Centro de Biologia Ambiental / Departamento de Biologia Animal
Can reproductive barriers maintain differentiation in face of global changes? A case study in Drosophila subobscura
Author(s): Matos, M, Bárbaro, M, Mira, M, Fragata, I, Simões, P, Lima, M, Lopes-Cunha, M, Kellen, B, Santos, J, Magalhães, S
Species with wide distributions may be highly differentiated across contrasting environments. While gene flow may help maintain similarities among populations, local adaptation may lead to their divergence, as well as promote reproductive isolation, further fostering evolutionary diversification. The interplay between these two processes is of major importance for Conservation, as it will determine if populations differentiate or become more similar in the long run, as a result of environmental changes such as those imposed by man. In Drosophila subobscura, populations are differentiated along a latitudinal gradient, but recent evidence indicates that northern populations are becoming more similar to southern ones. An important issue is how much populations from the extremes of the cline differ in mating preferences, as this might contribute to reduce genetic introgression when populations meet. To address this, we analyzed the evolutionary dynamics of reproductive isolation of D. subobscura populations derived from the extremes of the European cline, while adapting to a common, laboratorial environment. We show that mating performance increased during laboratory adaptation. In general northern populations had a better performance than southern ones, and this difference was sustained across generations. Moreover northern females preferred mates from their own populations while southern females preferred males from the north. The assortative mating of the northern populations was stable through time, while disassortative mating of the southern populations faded away during laboratory evolution. Overall this study suggests that reproductive barriers may slow down the genetic introgression due to migration to the north, an important finding in evolutionary and conservation terms.
School of Biological Sciences
Can we use molecular techniques to measure inbreeding in wild populations of highly inbred, bottlenecked species?
Author(s): Taylor, H, Ramstad, K, Kardos, M
Understanding the effects of inbreeding depression is important for viability assessment and effective management of rare and endangered species, but accurately measuring inbreeding in such species remains challenging. Highly inbred species that have experienced severe bottleneck events typically lack the behavioural pedigree information, high levels of genetic diversity and large population sizes (and thus sample sizes) required to accurately estimate individual inbreeding. This raises the question of whether investing resources into research in this area is worthwhile for conservation managers and, if so, what the best approach might be. We modeled the accuracy of pedigrees constructed using varying numbers of simulated microsatellite markers for the little spotted kiwi (Apteryx owenii), a species that has experienced a recent, severe bottleneck and that exhibits extremely low genetic variation. We found that the number of microsatellite markers required to reconstruct precise pedigrees and provide accurate inbreeding coefficients will be cost prohibitive for the majority of conservation studies. Alternative approaches, such as heterozygosity fitness correlations, would also require a prohibitively large number of neutral markers. Pairwise relatedness measures show promise for estimating inbreeding in this species and those with similar histories, but genomic measures such as runs of homozygosity (ROH) currently provide the most effective alternative for measuring inbreeding. We acknowledge that genomic methods may also prove too costly currently for many conservation programmes and emphasise that conservation managers should weigh the costs and benefits of alternative strategies prior to investing in genetic measures as part of their rescue strategies.
Institute of Biosciences
Characterization of MHC-class II DRB diversity in the lesser anteater (Tamandua tetradactyla)
Author(s): Clozato, CL, Moraes-Barros, N, Morgante, JS, Sommer, S
Studies of immune gene variation in the Major Histocompatibility Complex (MHC) provide a powerful tool to investigate patterns of adaptative genetic diversity shaped by natural selection. The use of MHC makers in population genetics has grown to a great extant in the past few years. However, studies with non-model species are still challenging due to the lack of a references and information of loci number. The lesser anteater is a medium sized mammal of the order Pilosa. The species is geographically widespread, found throughout South America in several types of habitats such as grasslands, savannas, forests and wetlands. Such flexibility on habitat use may lead to local adaptations reflected in the species’ MHC gene diversity, accounting for different parasite pressures in the environment. To understand the contribution of natural selection to Tamandua tetradactyla populations we described the diversity of the MHC Class II DRB exon 2 gene. At first, Single Strand Conformation Polymorphism (SSCP) was used to screen diversity in order to develop the optimal primer pair for sequential amplification (i.e., the one that catches most diversity and shows less null alleles). DRB exon 2 was amplified in ten gDNA samples from individuals trapped at different geographical locations using three primer sets. PCR products were run twice on SSCP gels and sequenced. A fragment of 198 base pairs (66 aminoacids) was obtained, and no indels were found. After choosing the best primer set, a total of 22 alleles were detected on the aminoacid level (TateDRB01 to TateDRB22), and 26 on the nucleotide level. Between four and eight alleles were found per individual (average of 4.7), indicating the presence of at least two DRB loci. Secondly, 50 samples derived from four different biomes of the species occurrence are currently analysed through Next Generation Sequencing (NGS) on a 454 Junior platform. This will allow the analyses of the genetic structure of MHC DRB gene in the species.
Characterizing and tracking MHC variation of chyrtridiomycosis affected Chiricahua leopard frogs over time in natural populations
Author(s): Mulder, KP, Savage, AE
The amphibian disease chytridiomycosis caused by the fungus Batrachochytrium dendrobatidis (Bd) has contributed to the decline and extirpation of numerous populations of Chiricahua leopard frogs (Lithobates chiricahuensis), an endangered species native to the Southwestern United States and Northern Mexico. Conservation efforts have focused on captive rearing of wild-caught egg masses and subsequent release following metamorphosis (called head-starting) to increase population sizes across the species range. The survival rate of released individuals is, however, heavily dependent on their ability to combat chytridiomycosis. In captivity, populations of other species of leopard frogs show differential survival to experimental Bd infections dependent on their genetic variation in the major histocompatability complex (MHC), a highly variable gene family in vertebrates known to be important in pathogen resistance. We used single locus 454 pyrosequencing to characterize MHC genetic variation in head-started Chiricahua leopard frogs that will be released and monitored for one year to determine survival rates and identify alleles that confer an advantage against Bd in a natural environment. This information will be used to identify candidate resistance alleles and add MHC-based marker assisted selection to captive breeding efforts, with the goal of increasing the success rate of head-starting efforts and mitigating the impact of Bd on natural populations of both Chiricahua leopard frogs as well as other amphibian species affected by chrytridiomycosis. This is a case study of how evolutionary genetic analyses of adaptive markers can assist conservation efforts in captive breeding.
Comparison of estimators of effective population size: variation and bias in the methods
Author(s): Jimenez-Mena, B, Hospital, F, Verrier, E
The effective population size (Ne) is a parameter of paramount importance in population genetics. Many estimators of Ne have been developed in the literature and each one uses different kinds of data (pedigree, molecular markers). But the various methods give very different estimates of Ne for the same population. Therefore, there is a need for an assessment of the consistency and reliability of the methods. The aim of our study is to analyze a few of them, making a comparison by using simulation data. A forward-in-time simulation of a multi-allelic population subjected to genetic drift was developed. We modelled a diploid population which reproduced randomly in discrete generations, with constant population size N. Self-fertilization was allowed. Selection, migration, and new mutations were assumed to not happen across generations. At each generation, Ne was estimated with various methods. We performed 700 replicates. We used the classical estimator 1/(2 x rate of Inbreeding). The coefficients of inbreeding were obtained by several ways: (i) the average pairwise coancestry derived from pedigree, (ii) the heterozygosity (He) computed from the observed allele frequencies. We also included in the comparison two estimators based on temporal changes in the allele frequency taken from the population at two points in time. We performed the comparisons varying different conditions: number of generations between sampled populations (d), initial allele configuration, and N. The results showed that the use of (ii) resulted in a huge range of Ne values, in some cases with extreme values as large as 1e+06. This is due to the large variation of the estimated values of He, which can lead to a bias in Ne. Increasing d reduced this variability of results and increased the accuracy of Ne estimation, but not very much. Estimations based on (i) resulted in very accurate estimates of Ne.
Department of Biological Sciences
Consistent patterns of return cross-species application of SNP chips
Author(s): Miller, JM, Kijas, JW, Heaton, MP, McEwan, JC, Coltman, DW
Recent advances in technology facilitated development of large sets of genetic markers for many taxa, though most often model or domestic organisms. Cross-species application of genomic technologies may allow for rapid marker discovery in wild relatives of taxa with well developed resources. We investigated cross-species application of three commercially available SNP chips (the OvineSNP50, BovineSNP50, and EquineSNP50 BeadChips) as a function of divergence time between the domestic source species and wild target species. Across all three chips we observed a consistent linear decrease in call rate (~1.5% per million years), while retention of polymorphisms showed an exponential decay. These results will allow researchers to predict the expected amplification rate and polymorphism of cross-species application for their taxa of interest, as well as provide a resource for estimating divergence times.
Department of Animal and Plant Sciences
Effects of seasonal conditions on mortality and fertility in Asian elephants: implications for conservation
Author(s): Mumby, HS, Courtiol, A, Mar, KU, Lummaa, V
In highly seasonal environments, many species maximise offspring survival by reproducing at the time of year with peak resource availability. However, elephants do not have a single breeding season with females undergoing reproductive cycles throughout the year. Whether females concentrate most births on periods of maximum offspring survival is unknown, as are the proximate factors that could affect seasonal variation in birth rate. Long-term effects of birth season on patterns of mortality and fertility are also yet to be investigated. These topics are of particular importance in elephants, which are extremely long-lived and endangered, as understanding variation in mortality and reproductive success could contribute towards conservation of the species. We use individual-based longitudinal data for 2350 semi-captive logging elephants from Myanmar that occupy regions with a tropical monsoon climate, to investigate immediate and long term fertility and mortality responses to season. We supplement this long-term data with a 1 year subsample of 70 elephants for which monthly measurements of body weight, body condition and stress hormone (cortisol) levels were collected, to investigate the physiological correlates of seasonal conditions. Our results show significant variation in probability of birth by month, and an interaction between birth order and probability of birth, with higher seasonality of births in first-born individuals. There was no long-term effect of birth month on mortality, but females born in the monsoon season subsequently had earlier peak in fertility and earlier age at last reproduction in comparison to those born in the cool or dry seasons. The seasonal pattern of births did not coincide with high rainfall periods, but was rather associated with seasonal variation in workload and also matches individual level variation in cortisol in the subsample. This is a rare test of effects of early conditions on individual fitness in a non-model species.
Department of Biology
Evolutionary conservation of large blue butterflies
Author(s): Nash, DR, Andersen, A
The large blue butterflies (genus Maculinea/Phengaris) are icons of invertebrate conservation. Their rarity is to a large extent due to their complex life cycle during which they exploit both specific host plants and specific host Myrmica ants, which must therefore co-occur. Even when both hosts are present in the same area, there is massive variation in the probability of adoption by and survival in different host ant nests. Over the last few decades we have learnt a great deal about some of the underlying causes of this variation, for example as a result of coevolutionary arms-races in chemical mimicry and the effects of variation in host ant social structure. Over the same period, there have been several attempts to reintroduce large blue butterflies to areas from which they have disappeared, with varying degrees of success. Here we examine to what extent the success of large blue butterfly reintroductions has been increased by a deeper understanding of their evolution, and the genetic and evolutionary consequences of reintroduction programs. We also examine how the success of future conservation efforts could be enhanced based on our current knowledge of the evolution and ecology of the large blue butterflies and their hosts.
DAFNAE & Department of Biodiversity and Molecular Ecology
Genetic diversity and population structure of the common frog (Rana temporaria) in the Trentino region (south-eastern Alps)
Author(s): Marchesini, A, Battisti, A, Vernesi, C
Amphibians are facing a dramatic decline worldwide, due to their high susceptibility to perturbations and global change. A decrease in genetic diversity can lead to loss of adaptability, and it is often associated with reduction in fitness. Amphibians seem to be particularly prone to such genetic processes, and a growing body of research shows that many amphibian populations are experiencing a reduction in genetic variation. In this study we investigated the levels of genetic diversity and population differentiation of the common frog (Rana temporaria) in the alpine region of Trentino. Rana temporaria is a widespread amphibian species in Europe and is not currently considered threatened; nevertheless, in some part of its range it has recently experienced localized declines. We analyzed polymorphism in a set of 12 SSR loci, in about 25 populations spread over the entire area of interest. Levels of genetic diversity were comparable to those found in other European populations, but a relatively high degree of heterogeneity among sites was recorded. We detected an irregular population structure, though a first general subdivision may be recognized between the populations belonging to the orographic right and left side of the Adige river. Some populations of the central part of the area showed lower levels of genetic variability, together with relatively strong differentiation. This subarea is characterized by a wide and anthropized valley run through by the Adige river: the suitable habitat for Rana temporaria is limited to isolated patches within an inhospitable landscape matrix. In addition, this area largely overlaps with the distribution of Rana dalmatina in the Trentino region. We discussed the effects of population density and potential competition (in terms of pond occupancy) on the recorded patterns of genetic diversity and population structure, highlighting the genetic peculiarity (and therefore conservation value) of some isolated populations.
Genomic consequences of inbreeding and hybridization in pigs and wild boars
Author(s): Bosse, M, Madsen, O, Megens, H, Frantz, LAF, Paudel, Y, Crooijmans, RPMA, Groenen, MAM
The maintenance of genetic diversity in (isolated) populations is essential for their adaptive ability. If standing variation is low, the susceptibility to a variety of diseases and environmental changes is elevated. Two haplotypes are IBD (identical by descent) when they originate from a common ancestor. If IBD haplotypes reunite within one diploid organism, it results in a region of homozygosity (ROH), which is an indication of recent inbreeding. The interplay of population demographic history and recombination rate is essential in the process of haplotype formation and distribution. In management of small, potential inbreed, populations, outcrossing is used to introduce new haplotypes in a population and hereby increase genetic diversity. This study utilizes the latest genomics tools to identify shared haplotype tracts between pigs (Sus scrofa) from different Eurasian wild boar and breed populations. Pigs are an excellent model species to study haplotype structure because of their complex demographic history, multiple domestication events and recent admixture. Next-generation sequencing enables a thorough and nearly ascertainment bias-free investigation of genome-wide patterns of haplotype sharing. Our study reveals patterns of inbreeding, and conserved, introgressed and selected haplotypes in the pig genome. Haplotypes that are shared between closely related individuals are longer and more abundant in the genome than haplotypes shared by distantly related individuals. Selection on introgressed haplotypes results in an over-representation of these haplotypes in a population. Nucleotide diversity in the genome is higher when at least one haplotype is shared with a distantly related individual, supporting the fundamental genetics theory behind outcrossing. Detailed mapping of the genomic distribution of variation enables a targeted approach to increase genetic diversity of captive and wild populations, which may facilitate conservation efforts in the near future.