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2. Male mate-searching strategies and female cues: how do male guppies find receptive females?

Author

Guevara-Fiore, P., Stapley, J., Krause, J., Ramnarine, I.W., and Watt, P.J.

Subjects
Zoology and wildlife conservation
Abstract

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.anbehav.2010.02.027 Byline: P. Guevara-Fiore (a), J. Stapley (a), J. Krause (b), I.W. Ramnarine (c), P.J. Watt (a) Abstract: Locating potential mates is critical to mating. We studied males' association with females and mate-searching patterns in the guppy, Poecilia reticulata, a promiscuous live-bearer. In the field, we examined whether male guppies respond differently to a shoal of conspecific fish based on the members of the shoal. We found that more males were attracted to shoals that contained receptive females than to shoals of nonreceptive females or males. We also conducted laboratory experiments to investigate how males use olfactory cues of nonreceptive and receptive females to search for and associate with females. We gave males the option to associate with nonreceptive females when olfactory cues of receptive or nonreceptive females were present and absent, and when olfactory cues were presented alone. Males associated with females most strongly when both cues were presented simultaneously, but when cues were presented separately males' association with females differed with respect to the olfactory cues that were added. Males associated with females equally with visual and olfactory cues presented separately when the odour cues were from receptive females. However, when the odour cues were from nonreceptive females, males associated with females less with olfactory than visual cues. Searching activity increased when males had access only to olfactory cues. Taken together these results suggest that olfactory cues influence males' association with females and searching behaviour, and these changes in behaviour are likely to maximize a male's opportunity to encounter receptive females. Author Affiliation: (a) Department of Animal & Plant Sciences, University of Sheffield, U.K. (b) Department of Ecology and Biology of Fishes, Institute of Freshwater Ecology and Inland Fisheries, Germany (c) Department of Life Sciences, University of the West Indies, Jamaica Article History: Received 23 July 2009; Revised 6 October 2009; Accepted 22 February 2010 Article Note: (miscellaneous) MS. number: 09-00494

Published
2010

3. A linkage map of the zebra finch Taeniopygia guttata provides new insights into avian genome evolution

Author

Stapley, J., Birkhead, T.R., Burke, T., and Slate, J.

Subjects
Zebra finch -- Research, Zebra finch -- Genetic aspects, Evolutionary biology -- Analysis, Chromosome mapping -- Research, Genomics -- Research, Biological sciences
Abstract

Passeriformes are the largest order of birds and one of the most widely studied groups in evolutionary biology and ecology. Until recently genomic tools in passerines relied on chicken genomic resources. Here we report the construction and analysis of a whole-genome linkage map for the zebra finch (Taeniopygia guttata) using a 354-bird pedigree. The map contains 876 SNPs dispersed across 45 linkage groups and we found only a few instances of interchromosomal rearrangement between the zebra finch and the chicken genomes. Interestingly, there was a greater than expected degree of intrachromosomal rearrangements compared to the chicken, suggesting that gene order is not conserved within avian chromosomes. At 1068 cM the map is approximately only one quarter the length of the chicken linkage map, providing further evidence that the chicken has an unusually high recombination rate. Male and female linkage-map lengths were similar, suggesting no heterochiasmy in the zebra finch. This whole-genome map is the first for any passerine and a valuable tool for the zebra finch genome sequence project and for studies of quantitative trait loci.

Published
2008

9. Red Carotenoid Coloration in the Zebra Finch Is Controlled by a Cytochrome P450 Gene Cluster

Author

Mundy, N.I., Stapley, J., Bennison, C., Tucker, R., Twyman, H., Kim, K.W., Burke, T., Birkhead, T.R., Andersson, S., Slate, J., Mundy, Nicholas [0000-0002-5545-1517], and Apollo - University of Cambridge Repository

Subjects
Male, animal structures, Agricultural and Biological Sciences(all), Biochemistry, Genetics and Molecular Biology(all), Pigmentation, Beak, Pigments, Biological, Tarsus, Animal, Retina, Avian Proteins, Cytochrome P-450 Enzyme System, Animals, Female, Finches
Abstract

Bright-red colors in vertebrates are commonly involved in sexual, social, and interspecific signaling [1-8] and are largely produced by ketocarotenoid pigments. In land birds, ketocarotenoids such as astaxanthin are usually metabolically derived via ketolation of dietary yellow carotenoids [9, 10]. However, the molecular basis of this gene-environment mechanism has remained obscure. Here we use the yellowbeak mutation in the zebra finch (Taeniopygia guttata) to investigate the genetic basis of red coloration. Wild-type ketocarotenoids were absent in the beak and tarsus of yellowbeak birds. The yellowbeak mutation mapped to chromosome 8, close to a cluster of cytochrome P450 loci (CYP2J2-like) that are candidates for carotenoid ketolases. The wild-type zebra finch genome was found to have three intact genes in this cluster: CYP2J19A, CYP2J19B, and CYP2J40. In yellowbeak, there are multiple mutations: loss of a complete CYP2J19 gene, a modified remaining CYP2J19 gene (CYP2J19(yb)), and a non-synonymous SNP in CYP2J40. In wild-type birds, CYP2J19 loci are expressed in ketocarotenoid-containing tissues: CYP2J19A only in the retina and CYP2J19B in the beak and tarsus and to a variable extent in the retina. In contrast, expression of CYP2J19(yb) is barely detectable in the beak of yellowbeak birds. CYP2J40 has broad tissue expression and shows no differences between wild-type and yellowbeak. Our results indicate that CYP2J19 genes are strong candidates for the carotenoid ketolase and imply that ketolation occurs in the integument in zebra finches. Since cytochrome P450 enzymes include key detoxification enzymes, our results raise the intriguing possibility that red coloration may be an honest signal of detoxification ability., Current Biology, 26 (11), ISSN:0960-9822, ISSN:1879-0445

Published
2016

10. Integrating different approaches in the definition of biological stocks: A northern Australian multi-jurisdictional fisheries example using grey mackerel, Scomberomorus semifasciatus

Author

Welch, D., Newman, Stephen, Buckworth, R., Ovenden, J., Broderick, D., Lester, R., Gribble, N., Ballagh, A., Charters, R., Stapley, J., Street, R., Garrett, R., Begg, G., Welch, D., Newman, Stephen, Buckworth, R., Ovenden, J., Broderick, D., Lester, R., Gribble, N., Ballagh, A., Charters, R., Stapley, J., Street, R., Garrett, R., and Begg, G.

Abstract

A holistic approach to stock structure studies utilises multiple different techniques on the same individuals sampled from selected populations and combines results across spatial and temporal scales to produce a weight of evidence conclusion. It is the most powerful and reliable source of information to use in formulating resource management and monitoring plans. Few examples of the use of a holistic approach in stock structure studies exist, although more recently this is changing. Using such an approach makes integration of results from each technique challenging. An integrated stock definition (ISD) approach for holistic stock structure studies was developed in this study to aid in the appropriate interpretation of stock structure results to guide the determination of fishery management units. The ISD approach is applied herein to a study of the northern Australian endemic grey mackerel, Scomberomorus semifasciatus (Scombridae). Analyses of genetic (mitochondrial DNA and microsatellites), parasite, otolith stable isotope, and growth data are synthesised to determine the stock structure of S. semifasciatus across northern Australia. Integration of the results from all techniques identified at least six S. semifasciatus stocks for management purposes. Further, the use of the ISD approach provided a simple basis for integrating multiple techniques and for their interpretation. The use of this holistic approach was a powerful tool in providing greater certainty about the appropriate management units for S. semifasciatus. Future stock structure studies investigating spatial management questions in the fisheries context should adopt a holistic approach and apply the ISD approach for a more accurate definition of biological stocks to improve fisheries management.

Published
2015

13. Spatial variation in life history reveals insight into connectivity and geographic population structure of a tropical estuarine teleost: King threadfin, Polydactylus macrochir

Author

Moore, B., Simpfendorfer, C., Newman, Stephen, Stapley, J., Allsop, Q., Sellin, M., Welch, D., Moore, B., Simpfendorfer, C., Newman, Stephen, Stapley, J., Allsop, Q., Sellin, M., and Welch, D.

Abstract

Understanding the life history of exploited fish species is not only critical in developing stock assessments and productivity models, but has a dual function in the delineation of connectivity and geographical population structure. In this study, patterns in growth and length and age at sex change of Polydactylus macrochir, an ecologically and economically important protandrous estuarine teleost, were examined to provide preliminary information on the species' connectivity and geographic structure across northern Australia. Considerable variation in life history parameters was observed among the 18 locations sampled. Both unconstrained and constrained (t 0=0) estimates of von Bertalanffy growth function parameters differed significantly among all neighbouring locations with the exception of two locations in Queensland's east coast and two in Queensland's Gulf of Carpentaria waters, respectively. Comparisons of back-calculated length-at-age 2 provided additional evidence for growth differences among some locations, but were not significantly different among locations in the south-eastern Gulf of Carpentaria or on Queensland's east coast. The length and age at sex change differed markedly among locations, with fish from the east coast of Australia changing sex from males to females at significantly greater lengths and ages than elsewhere. Sex change occurred earliest at locations within Queensland's Gulf of Carpentaria, where a large proportion of small, young females were recorded. The observed differences suggest that P. macrochir likely form a number of geographically and/or reproductively distinct groups in Australian waters and suggest that future studies examining connectivity and geographic population structure of estuarine fishes will likely benefit from the inclusion of comparisons of life history parameters. © 2012 Elsevier B.V.

Published
2012

14. Stock structure of the blue threadfin (Eleutheronema tetradactylum) across northern Australia derived from life-history characteristics

Author

Ballagh, A., Welch, D., Newman, Stephen, Allsop, Q., Stapley, J., Ballagh, A., Welch, D., Newman, Stephen, Allsop, Q., and Stapley, J.

Abstract

Life history characteristics were used to determine the stock structure of the polynemid Eleutheronema tetradactylum across northern Australia. Growth, estimated from back-calculated length-at-age from sagittal otoliths, and length at sex change were estimated from samples collected from 12 different locations across western, northern and eastern Australia between 2007 and 2009. Comparison of back-calculated length-at-age, growth and length at sex change between locations revealed significant variation in the life-history characteristics of E. tetradactylum across northern Australia, with significant differences detected in 43 of 45 location comparisons. Differences in otolith size relative to fish length also existed amongst locations. No differences in other morphometric relationships were detected. The results of this study provide evidence for a high degree of spatial population subdivision for E. tetradactylum across northern Australia, the finding of which has implications for E. tetradactylum fisheries throughout its range, and provides a biological basis for spatial management of the species in Australia. © 2012 Elsevier B.V.

Published
2012

15. Stock structure of blue threadfin Eleutheronema tetradactylum across northern Australia, as indicated by parasites

Author

Moore, B. R., Stapley, J., Allsop, Q., Newman, S. J., Ballagh, A., Welch, D. J., Lester, R. J. G., Moore, B. R., Stapley, J., Allsop, Q., Newman, S. J., Ballagh, A., Welch, D. J., and Lester, R. J. G.

Abstract

The parasite fauna of the blue threadfin Eleutheronema tetradactylum, collected from 14 sites across northern Australia, was examined to evaluate the degree of movement and subsequent stock structure of the fish. Univariate and multivariate analysis of nine ‘permanent’ parasite species [the nematodes Anisakis (type I) and Terranova (type II), the cestodes Otobothrium australe, Pterobothrium pearsoni, Pterobothrium sp. A, Callitetrarhynchus gracilis, Parotobothrium balli and Nybelinia sp., and the acanthocephalan Pomphorhynchus sp.] demonstrated little similarity between sites, indicating limited mixing and therefore long-term separation of post-juvenile fish. As such, the effects of fishing are likely to be localized within the current administrative boundaries, implying little need for interstate co-operative management. Within each jurisdiction, management of E. tetradactylum populations, including the establishment of harvest strategies and fishery regulations, should be conducted in a way that recognizes the resident nature of the fish.

Published
2011

16. Evaluating catch and mitigating risk in a multispecies, tropical, inshore shark fishery within the Great Barrier Reef World Heritage Area

Author

Harry, A. V., Tobin, A. J., Simpfendorfer, C. A., Welch, D. J., Mapleston, A., White, J., Williams, A. J., Stapley, J., Harry, A. V., Tobin, A. J., Simpfendorfer, C. A., Welch, D. J., Mapleston, A., White, J., Williams, A. J., and Stapley, J.

Abstract

Small-scale and artisanal fisheries for sharks exist in most inshore, tropical regions of the world. Although often important in terms of food security, their low value and inherent complexity provides an imposing hurdle to sustainable management. An observer survey of a small-scale commercial gill-net fishery operating within the Great Barrier Reef World Heritage area revealed at least 38 species of elasmobranch were present in the catch. Of the total elasmobranch catch, 95% was 25 species of Carcharhiniformes from the families Carcharhinidae, Hemigaleidae and Sphyrnidae. Individual species were captured in a variety of ways by the fishery, often with strongly biased sex ratios and in a variety of life stages (e.g. neonates, juveniles, adult). Despite this, the main carcharhiniform taxa captured could be qualitatively categorised into four groups based on similar catch characteristics, body size and similarities in life history: small coastal (<1000 mm); medium coastal (1000–2000 mm); large coastal/semi-pelagic (>2000 mm); and hammerheads. Such groupings can potentially be useful for simplifying management of complex multispecies fisheries. The idiosyncrasies of elasmobranch populations and how fisheries interact with them provide a challenge for management but, if properly understood, potentially offer underutilised options for designing management strategies.

Published
2011

17. Stock structure of blue threadfin Eleutheronema tetradactylum across northern Australia, as indicated by parasites

Author

Moore, B., Stapley, J., Allsop, Q., Newman, Stephen, Ballagh, A., Welch, D., Lester, R., Moore, B., Stapley, J., Allsop, Q., Newman, Stephen, Ballagh, A., Welch, D., and Lester, R.

Abstract

The parasite fauna of the blue threadfin Eleutheronema tetradactylum, collected from 14 sites across northern Australia, was examined to evaluate the degree of movement and subsequent stock structure of the fish. Univariate and multivariate analysis of nine 'permanent' parasite species [the nematodes Anisakis (type I) and Terranova (type II), the cestodes Otobothrium australe, Pterobothrium pearsoni, Pterobothrium sp. A, Callitetrarhynchus gracilis, Parotobothrium balli and Nybelinia sp., and the acanthocephalan Pomphorhynchus sp.] demonstrated little similarity between sites, indicating limited mixing and therefore long-term separation of post-juvenile fish. As such, the effects of fishing are likely to be localized within the current administrative boundaries, implying little need for interstate co-operative management. Within each jurisdiction, management of E. tetradactylum populations, including the establishment of harvest strategies and fishery regulations, should be conducted in a way that recognizes the resident nature of the fish. © 2011 The Authors. Journal of Fish Biology © 2011 The Fisheries Society of the British Isles.

Published
2011

18. Stock structure of blue threadfin Eleutheronema tetradactylum across northern Australia as inferred from stable isotopes in sagittal otolith carbonate

Author

Newman, Stephen, Pember, M., Rome, B., Mitsopoulos, G., Skepper, C., Allsop, Q., Saunders, T., Ballagh, A., Van Herwerden, L., Garrett, R., Gribble, N., Stapley, J., Meeuwig, J., Moore, B., Welch, D., Newman, Stephen, Pember, M., Rome, B., Mitsopoulos, G., Skepper, C., Allsop, Q., Saunders, T., Ballagh, A., Van Herwerden, L., Garrett, R., Gribble, N., Stapley, J., Meeuwig, J., Moore, B., and Welch, D.

Abstract

Stable isotopes of d18O and d13C in sagittal otolith carbonates were used to determine the stock structure of the polynemid Eleutheronema tetradactylum (Shaw) across tropical northern Australia, where this species is an important component of inshore commercial and recreational fisheries. Stable isotopes from the sagittal otolith carbonate of 470 fish from 11 discrete locations across western, northern and eastern Australia were sampled between 2007 and 2009. Analysis of these stable isotopes revealed different location-specific signatures, indicating strong population subdivision. The significant differences in the isotopic signatures of E. tetradactylum demonstrated that there is unlikely to be substantial movement of fish between these locations. The spatial separation of these populations indicates a complex fine spatial scale stock structure across northern Australia, with at least 11 stocks or management units present. The population subdivision of E. tetradactylum was evident along expansive stretches of open beach systems and within coastal embayments with no physical barriers such as headlands. These results indicate that optimal fisheries management will require a review of the current spatial arrangements, particularly the potential for localised depletion of stocks on small spatial scales. © 2011 Blackwell Publishing Ltd.

Published
2011

19. Stock structure of Grey Mackerel, Scomberomorus semifasciatus (Pisces: Scombridae) across northern Australia, based on otolith stable isotope chemistry

Author

Newman, S.J., Wright, I.W., Rome, B.M., Mackie, M.C., Lewis, P.D., Buckworth, R.C., Ballagh, A.C., Garrett, R.N., Stapley, J., Broderick, D., Ovenden, J.R., Welch, D.J., Newman, S.J., Wright, I.W., Rome, B.M., Mackie, M.C., Lewis, P.D., Buckworth, R.C., Ballagh, A.C., Garrett, R.N., Stapley, J., Broderick, D., Ovenden, J.R., and Welch, D.J.

Abstract

The stable isotopes of delta O-18 and delta C-13 in sagittal otolith carbonates were used to determine the stock structure of Grey Mackerel, Scomberomorus semifasciatus. Otoliths were collected from Grey Mackerel at ten locations representing much of their distributional and fisheries range across northern Australia from 2005 to 2007. Across this broad range (similar to 6500 km), fish from four broad locations-Western Australia (S1), Northern Territory and Gulf of Carpentaria (S2, S3, S4, S5, S6, S7), Queensland east coast mid and north sites (S8, S9) and Queensland east coast south site (S10)-had stable isotope values that were significantly different indicating stock separation. Otolith stable isotopes differed more between locations than among years within a location, indicating temporal stability across years. The spatial separation of these populations indicates a complex stock structure across northern Australia. Stocks of S. semifasciatus appear to be associated with large coastal embayments. These results indicate that optimal fisheries management may require a review of the current spatial arrangements, particularly in relation to the evidence of shared stocks in the Gulf of Carpentaria. Furthermore, as the population of S. semifasciatus in Western Australia exhibited high spatial separation from those at all the other locations examined, further research activities should focus on investigating additional locations within Western Australia for an enhanced determination of stock delineation. From the issue entitled "Proceedings of the 4th International Otolith Symposium, 24-28 August 2009, Monterey, California"

Published
2010

20. Defining the stock structure of northern Australia's threadfin salmon species

Author

Welch, D.J., Ballagh, A., Newman, S.J., Lester, R.J.G., Moore, B., Van Herwerden, L., Horne, J., Allsop, Q., Saunders, T., Stapley, J., Welch, D.J., Ballagh, A., Newman, S.J., Lester, R.J.G., Moore, B., Van Herwerden, L., Horne, J., Allsop, Q., Saunders, T., and Stapley, J.

Abstract

The requirement for Queensland, Northern Territory and Western Australian jurisdictions to ensure sustainable harvest of fish resources relies on robust information on the resource status. In northern Australia management of inshore fisheries that target blue threadfin (Eleutheronema tetradactylum) and king threadfin (Polydactylus macrochir) is independent for each of these jurisdictions. However, the lack of information on the stock structure and biology of threadfins means that the appropriate spatial scale of management is not known and assessment of the resource status is not possible. Establishing the stock structure of blue and king threadfin would also immensely improve the relevance of future resource assessments for fishery management of threadfins across northern Australia. This highlighted the urgent need for stock structure information for this species.

Published
2010

21. Novel microsatellite loci identified from the Australian eastern small-eyed snake (Elapidae: Rhinocephalus nigrescens) and cross species amplification in the related genus Suta

Author

Stapley, J, Hayes, CM, Webb, JK, Keogh, JS, Stapley, J, Hayes, CM, Webb, JK, and Keogh, JS

Abstract

A total of 15 microsatellite primers pairs were developed for the Australian small-eyed snake Rhinoplocephalus nigrescens. Five primers were used to screen 93 individuals of R. nigrescens and were also tested against eight species of the closely related genus Suta. Allelic diversity in R. nigrescens was high in three loci (12-27) and there was high heterozygosity (0.58-0.82). Observed heterozygosity did not deviate from Hardy-Weinberg expectations for the five loci tested. These primers will be useful in studies of population genetics and mating systems of small-eyed snakes and related species. © 2005 Blackwell Publishing Ltd.

Published
2005

23. Stock structure of blue threadfin Eleutheronema tetradactylum across northern Australia as inferred from stable isotopes in sagittal otolith carbonate

Author

NEWMAN, S. J., primary, PEMBER, M. B., additional, ROME, B. M., additional, MITSOPOULOS, G. E. A., additional, SKEPPER, C. L., additional, ALLSOP, Q., additional, SAUNDERS, T., additional, BALLAGH, A. C., additional, VAN HERWERDEN, L., additional, GARRETT, R. N., additional, GRIBBLE, N. A., additional, STAPLEY, J. M., additional, MEEUWIG, J. J., additional, MOORE, B. R., additional, and WELCH, D. J., additional

Published
2011
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26. A journey of self-discovery: an intervention involving massage, yoga and relaxation for children with emotional and behavioural difficulties attending primary schools.

Author

Powell L, Gilchrist M, and Stapley J

Subjects
PHYSICAL therapy, HUMAN behavior, PHYSICAL therapy education, SCHOOL attendance, SCHOOL day, YOGA, TEACHERS, CONFIDENCE, STUDENTS
Abstract

This study reports on an intervention involving massage, yoga and relaxation delivered to young children with emotional and behavioural difficulties. Children (n = 126) were invited to participate in the Self-discovery Programme (SDP) with parental consent. A total of 107 children aged 8-11 years completed the SDP and all measures. Children were allocated to a Control (n = 54) or Intervention (n = 53) group. The results indicate that children in the Intervention group showed improvements in self-confidence, social confidence, communication and contributions in class. Children in the Intervention group were noted by teachers to use skills learned on the SDP during the school day. [ABSTRACT FROM AUTHOR]

Published
2008
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32. The effect of some early synthetic insecticides on pest management practices

Author

Stapley, J H

Abstract

The use of insecticides is often advisable and sometimes essential; when a crop is threatened, it is necessary to take action which must be swift and effective. Integrated pest management is a concept which is now generally known and widely accepted and it is to be hoped that less effort will be expended in the future on partisan and often biased controversy, and that the judicious use of insecticides will be accepted as an integral part of pest management strategy.

Published
1979
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33. Insect pests of coconuts in the Pacific Region

Author

Stapley, J H

Abstract

A significant advance in the control of rhinoceros beetle has been achieved by the use of a chemical attractant and virus infection. Premature nutfall, due to the bug Amblypelta cocophaga, has been effectively reduced by replacing ground-nesting ants by tree-nesting ants, which are also inimical to another bug pest, Axiagastus. Biological control of coconut leaf beetle by the parasite Tetra-stichus brontispae is recommended except on young palms where it can be controlled chemically.

Published
1973
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34. The Ipswich Torcs

Author

Brailsford, John and Stapley, J. E.

Abstract

The hoard of gold torcs from Ipswich comprises five found in 1968, to which must be added a sixth found on 18 October 1970. The five found in 1968 were in immediate association with each other and are here numbered 1 to 5. The 1970 find, my number 6, may be accepted as from the same hoard but separated from the others during the course of earth-moving in the area concerned.All the torcs are outstanding examples of early Celtic craftsmanship, and the group is of exceptional technical interest and great sociological and economic significance.

Published
1972
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36. The Rice Leaf Roller in the Solomon Islands

Author

Stapley, J. H.

Subjects
Solomon Islands, Leaf Roller
Abstract

This article 'The Rice Leaf Roller in the Solomon Islands' appeared in the International Rice Research Newsletter series, created by the International Rice Research Institute (IRRI). The primary objective of this publication was to expedite communication among scientists concerned with the development of improved technology for rice and for rice based cropping systems. This publication will report what scientists are doing to increase the production of rice in as much as this crop feeds the most densely populated and land scarce nations in the world.

Published
1978
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44. Developing a community-based genetic nomenclature for anole lizards

Author

Kusumi Kenro, Kulathinal Rob J, Abzhanov Arhat, Boissinot Stephane, Crawford Nicholas G, Faircloth Brant C, Glenn Travis C, Janes Daniel E, Losos Jonathan B, Menke Douglas B, Poe Steven, Sanger Thomas J, Schneider Christopher J, Stapley Jessica, Wade Juli, and Wilson-Rawls Jeanne

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Comparative studies of amniotes have been hindered by a dearth of reptilian molecular sequences. With the genomic assembly of the green anole, Anolis carolinensis available, non-avian reptilian genes can now be compared to mammalian, avian, and amphibian homologs. Furthermore, with more than 350 extant species in the genus Anolis, anoles are an unparalleled example of tetrapod genetic diversity and divergence. As an important ecological, genetic and now genomic reference, it is imperative to develop a standardized Anolis gene nomenclature alongside associated vocabularies and other useful metrics. Results Here we report the formation of the Anolis Gene Nomenclature Committee (AGNC) and propose a standardized evolutionary characterization code that will help researchers to define gene orthology and paralogy with tetrapod homologs, provide a system for naming novel genes in Anolis and other reptiles, furnish abbreviations to facilitate comparative studies among the Anolis species and related iguanid squamates, and classify the geographical origins of Anolis subpopulations. Conclusions This report has been generated in close consultation with members of the Anolis and genomic research communities, and using public database resources including NCBI and Ensembl. Updates will continue to be regularly posted to new research community websites such as lizardbase. We anticipate that this standardized gene nomenclature will facilitate the accessibility of reptilian sequences for comparative studies among tetrapods and will further serve as a template for other communities in their sequencing and annotation initiatives.

Published
2011
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45. A comparison of SNPs and microsatellites as linkage mapping markers: lessons from the zebra finch (Taeniopygia guttata)

Author

Birkhead Tim R, Dawson Deborah A, Stapley Jessica, Ball Alexander D, Burke Terry, and Slate Jon

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Genetic linkage maps are essential tools when searching for quantitative trait loci (QTL). To maximize genome coverage and provide an evenly spaced marker distribution a combination of different types of genetic marker are sometimes used. In this study we created linkage maps of four zebra finch (Taeniopygia guttata) chromosomes (1, 1A, 2 and 9) using two types of marker, Single Nucleotide Polymorphisms (SNPs) and microsatellites. To assess the effectiveness and accuracy of each kind of marker we compared maps built with each marker type separately and with both types of marker combined. Linkage map marker order was validated by making comparisons to the assembled zebra finch genome sequence. Results We showed that marker order was less reliable and linkage map lengths were inflated for microsatellite maps relative to SNP maps, apparently due to differing error rates between the two types of marker. Guidelines on how to minimise the effects of error are provided. In particular, we show that when combining both types of marker the conventional process of building linkage maps, whereby the most informative markers are added to the map first, has to be modified in order to improve map accuracy. Conclusions When using multiple types and large numbers of markers to create dense linkage maps, the least error prone loci (SNPs) rather than the most informative should be used to create framework maps before the addition of other potentially more error prone markers (microsatellites). This raises questions about the accuracy of marker order and predicted recombination rates in previous microsatellite linkage maps which were created using the conventional building process, however, provided suitable error detection strategies are followed microsatellite-based maps can continue to be regarded as reasonably reliable.

Published
2010
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46. Establishing a basis for ecosystem management in the western Indian Ocean.

Author

Vousden, D., Scott, L. E. P., Sauer, W., Bornman, T. G., Ngoile, M., Stapley, J., and Lutjeharms, J. R. E.

Subjects
*MARINE ecosystem management, *OCEANOGRAPHY, *MARINE biology, *MARINE resources
Abstract

The article offers information on the Agulhas and Somali Current Large Marine Ecosystem (ASCLME), a multinational programme, which aims to provide understanding of marine resources for the benefit of island and coastal populations in the Indian Ocean region. The programme is implemented by the United Nations Development Programme. It focuses on building and collating information on oceanography, coastal livelihoods, organic pollution, fish spawning and nursery areas.

Published
2008

47. Teaching transposon classification as a means to crowd source the curation of repeat annotation - a tardigrade perspective.

Author

Peona V, Martelossi J, Almojil D, Bocharkina J, Brännström I, Brown M, Cang A, Carrasco-Valenzuela T, DeVries J, Doellman M, Elsner D, Espíndola-Hernández P, Montoya GF, Gaspar B, Zagorski D, Hałakuc P, Ivanovska B, Laumer C, Lehmann R, Boštjančić LL, Mashoodh R, Mazzoleni S, Mouton A, Nilsson MA, Pei Y, Potente G, Provataris P, Pardos-Blas JR, Raut R, Sbaffi T, Schwarz F, Stapley J, Stevens L, Sultana N, Symonova R, Tahami MS, Urzì A, Yang H, Yusuf A, Pecoraro C, and Suh A

Abstract

Background: The advancement of sequencing technologies results in the rapid release of hundreds of new genome assemblies a year providing unprecedented resources for the study of genome evolution. Within this context, the significance of in-depth analyses of repetitive elements, transposable elements (TEs) in particular, is increasingly recognized in understanding genome evolution. Despite the plethora of available bioinformatic tools for identifying and annotating TEs, the phylogenetic distance of the target species from a curated and classified database of repetitive element sequences constrains any automated annotation effort. Moreover, manual curation of raw repeat libraries is deemed essential due to the frequent incompleteness of automatically generated consensus sequences., Results: Here, we present an example of a crowd-sourcing effort aimed at curating and annotating TE libraries of two non-model species built around a collaborative, peer-reviewed teaching process. Manual curation and classification are time-consuming processes that offer limited short-term academic rewards and are typically confined to a few research groups where methods are taught through hands-on experience. Crowd-sourcing efforts could therefore offer a significant opportunity to bridge the gap between learning the methods of curation effectively and empowering the scientific community with high-quality, reusable repeat libraries., Conclusions: The collaborative manual curation of TEs from two tardigrade species, for which there were no TE libraries available, resulted in the successful characterization of hundreds of new and diverse TEs in a reasonable time frame. Our crowd-sourcing setting can be used as a teaching reference guide for similar projects: A hidden treasure awaits discovery within non-model organisms., (© 2024. The Author(s).)

Published
2024
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48. Plastic and genomic change of a newly established lizard population following a founder event.

Author

Sabolić I, Mira Ó, Brandt DYC, Lisičić D, Stapley J, Novosolov M, Bakarić R, Cizelj I, Glogoški M, Hudina T, Taverne M, Allentoft ME, Nielsen R, Herrel A, and Štambuk A

Subjects
Animals, Islands, Genetic Variation, Italy, Adaptation, Physiological genetics, Male, Lizards genetics, Phenotype, Genetics, Population, Founder Effect
Abstract

Understanding how phenotypic divergence arises among natural populations remains one of the major goals in evolutionary biology. As part of competitive exclusion experiment conducted in 1971, 10 individuals of Italian wall lizard (Podarcis siculus (Rafinesque-Schmaltz, 1810)) were transplanted from Pod Kopište Island to the nearby island of Pod Mrčaru (Adriatic Sea). Merely 35 years after the introduction, the newly established population on Pod Mrčaru Island had shifted their diet from predominantly insectivorous towards omnivorous and changed significantly in a range of morphological, behavioural, physiological and ecological characteristics. Here, we combine genomic and quantitative genetic approaches to determine the relative roles of genetic adaptation and phenotypic plasticity in driving this rapid phenotypic shift. Our results show genome-wide genetic differentiation between ancestral and transplanted population, with weak genetic erosion on Pod Mrčaru Island. Adaptive processes following the founder event are indicated by highly differentiated genomic loci associating with ecologically relevant phenotypic traits, and/or having a putatively adaptive role across multiple lizard populations. Diverged traits related to head size and shape or bite force showed moderate heritability in a crossing experiment, but between-population differences in these traits did not persist in a common garden environment. Our results confirm the existence of sufficient additive genetic variance for traits to evolve under selection while also demonstrating that phenotypic plasticity and/or genotype by environment interactions are the main drivers of population differentiation at this early evolutionary stage., (© 2023 John Wiley & Sons Ltd.)

Published
2024
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49. Two-speed genomes of Epichloe fungal pathogens show contrasting signatures of selection between species and across populations.

Author

Treindl AD, Stapley J, Croll D, and Leuchtmann A

Subjects
Genome, Poaceae genetics, Genomics, Plants genetics, Selection, Genetic, Epichloe genetics
Abstract

Antagonistic selection between pathogens and their hosts can drive rapid evolutionary change and leave distinct molecular footprints of past and ongoing selection in the genomes of the interacting species. Despite an increasing availability of tools able to identify signatures of selection, the genetic mechanisms underlying coevolutionary interactions and the specific genes involved are still poorly understood, especially in heterogeneous natural environments. We searched the genomes of two species of Epichloe plant pathogen for evidence of recent selection. The Epichloe genus includes highly host-specific species that can sterilize their grass hosts. We performed selection scans using genome-wide SNP data from seven natural populations of two co-occurring Epichloe sibling species specialized on different hosts. We found evidence of recent (and ongoing) selective sweeps across the genome in both species. However, selective sweeps were more abundant in the species with a larger effective population size. Sweep regions often overlapped with highly polymorphic AT-rich regions supporting the role of these genome compartments in adaptive evolution. Although most loci under selection were specific to individual populations, we could also identify several candidate genes targeted by selection in sweep regions shared among populations. The genes encoded small secreted proteins typical of fungal effectors and cell wall-degrading enzymes. By investigating the genomic signatures of selection across multiple populations and species, this study contributes to our understanding of complex adaptive processes in natural plant pathogen systems., (© 2023 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.)

Published
2024
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50. GWAS reveals a rapidly evolving candidate avirulence effector in the Cercospora leaf spot pathogen.

Author

Chen C, Keunecke H, Bemm F, Gyetvai G, Neu E, Kopisch-Obuch FJ, McDonald BA, and Stapley J

Subjects
Cercospora genetics, Mutation, Virulence genetics, Plant Diseases microbiology, Genome-Wide Association Study, Ascomycota genetics
Abstract

The major resistance gene BvCR4 recently bred into sugar beet hybrids provides a high level of resistance to Cercospora leaf spot caused by the fungal pathogen Cercospora beticola. The occurrence of pathogen strains that overcome BvCR4 was studied using field trials in Switzerland conducted under natural disease pressure. Virulence of a subset of these strains was evaluated in a field trial conducted under elevated artificial disease pressure. We created a new C. beticola reference genome and mapped whole genome sequences of 256 isolates collected in Switzerland and Germany. These were combined with virulence phenotypes to conduct three separate genome-wide association studies (GWAS) to identify candidate avirulence genes. We identified a locus associated with avirulence containing a putative avirulence effector gene named AvrCR4. All virulent isolates either lacked AvrCR4 or had nonsynonymous mutations within the gene. AvrCR4 was present in all 74 isolates from non-BvCR4 hybrids, whereas 33 of 89 isolates from BvCR4 hybrids carried a deletion. We also mapped genomic data from 190 publicly available US isolates to our new reference genome. The AvrCR4 deletion was found in only one of 95 unique isolates from non-BvCR4 hybrids in the United States. AvrCR4 presents a unique example of an avirulence effector in which virulent alleles have only recently emerged. Most likely these were selected out of standing genetic variation after deployment of BvCR4. Identification of AvrCR4 will enable real-time screening of C. beticola populations for the emergence and spread of virulent isolates., (© 2023 The Authors. Molecular Plant Pathology published by British Society for Plant Pathology and John Wiley & Sons Ltd.)

Published
2024
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