Conservation Genetics

Next-generation DNA sequencing reveals evolutionary trends in microsatellite abundance in reptiles

by Robert Murphy

Blair, C., V.H. Jiménez-Arcos, F.R. Méndez de la Cruz, and R.W. Murphy. In press. Next-generation DNA sequencing reveals evolutionary trends in microsatellite abundance in reptiles. Conservation Genetics Resources. COGR-D-12-01035R1.

Isolation and characterization of eleven novel polymorphic microsatellite loci in the spiny softshell turtle (Apalone spinifera)

by Robert Murphy

Davy, C.M., I.M. Conflitti, D. Storisteanu, and R.W. Murphy. In press. Isolation and characterization of eleven novel polymorphic microsatellite loci in the spiny softshell turtle (Apalone spinifera). Conservation Genetics Resources. COGR1022.

Application of Genetics to Conservation of Canadian Reptiles

by David Galbraith

Andrew A. Chek, Kent A. Prior, David A. Galbraith, Stephen C. Lougheed. 2007. Herpetological Conservation 2:113-130 (Chapter 7)

Conservation genetics is principally concerned with 2 endeavours. The 1st approach uses genetic data to inform... more Conservation genetics is principally concerned with 2 endeavours. The 1st approach uses genetic data to inform questions centred on relationships among individuals, populations, species or higher-level taxa. Such questions may relate to connectivity among populations (gene flow) and the effects of past or present fragmentation events, forensic applications (animal or plant derivative identification) or the evolutionary affinities among taxa (phylogeny). The 2nd approach emphasizes quantification of genetic diversity at various hierarchical levels, to understand immediate (inbreeding) or future (ability to adapt to changing environments) consequences of reduced genetic variation. Relatively few populations of Canada’s 43 species of reptiles have been investigated using genetic techniques, which is unfortunate, because theory suggests these peripheral populations can harbour unique genetic variants, or be substantially genetically diverged from core populations. Examples from Canada and elsewhere can be used to illustrate some of the main sorts of inquiry within the 2 areas outlined above. Genetic markers have been useful in clarifying the bounds and affinities of reptile taxa and the related task of assessing the value of the taxon. Genetic markers can offer indirect measures of gene flow/migration between populations, although these estimates are ideally anchored by ecological assessments (mark-recapture, radiotelemetry studies). Gene flow/migration is important in determining the proportion of genetic variation unique to a given population. Perhaps more practically, the extent to which populations are genetically connected determines the scale and geographic bounds of management units and the likelihood that a given population can recolonize an area where a neighbouring population has been extirpated. Small population size is correlated with the loss of genetic variation (for example, through founder effect or genetic drift), which may impair the future adaptive capacity of a population or species as a whole. Small population size also results in inbreeding, which can lead to the accumulation of deleterious alleles that reduce fitness and make the population decline further. Other applications of genetic markers include their use in determining the sex of individuals, important when the species is monomorphic, where the species is difficult to handle, or where only a sample of the individual is available. Genetic markers are also of use for investigations of mating systems. Which and how many males and females breed in a population may have important consequences for wild management, captive breeding, or reintroduction measures. Finally, genetic markers may be applied for forensic purposes: establishing the provenance or identity of an individual or part thereof. The relatively small proportion of Canadian reptiles genetically investigated is not a reflection of inadequate laboratory capacity or expertise. Our experience suggests there is a willing supply of both geneticists and students eager to carry out such work; financial resources are more often the limiting factor. Where resources are available, we suggest 3 areas of study that could contribute to Canadian reptile conservation: taxonomic studies, particularly where species are marked by geographic variation in morphology, or where the distribution of species is discontinuous or spans very different environments; studies of the conservation value of peripheral populations; and using genetic information and GIS tools to assess the effect of habitat disturbance on population connectivity over relatively short time scales.

Range-edge genetic diversity: locally poor extant southern patches maintain a regionally diverse hotspot in the seagrass Zostera marina

by Onno Diekmann

Molecular Ecology (2012) doi: 10.1111/j.1365-294X.2012.05500.x

Refugial populations at the rear edge are predicted to contain higher genetic diversity
than those resulting from... more Refugial populations at the rear edge are predicted to contain higher genetic diversity
than those resulting from expansion, such as in post-glacial recolonizations. However,
peripheral populations are also predicted to have decreased diversity compared to the
centre of a species’ distribution. We aim to test these predictions by comparing genetic
diversity in populations at the limits of distribution of the seagrass Zostera marina, with
populations in the species’ previously described central diversity ‘hotspot’. Zostera
marina populations show decreased allelic richness, heterozygosity and genotypic
richness in both the ‘rear’ edge and the ‘leading’ edge compared to the diversity ‘hotspot’
in the North Sea ⁄ Baltic region. However, when populations are pooled, genetic diversity
at the southern range is as high as in the North Sea ⁄ Baltic region while the ‘leading edge’
remains low in genetic diversity. The decreased genetic diversity in these southern
Iberian populations compared to more central populations is possibly the effect of drift
because of small effective population size, as a result of reduced habitat, low sexual
reproduction and low gene flow. However, when considering the whole southern edge of
distribution rather than per population, diversity is as high as in the central ‘hotspot’ in
the North Sea ⁄ Baltic region. We conclude that diversity patterns assessed per population
can mask the real regional richness that is typical of rear edge populations, which have
played a key role in the species biogeographical history and as marginal diversity
hotspots have very high conservation value.

Effective size of an Atlantic salmon (Salmo salar L.) metapopulation in Northern Spain

by Carlos Garcia de Leaniz

Kuparinen,A.; Tufto,J.; Consuegra,S.; Hindar,K.; Merilä,J.; Garcia de Leaniz,C. (2010). Cons. Genetics 11: 1559-1565

The genetic diversity of metapopulations is influenced not only by the effective sizes (Ne) of individual... more The genetic diversity of metapopulations is influenced not only by the effective sizes (Ne) of individual subpopulations, but also by the total effective size of the metapopulation (meta-Ne). We estimated meta-Ne of four neighbouring Atlantic salmon populations connected by gene flow using genetic estimates of subpopulation Nes and migration rates derived from capture-recapture data. The  was lower than the sum of s of the subpopulations, suggesting that genetic diversity harboured by the four river salmon metapopulation is lower than what would have been expected by viewing individual subpopulations separately. In addition,  was found to be sensitive to changes in  of the subpopulation from which net emigration rate was largest, so as that the genetic diversity of the metapopulation would be best preserved by avoiding any reductions in Ne of this subpopulation. Yet, this subpopulation is the one that has historically - and still is - experiencing the highest exploitation rate in the metapopulation system. Keywords: Atlantic salmon, conservation, effective population size, fisheries, metapopulation, Salmo salar L.

Microsatellite standardization and genotyping error in a large multi-partner research programme for conservation of Atlantic salmon (Salmo salar L.)

by Carlos Garcia de Leaniz

Ellis,J.S.; Gilbey,J.; Balstad,T.; Cherbonnel,C.; Consuegra,S.; Coughlan,J.; Cross,T.F.; Crozier,W.; Dillane,E.; Ensing,D.; García de Leániz,C.; Garcia-Vazquez,E.; Griffiths,A.M.; Hindar,K.; Hjorleifsdottir,S.; Knox,D.; Machado-Schiaffino,G.; McGinnity,P.; Meldrup,D.; Nielsen,E.E.; Primmer,C.R.; Prodöhl,P.; Vähä,J.-P.; Verspoor,E.; Wennevik,V.; Stevens,J.R. (2011). Genetica 139: 353-367

Microsatellite genotyping is a common DNAcharacterization technique in population, ecological andevolutionary genetics... more Microsatellite genotyping is a common DNAcharacterization technique in population, ecological andevolutionary genetics research. Since different alleles aresized relative to internal size-standards, different laboratoriesmust calibrate and standardize allelic designationswhen exchanging data. This interchange of microsatellitedata can often prove problematic. Here, 16 microsatelliteloci were calibrated and standardized for the Atlantic salmon,Salmo salar, across 12 laboratories. Althoughinconsistencies were observed, particularly due to differencesbetween migration of DNA fragments and actualallelic size ('size shifts'), inter-laboratory calibration wassuccessful. Standardization also allowed an assessment ofthe degree and partitioning of genotyping error. Notably,the global allelic error rate was reduced from 0.05 ± 0.01prior to calibration to 0.01 ± 0.002 post-calibration. Mosterrors were found to occur during analysis (i.e. when sizecallingalleles; the mean proportion of all errors that wereanalytical errors across loci was 0.58 after calibration). Noevidence was found of an association between the degreeof error and allelic size range of a locus, number of alleles,nor repeat type, nor was there evidence that genotypingerrors were more prevalent when a laboratory analyzedsamples outside of the usual geographic area theyencounter. The microsatellite calibration between laboratoriespresented here will be especially important forgenetic assignment of marine-caught Atlantic salmon,

Metapopulation dynamics of a diadromous galaxiid fish and potential effects of salmonid aquaculture

by Carlos Garcia de Leaniz

Vanhaecke,D.; Garcia de Leaniz,C.; Gajardo,G.; Thomas,C.J.; Consuegra,S. (2012). Freshwater Biology 57: 1241-1252.

1.Direct ecological effects of biological invasions have been widely documented, but indirect genetic effects on... more 1.Direct ecological effects of biological invasions have been widely documented, but indirect genetic effects on native species are poorly known. In many cases this is due to lack of information on the genetic structure of species affected by invasions.
2. We used microsatellite DNA loci to estimate the genetic structure and gene flow patterns of Galaxias maculatus, a galaxiid fish endemic to the Southern Hemisphere which is increasingly being threatened by salmonid invasions.
3. Analysis of nine diadromous populations of G. maculatus in Chilean Patagonia (an area heavily impacted by farming of non-native salmonids) indicates that dispersal is mostly a passive process, seemingly driven by wind and currents, and resulting in high gene flow and weak population structuring. 4.Gene flow was asymmetrical, with three populations acting as sources and six populations acting as sinks. Sinks had lower habitat quality and had a greater incidence of adults than sources, which consisted mostly of juveniles.
5.Rivers invaded by salmonid escapees experienced significantly higher aquaculture pressure than rivers where salmonid escapees were apparently absent, but no effect on genetic diversity of G. maculatus could be detected.
6.We discuss whether salmonid aquaculture might affect the demography and connectivity of galaxiid metapopulations: indirectly through habitat alteration and directly through escapes of predatory fish.

Genetic evidence for a distinct Pelodytes lineage in southwest Portugal: implications for the use of pre-developed microsatellite markers

by Onno Diekmann

Co-authored

For population genetic analyses of Parsley
frogs in Iberia we initially used microsatellite markersmore For population genetic analyses of Parsley
frogs in Iberia we initially used microsatellite markers
previously developed for Pelodytes punctatus in southwest
Portugal. However, several loci indicated a strong signal of
amplification failure for individuals from northern Spain.
Cryptic species or genetic entities are suspected to occur in
southwest Portugal on the basis of studies with other spe-
cies and understanding cryptic diversity is a concern as
amphibian habitat, temporary ponds in traditional Medi-
terranean farmland, is disappearing at a fast rate. Our study
revealed a new Pelodytes lineage in southwest Portugal
which appears to be discrete. However, the rare occurrence
of a distinct mitochondrial haplotype from its sister species,
despite no nuclear differentiation, is a signature of intro-
gression indicating that reproductive isolation is not
complete.

TaqMan assays for species identification of the red squirrel (Sciurus vulgaris) and the grey squirrel (Sciurus carolinensis)

by Denise O' Meara

Denise O'Meara, Peter Turner, Lee Coffey, Catherine O'Reilly

We have developed TaqMan based assays for species-specific identification of two species of squirrel found in the... more We have developed TaqMan based assays for species-specific identification of two species of squirrel found in the British Isles, the native red squirrel (Sciurus vulgaris) and the introduced North American grey squirrel (Sciurus carolinensis). These assays correctly identified tissue and hair samples of both species and there was no cross-species amplification. This is a useful method for non-invasive surveys to help conserve the red squirrel and manage the spread of the grey squirrel in the UK and Ireland.

A study of genetic differentiation and hybridization among oak species with divergent ecological and evolutionary profiles

by Charalambos Neophytou

Clonal diversity and conservation genetics of the medicinal plant Carapichea ipecacuanha (Rubiaceae)

by luiz Orlando de Oliveira

Combining genetic, historical and geographical data to reconstruct the dynamics of bioinvasions: application to the cane toad Bufo marinus.

by Mathias Currat

The hidden side of invasions: massive introgression by local genes

by Mathias Currat

Signals of recent spatial expansions in the grey mouse lemur (Microcebus murinus)

by Mathias Currat

Genetic variation in transferrin as a predictor for differentiation and evolution of caribou from eastern Canada

by Mike Ferguson

Røed, Ferguson, Crete and Beregrud. 1991. Genetic variation in transferrin as a predictor for differentiation and evolution of caribou from eastern Canada. Rangifer 11: 65-74.

Polyacrylamide gel electrophoresis was used to analyze transferrin variation in caribou populations from Manitoba,... more Polyacrylamide gel electrophoresis was used to analyze transferrin variation in caribou populations from Manitoba, Ontario, Quebec/Labrador, and Baffin Island, Northwest Territories in eastern Canada. The transferrin allele frequencies in these populations were compared with those previously reported for Canadian barren-ground caribou, Rangifer tarandus groenlandicus, Alaska caribou, R. t. granti, Peary caribou, R. t. pearyi, Svalbard reindeer, R. t. platyrhynchus, and Eurasian tundra reindeer, R. t. tarandus. A total of twenty different alleles were detected in the analyzed material, considerable genetic heterogeneity being detected between regions. Three alleles that were relatively common in caribou from Ontario, Manitoba and Quebec/Labrador, were present not present in R. t. granti, R. t. pearyi, R. t. tarandus or R. t. platyrhynchus, and present only at very low frequencies in R. t. groenlandicus. These findings, together with genetic identity analyses,suggest that the caribou in Manitoba, Ontario and Quebec/Labrador are mainly of the R. t. caribou type, and that little interbreeding has occurred with other subspecies. The large genetic distance in the transferrin locus between R. t. caribou and other subspecies of reindeer/caribou suggests that, during the late Wisconsin glaciation the ancestral populations of R. t. caribou survived in a refugium different from the ancestral populations of the other subspecies. Significant genetic differences between Baffin Island caribou and all other populations were mainly due to the presence of one allele which was in high frequency in Baffin Island caribou, but was absent, or present in very low frequencies, in all other caribou populations. The genetic differences between Baffin Island caribou and the other subspecies were greater than the differences between several of the currently recognized subspecies.

The coral genus Madracis. Speciation in corals and their symbionts

by Onno Diekmann

Conference Announcement: “In the Wake of the Basque Whalers: Cultural and Genetic Heritage of the Basques and the Native Americans of the North Atlantic”

by Roslyn Frank

Here is the program for the upcoming International Conference called “In the Wake of the Basque Whalers: Cultural and Genetic Heritage of the Basques and the Native Americans of the North Atlantic”, featuring speakers from across several disciplines and cultures. It will take place 21-22 September 2011 in Bilbao, Spain, on the campus of the University of the Basque Country. It has been coordinated by the BIOMICs unit of UPV/EHU, University of the Basque Country Research Group and the well known film maker, photographer and investigator Xabi Otero of JAUZARREA. The unique blend of presentations in the humanities and hard sciences that characterizes this conference is a reflection of the unique broad-based interdisciplinary approach promoted by the team of geneticists at the University of the Basque Country, most particularly by Dr. Marian M. de Pancorbo, Director of the UPV/EHU BIOMICS unit, and Dr. Sergio Cardoso.

The conference summary is as follows:

“The Basques established relations with Native Americans in the St.... more The conference summary is as follows:

“The Basques established relations with Native Americans in the St. Lawrence River area over many centuries, and evidence of this appears in historical records. A wealth of historical, archaeological and even language records have been preserved as a result of these relations. One can therefore assume that the DNA lineages may also bear witness to these relations, owing to the contribution resulting from the constant trade established with the Native Americans by our whale hunters, cod fishermen and fur traders from the Lower Middle Ages and up until the 20th century.”

The list of participants includes: Dr. Marian M. de Pancorbo (UPV/EHU), Xabi Otero (JAUZARREA), Juan Antonio Urbeltz (IKERFOLK Institute), Dr. Stephen Augustine (Museum of Civilisation, Hull-Ottawa, Traditional Mi’kmaq Chief, Restigouche), Dr. Paul Charest (Laval University, Québec), Ghislain Picard (Head of the Assembly of the First Nations of Québec and Labrador), Dr. Charles A. Martin (University of Montreal), Dr. Stephen Oppenheimer (University of Oxford), Dr. Daniel G. Bradley (Trinity College, Dublin), Dr. Sergio Cardoso (UPV/EHU), Jon Maia and Amets Arzallus, Dr. Roldán Jimeno Aranguren (Public University of Navarre), Dr. Jacques Lacoursière (Laval University, Québec), Dr. Miren Egaña Goya (Aranzadi Scientific Society, Donostia), Dr. Brad Loewen (University of Montreal), Dr. Peter Bakker (University of Aarhus, Denmark), Dr. Robert Grenier (Parks Canada, UNESCO), Xabier Agote (ALBAOLA Association, Pasaia), Dr. Aurélie Arcocha-Scarcia (Université Michel de Montaigen-Bordeaux3, Centre de Recherche sur la Langue et les Textes).

Sobre la conservacion de Ateles geoffroyi (Primates Atelidae) en El Salvador: consideraciones geneticas para la formacion de poblaciones en cautiverio

by Silvio Crespin

A collection of captive individuals can be used for a variety of conservation purposes, including the formation of... more A collection of captive individuals can be used for a variety of conservation purposes, including the formation of captive populations, with the intention of maintaining a high genetic variation and avoiding genetic drift. Consequently 18 A. geoffroyi individuals kept in captivity were genotyped applying three microsatellite loci (loci 1118, 311 and P2BH6), constituting the first study of genetic variation of this species in El Salvador. The amplification of the microsatellite fragments and subsequent identification of the genotypes employed nuclear DNA extracted from blood samples and hair follicles. Approximately 89% of the subjects were genotyped successfully, wherein an allelic dropout of 16% and 22% (loci 1118 and 311, respectively) occurred due probably to the presence of a mutation in the sequence of the flanking region. A high average expected heterozygosity (He = 0.717) was calculated, however, the observed heterozygosity is significantly less (F = 0.492). Computed exact tests confirm the collection of individuals would not be in Hardy-Weinberg equilibrium (HWE) for any of the three loci studied. Therefore, a population comprised by the gene pool of the individuals sampled would not be able to maintain constant allele frequencies if kept isolated from other populations, impeding its use in long term conservation efforts.

Argali abundance in the Afghan Pamir using capture-recapture modeling from fecal DNA.

by Vânia Costa

Harris RB, Winnie J, Amish SJ, Beja-Pereira A, Godinho R, Costa V, Luikart G

Estimating population size in a mark–recapture framework using DNA obtained from remotely collected genetic samples... more Estimating population size in a mark–recapture framework using DNA obtained from remotely collected genetic samples (e.g., feces) has become common in recent years but rarely has been used for ungulates. Using DNA extracted from fecal pellets, we estimated the size of an argali (Ovis ammon) population that was believed to be isolated from others within the Big Pamir Mountains, Afghanistan, an area where access was difficult and expensive. We used closed-capture models to estimate abundance, and Pradel models to examine closure assumptions, both as implemented in Program MARK. We also made visual counts of argali in the Big Pamirs, allowing comparison of count indices of abundance with modeled estimates. Our model-averaged estimate for female argali in the Big Pamir was 172 (95% CI  =  117–232), which was about 23% higher than our best assessment using uncorrected visual counts. However, mark–recapture models suggested that males were not a closed population; thus, we were unable to provide a meaningful estimate of overall population size. Males either suffered much higher mortality than females during the sampling period, or, more likely, males moved in and out of the Big Pamir area. Although information from DNA did not provide a clear overall population estimate, it suggested that the Big Pamir was not isolated from other argali populations, which could not have been confirmed with visual observations alone. Estimating argali population size using mark–recapture models and fecal DNA is feasible but may be too expensive for frequent monitoring of large and remote populations. Our study demonstrates the importance of sex identification and separate abundance estimation for each sex, especially if movement ecology differs by sex.

Patterns of Genetic Structuring In a Brown Trout (Salmo Trutta L.) Metapopulation

by Ilaria Coscia

Conservation Genetics 2010