Francis X. Villablanca

Consequences of a Genetic Bottleneck in California Condors: A Mitochondrial DNA Perspective

Mary S. Adams et al. — Fri, 18 Nov 2011 14:48:47 PST

The California Condor (Gymnogyps californianus) has recently survived a severe population bottleneck. The entire population was reduced to 27 individuals in 1982. The number of genetic founders was even smaller. We obtained 482 base pairs of DNA sequence from the mitochondrial control region (CR) of all founder individuals that potentially represented unique maternal haplotypes. Four unique haplotypes were present in the genetic founders. One of these haplotypes is unique to Topatopa, a male brought into captivity in 1967, whose haplotype will not persist in the future population. Haplotype diversity (h) was reduced by 25% between the founder population and our census of the 2002 population. Nucleotide diversity (θ) did not vary significantly between the founders and the current population. Our results provide insights into condor genetics. First, where recessive deleterious alleles have been expressed in progeny (e.g., chondrodystrophy) the breeding pair shares the same mitochondrial haplotype. Second, we identifi ed the presence of a nuclear copy of the mitochondrial control region and provide condor specific primer sequences to preferentially amplify DNA of mitochondrial origin. Third, we confirm low levels of genetic diversity in the captive population as suggested by previous research. Forth, we question whether the low level of diversity is a consequence of the 20th century bottleneck, or if diversity has been historically low over a much longer time scale.

Spatial and Temporal Continuity of Kangaroo Rat Populations Shown by Sequencing Mitochondrial DNA from Museum Specimens

W. Kelley Thomas et al. — Mon, 14 Nov 2011 10:42:09 PST

The advent of direct sequencing via the polymerase chain reaction (PCR) has opened up the possibility of molecular studies on museum specimens. Here we analyze genetic variation in populations over time by applying PCR to DNA extracted from museum specimens sampled from populations of one species over the last 78 years. Included in this study were 43 museum specimens of the Panamint kangaroo ratDipodomys panamintinus from localities representing each of three geographically distinct subspecies. These specimens were originally collected and prepared as dried skins in 1911, 1917, or 1937. For each specimen, a 225-bp segment of the mitochondrial genome was sequenced. These mitochondrial DNA sequences were compared to those of 63 specimens collected at the same localities in 1988. The three subspecies were nearly completely distinct. Only 2 of the 106 individuals shared mitochondrial types between subspecies. For all three localities, the diversity levels were maintained between the two temporal samples. The concordance observed between the two temporally separate phylogenies supports the use of museum specimens for phylogenetic inference. This study demonstrates the accuracy and routine nature of the use of museum specimens in the analysis of mitochondrial sequence variation in natural populations and, importantly, that a temporal aspect can now be added to such studies.

Invasion genetics of the Mediterranean fruit fly: variation in multiple nuclear introns

F. X. Villablanca et al. — Mon, 14 Nov 2011 10:42:07 PST

Biological invasions generally start from low initial population sizes, leading to reduced genetic variation in nuclear and especially mitochondrial DNA. Consequently, genetic approaches for the study of invasion history and population structure are difficult. An extreme example is the Mediterranean fruit fly, Ceratitis capitata (Medfly), for which successive invasions during this century have resulted in a loss of 60% of ancestral genetic variation in isozymes and 75% of variation in mitochondrial DNA. Using Medflies as an example, we present a new approach to invasion genetics that measures DNA sequence variation within introns from multiple nuclear loci. These loci are so variable that even relatively recently founded Medfly populations within California and Hawaii retain ample genetic diversity. Invading populations have only lost 35% of the ancestral genetic variation. Intron variation will allow high-resolution genetic characterization of invading populations in both natural and managed systems, although non-equilibrium methods of analysis may be necessary if the genetic diversity represents sorting ancestral polymorphism.

Invasion genetics of New World medflies: testing alternative colonization scenarios

Andrew J. Bohonak et al. — Mon, 14 Nov 2011 10:42:06 PST

The Mediterranean fruit fly (Ceratitis capitata) is an invasive agricultural pest with a wide host range and a nearly global distribution. Efforts to forgo the medfly''s spread into the United States are dependent on an understanding of population dynamics in newly established populations elsewhere. To explore the potential influence of demographic and historical parameters in six medfly populations distributed from Mexico to Peru, we created population genetic null models using Monte Carlo simulations. Null expectations for genetic differentiation (F _ST) were compared with actual sequence variation from four highly polymorphic nuclear loci. Four colonization scenarios that were modeled led to unique genetic signatures that could be used to interpret empirical data. Unless current gene flow across Latin America was assumed to be very high, we could reject colonizations consisting of multiple introductions, each of low genetic diversity. Further, if simulated populations were small (N _e = 5 × 10² individuals per population), small invasions from a single source consistently produced F _ST values comparable to those currently observed in Latin America. In contrast, only large invasions from diverse sources were compatible with the observed data for large populations (N _e 5 × 10³). This study demonstrates that alternative population genetic hypotheses can be tested empirically even when departures from equilibrium are extreme, and that population genetic theory can be used to explore the processes that underlie biological invasions.

Dynamics of mitochondrial DNA evolution in animals: Amplification and sequencing with conserved primers

T. D. Kocher et al. — Mon, 14 Nov 2011 10:42:04 PST

With a standard set of primers directed toward conserved regions, we have used the polymerase chain reaction to amplify homologous segments of mtDNA from more than 100 animal species, including mammals, birds, amphibians, fishes, and some invertebrates. Amplification and direct sequencing were possible using unpurified mtDNA from nanogram samples of fresh specimens and microgram amounts of tissues preserved for months in alcohol or decades in the dry state. The bird and fish sequences evolve with the same strong bias toward transitions that holds for mammals. However, because the light strand of birds is deficient in thymine, thymine to cytosine transitions are less common than in other taxa. Amino acid replacement in a segment of the cytochrome b gene is faster in mammals and birds than in fishes and the pattern of replacements fits the structural hypothesis for cytochrome b. The unexpectedly wide taxonomic utility of these primers offers opportunities for phylogenetic and population research.

Disparate Rates of Molecular Evolution in Cospeciating Hosts and Parasites

M. S. Hafner et al. — Mon, 14 Nov 2011 10:42:02 PST

DNA sequences for the gene encoding mitochondrial cytochrome oxidase I in a group of rodents (pocket gophers) and their ectoparasites (chewing lice) provide evidence for cospeciation and reveal different rates of molecular evolution in the hosts and their parasites. The overall rate of nucleotide substitution (both silent and replacement changes) is approximately three times higher in lice, and the rate of synonymous substitution (based on analysis of fourfold degenerate sites) is approximately an order of magnitude greater in lice. The difference in synonymous substitution rate between lice and gophers correlates with a difference of similar magnitude in generation times.

Low genetic diversity in an endangered species: recent or historic pattern?

Marjorie D. Matocq et al. — Mon, 14 Nov 2011 10:42:01 PST

Examining patterns of genetic diversity has become an integral component of many management plans concerning endangered species, yet interpreting the processes underlying such patterns remains challenging. We demonstrate low genetic diversity in a critically endangered small mammal population. A common interpretation of this pattern would be that it is the result of a known, recent decline in this population. We test this interpretation and find it to be incorrect. Instead, by using museum voucher specimens, we show that the pattern of low genetic diversity is historical. This study demonstrates the importance of choosing appropriate reference groups by which to interpret modern levels of genetic diversity in endangered species. We conclude that analysis of archival specimens may be essential in cases where genetic diversity is driving conservation management decisions because it may allow us to distinguish the effects of low genetic diversity from the process of losing diversity. We recognize that this approach can be limited due to several sampling issues: archival material may not be available, statistical power needs to be evaluated, sample sizes and sequence lengths may be suboptimal due to intrinsic difficulties associated with amplification of degraded DNA. These issues are discussed and possible solutions identified.

Is population genetics mired in the past?

Andrew J. Bohonak et al. — Mon, 14 Nov 2011 10:41:59 PST

Spatial and Temporal Aspects of Populations Revealed by Mitochondrial DNA

Francis X. Villablanca — Mon, 14 Nov 2011 10:41:58 PST

The evolutionary analysis of DNA sequences bridges phylogenetics and population genetics. Ancient DNA (aDNA) alJows the study of extinct genotypes, populations, and species, as well as dichronic comparisons of extant populations and species. Thus a DNA forges an empirical link between history and two inherently historical fields of research. Fortunately, the conceptual frameworks of phylogenetics and population genetics can easily be extended to encompass advances being made in the study of aDNA.