Deborah Dawson - Academia.edu (original) (raw)

Papers by Deborah Dawson

PLoS ONE, 2012

The exceptional biodiversity of Reunion Island is threatened by anthropogenic landscape changes t... more The exceptional biodiversity of Reunion Island is threatened by anthropogenic landscape changes that took place during the 350 years of human colonization. During this period the human population size increased dramatically from 250 to 800,000. The arrival of humans together with the development of agriculture, invasive species such as rats and cats, and deforestation has lead to the extinction of more than half of the original vertebrate species of the island. For the remaining species, significant work is being carried out to identify threats and conservation status, but little genetic work has been carried on some of the most endangered species. In the last decade theoretical studies have shown the ability of neutral genetic markers to infer the demographic history of endangered species and identify and date past population size changes (expansions or bottlenecks). In this study we provide the first genetic data on the critically endangered species the Reunion cuckoo-shrike Coracina newtoni. The Reunion cuckoo-shrike is a rare endemic forest bird surviving in a restricted 12-km 2 area of forested uplands and mountains. The total known population consists of less than one hundred individuals out of which 45 were genotyped using seventeen polymorphic microsatellite loci. We found a limited level of genetic variability and weak population structure, probably due to the limited geographic distribution. Using Bayesian methods, we identified a strong decline in population size during the Holocene, most likely caused by an ancient climatic or volcanic event around 5000 years ago. This result was surprising as it appeared in apparent contradiction with the accepted theory of recent population collapse due to deforestation and predator introduction. These results suggest that new methods allowing for more complex demographic models are necessary to reconstruct the demographic history of populations.

Conservation Genetics Resources, 2010

Genetic data are increasingly recognized for their utility in conservation programs. However, man... more Genetic data are increasingly recognized for their utility in conservation programs. However, many endangered species belong to families that have been understudied. Due to the urgency of their conservation status it is important to quickly identify polymorphic microsatellite loci from available resources. We show for the Réunion Cuckoo shrike Coracina newtoni, that this strategy can be very useful. Using 110 passerine microsatellite primer sets we identified eighteen polymorphic loci and tested them in 25 C. newtoni individuals. Following a Bonferroni correction one pair of loci displayed linkage disequilibrium (P-value \ 0.0001).

BMC research notes, Jan 19, 2017

The objective here is to identify highly polymorphic microsatellite loci for the Palaearctic swea... more The objective here is to identify highly polymorphic microsatellite loci for the Palaearctic sweat bee Lasioglossum malachurum. Sweat bees (Hymenoptera: Halictidae) are widespread pollinators that exhibit an unusually large range of social behaviours from non-social, where each female nests alone, to eusocial, where a single queen reproduces while the other members of the colony help to rear her offspring. They thus represent excellent models for understanding social evolution. 24 new microsatellite loci were successfully optimized. When amplified across 23-40 unrelated females, the number of alleles per locus ranged from 3 to 17 and the observed heterozygosities 0.45 to 0.95. Only one locus showed evidence of significant deviation from Hardy-Weinberg equilibrium. No evidence of linkage disequilibrium was found. These 24 loci will enable researchers to gain greater understanding of colony relationships within this species, an important model for the study of eusociality. Furthermore...

European Journal of Wildlife Research, 2016

Microsatellite loci are widely used in ecological and evolutionary studies to assess 19 inbreedin... more Microsatellite loci are widely used in ecological and evolutionary studies to assess 19 inbreeding, genetic parentage and population structure. Such loci are often species-specific and 20 optimised in multiplexes to allow for economical and efficient use. Here, we tested 11 microsatellite 21 loci designed for use in European bee-eaters (Merops apiaster), along with 31 loci designed in other 22 species, for their utility in European bee-eaters sampled on Susak Island, Croatia. Of these 42 loci, 20 23 were polymorphic in 38 individuals. These polymorphic loci were further assessed in a subset of 23 24 adults, excluding close relatives, which exhibited between three and 13 alleles each. All loci were 25 autosomal, as indicated by the presence of heterozygotes in both males and females. One of the 26 polymorphic loci exhibited low heterozygosity, three loci deviated from Hardy-Weinberg equilibrium 27 and three pairs of loci displayed linkage disequilibrium. The remaining selected eight cross-species 28 loci and seven loci isolated in European bee-eaters were combined with two sex-typing markers and 29 optimised in five multiplexes. A combination of 17 loci of varying degrees of polymorphism makes 30 this multiplex set particularly suitable for both parentage and spatial genetic analyses. This multiplex 31 set therefore provides a useful toolkit for studying kin selection and population genetics in the 32 cooperatively breeding European bee-eater and, potentially, in other closely related species. 33 Manuscript without track changes Click here to download Manuscript EJWR-S-15-00356-1_RESUBMITTED_FINAL.doc Click here to view linked References

Molecular Ecology Notes, 2006

We isolated 45 new Kentish plover (Charadrius alexandrinus) microsatellite loci. These were teste... more We isolated 45 new Kentish plover (Charadrius alexandrinus) microsatellite loci. These were tested for polymorphism in 42 Kentish plovers breeding in the Çukurova Delta, Turkey. Thirty-six of the 45 loci were polymorphic with observed heterozygosity varying between 0.22 and 0.93. Genotypes of individuals of known sex indicated that two loci were sex-linked (Calex-26 is located on the Z chromosome and Calex-31 on the W chromosome). Additionally, we tested all loci for amplification in four other species of Charadridae (Kittlitz's plover, Madagascar plover, three-banded plover and white-fronted plover). On average 34 loci amplified per species (range 29-36).

Molecular ecology, 2014

Discerning the relative roles of adaptive and nonadaptive processes in generating differences amo... more Discerning the relative roles of adaptive and nonadaptive processes in generating differences among populations and species, as well as how these processes interact, is a fundamental aim in biology. Both genetic and phenotypic divergence across populations can be the product of limited dispersal and gradual genetic drift across populations (isolation by distance), of colonization history and founder effects (isolation by colonization) or of adaptation to different environments preventing migration between populations (isolation by adaptation). Here, we attempt to differentiate between these processes using island populations of Berthelot's pipit (Anthus berthelotii), a passerine bird endemic to three Atlantic archipelagos. Using microsatellite markers and approximate Bayesian computation, we reveal that the northward colonization of this species ca. 8500 years ago resulted in genetic bottlenecks in the colonized archipelagos. We then show that high levels of genetic structure ex...

Molecular Ecology Notes, 2003

This is a repository copy of Isolation of 39 polymorphic microsatellite loci and the development ... more This is a repository copy of Isolation of 39 polymorphic microsatellite loci and the development of a fluorescently labelled marker set for the Eurasian badger.

Molecular Ecology Notes, 2003

This is a repository copy of Characterization of spotted hyena, Crocuta crocuta microsatellite loci.

Molecular Ecology Notes, 2003

including the URL of the record and the reason for the withdrawal request.

This is a repository copy of Isolation of polymorphic microsatellites in the stemless thistle (Ci... more This is a repository copy of Isolation of polymorphic microsatellites in the stemless thistle (Cirsium acaule) and their utility in other Cirsium species.

PLoS ONE, 2011

Fluctuating asymmetry (FA), a measure of developmental instability, has been hypothesized to incr... more Fluctuating asymmetry (FA), a measure of developmental instability, has been hypothesized to increase with genetic stress. Despite numerous studies providing empirical evidence for associations between FA and genome-wide properties such as multi-locus heterozygosity, support for single-locus effects remains scant. Here we test if, and to what extent, FA co-varies with single-and multilocus markers of genetic diversity in house sparrow (Passer domesticus) populations along an urban gradient. In line with theoretical expectations, FA was inversely correlated with genetic diversity estimated at genome level. However, this relationship was largely driven by variation at a single key locus. Contrary to our expectations, relationships between FA and genetic diversity were not stronger in individuals from urban populations that experience higher nutritional stress. We conclude that loss of genetic diversity adversely affects developmental stability in P. domesticus, and more generally, that the molecular basis of developmental stability may involve complex interactions between local and genome-wide effects. Further study on the relative effects of single-locus and genome-wide effects on the developmental stability of populations with different genetic properties is therefore needed.

Molecular Ecology Resources, 2009

We characterized 38 microsatellite loci in the European blackbird, Turdus merula. Thirtyseven loc... more We characterized 38 microsatellite loci in the European blackbird, Turdus merula. Thirtyseven loci were identified by testing 242 loci that had been originally isolated in other avian species. One additional locus was isolated from a European blackbird genomic library. All loci were characterized in 20-29 blackbirds from a population in the Czech Republic and displayed between two and 16 alleles, with observed heterozygosity ranging from 0.04 to 1.00. Thirty-seven loci could be assigned a chromosome location in the zebra finch (Taeniopygia guttata) genome based on sequence homology.

Molecular Ecology, 1998

Despite the interest that avian brood parasites provoke due to their reproductive strategy, and t... more Despite the interest that avian brood parasites provoke due to their reproductive strategy, and the wealth of published studies, their mating system is one of the least known aspects of their natural history. This study describes the first attempt to use genetics to characterize mating patterns in a brood parasite, the great spotted cuckoo (Clamator glandarius). We developed a set of microsatellite markers for this species that allowed us to determine the parentage of 78% of the chicks sampled, with a high probability of certainty (false parental inclusion probability, P FI = 2 × 10-4). Parentage analyses allowed us to determine mating patterns in the population, to show for the first time that there were several females laying in the same study site and sharing host nests, and that females used nests of two different host species in the same season. A total of 70% of the inferred mating relationships can be considered monogamous, and the rest were cases of genetic polygamy, although of unknown social structure. To ease parentage analyses, adult birds were successfully sexed using a combination of sexspecific PCR primers and SSCP techniques before parentage assignment.

Molecular Ecology, 2010

Cultural transmission is thought to be a mechanism by which migratory animals settle into habitat... more Cultural transmission is thought to be a mechanism by which migratory animals settle into habitats, but little evidence exists in wild populations because of the difficulty of following individuals over successive generations and wide geographical distances. Cultural inheritance of migration routes represents a mechanism whereby geographical isolation can arise between separate groups and could constrain individuals to potentially suboptimal sites within their range. Conversely, adopting the parental migratory route in adult life, rather than dispersing randomly, may increase an individual's reproductive success because that strategy has already been proven to allow successful breeding. We combined a pedigree of related light-bellied Brent geese (Branta bernicla hrota) with 6 years of observations of marked birds to calculate the dispersal distances of adult offspring from their parents in both Ireland and Iceland. In both countries, the majority of offspring were found to recruit into or near their parental sites, indicating migratory connectivity in the flyway. Despite this kin structure, we found no evidence of genetic differentiation using genotype data from 1127 individuals across 15 microsatellite loci. We suggest that the existence of migratory connectivity of subpopulations is far more common than previous research indicates and that cultural information may play an important role in structuring reproductive isolation among them.

Conservation Genetics - CONSERV GENET, 2002

Insect Molecular Biology, 2007

Although microsatellites are ubiquitous in eukaryota, the number of available markers varies stro... more Although microsatellites are ubiquitous in eukaryota, the number of available markers varies strongly among taxa. This meta-analysis was conducted on 32 insect species. Sequences were obtained from two assembled whole genomes, whole genome shotgun (WGS) sequences from 10 species and screening partial genomic libraries for microsatellites from 23 species. We have demonstrated: (1) strong differences in the abundance of microsatellites among species; (2) that microsatellites within species are often grouped into families based on similarities in their flanking sequences; (3) that the proportion of microsatellites grouped into families varies strongly among taxa; and (4) that microsatellite families were significantly more often associated with transposable elements-or their remnants-than unique microsatellite sequences.

Forensic Science International: Genetics, 2008

Developing short tandem repeat (STR) profiling systems for forensic identification is complicated... more Developing short tandem repeat (STR) profiling systems for forensic identification is complicated in animal species. Obtaining a representative number of individuals from populations, limited access to family groups and a lack of developed STR markers can make adhering to human forensic guidelines difficult. Furthermore, a lack of animal specific guidelines may explain why many wildlife forensic STR profiling systems developed to date have not appropriately addressed areas such as marker validation or the publication and analysis of population data necessary for the application of these tools to forensic science. Here we present a methodology used to develop an STR profiling system for a legally protected wildlife species, the Eurasian badger Meles meles. Ten previously isolated STR loci were selected based on their level of polymorphism, adherence to Hardy-Weinberg expectations and their fragment size. Each locus was individually validated with respect to its reproducibility, inheritance, species specificity, DNA template concentration and thermocycling parameters. The effects of chemical, substrate and environmental exposure were also investigated. All ten STR loci provided reliable and reproducible results, and optimal amplification conditions were defined. Allele frequencies from 20 representative populations in England and Wales are presented and used to calculate the level of population substructure (u) and inbreeding (f). Accounting for these estimates, the average probability of identity (PI ave) was 2.18 Â 10 À7. This case study can act as a framework for others attempting to develop wildlife forensic profiling systems.

Conservation Genetics Resources, 2010

We isolated 137 unique microsatellite loci from an enriched Light-bellied Brent goose (Branta ber... more We isolated 137 unique microsatellite loci from an enriched Light-bellied Brent goose (Branta bernicla hrota) genomic library. Thirty-seven polymorphic loci were characterised in 24 unrelated individuals sampled from a Light-bellied Brent goose population located at Ringneill quay in Strangford Lough, Northern Ireland. The 37 polymorphic loci displayed between 2 and 38 alleles. Sequence homology was used to assign a predicted chromosome location for 31 polymorphic loci (31 in the chicken (Gallus gallus) and 30 in the zebra finch (Taeniopygia guttata) assembled genome). Two polymorphic microsatellite loci were Z-linked based on the typing of known sex individuals (24 females and 25 females) and sequence homology.

Conservation Genetics Resources, 2011

The European badger (Meles meles) breeds plurally in lowland England and is important economicall... more The European badger (Meles meles) breeds plurally in lowland England and is important economically due to its link with bovine tuberculosis (Mycobacterium bovis) transmission. To understand disease transmission and facilitate effective management, it is vital to elucidate the social structure of badger groups. To improve parentage assignment and the discrimination of relatives, we isolated and characterised 21 polymorphic microsatellite loci in 24 individuals from Wytham Woods, Oxfordshire, UK. These 21 loci increased the discrimination power between fullsiblings and half-siblings from 71 to 88%, when added to the existing 31 loci. Similarly, the combined non-exclusion probability increased from 3.0 9 10-8 to 5.8 9 10-13. Newly isolated Mel-592 (FR745854) was X-linked, based on the genotypes of 48 known-sex individuals and will enhance the genetic sex-typing of badgers. Keywords European badger Á Meles meles Á Mustelidae Á Microsatellite Á Parentage Á X-chromosome linked locus Electronic supplementary material The online version of this article (

BMC Genomics, 2013

Background: Microsatellites are widely used for many genetic studies. In contrast to single nucle... more Background: Microsatellites are widely used for many genetic studies. In contrast to single nucleotide polymorphism (SNP) and genotyping-by-sequencing methods, they are readily typed in samples of low DNA quality/concentration (e.g. museum/non-invasive samples), and enable the quick, cheap identification of species, hybrids, clones and ploidy. Microsatellites also have the highest cross-species utility of all types of markers used for genotyping, but, despite this, when isolated from a single species, only a relatively small proportion will be of utility. Marker development of any type requires skill and time. The availability of sufficient "off-the-shelf" markers that are suitable for genotyping a wide range of species would not only save resources but also uniquely enable new comparisons of diversity among taxa at the same set of loci. No other marker types are capable of enabling this. We therefore developed a set of avian microsatellite markers with enhanced cross-species utility. Results: We selected highly-conserved sequences with a high number of repeat units in both of two genetically distant species. Twenty-four primer sets were designed from homologous sequences that possessed at least eight repeat units in both the zebra finch (Taeniopygia guttata) and chicken (Gallus gallus). Each primer sequence was a complete match to zebra finch and, after accounting for degenerate bases, at least 86% similar to chicken. We assessed primer-set utility by genotyping individuals belonging to eight passerine and four non-passerine species. The majority of the new Conserved Avian Microsatellite (CAM) markers amplified in all 12 species tested (on average, 94% in passerines and 95% in non-passerines). This new marker set is of especially high utility in passerines, with a mean 68% of loci polymorphic per species, compared with 42% in non-passerine species. Conclusions: When combined with previously described conserved loci, this new set of conserved markers will not only reduce the necessity and expense of microsatellite isolation for a wide range of genetic studies, including avian parentage and population analyses, but will also now enable comparisons of genetic diversity among different species (and populations) at the same set of loci, with no or reduced bias. Finally, the approach used here can be applied to other taxa in which appropriate genome sequences are available.

PLoS ONE, 2012

The exceptional biodiversity of Reunion Island is threatened by anthropogenic landscape changes t... more The exceptional biodiversity of Reunion Island is threatened by anthropogenic landscape changes that took place during the 350 years of human colonization. During this period the human population size increased dramatically from 250 to 800,000. The arrival of humans together with the development of agriculture, invasive species such as rats and cats, and deforestation has lead to the extinction of more than half of the original vertebrate species of the island. For the remaining species, significant work is being carried out to identify threats and conservation status, but little genetic work has been carried on some of the most endangered species. In the last decade theoretical studies have shown the ability of neutral genetic markers to infer the demographic history of endangered species and identify and date past population size changes (expansions or bottlenecks). In this study we provide the first genetic data on the critically endangered species the Reunion cuckoo-shrike Coracina newtoni. The Reunion cuckoo-shrike is a rare endemic forest bird surviving in a restricted 12-km 2 area of forested uplands and mountains. The total known population consists of less than one hundred individuals out of which 45 were genotyped using seventeen polymorphic microsatellite loci. We found a limited level of genetic variability and weak population structure, probably due to the limited geographic distribution. Using Bayesian methods, we identified a strong decline in population size during the Holocene, most likely caused by an ancient climatic or volcanic event around 5000 years ago. This result was surprising as it appeared in apparent contradiction with the accepted theory of recent population collapse due to deforestation and predator introduction. These results suggest that new methods allowing for more complex demographic models are necessary to reconstruct the demographic history of populations.

Conservation Genetics Resources, 2010

Genetic data are increasingly recognized for their utility in conservation programs. However, man... more Genetic data are increasingly recognized for their utility in conservation programs. However, many endangered species belong to families that have been understudied. Due to the urgency of their conservation status it is important to quickly identify polymorphic microsatellite loci from available resources. We show for the Réunion Cuckoo shrike Coracina newtoni, that this strategy can be very useful. Using 110 passerine microsatellite primer sets we identified eighteen polymorphic loci and tested them in 25 C. newtoni individuals. Following a Bonferroni correction one pair of loci displayed linkage disequilibrium (P-value \ 0.0001).

BMC research notes, Jan 19, 2017

The objective here is to identify highly polymorphic microsatellite loci for the Palaearctic swea... more The objective here is to identify highly polymorphic microsatellite loci for the Palaearctic sweat bee Lasioglossum malachurum. Sweat bees (Hymenoptera: Halictidae) are widespread pollinators that exhibit an unusually large range of social behaviours from non-social, where each female nests alone, to eusocial, where a single queen reproduces while the other members of the colony help to rear her offspring. They thus represent excellent models for understanding social evolution. 24 new microsatellite loci were successfully optimized. When amplified across 23-40 unrelated females, the number of alleles per locus ranged from 3 to 17 and the observed heterozygosities 0.45 to 0.95. Only one locus showed evidence of significant deviation from Hardy-Weinberg equilibrium. No evidence of linkage disequilibrium was found. These 24 loci will enable researchers to gain greater understanding of colony relationships within this species, an important model for the study of eusociality. Furthermore...

European Journal of Wildlife Research, 2016

Microsatellite loci are widely used in ecological and evolutionary studies to assess 19 inbreedin... more Microsatellite loci are widely used in ecological and evolutionary studies to assess 19 inbreeding, genetic parentage and population structure. Such loci are often species-specific and 20 optimised in multiplexes to allow for economical and efficient use. Here, we tested 11 microsatellite 21 loci designed for use in European bee-eaters (Merops apiaster), along with 31 loci designed in other 22 species, for their utility in European bee-eaters sampled on Susak Island, Croatia. Of these 42 loci, 20 23 were polymorphic in 38 individuals. These polymorphic loci were further assessed in a subset of 23 24 adults, excluding close relatives, which exhibited between three and 13 alleles each. All loci were 25 autosomal, as indicated by the presence of heterozygotes in both males and females. One of the 26 polymorphic loci exhibited low heterozygosity, three loci deviated from Hardy-Weinberg equilibrium 27 and three pairs of loci displayed linkage disequilibrium. The remaining selected eight cross-species 28 loci and seven loci isolated in European bee-eaters were combined with two sex-typing markers and 29 optimised in five multiplexes. A combination of 17 loci of varying degrees of polymorphism makes 30 this multiplex set particularly suitable for both parentage and spatial genetic analyses. This multiplex 31 set therefore provides a useful toolkit for studying kin selection and population genetics in the 32 cooperatively breeding European bee-eater and, potentially, in other closely related species. 33 Manuscript without track changes Click here to download Manuscript EJWR-S-15-00356-1_RESUBMITTED_FINAL.doc Click here to view linked References

Molecular Ecology Notes, 2006

We isolated 45 new Kentish plover (Charadrius alexandrinus) microsatellite loci. These were teste... more We isolated 45 new Kentish plover (Charadrius alexandrinus) microsatellite loci. These were tested for polymorphism in 42 Kentish plovers breeding in the Çukurova Delta, Turkey. Thirty-six of the 45 loci were polymorphic with observed heterozygosity varying between 0.22 and 0.93. Genotypes of individuals of known sex indicated that two loci were sex-linked (Calex-26 is located on the Z chromosome and Calex-31 on the W chromosome). Additionally, we tested all loci for amplification in four other species of Charadridae (Kittlitz's plover, Madagascar plover, three-banded plover and white-fronted plover). On average 34 loci amplified per species (range 29-36).

Molecular ecology, 2014

Discerning the relative roles of adaptive and nonadaptive processes in generating differences amo... more Discerning the relative roles of adaptive and nonadaptive processes in generating differences among populations and species, as well as how these processes interact, is a fundamental aim in biology. Both genetic and phenotypic divergence across populations can be the product of limited dispersal and gradual genetic drift across populations (isolation by distance), of colonization history and founder effects (isolation by colonization) or of adaptation to different environments preventing migration between populations (isolation by adaptation). Here, we attempt to differentiate between these processes using island populations of Berthelot's pipit (Anthus berthelotii), a passerine bird endemic to three Atlantic archipelagos. Using microsatellite markers and approximate Bayesian computation, we reveal that the northward colonization of this species ca. 8500 years ago resulted in genetic bottlenecks in the colonized archipelagos. We then show that high levels of genetic structure ex...

Molecular Ecology Notes, 2003

This is a repository copy of Isolation of 39 polymorphic microsatellite loci and the development ... more This is a repository copy of Isolation of 39 polymorphic microsatellite loci and the development of a fluorescently labelled marker set for the Eurasian badger.

Molecular Ecology Notes, 2003

This is a repository copy of Characterization of spotted hyena, Crocuta crocuta microsatellite loci.

Molecular Ecology Notes, 2003

including the URL of the record and the reason for the withdrawal request.

This is a repository copy of Isolation of polymorphic microsatellites in the stemless thistle (Ci... more This is a repository copy of Isolation of polymorphic microsatellites in the stemless thistle (Cirsium acaule) and their utility in other Cirsium species.

PLoS ONE, 2011

Fluctuating asymmetry (FA), a measure of developmental instability, has been hypothesized to incr... more Fluctuating asymmetry (FA), a measure of developmental instability, has been hypothesized to increase with genetic stress. Despite numerous studies providing empirical evidence for associations between FA and genome-wide properties such as multi-locus heterozygosity, support for single-locus effects remains scant. Here we test if, and to what extent, FA co-varies with single-and multilocus markers of genetic diversity in house sparrow (Passer domesticus) populations along an urban gradient. In line with theoretical expectations, FA was inversely correlated with genetic diversity estimated at genome level. However, this relationship was largely driven by variation at a single key locus. Contrary to our expectations, relationships between FA and genetic diversity were not stronger in individuals from urban populations that experience higher nutritional stress. We conclude that loss of genetic diversity adversely affects developmental stability in P. domesticus, and more generally, that the molecular basis of developmental stability may involve complex interactions between local and genome-wide effects. Further study on the relative effects of single-locus and genome-wide effects on the developmental stability of populations with different genetic properties is therefore needed.

Molecular Ecology Resources, 2009

We characterized 38 microsatellite loci in the European blackbird, Turdus merula. Thirtyseven loc... more We characterized 38 microsatellite loci in the European blackbird, Turdus merula. Thirtyseven loci were identified by testing 242 loci that had been originally isolated in other avian species. One additional locus was isolated from a European blackbird genomic library. All loci were characterized in 20-29 blackbirds from a population in the Czech Republic and displayed between two and 16 alleles, with observed heterozygosity ranging from 0.04 to 1.00. Thirty-seven loci could be assigned a chromosome location in the zebra finch (Taeniopygia guttata) genome based on sequence homology.

Molecular Ecology, 1998

Despite the interest that avian brood parasites provoke due to their reproductive strategy, and t... more Despite the interest that avian brood parasites provoke due to their reproductive strategy, and the wealth of published studies, their mating system is one of the least known aspects of their natural history. This study describes the first attempt to use genetics to characterize mating patterns in a brood parasite, the great spotted cuckoo (Clamator glandarius). We developed a set of microsatellite markers for this species that allowed us to determine the parentage of 78% of the chicks sampled, with a high probability of certainty (false parental inclusion probability, P FI = 2 × 10-4). Parentage analyses allowed us to determine mating patterns in the population, to show for the first time that there were several females laying in the same study site and sharing host nests, and that females used nests of two different host species in the same season. A total of 70% of the inferred mating relationships can be considered monogamous, and the rest were cases of genetic polygamy, although of unknown social structure. To ease parentage analyses, adult birds were successfully sexed using a combination of sexspecific PCR primers and SSCP techniques before parentage assignment.

Molecular Ecology, 2010

Cultural transmission is thought to be a mechanism by which migratory animals settle into habitat... more Cultural transmission is thought to be a mechanism by which migratory animals settle into habitats, but little evidence exists in wild populations because of the difficulty of following individuals over successive generations and wide geographical distances. Cultural inheritance of migration routes represents a mechanism whereby geographical isolation can arise between separate groups and could constrain individuals to potentially suboptimal sites within their range. Conversely, adopting the parental migratory route in adult life, rather than dispersing randomly, may increase an individual's reproductive success because that strategy has already been proven to allow successful breeding. We combined a pedigree of related light-bellied Brent geese (Branta bernicla hrota) with 6 years of observations of marked birds to calculate the dispersal distances of adult offspring from their parents in both Ireland and Iceland. In both countries, the majority of offspring were found to recruit into or near their parental sites, indicating migratory connectivity in the flyway. Despite this kin structure, we found no evidence of genetic differentiation using genotype data from 1127 individuals across 15 microsatellite loci. We suggest that the existence of migratory connectivity of subpopulations is far more common than previous research indicates and that cultural information may play an important role in structuring reproductive isolation among them.

Conservation Genetics - CONSERV GENET, 2002

Insect Molecular Biology, 2007

Although microsatellites are ubiquitous in eukaryota, the number of available markers varies stro... more Although microsatellites are ubiquitous in eukaryota, the number of available markers varies strongly among taxa. This meta-analysis was conducted on 32 insect species. Sequences were obtained from two assembled whole genomes, whole genome shotgun (WGS) sequences from 10 species and screening partial genomic libraries for microsatellites from 23 species. We have demonstrated: (1) strong differences in the abundance of microsatellites among species; (2) that microsatellites within species are often grouped into families based on similarities in their flanking sequences; (3) that the proportion of microsatellites grouped into families varies strongly among taxa; and (4) that microsatellite families were significantly more often associated with transposable elements-or their remnants-than unique microsatellite sequences.

Forensic Science International: Genetics, 2008

Developing short tandem repeat (STR) profiling systems for forensic identification is complicated... more Developing short tandem repeat (STR) profiling systems for forensic identification is complicated in animal species. Obtaining a representative number of individuals from populations, limited access to family groups and a lack of developed STR markers can make adhering to human forensic guidelines difficult. Furthermore, a lack of animal specific guidelines may explain why many wildlife forensic STR profiling systems developed to date have not appropriately addressed areas such as marker validation or the publication and analysis of population data necessary for the application of these tools to forensic science. Here we present a methodology used to develop an STR profiling system for a legally protected wildlife species, the Eurasian badger Meles meles. Ten previously isolated STR loci were selected based on their level of polymorphism, adherence to Hardy-Weinberg expectations and their fragment size. Each locus was individually validated with respect to its reproducibility, inheritance, species specificity, DNA template concentration and thermocycling parameters. The effects of chemical, substrate and environmental exposure were also investigated. All ten STR loci provided reliable and reproducible results, and optimal amplification conditions were defined. Allele frequencies from 20 representative populations in England and Wales are presented and used to calculate the level of population substructure (u) and inbreeding (f). Accounting for these estimates, the average probability of identity (PI ave) was 2.18 Â 10 À7. This case study can act as a framework for others attempting to develop wildlife forensic profiling systems.

Conservation Genetics Resources, 2010

We isolated 137 unique microsatellite loci from an enriched Light-bellied Brent goose (Branta ber... more We isolated 137 unique microsatellite loci from an enriched Light-bellied Brent goose (Branta bernicla hrota) genomic library. Thirty-seven polymorphic loci were characterised in 24 unrelated individuals sampled from a Light-bellied Brent goose population located at Ringneill quay in Strangford Lough, Northern Ireland. The 37 polymorphic loci displayed between 2 and 38 alleles. Sequence homology was used to assign a predicted chromosome location for 31 polymorphic loci (31 in the chicken (Gallus gallus) and 30 in the zebra finch (Taeniopygia guttata) assembled genome). Two polymorphic microsatellite loci were Z-linked based on the typing of known sex individuals (24 females and 25 females) and sequence homology.

Conservation Genetics Resources, 2011

The European badger (Meles meles) breeds plurally in lowland England and is important economicall... more The European badger (Meles meles) breeds plurally in lowland England and is important economically due to its link with bovine tuberculosis (Mycobacterium bovis) transmission. To understand disease transmission and facilitate effective management, it is vital to elucidate the social structure of badger groups. To improve parentage assignment and the discrimination of relatives, we isolated and characterised 21 polymorphic microsatellite loci in 24 individuals from Wytham Woods, Oxfordshire, UK. These 21 loci increased the discrimination power between fullsiblings and half-siblings from 71 to 88%, when added to the existing 31 loci. Similarly, the combined non-exclusion probability increased from 3.0 9 10-8 to 5.8 9 10-13. Newly isolated Mel-592 (FR745854) was X-linked, based on the genotypes of 48 known-sex individuals and will enhance the genetic sex-typing of badgers. Keywords European badger Á Meles meles Á Mustelidae Á Microsatellite Á Parentage Á X-chromosome linked locus Electronic supplementary material The online version of this article (

BMC Genomics, 2013

Background: Microsatellites are widely used for many genetic studies. In contrast to single nucle... more Background: Microsatellites are widely used for many genetic studies. In contrast to single nucleotide polymorphism (SNP) and genotyping-by-sequencing methods, they are readily typed in samples of low DNA quality/concentration (e.g. museum/non-invasive samples), and enable the quick, cheap identification of species, hybrids, clones and ploidy. Microsatellites also have the highest cross-species utility of all types of markers used for genotyping, but, despite this, when isolated from a single species, only a relatively small proportion will be of utility. Marker development of any type requires skill and time. The availability of sufficient "off-the-shelf" markers that are suitable for genotyping a wide range of species would not only save resources but also uniquely enable new comparisons of diversity among taxa at the same set of loci. No other marker types are capable of enabling this. We therefore developed a set of avian microsatellite markers with enhanced cross-species utility. Results: We selected highly-conserved sequences with a high number of repeat units in both of two genetically distant species. Twenty-four primer sets were designed from homologous sequences that possessed at least eight repeat units in both the zebra finch (Taeniopygia guttata) and chicken (Gallus gallus). Each primer sequence was a complete match to zebra finch and, after accounting for degenerate bases, at least 86% similar to chicken. We assessed primer-set utility by genotyping individuals belonging to eight passerine and four non-passerine species. The majority of the new Conserved Avian Microsatellite (CAM) markers amplified in all 12 species tested (on average, 94% in passerines and 95% in non-passerines). This new marker set is of especially high utility in passerines, with a mean 68% of loci polymorphic per species, compared with 42% in non-passerine species. Conclusions: When combined with previously described conserved loci, this new set of conserved markers will not only reduce the necessity and expense of microsatellite isolation for a wide range of genetic studies, including avian parentage and population analyses, but will also now enable comparisons of genetic diversity among different species (and populations) at the same set of loci, with no or reduced bias. Finally, the approach used here can be applied to other taxa in which appropriate genome sequences are available.