PeerJ Preprints: Geneticshttps://peerj.com/preprints/index.atom?journal=peerj&subject=1700Genetics articles published in PeerJ PreprintsDesign and reporting considerations for genetic screening testshttps://peerj.com/preprints/279222019-10-232019-10-23Jill HagenkordBirgit FunkeEmily QianMadhuri HegdeKevin B JacobsMatthew FerberMatthew LeboAdam H BuchananDavid Bick
Testing asymptomatic individuals for unsuspected conditions is not new to the medical and public health communities and protocols to develop screening tests are well-established. However, the application of screening principles to inherited diseases presents unique challenges. Unlike most screening tests, the natural history and disease prevalence of most rare inherited diseases in an unselected population are unknown. It is difficult or impossible to obtain a “truth set” cohort for clinical validation studies. As a result, it is not possible to accurately calculate clinical positive and negative predictive values for “likely pathogenic” genetic variants, which are commonly returned in genetic screening assays. In addition, many of the genetic conditions included in screening panels do not have clinical confirmatory tests. All of these elements are typically required to justify the development of a screening test, according to the World Health Organization screening principles. Nevertheless, as the cost of DNA sequencing continues to fall, more individuals are opting to undergo genomic testing in the absence of a clinical indication. Despite the challenges, reasonable estimates can be deduced and used to inform test design strategies. Here, we review test design principles and apply them to genetic screening.
Testing asymptomatic individuals for unsuspected conditions is not new to the medical and public health communities and protocols to develop screening tests are well-established. However, the application of screening principles to inherited diseases presents unique challenges. Unlike most screening tests, the natural history and disease prevalence of most rare inherited diseases in an unselected population are unknown. It is difficult or impossible to obtain a “truth set” cohort for clinical validation studies. As a result, it is not possible to accurately calculate clinical positive and negative predictive values for “likely pathogenic” genetic variants, which are commonly returned in genetic screening assays. In addition, many of the genetic conditions included in screening panels do not have clinical confirmatory tests. All of these elements are typically required to justify the development of a screening test, according to the World Health Organization screening principles. Nevertheless, as the cost of DNA sequencing continues to fall, more individuals are opting to undergo genomic testing in the absence of a clinical indication. Despite the challenges, reasonable estimates can be deduced and used to inform test design strategies. Here, we review test design principles and apply them to genetic screening.Endless forms of sexual selectionhttps://peerj.com/preprints/275842019-10-012019-10-01Willow R LindsayStaffan AnderssonBadreddine BererhiJacob HöglundArild JohnsenCharlotta KvarnemoErica H LederJan T LifjeldCalum E NinnesMats OlssonGeoff A ParkerTommaso PizzariAnna QvarnströmRebecca J SafranOla SvenssonScott Edwards
In recent years, the field of sexual selection has exploded, with advances in theoretical and empirical research complementing each other in exciting ways. This perspective piece is the product of a “stock-taking” workshop on sexual selection and conflict. Our aim is to identify and deliberate on outstanding questions and to stimulate discussion rather than provide a comprehensive overview of the entire field. These questions are organized into four thematic sections we deem essential to the field. First we focus on the evolution of mate choice and mating systems. Variation in mate quality can generate both competition and choice in the opposite sex, with implications for the evolution of mating systems. Limitations on mate choice may dictate the importance of direct vs. indirect benefits in mating decisions and consequently, mating systems, especially with regard to polyandry. Second, we focus on how sender and receiver mechanisms shape signal design. Mediation of honest signal content likely depends on integration of temporally variable social and physiological costs that are challenging to measure. We view the neuroethology of sensory and cognitive receiver biases as the main key to signal form and the ‘aesthetic sense’ proposed by Darwin. Since a receiver bias is sufficient to both initiate and drive ornament or armament exaggeration, without a genetically correlated or even coevolving receiver, this may be the appropriate ‘null model’ of sexual selection. Thirdly, we focus on the genetic architecture of sexually selected traits. Despite advances in modern molecular techniques, the number and identity of genes underlying performance, display and secondary sexual traits remains largely unknown. In-depth investigations into the genetic basis of sexual dimorphism in the context of long-term field studies will reveal constraints and trajectories of sexually selected trait evolution. Finally, we focus on sexual selection and conflict as drivers of speciation. Population divergence and speciation are often influenced by an interplay between sexual and natural selection. The extent to which sexual selection promotes or counteracts population divergence may vary depending on the genetic architecture of traits as well as the covariance between mating competition and local adaptation. Additionally, post-copulatory processes, such as selection against heterospecific sperm, may influence the importance of sexual selection in speciation. We propose that efforts to resolve these four themes can catalyze conceptual progress in the field of sexual selection, and we offer potential avenues of research to advance this progress.
In recent years, the field of sexual selection has exploded, with advances in theoretical and empirical research complementing each other in exciting ways. This perspective piece is the product of a “stock-taking” workshop on sexual selection and conflict. Our aim is to identify and deliberate on outstanding questions and to stimulate discussion rather than provide a comprehensive overview of the entire field. These questions are organized into four thematic sections we deem essential to the field. First we focus on the evolution of mate choice and mating systems. Variation in mate quality can generate both competition and choice in the opposite sex, with implications for the evolution of mating systems. Limitations on mate choice may dictate the importance of direct vs. indirect benefits in mating decisions and consequently, mating systems, especially with regard to polyandry. Second, we focus on how sender and receiver mechanisms shape signal design. Mediation of honest signal content likely depends on integration of temporally variable social and physiological costs that are challenging to measure. We view the neuroethology of sensory and cognitive receiver biases as the main key to signal form and the ‘aesthetic sense’ proposed by Darwin. Since a receiver bias is sufficient to both initiate and drive ornament or armament exaggeration, without a genetically correlated or even coevolving receiver, this may be the appropriate ‘null model’ of sexual selection. Thirdly, we focus on the genetic architecture of sexually selected traits. Despite advances in modern molecular techniques, the number and identity of genes underlying performance, display and secondary sexual traits remains largely unknown. In-depth investigations into the genetic basis of sexual dimorphism in the context of long-term field studies will reveal constraints and trajectories of sexually selected trait evolution. Finally, we focus on sexual selection and conflict as drivers of speciation. Population divergence and speciation are often influenced by an interplay between sexual and natural selection. The extent to which sexual selection promotes or counteracts population divergence may vary depending on the genetic architecture of traits as well as the covariance between mating competition and local adaptation. Additionally, post-copulatory processes, such as selection against heterospecific sperm, may influence the importance of sexual selection in speciation. We propose that efforts to resolve these four themes can catalyze conceptual progress in the field of sexual selection, and we offer potential avenues of research to advance this progress.Leveraging eDNA to detect and monitor hybrid zoneshttps://peerj.com/preprints/279962019-09-302019-09-30Kathryn StewartScott A. Taylor
Hybrid zones are important windows into evolutionary processes and our understanding of their significance and prevalence in nature has expanded quickly. Yet most hybridization research has restricted temporal and spatial resolution, limiting our ability to draw broad conclusions about evolutionary and conservation related outcomes. Here, we argue rapidly advancing environmental DNA (eDNA) methodology should be adopted for studies of hybrid zones to increase temporal sampling (contemporary and historical), to refine and geographically expand sampling density, and to collect data for taxa that are difficult to directly sample. Genomic data in the environment offer the potential for near real-time biological tracking and eDNA provides broad, as yet untapped potential to address eco-evolutionary questions.
Hybrid zones are important windows into evolutionary processes and our understanding of their significance and prevalence in nature has expanded quickly. Yet most hybridization research has restricted temporal and spatial resolution, limiting our ability to draw broad conclusions about evolutionary and conservation related outcomes. Here, we argue rapidly advancing environmental DNA (eDNA) methodology should be adopted for studies of hybrid zones to increase temporal sampling (contemporary and historical), to refine and geographically expand sampling density, and to collect data for taxa that are difficult to directly sample. Genomic data in the environment offer the potential for near real-time biological tracking and eDNA provides broad, as yet untapped potential to address eco-evolutionary questions.Inbreeding depression in one of the last DFTD-free wild populations of Tasmanian devilshttps://peerj.com/preprints/279852019-09-262019-09-26Rebecca M GooleyCarolyn J HoggSamantha FoxDavid PembertonKatherine BelovCatherine E Grueber
Background. Vulnerable species experiencing inbreeding depression are prone to localised extinctions because of their reduced fitness. For Tasmanian devils, the rapid spread of devil facial tumour disease (DFTD) has led to population declines and fragmentation across the species’ range. Here we show that one of the few remaining DFTD-free populations of Tasmanian devils is experiencing inbreeding depression. Moreover, this population has experienced a significant reduction in reproductive success over recent years.
Methods. We used 32 microsatellite loci to examine changes in genetic diversity and inbreeding in the wild population at Woolnorth, alongside field data on breeding success from females to test for inbreeding depression.
Results. We found that maternal internal relatedness has a negative impact on litter sizes. The results of this study imply that this population has entered an extinction vortex and that to protect the population, genetic rescue may be required. This study provides conservation managers with useful information for managing wild devils and provides support for the “Wild Devil Recovery Program” which is currently augmenting small, isolated populations.
Background. Vulnerable species experiencing inbreeding depression are prone to localised extinctions because of their reduced fitness. For Tasmanian devils, the rapid spread of devil facial tumour disease (DFTD) has led to population declines and fragmentation across the species’ range. Here we show that one of the few remaining DFTD-free populations of Tasmanian devils is experiencing inbreeding depression. Moreover, this population has experienced a significant reduction in reproductive success over recent years.Methods. We used 32 microsatellite loci to examine changes in genetic diversity and inbreeding in the wild population at Woolnorth, alongside field data on breeding success from females to test for inbreeding depression.Results. Wefound that maternal internal relatedness has a negative impact on litter sizes. The results of this study imply that this population has entered an extinction vortex and that to protect the population, genetic rescue may be required. This study provides conservation managers with useful information for managing wild devils and provides support for the “Wild Devil Recovery Program” which is currently augmenting small, isolated populations.A guide to carrying out a phylogenomic target sequence capture projecthttps://peerj.com/preprints/279682019-09-182019-09-18Tobias AndermannMaria Fernanda Torres JimenezPável Matos-MaravíRomina BatistaJosé L Blanco-PastorA. Lovisa S GustafssonLogan KistlerIsabel M LiberalBengt OxelmanChristine D BaconAlexandre Antonelli
High-throughput DNA sequencing techniques enable time- and cost-effective sequencing of large portions of the genome. Instead of sequencing and annotating whole genomes, many phylogenetic studies focus sequencing efforts on large sets of pre-selected loci, which further reduces costs and bioinformatic challenges while increasing sequencing depth. One common approach that enriches loci before sequencing is often referred to as target sequence capture. This technique has been shown to be applicable to phylogenetic studies of greatly varying evolutionary depth and has proven to produce powerful, large multi-locus DNA sequence datasets of selected loci, suitable for phylogenetic analyses. However, target capture requires careful theoretical and practical considerations, which will greatly affect the success of the experiment. Here we provide an easy-to-follow flowchart for adequately designing phylogenomic target capture experiments, and we discuss necessary considerations and decisions from the first steps in the lab to the final bioinformatic processing of the sequence data. We particularly discuss issues and challenges related to the taxonomic scope, sample quality, and available genomic resources of target capture projects and how these issues affect all steps from bait design to the bioinformatic processing of the data. Altogether this review outlines a roadmap for future target capture experiments and is intended to assist researchers with making informed decisions for designing and carrying out successful phylogenetic target capture studies
High-throughput DNA sequencing techniques enable time- and cost-effective sequencing of large portions of the genome. Instead of sequencing and annotating whole genomes, many phylogenetic studies focus sequencing efforts on large sets of pre-selected loci, which further reduces costs and bioinformatic challenges while increasing sequencing depth. One common approach that enriches loci before sequencing is often referred to as target sequence capture. This technique has been shown to be applicable to phylogenetic studies of greatly varying evolutionary depth and has proven to produce powerful, large multi-locus DNA sequence datasets of selected loci, suitable for phylogenetic analyses. However, target capture requires careful theoretical and practical considerations, which will greatly affect the success of the experiment. Here we provide an easy-to-follow flowchart for adequately designing phylogenomic target capture experiments, and we discuss necessary considerations and decisions from the first steps in the lab to the final bioinformatic processing of the sequence data. We particularly discuss issues and challenges related to the taxonomic scope, sample quality, and available genomic resources of target capture projects and how these issues affect all steps from bait design to the bioinformatic processing of the data. Altogether this review outlines a roadmap for future target capture experiments and is intended to assist researchers with making informed decisions for designing and carrying out successful phylogenetic target capture studiesDevelopment and characterization of novel cross-species tetranucleotide microsatellite markers for sterlet (Acipenser ruthenus) from Chinese sturgeon (Acipenser sinensis)https://peerj.com/preprints/279642019-09-172019-09-17Yacheng HuJing YangXueqing LiuKan XiaoBinzhong WangHejun Du
Sterlet (Acipenser ruthenus) is an important economic fish because of its nourishing caviar, isinglass and flesh. In order to facilitate the recovery of this species, the full understanding of its population genetic structure is necessary for taking appropriate management actions. However, genetic data on the use of nuclear loci in sterlet is still quite poor because microsatellite markers in sterlet that had been developed appeared to be polyploidy which add difficulties in studying the genetic of the sterlet. In this study, 24 tetranucleotide microsatellite markers were developed in sterlet from 160 microsatellite markers of the endangered Chinese sturgeon (Acipenser sinensis). Ten (ZHX76, ZHX64, Z194, Z217, Z184, Z242, Z250, Z258, Z268 and Z269) of the 24 loci showed disomic patterns while the rest loci showed tetrasomic patterns. In this paper, 24 microsatellite markers were characterized in 16 sterlet individuals and all of them were polymorphic with 2 to 7 alleles per locus. The Hardy-Weinberg departure value (d), polymorphic information content (PIC), the observed heterozygosity (HO), the Shannon-Wiener Diversity Indices (H') and the mean expected heterozygosity (HE) of all 24 polymorphic loci ranged from -0.334 to 0.484, 0.367 to 0.725, 0.438 to 1, 0.659 to 1.695, from 0.466 to 0.777, respectively. The markers described here will help in addressing practical problems such as the study of population genetics, conservation genetics and evolution in the polyploidy derivative nature of sterlet.
Sterlet (Acipenser ruthenus) is an important economic fish because of its nourishing caviar, isinglass and flesh. In order to facilitate the recovery of this species, the full understanding of its population genetic structure is necessary for taking appropriate management actions. However, genetic data on the use of nuclear loci in sterlet is still quite poor because microsatellite markers in sterlet that had been developed appeared to be polyploidy which add difficulties in studying the genetic of the sterlet. In this study, 24 tetranucleotide microsatellite markers were developed in sterlet from 160 microsatellite markers of the endangered Chinese sturgeon (Acipenser sinensis). Ten (ZHX76, ZHX64, Z194, Z217, Z184, Z242, Z250, Z258, Z268 and Z269) of the 24 loci showed disomic patterns while the rest loci showed tetrasomic patterns. In this paper, 24 microsatellite markers were characterized in 16 sterlet individuals and all of them were polymorphic with 2 to 7 alleles per locus. The Hardy-Weinberg departure value (d), polymorphic information content (PIC), the observed heterozygosity (HO), the Shannon-Wiener Diversity Indices (H') and the mean expected heterozygosity (HE) of all 24 polymorphic loci ranged from -0.334 to 0.484, 0.367 to 0.725, 0.438 to 1, 0.659 to 1.695, from 0.466 to 0.777, respectively. The markers described here will help in addressing practical problems such as the study of population genetics, conservation genetics and evolution in the polyploidy derivative nature of sterlet.Immunocytological analysis of chromosomes in meiotic prophase I of the paleotetraploid frog Xenopus laevishttps://peerj.com/preprints/279372019-09-052019-09-05Sergey MatveevskySergey StolyarovOxana Kolomiets
The African clawed frog Xenopus laevis (Pipidae, Anura, Amphibia) is a model object of cell and evolutionary biology. X. laevis is a paleotetraploid frog. For the first time, the results of an immunocytological analysis of the Xenopus chromosome behaviour in the meiotic prophase I based on synaptonemal complexes (SC) are presented. We identified all stages of meiosis prophase I, and determined the dynamics of the main proteins involved in the synapsis and repair of DNA DSBs. We did not find a homeologous synapsis.
The African clawed frog Xenopus laevis (Pipidae, Anura, Amphibia) is a model object of cell and evolutionary biology. X. laevis is a paleotetraploid frog. For the first time, the results of an immunocytological analysis of the Xenopus chromosome behaviour in the meiotic prophase I based on synaptonemal complexes (SC) are presented. We identified all stages of meiosis prophase I, and determined the dynamics of the main proteins involved in the synapsis and repair of DNA DSBs. We did not find a homeologous synapsis.The complete chloroplast genomes of seventeen Aegilops tauschii: Genome characteristic and comparative analysishttps://peerj.com/preprints/279322019-08-312019-08-31Qing SuLuxian LiuMengyu ZhaoCancan ZhangDale ZhangYouyong LiSuoping Li
As the diploid progenitor of common wheat, Aegilops tauschii Cosson (DD, 2n = 2x = 14) is regarded to be a potential genetic resource for improving common wheat, which is naturally distributed in central Eurasia, spreading from northern Syria and Turkey to western China. In this work, the chloroplast genomes of seventeen Ae. tauschii accessions showed 135 551~ 136 009 bp in length and contained the typical quadripartite structure of angiosperms. Meanwhile, a total of 127 functional genes, including 78 protein-coding genes, 4 rRNAs, 26 tRNAs, and 19 duplicated genes were identified. Overall genomic structure including gene number, gene order were well conserved with identical IR/SC boundary regions, but few variations predominantly were detected in non-coding regions (intergenic spacer regions). IR expansion and contraction with identical structure among 17 Aegilops tauschii accessions were not influence chloroplast genomes in length. Four cpDNA markers including rpl32-trnL-UAG, ccsA-ndhD, rbcL-psaI and rps18-rpl20 showed high nucleotide polymorphisms,which may be used to study on inter- and intra-specific genetic structure and diversity of Ae. tauschii. The ndhF gene in AY46 accession appeared the highest ω value, which might be involved in the adaptation to high altitude ecological environment during the evolution of AY46 accession. The phylogenetic relationships constructed by the complete genome sequences strongly support that Ae. tauschii in the Yellow River region might be directly originated from Central Asia rather than Xinjiang. The specific spreading route of Ae. tauschii revealed in this work, reflects the frequent cultural exchange through the silk road from one point of view. We confirmed that Ae. tauschii derived from monophyletic speciation rather than hybrid speciation at the chloroplast genome level.
As the diploid progenitor of common wheat, Aegilops tauschii Cosson (DD, 2n = 2x = 14) is regarded to be a potential genetic resource for improving common wheat, which is naturally distributed in central Eurasia, spreading from northern Syria and Turkey to western China. In this work, the chloroplast genomes of seventeen Ae. tauschii accessions showed 135 551~ 136 009 bp in length and contained the typical quadripartite structure of angiosperms. Meanwhile, a total of 127 functional genes, including 78 protein-coding genes, 4 rRNAs, 26 tRNAs, and 19 duplicated genes were identified. Overall genomic structure including gene number, gene order were well conserved with identical IR/SC boundary regions, but few variations predominantly were detected in non-coding regions (intergenic spacer regions). IR expansion and contraction with identical structure among 17 Aegilops tauschii accessions were not influence chloroplast genomes in length. Four cpDNA markers including rpl32-trnL-UAG, ccsA-ndhD, rbcL-psaI and rps18-rpl20 showed high nucleotide polymorphisms,which may be used to study on inter- and intra-specific genetic structure and diversity of Ae. tauschii. The ndhF gene in AY46 accession appeared the highest ω value, which might be involved in the adaptation to high altitude ecological environment during the evolution of AY46 accession. The phylogenetic relationships constructed by the complete genome sequences strongly support that Ae. tauschii in the Yellow River region might be directly originated from Central Asia rather than Xinjiang. The specific spreading route of Ae. tauschii revealed in this work, reflects the frequent cultural exchange through the silk road from one point of view. We confirmed that Ae. tauschii derived from monophyletic speciation rather than hybrid speciation at the chloroplast genome level.The detection of trans gene fragments of hEPO in gene doping model mice by Taqman qPCR assayhttps://peerj.com/preprints/279252019-08-292019-08-29Kai AokiTakehito SugasawaKouki YanazawaKoichi WatanabeTohru TakemasaYoshinori TakeuchiYuichi AitaNaoya YahagiYasuko YoshidaTomoaki KujiNanami SekineKaoru TakeuchiHaruna UedaYasushi KawakamiKazuhiro Takekoshi
BACKGROUND. With the rapid progress of genetic engineering and gene therapy methods, the World Anti-Doping Agency has raised concerns regarding gene doping, which is prohibited in sports. However, there is no standard method available for detecting transgenes delivered by injection of naked plasmids. Here, we developed a detection method for detecting transgenes delivered by injection of naked plasmids in a mouse model that mimics gene doping. METHODS. Whole blood from the tail tip and one piece of stool were used as pre-samples of injection. Next, a plasmid vector containing the human erythropoietin (hEPO) gene was injected into mice through intravenous (IV), intraperitoneal (IP), or local muscular (IM) injection. At 1, 2, 3, 6, 12, 24, and 48 h after injection, approximately 50 μL whole blood was collected from the tail tip. One piece of stool was collected at 6, 12, 24, and 48 h. From each sample, total DNA was extracted and transgene fragments were analyzed by Taqman quantitative PCR (qPCR) and SYBR green qPCR. RESULTS. In whole blood DNA samples evaluated by Taqman qPCR, the transgene fragments were detected at all time points in the IP sample and at 1, 2, 3, 6, and 12 h in the IV and IM samples. In the stool-DNA samples, the transgene fragments were detected at 6, 12, 24, and 48 h in the IV and IM samples by Taqman qPCR. In the analysis by SYBR green qPCR, the transgene fragments were detected at some time point in both specimens; however, many non-specific amplicons were detected. CONCLUSIONS. These results indicate that transgene fragments evaluated after each injection method of naked plasmids were detected in whole-blood and stool DNA samples. These findings may facilitate the development of methods for detecting gene doping.
BACKGROUND. With the rapid progress of genetic engineering and gene therapy methods, the World Anti-Doping Agency has raised concerns regarding gene doping, which is prohibited in sports. However, there is no standard method available for detecting transgenes delivered by injection of naked plasmids. Here, we developed a detection method for detecting transgenes delivered by injection of naked plasmids in a mouse model that mimics gene doping. METHODS. Whole blood from the tail tip and one piece of stool were used as pre-samples of injection. Next, a plasmid vector containing the human erythropoietin (hEPO) gene was injected into mice through intravenous (IV), intraperitoneal (IP), or local muscular (IM) injection. At 1, 2, 3, 6, 12, 24, and 48 h after injection, approximately 50 μL whole blood was collected from the tail tip. One piece of stool was collected at 6, 12, 24, and 48 h. From each sample, total DNA was extracted and transgene fragments were analyzed by Taqman quantitative PCR (qPCR) and SYBR green qPCR. RESULTS. In whole blood DNA samples evaluated by Taqman qPCR, the transgene fragments were detected at all time points in the IP sample and at 1, 2, 3, 6, and 12 h in the IV and IM samples. In the stool-DNA samples, the transgene fragments were detected at 6, 12, 24, and 48 h in the IV and IM samples by Taqman qPCR. In the analysis by SYBR green qPCR, the transgene fragments were detected at some time point in both specimens; however, many non-specific amplicons were detected. CONCLUSIONS. These results indicate that transgene fragments evaluated after each injection method of naked plasmids were detected in whole-blood and stool DNA samples. These findings may facilitate the development of methods for detecting gene doping.Impact of hybridisation in two Cossypha robin-chat species in southern Africahttps://peerj.com/preprints/279122019-08-212019-08-21Jean MollettNaadhirah MunshiCraig Symes
Chorister Robin-Chat Cossypha dichroa, a South African forest endemic, and Red-capped Robin-Chat C. natalensis, a widely distributed species in African forest and woodland, are inferred to hybridise in areas of sympatry. DNA was extracted from blood samples of C. dichroa (n = 18), C. natalensis (n = 47), and two phenotypic hybrids. The mitochondrial cytochrome c oxidase I (COI) gene was amplified by PCR and sequenced. Phylogenetic analysis was performed on the sequence data to investigate taxonomic status and putative interspecific hybridisation. Phenotypic hybrids grouped with C. natalensis, suggesting maternal parentage from that species. Intra- and interspecific genetic and geographic distances were compared between C. dichroa and C. natalensis to assess genetic introgression. Seven of the thirteen microsatellite primer pairs developed for C. natalensis cross amplified in C. dichroa. These seven markers were then used for further analysis. STRUCTURE v2.3.4 was used to assign individuals to a particular genetic cluster and determine any admixture. NEWHYBRIDS v1.1 was used to assign hybrid status to samples beyond the F1 generation. Despite the hybridisation events recorded between C. dichroa and C. natalensis they still form two separate clusters as expected, and two genetic clusters (K=2) were identified using STRUCTURE. These two species are proficient vocal mimics and it is likely that reproductive isolation mechanisms are overcome through vocalisations. Genotypic hybrids are evident in the sampled population and hybridisation and backcrossing across a zone of sympatry is occurring. However, hybridisation is expected to have very little evolutionary influence on the integrity of recently diverged species which retain reproductive isolation across a wide region of sympatry through call distinctness.
Chorister Robin-Chat Cossypha dichroa, a South African forest endemic, and Red-capped Robin-Chat C. natalensis, a widely distributed species in African forest and woodland, are inferred to hybridise in areas of sympatry. DNA was extracted from blood samples of C. dichroa (n = 18), C. natalensis (n = 47), and two phenotypic hybrids. The mitochondrial cytochrome c oxidase I (COI) gene was amplified by PCR and sequenced. Phylogenetic analysis was performed on the sequence data to investigate taxonomic status and putative interspecific hybridisation. Phenotypic hybrids grouped with C. natalensis, suggesting maternal parentage from that species. Intra- and interspecific genetic and geographic distances were compared between C. dichroa and C. natalensis to assess genetic introgression. Seven of the thirteen microsatellite primer pairs developed for C. natalensis cross amplified in C. dichroa. These seven markers were then used for further analysis. STRUCTURE v2.3.4 was used to assign individuals to a particular genetic cluster and determine any admixture. NEWHYBRIDS v1.1 was used to assign hybrid status to samples beyond the F1 generation. Despite the hybridisation events recorded between C. dichroa and C. natalensis they still form two separate clusters as expected, and two genetic clusters (K=2) were identified using STRUCTURE. These two species are proficient vocal mimics and it is likely that reproductive isolation mechanisms are overcome through vocalisations. Genotypic hybrids are evident in the sampled population and hybridisation and backcrossing across a zone of sympatry is occurring. However, hybridisation is expected to have very little evolutionary influence on the integrity of recently diverged species which retain reproductive isolation across a wide region of sympatry through call distinctness.