Tracing past human male movements in northern/eastern Africa and western Eurasia: new clues from Y-chromosomal haplogroups E-M78 and J-M12

Detailed population data were obtained on the distribution of novel biallelic markers that finely dissect the human Y-chromosome haplogroup E-M78. Among 6,501 Y chromosomes sampled in 81 human populations worldwide, we found 517 E-M78 chromosomes and assigned them to 10 subhaplogroups. Eleven microsatellite loci were used to further evaluate subhaplogroup internal diversification. The geographic and quantitative analyses of haplogroup and microsatellite diversity is strongly suggestive of a northeastern African origin of E-M78, with a corridor for bidirectional migrations between northeastern and eastern Africa (at least 2 episodes between 23.9-17.3 ky and 18.0-5.9 ky ago), trans-Mediterranean migrations directly from northern Africa to Europe (mainly in the last 13.0 ky), and flow from northeastern Africa to western Asia between 20.0 and 6.8 ky ago. A single clade within E-M78 (E-V13) highlights a range expansion in the Bronze Age of southeastern Europe, which is also detected by haplogroup J-M12. Phylogeography pattern of molecular radiation and coalescence estimates for both haplogroups are similar and reveal that the genetic landscape of this region is, to a large extent, the consequence of a recent population growth in situ rather than the result of a mere flow of western Asian migrants in the early Neolithic. Our results not only provide a refinement of previous evolutionary hypotheses but also well-defined time frames for past human movements both in northern/eastern Africa and western Eurasia.     

Mating patterns in a hybrid zone of fire-bellied toads (Bombina): inferences from adult and full-sib genotypes

We present two novel methods to infer mating patterns from genetic data. They differ from existing statistical methods of parentage inference in that they apply to populations that deviate from Hardy-Weinberg and linkage equilibrium, and so are suited for the study of assortative mating in hybrid zones. The core data set consists of genotypes at several loci for a number of full-sib clutches of unknown parentage. Our inference is based throughout on estimates of allelic associations within and across loci, such as heterozygote deficit and pairwise linkage disequilibrium. In the first method, the most likely parents of a given clutch are determined from the genotypic distribution of the associated adult population, given an explicit model of nonrandom mating. This leads to estimates of the strength of assortment. The second approach is based solely on the offspring genotypes and relies on the fact that a linear relation exists between associations among the offspring and those in the population of breeding pairs. We apply both methods to a sample from the hybrid zone between the fire-bellied toads Bombina bombina and B. variegata (Anura: Disco glossidae) in Croatia. Consistently, both approaches provide no evidence for a departure from random mating, despite adequate statistical power. Instead, B. variegata-like individuals among the adults contributed disproportionately to the offspring cohort, consistent with their preference for the type of breeding habitat in which this study was conducted.     

Directional migration in the Hindu castes: inferences from mitochondrial, autosomal and Y-chromosomal data

Genetic, ethnographic, and historical evidence suggests that the Hindu castes have been highly endogamous for several thousand years and that, when movement between castes does occur, it typically consists of females joining castes of higher social status. However, little is known about migration rates in these populations or the extent to which migration occurs between caste groups of low, middle, and high social status. To investigate these aspects of migration, we analyzed the largest collection of genetic markers collected to date in Hindu caste populations. These data included 45 newly typed autosomal short tandem repeat polymorphisms (STRPs), 411 bp of mitochondrial DNA sequence, and 43 Y-chromosomal single-nucleotide polymorphisms that were assayed in more than 200 individuals of known caste status sampled in Andrah Pradesh, in South India. Application of recently developed likelihood-based analyses to this dataset enabled us to obtain genetically derived estimates of intercaste migration rates. STRPs indicated migration rates of 1–2% per generation between high-, middle-, and low-status caste groups. We also found support for the hypothesis that rates of gene flow differ between maternally and paternally inherited genes. Migration rates were substantially higher in maternally than in paternally inherited markers. In addition, while prevailing patterns of migration involved movement between castes of similar rank, paternally inherited markers in the low-status castes were most likely to move into high-status castes. Our findings support earlier evidence that the caste system has been a significant, long-term source of population structuring in South Indian Hindu populations, and that patterns of migration differ between males and females.     

mtDNA variation predicts population size in humans and reveals a major Southern Asian chapter in human prehistory

The relative timing and size of regional human population growth following our expansion from Africa remain unknown. Human mitochondrial DNA (mtDNA) diversity carries a legacy of our population history. Given a set of sequences, we can use coalescent theory to estimate past population size through time and draw inferences about human population history. However, recent work has challenged the validity of using mtDNA diversity to infer species population sizes. Here we use Bayesian coalescent inference methods, together with a global data set of 357 human mtDNA coding-region sequences, to infer human population sizes through time across 8 major geographic regions. Our estimates of relative population sizes show remarkable concordance with the contemporary regional distribution of humans across Africa, Eurasia, and the Americas, indicating that mtDNA diversity is a good predictor of population size in humans. Plots of population size through time show slow growth in sub-Saharan Africa beginning 143-193 kya, followed by a rapid expansion into Eurasia after the emergence of the first non-African mtDNA lineages 50-70 kya. Outside Africa, the earliest and fastest growth is inferred in Southern Asia approximately 52 kya, followed by a succession of growth phases in Northern and Central Asia (approximately 49 kya), Australia (approximately 48 kya), Europe (approximately 42 kya), the Middle East and North Africa (approximately 40 kya), New Guinea (approximately 39 kya), the Americas (approximately 18 kya), and a second expansion in Europe (approximately 10-15 kya). Comparisons of relative regional population sizes through time suggest that between approximately 45 and 20 kya most of humanity lived in Southern Asia. These findings not only support the use of mtDNA data for estimating human population size but also provide a unique picture of human prehistory and demonstrate the importance of Southern Asia to our recent evolutionary past.     

African origin and global distribution patterns: Evidence inferred from phylogenetic and biogeographical analyses of ectomycorrhizal fungal genus Strobilomyces

Aim

The ectomycorrhizal genus Strobilomyces is widely distributed throughout many parts of the world, but its origin, divergence and distribution patterns remain largely unresolved. In this study, we aim to explore the species diversity, distribution and evolutionary patterns of Strobilomyces on a global scale by establishing a general phylogenetic framework with extensive sampling.

Location

Africa, Australasia, East Asia, Europe, North America, Central America and Southeast Asia.

Methods

The genealogical concordance phylogenetic species recognition method was used to delimit phylogenetic species. Divergence times were estimated using a Bayesian uncorrelated lognormal relaxed molecular clock. The ancestral area and host of Strobilomyces were inferred via the programs rasp and mesquite . The change of diversification rate over time was estimated using Ape, Laser and Bammtools software packages.

Results

We recognize a novel African clade and 49 phylogenetic species with morphological evidence, including 18 new phylogenetic species and 23 previously described ones. Strobilomyces probably originated in Africa, in association with Detarioideae/Phyllanthaceae/Monotoideae during the early Eocene. The dispersal to Southeast Asia can be explained by Wolfe's “Boreotropical migration” hypothesis. East Asia, Australasia, Europe and North/Central America are primarily the recipients of immigrant taxa during the Oligocene or later. A rapid radiation implied by one diversification shift was inferred within Strobilomyces during the Miocene.

Main conclusions

An unexpected phylogenetic species diversity within Strobilomyces was uncovered. The highest diversity, resulting probably from a rapid radiation, was found in East Asia. Dispersal played an important role in the current distribution pattern of Strobilomyces. The Palaeotropical disjunction is explained by species dispersal from Africa to Southeast Asia through boreotropical forests during the early Eocene. Species from the Northern Hemisphere and Australasia are largely derived from immigrant ancestors from Southeast Asia.     

Mating system variation in Veronica (Plantaginaceae): inferences from pollen/ovule ratios and other reproductive traits

The pollen–ovule ratio (P/O) is commonly used to estimate the mode of sexual reproduction in flowering plants. In previous studies, a clear correspondence has been detected between this character and the degree of autogamy. We here investigate variation in this character and its expected correlates in the genus Veronica (Plantaginaceae). Pollen–ovule ratios of 45 species representing eleven percent of all the species in the genus were investigated and compared with results from crossing experiments from previous studies. In addition, multiple populations of 17 of the 45 studied species were sampled and a controlled‐environment experiment was conducted to evaluate the extent of intraspecific variation. Moreover, relationships between P/O and other primary and secondary reproductive characters of the Veronica flower were investigated in relation to a phylogenetic hypothesis in order to determine the phylogenetic constraints on reproductive characters. The differences in P/O among species correspond well to the diversity of mating systems in Veronica and correlate well with other floral characters such as corolla size. These characters together seem to allow a powerful and fast tool to infer mating systems. However, causes for intraspecific variation of P/O, such as different cytotypes, ecotypes or different growth conditions, need to be considered.     

牦牛的分类学地位及起源研究:mtDNA D-loop序列的分析

牦牛的起源与属级分类学地位至今仍然存在一定的争议。我们测定了家养牦牛和野生牦牛线粒体控制区(D-loop)序列,并以此构建牦牛和牛属、野牛属、水牛属以及非洲水牛属相关种的系统发育树。研究结果表明线粒体D-loop区与Cytb基因序列在构建牛族的系统发育具有同样重要的价值。系统发育关系显示野牛属的灭绝种草原野牛与现存种美洲野牛先聚合为一单系群,然后再和牦牛形成一单系分支,表明牦牛与野牛属的草原野牛、美洲野牛亲缘关系最近,具有最近的共同祖先,而与牛属的其它亚洲物种亲缘关系较远。因此,本研究不支持将牦牛独立为牦牛属———Poephagus,牛属与野牛属在分类上也应合并为一个属。基于上述研究结果和化石证据,我们进一步对牦牛起源的历史背景进行了讨论,认为牦牛与野牛属的分化是由于第四纪气候变化在欧亚大陆发生的,野牛通过白令陆桥进入北美;冰期结束后,由于欧亚大陆其它地区温度升高,牦牛只能局限分布在较为寒冷的青藏高原;而野牛属在北美先后分化为草原野牛和美洲野牛,前者可能是后者的直接祖先。     

分子人类学与现代人的起源*

1953年Watson & Crick 对于DNA双螺旋结构模型的提出及对其遗传机理的解释,标志着现代分子生物学的诞生。其后短短50年的时间里,分子生物学在各个学科之间广泛渗透,相互促进,不断深入和发展。在以研究人类的起源和进化为首要任务的人类学领域,由于现代分子生物学理论和方法的应用,诞生了分子人类学这一全新的结合型分支学科,为人类学的发展提供了科学可信的研究方法和具发展前景的研究方向。系统地介绍了分子人类学的发展历史、研究方法及原理;另外,结合分子人类学在古人类学研究中的应用,讨论了关于现代人起源的“非洲起源说”和“多地区连续演化说”。Abstract: Since Watson & Crick put forward the double-helix model of DNA structure and hereditary mechanism in 1953, it is generally accepted that this event marks the birth of modern molecular biology. This new field of biology has experienced a flourishing development in the past 50 years. On one hand, the development of molecular biology has been deeply influencing many relative fields; on the other hand, its own proceeding pace has been accelerated by the reaction from the other fields. Anthropology is one of the fields most deeply impacted by the theory and method of molecular biology. Most importantly, molecular anthropology was born as a result of combination of molecular biology, anthropology as well as paleoanthropology. This new branch provides reliable method and vital direction for paleoanthropology. This paper systematically reviews the history, principle and method of molecular anthropology. Two hypotheses on the origin of modern human, which include “out-of-African theory” and “theory of multiregional evolution” are also discussed for the purpose of showing how molecular anthropology is applied in paleoanthropology.     

When recent and evolutionary histories meet: deciphering temporal events from contemporary patterns of mtDNA from fishers (Martes pennanti) in north‐eastern North America

The current spatial distribution of genetic lineages across a region should reflect the complex interplay of both historical and contemporary processes. Postglacial expansion and recolonization in the distant past, in combination with more recent events with anthropogenic effects such as habitat fragmentation and overexploitation, can help shape the pattern of genetic structure observed in contemporary populations. In this study, we characterize the spatial distribution of mtDNA lineages for fisher (Martes pennanti) in north‐eastern North America. The history of fishers in this region is well understood and thus provides an opportunity to interpret patterns of genetic structure in the light of known historical (e.g. recolonization from glacial refugia) and contemporary events (e.g. reintroductions, fragmentation and natural recolonization). Our results indicate that fishers likely recolonized north‐eastern North America from a single Pleistocene refugium. Three genetically distinct remnant populations persisted through the population declines of the 1800s and served as sources for multiple reintroductions and natural recolonizations that have restored the fisher throughout north‐eastern North America. However, the spatial genetic structure of genetic lineages across the region still reflects the three remnant populations.     

Probing the combination of erlotinib hydrochloride,an anticancer drug,and human serum albumin: Spectroscopic,molecular docking,and molecular dynamic analyses

Human serum albumin (HSA) is a globular and monomeric protein in plasma that transports many drugs and compounds. Binding of some drugs to HSA can lead to changes in its stability and biological function. We investigated the binding interactions between erlotinib hydrochloride (Erlo) and HSA. Erlo is used to treat lung, pancreatic, and some other cancers. Experimental data showed that the fluorescence emission of the protein was quenched by Erlo using a static quenching mechanism. The calculation of the binding constant, K_b (1.57 × 10⁵ M⁻¹ at 300 K), confirmed the existence of a moderate binding interaction between Erlo and HSA. The interaction was enthalpy driven, spontaneous, and exothermic. The calculated thermodynamic parameters in agreement with simulation and molecular docking data showed that van der Waals and hydrogen bond forces played an important role in the interaction process. Molecular docking results indicated that Erlo has more affinity to bind to subdomain IIA (site I) of HSA. Molecular dynamics simulation analysis showed that the protein is stable in the presence of Erlo under simulation conditions.     

Single cell human genomic analyses: a way to refine the knowledge of cellular heterogeneity origins in individual subject

Single cell genomics performed on individual human subjects' tumors, neural tissues, and sperm samples revealed the existence of genetic heterogeneity arising through either mutations in exomes, deletions, recombinations, and duplications of DNA sequences, as well as aneuploidy. These genetic changes happen during cell cycles followed by cell division. The aim of this review is to strictly focus on single cell human genomics and intends to deliver information that can help to refine fundamental knowledge relating to genetic causes of cellular heterogeneity origins in both healthy and disease states. Allogenic heterogeneity as well as heterogeneity origins of cells possessing the same genome with different gene expression patterns is not the subject of this review. Future research still requires: a) improvement for complete and errorless DNA acquisition and sequencing of not only selected parts of the genome, and b) analyses of more samples that contain millions of cells. These data will deliver a more precise comparative representation of genetic diversity among single cells in an individual human subject. Consequently, we will be able to better distinguish between the role of genetic, versus epigenetic, and stochastic factors in the cellular diversity of over 30 trillion cells present in a human body.     

Biogeographical patterns of genetic differentiation in dung beetles of the genus Trypocopris (Coleoptera, Geotrupidae) inferred from mtDNA and AFLP analyses

Aim To examine the phylogeography and population structure of three dung beetle species of the genus Trypocopris (Coleoptera, Geotrupidae). We wanted to test whether genetic differences and genealogies among populations were in accordance with morphologically described subspecies and we aimed to establish times of divergence among subspecies to depict the appropriate temporal framework of their phylogeographical differentiation. We also wished to investigate the historical demographic events and the relative influences of gene flow and drift on the distribution of genetic variability of the different populations. Location Europe (mostly Italy). Methods We collected adult males from dung pats from 15 Italian localities over the period 2000–2002. For sequence analysis, some dried specimens from Albania, Croatia, Slovakia and Spain were also used. We applied cytochrome oxidase I mitochondrial DNA sequencing and the amplified fragment length polymorphism (AFLP) technique to determine whether phylogeographical patterns within the three species support the proposed hypotheses of subspecies designations, and to detect further structure among populations that might mediate diversification. Results and main conclusions The results show a high concordance between the distribution of mtDNA variation and the main morphological groups recognized as subspecies, which thus may represent independent evolutionary units. The degree of mitochondrial divergence suggests that speciation events occurred during the Pliocene, while diversification of the main subspecific lineages took place in the Pleistocene, from c. 0.3 to 1.5 Ma. Mitochondrial and nuclear data also reveal that there is phylogeographical structuring among populations within each of the main groups and that both contemporary and historical processes determined this pattern of genetic structure. Geographical populations form monophyletic clades in both phylogenetic and network reconstructions. Despite the high levels of intrapopulational diversity, F_ST values indicate moderate but significant genetic differentiation among populations, and a Bayesian clustering analysis of the AFLP data clearly separates the geographical populations. Nucleotide and gene diversity estimates reveal interspecific differences in the degree of diversification among populations that may be related to the different ecological requirements of the three species.     

Energy and the rate of evolution: inferences from plant rDNA substitution rates in the western Pacific

In this study, we compare rDNA substitution rates for a group of closely related plant species in the western Pacific that exist in different biomes. The results of this comparison indicate higher rates of substitution for species living in habitats with greater biologically available energy. We interpret that finding as potentially important in understanding evolution because of its implication that substitution rate may be a function of biologically available energy and its correlate, productivity. The relevance of this research is twofold. First, contrasting closely related species across different biomes allows for a comparison between rates of molecular evolution across different energetic/productivity regimes while controlling for phylogenetically influenced variation. Second, the research indicates some of the design parameters for future studies that are required to explore the importance of this relationship among different groups of related organisms. If higher rates of molecular evolution where there is greater available energy are found to be widespread this might bring an additional dimension to the understanding of macroevolutionary pattern and process.     

A journey through time: exploring temporal patterns amongst digitized plant specimens from Australia

Online access to species occurrence records has opened new windows into investigating biodiversity patterns across multiple scales. The value of these records for research depends on their spatial, temporal, and taxonomic quality. We assessed temporal patterns in records from the Australasian Virtual Herbarium, asking: (1) How temporally consistent has collecting been across Australia? (2) Which areas of Australia have the most reliable records, in terms of temporal consistency and inventory completeness? (3) Are there temporal trends in the completeness of attribute information associated with records? We undertook a multi-step filtering procedure, then estimated temporal consistency and inventory completeness for sampling units (SUs) of 50?km ×?50?km. We found temporal bias in collecting, with 80% of records collected over the period 1970–1999. South-eastern Australia, the Wet Tropics in north-east Queensland, and parts of Western Australia have received the most consistent sampling effort over time, whereas much of central Australia has had low temporal consistency. Of the SUs, 18% have relatively complete inventories with high temporal consistency in sampling. We also determined that 25% of digitized records had missing attribute information. By identifying areas with low reliability, we can limit erroneous inferences about distribution patterns and identify priority areas for future sampling.     

Non-random patterns in the Yellowstone ecosystem: inferences from mammalian body size, order and biogeographical affinity

Aim Our aim was to investigate how the environment, species characteristics and historical factors at the subcontinental scale affect patterns of diversity. We used the assembly of the Yellowstone biota over the past 10,000 years as a natural experiment for investigating the processes that generate a modern non‐volant mammal species pool. Location The data represent species from throughout North America with special attention to the non‐volant mammals of Yellowstone National Park, USA. Methods We used digitized range maps to determine biogeographical affinity for all non‐volant mammals in the Rocky Mountains, Deserts and Great Plains biogeographical regions of North America. This biogeographical affinity, along with taxonomic order and body size class, was used to test whether non‐random patterns exist in the assemblage of Yellowstone non‐volant mammals. These characteristics were also used to investigate the strength of non‐random processes, such as habitat or taxon filtering, on particular groups of species or individual species. Results Our results indicated that the Yellowstone fauna is composed of a non‐random subset of mammals from specific body size classes and with particular biogeographical affinities. Analyses by taxonomic order found significantly more Carnivora from the Rocky Mountains region and significantly fewer Rodentia from the Deserts region than expected from random assembly. Analyses using body size classes revealed deviations from expectations, including several significant differences between the frequency distribution of regional body sizes and the distribution of those species found within Yellowstone. Main conclusions Our novel approach explores processes affecting species pool assembly in the Yellowstone region and elsewhere, and particularly identifies unique properties of species that may contribute to non‐random assembly. Focusing on the mechanisms generating diversity, not just current diversity patterns, will assist the design of conservation strategies given future environmental change scenarios.     

Flap flexibility amongst plasmepsins I,II, III,IV, and V: Sequence,structural, and molecular dynamics analyses

Herein, for the first time, we comparatively report the opening and closing of apo plasmepsin I – V. Plasmepsins belong the aspartic protease family of enzymes, and are expressed during the various stages of the P. falciparum lifecycle, the species responsible for the most lethal and virulent malaria to infect humans. Plasmepsin I, II, IV and HAP degrade hemoglobin from infected red blood cells, whereas plasmepsin V transport proteins crucial to the survival of the malaria parasite across the endoplasmic reticulum. Flap‐structures covering the active site of aspartic proteases (such as HIV protease) are crucial to the conformational flexibility and dynamics of the protein, and ultimately control the binding landscape. The flap‐structure in plasmepsins is made up of a flip tip in the N‐terminal lying perpendicular to the active site, adjacent to the flexible loop region in the C‐terminal. Using molecular dynamics, we propose three parameters to better describe the opening and closing of the flap‐structure in apo plasmepsins. Namely, the distance, d₁, between the flap tip and the flexible region; the dihedral angle, ?, to account for the twisting motion; and the TriCα angle, θ₁. Simulations have shown that as the flap‐structure twists, the flap and flexible region move apart opening the active site, or move toward each other closing the active site. The data from our study indicate that of all the plasmepsins investigated in the present study, Plm IV and V display the highest conformational flexibility and are more dynamic structures versus Plm I, II, and HAP. Proteins 2015; 83:1693–1705. © 2015 Wiley Periodicals, Inc.     

Mating behavior and thermoregulation of the reindeer warble fly,Hypoderma tarandi L. (Diptera: Oestridae)

Hypoderma (=Oedemagena) tarandi L. (Diptera: Oestridae) is characterized by a mating strategy in which both sexes meet and mate at two types of distinct topographical landmarks. In the expansive, treeless vidda (= tundra-like) biome, mating places are unique, rocky areas located along rivers and streams or in rocky areas of drying river and stream beds. In wooded valleys below the vidda, flies mated at certain topographical areas along dirt road tracks/paths. Thermoregulatory activities of males occupying perches at mating places included selection of substratum at perch site, orientation of body to sun's rays, crouching, stilting, and flights into upper cooler air. On warm sunny days males perched for just 1–2 min before flying up into cooler air to promote cooling. Laboratory and field studies revealed that flies could not metabolically cool down when held at 25–38°C. Time spent at mating places depended on temperature, duration of sunshine, and wind velocity. Males were very aggressive in pursuing allHypoderma-sized objects that passed by them or that landed near them, but they did not defend specific perch sites. Males either pursued and caught females in flight, or they hopped onto females that landed near them. During 5 years, 74 males and 14 females were seen at mating places. Dissection of six females caught at mating places revealed them to be recently eclosed flies full of fat body and with all eggs intact; two not paired with males were non-inseminated. Three experimentally paired females remainedin copulo for 10, 13, and 19.5 min.