What Are the Best Correlates of Predicted Extinction Risk?
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Effective Population Size and Genetic Conservation Criteria for Bull Trout
North American Journal of Fisheries Management 21:756±764, 2001 q Copyright by the American Fisheries Society 2001 Effective Population Size and Genetic Conservation Criteria for Bull Trout B. E. RIEMAN* U.S. Department of Agriculture Forest Service, Rocky Mountain Research Station, 316 East Myrtle, Boise, Idaho 83702, USA F. W. A LLENDORF Division of Biological Sciences, University of Montana, Missoula, Montana 59812, USA Abstract.ÐEffective population size (Ne) is an important concept in the management of threatened species like bull trout Salvelinus con¯uentus. General guidelines suggest that effective population sizes of 50 or 500 are essential to minimize inbreeding effects or maintain adaptive genetic variation, respectively. Although Ne strongly depends on census population size, it also depends on demographic and life history characteristics that complicate any estimates. This is an especially dif®cult problem for species like bull trout, which have overlapping generations; biologists may monitor annual population number but lack more detailed information on demographic population structure or life history. We used a generalized, age-structured simulation model to relate Ne to adult numbers under a range of life histories and other conditions characteristic of bull trout populations. Effective population size varied strongly with the effects of the demographic and environmental variation included in our simulations. Our most realistic estimates of Ne were between about 0.5 and 1.0 times the mean number of adults spawning annually. We conclude that cautious long-term management goals for bull trout populations should include an average of at least 1,000 adults spawning each year. Where local populations are too small, managers should seek to conserve a collection of interconnected populations that is at least large enough in total to meet this minimum. -
Genetic and Demographic Dynamics of Small Populations of Silene Latifolia
Heredity (2003) 90, 181–186 & 2003 Nature Publishing Group All rights reserved 0018-067X/03 $25.00 www.nature.com/hdy Genetic and demographic dynamics of small populations of Silene latifolia CM Richards, SN Emery and DE McCauley Department of Biological Sciences, Vanderbilt University, PO Box 1812, Station B, Nashville, TN 37235, USA Small local populations of Silene alba, a short-lived herbac- populations doubled in size between samples, while others eous plant, were sampled in 1994 and again in 1999. shrank by more than 75%. Similarly, expected heterozygosity Sampling included estimates of population size and genetic and allele number increased by more than two-fold in diversity, as measured at six polymorphic allozyme loci. individual populations and decreased by more than three- When averaged across populations, there was very little fold in others. When population-specific change in number change between samples (about three generations) in and change in measures of genetic diversity were considered population size, measures of within-population genetic together, significant positive correlations were found be- diversity such as number of alleles or expected hetero- tween the demographic and genetic variables. It is specu- zygosity, or in the apportionment of genetic diversity within lated that some populations were released from the and among populations as measured by Fst. However, demographic consequences of inbreeding depression by individual populations changed considerably, both in terms gene flow. of numbers of individuals and genetic composition. Some Heredity (2003) 90, 181–186. doi:10.1038/sj.hdy.6800214 Keywords: genetic diversity; demography; inbreeding depression; gene flow Introduction 1986; Lynch et al, 1995), the interaction of genetics and demography could also influence population persistence How genetics and demography interact to influence in common species, because it is generally accepted that population viability has been a long-standing question in even many abundant species are not uniformly distrib- conservation biology. -
Spatial Criteria Used in IUCN Assessment Overestimate Area of Occupancy for Freshwater Taxa
Spatial Criteria Used in IUCN Assessment Overestimate Area of Occupancy for Freshwater Taxa By Jun Cheng A thesis submitted in conformity with the requirements for the degree of Masters of Science Ecology and Evolutionary Biology University of Toronto © Copyright Jun Cheng 2013 Spatial Criteria Used in IUCN Assessment Overestimate Area of Occupancy for Freshwater Taxa Jun Cheng Masters of Science Ecology and Evolutionary Biology University of Toronto 2013 Abstract Area of Occupancy (AO) is a frequently used indicator to assess and inform designation of conservation status to wildlife species by the International Union for Conservation of Nature (IUCN). The applicability of the current grid-based AO measurement on freshwater organisms has been questioned due to the restricted dimensionality of freshwater habitats. I investigated the extent to which AO influenced conservation status for freshwater taxa at a national level in Canada. I then used distribution data of 20 imperiled freshwater fish species of southwestern Ontario to (1) demonstrate biases produced by grid-based AO and (2) develop a biologically relevant AO index. My results showed grid-based AOs were sensitive to spatial scale, grid cell positioning, and number of records, and were subject to inconsistent decision making. Use of the biologically relevant AO changed conservation status for four freshwater fish species and may have important implications on the subsequent conservation practices. ii Acknowledgments I would like to thank many people who have supported and helped me with the production of this Master’s thesis. First is to my supervisor, Dr. Donald Jackson, who was the person that inspired me to study aquatic ecology and conservation biology in the first place, despite my background in environmental toxicology. -
4 Genetics of Small Populations: the Case of the Laysan Finch
Case Studies in Ecology and Evolution DRAFT 4 Genetics of Small Populations: the case of the Laysan Finch In 1903, rabbits were introduced to a tiny island in the Hawaiian archipelago called Laysan Island. That island is only 187 ha in size, in the middle of the Pacific Ocean about 1000 km northeast of Hawaii. Despite the benign intentions for having rabbits on the island, the released rabbits quickly multiplied and devoured most of the vegetation. Oceanic islands are often home to unique or endemic species that have evolved in isolation. Laysan was no exception. Well-known examples of island endemics include the finches on the Galapagos Islands and the dodo that was only known from the islands of Mauritius. On Laysan there were several species of birds and plants that were known only from that single island. The introduced rabbits on the island destroyed the food supply for various species of land birds. Several endemic species of plants and animals were driven extinct, including the Laysan rail, the Laysan honeycreeper, the millerbird, and plants like the Laysan fan palm. Only 4 of 26 species of plants remained on the island in 1923, 20 years after the rabbits first arrived. Populations of other species declined to very small levels. One of the two surviving endemic land birds was a small finch called the Laysan finch, Telespiza cantans. After the rabbits were finally exterminated in 1923, the population of finches recovered on Laysan Island. Over the last four decades the average population size of on Laysan Island has been about 11,000 birds. -
Detecting Patterns of Species Diversification in the Presence of Both Rate Shifts and Mass Extinctions
Version dated: August 3, 2021 Detecting patterns of species diversification in the presence of both rate shifts and mass extinctions Sacha Laurent12, Marc Robinson-Rechavi12, and Nicolas Salamin12 1Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland 2Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland (Keywords: Phylogeny, Diversification, Mass Extinctions) Abstract Background: Recent methodological advances allow better examination of speciation and extinction processes and patterns. A major open question is the origin of large discrepancies in species number between groups of the same age. Existing frameworks to model this diversity either focus on changes between lineages, neglecting global effects such as mass arXiv:1404.5441v3 [q-bio.PE] 31 Aug 2015 extinctions, or focus on changes over time which would affect all lineages. Yet it seems probable that both lineages differences and mass extinctions affect the same groups. Results: Here we used simulations to test the performance of two widely used methods under complex scenarios of diversification. We report good performances, although with a tendency to over-predict events with increasing complexity of the scenario. Conclusion: Overall, we find that lineage shifts are better detected than mass extinctions. This work has significance to assess the methods currently used to estimate changes in diversification using phylogenetic trees. Our results also point toward the need to develop new models of diversification to expand our capabilities to analyse realistic and complex evolutionary scenarios. Background The estimation of the rates of speciation and extinction provides important information on the macro-evolutionary processes shaping biodiversity through time (Ricklefs 2007). Since the seminal paper by Nee et al: Nee et al. -
Amphibian Cascades Frog SOC X X Mountain Meadows, Bogs, Ponds Or
Taxa Species Species SMU/ESU/D Federal State BM CP CR EC KM NR WC WV NS Special needs Limiting factors Data gaps Conservation actions Key reference or plan, if available Common Scientific PS/Group Listing listing Name Name Status status Amphibian Cascades SOC X X Mountain meadows, bogs, ponds or potholes Montane species vulnerable to genetic Habitat requirements and how they may vary by Maintain connectivity of habitat. Monitor effects of fish http://www.fs.fed.us/psw/publications/documents/ frog above 2,400 feet elevation. Requires access isolation. Experiencing substantial elevation within the species' range. Habitat stocking and water quality on populations. Carefully manage psw_gtr244/psw_gtr244.pdf to permanent water. Lays eggs in shallow reductions in southern parts of range characteristics that could enhance migration livestock grazing in occupied wet meadows. Use prescribed sunny edges of ponds, or on low vegetation (e.g., CA). Potentially sensitive to and gene flow. Feeding habits. Effects of burning or hand-felling of trees periodically to set plant near ponds where warm sunlight speeds egg waterborne pathogens. pathogens airborne environmental pollution. succession. If reintroductions are warranted, use individuals development. Larvae may “school” in large Feasibility studies on reintroduction at historic from nearby populations and consult results of feasibility masses. sites. studies. Conservation actions in Oregon are particularly valuable given reductions in other parts of range. Amphibian Cascade X X Cold, fast-flowing, clear, permanent headwater Larvae take several years to reach sexual Basic inventory, abundance and population Maintain stream buffers to maintain cool water Howell, B.L. and N. M. Maggiulli. 2011. -
Understanding the Ecology of Extinction: Are We Close to the Critical Threshold?
Ann. Zool. Fennici 40: 71–80 ISSN 0003-455X Helsinki 30 April 2003 © Finnish Zoological and Botanical Publishing Board 2003 Understanding the ecology of extinction: are we close to the critical threshold? Tim G. Benton Institute of Biological Sciences, University of Stirling, FK9 4LA, UK (e-mail: [email protected]) Received 25 Nov. 2002, revised version received 20 Jan. 2003, accepted 21 Jan. 2003 Benton, T. G. 2003: Understanding the ecology of extinction: are we close to the critical threshold? — Ann. Zool. Fennici 40: 71–80. How much do we understand about the ecology of extinction? A review of recent lit- erature, and a recent conference in Helsinki gives a snapshot of the “state of the art”*. This “snapshot” is important as it highlights what we currently know, the tools avail- able for studying the process of extinction, its ecological correlates, and the theory concerning extinction thresholds. It also highlights that insight into the ecology of extinction can come from areas as diverse as the study of culture, the fossil record and epidemiology. Furthermore, it indicates where the gaps in knowledge and understand- ing exist. Of particular note is the need either to generate experimental data, or to make use of existing empirical data — perhaps through meta-analyses, to test general theory and guide its future development. Introduction IUCNʼs 2002 Red List, a total of 11 167 species are currently known to be threatened (http:// Few would argue that managing natural popu- www.redlist.org/info/tables/table1.html), though lations and their habitats is one of the greatest this is a gross underestimate of the true value, as, challenges for humans in the 21st century. -
Prominent Role of Invasive Species in Avian Biodiversity Loss
Biological Conservation 142 (2009) 2043–2049 Contents lists available at ScienceDirect Biological Conservation journal homepage: www.elsevier.com/locate/biocon Prominent role of invasive species in avian biodiversity loss Miguel Clavero a,b,*, Lluís Brotons a, Pere Pons b, Daniel Sol c a Grup d’Ecologia del Paisatge, Àrea de Biodiversitat, Centre Tecnològic Forestal de Catalunya, Pujada del Seminari s/n. 25280 Solsona, Catalonia, Spain b Departament de Ciències Ambientals, Universitat de Girona, Campus de Montilivi, 17071 Girona, Catalonia, Spain c CREAF-CSIC (Centre for Ecological Research and Applied Forestries—Spanish National Research Council), Autonomous University of Barcelona, E-08193 Bellaterra, Catalonia, Spain article info abstract Article history: The rise of extinction rates associated with human activities has led to a growing interest in identifying Received 20 January 2009 extinction-prone taxa and extinction-promoting drivers. Previous work has identified habitat alterations Received in revised form 23 March 2009 and invasive species as the major drivers of recent bird extinctions. Here, we extend this work to ask how Accepted 29 March 2009 these human-driven impacts differentially affect extinction-prone taxa, and if any specific driver pro- Available online 28 April 2009 motes taxonomic homogenization of avifauna. Like most previous studies, our analysis is based on global information of extinction drivers affecting threatened and extinct bird species from the IUCN Red List. Keywords: Unlike previous studies, we employ a multivariate statistical framework that allows us to identify the Extinction risk main gradients of variation in extinction drivers. By using these gradients, we show that bird families Extinction drivers Biotic homogenization with the highest extinction risk are primarily associated with threats posed by invasive species, once spe- Invasive species cies richness and phylogeny are taken into account. -
David M. Raup 1933–2015
David M. Raup 1933–2015 A Biographical Memoir by Michael Foote and Arnold I. Miller ©2017 National Academy of Sciences. Any opinions expressed in this memoir are those of the authors and do not necessarily reflect the views of the National Academy of Sciences. DAVID MALCOLM RAUP April 24, 1933–July 9, 2015 Elected to the NAS, 1979 David M. Raup, one of the most influential paleontolo- gists of the second half of the 20th century, infused the field with concepts from modern biology and established several major lines of research that continue today: Theoretical morphology. Why, despite eons of evolution, is the spectrum of realized biological forms such a tiny fraction of those that are theoretically possible? First-order patterns in the geologic history of biodiversity. Has biodiversity increased steadily over time? What does the answer imply about the biosphere and the nature of the fossil record? Mathematical modeling of evolution. What By Michael Foote patterns result, for example, from the structure of evolu- and Arnold I. Miller tionary trees? And what is the apparent order that emerges from stochastic processes? Biological extinction. What temporal patterns are evident in the history of life and what are their implications for the drivers of extinction and for Earth’s place in the cosmos? The pilot and the paleontologist In The Right Stuff(1979), author Tom Wolfe observed that the calm West Virginia drawl of the renowned test pilot and World War II ace Chuck Yeager could still be heard in the voices of virtually all commercial pilots, decades after Yeager became the first to break the sound barrier. -
Fish-Movement Ecology in High-Gradient Headwater Streams: Its Relevance to Fish Passage Restoration Through Stream Culvert Barriers
Fish-Movement Ecology in High-Gradient Headwater Streams: Its Relevance to Fish Passage Restoration Through Stream Culvert Barriers Hoffman, R., and Dunham, J. Open-File Report 2007–1140 U.S. Department of the Interior U.S. Geological Survey U.S. Department of the Interior DIRK KEMPTHORNE, Secretary U.S. Geological Survey Mark D. Myers, Director U.S. Geological Survey, Reston, Virginia 2007 Revised and reprinted: 2007 For product and ordering information: World Wide Web: http://www.usgs.gov/pubprod Telephone: 1-888-ASK-USGS For more information on the USGS—the Federal source for science about the Earth, its natural and living resources, natural hazards, and the environment: World Wide Web: http://www.usgs.gov Telephone: 1-888-ASK-USGS Suggested citation: Hoffman, R., and Dunham, J., 2007, Fish Movement Ecology in High Gradient Headwater Streams: Its Relevance to Fish Passage Restoration Through Stream Culvert Barriers: U.S. Geological Survey, OFR 2007- 1140, p. 40. Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government. Although this report is in the public domain, permission must be secured from the individual copyright owners to reproduce any copyrighted material contained within this report. ii Contents Contents ..............................................................................................................................................................................iii Executive Summary............................................................................................................................................................1 -
Long Term Evolutionary Responses to Whole Genome Duplication
Unicentre CH-1015 Lausanne http://serval.unil.ch Year : 2016 Long term evolutionary responses to whole genome duplication Sacha Laurent Sacha Laurent, 2016, Long term evolutionary responses to whole genome duplication Originally published at : Thesis, University of Lausanne Posted at the University of Lausanne Open Archive http://serval.unil.ch Document URN : urn:nbn:ch:serval-BIB_8E5536BAC6042 Droits d’auteur L'Université de Lausanne attire expressément l'attention des utilisateurs sur le fait que tous les documents publiés dans l'Archive SERVAL sont protégés par le droit d'auteur, conformément à la loi fédérale sur le droit d'auteur et les droits voisins (LDA). A ce titre, il est indispensable d'obtenir le consentement préalable de l'auteur et/ou de l’éditeur avant toute utilisation d'une oeuvre ou d'une partie d'une oeuvre ne relevant pas d'une utilisation à des fins personnelles au sens de la LDA (art. 19, al. 1 lettre a). A défaut, tout contrevenant s'expose aux sanctions prévues par cette loi. Nous déclinons toute responsabilité en la matière. Copyright The University of Lausanne expressly draws the attention of users to the fact that all documents published in the SERVAL Archive are protected by copyright in accordance with federal law on copyright and similar rights (LDA). Accordingly it is indispensable to obtain prior consent from the author and/or publisher before any use of a work or part of a work for purposes other than personal use within the meaning of LDA (art. 19, para. 1 letter a). Failure to do so will expose offenders to the sanctions laid down by this law. -
Forecasting Extinctions: Uncertainties and Limitations
Diversity 2009, 1, 133-150; doi:10.3390/d1020133 OPEN ACCESS diversity ISSN 2071-1050 www.mdpi.com/journal/diversity Review Forecasting Extinctions: Uncertainties and Limitations Richard J. Ladle 1,2 1 School of Geography and the Environment, Oxford University, South Parks Road, Oxford, UK; E-Mail: [email protected]; Tel.: +55-31-3899 1902; Fax: +55-31-3899-2735 2 Department of Agricultural and Environmental Engineering, Federal University of Viçosa, Viçosa, Brazil Received: 13 October 2009 / Accepted: 14 November 2009 / Published: 26 November 2009 Abstract: Extinction forecasting is one of the most important and challenging areas of conservation biology. Overestimates of extinction rates or the extinction risk of a particular species instigate accusations of hype and overblown conservation rhetoric. Conversely, underestimates may result in limited resources being allocated to other species/habitats perceived as being at greater risk. In this paper I review extinction models and identify the key sources of uncertainty for each. All reviewed methods which claim to estimate extinction probabilities have severe limitations, independent of if they are based on ecological theory or on rather subjective expert judgments. Keywords: extinction; uncertainty; forecasting; local extinction; viability 1. Introduction ―Prediction is very difficult, especially about the future‖ Nils Bohr, Nobel Prize winning physicist Preventing the extinction of species is probably the most emblematic objective of the global conservation movement. To fulfill this aim effectively requires that decision makers and environmental managers are provided with accurate information on: (1) the identities of specific species/populations with a high probability of going extinct without further interventions; (2) the predicted rates of extinction among a range of taxa in different geographic areas and biomes under various ecological scenarios.