Yvonne L. Chan

Serial SimCoal: A population genetics model for data from multiple populations and points in time

UNLABELLED We present Serial SimCoal, a program that models population genetic data from multiple time points, as with ancient DNA data. An extension of SIMCOAL, it also allows simultaneous modeling of complex demographic histories, and migration between multiple populations. Further, we incorporate a statistical package to calculate relevant summary statistics, which, for the first time allows users to investigate the statistical power provided by, conduct hypothesis-testing with, and explore sample size limitations of ancient DNA data. AVAILABILITY Source code and Windows/Mac executables at http://www.stanford.edu/group/hadlylab/ssc.html CONTACT senka@stanford.edu.

Genetic Response to Climatic Change: Insights from Ancient DNA and Phylochronology

Understanding how climatic change impacts biological diversity is critical to conservation. Yet despite demonstrated effects of climatic perturbation on geographic ranges and population persistence, surprisingly little is known of the genetic response of species. Even less is known over ecologically long time scales pertinent to understanding the interplay between microevolution and environmental change. Here, we present a study of population variation by directly tracking genetic change and population size in two geographically widespread mammal species (Microtus montanus and Thomomys talpoides) during late-Holocene climatic change. We use ancient DNA to compare two independent estimates of population size (ecological and genetic) and corroborate our results with gene diversity and serial coalescent simulations. Our data and analyses indicate that, with population size decreasing at times of climatic change, some species will exhibit declining gene diversity as expected from simple population genetic models, whereas others will not. While our results could be consistent with selection, independent lines of evidence implicate differences in gene flow, which depends on the life history strategy of species.

Bayesian estimation of the timing and severity of a population bottleneck from ancient DNA.

In this first application of the approximate Bayesian computation approach using the serial coalescent, we demonstrated the estimation of historical demographic parameters from ancient DNA. We estimated the timing and severity of a population bottleneck in an endemic subterranean rodent, Ctenomys sociabilis, over the last 10,000 y from two cave sites in northern Patagonia, Argentina. Understanding population bottlenecks is important in both conservation and evolutionary biology. Conservation implications include the maintenance of genetic variation, inbreeding, fixation of mildly deleterious alleles, and loss of adaptive potential. Evolutionary processes are impacted because of the influence of small populations in founder effects and speciation. We found a decrease from a female effective population size of 95,231 to less than 300 females at 2,890 y before present: a 99.7% decline. Our study demonstrates the persistence of a species depauperate in genetic diversity for at least 2,000 y and has implications for modes of speciation in the incredibly diverse rodent genus Ctenomys. Our approach shows promise for determining demographic parameters for other species with ancient and historic samples and demonstrates the power of such an approach using ancient DNA.

SUBSPECIFIC DIFFERENTIATION AND CONSERVATION OF SONG SPARROWS (MELOSPIZA MELODIA) IN THE SAN FRANCISCO BAY REGION INFERRED BY MICROSATELLITE LOCI ANALYSIS

Abstract We examined genetic population structure of five putative subspecies of Song Sparrows (Melospiza melodia) in the San Francisco Bay region (M. m. samuelis, M. m. maxillaris, M. m. pusillula, M. m. gouldii, and M. m. heermanni) at nine microsatellite loci to assist the development of Song Sparrow conservation and management strategies. We sampled nine populations from five putative subspecies and found low estimates of differentiation between populations within subspecies and between. Despite low estimates of divergence, genetic structure at the subspecies level was indicated by the larger amount of variance accounted for by subspecies than populations. We propose that a management unit encompassing the range of M. m. pusillula be given priority for conservation on the basis of the extent of genetic divergence shown by Cavalli-Sforza and Edwards chord distance, and the topology of an unweighted pair group cluster analysis supported by 100% of bootstrap replicates across loci. Although M. m. samuelis and M. m. maxillaris appear undifferentiated from M. m. heermanni, it remains possible that adaptive differences between those types were not identified with neutral loci.

ANCIENT DNA EVIDENCE OF PROLONGED POPULATION PERSISTENCE WITH NEGLIGIBLE GENETIC DIVERSITY IN AN ENDEMIC TUCO-TUCO (CTENOMYS SOCIABILIS)

Abstract We traced a population of Ctenomys sociabilis, a highly endemic South American tuco-tuco, through 1,000 years to assess its response to climatic change and recent human disturbance. Samples were obtained from a late-Holocene raptor roost in Parque Nacional Nahuel Huapi, Argentina, which produced a diverse and abundant rodent fauna, with >10 genera extending from the present to 950 ± 50 years ago (CAMS-45936). The site (Estancia Nahuel Huapi locality 1) was located near the center of the present geographic range of C. sociabilis, which occurs throughout 8 of 9 stratigraphic levels in the site. To examine genetic structure through time, we extracted ancient DNA from 16 teeth at those levels and from 1 modern tooth at the surface for a total of 17 specimens. Cytochrome-b sequences from ancient and modern specimens were compared with a modern tuco-tuco sequence from the extant local population. Our results show that of those 17 specimens, all but 1 had identical sequences. Further, these sequences were identical to a representative of the modern population. Thus, that population has remained genetically identical for at least 1,000 years in the face of climatic change, human disturbance, and proximity of other tuco-tuco species (C. haigi, C. maulinus) with adjacent geographic distributions. Our findings indicate that a population bottleneck contributing to low genetic diversity of C. sociabilis occurred before 1,000 years ago and that late-Holocene climatic change occurred without a corresponding impact on the genetic diversity of this species.

The contribution of island populations to in situ genetic conservation

Genetic variation is often lower within island populations, however islands may also harbor divergent genetic variation. The likelihood that insular populations are genetically diverse or divergent should be influenced by island size and isolation. We tested this assumption by comparing patterns of genetic variation across all major island song sparrow populations along the Pacific North American coast. Allelic richness was moderately lowered even on islands which are close to large, potential sources. The most significant differences in allelic richness occurred on very small or highly remote islands. Gene diversity was significantly lower only on remote or very small islands. We found that island populations contribute to regional genetic variation through both the amount of genetic variation and the uniqueness of that variation. The partitioning of this contribution was associated with the size and isolation of the island populations.

The effects of contemporary processes in maintaining the genetic structure of western song sparrows (Melospiza melodia)

Historic events and contemporary processes work in concert to create and maintain geographically partitioned variation and are instrumental in the generation of biodiversity. We sought to gain a better understanding of how contemporary processes such as movement and isolation influence the genetic structure of widely distributed vagile species such as birds. Song sparrows (Melospiza melodia) in western North America provide a natural system for examining the genetics of populations that have different patterns of geographic isolation and migratory behavior. We examined the population genetics of 576 song sparrows from 23 populations using seven microsatellite loci to assess genetic differentiation among populations and to estimate the effects of drift and immigration (gene flow) on each population. Sedentary, isolated populations were characterized by low levels of immigration and high levels of genetic drift, whereas those populations less isolated displayed signals of high gene flow and little differentiation from other populations. Contemporary dispersal rates from migratory populations, estimated by assignment test, were higher and occurred over larger distances than dispersal from sedentary populations but were also probably too low to counter the effects of drift in most populations. We suggest that geographic isolation and limited gene flow facilitated by migratory behavior are responsible for maintaining observed levels of differentiation among Pacific coastal song sparrow populations.

Concordant and Discordant Signals Between Genetic Data and Described Subspecies of Pacific Coast Song Sparrows

Abstract Song Sparrows (Melospiza melodia) provide one of North Americas best examples of geographic variation in phenotype, with approximately 26 described subspecies recognized. However, researchers have found inconsistent signals when making comparisons between subspecies and genetic markers. We examined seven microsatellite loci from 576 Song Sparrows of 23 western North American populations representing 13 recognized subspecies. We assessed the level of concordance between microsatellite genotypes and subspecies. We found that in some, but not all, instances neutral genetic structure corresponded to recognized phenotypic structure. However, some populations not currently recognized as subspecies were found to be genetically differentiated from all other populations that are considered to be the same subspecies. We suggest that a combination of phenotypic characters, behavioral traits, and multiple loci be used when assessing geographic variation in birds, and that sampling should be conducted in more than one location within broadly distributed subspecies.

Genetic variation over 10 000 years in Ctenomys: comparative phylochronology provides a temporal perspective on rarity, environmental change and demography

An understanding of how ecological traits influence past species response to environmental change can aid our future predictions of species persistence. We used ancient DNA and serial coalescent modelling in a hypothesis‐testing framework to reveal differences in temporal genetic variation over 10 000 years for two species of subterranean rodents that currently differ in rarity (abundance, range size and habitat specificity) and mating system, but that reside in the same volcanically active region. Comparative phylochronologic analyses indicated little genetic change and suggest genetic stability in the solitary widespread Ctenomys haigi over thousands of years. In contrast, we found a pattern of haplotypic turnover in the rare and currently endangered Ctenomys sociabilis. Serial coalescent modelling indicated that the best‐fit models of microevolutionary change included gene flow between isolated populations for this species. Although C. haigi and C. sociabilis are congeners that share many life history traits, they have behavioural, habitat‐preference and population‐size differences that may have resulted in contrasting patterns of temporal variation during periods of environmental change.

Archaeological evidence of validity of fish populations on unexploited reefs as proxy targets for modern populations.

Reef-fish management and conservation is hindered by a lack of information on fish populations prior to large-scale contemporary human impacts. As a result, relatively pristine sites are often used as conservation baselines for populations near sites affected by humans. This space-for-time approach can only be validated by sampling assemblages through time. We used archaeological remains to evaluate whether the remote, uninhabited Northwestern Hawaiian Islands (NWHI) might provide a reasonable proxy for a lightly exploited baseline in the Main Hawaiian Islands (MHI). We used molecular and morphological techniques to describe the taxonomic and size composition of the scarine parrotfish catches present in 2 archaeological assemblages from the MHI, compared metrics of these catches with modern estimates of reproductive parameters to evaluate whether catches represented by the archaeological material were consistent with sustainable fishing, and evaluated overlap between size structures represented by the archaeological material and modern survey data from the MHI and the NWHI to assess whether a space-for-time substitution is reasonable. The parrotfish catches represented by archaeological remains were consistent with sustainable fishing because they were dominated by large, mature individuals whose average size remained stable from prehistoric (AD approximately 1400-1700) through historic (AD 1700-1960) periods. The ancient catches were unlike populations in the MHI today. Overlap between the size structure of ancient MHI catches and modern survey data from the NWHI or the MHI was an order of magnitude greater for the NWHI comparison, a result that supports the validity of using the NWHI parrotfish data as a proxy for the MHI before accelerated, heavy human impacts in modern times.