Cephalopod species identification using integrated analysis of machine learning and deep learning approaches

Background Despite the high commercial fisheries value and ecological importance as prey item for higher marine predators, very limited taxonomic work has been done on cephalopods in Malaysia. Due to the soft-bodied nature of cephalopods, the identification of cephalopod species based on the beak hard parts can be more reliable and useful than conventional body morphology. Since the traditional method for species classification was time-consuming, this study aimed to develop an automated identification model that can identify cephalopod species based on beak images. Methods A total of 174 samples of seven cephalopod species were collected from the west coast of Peninsular Malaysia. Both upper and lower beaks were extracted from the samples and the left lateral views of upper and lower beak images were acquired. Three types of traditional morphometric features were extracted namely grey histogram of oriented gradient (HOG), colour HOG, and morphological shape descriptor (MSD). In addition, deep features were extracted by using three pre-trained convolutional neural networks (CNN) models which are VGG19, InceptionV3, and Resnet50. Eight machine learning approaches were used in the classification step and compared for model performance. Results The results showed that the Artificial Neural Network (ANN) model achieved the best testing accuracy of 91.14%, using the deep features extracted from the VGG19 model from lower beak images. The results indicated that the deep features were more accurate than the traditional features in highlighting morphometric differences from the beak images of cephalopod species. In addition, the use of lower beaks of cephalopod species provided better results compared to the upper beaks, suggesting that the lower beaks possess more significant morphological differences between the studied cephalopod species. Future works should include more cephalopod species and sample size to enhance the identification accuracy and comprehensiveness of the developed model.

The Trichohyalin-Like Protein Scaffoldin Is Expressed in the Multilayered Periderm during Development of Avian Beak and Egg Tooth

Scaffoldin, an S100 fused-type protein (SFTP) with high amino acid sequence similarity to the mammalian hair follicle protein trichohyalin, has been identified in reptiles and birds, but its functions are not yet fully understood. Here, we investigated the expression pattern of scaffoldin and cornulin, a related SFTP, in the developing beaks of birds. We determined the mRNA levels of both SFTPs by reverse transcription polymerase chain reaction (RT-PCR) in the beak and other ectodermal tissues of chicken (Gallus gallus) and quail (Coturnix japonica) embryos. Immunohistochemical staining was performed to localize scaffoldin in tissues. Scaffoldin and cornulin were expressed in the beak and, at lower levels, in other embryonic tissues of both chickens and quails. Immunohistochemistry revealed scaffoldin in the peridermal compartment of the egg tooth, a transitory cornified protuberance (caruncle) on the upper beak which breaks the eggshell during hatching. Furthermore, scaffoldin marked a multilayered peridermal structure on the lower beak. The results of this study suggest that scaffoldin plays an evolutionarily conserved role in the development of the avian beak with a particular function in the morphogenesis of the egg tooth.

Comparative performance and haematological profile of cockerel chickens debeaked at varied length and at different ages

An experiment was conducted to determine the comparative performance of cockerel chickens debeaked at varied length and at different ages. One hundred and ninety-five cockerel birds were purchased from a reputable hatchery, brooded and randomly allotted into 4 treatments of three replicates and 15 birds per replicate. Treatment 1 (T1) served as the control which contained 15 birds that were allotted into 3 replicates without debeaking. At the 4th week, 45 birds were debeaked at varied degrees of debeaking to form treatments 2, 3 and 4 respectively as follows: T2- 1/2 of upper beak and 1/2 of lower beak debeaked using 5 birds per replicate and 3 replicates per treatment, T3-1/2 of upper beak and 1/3 of lower beak debeaked using 5 birds per replicate and 3 replicates per treatment and T4- 1/3 of upper beak and ½ of lower beak were debeaked using 5 birds per replicate and 3 replicates per treatment as it was done in all other treatments. Also, the same procedures used for all the treatments in the 4th week as demonstrated above were repeated in the sixth, eighth and tenth week of age respectively so as to reflect the treatment effect at different ages. Data collected include: initial and final weight, daily feed intake, body weight gain and of haematological parameters. Results showed that varied degrees of debeaking examined significantly affected (p< 0.05) all the performance parameters considered:body weight gain, FCR, heterophil/lymphocyte ratio etc. It was therefore concluded that farmers should imbibe the practice of cutting half of the upper beak and half of the lower beak or one third of the upper beak and half of the lower beak (T2) preferably at the earlier stages of the birds' life as they gave better values for the performance parameters considered.

Functional Significance of Anatomical Accommodation in the Skull of Common Hoopoe, Upupa Epops (Bucerotiformes, Upupidae)

The present study aims to supplement anatomical data about the cranial skeleton and describe some cranial modifications of the common hoopoe, Upupa epops Linnaeus, 1758, by using several techniques. The common hoopoe has small skull and characterized by presence of air space (pneumatization) within their bones. The degree of pneumatization increased especially within the temporal region. The skull of the common hoopoe possesses different types of kinetic hinges; one hinge locates between frontal and nasal region (frontonasal hinge) allows depression/elevation of upper beak relative to brain case. The other one exhibits between the upper beak and jugal bar (maxilla-jugal hinge). The skull of the common hoopoe characterizes by presence of powerful jaw ligamentous system. One of these ligaments exhibits ossification (Lig. Jugomandibularis medialis). In addition, a long mandibular symphysis observes between the two rami of the anterior third of the lower beak. This mandibular symphysis seems longer in the dorsal surface than the ventral one form ventral gap between the two rami of mandible. These modifications of the cranial skeleton of common hoopoe and jaw ligaments consider features of adaptation for probe mechanism, as well as exhibit its phylogenetic relationship with other avian species.

Recent findings of Ommastrephes bartramii (Cephalopoda: Ommastrephidae) in the eastern Mediterranean and the implication on its range expansion

The neon flying squid Ommastrephes bartramii is found circumglobally in subtropical, temperate waters and sustains important fisheries in the North Pacific, but it is rarely encountered in the Mediterranean Sea. During the last decade, and particularly since 2004, the frequency of its presence in the Aegean Sea and nearby regions has increased, raising a question about a change in the species distribution and abundance in this area. In this study, we reviewed the literature on O. bartramii findings in the Mediterranean Sea and present new data describing body and beak morphometry, diet and the maturity of specimens recently collected from the easternmost basins. According to data from the entire Mediterranean Sea, collected individuals reached 66 cm in mantle length (ML), wherein only females were larger than 32 cm in ML. An isometric growth in body weight (BW) was shown, whereas the lower beak rostral length (LRL) was allometrically positive in relation to the ML. Occasional catches by jigs during experimental cruises provided most of the individuals recorded in the period from 1982-1992. In contrast, the most recent records are primarily comprised of mature females collected on or near the shore in the eastern basin and of predominantly smaller individuals from the western basin caught by professional jigging fisheries. The distribution of the specimen recorded from the Aegean Sea indicates an association between the species distribution and the circulation of the warm Levantine Intermediate Water. The more frequent observations of moribund spawning females at the periphery of the Cretan Sea are indicative of a spawning ground at this area. The suspected recent increase of O. bartramii abundance in both the northeastern and northwestern basins might be due to the warming of upper sea layers, which has been observed since the mid-1980s and is considered to be the main factor driving the northward expansion of the warm-water species’ range within the Mediterranean Sea.

Systematics of the Onychoteuthidae Gray, 1847 (Cephalopoda: Oegopsida)

Squids in the family Onychoteuthidae Gray, 1847, have been reported from every ocean but the Arctic, are taken frequently in deep-sea fisheries bycatch, and are ecologically important in the diets of many marine predators including cetaceans, pinnipeds, sharks, and seabirds. However, the diversity and systematics of the family have remained poorly understood. Of the 60+ nominal species, 12–14 have generally been accepted in recent studies. Challenges to clarity include insufficient species descriptions, original descriptions published in eight languages and often based solely on early life stages, non-designation or subsequent loss of type material, and the existence of several unresolved species complexes. In light of the general systematic disarray of the Onychoteuthidae, a global revision of the family follows, based on ~1500 specimens examined from 19 repositories. Type material has been examined wherever possible (although, for some species, photographs of type specimens, original illustrations, and/or the original descriptions have provided the only information available). For all 25 species treated in this revision, descriptions and illustrations are provided to a consistent standard that will enable their reidentification. External and internal morphological characters and states are described for subadult to adult stages of most species, with external characters reported through ontogeny as permitted by available material. Historically important characters are treated (general external morphology, body proportions, tentacle clubs, photophores, gladius, lower beak, radula), augmented by several more recently recognised characters (palatine teeth, detailed morphology of the tentacular hooks in adults, tentacular suckers in paralarvae, chromatophore patterns). The systematic value of both historical and new morphological characters at the generic and species levels is discussed; at all ontogenetic stages, tentacular club and hook morphology are considered the most valuable characters, although body proportions and gladius also prove useful. In the interest of systematic stability, neotypes are also designated for four species in which type specimens were not previously designated [Onykia (Onykia) loennbergii Ishikawa & Wakiya, 1914; Onychoteuthis borealijaponica Okada, 1927] or have been subsequently lost [Onykia (Onykia) carriboea Lesueur, 1821; Onykia (Onykia) robsoni Adam, 1962]. Partial resolution of the Onychoteuthis banksii complex has been possible in the Pacific and Atlantic Oceans, resulting in: the resurrection of Onychoteuthis bergii Lichtenstein, 1818, and Onychoteuthis aequimanus Gabb, 1868; the description of two new species in an earlier publication (Onychoteuthis lacrima Bolstad & Seki, and Onychoteuthis prolata Bolstad, Vecchione & Young, in Bolstad, 2008) and another herein, Onychoteuthis horstkottei sp. nov.; and the expansion of one species’ recognised distribution (Onychoteuthis compacta Berry, 1913) to include the Atlantic Ocean. The genus Moroteuthis Verrill, 1881, is considered a junior synonym of Onykia Lesueur, 1821, in accordance with the findings of several earlier authors. However, morphological differences in the species ‘Moroteuthis’ ingens Smith, 1881, necessitate the resurrection of the subgenus Moroteuthopsis Pfeffer, 1908, with all other Onykia species placed into the nominate subgenus Onykia (Onykia). Sexual dimorphism is reported in the beaks of Onykia (Moroteuthopsis) ingens (new comb.). Morphological and historical genetic data suggest a more distant relationship between Onykia and the species ‘Moroteuthis’ knipovitchi Filippova, 1972, than was suggested by earlier classifications. This species is therefore placed into Filippovia gen. nov., described herein. ‘Onykia’ rancureli (Okutani, 1981) and C. youngorum sp. nov. are placed into Callimachus gen. nov., according to morphological and genetic data. Given that the majority of available onychoteuthid material was collected after 1950, resulting in the descriptions of over half of the generally accepted genera and species since 1960, ongoing collection programmes are necessary to further resolve onychoteuthid systematics.

Ultraviolet Beak Spots in King and Emperor Penguins

In seabirds, colors of feathers and external tissues have only recently been studied, and ultraviolet (UV) color has not yet been detected. Using live individuals as well as museum skins, we found UV peaks of reflectance in two large Aptenodytes species, King (A. patagonicus) and Emperor (A. forsteri) Penguins. UV reflectance did not occur on the feathers, claws, or skin of these species, nor did we find UV reflectance in five other genera of penguins (11 species). UV peaks overlapped with spots of color on the lower beak that appeared orange for human observers, and beak spots differed slightly in location between the two species. Adults of both sexes possessed these UV markings, but they were lacking in juveniles, as was the orange color of the beak spot, and auricular patches used for selecting mates. Finally, measurements of free-ranging King Penguins showed that recently paired birds had higher UV reflectance than courting ones, suggesting possible roles of UV beak spots in pairing and as an indicator of sexual maturity. Manchas Ultravioleta en el Pico de los Pingüinos Aptenodytes patagonicus y A. forsteri Resumen. En las aves marinas, los colores de las plumas y los tejidos externos sólo han sido estudiados recientemente, y el color ultravioleta (UV) todavía no se ha detectado. En individuos vivos así como en pieles de museo, nosotros encontramos picos de reflectancia UV en dos especies de pingüinos, Aptenodytes patagonicus y A. forsteri. El color UV no se encontró en las plumas, las garras o la piel de estas especies, ni encontramos color UV en otros cinco géneros de pingüinos (11 especies). Los puntos UV se encontraban superpuestos con manchas de color ubicadas en la parte baja del pico que parecían anaranjadas para los observadores humanos. Las manchas del pico difirieron levemente en forma y localización entre las dos especies. Los adultos de ambos sexos presentaron las manchas UV, pero éstas no estaban presentes en los juveniles, al igual que el color anaranjado de la mancha del pico y los parches auriculares empleados en la selección de parejas. Medidas tomadas en individuos libres de la especie A. patagonicus demostraron que los que se habían apareado recientemente tenían presentaban reflectancias de UV mayores que las de aquellos que aún estaban cortejando, lo que sugiere un posible papel de las manchas UV del pico en el apareamiento y como indicadoras de la madurez sexual.

Analysis of beak morphometry of the horned octopus Eledone cirrhosa (Cephalopoda: Octopoda) in the Thracian Sea (NE Mediterranean)

Cephalopod beaks are chitinous structures situated in the buccal mass lying at the base of their arms. Because they are among the few hard structures of cephalopods with high resistance to erosion during digestive process in predator stomachs, the study of the beak morphometry is of major importance for the species taxonomy, as well as, for the size estimation of the cephalopods consumed. In this study new information is provided on the dimensions and pigmentation process of the upper and lower beak of the horned octopus Eledone cirrhosa derived from 67 female and 47 male specimens caught by trawl in the Thracian Sea (NE Mediterranean). The growth of both beaks was allometric in relation to the mantle length and body weight. According to the results of covariance analysis, no difference was found in growth pattern of beaks between sexes. Four degrees of pigmentation were identified in both upper and lower beaks, the darkening process starting in females at a smaller size.

Adelieledone, a new genus of octopodid from the Southern Ocean

The syntypes of the endemic Southern Ocean octopodid Pareledone polymorpha (Robson, 1930) were re-examined and measurements, counts and indices are presented. The two forms described by Robson, namely oblonga and affinis, are determined to have no taxonomic validity. The species polymorpha shows morphological similarities with Pareledone adelieana (Berry, 1917) but differs in relative arm lengths, sucker counts, external colouration and size at maturity. Both species are transferred to the new genus Adelieledone, which is separated from the genus Pareledone s.s. by the transverse ridges in the ligula groove of the hectocotylus, the sharp tip of the lower beak, the enlarged posterior salivary glands, the absence of stylets and by skin sculpture, especially by the presence of two longitudinal integumentary ridges on the dorsal mantle. A new species, Adelieledone piatkowski, is described from the Antarctic Peninsula. Beak morphology can discriminate the genera in predator studies.

Giant squid beaks: implications for systematics

The systematic position of the giant squid Architeuthis remains unresolved but comparison of beak morphometrics is an approach that has not been attempted before. Additional data for the relationship between mantle length (ML) and lower beak rostral length (LRL) suggest that Architeuthis sp. in the North Atlantic, South Africa and New Zealand are parts of the same asymptotic relationship. Comparison of beak dimensions of Architeuthis from the North Atlantic, South Africa and New Zealand with those of two distinct species of Todarodes, from the Mediterranean and southern Africa, indicate that there may be only one species of Architeuthis in these three regions. No consistent morphological evidence has yet been found to indicate more than one species of Architeuthis in the Atlantic or in the southern hemisphere.