Genome‐wide detection of CNVs associated with beak deformity in chickens using high‐density 600K SNP arrays

Beak deformity (crossed beaks) is found in several indigenous chicken breeds including Beijing‐You studied here. Birds with deformed beaks have reduced feed intake and poor production performance. Recently, copy number variation (CNV) has been examined in many species and is recognized as a source of genetic variation, especially for disease phenotypes. In this study, to unravel the genetic mechanisms underlying beak deformity, we performed genome‐wide CNV detection using Affymetrix chicken high‐density 600K data on 48 deformed‐beak and 48 normal birds using penncnv . As a result, two and eight CNV regions (CNVRs) covering 0.32 and 2.45 Mb respectively on autosomes were identified in deformed‐beak and normal birds respectively. Further RT‐qPCR studies validated nine of the 10 CNVRs. The ratios of six CNVRs were significantly different between deformed‐beak and normal birds (P < 0.01). Within these six regions, three and 21 known genes were identified in deformed‐beak and normal birds respectively. Bioinformatics analysis showed that these genes were enriched in six GO terms and one KEGG pathway. Five candidate genes in the CNVRs were further validated using RT‐qPCR. The expression of LRIG2 (leucine rich repeats and immunoglobulin like domains 2) was lower in birds with deformed beaks (P < 0.01). Therefore, the LRIG2 gene could be considered a key factor in view of its known functions and its potential roles in beak deformity. Overall, our results will be helpful for future investigations of the genomic structural variations underlying beak deformity in chickens.     

The skull evolution of oviraptorosaurian dinosaurs: the role of niche partitioning in diversification

Oviraptorosaurs are bird‐like theropod dinosaurs that thrived in the final pre‐extinction ecosystems during the latest Cretaceous, and the beaked, toothless skulls of derived species are regarded as some of the most peculiar among dinosaurs. Their aberrant morphologies are hypothesized to have been caused by rapid evolution triggered by an ecological/biological driver, but little is known about how their skull shapes and functional abilities diversified. Here, we use quantitative techniques to study oviraptorosaur skull form and mandibular function. We demonstrate that the snout is particularly variable, that mandibular form and upper/lower beak form are significantly correlated with phylogeny, and that there is a strong and significant correlation between mandibular function and mandible/lower beak shape, suggesting a form–function association. The form–function relationship and phylogenetic signals, along with a moderate allometric signal in lower beak form, indicate that similar mechanisms governed beak shape in oviraptorosaurs and extant birds. The two derived oviraptorosaur clades, oviraptorids and caenagnathids, are significantly separated in morphospace and functional space, indicating that they partitioned niches. Oviraptorids coexisting in the same ecosystem are also widely spread in morphological and functional space, suggesting that they finely partitioned feeding niches, whereas caenagnathids exhibit extreme disparity in beak size. The diversity of skull form and function was likely key to the diversification and evolutionary success of oviraptorosaurs in the latest Cretaceous.     

东太平洋公海茎柔鱼饵料中鱼类和头足类组成初步分析

茎柔鱼(Dosidicus gigas)广泛分布于东太平洋海域,在海洋生态系统中扮演着重要角色。本研究根据2019年6—12月我国鱿钓生产船在东太平洋公海采集的62尾茎柔鱼样本,对其胃含物残留的4131个耳石和75个角质颚样本进行鉴定分析。结果表明: 茎柔鱼主要摄食鱼类10种、头足类4种。从摄食饵料的出现频率和数量百分比来看,主要摄食的鱼类饵料为荧串光鱼、朗明灯鱼和墨西哥尾灯鱼,荧串光鱼在不同胴长组的茎柔鱼胃内均有出现,是茎柔鱼最重要的饵料;摄食的头足类主要有茎柔鱼、鸢乌贼和爪乌贼。随着胴长的增大,茎柔鱼摄食的饵料种类不断增加,头足类和灯笼鱼饵料比例增加,且摄食的饵料尺寸增大,摄食营养结构发生改变,摄食营养水平随之提高。研究结果可为评估不同饵料生物在茎柔鱼食性转变过程中的食物贡献提供基础资料。     

Naris and beak malformation caused by the parasitic fly, Philornis downsi (Diptera: Muscidae), in Darwin's small ground finch, Geospiza fuliginosa (Passeriformes: Emberizidae)

Parasites induce phenotypic modifications in their hosts, which can compromise host fitness. For example, the parasitic fly Philornis downsi , which was recently introduced to the Galápagos Islands, causes severe naris and beak malformation in Darwin's finches. The fly larvae feed on tissues from the nares of developing finch nestlings, thereby altering the size and shape of the nares and beak. Although the parasitism is age-specific (adult finches are not parasitized), naris and beak malformations persist into adulthood as parasite-induced malformations. We systematically examined adult populations of Darwin's small ground finch, Geospiza fuliginosa , on the islands of Santa Cruz for P. downsi -induced malformation. We found that malformed birds had significantly longer nares, and shorter, shallower beaks, than birds considered to be normal (i.e. with no nares or beak malformation). In addition, normal birds showed an isometry between naris length and beak dimensions (beak length feather and beak depth), which was not found in malformed birds. These differences suggest that beak morphology was influenced by P. downsi parasitism. Interestingly, we did not find any evidence of developmental impairment (smaller body size) or reduced foraging efficiency (lower body condition) between normal and malformed birds. Our findings of P. downsi -induced malformation raise new questions about the evolutionary trajectory and conservation status for this group of birds.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 98 , 577–585.     

A developing paradigm for the development of bird beaks

Some adaptive radiations are notable for extreme interspecific diversification in one or a few adult traits. How and why have trait differences evolved? Natural and sexual selection often provide answers to the question of why. An answer to the question of how is to be found in the genetic control of the phenotypic traits, especially in the early stages of development, when interspecific differences first become expressed. Recent studies of the molecular genetic control of beak development in Darwin's finches have shown that a signalling molecule (BMP4) plays a key role in the development of large and deep beaks. Expression of this molecule occurs earlier (heterochrony) and at higher levels in species with deep beaks compared with species with more pointed beaks. The implication of this finding is that variation in the regulation of one or a few genes that are expressed early could be the source of evolutionarily significant variation that is subject to natural selection in speciation and adaptive radiation. This view is reinforced by parallel findings with the same signalling molecule in the development of jaw morphology in cichlid fish of the Great Lakes of Africa. Further research into regulatory mechanisms is to be expected, as well as extension to other examples of radiation such as honeycreepers in Hawaii and Anolis lizards in the Caribbean. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 88 , 17–22.     

Functional morphology of the cephalopod buccal mass: a novel joint type

The arrangement of the musculature and connective tissues of the buccal mass of the coleoid cephalopods Octopus bimaculoides, Sepia officinalis, and Loliguncula brevis was examined using dissection and histology. Serial sections in three mutually perpendicular planes were used to identify the muscles and connective tissues responsible for beak movements and stability and to describe their morphology and fiber trajectories. Four major beak muscles were identified: the anterior, posterior, superior, and lateral mandibular muscles. The anterior, posterior, and superior mandibular muscles connect the upper beak and the lower beak. Although the lateral mandibular muscles originate on the upper beak, they do not connect to the lower beak and instead insert on a connective tissue sheath surrounding the buccal mass. Examination of the fibers of the lateral mandibular muscles reveals that they have the organization of a muscular hydrostat, with muscle fibers oriented in three mutually perpendicular orientations. Although the beaks are capable of complex opening, closing, and shearing movements, they do not contact one another and are instead connected only by the musculature of the buccal mass. Based on the morphological analysis and observations of freshly dissected beaks undergoing the stereotyped bite cycle, the functional role of the beak muscles is hypothesized. The anterior and superior mandibular muscles are likely responsible for beak closing and shearing movements. The posterior mandibular muscle is likely also involved in beak closing, but may act synergistically with the lateral mandibular muscles to open the beaks. The lateral mandibular muscles may use a muscular-hydrostatic mechanism to control the location of the pivot between the beaks and to generate the force required for beak opening. The lack of contact between the beaks and the morphology of the lateral mandibular muscles suggests that the buccal mass of coleoid cephalopods may represent a previously unexamined flexible joint mechanism. The term "muscle articulation" is proposed here to denote the importance of the musculature in the function of such a joint.     

Beak from the body chamber of an Early Carboniferous shelled longiconic coleoid cephalopod from Arkansas,USA

Here we report the discovery of an Early Carboniferous (Late Visean) 3D cephalopod beak displaying significant similarity to the lower beak of Recent coleoids. It was uncovered in a fragmentarily preserved, longiconic shell from the Moorefield Formation in Arkansas, USA. This shell comprises a fractured 29‐mm‐long body chamber having a maximum diameter of ~14 mm and showing an indistinct pro‐ostracum‐like structure. The beak‐bearing shell could easily have been mistaken for a bactritid or orthocerid if it were not for a coleoid‐type, weakly mineralized, evidently organic‐rich shell wall which shows a lamello‐columnar ultrastructure of a bulk of shell wall thickness and plate ultrastructure of thin outer layer. The specimen is assigned to an as‐yet unnamed shelled coleoid of a so far unknown high‐level taxonomic group. A partially exposed, 4.0‐mm‐long portion of the beak is the lower beak in oblique view from its left side. It exhibits fractured anthracite‐like black, apparently originally chitin material, helmet‐like general shape, broad hood with narrow shallow median groove and small notch posteriorly, pronounced pointed, non‐biomineralized upside belt rostrum, high shoulder and about a 90–100 degrees jaw angle. A broad hood and massive rostrum emphasize its similarity to the lower mandible of Recent Vampyroteuthis and signify that its unique, among living coleoids, structure has been existed for at least since Late Visean time (~333 my).     

Smaller beaks for colder winters: Thermoregulation drives beak size evolution in Australasian songbirds

Birds’ beaks play a key role in foraging, and most research on their size and shape has focused on this function. Recent findings suggest that beaks may also be important for thermoregulation, and this may drive morphological evolution as predicted by Allen's rule. However, the role of thermoregulation in the evolution of beak size across species remains largely unexplored. In particular, it remains unclear whether the need for retaining heat in the winter or dissipating heat in the summer plays the greater role in selection for beak size. Comparative studies are needed to evaluate the relative importance of these functions in beak size evolution. We addressed this question in a clade of birds exhibiting wide variation in their climatic niche: the Australasian honeyeaters and allies (Meliphagoidea). Across 158 species, we compared species’ climatic conditions extracted from their ranges to beak size measurements in a combined spatial‐phylogenetic framework. We found that winter minimum temperature was positively correlated with beak size, while summer maximum temperature was not. This suggests that while diet and foraging behavior may drive evolutionary changes in beak shape, changes in beak size can also be explained by the beak's role in thermoregulation, and winter heat retention in particular.     

A new Lower Cretaceous bird from China and tooth reduction in early avian evolution

A new avian genus and species, Zhongjianornis yangi gen. et sp. nov., is reported from the Lower Cretaceous lacustrine deposits of the Jiufotang Formation in Liaoning, northeast China. The new taxon is characterized by possessing the following combination of features: upper and lower jaws toothless, snout pointed, humerus with large and robust deltopectoral crest, second phalanx of the major manual digit longer than the first phalanx, unguals of the alular and major digits of similar length and significantly shorter than the corresponding penultimate phalanges, tibiotarsus slender and more than twice the length of the tarsometatarsus, and metatarsal IV longer than the other metatarsals. Phylogenetic analysis indicates that Zhongjianornis is phylogenetically basal to Confuciusornis and the dominant Mesozoic avian groups, Enantiornithes and Ornithurae, and therefore provides significant new information regarding the diversification of birds in the Early Cretaceous. It also represents the most basal bird that completely lacks teeth, suggesting that tooth loss was more common than expected in early avian evolution and that the avian beak appeared independently in several avian lineages, most probably as a response to selective pressure for weight reduction. Finally, the presence of a significantly enlarged humeral deltopectoral crest suggests that Zhongjianornis shares with other basal birds such as Jeholornis, Sapeornis and Confuciusornis a distinctive mode of adaptation for flight contrasting with that seen in more advanced birds, which instead possess an elongated sternum and a prominent keel.