Genetic mating system and population history of the endangered Western Yellow-breasted Chat (Icteria virens auricollis) in British Columbia, Canada

2011 ◽  
Vol 89 (10) ◽  
pp. 881-891 ◽  
Author(s):  
Carolina I. Miño ◽  
Ingrid L. Pollet ◽  
Christine A. Bishop ◽  
Michael A. Russello
Keyword(s):  
British Columbia ◽  
Mating System ◽  
Demographic History ◽  
Population Decline ◽  
Population History ◽  
Breeding Habitat ◽  
Neotropical Migrant ◽  
Extra Pair Paternity ◽  
Icteria Virens ◽  
Genetic Mating System

The Western Yellow-breasted Chat ( Icteria virens auricollis (Deppe, 1830)) is a Neotropical migrant, with a Canadian distribution restricted to breeding populations in southern British Columbia. Given its small population size and diminishing breeding habitat, Yellow-breasted Chats are federally endangered in Canada. We used genotypic data at eight microsatellite loci to assess genetic diversity, reconstruct population structure and demographic history, and characterize genetic mating system of Yellow-breasted Chats sampled across 60 nesting sites at five locations in the Okanagan Valley (n = 148). Microsatellite-based analyses indicated lack of significant genetic differentiation among breeding sites and no genetic evidence of population decline. Parentage assignments indicated moderate levels of extra-pair paternity, with 30.7% offspring not sired by attending males. Patterns of sibship among nestlings revealed 49.1% of the clutches were composed entirely of full-siblings, with half-siblings and unrelated nestlings present in some broods. These findings suggest that extra-pair paternity is common in Yellow-breasted Chats, similar to other avian species, and present the first evidence of conspecific brood parasitism in warblers. Our findings add to a growing body of research informing the need to establish a national park in the south Okanagan to preserve critical habitat and connect populations of species at risk.

scholarly journals An Integrated Framework for the Inference of Viral Population History From Reconstructed Genealogies

Genetics ◽  
2000 ◽  
Vol 155 (3) ◽  
pp. 1429-1437
Author(s):  
Oliver G Pybus ◽  
Andrew Rambaut ◽  
Paul H Harvey
Keyword(s):  
Maximum Likelihood ◽  
Sequence Data ◽  
Demographic History ◽  
Population History ◽  
Maximum Likelihood Estimates ◽  
Viral Population ◽  
True Parameter ◽  
Subtype B ◽  
Exponential Growth Model ◽  
Parameter Values

Abstract We describe a unified set of methods for the inference of demographic history using genealogies reconstructed from gene sequence data. We introduce the skyline plot, a graphical, nonparametric estimate of demographic history. We discuss both maximum-likelihood parameter estimation and demographic hypothesis testing. Simulations are carried out to investigate the statistical properties of maximum-likelihood estimates of demographic parameters. The simulations reveal that (i) the performance of exponential growth model estimates is determined by a simple function of the true parameter values and (ii) under some conditions, estimates from reconstructed trees perform as well as estimates from perfect trees. We apply our methods to HIV-1 sequence data and find strong evidence that subtypes A and B have different demographic histories. We also provide the first (albeit tentative) genetic evidence for a recent decrease in the growth rate of subtype B.

Phylogeographic structure and gene flow of Himalayan snowcock (Tetraogallus himalayensis)

2010 ◽  
Vol 60 (4) ◽  
pp. 449-465
Author(s):  
Wen Longying ◽  
Zhang Lixun ◽  
An Bei ◽  
Luo Huaxing ◽  
Liu Naifa ◽  
...  
Keyword(s):  
Demographic History ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Population Expansion ◽  
Population History ◽  
Tibet Plateau ◽  
Phylogeographic Structure ◽  
Mitochondrial Cytochrome B ◽  
History Of ◽  
Qinghai Tibet Plateau

AbstractWe have used phylogeographic methods to investigate the genetic structure and population history of the endangered Himalayan snowcock (Tetraogallus himalayensis) in northwestern China. The mitochondrial cytochrome b gene was sequenced of 102 individuals sampled throughout the distribution range. In total, we found 26 different haplotypes defined by 28 polymorphic sites. Phylogenetic analyses indicated that the samples were divided into two major haplogroups corresponding to one western and one eastern clade. The divergence time between these major clades was estimated to be approximately one million years. An analysis of molecular variance showed that 40% of the total genetic variability was found within local populations, 12% among populations within regional groups and 48% among groups. An analysis of the demographic history of the populations suggested that major expansions have occurred in the Himalayan snowcock populations and these correlate mainly with the first and the second largest glaciations during the Pleistocene. In addition, the data indicate that there was a population expansion of the Tianshan population during the uplift of the Qinghai-Tibet Plateau, approximately 2 million years ago.

scholarly journals Comparing maternal genetic variation across two millennia reveals the demographic history of an ancient human population in southwest Turkey

2016 ◽  
Vol 3 (2) ◽  
pp. 150250 ◽  
Author(s):  
Claudio Ottoni ◽  
Rita Rasteiro ◽  
Rinse Willet ◽  
Johan Claeys ◽  
Peter Talloen ◽  
...  
Keyword(s):  
Demographic History ◽  
Population Decline ◽  
Fifth Century ◽  
Seventh Century ◽  
Human Occupation ◽  
Dna Variation ◽  
Genetic Discontinuity ◽  
History Of ◽  
The City ◽  
Modern Sample

More than two decades of archaeological research at the site of Sagalassos, in southwest Turkey, resulted in the study of the former urban settlement in all its features. Originally settled in late Classical/early Hellenistic times, possibly from the later fifth century BCE onwards, the city of Sagalassos and its surrounding territory saw empires come and go. The Plague of Justinian in the sixth century CE, which is considered to have caused the death of up to a third of the population in Anatolia, and an earthquake in the seventh century CE, which is attested to have devastated many monuments in the city, may have severely affected the contemporary Sagalassos community. Human occupation continued, however, and Byzantine Sagalassos was eventually abandoned around 1200 CE. In order to investigate whether these historical events resulted in demographic changes across time, we compared the mitochondrial DNA variation of two population samples from Sagalassos (Roman and Middle Byzantine) and a modern sample from the nearby town of Ağlasun. Our analyses revealed no genetic discontinuity across two millennia in the region and Bayesian coalescence-based simulations indicated that a major population decline in the area coincided with the final abandonment of Sagalassos, rather than with the Plague of Justinian or the mentioned earthquake.

scholarly journals Population Dynamics in Pre-Modern China

2013 ◽  
Author(s):  
Zhongwei Zhao
Keyword(s):  
Economic Development ◽  
Population Growth ◽  
Chinese Population ◽  
Environmental Changes ◽  
Demographic History ◽  
Social Institutions ◽  
Population History ◽  
Chinese History ◽  
Population Changes ◽  
The Past

China constituted one of the earliest civilizations in the world. During most of the past two millennia, China was also one of the most advanced economies and the home of around a quarter of the world’s population. By the start of the first millennium, the Chinese population was already about sixty million. In the next two thousand years, China’s population growth and economic development significantly influenced the world’s population changes and history. Partly for these reasons, in the study of population and social history, China’s historical population growth, demographic regimes, marriage patterns, and household formation systems are frequently used as examples in the discussion of population changes, microsocial structure, and their relationships with natural resources and economic development in past times. Population changes were one of the key components of Chinese history. The size and density of the population, the rise and fall of fertility and mortality, and the increase and decrease of population movements were not only related to demographic factors such as age structure. They were also strongly affected by political and economic conditions, social institutions and cultural traditions, and natural and social environments. Therefore, studies of demographic history, those conducted recently in particular, often shed new light on economic, political, social, and environmental changes in the past. This bibliography, through reviewing major works published in Chinese and English, provides an introduction to China’s main historical population data sources, major research questions, and debates in the study of Chinese population history. It also introduces recent advances in Chinese historical demography and important research findings made by these developments.

scholarly journals Population structure and demographic history of the chukar partridge Alectoris chukar in China

2013 ◽  
Vol 59 (4) ◽  
pp. 458-474 ◽  
Author(s):  
Sen Song ◽  
Shijie Bao ◽  
Ying Wang ◽  
Xinkang Bao ◽  
Bei An ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
North America ◽  
Demographic History ◽  
Population Expansion ◽  
Northwest China ◽  
Population History ◽  
Extant Species ◽  
History Of ◽  
Chukar Partridge

Abstract Pleistocene climate fluctuations have shaped the patterns of genetic diversity observed in extant species. Although the effects of recent glacial cycles on genetic diversity have been well studied on species in Europe and North America, genetic legacy of species in the Pleistocene in north and northwest of China where glaciations was not synchronous with the ice sheet development in the Northern Hemisphere or or had little or no ice cover during the glaciations’ period, remains poorly understood. Here we used phylogeographic methods to investigate the genetic structure and population history of the chukar partridge Alec-toris chukar in north and northwest China. A 1,152 – 1,154 bp portion of the mtDNA CR were sequenced for all 279 specimens and a total number of 91 haplotypes were defined by 113 variable sites. High levels of gene flow were found and gene flow estimates were greater than 1 for most population pairs in our study. The AMOVA analysis showed that 81% and 16% of the total genetic variability was found within populations and among populations within groups, respectively. The demographic history of chukar was examined using neutrality tests and mismatch distribution analyses and results indicated Late Pleistocene population expansion. Results revealed that most populations of chukar experienced population expansion during 0.027 ? 0.06 Ma. These results are at odds with the results found in Europe and North America, where population expansions occurred after Last Glacial Maximum (LGM, 0.023 to 0.018 Ma). Our results are not consistent with the results from avian species of Tibetan Plateau, either, where species experienced population expansion following the retreat of the extensive glaciation period (0.5 to 0.175 Ma).

Monogamy with exceptions: Social and genetic mating system in a bird species with high paternal investment

Behaviour ◽  
2005 ◽  
Vol 142 (8) ◽  
pp. 1093-1114 ◽  
Author(s):  
Peter Pechacek ◽  
Klaus G. Michalek ◽  
Hans Winkler ◽  
Donald Blomqvist
Keyword(s):  
Mating System ◽  
Bird Species ◽  
Paternal Investment ◽  
Genetic Mating System

scholarly journals Applicability of the Mutation–Selection Balance Model to Population Genetics of Heterozygous Protein-Truncating Variants in Humans

2019 ◽  
Vol 36 (8) ◽  
pp. 1701-1710 ◽  
Author(s):  
Donate Weghorn ◽  
Daniel J Balick ◽  
Christopher Cassa ◽  
Jack A Kosmicki ◽  
Mark J Daly ◽  
...  
Keyword(s):  
Population Genetics ◽  
De Novo ◽  
Demographic History ◽  
Purifying Selection ◽  
Population History ◽  
Balance Model ◽  
Data Set ◽  
Stochastic Force ◽  
Drift Estimation ◽  
Human Genes

Abstract The fate of alleles in the human population is believed to be highly affected by the stochastic force of genetic drift. Estimation of the strength of natural selection in humans generally necessitates a careful modeling of drift including complex effects of the population history and structure. Protein-truncating variants (PTVs) are expected to evolve under strong purifying selection and to have a relatively high per-gene mutation rate. Thus, it is appealing to model the population genetics of PTVs under a simple deterministic mutation–selection balance, as has been proposed earlier (Cassa et al. 2017). Here, we investigated the limits of this approximation using both computer simulations and data-driven approaches. Our simulations rely on a model of demographic history estimated from 33,370 individual exomes of the Non-Finnish European subset of the ExAC data set (Lek et al. 2016). Additionally, we compared the African and European subset of the ExAC study and analyzed de novo PTVs. We show that the mutation–selection balance model is applicable to the majority of human genes, but not to genes under the weakest selection.

scholarly journals Do Some Northern Goshawk Nest Areas Consistently Fledge More Young Than Others?

The Condor ◽  
2002 ◽  
Vol 104 (2) ◽  
pp. 343-352
Author(s):  
Erica L. McClaren ◽  
Patricia L. Kennedy ◽  
Sarah R. Dewey
Keyword(s):  
British Columbia ◽  
New Mexico ◽  
Spatial Patterns ◽  
Vancouver Island ◽  
Breeding Habitat ◽  
Habitat Characteristics ◽  
Accipiter Gentilis ◽  
Uinta Mountains ◽  
Northern Goshawk ◽  
Jemez Mountains

Abstract In long-lived raptors, research suggests that some nest areas consistently fledge more young than others, with the majority of young in the population being produced by a few females. If this claim were true for Northern Goshawk (Accipiter gentilis) populations, it would benefit land managers to identify high-quality goshawk breeding habitat. We examined whether the number of young fledged varied spatially among Northern Goshawk nest areas within three study areas where long-term reproductive data from goshawks were available: (1) Vancouver Island, British Columbia; (2) Jemez Mountains, New Mexico; and (3) Uinta Mountains, Utah. A mixed-model ANOVA indicated there was minimal spatial variation in nest productivity among nest areas within the three study locations. Rather, nest areas exhibited high temporal variability in nest productivity within each study area. These results suggest that temporal patterns such as local weather and fluctuating prey populations influenced Northern Goshawk reproduction more than spatial patterns such as habitat characteristics. Nest productivity may inadequately reflect spatial patterns in goshawk reproduction and so it would be premature to assume that habitat quality for Northern Goshawks was equal among nest areas within these study areas. Future research should examine spatial variability among nest areas in adult and juvenile survival rates to gain a complete picture of population responses to habitat change. ¿Se Producen Consistentemente Más Volantones de Accipiter gentilis en Algunos Sitios de Anidación que en Otros? Resumen. Investigaciones en aves rapaces longevas sugieren que consistentemente más polluelos empluman en algunos sitios de anidación que en otros y que la mayoría de los juveniles en la población son producidos por unas pocas hembras. Si esto fuera cierto para poblaciones de Accipiter gentilis, ayudaría a las autoridades ambientales a identificar hábitat reproductivo de alta calidad para la especie. Evaluamos si el número de polluelos emplumados varió espacialmente entre sitios de anidación de A. gentilis dentro de tres áreas de estudio para las cuales había datos reproductivos de largo plazo disponibles: (1) Vancouver Island, British Columbia; (2) Jemez Mountains, New Mexico; y (3) Uinta Mountains, Utah. Un modelo mixto de análisis de varianza indicó que la variación espacial en la productividad de los nidos entre sitios de anidación dentro de las tres áreas de estudio fue mínima. En cambio, los sitios de anidación presentaron una alta variabilidad temporal en la productividad de los nidos dentro de cada área de estudio. Estos resultados sugieren que los patrones temporales como el clima y las fluctuaciones de las poblaciones de presas influencian la reproducción de A. gentilis más que los patrones espaciales como las características del hábitat. La productividad de los nidos puede reflejar inadecuadamente los patrones espaciales de la reproducción de A. gentilis, de modo que sería prematuro suponer que la calidad de hábitat fue igual entre los sitios de anidación dentro de las áreas de estudio. Para tener una perspectiva completa de la respuesta de las poblaciones a cambios en el ambiente, investigaciones futuras deberían examinar la variabilidad espacial entre sitios de anidación en las tasas de supervivencia de aves adultas y juveniles.

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