Effective population sizes and temporal stability of genetic structure in Rana pipiens, the northern leopard frog

Although studies of population genetic structure are very common, whether genetic structure is stable over time has been assessed for very few taxa. The question of stability over time is particularly interesting for frogs because it is not clear to what extent frogs exist in dynamic metapopulations with frequent extinction and recolonization, or in stable patches at equilibrium between drift and gene flow. In this study we collected tissue samples from the same five populations of leopard frogs, Rana pipiens, over a 22-30 year time interval (11-15 generations). Genetic structure among the populations was very stable, suggesting that these populations were not undergoing frequent extinction and colonization. We also estimated the effective size of each population from the change in allele frequencies over time. There exist few estimates of effective size for frog populations, but the data available suggest that ranid frogs may have much larger ratios of effective size (Ne) to census size (Nc) than toads (bufonidae). Our results indicate that R. pipiens populations have effective sizes on the order of hundreds to at most a few thousand frogs, and Ne/Nc ratios in the range of 0.1-1.0. These estimates of Ne/Nc are consistent with those estimated for other Rana species. Finally, we compared the results of three temporal methods for estimating Ne. Moment and pseudolikelihood methods that assume a closed population gave the most similar point estimates, although the moment estimates were consistently two to four times larger. Wang and Whitlock's new method that jointly estimates Ne and the rate of immigration into a population (m) gave much smaller estimates of Ne and implausibly large estimates of m. This method requires knowing allele frequencies in the source of immigrants, but was thought to be insensitive to inexact estimates. In our case the method may have failed because we did not know the true source of immigrants for each population. The method may be more sensitive to choice of source frequencies than was previously appreciated, and so should be used with caution if the most likely source of immigrants cannot be identified clearly.     

The conditional relationship between English language proficiency and earnings among US immigrants

Using the 2000 US census data for immigrants of twenty language groups resided in metropolitan areas, we test the hypothesis that the rate of returns (in earnings) to English proficiency is not constant but varies with the language environment (as defined by group size, segregation, linguistic heterogeneity and inequality) in which immigrants are embedded. Results from our hierarchical model indicate that while an increase in the size and segregation of the language group diminishes returns to English proficiency, a rise in linguistic heterogeneity and inequality in the metropolitan area has the opposite effects. This study expands the scope of the previous studies by identifying conditions under which returns to English proficiency among immigrants are modified by a set of contextual factors often overlooked.     

Unmodern Synthesis: Developmental Hierarchies and the Origin of Phenotypes

The question of whether the modern evolutionary synthesis requires an extension has recently become a topic of discussion, and a source of controversy. We suggest that this debate is, for the most part, not about the modern synthesis at all. Rather, it is about the extent to which genetic mechanisms can be regarded as the primary determinants of phenotypic characters. The modern synthesis has been associated with the idea that phenotypes are the result of gene products, while supporters of the extended synthesis have suggested that environmental factors, along with processes such as epigenetic inheritance, and niche construction play an important role in character formation. We argue that the methodology of the modern evolutionary synthesis has been enormously successful, but does not provide an accurate characterization of the origin of phenotypes. For its part, the extended synthesis has yet to be transformed into a testable theory, and accordingly, has yielded few results. We conclude by suggesting that the origin of phenotypes can only be understood by integrating findings from all levels of the organismal hierarchy. In most cases, parts and processes from a single level fail to accurately explain the presence of a given phenotypic trait.     

Augmenting superpopulation capture-recapture models with population assignment data

Summary Ecologists applying capture–recapture models to animal populations sometimes have access to additional information about individuals' populations of origin (e.g., information about genetics, stable isotopes, etc.). Tests that assign an individual's genotype to its most likely source population are increasingly used. Here we show how to augment a superpopulation capture–recapture model with such information. We consider a single superpopulation model without age structure, and split each entry probability into separate components due to births in situ and immigration. We show that it is possible to estimate these two probabilities separately. We first consider the case of perfect information about population of origin, where we can distinguish individuals born in situ from immigrants with certainty. Then we consider the more realistic case of imperfect information, where we use genetic or other information to assign probabilities to each individual's origin as in situ or outside the population. We use a resampling approach to impute the true population of origin from imperfect assignment information. The integration of data on population of origin with capture–recapture data allows us to determine the contributions of immigration and in situ reproduction to the growth of the population, an issue of importance to ecologists. We illustrate our new models with capture–recapture and genetic assignment data from a population of banner‐tailed kangaroo rats Dipodomys spectabilis in Arizona.     

与中国现代人起源问题有联系的分子生物学研究成果的讨论

本文简略介绍最近几年发表的与中国现代人起源有直接和间接关系的几篇分子生物学论文,结合中国的人类化石、旧石器、古哺乳动物学和亚洲西部的旧石器以及分子生物学研究的新资料,论证根据Y染色体一些基因的分析认为中国的古老人类被来自非洲的现代人完全替代的推论不能成立。古人类学的研究已经显示人类进化是十分复杂的过程,新的分子生物学论文也显示人类的分子进化比过去认识的远为复杂。在对新信息进行解释和推论时必须对这样的复杂性保持深刻清醒的认识,人类进化不可能既是这样又是那样,只有将各个有关学科得来的信息进行综合思考才可望使得根据这些信息得出的推论趋于协调,对人类进化的认识逐渐接近真实。     

Connectivity dominates larval replenishment in a coastal reef fish metapopulation

Direct estimates of larval retention and connectivity are essential to understand the structure and dynamics of marine metapopulations, and optimize the size and spacing of reserves within networks of marine-protected areas (MPAs). For coral reef fishes, while there are some empirical estimates of self-recruitment at isolated populations, exchange among sub-populations has been rarely quantified. Here, we used microsatellite DNA markers and a likelihood-based parentage analysis to assess the relative magnitude of self-recruitment and exchange among eight geographically distinct sub-populations of the panda clownfish Amphiprion polymnus along 30 km of coastline near Port Moresby, Papua New Guinea. In addition, we used an assignment/exclusion test to identify immigrants arriving from genetically distinct sources. Overall, 82 per cent of the juveniles were immigrants while 18 per cent were progeny of parents genotyped in our focal metapopulation. Of the immigrants, only 6 per cent were likely to be genetically distinct from the focal metapopulation, suggesting most of the connectivity is among sub-populations from a rather homogeneous genetic pool. Of the 18 per cent that were progeny of known adults, two-thirds dispersed among the eight sub-populations and only one-third settled back into natal sub-populations. Comparison of our data with previous studies suggested that variation in dispersal distances is likely to be influenced by the geographical setting and spacing of sub-populations.     

Dental perspectives on the population history of Southeast Asia

This article uses metric and nonmetric dental data to test the "two-layer" or immigration hypothesis whereby Southeast Asia was initially occupied by an "Australo-Melanesian" population that later underwent substantial genetic admixture with East Asian immigrants associated with the spread of agriculture from the Neolithic period onwards. We examined teeth from 4,002 individuals comprising 42 prehistoric and historic samples from East Asia, Southeast Asia, Australia, and Melanesia. For the odontometric analysis, dental size proportions were compared using factor analysis and Q-mode correlation coefficients, and overall tooth size was also compared between population samples. Nonmetric population affinities were estimated by Smith's distances, using the frequencies of 16 tooth traits. The results of both the metric and nonmetric analyses demonstrate close affinities between recent Australo-Melanesian samples and samples representing early Southeast Asia, such as the Early to Middle Holocene series from Vietnam, Malaysia, and Flores. In contrast, the dental characteristics of most modern Southeast Asians exhibit a mixture of traits associated with East Asians and Australo-Melanesians, suggesting that these populations were genetically influenced by immigrants from East Asia. East Asian metric and/or nonmetric traits are also found in some prehistoric samples from Southeast Asia such as Ban Kao (Thailand), implying that immigration probably began in the early Neolithic. Much clearer influence of East Asian immigration was found in Early Metal Age Vietnamese and Sulawesi samples. Although the results of this study are consistent with the immigration hypothesis, analysis of additional Neolithic samples is needed to determine the exact timing of population dispersals into Southeast Asia.     

The apple,the tree,and a space to grow in

The idea for the study presented in Spanish Legacies: the coming of age of the second generation was sparked by the series of unrests from immigrant youths in a number of cities across Europe. The discontent expressed by the young generation of immigrants presented a sharp indicator of how little is known about young people of foreign origin growing up as immigrant residents in Europe, despite their significant number (10 per cent in France, 13 per cent in Spain and 15 per cent in Ireland by 2010). The success or failure of immigrants’ integrational processes, considering cultural factors and language barriers as challenges experienced by immigrants, can have major political and social impact on the regions where they reside. It is these challenges that are investigated in depth, in this book.     

Contribution of Immigration to Adolescent Fertility in Spain Considering the Reproductive Pattern in the Country of Origin

Adolescent fertility displays a trend that does not follow—and even runs contrary to—the general temporal fertility pattern. Multiple factors determine this trend, including socioeconomic conditions and cultural patterns at both immigrants’ place of origin of and their destination. This article analyzes adolescent fertility in Spain with regard to country of maternal origin using records of deliveries (1980–2008) and information from countries with high immigration rates to Spain. After 1980, deliveries to adolescents diminished; after 1996, only Spanish-born adolescents continued this downward trend, but not immigrants. The factors responsible for these differences are diverse and related to the characteristics of the immigrants themselves, in addition to the situation of immigrants in the Spanish context.     

Using mitochondrial and nuclear DNA markers to reconstruct human evolution

Molecular genetic data have greatly improved our ability to test hypotheses about human evolution. During the past decade, a large amount of nuclear and mitochondrial data have been collected from diverse human populations. Taken together, these data indicate that modern humans are a relatively young species. African populations show the largest amount of genetic diversity, and they are the most genetically divergent population. Modern human populations expanded in size first on the African continent. These findings support a recent African origin of modern humans, but this conclusion should be tempered by the possible effects of factors such as gene flow, population size differences, and natural selection. BioEssays 20:126–136, 1998. © 1998 John Wiley & Sons, Inc.     

Immigration and the cost of ethnic subordination: the case of Israeli society

This study focuses on earnings disadvantages experienced by three ethnic groups of Jewish immigrants in Israel. Data were obtained from the 2011 Income Survey gathered by the Israel Central Bureau of Statistics. The findings reveal that when compared to Israeli-born, all ethnic groups are disadvantaged in earnings attainment in the first generation. The earnings disadvantages of immigrants as compared to Israeli-born decrease with the passage of time and become negligible in the second generation. To disentangle the impact on earnings penalty of ethnic origin from that of immigrant status, a procedure for decomposing mean differences between groups is introduced. The analysis reveals that earnings disadvantage among Ashkenazim and Soviet immigrants can be attributed to immigrant status but not to ethnicity. By contrast, earnings penalties among Sephardim immigrants can be attributed to both ethnicity and immigrant status. The implications of the long-lasting effect of ethnicity versus the short-term effect of immigrant status are discussed.     

Dissemination pathways of common bean (Phaseolus vulgaris,Fabaceae) deduced from phaseolin electrophoretic variability. I. The Americas

Dissemination pathways of common bean (Phaseolus vulgaris) cultivars from their areas of domestication to other parts of the Americas were determined using phaseolin type, as determined by 1-dimensional SDS/PAGE. Common bean cultivars of lowland South America exhibited approximately equal numbers of ‘S’ and ‘T’ phaseolin types. ‘S2019 cultivars of that region may have been introduced along a route starting in Middle America and leading into Colombia, Venezuela, and eventually Brazil. ‘T’ phaseolin cultivars in lowland South America may have been introduced directly from the Andes or indirectly by European immigrants. In the southwestern U.S.A., most of the cultivars showed an ‘S’ phaseolin, confirming the Middle American origin of these cultivars, as suggested previously by the archaeological record. In northeastern U.S.A. and Canada, the ‘T’and ‘C’ phaseolin types were more frequent than the ‘S’ phaseolin cultivars. While most of the former were possibly introduced into that region by European immigrants, most of the latter may have been introduced by the pre-Columbian Indian populations. Seed size analysis revealed that ‘T’ or ‘C’ phaseolin cultivars had significantly larger seeds than ‘S’ phaseolin cultivars, as had been observed previously in Middle America and the Andes. The phaseolin types of commercial seed types and of early northeastern U.S. cultivars are discussed.     

Analysis of features contributing to activity of the single-stranded origin of Bacillus plasmid pBAA1.

The features which contribute to the activity of the single-stranded origin of the Bacillus plasmid pBAA1 were investigated. This origin is contained on a DNA fragment greater than 116 but less than 191 bases in size. There is the potential to form three stem-loop structures within this fragment. Comparison of the sequence of this origin from pBAA1 with the sequence of a homologous fragment from the Bacillus thuringiensis plasmid pGI2 indicates that both the structure and the relative positioning of the predicted stem-loops are important for origin activity. Deletion analysis suggests that it is the structure of stem-loop III which is important, because it can be replaced by a nonrelated dyad element without significant loss of origin activity. Three sequence motifs are conserved between the origins from pBAA1 and pGI2. Mutation of motif 1 leads to attenuation of single-stranded origin activity. A second motif (motif 3) shares significant homology with a group of single-strand initiation (ssi) sites found on plasmids isolated from Escherichia coli, suggesting that it also contributes to single-stranded origin activity. Our results also indicate that RNA polymerase is utilized to synthesize the RNA primer at the pBAA1 single-stranded origin and that this origin can function in both Bacillus subtilis and Staphylococcus aureus.     

The Case for a Single‐Plastid Origin Revisited: Convergent Evolution in Organellar Gene Content

Three eukaryotic lineages generally are believed to have plastids that are primary in origin; that is, descended directly from a cyanobacterial endosymbiont. The recovery of these plastids as a monophyletic group in most molecular phylogenetic analyses, along with similarities in genome content and protein targeting mechanisms, have been cited as strong evidence in support of the hypothesis of a single endosymbiotic origin of all plastids. Although these data indeed are consistent with a single plastid origin, they also are consistent with the proposition of multiple endosymbiotic origins. Each hypothesis requires certain evolutionary assumptions in order to be reconciled with all existing data; at present, it is unclear which of these assumptions most likely reflect the historical process that gave rise to plastid diversity. Here we examine similarities in gene content among representatives of the three primary plastid lineages, using as a control the genome of a mitochondrion that almost certainly originated as an independent endosymbiotic association. To minimize metabolic constraints on gene retention we focus on two datasets, ribosomal protein and transfer RNA genes, neither of which is tied directly to specific organellar functions. Analyses of all possible pair‐wise comparisons among the three plastids and mitochondrion indicate that genomic similarities are most consistent with convergent evolution due to constraints on gene loss, rather than with hypothesized shared evolutionary histories. We find no evidence of phylogenetic signal in the pattern of gene loss overlying this convergence. In light of these results, we address other lines of evidence and arguments that have been raised in support of a single plastid origin.     

Inferring origins of migrating insects using isoscapes: a case study using the true armyworm,Mythimna unipuncta,in North America

1. Many important insect pests undertake seasonal migrations at continental scales in response to changes in resource quality and availability. The frequency and timing of these events could be influenced by the impact of climate change on the suitability of the different sites exploited throughout the year, yet, in many cases, little is known about the origin of seasonal populations, as tracking insect movements is extremely challenging due to their small body size. 2. The use of stable isotope measurements in insect tissues combined with the development of tissue‐specific ‘isoscapes’ of modelled geographic isotope patterns presents a potentially valuable but rarely used approach for obtaining such information on important pest species. In this paper it is illustrated how stable hydrogen isotope analyses (δ²H) in wing chitin of the true armyworm (Mythimna (Psuedaletia) unipuncta Haworth), a seasonal migrant, clearly delineated between 2016 spring immigrants and later locally produced moths in southern Ontario, Canada. 3. It is shown that adult moths captured in early fall in Texas were immigrants from farther north, the first direct confirmation of a southward return migration of this species. Stable carbon isotope (δ¹³C) measurements indicated that spring immigrants in Ontario and autumn immigrants in Texas were from exclusively C3 biomes. Stable nitrogen isotope (δ¹⁵N) measurements also provided information on the probability of individuals coming from agriculturally intensive (i.e. higher δ¹⁵N) sites. Finally, several recommendations are provided regarding future research that could improve the Bayesian assignment models and thus improve assignment accuracy.     

Autosomal STRs Provide Genetic Evidence for the Hypothesis That Tai People Originate from Southern China

Tai people are widely distributed in Thailand, Laos and southwestern China and are a large population of Southeast Asia. Although most anthropologists and historians agree that modern Tai people are from southwestern China and northern Thailand, the place from which they historically migrated remains controversial. Three popular hypotheses have been proposed: northern origin hypothesis, southern origin hypothesis or an indigenous origin. We compared the genetic relationships between the Tai in China and their “siblings” to test different hypotheses by analyzing 10 autosomal microsatellites. The genetic data of 916 samples from 19 populations were analyzed in this survey. The autosomal STR data from 15 of the 19 populations came from our previous study (Lin et al., 2010). 194 samples from four additional populations were genotyped in this study: Han (Yunnan), Dai (Dehong), Dai (Yuxi) and Mongolian. The results of genetic distance comparisons, genetic structure analyses and admixture analyses all indicate that populations from northern origin hypothesis have large genetic distances and are clearly differentiated from the Tai. The simulation-based ABC analysis also indicates this. The posterior probability of the northern origin hypothesis is just 0.04 [95%CI: (0.01–0.06)]. Conversely, genetic relationships were very close between the Tai and populations from southern origin or an indigenous origin hypothesis. Simulation-based ABC analyses were also used to distinguish the southern origin hypothesis from the indigenous origin hypothesis. The results indicate that the posterior probability of the southern origin hypothesis [0.640, 95%CI: (0.524–0.757)] is greater than that of the indigenous origin hypothesis [0.324, 95%CI: (0.211–0.438)]. Therefore, we propose that the genetic evidence does not support the hypothesis of northern origin. Our genetic data indicate that the southern origin hypothesis has higher probability than the other two hypotheses statistically, suggesting that the Tai people most likely originated from southern China.     

Participation of non‐English‐speaking‐background immigrants in work‐related training

This article uses representative data on a sample of Australian workers to examine whether non‐English‐speaking‐background [NESB] immigrants are disadvantaged in terms of access to, and participation in, employment‐related training. Results from the estimation of logit models explaining participation in various types of training indicate that NESB immigrant workers have much lower probabilities of receiving training, even after holding other individual and employment characteristics constant. Further, this differential was generally found to be most pronounced for those immigrants with English‐language difficulties. Decomposition of the training differential, however, suggests that part of the explanation for the lesser incidence of training among NESB immigrants may well lie in employer‐based discrimination.     

Differentials of Yayoi immigration to Japanas derived from dental metrics

A major influx of new people, today termed Yayoi, migrated from the East Asian continent into the Japanese archipelago during the Aeneolithic and Protohistoric periods and interbred with the preexisting Jomon people. This study classifies ancient and more modern Japanese into natives or immigrants using discriminant analysis based on dental measurements in order to reconstruct the initial impact of the immigrants and the temporal and geographical differentials of mixture with the preexisting people. The results suggest that the earliest immigrants diffused into central Japan, including the Kanto region. The proportion of immigrant origin in the protohistoric Kofun was less in eastern Japan (72%) as compared to western Japan (81%-90%). The proportion of the immigrants in the Kanto District decreased during the medieval period (63%) and increased again in the early modern Edo and later modern times (75%), which might indicate that the gene flow still was occurring from west to east even in these times. Assuming the estimated proportions of either group reflect the intermixture ratio, the recent Japanese people may be regarded as hybrid of the native and immigrant groups with the following approximate ratios: 1:3 for the Kanto Japanese, 2:3 for the Ryukyu Islanders and 7:3 for the Hokkaido Ainu. These estimations support the "dual structure model" formed by Hanihara (1991) for explaining the population history of Japan.     

Educational performance of native and immigrant children from various countries of origin

Mostly due to the lack of suitable data, cross-national research on the integration of migrant pupils is still scarce. We aim to fill this gap by addressing the question of the extent to which native and first- and second-generation migrants from various regions of origin, living in thirteen different countries of destination, differ in their scholastic ability. Using the PISA 2003 data, we focus primarily on the impact of origin and destination effects on the scholastic achievement of migrants.

The results indicate that family characteristics and origin and destination effects can offer a significant contribution to the explanation of difference in scholastic knowledge between natives and first- and second-generation migrants. However, certain primary origin and destination effects, as well as interactions between these and family characteristics, remain significant and substantive after controlling for family characteristics, suggesting serious integration problems in the case of migrants from a few regions of origin in some European countries of destination.     

The Influence of Kinship on Familiar Natal Migrant Rhesus Macaques (Macaca mulatta)

In most primate species, females remain in the natal group with kin while males disperse away from kin around the time of puberty. Philopatric females bias their social behavior toward familiar maternal and paternal kin in several species, but little is known about kin bias in the dispersing sex. Male dispersal is likely to be costly because males encounter an increased risk of predation and death, which might be reduced by dispersing together with kin and/or familiar males (individuals that were born and grew up in same natal group) or into a group containing kin and/or familiar males. Here we studied the influence of kinship on familiar natal migrant rhesus macaques (Macaca mulatta) on Cayo Santiago, Puerto Rico, by combining demographic, behavioral, and genetic data. Our data suggest that kinship influences spatial proximity between recent natal immigrants and males familiar to them. Immigrants were significantly nearer to more closely related familiar males than to more distantly related individuals. Within a familiar subgroup, natal migrants were significantly closer to maternal kin, followed by paternal kin, then non-kin, and finally to males related via both the maternal and paternal line. Spatial proximity between natal immigrants and familiar males did not decrease over time in the new group, suggesting that there is no decline in associations between these individuals within the first months of immigration. Overall, our results might indicate that kinship is important for the dispersing sex, at least during natal dispersal when kin are still available.