Morphometric dataset of Varanus salvator for non-invasive sex identification using machine learning.

Reliable sex identification in Varanus salvator traditionally relied on invasive methods like genetic analysis or dissection, as less invasive techniques such as hemipenes inversion are unreliable. Given the ecological importance of this species and skewed sex ratios in disturbed habitats, a dataset that allows ecologists or zoologists to study the sex determination of the lizard is crucial. We present a new dataset containing morphometric measurements of V. salvator individuals from the skin trade, with sex confirmed by dissection post- measurement. The dataset consists of a mixture of primary and secondary data such as weight, skull size, tail length, condition etc. and can be used in modelling studies for ecological and conservation research to monitor the sex ratio of this species. Validity was demonstrated by training and testing six machine learning models. This dataset has the potential to streamline sex determination, offering a non-invasive alternative to complement existing methods in V. salvator research, mitigating the need for invasive procedures.

Mandibular and dental measurements for sex determination using machine learning.

The present study tested the combination of mandibular and dental dimensions for sex determination using machine learning. Lateral cephalograms and dental casts were used to obtain mandibular and mesio-distal permanent teeth dimensions, respectively. Univariate statistics was used for variables selection for the supervised machine learning model (alpha = 0.05). The following algorithms were trained: logistic regression, gradient boosting classifier, k-nearest neighbors, support vector machine, multilayer perceptron classifier, decision tree, and random forest classifier. A threefold cross-validation approach was adopted to validate each model. The areas under the curve (AUC) were computed, and ROC curves were constructed. Three mandibular-related measurements and eight dental size-related dimensions were used to train the machine learning models using data from 108 individuals. The mandibular ramus height and the lower first molar mesio-distal size exhibited the greatest predictive capability in most of the evaluated models. The accuracy of the models varied from 0.64 to 0.74 in the cross-validation stage, and from 0.58 to 0.79 when testing the data. The logistic regression model exhibited the highest performance (AUC = 0.84). Despite the limitations of this study, the results seem to show that the integration of mandibular and dental dimensions for sex prediction would be a promising approach, emphasizing the potential of machine learning techniques as valuable tools for this purpose.

Preference and Disclosure of Fetal Gender to Pregnant Women during Prenatal Ultrasonography in South South Nigeria.

BACKGROUND: Ultrasound scan (USS) in pregnancy has become a common diagnostic tool used in the assessment of pregnancy in recent time. In the course of routine pregnancy assessment using USS, some pregnant women will request to know the sex of their unborn babies. Their reasons for wanting to know the gender of their baby could be either for social reason like planning for an unborn child or their desire for a preferred gender. AIM: The aim of the study was to evaluate gender preferences and disclosure of foetal sex at prenatal USS. METHODS: This was a cross-sectional study conducted at the antenatal clinic of Central Hospital Agbor, Delta State, Nigeria. A total of 235 consecutive consenting women who came for antenatal care (ANC) registration were recruited for the study after obtaining their informed written consent. Questionnaire was used to seek for their sociodemographic characteristics, preference and desires for foetal gender disclosure, reasons for gender disclosure, and awareness of USS accuracy for gender determination. RESULTS: The desire to know the sex of baby was high (99.6%). The major reason for wanting to know the sex of baby was to plan for the unborn child (47.7%) and maternal curiosity (37.0%). Majority of the women (57.4%) had no gender preference. Sixty percent (60%) were not aware that USS sex diagnosis could be wrong. CONCLUSION: There is a strong desire by pregnant women to know the sex of their babies at routine USS. Considering the fact that many of the women were not aware that there could be wrong diagnosis at prenatal ultrasound, it is suggested that adequate counselling be given before fetal sex disclosure.

Molecular sexing of birds using quantitative PCR (qPCR) of sex-linked genes and logistic regression models.

The ability to sex individuals is an important component of many behavioural and ecological investigations and provides information for demographic models used in conservation and species management. However, many birds are difficult to sex using morphological characters or traditional molecular sexing methods. In this study, we developed probabilistic models for sexing birds using quantitative PCR (qPCR) data. First, we quantified distributions of gene copy numbers at a set of six sex-linked genes, including the sex-determining gene DMRT1, for individuals across 17 species and seven orders of birds (n = 150). Using these data, we built predictive logistic models for sex identification and tested their performance with independent samples from 51 species and 13 orders (n = 209). Models using the two loci most highly correlated with sex had greater accuracy than models using the full set of sex-linked loci, across all taxonomic levels of analysis. Sex identification was highly accurate when individuals to be assigned were of species used in model building. Our analytical approach was widely applicable across diverse neognath bird lineages spanning millions of years of evolutionary divergence. Unlike previous methods, our probabilistic framework incorporates uncertainty around qPCR measurements as well as biological variation within species into decision-making rules. We anticipate that this method will be useful for sexing birds, including those of high conservation concern and/or subsistence value, that have proven difficult to sex using traditional approaches. Additionally, the general analytical framework presented in this paper may also be applicable to other organisms with sex chromosomes.

Sex identification of birds in Taipei Zoo.

As a conservation and breeding institution for birds, Taipei Zoo plays an important role in restoring endangered species. As approximately half of all bird species are monomorphic, precisely confirming the sex of individuals is critical for the management of ex-situ conservation breeding populations, as well as for understanding the sex ratio of those in the wild. Generally, PCR is used more reliably for sex determination versus traditional methods such as plumage, behavior or hormone levels. Nevertheless, the various primer sets and annealing temperatures vary between species, and so inaccurate sexing can occasionally happen due to inadequate PCR conditions. To reduce the probability of misidentification, and to establish a PCR condition database for sex determination across the diverse range of avian taxa, we tested multiple primer sets and annealing temperatures for amplification of the bird sex-specific gene fragments (CHD1) for each captive or rescued avian species held at Taipei Zoo since 2014. A total of 162 species across 22 orders were tested using one or two primer sets. One hundred and fifty-five species were successfully sexed by the primer set 2550F/2718R and the success rate of sex typing reached over 90% of species tested in each order. Most species have suitable PCR annealing temperatures between 45°C and 55°C, and the species in the same avian taxa showed similar results in temperature. This indicates that it is possible to select the annealing temperature of other species in the same family when the species had not been tested before. We expect this study will improve the success rate of identifying sex by using applicable PCR conditions and reduce the time for searching references every time before attempts to PCR sex birds.

Determinação do sexo a partir da morfometria geométrica e mensurações em imagens tridimensionais de dentes caninos / Sex determination from geometric morphometry and measurements in three-dimensional images of canine teeth

O presente estudo teve como objetivo avaliar a determinação do sexo por meio da análise geométrica e de mensurações a partir de imagens tridimensionais de dentes caninos, advindas de escaneamento intraoral, no Autodesk MeshMixer, bem como elaborar um roteiro prático para servir de guia na manipulação e coleta de dados nesse software. Trata-se de um estudo do tipo cego e transversal, dividido em duas etapas. Inicialmente, foram selecionadas imagens de 127 caninos (65 femininos e 63 masculinos) para a análise morfométrica geométrica, utilizando a marcação de 50 pontos, distribuídos em 27 pontos para contorno e 23 pontos para delimitação da forma das superfícies vestibular e lingual. Cada ponto de referência recebeu um valor para as coordenadas x, y e z, representando a sua posição. Na análise estatística dos dados foi utilizado um software específico para análise morfométrica geométrica, o MorphoJ, no qual foram importados os dados e submetidos à Análise Ajustada de Procrustes, Análise Discriminante e Análise da Variação Canônica. Não foram exibidas diferenças significativas para distribuição do sexo nas analises anteriores. Ainda, os dados relativos ao tamanho do centroide gerado no MorphoJ foram importados para o IBM SPSS Statistics 22.0 e submetidos ao teste t student, resultando em uma diferença estatística para o sexo. Para a aplicabilidade das mensurações digitais, foram utilizadas imagens de 345 caninos (191 femininos e 154 masculinos). Foram realizadas medidas das distâncias mesiodistais, vestibulolinguais, cervicoincisais (altura) e distâncias intercaninas de 5 pontos estabelecidos em cada canino (cúspide, cervical por vestibular e lingual, ponto máximo mesial e lingual). Todas as médias foram maiores para o sexo masculino e, com exceção da altura do elemento 33, apresentaram diferenças significativas para o sexo (p<0,05). As mensurações mesiodistais, vestibulolinguais e intercaninas (com exceção do ponto cervical por lingual), apresentaram uma boa acurácia, representadas por valores de áreas sobre a curva ROC maiores do que 0,7. O Autodesk MeshMixer apresentou-se como um ótimo auxiliar e de grande contribuição para análises dentro da Antropologia Forense. Apesar dos caninos serem elementos altamente dimórficos, para a análise morfométrica, não foram exibidas diferenças estatísticas na análise discriminante. Porém, o tamanho do centroide apresentou diferenças estatísticas e com médias maiores para o sexo masculino. As medidas realizadas nos dentes caninos apresentaram diferenças estatísticas para o sexo, com boas classificações na análise discriminante e com boas predições sexuais de acordo com os valores de especificidade e sensibilidade. A aplicabilidade de técnicas digitais de mensuração exibiu bons resultados, concordando esses dados obtidos com estudos que utilizaram as técnicas manuais de medida.

SRY gene isolation from teeth for forensic gender identification-An observational study.

Personal identification in forensics is possible with gender determination using DNA (deoxyribonucleic acid) analysis. DNA isolation from teeth samples subjected to extreme temperatures has been shown to predict the gender of the deceased. However, the literature lacks studies on DNA extracted from tooth samples exposed to freezing temperatures. This study aimed to isolate the SRY gene from the extirpated pulp of teeth that were subjected to varying temperatures for gender identification. Thirty teeth with vital pulps, divided into 3 groups were included in the study. Each group consisted of 5 male and 5 female tooth samples. The groups were exposed to diverse environmental factors for three weeks. Group 1: room temperature (R group); Group 2: high temperature (H group) and Group 3: freezing temperature (F group). Later, DNA was isolated from the pulp tissue, and the SRY gene was amplified using PCR (Polymerase Chain Reaction). The Sensitivity and Specificity of the results were analyzed. SRY gene detected in the study samples identified accurate gender with a 46.70% Sensitivity and 93.30% Specificity. Significant difference was found in the correlation between gene expression and gender among the three groups (p = 1.000). The study validates that dental pulp tissue can be a reliable source for DNA extraction. And SRY gene amplification from teeth exposed to diverse environmental conditions. Further investigations are required to validate its application in forensics.

Sex determination by ultrasonography prior to artificial breeding of the pufferfish Arothron manilensis (Tetraodontiformes, Tetraodontidae).

Artificial breeding was induced in the pufferfish Arothron manilensis following ultrasonographic sex determination. Hormonal treatment of mature male and female specimens followed the collection (and measurement) of fully developed eggs by cannulation. Fertilized eggs (0.85 ± 0.02 mm diameter) were spherical, demersal and individually adhesive. Hatching occurred 5 days after fertilization, larvae being 2.23 ± 0.15 mm in total length and 2.08 ± 0.14 mm in notochord length. The larvae had all died within 14 days of hatching. To improve artificial breeding techniques for A. manilensis, it is necessary to determine more appropriate timing for hormone injection, as well as feeding nutrient-enhanced SS type Brachionus sp. to newly hatched larvae.

Palatal rugae as an unique and stable marker in personal identification-An interracial pilot study.

Background: In post-mortem scenarios, often it is a very difficult process to establish a person's identity. Rugae are unique in that they are protected from trauma as they are insulated from heat by tongue and buccal pad of fat unlike fingerprint or lip print that is prone to destruction. Aim and Objectives: This study was aimed to compare the palatal rugae among people of different races. The sole objectives of the study were to assess the predominant pattern in the selected groups, reliability of rugae pattern in personal identification, to evaluate reliability of sex determination and to compare the total number of rugae on right and left sides of the palate among the males and females. Study Design: A total of 90 subjects were enrolled into the study and divided into three groups that are African, Dravidian and Mongoloid population. Shapes of rugae present were analyzed according to the classification given by Kapali et al. (1997) and Thomas & Kotze (1983). Result: The predominant rugae shape in African and Dravidian population was wavy pattern, whereas Mongoloid race was predominant in curve pattern. African and Dravidian males were predominant in wavy pattern when compared to Mongoloid males where unification type was more predominant. Conclusion: A statistically significant association between the rugae shape in three populations exists, although subtle yet definite.

A review of the recent advances for the in ovo sexing of chicken embryos using optical sensing techniques.

The culling of day-old male chicks has caused ethical and economic concerns. Traditional approaches for detecting the in ovo sex of chicken embryos involve opening the eggshell and inner membrane, which are destructive, time-consuming, and inefficient. Therefore, noncontact optical sensing techniques have been examined for the in ovo sexing of chicken embryos. Compared with traditional methods, optical sensing can increase determination throughput and frequency for the rapid sexing of chicken embryos. This paper presented a comprehensive review of the different optical sensing techniques used for the in ovo sexing of chicken embryos, including visible and near-infrared (Vis-NIR) spectroscopy, hyperspectral imaging, Raman spectroscopy, fluorescence spectroscopy, and machine vision, discussing their advantages and disadvantages. In addition, the latest research regarding different detection algorithms and models for the in ovo sexing of chicken embryos was summarized. Therefore, this paper provides updated information regarding the optical sensing techniques that can be used in the poultry industry and related research.

SNP Panel and Genomic Sex Identification in Atlantic Halibut (Hippoglossus hippoglossus).

The ability to identify sex is necessary in population biology for a proper understanding of the dynamics of a population. In Atlantic halibut, phenotypic sex identification is not possible due to the lack of significant external morphological differences. We developed an Illumina SNP panel for Atlantic halibut with 4000 SNPs spread evenly throughout the genome with a minor allele frequency MAF ≥ 0.4, except for N = 249 SNPs located in a sex-determining region on chromosome 12, N = 176 of these SNPs were selected to genetically identify male and female individuals using a DAPC analysis. The genomic identification of sex allows for non-lethal sex determination and validation of sex identification in the field. The SNP panel is a new genomic resource for Atlantic halibut that will make it possible to generate the genotypic data for the large number of individuals needed to estimate population abundance using genomics and the Close Kin Mark Recapture (CKMR) approach, an emerging component of fisheries management and stock monitoring.

Bioimpedance-Measurement-Based Non-Invasive Method for In Ovo Chicken Egg Sexing.

Day-old male chick culling is one of the world's most inhumane problems in the poultry industry. Every year, seven billion male chicks are slaughtered in laying-hen hatcheries due to their higher feed exchange rate, lower management than female chicks, and higher production costs. This study describes a novel non-invasive method for determining the gender of chicken eggs. During the incubation period of fourteen days, four electrodes were attached to each egg for data collection. On the last day of incubation, a standard polymerase chain reaction (PCR)-based chicken gender determination protocol was applied to the eggs to obtain the gender information. A relationship was built between the collected data and the egg's gender, and it was discovered to have a reliable connection, indicating that the chicken egg gender can be determined by measuring the impedance data of the eggs on day 9 of incubation with the four electrodes set and using the self-normalization technique. This is a groundbreaking discovery, demonstrating that impedance spectroscopy can be used to sex chicken eggs before they hatch, relieving the poultry industry of such an ethical burden.

Utilization of a Gender-Based Sorting Machine for Crustacean Selection in Bioconcentration Studies with the Freshwater Amphipod Hyalella azteca.

Bioconcentration factors (BCFs) are determined by fish flow-through tests performed according to Organisation for Economic Co-operation and Development test guideline 305. These are time-consuming and expensive and use a large number of animals. An alternative test design using the freshwater amphipod Hyalella azteca for bioconcentration studies has been recently developed and demonstrated a high potential. For bioconcentration studies using H. azteca, male amphipods are preferred compared with female organisms. Manual sexing of male adult amphipods is, however, time-consuming and requires care and skill. A new fully automatic sorting and dispensing machine for H. azteca based on image analysis has recently been developed by the company Life Science Methods. Nevertheless, an anesthesia step is necessary prior to the automatic selection. In the present study, we show that a single-pulse of 90 min of tricaine at the concentration of 1 g/L can be used and is recommended to select H. azteca males manually or automatically using the sorting machine. In the second part, we demonstrate that the machine has the ability to select, sort, and disperse the males of a culture batch of H. azteca as efficiently as manual procedures. In the last part of the study, BCFs of two organic substances were evaluated using the H. azteca bioconcentration test (HYBIT) protocol, with an anesthetizing step and robotic selection compared with manual selection without an anesthetizing step. The different BCF values obtained were in accordance with those indicated in the literature and showed that an anesthetizing step had no effect on the BCF values. Therefore, these data validated the interest in this sorting machine for selecting males to perform bioconcentrations studies with H. azteca. Environ Toxicol Chem 2023;42:1075-1084. © 2023 SETAC.

Highly sensitive and quick in ovo sexing of domestic chicken eggs by two-wavelength fluorescence spectroscopy.

The in ovo sexing of chicken eggs is a current task and a prerequisite to overcome the mass killing of male day-old chicks from laying lines. Although various methods have been developed and tested in recent years, practicable methods for sex determination are still missing which can be applicated in poultry hatcheries before the chicken embryo is capable of nociception and pain sensation. Optical spectroscopic methods enable an early determination of the sex. In this study, a novel method based on two-wavelength in ovo fluorescence excitation is described. More than 1600 eggs were examined. In ovo fluorescence was sequentially excited at 532 nm and 785 nm. The fluorescence intensities of the spectral regions behave inversely with respect to sex. It is shown that the observed sex-related differences in the fluorescence intensities are based on the embryonic hemoglobin synthesis. The accuracy of sex determination is 96% for both sexes. The hatching rate is not reduced compared to an equivalent reference group.

The Use of Levels One and Two Dermatoglyphics for Sex Identification in University of Ibadan Community, Southwest Nigeria.

Dermatoglyphic traits are genetically determined and remain constant until death. Dermatoglyphics features are arranged from patterns, minutiae and ridgeology. This study utilized patterns and minutiae details of fingerprints as a means of sexual differentiation amongst the University of Ibadan community. Three hundred and eighty-four (192 males and 192 females) participants from the University of Ibadan community were recruited using multistage sampling technique. Fingerprints were obtained using fingerprint scanner Dermalog LF10, Hamburg, Germany. GraphPad Prism 7.0 was used for the test of mean of variables. Ulnar loop, whorl and radial loop patterns were found to be predominantly distributed in both male and female in that order. However, the arch pattern was significantly different between female and male. The male subjects had significantly higher total finger ridge count (TFRC). All the analysed minutiae were significantly different between male and female except bridge. The arch pattern, TFRC and level 2 details (minutiae) of dermatoglyphics could be used as markers for sexual differentiation.

Highly sensitive sex determination method using the exon 1 region of the amelogenin gene.

Sex determination is a crucial factor in the identification of unidentified human remains. Sex determination by DNA analysis is particularly useful because it can be applied to samples for which morphological characteristics are unavailable. Because samples handled in forensic DNA typing are easily degraded by environmental factors and microorganisms, there is a need for a method that can accurately determine sex even in highly decayed samples. Previous studies mainly used sex differences in an intron of the amelogenin gene. However, this region is highly polymorphic, and there are cases where accurate sexing cannot be performed because of genetic mutations in the target region. Thus, for reliable sex determination, it is desirable to select loci with as few non-sexual polymorphisms as possible. In this study, we focused on the exon 1 region of the amelogenin gene, which has very little polymorphism other than sex differences. We developed a primer set for sex determination and compared it with the GlobalFiler™ PCR Amplification Kit (GF), which is widely used for forensic DNA typing. The results showed that the amount of DNA required for accurate sex determination was 25 pg for both methods, achieving equivalent sensitivity. Next, we compared the two methods using ancient human skeletons and found that the present method with its shorter amplicon was considerably superior to GF. The present method is simple, rapid, inexpensive, and suitable for analyzing highly degraded samples. Therefore, this method is expected to contribute to forensic sciences and physical anthropology.

Genetic determination and JARID2 over-expression in a thermal incubation experiment in Casque-Headed Lizard.

Non-avian reptiles, unlike mammals and birds, have undergone numerous sex determination changes. Casque-Headed Lizards have replaced the ancestral XY system shared across pleurodonts with a new pair of XY chromosomes. However, the evolutionary forces that triggered this transition have remained unclear. An interesting hypothesis suggests that species with intermediate states, with sex chromosomes but also thermal-induced sex reversal at specific incubation temperatures, could be more susceptible to sex determination turnovers. We contrasted genotypic data (presence/absence of the Y chromosome) against the histology of gonads of embryos from stages 35-37 incubated at various temperatures, including typical male-producing (26°C) and female-producing (32°C) temperatures. Our work apparently reports for the first time the histology of gonads, including morphological changes, from stages 35-37 of development in the family Corytophanidae. We also observed that all embryos developed hemipenes, suggesting sex-linked developmental heterochrony. We observed perfect concordance between genotype and phenotype at all temperatures. However, analysis of transcriptomic data from embryos incubated at 26°C and 32°C identified transcript variants of the chromatin modifiers JARID2 and KDM6B that have been linked to temperature-dependent sex determination in other reptiles. Our work tested the validity of a mixed sex determination system in the family Corytophanidae. We found that XY chromosomes are dominant; however, our work supports the hypothesis of a conserved transcriptional response to incubation temperatures across non-avian reptiles that could be a reminiscence of an ancestral sex determination system.