Genetic assessment of captive breeding program of Indian Pangolin: implications for conservation and management

BACKGROUND

Captive breeding programs play a vital role in conservation of threatened species, necessitating an understanding of genetic diversity among captive individuals to ensure long-term genetic viability, appropriate mate selection, and successful reintroduction to native habitats.

METHODS AND RESULTS

We did not observe any recent genetic bottleneck, and population showed moderate genetic diversity. The estimated effective population size, representing individuals capable of contributing genetically to future generations, was estimated as 18.6 individuals (11.4-35.1 at 95% CI). Based on the genetic make-up and allelic diversity, we found seventeen pangolins (11 females and 6 males) were genetically unrelated and relatively more potent than others.

CONCLUSION

In this study, we evaluated the captive breeding program of the Indian pangolin population at the Pangolin Conservation Breeding Centre in Nandankanan Zoological Park, Bhubaneswar, Odisha. We highlight the significance of genetic monitoring within the captive population of Indian pangolin for preserving genetic diversity and ensuring the long-term survival of the species. We established the genetic profiles of all 29 pangolins and identified 17 pangolins to be prioritized for enhanced breeding and future zoo exchange programs. We appreciate the zoo authorities for promoting genetic assessment of pangolin for better and more effective monitoring of the captive breeding of the endangered Indian pangolin.

Cryogenic storage increases the longevity of butternut (Juglans cinerea, L.) seed embryogenic axes

Butternut (Juglans cinerea L.), a species listed as endangered, is currently undergoing rapid decline due to habitat loss and the introduction of Ophiognomonia clavigignenti-juglandacearum, a non-native pathogen causing butternut canker. The decline of butternut has led to the development of cryobiological methods for the ex-situ conservation of the species since viability is not maintained using conventional methods. In this study, we assess the survivability and growth of butternut embryogenic axes into plantlets after 7 years of cryopreservation. Results show that cryopreservation is a highly effective method for the long-term storage of embryogenic axes since both survival and subsequent acclimatization into plantlets was successful with an average of 76% survival and 71% acclimatization, respectively. These results surpass the actual duration viability for non-cryogenic storage of butternut seed and we hope that future testing will result in longer term success of this cryobiological method and provide much needed germplasm for future restoration.

Single nucleotide polymorphism (SNP) markers for genetic diversity and population structure study in Ethiopian barley (Hordeum vulgare L.) germplasm

BACKGROUND

High-density single nucleotide polymorphisms (SNPs) are the most abundant and robust form of genetic variants and hence make highly favorable markers to determine the genetic diversity and relationship, enhancing the selection of breeding materials and the discovery of novel genes associated with economically important traits. In this study, a total of 105 barley genotypes were sampled from various agro-ecologies of Ethiopia and genotyped using 10 K single nucleotide polymorphism (SNP) markers. The refined dataset was used to assess genetic diversity and population structure.

RESULTS

The average gene diversity was 0.253, polymorphism information content (PIC) of 0.216, and minor allelic frequency (MAF) of 0.118 this revealed a high genetic variation in barley genotypes. The genetic differentiation also showed the existence of variations, ranging from 0.019 to 0.117, indicating moderate genetic differentiation between barley populations. Analysis of molecular variance (AMOVA) revealed that 46.43% and 52.85% of the total genetic variation occurred within the accessions and populations, respectively. The heat map, principal components and population structure analysis further confirm the presence of four distinct clusters.

CONCLUSIONS

This study confirmed that there is substantial genetic variation among the different barley genotypes. This information is useful in genomics, genetics and barley breeding.

DNA matchmaking in captive facilities: a case study with tigers

BACKGROUND

Genetics driven interventions if adopted in conservation breeding projects may enhance the overall success by prioritizing breeding among genetically most competent individuals and delaying or completely diminishing the ill effects of inbreeding.

METHODS AND RESULTS

In the present study, we investigated genetic make-up of 15 tigers housed at five different captive facilities of West Bengal in India and report the moderate level of genetic variation. We identified five tigers based on individual genetic attributes that may be prioritized for future breeding or animal exchange programmes. The occurrence of first and second order related individuals in captivity require management attention and they should be paired considering their immediate genetic background.

CONCLUSION

Considering tiger as a case study, we highlight the use of genetic assessment and necessity to validate the studbook records in formulating adaptive management strategies for long-term conservation and management of species of interest.

Mortality analysis of captive red panda cubs within Chengdu, China

Background

The red panda has been classified as an endangered species due to the decreased number in the world and disease is considered as a great threat to the health and survival of the cubs in captivity.

Results

This study analyzed 32 red panda cub mortalities (15 females and 17 males, age less than two months) through gross necropsy, microbiological examination, and histopathological observation at the Chengdu Research Base of Giant Panda Breeding, China, during 2014–2020. The results showed that screenings for canine distemper virus, canine parvovirus, rotavirus and parasite infection were all negative, however bacteria such as Klebsiella pneumoniae, Proteus mirabilis, Escherichia coli, Enterococcus faecalis, Pseudomonas were isolated from the tissue samples of some cubs. The major causes of death were respiratory (43.75%) and digestive system disease (28.13%), followed by cardiovascular disease (12.5%) and neonatal stillbirths (9.38%). Renal system diseases and trauma were also detected, at lower incidence (one case for each). The mortality rate within 15 days of birth was 68.75% and gradually decreased with age, there was no significant difference in gender.

Conclusion

This study can provide a scientific basis for the analysis of the cause of death among red panda cubs in captivity, so as to improve the survival rate, help build the captive population and further the ex-situ conservation management of this endangered species. Additionally, our research may also provide insights into the in-situ conservation of wild red pandas by identifying emerging disease threats within the wild population and potential treatment for rescued individuals.

A noteworthy case of rewilding Chinese yew from a garden population in eastern China

Chinese yew (Taxus wallichiana var. mairei) is ranked as a rare and endangered plant of first-grade protection of China. It has been widely cultivated in 17 provinces of China over the past few decades. However, little is known about the dispersion, rewilding, and ecological influence of Chinese yew’s offspring during cultivation. Here, we report a noteworthy case of this species, via ex situ conservation, which has successfully spread into different secondary forests, thus forming a stable regenerating population in eastern China. The establishment of this yew population, which has > 900 individuals and 7 ha area, can be ascribed to two key ecological factors: (1) secondary forest near the parent yews that provided suitable microhabitats in which progeny yews could germinate and grow, and (2) seed-foraging and transportation by native birds. Thus, this case may offer a pathway for conserving endangered Chinese Taxus species, which can attract frugivorous birds to disperse their seeds. In addition, it is necessary to monitor the growth performance of progeny population in the field.

Ex-situ conservation of wheat genetic resources from Saudi Arabia

Wheat (Triticum L.) is one of the major food crops of the world, and an important component of food security. The aim of this study was to collect and preserve seeds of wheat growing in eight regions of the Kingdom of Saudi Arabia (Al-Qassim, Asir, Al-Taif, Najran, AL-Baha, Jazan, Al-Madinah and Wadi Al-Dawasir) where wheat has been cultivated since ancient times. Sixty-one accessions/samples of wheat (Triticum aestivum) were collected and placed in dry storage (ex-situ conservation) at −18 °C (i.e. permanent storage). The accessions of local wheat have the ability to grow under harsh environmental conditions such as (high temperature, drought and salinity). Most of these samples were collected directly from farms, but a few were collected from markets. The most important criteria for ex-situ conservation is that seeds need to have a low moisture content (MC) and a high percentage viability. Seed MC was measured for all 61 accessions by the oven-drying method and seed viability was tested in three ways: percentage of germination, tetrazolium chloride testing, and X-ray radiography.

The seed MC of the 61 accessions was uniformly very low (0.10–0.12%), and 97 to 100% of the seeds were viable. Thus, all 61 wheat accessions collected in this study have the initial requirements to remain viable for long periods of time in ex-situ conservation in the gene seed bank.

Effects of personality and rearing-history on the welfare of captive Asiatic lions (Panthera leo persica)

Background

The long-term success of ex-situ conservation programmes depends on species-appropriate husbandry and enrichment practices complemented by an accurate welfare assessment protocol. Zoos and conservation breeding programmes should employ a bottom-up approach to account for intraspecific variations in measures of animal welfare. We studied 35 (14:21) captive Asiatic lions in Sakkarbaug Zoological Garden, Junagadh, India to understand the implications of individual variations on welfare measures. We categorized the subjects based on personality traits (bold or shy), rearing history (wild-rescued or captive-raised), sex, and social-grouping. We explored the association of these categorical variables on welfare indices such as behavioural diversity, latency to approach novel objects, enclosure usage and aberrant repetitive behaviours. Further, we assessed the inter-relationships between different behavioural measures of welfare.

Results

Our results show that intraspecific variations based on rearing-history and personality traits are significantly associated with the welfare states of captive Asiatic lions. Asiatic lions with bold personality traits (M = 0.50, SD = 0.12, N = 21) and those raised in captivity (M = 0.47, SD = 0.12, N = 16) used enclosure space more homogenously compared to shy (M = 0.71, SD = 0.15, N = 14) and wild-rescued (M = 0.67, SD = 0.15, N = 19) animals. Behaviour diversity was significantly higher in captive-raised (M = 1.26, SD = 0.3, N = 16) and bold (M = 1.23, SD = 0.26, N = 21) subjects compared to wild-rescued (M = 0.83, SD = 0.35, N = 19) and shy (M = 0.73, SD = 0.34, N = 14) individuals. Aberrant repetitive behaviours (stereotypy) were significantly lower in bold (M = 7.01, SD = 4, N = 21) and captive-raised (M = 7.74, SD = 5.3) individuals compared to wild-rescued (M = 13.12, SD = 6.25, N = 19) and shy (M = 16.13, SD = 5.4, N = 16) lions. Sex and social-grouping of subjects did not show significant associations with behavioural welfare indices. Interestingly, behaviour diversity was reliably predicted by the enclosure usage patterns and aberrant repetitive behaviours displayed by subjects.

Discussion

Our findings underline the importance of individual-centric, behaviour-based, and multi-dimensional welfare assessment approaches in ex-situ conservation programmes. The results suggest that behavioural welfare indices complemented with individual variations can explain inter-individual differences in behavioural welfare measure outcomes of Asiatic lions. These findings also provide zoo managers with a non-invasive tool to reliably assess and improve husbandry practices for Asiatic lions. Understanding the unique welfare requirement of individuals in captivity will be crucial for the survival of the species.

Botanic gardens should lead the way to create a "Garden Earth" in the Anthropocene

The strength and expertise that botanic gardens bring to conservation are based on their detailed knowledge and understanding of the care, management, and biology of a diversity of plant species. This emphasis on the organism has led to many ex-situ and in-situ conservation programs aimed at protecting endangered species, restoring threatened populations, and establishing living plant and seed collections of endangered species. In China, the scale and pace of change in land and resource use, often leading to environmental degradation, has created a strong emphasis on improving environmental conditions. If done properly, being "green" can be a surprisingly complex issue, because it should encompass and exploit the whole of plant diversity and function. Unfortunately, 'green' often includes a small portion of this whole. Earth's rich plant diversity presents considerable opportunity but requires expertise and knowledge for stable and beneficial management. With the dawning of the Anthropocene, we should strive to live on a "Garden Earth", where we design and manage our environments, both built and natural, to create a healthy, beneficial living landscape for people and other organisms. The staff of botanic gardens worldwide and the living collections they maintain embody the best examples of sustainable, beautiful, and beneficial environments that thrive on plant diversity. This expertise should be a fundamental resource for agencies in all sectors responsible for managing and designing "green" infrastructure. Botanic gardens should actively engage and contribute to these opportunities, from large public infrastructure projects to small private conservation efforts. Here, we discuss several ongoing conservation efforts, primarily in China, and attempt to identify areas where botanic gardens could make a significant and meaningful difference.

Systematic review on the conservation genetics of African savannah elephants

Background

In this paper we review the conservation genetics of African savannah elephants, aiming to understand the spatio-temporal research trends and their underlying factors. As such, we explore three questions associated to the conservation genetics and molecular ecology of these elephants: (1) what are the research trends concerning the conservation genetics of Loxodonta africana? (2) Do richer countries conduct more research on the genetics of African elephants? (3) Which attributes influence where scholars conduct their research?

Materials and Methods

We examined available peer-reviewed publications from 1993 to 2014 in complementary online databases, including the ISI/Web of Science (WoS), Scopus and Google Scholar (GS), and searched for publications in scientific journals as well as in the reference section of these publications. We analyzed the annual trend of publications in this field of research, including the number of authors, levels of collaboration among authors, year of publication, publishing journal and the countries from where genetic samples were collected. Additionally, we identified main research clusters, authors, and institutional collaborations, based on co-citation and co-occurrence networks.

Results

We found that during the study period there was a positive trend in the number of publications and a reduction in the number of authors per paper. Twenty-five countries contributed, with the majority of publications authored by researchers in the USA, Kenya and South Africa. The majority of samples were collected in Kenya, Tanzania and South Africa. Research outputs are associated with the existence of long-term conservation/research projects and research potential as measured by the literacy rate and the number of higher education institutions in a country. Five research clusters were identified, focusing on the origin and evolution of the species, methodological issues and the relatedness among elephant species.

Conclusions

Research in this field should be expanded to additional countries harboring elephant populations to enable a more comprehensive understanding of the population structure and genetic differentiation of the species, and to cope with challenges associated with the conservation of the species such as illegal hunting, habitat fragmentation, species reintroduction and climate change.

Influence of ethnic traditional cultures on genetic diversity of rice landraces under on-farm conservation in southwest China

BACKGROUND

Crop genetic resources are important components of biodiversity. However, with the large-scale promotion of mono-cropping, genetic diversity has largely been lost. Ex-situ conservation approaches were widely used to protect traditional crop varieties worldwide. However, this method fails to maintain the dynamic evolutionary processes of crop genetic resources in their original habitats, leading to genetic diversity reduction and even loss of the capacity of resistance to new diseases and pests. Therefore, on-farm conservation has been considered a crucial complement to ex-situ conservation. This study aimed at clarifying the genetic diversity differences between ex-situ conservation and on-farm conservation and to exploring the influence of traditional cultures on genetic diversity of rice landraces under on-farm conservation.

METHODS

The conservation status of rice landrace varieties, including Indica and Japonica, non-glutinous rice (Oryza sativa) and glutinous rice (Oryza sativa var. glutinosa Matsum), was obtained through ethno-biology investigation method in 12 villages of ethnic groups from Guizhou, Yunnan and Guangxi provinces of China. The genetic diversity between 24 pairs of the same rice landraces from different times were compared using simple sequence repeat (SSR) molecular markers technology. The landrace paris studied were collected in 1980 and maintained ex-situ, while 2014 samples were collected on-farm in southwest of China.

RESULTS

The results showed that many varieties of rice landraces have been preserved on-farm by local farmers for hundreds or thousands of years. The number of alleles (Na), effective number of alleles (Ne), Nei genetic diversity index (He) and Shannon information index (I) of rice landraces were significantly higher by 12.3-30.4 % under on-farm conservation than under ex-situ conservation. Compared with the ex-situ conservation approach, rice landraces under on-farm conservation programs had more alleles and higher genetic diversity. In every site we investigated, ethnic traditional cultures play a positive influence on rice landrace variety diversity and genetic diversity.

CONCLUSION

Most China's rice landraces were conserved in the ethnic areas of southwest China. On-farm conservation can effectively promote the allelic variation and increase the genetic diversity of rice landraces over the past 35 years. Moreover, ethnic traditional culture practices are a crucial foundation to increase genetic diversity of rice landraces and implement on-farm conservation.

Development of sperm cryopreservation protocol of endangered spiny eel, Mastacembelus armatus (Lacepede 1800) for ex-situ conservation

The study was conducted to develop sperm cryopreservation protocol for the endangered spiny eel, Mastacembelus armatus as well as to use the cryopreserved sperm in breeding. Activation of sperm was evaluated by observing motility in different osmolalities of NaCl solution (48-319 mOsmol/kg) and found that sperm motility decreased with increasing osmolality of the NaCl solution and it was totally inhibited at 319 mOsmol/kg. The highest motility and swimming duration of sperm were observed as 14.5 ± 0.5 min and 4.75 ± 0.25 min at 128 mOsmol/kg and 67 mOsmol/kg, respectively. The concentration of sperm was found to be 1.75 × 10¹⁰ to 2.25 × 10¹⁰ cells/ml. Evaluation of toxicity of cryoprotectants of dimethyl sulfoxide (Me₂SO) and methanol to sperm was performed at 5, 10 and 15% concentrations during 5-30 min incubation period and found that cryoprotectants with 5 and 10% concentrations produced better motility up to 10 min incubation. In the selection of suitable diluent for cryopreservation of sperm, Alsever's solution with 10% Me₂SO performed best producing 91.67 ± 1.67% and 65 ± 2.89% equilibration and post-thaw motility, respectively. In breeding trials, sperm preserved with Alsever's solution plus Me₂SO produced more or less similar fertilization (82.25 ± 4.46%) and hatching (12 ± 0.65%) to those preserved with 0.9% NaCl solution plus Me₂SO as 79.88 ± 4.67% and 11 ± 0.46% fertilization and hatching respectively. Fresh sperm used as control produced 87.63 ± 3.6% and 14 ± 0.5% fertilization and hatching respectively. Both cryopreserved and fresh sperm-derived fry performed well but the control fry showed a significantly better (P < 0.05) growth. Fry derived from four diluents did not show any significant (P > 0.05) growth difference but Alsever's solution plus Me₂SO produced better results.