scholarly journals Across-Species Pose Estimation in Poultry Based on Images Using Deep Learning

2021 ◽  
Vol 2 ◽  
Author(s):  
Jan Erik Doornweerd ◽  
Gert Kootstra ◽  
Roel F. Veerkamp ◽  
Esther D. Ellen ◽  
Jerine A. J. van der Eijk ◽  
...  
Keyword(s):  
Pose Estimation ◽  
Genetic Parameters ◽  
Single Species ◽  
Target Species ◽  
Data Annotation ◽  
Future Studies ◽  
Test Sets ◽  
Species Performance ◽  
Direct Use ◽  
Pixel Error

Animal pose-estimation networks enable automated estimation of key body points in images or videos. This enables animal breeders to collect pose information repeatedly on a large number of animals. However, the success of pose-estimation networks depends in part on the availability of data to learn the representation of key body points. Especially with animals, data collection is not always easy, and data annotation is laborious and time-consuming. The available data is therefore often limited, but data from other species might be useful, either by itself or in combination with the target species. In this study, the across-species performance of animal pose-estimation networks and the performance of an animal pose-estimation network trained on multi-species data (turkeys and broilers) were investigated. Broilers and turkeys were video recorded during a walkway test representative of the situation in practice. Two single-species and one multi-species model were trained by using DeepLabCut and tested on two single-species test sets. Overall, the within-species models outperformed the multi-species model, and the models applied across species, as shown by a lower raw pixel error, normalized pixel error, and higher percentage of keypoints remaining (PKR). The multi-species model had slightly higher errors with a lower PKR than the within-species models but had less than half the number of annotated frames available from each species. Compared to the single-species broiler model, the multi-species model achieved lower errors for the head, left foot, and right knee keypoints, although with a lower PKR. Across species, keypoint predictions resulted in high errors and low to moderate PKRs and are unlikely to be of direct use for pose and gait assessments. A multi-species model may reduce annotation needs without a large impact on performance for pose assessment, however, with the recommendation to only be used if the species are comparable. If a single-species model exists it could be used as a pre-trained model for training a new model, and possibly require a limited amount of new data. Future studies should investigate the accuracy needed for pose and gait assessments and estimate genetic parameters for the new phenotypes before pose-estimation networks can be applied in practice.

scholarly journals Genetic Variability, Correlation among Agronomic Traits, and Genetic Progress in a Sugarcane Diversity Panel

Agriculture ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 533
Author(s):  
Fernanda Zatti Barreto ◽  
Thiago Willian Almeida Balsalobre ◽  
Roberto Giacomini Chapola ◽  
Antonio Augusto Franco Garcia ◽  
Anete Pereira Souza ◽  
...  
Keyword(s):  
Genetic Parameters ◽  
Mixed Model ◽  
Agronomic Traits ◽  
Average Increase ◽  
Genetic Progress ◽  
Breeding Programs ◽  
Future Studies ◽  
Diversity Panel ◽  
Adjusted Means ◽  
Historical Series

Sugarcane breeding programs require 15 years of experimentation to create more productive cultivars, and estimates of genetic progress can indicate the efficiency of breeding programs. In this study, we used a diversity panel, the Brazilian Panel of Sugarcane Genotypes (BPSG), with the following objectives: (i) to estimate, through a mixed model, the adjusted means and genetic parameters of ten traits evaluated over three harvest years; (ii) to estimate genotypic correlation among those traits; and (iii) to estimate genetic progress over six decades of breeding. The heritabilities ranged from 0.43 to 0.88, and we detected 42 significant correlations, 9 negative and 33 positive. Over six decades, the sucrose-related traits BRIX, POL%C, and POL%J showed an average increase per decade of 0.27 °Brix (0.26% and 0.31%, respectively). Stalk number, height, and weight of the plot, and cane and sucrose yields revealed average increases per decade of 3.27 stalks, 0.06 m, 9.42 kg, 11.22 t/ha, and 2.08 t/ha, respectively. The genetic progress of the main agronomic traits is discussed through a historical series of sugarcane genotypes present in the BPSG. The findings of this study could contribute to the management of new breeding strategies and allow for future studies of associative mapping.

Quantitative Detection of Species-Specific DNA in Feedstuffs and Fish Meals

2005 ◽  
Vol 68 (6) ◽  
pp. 1217-1221 ◽  
Author(s):  
PAVEL KRCMAR ◽  
EVA RENCOVA
Keyword(s):  
Mitochondrial Dna ◽  
Real Time ◽  
Dna Sequences ◽  
Real Time Pcr ◽  
Single Species ◽  
Absolute Quantification ◽  
Quantitative Detection ◽  
Vertebrate Species ◽  
Target Species ◽  
Species Specific

A sensitive and rapid method for the quantitative detection of bovine-, ovine-, swine-, and chicken-specific mitochondrial DNA sequences based on real-time PCR has been developed. The specificity of the primers and probes for real-time PCR has been tested using DNA samples of other vertebrate species that may also be present in rendered products. The quantitative detection was performed with dual-labeled probes (TaqMan) using absolute quantification with external standards of single species meat-and-bone meals. This method facilitates the detection of 0.01% of the target species–derived material in concentrate feed mixtures and fish meals.

scholarly journals Declassifying Myrmecophily in the Coleoptera to Promote the Study of Ant-Beetle Symbioses

2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
Glené Mynhardt
Keyword(s):  
Classification Scheme ◽  
Morphological Characteristics ◽  
Behavioral Data ◽  
Target Species ◽  
Classification Schemes ◽  
Future Studies ◽  
Symbiotic Associations ◽  
Behavioral Studies ◽  
Morphological Adaptations ◽  
Evolutionary Studies

The symbiotic associations between beetles and ants have been observed in at least 35 beetle families. Among myrmecophiles, beetles exhibit the most diverse behavioral and morphological adaptations to a life with ants. These various associations have historically been grouped into discrete but overlapping behavioral categories, many of which are still used in the modern literature. While these behavioral classifications provide a rich foundation for the study of ant-beetle symbioses, the application of these systems in future studies may be less than effective. Since morphological characteristics often provide the only information of myrmecophilous beetles, they should be studied in a species-by-species fashion, as behavioral data are often limited or unavailable. Similarly, behavioral studies should focus on the target species at hand, avoiding discrete classification schemes. I formally propose the rejection of any classification scheme, in order to promote future studies of myrmecophily in both taxonomic and evolutionary studies.

scholarly journals Evolution of the patella and patelloid in marsupial mammals

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9760
Author(s):  
Alice L. Denyer ◽  
Sophie Regnault ◽  
John R. Hutchinson
Keyword(s):  
Maximum Likelihood ◽  
Developmental Plasticity ◽  
Ct Scanning ◽  
Reconstruction Algorithm ◽  
Single Species ◽  
Character State ◽  
Sesamoid Bone ◽  
Future Studies ◽  
Marsupial Species ◽  
Complex Patterns

The musculoskeletal system of marsupial mammals has numerous unusual features beyond the pouch and epipubic bones. One example is the widespread absence or reduction (to a fibrous “patelloid”) of the patella (“kneecap”) sesamoid bone, but prior studies with coarse sampling indicated complex patterns of evolution of this absence or reduction. Here, we conducted an in-depth investigation into the form of the patella of extant marsupial species and used the assembled dataset to reconstruct the likely pattern of evolution of the marsupial patella. Critical assessment of the available literature was followed by examination and imaging of museum specimens, as well as CT scanning and histological examination of dissected wet specimens. Our results, from sampling about 19% of extant marsupial species-level diversity, include new images and descriptions of the fibrocartilaginous patelloid in Thylacinus cynocephalus (the thylacine or “marsupial wolf”) and other marsupials as well as the ossified patella in Notoryctes ‘marsupial moles’, Caenolestes shrew opossums, bandicoots and bilbies. We found novel evidence of an ossified patella in one specimen of Macropus rufogriseus (Bennett’s wallaby), with hints of similar variation in other species. It remains uncertain whether such ossifications are ontogenetic variation, unusual individual variation, pathological or otherwise, but future studies must continue to be conscious of variation in metatherian patellar sesamoid morphology. Our evolutionary reconstructions using our assembled data vary, too, depending on the reconstruction algorithm used. A maximum likelihood algorithm favours ancestral fibrocartilaginous “patelloid” for crown clade Marsupialia and independent origins of ossified patellae in extinct sparassodonts, peramelids, notoryctids and caenolestids. A maximum parsimony algorithm favours ancestral ossified patella for the clade [Marsupialia + sparassodonts] and subsequent reductions into fibrocartilage in didelphids, dasyuromorphs and diprotodonts; but this result changed to agree more with the maximum likelihood results if the character state reconstructions were ordered. Thus, there is substantial homoplasy in marsupial patellae regardless of the evolutionary algorithm adopted. We contend that the most plausible inference, however, is that metatherians independently ossified their patellae at least three times in their evolution. Furthermore, the variability of the patellar state we observed, even within single species (e.g. M. rufogriseus), is fascinating and warrants further investigation, especially as it hints at developmental plasticity that might have been harnessed in marsupial evolution to drive the complex patterns inferred here.

scholarly journals Single-Species Co-management Improves Fish Assemblage Structure and Composition in a Tropical River

2021 ◽  
Vol 9 ◽  
Author(s):  
Wendell M. Medeiros-Leal ◽  
Leandro Castello ◽  
Carlos E. C. Freitas ◽  
Flávia K. Siqueira-Souza
Keyword(s):  
Fish Assemblage ◽  
Amazon Basin ◽  
Fish Assemblages ◽  
Single Species ◽  
Floodplain Lakes ◽  
Fish Diversity ◽  
Fish Assemblage Structure ◽  
Target Species ◽  
Limited Access ◽  
Positive Effects

Co-management is increasingly recognized as an effective model for managing fisheries, but little information exists on whether co-management can produce effects in species other than the target species. Fishery co-management in the tropics, where fish diversity is high and fish catches tend to be multispecies, is prone to produce assemblage-wide effects via alterations in the food web and changes in the overall capture of non-target species. Here, we assessed the effects of co-management for the species Arapaima sp. in relation to the structure and composition of the overall fish assemblage in floodplain lakes of the central Amazon Basin. These floodplain lakes are managed under a system of zoning of fishing activities. We used data from surveys of six floodplain lakes, including two lakes of each of three categories (lakes where fishing is prohibited, limited-access lakes, and open fishing lakes). The surveys were carried out before and after implementation of co-management, through gillnet fishing. The study area was the lower Solimões River, in the Amazon Basin, Brazil. Statistical models showed significant changes in the composition and structure of the fish assemblages after the implementation of the co-management, regardless of the zoning category. Through regulation of gear use and fishing practices, co-management allowed the colonization of species that had not been present before, which lead to higher richness and consequently increased fish sizes, abundance and biomass. Species of sedentary habits, migrants of short and medium distances, with commercial importance benefited the most from co-management. In the results presented in temporal scale, it was possible to observe a potential spillover effect being provided by the lakes where fishing is prohibited (no-take zones) and those of limited access that benefited those open to fishing. Thus, co-management had positive effects in the structure and composition of fish assemblages in all lakes, regardless of zoning category.

scholarly journals Elucidating Patterns in the Occurrence of Threatened Ground-Dwelling Marsupials Using Camera-Traps

Animals ◽  
2019 ◽  
Vol 9 (11) ◽  
pp. 913 ◽  
Author(s):  
Claridge ◽  
Paull ◽  
Welbourne
Keyword(s):  
Mammalian Species ◽  
Sampling Strategy ◽  
Single Species ◽  
Camera Traps ◽  
Target Species ◽  
Baseline Information ◽  
The Relationship ◽  
Term Monitoring ◽  
Survey Effort

Establishing trends in endangered fauna against management efforts is a key but often challenging enterprise. Camera-traps offer a new and literal window into monitoring many different mammalian species. Getting it right demands seeking baseline information about how often target species interact with these devices, prior to setting a long-term monitoring strategy. We used a camera-trap array to collect detection data on three species of threatened ground-dwelling marsupials in south-eastern mainland Australia. Over a four-year period, occupancy estimates for two species of bandicoot (southern brown bandicoot Isoodon obesulus and long-nosed bandicoot Perameles nasuta) and a single species of rat-kangaroo (long-nosed potoroo Potorous tridatylus) were generated. These estimates were variously robust depending on visitation history, but nevertheless indicated persistence of these rare and otherwise under threat species. Detection probability for each species differed between study areas, type of management and with complexity of ground and shrub vegetation cover. The relationship between detection and vegetation structure dictated that survey effort was only robust where conditions were optimal for a given species. Outside of that further survey effort would be required to have confidence in survey outcome. In the future this would demand a different sampling strategy, be that through lengthening survey time or adding additional camera units at sites.

scholarly journals Genetic Analysis of Major Carcass Traits of Korean Hanwoo Males Raised for Thirty Months

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1792
Author(s):  
Mahboob Alam ◽  
Soo Hyun Lee ◽  
Do Hyun Lee ◽  
Chungil Cho ◽  
Mi Na Park
Keyword(s):  
Genetic Parameters ◽  
Carcass Traits ◽  
Production Cycle ◽  
Marbling Score ◽  
Multiple Trait ◽  
Muscle Area ◽  
Eye Muscle ◽  
Future Studies ◽  
Genetic Potential ◽  
First Time

Understanding animals’ genetic potential for carcass traits is the key to genetic improvements in any beef cattle. In this study, we investigated the genetic merits of carcass traits using Hanwoo males raised in a 30-month production system (PROD30). We achieved this using a dataset comprising 6092 Hanwoo males born between 2005 and 2017 and measures of four carcass traits (carcass weight, CWT; eye muscle area, EMA; backfat thickness, BFT; and marbling score, MS). Genetic parameters were estimated using a multiple-trait animal model through the AIREMLF90 program. According to the multiple-trait model, the h2 of CWT, EMA, BFT, and MS were 0.35 ± 0.04, 0.43 ± 0.05, 0.48 ± 0.05, and 0.56 ± 0.05, respectively. The strongest genetic correlation (rg) was obtained between CWT and EMA (0.49 ± 0.07), whereas it was negligible between CWT and BFT. EMA and MS were also moderately correlated, whereas there was a relatively low negative correlation between EMA and BFT (−0.26 ± 0.08). Our study revealed a consistent indirect genetic improvement in animals from 2005 onwards. Although Hanwoo improvement has mainly focused on males under a 24-month production cycle, we observed PROD30 males to have somewhat similar genetic potential. Our results provide useful insights into the genetic merits of PROD30 males for the first time, which may facilitate future studies on them and their integration into the Hanwoo National Evaluation for genomic selection.

scholarly journals Biology of tiny animals: three new species of minute salamanders (Plethodontidae:Thorius) from Oaxaca, Mexico

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2694 ◽  
Author(s):  
Gabriela Parra-Olea ◽  
Sean M. Rovito ◽  
Mario García-París ◽  
Jessica A. Maisano ◽  
David B. Wake ◽  
...  
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
Taxonomic Status ◽  
Single Species ◽  
Molecular Data ◽  
Future Studies ◽  
Sierra Madre ◽  
Disjunct Populations ◽  
Sierra Madre Del Sur ◽  
Three New Species

We describe three new species of minute salamanders, genusThorius, from the Sierra Madre del Sur of Oaxaca, Mexico. Until now only a single species,T. minutissimus, has been reported from this region, although molecular data have long shown extensive genetic differentiation among geographically disjunct populations. AdultThorius pinicolasp. nov.,T. longicaudussp. nov., andT. tlaxiacussp. nov. are larger thanT. minutissimusand possess elliptical rather than oval nostrils;T. pinicolaandT. longicaudusalso have longer tails. All three new species occur west of the range ofT. minutissimus, which has the easternmost distribution of any member of the genus. The new species are distinguished from each other and from other namedThoriusin Oaxaca by a combination of adult body size, external morphology and osteology, and by protein characters (allozymes) and differences in DNA sequences. In addition, we redescribeT. minutissimusand a related species,T. narisovalis, to further clarify the taxonomic status of Oaxacan populations and to facilitate future studies of the remaining genetically differentiatedThoriusthat cannot be satisfactorily assigned to any named species. Populations of all five species considered here appear to have declined dramatically over the last one or two decades and live specimens are difficult to find in nature.Thoriusmay be the most endangered genus of amphibians in the world. All species may go extinct before the end of this century.

Ecosystem Considerations in Fisheries Management: Theory and Practice

2005 ◽  
Vol 20 (3) ◽  
pp. 381-422 ◽  
Author(s):  
Scott Parsons
Keyword(s):  
Fisheries Management ◽  
Single Species ◽  
Ecosystem Approach ◽  
Theory And Practice ◽  
Target Species ◽  
Management Measures ◽  
Species Analysis ◽  
Recent Developments ◽  
Fishing Fleets ◽  
Management Approaches

AbstractThis article examines recent developments with respect to the development and application of an ecosystem approach in marine fisheries management. A number of international fisheries legal instruments now include explicit references to ecosystem considerations. While there has been general agreement on the need to take ecosystem considerations into account, there is no clarity or consensus on how this can best be done. Various definitions of an ecosystem approach emphasise that the focus must be on managing the human activities, which are part of, and impact on, marine ecosystems. An ecosystem approach is neither inconsistent with, nor a replacement for, existing fisheries management approaches—it is not a panacea for the problems confronting world fisheries. Realistically, we can only move to an ecosystem approach incrementally, starting with more rigorous/cautious application and extension of single species methods. A key element of any ecosystem approach will likely be to set harvest rates for target species at even lower conservative levels than might be suggested by single species analysis. Fisheries management measures should also ensure the protection not only of target species, but also of non-target, associated or dependent species. Reducing the killing power of the world's fishing fleets is an essential component of ecosystem-based fisheries management.

scholarly journals The impacts of different management strategies and environmental forcing in ecological communities

2006 ◽  
Vol 273 (1600) ◽  
pp. 2491-2499 ◽  
Author(s):  
Katja Enberg ◽  
Mike S Fowler ◽  
Esa Ranta
Keyword(s):  
Species Interactions ◽  
Management Strategies ◽  
Single Species ◽  
Target Population ◽  
Population Management ◽  
Community Response ◽  
Ecological Communities ◽  
Target Species ◽  
Community Members ◽  
Environmental Forcing

Understanding the effects of population management on the community a target species belongs to is of key importance for successful management. It is known that the removal or extinction of a single species in a community may lead to extinctions of other community members. In our study, we assess the impacts of population management on competitive communities, studying the response of both locally stable and unstable communities of varying size (between four and 10 species) to three different management strategies; harvesting of a target species, harvesting with non-targeted catch, and stocking of the target species. We also studied the consequences of selecting target species with different relative abundances, as well as the effects of varying environmental conditions. We show here how the effects of management in competitive communities extend far beyond the target population. A crucial role is played by the underlying stability properties of the community under management. In general, locally unstable communities are more vulnerable to perturbation through management. Furthermore, the community response is shown to be sensitive to the relative density of the target species. Of considerable interest is the result that even a small (2.5%) increase in the population size of the target species through stocking may lead to extinction of other community members. These results emphasize the importance of considering and understanding multi-species interactions in population management.

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