis machos adultos de morcego de cada espécie: Noctilio leporinus (piscívoro), Phyllostomus hastatus (carnívoros/onívoros) e Carollia perspicillata (frugívoro). Eles foram seccionados em série e transversalmente, cortados e corados com coloração rápida cresil-violeta. tolet. O grupo SOC foi medido como 640 ± 70 µm no morcego N. leporinus, 480 ± 50 µm no P. hastatus e 240 ± 30 µm no morcego C. perspicillata. Os principais núcleos do grupo SOC dos três morcegos foram o LSO e o MSO e o MNTB. O MSO e o LSO foram muito bem desenvolvidos em morcegos N. leporinus. A MSO de N. leporinus foi subdividida em DMSO e VMSO. O principal tipo de células presentes na MSO e LSO são as células multipolares de coloração escura em todos os morcegos. Os MSO bem desenvolvidos e LSO de morcegos N. leporinus indicam que estes morcegos são altamente sensíveis a sons de baixa frequência e diferenças de intensidade interaural, que ajudaram estes morcegos a se alimentarem na superfície da água usando vários tipos de sinais de ecolocalização. O tamanho médio de SOC em morcegos de P. hastatus e C. perspicillata pode ser atribuído ao fato destes morcegos usarem visão e olfato junto com a ecolocalização para forragear.

Cytoarchitecture of the superior olivary complex of three neotropical species of bats (Noctilio leporinus, Phyllostomus hastatus and Carollia perspicillata) with different foraging behavior / Citoarquitetura do complexo olivar superior de três espécies neotropicais de morcegos (Noctilio leporinus, Phyllostomus hastatus e Carollia perspicillata) com diferentes comportamentos de forrageamento

The understanding of the echolocation by studying different auditory nuclei of echolocating bats can be an important link in elucidating questions arising in relation to their foraging behavior. The superior olivary complex (SOC) is the primary center for processing the binaural cues used in sound localization since echo locating bats rely on acoustic cues to navigate and capture prey while in flight. The present study was taken to test the hypothesis that the SOC of echolocating neotropical bats with different foraging behavior will exhibit morphological variations in relative size, degree of complexity and spatial distribution. The brains were collected from six male adult bats of each species: Noctilio leporinus (fish eating), Phyllostomus hastatus (carnivorous/omnivorous) and Carollia perspicillata (fruit eating). They were double-embedded and transverse serial sections were cut and stained with cresyl fast violet. The SOC measured as 640 ± 70 µm in the N. leporinus bat, 480 ± 50 µm in the P. hastatus and 240 ± 30 µm in the C. perspicillata bat. The principal nuclei of the SOC of in all three bats were the LSO, MSO and MNTB. The MSO and LSO were very well developed in N. leporinus bats. The MSO of N. leporinus bat subdivided into DMSO and VMSO. The main cell type of cells present in MSO and LSO are dark staining multipolar cells in all the bats studied. The well-developed MSO and LSO of N. leporinus bats indicate that these bats are highly sensitive to low frequency sounds and interaural intensity differences, which help these bats to forage over water by using various types of echolocation signals. The average size of SOC in P. hastatus and C. perspicillata bats can be attributed to the fact that these bats use vision and smell along with echolocation to forage the food.(AU)

O entendimento da ecolocalização pelo estudo de diferentes núcleos auditivos de morcegos pode ser um elo importante na elucidação das inúmeras questões que surgem em relação ao seu comportamento de forrageamento. O complexo olivar superior (SOC) é o principal centro de processamento das pistas binaurais usadas na localização do som, já que os morcegos ecolocalizadores contam com sinais acústicos para navegar e capturar as presas durante o vôo. O presente estudo foi realizado para testar a hipótese de que morcegos que usam a ecolocalização para diferentes comportamentos de forrageamento irão variar na estrutura, tamanhos relativos e grau de complexidade e distribuição espacial do grupo SOC. Os cérebros foram coletados de seis machos adultos de morcego de cada espécie: Noctilio leporinus (piscívoro), Phyllostomus hastatus (carnívoros/onívoros) e Carollia perspicillata (frugívoro). Eles foram seccionados em série e transversalmente, cortados e corados com coloração rápida cresil-violeta. tolet. O grupo SOC foi medido como 640 ± 70 µm no morcego N. leporinus, 480 ± 50 µm no P. hastatus e 240 ± 30 µm no morcego C. perspicillata. Os principais núcleos do grupo SOC dos três morcegos foram o LSO e o MSO e o MNTB. O MSO e o LSO foram muito bem desenvolvidos em morcegos N. leporinus. A MSO de N. leporinus foi subdividida em DMSO e VMSO. O principal tipo de células presentes na MSO e LSO são as células multipolares de coloração escura em todos os morcegos. Os MSO bem desenvolvidos e LSO de morcegos N. leporinus indicam que estes morcegos são altamente sensíveis a sons de baixa frequência e diferenças de intensidade interaural, que ajudaram estes morcegos a se alimentarem na superfície da água usando vários tipos de sinais de ecolocalização. O tamanho médio de SOC em morcegos de P. hastatus e C. perspicillata pode ser atribuído ao fato destes morcegos usarem visão e olfato junto com a ecolocalização para forragear.(AU)

Cytoarchitecture of the superior olivary complex of three neotropical species of bats (Noctilio leporinus, Phyllostomus hastatus and Carollia perspicillata) with different foraging behavior.

The understanding of the echolocation by studying different auditory nuclei of echolocating bats can be an important link in elucidating questions arising in relation to their foraging behavior. The superior olivary complex (SOC) is the primary center for processing the binaural cues used in sound localization since echo locating bats rely on acoustic cues to navigate and capture prey while in flight. The present study was taken to test the hypothesis that the SOC of echolocating neotropical bats with different foraging behavior will exhibit morphological variations in relative size, degree of complexity and spatial distribution. The brains were collected from six male adult bats of each species: Noctilio leporinus (fish eating), Phyllostomus hastatus (carnivorous/omnivorous) and Carollia perspicillata (fruit eating). They were double-embedded and transverse serial sections were cut and stained with cresyl fast violet. The SOC measured as 640 ± 70 µm in the N. leporinus bat, 480 ± 50 µm in the P. hastatus and 240 ± 30 µm in the C. perspicillata bat. The principal nuclei of the SOC of in all three bats were the LSO, MSO and MNTB. The MSO and LSO were very well developed in N. leporinus bats. The MSO of N. leporinus bat subdivided into DMSO and VMSO. The main cell type of cells present in MSO and LSO are dark staining multipolar cells in all the bats studied. The well-developed MSO and LSO of N. leporinus bats indicate that these bats are highly sensitive to low frequency sounds and interaural intensity differences, which help these bats to forage over water by using various types of echolocation signals. The average size of SOC in P. hastatus and C. perspicillata bats can be attributed to the fact that these bats use vision and smell along with echolocation to forage the food.

Echolocation adaptations during high-speed roost re-entry for Brazilian free-tailed bats (Tadarida brasiliensis).

Some bats re-enter their cave while using echolocation at very high speeds, but this behavior is poorly studied. Thermal imaging and an array of ultrasonic microphones were used to investigate the acoustic adaptations made during high-speed re-entry for single bats entering a cave. There was a significant overall effect between bat, distance to the ground, and its flight speed on pulse duration and interpulse interval (IPI). The data imply that overall bats reduce pulse duration, IPI, and bandwidth as they approach the cave and slow down, but the behavior changes among individuals.

Forward masking enhances the auditory brainstem response in the free-tailed bat, Tadarida brasiliensis, during a critical time window for sonar reception.

Forward masking is a widespread auditory phenomenon in which the response to one sound transiently reduces the response to a succeeding sound. This study used auditory brainstem responses to measure temporal masking effects in the free-tailed bat, Tadarida brasiliensis. A digital subtraction protocol was used to isolate responses to the second of a pair of pulses varying in interval, revealing a suppression phase lasting <4 ms followed by an enhancement phase lasting 4-15 ms during which the ABR waveform was amplified up to 100%. The results suggest echolocating bats possess adaptations for enhancing sonar receiver gain shortly after pulse emission.

The effect of local land use on aerial insectivorous bats (Chiroptera) within the two dominating crop types in the Northern-Caribbean lowlands of Costa Rica.

Land transformation into agricultural areas and the intensification of management practices represent two of the most devastating threats to biodiversity worldwide. Within this study, we investigated the effect of intensively managed agroecosystems on bat activity and species composition within two focal areas differing in landscape structure. We sampled bats via acoustic monitoring and insects with flight interception traps in banana and pineapple monoculture plantations and two nearby protected forested areas within the area of Sarapiquí, Costa Rica. Our results revealed that general occurrence and feeding activity of bats was higher above plantations compared to forested areas. We also recorded higher species richness at recording sites in plantations. This trend was especially strong within a fragmented landscape, with only four species recorded in forests, but 12 above pineapple plantations. Several bat species, however, occurred only once or twice above plantations, and forest specialist species such as Centronycteris centralis, Myotis riparius and Pteronotus mesoamericanus were only recorded at forest sites. Our results indicated, that mostly mobile open space and edge foraging bat species can use plantations as potential foraging habitat and might even take advantage of temporal insect outbreaks. However, forests are vital refugia for several species, including slower flying forest specialists, and thus a prerequisite to safeguard bat diversity within agricultural dominated landscapes.

Sound Generating Structures of the Humpback Dolphin Sousa plumbea (Cuvier, 1829) and the Directionality in Dolphin Sounds.

The macroscopic morphology of structures involved in sound generation in the Indian Ocean humpback dolphin (Sousa plumbea) were described for the first time using computed tomography imaging and standard gross dissection techniques. The Indian Ocean humpback dolphin may represent a useful comparative model to the bottlenose dolphin (Tursiops sp.) to provide insights into the functional anatomy of the sound production in dolphins, since these coastal dolphins exhibit similar body size and share similarities on acoustic behavior. The general arrangement of sound generating structures, that is, air sacs and muscles, was similar in both the bottlenose dolphin and the Indian Ocean humpback dolphin. The main difference between the two species existed in a small left posterior branch of the melon in the Indian Ocean humpback dolphin, which was not found in the bottlenose dolphin and might reflect an adaptation of directionality for high frequency communication sounds as seen in some other delphinids (e.g., Lagenorhynchus sp., Grampus griseus). Thus, this may be the main reason for the asymmetry of the sound production structures in dolphins. Additionally, the longer rostrum in Indian Ocean humpback dolphins might suggest a more directional echolocation beam compared to the Lahille's bottlenose dolphin. Anat Rec, 302:849-860, 2019. © 2018 Wiley Periodicals, Inc.

Coexistence of two sympatric cryptic bat species in French Guiana: insights from genetic, acoustic and ecological data.

BACKGROUND: The distinction between lineages of neotropical bats from the Pteronotus parnellii species complex has been previously made according to mitochondrial DNA, and especially morphology and acoustics, in order to separate them into two species. In these studies, either sample sizes were too low when genetic and acoustic or morphological data were gathered on the same individuals, or genetic and other data were collected on different individuals. In this study, we intensively sampled bats in 4 caves and combined all approaches in order to analyse genetic, morphologic, and acoustic divergence between these lineages that live in the same caves in French Guiana. RESULTS: A multiplex of 20 polymorphic microsatellite markers was developed using the 454-pyrosequencing technique to investigate for the first time the extent of reproductive isolation between the two lineages and the population genetic structure within lineages. We genotyped 748 individuals sampled between 2010 and 2015 at the 20 nuclear microsatellite loci and sequenced a portion of the cytochrome c oxydase I gene in a subset of these. Two distinct, non-overlapping haplogroups corresponding to cryptic species P. alitonus and P. rubiginosus were revealed, in accordance with previous findings. No spatial genetic structure between caves was detected for both species. Hybridization appeared to be quite limited (0.1-4%) using microsatellite markers whereas introgression was more common (7.5%) and asymmetric for mitochondrial DNA (mtDNA). CONCLUSIONS: The extremely low rate of hybridization could be explained by differences in life cycle phenology between species as well as morphological and acoustical distinction between sexes in one or the other species. Taken together, these results add to our growing understanding of the nature of species boundaries in Pteronotus parnelli, but deserve more in-depth studies to understand the evolutionary processes underlying asymmetric mtDNA introgression in this group of cryptic species.

Species-level classification of beaked whale echolocation signals detected in the northern Gulf of Mexico.

This study presents and evaluates several methods for automated species-level classification of echolocation clicks from three beaked whale species recorded in the northern Gulf of Mexico. The species included are Cuvier's and Gervais' beaked whales, as well as an unknown species denoted Beaked Whale Gulf. An optimal feature set for discriminating the three click types while also separating detected clicks from unidentified delphinids was determined using supervised step-wise discriminant analysis. Linear and quadratic discriminant analyses both achieved error rates below 1% with three features, determined by tenfold cross validation. The waveform fractal dimension was found to be a highly ranked feature among standard spectral and temporal parameters. The top-ranking features were Higuchi's fractal dimension, spectral centroid, Katz's fractal dimension, and -10 dB duration. Six clustering routines, including four popular network-based algorithms, were also evaluated as unsupervised classification methods using the selected feature set. False positive rates of 0.001 and 0.024 were achieved by Chinese Whispers and spectral clustering, respectively, across 200 randomized trials. However, Chinese Whispers clustering yielded larger false negative rates. Spectral clustering was further tested on clicks from encounters of beaked, sperm, and pilot whales in the Tongue of the Ocean, Bahamas.

Automated classification of dolphin echolocation click types from the Gulf of Mexico.

Delphinids produce large numbers of short duration, broadband echolocation clicks which may be useful for species classification in passive acoustic monitoring efforts. A challenge in echolocation click classification is to overcome the many sources of variability to recognize underlying patterns across many detections. An automated unsupervised network-based classification method was developed to simulate the approach a human analyst uses when categorizing click types: Clusters of similar clicks were identified by incorporating multiple click characteristics (spectral shape and inter-click interval distributions) to distinguish within-type from between-type variation, and identify distinct, persistent click types. Once click types were established, an algorithm for classifying novel detections using existing clusters was tested. The automated classification method was applied to a dataset of 52 million clicks detected across five monitoring sites over two years in the Gulf of Mexico (GOM). Seven distinct click types were identified, one of which is known to be associated with an acoustically identifiable delphinid (Risso's dolphin) and six of which are not yet identified. All types occurred at multiple monitoring locations, but the relative occurrence of types varied, particularly between continental shelf and slope locations. Automatically-identified click types from autonomous seafloor recorders without verifiable species identification were compared with clicks detected on sea-surface towed hydrophone arrays in the presence of visually identified delphinid species. These comparisons suggest potential species identities for the animals producing some echolocation click types. The network-based classification method presented here is effective for rapid, unsupervised delphinid click classification across large datasets in which the click types may not be known a priori.

Testing Convergent Evolution in Auditory Processing Genes between Echolocating Mammals and the Aye-Aye, a Percussive-Foraging Primate.

Several taxonomically distinct mammalian groups-certain microbats and cetaceans (e.g., dolphins)-share both morphological adaptations related to echolocation behavior and strong signatures of convergent evolution at the amino acid level across seven genes related to auditory processing. Aye-ayes (Daubentonia madagascariensis) are nocturnal lemurs with a specialized auditory processing system. Aye-ayes tap rapidly along the surfaces of trees, listening to reverberations to identify the mines of wood-boring insect larvae; this behavior has been hypothesized to functionally mimic echolocation. Here we investigated whether there are signals of convergence in auditory processing genes between aye-ayes and known mammalian echolocators. We developed a computational pipeline (Basic Exon Assembly Tool) that produces consensus sequences for regions of interest from shotgun genomic sequencing data for nonmodel organisms without requiring de novo genome assembly. We reconstructed complete coding region sequences for the seven convergent echolocating bat-dolphin genes for aye-ayes and another lemur. We compared sequences from these two lemurs in a phylogenetic framework with those of bat and dolphin echolocators and appropriate nonecholocating outgroups. Our analysis reaffirms the existence of amino acid convergence at these loci among echolocating bats and dolphins; some methods also detected signals of convergence between echolocating bats and both mice and elephants. However, we observed no significant signal of amino acid convergence between aye-ayes and echolocating bats and dolphins, suggesting that aye-aye tap-foraging auditory adaptations represent distinct evolutionary innovations. These results are also consistent with a developing consensus that convergent behavioral ecology does not reliably predict convergent molecular evolution.

Amazon river dolphins (Inia geoffrensis) modify biosonar output level and directivity during prey interception in the wild.

Toothed whales have evolved to live in extremely different habitats and yet they all rely strongly on echolocation for finding and catching prey. Such biosonar-based foraging involves distinct phases of searching for, approaching and capturing prey, where echolocating animals gradually adjust sonar output to actively shape the flow of sensory information. Measuring those outputs in absolute levels requires hydrophone arrays centred on the biosonar beam axis, but this has never been done for wild toothed whales approaching and capturing prey. Rather, field studies make the assumption that toothed whales will adjust their biosonar in the same manner to arrays as they will when approaching prey. To test this assumption, we recorded wild botos (Inia geoffrensis) as they approached and captured dead fish tethered to a hydrophone in front of a star-shaped seven-hydrophone array. We demonstrate that botos gradually decrease interclick intervals and output levels during prey approaches, using stronger adjustment magnitudes than predicted from previous boto array data. Prey interceptions are characterised by high click rates, but although botos buzz during prey capture, they do so at lower click rates than marine toothed whales, resulting in a much more gradual transition from approach phase to buzzing. We also demonstrate for the first time that wild toothed whales broaden biosonar beamwidth when closing in on prey, as is also seen in captive toothed whales and bats, thus resulting in a larger ensonified volume around the prey, probably aiding prey tracking by decreasing the risk of prey evading ensonification.