The deep population history of northern East Asia from the Late Pleistocene to the Holocene

1. Download : Download high-res image (291KB)
2. Download : Download full-size image

     

The population history of extant and extinct hyenas

We have analyzed partial DNA sequences of the mitochondrialcytochrome b gene from extant striped, brown, and spotted hyenasas well as from Pleistocene cave hyenas. Sequences of the Pleistocenecave hyenas from Eurasia and modern spotted hyenas from Africaare intermixed in phylogenetic analyses, questioning any taxonomicdelineation between the two groups. Contrary to cave hyenasin Eurasia, spotted hyenas in Africa show a phylogeographicpattern with little geographical overlap between two mitochondrialDNA (mtDNA) clades, suggesting two Pleistocene refugia in thenorth and south of Africa. Our results, furthermore, suggestthree waves of migration from Africa to Eurasia for spottedhyenas, around 3, 1, and 0.3 MYA. A recent emigration of stripedhyenas from Africa to Eurasia took place less than 0.1 MYA,resulting in a dramatic expansion of the geographical rangeof striped hyenas. In striped hyenas and within the geographicalrange of mtDNA clades in spotted hyenas, we found identicalsequences several thousand kilometers apart, indicating a highrate of migration during the Pleistocene as well as the Holocene.Both striped and brown hyenas show low amounts of genetic diversity,with the latter ones displaying just a single haplotype.     

Genetic diversity of endangered brown bear (Ursus arctos) populations at the crossroads of Europe, Asia and Africa

Aim  Middle East brown bears ( Ursus arctos syriacus Hemprich and Ehrenberg, 1828) are presently on the edge of extinction. However, little is known of their genetic diversity. This study investigates that question as well as that of Middle East brown bear relationships to surrounding populations of the species.
Location  Middle East region of south-western Asia.
Methods  We performed DNA analyses on 27 brown bear individuals. Twenty ancient bone samples (Late Pleistocene to 20th century) from natural populations and seven present-day samples obtained from captive individuals were analysed.
Results  Phylogenetic analyses of the mitochondrial sequences obtained from seven ancient specimens identify three distinct maternal clades, all unrelated to one recently described from North Africa. Brown bears from Iran exhibit striking diversity (three individuals, three haplotypes) and form a unique clade that cannot be linked to any extant one. Individuals from Syria belong to the Holarctic clade now observed in Eastern Europe, Turkey, Japan and North America. Specimens from Lebanon surprisingly appear as tightly linked to the clade of brown bears now in Western Europe. Moreover, we show that U. a. syriacus in captivity still harbour haplotypes closely linked to those found in ancient individuals.
Main conclusion  This study brings important new information on the genetic diversity of brown bear populations at the crossroads of Europe, Asia and Africa. It reveals a high level of diversity in Middle East brown bears and extends the historical distribution of the Western European clade to the East. Our analyses also suggest the value of a specific breeding programme for captive populations.     

Sixty years of anthropogenic pressure: a spatio-temporal genetic analysis of brown trout populations subject to stocking and population declines

Analyses of historical samples can provide invaluable information on changes to the genetic composition of natural populations resulting from human activities. Here, we analyse 21 microsatellite loci in historical (archived scales from 1927 to 1956) and contemporary samples of brown trout ( Salmo trutta ) from six neighbouring rivers in Denmark, to compare the genetic structure of wild populations before and after population declines and stocking with nonlocal strains of hatchery trout. We show that all populations have been strongly affected by stocking, with admixture proportions ranging from 14 to 64%. Historical population genetic structure was characterized by isolation by distance and by positive correlations between historical effective population sizes and habitat area within river systems. Contemporary population genetic structure still showed isolation by distance, but also reflected differences among populations in hatchery trout admixture proportions. Despite significant changes to the genetic composition within populations over time, dispersal rates among populations were roughly similar before and after stocking. We also assessed whether population declines or introgression by hatchery strain trout should be the most significant conservation concern in this system. Based on theoretical considerations, we argue that population declines have had limited negative effects for the persistence of adaptive variation, but admixture with hatchery trout may have resulted in reduced local adaptation. Collectively, our study demonstrates the usefulness of analysing historical samples for identifying the most important consequences of human activities on the genetic structure of wild populations.     

Using archaeogenomic and computational approaches to unravel the history of local adaptation in crops

Our understanding of the evolution of domestication has changed radically in the past 10 years, from a relatively simplistic rapid origin scenario to a protracted complex process in which plants adapted to the human environment. The adaptation of plants continued as the human environment changed with the expansion of agriculture from its centres of origin. Using archaeogenomics and computational models, we can observe genome evolution directly and understand how plants adapted to the human environment and the regional conditions to which agriculture expanded. We have applied various archaeogenomics approaches as exemplars to study local adaptation of barley to drought resistance at Qasr Ibrim, Egypt. We show the utility of DNA capture, ancient RNA, methylation patterns and DNA from charred remains of archaeobotanical samples from low latitudes where preservation conditions restrict ancient DNA research to within a Holocene timescale. The genomic level of analyses that is now possible, and the complexity of the evolutionary process of local adaptation means that plant studies are set to move to the genome level, and account for the interaction of genes under selection in systems-level approaches. This way we can understand how plants adapted during the expansion of agriculture across many latitudes with rapidity.     

Complex population history of two Anopheles dirus mosquito species in Southeast Asia suggests the influence of Pleistocene climate change rather than human-mediated effects

Anopheles dirus and Anopheles baimaii are closely related species which feed on primates, particularly humans, and transmit malaria in the tropical forests of mainland Southeast Asia. Here, we report an in-depth phylogeographic picture based on 269 individuals from 21 populations from mainland Southeast Asia. Analysis of 1537 bp of mtDNA sequence revealed that the population history of A. baimaii is far more complex than previously thought. An old expansion (pre-300 kyr BP) was inferred in northern India/Bangladesh with a wave of south-eastwards expansion arriving at the Thai border (ca 135-173 kyr BP) followed by leptokurtic dispersal very recently (ca 16 kyr BP) into peninsular Thailand. The long and complex population history of these anthropophilic species suggests their expansions are not in response to the relatively recent (ca 40 kyr BP) human expansions in mainland Southeast Asia but, rather, fit well with our understanding of Pleistocene climatic change there.     

古DNA技术在人类墓葬遗骸研究中的应用及进展

考古工作中得到的生物遗骸由于长期的风化,自然侵蚀等因素的影响,遗骸本身含有的古代生物的DNA的大部分会分解,使得对遗骸中的生物遗传信息研究变得非常困难.可将现代生物工程的PCR技术应用到考古工作中,该技术能够对残存的微量DNA进行大量的生物体外扩增,得到更多的古代生物的遗传信息,提高时遗骸种属鉴定的准确性.通过对出土的人类遗骸中微量DNA的扩增、测试和遗骸间DNA序列的对比,在计算机软件的帮助下与已知的人类DNA序列进行比较,能确定同一墓葬中不同遗骸的亲缘关系和该遗骸群体在整个人类进化体系中的位置.对这一试验过程的一些方法、技术、研究进展和目前仍然面临的一些问题作了介绍.     

Multilocus genotypes from Charles Darwin's finches: biodiversity lost since the voyage of the Beagle

Genetic analysis of museum specimens offers a direct window into a past that can predate the loss of extinct forms. We genotyped 18 Galápagos finches collected by Charles Darwin and companions during the voyage of the Beagle in 1835, and 22 specimens collected in 1901. Our goals were to determine if significant genetic diversity has been lost since the Beagle voyage and to determine the genetic source of specimens for which the collection locale was not recorded. Using ‘ancient’ DNA techniques, we quantified variation at 14 autosomal microsatellite loci. Assignment tests showed several museum specimens genetically matched recently field-sampled birds from their island of origin. Some were misclassified or were difficult to classify. Darwin''s exceptionally large ground finches (Geospiza magnirostris) from Floreana and San Cristóbal were genetically distinct from several other currently existing populations. Sharp-beaked ground finches (Geospiza difficilis) from Floreana and Isabela were also genetically distinct. These four populations are currently extinct, yet they were more genetically distinct from congeners than many other species of Darwin''s finches are from each other. We conclude that a significant amount of the finch biodiversity observed and collected by Darwin has been lost since the voyage of the Beagle.     

Dynamic elements of replication protein A at the crossroads of DNA replication,recombination, and repair

Abstract

The heterotrimeric eukaryotic Replication protein A (RPA) is a master regulator of numerous DNA metabolic processes. For a long time, it has been viewed as an inert protector of ssDNA and a platform for assembly of various genome maintenance and signaling machines. Later, the modular organization of the RPA DNA binding domains suggested a possibility for dynamic interaction with ssDNA. This modular organization has inspired several models for the RPA-ssDNA interaction that aimed to explain how RPA, the high-affinity ssDNA binding protein, is replaced by the downstream players in DNA replication, recombination, and repair that bind ssDNA with much lower affinity. Recent studies, and in particular single-molecule observations of RPA-ssDNA interactions, led to the development of a new model for the ssDNA handoff from RPA to a specific downstream factor where not only stability and structural rearrangements but also RPA conformational dynamics guide the ssDNA handoff. Here we will review the current knowledge of the RPA structure, its dynamic interaction with ssDNA, and how RPA conformational dynamics may be influenced by posttranslational modification and proteins that interact with RPA, as well as how RPA dynamics may be harnessed in cellular decision making.     

Ancient population genomics and the study of evolution

Recently, the study of ancient DNA (aDNA) has been greatly enhanced by the development of second-generation DNA sequencing technologies and targeted enrichment strategies. These developments have allowed the recovery of several complete ancient genomes, a result that would have been considered virtually impossible only a decade ago. Prior to these developments, aDNA research was largely focused on the recovery of short DNA sequences and their use in the study of phylogenetic relationships, molecular rates, species identification and population structure. However, it is now possible to sequence a large number of modern and ancient complete genomes from a single species and thereby study the genomic patterns of evolutionary change over time. Such a study would herald the beginnings of ancient population genomics and its use in the study of evolution. Species that are amenable to such large-scale studies warrant increased research effort. We report here progress on a population genomic study of the Adélie penguin (Pygoscelis adeliae). This species is ideally suited to ancient population genomic research because both modern and ancient samples are abundant in the permafrost conditions of Antarctica. This species will enable us to directly address many of the fundamental questions in ecology and evolution.     

Demographic history and population structure of the Antarctic silverfish Pleuragramma antarcticum

The Antarctic silverfish Pleuragramma antarcticum (Nototheniidae) is the most abundant pelagic fish inhabiting Antarctic waters. In this study we investigated, through partial sequencing of the D-loop mitochondrial region, samples collected at four different locations in the Southern Ocean, three in the Atlantic and one in the Pacific sector. Sampling was replicated in two different years at two locations. Sequence analysis showed a remarkably high polymorphism, with 110 haplotypes over the 256 investigated specimens, and about 80% of haplotypes occurring only once. Neutrality tests indicated that all samples were not at mutation-drift equilibrium, and suggested a past population expansion. This result was supported by the presence of a star-like topology in the D-loop gene tree, and by results of mismatch distribution. The start of the expansion was dated, using a specifically calibrated clock, between 111 and 126 thousand years ago. This value corresponds to the start of the cooling period that led to the last glaciation peak, and is in close agreement with a recently suggested range expansion for pelagic Antarctic ecosystems. Analysis of molecular variation indicated a small, though highly significant, value of differentiation between samples. This result, together with the lack of association between clades and geographical locations, indicates a weak population structure for the species.     

The impact of past climate change on genetic variation and population connectivity in the Icelandic arctic fox

Previous studies have suggested that the presence of sea ice is an important factor in facilitating migration and determining the degree of genetic isolation among contemporary arctic fox populations. Because the extent of sea ice is dependent upon global temperatures, periods of significant cooling would have had a major impact on fox population connectivity and genetic variation. We tested this hypothesis by extracting and sequencing mitochondrial control region sequences from 17 arctic foxes excavated from two late-ninth-century to twelfth-century AD archaeological sites in northeast Iceland, both of which predate the Little Ice Age (approx. sixteenth to nineteenth century). Despite the fact that five haplotypes have been observed in modern Icelandic foxes, a single haplotype was shared among all of the ancient individuals. Results from simulations within an approximate Bayesian computation framework suggest that the rapid increase in Icelandic arctic fox haplotype diversity can only be explained by sea-ice-mediated fox immigration facilitated by the Little Ice Age.     

Historical DNA reveals the demographic history of Atlantic cod (Gadus morhua) in medieval and early modern Iceland

Atlantic cod (Gadus morhua) vertebrae from archaeological sites were used to study the history of the Icelandic Atlantic cod population in the time period of 1500–1990. Specifically, we used coalescence modelling to estimate population size and fluctuations from the sequence diversity at the cytochrome b (cytb) and Pantophysin I (PanI) loci. The models are consistent with an expanding population during the warm medieval period, large historical effective population size (N_E), a marked bottleneck event at 1400–1500 and a decrease in N_E in early modern times. The model results are corroborated by the reduction of haplotype and nucleotide variation over time and pairwise population distance as a significant portion of nucleotide variation partitioned across the 1550 time mark. The mean age of the historical fished stock is high in medieval times with a truncation in age in early modern times. The population size crash coincides with a period of known cooling in the North Atlantic, and we conclude that the collapse may be related to climate or climate-induced ecosystem change.     

Human settlement history between Sunda and Sahul: a focus on East Timor (Timor-Leste) and the Pleistocenic mtDNA diversity

Background

Distinct, partly competing, “waves” have been proposed to explain human migration in(to) today’s Island Southeast Asia and Australia based on genetic (and other) evidence. The paucity of high quality and high resolution data has impeded insights so far. In this study, one of the first in a forensic environment, we used the Ion Torrent Personal Genome Machine (PGM) for generating complete mitogenome sequences via stand-alone massively parallel sequencing and describe a standard data validation practice.

Results

In this first representative investigation on the mitochondrial DNA (mtDNA) variation of East Timor (Timor-Leste) population including >300 individuals, we put special emphasis on the reconstruction of the initial settlement, in particular on the previously poorly resolved haplogroup P1, an indigenous lineage of the Southwest Pacific region. Our results suggest a colonization of southern Sahul (Australia) >37 kya, limited subsequent exchange, and a parallel incubation of initial settlers in northern Sahul (New Guinea) followed by westward migrations <28 kya.

Conclusions

The temporal proximity and possible coincidence of these latter dispersals, which encompassed autochthonous haplogroups, with the postulated “later” events of (South) East Asian origin pinpoints a highly dynamic migratory phase.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-014-1201-x) contains supplementary material, which is available to authorized users.     

Genetic population structure and contemporary dispersal patterns of a recent European invader, the Chinese mitten crab, Eriocheir sinensis

Genetic studies of recently established populations are challenging because the assumption of equilibrium underlying many analyses is likely to be violated. Using microsatellites, we investigated determinants of genetic structure and migration among invasive European-Chinese mitten crab populations, applying a combination of traditional population genetic analyses and nonequilibrium Bayesian methods. Consistent with their recent history, invasive populations showed much lower levels of genetic diversity than a native Chinese population, indicative of recent bottlenecks. Population differentiation was generally low but significant and especially pronounced among recently established populations. Significant differentiation among cohorts from the same geographical location (River Thames) suggests the low effective population size and associated strong genetic drift that would be anticipated from a very recent colonization. An isolation-by-distance pattern appears to be driven by an underlying correlation between geographical distance and population age, suggesting that cumulative homogenizing gene flow reduces founder bottleneck-associated genetic differentiation between longer-established populations. This hypothesis was supported by a coalescent analysis, which supported a drift + gene flow model as more likely than a model excluding gene flow. Furthermore, admixture analysis identified several recent migrants between the UK and Continental European population clusters. Admixture proportions were significantly predicted by the volume of shipping between sites, indicating that human-mediated transport remains a significant factor for dispersal of mitten crabs after the initial establishment of populations. Our study highlights the value of nonequilibrium methods for the study of invasive species, and also the importance of evaluating nonequilibrium explanations for isolation by distance patterns.     

Population prehistory of East Asia and the pacific as viewed from craniofacial morphology: The basic populations in East Asia,VII

Distance analyses were applied to 11 craniofacial measurements recorded in samples from East and Southeast Asia, Australia, Melanesia, Polynesia, and Micronesia for the purpose of assessing the biological affinities and possible origins of these populations. A clear separation between Australomelanesians and other populations from East and Southeast Asia and the Pacific is evident. The craniofacial variations suggest that the generalized Asian populations (Negritos, Dayaks, Lesser Sunda Islands, etc.) represent at least part of the morphological background of not only the majority of present Southeast Asians, but also the Neolithic Jomon people and their lineage in Japan, Polynesians, and western Micronesians. The original craniofacial features of Southeast Asians may have occurred as the result of convergent microevolution due to similar environmental conditions such as tropical rain forest. This supports the local-evolution hypothesis for modern Southeast Asian craniofacial features. © 1993 Wiley-Liss, Inc.     

The limits of mtDNA phylogeography: complex patterns of population history in a highly structured Iberian lizard are only revealed by the use of nuclear markers

Phylogeographic analyses based on the sole use of the mitochondrial DNA (mtDNA) molecule reveal only a small part of the evolutionary history of a species or a set of related species. In this study, we have combined the application of slow- and fast-evolving nuclear markers (proteins and microsatellites, respectively) together with the analysis of two-gene genealogies to further understand the history of the Iberian endemic Schreiber's green lizard, Lacerta schreiberi, a species for which a well established phylogeographical scenario is available. In sharp contrast with the observation of four divergent and almost allopatric mtDNA clades, our nuclear data revealed how two groups of populations diverged, persisted and began to admix along the mountains of the Iberian Central System. In addition, the combination of mtDNA and nuclear data showed how the core area of the species distribution responded to ice ages, first by relatively old processes of population expansion to the south followed by episodes of contraction that are at the origin of present-day isolates, and more recently by a postglacial expansion to the Iberian Northwest where new habitats were made available after climatic amelioration. Taken together with recently published results for a variety of other organisms, our results suggest that complex processes of fragmentation, expansion and admixture can only be properly addressed through the use of several and complementary types of molecular markers. Finally, we also suggest that southern European refugia are both hotspots and melting pots of genetic diversity.     

Genetic discontinuity, breeding-system change and population history of Arabis alpina in the Italian Peninsula and adjacent Alps

Arabis alpina is a widespread plant of European arctic and alpine environments and belongs to the same family as Arabidopsis thaliana. It grows in all major mountain ranges within the Italian glacial refugia and populations were sampled over a 1300 km transect from Sicily to the Alps. Diversity was studied in nuclear and chloroplast genome markers, combining phylogeographical and population genetic approaches. Alpine populations had significantly lower levels of nuclear genetic variation compared to those in the Italian Peninsula, and this is associated with a pronounced change in within-population inbreeding. Alpine populations were significantly inbred (F(IS) = 0.553), possibly reflecting a change to the self-incompatibility system during leading edge colonization. The Italian Peninsula populations were approaching Hardy-Weinberg equilibrium (outbreeding, F(IS) = 0.076) and genetic variation was highly structured, consistent with independent local 'refugia within refugia' and the fragmentation of an established population by Quaternary climate oscillations. There is very little evidence of genetic exchange between the Alps and the Italian Peninsula main distribution ranges. The Alps functioned as a glacial sink for A. alpina, while the Italian Peninsula remains a distinct and separate long-term refugium. Comparative analysis indicated that inbreeding populations probably recolonized the Alps twice: (i) during a recent postglacial colonization of the western Alps from a Maritime Alps refugium; and (ii) separately into the central Alps from a source outside the sampling range. The pronounced geographical structure and inbreeding discontinuities are significant for the future development of A. alpina as a model species.