1
|
Leon-Apodaca AV, Kumar M, Del Castillo A, Conroy GC, Lamont RW, Ogbourne S, Cairns KM, Borburgh L, Behrendorff L, Subramanian S, Szpiech ZA. Genomic consequences of isolation and inbreeding in an island dingo population. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.15.557950. [PMID: 37745583 PMCID: PMC10516007 DOI: 10.1101/2023.09.15.557950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Dingoes come from an ancient canid lineage that originated in East Asia around 8000-11,000 years BP. As Australia's largest terrestrial predator, dingoes play an important ecological role. A small, protected population exists on a world heritage listed offshore island, K'gari (formerly Fraser Island). Concern regarding the persistence of dingoes on K'gari has risen due to their low genetic diversity and elevated inbreeding levels. However, whole-genome sequencing data is lacking from this population. Here, we include five new whole-genome sequences of K'gari dingoes. We analyze a total of 18 whole genome sequences of dingoes sampled from mainland Australia and K'gari to assess the genomic consequences of their demographic histories. Long (>1 Mb) runs of homozygosity (ROH) - indicators of inbreeding - are elevated in all sampled dingoes. However, K'gari dingoes showed significantly higher levels of very long ROH (>5 Mb), providing genomic evidence for small population size, isolation, inbreeding, and a strong founder effect. Our results suggest that, despite current levels of inbreeding, the K'gari population is purging strongly deleterious mutations, which, in the absence of further reductions in population size, may facilitate the persistence of small populations despite low genetic diversity and isolation. However, there may be little to no purging of mildly deleterious alleles, which may have important long-term consequences, and should be considered by conservation and management programs. SIGNIFICANCE A long-standing question in conservation genetics is whether long-term isolation and elevated levels of inbreeding always leads to inevitable population extinction. Here we conduct the first-ever whole-genome analysis of a population of dingoes living in long-term isolation on an island off the coast of Australia (K'gari). We show that these animals are beset by very low genetic diversity, likely the result of extensive inbreeding, and an elevated number of deleterious homozygotes. However, our results suggest that these dingoes are likely purging highly deleterious alleles, which may have allowed them to persist long term despite their extremely small population (<200 individuals).
Collapse
|
2
|
Schmökel H, Farrell A, Balisi MF. Subchondral defects resembling osteochondrosis dissecans in joint surfaces of the extinct saber-toothed cat Smilodon fatalis and dire wolf Aenocyon dirus. PLoS One 2023; 18:e0287656. [PMID: 37436967 DOI: 10.1371/journal.pone.0287656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/10/2023] [Indexed: 07/14/2023] Open
Abstract
Skeletal disease may hamper the behavior of large predators both living and extinct. We investigated the prevalence of osteochondrosis dissecans (OCD), a developmental bone disease affecting the joints, in two Ice Age predators: the saber-toothed cat Smilodon fatalis and dire wolf Aenocyon dirus. As published cases in modern Felidae and wild Canidae are rare, we predicted that subchondral defects resembling OCD would be rare in the extinct predators. We examined limb joints in juvenile and adult S. fatalis: 88 proximal humeri (shoulder), 834 distal femora (stifle), and 214 proximal tibiae. We also examined limb joints in juvenile and adult A. dirus: 242 proximal humeri, 266 distal femora, and 170 proximal tibiae. All specimens are from the Late Pleistocene Rancho La Brea fossil locality in Los Angeles, California, USA. While the Smilodon shoulder and tibia showed no subchondral defects, subchondral defects in the Smilodon femur had a prevalence of 6%; most defects were small (<7mm); and nine adult stifles with defects also showed osteoarthritis. Subchondral defects in the A. dirus femur had a prevalence of 2.6%; most defects were large (>12mm); and five stifles further developed mild osteoarthritis. Subchondral defects in the A. dirus shoulder had a prevalence of 4.5%; most defects were small, and three shoulders developed moderate osteoarthritis. No defects were found in the A. dirus tibia. Contrary to our prediction, we found a high prevalence of subchondral defects in the stifle and shoulder of S. fatalis and A. dirus resembling OCD found in humans and other mammals. As modern dogs affected by OCD are highly inbred, this high prevalence in the fossil taxa may suggest that they experienced inbreeding as they approached extinction. The deep-time history of this disease supports the need for monitoring of animal domestication, as well as conservation, to avoid unexpected surges in OCD under conditions like inbreeding.
Collapse
Affiliation(s)
- Hugo Schmökel
- Evidensia Academy, Division of Orthopaedics, Stockholm, Sweden
| | - Aisling Farrell
- La Brea Tar Pits and Museum, National History Museums of Los Angeles County, Los Angeles, California, United States of America
| | - Mairin F Balisi
- La Brea Tar Pits and Museum, National History Museums of Los Angeles County, Los Angeles, California, United States of America
- Raymond M. Alf Museum of Palaeontology, Claremont, California, United States of America
| |
Collapse
|
3
|
Wikenros C, Di Bernardi C, Zimmermann B, Åkesson M, Demski M, Flagstad Ø, Mattisson J, Tallian A, Wabakken P, Sand H. Scavenging patterns of an inbred wolf population in a landscape with a pulse of human-provided carrion. Ecol Evol 2023; 13:e10236. [PMID: 37415640 PMCID: PMC10319521 DOI: 10.1002/ece3.10236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 04/28/2023] [Accepted: 06/13/2023] [Indexed: 07/08/2023] Open
Abstract
Scavenging is an important part of food acquisition for many carnivore species that switch between scavenging and predation. In landscapes with anthropogenic impact, humans provide food that scavenging species can utilize. We quantified the magnitude of killing versus scavenging by gray wolves (Canis lupus) in Scandinavia where humans impact the ecosystem through hunter harvest, land use practices, and infrastructure. We investigated the cause of death of different animals utilized by wolves, and examined how the proportion of their consumption time spent scavenging was influenced by season, wolf social affiliation, level of inbreeding, density of moose (Alces alces) as their main prey, density of brown bear (Ursus arctos) as an intraguild competitor, and human density. We used data from 39 GPS-collared wolves covering 3198 study days (2001-2019), including 14,205 feeding locations within space-time clusters, and 1362 carcasses utilized by wolves. Most carcasses were wolf-killed (80.5%) while a small part had died from other natural causes (1.9%). The remaining had either anthropogenic mortality causes (4.7%), or the cause of death was unknown (12.9%). Time spent scavenging was higher during winter than during summer and autumn. Solitary wolves spent more time scavenging than pack-living individuals, likely because individual hunting success is lower than pack success. Scavenging time increased with the mean inbreeding coefficient of the adult wolves, possibly indicating that more inbred individuals resort to scavenging, which requires less body strength. There was weak evidence for competition between wolves and brown bears as well as a positive relationship between human density and time spent scavenging. This study shows how both intrinsic and extrinsic factors drive wolf scavenging behavior, and that despite a high level of inbreeding and access to carrion of anthropogenic origin, wolves mainly utilized their own kills.
Collapse
Affiliation(s)
- Camilla Wikenros
- Grimsö Wildlife Research Station, Department of EcologySwedish University of Agricultural SciencesRiddarhyttanSweden
| | - Cecilia Di Bernardi
- Grimsö Wildlife Research Station, Department of EcologySwedish University of Agricultural SciencesRiddarhyttanSweden
- Department of Biology and Biotechnologies “Charles Darwin”University of Rome La SapienzaRomeItaly
| | - Barbara Zimmermann
- Faculty of Applied Ecology, Agricultural Sciences and BiotechnologyInland Norway University of Applied SciencesElverumNorway
| | - Mikael Åkesson
- Grimsö Wildlife Research Station, Department of EcologySwedish University of Agricultural SciencesRiddarhyttanSweden
| | - Maike Demski
- County Administrative Board of NorrbottenLuleåSweden
| | | | - Jenny Mattisson
- Norwegian Institute for Nature Research (NINA)TrondheimNorway
| | - Aimee Tallian
- Norwegian Institute for Nature Research (NINA)TrondheimNorway
| | - Petter Wabakken
- Faculty of Applied Ecology, Agricultural Sciences and BiotechnologyInland Norway University of Applied SciencesElverumNorway
| | - Håkan Sand
- Grimsö Wildlife Research Station, Department of EcologySwedish University of Agricultural SciencesRiddarhyttanSweden
| |
Collapse
|
4
|
Smeds L, Ellegren H. From high masked to high realized genetic load in inbred Scandinavian wolves. Mol Ecol 2022; 32:1567-1580. [PMID: 36458895 DOI: 10.1111/mec.16802] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 11/17/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022]
Abstract
When new mutations arise at functional sites they are more likely to impair than improve fitness. If not removed by purifying selection, such deleterious mutations will generate a genetic load that can have negative fitness effects in small populations and increase the risk of extinction. This is relevant for the highly inbred Scandinavian wolf (Canis lupus) population, founded by only three wolves in the 1980s and suffering from inbreeding depression. We used functional annotation and evolutionary conservation scores to study deleterious variation in a total of 209 genomes from both the Scandinavian and neighbouring wolf populations in northern Europe. The masked load (deleterious mutations in heterozygote state) was highest in Russia and Finland with deleterious alleles segregating at lower frequency than neutral variation. Genetic drift in the Scandinavian population led to the loss of ancestral alleles, fixation of deleterious variants and a significant increase in the per-individual realized load (deleterious mutations in homozygote state; an increase by 45% in protein-coding genes) over five generations of inbreeding. Arrival of immigrants gave a temporary genetic rescue effect with ancestral alleles re-entering the population and thereby shifting deleterious alleles from homozygous into heterozygote genotypes. However, in the absence of permanent connectivity to Finnish and Russian populations, inbreeding has then again led to the exposure of deleterious mutations. These observations provide genome-wide insight into the magnitude of genetic load and genetic rescue at the molecular level, and in relation to population history. They emphasize the importance of securing gene flow in the management of endangered populations.
Collapse
Affiliation(s)
- Linnéa Smeds
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Hans Ellegren
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| |
Collapse
|
5
|
Wilson LAB. Developmental instability in domesticated mammals. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2022; 338:484-494. [PMID: 34813170 DOI: 10.1002/jez.b.23108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
Measures of fluctuating asymmetry (FA) have been adopted widely as an estimate of developmental instability. Arising from various sources of stress, developmental instability is associated with an organism's capacity to maintain fitness. The process of domestication has been framed as an environmental stress with human-specified parameters, suggesting that FA may manifest to a larger degree among domesticates compared to their wild relatives. This study used three-dimensional geometric morphometric landmark data to (a) quantify the amount of FA in the cranium of six domestic mammal species and their wild relatives and, (b) provide novel assessment of the commonalities and differences across domestic/wild pairs concerning the extent to which random variation arising from the developmental system assimilates into within-population variation. The majority of domestic mammals showed greater disparity for asymmetric shape, however, only two forms (Pig, Dog) showed significantly higher disparity as well as a higher degree of asymmetry compared to their wild counterparts (Wild Boar, Wolf). Contra to predictions, most domestic and wild forms did not show a statistically significant correspondence between symmetric shape variation and FA, however, a moderate correlation value was recorded for most pairs (r-partial least squares >0.5). Within pairs, domestic and wild forms showed similar correlation magnitudes for the relationship between the asymmetric and symmetric components. In domesticates, new variation may therefore retain a general, conserved pattern in the gross structuring of the cranium, whilst also being a source for response to selection on specific features.
Collapse
Affiliation(s)
- Laura A B Wilson
- School of Archaeology and Anthropology, The Australian National University, Canberra, ACT, Australia
- School of Biological, Earth, and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| |
Collapse
|
6
|
Viluma A, Flagstad Ø, Åkesson M, Wikenros C, Sand H, Wabakken P, Ellegren H. Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population. Genome Res 2022; 32:449-458. [PMID: 35135873 PMCID: PMC8896455 DOI: 10.1101/gr.276070.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 12/30/2021] [Indexed: 11/25/2022]
Abstract
Genetic drift can dramatically change allele frequencies in small populations and lead to reduced levels of genetic diversity, including loss of segregating variants. However, there is a shortage of quantitative studies of how genetic diversity changes over time in natural populations, especially on genome-wide scales. Here, we analyzed whole-genome sequences from 76 wolves of a highly inbred Scandinavian population, founded by only one female and two males, sampled over a period of 30 yr. We obtained chromosome-level haplotypes of all three founders and found that 10%–24% of their diploid genomes had become lost after about 20 yr of inbreeding (which approximately corresponds to five generations). Lost haplotypes spanned large genomic regions, as expected from the amount of recombination during this limited time period. Altogether, 160,000 SNP alleles became lost from the population, which may include adaptive variants as well as wild-type alleles masking recessively deleterious alleles. Although not sampled, we could indirectly infer that the two male founders had megabase-sized runs of homozygosity and that all three founders showed significant haplotype sharing, meaning that there were on average only 4.2 unique haplotypes in the six copies of each autosome that the founders brought into the population. This violates the assumption of unrelated founder haplotypes often made in conservation and management of endangered species. Our study provides a novel view of how whole-genome resequencing of temporally stratified samples can be used to visualize and directly quantify the consequences of genetic drift in a small inbred population.
Collapse
|
7
|
Šnjegota D, Stronen AV, Boljte B, Ćirović D, Djan M, Huber D, Jelenčič M, Konec M, Kusak J, Skrbinšek T. Population genetic structure of wolves in the northwestern Dinaric-Balkan region. Ecol Evol 2021; 11:18492-18504. [PMID: 35003687 PMCID: PMC8717286 DOI: 10.1002/ece3.8444] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 11/29/2022] Open
Abstract
The Balkan Peninsula and the Dinaric Mountains possess extraordinary biodiversity and support one of the largest and most diverse wolf (Canis lupus) populations in Europe. Results obtained with diverse genetic markers show west-east substructure, also seen in various other species, despite the absence of obvious barriers to movement. However, the spatial extent of the genetic clusters remains unresolved, and our aim was to combine fine-scale sampling with population and spatial genetic analyses to improve resolution of wolf genetic clusters. We analyzed 16 autosomal microsatellites from 255 wolves sampled in Slovenia, Croatia, Bosnia and Herzegovina (BIH), and Serbia and documented three genetic clusters. These comprised (1) Slovenia and the regions of Gorski kotar and Lika in Croatia, (2) the region of Dalmatia in southern Croatia and BIH, and (3) Serbia. When we mapped the clusters geographically, we observed west-east genetic structure across the study area, together with some specific structure in BIH-Dalmatia. We observed that cluster 1 had a smaller effective population size, consistent with earlier reports of population recovery since the 1980s. Our results provide foundation for future genomic studies that would further resolve the observed west-east population structure and its evolutionary history in wolves and other taxa in the region and identify focal areas for habitat conservation. They also have immediate importance for conservation planning for the wolves in one of the most important parts of the species' European range.
Collapse
Affiliation(s)
- Dragana Šnjegota
- Department of Biology and EcologyFaculty of Natural Sciences and MathematicsUniversity of Banja LukaBanja LukaBosnia and Herzegovina
| | - Astrid Vik Stronen
- Department of BiologyBiotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
| | - Barbara Boljte
- Department of BiologyBiotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
| | - Duško Ćirović
- Faculty of BiologyUniversity of BelgradeBelgradeSerbia
| | - Mihajla Djan
- Department of Biology and EcologyFaculty of SciencesUniversity of Novi SadNovi SadSerbia
| | - Djuro Huber
- Department of BiologyFaculty of Veterinary MedicineUniversity of ZagrebZagrebCroatia
| | - Maja Jelenčič
- Department of BiologyBiotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
| | - Marjeta Konec
- Department of BiologyBiotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
| | - Josip Kusak
- Department of BiologyFaculty of Veterinary MedicineUniversity of ZagrebZagrebCroatia
| | - Tomaž Skrbinšek
- Department of BiologyBiotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
| |
Collapse
|
8
|
Martins FP, Souza EC, Bernardes FCS, Abidu-Figueiredo M, Kasper CB, de Souza-Junior P. Anatomical variations in cervical vertebrae in two species of neotropical canids: What is the meaning? Anat Histol Embryol 2020; 50:212-217. [PMID: 32857880 DOI: 10.1111/ahe.12609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 07/03/2020] [Accepted: 08/05/2020] [Indexed: 11/30/2022]
Abstract
Anatomical variation in wild canids is rarely described. Altered shapes, uni- or bilaterally situated, were observed in ventral laminae of C6 and/or in C7 vertebral body of two fox species: Lycalopex gymnocercus and Cerdocyon thous. The specimens were young adults, collected dead on highways in southern Brazil. Deformities were considered anatomical variations because apparently there was no interference in function. The occurrence of such variations in two related species from the same area can suggest an environmental common cause rather than genetic issues. Future studies may deepen the understanding between cause and effect of these vertebral deformities in wild canids.
Collapse
Affiliation(s)
- Felipe Pratalli Martins
- Laboratory of Animal Anatomy, Federal University of Pampa (UNIPAMPA), Uruguaiana, RS, Brazil
| | - Erick Candiota Souza
- Laboratory of Animal Anatomy, Federal University of Pampa (UNIPAMPA), Uruguaiana, RS, Brazil
| | | | - Marcelo Abidu-Figueiredo
- Department of Animal and Human Anatomy, Federal Rural University of Rio de Janeiro (UFRRJ), Seropédica, RJ
| | - Carlos Benhur Kasper
- Birds and Mammals Laboratory, Federal University of Pampa (UNIPAMPA), São Gabriel, RS, Brazil
| | - Paulo de Souza-Junior
- Laboratory of Animal Anatomy, Federal University of Pampa (UNIPAMPA), Uruguaiana, RS, Brazil
| |
Collapse
|
9
|
Robinson JA, Räikkönen J, Vucetich LM, Vucetich JA, Peterson RO, Lohmueller KE, Wayne RK. Genomic signatures of extensive inbreeding in Isle Royale wolves, a population on the threshold of extinction. SCIENCE ADVANCES 2019; 5:eaau0757. [PMID: 31149628 PMCID: PMC6541468 DOI: 10.1126/sciadv.aau0757] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 04/23/2019] [Indexed: 05/08/2023]
Abstract
The observation that small isolated populations often suffer reduced fitness from inbreeding depression has guided conservation theory and practice for decades. However, investigating the genome-wide dynamics associated with inbreeding depression in natural populations is only now feasible with relatively inexpensive sequencing technology and annotated reference genomes. To characterize the genome-wide effects of intense inbreeding and isolation, we performed whole-genome sequencing and morphological analysis of an iconic inbred population, the gray wolves (Canis lupus) of Isle Royale. Through population genetic simulations and comparison with wolf genomes from a variety of demographic histories, we find evidence that severe inbreeding depression in this population is due to increased homozygosity of strongly deleterious recessive mutations. Our results have particular relevance in light of the recent translocation of wolves from the mainland to Isle Royale, as well as broader implications for management of genetic variation in the fragmented landscape of the modern world.
Collapse
Affiliation(s)
- Jacqueline A. Robinson
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
- Corresponding author.
| | - Jannikke Räikkönen
- Department of Environmental Research and Monitoring, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden
| | - Leah M. Vucetich
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - John A. Vucetich
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Rolf O. Peterson
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| |
Collapse
|
10
|
Latham KJ, Losey RJ. Spondylosis deformans as an indicator of transport activities in archaeological dogs: A systematic evaluation of current methods for assessing archaeological specimens. PLoS One 2019; 14:e0214575. [PMID: 30995245 PMCID: PMC6469781 DOI: 10.1371/journal.pone.0214575] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 03/16/2019] [Indexed: 11/18/2022] Open
Abstract
Over the past several decades archaeologists have used the spinal pathology spondylosis deformans as an indicator that archaeological dogs were used to pull or carry loads. This interpretive approach is largely based upon observations of prehistoric dog remains and archaeologist's interpretations of veterinary literature on recent sled dogs and other draft animals. However, no comparative large-scale studies of the occurrence of spondylosis deformans in wild canids, transport dogs, and dogs never involved in pulling or carrying loads have been published. To evaluate the reliability of spondylosis deformans in archaeological dogs as an indicator of participation in transport activities, 136 modern non-transport dogs, 19 sled dogs, and 241 wolves were systematically analyzed for the occurrence of spondylosis deformans. Our results indicate this pathology is not a reliable skeletal indicator of dog transport because the disease is prevalent in both dogs and wolves, regardless of their occupational histories. Numerous factors correlate with the occurrence and manifestation of this disease in canids, including age, body size, sex, and inbreeding. As such, it remains extremely challenging to identify specific etiologies for spondylosis deformans in archaeological specimens.
Collapse
Affiliation(s)
- Katherine J. Latham
- Department of Anthropology, University of Alberta, Edmonton, Alberta, Canada
- * E-mail:
| | - Robert J. Losey
- Department of Anthropology, University of Alberta, Edmonton, Alberta, Canada
| |
Collapse
|
11
|
Mpenda F, Schilling M, Campbell Z, Mngumi E, Buza J. The genetic diversity of local african chickens: A potential for selection of chickens resistant to viral infections. J APPL POULTRY RES 2019. [DOI: 10.3382/japr/pfy063] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
|
12
|
Robinson JA, Brown C, Kim BY, Lohmueller KE, Wayne RK. Purging of Strongly Deleterious Mutations Explains Long-Term Persistence and Absence of Inbreeding Depression in Island Foxes. Curr Biol 2018; 28:3487-3494.e4. [PMID: 30415705 DOI: 10.1016/j.cub.2018.08.066] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Revised: 07/03/2018] [Accepted: 08/31/2018] [Indexed: 11/19/2022]
Abstract
The recovery and persistence of rare and endangered species are often threatened by genetic factors, such as the accumulation of deleterious mutations, loss of adaptive potential, and inbreeding depression [1]. Island foxes (Urocyon littoralis), the dwarfed descendants of mainland gray foxes (Urocyon cinereoargenteus), have inhabited California's Channel Islands for >9,000 years [2-4]. Previous genomic analyses revealed that island foxes have exceptionally low levels of diversity and elevated levels of putatively deleterious variation [5]. Nonetheless, all six populations have persisted for thousands of generations, and several populations rebounded rapidly after recent severe bottlenecks [6, 7]. Here, we combine morphological and genomic data with population-genetic simulations to determine the mechanism underlying the enigmatic persistence of these foxes. First, through analysis of genomes from 1929 to 2009, we show that island foxes have remained at small population sizes with low diversity for many generations. Second, we present morphological data indicating an absence of inbreeding depression in island foxes, confirming that they are not afflicted with congenital defects common to other small and inbred populations. Lastly, our population-genetic simulations suggest that long-term small population size results in a reduced burden of strongly deleterious recessive alleles, providing a mechanism for the absence of inbreeding depression in island foxes. Importantly, the island fox illustrates a scenario in which genetic restoration through human-assisted gene flow could be a counterproductive or even harmful conservation strategy. Our study sheds light on the puzzle of island fox persistence, a unique success story that provides a model for the preservation of small populations.
Collapse
Affiliation(s)
- Jacqueline A Robinson
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Caitlin Brown
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Bernard Y Kim
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| |
Collapse
|
13
|
Gómez-Sánchez D, Olalde I, Sastre N, Enseñat C, Carrasco R, Marques-Bonet T, Lalueza-Fox C, Leonard JA, Vilà C, Ramírez O. On the path to extinction: Inbreeding and admixture in a declining grey wolf population. Mol Ecol 2018; 27:3599-3612. [DOI: 10.1111/mec.14824] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 07/13/2018] [Accepted: 07/16/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Daniel Gómez-Sánchez
- Ciencies Experimetals i de la Salut; Institut de Biologia Evolutiva (Universitat Pompeu Fabra - CSIC); Barcelona Spain
| | - Iñigo Olalde
- Ciencies Experimetals i de la Salut; Institut de Biologia Evolutiva (Universitat Pompeu Fabra - CSIC); Barcelona Spain
| | - Natalia Sastre
- Departament de Ciència Animal i dels Aliments; Facultat de Veterinària, Servei Veterinari de Genètica Molecular; Universitat Autònoma de Barcelona; Bellaterra Spain
- Department of Ecology and Evolutionary Biology; UCLA; Los Angeles California
| | | | - Rafael Carrasco
- Departamento de Biologia Animal, Biologia Vegetal y Ecología; Universidad de Jaén (UJA); Jaen Spain
| | - Tomas Marques-Bonet
- Ciencies Experimetals i de la Salut; Institut de Biologia Evolutiva (Universitat Pompeu Fabra - CSIC); Barcelona Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA); Barcelona Spain
- Centro Nacional de Análisis Genómico (CNAG); Barcelona Spain
| | - Carles Lalueza-Fox
- Ciencies Experimetals i de la Salut; Institut de Biologia Evolutiva (Universitat Pompeu Fabra - CSIC); Barcelona Spain
| | - Jennifer A. Leonard
- Conservation and Evolutionary Genetics Group; Estación Biológica de Doñana (EBD-CSIC); Seville Spain
| | - Carles Vilà
- Conservation and Evolutionary Genetics Group; Estación Biológica de Doñana (EBD-CSIC); Seville Spain
| | - Oscar Ramírez
- Ciencies Experimetals i de la Salut; Institut de Biologia Evolutiva (Universitat Pompeu Fabra - CSIC); Barcelona Spain
- Vetgenomics S.L.; Bellaterra Spain
| |
Collapse
|
14
|
Hindrikson M, Remm J, Pilot M, Godinho R, Stronen AV, Baltrūnaité L, Czarnomska SD, Leonard JA, Randi E, Nowak C, Åkesson M, López-Bao JV, Álvares F, Llaneza L, Echegaray J, Vilà C, Ozolins J, Rungis D, Aspi J, Paule L, Skrbinšek T, Saarma U. Wolf population genetics in Europe: a systematic review, meta-analysis and suggestions for conservation and management. Biol Rev Camb Philos Soc 2016; 92:1601-1629. [PMID: 27682639 DOI: 10.1111/brv.12298] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 08/01/2016] [Accepted: 08/26/2016] [Indexed: 01/04/2023]
Abstract
The grey wolf (Canis lupus) is an iconic large carnivore that has increasingly been recognized as an apex predator with intrinsic value and a keystone species. However, wolves have also long represented a primary source of human-carnivore conflict, which has led to long-term persecution of wolves, resulting in a significant decrease in their numbers, genetic diversity and gene flow between populations. For more effective protection and management of wolf populations in Europe, robust scientific evidence is crucial. This review serves as an analytical summary of the main findings from wolf population genetic studies in Europe, covering major studies from the 'pre-genomic era' and the first insights of the 'genomics era'. We analyse, summarize and discuss findings derived from analyses of three compartments of the mammalian genome with different inheritance modes: maternal (mitochondrial DNA), paternal (Y chromosome) and biparental [autosomal microsatellites and single nucleotide polymorphisms (SNPs)]. To describe large-scale trends and patterns of genetic variation in European wolf populations, we conducted a meta-analysis based on the results of previous microsatellite studies and also included new data, covering all 19 European countries for which wolf genetic information is available: Norway, Sweden, Finland, Estonia, Latvia, Lithuania, Poland, Czech Republic, Slovakia, Germany, Belarus, Russia, Italy, Croatia, Bulgaria, Bosnia and Herzegovina, Greece, Spain and Portugal. We compared different indices of genetic diversity in wolf populations and found a significant spatial trend in heterozygosity across Europe from south-west (lowest genetic diversity) to north-east (highest). The range of spatial autocorrelation calculated on the basis of three characteristics of genetic diversity was 650-850 km, suggesting that the genetic diversity of a given wolf population can be influenced by populations up to 850 km away. As an important outcome of this synthesis, we discuss the most pressing issues threatening wolf populations in Europe, highlight important gaps in current knowledge, suggest solutions to overcome these limitations, and provide recommendations for science-based wolf conservation and management at regional and Europe-wide scales.
Collapse
Affiliation(s)
- Maris Hindrikson
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51014, Tartu, Estonia
| | - Jaanus Remm
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51014, Tartu, Estonia
| | - Malgorzata Pilot
- School of Life Sciences, University of Lincoln, Green Lane, LN6 7DL, Lincoln, UK
| | - Raquel Godinho
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Astrid Vik Stronen
- Department of Chemistry and Bioscience, Section of Biology and Environmental Science, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg Øst, Denmark
| | - Laima Baltrūnaité
- Laboratory of Mammalian Biology, Nature Research Centre, Akademijos 2, 08412, Vilnius, Lithuania
| | - Sylwia D Czarnomska
- Mammal Research Institute Polish Academy of Sciences, Waszkiewicza 1, 17-230, Białowieża, Poland
| | - Jennifer A Leonard
- Department of Integrative Ecology, Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Avd. Americo Vespucio s/n, 41092, Seville, Spain
| | - Ettore Randi
- Department of Chemistry and Bioscience, Section of Biology and Environmental Science, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg Øst, Denmark
- Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), 40064, Ozzano dell'Emilia, Bologna, Italy
| | - Carsten Nowak
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Clamecystrasse 12, 63571, Gelnhausen, Germany
| | - Mikael Åkesson
- Department of Ecology, Grimsö Wildlife Research Station, Swedish University of Agricultural Sciences, SE-730 91, Riddarhyttan, Sweden
| | | | - Francisco Álvares
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - Luis Llaneza
- ARENA Asesores en Recursos Naturales S.L. c/Perpetuo Socorro, n° 12 Entlo 2B, 27003, Lugo, Spain
| | - Jorge Echegaray
- Department of Integrative Ecology, Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Avd. Americo Vespucio s/n, 41092, Seville, Spain
| | - Carles Vilà
- Department of Integrative Ecology, Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Avd. Americo Vespucio s/n, 41092, Seville, Spain
| | - Janis Ozolins
- Latvian State Forest Research Institute "Silava", Rigas iela 111, LV-2169, Salaspils, Latvia
| | - Dainis Rungis
- Latvian State Forest Research Institute "Silava", Rigas iela 111, LV-2169, Salaspils, Latvia
| | - Jouni Aspi
- Department of Genetics and Physiology, University of Oulu, 90014, Oulu, Finland
| | - Ladislav Paule
- Department of Phytology, Faculty of Forestry, Technical University, T.G. Masaryk str. 24, SK-96053, Zvolen, Slovakia
| | - Tomaž Skrbinšek
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Vecna pot 111, 1000, Ljubljana, Slovenia
| | - Urmas Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51014, Tartu, Estonia
| |
Collapse
|
15
|
Janssens LAA, Street M, Miller R, Hazewinkel HAW, Giemsch L, Schmitz R. The oldest case yet reported of osteoarthritis in a dog: an archaeological and radiological evaluation. J Small Anim Pract 2016; 57:568-574. [PMID: 27581723 DOI: 10.1111/jsap.12548] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 04/22/2016] [Accepted: 05/06/2016] [Indexed: 11/28/2022]
Abstract
A century ago the remains of a dog skeleton were found in an archaeological double human burial, near Bonn-Oberkassel (Germany). Recent re-examination of the dog remains revealed that they were about 14,500 years old. Based on the growth plates, the animal was considered to be approximately 7·5 months old at the time of death. Based on the minimal humeral diameter, it was calculated that it was approximately 0·47 m tall at the shoulder and weighed approximately 15·7 kg. The right proximal ulna of this skeleton showed osteoarthritis, manifested by an osteophyte of 5×3×1·5 mm3 at its cranial edge, with no identified primary developmental causes for osteoarthritis. Osteochondritis dissecans, joint incongruity and trauma are possible aetiologies. The left ulna did not reveal any abnormalities.
Collapse
Affiliation(s)
- L A A Janssens
- Clinic for Orthopaedic Surgery of Companion Animals, 3068SB Rotterdam, The Netherlands. .,Department of Archaeology, University of Leiden, 2333 CC Leiden, The Netherlands.
| | - M Street
- Monrepos Archaeological Research Centre and Museum for Human Behavioural Evolution, 56567 Neuwied, Germany
| | - R Miller
- Service of Prehistory, University of Liège, 4000 Liège, Belgium
| | - H A W Hazewinkel
- Department of Clinical Sciences of Companion Animals, Utrecht University, 3508TD Utrecht, The Netherlands
| | - L Giemsch
- Archäologisches Museum Frankfurt, Karmelitergasse 1D-60311 Frankfurt am Main, Germany
| | - R Schmitz
- LVR-Landesmuseum Bonn, Rheinisches Landesmuseum für Archäologie, Kunst- und Kulturgeschichte, Bachstraße 5-953115 Bonn, Germany
| |
Collapse
|
16
|
Trask AE, Bignal EM, McCracken DI, Monaghan P, Piertney SB, Reid JM. Evidence of the phenotypic expression of a lethal recessive allele under inbreeding in a wild population of conservation concern. J Anim Ecol 2016; 85:879-91. [PMID: 26996516 DOI: 10.1111/1365-2656.12503] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 01/15/2016] [Indexed: 11/27/2022]
Abstract
Deleterious recessive alleles that are masked in outbred populations are predicted to be expressed in small, inbred populations, reducing both individual fitness and population viability. However, there are few definitive examples of phenotypic expression of lethal recessive alleles under inbreeding conditions in wild populations. Studies that demonstrate the action of such alleles, and infer their distribution and dynamics, are required to understand their potential impact on population viability and inform management responses. The Scottish population of red-billed choughs (Pyrrhocorax pyrrhocorax), which currently totals <60 breeding pairs and is of major conservation concern, has recently been affected by lethal blindness in nestlings. We used family data to show that the pattern of occurrence of blindness within and across affected families that produced blind nestlings was exactly 0·25, matching that expected given a single-locus autosomal lethal recessive allele. Furthermore, the observed distribution of blind nestlings within affected families did not differ from that expected given Mendelian inheritance of such an allele. Relatedness estimates showed that individuals from affected families were not more closely related to each other than they were to individuals from unaffected families that did not produce blind nestlings. Blind individuals tended to be less heterozygous than non-blind individuals, as expected if blindness was caused by the expression of a recessive allele under inbreeding. However, there was no difference in the variance in heterozygosity estimates, suggesting that some blind individuals were relatively outbred. These results suggest carriers of the blindness allele may be widely distributed across contemporary families rather than restricted to a single family lineage, implying that the allele has persisted across multiple generations. Blindness occurred at low frequency (affecting 1·6% of observed nestlings since 1981). However, affected families had larger initial brood sizes than unaffected families. Such high fecundity of carriers of a lethal recessive allele might reflect overdominance, potentially reducing purging and increasing allele persistence probability. We thereby demonstrate the phenotypic expression of a lethal recessive allele in a wild population of conservation concern, and provide a general framework for inferring allele distribution and persistence and informing management responses.
Collapse
Affiliation(s)
- Amanda E Trask
- Institute of Biological & Environmental Sciences, School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
| | - Eric M Bignal
- Scottish Chough Study Group, Kindrochaid, Bridgend, Isle of Islay, Argyll, PA44 7PT, UK
| | - Davy I McCracken
- Future Farming Systems, Scotland's Rural College, Auchincruive, Ayr, KA6 5HW, UK
| | - Pat Monaghan
- College of Medical, Veterinary & Life Sciences, University of Glasgow, Graham Kerr Building, Glasgow, G12 8QQ, UK
| | - Stuart B Piertney
- Institute of Biological & Environmental Sciences, School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
| | - Jane M Reid
- Institute of Biological & Environmental Sciences, School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
| |
Collapse
|
17
|
Genetic contribution from a zoo population can increase genetic variation in the highly inbred wild Swedish wolf population. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0738-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
18
|
Driscoll CC, Driscoll JG, Hazekamp C, Mitton JB, Wehausen JD. A tale of two markers: Population genetics of colorado rocky mountain bighorn sheep estimated from microsatellite and mitochondrial data. J Wildl Manage 2015. [DOI: 10.1002/jwmg.895] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Catherine C. Driscoll
- Department of Ecology and Evolutionary Biology; University of Colorado; Campus Box 224, Boulder CO 80309-0334
| | | | - Corey Hazekamp
- University of Massachusetts; 100 Morrissey Boulevard, Boston MA 02125-3393
| | - Jeffry B. Mitton
- Department of Ecology and Evolutionary Biology; University of Colorado; Campus Box 224, Boulder CO 80309-0334
| | - John D. Wehausen
- University of California San Diego; White Mountain Research Station; 3000 East Line Street, Bishop CA 93514
| |
Collapse
|
19
|
Hössjer O, Olsson F, Laikre L, Ryman N. Metapopulation inbreeding dynamics, effective size and subpopulation differentiation--A general analytical approach for diploid organisms. Theor Popul Biol 2015; 102:40-59. [PMID: 25875853 DOI: 10.1016/j.tpb.2015.03.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 03/18/2015] [Accepted: 03/23/2015] [Indexed: 11/26/2022]
Abstract
Motivated by problems in conservation biology we study genetic dynamics in structured populations of diploid organisms (monoecious or dioecious). Our analysis provides an analytical framework that unifies substantial parts of previous work in terms of exact identity by descent (IBD) and identity by state (IBS) recursions. We provide exact conditions under which two structured haploid and diploid populations are equivalent, and some sufficient conditions under which a dioecious diploid population can be treated as a monoecious diploid one. The IBD recursions are used for computing local and metapopulation inbreeding and coancestry effective population sizes and for predictions of several types of fixation indices over different time horizons.
Collapse
Affiliation(s)
- Ola Hössjer
- Department of Mathematics, Division of Mathematical Statistics, Stockholm University, SE 106 91 Stockholm, Sweden.
| | - Fredrik Olsson
- Department of Mathematics, Division of Mathematical Statistics, Stockholm University, SE 106 91 Stockholm, Sweden.
| | - Linda Laikre
- Department of Zoology, Division of Population Genetics, Stockholm University, SE 106 91 Stockholm, Sweden.
| | - Nils Ryman
- Department of Zoology, Division of Population Genetics, Stockholm University, SE 106 91 Stockholm, Sweden.
| |
Collapse
|
20
|
Tison JL, Blennow V, Palkopoulou E, Gustafsson P, Roos A, Dalén L. Population structure and recent temporal changes in genetic variation in Eurasian otters from Sweden. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0664-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
21
|
Räikkönen J, Vucetich JA, Vucetich LM, Peterson RO, Nelson MP. What the Inbred Scandinavian Wolf Population Tells Us about the Nature of Conservation. PLoS One 2013; 8:e67218. [PMID: 23805301 PMCID: PMC3689695 DOI: 10.1371/journal.pone.0067218] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2012] [Accepted: 05/19/2013] [Indexed: 11/17/2022] Open
Abstract
The genetic aspects of population health are critical, but frequently difficult to assess. Of concern has been the genetic constitution of Scandinavian wolves (Canis lupus), which represent an important case in conservation. We examined the incidence of different congenital anomalies for 171 Scandinavian wolves, including the immigrant founder female, born during a 32-year period between 1978 and 2010. The incidence of anomalies rose from 13% to 40% throughout the 32-year study period. Our ability to detect this increase was likely facilitated by having considered multiple kinds of anomaly. Many of the found anomalies are likely associated with inbreeding or some form of genetic deterioration. These observations have implications for understanding the conservation needs of Scandinavian wolves. Moreover, these observations and the history of managing Scandinavian wolves focus attention on a broader question, whether conservation is merely about avoiding extinction of remnant populations, or whether conservation also entails maintaining genetic aspects of population health.
Collapse
Affiliation(s)
- Jannikke Räikkönen
- Swedish Museum of Natural History, Department of Contaminant Research, Stockholm, Sweden
| | | | | | | | | |
Collapse
|
22
|
Laikre L, Jansson M, Allendorf FW, Jakobsson S, Ryman N. Hunting effects on favourable conservation status of highly inbred Swedish wolves. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2013; 27:248-253. [PMID: 23282216 DOI: 10.1111/j.1523-1739.2012.01965.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 08/01/2012] [Indexed: 06/01/2023]
Abstract
The wolf (Canis lupus) is classified as endangered in Sweden by the Swedish Species Information Centre, which is the official authority for threat classification. The present population, which was founded in the early 1980s, descends from 5 individuals. It is isolated and highly inbred, and on average individuals are more related than siblings. Hunts have been used by Swedish authorities during 2010 and 2011 to reduce the population size to its upper tolerable level of 210 wolves. European Union (EU) biodiversity legislation requires all member states to promote a concept called "favourable conservation status" (FCS) for a series of species including the wolf. Swedish national policy stipulates maintenance of viable populations with sufficient levels of genetic variation of all naturally occurring species. Hunting to reduce wolf numbers in Sweden is currently not in line with national and EU policy agreements and will make genetically based FCS criteria less achievable for this species. We suggest that to reach FCS for the wolf in Sweden the following criteria need to be met: (1) a well-connected, large, subdivided wolf population over Scandinavia, Finland, and the Russian Karelia-Kola region should be reestablished, (2) genetically effective size (Ne ) of this population is in the minimum range of Ne = 500-1000, (3) Sweden harbors a part of this total population that substantially contributes to the total Ne and that is large enough to not be classified as threatened genetically or according to IUCN criteria, and (4) average inbreeding levels in the Swedish population are <0.1.
Collapse
Affiliation(s)
- Linda Laikre
- Department of Zoology, Stockholm University, Stockholm, Sweden.
| | | | | | | | | |
Collapse
|
23
|
Jansson E, Ruokonen M, Kojola I, Aspi J. Rise and fall of a wolf population: genetic diversity and structure during recovery, rapid expansion and drastic decline. Mol Ecol 2012; 21:5178-93. [DOI: 10.1111/mec.12010] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 08/02/2012] [Accepted: 08/03/2012] [Indexed: 11/29/2022]
Affiliation(s)
- E. Jansson
- Department of Biology; University of Oulu; PO Box 3000; Oulu; FIN-90014; Finland
| | - M. Ruokonen
- Department of Biology; University of Oulu; PO Box 3000; Oulu; FIN-90014; Finland
| | - I. Kojola
- Finnish Game and Fisheries Research Institute; Rakentajantie 3; PO Box 413; Oulu; FIN-90014; Finland
| | - J. Aspi
- Department of Biology; University of Oulu; PO Box 3000; Oulu; FIN-90014; Finland
| |
Collapse
|
24
|
Geffen E, Kam M, Hefner R, Hersteinsson P, Angerbjörn A, Dalèn L, Fuglei E, Norèn K, Adams JR, Vucetich J, Meier TJ, Mech LD, Vonholdt BM, Stahler DR, Wayne RK. Kin encounter rate and inbreeding avoidance in canids. Mol Ecol 2011; 20:5348-58. [PMID: 22077191 DOI: 10.1111/j.1365-294x.2011.05358.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Mating with close kin can lead to inbreeding depression through the expression of recessive deleterious alleles and loss of heterozygosity. Mate selection may be affected by kin encounter rate, and inbreeding avoidance may not be uniform but associated with age and social system. Specifically, selection for kin recognition and inbreeding avoidance may be more developed in species that live in family groups or breed cooperatively. To test this hypothesis, we compared kin encounter rate and the proportion of related breeding pairs in noninbred and highly inbred canid populations. The chance of randomly encountering a full sib ranged between 1-8% and 20-22% in noninbred and inbred canid populations, respectively. We show that regardless of encounter rate, outside natal groups mates were selected independent of relatedness. Within natal groups, there was a significant avoidance of mating with a relative. Lack of discrimination against mating with close relatives outside packs suggests that the rate of inbreeding in canids is related to the proximity of close relatives, which could explain the high degree of inbreeding depression observed in some populations. The idea that kin encounter rate and social organization can explain the lack of inbreeding avoidance in some species is intriguing and may have implications for the management of populations at risk.
Collapse
Affiliation(s)
- Eli Geffen
- Department of Zoology, Tel Aviv University, Tel Aviv 69978, Israel.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
|
26
|
Spiering PA, Szykman Gunther M, Somers MJ, Wildt DE, Walters M, Wilson AS, Maldonado JE. Inbreeding, heterozygosity and fitness in a reintroduced population of endangered African wild dogs (Lycaon pictus). CONSERV GENET 2010. [DOI: 10.1007/s10592-010-0147-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
|
27
|
Hagenblad J, Olsson M, Parker HG, Ostrander EA, Ellegren H. Population genomics of the inbred Scandinavian wolf. Mol Ecol 2009; 18:1341-51. [PMID: 19368642 DOI: 10.1111/j.1365-294x.2009.04120.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The Scandinavian wolf population represents one of the genetically most well-characterized examples of a severely bottlenecked natural population (with only two founders), and of how the addition of new genetic material (one immigrant) can at least temporarily provide a 'genetic rescue'. However, inbreeding depression has been observed in this population and in the absence of additional immigrants, its long-term viability is questioned. To study the effects of inbreeding and selection on genomic diversity, we performed a genomic scan with approximately 250 microsatellite markers distributed across all autosomes and the X chromosome. We found linkage disequilibrium (LD) that extended up to distances of 50 Mb, exceeding that of most outbreeding species studied thus far. LD was particularly pronounced on the X chromosome. Overall levels of observed genomic heterozygosity did not deviate significantly from simulations based on known population history, giving no support for a general selection for heterozygotes. However, we found evidence supporting balancing selection at a number of loci and also evidence suggesting directional selection at other loci. For markers on chromosome 23, the signal of selection was particularly strong, indicating that purifying selection against deleterious alleles may have occurred even in this very small population. These data suggest that population genomics allows the exploration of the effects of neutral and non-neutral evolution on a finer scale than what has previously been possible.
Collapse
Affiliation(s)
- Jenny Hagenblad
- Department of Physics, Chemistry and Biology, Linköping University, Sweden
| | | | | | | | | |
Collapse
|
28
|
|
29
|
Aspi J, Roininen E, Kiiskilä J, Ruokonen M, Kojola I, Bljudnik L, Danilov P, Heikkinen S, Pulliainen E. Genetic structure of the northwestern Russian wolf populations and gene flow between Russia and Finland. CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9642-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
30
|
Vonholdt BM, Stahler DR, Smith DW, Earl DA, Pollinger JP, Wayne RK. The genealogy and genetic viability of reintroduced Yellowstone grey wolves. Mol Ecol 2008; 17:252-74. [PMID: 17877715 DOI: 10.1111/j.1365-294x.2007.03468.x] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The recovery of the grey wolf in Yellowstone National Park is an outstanding example of a successful reintroduction. A general question concerning reintroduction is the degree to which genetic variation has been preserved and the specific behavioural mechanisms that enhance the preservation of genetic diversity and reduce inbreeding. We have analysed 200 Yellowstone wolves, including all 31 founders, for variation in 26 microsatellite loci over the 10-year reintroduction period (1995-2004). The population maintained high levels of variation (1995 H(0) = 0.69; 2004 H(0) = 0.73) with low levels of inbreeding (1995 F(IS) = -0.063; 2004 F(IS) = -0.051) and throughout, the population expanded rapidly (N(1995) = 21; N(2004) = 169). Pedigree-based effective population size ratios did not vary appreciably over the duration of population expansion (1995 N(e)/N(g) = 0.29; 2000 N(e)/N(g) = 0.26; 2004 N(e)/N(g) = 0.33). We estimated kinship and found only two of 30 natural breeding pairs showed evidence of being related (average r = -0.026, SE = 0.03). We reconstructed the genealogy of 200 wolves based on genetic and field data and discovered that they avoid inbreeding through a wide variety of behavioural mechanisms including absolute avoidance of breeding with related pack members, male-biased dispersal to packs where they breed with nonrelatives, and female-biased subordinate breeding. We documented a greater diversity of such population assembly patterns in Yellowstone than previously observed in any other natural wolf population. Inbreeding avoidance is nearly absolute despite the high probability of within-pack inbreeding opportunities and extensive interpack kinship ties between adjacent packs. Simulations showed that the Yellowstone population has levels of genetic variation similar to that of a population managed for high variation and low inbreeding, and greater than that expected for random breeding within packs or across the entire breeding pool. Although short-term losses in variation seem minimal, future projections of the population at carrying capacity suggest significant inbreeding depression will occur without connectivity and migratory exchange with other populations.
Collapse
Affiliation(s)
- Bridgett M Vonholdt
- University of California, Los Angeles, Ecology and Evolutionary Biology, 621 Charles E. Young Dr South, Los Angeles, CA 90095, USA
| | | | | | | | | | | |
Collapse
|
31
|
Kirschning J, Zachos FE, Cirovic D, Radovic IT, Hmwe SS, Hartl GB. Population Genetic Analysis of Serbian Red Foxes (Vulpes vulpes) by Means of Mitochondrial Control Region Sequences. Biochem Genet 2007; 45:409-20. [PMID: 17265184 DOI: 10.1007/s10528-007-9082-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A population genetic analysis based on sequences of the mitochondrial control region in 110 red foxes from five sampling localities in northern Serbia was carried out. The analysis yielded nine different haplotypes. Neither haplotype phylogeny nor their distribution was in accordance with the geographic location of the populations. In particular, the data failed to detect an unequivocal influence of the two big rivers, the Danube and the Tisza, separating the populations studied. Population differentiation was altogether low, without any relationship to the rivers as possible migration barriers. Although the possibility of foxes crossing the rivers over bridges or by swimming, thus keeping up gene flow, cannot be ruled out, it is most probable that the control region sequences are not sensitive enough to resolve small-scale population relationships but rather show patterns determined by stochastic processes such as genetic drift or lineage sorting.
Collapse
Affiliation(s)
- Julia Kirschning
- Zoological Institute, Christian-Albrechts-University, Olshausenstrasse 40, 24118, Kiel, Germany
| | | | | | | | | | | |
Collapse
|
32
|
Bensch S, Andrén H, Hansson B, Pedersen HC, Sand H, Sejberg D, Wabakken P, Akesson M, Liberg O. Selection for heterozygosity gives hope to a wild population of inbred wolves. PLoS One 2006; 1:e72. [PMID: 17183704 PMCID: PMC1762340 DOI: 10.1371/journal.pone.0000072] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2006] [Accepted: 11/07/2006] [Indexed: 12/13/2022] Open
Abstract
Recent analyses have questioned the usefulness of heterozygosity estimates as measures of the inbreeding coefficient (f), a finding that may have dramatic consequences for the management of endangered populations. We confirm that f and heterozygosity is poorly correlated in a wild and highly inbred wolf population. Yet, our data show that for each level of f, it was the most heterozygous wolves that established themselves as breeders, a selection process that seems to have decelerated the loss of heterozygosity in the population despite a steady increase of f. The markers contributing to the positive relationship between heterozygosity and breeding success were found to be located on different chromosomes, but there was a substantial amount of linkage disequilibrium in the population, indicating that the markers are reflecting heterozygosity over relatively wide genomic regions. Following our results we recommend that management programs of endangered populations include estimates of both f and heterozygosity, as they may contribute with complementary information about population viability.
Collapse
Affiliation(s)
- Staffan Bensch
- Department of Animal Ecology, Lund University, Lund, Sweden.
| | | | | | | | | | | | | | | | | |
Collapse
|