| 1. |
- Graham, Stuart, et al.
(author)
-
The utility of effective population size in population management 1 : estimating contemporary effective size
- 2016
-
Journal article (other academic/artistic)abstract
- Estimates of effective population size (Ne) are highly desirable in managed populations because they are informative of the rate at which genetic variation is being lost through the processes of genetic drift or inbreeding. Due to the notorious difficulty of accurate Ne estimation in natural populations, myriad estimation methods have been developed over the last 50 years. Conservation practitioners and researchers who are unfamiliar with the Ne estimation literature are now faced with an overwhelming amount of choice when selecting an estimation method and, unfortunately, the resources available to help them make this decision rarely consider the practicalities of implementing these methods. This review aims to alleviate this problem by explicitly considering these practicalities while describing and comparing the most popular estimation methods available. We begin by clearly describing how estimates of Ne can be used in population management. We then go on to describe the most popular methods available for Ne estimation, stating the assumptions that are made and the data that are required. The review concludes with recommendations of the most appropriate estimation methods given specific motivations for estimating Ne and the types of data that are practical to collect.
|
|
| 2. |
- Griesser, Michael, et al.
(author)
-
Experience buffers extrinsic mortality in a group-living bird species
- 2017
-
In: Oikos. - : Wiley. - 0030-1299 .- 1600-0706. ; 126:9, s. 1258-1268
-
Journal article (peer-reviewed)abstract
- Extrinsic mortality has a strong impact on the evolution of life-histories, prey morphology and behavioural adaptations, but for many animals the causes of mortality are poorly understood. Predation is an important driver of extrinsic mortality and mobile animals form groups in response to increased predation risk. Furthermore, in many species juveniles suffer higher mortality than older individuals, which may reflect a lower phenotypic quality, lower competitiveness, or a lack of antipredator or foraging skills. Here we assessed the causes of mortality for 371 radio tagged Siberian jays. This sedentary bird species lives in family groups that contain a breeding pair as well as related and unrelated non-breeders. Ninety-five percent of death were due to predation (n = 59 out of 62 individuals) and most individuals were killed by Accipiter hawks. Multivariate Cox proportional hazards models showed that non-breeders had a lower survival than breeders, but only in territories in managed forest with little visual cover. Examining breeders, only sex influenced survival with males having a lower survival than females. For non-breeders, juveniles had lower survival than older non-breeders, and those on managed territories had lower survival than those on unmanaged territories. Additionally, a low feather quality reduced the survival probability of non-breeders only. Thus, living on managed territories and having a low feature quality affected only non-breeders, particularly juveniles. These findings add to previous research demonstrating that juvenile Siberian jays acquire critical antipredator skills from experienced group members. Thus, experience can buffer extrinsic mortality, highlighting that group living not only provides safety in numbers, but also provide social opportunities to learn critical life-skills.
|
|
| 3. |
- Kozma, Radoslav, 1987-, et al.
(author)
-
Genomic regions of speciation and adaptation among three species of grouse
- 2019
-
In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9
-
Journal article (peer-reviewed)abstract
- Understanding the molecular basis of adaption is one of the central goals in evolutionary biology and when investigated across sister species it can provide detailed insight into the mechanisms of speciation. Here, we sequence the genomes of 34 individuals from three closely related grouse species in order to uncover the genomic architecture of speciation and the genes involved in adaptation. We identify 6 regions, containing 7 genes that show lineage specific signs of differential selection across the species. These genes are involved in a variety of cell processes ranging from stress response to neural, gut, olfactory and limb development. Genome wide neutrality test statistics reveal a strong signal of population expansion acting across the genomes. Additionally, we uncover a 3.5 Mb region on chromosome 20 that shows considerably lower levels of differentiation across the three grouse lineages, indicating possible action of uniform selection in this region.
|
|
| 4. |
- Kozma, Radoslav, 1987-
(author)
-
Inferring demographic history and speciation of grouse using whole genome sequences
- 2016
-
Doctoral thesis (other academic/artistic)abstract
- From an ecological perspective, knowledge of demographic history is highly valuable because population size fluctuations can be matched to known climatic events, thereby revealing great insight into a species’ reaction to past climate change. This in turn enables us to predict how they might respond to future climate scenarios. Prominently, with the advent of high-throughput sequencing it is now becoming possible to assemble genomes of non-model organisms thereby providing unprecedented resolution to the study of demographic history and speciation. This thesis utilises four species of grouse (Aves, subfamily Tetraoninae) in order to explore the demographic history and speciation within this lineage; the willow grouse, red grouse, rock ptarmigan and the black grouse. I, and my co-authors, begin by reviewing the plethora of methods used to estimate contemporary effective population size (Ne) and demographic history that are available to animal conservation practitioners. We find that their underlying assumptions and necessary input data can bias in their application, and thus we provide a summary of their applicability.I then use the whole genomes of the black grouse, willow grouse and rock ptarmigan to infer their population dynamics within the last million years. I find three dominant periods that shape their demographic history: early Pleistocene cooling (3-0.9 Mya), the mid-Brunhes event (430 kya) and the last glacial period (110-10 kya). I also find strong signals of local population history – recolonization and subdivision events – affecting their demography. In the subsequent study, I explore the grouse dynamics within the last glacial period in more detail by including more distant samples and using ecological modelling to track habitat distribution changes. I further uncover strong signals of local population history, with multiple fringe populations undergoing severe bottlenecks. I also determine that future climate change is expected to drastically constrict the distribution of the studied grouse.Lastly, I use whole genome sequencing to uncover 6 highly differentiated regions, containing 7 genes, hinting at their role in adaptation and speciation in three grouse taxa. I also locate a region of low differentiation, containing the Agouti pigmentation gene, indicating its role in the grouse plumage coloration.
|
|
| 5. |
- Kozma, Radoslav, 1987-, et al.
(author)
-
Insight into speciation and adaptation in grouse as revealed by whole genome sequencing
-
Other publication (other academic/artistic)abstract
- Understanding the molecular basis of adaption is one of the central goals in evolutionary biology and when investigated across sister species it can provide detailed insight into the mechanisms of speciation. The grouse (subfamily Tetraoninae) constitute an avian lineage whose members inhabit a wide variety of habitats and possess diverse plumage traits and as such offer an interesting case study. Here, we sequence the genomes of 34 individuals comprising three grouse taxa; the willow grouse (Lagopus lagopus lagopus), the red grouse (Lagopus lagopus scoticus) and the rock ptarmigan (Lagopus muta) in order to uncover the genomic architecture of speciation and the genes involved in adaptation. We identify 6 regions, containing 7 genes that show consistent signs of differential selection across the species. These genes are highly involved in a variety of cell processes ranging from stress response to neural, gut, olfactory and limb development. Genome wide neutrality test statistics also reveal a strong signal of population expansion acting across the genomes, which is in line with previous demographic studies in these systems. Additionally, we uncover a 3.5Mb region on chromosome 20 that shows considerably lower levels of differentiation across the three grouse lineages, indicating the action of uniform selection. The Agouti gene, which is integral in the pigmentation pathway, lies at the 5' start of this region hinting at the conserved development of brown plumage across the three taxa. Together, our results provide a key step in the exploration of grouse speciation and adaptation.
|
|
| 6. |
- Kozma, Radoslav, 1987-, et al.
(author)
-
Looking into the past : the reaction of three grouse species to climate change over the last million years using whole genome sequences
- 2016
-
In: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 25:2, s. 570-580
-
Journal article (peer-reviewed)abstract
- Tracking past population fluctuations can give insight into current levels of genetic variation present within species. Analysing population dynamics over larger timescales can be aligned to known climatic changes to determine the response of species to varying environments. Here, we applied the Pairwise Sequentially Markovian Coalescent (PSMC) model to infer past population dynamics of three widespread grouse species; black grouse, willow grouse and rock ptarmigan. This allowed the tracking of the effective population size (Ne) of all three species beyond 1 Mya, revealing that (i) early Pleistocene cooling (~2.5 Mya) caused an increase in the willow grouse and rock ptarmigan populations, (ii) the mid-Brunhes event (~430 kya) and following climatic oscillations decreased the Ne of willow grouse and rock ptarmigan, but increased the Ne of black grouse and (iii) all three species reacted differently to the last glacial maximum (LGM) – black grouse increased prior to it, rock ptarmigan experienced a severe bottleneck and willow grouse was maintained at large population size. We postulate that the varying PSMC signal throughout the LGM depicts only the local history of the species. Nevertheless, the large population fluctuations in willow grouse and rock ptarmigan indicate that both species are opportunistic breeders while black grouse tracks the climatic changes more slowly and is maintained at lower Ne. Our results highlight the usefulness of the PSMC approach in investigating species’ reaction to climate change in the deep past, but also that caution should be taken in drawing general conclusions about the recent past.
|
|
| 7. |
- Kozma, Radoslav, 1987-, et al.
(author)
-
Past and potential future population dynamics of three grouse species using ecological and whole genome coalescent modeling
- 2018
-
In: Ecology and Evolution. - : Wiley. - 2045-7758. ; 8:13, s. 6671-6681
-
Journal article (peer-reviewed)abstract
- Studying demographic history of species provides insight into how the past has shaped the current levels of overall biodiversity and genetic composition of species, but also how these species may react to future perturbations. Here we investigated the demographic history of the willow grouse (Lagopus lagopus), rock ptarmigan (Lagopus muta), and black grouse (Tetrao tetrix) through the Late Pleistocene using two complementary methods and whole genome data. Species distribution modeling (SDM) allowed us to estimate the total range size during the Last Interglacial (LIG) and Last Glacial Maximum (LGM) as well as to indicate potential population subdivisions. Pairwise Sequentially Markovian Coalescent (PSMC) allowed us to assess fluctuations in effective population size across the same period. Additionally, we used SDM to forecast the effect of future climate change on the three species over the next 50years. We found that SDM predicts the largest range size for the cold-adapted willow grouse and rock ptarmigan during the LGM. PSMC captured intraspecific population dynamics within the last glacial period, such that the willow grouse and rock ptarmigan showed multiple bottlenecks signifying recolonization events following the termination of the LGM. We also see signals of population subdivision during the last glacial period in the black grouse, but more data are needed to strengthen this hypothesis. All three species are likely to experience range contractions under future warming, with the strongest effect on willow grouse and rock ptarmigan due to their limited potential for northward expansion. Overall, by combining these two modeling approaches, we have provided a multifaceted examination of the biogeography of these species and how they have responded to climate change in the past. These results help us understand how cold-adapted species may respond to future climate changes.
|
|
| 8. |
- Kozma, Radoslav, 1987-, et al.
(author)
-
The utility of effective population size in population management 2 : estimating demographic history
- 2016
-
Journal article (other academic/artistic)abstract
- Elucidating demographic history by tracking the fluctuations of effective population size (Ne) through time has helped uncover interesting insight into the ecology and evolutionary history of a wide array of populations and species. This field of research has seen many exciting methods put forth that together can retrieve the demographic history across many time scales and as such, it is becoming a very useful tool available for conservation practitioners. However, due to the inherent difficulties associated with estimating Ne, the literature can be very technical it is often unclear how methods differ in their assumptions and data requirements. Thus, the choice of which method to use for what purpose can be an extremely difficult one. With this review, we aim to first describe the major methods used to estimate demographic history and clarify their underlying requirements and assumptions. We then highlight some of the overarching motives to understand past Ne fluctuations and we conclude with advice about which methods to use to address these specific motives with a particular focus on the temporal resolution required.
|
|
| 9. |
- Rózsa, Jani, et al.
(author)
-
Effects of a range expansion on adaptive and neutral genetic diversity in dispersal limited Hazel grouse (Bonasa bonasia) in the French Alps
- 2016
-
In: Conservation Genetics. - : Springer Science and Business Media LLC. - 1566-0621 .- 1572-9737. ; 17:2, s. 401-412
-
Journal article (peer-reviewed)abstract
- Biogeographic range expansions, when related to dispersal limitation, may have counter intuitive effects on genetic diversity. At range margins the relative roles of demographic changes, connectivity and genetic diversity need to be integrated for a successful assessment of population viability. Historically the Hazel grouse (Bonasa bonasia) in France was found in the north of the French Alps and also in a disjunct population in the nearby Jura Mountains. The species has recently undergone a range expansion in a north to south axis in the Alps. Local population size estimates and migration patterns during expansion have previously been studied. In this study, we performed genotyping at neutral (microsatellite) and adaptive (MHC) genetic markers in Hazel grouse. We compared diversity and differentiation (FST and DEST) at three sampling localities along the expansion axis in the French Alps and Jura, as well as at two sampling localities in Sweden, where the population has had a long-term continuous and stable distribution. Strong serial founder effects were found between the French localities, resulting in stronger isolation further south, with a relatively high neutral differentiation (pair-wise FST = 0.117). However, the loss of adaptive diversity MHC was slight. No adaptive differentiation (MHC DEST = −0.015) was observed, thus, the French localities can be considered uniform units with regard to MHC diversity, a criterion to treat populations in these localities as a management unit.
|
|
| 10. |
- Wang, Biao, et al.
(author)
-
Transcriptome sequencing of black grouse (Tetrao tetrix) for immune gene discovery and microsatellite development
- 2012
-
In: Open Biology. - : The Royal Society. - 2046-2441. ; 2, s. 120054-
-
Journal article (peer-reviewed)abstract
- The black grouse (Tetrao tetrix) is a galliform bird species that is important forboth ecological studies and conservation genetics. Here, we report the sequencing of the spleen transcriptome of black grouse using 454 GS FLX Titanium sequencing. We performed a large-scale gene discovery analysis with a focus on genes that might be related to fitness in this species and also identified a large set of microsatellites. In total, we obtained 182 179 quality-filtered sequencing reads that we assembled into 9035 contigs. Using these contigs and 15 794 length-filtered (greater than 200 bp) singletons, we identified 7762 transcripts that appear to be homologues of chicken genes. A specific BLAST search with an emphasis on immune genes found 308 homologous chicken genes that have immune function, including ten major histocompatibility complex-related genes located on chicken chromosome 16. We also identified 1300 expressed sequence tag microsatellites and were able to design suitable flanking primers for 526 of these. A preliminary test of the polymorphism of the microsatellites found 10 polymorphic microsatellites of the 102 tested. Genomic resources generated in this study should greatly benefit future ecological, evolutionary and conservation genetic studies on this species.
|
|
