Population genetics (Biology)

Population Structure and Gene Evolution In Saccharomyces Cerevisiae

by Jeffrey Townsend

The fully sequenced genomes of four species within the Saccharomyces sensu stricto complex provide a wealth of... more The fully sequenced genomes of four species within the Saccharomyces sensu stricto complex provide a wealth of information for molecular-evolutionary inference. Yet virtually nothing is known about population-genetic variation within these species, including the molecular-biological and genetic-model organism S. cerevisiae. Here we investigate the population-genetic variation and population structure of S. cerevisiae by sequencing the four loci CDC19, PHD1, FZF1 and SSU1 in 27 strains. Sequence analysis demonstrates a distinct population structure in S. cerevisiae, distinguishing strains collected from a Pennsylvanian oak forest and strains collected from vineyards, perhaps due to ecological rather than geographic factors. The low level of conflict observed between the gene trees estimated for each locus implies moderate recombination in nature. High polymorphism in the gene SSU1 provides evidence of diversifying selection on its protein product, a sulfite exporter, perhaps associated with the use of sulfur-based fungicides in vineyards. FZF1, encoding a transcription factor regulating the expression level of SSU1, displays even greater polymorphism. This, the first multilocus sequence study of population structure in natural isolates of S. cerevisiae, is the first study to demonstrate population structure within S. cerevisiae, and the first study to detect historical selection on a locus important to the natural history of wine yeast.

A multilevel approach to predict toxicity in copepod populations: Assessment of growth, genetics, and population structure

by Mats Grahn

Evidence of population genetic effects of long-term exposure to contaminated sediments--A multi-endpoint study with copepods

by Mats Grahn

Genetic, morphological, and feather isotope variation of migratory willow warblers show gradual divergence in a ring

by Mats Grahn

MEDEA SELFISH GENETIC ELEMENTS AS TOOLS FOR ALTERING TRAITS OF WILD POPULATIONS: A THEORETICAL ANALYSIS

by Jessica Su

One strategy for controlling transmission of insect-borne disease involves replacing the native insect population with... more One strategy for controlling transmission of insect-borne disease involves replacing the native insect population with transgenic animals unable to transmit disease. Population replacement requires a drive mechanism to ensure the rapid spread of linked transgenes, the presence of which may result in a fitness cost to carriers. Medea selfish genetic elements have the feature that when present in a female, only offspring that inherit the element survive, a behavior that can lead to spread. Here, we derive equations that describe the conditions under which Medea elements with a fitness cost will spread, and the equilibrium allele frequencies are achieved. Of particular importance, we show that whenever Medea spreads, the non-Medea genotype is driven out of the population, and we estimate the number of generations required to achieve this goal for Medea elements with different fitness costs and male-only introduction frequencies. Finally, we characterize two contexts in which Medea elements with fitness costs drive the non-Medea allele from the population: an autosomal element in which not all Medea-bearing progeny of a Medea- bearing mother survive, and an X-linked element in species in which X/Y individuals are male. Our results suggest that Medea elements can drive population replacement under a wide range of conditions.

Role of recent and old riverine barriers in fine-scale population genetic structure of Geoffroy's tamarin (Saguinus geoffroyi) in the Panama Canal watershed

by Sam Diaz-Munoz

Ecology and Evolution (Early View 2011)

The role of physical barriers in promoting population divergence and genetic structuring is well known. While it is... more The role of physical barriers in promoting population divergence and genetic structuring is well known. While it is well established that animals can show genetic structuring at small spatial scales, less well-resolved is how the timing of the appearance of barriers affects population structure. This study uses the Panama Canal watershed as a test of the effects of old and recent riverine barriers in creating population structure in Saguinus geoffroyi, a small cooperatively breeding Neotropical primate. Mitochondrial sequences and microsatellite genotypes from three sampling localities revealed genetic structure across the Chagres River and the Panama Canal, suggesting that both waterways act as barriers to gene flow. F-statistics and exact tests of population differentiation suggest population structure on either side of both riverine barriers. Genetic differentiation across the Canal, however, was less than observed across the Chagres. Accordingly, Bayesian clustering algorithms detected between two and three populations, with localities across the older Chagres River always assigned as distinct populations. While conclusions represent a preliminary assessment of genetic structure of S. geoffroyi, this study adds to the evidence indicating that riverine barriers create genetic structure across a wide variety of taxa in the Panama Canal watershed and highlights the potential of this study area for discerning modern from historical influences on observed patterns of population genetic structure.

Palaeolithic Continuity Refugium Theory: A New Approach to the Linguistic Prehistory of Europe. Azken Glaziazio Handiko Babeslekua eta Euskara. Bergara, 2011-10-19

by Roslyn Frank

The following .pdf is a copy of the Power Point presentation that I gave on October 19, 2011, in the Irizar Jauregiko Aretoa, Bergara, Euskal Herria. It is a bilingual presentation. Its title in Basque is Azken Glaziazio Handiko Babeslekua eta Euskara while in Spanish it is “El Refugio de la Última Glaciación y el Euskara”. And the English translation would be “The Last Glacial Maximum: The Franco-Cantabrian Refuge and the Basque Language”.

The talk is an overview of the data, genetic, archaeological and linguistic, which support the Paleolithic Continuity... more The talk is an overview of the data, genetic, archaeological and linguistic, which support the Paleolithic Continuity Refuguim Theory (PCRT) of European prehistory. More specifically, based on the findings of genetics (studies of Y-chromosome and mtDNA), the following hypothesis has been brought forward for testing. It argues that during the Last Glacial Maximum (LGM), the hunter-gatherers of Europe retreated to the south of Europe, settling into three refugia, one in the Balkans, one in the Ukraine and a third in the Franco-Cantabrian zone, a geographic location where the Basque people and their language have survived.

According to the results of various teams of geneticists, at the end of the LGM along with the warming of the climate that ensued, the hunter-gatherers inhabiting this refuge slowly moved north and westward to take advantage of the food resources in the newly opened territories. Studies of Basque DNA (paternally transmitted Y-chromosome and maternally transmitted mtDNA) have shown significant similarities between Basques and populations inhabiting present and former Celtic-speaking zones along the Atlantic Façade. Furthermore, various haplogroups found among the Basques show up in other populations of European descent, leading the geneticists to argue that this situation might best be explained by positing out-migration from this zone over a period of several thousands of years, starting at the end of the LGM.

Moreover, it follows that members of Basque-speaking population of this zone might well trace their descent from the same populations that began to move out of this geographical region as the ice sheets retreated.

In 2006, a multidisciplinary team of researchers –composed of geographers, archaeologists and geneticists, namely, Dr. William Davies, Dr. Paul Pettitt, Dr. Lee Hazelwood and Dr. Martin Richards coordinated by Dr. Clive Gamble– described the situation this way:

“A major population expansion occurred in Western Europe during the Late Glacial (15-11.5ka CAL PB) as the OIS2 ice sheets retreated and unglaciated areas in the north became available for re-settlement. Phlylogeographic analysis using molecular evidence assigns 60% of the European mitochondrial DNA lineages (Richards et al. 2000), and an even higher proportion of West European Y-chromosome lineages (Semino et al. 2000), to a population bottleneck prior to an expansion from southwest to northern Europe (Torroni et al. 1998; Torroni et al. 2001; Achilli et al. 2004; Rootsi et al. 2004; Pereira et al. 2005)” (Gamble et al. 2006: 1-2).

The key question posed by the research concerns the language that was being spoken by the hunter-gatherer populations when they moved out of this refuge. Gamble et al. was the first team of researchers to pose this question explicitly:

“The growing evidence that the major signal in European genetic lineages predates the Neolithic, however, creates serious problems for the agriculturalist perspective. If western Europe was, to a large extent, repopulated from northeast Iberia [Franco-Cantabrian zone] then, since place-name evidence suggests that people in this source region spoke languages related to Basque before the advent of Indo-European, the obvious corollary would seem to be that the expanding human groups should have been Basque speakers” (Gamble et al. 2005: 209).

The presentation lays out the methodology has been developed to test the validity of the corollary that Gamble et al. set forth in 2005. The latter section of the .pdf discusses the methodology and applies it to a concrete data set. The approach is a comparative one. It takes morpho-syntactic elements classified as Proto-Indo-European and compares them to what appear to be their counterparts in Euskara. Tests are then applied to determine the nature of the lineage of the two sets of morphemes in question. The PIE elements are ones recognized as common across IE languages and, therefore, as constituting the most archaic strata of these languages. However, until now IE research model has not sought to explain the origin of the elements themselves.

Keeping in mind the results of the genetic studies cited above, the Basque language becomes a possible candidate for additional comparative work. Moreover, by focusing on reconstructing morphemic lineages, not languages, the PCRT approach to the data allows for a more fine-grained analysis of the linguistic evidence.

Selected Referencias:
• Achilli, A. et al. 2004. The molecular dissection of mtDNA haplogroup H confirms that the Franco-Cantabrian glacial refuge was a major source for the European gene pool. American Journal of Human Genetics 75 (5): 910-918.
• Brugmann, K 1891. A Comparative Grammar of the Indo-Germanic Languages. Vol. II. Morphology (Stem-formation and inflexion). Part 1. New York: B. Westermann & Co. http://books.google.com/books?id=eWsKAAAAIAAJ&printsec=frontcover&dq=brugmann+%22comparative+grammar+of+the+indo+germanic+languages%22#PPR2,M1
• Cardoso Martín, S. 2008. Diversidad del genoma mitocondrial en poblaciones autóctonas de la Cornisa Cantábrica: Huellas de la recolonización postglacial de Europa. Gasteiz: University of the Basque Country.
• Cardoso Martín, S. et al. 2011. The maternal legacy of Basques in Northern Navarre: New Insights into the Mitocondrial DNA diversity of the Franco-Cantabria Area. Journal of Physical Anthrpology 145 (3): 480-488.
• Dupanloup, I., et al. 2004. Estimating the impact of prehistoric admixture on the genome of Europeans. Molecular Biology and Evolution 21 (7): 1361-1372.
• Frank, R. M. 2008. Palaeolithic Continuity Refugium Theory (PCRT): Hamalau and its linguistic and cultural relatives. Part 1. Insula 4 (December): 61-131. Cagliari, Sardinia.
• Frank, R. M. in prep. Rethinking the Linguistic Landscape of Europe: The Indo-European "Homeland" in light of Palaeolithic Continuity Refugium Theory (PCRT).
• Gamble, C. et al. 2005. The archaeological and genetic foundations of the European population during the Late Glacial: Implications for 'agricultural thinking'. Cambridge Archaeological Journal 15 (2): 193-223.
• Gamble, C. et al. 2006. The Late Glacial ancestry of Europeans: Combining genetic and archaeological evidence. Documenta Praehistorica 33: 1-10. http://arheologija.ff.uni-lj.si/documenta/pdf33/gamble33.pdf.
• Haspelmath, M. 2007. Pre-established categories don't exist: Consequences for language description and typology. Linguistic Typology 11 (1): 119-132.
• Haspelmath, M. 2010. Comparative concepts and descriptive categories in cross-linguistic studies. Language 86 (3): 663-687.
• Oppenheimer, S. 2006. The Origins of the British - A Genetic Detective Story. Constable and Robinson.
• Tovar A. 1954. El sufijo -ko: Indoeuropeo y circumindoeuropeo. Archivo glottologico italiano 39: 56-64.
• Tovar A. 1970a. The Basque language and the Indo-European spread to the West. In: George Cardona (ed.), Papers Presented at the Third Indo-European Conference at the University of Pennsylvania: Indo-European and Indo-Europeans, 267-278. Philadelphia, Pennsylvania: University of Pennsylvania Press.
• Torroni, A., et al. 2001. A signal, from human mtDNA, of postglacial recolonization in Europe. American Journal of Human Genetics. 69:844-852.
• Wilson, J. et al. 2001. Genetic evidence of different male and female roles during cultural transitions in the British Isles. Proceedings of the National Academy of Sciences, USA 98(9): 5078-5083.

Nestmate relatedness and population genetic structure of the Australian social crab spider Diaea ergandros (Araneae: Thomisidae)

by Theodore Evans

Molecular Ecology 1, 2307-2316

We characterized the population genetic structure of the Australian social spider Diaea ergandros using polymorphic... more We characterized the population genetic structure of the Australian social spider Diaea ergandros using polymorphic allozyme markers. Our main objectives were to understand the social organization of D. ergandros and discern patterns of gene flow across distantly separated geographical areas. Spiders were sampled from nests located within 100 m wide locales, which were distributed within larger 50 km wide regions. Our results indicated that nestmates could have been produced by a single mother and father in 88.9% of D. ergandros nests. The remainder of nests contained spiders that were probably produced by polyandrous females or were immigrants from foreign nests. Nestmate relatedness was relatively high (r = 0.44) and did not differ significantly between the sexes or among juvenile, subadult and adult life stages. We also discovered that D. ergandros populations were highly structured, with significant differentiation detected among locales (FLR = 0.23) and regions (FRT = 0.081). Spiders within locales were also substantially inbred (FIL = 0.15). Overall, our data show that significant population subdivision exists in D. ergandros populations, and we suggest that the poor dispersal ability of Diaea spiders can account for the observed genetic structure.

Microsatellite markers in the primitive termite Mastotermes darwiniensis

by Theodore Evans

Molecular Ecology Notes 1, 250-251

We developed 10 microsatellite loci in the primitive termite Mastotermes darwiniensis. The number of alleles per locus... more We developed 10 microsatellite loci in the primitive termite Mastotermes darwiniensis. The number of alleles per locus ranged from four to 15, and the expected heterozygosites spanned from 0.21 to 0.90, in a sample of 40 workers collected from the Northern Territory, Australia. We also determined that only two loci amplified in five other termite species. The low frequency of cross-amplification probably resulted from the high level of phylogenetic divergence between M. darwiniensis and the other taxa. Thus, although the loci are not widely applicable, they should prove effective in elucidating the genetic structure of M. darwiniensis populations.

Molecular diversity after a range expansion in heterogeneous environments

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.

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).

The ephemeral shorebird: population history of ruffs

by Yvonne Verkuil

Doctoral thesis, July 2010

Ruffs are migrant shorebirds of inland habitats. This thesis describes seasonal migration and changes in range... more Ruffs are migrant shorebirds of inland habitats. This thesis describes seasonal migration and changes in range occupation of ruffs, and presents a comparative analysis of the population genetics of ruffs and related shorebird species. Two hypotheses about shorebird evolution are addressed. Firstly, it is questioned whether instead of evolutionary constraints on migration routes (inflexible migration hypothesis), flexible routing might better explain observations on migration in shorebirds. Secondly, we test whether genetic variation in ruff and other inland, freshwater shorebirds is higher than in marine, coastal shorebirds (habitat dichotomy hypothesis).

Characterization of polymorphic microsatellite DNA markers in the black‐tailed godwit (Limosa limosa: Aves)

by Yvonne Verkuil

Molecular Ecology Resources 9, 1415-1418, 2009

We isolated and tested 16 microsatellite loci in black-tailed godwits from the Netherlands (Limosa limosa limosa), and... more We isolated and tested 16 microsatellite loci in black-tailed godwits from the Netherlands (Limosa limosa limosa), and from Australasia (subspecies melanuroides). One locus was
monomorphic, two loci had null-alleles and one was significantly heterozygote deficient. The remaining 12 polymorphic loci had on average 7.9 alleles (range 5–11) and the mean expected heterozygosity was 0.69. No significant linkage disequilibrium between the loci was observed and all loci were autosomal. Fourteen loci were successfully cross-amplified in bar-tailed godwit (Limosa lapponica).

De la genética a la cinética

by Alejandro Fernández Villaverde

AF Villaverde, JR Banga (2011) Investigación y Ciencia, 418, pp. 12-13

New insights on the taxonomy and population structure of Bryde’s whale” species across the Indo-Western Pacific

by Francine Kershaw

Kershaw, F., Leslie, M.S., Collins, T., Mansur, R.M., Smith, B.D., Minton, G., Baldwin, R., LeDuc, R.G., Anderson, C., Brownell, R.L. Jr. & Rosenbaum, H.C. (2011). New insights on the taxonomy and population structure of Bryde’s whale” species across the Indo-Western Pacific. Paper SC/63/O19 presented to IWC Scientific Committee, June 2011, Tromso, Norway (unpublished).

Phylogenetic and population genetic divergence correspond with habitat for the pathogen Colletotrichum cereale and allied taxa across diverse grass communities

by Jo Anne Crouch

Over the past decade, the emergence of anthracnose disease has newly challenged the health of turfgrasses on North... more Over the past decade, the emergence of anthracnose disease has newly challenged the health of turfgrasses on North American golf courses, resulting in considerable economic loss. The fungus responsible for the outbreaks, Colletotrichum cereale, has also been identified from numerous natural grasses and cereal crops, although disease symptoms are generally absent. Here we utilize phylogenetic and population genetic analyses to determine the role of ecosystem in the advancement of turfgrass anthracnose and assess whether natural grass and/or cereal inhabitants are implicated in the epidemics. Using a four-gene nucleotide data set to diagnose the limits of phylogenetic species and population boundaries, we find that the graminicolous Colletotrichum diverged from a common ancestor into distinct lineages correspondent with host physiology (C3 or C4 photosynthetic pathways). In the C4 lineage, which includes the important cereal pathogens Colletotrichum graminicola, C. sublineolum, C. falcatum, C. eleusines, C. caudatum and several novel species, host specialization predominates, with host-associated lineages corresponding to isolated sibling species. Although the C3 lineage--C. cereale--is comprised of one wide host-range species, it is divided into 10 highly specialized populations corresponding to ecosystem and/or host plant, along with a single generalist population spread across multiple habitat types. Extreme differentiation between the specialized C. cereale populations suggests that asymptomatic nonturfgrass hosts are unlikely reservoirs of infectious disease propagules, but gene flow between the generalist population and the specialized genotypes provides an indirect mechanism for genetic exchange between otherwise isolated populations and ecosystems.

Isolation of Highly Polymorphic Microsatellite Loci for a Species With a Large Genome Size: Sharp-Ribbed Salamander (Pleurodeles Waltl)

by Onno Diekmann

Permanent Genetic Resources Added to Molecular Ecology Resources Database 1 May 2009–31 July 2009

by Onno Diekmann

Teske, P.R., Zardi, G.I., McQuaid, C.D., Papadopoulos, I., Barker, N.P., Edkins, M.T. & Griffiths, C.L. (2007). Implications of life history on genetic structure and migration rates of southern African coastal invertebrates: planktonic, abbreviated and direct development.

by Nigel Barker

Marine Biology 152: 697-711.