Population genomic data reveal low genetic diversity,divergence and local adaptation among threatened Reeves's Pheasant(Syrmaticus reevesii)

Population genomic data could provide valuable information for conservation efforts;however,limited studies have been conducted to investigate the genetic status of threatened pheasants.Reeves’s Pheasant(Syrmaticus reevesii)is facing population decline,attributed to increases in habitat loss.There is a knowledge gap in understanding the genomic status and genetic basis underlying the local adaptation of this threatened bird.Here,we used population genomic data to assess population structure,genetic diversity,inbreeding patterns,and genetic divergence.Furthermore,we identified candidate genes linked with adaptation across the current distribution of Reeves’s Pheasant.The present study assembled the first de novo genome sequence of Reeves’s Pheasant and annotated 19,458 genes.We also sequenced 30 individuals from three populations(Dabie Mountain,Shennongjia,Qinling Mountain)and found that there was clear population structure among those populations.By comparing with other threatened species,we found that Reeves’s Pheasants have low genetic diversity.Runs of homozygosity suggest that the Shennongjia population has experienced serious inbreeding.The demographic history results indicated that three populations experienced several declines during the glacial period.Local adaptative analysis among the populations identified 241 candidate genes under directional selection.They are involved in a large variety of processes,including the immune response and pigmentation.Our results suggest that the three populations should be considered as three different conservation units.The current study provides genetic evidence for conserving the threatened Reeves’s Pheasant and provides genomic resources for global biodiversity management.

The clutch size,incubation behavior of Reeves’s Pheasant(Syrmaticus reevesii) and their responses to ambient temperature and precipitation

Weather conditions play a pivotal role in embryo development and parental incubation costs,potentially impacting the clutch size and incubation behavior of birds.Understanding these effects is crucial for bird conservation.Reeves’ s Pheasant(Syrmaticus reevesii) is a threatened species endemic to China,which is characterized by female-only incubation.However,there is a lack of information regarding the impact of weather conditions on clutch size and incubation behavior in this species.Using satellite tracking,we tracked 27 wild female Reeves’ s Pheasants from 2020 to 2023 in Hubei Province,China.We explored their clutch size and incubation behavior,as well as their responses to ambient temperature and precipitation.Clutch size averaged 7.75 ±1.36,had an association with average ambient temperature and average daily precipitation during the egglaying period,and was potentially linked to female breeding attempts.Throughout the incubation period,females took an average of 0.73 ±0.46 recesses every 24 h,with an average recess duration of 100.80 ±73.37 min and an average nest attendance of 92.98 ±5.27%.They showed a unimodal recess pattern in which nest departures peaked primarily between 13:00 and 16:00.Furthermore,females rarely left nests when daily precipitation was high.Recess duration and nest attendance were influenced by the interaction between daily mean ambient temperature and daily precipitation,as well as day of incubation.Additionally,there was a positive correlation between clutch size and recess duration.These results contribute valuable insights into the lifehistory features of this endangered species.

Phylogenetic Relationships of Monal Pheasants Lophophorus Inferred from Sequences of Mitochondrial Cytochrome b Gene

The phylogeny of the monal pheasants (Lophophorus) and their relationships to some species of the genera Tragopan,Pucrasia and Ithaginis were studied by comparing mitochondrial cytochrome b (cyt b) nucleotide sequences.The molecular phylogenetic trees show that:①the genus Tragopan and the genus Pucrasia share a common ancestor which is the sister taxon of the ancestor of the genus Lophophorus;②the genus Lophophorus had evolved into two branches:One was the Sclaters Monal;the other included the Chinese Monal and the Himalayan Monal.Considering its molecular phylogeny,distribution patterns and morphological evidences,the genus Lophophorus might originate in the Hengduan mountains region of southwestern China.

Modeling foraging habitats of Hume’s Pheasant (Syrmaticus humiae) in Dazhong Mountain, Yunnan, southwestern China

We modeled foraging habitats of Hume’s Pheasant (Syrmaticus humiae) on a macro-habitat level using ArcGIS in an attempt to provide scientific reference for management and restoration of habitats. Field work was conducted from March to April in 2006 and 2008, and from October to November in 2005 and 2008 in Dazhong Mountain, Yunnan Province, southwestern China. The selection of ecological factors was estimated by means of a resource selection index, distance analysis and the method of hierarchical habitat selection. The foraging habitat patches were modeled spatially by ArcGIS. The results show that actual and potential foraging patches overlapped considerably in spring and autumn. The number and total areas of patches in the autumn were smaller than those in the spring. The minimum and average areas of patches in the autumn were larger than those in the spring, while the maximum areas of actual and potential foraging patches in the autumn were equal to those in the spring. Similarity in the selection for survival and safety consideration in both seasons was the main strategy for landscape factors of habitats by Hume’s Pheasant, while seasonal difference in selecting a landscape matrix was their secondary strategy, affecting landscape factors in the habitat. Changes of foraging patches in both seasons reflect a difference of resources requirement by the bird. Fragmentation and miniaturization of foraging patches would result in the formation of a meta-population of Hume’s Pheasant.

Home range and habitat composition of male Reeves's Pheasants in an agricultural-forest plantation landscape in central China:a preliminary report

We present a preliminary examination of the home range and habitat use of male Reeves's Pheasants (Syrmaticus reevesii) in an agricultural-forest plantation landscape on the Xianjuding Forest Farm, Hubei Province, central China. Fieldwork was carried out from March to August in 2003. The home range of males averaged 33.17 ± 12.55 ha by MCP (minimum convex polygon) and 21.05 ± 5.61 ha by a 95% fixed kernel estimator. The core area by a 60% fixed kernel estimator was 3.92 ± 0.27 ha. We did not detect significant seasonal variations in home range, core area and movement in this farm. Chinese fir (Cunninghamia lanceolata) plantations were the dominant habitat type within the home ranges and core areas. The males used their habitat non-randomly in spring and summer, preferred the fir plantations and avoided broadleaf forests in both seasons. In addition, the males used shrubs less than were available in the spring. The vegetation structure of different habitats may be the leading factor affecting the use of the habitats.

Blue-eared Pheasant:a forest bird endemic to China

The Blue-eared Pheasant (Crossoptilon auritum) is an important bird species,endemic to China and is ranked as a second grade key protected wildlife species in China.These birds are only found in the mountainous regions of Qinghai,Gansu and Sichuan provinces and the Ningxia Hui Autonomous Region.In order to understand systematically the existing information on the biology of the Blue-eared Pheasant,we provide updated information on its habitat,activity,nest-site features,breeding biology,feeding habits,population status and conservation of this pheasant by integrating published data with the information from our field surveys,conducted from 2006 to 2008 in the Gaihai-zecha National Nature Reserve,Gansu.

Hainan Peacock Pheasant (Polyplectron katsumatae):an endangered and rare tropical forest bird

The Hainan Peacock Pheasant (Polyplectron katsumatae),the smallest allied species of somber forest peacock pheasants among the taxa of Polyplectron spp.,is a rare tropical forest bird endemic to China,and distributed only in the mountainous region of central and southwestern Hainan Island dominated by evergreen broadleaf forests.By integrating references and unpublished data based on our field surveys,we presented information on species status,distribution and population,habitat and home range,breeding ecology and conservation of the Hainan Peacock Pheasant.Future investigation should focus on its life history traits in relation to vulnerability.Considering its limited distribution and small population size,it has recently been recognized as "Endangered" by the IUCN Red List to prevent loss of this island endemic.

Parapatric speciation with recurrent gene flow of two sexual dichromatic pheasants

Understanding speciation has long been a fundamental goal of evolutionary biology.It is widely accepted that speciation requires an interruption of gene flow to generate strong reproductive isolation between species.The mechanism of how speciation in sexually dichromatic species operates in the face of gene flow remains an open question.Two species in the genus Chrysolophus,the Golden Pheasant(C.pictus)and Lady Amherst’s Pheasant(C.amherstiae),both of which exhibit significant plumage dichromatism,are currently parapatric in southwestern China with several hybrid recordings in field.In this study,we estimated the pattern of gene flow during the speciation of the two pheasants using the Approximate Bayesian Computation(ABC)method based on data from multiple genes.Using a newly assembled de novo genome of Lady Amherst’s Pheasant and resequencing of widely distributed individuals,we reconstructed the demographic history of the two pheasants by the PSMC(pairwise sequentially Markovian coalescent)method.The results provide clear evidence that the gene flow between the two pheasants was consistent with the predictions of the isolation with migration model during divergence,indicating that there was long-term gene flow after the initial divergence(ca.2.2 million years ago).The data further support the occurrence of secondary contact between the parapatric populations since around 30 kya with recurrent gene flow to the present,a pattern that may have been induced by the population expansion of the Golden Pheasant in the late Pleistocene.The results of the study support the scenario of speciation between the Golden Pheasant and Lady Amherst’s Pheasant with cycles of mixing-isolation-mixing,possibly due to the dynamics of geographical context in the late Pleistocene.The two species provide a good research system as an evolutionary model for testing reinforcement selection in speciation.

Winter diet and digestive tract of the Golden Pheasant(Chrysolophus pictus) in the Qinling Mountains,China

The winter diet and morphological structure of the gastrointestinal tract of the Golden Pheasant(Chrysolophus pictus) was investigated in the Qinling Mountains,Shaanxi Province in 2002/2003.Individual food items in crops were identified by species,where possible,using standard taxonomic methods.The Golden Pheasant consumes exclusively vegetarian foods in the winter,of at least 14 plant species,such as crops and other vegetable species.The digestive tract of the Golden Pheasant is composed of an oesophagus,a stomach,a relatively long intestine measuring 3.4 × standard body length,two fully-developed caeca and a relatively short colon,typical for herbivorous birds.Pebbles of different sizes(0.5-3 mm in diameter) were very frequent in the gizzard.The average dry weight of the pebbles was 10.4±2.5 g and was positively correlated with the weight of digesta in the gizzard(Pearson r = 0.747,p < 0.01,n = 37).The mucosa surface pH of the digestive tract of the Golden Pheasant was slightly acidic,but higher in the crop and gizzard.

Genetic evidence for male-biased dispersal in Elliot's Pheasant (Syrmaticus ellioti) in China

Sex-biased dispersal,in which individuals of one sex tend to disperse and breed at a greater distance from their natal site than individuals of the opposite sex,appears to be common in vertebrate organisms and is very important to population structures and dynamics.Many studies have documented the dispersal patterns of monogamous birds; however,observations and data are few for polygynous birds.In our study,we report on the indication of sex-biased dispersal in Elliot's Pheasant (Syrmaticus ellioti),a vulnerable species endemic to China,using polymorphic DNA microsatellite loci (105 individual birds and seven loci) and mitochondrial DNA control-region sequences (63 birds).Contrary to the traditional concept that males are the more philopatric sex and females the more dispersing sex in birds,all the genetic information extracted from the two markers suggests that male-biased dispersal is predominant in Elliot's Pheasant.We argue that polygynous species in Galliformes without lekking behavior are more likely to exhibit male-biased dispersal patterns,consistent with the expected results based on the polygynous mating system of Elliot's Pheasant.

Expression levels of GSTA2 and APOD genes might be associated with carotenoid coloration in golden pheasant(Chrysolophus pictus) plumage

Carotenoids, which generate yellow, orange, and red colors, are crucial pigments in avian plumage. Investigations into genes associated with carotenoid- based coloration in avian species are important; however, such research is difficult because carotenoids cannot be synthetized in vertebrates as they are only derived from dietary sources. Here, the golden pheasant （Chrysolophus pictus） was used as a model in analysis of candidate gene expression profiles implicated in carotenoid binding and deposition. Using mass and Raman spectrometry to confirm the presence of carotenoids in golden pheasant feathers, we found C40H540 and C40H5602 in feathers with yellow to red colors, and in the rachis of iridescent feathers. The global gene expression profiles in golden pheasant skins were analyzed by RNA-seq and all six carotenoid binding candidate genes sequenced were studied by real- time PCR. STAR4, GSTA2, Scarbl, and APOD in feather follicles showed different expressions in red breast and orange nape feathers compared with that of iridescent mantle feathers. Further comparison of golden pheasant yellow rump and Lady Amherst＇s pheasant （Chrysolophus amherstiae） white nape feathers suggested that GSTA2 and APOD played a potential role in carotenoid-based coloration in golden pheasant.

Seasonal variations in the energy budget of Elliot's pheasant (Syrmaticus ellioti) in cage

This study aimed to discuss the energy budget of Elliot's pheasant Syrmaticus ellioti in different seasons, with life and health, good growth and normal digestion of Elliot's pheasant as the tested objects, The energy budget of Elliot's pheasant was measured by daily collection of the trial pheasants' excrement in the biological garden of Guangxi Normal University from March 2011 to February 2012. The results showed that the gross energy consumption, metabolic energy and excrement energy varied by season, increasing as temperature decreased. There was significant difference in gross energy consumption, metabolic energy, excrement energy between adults and nonages. There was also a trend that food digestibility of pheasants increases as temperature increases. In the same season, the food digestibility of adults was better than that of nonages. Throughout spring, summer, autumn and winter, the metabolic energy of 4-year adults were 305.77±13.40 kJ/d, 263.67±11.89 kJ/d, 357.23±25.49 kJ/d and 403.12±24.91 kJ/d, respectively, and the nonages were 284.86±17.22 kJ/d, 284. 66±15.16 kJ/d, 402. 26±31.46 kJ/d and 420. 30±31.98 kJ/d, respectively. The minimum metabolic energies were 247.65±21.81 g, 265.86±26.53 g, respectively for each group, detected between 4-year adults and 1-year nonages. Further study is needed to determine whether 29.6 C is the optimal temperature for the Elliot's pheasant.

Nest survival rate of Reeves＇s pheasant(Syrmaticus reevesii) based on artificial nest experiments

To explore the nest survival rate of Reeves＇ s pheasant（Syrmaticus reevesii） and the nest-site factors that affect it, we conducted artificial nest experiments with reference to natural nests at Dongzhai National Nature Reserve（DNNR）, Henan Province and Pingjingguan, Hubei Province from April to June 2014 simulating the situation in its early and later breeding season. We also determined distance characteristics of the nest sites by Arc GIS 10.0. Nest survival models were constructed in Program MARK for data analysis. Results indicated that in the early breeding season, the apparent survival rate（ASR） in DNNR（52.4%） was significantly greater than that in Pingjingguan（13.5%）, and the ASR in the later breeding season in DNNR（26.7%） was not indistinctively correlated with Pingjingguan（3.2%）. The daily survival rate（DSR） in the later breeding season was 93.8% in DNNR and 92.0% in Pingjingguan, respectively. The DSRs were both negatively correlated with nest distance to forest edges and settlements. The DSR in Pingjingguan was positively correlated with nest distance to paths and negatively correlated with nest distance to water sources. However, the DSR in DNNR was negatively correlated with nest distance to paths but positively correlated with nest distance to water sources.

Muscle architecture of the forelimb of the Golden Pheasant(Chrysolophus pictus)(Aves: Phasianidae)and its implications for functional capacity in flight

Background: Flight is the central avian adaptation in evolution. Wing muscles form an important anatomical basis for avian flight, affecting wing performance and determine modes of flight. However, the roles of distal muscles in adjusting the wing, as well as their functional specializations, remain largely unknown. The importance of muscle fiber architecture has long been recognized. In this study, we provide quantitative anatomical data on the muscle architecture of the forelimb of the Golden Pheasant(Chrysolophus pictus), with an emphasis on brachial,antebrachial and manual segments.Methods: The forelimbs of five Golden Pheasants were dissected and detailed measurements of all muscles were made, including muscle mass, muscle belly length, fascicle length. From these values, muscle volume, physiological cross-sectional area(PCSA) and maximum isometric force were derived.Results: General trends such as the distribution of muscle mass, fascicle length and the ratio of tendon length/belly length are revealed. Comparing PCSAs between antebrachial depressors and elevators and between intrinsics of the alular digit and major digit yielded significant differences(p < 0.05). Pronounced development of the antebrachial depressors suggests that ventral rotation of the distal half of the wing is a pivotal factor in shape change and orientation modulation. Large PCSAs in tandem with the force generation capability of the major digit intrinsics may help stabilize the digits while enhancing support of the primary feathers. The architectural properties of the alular digit confirm that alular adjustment is essential to rapid adduction and abduction.Conclusions: These observations illustrate the underlying structural basis for the functional capacities of the distal forelimb muscles and may provide additional information useful in further biomechanical and in vivo investigations.

Population survey and conservation assessment of the globally threa- tened cheer pheasant （Catreus wallicht） in Jhelum Valley, Azad Kas- hmir, Pakistan

The cheer pheasant Catreus wallichi is a globally threatened species that inhabits the western Himalayas. Though it is well established that the species is threatened and its numbers declining, updated definitive estimates are lacking, so in 2011, we conducted a survey to assess the density, population size, and threats to the species in Jhelum valley, Azad Kashmir, which holds the largest known population of cheer pheasants in Pakistan. We conducted dawn call count surveys at 17 points clustered in three survey zones of the valley, 11 of which had earlier been used for a 2002-2003 survey of the birds. Over the course of our survey, 113 birds were recorded. Mean density of cheer pheasant in the valley was estimated at 11.8±6.47 pairs per km2, with significant differences in terms of both counts and estimated density of cheer were significantly different across the three survey zones, with the highest in the Chinari region and the lowest, that is the area with no recorded sightings of the pheasants, in Gari Doppata. The total breeding population of cheer pheasants is estimated to be some 2 490 pairs, though this does not consider the actual area of occupancy in the study area. On the whole, more cheer pheasants were recorded in this survey than from the same points in 2002-2003, indicating some success in population growth. Unfortunately, increasing human settlement, fires, livestock grazing, hunting, and the collection of non-timber forest products continue to threaten the population of cheer in the Jhelum valley. To mitigate these potential impacts, some degree of site protection should be required for the conservation of cheer pheasants in Pakistan, and more effective monitoring of the species is clearly needed.

Normal Bacterial Floras in Intestinal Tract of Ring-Necked Pheasant

The normal bacterial floras in intestinal tract of ring-necked pheasant were investigated. Eight age groups were chosen. Samples of intestines were diluted in 10 fold series and incubated on different selective media. Atter incubation. aimed bacterial colonies were counted then the number of CFU/g of gut inclusions was evaluated. The data were analyzed in statistics. The physiological values of eight main normal bacterial floras were obtained. The eubiosis of normal bacterial floras in intestinal tract of ring-necked pheasant was established from its age of 10 days old to 30 days old. The dominant bacterial floras were bifidobacterium, lactobacillus and bacteroideceae.

Functional and phylogenetic structures of pheasants in China

Biodiversity has been subjected to increasing anthropogenic pressures.It is critical to understand the different processes that govern community assembly and species coexistence under biogeographic processes and anthropogenic events.Pheasants(Aves:Phasianidae)are highly threatened birds and China supports the richest pheasant species worldwide.Unravelling the spatial patterns and underlying factors associated with multidimensional biodiversity of species richness(SR),functional diversity(FD),and phylogenetic diversity(PD)of pheasants in China is helpful to understand not only the processes that govern pheasant community assembly and species coexistence,but also pheasant biodiversity conservation.We used a total of 45 pheasant species in China and analyzed the SR,FD,PD,and functional and phylogenetic structures by integrating species distribution maps,functional traits and phylogenies based on 50 km×50 km grid cells.We further used simultaneous autoregressive(SAR)models to explore the factors that determined these patterns.The southern Qinghai-Tibetan Plateau(QTP),Hengduan Mountains,southwestern Mountains,the east of the Qilian Mountains,the Qinling,southern China displayed higher SR,FD,and PD,which were determined by elevation,habitat heterogeneity,temperature seasonality,and vegetation cover.Elevation primarily determined the functional and phylogenetic structures of the pheasant communities.Assemblages in the highlands were marked by functional and phylogenetic clustering,particularly in the QTP,whereas the lowlands in eastern China comprised community overdispersion.Clustered pheasant assemblages were composed of young lineages.Patterns of functional and phylogenetic structures and richness-controlled functional and phylogenetic diversity differed between regions,suggesting that phylogenetic structures are not a good proxy for identifying functional structures.We revealed the significant role of elevation in pheasant community assemblages in China.Highlands interacted with community clustering,whereas lowlands interacted with overdispersion,supporting the environmental filtering hypothesis.Biogeographical drivers other than anthropogenic factor determined biodiversity of pheasants at the present scale of China.This study provides complementary background resources for multi-dimensional pheasant biodiversity and provides insights into avian biodiversity patterns in China.

Seasonal variations in the energy budget of Elliot’s pheasant (Syrmaticus ellioti) in cage

This study aimed to discuss the energy budget of Elliot’s pheasant Syrmaticus ellioti in different seasons,with life and health,good growth and normal digestion of Elliot’s pheasant as the tested objects,The energy budget of Elliot’s pheasant was measured by daily collection of the trial pheasants’excrement in the biological garden of Guangxi Normal University from March 2011 to February 2012.The results showed that the gross energy consumption,metabolic energy and excrement energy varied by season,increasing as temperature decreased.There was significant difference in gross energy consumption,metabolic energy,excrement energy between adults and nonages.There was also a trend that food digestibility of pheasants increases as temperature increases.In the same season,the food digestibility of adults was better than that of nonages.Throughout spring,summer,autumn and winter,the metabolic energy of 4-year adults were 305.77±13.40 kJ/d,263.67±11.89 kJ/d,357.23±25.49 kJ/d and 403.12±24.91 kJ/d,respectively,and the nonages were 284.86±17.22 kJ/d,284.66±15.16 kJ/d,402.26±31.46 kJ/d and 420.30±31.98 kJ/d,respectively.The minimum metabolic energies were 247.65±21.81 g,265.86±26.53 g,respectively for each group,detected between 4-year adults and 1-year nonages.Further study is needed to determine whether 29.6 C is the optimal temperature for the Elliot’s pheasant.

Genetic Variation of Grey-rumped Pheasant (Torquatus group) Populations in China

The polymerase chain reaction combined with direct sequencing was employed to deduce the variety of the grey-rumped pheasant populations in China. Totally 1079 basepair sequences of mitochondrial DNA （mtDNA） control-region gene were analyzed from 121 grey-rumpod pheasants obtained from 13 Chinese lo- calities, 76 variable sites resulted in 91 haplotypes. These populations possessed a high level of genetic diversity, indicating that during their evolution effective population size and polymorphism were not reduced by climatic fluctuations in the Pleistocene ice ages. Phylogenetie analysis indicates that all populations were clustered into two groups, western and eastern. The degree of population differentiation presumably results from a low gene flow （ N, = 0. 33, F,, = 0. 60, P 〈 0. 001 ） between the two groups, and the divergence occurred in the years （2.1 ×10^5 - 2.2 × 105 ）. The genetic structure of grey-rumped pheasants in China ap- pears to be the result of the uplift of Qinghai-Tibet Plateau, the existence of Qinling Mountains and Liupan Mountains and cyclical climatic oscillations during the late Pleistocene.