Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Reconstructing the origins and dispersal of the Polynesian bottle gourd (Lagenaria siceraria)

The origin of the Polynesian bottle gourd (Lagenaria siceraria), an important crop species in prehistoric Polynesia, has remained elusive. Most recently, a South American origin has been favored as the bottle gourd could have been introduced from this continent with the sweet potato by Polynesian voyagers around A.D. 1,000. To test the hypothesis of an American origin for the Polynesian bottle gourd, we developed seven markers specific to bottle gourd (two chloroplast and five nuclear). The nuclear markers were developed using a new technique where polymorphic inter simple sequence repeat (ISSR) markers are converted into single-locus polymerase chain reaction and sequencing markers--an approach that will be useful for developing markers in other taxa. All seven markers were sequenced in 36 cultivars of bottle gourd from Asia, the Americas, and Polynesia. The results support a dual origin for the Polynesian bottle gourd: the chloroplast markers are exclusively of Asian origin, but the nuclear markers show alleles originating in both the Americas and Asia. Because hybridization of Polynesian bottle gourds with post-European introductions cannot be excluded, ancient DNA from archaeological material will be useful for further elucidating the prehistoric movements of this species in Polynesia. This work has implications not only for the dispersal of the Polynesian bottle gourd but also for the domestication and dispersal of the species as a whole.     

薇甘菊不同时期的营养繁殖及其生物量分配特征

薇甘菊是世界热带、亚热带地区最具危险性的外来植物之一,较强的无性生长与繁殖是其种群快速建立和扩散的主要原因。该实验采用生长期(40d、30d、20d、10d)和养分(1倍Hoagland’s营养液、清水+土壤、清水)二因子设计,探讨薇甘菊根、茎、叶的营养生长与繁殖和生物量分配特征。结果显示:(1)生长期对薇甘菊茎的存活率和养分对薇甘菊茎的净增生物量比例具有极显著影响(P<0.01),但对其他指标影响均不显著(P>0.05);生长期和养分互作除对薇甘菊根的存活率和茎的分枝数影响不显著外,对其他指标影响均达到极显著(P<0.01)。(2)所有薇甘菊根处理中的存活率为0,茎的分枝数在各处理之间的差异不显著。(3)随着生长期和养分增加,薇甘菊茎和叶的存活率及其生物量逐渐提高,且茎的分枝长、叶的分枝长及其分枝数逐渐提高,但中等养分更有利于提高生长期较短的薇甘菊叶的存活率、分枝长、分枝数及生物量。研究表明,薇甘菊不同营养器官在不同生长期和养分条件具有不同的存活情况以及形态可塑性和生物量分配特征。     

mtDNA variation of aboriginal Siberians reveals distinct genetic affinities with Native Americans.

The mtDNA variation of 411 individuals from 10 aboriginal Siberian populations was analyzed in an effort to delineate the relationships between Siberian and Native American populations. All mtDNAs were characterized by PCR amplification and restriction analysis, and a subset of them was characterized by control region sequencing. The resulting data were then compiled with previous mtDNA data from Native Americans and Asians and were used for phylogenetic analyses and sequence divergence estimations. Aboriginal Siberian populations exhibited mtDNAs from three (A, C, and D) of the four haplogroups observed in Native Americans. However, none of the Siberian populations showed mtDNAs from the fourth haplogroup, group B. The presence of group B deletion haplotypes in East Asian and Native American populations but their absence in Siberians raises the possibility that haplogroup B could represent a migratory event distinct from the one(s) which brought group A, C, and D mtDNAs to the Americas. Our findings support the hypothesis that the first humans to move from Siberia to the Americas carried with them a limited number of founding mtDNAs and that the initial migration occurred between 17,000-34,000 years before present.     

Reviewing the history of HIV-1: spread of subtype B in the Americas

The dispersal of HIV-1 subtype B (HIV-1B) is a reflection of the movement of human populations in response to social, political, and geographical issues. The initial dissemination of HIV-1B outside Africa seems to have included the passive involvement of human populations from the Caribbean in spreading the virus to the United States. However, the exact pathways taken during the establishment of the pandemic in the Americas remain unclear. Here, we propose a geographical scenario for the dissemination of HIV-1B in the Americas, based on phylogenetic and genetic statistical analyses of 313 available sequences of the pol gene from 27 countries. Maximum likelihood and bayesian inference methods were used to explore the phylogenetic relationships between HIV-1B sequences, and molecular variance estimates were analyzed to infer the genetic structure of the viral population. We found that the initial dissemination and subsequent spread of subtype B in the Americas occurred via a single introduction event in the Caribbean around 1964 (1950-1967). Phylogenetic trees present evidence of several primary outbreaks in countries in South America, directly seeded by the Caribbean epidemic. Cuba is an exception insofar as its epidemic seems to have been introduced from South America. One clade comprising isolates from different countries emerged in the most-derived branches, reflecting the intense circulation of the virus throughout the American continents. Statistical analysis supports the genetic compartmentalization of the virus among the Americas, with a close relationship between the South American and Caribbean epidemics. These findings reflect the complex establishment of the HIV-1B pandemic and contribute to our understanding between the migration process of human populations and virus diffusion.     

A Review of Coralilla (<Emphasis Type="Italic">Antigonon leptopus</Emphasis>): An Invasive and Popular Urban Bush Medicine in Jamaica

Antigonon leptopus is a smothering, habitat-transforming vine with showy pink flowers. Originating in Mexico, it is now widespread or invasive on tropical islands around the world, including the West Indies, as a consequence of active human dispersal and disturbance. Using mixed methods research, we assessed the species’ (1) historical geographic spread throughout the Americas, (2) local ethnobotanical importance in Jamaica, and (3) biomedical potential as an herbal medicine. Methods included georeferencing of time-stamped herbarium collections from pre-1900 to 2016, literature review, and ethnobotanical research in rural and urban Jamaica (n?=?58 participants). Results demonstrated that A. leptopus has spread aggressively in the West Indies since the 1950s. It has become a problematic invasive species in urban Jamaica, which has likely facilitated its local popularity as an herbal medicine. In urban Jamaica, ethnobotanical interviews ranked the species as the fourth most frequently reported medicinal plant. In contrast, A. leptopus was present but did not dominate the vegetation in rural Jamaica, and was never mentioned during interviews. The biomedical literature offers limited support for its biological activity, while showing no acute toxic effects. The ethnobotany of A. leptopus showcases the dynamic interplay between people, plants, and the environment.     

Updating the geographical distribution and frequency of Aedes albopictus in Brazil with remarks regarding its range in the Americas

The geographical distribution of Aedes albopictus in Brazil was updated according to the data recorded across the country over the last eight years. Countrywide house indexes (HI) for Ae. albopictus in urban and suburban areas were described for the first time using a sample of Brazilian municipalities. This mosquito is currently present in at least 59% of the Brazilian municipalities and in 24 of the 27 federal units (i.e., 26 states and the Federal District). In 34 Brazilian municipalities, the HI values for Ae. albopictus were higher than those recorded for Ae. aegypti, reaching figures as high as HI = 7.72 in the Southeast Region. Remarks regarding the current range of this mosquito species in the Americas are also presented. Nineteen American countries are currently infested and few mainland American countries have not confirmed the occurrence of Ae. albopictus. The large distribution and high frequency of Ae. albopictus in the Americas may become a critical factor in the spread of arboviruses like chikungunya in the new world.     

mtDNA diversity in Chukchi and Siberian Eskimos: implications for the genetic history of Ancient Beringia and the peopling of the New World.

The mtDNAs of 145 individuals representing the aboriginal populations of Chukotka-the Chukchi and Siberian Eskimos-were subjected to RFLP analysis and control-region sequencing. This analysis showed that the core of the genetic makeup of the Chukchi and Siberian Eskimos consisted of three (A, C, and D) of the four primary mtDNA haplotype groups (haplogroups) (A-D) observed in Native Americans, with haplogroup A being the most prevalent in both Chukotkan populations. Two unique haplotypes belonging to haplogroup G (formerly called "other" mtDNAs) were also observed in a few Chukchi, and these have apparently been acquired through gene flow from adjacent Kamchatka, where haplogroup G is prevalent in the Koryak and Itel'men. In addition, a 16111C-->T transition appears to delineate an "American" enclave of haplogroup A mtDNAs in northeastern Siberia, whereas the 16192C-->T transition demarcates a "northern Pacific Rim" cluster within this haplogroup. Furthermore, the sequence-divergence estimates for haplogroups A, C, and D of Siberian and Native American populations indicate that the earliest inhabitants of Beringia possessed a limited number of founding mtDNA haplotypes and that the first humans expanded into the New World approximately 34,000 years before present (YBP). Subsequent migration 16,000-13,000 YBP apparently brought a restricted number of haplogroup B haplotypes to the Americas. For millennia, Beringia may have been the repository of the respective founding sequences that selectively penetrated into northern North America from western Alaska.     

Brief communication: DNA from early Holocene American dog

We present the oldest genetically identified dog in the Americas, directly dated to 9,260 ± 170 Cal. B.P. The DNA was extracted from an occipital condyle imbedded in a human paleofecal sample from Hinds Cave in southwest Texas. A 368 base pair fragment of the mitochondrial genome control region was sequenced. These data were analyzed with comparable data, which included other ancient dogs and extant dogs, wolves and coyotes from around the world. Compiled with published data, our results characterize ancient American dogs within clades rooted by Eurasian wolves. In the Americas, these data provide no evidence of local interbreeding with wolves. This is a departure from the genetic pattern in other areas of the world where interbreeding with local wolf populations is apparent. Our discovery of domestic dog bone in a human paleofecal sample provides the earliest direct evidence for human consumption of dogs in the New World. These data support the hypothesis that dogs were a food source for early Paleoamericans.     

Population genetic analysis of cat populations from Mexico, Colombia, Bolivia, and the Dominican Republic: Identification of different gene pools in Latin America

In this paper we identify new genetic profiles of eight Latin American cat populations. In addition, we combine data from the present study and previously published data on 70 other American and European populations to discuss (1) the points of introduction of mutant alleles for cat coat phenotypes from Europe into Latin America, (2) the heterozygosity levels at these loci in the current Latin American cat populations, (3) the level of genetic heterogeneity among Latin American cat populations, and how this compares with levels found in North American and European cat populations, and (4) how many different cat gene pools are currently present in Latin America. We also include in our purview historical records of human migrations from Europe to and within the Americas. Our analyses clearly support the view that the current genetic profiles and structuring of cat populations in Latin America can be largely explained by the historical migration patterns of humans. This work is dedicated to the memory of Dr Roy Robinson. May he rest in peace.     

Brief communication: The Uto-Aztecan premolar in early hunter-gatherers from South-Central North America

The Uto‐Aztecan premolar is a discrete dental trait found in low frequency (<2%) among world populations. The highest frequencies of the trait have been found among the indigenous populations of North America and, to a lesser extent, South America. Because of the trait's relatively higher frequency in the Western Hemisphere, the antiquity and distribution of the feather is important for reconstructing the biocultural interactions of prehistoric populations. While early research concluded that the Uto‐Aztecan premolar originated in the American Southwest around 4,000 years Before Present (BP), more recent studies have discovered the trait across the Americas and in parts of Europe and Asia. For this study, over 300 dentitions representing foragers and farmers in south‐central North America were examined. The trait was found in relatively high frequency (over 11%) in Archaic hunter‐gatherer populations from Central Texas, with high frequencies also found in the adjacent western Gulf Coastal Plain. The presence of this trait in Early Archaic populations suggests that the trait was present by 8,000 BP and persisted at a high frequency into the Late Archaic period. Am J Phys Anthropol 149:318–322, 2012. © 2012 Wiley Periodicals, Inc.     

Early South Americans Cranial Morphological Variation and the Origin of American Biological Diversity

Recent South Americans have been described as presenting high regional cranial morphological diversity when compared to other regions of the world. This high diversity is in accordance with linguistic and some of the molecular data currently available for the continent, but the origin of this diversity has not been satisfactorily explained yet. Here we explore if this high morphological variation was already present among early groups in South America, in order to refine our knowledge about the timing and origins of the modern morphological diversity. Between-group (Fst estimates) and within-group variances (trace of within-group covariance matrix) of the only two early American population samples available to date (Lagoa Santa and Sabana de Bogotá) were estimated based on linear craniometric measurements and compared to modern human cranial series representing six regions of the world, including the Americas. The results show that early Americans present moderate within-group diversity, falling well within the range of modern human groups, despite representing almost three thousand years of human occupation. The between-group variance apportionment is very low between early Americans, but is high among recent South American groups, who show values similar to the ones observed on a global scale. Although limited to only two early South American series, these results suggest that the high morphological diversity of native South Americans was not present among the first human groups arriving in the continent and must have originated during the Middle Holocene, possibly due to the arrival of new morphological diversity coming from Asia during the Holocene.     

Identification and characterisation of the Plasmodium vivax rhoptry-associated protein 2

Plasmodium vivax is currently the most widespread of the four parasite species causing malaria in humans around the world. It causes more than 75 million clinical episodes per year, mainly on the Asian and American continents. Identifying new antigens to be further tested as anti-P. vivax vaccine candidates has been greatly hampered by the difficulty of maintaining this parasite cultured in vitro. Taking into account that one of the most promising vaccine candidates against Plasmodium falciparum is the rhoptry-associated protein 2, we have identified the P. falciparum rhoptry-associated protein 2 homologue in P. vivax in the present study. This protein has 400 residues, having an N-terminal 21 amino-acid stretch compatible with a signal peptide and, as occurs with its falciparum homologue, it lacks repeat sequences. The protein is expressed in asexual stage P. vivax parasites and polyclonal sera raised against this protein recognised a 46 kDa band in parasite lysate in a Western blot assay.     

The Phylogeographic History of the New World Screwworm Fly,Inferred by Approximate Bayesian Computation Analysis

Insect pest phylogeography might be shaped both by biogeographic events and by human influence. Here, we conducted an approximate Bayesian computation (ABC) analysis to investigate the phylogeography of the New World screwworm fly, Cochliomyia hominivorax, with the aim of understanding its population history and its order and time of divergence. Our ABC analysis supports that populations spread from North to South in the Americas, in at least two different moments. The first split occurred between the North/Central American and South American populations in the end of the Last Glacial Maximum (15,300-19,000 YBP). The second split occurred between the North and South Amazonian populations in the transition between the Pleistocene and the Holocene eras (9,100-11,000 YBP). The species also experienced population expansion. Phylogenetic analysis likewise suggests this north to south colonization and Maxent models suggest an increase in the number of suitable areas in South America from the past to present. We found that the phylogeographic patterns observed in C. hominivorax cannot be explained only by climatic oscillations and can be connected to host population histories. Interestingly we found these patterns are very coincident with general patterns of ancient human movements in the Americas, suggesting that humans might have played a crucial role in shaping the distribution and population structure of this insect pest. This work presents the first hypothesis test regarding the processes that shaped the current phylogeographic structure of C. hominivorax and represents an alternate perspective on investigating the problem of insect pests.     

云南假泽兰属植物及薇甘菊的危害

外来入侵生物对生态系统产生的影响十分巨大,已经成为国家生态安全的严重隐患。自上世纪90年代末期以来,入侵植物薇甘菊（Mikania micrantha H．B．K．）在我国的生态危害引起了社会各界的广泛关注。但是,至今我国所有关于薇甘菊的文献中,均末提及该种在云南的分布。作者通过实地调查和查阅昆明植物研究所的相关标本,确认云南分布有两种假泽兰属植物,即假泽兰（Mikania cordata （Burm．f．）B．L．Robinson）和薇甘菊（M．micrantha）,并介绍了薇甘菊在云南西南部德宏州的危害现状。根据薇甘菊的生物学习性,作者预测薇甘菊将进一步在德宏州扩散,还可能入侵到与德宏州气候相似的其他地区,有关政府部门和研究机构对此问题应该给予高度重视。     

Mitochondrial population genomics supports a single pre-Clovis origin with a coastal route for the peopling of the Americas

It is well accepted that the Americas were the last continents reached by modern humans, most likely through Beringia. However, the precise time and mode of the colonization of the New World remain hotly disputed issues. Native American populations exhibit almost exclusively five mitochondrial DNA (mtDNA) haplogroups (A-D and X). Haplogroups A-D are also frequent in Asia, suggesting a northeastern Asian origin of these lineages. However, the differential pattern of distribution and frequency of haplogroup X led some to suggest that it may represent an independent migration to the Americas. Here we show, by using 86 complete mitochondrial genomes, that all Native American haplogroups, including haplogroup X, were part of a single founding population, thereby refuting multiple-migration models. A detailed demographic history of the mtDNA sequences estimated with a Bayesian coalescent method indicates a complex model for the peopling of the Americas, in which the initial differentiation from Asian populations ended with a moderate bottleneck in Beringia during the last glacial maximum (LGM), around approximately 23,000 to approximately 19,000 years ago. Toward the end of the LGM, a strong population expansion started approximately 18,000 and finished approximately 15,000 years ago. These results support a pre-Clovis occupation of the New World, suggesting a rapid settlement of the continent along a Pacific coastal route.     

Molecular phylogeny and diversification history of Prosopis (Fabaceae: Mimosoideae)

The genus Prosopis is an important member of arid and semiarid environments around the world. To study Prosopis diversification and evolution, a combined approach including molecular phylogeny, molecular dating, and character optimization analysis was applied. Phylogenetic relationships were inferred from five different molecular markers ( mat K- trn K, trn L- trn F, trn S- psb C, G3pdh, NIA). Taxon sampling involved a total of 30 Prosopis species that represented all Sections and Series and the complete geographical range of the genus. The results suggest that Prosopis is not a natural group. Molecular dating analysis indicates that the divergence between Section Strombocarpa and Section Algarobia plus Section Monilicarpa occurred in the Oligocene, contrasting with a much recent diversification (Late Miocene) within each of these groups. The diversification of the group formed by species of Series Chilenses, Pallidae, and Ruscifoliae is inferred to have started in the Pliocene, showing a high diversification rate. The moment of diversification within the major lineages of American species of Prosopis is coincident with the spreading of arid areas in the Americas, suggesting a climatic control for diversification of the group. Optimization of habitat parameters suggests an ancient occupation of arid environments by Prosopis species.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 621–640.     

A reevaluation of the Native American mtDNA genome diversity and its bearing on the models of early colonization of Beringia

The Americas were the last continents to be populated by humans, and their colonization represents a very interesting chapter in our species' evolution in which important issues are still contentious or largely unknown. One difficult topic concerns the details of the early peopling of Beringia, such as for how long it was colonized before people moved into the Americas and the demography of this occupation. A recent work using mitochondrial genome (mtDNA) data presented evidence for a so called "three-stage model" consisting of a very early expansion into Beringia followed by approximately 20,000 years of population stability before the final entry into the Americas. However, these results are in disagreement with other recent studies using similar data and methods. Here, we reanalyze their data to check the robustness of this model and test the ability of Native American mtDNA to discriminate details of the early colonization of Beringia. We apply the Bayesian Skyline Plot approach to recover the past demographic dynamic underpinning these events using different mtDNA data sets. Our results refute the specific details of the "three-stage model", since the early stage of expansion into Beringia followed by a long period of stasis could not be reproduced in any mtDNA data set cleaned from non-Native American haplotypes. Nevertheless, they are consistent with a moderate population bottleneck in Beringia associated with the Last Glacial Maximum followed by a strong population growth around 18,000 years ago as suggested by other recent studies. We suggest that this bottleneck erased the signals of ancient demographic history from recent Native American mtDNA pool, and conclude that the proposed early expansion and occupation of Beringia is an artifact caused by the misincorporation of non-Native American haplotypes.     

Criteria for Native Food Plant Collection in Northeastern Brazil

Different criteria are used by human populations around the world in the selection of preferred natural resources. In this study, the following hypotheses were tested: 1) the preference for food native species is related to the number of uses for which the species are cited; 2) the categories of food and medicinal use equally influence the selection of a species as preferred; 3) the preference among native food species is related to its frequency and abundance in the areas of collection. Data collection on species preference was conducted in communities located near the Araripe National Forest (FLONA) in Ceará, Northeastern, Brazil. Both the hypothesis that the preference would relate to the number of uses attributed to species and the hypothesis that food and medicinal categories equally influence the selection of species as preferred ones were corroborated. It was concluded in this study that people optimize both use and collection of native resources using criteria such as the versatility of uses for species and the abundance of the resource in the preferred collection areas. It is believed that this trend may be an adaptive strategy adopted by local communities for the exploitation of native resources.     

Polyploidy in invasive plant species of Singapore

Singapore is a recognized global hotspot for invasive species and many introduced plant species have become major weeds there. Some of the common invasive taxa, such as Asystasia gangetica ssp. micrantha , Mimosa pigra , Neptunia plena , Panicum maximum , and Urochloa mutica , are spread over large areas and dominate the indigenous flora in some habitats. In a study aimed at understanding the relationship between polyploidy and invasiveness, we show that all the investigated invasive taxa are polyploids. A. gangetica ssp. micrantha , N. plena , and P. maximum vary in chromosome number and ploidy level across the world, but we recorded only one chromosome count for each of these species in Singapore. Similarly, the cytology of M. pigra and U. mutica also revealed that these species are polyploid, each with only one chromosome number across all populations. The results indicate that one polyploid line in each of these species has been selected favourably and has become invasive. We also show that all the species exhibit normal male meiosis and possess high percentages of pollen fertility. Based on the present study and an analysis of previously reported ploidy levels, we suggest that these taxa are probably of allopolyploid origin. We conclude that polyploidy and an effective reproductive system are a perfect mix for successful invasion by these species in Singapore.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 151 , 395–403.     

薇甘菊对香港郊野公园植物群落危害的分析

从薇甘菊(Mikania micrantha)对不同类型群落的危害,群落中各植物种类受薇甘菊危害的程度,以及薇甘菊与群落中主要乔木和灌木的种间联结性等方面,对香港郊野公园植物群落受薇甘菊危害状况进行了分析。研究样地所在的植被受薇甘菊的危害严重,草灌丛中薇甘菊的平均覆盖率高达80%,灌木群落中薇甘菊的平均覆盖率为60%左右,常绿阔叶林中的薇甘菊覆盖率平均约为30%。对香港郊野公园受薇甘菊危害的植物种类分析表明:受薇甘菊危害最大的主要是乔木和灌木,草本和藤本的受害比例和受害程度相对较小。受薇甘菊危害的乔木有30种,占群落中乔木的62.50%;受薇甘菊危害的灌木有29种,占群落中灌木的70.73%;受薇甘菊危害的草本植物有10种,占群落中草本植物的33.33%。通过无样方法采用2×2列联表的χ2检验对薇甘菊与群落中主要乔木和灌木的种间联结性分析表明:与薇甘菊呈正联结的乔木有12种,占主要乔木(28种)的42.86%,这些种大多是阳生性乔木;与薇甘菊呈负联结的乔木有16种,占主要乔木的57.16%。与薇甘菊呈正联结的灌木有11种,占主要灌木(19种)的57.89%,多是阳生性灌木;与薇甘菊呈负联结的灌木有8种,占主要灌木的42.11%,这些种大多数也是阳生性灌木,仅九节是耐阴性灌木。