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Summers J, Cosgrove EJ, Bowman R, Fitzpatrick JW, Chen N. Impacts of increasing isolation and environmental variation on Florida Scrub-Jay demography. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.10.575127. [PMID: 38260596 PMCID: PMC10802623 DOI: 10.1101/2024.01.10.575127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Isolation caused by anthropogenic habitat fragmentation can destabilize populations. Populations relying on the inflow of immigrants can face reduced fitness due to inbreeding depression as fewer new individuals arrive. Empirical studies of the demographic consequences of isolation are critical to understand how populations persist through changing conditions. We used a 34-year demographic and environmental dataset from a population of cooperatively-breeding Florida Scrub-Jays ( Aphelocoma coerulescens ) to create mechanistic models linking environmental and demographic factors to population growth rates. We found that the population has not declined despite both declining immigration and increasing inbreeding, owing to a coinciding response in breeder survival. We find evidence of density-dependent immigration, breeder survival, and fecundity, indicating that interactions between vital rates and local density play a role in buffering the population against change. Our study elucidates the impacts of isolation on demography and how long-term stability is maintained via demographic responses.
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Vieu JC, Koubínová D, Grant JR. Population Genetic Structure and Diversity of Cryptic Species of the Plant Genus Macrocarpaea (Gentianaceae) from the Tropical Andes. PLANTS (BASEL, SWITZERLAND) 2023; 12:1710. [PMID: 37111932 PMCID: PMC10145315 DOI: 10.3390/plants12081710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/29/2023] [Accepted: 04/14/2023] [Indexed: 06/19/2023]
Abstract
The Pleistocene climatic oscillations (PCO) that provoked several cycles of glacial-interglacial periods are thought to have profoundly affected species distribution, richness and diversity around the world. While the effect of the PCO on population dynamics at temperate latitudes is well known, considerable questions remain about its impact on the biodiversity of neotropical mountains. Here, we use amplified fragment length polymorphism molecular markers (AFLPs) to investigate the phylogeography and genetic structure of 13 plant species belonging to the gentian genus Macrocarpaea (Gentianaceae) in the tropical Andes. These woody herbs, shrubs or small trees show complex and potentially reticulated relationships, including cryptic species. We show that populations of M. xerantifulva in the dry system of the Rio Marañón in northern Peru have lower levels of genetic diversity compared to other sampled species. We suggest that this is due to a recent demographic bottleneck resulting from the contraction of the montane wet forests into refugia because of the expansion of the dry system into the valley during the glacial cycles of the PCO. This may imply that the ecosystems of different valleys of the Andes might have responded differently to the PCO.
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3
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Maes T, De Corte Z, Vangestel C, Virgilio M, Smitz N, Djuikwo-Teukeng FF, Papadaki MI, Huyse T. Large-scale and small-scale population genetic structure of the medically important gastropod species Bulinus truncatus (Gastropoda, Heterobranchia). Parasit Vectors 2022; 15:328. [PMID: 36123605 PMCID: PMC9484234 DOI: 10.1186/s13071-022-05445-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/12/2022] [Indexed: 11/11/2022] Open
Abstract
Background Gastropod snails remain strongly understudied, despite their important role in transmitting parasitic diseases. Knowledge of their distribution and population dynamics increases our understanding of the processes driving disease transmission. We report the first study to use high-throughput sequencing (HTS) to elucidate the population genetic structure of the hermaphroditic snail Bulinus truncatus (Gastropoda, Heterobranchia) on a regional (17–150 km) and inter-regional (1000–5400 km) scale. This snail species acts as an intermediate host of Schistosoma haematobium and Schistosoma bovis, which cause human and animal schistosomiasis respectively. Methods Bulinus truncatus snails were collected in Senegal, Cameroon, Egypt and France and identified through DNA barcoding. A single-end genotyping-by-sequencing (GBS) library, comprising 87 snail specimens from the respective countries, was built and sequenced on an Illumina HiSeq 2000 platform. Reads were mapped against S. bovis and S. haematobium reference genomes to identify schistosome infections, and single nucleotide polymorphisms (SNPs) were scored using the Stacks pipeline. These SNPs were used to estimate genetic diversity, assess population structure and construct phylogenetic trees of B. truncatus. Results A total of 10,750 SNPs were scored and used in downstream analyses. The phylogenetic analysis identified five clades, each consisting of snails from a single country but with two distinct clades within Senegal. Genetic diversity was low in all populations, reflecting high selfing rates, but varied between locations due to habitat variability. Significant genetic differentiation and isolation by distance patterns were observed at both spatial scales, indicating that gene flow is not strong enough to counteract the effects of population bottlenecks, high selfing rates and genetic drift. Remarkably, the population genetic differentiation on a regional scale (i.e. within Senegal) was as large as that between populations on an inter-regional scale. The blind GBS technique was able to pick up parasite DNA in snail tissue, demonstrating the potential of HTS techniques to further elucidate the role of snail species in parasite transmission. Conclusions HTS techniques offer a valuable toolbox to further investigate the population genetic patterns of intermediate schistosome host snails and the role of snail species in parasite transmission. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05445-x.
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Affiliation(s)
- Tim Maes
- Department of Biology, Katholieke Universiteit Leuven, Ch. Deberiotstraat 32, 3000, Leuven, Belgium. .,Royal Museum for Central Africa, Leuvensesteenweg 13, 3080, Tervuren, Belgium.
| | - Zoë De Corte
- Royal Museum for Central Africa, Leuvensesteenweg 13, 3080, Tervuren, Belgium.,Royal Belgian Institute of Natural Sciences, Vautierstraat 29, 1000, Brussels, Belgium
| | - Carl Vangestel
- Royal Belgian Institute of Natural Sciences, Vautierstraat 29, 1000, Brussels, Belgium.,Terrestrial Ecology Unit, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | | | - Nathalie Smitz
- Royal Museum for Central Africa, Leuvensesteenweg 13, 3080, Tervuren, Belgium
| | | | - Maria Ioanna Papadaki
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Tine Huyse
- Department of Biology, Katholieke Universiteit Leuven, Ch. Deberiotstraat 32, 3000, Leuven, Belgium.,Royal Museum for Central Africa, Leuvensesteenweg 13, 3080, Tervuren, Belgium
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4
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Fingerprinting, structure, and genetic relationships among selected accessions of blue honeysuckle (Lonicera caerulea L.) from European collections. BIOTECHNOLOGY REPORTS 2022; 34:e00721. [PMID: 35686005 PMCID: PMC9171449 DOI: 10.1016/j.btre.2022.e00721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/10/2022] [Accepted: 03/14/2022] [Indexed: 11/28/2022]
Abstract
Scarcely on December 13, 2018, L. caerulea fruits were included in the list of novel foods in EU. Hence, the growing interest in L. caerulea extends to its genome. R-ISSR explores other than the RAPD, ISSR, AFLP, and RFLP techniques part of genome and analyze other range of genetic variability. R-ISSR markers could be used for Lonicera core germplasm collection, development of SCARs, genetic map construction, barcoding, protection of variety rights, MAS, and genomic selection.
Due to its value and economic importance, the genome of Lonicera caerulea L. has been widely studied in various fields of science. In this study the genetic structure and relationships between 24 accessions of L. caerulea of different origins were assessed. A total of 692, 814, and 258 loci were amplified using 43 RAPD (random amplified polymorphic DNA), 40 ISSR (intersimple sequence repeat), and 20 R-ISSR (RAPD+ISSR) primers, respectively. Among the amplified loci, 66–78% were polymorphic and 12–20% were private. Selected R-ISSR sequences were detected in Lonicera japonica transcripts. Cluster and STRUCTURE analyses performed for each of the techniques revealed the existing differences and unknown similarities between the genotypes. The r-factor values calculated in the Mantel test indicated highly significant positive correlations between the Nei distance matrices, similar to the FST values (FST_RAPD = 0.223, FST_ISSR = 0.279, FST_R-ISSR = 0.363) determined in the analysis of molecular variance. It was found that 78%, 72%, and 64% of the genetic variations were related to the differences observed within the populations, which suggest that the variations are mainly reflected in the differences among the genotypes. The principal coordinate analysis showed greater differences between the mean distances of the Lonicera genotype pair and the actual distances of the same pairs on the Nei matrix compared to multidimensional scaling. These differences were 45%, 56%, and 42% higher for RAPD, ISSR and R-ISSR, respectively.
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5
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Nguyen TN, Chen N, Cosgrove EJ, Bowman R, Fitzpatrick JW, Clark AG. Dynamics of reduced genetic diversity in increasingly fragmented populations of Florida
Scrub‐Jays
,
Aphelocoma coerulescens. Evol Appl 2022; 15:1018-1027. [PMID: 35782006 PMCID: PMC9234620 DOI: 10.1111/eva.13421] [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: 12/16/2021] [Revised: 04/04/2022] [Accepted: 05/04/2022] [Indexed: 11/29/2022] Open
Abstract
Understanding the genomic consequences of population decline is important for predicting species' vulnerability to intensifying global change. Empirical information about genomic changes in populations in the early stages of decline, especially for those still experiencing immigration, remains scarce. We used 7834 autosomal SNPs and demographic data for 288 Florida scrub jays (Aphelocoma coerulescens; FSJ) sampled in 2000 and 2008 to compare levels of genetic diversity, inbreeding, relatedness, and lengths of runs of homozygosity (ROH) between two subpopulations within dispersal distance of one another but have experienced contrasting demographic trajectories. At Archbold Biological Station (ABS), the FSJ population has been stable because of consistent habitat protection and management, while at nearby Placid Lakes Estates (PLE), the population declined precipitously due to suburban development. By the onset of our sampling in 2000, birds in PLE were already less heterozygous, more inbred, and on average more related than birds in ABS. No significant changes occurred in heterozygosity or inbreeding across the 8‐year sampling interval, but average relatedness among individuals decreased in PLE, thus by 2008 average relatedness did not differ between sites. PLE harbored a similar proportion of short ROH but a greater proportion of long ROH than ABS, suggesting one continuous population of shared demographic history in the past, which is now experiencing more recent inbreeding. These results broadly uphold the predictions of simple population genetic models based on inferred effective population sizes and rates of immigration. Our study highlights how, in just a few generations, formerly continuous populations can diverge in heterozygosity and levels of inbreeding with severe local population decline despite ongoing gene flow.
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Affiliation(s)
- Tram N. Nguyen
- Department of Ecology and Evolutionary Biology Cornell University Ithaca NY USA
- Cornell Lab of Ornithology Ithaca NY USA
| | - Nancy Chen
- Department of Biology University of Rochester Rochester NY USA
| | - Elissa J. Cosgrove
- Department of Molecular Biology and Genetics Cornell University Ithaca NY USA
| | - Reed Bowman
- Avian Ecology Lab, Archbold Biological Station, Venus FL USA
| | - John W. Fitzpatrick
- Department of Ecology and Evolutionary Biology Cornell University Ithaca NY USA
- Cornell Lab of Ornithology Ithaca NY USA
| | - Andrew. G. Clark
- Department of Ecology and Evolutionary Biology Cornell University Ithaca NY USA
- Avian Ecology Lab, Archbold Biological Station, Venus FL USA
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6
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Breininger DR, Carter GM, Legare SA, Payne WV, Stolen ED, Breininger DJ, Lyon JE. Multistate modeling of Florida scrub‐jay adult survival and breeding transitions. Ecosphere 2022. [DOI: 10.1002/ecs2.3991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- David R. Breininger
- Herndon Solutions Group, LLC NASA Environmental and Medical Contract Kennedy Space Center Florida USA
| | - Geoffrey M. Carter
- Herndon Solutions Group, LLC NASA Environmental and Medical Contract Kennedy Space Center Florida USA
| | - Stephanie A. Legare
- Herndon Solutions Group, LLC NASA Environmental and Medical Contract Kennedy Space Center Florida USA
| | - William V. Payne
- Herndon Solutions Group, LLC NASA Environmental and Medical Contract Kennedy Space Center Florida USA
| | - Eric D. Stolen
- Herndon Solutions Group, LLC NASA Environmental and Medical Contract Kennedy Space Center Florida USA
| | | | - James E. Lyon
- Merritt Island National Wildlife Refuge Titusville Florida USA
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7
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Limeira DM, Santos MH, Mateus RP, Ruas CDF, Almeida MCD, Moreira Filho O, Artoni RF. Molecular data reveal a complex population genetic structure for Psalidodon scabripinnis (Teleostei: Characidae) in the Atlantic Rainforest, Brazil. Genet Mol Biol 2022; 45:e20210048. [PMID: 35238328 PMCID: PMC8892460 DOI: 10.1590/1678-4685-gmb-2021-0048] [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: 02/15/2021] [Accepted: 12/08/2021] [Indexed: 11/23/2022] Open
Abstract
Recently renamed, Psalidodon scabripinnis populations of Serra da Mantiqueira, previously known as Astyanax scabripinnis have been deeply studied in the last years. These populations are small and isolated and occur very close to the watershed between Paraíba do Sul River basin and Upper Paraná River basin, in Serra da Mantiqueira region in the Atlantic Rainforest. These conditions arouse the interest in knowing theor genetic conservation status and how they responded to the separation between the two rivers basins. Therefore, we accessed the genetic diversity of five P. scabripinnis populations of this region with microsatellites and mitochondrial data. The results showed a complex structure pattern that doesn’t match the simple basin separation and a reasonably conservation status when compared with other populations of the same family or with similar natural history.
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8
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Ferguson SH, Yurkowski DJ, Hudson JM, Edkins T, Willing C, Watt CA. Larger body size leads to greater female beluga whale ovarian reproductive activity at the southern periphery of their range. Ecol Evol 2021; 11:17314-17322. [PMID: 34938510 PMCID: PMC8668808 DOI: 10.1002/ece3.8367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 10/05/2021] [Accepted: 11/02/2021] [Indexed: 12/22/2022] Open
Abstract
Identification of phenotypic characteristics in reproductively successful individuals provides important insights into the evolutionary processes that cause range shifts due to environmental change. Female beluga whales (Delphinapterus leucas) from the Baffin Bay region (BB) of the Canadian Arctic in the core area of the species' geographic range have larger body size than their conspecifics at the southern range periphery in Hudson Bay (HB). We investigated the mechanism for this north and south divergence as it relates to ovarian reproductive activity (ORA = total corpora) that combines morphometric data with ovarian corpora counted from female reproductive tracts. Our study aim was to assess the relative influence of age and body size of female beluga whale on ORA in the two populations. Female beluga whale ORA increased more quickly with age (63% partial variation explained) in BB than in HB (41%). In contrast, body length in HB female beluga whales accounted for considerably more of the total variation (12% vs. 1%) in ORA compared to BB whales. We speculate that female HB beluga whale ORA was more strongly linked with body length due to higher population density resulting in food competition that favors the energetic advantages of larger body size during seasonal food limitations. Understanding the evolutionary mechanism of how ORA varies across a species' range will assist conservation efforts in anticipating and mitigating future challenges associated with a warming planet.
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Affiliation(s)
- Steven H. Ferguson
- Fisheries and Oceans CanadaFreshwater InstituteWinnipegManitobaCanada
- Biological SciencesUniversity of ManitobaWinnipegManitobaCanada
| | - David J. Yurkowski
- Fisheries and Oceans CanadaFreshwater InstituteWinnipegManitobaCanada
- Biological SciencesUniversity of ManitobaWinnipegManitobaCanada
| | - Justine M. Hudson
- Fisheries and Oceans CanadaFreshwater InstituteWinnipegManitobaCanada
| | - Tera Edkins
- Fisheries and Oceans CanadaFreshwater InstituteWinnipegManitobaCanada
| | | | - Cortney A. Watt
- Fisheries and Oceans CanadaFreshwater InstituteWinnipegManitobaCanada
- Biological SciencesUniversity of ManitobaWinnipegManitobaCanada
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9
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Parker E, Dornburg A, Struthers CD, Jones CD, Near TJ. Phylogenomic species delimitation dramatically reduces species diversity in an Antarctic adaptive radiation. Syst Biol 2021; 71:58-77. [PMID: 34247239 DOI: 10.1093/sysbio/syab057] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 07/06/2021] [Accepted: 06/30/2021] [Indexed: 11/14/2022] Open
Abstract
Application of genetic data to species delimitation often builds confidence in delimitations previously hypothesized using morphological, ecological, and geographic data and frequently yields recognition of previously-undescribed cryptic diversity. However, a recent critique of genomic data-based species delimitation approaches is that they have the potential to conflate population structure with species diversity, resulting in taxonomic oversplitting. The need for an integrative approach to species delimitation, in which molecular, morphological, ecological, and geographic lines of evidence are evaluated together, is becoming increasingly apparent. Here, we integrate phylogenetic, population genetic, and coalescent analyses of genome-wide sequence data with investigation of variation in multiple morphological traits to delimit species within the Antarctic barbeled plunderfishes (Artedidraconidae: Pogonophryne). Pogonophryne currently comprises 29 valid species, most of which are distinguished solely by variation in ornamentation of the mental barbel that projects from the lower jaw, a structure previously shown to vary widely within a single species. However, our genomic and phenotypic analyses result in a dramatic reduction in the number of distinct species recognized within the clade, providing evidence to support the recognition of no more than six species. We propose to synonymize 24 of the currently recognized species with five species of Pogonophryne. We find genomic and phenotypic evidence for a new species of Pogonophryne from specimens collected in the Ross Sea. Our findings represent a rare example in which application of molecular data provides evidence of taxonomic oversplitting on the basis of morphology, clearly demonstrating the utility of an integrative species delimitation framework.
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Affiliation(s)
- Elyse Parker
- Department of Ecology & Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA
| | - Alex Dornburg
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, Charlotte, NC 28223, USA
| | - Carl D Struthers
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| | - Christopher D Jones
- Antarctic Ecosystem Research Division, NOAA Southwest Fisheries Science Center, La Jolla, CA 92037, USA
| | - Thomas J Near
- Department of Ecology & Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA.,Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA
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10
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Lawson DM, Williams CK, Lavretsky P, Howell DL, Fuller JC. Mallard–Black Duck Hybridization and Population Genetic Structure in North Carolina. J Wildl Manage 2021. [DOI: 10.1002/jwmg.22085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Daniel M. Lawson
- University of Delaware, 531 South College Avenue Newark DE 19716 USA
| | | | - Philip Lavretsky
- University of Texas at El Paso, 500 W University Avenue El Paso TX 79968 USA
| | - Douglas L. Howell
- North Carolina Wildlife Resources Commission 132 Marine Drive Edenton NC 27699 USA
| | - Joseph C. Fuller
- North Carolina Wildlife Resources Commission 132 Marine Drive Edenton NC 27699 USA
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11
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Miller KE, Risch R, Garcia J. Long-Distance Dispersal in a Sedentary Species, Aphelocoma coerulescens (Florida Scrub-Jay), in Northern Florida. SOUTHEAST NAT 2021. [DOI: 10.1656/058.020.0118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Karl E. Miller
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, 1105 SW Williston Road, Gainesville, FL 32601
| | | | - Jay Garcia
- Ocala National Forest, Umatilla, FL 32784
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12
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Yannic G, Helfer V, Sermier R, Schmidt BR, Fumagalli L. Fine scale genetic structure in fire salamanders (Salamandra salamandra) along a rural-to-urban gradient. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01335-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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13
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Lehnen SE, Sternberg MA, Swarts HM, Sesnie SE. Evaluating population connectivity and targeting conservation action for an endangered cat. Ecosphere 2021. [DOI: 10.1002/ecs2.3367] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Sarah E. Lehnen
- Division of Biological Sciences U.S. Fish and Wildlife Service P.O. Box 1306 Albuquerque New Mexico87103USA
| | - Mitch A. Sternberg
- South Texas Refuge Complex U.S. Fish and Wildlife Service 3325 Green Jay Road Alamo Texas78516USA
| | - Hilary M. Swarts
- Laguna Atascosa National Wildlife Refuge U.S. Fish and Wildlife Service 22817 Ocelot Road Los Fresnos Texas78566USA
| | - Steven E. Sesnie
- Division of Biological Sciences U.S. Fish and Wildlife Service P.O. Box 1306 Albuquerque New Mexico87103USA
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14
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Curry CJ, Davis BW, Bertola LD, White PA, Murphy WJ, Derr JN. Spatiotemporal Genetic Diversity of Lions Reveals the Influence of Habitat Fragmentation across Africa. Mol Biol Evol 2021; 38:48-57. [PMID: 32667997 PMCID: PMC8480188 DOI: 10.1093/molbev/msaa174] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Direct comparisons between historical and contemporary populations allow for detecting changes in genetic diversity through time and assessment of the impact of habitat fragmentation. Here, we determined the genetic architecture of both historical and modern lions to document changes in genetic diversity over the last century. We surveyed microsatellite and mitochondrial genome variation from 143 high-quality museum specimens of known provenance, allowing us to directly compare this information with data from several recently published nuclear and mitochondrial studies. Our results provide evidence for male-mediated gene flow and recent isolation of local subpopulations, likely due to habitat fragmentation. Nuclear markers showed a significant decrease in genetic diversity from the historical (HE = 0.833) to the modern (HE = 0.796) populations, whereas mitochondrial genetic diversity was maintained (Hd = 0.98 for both). Although the historical population appears to have been panmictic based on nDNA data, hierarchical structure analysis identified four tiers of genetic structure in modern populations and was able to detect most sampling locations. Mitogenome analyses identified four clusters: Southern, Mixed, Eastern, and Western and were consistent between modern and historically sampled haplotypes. Within the last century, habitat fragmentation caused lion subpopulations to become more geographically isolated as human expansion changed the African landscape. This resulted in an increase in fine-scale nuclear genetic structure and loss of genetic diversity as lion subpopulations became more differentiated, whereas mitochondrial structure and diversity were maintained over time.
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Affiliation(s)
- Caitlin J Curry
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX
| | - Laura D Bertola
- Department of Biology, City College of New York, New York, NY
| | - Paula A White
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California Los Angeles, Los Angeles, CA
| | - William J Murphy
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX
| | - James N Derr
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX
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15
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Selz OM, Dönz CJ, Vonlanthen P, Seehausen O. A taxonomic revision of the whitefish of lakes Brienz and Thun, Switzerland, with descriptions of four new species (Teleostei, Coregonidae). Zookeys 2020; 989:79-162. [PMID: 33223897 PMCID: PMC7669820 DOI: 10.3897/zookeys.989.32822] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 08/07/2019] [Indexed: 12/16/2022] Open
Abstract
The alpha taxonomy of the endemic whitefish of lakes Brienz and Thun, Switzerland, is revised. We evaluate the status of seven known species: Coregonus steinmanni sp. nov., Coregonus profundus sp. nov. and Coregonus acrinasus sp. nov. are endemic to Lake Thun; Coregonus Brienzii sp. nov. is endemic to Lake Brienz; and C. alpinus, C. albellus, and C. fatioi from lakes Brienz and Thun are redescribed. One of these species, C. alpinus, is revised, since the lectotype for this species is incongruent with the species description given by Kottelat (1997) and Kottelat and Freyhof (2007). The name C. alpinus is thus retained for the lectotype designated by Kottelat (1997) and a new description of this taxon provided. For the species otherwise described by Kottelat (1997) and Kottelat and Freyhof (2007) as C. alpinus the new name C. profundus is designated. Coregonus acrinasus is genetically partially of allochthonous origin, closely related to the radiation of Lake Constance, and we therefore compare it to all recognized species of Lake Constance, C. wartmanni, C. macrophthalmus, C. arenicolus, and C. gutturosus.
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Affiliation(s)
- Oliver M Selz
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland Swiss Federal Institute of Aquatic Science and Technology Kastanienbaum Switzerland.,Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland University of Bern Bern Switzerland
| | - Carmela J Dönz
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland Swiss Federal Institute of Aquatic Science and Technology Kastanienbaum Switzerland.,Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland University of Bern Bern Switzerland
| | - Pascal Vonlanthen
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland Swiss Federal Institute of Aquatic Science and Technology Kastanienbaum Switzerland.,Aquabios GmbH, Les Fermes 57, 1792 Cordast, Switzerland Aquabios GmbH Cordast Switzerland
| | - Ole Seehausen
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland Swiss Federal Institute of Aquatic Science and Technology Kastanienbaum Switzerland.,Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland University of Bern Bern Switzerland
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16
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Wu Y, Bogdanowicz SM, Andres JA, Vieira KA, Wang B, Cossé A, Pfister SE. Tracking invasions of a destructive defoliator, the gypsy moth (Erebidae: Lymantria dispar): Population structure, origin of intercepted specimens, and Asian introgression into North America. Evol Appl 2020; 13:2056-2070. [PMID: 32908604 PMCID: PMC7463338 DOI: 10.1111/eva.12962] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/03/2020] [Accepted: 03/04/2020] [Indexed: 12/30/2022] Open
Abstract
Genetic data can help elucidate the dynamics of biological invasions, which are fueled by the constant expansion of international trade. The introduction of European gypsy moth (Lymantria dispar dispar) into North America is a classic example of human-aided invasion that has caused tremendous damage to North American temperate forests. Recently, the even more destructive Asian gypsy moth (mainly L. d. asiatica and L. d. japonica) has been intercepted in North America, mostly transported by cargo ships. To track invasion pathways, we developed a diagnostic panel of 60 DNA loci (55 nuclear and 5 mitochondrial) to characterize worldwide genetic differentiation within L. dispar and its sister species L. umbrosa. Hierarchical analyses supported strong differentiation and recovered five geographic groups that correspond to (1) North America, (2) Europe plus North Africa and Middle East, (3) the Urals, Central Asia, and Russian Siberia, (4) continental East Asia, and (5) the Japanese islands. Interestingly, L. umbrosa was grouped with L. d. japonica, and the introduced North American population exhibits remarkable distinctiveness from contemporary European counterparts. Each geographic group, except for North America, shows additional lower-level structures when analyzed individually, which provided the basis for inference of the origin of invasive specimens. Two assignment approaches consistently identified a coastal area of continental East Asia as the major source for Asian invasion during 2014-2015, with Japan being another source. By analyzing simulation and laboratory crosses, we further provided evidence for the occurrence of natural Asian-North American hybrids in the Pacific Northwest, raising concerns for introgression of Asian alleles that may accelerate range expansion of gypsy moth in North America. Our study demonstrates how genetic data contribute to bio-surveillance of invasive species with results that can inform regulatory management and reduce the frequency of trade-associated invasions.
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Affiliation(s)
- Yunke Wu
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNYUSA
- United States Department of AgricultureAPHIS, PPQ, S&T, Otis LaboratoryBuzzards BayMAUSA
| | | | - Jose A. Andres
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNYUSA
| | - Kendra A. Vieira
- United States Department of AgricultureAPHIS, PPQ, S&T, Otis LaboratoryBuzzards BayMAUSA
| | - Baode Wang
- United States Department of AgricultureAPHIS, PPQ, S&T, Otis LaboratoryBuzzards BayMAUSA
| | - Allard Cossé
- United States Department of AgricultureAPHIS, PPQ, S&T, Otis LaboratoryBuzzards BayMAUSA
| | - Scott E. Pfister
- United States Department of AgricultureAPHIS, PPQ, S&T, Otis LaboratoryBuzzards BayMAUSA
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17
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Termignoni-Garcia F, Louder MIM, Balakrishnan CN, O’Connell L, Edwards SV. Prospects for sociogenomics in avian cooperative breeding and parental care. Curr Zool 2020; 66:293-306. [PMID: 32440290 PMCID: PMC7233861 DOI: 10.1093/cz/zoz057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/20/2019] [Indexed: 01/08/2023] Open
Abstract
For the last 40 years, the study of cooperative breeding (CB) in birds has proceeded primarily in the context of discovering the ecological, geographical, and behavioral drivers of helping. The advent of molecular tools in the early 1990s assisted in clarifying the relatedness of helpers to those helped, in some cases, confirming predictions of kin selection theory. Methods for genome-wide analysis of sequence variation, gene expression, and epigenetics promise to add new dimensions to our understanding of avian CB, primarily in the area of molecular and developmental correlates of delayed breeding and dispersal, as well as the ontogeny of achieving parental status in nature. Here, we outline key ways in which modern -omics approaches, in particular genome sequencing, transcriptomics, and epigenetic profiling such as ATAC-seq, can be used to add a new level of analysis of avian CB. Building on recent and ongoing studies of avian social behavior and sociogenomics, we review how high-throughput sequencing of a focal species or clade can provide a robust foundation for downstream, context-dependent destructive and non-destructive sampling of specific tissues or physiological states in the field for analysis of gene expression and epigenetics. -Omics approaches have the potential to inform not only studies of the diversification of CB over evolutionary time, but real-time analyses of behavioral interactions in the field or lab. Sociogenomics of birds represents a new branch in the network of methods used to study CB, and can help clarify ways in which the different levels of analysis of CB ultimately interact in novel and unexpected ways.
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Affiliation(s)
- Flavia Termignoni-Garcia
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Matthew I M Louder
- International Research Center for Neurointelligence, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | | | - Lauren O’Connell
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
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18
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González‐Serna MJ, Cordero PJ, Ortego J. Insights into the neutral and adaptive processes shaping the spatial distribution of genomic variation in the economically important Moroccan locust ( Dociostaurus maroccanus). Ecol Evol 2020; 10:3991-4008. [PMID: 32489626 PMCID: PMC7244894 DOI: 10.1002/ece3.6165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 02/12/2020] [Accepted: 02/18/2020] [Indexed: 11/11/2022] Open
Abstract
Understanding the processes that shape neutral and adaptive genomic variation is a fundamental step to determine the demographic and evolutionary dynamics of pest species. Here, we use genomic data obtained via restriction site-associated DNA sequencing to investigate the genetic structure of Moroccan locust (Dociostaurus maroccanus) populations from the westernmost portion of the species distribution (Iberian Peninsula and Canary Islands), infer demographic trends, and determine the role of neutral versus selective processes in shaping spatial patterns of genomic variation in this pest species of great economic importance. Our analyses showed that Iberian populations are characterized by high gene flow, whereas the highly isolated Canarian populations have experienced strong genetic drift and loss of genetic diversity. Historical demographic reconstructions revealed that all populations have passed through a substantial genetic bottleneck around the last glacial maximum (~21 ka BP) followed by a sharp demographic expansion at the onset of the Holocene, indicating increased effective population sizes during warm periods as expected from the thermophilic nature of the species. Genome scans and environmental association analyses identified several loci putatively under selection, suggesting that local adaptation processes in certain populations might not be impeded by widespread gene flow. Finally, all analyses showed few differences between outbreak and nonoutbreak populations. Integrated pest management practices should consider high population connectivity and the potential importance of local adaptation processes on population persistence.
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Affiliation(s)
- María José González‐Serna
- Grupo de Investigación de la Biodiversidad Genética y CulturalInstituto de Investigación en Recursos Cinegéticos – IREC – (CSIC, UCLM, JCCM)Ciudad RealSpain
| | - Pedro J. Cordero
- Grupo de Investigación de la Biodiversidad Genética y CulturalInstituto de Investigación en Recursos Cinegéticos – IREC – (CSIC, UCLM, JCCM)Ciudad RealSpain
- Departamento de Ciencia y Tecnología Agroforestal y GenéticaEscuela Técnica Superior de Ingenieros Agrónomos (ETSIA)Universidad de Castilla‐La Mancha (UCLM)Ciudad RealSpain
| | - Joaquín Ortego
- Department of Integrative EcologyEstación Biológica de Doñana – EBD – (CSIC)SevilleSpain
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Cayuela H, Besnard A, Cote J, Laporte M, Bonnaire E, Pichenot J, Schtickzelle N, Bellec A, Joly P, Léna J. Anthropogenic disturbance drives dispersal syndromes, demography, and gene flow in amphibian populations. ECOL MONOGR 2020. [DOI: 10.1002/ecm.1406] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Hugo Cayuela
- Univ. Lyon Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR5023 LEHNA F‐69622 Villeurbanne France
- EPHE, UM, SupAgro, IRD, INRA, UMR 5175 CEFE, CNRS PSL Research University Montpellier F‐34293 France
| | - Aurélien Besnard
- EPHE, UM, SupAgro, IRD, INRA, UMR 5175 CEFE, CNRS PSL Research University Montpellier F‐34293 France
| | - Julien Cote
- CNRS, Université Toulouse III Paul Sabatier, ENFA UMR5174EDB (Laboratoire Évolution & Diversité Biologique) 118 route de Narbonne F‐31062 Toulouse France
| | - Martin Laporte
- EPHE, UM, SupAgro, IRD, INRA, UMR 5175 CEFE, CNRS PSL Research University Montpellier F‐34293 France
| | - Eric Bonnaire
- Office National des Forêts Agence de Verdun 55100 Verdun France
| | - Julian Pichenot
- Centre de Recherche et Formation en Eco‐éthologie (CERFE) CERFE 08240 Boult‐aux‐Bois France
| | - Nicolas Schtickzelle
- Earth and Life Institute Biodiversity Research Centre Université Catholique de Louvain 1348 Louvain‐la‐Neuve Belgium
| | - Arnaud Bellec
- Univ. Lyon Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR5023 LEHNA F‐69622 Villeurbanne France
| | - Pierre Joly
- Univ. Lyon Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR5023 LEHNA F‐69622 Villeurbanne France
| | - Jean‐Paul Léna
- Univ. Lyon Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR5023 LEHNA F‐69622 Villeurbanne France
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Tringali A, Sherer DL, Cosgrove J, Bowman R. Life history stage explains behavior in a social network before and during the early breeding season in a cooperatively breeding bird. PeerJ 2020; 8:e8302. [PMID: 32095315 PMCID: PMC7020825 DOI: 10.7717/peerj.8302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 11/26/2019] [Indexed: 12/03/2022] Open
Abstract
In species with stage-structured populations selection pressures may vary between different life history stages and result in stage-specific behaviors. We use life history stage to explain variation in the pre and early breeding season social behavior of a cooperatively breeding bird, the Florida scrub-jay (Aphelocoma coerulescens) using social network analysis. Life history stage explains much of the variation we observed in social network position. These differences are consistent with nearly 50 years of natural history observations and generally conform to a priori predictions about how individuals in different stages should behave to maximize their individual fitness. Where the results from the social network analysis differ from the a priori predictions suggest that social interactions between members of different groups are more important for breeders than previously thought. Our results emphasize the importance of accounting for life history stage in studies of individual social behavior.
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Affiliation(s)
- Angela Tringali
- Avian Ecology Program, Archbold Biological Station, Venus, FL, United States of America
| | - David L Sherer
- Avian Ecology Program, Archbold Biological Station, Venus, FL, United States of America.,Department of Biology, University of Central Florida, Orlando, FL, United States of America
| | - Jillian Cosgrove
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, United States of America
| | - Reed Bowman
- Avian Ecology Program, Archbold Biological Station, Venus, FL, United States of America
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21
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Genetic analysis of red deer (Cervus elaphus) administrative management units in a human-dominated landscape. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01248-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
AbstractRed deer (Cervus elaphus) throughout central Europe are influenced by different anthropogenic activities including habitat fragmentation, selective hunting and translocations. This has substantial impacts on genetic diversity and the long-term conservation of local populations of this species. Here we use genetic samples from 480 red deer individuals to assess genetic diversity and differentiation of the 12 administrative management units located in Schleswig Holstein, the northernmost federal state in Germany. We applied multiple analytical approaches and show that the history of local populations (i.e., translocations, culling of individuals outside of designated red deer zones, anthropogenic infrastructures) potentially has led to low levels of genetic diversity. Mean expected heterozygosity was below 0.6 and we observed on average 4.2 alleles across 12 microsatellite loci. Effective population sizes below the recommended level of 50 were estimated for multiple local populations. Our estimates of genetic structure and gene flow show that red deer in northern Germany are best described as a complex network of asymmetrically connected subpopulations, with high genetic exchange among some local populations and reduced connectivity of others. Genetic diversity was also correlated with population densities of neighboring management units. Based on these findings, we suggest that connectivity among existing management units should be considered in the practical management of the species, which means that some administrative management units should be managed together, while the effective isolation of other units needs to be mitigated.
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22
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Putnam AS, Nguyen TN, Mott A, Korody ML, Ryder OA. Assessing possible hybridization among managed Nubian ibex in North America. Zoo Biol 2019; 39:121-128. [PMID: 31833594 DOI: 10.1002/zoo.21527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 10/21/2019] [Accepted: 11/07/2019] [Indexed: 11/06/2022]
Abstract
Hybridization among closely related species is a concern in zoo and aquarium populations where unpedigreed animals are frequently exchanged with the private sector. In this study, we examine possible hybridization in a group of Nubian ibex (Capra nubiana) imported into the Association of Zoos and Aquariums' (AZA) Species Survival Program (SSP) from a private institution. These individuals appeared smaller in stature than adult SSP Nubian ibex and were excluded from breeding recommendations over the concern that they were hybrids. Twenty-six microsatellites were used to rule out recent hybridization with domestic goats, Siberian ibex (Capra sibirica), and Alpine ibex (Capra ibex). We argue that natural phenotypic variation across the large geographic range of Nubian ibex may account for the small stature of the imported ibex, as private institutions may have historically acquired individuals from locations that differed from the SSP founders. However, the imported Nubian ibex appeared genetically differentiated from the SSP Nubian ibex and may represent a source of genetic variation for the managed population.
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Affiliation(s)
- Andrea S Putnam
- Department of Life Sciences, San Diego Zoo Global, San Diego, California
| | - Tram N Nguyen
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York
| | | | - Marisa L Korody
- Institute for Conservation Research, San Diego Zoo Global, San Diego, California
| | - Oliver A Ryder
- Institute for Conservation Research, San Diego Zoo Global, San Diego, California
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23
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Li M, Li B, Jiang S, Zhao Y, Xu X, Wu J. Microsatellite-based analysis of genetic structure and gene flow of Mythimna separata (Walker) (Lepidoptera: Noctuidae) in China. Ecol Evol 2019; 9:13426-13437. [PMID: 31871655 PMCID: PMC6912921 DOI: 10.1002/ece3.5799] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 09/23/2019] [Accepted: 10/11/2019] [Indexed: 11/27/2022] Open
Abstract
The oriental armyworm, Mythimna separata, is a serious agricultural pest in China. Seasonal and roundtrip migration has recently led to sudden, localized outbreaks and crop losses. To evaluate genetic differentiation between populations in eastern and western China and elucidate gene flow, the genetic structure of 20 natural populations from nine provinces was examined using seven microsatellite markers. The results indicated high genetic diversity. However, little to moderate (0 < F ST < 0.15) genetic differentiation was detected, and there was no correlation between genetic distance and geographical distance. Bayesian clustering analysis identified three groups whereas discriminant analysis of principal components identified ten clusters that were considered as two clear-cut clusters and one admixed group. Gene flow occurred frequently in most population pairs, and an asymmetrical migration rate was detected in several pairwise population comparisons. The bottleneck test showed that few populations had experienced recent bottlenecks. Correspondingly, large-scale and long-distance migration of M. separata has caused low genetic differentiation and frequent gene exchange. Our findings are important for studying genetic evolution and help to improve predictions of M. separata outbreaks in China.
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Affiliation(s)
- Mei‐Mei Li
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Plant ProtectionNorthwest A & F UniversityYanglingChina
| | - Bo‐Liao Li
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Plant ProtectionNorthwest A & F UniversityYanglingChina
| | - Shi‐Xiong Jiang
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Plant ProtectionNorthwest A & F UniversityYanglingChina
| | - Yu‐Wan Zhao
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Plant ProtectionNorthwest A & F UniversityYanglingChina
| | - Xiang‐Li Xu
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Plant ProtectionNorthwest A & F UniversityYanglingChina
| | - Jun‐Xiang Wu
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Plant ProtectionNorthwest A & F UniversityYanglingChina
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24
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Carroll RP, Litvaitis MK, Clements SJ, Stevens CL, Litvaitis JA. History matters: contemporary versus historic population structure of bobcats in the New England region, USA. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01170-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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25
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Tanhuanpää P, Heinonen M, Bitz L, Rokka VM. Genetic diversity and structure in the northern populations of European hazelnut ( Corylus avellana L.). Genome 2019; 62:537-548. [PMID: 31170350 DOI: 10.1139/gen-2018-0193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
European hazelnut (Corylus avellana L.) is a strictly cross-pollinated diploid tree species, which has its northernmost populations in Fennoscandia, and it was one of the first species to recolonize northern Europe after the last ice age. Hazelnut produces edible nuts in Finland but nowadays they are underutilized as food, and currently no breeding programmes exist. In the present study, 300 hazelnut specimens were collected from 20 different locations (= populations) in Finland, and they were genetically analyzed using nine simple sequence repeat (SSR) markers. Most of the genetic diversity existed within populations (83%). According to different genetic analyses (STRUCTURE, principal coordinates analysis, and clustering), a general lack of structure was observed, suggesting extensive gene flow among hazelnuts between 17 investigated populations. However, genetic structuring was clearly observed in three populations: Hakavuori, Mustiala, and Pähkinämäki, which might have become isolated due to geographical barriers that kept them separate, diminishing gene flow from other populations. Studying the diversity of European hazelnut is of great interest for understanding population genetics of a species distributed in its marginal areas in the north, and the results are also valuable for further uses in plant conservation, selection, and possible future breeding actions in Finland.
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Affiliation(s)
- Pirjo Tanhuanpää
- Production Systems, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland.,Production Systems, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland
| | - Maarit Heinonen
- Production Systems, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland.,Production Systems, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland
| | - Lidija Bitz
- Production Systems, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland.,Production Systems, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland
| | - Veli-Matti Rokka
- Production Systems, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland.,Production Systems, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland
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26
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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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27
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Distribution, fine-scale subdivision, and population size of San Joaquin kit foxes in the Ciervo-Panoche Natural Area, California. CONSERV GENET 2019. [DOI: 10.1007/s10592-018-1122-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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28
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GENETIC DIVERSITY OF YELLOW-BILLED MAGPIES ( PICA NUTALLI) BEFORE AND AFTER A WEST NILE VIRUS EPIDEMIC. J Wildl Dis 2019; 55:316-324. [PMID: 30628856 DOI: 10.7589/2018-01-023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The appearance of West Nile virus (WNV) coincided with declines in California, US bird populations beginning in 2004, and particularly affected corvid populations, including Yellow-billed Magpies ( Pica nutalli), an endemic species to California. Our objective was to determine if the timing of the WNV epidemic correlated with changes in the genetic diversity or population structure of magpies. We hypothesized the declines in magpie abundance from WNV would lead to genetic bottlenecks and reduced genetic diversity, but not to changes in population genetic structure. To test these hypotheses, we genetically typed magpie samples collected during the Dead Bird Survey before WNV arrived (2002-04), immediately after WNV arrived in late 2004 (2006-08), and several generations after the onset of the epidemic (2009-11). For each of these three time periods, we tested for genetic bottlenecks, estimated genetic heterozygosity, allelic richness, relatedness, effective population sizes, and genetic structure, with the use of 10 nuclear microsatellite loci. Although there was no evidence for spatial or temporal genetic structure, genetic-diversity estimates were similar or below estimates for endangered corvid species. Measures of genetic diversity were consistent across time periods. In contrast to our expectation, we detected a genetic bottleneck prior to the WNV epidemic, which may have coincided with severe drought conditions in California, increasing human population size in magpie range, and an estimated 33% decrease in population size. We found weak evidence to support a bottleneck after the introduction of WNV in California. Our results suggest the WNV epidemic did not have additional catastrophic effects on the neutral genetic diversity of P. nutalli in the sampled areas. However, because we detected lower heterozygosity in Yellow-billed Magpies than has been reported in closely related endangered species, this species is of conservation concern and should be monitored to detect further population declines or loss of genetic diversity.
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29
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Nigenda-Morales SF, Gompper ME, Valenzuela-Galván D, Lay AR, Kapheim KM, Hass C, Booth-Binczik SD, Binczik GA, Hirsch BT, McColgin M, Koprowski JL, McFadden K, Wayne RK, Koepfli KP. Phylogeographic and diversification patterns of the white-nosed coati (Nasua narica): Evidence for south-to-north colonization of North America. Mol Phylogenet Evol 2018; 131:149-163. [PMID: 30468940 DOI: 10.1016/j.ympev.2018.11.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 11/12/2018] [Accepted: 11/16/2018] [Indexed: 11/30/2022]
Abstract
White-nosed coatis (Nasua narica) are widely distributed throughout North, Central, and South America, but the patterns of temporal and spatial diversification that have contributed to this distribution are unknown. In addition, the biogeographic history of procyonid species in the Americas remains contentious. Using sequences from three mitochondrial loci (Cytochrome b, NAHD5 and 16S rRNA; 2201 bp) and genotypes from 11 microsatellite loci, we analyzed genetic diversity to determine phylogeographic patterns, genetic structure, divergence times, and gene flow among Nasua narica populations throughout the majority of the species' range. We also estimated the ancestral geographic range of N. narica and other procyonid species. We found a high degree of genetic structure and divergence among populations that conform to five evolutionarily significant units. The most southerly distributed population (Panama) branched off much earlier (∼3.8 million years ago) than the northern populations (<1.2 million years ago). Estimated gene flow among populations was low and mostly northwards and westwards. The phylogeographic patterns within N. narica are associated with geographic barriers and habitat shifts likely caused by Pliocene-Pleistocene climate oscillations. Significantly, our findings suggest the dispersal of N. narica was south-to-north beginning in the Pliocene, not in the opposite direction during the Pleistocene as suggested by the fossil record, and that the most recent common ancestor for coati species was most likely distributed in South or Central America six million years ago. Our study implies the possibility that the diversification of Nasua species, and other extant procyonid lineages, may have occurred in South America.
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Affiliation(s)
- Sergio F Nigenda-Morales
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Matthew E Gompper
- School of Natural Resources, University of Missouri, Columbia, MO 65211, USA
| | - David Valenzuela-Galván
- Departamento de Ecología Evolutiva, Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico
| | - Anna R Lay
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Karen M Kapheim
- Department of Biology, Utah State University, Logan, UT 84322, USA
| | | | | | | | - Ben T Hirsch
- Zoology and Ecology, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
| | - Maureen McColgin
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - John L Koprowski
- School of Natural Resources and the Environment, The University of Arizona, Tucson, AZ 85721, USA
| | - Katherine McFadden
- College of Agriculture, Forestry and Life Sciences, Clemson University, Clemson, SC 29634, USA
| | - Robert K Wayne
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Klaus-Peter Koepfli
- Smithsonian Conservation Biology Institute, National Zoological Park, Washington, D.C. 20008, USA; Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, Saint Petersburg 199034, Russian Federation.
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Chabot AA, Hobson KA, Van Wilgenburg SL, Pérez GE, Lougheed SC. Migratory connectivity in the Loggerhead Shrike ( Lanius ludovicianus). Ecol Evol 2018; 8:10662-10672. [PMID: 30519396 PMCID: PMC6262747 DOI: 10.1002/ece3.4415] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 04/15/2018] [Accepted: 05/06/2018] [Indexed: 11/10/2022] Open
Abstract
AIM We combine genetic and stable isotope data to quantify migration patterns in Loggerhead Shrike (Lanius ludovicianus), a species of conservation concern in North America, to assess how connectivity differs and impacts population evolution, ecology, and conservation. LOCATION We sampled shrikes across the majority of their nonbreeding range, from the Atlantic Coast to the western United States east of the Rocky Mountains and throughout Mexico. METHODS Our study used a Bayesian framework using δ2Hf from a breeding season origin feather and nuclear genetic microsatellite markers to distinguish between co-occurring migratory and nonmigratory individuals on the wintering grounds and, for migrants, to assign individuals to a breeding ground origin and genetic group. RESULTS Migratory shrikes were present throughout the nonbreeding range but the proportion differed among sample areas. Four main wintering areas were identified. Connectivity ranged from weakly negative in birds wintering on the Atlantic Coast to strongly positive between wintering grounds in the southwestern United States and Mexico and northwestern breeding populations. Connectivity was weakest in L. l. migrans, and strongest in L. l. mexicanus and L. l. excubitorides. Although believed to be nonmigratory, long-distance movements of individuals were observed in L. ludovicianus and L. l. mexicanus. Our data support a pattern of chain migration, again most notable in the western half of the species nonbreeding range, and differential migration based on age. MAIN CONCLUSIONS Our study provides of one such of the first quantitative measures of migratory connectivity and is among the first studies of a short-distance migratory passerine in North America. The higher migratory connectivity among western, versus eastern populations, and less severe population declines attributable to habitat loss or reproductive success, may result in more localized and/or less severe limiting factors for western populations and more severe on the Atlantic coast and Mississippi Alluvial Valley wintering grounds.
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Affiliation(s)
- Amy A. Chabot
- Department of BiologyQueen's UniversityKingstonOntario
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Geneva AJ, Kreit AM, Neiffer S, Tsang S, Horwitz RJ. Regional population structure of the endangered Bridle Shiner (Notropis bifrenatus). CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1074-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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32
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Doenz CJ, Bittner D, Vonlanthen P, Wagner CE, Seehausen O. Rapid buildup of sympatric species diversity in Alpine whitefish. Ecol Evol 2018; 8:9398-9412. [PMID: 30377510 PMCID: PMC6194267 DOI: 10.1002/ece3.4375] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 05/22/2018] [Accepted: 06/18/2018] [Indexed: 12/11/2022] Open
Abstract
Adaptive radiations in postglacial fish offer excellent settings to study the evolutionary mechanisms involved in the rapid buildup of sympatric species diversity from a single lineage. Here, we address this by exploring the genetic and ecological structure of the largest Alpine whitefish radiation known, that of Lakes Brienz and Thun, using microsatellite data of more than 2000 whitefish caught during extensive species-targeted and habitat-randomized fishing campaigns. We find six strongly genetically and ecologically differentiated species, four of which occur in both lakes, and one of which was previously unknown. These four exhibit clines of genetic differentiation that are paralleled in clines of eco-morphological and reproductive niche differentiation, consistent with models of sympatric ecological speciation along environmental gradients. In Lake Thun, we find two additional species, a profundal specialist and a species introduced in the 1930s from another Alpine whitefish radiation. Strong genetic differentiation between this introduced species and all native species of Lake Thun suggests that reproductive isolation can evolve among allopatric whitefish species within 15,000 years and persist in secondary sympatry. Consistent with speciation theory, we find stronger correlations between genetic and ecological differentiation for sympatrically than for allopatrically evolved species.
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Affiliation(s)
- Carmela J. Doenz
- Division of Aquatic EcologyInstitute of Ecology and EvolutionUniversity of BernBernSwitzerland
- Department of Fish Ecology & EvolutionCenter for Ecology, Evolution and BiogeochemistryEawag Swiss Federal Institute of Aquatic Science and TechnologyKastanienbaumSwitzerland
| | - David Bittner
- Department of Fish Ecology & EvolutionCenter for Ecology, Evolution and BiogeochemistryEawag Swiss Federal Institute of Aquatic Science and TechnologyKastanienbaumSwitzerland
- Fischereiverwaltung Kanton AargauAarauSwitzerland
| | - Pascal Vonlanthen
- Department of Fish Ecology & EvolutionCenter for Ecology, Evolution and BiogeochemistryEawag Swiss Federal Institute of Aquatic Science and TechnologyKastanienbaumSwitzerland
- Aquabios GmbHLes FermesCordastSwitzerland
| | - Catherine E. Wagner
- Department of Fish Ecology & EvolutionCenter for Ecology, Evolution and BiogeochemistryEawag Swiss Federal Institute of Aquatic Science and TechnologyKastanienbaumSwitzerland
- Biodiversity Institute & Department of BotanyUniversity of WyomingLaramieWYUSA
| | - Ole Seehausen
- Division of Aquatic EcologyInstitute of Ecology and EvolutionUniversity of BernBernSwitzerland
- Department of Fish Ecology & EvolutionCenter for Ecology, Evolution and BiogeochemistryEawag Swiss Federal Institute of Aquatic Science and TechnologyKastanienbaumSwitzerland
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33
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Greenhorn JE, Bowman J, Wilson PJ. Genetic monitoring suggests increasing structure following recolonization by fishers. J Wildl Manage 2018. [DOI: 10.1002/jwmg.21495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Janet E. Greenhorn
- Environmental and Life Sciences Graduate Program; Trent University; 2140 East Bank Drive Peterborough ON K9L 0G2 Canada
| | - Jeff Bowman
- Wildlife Research and Monitoring Section; Ontario Ministry of Natural Resources and Forestry; 2140 East Bank Drive Peterborough ON K9L 0G2 Canada
| | - Paul J. Wilson
- Department of Biology; Trent University; 2140 East Bank Drive Peterborough ON K9L 0G2 Canada
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Maraci Ö, Özkan H, Bilgin R. Phylogeny and genetic structure in the genus Secale. PLoS One 2018; 13:e0200825. [PMID: 30024916 PMCID: PMC6053196 DOI: 10.1371/journal.pone.0200825] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 06/29/2018] [Indexed: 11/18/2022] Open
Abstract
Secale L. is a small but important genus that includes cultivated rye. Although genetic diversity of cultivated rye is high, patterns of genetic diversity in the whole genus, and potential factors affecting the distribution of genetic diversity remain elusive. The population structure and distribution of genetic variation within Secale, and its correlation with taxonomic delimitation, cultivation status or spatial distribution in relation to geography and climate zones were analyzed in this study. A collection of 726 individual plants derived from 139 different accessions representing Secale cereale, S. vavilovii, S. strictum, and S. sylvestre were investigated using SSR analysis and sequence diversity analysis of a nuclear EST region. Our results indicated that perennial S. strictum subspecies are genetically divergent from annual forms of the genus. Existence of two distinct clusters within the annual taxa was observed, one corresponding to samples from Asia, and a second to those outside of Asia. No clear genetic structure was observed between different annual species/subspecies, indicating introgression between these taxa. The analysis of cultivated rye revealed that landrace populations from the Middle East have the highest genetic diversity, supporting the idea of the area being the center of origin for cultivated rye. Considering high adaptive potential of those populations, Middle Eastern landraces should be regarded as genetic resources reservoirs for new niches and future breeding programs.
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Affiliation(s)
- Öncü Maraci
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany
- Evolutionary Biology, Bielefeld University, Bielefeld, Germany
- Institute of Environmental Sciences, Boğaziçi University, Istanbul, Turkey
- * E-mail:
| | - Hakan Özkan
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana,Turkey
| | - Raşit Bilgin
- Institute of Environmental Sciences, Boğaziçi University, Istanbul, Turkey
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Lam AW, Gueuning M, Kindler C, Van Dam M, Alvarez N, Panjaitan R, Shaverdo H, White LT, Roderick GK, Balke M. Phylogeography and population genomics of a lotic water beetle across a complex tropical landscape. Mol Ecol 2018; 27:3346-3356. [PMID: 30010208 DOI: 10.1111/mec.14796] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 06/06/2018] [Accepted: 06/11/2018] [Indexed: 11/30/2022]
Abstract
The habitat template concept applied to a freshwater system indicates that lotic species, or those which occupy permanent habitats along stream courses, are less dispersive than lentic species, or those that occur in more ephemeral aquatic habitats. Thus, populations of lotic species will be more structured than those of lentic species. Stream courses include both flowing water and small, stagnant microhabitats that can provide refuge when streams are low. Many species occur in these microhabitats but remain poorly studied. Here, we present population genetic data for one such species, the tropical diving beetle Exocelina manokwariensis (Dytiscidae), sampled from six localities along a ~300 km transect across the Birds Head Peninsula of New Guinea. Molecular data from both mitochondrial (CO1 sequences) and nuclear (ddRAD loci) regions document fine-scale population structure across populations that are ~45 km apart. Our results are concordant with previous phylogenetic and macroecological studies that applied the habitat template concept to aquatic systems. This study also illustrates that these diverse but mostly overlooked microhabitats are promising study systems in freshwater ecology and evolutionary biology. With the advent of next-generation sequencing, fine-scale population genomic studies are feasible for small nonmodel organisms to help illuminate the effect of habitat stability on species' natural history, population structure and geographic distribution.
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Affiliation(s)
- Athena Wai Lam
- SNSB-Zoologische Staatssammlung München, Munich, Germany
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, California
| | - Morgan Gueuning
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, Switzerland
- Competence Division for Research Technology and Knowledge Exchange, Method Development and Analytics, Agroscope, Wädenswil, Switzerland
- Institute of Biology, University of Neuchatel, Neuchatel, Switzerland
| | | | - Matthew Van Dam
- SNSB-Zoologische Staatssammlung München, Munich, Germany
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, California
| | - Nadir Alvarez
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, Switzerland
| | - Rawati Panjaitan
- Department of Biology, Faculty of Sciences and Mathematics, State University of Papua (UNIPA), Manokwari, West Papua, Indonesia
| | | | - Lloyd T White
- School of Earth and Environmental Sciences, University of Wollongong, New South Wales, Australia
| | - George K Roderick
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California
| | - Michael Balke
- SNSB-Zoologische Staatssammlung München, Munich, Germany
- GeoBioCenter, Ludwig-Maximilians-Universität München, Munich, Germany
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Babst-Kostecka A, Schat H, Saumitou-Laprade P, Grodzińska K, Bourceaux A, Pauwels M, Frérot H. Evolutionary dynamics of quantitative variation in an adaptive trait at the regional scale: The case of zinc hyperaccumulation in Arabidopsis halleri. Mol Ecol 2018; 27:3257-3273. [PMID: 30010225 DOI: 10.1111/mec.14800] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 06/23/2018] [Accepted: 07/09/2018] [Indexed: 01/06/2023]
Abstract
Metal hyperaccumulation in plants is an ecological trait whose biological significance remains debated, in particular because the selective pressures that govern its evolutionary dynamics are complex. One of the possible causes of quantitative variation in hyperaccumulation may be local adaptation to metalliferous soils. Here, we explored the population genetic structure of Arabidopsis halleri at fourteen metalliferous and nonmetalliferous sampling sites in southern Poland. The results were integrated with a quantitative assessment of variation in zinc hyperaccumulation to trace local adaptation. We identified a clear hierarchical structure with two distinct genetic groups at the upper level of clustering. Interestingly, these groups corresponded to different geographic subregions, rather than to ecological types (i.e., metallicolous vs. nonmetallicolous). Also, approximate Bayesian computation analyses suggested that the current distribution of A. halleri in southern Poland could be relictual as a result of habitat fragmentation caused by climatic shifts during the Holocene, rather than due to recent colonization of industrially polluted sites. In addition, we find evidence that some nonmetallicolous lowland populations may have actually derived from metallicolous populations. Meanwhile, the distribution of quantitative variation in zinc hyperaccumulation did separate metallicolous and nonmetallicolous accessions, indicating more recent adaptive evolution and diversifying selection between metalliferous and nonmetalliferous habitats. This suggests that zinc hyperaccumulation evolves both ways-towards higher levels at nonmetalliferous sites and lower levels at metalliferous sites. Our results open a new perspective on possible evolutionary relationships between A. halleri edaphic types that may inspire future genetic studies of quantitative variation in metal hyperaccumulation.
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Affiliation(s)
- Alicja Babst-Kostecka
- W. Szafer Institute of Botany, Department of Ecology, Polish Academy of Sciences, Krakow, Poland
- CNRS, UMR 8198 - Evo-Eco-Paleo, Université de Lille - Sciences et Technologies, Villeneuve d'Ascq, France
| | - Henk Schat
- Institute of Ecological Science, Free University of Amsterdam, Amsterdam, The Netherlands
| | - Pierre Saumitou-Laprade
- CNRS, UMR 8198 - Evo-Eco-Paleo, Université de Lille - Sciences et Technologies, Villeneuve d'Ascq, France
| | - Krystyna Grodzińska
- W. Szafer Institute of Botany, Department of Ecology, Polish Academy of Sciences, Krakow, Poland
| | - Angélique Bourceaux
- CNRS, UMR 8198 - Evo-Eco-Paleo, Université de Lille - Sciences et Technologies, Villeneuve d'Ascq, France
| | - Maxime Pauwels
- CNRS, UMR 8198 - Evo-Eco-Paleo, Université de Lille - Sciences et Technologies, Villeneuve d'Ascq, France
| | - Hélène Frérot
- CNRS, UMR 8198 - Evo-Eco-Paleo, Université de Lille - Sciences et Technologies, Villeneuve d'Ascq, France
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37
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Jenkins DA, Yannic G, Schaefer JA, Conolly J, Lecomte N. Population structure of caribou in an ice-bound archipelago. DIVERS DISTRIB 2018. [DOI: 10.1111/ddi.12748] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Deborah. A. Jenkins
- Environmental and Life Sciences Graduate Program; Trent University; Peterborough ON Canada
- Canada Research Chair in Polar and Boreal Ecology and Centre d'Études Nordiques; University of Moncton; Moncton NB Canada
| | - Glenn Yannic
- University of Grenoble Alpes; University of Savoie Mont Blanc; CNRS; LECA (Laboratoire d'Ecologie Alpine); Le Bourget-du-Lac France
| | | | - James Conolly
- Department of Anthropology; Trent University; Peterborough ON Canada
| | - Nicolas Lecomte
- Canada Research Chair in Polar and Boreal Ecology and Centre d'Études Nordiques; University of Moncton; Moncton NB Canada
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38
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Spatial variation in anthropogenic mortality induces a source–sink system in a hunted mesopredator. Oecologia 2018; 186:939-951. [DOI: 10.1007/s00442-018-4072-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 01/15/2018] [Indexed: 11/25/2022]
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39
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Geography and past climate changes have shaped the evolution of a widespread lizard from the Chilean hotspot. Mol Phylogenet Evol 2017; 116:157-171. [DOI: 10.1016/j.ympev.2017.08.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 08/22/2017] [Accepted: 08/24/2017] [Indexed: 11/21/2022]
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40
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Kozal LC, Simmons JW, Mollish JM, MacGuigan DJ, Benavides E, Keck BP, Near TJ. Phylogenetic and Morphological Diversity of theEtheostoma zonistiumSpecies Complex with the Description of a New Species Endemic to the Cumberland Plateau of Alabama. BULLETIN OF THE PEABODY MUSEUM OF NATURAL HISTORY 2017. [DOI: 10.3374/014.058.0202] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Logan C. Kozal
- Department of Ecology and Evolutionary Biology, Osborn Memorial Labs, Yale University, New Haven CT 06520-8106 USA
- Berkeley College, Yale University, New Haven CT 06520-8106 USA
| | - Jeffrey W. Simmons
- Resources and River Management, Tennessee Valley Authority, Chattanooga, TN 37402-2881 USA
| | - Jon Michael Mollish
- Resources and River Management, Tennessee Valley Authority, Chattanooga, TN 37402-2881 USA
| | - Daniel J. MacGuigan
- Department of Ecology and Evolutionary Biology, Osborn Memorial Labs, Yale University, New Haven CT 06520-8106 USA
| | - Edgar Benavides
- Department of Ecology and Evolutionary Biology, Osborn Memorial Labs, Yale University, New Haven CT 06520-8106 USA
| | - Benjamin P. Keck
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996 USA
| | - Thomas J. Near
- Department of Ecology and Evolutionary Biology, Osborn Memorial Labs, Yale University, New Haven CT 06520-8106 USA; Peabody Museum of Natural History, Yale University, New Haven, CT 06520-8106 USA
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Dealing with AFLP genotyping errors to reveal genetic structure in Plukenetia volubilis (Euphorbiaceae) in the Peruvian Amazon. PLoS One 2017; 12:e0184259. [PMID: 28910307 PMCID: PMC5598967 DOI: 10.1371/journal.pone.0184259] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 08/20/2017] [Indexed: 12/04/2022] Open
Abstract
An analysis of the population structure and genetic diversity for any organism often depends on one or more molecular marker techniques. Nonetheless, these techniques are not absolutely reliable because of various sources of errors arising during the genotyping process. Thus, a complex analysis of genotyping error was carried out with the AFLP method in 169 samples of the oil seed plant Plukenetia volubilis L. from small isolated subpopulations in the Peruvian Amazon. Samples were collected in nine localities from the region of San Martin. Analysis was done in eight datasets with a genotyping error from 0 to 5%. Using eleven primer combinations, 102 to 275 markers were obtained according to the dataset. It was found that it is only possible to obtain the most reliable and robust results through a multiple-level filtering process. Genotyping error and software set up influence both the estimation of population structure and genetic diversity, where in our case population number (K) varied between 2–9 depending on the dataset and statistical method used. Surprisingly, discrepancies in K number were caused more by statistical approaches than by genotyping errors themselves. However, for estimation of genetic diversity, the degree of genotyping error was critical because descriptive parameters (He, FST, PLP 5%) varied substantially (by at least 25%). Due to low gene flow, P. volubilis mostly consists of small isolated subpopulations (ΦPT = 0.252–0.323) with some degree of admixture given by socio-economic connectivity among the sites; a direct link between the genetic and geographic distances was not confirmed. The study illustrates the successful application of AFLP to infer genetic structure in non-model plants.
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Lombaert E, Ciosi M, Miller NJ, Sappington TW, Blin A, Guillemaud T. Colonization history of the western corn rootworm (Diabrotica virgifera virgifera) in North America: insights from random forest ABC using microsatellite data. Biol Invasions 2017. [DOI: 10.1007/s10530-017-1566-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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43
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Botero-Delgadillo E, Quirici V, Poblete Y, Cuevas É, Kuhn S, Girg A, Teltscher K, Poulin E, Kempenaers B, Vásquez RA. Variation in fine-scale genetic structure and local dispersal patterns between peripheral populations of a South American passerine bird. Ecol Evol 2017; 7:8363-8378. [PMID: 29075455 PMCID: PMC5648682 DOI: 10.1002/ece3.3342] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 07/23/2017] [Accepted: 08/01/2017] [Indexed: 12/24/2022] Open
Abstract
The distribution of suitable habitat influences natal and breeding dispersal at small spatial scales, resulting in strong microgeographic genetic structure. Although environmental variation can promote interpopulation differences in dispersal behavior and local spatial patterns, the effects of distinct ecological conditions on within‐species variation in dispersal strategies and in fine‐scale genetic structure remain poorly understood. We studied local dispersal and fine‐scale genetic structure in the thorn‐tailed rayadito (Aphrastura spinicauda), a South American bird that breeds along a wide latitudinal gradient. We combine capture‐mark‐recapture data from eight breeding seasons and molecular genetics to compare two peripheral populations with contrasting environments in Chile: Navarino Island, a continuous and low density habitat, and Fray Jorge National Park, a fragmented, densely populated and more stressful environment. Natal dispersal showed no sex bias in Navarino but was female‐biased in the more dense population in Fray Jorge. In the latter, male movements were restricted, and some birds seemed to skip breeding in their first year, suggesting habitat saturation. Breeding dispersal was limited in both populations, with males being more philopatric than females. Spatial genetic autocorrelation analyzes using 13 polymorphic microsatellite loci confirmed the observed dispersal patterns: a fine‐scale genetic structure was only detectable for males in Fray Jorge for distances up to 450 m. Furthermore, two‐dimensional autocorrelation analyzes and estimates of genetic relatedness indicated that related males tended to be spatially clustered in this population. Our study shows evidence for context‐dependent variation in natal dispersal and corresponding local genetic structure in peripheral populations of this bird. It seems likely that the costs of dispersal are higher in the fragmented and higher density environment in Fray Jorge, particularly for males. The observed differences in microgeographic genetic structure for rayaditos might reflect the genetic consequences of population‐specific responses to contrasting environmental pressures near the range limits of its distribution.
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Affiliation(s)
- Esteban Botero-Delgadillo
- Instituto de Ecología y Biodiversidad Departamento de Ciencias Ecológicas Facultad de Ciencias Universidad de Chile Santiago Chile.,SELVA: Research for conservation in the Neotropics Bogotá Colombia
| | - Verónica Quirici
- Departamento de Ecología y Biodiversidad Facultad de Ecología y Recursos Naturales Universidad Andrés Bello Santiago Chile.,Centro de Investigación Para la Sustentabilidad Universidad Andrés Bello Santiago Chile
| | - Yanina Poblete
- Instituto de Ecología y Biodiversidad Departamento de Ciencias Ecológicas Facultad de Ciencias Universidad de Chile Santiago Chile.,Instituto de Ciencias Naturales Universidad de las Américas Santiago Chile
| | - Élfego Cuevas
- Doctorado en Medicina de la Conservación Facultad de Ecología y Recursos Naturales Universidad Andrés Bello Santiago Chile
| | - Sylvia Kuhn
- Department of Behavioural Ecology and Evolutionary Genetics Max Plank Institute for Ornithology Seewiesen Germany
| | - Alexander Girg
- Department of Behavioural Ecology and Evolutionary Genetics Max Plank Institute for Ornithology Seewiesen Germany
| | - Kim Teltscher
- Department of Behavioural Ecology and Evolutionary Genetics Max Plank Institute for Ornithology Seewiesen Germany
| | - Elie Poulin
- Instituto de Ecología y Biodiversidad Departamento de Ciencias Ecológicas Facultad de Ciencias Universidad de Chile Santiago Chile
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics Max Plank Institute for Ornithology Seewiesen Germany
| | - Rodrigo A Vásquez
- Instituto de Ecología y Biodiversidad Departamento de Ciencias Ecológicas Facultad de Ciencias Universidad de Chile Santiago Chile
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Danner JE, Fleischer RC, Danner RM, Moore IT. Genetic population structure in an equatorial sparrow: roles for culture and geography. J Evol Biol 2017; 30:1078-1093. [PMID: 28294451 DOI: 10.1111/jeb.13065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 03/03/2017] [Accepted: 03/06/2017] [Indexed: 11/29/2022]
Abstract
Female preference for local cultural traits has been proposed as a barrier to breeding among animal populations. As such, several studies have found correlations between male bird song dialects and population genetics over relatively large distances. To investigate whether female choice for local dialects could act as a barrier to breeding between nearby and contiguous populations, we tested whether variation in male song dialects explains genetic structure among eight populations of rufous-collared sparrows (Zonotrichia capensis) in Ecuador. Our study sites lay along a transect, and adjacent study sites were separated by approximately 25 km, an order of magnitude less than previously examined for this and most other species. This transect crossed an Andean ridge and through the Quijos River Valley, both of which may be barriers to gene flow. Using a variance partitioning approach, we show that song dialect is important in explaining population genetics, independent of the geographic variables: distance, the river valley and the Andean Ridge. This result is consistent with the hypothesis that song acts as a barrier to breeding among populations in close proximity. In addition, songs of contiguous populations differed by the same degree or more than between two populations previously shown to exhibit female preference for local dialect, suggesting that birds from these populations would also breed preferentially with locals. As expected, all geographic variables (distance, the river valley and the Andean Ridge) also predicted population genetic structure. Our results have important implications for the understanding whether, and at what spatial scale, culture can affect population divergence.
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Affiliation(s)
- J E Danner
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, Washington, DC, USA.,Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - R C Fleischer
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, Washington, DC, USA
| | - R M Danner
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - I T Moore
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
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MacGuigan DJ, Geneva AJ, Glor RE. A genomic assessment of species boundaries and hybridization in a group of highly polymorphic anoles ( distichus species complex). Ecol Evol 2017; 7:3657-3671. [PMID: 28616163 PMCID: PMC5468153 DOI: 10.1002/ece3.2751] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 08/12/2016] [Accepted: 12/22/2016] [Indexed: 02/05/2023] Open
Abstract
Delimiting young species is one of the great challenges of systematic biology, particularly when the species in question exhibit little morphological divergence. Anolis distichus, a trunk anole with more than a dozen subspecies that are defined primarily by dewlap color, may actually represent several independent evolutionary lineages. To test this, we utilized amplified fragment length polymorphisms (AFLP) genome scans and genetic clustering analyses in conjunction with a coalescent‐based species delimitation method. We examined a geographically widespread set of samples and two heavily sampled hybrid zones. We find that genetic divergence is associated with a major biogeographic barrier, the Hispaniolan paleo‐island boundary, but not with dewlap color. Additionally, we find support for hypotheses regarding colonization of two Hispaniolan satellite islands and the Bahamas from mainland Hispaniola. Our results show that A. distichus is composed of seven distinct evolutionary lineages still experiencing a limited degree of gene flow. We suggest that A. distichus merits taxonomic revision, but that dewlap color cannot be relied upon as the primary diagnostic character.
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Affiliation(s)
- Daniel J MacGuigan
- Department of Ecology and Evolutionary Biology Yale University New Haven CT USA
| | - Anthony J Geneva
- Department of Organismic and Evolutionary Biology Harvard University Cambridge MA USA
| | - Richard E Glor
- Herpetology Division Biodiversity Institute University of Kansas Lawrence KS USA.,Department of Ecology and Evolutionary Biology University of Kansas Lawrence KS USA
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Limited Dispersal and Significant Fine - Scale Genetic Structure in a Tropical Montane Parrot Species. PLoS One 2016; 11:e0169165. [PMID: 28033364 PMCID: PMC5199109 DOI: 10.1371/journal.pone.0169165] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 12/13/2016] [Indexed: 11/19/2022] Open
Abstract
Tropical montane ecosystems are biodiversity hotspots harbouring many endemics that are confined to specific habitat types within narrow altitudinal ranges. While deforestation put these ecosystems under threat, we still lack knowledge about how heterogeneous environments like the montane tropics promote population connectivity and persistence. We investigated the fine-scale genetic structure of the two largest subpopulations of the endangered El Oro parakeet (Pyrrhura orcesi) endemic to the Ecuadorian Andes. Specifically, we assessed the genetic divergence between three sites separated by small geographic distances but characterized by a heterogeneous habitat structure. Although geographical distances between sites are small (3-17 km), we found genetic differentiation between all sites. Even though dispersal capacity is generally high in parrots, our findings indicate that dispersal is limited even on this small geographic scale. Individual genotype assignment revealed similar genetic divergence across a valley (~ 3 km distance) compared to a continuous mountain range (~ 13 km distance). Our findings suggest that geographic barriers promote genetic divergence even on small spatial scales in this endangered endemic species. These results may have important implications for many other threatened and endemic species, particularly given the upslope shift of species predicted from climate change.
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48
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Rojas ER, Sueur C, Henry PY, Doligez B, Wey G, Dehorter O, Massemin S. Network Analysis Shows Asymmetrical Flows within a Bird Metapopulation. PLoS One 2016; 11:e0166701. [PMID: 27893770 PMCID: PMC5125599 DOI: 10.1371/journal.pone.0166701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 11/02/2016] [Indexed: 11/19/2022] Open
Abstract
How the spatial expansion of a species changes at a human time scale is a process difficult to determine. We studied the dispersal pattern of the French white stork population, using a 21-year ringing/resighting dataset. We used the graph-theory to investigate the strength of links between 5 populations (North-East, North-West, Centre, West, and South) and to determine factors important for the birds’ movements. Two clusters of populations were identified within the metapopulation, with most frequent movements of individuals between North-Eastern and Centre populations, and between North-Western and Western populations. Exchanges of individuals between populations were asymmetrical, where North-Eastern and North-Western populations provided more emigrants than they received immigrants. Neither the geographical distance between populations, nor the difference in densities influenced the number of individuals exchanging between populations. The graph-theory approach provides a dynamic view of individual movements within a metapopulation and might be useful for future population studies in the context of conservation.
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Affiliation(s)
| | | | - Pierre-Yves Henry
- Mécanismes adaptatifs et Evolution (MECADEV UMR7179), Sorbonne Universités, MNHN, CNRS, Muséum National d'Histoire Naturelle, 1 avenue du Petit Château, Brunoy, France
- Centre de Recherches sur la Biologie des Populations d’Oiseaux (CRBPO), Centre d’Ecologie et des Sciences de la Conservation (CESCO UMR7204), Sorbonne Universités, MNHN, CNRS, UPMC, Muséum National d’Histoire Naturelle, Paris, France
| | - Blandine Doligez
- UMR CNRS 5558 –LBBE, "Biométrie et Biologie Évolutive", Villeurbanne cedex, France
| | - Gérard Wey
- Groupe Cigognes France & APRECIAL, Colmar, France
| | - Olivier Dehorter
- Centre de Recherches sur la Biologie des Populations d’Oiseaux (CRBPO), Centre d’Ecologie et des Sciences de la Conservation (CESCO UMR7204), Sorbonne Universités, MNHN, CNRS, UPMC, Muséum National d’Histoire Naturelle, Paris, France
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Soro A, Quezada-Euan JJG, Theodorou P, Moritz RFA, Paxton RJ. The population genetics of two orchid bees suggests high dispersal, low diploid male production and only an effect of island isolation in lowering genetic diversity. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0912-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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50
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Fant JB, Price AL, Larkin DJ. The influence of habitat disturbance on genetic structure and reproductive strategies within stands of native and non-native Phragmites australis
(common reed). DIVERS DISTRIB 2016. [DOI: 10.1111/ddi.12492] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Jeremie B. Fant
- Plant Science and Conservation; Chicago Botanic Garden; 1000 Lake Cook Road Glencoe IL 60022 USA
- Plant Biology and Conservation; Northwestern University; Evanston IL 60208 USA
| | - Amy L. Price
- Plant Science and Conservation; Chicago Botanic Garden; 1000 Lake Cook Road Glencoe IL 60022 USA
- Plant Biology and Conservation; Northwestern University; Evanston IL 60208 USA
| | - Daniel J. Larkin
- Plant Science and Conservation; Chicago Botanic Garden; 1000 Lake Cook Road Glencoe IL 60022 USA
- Department of Fisheries, Wildlife, and Conservation Biology; Minnesota Aquatic Invasive Species Research Center; University of Minnesota; St. Paul MN 55108 USA
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