Genetic and Phylogenetic Analyses of Endangered Species

O’Brien, SJ

doi:10.1146/annurev.genet.28.1.467

Cited by 25 publications

(30 citation statements)

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“…(Gravuer et al 2005), but there are no guidelines to indicate which features and what levels of significance will indicate whether plants from particular populations can be safely associated. Base sequences give precise information about divergence in certain genetic regions, but may not be representative of variation in the entire genome and may not pertain to fitness (O'Brien 1994). Breeding systems also complicate assessment of appropriate levels of variation for a population (Falk et al 1996).…”

Section: Enriching the Gene Pool Of Declining Populationsmentioning

confidence: 99%

Is transplanting an effective means of preserving vegetation?

Fahselt

2007

Can. J. Bot.

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Transplantation to new locations is used widely to propagate horticultural and agricultural species but is also promoted as a means of relocating whole communities that stand in the way of development. It may be used as well to move vegetation from the field for experimentation under controlled conditions. Transplantation has not in the past been considered a reliable means of conserving threatened species or reproducing functional characteristics of natural communities, and has been regarded by many as highly ineffective. However, its potential must now be re-examined because of the many recent transplant attempts as well as advances in related fields. Recent trials illustrate that individual endangered species are still particularly difficult to transplant and displaced multi-species sods are almost always changed in the process. Exact reconstruction of communities from individual components is next to impossible because the full complement of species, including critical microbial components, is almost never known. Owing to a limited understanding of phenology, reproduction, functional roles, and interrelationships among constituent microbes, cryptogams, vascular plants, and fauna, transplants may be placed into sites with both biological and physical insufficiencies. Genetic diversity may be lost or, if genotypes from diverse sources are mixed, outbreeding depression may result. Recent advances in soil science, microbial ecology, and population genetics have in some cases improved the effectiveness of transplantation, but new insights mainly permit a fuller appreciation of the causes of failure. Home-site advantage has been demonstrated, and habitat protection appears to be the best and perhaps only reliable way of preserving intact natural communities and rare species. Furthermore, experimentation with vegetational mats under controlled conditions may have little relevance to natural ecosystems.Key words: vegetation, simulation, transplantation, conservation, home-site advantage.Résumé : On utilise souvent la transplantation sur de nouveaux sites pour propager les plantes et stabiliser les paysages perturbés, cependant plusieurs considèrent ce procédé hautement inefficace comme méthode fiable pour conserver les espè-ces menacées et les communautés naturelles. Tout de même, on doit réexaminer sa pertinence, compte tenu de nombreux essais récents de transplantation, ainsi que de progrès dans les domaines connexes. Dans des essais récents, on a constaté, que les espèces menacées demeurent particulièrement difficiles à transplanter, et que le patron des communautés en tapis d'espèces multiples, se modifie presque toujours au cours du processus. La reconstruction exacte des communautés, à partir des composantes individuelles frôle l'impossible parce que l'apport de la totalité des espèces, incluant les composantes microbiennes, demeure presque toujours un inconnu. Comme on comprend peu la phénologie, la reproduction, les rôles fonctionnels et les interrelations entre les microbes, les cryptogames, les p...

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Section: Enriching the Gene Pool Of Declining Populationsmentioning

confidence: 99%

Is transplanting an effective means of preserving vegetation?

Fahselt

2007

Can. J. Bot.

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“…Causes for immunologic suppression in manatees include low water temperature (4) and a reduction in population size. Reduced diversity of genes that mediate immune defenses, particularly the major histocompatibility complex genes, due to genetic bottlenecks can lead to increased population sensitivity to infectious agents (12), and an increased prevalence and severity of PV-related pathology is often seen in populations that went through a historic genetic bottleneck (15,20,21).…”

Section: Vol 78 2004 Notes 12699mentioning

confidence: 99%

Characterization of a Novel Close-to-Root Papillomavirus from a Florida Manatee by Using Multiply Primed Rolling-Circle Amplification: Trichechus manatus latirostris Papillomavirus Type 1

Rector

Bossart

Ghim

et al. 2004

J Virol

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By using an isothermal multiply primed rolling-circle amplification protocol, the complete genomic DNA of a novel papillomavirus was amplified from a skin lesion biopsy of a Florida manatee (Trichechus manatus latirostris), one of the most endangered marine mammals in United States coastal waters. The nucleotide sequence, genome organization, and phylogenetic position of the Trichechus manatus latirostris papillomavirus type 1 (TmPV-1) were determined. TmPV-1 is the first virus isolated from the order of Sirenia. A phylogenetic analysis shows that TmPV-1 is only distantly related to other papillomavirus sequences, and it appears in our phylogenetic tree as a novel close-to-root papillomavirus genus.Papillomaviruses (PVs) are a large group of epitheliotropic pathogens that cause proliferations of the stratified squamous epithelium in a wide variety of host species. Ninety-three different types of human PV (HPV), causing a wide spectrum of genotype-specific lesions (22), have been completely genomically characterized (9). Although only a limited number of nonhuman PVs have been fully characterized, they cover a broad range of host species (9,14,16). Considering the numerous partial sequences of putative novel animal PVs published recently (2) and the large number of suspected PV infections in animals, based on clinical, histopathological, electron microscopic, and immunohistochemical findings (14), the PV genotype variety in nonhuman vertebrates might exceed that of the HPVs, and every vertebrate species could have its own set of PVs.The Florida manatee (Trichechus manatus latirostris) belongs to the order of Sirenia and is presently listed as an endangered species. Natural disease in manatees is uncommon (3,7,8), and the majority of manatee deaths are directly or indirectly attributable to human activities, as is the case for collisions with watercrafts and habitat degradation (3). In 1997, seven captive manatees from the Homosassa Springs State Wildlife Park, Homosassa, Florida, developed multiple pedunculated cutaneous papillomas, distributed over the leading contact regions of the anterior body. Four of these animals subsequently developed topically and clinically distinct sessile papillomas which were more diffuse and numerous and frequently showed a linear distribution along lines of scratch marks or trauma. In both lesion types, PVs were suspected as a causative agent, based on histological, ultrastructural, and immunohistochemical data (5). Papillomatous skin lesions have since been observed in free-ranging Florida manatees, and fragmental PV DNA sequences were obtained from these lesions by degenerate primer PCR (

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“…This loss of additive genetic variation decreases heritability (i.e., the proportion of phenotypic variation (V P ) that is heritable, h 2 ϭ V A /V P ). Decreases in heritability can then be directly related to decreases in adaptive potential by the standard breeder's equation, R ϭ h 2 S. These expectations have been validated in several experimental studies, which have measured either heritability (Whitlock and Fowler 1999;Saccheri et al 2001) or the response to artificial selection (James 1971;Frankham 1980;Franklin 1980;Lopez-Fanjul et al 1989;Wade et al 1996) immediately following bottleneck events.If the loss of genetic variation occurs gradually over an extended number of generations (e.g., O'Brien 1994;Taylor et al 1994), rather than during a rapid bottleneck event, then this basic drift model must be extended to incorporate the polygenic mutation rate (V M ). Under the drift-mutation (DM) model, the expected change in additive genetic variance is V M Ϫ V A /2N e each generation (Clayton and Robertson 1955), which eventually leads to a nonzero heritability of 2N e V M /…”

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confidence: 99%

“…If the loss of genetic variation occurs gradually over an extended number of generations (e.g., O'Brien 1994;Taylor et al 1994), rather than during a rapid bottleneck event, then this basic drift model must be extended to incorporate the polygenic mutation rate (V M ). Under the drift-mutation (DM) model, the expected change in additive genetic variance is V M Ϫ V A /2N e each generation (Clayton and Robertson 1955), which eventually leads to a nonzero heritability of 2N e V M / (2N e V M ϩ V E ) once drift-mutation equilibrium has been established (Lynch and Hill 1986).…”

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confidence: 99%

Modeling the Adaptive Potential of Isolated Populations: Experimental Simulations Using Drosophila

Bouzat¹

2005

Evolution

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Abstract. The genetic variability underlying many morphological and stress resistance traits may largely depend on the effects of genetic drift balanced by polygenic mutation. This model of adaptive potential has played a central role in the minimum viable population size concept and has been used to predict the effective population size necessary to prevent extinction within changing environments. However, there have been few long-term experimental studies of adaptive potential within isolated populations, and no study has thus far provided an experimental test of the driftmutation model of quantitative genetic variation. Using the sternopleural bristle number of Drosophila melanogaster as a model quantitative trait, we performed repeated measurements of adaptive potential on 15 replicate populations of two and 10 male-female pairs over 30 and 77 generations, respectively. Declines in adaptive potential were analyzed by comparing observed and expected changes in realized heritability over time. The only significant model deviation occurred immediately after bottlenecks of two pairs, in which greater than expected declines in realized heritability were observed. This result suggests that changes in allelic diversity during bottleneck events may be as important as changes in heterozygosity in determining adaptive potential. Drift-mutation model expectations were otherwise realized over all generations. Our results validate the use of the drift-mutation model as a tool for understanding the dynamics of adaptive potential for peripheral fitness characters, but suggest caution in applying this model to recently bottlenecked populations.Key words. Drift, genetic variation, heritability, heterozygosity, inbreeding, selection. The potential for populations to undergo short-term adaptive change depends upon the extent of genetic variability present among individuals (Fisher 1930). Processes affecting genetic variability within populations are therefore of special interest to the study of evolution and the preservation of endangered species (Lynch 1996;Hill 2000;Frankham et al. 2002). In isolated populations of small size, the amount of variation lost by genetic drift is much greater than that regenerated by polygenic mutation. As a consequence, small populations may lack the genetic variation required to respond adaptively to environmental selection pressures, which may elevate the extinction risk of such populations (Geber and Dawson 1993;Hoffman and Blows 1993;Lynch and Lande 1993;Burger and Lynch 1995). The development of theoretical models has thus been pursued with the aim of predicting changes in genetic variability and adaptive potential within small populations (Clayton and Robertson 1955;Lande 1976;Lynch and Hill 1986). These approaches have been useful for estimating the effective population size necessary to maintain high levels of adaptive potential (i.e., additive genetic variation; Franklin 1980; Lande and Barrowclough 1987;Franklin and Frankham 1998). To maintain adaptive potential within a population, th...

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Genetic and Phylogenetic Analyses of Endangered Species

Cited by 25 publications

References 0 publications

Is transplanting an effective means of preserving vegetation?

Is transplanting an effective means of preserving vegetation?

Characterization of a Novel Close-to-Root Papillomavirus from a Florida Manatee by Using Multiply Primed Rolling-Circle Amplification: Trichechus manatus latirostris Papillomavirus Type 1

Modeling the Adaptive Potential of Isolated Populations: Experimental Simulations Using Drosophila

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