The effects of scaling on age, sex and size relationships in Red-legged Partridges

Genomic diversity and signals of selection processes in wild and farm-reared red-legged partridges (Alectoris rufa)

The genetic dynamics of wild populations with releases of farm-reared reinforcements are very complex. These releases can endanger wild populations through genetic swamping or by displacing them. We assessed the genomic differences between wild and farm-reared red-legged partridges (Alectoris rufa) and described differential selection signals between both populations. We sequenced the whole genome of 30 wild and 30 farm-reared partridges. Both partridges had similar nucleotide diversity (π). Farm-reared partridges had a more negative Tajima's D and more and longer regions of extended haplotype homozygosity than wild partridges. We observed higher inbreeding coefficients (F_IS and F_ROH) in wild partridges. Selective sweeps (Rsb) were enriched with genes that contribute to the reproductive, skin and feather colouring, and behavioural differences between wild and farm-reared partridges. The analysis of genomic diversity should inform future decisions for the preservation of wild populations.

Novel genome reveals susceptibility of popular gamebird, the red-legged partridge (Alectoris rufa, Phasianidae), to climate change

We produced a high-quality de novo genome assembly of the red-legged partridge A. rufa, the first reference genome of its genus, by utilising novel 10× Chromium technology. The estimated genome size was 1.19 Gb with an overall genome heterozygosity of 0.0022; no runs of homozygosity were observed. In total, 21,589 protein coding genes were identified and assigned to 16,772 orthologs. Of these, 201 emerged as unique to Alectoris and were enriched for positive regulation of epithelial cell migration, viral genome integration and maturation. Using PSMC analysis, we inferred a major demographic decline commencing ~140,000 years ago, consistent with forest expansion and reduction of open habitats during the Eemian interglacial. Present-day populations exhibit the historically lowest genetic diversity. Besides implications for management and conservation, this genome also promises key insights into the physiology of these birds with a view to improving poultry husbandry practices.

Measuring body dimensions of leopards (Panthera pardus) from camera trap photographs

Measurement of body dimensions of carnivores usually requires the chemical immobilization of subjects. This process can be dangerous, costly and potentially harmful to the target individuals. Development of an alternative, inexpensive, and non-invasive method therefore warrants attention. The objective of this study was to test whether it is possible to obtain accurate measurements of body dimensions of leopards from camera trap photographs. A total of 10 leopards (Panthera pardus) were captured and collared at Malilangwe Wildlife Reserve, Zimbabwe from May 7 to June 20, 2017 and four body measurements namely shoulder height, head-to-tail, body, and tail length were recorded. The same measurements were taken from 101 scaled photographs of the leopards recorded during a baited-camera trapping (BCT) survey conducted from July 1 to October 22, 2017 and differences from the actual measurements calculated. Generalized Linear Mixed Effects Models were used to determine the effect of type of body measurement, photographic scale, posture, and sex on the accuracy of the photograph-based measurements. Type of body measurement and posture had a significant influence on accuracy. Least squares means of absolute differences between actual and photographic measurements showed that body length in the level back-straight forelimb-parallel tail posture was measured most accurately from photographs (2.0 cm, 95% CI [1.5–2.7 cm]), while head-to-tail dimensions in the arched back-bent forelimb-parallel tail posture were least accurate (8.3 cm, 95% CI [6.1–11.2 cm]). Using the BCT design, we conclude that it is possible to collect accurate morphometric data of leopards from camera trap photographs. Repeat measurements over time can provide researchers with vital body size and growth rate information which may help improve the monitoring and management of species of conservation concern, such as leopards.

Body proportions for the facilitation of walking, running and flying: the case of partridges

Background

Predation is one of the most important natural selection forces. Prey species can optimize feeding behavior and escape from predators based on mobility conditioned by body proportions. With age, mobility capacity increases and individuals are more efficient in finding resources and safety (e.g., food and refuge). Birds’ mobility is driven by the dimensions, of the head and torso, as well as the extremities and flight feathers. To assess the relationship between body traits and to understand how body proportions are organized in wild Red-legged partridges (Alectoris rufa), we used biometric data from nearly 14,000 individuals, obtained during a long-term study (1988–2011) on a wild population.

Results

We used GLMs and regressions to model the relationship between body mass and the size of body parts. We found that wing length was the morphological part best explained by other body trait measures. Wing length models were better predictors in juveniles than in adults and in females than in males. Wing length and feather length, mass and total length are the most strongly related parts; mass and wing length, total length and feather length are moderately related. The association between mass and wing length is intermediated by feather length and total length.

Conclusions

Social inclusion, feeding and predator evasion may be affected by body structure intermediated by mobility and health. Our results suggest that proportions of the body, extremities and flight feathers drive mobility which is intimately associated with ecology, biological efficiency, health and physical optimization. Our findings showed that wing size was strongly allied to other body part measurements, enhancing the importance of body structure conformation for flight. Our study highlights the scaled relationship of body structure among age-sex classes and its relevance to social cohesion, flock movement and the balance between predation and starvation.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1295-x) contains supplementary material, which is available to authorized users.