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Penttinen I, Nebel C, Stjernberg T, Kvist L, Ponnikas S, Laaksonen T. Large-scale genotypic identification reveals density-dependent natal dispersal patterns in an elusive bird of prey. MOVEMENT ECOLOGY 2024; 12:16. [PMID: 38360667 PMCID: PMC10870540 DOI: 10.1186/s40462-023-00447-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 12/30/2023] [Indexed: 02/17/2024]
Abstract
BACKGROUND Natal dispersal, the distance between site of birth and site of first breeding, has a fundamental role in population dynamics and species' responses to environmental changes. Population density is considered a key driver of natal dispersal. However, few studies have been able to examine densities at both the natal and the settlement site, which is critical for understanding the role of density in dispersal. Additionally, the role of density on natal dispersal remains poorly understood in long-lived and slowly reproducing species, due to their prolonged dispersal periods and often elusive nature. We studied the natal dispersal of the white-tailed eagle (Haliaeetus albicilla) in response to local breeder densities. We investigated the effects of the number of active territories around the natal site on (a) natal dispersal distance and (b) the difference between natal and settlement site breeder density. We were interested in whether eagles showed tendencies of conspecific attraction (positive density-dependence) or intraspecific competition (negative density-dependence) and how this related to settlement site breeder density. METHODS We used a combination of long-term visual and genotypic identification to match individuals from their breeding site to their natal nest. We identified natal dispersal events for 355 individuals hatched between 1984 and 2015 in the Baltic Sea coast and Arctic areas of Finland. Of those, 251 were identified by their genotype. RESULTS Individuals born in high-density areas dispersed shorter distances than those born in low-density areas, but settled at lower density breeding sites in comparison to their natal site. Eagles born in low natal area densities dispersed farther but settled in higher density breeding sites compared to their natal site. CONCLUSIONS We show that eagles might be attracted by conspecifics (positive density-dependence) to identify high-quality habitats or find mates, but do not settle in the most densely populated areas. This indicates that natal dispersal is affected by an interplay of conspecific attraction and intraspecific competition, which has implications for population dynamics of white-tailed eagles, but also other top predators. Furthermore, our study demonstrates the value of long-term collection of both nestling and (non-invasive) adult DNA samples, and thereafter using genotype matching to identify individuals in long-lived and elusive species.
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Affiliation(s)
- Ida Penttinen
- Department of Biology, University of Turku, Turku, Finland.
| | - Carina Nebel
- Department of Biology, University of Turku, Turku, Finland
| | - Torsten Stjernberg
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Laura Kvist
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Suvi Ponnikas
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Toni Laaksonen
- Department of Biology, University of Turku, Turku, Finland
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Awadi A, Ben Slimen H, Smith S, Makni M, Suchentrunk F. Patterns of evolution in MHC class II DQA and DQB exon 2 genes of Alpine mountain hares, Lepus timidus varronis, and sympatric and parapatric brown hares, L. europaeus, from Switzerland. Immunogenetics 2024; 76:37-50. [PMID: 38114658 DOI: 10.1007/s00251-023-01328-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/14/2023] [Indexed: 12/21/2023]
Abstract
In natural populations, hybridization is known to occur between a wide range of species. However, its evolutionary significance is less clear. Genes involved in fighting pathogens are considered excellent candidates for studying adaptive introgression, although both introgression and balancing selection can generate similar patterns of diversity and differentiation. Here, we compared DQA and DQB MHC class II and microsatellite allelic diversity of sympatric and parapatric mountain (Lepus timidus) and brown hare (L. europaeus) populations from Switzerland. We detected higher genetic diversity in brown hares compared to mountain hares at both MHC and microsatellite loci. We consider the observed patterns of microsatellite diversity both for L. europaeus and L. timidus as result of stochastic demographic processes while the pattern of MHC polymorphism of the studied hare populations can be explained by pathogen-driven selection. Rare bidirectional gene flow between both hare species seems to occur specifically for MHC alleles. However, the high number of shared alleles showing similar high frequency in both species suggests that reciprocally exchanged MHC alleles are being maintained via balancing selection. Adaptation to similar pathogen communities can also lead to parallel selection of MHC alleles. Positive selection, recombination and mutations have played different roles in shaping the patterns of MHC allelic diversity in and differentiation between both species. Results for the latter evolutionary forces do not show a better matching between the sympatric populations compared to the parapatric ones, suggesting a minor role of introgression for the observed evolutionary patterns of the studied hare species.
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Affiliation(s)
- A Awadi
- Laboratory of Functional Physiology and Valorization of Bioresources, Higher Institute of Biotechnology of Béja, University of Jendouba, Béja, 9000, Tunisia
| | - H Ben Slimen
- Laboratory of Functional Physiology and Valorization of Bioresources, Higher Institute of Biotechnology of Béja, University of Jendouba, Béja, 9000, Tunisia.
| | - S Smith
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstrasse 1, Vienna, 1160, Austria
| | - M Makni
- Faculty of Sciences of Tunis, LR01ES05 Biochimie et Biotechnologie, University of Tunis El Manar, Tunis, 2092, Tunisia
| | - F Suchentrunk
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Savoyenstrasse 1, Vienna, 1160, Austria
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Byrne AW, Marnell F, Barrett D, Reid N, Hanna REB, McElroy MC, Casey M. Rabbit Haemorrhagic Disease Virus 2 (RHDV2; GI.2) in Ireland Focusing on Wild Irish Hares (Lepus timidus hibernicus): An Overview of the First Outbreaks and Contextual Review. Pathogens 2022; 11:pathogens11030288. [PMID: 35335613 PMCID: PMC8953227 DOI: 10.3390/pathogens11030288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 12/01/2022] Open
Abstract
Rabbit haemorrhagic disease virus 2 (RHDV2; GI.2) is a pathogenic lagovirus that emerged in 2010, and which now has a global distribution. Outbreaks have been associated with local population declines in several lagomorph species, due to rabbit haemorrhagic disease (RHD)-associated mortality raising concerns for its potential negative impact on threatened or vulnerable wild populations. The Irish hare (Lepus timidus hibernicus) is endemic to Ireland, and is of conservation interest. The first cases of RHDV2 in Ireland were reported in domestic rabbits (Oryctolagus cuniculus) in 2016, soon followed by the first known case in a wild rabbit also in 2016, from a population reported to be experiencing high fatalities. During summer 2019, outbreaks in wild rabbits were confirmed in several locations throughout Ireland. Six cases of RHDV2 in wild hares were confirmed between July and November 2019, at four locations. Overall, 27 cases in wildlife were confirmed in 2019 on the island of Ireland, with a predominantly southern distribution. Passive surveillance suggests that the Irish hare is susceptible to lethal RHDV2 infection, and that spillover infection to hares is geographically widespread in eastern areas of Ireland at least, but there is a paucity of data on epidemiology and population impacts. A literature review on RHD impact in closely related Lepus species suggests that intraspecific transmission, spillover transmission, and variable mortality occur in hares, but there is variability in reported resistance to severe disease and mortality amongst species. Several key questions on the impact of the pathogen in Irish hares remain. Surveillance activities throughout the island of Ireland will be important in understanding the spread of infection in this novel host.
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Affiliation(s)
- Andrew W. Byrne
- One-Health Scientific Support Unit, Department of Agriculture, Food and the Marine, Agriculture House, D02 WK12 Dublin, Ireland;
- Correspondence: or
| | - Ferdia Marnell
- Department of Housing, Local Government and Heritage, National Parks and Wildlife Service (NPWS), D07 N7CV Dublin, Ireland;
| | - Damien Barrett
- One-Health Scientific Support Unit, Department of Agriculture, Food and the Marine, Agriculture House, D02 WK12 Dublin, Ireland;
| | - Neil Reid
- Institute of Global Food Security (IGFS), School of Biological Sciences, Queen’s University Belfast, Belfast BT9 5DL, UK;
| | - Robert E. B. Hanna
- Veterinary Science Division (VSD), Agri-Food and Biosciences Institute, Stormont, Belfast BT4 3SD, UK;
| | - Máire C. McElroy
- Bacteriology and Parasitology Division, Department of Agriculture, Food and the Marine, Agriculture House, Backweston, W23 VW2C Dublin, Ireland;
| | - Mícheál Casey
- Regional Veterinary Laboratories (RVL) Division, Department of Agriculture, Food and the Marine, Agriculture House, Backweston, W23 VW2C Dublin, Ireland;
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Kumar B, Cheng J, Ge D, Xia L, Yang Q. Phylogeography and ecological niche modeling unravel the evolutionary history of the Yarkand hare, Lepus yarkandensis (Mammalia: Leporidae), through the Quaternary. BMC Evol Biol 2019; 19:113. [PMID: 31153378 PMCID: PMC6545225 DOI: 10.1186/s12862-019-1426-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 04/22/2019] [Indexed: 01/29/2023] Open
Abstract
Background The Taklimakan Desert in China is characterized by unique geological and historical dynamics and endemic flora and fauna, but the influence of historical climate oscillations on the evolutionary history of endemic animals is poorly understood. Lepus yarkandensis is an oases-dependent Near Threatened species that lives in fragmented oasis habitats in the Taklimakan Desert, China. We investigated the geological and climatic impacts on its geographical differentiation, demographic history and influence of Pleistocene glacial-interglacial cycles on the evolutionary history of L. yarkandensis. Further, studied the impact of climatic oscillation based modification on phylogeography, distribution and diversification pattern of Yarkand hare by using Cytb (1140 bp), MGF (592 bp) and SPTBN1 (619 bp) markers. Ecological niche modeling (ENM) revealed the evolutionary history of this species in response to climate change during the Quaternary. Paleodistribution modeling was used to identify putative refugia and estimate their historical distributions. Results Both historical demographic analyses and climatic niche modeling revealed strong effects of glacial climate changes, suggesting recurrent range contractions and expansions. The EBSP results indicated clear population expansion of L. yarkandensis since the Pleistocene. In the “early Pleistocene”, the demographic expansion continued from 0.83 MYA to the last glacial period. The ENM analysis supported a wide distribution of Lepus yarkandensis at high altitudes during the last interglacial (LIG) period. During the last glacial maximum (LGM), the suitable climate was reduced and restricted to the western part of the Taklimakan Desert. Conclusions Inland aridification, oasis evolution and river flow played major roles in the population differentiation and demographic history of Yarkand hares. Historically, the large, continuous oases in the Taklimakan Desert contained a viable and unique population of L. yarkandensis. The fragmented desert environment might have caused low gene flow between individuals or groups, thus leading to predominant genetic differentiation. The Pleistocene climatic cycles triggered the diversification and expansion of this species during cold and warm periods, respectively, leading to multiple colonization events within the Taklimakan Desert. These events might be due to the expansion of the Taklimakan Desert during the Middle Pleistocene. Yarkand hare previously occupied vast areas at low and intermediate altitudes in Xinjiang, Gansu, Shanxi, Henan and Shaanxi Provinces in China. The past aridification, climate change-induced oasis modifications, changes in river volumes and flow directions, and human activities all affected the population demography and phylogeography of the Yarkand hare. Electronic supplementary material The online version of this article (10.1186/s12862-019-1426-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Brawin Kumar
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China.,International College, University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Jilong Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Lin Xia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China
| | - Qisen Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China.
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The evolutionary history of the Cape hare (Lepus capensis sensu lato): insights for systematics and biogeography. Heredity (Edinb) 2019; 123:634-646. [PMID: 31073237 DOI: 10.1038/s41437-019-0229-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 04/11/2019] [Accepted: 04/19/2019] [Indexed: 12/27/2022] Open
Abstract
Inferring the phylogeography of species with large distributions helps deciphering major diversification patterns that may occur in parallel across taxa. Here, we infer the evolutionary history of the Cape hare, Lepus capensis sensu lato, a species distributed from southern Africa to Asia, by analyzing variation at 18 microsatellites and 9 DNA (1 mitochondrial and 8 nuclear) sequenced loci, from field and museum-collected samples. Using a combination of assignment and coalescent-based methods, we show that the Cape hare is composed of five evolutionary lineages, distributed in distinct biogeographic regions-north-western Africa, eastern Africa, southern Africa, the Near East and the Arabian Peninsula. A deep phylogenetic break possibly dating to the Early Pleistocene was inferred between the African and Asian L. capensis groups, and the latter appear more closely related to other Eurasian hare species than to African Cape hares. The inferred phylogeographic structure is shared by numerous taxa distributed across the studied range, suggesting that environmental changes, such as the progressive aridification of the Saharo-Arabian desert and the fluctuations of savannah habitats in Sub-Saharan Africa, had comparable impacts across species. Fine-scale analyses of the western Sahara-Sahel populations showed rich fragmentation patterns for mitochondrial DNA but not for microsatellites, compatible with the environmental heterogeneity of the region and female philopatry. The complex evolutionary history of L. capensis sensu lato, which possibly includes interspecific gene flow, is not reflected by taxonomy. Integrating evolutionary inference contributes to an improved characterization of biodiversity, which is fundamental to foster the conservation of relevant evolutionary units.
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Canu A, Scandura M, Luchetti S, Cossu A, Iacolina L, Bazzanti M, Apollonio M. Influence of management regime and population history on genetic diversity and population structure of brown hares (Lepus europaeus) in an Italian province. EUR J WILDLIFE RES 2013. [DOI: 10.1007/s10344-013-0731-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Canu A, Suchentrunk F, Cossu A, Foddai R, Iacolina L, Ben Slimen H, Apollonio M, Scandura M. Differentiation under isolation and genetic structure of Sardinian hares as revealed by craniometric analysis, mitochondrial DNA and microsatellites. J ZOOL SYST EVOL RES 2012. [DOI: 10.1111/j.1439-0469.2012.00671.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Dubey S, Sumner J, Pike DA, Keogh JS, Webb JK, Shine R. Genetic Connectivity among Populations of an Endangered Snake Species from Southeastern Australia (Hoplocephalus bungaroides, Elapidae). Ecol Evol 2012; 1:218-27. [PMID: 22393497 PMCID: PMC3287295 DOI: 10.1002/ece3.25] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 08/02/2011] [Accepted: 08/03/2011] [Indexed: 11/10/2022] Open
Abstract
For endangered species that persist as apparently isolated populations within a previously more extensive range, the degree of genetic exchange between those populations is critical to conservation and management. A lack of gene flow can exacerbate impacts of threatening processes and delay or prevent colonization of sites after local extirpation. The broad-headed snake, Hoplocephalus bungaroides, is a small venomous species restricted to a handful of disjunct reserves near Sydney, Australia. Mark-recapture studies have indicated low vagility for this ambush predator, suggesting that gene flow also may be low. However, our analyses of 11 microsatellite loci from 163 snakes collected in Morton National Park, from six sites within a 10-km diameter, suggest relatively high rates of gene flow among sites. Most populations exchange genes with each other, with one large population serving as a source area and smaller populations apparently acting as sinks. About half of the juvenile snakes, for which we could reliably infer parentage, were collected from populations other than those in which we collected their putative parents. As expected from the snakes' reliance on rocky outcrops during cooler months of the year, most gene flow appears to be along sandstone plateaux rather than across the densely forested valleys that separate plateaux. The unexpectedly high rates of gene flow on a landscape scale are encouraging for future conservation of this endangered taxon. For example, wildlife managers could conserve broad-headed snakes by restoring habitats near extant source populations in areas predicted to be least affected by future climate change.
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Affiliation(s)
- Sylvain Dubey
- School of Biological Sciences, University of SydneyNSW 2006 Australia
| | - Joanna Sumner
- Museum Victoria11 Nicholson St, Carlton Gardens, VIC 3053, Australia
| | - David A Pike
- School of Biological Sciences, University of SydneyNSW 2006 Australia
- Present address: School of Marine and Tropical Biology, James Cook UniversityAustralia
| | - J Scott Keogh
- Research School of Biology, The Australian National UniversityCanberra, ACT 0200, Australia
| | - Jonathan K Webb
- School of Biological Sciences, University of SydneyNSW 2006 Australia
| | - Richard Shine
- School of Biological Sciences, University of SydneyNSW 2006 Australia
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O'MEARA DENISEB, EDWARDS CEIRIDWENJ, SLEEMAN DPADDY, CROSS TOMF, STATHAM MARKJ, MCDOWELL JANR, DILLANE EILEEN, COUGHLAN JAMIEP, O'LEARY DAVID, O'REILLY CATHERINE, BRADLEY DANIELG, CARLSSON JENS. Genetic structure of Eurasian badgers Meles meles (Carnivora: Mustelidae) and the colonization history of Ireland. Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.01927.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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MCDEVITT ALLAND, RAMBAU RAMUGONDOV, O'BRIEN JOHN, MCDEVITT CDAMIEN, HAYDEN THOMASJ, SEARLE JEREMYB. Genetic variation in Irish pygmy shrews Sorex minutus (Soricomorpha: Soricidae): implications for colonization history. Biol J Linn Soc Lond 2009. [DOI: 10.1111/j.1095-8312.2009.01218.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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McDevitt AD, Edwards CJ, O’Toole P, O’Sullivan P, O’Reilly C, Carden RF. Genetic structure of, and hybridisation between, red (Cervus elaphus) and sika (Cervus nippon) deer in Ireland. Mamm Biol 2009. [DOI: 10.1016/j.mambio.2009.03.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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MELO-FERREIRA J, ALVES PC, FREITAS H, FERRAND N, BOURSOT P. The genomic legacy from the extinctLepus timidusto the three hare species of Iberia: contrast between mtDNA, sex chromosomes and autosomes. Mol Ecol 2009; 18:2643-58. [DOI: 10.1111/j.1365-294x.2009.04221.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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