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1. A Taxonomically-verified and Vouchered Checklist of the Vascular Plants of the Republic of Guinea

Author

Gosline, George, Bidault, Ehoarn, van der Burgt, Xander, Cahen, Daniel, Challen, Gill, Condé, Nagnouma, Couch, Charlotte, Couvreur, Thomas L. P., Dagallier, Léo-Paul M. J., Darbyshire, Iain, Dawson, Sally, Doré, Tokpa Seny, Goyder, David, Grall, Aurélie, Haba, Pépé, Haba, Pierre, Harris, David, Hind, D. J. Nicholas, Jongkind, Carel, Konomou, Gbamon, Larridon, Isabel, Lewis, Gwilym, Ley, Alexandra, Lock, Michael, Lucas, Eve, Magassouba, Sékou, Mayo, Simon, Molmou, Denise, Monro, Alexandre, Onana, Jean Michel, Paiva, Jorge, Paton, Alan, Phillips, Sylvia, Prance, Ghillean, Quintanar, Alejandro, Rokni, Saba, Shah, Toral, Schrire, Brian, Schuiteman, André, Simões, Ana Rita Giraldes, Sosef, Marc, Stévart, Tariq, Stone, R. Doug, Utteridge, Tim, Wilkin, Paul, Xanthos, Martin, Nic Lughadha, Eimear, and Cheek, Martin

Published
2023
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6. Indigenous crop diversity maintained despite the introduction of major global crops in an African centre of agrobiodiversity

Author

Rampersad, Chris, primary, Geto, Tesfu, additional, Samuel, Tarekegn, additional, Abebe, Meseret, additional, Gomez, Marybel Soto, additional, Pironon, Samuel, additional, Büchi, Lucie, additional, Haggar, Jeremy, additional, Stocks, Jonathan, additional, Ryan, Philippa, additional, Buggs, Richard J. A., additional, Demissew, Sebsebe, additional, Wilkin, Paul, additional, Abebe, Wendawek M., additional, and Borrell, James S., additional

Published
2023
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9. Wild edible yams from Madagascar: New insights into nutritional composition support their use for food security and conservation.

Author

Ratsimbazafy, Mirana K., Sharp, Paul A., Razanamparany, Louisette, Rajaonah, Mamy Tiana, Rakotoarison, Feno, Khoja, Kholoud K., Wilkin, Paul, and Howes, Melanie‐Jayne R.

Subjects
FOOD conservation, YAMS, FOOD security, EDIBLE mushrooms, CAROTENES, IRON
Abstract

Yams (Dioscorea species) are an important food resource in Madagascar, where both cultivated winged yam (D. alata) and wild edible yams are consumed. However, there is limited knowledge on the nutrient composition of wild edible yams in Madagascar, and on how they compare with the cultivated winged yam. Therefore, in this study, nine wild edible yam species, one with two subspecies from Madagascar (D. bako, D. buckleyana, D. irodensis, D. maciba, D. orangeana, D. pteropoda, D. sambiranensis subsp. bardotiae and subsp. sambiranensis, D. seriflora, and Dioscorea species Ovy valiha), were analyzed for their nutrient composition, compared with cultivated D. alata. They include 6/6 of the most favored wild edible yam species in Madagascar. New nutrient composition data (protein, carbohydrate/starch, energy, lipid, β‐carotene, and minerals) are presented for these nine wild edible yam species. The results show that they contain comparable levels of lipids and starch to D. alata, but none are better sources of protein than D. alata. The results show that D. irodensis contains a significantly higher β‐carotene content when compared to all other edible yams analyzed, and that D. buckleyana, D. irodensis, and D. sambiranensis subsp. bardotiae have a higher calcium content than cultivated D. alata, while all nine wild edible yam species analyzed contain a higher iron content, compared to cultivated D. alata. The nutrient composition data presented could provide new incentives to conserve wild edible yams and inform on strategies to select Dioscorea species for sustainable cultivation and use, providing opportunities to enhance future food security in Madagascar. [ABSTRACT FROM AUTHOR]

Published
2024
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10. Checklist of the Vascular Plants of the Republic of Guinea -- printable format

Author

Gosline, George, Bidault, Ehoarn, Burgt, Xander van der, Cahen, Daniel, Challen, Gill, Condé, Nagnouma, Couch, Charlotte, Couvreur, Thomas L.P ., Dagallier, Léo-Paul M.J., Dawson, Sally, Doré, Tokpa Seny, Goyder, David, Grall, Aurélie, Haba, Pépé, Haba, Pierre, Harris, David, Hind, D.J. Nicholas, Jongkind, Carel, Konomou, Gbamom, Larridon, Isabel, Lewis, Gwilym, Ley, Alexandra, Lock, Michael, Lucas, Eve, Magassouba, Sékou, Mayo, Simon, Molmou, Denise, Monro, Alexandre, Onana, Jean Michel, Paiva, Jorge, Paton, Alan, Phillips, Sylvia, Prance, Ghillian, Quintanar, Alejandro, Rokni, Saba, Shah, Toral, Schrire, Brian, Schuiteman, André, Simões, Ana Rita Giraldes, Sosef, Marc, Stévart, Tariq, Stone, R. Doug, Utteridge, Tim, Wilkin, Paul, Xanthos, Martin, Nic Lughadha, Eimear, and Cheek, Martin

Subjects
Flora, West Africa, Taxonomic checklist
Abstract

The Checklist of the Vascular Plants of the Republic of Guinea (CVPRG) is a specimen-based, expert-validated knowledge product, which provides a concise synthesis and overview of current knowledge on 3898 vascular plant species documented from Guinea (Conakry), West Africa, including their accepted names and synonyms, as well as their distribution and status within Guinea (indigenous or introduced, endemic or not). The CVPRG is generated automatically from the Guinea Collections Database and the Guinea Names Backbone Database, both developed and maintained at the Royal Botanic Gardens, Kew, in collaboration with the staff of the National Herbarium of Guinea. A total of 3505 indigenous vascular plant species are reported of which 3328 are flowering plants (angiosperms); this represents a 26% increase in known indigenous angiosperms since the last floristic overview. Intended as a reference for scientists documenting the diversity and distribution of the Guinea flora, the CVPRG will also inform those seeking to safeguard the rich plant diversity of Guinea and the societal, ecological and economic benefits accruing from these biological resources., This file is a printable version of the GBIF checklist dataset of the same name stored at https://doi.org/10.15468/f5gb45 . It is described in a forthcoming paper "A Taxonomically-verified and Vouchered Checklist of the Vascular Plants of the Republic of Guinea", Gosline et al., in Scientific Data.

Published
2023
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11. Genomic, spatial and morphometric data for discrimination of four species in the Mediterranean Tamus clade of yams (Dioscorea, Dioscoreaceae)

Author

Campos, Miguel, primary, Kelley, Emma, additional, Gravendeel, Barbara, additional, Médail, Frédéric, additional, Christenhusz, J M Maarten, additional, Fay, Michael F, additional, Catalán, Pilar, additional, Leitch, Ilia J, additional, Forest, Félix, additional, Wilkin, Paul, additional, and Viruel, Juan, additional

Published
2023
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12. Madagascar’s extraordinary biodiversity: Evolution, distribution, and use

Author

Antonelli, Alexandre, primary, Smith, Rhian J., additional, Perrigo, Allison L., additional, Crottini, Angelica, additional, Hackel, Jan, additional, Testo, Weston, additional, Farooq, Harith, additional, Torres Jiménez, Maria F., additional, Andela, Niels, additional, Andermann, Tobias, additional, Andriamanohera, Andotiana M., additional, Andriambololonera, Sylvie, additional, Bachman, Steven P., additional, Bacon, Christine D., additional, Baker, William J., additional, Belluardo, Francesco, additional, Birkinshaw, Chris, additional, Borrell, James S., additional, Cable, Stuart, additional, Canales, Nataly A., additional, Carrillo, Juan D., additional, Clegg, Rosie, additional, Clubbe, Colin, additional, Cooke, Robert S. C., additional, Damasco, Gabriel, additional, Dhanda, Sonia, additional, Edler, Daniel, additional, Faurby, Søren, additional, de Lima Ferreira, Paola, additional, Fisher, Brian L., additional, Forest, Félix, additional, Gardiner, Lauren M., additional, Goodman, Steven M., additional, Grace, Olwen M., additional, Guedes, Thaís B., additional, Henniges, Marie C., additional, Hill, Rowena, additional, Lehmann, Caroline E. R., additional, Lowry, Porter P., additional, Marline, Lovanomenjanahary, additional, Matos-Maraví, Pável, additional, Moat, Justin, additional, Neves, Beatriz, additional, Nogueira, Matheus G. C., additional, Onstein, Renske E., additional, Papadopulos, Alexander S. T., additional, Perez-Escobar, Oscar A., additional, Phelps, Leanne N., additional, Phillipson, Peter B., additional, Pironon, Samuel, additional, Przelomska, Natalia A. S., additional, Rabarimanarivo, Marina, additional, Rabehevitra, David, additional, Raharimampionona, Jeannie, additional, Rajaonah, Mamy Tiana, additional, Rajaonary, Fano, additional, Rajaovelona, Landy R., additional, Rakotoarinivo, Mijoro, additional, Rakotoarisoa, Amédée A., additional, Rakotoarisoa, Solofo E., additional, Rakotomalala, Herizo N., additional, Rakotonasolo, Franck, additional, Ralaiveloarisoa, Berthe A., additional, Ramirez-Herranz, Myriam, additional, Randriamamonjy, Jean Emmanuel N., additional, Randriamboavonjy, Tianjanahary, additional, Randrianasolo, Vonona, additional, Rasolohery, Andriambolantsoa, additional, Ratsifandrihamanana, Anitry N., additional, Ravololomanana, Noro, additional, Razafiniary, Velosoa, additional, Razanajatovo, Henintsoa, additional, Razanatsoa, Estelle, additional, Rivers, Malin, additional, Sayol, Ferran, additional, Silvestro, Daniele, additional, Vorontsova, Maria S., additional, Walker, Kim, additional, Walker, Barnaby E., additional, Wilkin, Paul, additional, Williams, Jenny, additional, Ziegler, Thomas, additional, Zizka, Alexander, additional, and Ralimanana, Hélène, additional

Published
2022
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13. Madagascar’s extraordinary biodiversity: Threats and opportunities

Author

Ralimanana, Hélène, primary, Perrigo, Allison L., additional, Smith, Rhian J., additional, Borrell, James S., additional, Faurby, Søren, additional, Rajaonah, Mamy Tiana, additional, Randriamboavonjy, Tianjanahary, additional, Vorontsova, Maria S., additional, Cooke, Robert S. C., additional, Phelps, Leanne N., additional, Sayol, Ferran, additional, Andela, Niels, additional, Andermann, Tobias, additional, Andriamanohera, Andotiana M., additional, Andriambololonera, Sylvie, additional, Bachman, Steven P., additional, Bacon, Christine D., additional, Baker, William J., additional, Belluardo, Francesco, additional, Birkinshaw, Chris, additional, Cable, Stuart, additional, Canales, Nataly A., additional, Carrillo, Juan D., additional, Clegg, Rosie, additional, Clubbe, Colin, additional, Crottini, Angelica, additional, Damasco, Gabriel, additional, Dhanda, Sonia, additional, Edler, Daniel, additional, Farooq, Harith, additional, de Lima Ferreira, Paola, additional, Fisher, Brian L., additional, Forest, Félix, additional, Gardiner, Lauren M., additional, Goodman, Steven M., additional, Grace, Olwen M., additional, Guedes, Thaís B., additional, Hackel, Jan, additional, Henniges, Marie C., additional, Hill, Rowena, additional, Lehmann, Caroline E. R., additional, Lowry, Porter P., additional, Marline, Lovanomenjanahary, additional, Matos-Maraví, Pável, additional, Moat, Justin, additional, Neves, Beatriz, additional, Nogueira, Matheus G. C., additional, Onstein, Renske E., additional, Papadopulos, Alexander S. T., additional, Perez-Escobar, Oscar A., additional, Phillipson, Peter B., additional, Pironon, Samuel, additional, Przelomska, Natalia A. S., additional, Rabarimanarivo, Marina, additional, Rabehevitra, David, additional, Raharimampionona, Jeannie, additional, Rajaonary, Fano, additional, Rajaovelona, Landy R., additional, Rakotoarinivo, Mijoro, additional, Rakotoarisoa, Amédée A., additional, Rakotoarisoa, Solofo E., additional, Rakotomalala, Herizo N., additional, Rakotonasolo, Franck, additional, Ralaiveloarisoa, Berthe A., additional, Ramirez-Herranz, Myriam, additional, Randriamamonjy, Jean Emmanuel N., additional, Randrianasolo, Vonona, additional, Rasolohery, Andriambolantsoa, additional, Ratsifandrihamanana, Anitry N., additional, Ravololomanana, Noro, additional, Razafiniary, Velosoa, additional, Razanajatovo, Henintsoa, additional, Razanatsoa, Estelle, additional, Rivers, Malin, additional, Silvestro, Daniele, additional, Testo, Weston, additional, Torres Jiménez, Maria F., additional, Walker, Kim, additional, Walker, Barnaby E., additional, Wilkin, Paul, additional, Williams, Jenny, additional, Ziegler, Thomas, additional, Zizka, Alexander, additional, and Antonelli, Alexandre, additional

Published
2022
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15. Maintenance and expansion of genetic and trait variation following domestication in a clonal crop

Author

Biswas, Manosh, Papadopulos, Alexander, White, Oliver, Demissew, Sebsebe, Wilkin, Paul, Nichols, Richard, Borrell, James, Abebe, Wendawek, Kebede, Firew, Woldeyes, Feleke, Heslop-Harrison, Pat, Dussert, Yann, Schwarzacher, Trude, and Buggs, Richard

Subjects
bepress|Life Sciences|Agriculture, bepress|Life Sciences|Genetics and Genomics|Genomics, bepress|Life Sciences, bepress|Life Sciences|Agriculture|Biosecurity, bepress|Life Sciences|Genetics and Genomics, bepress|Life Sciences|Bioinformatics, bepress|Life Sciences|Plant Sciences
Abstract

Clonal propagation enables favourable crop genotypes to be rapidly selected and multiplied. However, the absence of sexual propagation can lead to low genetic diversity and accumulation of deleterious mutations, which may eventually render crops less resilient to pathogens or environmental change. To better understand this trade-off, we characterise the domestication and contemporary genetic diversity of Enset (Ensete ventricosum), an indigenous African relative of bananas (Musa) and principal starch staple for 20 million Ethiopians. Wild enset is strictly sexually outcrossing, but in cultivation is exclusively propagated clonally and associated with diversification and specialisation into hundreds of named landraces. We applied tGBS sequencing to generate genome-wide genotypes for 192 accessions from across enset’s cultivated distribution, and surveyed 1340 farmers on enset agronomic traits. Overall, reduced heterozygosity in the domesticated lineage was consistent with a domestication bottleneck that retained 37% of wild diversity. However, excess low frequency putatively deleterious missense mutations present as heterozygotes suggested accumulation of mutational load in clonal domesticated lineages. Our evidence indicates that the major domesticated lineages initially arose through historic sexual recombination associated with a domestication bottleneck, followed by amplification of favourable genotypes through an extended period of clonal propagation. Among domesticated lineages we found significant phylogenetic signal for multiple farmer identified food, nutrition and disease resistance traits and little evidence of contemporary recombination. Development of future-climate adapted genotypes may require crop breeding, but outcrossing risks exposing deleterious alleles as homozygotes. This trade-off may partly explain the ubiquity and persistence of clonal propagation over recent centuries of comparative climate stability.

Published
2022
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17. Genomic, spatial and morphometric data for discrimination of four species in the Mediterranean Tamus clade of yams (Dioscorea, Dioscoreaceae)

Author

Campos, Miguel, primary, Kelley, Emma, additional, GRAVENDEEL, Barbara, additional, Médail, Frédéric, additional, Christenhusz, J. M. Maarten, additional, Fay, Michael F., additional, Catalán, Pilar, additional, Leitch, Ilia J., additional, Forest, Félix, additional, Wilkin, Paul, additional, and Viruel, Juan, additional

Published
2022
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18. Maintenance and expansion of genetic and trait variation following domestication in a clonal crop.

Author

White, Oliver W., Biswas, Manosh Kumar, Abebe, Wendawek M., Dussert, Yann, Kebede, Firew, Nichols, Richard A., Buggs, Richard J. A., Demissew, Sebsebe, Woldeyes, Feleke, Papadopulos, Alexander S. T., Schwarzacher, Trude, Heslop‐Harrison, Pat J. S., Wilkin, Paul, and Borrell, James S.

Subjects
GENETIC variation, GENETIC load, PLANT breeding, BANANAS, DIET in disease, MISSENSE mutation, NATURAL immunity
Abstract

Clonal propagation enables favourable crop genotypes to be rapidly selected and multiplied. However, the absence of sexual propagation can lead to low genetic diversity and accumulation of deleterious mutations, which may eventually render crops less resilient to pathogens or environmental change. To better understand this trade‐off, we characterize the domestication and contemporary genetic diversity of Enset (Ensete ventricosum), an indigenous African relative of bananas (Musa) and a principal starch staple for 20 million Ethiopians. Wild enset reproduction occurs strictly by sexual outcrossing, but for cultivation, it is propagated clonally and associated with diversification and specialization into hundreds of named landraces. We applied tGBS sequencing to generate genome‐wide genotypes for 192 accessions from across enset's cultivated distribution, and surveyed 1340 farmers on enset agronomic traits. Overall, reduced heterozygosity in the domesticated lineage was consistent with a domestication bottleneck that retained 37% of wild diversity. However, an excess of putatively deleterious missense mutations at low frequency present as heterozygotes suggested an accumulation of mutational load in clonal domesticated lineages. Our evidence indicates that the major domesticated lineages initially arose through historic sexual recombination associated with a domestication bottleneck, followed by the amplification of favourable genotypes through an extended period of clonal propagation. Among domesticated lineages, we found a significant phylogenetic signal for multiple farmer‐identified food, nutrition and disease resistance traits and little evidence of contemporary recombination. The development of future‐climate adapted genotypes may require crop breeding, but outcrossing risks exposing deleterious alleles as homozygotes. This trade‐off may partly explain the ubiquity and persistence of clonal propagation over recent centuries of comparative climate stability. [ABSTRACT FROM AUTHOR]

Published
2023
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19. Madagascar's extraordinary biodiversity : Evolution, distribution, and use

Author

Antonelli, Alexandre, Smith, Rhian J., Perrigo, Allison L., Crottini, Angelica, Hackel, Jan, Testo, Weston, Farooq, Harith, Jimenez, Maria F. Torres, Andela, Niels, Andermann, Tobias, Andriamanohera, Andotiana M., Andriambololonera, Sylvie, Bachman, Steven P., Bacon, Christine D., Baker, William J., Belluardo, Francesco, Birkinshaw, Chris, Borrell, James S., Cable, Stuart, Canales, Nataly A., Carrillo, Juan D., Clegg, Rosie, Clubbe, Colin, Cooke, Robert S. C., Damasco, Gabriel, Dhanda, Sonia, Edler, Daniel, Faurby, Soren, Ferreira, Paola de Lima, Fisher, Brian L., Forest, Felix, Gardiner, Lauren M., Goodman, Steven M., Grace, Olwen M., Guedes, Thais B., Henniges, Marie C., Hill, Rowena, Lehmann, Caroline E. R., Lowry, Porter P., II, Marline, Lovanomenjanahary, Matos-Maravi, Pavel, Moat, Justin, Neves, Beatriz, Nogueira, Matheus G. C., Onstein, Renske E., Papadopulos, Alexander S. T., Perez-Escobar, Oscar A., Phelps, Leanne N., Phillipson, Peter B., Pironon, Samuel, Przelomska, Natalia A. S., Rabarimanarivo, Marina, Rabehevitra, David, Raharimampionona, Jeannie, Rajaonah, Mamy Tiana, Rajaonary, Fano, Rajaovelona, Landy R., Rakotoarinivo, Mijoro, Rakotoarisoa, Amedee A., Rakotoarisoa, Solofo E., Rakotomalala, Herizo N., Rakotonasolo, Franck, Ralaiveloarisoa, Berthe A., Ramirez-Herranz, Myriam, Randriamamonjy, Jean Emmanuel N., Randriamboavonjy, Tianjanahary, Randrianasolo, Vonona, Rasolohery, Andriambolantsoa, Ratsifandrihamanana, Anitry N., Ravololomanana, Noro, Razafiniary, Velosoa, Razanajatovo, Henintsoa, Razanatsoa, Estelle, Rivers, Malin, Sayol, Ferran, Silvestro, Daniele, Vorontsova, Maria S., Walker, Kim, Walker, Barnaby E., Wilkin, Paul, Williams, Jenny, Ziegler, Thomas, Zizka, Alexander, Ralimanana, Helene, Antonelli, Alexandre, Smith, Rhian J., Perrigo, Allison L., Crottini, Angelica, Hackel, Jan, Testo, Weston, Farooq, Harith, Jimenez, Maria F. Torres, Andela, Niels, Andermann, Tobias, Andriamanohera, Andotiana M., Andriambololonera, Sylvie, Bachman, Steven P., Bacon, Christine D., Baker, William J., Belluardo, Francesco, Birkinshaw, Chris, Borrell, James S., Cable, Stuart, Canales, Nataly A., Carrillo, Juan D., Clegg, Rosie, Clubbe, Colin, Cooke, Robert S. C., Damasco, Gabriel, Dhanda, Sonia, Edler, Daniel, Faurby, Soren, Ferreira, Paola de Lima, Fisher, Brian L., Forest, Felix, Gardiner, Lauren M., Goodman, Steven M., Grace, Olwen M., Guedes, Thais B., Henniges, Marie C., Hill, Rowena, Lehmann, Caroline E. R., Lowry, Porter P., II, Marline, Lovanomenjanahary, Matos-Maravi, Pavel, Moat, Justin, Neves, Beatriz, Nogueira, Matheus G. C., Onstein, Renske E., Papadopulos, Alexander S. T., Perez-Escobar, Oscar A., Phelps, Leanne N., Phillipson, Peter B., Pironon, Samuel, Przelomska, Natalia A. S., Rabarimanarivo, Marina, Rabehevitra, David, Raharimampionona, Jeannie, Rajaonah, Mamy Tiana, Rajaonary, Fano, Rajaovelona, Landy R., Rakotoarinivo, Mijoro, Rakotoarisoa, Amedee A., Rakotoarisoa, Solofo E., Rakotomalala, Herizo N., Rakotonasolo, Franck, Ralaiveloarisoa, Berthe A., Ramirez-Herranz, Myriam, Randriamamonjy, Jean Emmanuel N., Randriamboavonjy, Tianjanahary, Randrianasolo, Vonona, Rasolohery, Andriambolantsoa, Ratsifandrihamanana, Anitry N., Ravololomanana, Noro, Razafiniary, Velosoa, Razanajatovo, Henintsoa, Razanatsoa, Estelle, Rivers, Malin, Sayol, Ferran, Silvestro, Daniele, Vorontsova, Maria S., Walker, Kim, Walker, Barnaby E., Wilkin, Paul, Williams, Jenny, Ziegler, Thomas, Zizka, Alexander, and Ralimanana, Helene

Abstract

Madagascar's biota is hyperdiverse and includes exceptional levels of endemicity. We review the current state of knowledge on Madagascar's past and current terrestrial and freshwater biodiversity by compiling and presenting comprehensive data on species diversity, endemism, and rates of species description and human uses, in addition to presenting an updated and simplified map of vegetation types. We report a substantial increase of records and species new to science in recent years; however, the diversity and evolution of many groups remain practically unknown (e.g., fungi and most invertebrates). Digitization efforts are increasing the resolution of species richness patterns and we highlight the crucial role of field- and collections-based research for advancing biodiversity knowledge and identifying gaps in our understanding, particularly as species richness corresponds closely to collection effort. Phylogenetic diversity patterns mirror that of species richness and endemism in most of the analyzed groups. We highlight humid forests as centers of diversity and endemism because of their role as refugia and centers of recent and rapid radiations. However, the distinct endemism of other areas, such as the grassland-woodland mosaic of the Central Highlands and the spiny forest of the southwest, is also biologically important despite lower species richness. The documented uses of Malagasy biodiversity are manifold, with much potential for the uncovering of new useful traits for food, medicine, and climate mitigation. The data presented here showcase Madagascar as a unique " living laboratory" for our understanding of evolution and the complex interactions between people and nature. The gathering and analysis of biodiversity data must continue and accelerate if we are to fully understand and safeguard this unique subset of Earth's biodiversity.

Published
2022
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20. Madagascar's extraordinary biodiversity : Threats and opportunities

Author

Ralimanana, Helene, Perrigo, Allison L., Smith, Rhian J., Borrell, James S., Faurby, Soren, Rajaonah, Mamy Tiana, Randriamboavonjy, Tianjanahary, Vorontsova, Maria S., Cooke, Robert S. C., Phelps, Leanne N., Sayol, Ferran, Andela, Niels, Andermann, Tobias, Andriamanohera, Andotiana M., Andriambololonera, Sylvie, Bachman, Steven P., Bacon, Christine D., Baker, William J., Belluardo, Francesco, Birkinshaw, Chris, Cable, Stuart, Canales, Nataly A., Carrillo, Juan D., Clegg, Rosie, Clubbe, Colin, Crottini, Angelica, Damasco, Gabriel, Dhanda, Sonia, Edler, Daniel, Farooq, Harith, Ferreira, Paola de Lima, Fisher, Brian L., Forest, Felix, Gardiner, Lauren M., Goodman, Steven M., Grace, Olwen M., Guedes, Thais B., Hackel, Jan, Henniges, Marie C., Hill, Rowena, Lehmann, Caroline E. R., Lowry, Porter P., II, Marline, Lovanomenjanahary, Matos-Maravi, Pavel, Moat, Justin, Neves, Beatriz, Nogueira, Matheus G. C., Onstein, Renske E., Papadopulos, Alexander S. T., Perez-Escobar, Oscar A., Phillipson, Peter B., Pironon, Samuel, Przelomska, Natalia A. S., Rabarimanarivo, Marina, Rabehevitra, David, Raharimampionona, Jeannie, Rajaonary, Fano, Rajaovelona, Landy R., Rakotoarinivo, Mijoro, Rakotoarisoa, Amedee A., Rakotoarisoa, Solofo E., Rakotomalala, Herizo N., Rakotonasolo, Franck, Ralaiveloarisoa, Berthe A., Ramirez-Herranz, Myriam, Randriamamonjy, Jean Emmanuel N., Randrianasolo, Vonona, Rasolohery, Andriambolantsoa, Ratsifandrihamanana, Anitry N., Ravololomanana, Noro, Razafiniary, Velosoa, Razanajatovo, Henintsoa, Razanatsoa, Estelle, Rivers, Malin, Silvestro, Daniele, Testo, Weston, Jimenez, Maria F. Torres, Walker, Kim, Walker, Barnaby E., Wilkin, Paul, Williams, Jenny, Ziegler, Thomas, Zizka, Alexander, Antonelli, Alexandre, Ralimanana, Helene, Perrigo, Allison L., Smith, Rhian J., Borrell, James S., Faurby, Soren, Rajaonah, Mamy Tiana, Randriamboavonjy, Tianjanahary, Vorontsova, Maria S., Cooke, Robert S. C., Phelps, Leanne N., Sayol, Ferran, Andela, Niels, Andermann, Tobias, Andriamanohera, Andotiana M., Andriambololonera, Sylvie, Bachman, Steven P., Bacon, Christine D., Baker, William J., Belluardo, Francesco, Birkinshaw, Chris, Cable, Stuart, Canales, Nataly A., Carrillo, Juan D., Clegg, Rosie, Clubbe, Colin, Crottini, Angelica, Damasco, Gabriel, Dhanda, Sonia, Edler, Daniel, Farooq, Harith, Ferreira, Paola de Lima, Fisher, Brian L., Forest, Felix, Gardiner, Lauren M., Goodman, Steven M., Grace, Olwen M., Guedes, Thais B., Hackel, Jan, Henniges, Marie C., Hill, Rowena, Lehmann, Caroline E. R., Lowry, Porter P., II, Marline, Lovanomenjanahary, Matos-Maravi, Pavel, Moat, Justin, Neves, Beatriz, Nogueira, Matheus G. C., Onstein, Renske E., Papadopulos, Alexander S. T., Perez-Escobar, Oscar A., Phillipson, Peter B., Pironon, Samuel, Przelomska, Natalia A. S., Rabarimanarivo, Marina, Rabehevitra, David, Raharimampionona, Jeannie, Rajaonary, Fano, Rajaovelona, Landy R., Rakotoarinivo, Mijoro, Rakotoarisoa, Amedee A., Rakotoarisoa, Solofo E., Rakotomalala, Herizo N., Rakotonasolo, Franck, Ralaiveloarisoa, Berthe A., Ramirez-Herranz, Myriam, Randriamamonjy, Jean Emmanuel N., Randrianasolo, Vonona, Rasolohery, Andriambolantsoa, Ratsifandrihamanana, Anitry N., Ravololomanana, Noro, Razafiniary, Velosoa, Razanajatovo, Henintsoa, Razanatsoa, Estelle, Rivers, Malin, Silvestro, Daniele, Testo, Weston, Jimenez, Maria F. Torres, Walker, Kim, Walker, Barnaby E., Wilkin, Paul, Williams, Jenny, Ziegler, Thomas, Zizka, Alexander, and Antonelli, Alexandre

Abstract

Madagascar's unique biota is heavily affected by human activity and is under intense threat. Here, we review the current state of knowledge on the conservation status of Madagascar's terrestrial and freshwater biodiversity by presenting data and analyses on documented and predicted species-level conservation statuses, the most prevalent and relevant threats, ex situ collections and programs, and the coverage and comprehensiveness of protected areas. The existing terrestrial protected area network in Madagascar covers 10.4% of its land area and includes at least part of the range of the majority of described native species of vertebrates with known distributions (97.1% of freshwater fishes, amphibians, reptiles, birds, and mammals combined) and plants (67.7%). The overall figures are higher for threatened species (97.7% of threatened vertebrates and 79.6% of threatened plants occurring within at least one protected area). International Union for Conservation of Nature (IUCN) Red List assessments and Bayesian neural network analyses for plants identify overexploitation of biological resources and unsustainable agriculture as themost prominent threats to biodiversity. We highlight five opportunities for action at multiple levels to ensure that conservation and ecological restoration objectives, programs, and activities take account of complex underlying and interacting factors and produce tangible benefits for the biodiversity and people of Madagascar.

Published
2022
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21. Madagascar’s extraordinary biodiversity:Evolution, distribution, and use

Author

Antonelli, Alexandre, Smith, Rhian J., Perrigo, Allison L., Crottini, Angelica, Hackel, Jan, Testo, Weston, Farooq, Harith, Torres Jiménez, Maria F., Andela, Niels, Andermann, Tobias, Andriamanohera, Andotiana M., Andriambololonera, Sylvie, Bachman, Steven P., Bacon, Christine D., Baker, William J., Belluardo, Francesco, Birkinshaw, Chris, Borrell, James S., Cable, Stuart, Canales, Nataly A., Carrillo, Juan D., Clegg, Rosie, Clubbe, Colin, Cooke, Robert S. C., Damasco, Gabriel, Dhanda, Sonia, Edler, Daniel, Faurby, Søren, de Lima Ferreira, Paola, Fisher, Brian L., Forest, Félix, Gardiner, Lauren M., Goodman, Steven M., Grace, Olwen M., Guedes, Thaís B., Henniges, Marie C., Hill, Rowena, Lehmann, Caroline E. R., Lowry, Porter P., Marline, Lovanomenjanahary, Matos-Maraví, Pável, Moat, Justin, Neves, Beatriz, Nogueira, Matheus G. C., Onstein, Renske E., Papadopulos, Alexander S. T., Perez-Escobar, Oscar A., Phelps, Leanne N., Phillipson, Peter B., Pironon, Samuel, Przelomska, Natalia A. S., Rabarimanarivo, Marina, Rabehevitra, David, Raharimampionona, Jeannie, Rajaonah, Mamy Tiana, Rajaonary, Fano, Rajaovelona, Landy R., Rakotoarinivo, Mijoro, Rakotoarisoa, Amédée A., Rakotoarisoa, Solofo E., Rakotomalala, Herizo N., Rakotonasolo, Franck, Ralaiveloarisoa, Berthe A., Ramirez-Herranz, Myriam, Randriamamonjy, Jean Emmanuel N., Randriamboavonjy, Tianjanahary, Randrianasolo, Vonona, Rasolohery, Andriambolantsoa, Ratsifandrihamanana, Anitry N., Ravololomanana, Noro, Razafiniary, Velosoa, Razanajatovo, Henintsoa, Razanatsoa, Estelle, Rivers, Malin, Sayol, Ferran, Silvestro, Daniele, Vorontsova, Maria S., Walker, Kim, Walker, Barnaby E., Wilkin, Paul, Williams, Jenny, Ziegler, Thomas, Zizka, Alexander, Ralimanana, Hélène, Antonelli, Alexandre, Smith, Rhian J., Perrigo, Allison L., Crottini, Angelica, Hackel, Jan, Testo, Weston, Farooq, Harith, Torres Jiménez, Maria F., Andela, Niels, Andermann, Tobias, Andriamanohera, Andotiana M., Andriambololonera, Sylvie, Bachman, Steven P., Bacon, Christine D., Baker, William J., Belluardo, Francesco, Birkinshaw, Chris, Borrell, James S., Cable, Stuart, Canales, Nataly A., Carrillo, Juan D., Clegg, Rosie, Clubbe, Colin, Cooke, Robert S. C., Damasco, Gabriel, Dhanda, Sonia, Edler, Daniel, Faurby, Søren, de Lima Ferreira, Paola, Fisher, Brian L., Forest, Félix, Gardiner, Lauren M., Goodman, Steven M., Grace, Olwen M., Guedes, Thaís B., Henniges, Marie C., Hill, Rowena, Lehmann, Caroline E. R., Lowry, Porter P., Marline, Lovanomenjanahary, Matos-Maraví, Pável, Moat, Justin, Neves, Beatriz, Nogueira, Matheus G. C., Onstein, Renske E., Papadopulos, Alexander S. T., Perez-Escobar, Oscar A., Phelps, Leanne N., Phillipson, Peter B., Pironon, Samuel, Przelomska, Natalia A. S., Rabarimanarivo, Marina, Rabehevitra, David, Raharimampionona, Jeannie, Rajaonah, Mamy Tiana, Rajaonary, Fano, Rajaovelona, Landy R., Rakotoarinivo, Mijoro, Rakotoarisoa, Amédée A., Rakotoarisoa, Solofo E., Rakotomalala, Herizo N., Rakotonasolo, Franck, Ralaiveloarisoa, Berthe A., Ramirez-Herranz, Myriam, Randriamamonjy, Jean Emmanuel N., Randriamboavonjy, Tianjanahary, Randrianasolo, Vonona, Rasolohery, Andriambolantsoa, Ratsifandrihamanana, Anitry N., Ravololomanana, Noro, Razafiniary, Velosoa, Razanajatovo, Henintsoa, Razanatsoa, Estelle, Rivers, Malin, Sayol, Ferran, Silvestro, Daniele, Vorontsova, Maria S., Walker, Kim, Walker, Barnaby E., Wilkin, Paul, Williams, Jenny, Ziegler, Thomas, Zizka, Alexander, and Ralimanana, Hélène

Abstract

Madagascar’s biota is hyperdiverse and includes exceptional levels of endemicity. We review the current state of knowledge on Madagascar’s past and current terrestrial and freshwater biodiversity by compiling and presenting comprehensive data on species diversity, endemism, and rates of species description and human uses, in addition to presenting an updated and simplified map of vegetation types. We report a substantial increase of records and species new to science in recent years; however, the diversity and evolution of many groups remain practically unknown (e.g., fungi and most invertebrates). Digitization efforts are increasing the resolution of species richness patterns and we highlight the crucial role of field- and collections-based research for advancing biodiversity knowledge and identifying gaps in our understanding, particularly as species richness corresponds closely to collection effort. Phylogenetic diversity patterns mirror that of species richness and endemism in most of the analyzed groups. We highlight humid forests as centers of diversity and endemism because of their role as refugia and centers of recent and rapid radiations. However, the distinct endemism of other areas, such as the grassland-woodland mosaic of the Central Highlands and the spiny forest of the southwest, is also biologically important despite lower species richness. The documented uses of Malagasy biodiversity are manifold, with much potential for the uncovering of new useful traits for food, medicine, and climate mitigation. The data presented here showcase Madagascar as a unique “living laboratory” for our understanding of evolution and the complex interactions between people and nature. The gathering and analysis of biodiversity data must continue and accelerate if we are to fully understand and safeguard this unique subset of Earth’s biodiversity.

Published
2022

22. Madagascar’s extraordinary biodiversity:Threats and opportunities

Author

Ralimanana, Hélène, Perrigo, Allison L., Smith, Rhian J., Borrell, James S., Faurby, Søren, Rajaonah, Mamy Tiana, Randriamboavonjy, Tianjanahary, Vorontsova, Maria S., Cooke, Robert S. C., Phelps, Leanne N., Sayol, Ferran, Andela, Niels, Andermann, Tobias, Andriamanohera, Andotiana M., Andriambololonera, Sylvie, Bachman, Steven P., Bacon, Christine D., Baker, William J., Belluardo, Francesco, Birkinshaw, Chris, Cable, Stuart, Canales, Nataly A., Carrillo, Juan D., Clegg, Rosie, Clubbe, Colin, Crottini, Angelica, Damasco, Gabriel, Dhanda, Sonia, Edler, Daniel, Farooq, Harith, de Lima Ferreira, Paola, Fisher, Brian L., Forest, Félix, Gardiner, Lauren M., Goodman, Steven M., Grace, Olwen M., Guedes, Thaís B., Hackel, Jan, Henniges, Marie C., Hill, Rowena, Lehmann, Caroline E. R., Lowry, Porter P., Marline, Lovanomenjanahary, Matos-Maraví, Pável, Moat, Justin, Neves, Beatriz, Nogueira, Matheus G. C., Onstein, Renske E., Papadopulos, Alexander S. T., Perez-Escobar, Oscar A., Phillipson, Peter B., Pironon, Samuel, Przelomska, Natalia A. S., Rabarimanarivo, Marina, Rabehevitra, David, Raharimampionona, Jeannie, Rajaonary, Fano, Rajaovelona, Landy R., Rakotoarinivo, Mijoro, Rakotoarisoa, Amédée A., Rakotoarisoa, Solofo E., Rakotomalala, Herizo N., Rakotonasolo, Franck, Ralaiveloarisoa, Berthe A., Ramirez-Herranz, Myriam, Randriamamonjy, Jean Emmanuel N., Randrianasolo, Vonona, Rasolohery, Andriambolantsoa, Ratsifandrihamanana, Anitry N., Ravololomanana, Noro, Razafiniary, Velosoa, Razanajatovo, Henintsoa, Razanatsoa, Estelle, Rivers, Malin, Silvestro, Daniele, Testo, Weston, Torres Jiménez, Maria F., Walker, Kim, Walker, Barnaby E., Wilkin, Paul, Williams, Jenny, Ziegler, Thomas, Zizka, Alexander, Antonelli, Alexandre, Ralimanana, Hélène, Perrigo, Allison L., Smith, Rhian J., Borrell, James S., Faurby, Søren, Rajaonah, Mamy Tiana, Randriamboavonjy, Tianjanahary, Vorontsova, Maria S., Cooke, Robert S. C., Phelps, Leanne N., Sayol, Ferran, Andela, Niels, Andermann, Tobias, Andriamanohera, Andotiana M., Andriambololonera, Sylvie, Bachman, Steven P., Bacon, Christine D., Baker, William J., Belluardo, Francesco, Birkinshaw, Chris, Cable, Stuart, Canales, Nataly A., Carrillo, Juan D., Clegg, Rosie, Clubbe, Colin, Crottini, Angelica, Damasco, Gabriel, Dhanda, Sonia, Edler, Daniel, Farooq, Harith, de Lima Ferreira, Paola, Fisher, Brian L., Forest, Félix, Gardiner, Lauren M., Goodman, Steven M., Grace, Olwen M., Guedes, Thaís B., Hackel, Jan, Henniges, Marie C., Hill, Rowena, Lehmann, Caroline E. R., Lowry, Porter P., Marline, Lovanomenjanahary, Matos-Maraví, Pável, Moat, Justin, Neves, Beatriz, Nogueira, Matheus G. C., Onstein, Renske E., Papadopulos, Alexander S. T., Perez-Escobar, Oscar A., Phillipson, Peter B., Pironon, Samuel, Przelomska, Natalia A. S., Rabarimanarivo, Marina, Rabehevitra, David, Raharimampionona, Jeannie, Rajaonary, Fano, Rajaovelona, Landy R., Rakotoarinivo, Mijoro, Rakotoarisoa, Amédée A., Rakotoarisoa, Solofo E., Rakotomalala, Herizo N., Rakotonasolo, Franck, Ralaiveloarisoa, Berthe A., Ramirez-Herranz, Myriam, Randriamamonjy, Jean Emmanuel N., Randrianasolo, Vonona, Rasolohery, Andriambolantsoa, Ratsifandrihamanana, Anitry N., Ravololomanana, Noro, Razafiniary, Velosoa, Razanajatovo, Henintsoa, Razanatsoa, Estelle, Rivers, Malin, Silvestro, Daniele, Testo, Weston, Torres Jiménez, Maria F., Walker, Kim, Walker, Barnaby E., Wilkin, Paul, Williams, Jenny, Ziegler, Thomas, Zizka, Alexander, and Antonelli, Alexandre

Abstract

Madagascar’s unique biota is heavily affected by human activity and is under intense threat. Here, we review the current state of knowledge on the conservation status of Madagascar’s terrestrial and freshwater biodiversity by presenting data and analyses on documented and predicted species-level conservation statuses, the most prevalent and relevant threats, ex situ collections and programs, and the coverage and comprehensiveness of protected areas. The existing terrestrial protected area network in Madagascar covers 10.4% of its land area and includes at least part of the range of the majority of described native species of vertebrates with known distributions (97.1% of freshwater fishes, amphibians, reptiles, birds, and mammals combined) and plants (67.7%). The overall figures are higher for threatened species (97.7% of threatened vertebrates and 79.6% of threatened plants occurring within at least one protected area). International Union for Conservation of Nature (IUCN) Red List assessments and Bayesian neural network analyses for plants identify overexploitation of biological resources and unsustainable agriculture as the most prominent threats to biodiversity. We highlight five opportunities for action at multiple levels to ensure that conservation and ecological restoration objectives, programs, and activities take account of complex underlying and interacting factors and produce tangible benefits for the biodiversity and people of Madagascar.

Published
2022

23. Uses and benefits of digital sequence information from plant genetic resources:Lessons learnt from botanical collections

Author

Cowell, Carly, Paton, Alan, Borrell, James S., Williams, China, Wilkin, Paul, Antonelli, Alexandre, Baker, William J., Buggs, Richard, Fay, Michael F., Gargiulo, Roberta, Grace, Olwen M., Kuhnhäuser, Benedikt G., Woudstra, Yannick, Kersey, Paul J., Cowell, Carly, Paton, Alan, Borrell, James S., Williams, China, Wilkin, Paul, Antonelli, Alexandre, Baker, William J., Buggs, Richard, Fay, Michael F., Gargiulo, Roberta, Grace, Olwen M., Kuhnhäuser, Benedikt G., Woudstra, Yannick, and Kersey, Paul J.

Abstract

Digitized molecular data are vital to numerous aspects of scientific research and genetic resource use. The Convention on Biological Diversity currently refers to this as “Digital Sequence Information” (DSI), a term not widely adopted by science and lacking a clear definition. There are concerns over the access to genetic resources and absence of benefit sharing by provider countries. Open access to DSI might exacerbate this, which is leading to increasing policy interventions and restricted access to genetic resources and DSI. We analyze current international debate and proposed solutions and provide case studies of DSI use producing tangible benefits for the provider countries and scientific research, demonstrating the importance of open access DSI to achieving conservation goals. Summary: Substantial advances in DNA sequencing over the last decades hold great potential to enhance food security and sustainable use of global biodiversity, benefiting the world's poorest people. Digital Sequence Information (DSI) plays a crucial role in catalyzing research applications that can contribute to international societal and biodiversity conservation targets. However, benefit sharing relating to DSI is difficult to identify and hindered by the lack of clear international governance and legislation, which in turn has led to a reluctance to make DSI publicly and freely available. Critically, no precise definition exists under the Convention on Biological Diversity (CBD), the Nagoya Protocol (NP), or the International Treaty for Plant Genetic Resources for Food and Agriculture (ITPGRFA). The key difference between DSI and biological resources, for which access and use are highly regulated under those frameworks, is that information is nonphysical. Information can be replicated and used without movement of, or access to, physical specimens. Thus, regulating the use of DSI is extremely challenging and remains controversial. Here, we review the regulation of DSI and the possib

Published
2022

24. Introduced crops supplement rather than replace indigenous crops in an African center of agrobiodiversity

Author

Rampersad, Chris, primary, Geto, Tesfu, additional, Samuel, Tarekegn, additional, Abebe, Meseret, additional, Soto Gomez, Marybel, additional, Pironon, Samuel, additional, Buchi, Lucie, additional, Haggar, Jeremy, additional, Stocks, Jonathan, additional, Ryan, Philippa, additional, Buggs, Richard J A, additional, Demissew, Sebsebe, additional, Wilkin, Paul, additional, and Borrell, James S, additional

Published
2022
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25. The Genetic Diversity of Enset (Ensete ventricosum) Landraces Used in Traditional Medicine Is Similar to the Diversity Found in Non-medicinal Landraces

Author

Nuraga, Gizachew Woldesenbet, primary, Feyissa, Tileye, additional, Tesfaye, Kassahun, additional, Biswas, Manosh Kumar, additional, Schwarzacher, Trude, additional, Borrell, James S., additional, Wilkin, Paul, additional, Demissew, Sebsebe, additional, Tadele, Zerihun, additional, and Heslop-Harrison, J. S. (Pat), additional

Published
2022
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27. Uses and benefits of digital sequence information from plant genetic resources: Lessons learnt from botanical collections.

Author

Cowell, Carly, Paton, Alan, Borrell, James S., Williams, China, Wilkin, Paul, Antonelli, Alexandre, Baker, William J., Buggs, Richard, Fay, Michael F., Gargiulo, Roberta, Grace, Olwen M., Kuhnhäuser, Benedikt G., Woudstra, Yannick, and Kersey, Paul J.

Subjects
GENETIC resources utilization, PLANT germplasm, BIODIVERSITY, DNA, GERMPLASM conservation, NATURAL resources
Abstract

Societal Impact Statement: Digitized molecular data are vital to numerous aspects of scientific research and genetic resource use. The Convention on Biological Diversity currently refers to this as "Digital Sequence Information" (DSI), a term not widely adopted by science and lacking a clear definition. There are concerns over the access to genetic resources and absence of benefit sharing by provider countries. Open access to DSI might exacerbate this, which is leading to increasing policy interventions and restricted access to genetic resources and DSI. We analyze current international debate and proposed solutions and provide case studies of DSI use producing tangible benefits for the provider countries and scientific research, demonstrating the importance of open access DSI to achieving conservation goals. Summary: Substantial advances in DNA sequencing over the last decades hold great potential to enhance food security and sustainable use of global biodiversity, benefiting the world's poorest people. Digital Sequence Information (DSI) plays a crucial role in catalyzing research applications that can contribute to international societal and biodiversity conservation targets. However, benefit sharing relating to DSI is difficult to identify and hindered by the lack of clear international governance and legislation, which in turn has led to a reluctance to make DSI publicly and freely available. Critically, no precise definition exists under the Convention on Biological Diversity (CBD), the Nagoya Protocol (NP), or the International Treaty for Plant Genetic Resources for Food and Agriculture (ITPGRFA). The key difference between DSI and biological resources, for which access and use are highly regulated under those frameworks, is that information is nonphysical. Information can be replicated and used without movement of, or access to, physical specimens. Thus, regulating the use of DSI is extremely challenging and remains controversial. Here, we review the regulation of DSI and the possible future steps by the international community, in the context of the benefit‐sharing obligations of the CBD, NP, and ITPGRFA. We highlight how multilateral agreements work in practice and are a solution to this impasse. We provide case studies demonstrating how the Royal Botanic Gardens, Kew, and its collaborators address the uncertainty surrounding the use of DSI, illustrating tangible and equitable benefits that have arisen from such use. We conclude that open access to DSI is needed for scientific research and international policy. [ABSTRACT FROM AUTHOR]

Published
2022
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28. Madagascar’s extraordinary biodiversity: Threats and opportunities

Author

Gardiner, Lauren, Ralimanana, Hélène [0000-0002-7963-5644], Perrigo, Allison L [0000-0002-6565-6305], Smith, Rhian J [0000-0003-2836-0246], Borrell, James S [0000-0001-9902-7681], Faurby, Søren [0000-0002-2974-2628], Rajaonah, Mamy Tiana [0000-0002-3117-4180], Randriamboavonjy, Tianjanahary [0000-0001-5767-3992], Vorontsova, Maria S [0000-0003-0899-1120], Cooke, Robert SC [0000-0003-0601-8888], Phelps, Leanne N [0000-0002-7385-3907], Sayol, Ferran [0000-0003-3540-7487], Andermann, Tobias [0000-0002-0932-1623], Andriamanohera, Andotiana M [0000-0001-9853-0613], Bachman, Steven P [0000-0003-1085-6075], Bacon, Christine D [0000-0003-2341-2705], Baker, William J [0000-0001-6727-1831], Belluardo, Francesco [0000-0002-3967-2686], Cable, Stuart [0000-0001-7119-9844], Canales, Nataly A [0000-0003-3241-8607], Carrillo, Juan D [0000-0003-2475-3341], Clegg, Rosie [0000-0002-7073-2093], Clubbe, Colin [0000-0002-0532-1722], Crottini, Angelica [0000-0002-8505-3050], Dhanda, Sonia [0000-0002-5440-9229], Edler, Daniel [0000-0001-5420-0591], Farooq, Harith [0000-0001-9031-2785], de Lima Ferreira, Paola [0000-0002-6957-4243], Fisher, Brian L [0000-0002-4653-3270], Forest, Félix [0000-0002-2004-433X], Gardiner, Lauren M [0000-0002-8843-0317], Goodman, Steven M [0000-0001-9318-0570], Grace, Olwen M [0000-0003-1431-2761], Guedes, Thaís B [0000-0003-3318-7193], Hackel, Jan [0000-0002-9657-5372], Hill, Rowena [0000-0002-1046-5528], Lehmann, Caroline ER [0000-0002-6825-124X], Lowry, Porter P [0000-0002-8047-5019], Marline, Lovanomenjanahary [0000-0002-6181-0440], Matos-Maraví, Pável [0000-0002-2885-4919], Moat, Justin [0000-0002-5513-3615], Neves, Beatriz [0000-0002-6469-7930], Nogueira, Matheus GC [0000-0001-7256-2166], Onstein, Renske E [0000-0002-2295-3510], Perez-Escobar, Oscar A [0000-0001-9166-2410], Phillipson, Peter B [0000-0001-8390-0079], Pironon, Samuel [0000-0002-8937-7626], Przelomska, Natalia AS [0000-0001-9207-4565], Rabarimanarivo, Marina [0000-0001-5049-9151], Rabehevitra, David [0000-0003-2763-5754], Rakotoarinivo, Mijoro [0000-0001-6644-5107], Ralaiveloarisoa, Berthe A [0000-0002-4046-9028], Ramirez-Herranz, Myriam [0000-0002-4715-9372], Rasolohery, Andriambolantsoa [0000-0002-9686-262X], Razanajatovo, Henintsoa [0000-0001-8084-6791], Razanatsoa, Estelle [0000-0002-7219-1411], Rivers, Malin [0000-0001-9690-1353], Silvestro, Daniele [0000-0003-0100-0961], Testo, Weston [0000-0003-3194-5763], Torres Jiménez, Maria F [0000-0002-7177-4164], Walker, Kim [0000-0002-2617-4768], Walker, Barnaby E [0000-0002-3884-671X], Wilkin, Paul [0000-0003-4982-7175], Williams, Jenny [0000-0003-3392-0738], Ziegler, Thomas [0000-0002-4797-609X], Zizka, Alexander [0000-0002-1680-9192], Antonelli, Alexandre [0000-0003-1842-9297], and Apollo - University of Cambridge Repository

Subjects
Mammals, Endangered Species, Madagascar, Animals, Humans, Bayes Theorem, Biodiversity, Plants, Biota
Abstract

Madagascar’s unique biota is heavily impacted by human activity and under intense threat. Here, we review the current state of knowledge on the conservation status of Madagascar’s terrestrial and freshwater biodiversity by presenting data and analyses on documented and predicted species-level conservation status, the most prevalent and relevant threats, ex situ collections and programs, and the coverage and comprehensiveness of protected areas. The existing terrestrial protected area network in Madagascar covers 10.4% of its land area and includes at least part of the range of thmajority of described native species of vertebrates with known distributions (97.1% of freshwater fishes, amphibians, reptiles, birds and mammals combined) and plants (67.7%). The overall figures are higher for threatened species (97.7% of threatened vertebrates and 79.6% of threatened plants occurring within at least one protected area). IUCN Red List assessments and Bayesian neural network analyses for plants identify overexploitation of biological resources and unsustainable agriculture as the most prominent threats to biodiversity. We highlight five opportunities for action at multiple levels to ensure that conservation and ecological restoration objectives, programs and activities take account of complex underlying and interacting factors and produce tangible benefits for the biodiversity and people of Madagascar.

Published
2022

29. A Bioinformatic Pipeline to Estimate Ploidy Level from Target Capture Sequence Data Obtained from Herbarium Specimens.

Author

Viruel J, Hidalgo O, Pokorny L, Forest F, Gravendeel B, Wilkin P, and Leitch IJ

Subjects
Genome, Plant, DNA, Plant, Polymorphism, Single Nucleotide, Chromosomes, Plant, Flow Cytometry, Plants classification, Plants genetics, Ploidies, Software
Abstract

Whole genome duplications (WGD) are frequent in many plant lineages; however, ploidy level variation is unknown in most species. The most widely used methods to estimate ploidy levels in plants are chromosome counts, which require living specimens, and flow cytometry estimates, which necessitate living or relatively recently collected samples. Newly described bioinformatic methods have been developed to estimate ploidy levels using high-throughput sequencing data, and these have been optimized in plants by calculating allelic ratio values from target capture data. This method relies on the maintenance of allelic ratios from the genome to the sequence data. For example, diploid organisms will generate allelic data in a 1:1 proportion, with an increasing number of possible allelic ratio combinations occurring in individuals with higher ploidy levels. In this chapter, we explain step-by-step this bioinformatic approach for the estimation of ploidy level., (© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Published
2023
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