Understanding the degree of genetic population differentiation is important in conservation genet... more Understanding the degree of genetic population differentiation is important in conservation genetics for inferring gene flow between populations and for identifying small and isolated threatened populations. We evaluated the genetic variation within and between three populations of the rock firefinch (Lagonosticta sanguinodorsalis), a range restricted firefinch endemic to Nigeria and Cameroon. The populations were closely located (c. 100 km apart) within the species' core distribution in Central Nigeria. We found that the populations had similar levels of gene diversities (H E) and low but significant inbreeding coefficients (F IS). Despite the short distance between populations there was a weak but significant population structure, which indicates that the populations are somewhat isolated and affected by drift within the species' core distribution in Nigeria. The knowledge of the genetic status of the rock firefinch will serve as a foundation to future studies to help understand population demography and for managing and maintaining viable populations.
Lion faecal samples, collected in the field between 1 hour to 1 week after defecation were preser... more Lion faecal samples, collected in the field between 1 hour to 1 week after defecation were preserved in three different media (ethanol, ASL buffer and Two-step storage). The aim was to determine which faecal DNA field preservation method best enhances PCR amplification success. Samples stored in ethanol showed a significantly higher amplification success of microsatellite loci than samples stored in the other two media. In contrast, amplification success of a mitochondrial locus was similar among the samples stored in the three types of media. We reviewed twelve previous studies that employed different media for the storage of faeces, although patterns of success were not fully consistent among different media, ethanol storage was scored highest in the majority of these tests.
Knowledge of which genes and pathways are affected by inbreeding may help understanding the genet... more Knowledge of which genes and pathways are affected by inbreeding may help understanding the genetic basis of inbreeding depression, the potential for purging (selection against deleterious recessive alleles) and the transition from outcrossing to selfing. Arabidopsis lyrata is a predominantly self-incompatible perennial plant, closely related to the selfing model species A. thaliana. To examine how inbreeding affects gene expression, we compared the transcriptome of experimentally selfed and outcrossed A. lyrata originating from two Scandinavian populations that express similar inbreeding depression for fitness (∂≈0.80). The number of genes significantly differentially expressed between selfed and outcrossed individuals were 2.5 times higher in the Norwegian population (≈500 genes) than in the Swedish population (≈200 genes). In both populations a majority of genes were up-regulated upon selfing (≈80%). Functional annotation analysis of the differentially expressed genes showed that...
Despite virtually identical DNA sequences between the sexes, sexual dimorphism is a widespread ph... more Despite virtually identical DNA sequences between the sexes, sexual dimorphism is a widespread phenomenon in nature. To a large extent the systematic differences between the sexes must therefore arise from processes involving gene regulation. In accordance, sexual dimorphism in gene expression is common and extensive. Genes with sexually dimorphic regulation are known to evolve rapidly, both in DNA sequence and in gene expression profile. Studies of gene expression in related species can shed light on the flexibility, or degree of conservation, of the gene expression profiles underlying sexual dimorphism. We have studied the extent of sexual dimorphism in gene expression in the brain of two species of songbirds, the zebra finch (Taeniopygia guttata) and the common whitethroat (Sylvia communis), using large-scale microarray technology. Sexual dimorphism in gene expression was extensive in both species, and predominantly sex-linked: most genes identified were male-biased and Z-linked....
Evolutionary molecular studies of island radiations may lead to insights in the role of vicarianc... more Evolutionary molecular studies of island radiations may lead to insights in the role of vicariance, founder events, population size and drift in the processes of population differentiation. We evaluate the degree of population genetic differentiation and fixation of the Canary Islands blue tit subspecies complex using microsatellite markers and aim to get insights in the population history using coalescence based methods. The Canary Island populations were strongly genetically differentiated and had reduced diversity with pronounced fixation including many private alleles. In population structure models, the relationship between the central island populations (La Gomera, Tenerife and Gran Canaria) and El Hierro was difficult to disentangle whereas the two European populations showed consistent clustering, the two eastern islands (Fuerteventura and Lanzarote) and Morocco weak clustering, and La Palma a consistent unique lineage. Coalescence based models suggested that the European mainland forms an outgroup to the Afrocanarian population, a split between the western island group (La Palma and El Hierro) and the central island group, and recent splits between the three central islands, and between the two eastern islands and Morocco, respectively. It is clear that strong genetic drift and low level of concurrent gene flow among populations have shaped complex allelic patterns of fixation and skewed frequencies over the archipelago. However, understanding the population history remains challenging; in particular, the pattern of extreme divergence with low genetic diversity and yet unique genetic material in the Canary Island system requires an explanation. A potential scenario is population contractions of a historically large and genetically variable Afrocanarian population, with vicariance and drift following in the wake. The suggestion from sequence-based analyses of a Pleistocene extinction of a substantial part of North Africa and a Pleistocene/Holocene eastward re-colonisation of western North Africa from the Canaries remains possible.
Dosage compensation, the process whereby expression of sex-linked genes remains similar between s... more Dosage compensation, the process whereby expression of sex-linked genes remains similar between sexes (despite heterogamety) and balanced with autosomal expression, was long believed to be essential. However, recent research has shown that several lineages, including birds, butterflies, monotremes and sticklebacks, lack chromosome-wide dosage compensation mechanisms and do not completely balance the expression of sex-linked and autosomal genes. To obtain further understanding of avian sex-biased gene expression, we studied Z-linked gene expression in the brain of two songbirds of different genera (zebra finch, Taeniopygia guttata, and common whitethroat, Sylvia communis) using microarray technology. In both species, the male-bias in gene expression was significantly higher for Z than for autosomes, although the ratio of Z-linked to autosomal expression (Z:A) was relatively close to one in both sexes (range: 0.89-1.01). Interestingly, the Z-linked male-bias in gene expression increased with expression level, and genes with low expression showed the lowest degree of sex-bias. These results support the view that the heterogametic females have up-regulated their single Z-linked homologues to a high extent when the W-chromosome degraded and thereby managed to largely balance their Z:A expression with the exception of highly expressed genes. The male-bias in highly expressed genes points towards male-driven selection on Z-linked loci, and this and other possible hypotheses are discussed.
Background: In a rapidly changing world, it is of fundamental importance to understand processes ... more Background: In a rapidly changing world, it is of fundamental importance to understand processes constraining or facilitating adaptation through microevolution. As different traits of an organism covary, genetic correlations are expected to affect evolutionary trajectories. However, only limited empirical data are available. Methodology/Principal Findings: We investigate the extent to which multivariate constraints affect the rate of adaptation, focusing on four morphological traits often shown to harbour large amounts of genetic variance and considered to be subject to limited evolutionary constraints. Our data set includes unique long-term data for seven bird species and a total of 10 populations. We estimate population-specific matrices of genetic correlations and multivariate selection coefficients to predict evolutionary responses to selection. Using Bayesian methods that facilitate the propagation of errors in estimates, we compare (1) the rate of adaptation based on predicted response to selection when including genetic correlations with predictions from models where these genetic correlations were set to zero and (2) the multivariate evolvability in the direction of current selection to the average evolvability in random directions of the phenotypic space. We show that genetic correlations on average decrease the predicted rate of adaptation by 28%. Multivariate evolvability in the direction of current selection was systematically lower than average evolvability in random directions of space. These significant reductions in the rate of adaptation and reduced evolvability were due to a general nonalignment of selection and genetic variance, notably orthogonality of directional selection with the size axis along which most (60%) of the genetic variance is found. Conclusions: These results suggest that genetic correlations can impose significant constraints on the evolution of avian morphology in wild populations. This could have important impacts on evolutionary dynamics and hence population persistence in the face of rapid environmental change.
This survey was conducted in two protected areas in Nigeria to genetically identify individual li... more This survey was conducted in two protected areas in Nigeria to genetically identify individual lions and to determine the genetic variation within and between the populations. We used faecal sample DNA, a non-invasive alternative to the risky and laborious task of taking samples directly from the animals, often preceded by catching and immobilization. Data collection in Yankari Game Reserve (YGR) spanned through a period of five years (2008-2012), whereas data in Kainji Lake National Park (KLNP) was gathered for a period of three years (2009, 2010 and 2012). We identified a minimum of eight individuals (2 males, 3 females, 3 unknown) from YGR and a minimum of ten individuals (7 males, 3 females) from KLNP. The two populations were found to be genetically distinct as shown by the relatively high fixation index (F ST = 0.17) with each population exhibiting signs of inbreeding (YGR F IS = 0.49, KLNP F IS = 0.38). The genetic differentiation between the Yankari and Kainji lions is assumed to result from large spatial geographic distance and physical barriers reducing gene flow between these two remaining wild lion populations in Nigeria. To mitigate the probable inbreeding depression in the lion populations within Nigeria it might be important to transfer lions between parks or reserves or to reintroduce lions from the zoos back to the wild.
In line with inbreeding theory, genetic diversity at a set of molecular markers may explain varia... more In line with inbreeding theory, genetic diversity at a set of molecular markers may explain variation in fitness-associated traits in partially inbred populations, and such associations will appear as 'genotype-fitness correlations'. An individual genetic diversity index specifically used for microsatellites is 'mean d 2 ', i.e. the mean squared distance between alleles. The original hypothesis for mean d 2-fitness correlations assumes that mean d 2 captures fitness effects at both ends of the inbreeding-outbreeding spectrum. This hypothesis received strong criticism from work showing that even a plain diversity estimate such as multi-locus heterozygosity (MLH) outperforms mean d 2 as a predictor of the inbreeding coefficient and fitness in most realistic situations. Despite this critique, the mean d 2-approach is still used frequently in ecological and evolutionary research, producing results suggesting that mean d 2 sometimes provides a stronger prediction of fitness than does MLH. In light of the critique, such results are unexpected, but potential explanations for them may exist (at least hypothetically), including scenarios based on close linkage and recent admixture. Nevertheless, a major caveat is that it is very difficult to predict a priori if mean d 2 will improve the genotype-fitness correlation, which in turn makes objective interpretations difficult. Mean d 2-fitness associations are potentially interesting, but the fact that we cannot easily understand them is problematic and should be thoroughly addressed in each study. Therefore, instead of hastily reached interpretations of mean d 2-fitness correlations, conclusions need support from complementary analyses, e.g. verifying admixture of genetically structured populations.
Allopatry and allopatric speciation can arise through two different mechanisms: vicariance or col... more Allopatry and allopatric speciation can arise through two different mechanisms: vicariance or colonization through dispersal. Distinguishing between these different allopatric mechanisms is difficult and one of the major challenges in biogeographical research. Here, we address whether allopatric isolation in an endemic island lizard is the result of vicariance or dispersal. We estimated the amount and direction of gene flow during the divergence of isolated islet populations and subspecies of the endemic Skyros wall lizard Podarcis gaigeae, a phenotypically variable species that inhabits a major island and small islets in the Greek archipelago. We applied isolation-with-migration models to estimate population divergence times, population sizes and gene flow between islet-mainland population pairs. Divergence times were significantly correlated with independently estimated geological divergence times. This correlation strongly supports a vicariance scenario where islet populations have sequentially become isolated from the major island. We did not find evidence for significant gene flow within P. g. gaigeae. However, gene-flow estimates from the islet to the mainland populations were positively affected by islet area and negatively by distance between the islet and mainland. We also found evidence for gene flow from one subspecies (P. g. weigandi) into another (P. g. gaigeae), but not in the other direction. Ongoing gene flow between the subspecies suggests that even in this geographically allopatric scenario with the sea posing a strong barrier to dispersal, divergence with some gene flow is still feasible.
Knowledge of relatedness between pairs of individuals plays an important role in many research ar... more Knowledge of relatedness between pairs of individuals plays an important role in many research areas including evolutionary biology, quantitative genetics, and conservation. Pairwise relatedness estimation methods based on genetic data from highly variable molecular markers are now used extensively as a substitute for pedigrees. Although the sampling variance of the estimators has been intensively studied for the most common simple genetic relationships, such as unrelated, half- and full-sib, or parent–offspring, little attention has been paid to the average performance of the estimators, by which we mean the performance across all pairs of individuals in a sample. Here we apply two measures to quantify the average performance: first, misclassification rates between pairs of genetic relationships and, second, the proportion of variance explained in the pairwise relatedness estimates by the true population relatedness composition (i.e., the frequencies of different relationships in t...
I examine the relationship between reproductive success and marker-based relatedness (MBR; inferr... more I examine the relationship between reproductive success and marker-based relatedness (MBR; inferred from variation at 21 microsatellite loci) of pair-mates in a semi-isolated population of great reed warblers (Acrocephalus arundinaceus) over a 12 year period. There was a negative relationship between egg-hatching success and MBR, but no association between MBR and three other components of fitness (clutch size, proportion of fledglings and recruits). The relationship between hatchability and MBR was non-linear, with high hatching rates at low and intermediate levels of MBR and a sudden decline in hatching success among the small number of pairs with high MBR (<4% of the sample). It is likely that the decrease in fitness at high MBR was due to effects of homozygosity at genome-wide distributed loci, as opposed to effects of fitness loci in the local chromosomal vicinity of particular markers. This conclusion relies on the fact that similar results were found in another study of the same population that was based on DNA-fingerprinting band-sharing, and that there was a strong correlation between MBR and pedigree-based relatedness. The negative relationship between MBR and hatchability was especially pronounced in the first study years and levelled off in later years. This time-dependent effect of MBR on hatchability was not caused by a simultaneous temporal decrease in MBR, and may instead reflect the importance of other processes such as genotype • environment interactions or purging of deleterious recessive alleles.
Background: The major histocompatibility complex (MHC) is an important component of the vertebrat... more Background: The major histocompatibility complex (MHC) is an important component of the vertebrate immune system and is frequently used to characterise adaptive variation in wild populations due to its co-evolution with pathogens. Passerine birds have an exceptionally diverse MHC with multiple gene copies and large numbers of alleles compared to other avian taxa. The Nesospiza bunting species complex (two species on Nightingale Island; one species with three sub-species on Inaccessible Island) represents a rapid adaptive radiation at a small, isolated archipelago, and is thus an excellent model for the study of adaptation and speciation. In this first study of MHC in Nesospiza buntings, we aim to characterize MHCIIβ variation, determine the strength of selection acting at this gene region and assess the level of shared polymorphism between the Nesospiza species complex and its putative sister taxon, Rowettia goughensis, from Gough Island. Results: In total, 23 unique alleles were found in 14 Nesospiza and 2 R. goughensis individuals encoding at least four presumably functional loci and two pseudogenes. There was no evidence of ongoing selection on the peptide binding region (PBR). Of the 23 alleles, 15 were found on both the islands inhabited by Nesospiza species, and seven in both Nesospiza and Rowettia; indications of shared, ancestral polymorphism. A gene tree of Nesospiza MHCIIβ alleles with several other passerine birds shows three highly supported Nesospiza-specific groups. All R. goughensis alleles were shared with Nesospiza, and these alleles were found in all three Nesospiza sequence groups in the gene tree, suggesting that most of the observed variation predates their phylogenetic split. Conclusions: Lack of evidence of selection on the PBR, together with shared polymorphism across the gene tree, suggests that population variation of MHCIIβ among Nesospiza and Rowettia is due to ancestral polymorphism rather than local selective forces. Weak or no selection pressure could be attributed to low parasite load at these isolated Atlantic islands. The deep divergence between the highly supported Nesospiza-specific sequence Groups 2 and 3, and the clustering of Group 3 close to the distantly related passerines, provide strong support for preserved ancestral polymorphism, and present evidence of one of the rare cases of extensive ancestral polymorphism in birds.
Background: Patterns of spatial variation in discrete phenotypic traits can be used to draw infer... more Background: Patterns of spatial variation in discrete phenotypic traits can be used to draw inferences about the adaptive significance of traits and evolutionary processes, especially when compared to patterns of neutral genetic variation. Population divergence in adaptive traits such as color morphs can be influenced by both local ecology and stochastic factors such as genetic drift or founder events. Here, we use quantitative color measurements of males and females of Skyros wall lizard, Podarcis gaigeae, to demonstrate that this species is polymorphic with respect to throat color, and the morphs form discrete phenotypic clusters with limited overlap between categories. We use divergence in throat color morph frequencies and compare that to neutral genetic variation to infer the evolutionary processes acting on islet-and mainland populations. Results: Geographically close islet-and mainland populations of the Skyros wall lizard exhibit strong divergence in throat color morph frequencies. Population variation in throat color morph frequencies between islets was higher than that between mainland populations, and the effective population sizes on the islets were small (N e :s < 100). Population divergence (F ST) for throat color morph frequencies fell within the neutral F ST-distribution estimated from microsatellite markers, and genetic drift could thus not be rejected as an explanation for the pattern. Moreover, for both comparisons among mainland-mainland population pairs and between mainland-islet population pairs, morph frequency divergence was significantly correlated with neutral divergence, further pointing to some role for genetic drift in divergence also at the phenotypic level of throat color morphs. Conclusions: Genetic drift could not be rejected as an explanation for the pattern of population divergence in morph frequencies. In spite of an expected stabilising selection, throat color frequencies diverged in the islet populations. These results suggest that there is an interaction between selection and genetic drift causing divergence even at a phenotypic level in these small, subdivided populations.
Substantial genetic variation is hypothesised to be necessary for the long-term survival of speci... more Substantial genetic variation is hypothesised to be necessary for the long-term survival of species. Therefore, a major aim in conservation is to maintain and restore variation in small and endangered populations. However, in most populations the amount of genetic variation and, thus, the potential threats posed by limited variation are unknown. In the present study, we assess genetic variation, both at 10 microsatellite loci and at the major histocompatibility complex (MHC), in three closely related Acrocephalus warbler species with contrasting demographies. We found that the recently bottlenecked, island endemic, Seychelles warbler (A. sechellensis; SW) has substantially reduced microsatellite and MHC diversity compared to the widespread great reed warbler (A. arundinaceus; GRW). In contrast, another endangered species with a small breeding range, the Basra reed warbler (A. griseldis; BRW), harboured as much variation as did the GRW. This suggests that significant genetic variation and, therefore, adaptive potential, remains in the BRW-a situation that should hold as long as its habitat and numbers are maintained. Our study is one of the first to assess genetic variation at both 'non-critical' microsatellite markers and 'critical' MHC loci within endangered species. The two types of loci provided a similar picture of the genetic variation in the species we studied, but this has not been the case in studies of some other species. Using a combination of specific functional loci and genome-wide random markers appears to be the best way to assess the threat posed by reduced genetic diversity.
Proceedings of the Royal Society B: Biological Sciences, 2014
In a broad range of species—including humans—it has been demonstrated that telomere length declin... more In a broad range of species—including humans—it has been demonstrated that telomere length declines throughout life and that it may be involved in cell and organismal senescence. This potential link to ageing and thus to fitness has triggered recent interest in understanding how variation in telomere length is inherited and maintained. However, previous studies suffer from two main drawbacks that limit the possibility of understanding the relative importance of genetic, parental and environmental influences on telomere length variation. These studies have been based on (i) telomere lengths measured at different time points in different individuals, despite the fact that telomere length changes over life, and (ii) parent–offspring regression techniques, which do not enable differentiation between genetic and parental components of inheritance. To overcome these drawbacks, in our study of a songbird, the great reed warbler, we have analysed telomere length measured early in life in bo...
Proceedings of the Royal Society B: Biological Sciences, 2005
Linkage maps are lacking for many highly influential model organisms in evolutionary research, in... more Linkage maps are lacking for many highly influential model organisms in evolutionary research, including all passerine birds. Consequently, their full potential as research models is severely hampered. Here, we provide a partial linkage map and give novel estimates of sex-specific recombination rates in a passerine bird, the great reed warbler (Acrocephalus arundinaceus). Linkage analysis of genotypic data at 51 autosomal microsatellites and seven markers on the Z-chromosome (one of the sex chromosomes) from an extended pedigree resulted in 12 linkage groups with 2–8 loci. A striking feature of the map was the pronounced sex-dimorphism: males had a substantially lower recombination rate than females, which resulted in a suppressed autosomal map in males (sum of linkage groups: 110.2 cM) compared to females (237.2 cM; female/male map ratio: 2.15). The sex-specific recombination rates will facilitate the building of a denser linkage map and cast light on hypotheses about sex-specific ...
Understanding the degree of genetic population differentiation is important in conservation genet... more Understanding the degree of genetic population differentiation is important in conservation genetics for inferring gene flow between populations and for identifying small and isolated threatened populations. We evaluated the genetic variation within and between three populations of the rock firefinch (Lagonosticta sanguinodorsalis), a range restricted firefinch endemic to Nigeria and Cameroon. The populations were closely located (c. 100 km apart) within the species' core distribution in Central Nigeria. We found that the populations had similar levels of gene diversities (H E) and low but significant inbreeding coefficients (F IS). Despite the short distance between populations there was a weak but significant population structure, which indicates that the populations are somewhat isolated and affected by drift within the species' core distribution in Nigeria. The knowledge of the genetic status of the rock firefinch will serve as a foundation to future studies to help understand population demography and for managing and maintaining viable populations.
Lion faecal samples, collected in the field between 1 hour to 1 week after defecation were preser... more Lion faecal samples, collected in the field between 1 hour to 1 week after defecation were preserved in three different media (ethanol, ASL buffer and Two-step storage). The aim was to determine which faecal DNA field preservation method best enhances PCR amplification success. Samples stored in ethanol showed a significantly higher amplification success of microsatellite loci than samples stored in the other two media. In contrast, amplification success of a mitochondrial locus was similar among the samples stored in the three types of media. We reviewed twelve previous studies that employed different media for the storage of faeces, although patterns of success were not fully consistent among different media, ethanol storage was scored highest in the majority of these tests.
Knowledge of which genes and pathways are affected by inbreeding may help understanding the genet... more Knowledge of which genes and pathways are affected by inbreeding may help understanding the genetic basis of inbreeding depression, the potential for purging (selection against deleterious recessive alleles) and the transition from outcrossing to selfing. Arabidopsis lyrata is a predominantly self-incompatible perennial plant, closely related to the selfing model species A. thaliana. To examine how inbreeding affects gene expression, we compared the transcriptome of experimentally selfed and outcrossed A. lyrata originating from two Scandinavian populations that express similar inbreeding depression for fitness (∂≈0.80). The number of genes significantly differentially expressed between selfed and outcrossed individuals were 2.5 times higher in the Norwegian population (≈500 genes) than in the Swedish population (≈200 genes). In both populations a majority of genes were up-regulated upon selfing (≈80%). Functional annotation analysis of the differentially expressed genes showed that...
Despite virtually identical DNA sequences between the sexes, sexual dimorphism is a widespread ph... more Despite virtually identical DNA sequences between the sexes, sexual dimorphism is a widespread phenomenon in nature. To a large extent the systematic differences between the sexes must therefore arise from processes involving gene regulation. In accordance, sexual dimorphism in gene expression is common and extensive. Genes with sexually dimorphic regulation are known to evolve rapidly, both in DNA sequence and in gene expression profile. Studies of gene expression in related species can shed light on the flexibility, or degree of conservation, of the gene expression profiles underlying sexual dimorphism. We have studied the extent of sexual dimorphism in gene expression in the brain of two species of songbirds, the zebra finch (Taeniopygia guttata) and the common whitethroat (Sylvia communis), using large-scale microarray technology. Sexual dimorphism in gene expression was extensive in both species, and predominantly sex-linked: most genes identified were male-biased and Z-linked....
Evolutionary molecular studies of island radiations may lead to insights in the role of vicarianc... more Evolutionary molecular studies of island radiations may lead to insights in the role of vicariance, founder events, population size and drift in the processes of population differentiation. We evaluate the degree of population genetic differentiation and fixation of the Canary Islands blue tit subspecies complex using microsatellite markers and aim to get insights in the population history using coalescence based methods. The Canary Island populations were strongly genetically differentiated and had reduced diversity with pronounced fixation including many private alleles. In population structure models, the relationship between the central island populations (La Gomera, Tenerife and Gran Canaria) and El Hierro was difficult to disentangle whereas the two European populations showed consistent clustering, the two eastern islands (Fuerteventura and Lanzarote) and Morocco weak clustering, and La Palma a consistent unique lineage. Coalescence based models suggested that the European mainland forms an outgroup to the Afrocanarian population, a split between the western island group (La Palma and El Hierro) and the central island group, and recent splits between the three central islands, and between the two eastern islands and Morocco, respectively. It is clear that strong genetic drift and low level of concurrent gene flow among populations have shaped complex allelic patterns of fixation and skewed frequencies over the archipelago. However, understanding the population history remains challenging; in particular, the pattern of extreme divergence with low genetic diversity and yet unique genetic material in the Canary Island system requires an explanation. A potential scenario is population contractions of a historically large and genetically variable Afrocanarian population, with vicariance and drift following in the wake. The suggestion from sequence-based analyses of a Pleistocene extinction of a substantial part of North Africa and a Pleistocene/Holocene eastward re-colonisation of western North Africa from the Canaries remains possible.
Dosage compensation, the process whereby expression of sex-linked genes remains similar between s... more Dosage compensation, the process whereby expression of sex-linked genes remains similar between sexes (despite heterogamety) and balanced with autosomal expression, was long believed to be essential. However, recent research has shown that several lineages, including birds, butterflies, monotremes and sticklebacks, lack chromosome-wide dosage compensation mechanisms and do not completely balance the expression of sex-linked and autosomal genes. To obtain further understanding of avian sex-biased gene expression, we studied Z-linked gene expression in the brain of two songbirds of different genera (zebra finch, Taeniopygia guttata, and common whitethroat, Sylvia communis) using microarray technology. In both species, the male-bias in gene expression was significantly higher for Z than for autosomes, although the ratio of Z-linked to autosomal expression (Z:A) was relatively close to one in both sexes (range: 0.89-1.01). Interestingly, the Z-linked male-bias in gene expression increased with expression level, and genes with low expression showed the lowest degree of sex-bias. These results support the view that the heterogametic females have up-regulated their single Z-linked homologues to a high extent when the W-chromosome degraded and thereby managed to largely balance their Z:A expression with the exception of highly expressed genes. The male-bias in highly expressed genes points towards male-driven selection on Z-linked loci, and this and other possible hypotheses are discussed.
Background: In a rapidly changing world, it is of fundamental importance to understand processes ... more Background: In a rapidly changing world, it is of fundamental importance to understand processes constraining or facilitating adaptation through microevolution. As different traits of an organism covary, genetic correlations are expected to affect evolutionary trajectories. However, only limited empirical data are available. Methodology/Principal Findings: We investigate the extent to which multivariate constraints affect the rate of adaptation, focusing on four morphological traits often shown to harbour large amounts of genetic variance and considered to be subject to limited evolutionary constraints. Our data set includes unique long-term data for seven bird species and a total of 10 populations. We estimate population-specific matrices of genetic correlations and multivariate selection coefficients to predict evolutionary responses to selection. Using Bayesian methods that facilitate the propagation of errors in estimates, we compare (1) the rate of adaptation based on predicted response to selection when including genetic correlations with predictions from models where these genetic correlations were set to zero and (2) the multivariate evolvability in the direction of current selection to the average evolvability in random directions of the phenotypic space. We show that genetic correlations on average decrease the predicted rate of adaptation by 28%. Multivariate evolvability in the direction of current selection was systematically lower than average evolvability in random directions of space. These significant reductions in the rate of adaptation and reduced evolvability were due to a general nonalignment of selection and genetic variance, notably orthogonality of directional selection with the size axis along which most (60%) of the genetic variance is found. Conclusions: These results suggest that genetic correlations can impose significant constraints on the evolution of avian morphology in wild populations. This could have important impacts on evolutionary dynamics and hence population persistence in the face of rapid environmental change.
This survey was conducted in two protected areas in Nigeria to genetically identify individual li... more This survey was conducted in two protected areas in Nigeria to genetically identify individual lions and to determine the genetic variation within and between the populations. We used faecal sample DNA, a non-invasive alternative to the risky and laborious task of taking samples directly from the animals, often preceded by catching and immobilization. Data collection in Yankari Game Reserve (YGR) spanned through a period of five years (2008-2012), whereas data in Kainji Lake National Park (KLNP) was gathered for a period of three years (2009, 2010 and 2012). We identified a minimum of eight individuals (2 males, 3 females, 3 unknown) from YGR and a minimum of ten individuals (7 males, 3 females) from KLNP. The two populations were found to be genetically distinct as shown by the relatively high fixation index (F ST = 0.17) with each population exhibiting signs of inbreeding (YGR F IS = 0.49, KLNP F IS = 0.38). The genetic differentiation between the Yankari and Kainji lions is assumed to result from large spatial geographic distance and physical barriers reducing gene flow between these two remaining wild lion populations in Nigeria. To mitigate the probable inbreeding depression in the lion populations within Nigeria it might be important to transfer lions between parks or reserves or to reintroduce lions from the zoos back to the wild.
In line with inbreeding theory, genetic diversity at a set of molecular markers may explain varia... more In line with inbreeding theory, genetic diversity at a set of molecular markers may explain variation in fitness-associated traits in partially inbred populations, and such associations will appear as 'genotype-fitness correlations'. An individual genetic diversity index specifically used for microsatellites is 'mean d 2 ', i.e. the mean squared distance between alleles. The original hypothesis for mean d 2-fitness correlations assumes that mean d 2 captures fitness effects at both ends of the inbreeding-outbreeding spectrum. This hypothesis received strong criticism from work showing that even a plain diversity estimate such as multi-locus heterozygosity (MLH) outperforms mean d 2 as a predictor of the inbreeding coefficient and fitness in most realistic situations. Despite this critique, the mean d 2-approach is still used frequently in ecological and evolutionary research, producing results suggesting that mean d 2 sometimes provides a stronger prediction of fitness than does MLH. In light of the critique, such results are unexpected, but potential explanations for them may exist (at least hypothetically), including scenarios based on close linkage and recent admixture. Nevertheless, a major caveat is that it is very difficult to predict a priori if mean d 2 will improve the genotype-fitness correlation, which in turn makes objective interpretations difficult. Mean d 2-fitness associations are potentially interesting, but the fact that we cannot easily understand them is problematic and should be thoroughly addressed in each study. Therefore, instead of hastily reached interpretations of mean d 2-fitness correlations, conclusions need support from complementary analyses, e.g. verifying admixture of genetically structured populations.
Allopatry and allopatric speciation can arise through two different mechanisms: vicariance or col... more Allopatry and allopatric speciation can arise through two different mechanisms: vicariance or colonization through dispersal. Distinguishing between these different allopatric mechanisms is difficult and one of the major challenges in biogeographical research. Here, we address whether allopatric isolation in an endemic island lizard is the result of vicariance or dispersal. We estimated the amount and direction of gene flow during the divergence of isolated islet populations and subspecies of the endemic Skyros wall lizard Podarcis gaigeae, a phenotypically variable species that inhabits a major island and small islets in the Greek archipelago. We applied isolation-with-migration models to estimate population divergence times, population sizes and gene flow between islet-mainland population pairs. Divergence times were significantly correlated with independently estimated geological divergence times. This correlation strongly supports a vicariance scenario where islet populations have sequentially become isolated from the major island. We did not find evidence for significant gene flow within P. g. gaigeae. However, gene-flow estimates from the islet to the mainland populations were positively affected by islet area and negatively by distance between the islet and mainland. We also found evidence for gene flow from one subspecies (P. g. weigandi) into another (P. g. gaigeae), but not in the other direction. Ongoing gene flow between the subspecies suggests that even in this geographically allopatric scenario with the sea posing a strong barrier to dispersal, divergence with some gene flow is still feasible.
Knowledge of relatedness between pairs of individuals plays an important role in many research ar... more Knowledge of relatedness between pairs of individuals plays an important role in many research areas including evolutionary biology, quantitative genetics, and conservation. Pairwise relatedness estimation methods based on genetic data from highly variable molecular markers are now used extensively as a substitute for pedigrees. Although the sampling variance of the estimators has been intensively studied for the most common simple genetic relationships, such as unrelated, half- and full-sib, or parent–offspring, little attention has been paid to the average performance of the estimators, by which we mean the performance across all pairs of individuals in a sample. Here we apply two measures to quantify the average performance: first, misclassification rates between pairs of genetic relationships and, second, the proportion of variance explained in the pairwise relatedness estimates by the true population relatedness composition (i.e., the frequencies of different relationships in t...
I examine the relationship between reproductive success and marker-based relatedness (MBR; inferr... more I examine the relationship between reproductive success and marker-based relatedness (MBR; inferred from variation at 21 microsatellite loci) of pair-mates in a semi-isolated population of great reed warblers (Acrocephalus arundinaceus) over a 12 year period. There was a negative relationship between egg-hatching success and MBR, but no association between MBR and three other components of fitness (clutch size, proportion of fledglings and recruits). The relationship between hatchability and MBR was non-linear, with high hatching rates at low and intermediate levels of MBR and a sudden decline in hatching success among the small number of pairs with high MBR (<4% of the sample). It is likely that the decrease in fitness at high MBR was due to effects of homozygosity at genome-wide distributed loci, as opposed to effects of fitness loci in the local chromosomal vicinity of particular markers. This conclusion relies on the fact that similar results were found in another study of the same population that was based on DNA-fingerprinting band-sharing, and that there was a strong correlation between MBR and pedigree-based relatedness. The negative relationship between MBR and hatchability was especially pronounced in the first study years and levelled off in later years. This time-dependent effect of MBR on hatchability was not caused by a simultaneous temporal decrease in MBR, and may instead reflect the importance of other processes such as genotype • environment interactions or purging of deleterious recessive alleles.
Background: The major histocompatibility complex (MHC) is an important component of the vertebrat... more Background: The major histocompatibility complex (MHC) is an important component of the vertebrate immune system and is frequently used to characterise adaptive variation in wild populations due to its co-evolution with pathogens. Passerine birds have an exceptionally diverse MHC with multiple gene copies and large numbers of alleles compared to other avian taxa. The Nesospiza bunting species complex (two species on Nightingale Island; one species with three sub-species on Inaccessible Island) represents a rapid adaptive radiation at a small, isolated archipelago, and is thus an excellent model for the study of adaptation and speciation. In this first study of MHC in Nesospiza buntings, we aim to characterize MHCIIβ variation, determine the strength of selection acting at this gene region and assess the level of shared polymorphism between the Nesospiza species complex and its putative sister taxon, Rowettia goughensis, from Gough Island. Results: In total, 23 unique alleles were found in 14 Nesospiza and 2 R. goughensis individuals encoding at least four presumably functional loci and two pseudogenes. There was no evidence of ongoing selection on the peptide binding region (PBR). Of the 23 alleles, 15 were found on both the islands inhabited by Nesospiza species, and seven in both Nesospiza and Rowettia; indications of shared, ancestral polymorphism. A gene tree of Nesospiza MHCIIβ alleles with several other passerine birds shows three highly supported Nesospiza-specific groups. All R. goughensis alleles were shared with Nesospiza, and these alleles were found in all three Nesospiza sequence groups in the gene tree, suggesting that most of the observed variation predates their phylogenetic split. Conclusions: Lack of evidence of selection on the PBR, together with shared polymorphism across the gene tree, suggests that population variation of MHCIIβ among Nesospiza and Rowettia is due to ancestral polymorphism rather than local selective forces. Weak or no selection pressure could be attributed to low parasite load at these isolated Atlantic islands. The deep divergence between the highly supported Nesospiza-specific sequence Groups 2 and 3, and the clustering of Group 3 close to the distantly related passerines, provide strong support for preserved ancestral polymorphism, and present evidence of one of the rare cases of extensive ancestral polymorphism in birds.
Background: Patterns of spatial variation in discrete phenotypic traits can be used to draw infer... more Background: Patterns of spatial variation in discrete phenotypic traits can be used to draw inferences about the adaptive significance of traits and evolutionary processes, especially when compared to patterns of neutral genetic variation. Population divergence in adaptive traits such as color morphs can be influenced by both local ecology and stochastic factors such as genetic drift or founder events. Here, we use quantitative color measurements of males and females of Skyros wall lizard, Podarcis gaigeae, to demonstrate that this species is polymorphic with respect to throat color, and the morphs form discrete phenotypic clusters with limited overlap between categories. We use divergence in throat color morph frequencies and compare that to neutral genetic variation to infer the evolutionary processes acting on islet-and mainland populations. Results: Geographically close islet-and mainland populations of the Skyros wall lizard exhibit strong divergence in throat color morph frequencies. Population variation in throat color morph frequencies between islets was higher than that between mainland populations, and the effective population sizes on the islets were small (N e :s < 100). Population divergence (F ST) for throat color morph frequencies fell within the neutral F ST-distribution estimated from microsatellite markers, and genetic drift could thus not be rejected as an explanation for the pattern. Moreover, for both comparisons among mainland-mainland population pairs and between mainland-islet population pairs, morph frequency divergence was significantly correlated with neutral divergence, further pointing to some role for genetic drift in divergence also at the phenotypic level of throat color morphs. Conclusions: Genetic drift could not be rejected as an explanation for the pattern of population divergence in morph frequencies. In spite of an expected stabilising selection, throat color frequencies diverged in the islet populations. These results suggest that there is an interaction between selection and genetic drift causing divergence even at a phenotypic level in these small, subdivided populations.
Substantial genetic variation is hypothesised to be necessary for the long-term survival of speci... more Substantial genetic variation is hypothesised to be necessary for the long-term survival of species. Therefore, a major aim in conservation is to maintain and restore variation in small and endangered populations. However, in most populations the amount of genetic variation and, thus, the potential threats posed by limited variation are unknown. In the present study, we assess genetic variation, both at 10 microsatellite loci and at the major histocompatibility complex (MHC), in three closely related Acrocephalus warbler species with contrasting demographies. We found that the recently bottlenecked, island endemic, Seychelles warbler (A. sechellensis; SW) has substantially reduced microsatellite and MHC diversity compared to the widespread great reed warbler (A. arundinaceus; GRW). In contrast, another endangered species with a small breeding range, the Basra reed warbler (A. griseldis; BRW), harboured as much variation as did the GRW. This suggests that significant genetic variation and, therefore, adaptive potential, remains in the BRW-a situation that should hold as long as its habitat and numbers are maintained. Our study is one of the first to assess genetic variation at both 'non-critical' microsatellite markers and 'critical' MHC loci within endangered species. The two types of loci provided a similar picture of the genetic variation in the species we studied, but this has not been the case in studies of some other species. Using a combination of specific functional loci and genome-wide random markers appears to be the best way to assess the threat posed by reduced genetic diversity.
Proceedings of the Royal Society B: Biological Sciences, 2014
In a broad range of species—including humans—it has been demonstrated that telomere length declin... more In a broad range of species—including humans—it has been demonstrated that telomere length declines throughout life and that it may be involved in cell and organismal senescence. This potential link to ageing and thus to fitness has triggered recent interest in understanding how variation in telomere length is inherited and maintained. However, previous studies suffer from two main drawbacks that limit the possibility of understanding the relative importance of genetic, parental and environmental influences on telomere length variation. These studies have been based on (i) telomere lengths measured at different time points in different individuals, despite the fact that telomere length changes over life, and (ii) parent–offspring regression techniques, which do not enable differentiation between genetic and parental components of inheritance. To overcome these drawbacks, in our study of a songbird, the great reed warbler, we have analysed telomere length measured early in life in bo...
Proceedings of the Royal Society B: Biological Sciences, 2005
Linkage maps are lacking for many highly influential model organisms in evolutionary research, in... more Linkage maps are lacking for many highly influential model organisms in evolutionary research, including all passerine birds. Consequently, their full potential as research models is severely hampered. Here, we provide a partial linkage map and give novel estimates of sex-specific recombination rates in a passerine bird, the great reed warbler (Acrocephalus arundinaceus). Linkage analysis of genotypic data at 51 autosomal microsatellites and seven markers on the Z-chromosome (one of the sex chromosomes) from an extended pedigree resulted in 12 linkage groups with 2–8 loci. A striking feature of the map was the pronounced sex-dimorphism: males had a substantially lower recombination rate than females, which resulted in a suppressed autosomal map in males (sum of linkage groups: 110.2 cM) compared to females (237.2 cM; female/male map ratio: 2.15). The sex-specific recombination rates will facilitate the building of a denser linkage map and cast light on hypotheses about sex-specific ...
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Papers by Bengt Hansson