Browsing by Author "Salmona, Jordi"
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- Conservation Status and Abundance of the Crowned Sifaka (Propithecus coronatus)Publication . Salmona, Jordi; Rasolondraibe, Emmanuel; Jan, Fabien; Besolo, Aubin; Rakotoarisoa, Heriniaina; Meyler, Sam Viana; Wohlhauser, Sébastien; Rabarivola, Clément; Chikhi, LounèsThe crowned sifaka (Propithecus coronatus) is Endangered. It has a large but highly fragmented distribution; its known range extends from the Betsiboka River in the north of Madagascar, to the Mahavavy River in the north-west, and down to the Tsiribihina River in the south-west. The species lives in forest habitats that are highly and increasingly fragmented and are continuously suffering perturbations and destruction. In order to carry out effective conservation measures targeting P. coronatus, its conservation status needs to be updated so that measures can be taken before anthropogenic or natural environmental changes lead to the extirpation of the species in most of its forests. We (i) identified forest fragments where the species is still present and (ii) using the line-transect “Distance” sampling method, estimated the population size and density in the principal remaining forest fragments in the northern part of its range, including both protected and unprotected areas. We visited most of the forests in the northern part of its range in order to update the current area of occupancy, and to rate the state of its forests using a qualitative “forest quality index.” Our survey results have shown that (i) a large number of forests have disappeared or decreased in size in the last 10 years, and (ii) population densities vary considerably among forest fragments (ranging from 49 to 309 individuals per km²), with some very high densities in forests located along the Mahavavy River and in the Antrema area. Their abundance in the area surveyed is likely to be between 4,226 and 36,672 individuals, and most probably above 10,000. It is difficult to extrapolate from these estimates to the total abundance across the species’ entire range, but we estimate that it is likely to be large, probably between 130,000 and 220,000 individuals. Unfortunately, many field observations suggest that its populations continue to decline at a high rate due to habitat loss and hunting, and we argue for the re-evaluation of the conservation status from Endangered A2cd to Endangered A4acd, and the need to survey the rest of the range of P.coronatus.
- Effective Population Size Dynamics and the Demographic Collapse of Bornean Orang-UtansPublication . Sharma, Reeta; Arora, Natasha; Goossens, Benoit; Nater, Alexander; Morf, Nadja; Salmona, Jordi; Bruford, Michael W.; Van Schaik, Carel P.; Krützen, Michael; Chikhi, LounèsBornean orang-utans experienced a major demographic decline and local extirpations during the Pleistocene and Holocene due to climate change, the arrival of modern humans, of farmers and recent commercially-driven habitat loss and fragmentation. The recent loss of habitat and its dramatic fragmentation has affected the patterns of genetic variability and differentiation among the remaining populations and increased the extinction risk of the most isolated ones. However, the contribution of recent demographic events to such genetic patterns is still not fully clear. Indeed, it can be difficult to separate the effects of recent anthropogenic fragmentation from the genetic signature of prehistoric demographic events. Here, we investigated the genetic structure and population size dynamics of orang-utans from different sites. Altogether 126 individuals were analyzed and a full-likelihood Bayesian approach was applied. All sites exhibited clear signals of population decline. Population structure is known to generate spurious bottleneck signals and we found that it does indeed contribute to the signals observed. However, population structure alone does not easily explain the observed patterns. The dating of the population decline varied across sites but was always within the 200-2000 years period. This suggests that in some sites at least, orang-utan populations were affected by demographic events that started before the recent anthropogenic effects that occurred in Borneo. These results do not mean that the recent forest exploitation did not leave its genetic mark on orang-utans but suggests that the genetic pool of orang-utans is also impacted by more ancient events. While we cannot identify the main cause for this decline, our results suggests that the decline may be related to the arrival of the first farmers or climatic events, and that more theoretical work is needed to understand how multiple demographic events impact the genome of species and how we can assess their relative contributions.
- Genomics and the challenging translation into conservation practicePublication . Shafer, Aaron B.A.; Wolf, Jochen B.W.; Alves, Paulo C.; Bergström, Linnea; Bruford, Michael W.; Brännström, Ioana; Colling, Guy; Dalén, Love; De Meester, Luc; Ekblom, Robert; Fawcett, Katie D.; Fior, Simone; Hajibabaei, Mehrdad; Hill, Jason A.; Hoezel, A. Rus; Höglund, Jacob; Jensen, Evelyn L.; Krause, Johannes; Kristensen, Torsten N.; Krützen, Michael; McKay, John K.; Norman, Anita J.; Ogden, Rob; Österling, E. Martin; Ouborg, N. Joop; Piccolo, John; Popović, Danijela; Primmer, Craig R.; Reed, Floyd A.; Roumet, Marie; Salmona, Jordi; Schenekar, Tamara; Schwartz, Michael K.; Segelbacher, Gernot; Senn, Helen; Thaulow, Jens; Valtonen, Mia; Veale, Andrew; Vergeer, Philippine; Vijay, Nagarjun; Vilà, Carles; Weissensteiner, Matthias; Wennerström, Lovisa; Wheat, Christopher W.; Zieliński, PiotrThe global loss of biodiversity continues at an alarming rate. Genomic approaches have been suggested as a promising tool for conservation practice as scaling up to genome-wide data can improve traditional conservation genetic inferences and provide qualitatively novel insights. However, the generation of genomic data and subsequent analyses and interpretations remain challenging and largely confined to academic research in ecology and evolution. This generates a gap between basic research and applicable solutions for conservation managers faced with multifaceted problems. Before the real-world conservation potential of genomic research can be realized, we suggest that current infrastructures need to be modified, methods must mature, analytical pipelines need to be developed, and successful case studies must be disseminated to practitioners.
- New density estimates of a threatened sifaka species (Propithecus coquereli) in Ankarafantsika National ParkPublication . Kun-Rodrigues, Célia; Salmona, Jordi; Besolo, Aubin; Rasolondraibe, Emmanuel; Rabarivola, Clément; Marques, Tiago A.; Chikhi, LounèsPropithecus coquereli is one of the last sifaka species for which no reliable and extensive density estimates are yet available. Despite its endangered conservation status [IUCN, 2012] and recognition as a flagship species of the northwestern dry forests of Madagascar, its population in its last main refugium, the Ankarafantsika National Park (ANP), is still poorly known. Using line transect distance sampling surveys we estimated population density and abundance in the ANP. Furthermore, we investigated the effects of road, forest edge, river proximity and group size on sighting frequencies, and density estimates. We provide here the first population density estimates throughout the ANP. We found that density varied greatly among surveyed sites (from 5 to ∼100 ind/km2) which could result from significant (negative) effects of road, and forest edge, and/or a (positive) effect of river proximity. Our results also suggest that the population size may be ∼47,000 individuals in the ANP, hinting that the population likely underwent a strong decline in some parts of the Park in recent decades, possibly caused by habitat loss from fires and charcoal production and by poaching. We suggest community-based conservation actions for the largest remaining population of Coquerel's sifaka which will (i) maintain forest connectivity; (ii) implement alternatives to deforestation through charcoal production, logging, and grass fires; (iii) reduce poaching; and (iv) enable long-term monitoring of the population in collaboration with local authorities and researchers.
- Noninvasive molecular sexing: An evaluation and validation of the SRY- and amelogenin-based method in three new lemur speciesPublication . Vanpé, Cécile; Salmona, Jordi; Pais, Isa; Kun-Rodrigues, Célia; Pichon, Claire; Meyler, Samuel Viana; Rabarivola, Clément; Lewis, Rebecca J.; Ibouroi, Mohamed Thani; Chikhi, LounèsMany lemur species are arboreal, elusive, and/or nocturnal and are consequently difficult to approach, observe and catch. In addition, most of them are endangered. For these reasons, non-invasive sampling is especially useful in primates including lemurs. A key issue in conservation and ecological studies is to identify the sex of the sampled individuals to investigate sex-biased dispersal, parentage, social organization and population sex ratio. Several molecular tests of sex are available in apes and monkeys, but only a handful of them work in the lemuriform clade. Among these tests, the coamplification of the SRY gene with the amelogenin X gene using strepsirhine-specific X primers seems particularly promising, but the reliability and validity of this sexing test have not been properly assessed yet. In this study, we (i) show that this molecular sexing test works on three additional lemur species (Microcebus tavaratra, Propithecus coronatus and P. verreauxi) from two previously untested genera and one previously untested family, suggesting that these markers are likely to be universal among lemurs and other strepsirrhines; (ii) provide the first evidence that this PCR-based sexing test works on degraded DNA obtained from noninvasive samples; (iii) validate the approach using a large number of known-sex individuals and a multiple-tubes approach, and show that mismatches between the field sex and the final molecular consensus sex occur in less than 10% of all the samples and that most of these mismatches were likely linked to incorrect sex determinations in the field rather than genotyping errors.
- Signature of a Pre-Human Population Decline in the Critically Endangered Reunion Island Endemic Forest Bird Coracina newtoniPublication . Salmona, Jordi; Salamolard, Marc; Fouillot, Damien; Ghestemme, Thomas; Larose, Jerry; Centon, Jean-François; Sousa, Vitor; Dawson, Deborah A.; Thebaud, Christophe; Chikhi, LounèsThe exceptional biodiversity of Reunion Island is threatened by anthropogenic landscape changes that took place during the 350 years of human colonization. During this period the human population size increased dramatically from 250 to 800,000. The arrival of humans together with the development of agriculture, invasive species such as rats and cats, and deforestation has lead to the extinction of more than half of the original vertebrate species of the island. For the remaining species, significant work is being carried out to identify threats and conservation status, but little genetic work has been carried on some of the most endangered species. In the last decade theoretical studies have shown the ability of neutral genetic markers to infer the demographic history of endangered species and identify and date past population size changes (expansions or bottlenecks). In this study we provide the first genetic data on the critically endangered species the Reunion cuckoo-shrike Coracina newtoni. The Reunion cuckoo-shrike is a rare endemic forest bird surviving in a restricted 12-km(2) area of forested uplands and mountains. The total known population consists of less than one hundred individuals out of which 45 were genotyped using seventeen polymorphic microsatellite loci. We found a limited level of genetic variability and weak population structure, probably due to the limited geographic distribution. Using Bayesian methods, we identified a strong decline in population size during the Holocene, most likely caused by an ancient climatic or volcanic event around 5000 years ago. This result was surprising as it appeared in apparent contradiction with the accepted theory of recent population collapse due to deforestation and predator introduction. These results suggest that new methods allowing for more complex demographic models are necessary to reconstruct the demographic history of populations.