Empirical Assessment of Non-Invasive Population Genetics in Bats: Comparison of DNA Quality from Faecal and Tissue Samples

Boston, Emma S. M.; Puechmaille, Sébastien J.; Scott, David D.; Buckley, Daniel J.; Lundy, Mathieu G.; Montgomery, Ian; Prodöhl, Paulo A.; Teeling, Emma C.

doi:10.3161/150811012x654259

Cited by 31 publications

(36 citation statements)

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“…) that have been shown to provide results similar to tissue samples (Boston et al . ). Whole genomic DNA was extracted using either a modified salt–chloroform extraction as described in Puechmaille et al .…”

Section: Methodsmentioning

confidence: 97%

Phylogeography and postglacial recolonization of Europe by Rhinolophus hipposideros: evidence from multiple genetic markers

et al. 2013

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The demographic history of Rhinolophus hipposideros (lesser horseshoe bat) was reconstructed across its European, North African and Middle-Eastern distribution prior to, during and following the most recent glaciations by generating and analysing a multimarker data set. This data set consisted of an X-linked nuclear intron (Bgn; 543 bp), mitochondrial DNA (cytb-tRNA-control region; 1630 bp) and eight variable microsatellite loci for up to 373 individuals from 86 localities. Using this data set of diverse markers, it was possible to determine the species' demography at three temporal stages. Nuclear intron data revealed early colonization into Europe from the east, which pre-dates the Quaternary glaciations. The mtDNA data supported multiple glacial refugia across the Mediterranean, the largest of which were found in the Ibero-Maghreb region and an eastern location (Anatolia/Middle East)-that were used by R. hipposideros during the most recent glacial cycles. Finally, microsatellites provided the most recent information on these species' movements since the Last Glacial Maximum and suggested that lineages that had diverged into glacial refugia, such as in the Ibero-Maghreb region, have remained isolated. These findings should be used to inform future conservation management strategies for R. hipposideros and show the power of using a multimarker data set for phylogeographic studies.

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Section: Methodsmentioning

confidence: 97%

Phylogeography and postglacial recolonization of Europe by Rhinolophus hipposideros: evidence from multiple genetic markers

et al. 2013

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“…Individuals were genotyped using 19 nuclear microsatellite markers and one mitochondrial microsatellite marker. The following nuclear markers were used: EF15 [32]; b22 [33]; A2-Mluc, A13-Mluc, E5-Mluc, G6-Mluc, G30-Mluc, G31-Mluc [34], D15, H19, H23, H29 [35]; Mnatt-1, Mnatt-2 [36]; Mschreib3 [37]; Mnatt-8, Mnatt-11 [38]; FV5AP [39] and GZBYR (5′-TCCTTGTCACTATAAGCTCAGTGG-3′ (forward); 5′-CCAGGCAATAGTCTCCTAGCAC-3′ (reverse)). The 5′ end of the reverse primers FV5AP and G30-Mluc were PIG-tailed [40] with the sequence GTTT and the 5′ end of the reverse primer G31-Mluc with the sequence GTTTT to facilitate adenylation.…”

Section: Methodsmentioning

confidence: 99%

Evidence for genetic variation in Natterer’s bats (Myotis nattereri) across three regions in Germany but no evidence for co-variation with their associated astroviruses

et al. 2017

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BackgroundAs bats have recently been described to harbor many different viruses, several studies have investigated the genetic co-variation between viruses and different bat species. However, little is known about the genetic co-variation of viruses and different populations of the same bat species, although such information is needed for an understanding of virus transmission dynamics within a given host species. We hypothesized that if virus transmission between host populations depends on events linked to gene flow in the bats, genetic co-variation should exist between host populations and astroviruses.ResultsWe used 19 nuclear and one mitochondrial microsatellite loci to analyze the genetic population structure of the Natterer’s bat (Myotis nattereri) within and among populations at different geographical scales in Germany. Further, we correlated the observed bat population structure to that of partial astrovirus sequences (323–394 nt fragments of the RNA-dependent RNA polymerase gene) obtained from the same bat populations. Our analyses revealed that the studied bat colonies can be grouped into three distinct genetic clusters, corresponding to the three geographic regions sampled. Furthermore, we observed an overall isolation-by-distance pattern, while no significant pattern was observed within a geographic region. Moreover, we found no correlation between the genetic distances among the bat populations and the astrovirus sequences they harbored. Even though high genetic similarity of some of the astrovirus haplotypes found in several different regions was detected, identical astrovirus haplotypes were not shared between different sampled regions.ConclusionsThe genetic population structure of the bat host suggests that mating sites where several local breeding colonies meet act as stepping-stones for gene flow. Identical astrovirus haplotypes were not shared between different sampled regions suggesting that astroviruses are mostly transmitted among host colonies at the local scale. Nevertheless, high genetic similarity of some of the astrovirus haplotypes found in several different regions implies that occasional transmission across regions with subsequent mutations of the virus haplotypes does occur.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0856-0) contains supplementary material, which is available to authorized users.

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“…; 72–88 % in Boston et al . ). Concerning the QI threshold, all samples were above QI > 0.5, 18 (94.7% of the total) had a QI > 0.7 and 15 (78.9%) had a QI > 0.8.…”

Section: Discussionmentioning

confidence: 97%

Historical and non‐invasive samples: a study case of genotyping errors in newly isolated microsatellites for the lesser anteater (Tamandua tetradactyla L., Pilosa)

Clozato

Moraes‐Barros

Santos

et al. 2014

Molecular Ecology Resources

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Tamandua tetradactyla (Pilosa), the lesser anteater, is a medium-size mammal from South America. Its wide distribution through different landscapes, solitary and nocturnal habits, and the difficulty to capture and contain specimens limit the amount of individuals and populations sampled during fieldworks. These features along with the lack of specific molecular markers for the lesser anteater might be the causes for paucity in population genetic studies for the species. Historical samples from museum specimens, such as skins, and non-invasive samples, such as plucked hair, can be supplementary sources of DNA samples. However, the DNA quantity and quality of these samples may be limiting factors in molecular studies. In this study, we describe nine microsatellite loci for T. tetradactyla and test the amplification success, data reliability and estimate errors on both historical and non-invasive sample sets. We tested nine polymorphic microsatellites and applied the quality index approach to evaluate the relative performance in genotype analysis of 138 historical samples (study skin) and 19 non-invasive samples (plucked hair). The observed results show a much superior DNA quality of non-invasive over historical samples and support the quality index analysis as a practical tool to exclude samples with doubtful performance in genetic studies. We also found a relationship between the age of non-invasive samples and DNA quality, but lack of evidence of this pattern for historical samples.

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Empirical Assessment of Non-Invasive Population Genetics in Bats: Comparison of DNA Quality from Faecal and Tissue Samples

Cited by 31 publications

References 31 publications

Phylogeography and postglacial recolonization of Europe by Rhinolophus hipposideros: evidence from multiple genetic markers

Phylogeography and postglacial recolonization of Europe by Rhinolophus hipposideros: evidence from multiple genetic markers

Evidence for genetic variation in Natterer’s bats (Myotis nattereri) across three regions in Germany but no evidence for co-variation with their associated astroviruses

Historical and non‐invasive samples: a study case of genotyping errors in newly isolated microsatellites for the lesser anteater (Tamandua tetradactyla L., Pilosa)

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