Australian and Pacific contributions to the genetic diversity of Norfolk Island feral chickens

Words matter: how ecologists discuss managed and non-managed bees and birds

Effectively promoting the stability and quality of ecosystem services involves the successful management of domesticated species and the control of introduced species. In the pollinator literature, interest and concern regarding pollinator species and pollinator health dramatically increased in recent years. Concurrently, the use of loaded terms when discussing domesticated and non-native species may have increased. As a result, pollinator ecology has inherited both the confusion associated with invasion biology’s lack of a standardized terminology to describe native, managed, or introduced species as well as loaded terms with very strong positive or negative connotations. The recent explosion of research on native bees and alternative pollinators, coupled with the use of loaded language, has led to a perceived divide between native bee and managed bee researchers. In comparison, the bird literature discusses the study of managed (poultry) and non-managed (all other birds) species without an apparent conflict with regard to the use of terms with strong connotations or sentiment. Here, we analyze word usage when discussing non-managed and managed bee and bird species in 3614 ecological and evolutionary biology papers published between 1990 and 2019. Using time series analyses, we demonstrate how the use of specific descriptor terms (such as wild, introduced, and exotic) changed over time. We then conducted co-citation network analyses to determine whether papers that share references have similar terminology and sentiment. We predicted a negative language bias towards introduced species and positive language bias towards native species. We found an association between the term invasive and bumble bees and we observed significant increases in the usage of more ambiguous terms to describe non-managed species, such as wild. We detected a negative sentiment associated with the research area of pathogen spillover in bumble bees, which corroborates the subjectivity that language carries. We recommend using terms that acknowledge the role of human activities on pathogen spillover and biological invasions. Avoiding the usage of loaded terms when discussing managed and non-managed species will advance our understanding and promote effective and productive communication across scientists, general public, policy makers and other stake holders in our society.

Evaluation of non-linear growth curve models in the Vietnamese indigenous Mia chicken

Understanding of animal growth is important for the improvement of management and feeding practices; however, little is known about the growth curve in Vietnamese indigenous chicken. This study was performed to determine the most appropriate models for describing the growth curve of Vietnamese Mia chicken. The study evaluated the performances of the Logistic, Gompertz, Richards, and Bridges models of body weights in 224 Mia chickens. Models were fitted using minpack.lm package in R software and Akaike's information criterion and Bayesian information criterion were used for model comparison. Based on these criteria, the Gompertz and Bridges were the best models for males and females, respectively. Estimated asymmetric weights (α) were ranged from 2,241.91 ± 14.74 (g) (Logistic) to 2,623.86 ± 30.23 (g) (Gompertz) for males and from 1,537.36 ± 10.97 (g) (Logistic) and 1,958.36 ± 72.92 (g) (Bridges) for females, respectively. The age at the inflection point was estimated from 9.32 to 10.5 weeks and from 8.51 to 9.86 weeks for males and females, respectively. In conclusion, the Gompertz model is the most suitable model for describing the growth curve of Mia chicken. The parameters obtained from growth models could help define feeding programs to meet nutritional needs from hatching to the age of maximum growth, reproduction programs, and marketing strategies.

Complete mitochondrial genome sequence of Tosa-Jidori sheds light on the origin and evolution of Japanese native chickens

OBJECTIVE

In Japan, approximately 50 breeds of indigenous domestic chicken, called Japanese native chickens (JNCs), have been developed. JNCs gradually became established based on three major original groups, "Jidori", "Shoukoku", and "Shamo". Tosa-Jidori is a breed of Jidori, and archival records as well as its morphologically primitive characters suggest an ancient origin. Although Jidori is thought to have been introduced from East Asia, a previous study based on mitochondrial D-loop sequences demonstrated that Tosa-Jidori belongs to haplogroup D, which is abundant in Southeast Asia but rare in other regions, and a Southeast Asian origin for Tosa-Jidori was therefore suggested. The relatively small size of the D-loop region offers limited resolution in comparison with mitogenome phylogeny. This study was conducted to determine the phylogenetic position of the Tosa-Jidori breed based on complete mitochondrial D-loop and mitogenome sequences, and to clarify its evolutionary relationships, possible maternal origin and routes of introduction into Japan.

METHODS

Maximum likelihood and parsimony trees were based on 133 chickens and consisted of 86 mitogenome sequences as well as 47 D-loop sequences.

RESULTS

This is the first report of the complete mitogenome not only for the Tosa-Jidori breed, but also for a member of one of the three major original groups of JNCs. Our phylogenetic analysis based on D-loop and mitogenome sequences suggests that Tosa-Jidori individuals characterized in this study belong to the haplogroup D as well as the sub-haplogroup E1.

CONCLUSION

The sub-haplogroup E1 is relatively common in East Asia, and so although the Southeast Asian origin hypothesis cannot be rejected, East Asia is another possible origin of Tosa-Jidori. This study highlights the complicated origin and breeding history of Tosa-Jidori and other JNC breeds.

Origin and evolutionary history of domestic chickens inferred from a large population study of Thai red junglefowl and indigenous chickens

In this study, we aimed to elucidate the origin of domestic chickens and their evolutionary history over the course of their domestication. We conducted a large-scale genetic study using mitochondrial DNA D-loop sequences and 28 microsatellite DNA markers to investigate the diversity of 298 wild progenitor red junglefowl (Gallus gallus) across two subspecies (G. g. gallus and G. g. spadiceus) from 12 populations and 138 chickens from 10 chicken breeds indigenous to Thailand. Twenty-nine D-loop sequence haplotypes were newly identified: 14 and 17 for Thai indigenous chickens and red junglefowl, respectively. Bayesian clustering analysis with microsatellite markers also revealed high genetic diversity in the red junglefowl populations. These results suggest that the ancestral populations of Thai indigenous chickens were large, and that a part of the red junglefowl population gene pool was not involved in the domestication process. In addition, some haplogroups that are distributed in other countries of Southeast Asia were not observed in either the red junglefowls or the indigenous chickens examined in the present study, suggesting that chicken domestication occurred independently across multiple regions in Southeast Asia.

European and Asian contribution to the genetic diversity of mainland South American chickens

Chickens (Gallus gallus domesticus) from the Americas have long been recognized as descendants of European chickens, transported by early Europeans since the fifteenth century. However, in recent years, a possible pre-Columbian introduction of chickens to South America by Polynesian seafarers has also been suggested. Here, we characterize the mitochondrial control region genetic diversity of modern chicken populations from South America and compare this to a worldwide dataset in order to investigate the potential maternal genetic origin of modern-day chicken populations in South America. The genetic analysis of newly generated chicken mitochondrial control region sequences from South America showed that the majority of chickens from the continent belong to mitochondrial haplogroup E. The rest belongs to haplogroups A, B and C, albeit at very low levels. Haplogroup D, a ubiquitous mitochondrial lineage in Island Southeast Asia and on Pacific Islands is not observed in continental South America. Modern-day mainland South American chickens are, therefore, closely allied with European and Asian chickens. Furthermore, we find high levels of genetic contributions from South Asian chickens to those in Europe and South America. Our findings demonstrate that modern-day genetic diversity of mainland South American chickens appear to have clear European and Asian contributions, and less so from Island Southeast Asia and the Pacific Islands. Furthermore, there is also some indication that South Asia has more genetic contribution to European chickens than any other Asian chicken populations.

Genetic diversity of 21 experimental chicken lines with diverse origins and genetic backgrounds

The genetic characteristics and diversity of 21 experimental chicken lines registered with the National BioResource Project of Japan were examined using mitochondrial D-loop sequences and 54 microsatellite DNA markers. A total of 12 haplotypes were detected in the 500-bp mitochondrial DNA sequences of the hypervariable segment I for 349 individuals of 21 lines. The 12 haplotypes belonged to three (A, D, and E) haplogroups, out of the eight (A‒H) common haplogroups in domestic chickens and red junglefowls. The haplogroups A and D were widely represented in indigenous chickens in the Asian and Pacific regions, and the haplogroup E was the most prevalent in domestic chickens. Genetic clustering by discriminant analysis of principal components with microsatellite markers divided 681 individuals of 21 lines into three groups that consisted of Fayoumi-, European-, and Asian- derived lines. In each of the cladograms constructed with Nei's genetic distances based on allele frequencies and the membership coefficients provided by STRUCTURE and with the genetic distance based on the proportion of shared alleles, the genetic relationships coincided well with the breeding histories of the lines. Microsatellite markers showed remarkably lower genetic heterozygosities (less than 0.1 observed heterozygosity) for eight lines (GSP, GSN/1, YL, PNP, BM-C, WL-G, BL-E, and #413), which have been maintained as closed colonies for more than 40 years (except for #413), indicating their usefulness as experimental chicken lines in laboratory animal science research.

Bayesian Statistics in Archaeology

Null hypothesis significance testing (NHST) is the most common statistical framework used by scientists, including archaeologists. Owing to increasing dissatisfaction, however, Bayesian inference has become an alternative to these methods. In this article, we review the application of Bayesian statistics to archaeology. We begin with a simple example to demonstrate the differences in applying NHST and Bayesian inference to an archaeological problem. Next, we formally define NHST and Bayesian inference, provide a brief historical overview of their development, and discuss the advantages and limitations of each method. A review of Bayesian inference and archaeology follows, highlighting the applications of Bayesian methods to chronological, bioarchaeological, zooarchaeological, ceramic, lithic, and spatial analyses. We close by considering the future applications of Bayesian statistics to archaeological research.

Genetic diversity of Jiangsu native chicken breeds assessed with the mitochondrial DNA D-loop region

1. The objective of this study was to determine the origin and evolution of chickens from 5 native breeds that are traditionally raised in Jiangsu Province. 2. To address this question, the complete mitochondrial DNA D-loop sequence of 149 chickens from 5 native breeds of Jiangsu Province was analysed. 3. Sequence read lengths of the native breeds were 1231 to 1232 bp, with a single-base deletion from the 859 bp site in the 1231 bp haplotype. A total of 33 variable sites that defined 19 haplotypes were identified. The average haplotype diversity and nucleotide diversity were 0.862 ± 0.017 and 0.00591 ± 0.00135. 4. Phylogenetic analysis showed that genetic structure of the mtDNA haplotypes of Jiangsu chickens are distributed across 5 clades (haplogroups): Clades A, B, C, D, and E. However, most of the individuals characterised in this study belonged to clades A and B. 5. The results of this study indicate that Jiangsu chicken populations have relatively low nucleotide and haplotype diversity and likely share 5 common maternal lineages.

On the origins and genetic diversity of South American chickens: one step closer

Local chicken populations are a major source of food in the rural areas of South America. However, very little is known about their genetic composition and diversity. Here, we analyzed five populations from South America to investigate their maternal genetic origin and diversity, hoping to mitigate the lack of information on local chicken populations from this region. We also included three populations of chicken from the Iberian Peninsula and one from Easter Island, which are potential sources of the first chickens introduced in South America. The obtained sequencing data from South American chickens indicate the presence of four haplogroups (A, B, E and D) that can be further subdivided into nine sub-haplogroups. Of these, four (B1, D1a, E1a(b), E1b) were absent from local Iberian Peninsula chickens and one (D1a) was present only on Easter Island. The presence of the sub-haplogroups A1a(b) and E1a(b) in South America, previously only observed in Eastern Asia, and the significant population differentiation between Iberian Peninsula and South American populations, suggest a second maternal source of the extant genetic pool in South American chickens.

Multiple maternal origins of Indonesian crowing chickens revealed by mitochondrial DNA analysis

The utilization of Indonesian crowing chickens is increasing; as such, assessing their genetic structures is important to support the conservation of their genetic resources. This study analyzes the matrilineal evolution of Indonesian crowing chickens based on the mtDNA displacement loop D-loop region to clarify their phylogenetic relationships, possible maternal origin, and possible routes of chicken dispersal. The neighbor-joining tree reveals that the majority of Indonesian crowing chickens belong to haplogroups B, D, and E, but haplogroup D harbored most of them. The Bayesian analysis also reveals that Indonesian crowing chickens derive from Bekisar chicken, a hybrid of the green junglefowl, suggesting the possible contribution of green junglefowl to chicken domestication. There appear at least three maternal lineages of Indonesian chicken origins indicated by the median network profile of mtDNA D-loop haplotypes, namely (1) Chinese; (2) Chinese, Indian, and other Southeast Asian chickens; and (3) Indian, Chinese, Southeast Asian, Japanese, and European chickens. Chicken domestication might be centered in China, India, Indonesia, and other Southeast Asian countries, supporting multiple maternal origins of Indonesian crowing chickens. A systematic breeding program of indigenous chickens will be very important to retain the genetic diversity for future use and conservation.