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Natusch D, Aust PW, Caraguel C, Taggart PL, Ngo VT, Alexander GJ, Shine R, Coulson T. Python farming as a flexible and efficient form of agricultural food security. Sci Rep 2024; 14:5419. [PMID: 38485710 PMCID: PMC10940618 DOI: 10.1038/s41598-024-54874-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 02/17/2024] [Indexed: 03/18/2024] Open
Abstract
Diminishing natural resources and increasing climatic volatility are impacting agri-food systems, prompting the need for sustainable and resilient alternatives. Python farming is well established in Asia but has received little attention from mainstream agricultural scientists. We measured growth rates in two species of large pythons (Malayopython reticulatus and Python bivittatus) in farms in Thailand and Vietnam and conducted feeding experiments to examine production efficiencies. Pythons grew rapidly over a 12-month period, and females grew faster than males. Food intake and growth rates early in life were strong predictors of total lifetime growth, with daily mass increments ranging from 0.24 to 19.7 g/day for M. reticulatus and 0.24 to 42.6 g/day for P. bivittatus, depending on food intake. Pythons that fasted for up to 4.2 months lost an average of 0.004% of their body mass per day, and resumed rapid growth as soon as feeding recommenced. Mean food conversion rate for dressed carcasses was 4.1%, with useable products (dressed carcass, skin, fat, gall bladder) comprising 82% of the mass of live animals. In terms of food and protein conversion ratios, pythons outperform all mainstream agricultural species studied to date. The ability of fasting pythons to regulate metabolic processes and maintain body condition enhances food security in volatile environments, suggesting that python farming may offer a flexible and efficient response to global food insecurity.
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Affiliation(s)
- D Natusch
- School of Natural Sciences, Macquarie University, Sydney, NSW, 2109, Australia.
| | - P W Aust
- Department of Zoology, University of Oxford, Oxford, UK
- Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - C Caraguel
- School of Animal & Veterinary Science, The University of Adelaide, Adelaide, SA, 5371, Australia
| | - P L Taggart
- School of Animal & Veterinary Science, The University of Adelaide, Adelaide, SA, 5371, Australia
| | - V T Ngo
- National Key Laboratory, Institute of Tropical Biology, Vietnamese Academy of Sciences and Technology, 9/621 Hanoi Highway, Thu Duc City, Ho Chi Minh City, Vietnam
| | - G J Alexander
- Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - R Shine
- School of Natural Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - T Coulson
- Department of Zoology, University of Oxford, Oxford, UK
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Affiliation(s)
- M. J. Brouard
- E2D Ecological and Evolutionary Dynamics Department of Zoology University of Oxford Oxford UK
| | | | - S. Dressen
- DER GRÜNE ZOO WUPPERTAL Wuppertal Germany
| | - T. Coulson
- E2D Ecological and Evolutionary Dynamics Department of Zoology University of Oxford Oxford UK
| | - A. F. Malo
- GLOCEE - Global Change Ecology and Evolution Group Universidad de Alcala Madrid Spain
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Murray PG, Hanson D, Coulson T, Stevens A, Whatmore A, Poole RL, Mackay DJ, Black GCM, Clayton PE. 3-M syndrome: a growth disorder associated with IGF2 silencing. Endocr Connect 2013; 2:225-35. [PMID: 24148222 PMCID: PMC3847915 DOI: 10.1530/ec-13-0065] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 10/22/2013] [Indexed: 12/30/2022]
Abstract
3-M syndrome is an autosomal recessive disorder characterised by pre- and post-natal growth restriction, facial dysmorphism, normal intelligence and radiological features (slender long bones and tall vertebral bodies). It is known to be caused by mutations in the genes encoding cullin 7, obscurin-like 1 and coiled-coil domain containing 8. The mechanisms through which mutations in these genes impair growth are unclear. The aim of this study was to identify novel pathways involved in the growth impairment in 3-M syndrome. RNA was extracted from fibroblast cell lines derived from four 3-M syndrome patients and three control subjects, hybridised to Affymetrix HU 133 plus 2.0 arrays with quantitative real-time PCR used to confirm changes found on microarray. IGF-II protein levels in conditioned cell culture media were measured by ELISA. Of the top 10 downregulated probesets, three represented IGF2 while H19 was identified as the 23rd most upregulated probeset. QRT-PCR confirmed upregulation of H19 (P<0.001) and downregulation of IGF2 (P<0.001). Levels of IGF-II secreted into conditioned cell culture medium were higher for control fibroblasts than those for 3-M fibroblasts (10.2±2.9 vs 0.6±0.9 ng/ml, P<0.01). 3-M syndrome is associated with a gene expression profile of reduced IGF2 expression and increased H19 expression similar to that found in Silver-Russell syndrome. Loss of autocrine IGF-II in the growth plate may be associated with the short stature seen in children with 3-M syndrome.
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Affiliation(s)
- P G Murray
- Centre for Paediatrics and Child HealthInstitute of Human Development, Faculty of Medical and Human Sciences, University of ManchesterManchesterUK
- 5th Floor Research, Royal Manchester Children's HospitalCentral Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences CentreOxford Road, Manchester, M13 9WLUK
| | - D Hanson
- Centre for Paediatrics and Child HealthInstitute of Human Development, Faculty of Medical and Human Sciences, University of ManchesterManchesterUK
| | - T Coulson
- Centre for Paediatrics and Child HealthInstitute of Human Development, Faculty of Medical and Human Sciences, University of ManchesterManchesterUK
| | - A Stevens
- Centre for Paediatrics and Child HealthInstitute of Human Development, Faculty of Medical and Human Sciences, University of ManchesterManchesterUK
| | - A Whatmore
- Centre for Paediatrics and Child HealthInstitute of Human Development, Faculty of Medical and Human Sciences, University of ManchesterManchesterUK
| | - R L Poole
- Faculty of MedicineUniversity of SouthamptonSouthamptonUK
| | - D J Mackay
- Faculty of MedicineUniversity of SouthamptonSouthamptonUK
| | - G C M Black
- Centre for Genetic Medicine, Institute of Human DevelopmentFaculty of Medical and Human Sciences, University of ManchesterManchesterUK
- Genetic Medicine, St Mary's HospitalCentral Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences CentreOxford Road, Manchester, M13 9WLUK
| | - P E Clayton
- Centre for Paediatrics and Child HealthInstitute of Human Development, Faculty of Medical and Human Sciences, University of ManchesterManchesterUK
- 5th Floor Research, Royal Manchester Children's HospitalCentral Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences CentreOxford Road, Manchester, M13 9WLUK
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Kanda RK, Tristem M, Coulson T. Exploring the effects of immunity and life history on the dynamics of an endogenous retrovirus. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120505. [PMID: 23938754 DOI: 10.1098/rstb.2012.0505] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mammalian DNA is littered with the signatures of past retroviral infections. For example, at least 8% of the human genome can be attributed to endogenous retroviruses (ERVs). We take a single-locus approach to develop a simple susceptible-infected-recovered model to investigate the circumstances under which a disease-causing retrovirus can become incorporated into the host genome and spread through the host population if it were to confer an immunological advantage. In the absence of any fitness benefit provided by the long terminal repeat (LTR), we conclude that signatures of ERVs are likely to go to fixation within a population when the probability of evolving cellular/humoral immunity to a related exogenous version of the virus is extremely small. We extend this model to examine whether changing the speed of the host life history influences the likelihood that an exogenous retrovirus will incorporate and spread to fixation. Our results reveal the parameter space under which incorporation of exogenous retroviruses into a host genome may be beneficial to the host. In our final model, we find that the likelihood of an LTR reaching fixation in a host population is not strongly affected by host life history.
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Affiliation(s)
- R K Kanda
- Department of Zoology, University of Oxford, , Tinbergen Building, South Parks Road, Oxford OX1 3PS, UK
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Bateman AW, Ozgul A, Nielsen JF, Coulson T, Clutton-Brock TH. Social structure mediates environmental effects on group size in an obligate cooperative breeder,Suricata suricatta. Ecology 2013; 94:587-97. [DOI: 10.1890/11-2122.1] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Hanson D, Murray PG, Coulson T, Sud A, Omokanye A, Stratta E, Sakhinia F, Bonshek C, Wilson LC, Wakeling E, Temtamy SA, Aglan M, Rosser EM, Mansour S, Carcavilla A, Nampoothiri S, Khan WI, Banerjee I, Chandler KE, Black GCM, Clayton PE. Mutations in CUL7, OBSL1 and CCDC8 in 3-M syndrome lead to disordered growth factor signalling. J Mol Endocrinol 2012; 49:267-75. [PMID: 23018678 DOI: 10.1530/jme-12-0034] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
3-M syndrome is a primordial growth disorder caused by mutations in CUL7, OBSL1 or CCDC8. 3-M patients typically have a modest response to GH treatment, but the mechanism is unknown. Our aim was to screen 13 clinically identified 3-M families for mutations, define the status of the GH-IGF axis in 3-M children and using fibroblast cell lines assess signalling responses to GH or IGF1. Eleven CUL7, three OBSL1 and one CCDC8 mutations in nine, three and one families respectively were identified, those with CUL7 mutations being significantly shorter than those with OBSL1 or CCDC8 mutations. The majority of 3-M patients tested had normal peak serum GH and normal/low IGF1. While the generation of IGF binding proteins by 3-M cells was dysregulated, activation of STAT5b and MAPK in response to GH was normal in CUL7(-/-) cells but reduced in OBSL1(-/-) and CCDC8(-/-) cells compared with controls. Activation of AKT to IGF1 was reduced in CUL7(-/-) and OBSL1(-/-) cells at 5 min post-stimulation but normal in CCDC8(-/-) cells. The prevalence of 3-M mutations was 69% CUL7, 23% OBSL1 and 8% CCDC8. The GH-IGF axis evaluation could reflect a degree of GH resistance and/or IGF1 resistance. This is consistent with the signalling data in which the CUL7(-/-) cells showed impaired IGF1 signalling, CCDC8(-/-) cells showed impaired GH signalling and the OBSL1(-/-) cells showed impairment in both pathways. Dysregulation of the GH-IGF-IGF binding protein axis is a feature of 3-M syndrome.
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Affiliation(s)
- D Hanson
- Paediatric Endocrinology, School of Biomedicine, Manchester Academic Health Sciences Centre, University of Manchester, Manchester M13 9WL, UK
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Chauvenet ALM, Ewen JG, Armstrong DP, Coulson T, Blackburn TM, Adams L, Walker LK, Pettorelli N. Does supplemental feeding affect the viability of translocated populations? The example of the hihi. Anim Conserv 2012. [DOI: 10.1111/j.1469-1795.2012.00522.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - J. G. Ewen
- Institute of Zoology; Zoological Society of London; London; UK
| | - D. P. Armstrong
- Wildlife Ecology Group; Institute of Natural Resources; Massey University; Palmerston North; New Zealand
| | - T. Coulson
- Division of Biology; Imperial College London; Silwood Park Campus; Ascot; Berkshire; UK
| | | | - L. Adams
- Department of Conservation Wellington Conservancy Office; Wellington; New Zealand
| | | | - N. Pettorelli
- Institute of Zoology; Zoological Society of London; London; UK
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Coulson T, MacNulty DR, Stahler DR, vonHoldt B, Wayne RK, Smith DW. Modeling Effects of Environmental Change on Wolf Population Dynamics, Trait Evolution, and Life History. Science 2011; 334:1275-8. [DOI: 10.1126/science.1209441] [Citation(s) in RCA: 160] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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McConville AJ, Grachev I, Keane A, Coulson T, Bekenov AB, Milner-Gulland EJ. Reconstructing the observation process to correct for changing detection probability of a critically endangered species. ENDANGER SPECIES RES 2009. [DOI: 10.3354/esr00166] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Coulson T, Ezard THG, Pelletier F, Tavecchia G, Stenseth NC, Childs DZ, Pilkington JG, Pemberton JM, Kruuk LEB, Clutton-Brock TH, Crawley MJ. ESTIMATING THE FUNCTIONAL FORM FOR THE DENSITY DEPENDENCE FROM LIFE HISTORY DATA. Ecology 2008; 89:1661-74. [DOI: 10.1890/07-1099.1] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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King R, Brooks SP, Coulson T. Analyzing complex capture-recapture data in the presence of individual and temporal covariates and model uncertainty. Biometrics 2008; 64:1187-95. [PMID: 18325067 DOI: 10.1111/j.1541-0420.2008.00991.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
SUMMARY We consider the issue of analyzing complex ecological data in the presence of covariate information and model uncertainty. Several issues can arise when analyzing such data, not least the need to take into account where there are missing covariate values. This is most acutely observed in the presence of time-varying covariates. We consider mark-recapture-recovery data, where the corresponding recapture probabilities are less than unity, so that individuals are not always observed at each capture event. This often leads to a large amount of missing time-varying individual covariate information, because the covariate cannot usually be recorded if an individual is not observed. In addition, we address the problem of model selection over these covariates with missing data. We consider a Bayesian approach, where we are able to deal with large amounts of missing data, by essentially treating the missing values as auxiliary variables. This approach also allows a quantitative comparison of different models via posterior model probabilities, obtained via the reversible jump Markov chain Monte Carlo algorithm. To demonstrate this approach we analyze data relating to Soay sheep, which pose several statistical challenges in fully describing the intricacies of the system.
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Affiliation(s)
- R King
- School of Mathematics and Statistics, University of St Andrews, North Haugh, St Andrews, Fife, UK.
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Abstract
The shape of the association between age and the cost of reproduction varies across species. However, it is unclear whether there are any general patterns in the way the cost of reproduction varies with life history, taxon or ecological function. Using a simple theoretical method, we identified three characteristic patterns to describe the age-related survival cost of reproduction. The most frequent pattern is an approximately exponential decay (ED) with increasing age. Two additional u-shaped patterns were identified, where the cost of reproduction was higher for young and old individuals compared with intermediate-aged individuals. The majority of these u-shaped curves suggested higher costs of reproduction at older ages (RQ), with the rest suggesting a higher cost at young ages (LQ). While predators were most likely to exhibit ED-shaped cost curves, herbivores were equally likely to exhibit ED and RQ curves; birds were likely to exhibit ED-shaped curves and mammals were split equally between ED and RQ curves. These findings suggest that there may be predictable differences in the age-related shape of the cost of reproduction between species, but further research is required to identify the mechanisms generating such differences.
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Affiliation(s)
- G Proaktor
- Division of Biology, Centre for Population Biology, Imperial College, Silwood Park, Ascot, Berkshire SL5 7PY, UK.
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15
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Abstract
1. We investigate the evolutionary responses to harvesting in ungulates using a state-dependent, stochastic, density-dependent individual-based model of red deer Cervus elaphus (L.) females subject to different harvesting regimes. 2. The population's mean weight at first reproduction shifts towards light weights as harvesting increases, and its distribution changes from a single peak distribution under very low or high harvest rates, to a bimodal distribution under intermediate harvest rates. 3. These results suggest that, consistent with previous studies on aquatic species, harvesting-induced mortality may drive adaptive responses in ungulates by reducing the fitness benefits from adult survival and growth in favour of early and lightweight reproduction. 4. Selective harvesting for heavy animals has no additional effect on the evolutionarily stable strategy, suggesting that harvest rate is more important than the degree of selectivity in driving adaptive responses. However, selective harvesting of light females is positively associated with maturation weights even higher than those of a nonharvested population, probably due to the reduction in the fitness value of the offspring. 5. The average number of weight at maturation strategies in the population declines but the total number of strategies across all simulations increases with harvest rate, suggesting that harvesting-induced selection on weight at maturity overcomes the increase in strategy diversity expected from density-dependent release. 6. Yield initially increases with harvesting due to enhanced productivity of light females experiencing density-dependent release. However, it crashes under intense harvesting resulting in a population skewed to light, young and, therefore, less reproductive animals.
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Affiliation(s)
- G Proaktor
- Division of Biology and Centre for Population Biology, Imperial College, Silwood Park, Ascot, Berkshire, SL5 7PY, UK.
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16
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Abstract
1. The decomposition of population growth rate into contributions from different demographic rates has many applications, ranging from evolutionary biology to conservation and management. Demographic rates with low variance may be pivotal for population persistence, but variable rates can have a dramatic influence on population growth rate. 2. In this study, the mean and variance in population growth rate (lambda) is decomposed into contributions from different ages and demographic rates using prospective and retrospective matrix analyses for male and female components of an increasing common tern (Sterna hirundo) population. 3. Three main results emerged: (1) subadult return was highly influential in prospective and retrospective analyses; (2) different age-classes made different contributions to variation in lambda: older age classes consistently produced offspring whereas young adults performed well only in high quality years; and (3) demographic rate covariation explained a significant proportion of variation in both sexes. A large contribution to lambda did not imply a large contribution to its variation. 4. This decomposition strengthens the argument that the relationship between variation in demographic rates and variation in lambda is complex. Understanding this relationship and its consequences for population persistence and evolutionary change demands closer examination of the lives, and deaths, of the individuals within populations within species.
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Affiliation(s)
- T H G Ezard
- Division of Biology, Faculty of Life Sciences, Imperial College at Silwood Park, Ascot, Berkshire SL5 7PY, UK.
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18
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Abstract
This article presents a Bayesian analysis of mark-recapture-recovery data on Soay sheep. A reversible jump Markov chain Monte Carlo technique is used to determine age classes of common survival, and to model the survival probabilities in those classes using logistic regression. This involves environmental and individual covariates, as well as random effects. Auxiliary variables are used to impute missing covariates measured on individual sheep. The Bayesian approach suggests different models from those previously obtained using classical statistical methods. Following model averaging, features that were not previously detected, and which are of ecological importance, are identified.
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Affiliation(s)
- R King
- School of Mathematics and Statistics, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9SS, UK
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Coulson T, Benton TG, Lundberg P, Dall SRX, Kendall BE, Gaillard JM. Estimating individual contributions to population growth: evolutionary fitness in ecological time. Proc Biol Sci 2006; 273:547-55. [PMID: 16537125 PMCID: PMC1560056 DOI: 10.1098/rspb.2005.3357] [Citation(s) in RCA: 162] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Ecological and evolutionary change is generated by variation in individual performance. Biologists have consequently long been interested in decomposing change measured at the population level into contributions from individuals, the traits they express and the alleles they carry. We present a novel method of estimating individual contributions to population growth and changes in distributions of quantitative traits and alleles. An individual's contribution to population growth is an individual's realized annual fitness. We demonstrate how the quantities we develop can be used to address a range of empirical questions, and provide an application to a detailed dataset of Soay sheep. The approach provides results that are consistent with those obtained using lifetime estimates of individual performance, yet is substantially more powerful as it allows lifetime performance to be decomposed into annual survival and fecundity contributions.
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Affiliation(s)
- T Coulson
- Imperial College Division of Biology and Centre for Population Biology, Faculty of Life Sciences Silwood Park, Ascot, Berkshire SL5 7PY, UK.
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Nussey DH, Coltman DW, Coulson T, Kruuk LEB, Donald A, Morris SJ, Clutton-Brock TH, Pemberton J. Rapidly declining fine-scale spatial genetic structure in female red deer. Mol Ecol 2005; 14:3395-405. [PMID: 16156811 DOI: 10.1111/j.1365-294x.2005.02692.x] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A growing literature now documents the presence of fine-scale genetic structure in wild vertebrate populations. Breeding population size, levels of dispersal and polygyny--all hypothesized to affect population genetic structure--are known to be influenced by ecological conditions experienced by populations. However the possibility of temporal or spatial variation in fine-scale genetic structure as a result of ecological change is rarely considered or explored. Here we investigate temporal variation in fine-scale genetic structure in a red deer population on the Isle or Rum, Scotland. We document extremely fine-scale spatial genetic structure (< 100 m) amongst females but not males across a 24-year study period during which resource competition has intensified and the population has reached habitat carrying capacity. Based on census data, adult deer were allocated to one of three subpopulations in each year of the study. Global F(ST) estimates for females generated using these subpopulations decreased over the study period, indicating a rapid decline in fine-scale genetic structure of the population. Global F(ST) estimates for males were not different from zero across the study period. Using census and genetic data, we illustrate that, as a consequence of a release from culling early in the study period, the number of breeding females has increased while levels of polygyny have decreased in this population. We found little evidence for increasing dispersal between subpopulations over time in either sex. We argue that both increasing female population size and decreasing polygyny could explain the decline in female population genetic structure.
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Affiliation(s)
- D H Nussey
- Institute of Evolutionary Biology, University of Edinburgh, EH9 3JT, UK.
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21
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Abstract
Many recent studies report that individual heterozygosity at a handful of apparently neutral microsatellite markers is correlated with key components of fitness, with most studies invoking inbreeding depression as the likely underlying mechanism. The implicit assumption is that an individual's inbreeding coefficient can be estimated reliably using only 10 or so markers, but the validity of this assumption is unclear. Consequently, we have used individual-based simulations to examine the conditions under which heterozygosity and inbreeding are likely to be correlated. Our results indicate that the parameter space in which this occurs is surprisingly narrow, requiring that inbreeding events are both frequent and severe, for example, through selfing, strong population structure and/or high levels of polygyny. Even then, the correlations are strong only when large numbers of loci (~200) can be deployed to estimate heterozygosity. With the handful of markers used in most studies, correlations only become likely under the most extreme scenario we looked at, namely 20 demes of 20 individuals coupled with strong polygyny. This finding is supported by the observation that heterozygosity is only weakly correlated among markers within an individual, even in a dataset comprising 400 markers typed in diverse human populations, some of which favour consanguineous marriages. If heterozygosity and inbreeding coefficient are generally uncorrelated, then heterozygosity-fitness correlations probably have little to do with inbreeding depression. Instead, one would need to invoke chance linkage between the markers used and one or more gene(s) experiencing balancing selection. Unfortunately, both explanations sit somewhat uncomfortably with current understanding. If inbreeding is the dominant mechanism, then our simulations indicate that consanguineous mating would have to be vastly more common than is predicted for most realistic populations. Conversely, if heterosis provides the answer, there need to be many more polymorphisms with major fitness effects and higher levels of linkage disequilibrium than are generally assumed.
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Affiliation(s)
- F Balloux
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.
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Hallett TB, Coulson T, Pilkington JG, Clutton-Brock TH, Pemberton JM, Grenfell BT. Why large-scale climate indices seem to predict ecological processes better than local weather. Nature 2004; 430:71-5. [PMID: 15229599 DOI: 10.1038/nature02708] [Citation(s) in RCA: 256] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2004] [Accepted: 05/24/2004] [Indexed: 11/08/2022]
Abstract
Large-scale climatic indices such as the North Atlantic Oscillation are associated with population dynamics, variation in demographic rates and values of phenotypic traits in many species. Paradoxically, these large-scale indices can seem to be better predictors of ecological processes than local climate. Using detailed data from a population of Soay sheep, we show that high rainfall, high winds or low temperatures at any time during a 3-month period can cause mortality either immediately or lagged by a few days. Most measures of local climate used by ecologists fail to capture such complex associations between weather and ecological process, and this may help to explain why large-scale, seasonal indices of climate spanning several months can outperform local climatic factors. Furthermore, we show why an understanding of the mechanism by which climate influences population ecology is important. Through simulation we demonstrate that the timing of bad weather within a period of mortality can have an important modifying influence on intraspecific competition for food, revealing an interaction between climate and density dependence that the use of large-scale climatic indices or inappropriate local weather variables might obscure.
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Affiliation(s)
- T B Hallett
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
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23
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Abstract
Grazing by hill sheep and red deer prevents the regeneration of woodland in many parts of the Scottish Highlands and has also led to extensive loss of heather cover. Conservation bodies claim that there has been a rapid rise in Highland deer numbers caused by inadequate management and that these need to be drastically reduced. Here we show that the recent increase in red deer stocks has probably been overestimated and suggest that the gradual rise in numbers since 1970 may be a consequence of a reduction in sheep stocks and of changes in winter weather, rather than of a reduction in culling rate. Although there would be environmental benefits in reducing deer numbers, there is an equal need to reduce the numbers of hill sheep in many parts of the Highlands.
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Affiliation(s)
- T H Clutton-Brock
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK.
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Abstract
Van Tienderen recently published a method that links selection gradients between a phenotypic trait and multiple fitness components with the effects of these fitness components on the population growth rate (mean absolute fitness). The method allows selection to be simultaneously estimated across multiple fitness components in a population dynamic framework. In this paper we apply the method to a population of red deer living in the North Block of the Isle of Rum, Scotland. We show that (1) selection on birth date and birth weight can operate through multiple fitness components simultaneously; (2) our estimates of the response to selection are consistent with the observed change in trait values that we cannot explain with environmental and phenotypic covariates; (3) selection on both traits has fluctuated over the course of the study; (4) selection operates through different fitness components in different years; and (5) no environmental covariates correlate with selection because different fitness components respond to density and climatic variation in contrasting ways.
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Affiliation(s)
- T Coulson
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, United Kingdom.
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Milner-Gulland EJ, Bukreeva OM, Coulson T, Lushchekina AA, Kholodova MV, Bekenov AB, Grachev IA. Conservation: Reproductive collapse in saiga antelope harems. Nature 2003; 422:135. [PMID: 12634775 DOI: 10.1038/422135a] [Citation(s) in RCA: 182] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- E J Milner-Gulland
- Department of Environmental Science and Technology, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.
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Coulson T, Kruuk LEB, Tavecchia G, Pemberton JM, Clutton-Brock TH. ESTIMATING SELECTION ON NEONATAL TRAITS IN RED DEER USING ELASTICITY PATH ANALYSIS. Evolution 2003. [DOI: 10.1554/03-126] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Abstract
Attempts to relate species differences in population dynamics to variation in life histories rely on the assumption that the causes of contrasts in demography are sufficiently simple to be derived from first principles. Here, we investigate the causes of contrasts in dynamics between two ungulate populations on Hebridean islands (red deer and Soay sheep) and show that differences in stability, as well as in the effects of variation in density and climate, are related to differences in timing of reproduction relative to seasonal variation in resource abundance. In both populations, attempts to predict changes in population size sufficiently accurately for the results to be useful for management purposes require a knowledge of the responses of different age and sex categories to changes in density and climate, as well as of population structure.
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Affiliation(s)
- T H Clutton-Brock
- Large Animal Research Group, Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
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Salt J, Sellars V, Shemilt J, Boyd S, Coulson T, McCool S. The Scottish Centre for Autism preschool treatment programme. I: A developmental approach to early intervention. Autism 2001; 5:362-73. [PMID: 11777254 DOI: 10.1177/1362361301005004003] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Early intervention is an area of intense current interest for parents and professionals. This article describes a mainstream National Health Service (NHS) approach to early intervention, developed at the Scottish Centre for Autism. The aims of treatment are to improve the child's early social communication and social interaction skills, leading to the potential development of play and flexibility of behaviour. This is achieved by 1:1 intensive treatment by trained therapists, and a schedule of parent training. The treatment protocol incorporates a child led approach; the use of imitation as a therapeutic strategy; using language contingent on activities; and the introduction of flexibility into play and social exchanges.
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Affiliation(s)
- J Salt
- Scottish Centre for Autism, Department of Child and Family Psychiatry, Yorkhill NHS Trust, Glasgow, UK.
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31
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Abstract
The relationship between fitness and parental similarity has been dominated by studies of how inbreeding depression lowers fecundity in incestuous matings. A widespread implicit assumption is that adult fitness (reproduction) of individuals born to parents who are not unusually closely related is more or less equal. Examination of three long-lived vertebrates, the long-finned pilot whale, the grey seal and the wandering albatross reveals significant negative relationships between parental similarity and genetic estimates of reproductive success. This effect could, in principle, be driven by a small number of low quality, inbred individuals. However, when the data are partitioned into individuals with above average and below average parental similarity, we find no evidence that the slopes differ, suggesting that the effect is more or less similar across the full range of parental similarity values. Our results thus uncover a selective pressure that favours not only inbreeding avoidance, but also the selection of maximally dissimilar mates.
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Affiliation(s)
- W Amos
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
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32
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Coulson T, Catchpole EA, Albon SD, Morgan BJ, Pemberton JM, Clutton-Brock TH, Crawley MJ, Grenfell BT. Age, sex, density, winter weather, and population crashes in Soay sheep. Science 2001; 292:1528-31. [PMID: 11375487 DOI: 10.1126/science.292.5521.1528] [Citation(s) in RCA: 737] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Quantifying the impact of density, extrinsic climatic fluctuations, and demography on population fluctuations is a persistent challenge in ecology. We analyzed the effect of these processes on the irregular pattern of population crashes of Soay sheep on the St. Kilda archipelago, United Kingdom. Because the age and sex structure of the population fluctuates independently of population size, and because animals of different age and sex respond in different ways to density and weather, identical weather conditions can result in different dynamics in populations of equal size. In addition, the strength of density-dependent processes is a function of the distribution of weather events. Incorporating demographic heterogeneities into population models can influence dynamics and their response to climate change.
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Affiliation(s)
- T Coulson
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK.
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33
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Abstract
A recent study by Brook et al. empirically tested the performance of population viability analysis (PVA) using data from 21 populations across a wide range of species. The study concluded that PVAs are good at predicting the future dynamics of populations. We suggest that this conclusion is a result of a bias in the studies that Brook et al. included in their analyses. We present arguments that PVAs can only be accurate at predicting extinction probabilities if data are extensive and reliable, and if the distribution of vital rates between individuals and years can be assumed stationary in the future, or if any changes can be accurately predicted. In particular, we note that although catastrophes are likely to have precipitated many extinctions, estimates of the probability of catastrophes are unreliable.
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Coulson T, Milner-Gulland EJ, Clutton-Brock T. The relative roles of density and climatic variation on population dynamics and fecundity rates in three contrasting ungulate species. Proc Biol Sci 2000; 267:1771-9. [PMID: 12233776 PMCID: PMC1690729 DOI: 10.1098/rspb.2000.1209] [Citation(s) in RCA: 189] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The relative influences of density-dependent and -independent processes on vital rates and population dynamics have been debated in ecology for over half a century, yet it is only recently that both processes have been shown to operate within the same population. However, generalizations on the role of each process across species are rare. Using a process-orientated generalized linear modelling approach we show that variations in fecundity rates in populations of three species of ungulates with contrasting life histories are associated with density and winter weather in a remarkably similar manner. However, there are differences and we speculate that they are a result of differences in size between the species. Much previous research exploring the association between vital rates, population dynamics and density-dependent and -independent processes has used pattern-orientated approaches to decompose time-series into contributions from density-dependent and -independent processes. Results from these analyses are sometimes used to infer associations between vital rates, density and climatic variables. We compare results from pattern-orientated analyses of time-series with process-orientated analyses and report that the two approaches give different results. The approach of analysing relationships between vital rates, density and climatic variables may detect important processes influencing population dynamics that time-series methodologies may overlook.
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Affiliation(s)
- T Coulson
- Institute of Zoology, Zoological Society of London, Regent's Park, UK
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Abstract
Chronic helminth infection induces a type-2 cellular immune response. In contrast to this, mycobacterial infections commonly induce a type-1 immune response which is considered protective. Type-2 responses and diminished type-1 responses to mycobacteria have been previously correlated with active infection states such as pulmonary tuberculosis and lepromatous leprosy. The present study examines the immune responses of children exposed to both the helminth parasite Onchocerca volvulus and the mycobacterial infections, Mycobacterium tuberculosis and M. leprae. Proliferation of peripheral blood mononuclear cells (PBMC) and production of IL-4 in response to both helminth and mycobacterial antigen (PPD) decreased dramatically with increasing microfilarial (MF) density. Although interferon-gamma (IFN-gamma) production strongly correlated with cellular proliferation, it was surprisingly not related to MF density for either antigen. IL-4 production in response to helminth antigen and PPD increased with ascending children's age. IFN-gamma and cellular proliferation to PPD were not related to age, but in response to helminth antigen were significantly higher in children of age 9-12 years than children of either the younger age group (5-8 years) or the older group (13-16 years). Thus, there was a MF density-related down-regulation of cellular responsiveness and age-related skewing toward type 2 which was paralleled in response to both the helminth antigen and PPD. This parasite-induced immunomodulation of the response to mycobacteria correlates with a previous report of doubled incidence of lepromatous leprosy in onchocerciasis hyperendemic regions. Moreover, this demonstration that helminth infection in humans can modulate the immune response to a concurrent infection or immunological challenge is of critical importance to future vaccination strategies.
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Affiliation(s)
- G R Stewart
- Department of Biology, Imperial College of Science Technology and Medicine, St Mary's Campus, London, UK
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