Toward a Noninvasive Inuit Polar Bear Survey: Genetic Data from Polar Bear Hair Snags

in Wildlife Society Bulletin (in press)

Combined Mitochondrial and Nuclear Markers Revealed a Deep Vicariant History for Leopoldamys neilli, a Cave-Dwelling Rodent of Thailand

in PLoS ONE (2012), 7(10), 47670

Background: Historical biogeography and evolutionary processes of cave taxa have been widely studied in temperate regions. However, Southeast Asian cave ecosystems remain largely unexplored despite their ... [more ▼]

Background: Historical biogeography and evolutionary processes of cave taxa have been widely studied in temperate regions. However, Southeast Asian cave ecosystems remain largely unexplored despite their high scientific interest. Here we studied the phylogeography of Leopoldamys neilli, a cave-dwelling murine rodent living in limestone karsts of Thailand, and compared the molecular signature of mitochondrial and nuclear markers. Methodology/Principal Findings: We used a large sampling (n = 225) from 28 localities in Thailand and a combination of mitochondrial and nuclear markers with various evolutionary rates (two intronic regions and 12 microsatellites). The evolutionary history of L. neilli and the relative role of vicariance and dispersal were investigated using ancestral range reconstruction analysis and Approximate Bayesian computation (ABC). Both mitochondrial and nuclear markers support a large-scale population structure of four main groups (west, centre, north and northeast) and a strong finer structure within each of these groups. A deep genealogical divergence among geographically close lineages is observed and denotes a high population fragmentation. Our findings suggest that the current phylogeographic pattern of this species results from the fragmentation of a widespread ancestral population and that vicariance has played a significant role in the evolutionary history of L. neilli. These deep vicariant events that occurred during Plio-Pleistocene are related to the formation of the Central Plain of Thailand. Consequently, the western, central, northern and northeastern groups of populations were historically isolated and should be considered as four distinct Evolutionarily Significant Units (ESUs). Conclusions/Significance: Our study confirms the benefit of using several independent genetic markers to obtain a comprehensive and reliable picture of L. neilli evolutionary history at different levels of resolution. The complex genetic structure of Leopoldamys neilli is supported by congruent mitochondrial and nuclear markers and has been influenced by the geological history of Thailand during Plio-Pleistocene. [less ▲]

The optimization of microsatellite genotyping and genetic sexing of non-invasively collected polar bear tissue: Implications for monitoring and census.

Conference (2012, April)

The monitoring of Polar Bears in Canada has been completed largely through management unit (MU) wide capture-mark-recapture (CMR) surveys. While this data is very useful at the time of collection, these ... [more ▼]

The monitoring of Polar Bears in Canada has been completed largely through management unit (MU) wide capture-mark-recapture (CMR) surveys. While this data is very useful at the time of collection, these surveys are expensive and take time to plan and execute; cannot be feasibly executed across the polar bear range at intervals that reflect the expected rapid environmental changes in the Arctic; and are disdained by the Inuit as being invasive. As part of recent efforts to explore less expensive and non-invasive methods to monitor polar bears (see Wong et al & Van Coevderden de Groot et al this conference) we are evaluating genetic information obtained from non-invasively collected polar bear tissue. In this work we report on the genetic data obtained from non-invasively collected harisnags recovered from sampling stations erected between May-June 2006-2009 in M’Clintock Channel, Nunavut. Across the 4 years 344 hair snags were collected; following Paetkau (2004) we optimized 6 microsatellite loci to reliably amplify polar bear DNA from this tissue and we modified the procedure of Pages et al (2009) to reliably genetically sex these tissues. Our estimates for two common errors with this type of tissue across all loci – allelic dropout (0.026) and false allele (0.03) - were both less than p =.05. This suggests these errors are not going to significantly affect the accuracy of the consensus genotypes collected from these data. Using consensus genotypes from relevant hairsnags, we posit a minimum of 59 (max 82) unique bears entered our sampling stations. Of these, 24% were female, 64% were male, and 12% could not be sexed. We resampled 2 bears in 2006, 1 in 2007, 0 bears in 2008 and 14 bears in 2009 – the 2009 value reflects significantly increased sampling effort in 2009. Five bears were re-sampled between the non-invasive surveys in 2006-2009. When comparing our data to a subset of cubs and subadults captured during the Taylor et al. (2006) CMR survey of M’Clintock Channel (MU), we found 6 genotype matches. Our sampling stations may have a male bias as the sex ratio from the 1998-2000 CMR study was 42.1% ♂ (Taylor et al 2006) vs. 64% ♂ (this study). We cannot accurately determine the age bias (but see Wong et al this conference). Genetic data from Polar bear faecal samples may provide an unbiased sex and age sample of polar bears in any MU. Any data from these samples will help refine hairsnag derived MKNA estimate of polar bears from any MU. Here we report on our efforts to genotype and genetically sex 95 faecals we have collected from M’Clintock Channel from 2006-2009. Finally, we discuss the implications of these findings, results from other noninvasive work (Wong et al & Van Coevderden de Groot et al this conference) and ongoing/proposed work in the context of i) a non-invasive Inuit-based polar bear activity and health survey, and ii) a more rigorous census method which may allow more precise adjustments of harvest levels than currently possible using infrequently collected CMR data only. [less ▲]

Molecular phylogeny and systematics of Dipodoidea: a test of morphology-based hypotheses

in Zoologica Scripta (2012)

The superfamily Dipodoidea (Rodentia, Myomorpha) in its current interpretation contains a single family subdivided into six subfamilies. Four of them include morphologically specialized bipedal arid ... [more ▼]

The superfamily Dipodoidea (Rodentia, Myomorpha) in its current interpretation contains a single family subdivided into six subfamilies. Four of them include morphologically specialized bipedal arid-dwelling jerboas (Dipodinae – three-toed jerboas, Allactaginae – fivetoed jerboas, Cardiocraniinae – pygmy jerboas and Euchoreutinae – long-eared jerboas), the other two are represented by more generalized quadrupedal taxa (Zapodinae – jumping mice and Sminthinae – birch mice). Despite considerable effort from morphologists, the taxonomy as well as the phylogeny of the Dipodoidea remains controversial. Strikingly, molecular approach has never been envisaged to investigate these questions. In this study, the phylogenetic relationships among the main dipodoid lineages were reconstructed for the first time using DNA sequence data from four nuclear genes (IRBP, GHR, BRCA1, RAG1). No evidence of conflict among genes was revealed. The same robustly supported tree topology was inferred from the concatenated alignment whatever the phylogenetic methods used (maximum parsimony, maximum-likelihood and Bayesian phylogenetic methods). Sminthinae branches basally within the dipodoids followed by Zapodinae. Monophyletic Cardiocraniinae is sister to all other jerboas. Within the latter, the monophyly of both Dipodinae and Allactaginae is highly supported. The relationships between Dipodinae, Allactaginae and Euchoreutinae should be regarded as unresolved trichotomy. Morphological hypotheses were confronted to findings based on the presented molecular data. As a result, previously proposed sister group relationships between Euchoreutes and Sicista, Paradipus and Cardiocraniinae as well as the monophyly of Cardiocaniinae + Dipodinae were rejected. However, the latter association is consistently supported by most morphological analyses. The basis of the obvious conflict between genes and morphology remains unclear. Suggested modifications to the taxonomy of Dipodoidea imply recognition of three families: Sminthidae, Zapodidae and Dipodidae, the latter including Cardiocraniinae, Euchoreutinae, Allactaginae and Dipodinae as subfamilies. [less ▲]

Evidence of complex phylogeographic structure for the threatened rodent Leopoldamys neilli endemic to limestone karsts of Thailand

Conference (2011, July 21)

Limestone karsts are highly threatened biodiversity hotspots supporting huge levels of endemic species. Karsts are patchy distributed within Southeast Asia and their isolation from one another give them ... [more ▼]

Limestone karsts are highly threatened biodiversity hotspots supporting huge levels of endemic species. Karsts are patchy distributed within Southeast Asia and their isolation from one another give them the features of “islands on the continent”. We have studied the phylogeography of Neill’s Rat Leopoldamys neilli, a threatened murine rodent species endemic to limestone karsts of Thailand, in order to assess the influence of its endemicity to karst habitat on its phylogeographic pattern. Two hundred twenty-two individuals of L. neilli were collected in 26 limestone karsts throughout the geographical range of this species and were used in this study. Phylogeographic structure and population genetics of L. neilli were investigated on the basis of two mitochondrial markers, the cytochrome b gene and the cytochrome c oxydase subunit I gene, two nuclear fragments, the β-fibrinogen intron 7 and the intron 1 of the X-linked gene G6pd, and 12 microsatellite loci. Our study gave evidence of a complex and strong geographic structure of the genetic diversity for L. neilli. Several highly differentiated genetic lineages were observed throughout Thailand. These results suggest a severe fragmentation of L. neilli’s populations, correlated to the fragmented distribution of its habitat and highlight its high endemicity to limestone karsts. In conclusion, this study revealed an unexpected high level of intraspecific diversity within L. neilli. These results consolidate the importance to strengthen the protection of limestone habitats and to preserve not only their huge interspecific but also intraspecific diversity. [less ▲]

When morphometrics meet genetics: the case of the common dormouse, Muscardinus avellanarius

Poster (2011, July)

The aim of the study is to apply geometric morphometrics to the study of evolutionary processes that might have driven intra-specific differentiation of the common dormouse Muscardinus avellanarius in ... [more ▼]

The aim of the study is to apply geometric morphometrics to the study of evolutionary processes that might have driven intra-specific differentiation of the common dormouse Muscardinus avellanarius in Europe. The analysis of phenotypic features appears as a valuable complement to genetic analyses, providing a insight into evolutionary processes such as differentiation by vicariance or adaptation to different environments. Previous genetic studies based on mtDNA genes revealed a complex phylogeographic pattern for the common dormouse with the presence of two highly divergent lineages subdivided into geographic sublineages. We thus investigated whether this genetic differentiation leads to morphometric differences. We examined 150 museum specimens of dormouse from 34 localities in 12 countries. For each specimen, the size and shape of the first upper molar was quantified using an outline analysis based on Fourier methods. A geographic structure emerges from the morphometric pattern of differentiation, partially corresponding to the expectations based on the genetic results. The main differentiation, however, was unexpected and revealed a divergent Austrian cluster. This region was not documented so far for genetic analyses and morphometric data therefore challenge a more extensive sampling of this species that might reveal the existence of a further lineage. [less ▲]

Phylogenetic position of the Ohiya rat (Srilankamys ohiensis) based on mitochondrial and nuclear gene sequence analysis

in Zoologica Scripta (2011), 40(6), 545-553

We investigated the phylogenetic position the Ohiya rat, endemic to Sri Lanka, Srilankamys (Rodentia, Murinae), within the tribe Rattini based on the combined analysis of three independent genes (a ... [more ▼]

We investigated the phylogenetic position the Ohiya rat, endemic to Sri Lanka, Srilankamys (Rodentia, Murinae), within the tribe Rattini based on the combined analysis of three independent genes (a mitochondrial one and two nuclear exons). Three major lineages (the Maxomys, the Dacnomys and the Rattus divisions) were retrieved as monophyletic groups within the tribe Rattini. Srilankamys was not affiliated to any of the representatives of the Dacnomys division as it was supposed based on morphological characters, but clearly appeared as the first genus to diverge among the Rattus division. The Mindanao Shrew Mouse, Crunomys melanius, emerged as a part of the Maxomys division raising questions about the validity of the Crunomys and the Maxomys divisions as currently defined. Molecular date of divergence between Srilankamys and the other representatives of the Rattus division falls within the interval 6.7 ± 0.74 Mya, coinciding with the time of the isolation of Sri Lanka from the Deccan peninsula and the aridification period owing to the climate change at the end of the Miocene epoch. We suggest that the isolation of Sri Lanka from the continent, reinforced by the action of a seasonal monsoon-dominated climate, would have led to the isolation of some ancestral rodents of the Rattus division, which would have differentiated later into the Ohiya rat by a vicariant process. In a more general point of view, our study supports the previous results obtained on other organisms and evidence that Sri Lanka appears to be characterized by a particular fauna as compared to the Indian mainland. This island would therefore be considered as a specific distinct hotspot of biodiversity. [less ▲]

Inter- and Intraspecific Genetic Biodiversity in South East Asian Rodents: New Insights for Their Conservation

in Zachos, F. E.; Habel, J. C. (Eds.) Biodiversity Hotspots (2011)

South East Asia displays a high level of mammal endemism and the highest number of threatened and data deficient mammal species. However, the South East Asian biodiversity is still highly unexplored ... [more ▼]

South East Asia displays a high level of mammal endemism and the highest number of threatened and data deficient mammal species. However, the South East Asian biodiversity is still highly unexplored. Because of the runaway global changes, a better biological knowledge of this region is urgently required to improve the conservation and the management of its biodiversity. The first aim of this chapter is to present recent published data on a biodiversity inventory of the Rattini murine rodents from this region based on molecular markers (Page`s et al., 2009). In this first study, we applied the method proposed by Pons et al. (2006) that determines with no a priori the locations of ancestral nodes that define putative species in order to investigate the current taxonomy of the Rattini tribe. Our second aim concerns the intraspecific genetic structure of a rare and threatened South East Asian mammal species: the murine rodent Leopoldamys neilli, endemic to karst habitats . In this latter study, our results evidenced a high geographic structure of the genetic diversity of this species. The observed highly divergent genetic lineages would have to be considered as distinct evolutionary units or at least as Management units. These results are essential for the best conservation issues of species endemic to karsts and to South East Asia, in general. In this chapter, we therefore highlight that South East Asia would not be only a hotspot of interspecific but also of intraspecific biodiversity. [less ▲]

Thai limestone karsts: an impending biodiversity crisis

in The 1st EnvironmentAsia International Conference (2011)

Due to the high level of endemic species that they support and the high threats they are facing, such as unsustainable limestone quarrying, hunting and urbanization, limestone karsts are recognized as ... [more ▼]

Due to the high level of endemic species that they support and the high threats they are facing, such as unsustainable limestone quarrying, hunting and urbanization, limestone karsts are recognized as biodiversity hotspots needing urgent protection. The first aim of our study was to investigate the mammal rodent diversity of Thai limestone karsts. Our second aim was to examine the diversity at a finer scale than the species level (intraspecific biodiversity) using phylogeographic approaches. Therefore, we studied the phylogeographic structure of a threatened rodent, endemic to limestone karsts of Thailand, the Murinae Leopoldamys neilli. We sampled 76 limestone karsts in whole Thailand and live-trapped 444 rodents including 115 Leopoldamys neilli. Our study revealed an important rodent diversity in Thai limestone karsts. Besides endemic rodent species, karsts also host typical forest species to which they provide forest refugia in deforested regions. At the intraspecific level, our study revealed an unexpected high level of genetic differentiation within the rodent species L. neilli. As each limestone area of Thailand is characterized by a particular genetic lineage of L. neilli, the destruction of these karsts would lead to the disappearance of unique intraspecific strains not found elsewhere. Our results highlight the importance of protecting limestone habitats to preserve not only their interspecific but also intraspecific rodent diversity that is highly threatened as more than 20% of limestone karsts in Thailand have already been quarried. Management plans of limestone, a non-renewable resource, should urgently take into account this high biological importance of karsts. [less ▲]

Revisiting the taxonomy of the Rattini tribe: a phylogeny-based delimitation of species boundaries

Conference (2010, April)

Rodents are recognized as hosts for at least 60 zoonotic diseases and may represent a serious threat for human health. In the context of global environmental changes and increasing mobility of humans and ... [more ▼]

Rodents are recognized as hosts for at least 60 zoonotic diseases and may represent a serious threat for human health. In the context of global environmental changes and increasing mobility of humans and animals, contacts between pathogens and potential animal hosts and vectors are modified, amplifying the risk of disease emergence. An accurate identification of each rodent at a specific level is needed in order to understand their implications in the transmission of diseases. Among the Muridae, the Rattini tribe encompasses 167 species inhabiting South East Asia, a hotspot of both biodiversity and emerging and re-emerging diseases. The region faces growing economical development that affects habitats, biodiversity and health. Rat species have been demonstrated as significant hosts of pathogens but are still difficult to recognize at a specific level using morphological criteria. DNA-barcoding methods appear as accurate tools for rat species identification but their use is hampered by the need of reliable identification of reference specimens. In this study, we explore and highlight the limits of the current taxonomy of the Rattini tribe. We used the DNA sequence information itself as the primary information source to establish group membership and estimate putative species boundaries. We sequenced two mitochondrial and one nuclear genes from 122 rat samples to perform phylogenetic reconstructions. The method of Pons and colleagues (2006) that determines, with no prior expectations, the locations of ancestral nodes defining putative species was then applied to our dataset. To give an appropriate name to each cluster recognized as a putative species, we reviewed information from the literature and obtained sequences from a museum holotype specimen following the ancient DNA criteria. [less ▲]