Sex identification in falcons using microsatellite DNA markers

Minimally Invasive Sampling Methods for Molecular Sexing of Wild and Companion Birds

Birds are highly social and must be paired in order to increase their welfare. Most bird species are monomorphic; therefore, molecular sexing helps provide appropriate welfare for birds. Moreover, early sex determination can be of great value for bird owners. The aim of this study was to demonstrate that sex identification in birds achieved using molecular methods and samples collected via minimally invasive methods is fast, efficient, and accurate. A total of 100 samples (29 paired samples of feathers and oral swabs and 14 tripled samples of feathers, oral swabs, and blood) from 43 birds were included in this study, as follows: wild birds (Falconiformes, Accipitriformes, landfowl-Galliformes, waterfowl-Anseriformes) and companion birds (Passeriformes, Psittaciformes-large-, medium-, and small-sized parrots). Amplification of CHD1-Z and CHD1-W genes was performed via conventional PCR. The results obtained from feathers were compared to those obtained from oral swabs and to those obtained from blood samples, where applicable. The obtained results show that all types of samples can be used for molecular sexing of all studied bird species. To the best of our knowledge, the present study reports, for the first time, molecular sex identification in Red Siskin (Carduelis cucullata) and Goldfinch (Carduelis carduelis major). For higher accuracy, our recommendation is to use minimally invasive samples (oral swabs and feathers) and to test both types of samples for each bird instead of blood samples.

Hard times in the city - attractive nest sites but insufficient food supply lead to low reproduction rates in a bird of prey

INTRODUCTION

Urbanization is a global phenomenon that is encroaching on natural habitats and decreasing biodiversity, although it is creating new habitats for some species. The Eurasian kestrel (Falco tinnunculus) is frequently associated with urbanized landscapes but it is unclear what lies behind the high densities of kestrels in the urban environment.

RESULTS

Occupied nest sites in the city of Vienna, Austria were investigated along a gradient of urbanization (percentage of land covered by buildings or used by traffic). Field surveys determined the abundance of potential prey (birds and rodents) and the results were compared to the birds' diets. A number of breeding parameters were recorded over the course of three years. The majority of kestrels breed in semi-natural cavities in historic buildings. Nearest neighbour distances (NND) were smallest and reproductive success lowest in the city centre. Abundance of potential prey was not found to relate to the degree of urbanization but there was a significant shift in the birds' diets from a heavy reliance on rodents in the outskirts of the city to feeding more on small birds in the centre. The use of urban habitats was associated with higher nest failure, partly associated with predation and nest desertion, and with significantly lower hatching rates and smaller fledged broods.

CONCLUSIONS

High breeding densities in urban habitats do not necessarily correlate with high habitat quality. The high density of kestrel nests in the city centre is probably due to the ready availability of breeding cavities. Highly urbanized areas in Vienna are associated with unexpected costs for the city dwelling-raptor, in terms both of prey availability and of reproductive success. The kestrel appears to be exploiting the urban environment but given the poor reproductive performance of urban kestrels it is likely that the species is falling into an ecological trap.

Improved molecular assay for sex identification of the endangered crested Ibis (Nipponia nippon) based on the CHD1 gene and a sex-linked microsatellite locus

Sex Identification of monomorphic birds, especially endangered avian species, is essential for ecological study and biodiversity conservation. In this study, two popular primer sets of 2550F/2718R and P2/P8, which were designed to amplify different fragments of chromodomain-helicase-DNA binding protein 1 (CHD1) genes mapped on both Z and W chromosomes in birds, were used to identify for the first time the sex of individuals of the endangered species crested ibis (Nipponia nippon) in a large number of samples. An improved primer set of 2467F/2530R was re-designed to be specific to crested ibis following their conserved sequences derived from the 2550F/2718R primers. PCR products of the new primers were conveniently visualized with two bands of 552 base pairs (bp) and 358 bp for females, but a single band of 552 bp for males in routine 1.8% agarose gel. Similarly, the P2/P8 primer set amplified two fragments of 398 bp and 381 bp from females but one fragment of 398 bp from males; however, a high resolution involving 10% Polyacrylamide gel had to be employed to resolve the 17 bp insertions/deletions (in/dels) present between the two amplicons in females. In addition, a microsatellite locus NnNF05 was validated to be sex-linked and shown to be effective in the sexing of crested ibis, supporting its utility in non-invasive sampling. This study provides a rapid, convenient, and reliable molecular assay for improving sex identification in the monomorphic and monogamous crested ibis, and thus facilitates the selection of breeding pairs in captive programs and reintroduction initiatives.

Molecular sexing of threatened Gyps vultures: an important strategy for conservation breeding and ecological studies

During the last two decades populations of three resident species of Gyps vulture have declined dramatically and are now threatened with extinction in South Asia. Sex identification of vultures is of key importance for the purpose of conservation breeding as it is desirable to have an equal sex ratio in these monogamous species which are housed together in large colony aviaries. Because vultures are monomorphic, with no differences in external morphology or plumage colour between the sexes, other methods are required for sex identification. Molecular methods for sex identification in birds rely on allelic length or nucleotide sequence discrimination of the chromohelicase-DNA binding (CHD) gene located on male and female chromosomes ZZ and ZW, respectively. We characterized the partial sequences of CHD alleles from Gyps indicus, Gyps bengalensis, Gyps himalayensis and Aegypius monachus and analysed the applicability of five molecular methods of sex identification of 46 individual vultures including 26 known-sex G. bengalensis and G. indicus. The results revealed that W-specific PCR in combination with ZW-common PCR is a quick, accurate and simple method, and is ideal for sex identification of vultures. The method is also suitable to augment ecological studies for identifying sex of these endangered birds during necropsy examinations especially when gonads are not apparent, possibly due to regression during non-breeding seasons.

Microsatellite resources for Passeridae species: a predicted microsatellite map of the house sparrow Passer domesticus

We identified microsatellite sequences of potential utility in the house sparrow (Passer domesticus) and assigned their predicted genome locations. These sequences included newly isolated house sparrow loci, which we fully characterized. Many of the newly isolated loci were polymorphic in two other species of Passeridae: Berthelot's pipit Anthus berthelotii and zebra finch Taeniopygia guttata. In total, we identified 179 microsatellite markers that were either isolated directly from, or are of known utility in, the house sparrow. Sixty-seven of these markers were designed from unique sequences that we isolated from a house sparrow genomic library. These new markers were combined with 36 house sparrow markers isolated by other studies and 76 markers isolated from other passerine species but known to be polymorphic in the house sparrow. We utilized sequence homology to assign chromosomal locations for these loci in the assembled zebra finch genome. One hundred and thirty-four loci were assigned to 25 different autosomes and eight loci to the Z chromosome. Examination of the genotypes of known-sex house sparrows for 37 of the new loci revealed a W-linked locus and an additional Z-linked locus. Locus Pdoμ2, previously reported as autosomal, was found to be Z-linked. These loci enable the creation of powerful and cost-effective house sparrow multiplex primer sets for population and parentage studies. They can be used to create a house sparrow linkage map and will aid the identification of quantitative trait loci in passerine species.

Validation of Spilornis cheela hoya TaqMan probes for potential gender identification of many Accipitridae species

The objective of this study was to test the hypothesis that genders of Accipitridae species, with the same or similar sequences to our previously proposed Spilornis cheela hoya (S. c. hoya) chromo-helicase-DNA binding protein (CHD)-W-specific and CHD-ZW-common TaqMan probes, can be successfully determined. Eight species of Accipitridae with known genders were collected. After PCR, TA cloning, sequencing, and alignment analyses, sequence length differences of Griffiths P2/P8 PCR amplicons between CHD-Z and CHD-W genes ranged from 2 to 19 bp for these Accipitridae species, and they were unsolved in 3% agarose gel. Using our previous proposed S. c. hoya TaqMan probes, the genders of Circaetus gallicus, completely homologous to the sequences for these CHD probes, were successfully identified. With one nucleotide difference to S. c. hoya CHD-W-specific probe, gender identification of Accipiter gularis, Accipiter soloensis, Accipiter trivirgatus, Accipiter virgatus, and Butastur indicus were validated. With two nucleotide differences in the CHD-W-specific probe and one nucleotide difference in the CHD-ZW-common probe, Pernis ptilorhyncus also performed well for gender identification. In conclusion, the S. c. hoyaCHD probes, coupled with the Griffiths P2/P8 primers, were validated to provide accurate and high-throughput gender identification for many Accipitridae species.

A non-invasive test for sex identification in Short-toed Eagle (Circaetus gallicus)

Knowledge of the sex of individuals in natural populations greatly facilitates evolutionary ecology, breeding systems and genetics. Therefore, the development of a simple, not stressing and objective sexing test would facilitate conservation of the Short-toed Eagle (Circaetus gallicus), an endangered Accipitridae species living mainly in southern Europe and Asia. A PCR test was used employing primers that amplify two homologous fragments of both the CHD-W gene, unique of females, and the CHD-Z, occurring in the two sexes. The analysis of the PCR products obtained from blood DNA showed a band of about 380 bp, apparently unique in all individuals. The alignment of the sequences of the two fragments revealed that CHD-W is only 9 bp longer than CHD-Z (387 vs. 378 bp) while CHD-Z lacks the restriction site for Asp700I. After digestion male PCR products showed a unique band of 378 bp while fragments belonging to females resolved into three bands (378, 280 and 107 bp). Using feathers as DNA sources, the individual patterns obtained were identical with the corresponding blood DNA samples. This sexing technique is objective and non-invasive and could be useful for verifying the sex ratio theories and improving the management.

Sex identification by alternative polymerase chain reaction methods in falconiformes

A number of avian species are difficult to sex morphologically, especially as nestlings. Like other avian species, many species of Falconiformes are sexually monomorphic. Therefore, it is desirable that new methods based on DNA analysis are established in Falconiformes and other sexual monomorphic species. We identified sex in Falconiformes by two alternative methods. First, we used a sexing method based on the intronic length variation between CHD1W and CHD1Z using primers flanking the intron. In this method, two species of Falconidae could be identified for sexing. However, six species of Accipitridae could not, because they have few length variations. The second method used was based on differences in sequences between CHD1W and CHD1Z. From sequence analysis, a 3'-terminal mismatch primer on point mutation conserved among Falconiformes was designed, and identification of sex with the amplification refractory mutation system (ARMS) was performed. This method could identify sex in all species tested. In addition, because the 3'-terminal mismatch primer was designed on a point mutation conserved among Falconiformes, ARMS with these primers may identify sex in all Falconiformes. These are simple and rapid sexing methods, since only polymerase chain reaction (PCR) and agarose electrophoresis are required. In conclusion, sex identification by an alternative PCR approach based on intronic length variation and on differences in sequences between CHD1W and CHD1Z proved applicable to and useful for Falconiformes.

Evolutionary genetics. Clonal inheritance of avian mitochondrial DNA

We have taken a new approach to test the commonly accepted, but recently questioned, principle of clonal inheritance of vertebrate mitochondrial DNA (mtDNA) by relating its inheritance to a female-specific marker of nuclear DNA. Whereas this is impossible in organisms with male heterogamy (such as mammals), we show here that genealogies of mtDNA and the female-specific W chromosome of a bird species are completely concordant. Our results indicate that inheritance of mtDNA is free of detectable recombination effects over an evolutionary timescale.