青藏高原钻叶龙胆的遗传分化与种群动态历史研究

青藏高原是全球生物多样性中心之一,是研究物种形成和适应性进化的热点地区.龙胆属小龙胆组(Gen-tiana section Chondrophyllae s.l.)占整个龙胆属物种数目的 近一半,以青藏高原为分化中心,但组内物种的遗传分化及其影响因素并不清楚.该研究以小龙胆组青藏高原特有植物——钻叶龙胆(G.hayna...     

青藏高原岷县龙胆的遗传分化与种群动态历史分析

青藏高原是全球生物多样性中心之一,是研究物种形成和适应性进化的热点地区。岷县龙胆（Gentiana algida var. purdomii）是青藏高原地区特有植物,具有很高的药用价值。本研究以岷县龙胆种群为对象,基于不同遗传方式的分子标记,通过种群遗传结构、遗传分化、种群动态历史和物种分布模型等分析,探讨其在青藏高原的分化历史。结果表明：岷县龙胆具有高的遗传多样性,叶绿体数据表明种内遗传分化程度很高（F_ST=0.452）,但核基因数据表明种内遗传分化程度很低（F_ST=0.022）,揭示岷县龙胆种内存在强烈的基因流。种群动态历史分析表明岷县龙胆种群大小经历了近期扩张,物种分布模型的结果表明岷县龙胆在末次盛冰期以来分布范围略有扩张。分子钟模型的结果表明岷县龙胆种内的遗传分化主要发生在第四纪冰期以来。以上结果一致表明,第四纪气候波动是岷县龙胆分化的主要外部因素。本研究为龙胆属及青藏高原植物类群的物种分化、适应性研究以及资源开发与保护提供了参考。     

Origin of the disjunct distribution of flower colour polymorphism within Limonium wrightii (Plumbaginaceae) in the Ryukyu Archipelago

The sea lavender, Limonium wrightii , has six morphs of flower colour variation. The geographical distribution of flower colour morphs is disjunct; the distribution of the pink flower morph is divided into two subregions, and that of the yellow flower morph intervenes between them. The present study aimed to examine the origin of this apparent distribution pattern of flower colour in L. wrightii . Two main hypotheses (i.e. past dispersal events and phenotypic changes by natural selection and/or stochastic processes) have been proposed to account for the origin of leapfrog distribution patterns. To determine which hypothesis was applicable, we conducted a molecular phylogenetic analysis using sequence variation in chloroplast DNA (three regions of intergenic spacers, trnG - trnfM , trnV - trnM , and psbA-trnH ). We sequenced 58 accessions of L. wrightii frin 28 islands in the Ryukyu Archipelago and the Izu-Ogasawara Islands, located south of the Japanese mainland, and 12 accessions of four congeneric species. Within L. wrightii , we obtained four lineages of ten haplotypes. These lineages and haplotypes did not correlate with the different flower colours. These results indicate that the formation processes of populations are complex. The haplotypes of the pink flower morph did not show a sister relationship between the two disjunct subregions, indicating that the disjunct populations of the pink flower morphs are unlikely to share the pink flower colour as a result of common ancestry. We conclude that the observed leapfrog distribution pattern is caused by natural selection and/or stochastic processes.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 709–717.     

Fine-Scale Genetic Structure in the United Arab Emirates Reflects Endogamous and Consanguineous Culture,Population History,and Geography

The indigenous population of the United Arab Emirates (UAE) has a unique demographic and cultural history. Its tradition of endogamy and consanguinity is expected to produce genetic homogeneity and partitioning of gene pools while population movements and intercontinental trade are likely to have contributed to genetic diversity. Emiratis and neighboring populations of the Middle East have been underrepresented in the population genetics literature with few studies covering the broader genetic history of the Arabian Peninsula. Here, we genotyped 1,198 individuals from the seven Emirates using 1.7 million markers and by employing haplotype-based algorithms and admixture analyses, we reveal the fine-scale genetic structure of the Emirati population. Shared ancestry and gene flow with neighboring populations display their unique geographic position while increased intra- versus inter-Emirati kinship and sharing of uniparental haplogroups, reflect the endogamous and consanguineous cultural traditions of the Emirates and their tribes.     

Demographic History and Genomic Response to Environmental Changes in a Rapid Radiation of Wild Rats

For organisms to survive and prosper in a harsh environment, particularly under rapid climate change, poses tremendous challenges. Recent studies have highlighted the continued loss of megafauna in terrestrial ecosystems and the subsequent surge of small mammals, such as rodents, bats, lagomorphs, and insectivores. However, the ecological partitioning of these animals will likely lead to large variation in their responses to environmental change. In the present study, we investigated the evolutionary history and genetic adaptations of white-bellied rats (Niviventer Marshall, 1976), which are widespread in the natural terrestrial ecosystems in Asia but also known as important zoonotic pathogen vectors and transmitters. The southeastern Qinghai-Tibet Plateau was inferred as the origin center of this genus, with parallel diversification in temperate and tropical niches. Demographic history analyses from mitochondrial and nuclear sequences of Niviventer demonstrated population size increases and range expansion for species in Southeast Asia, and habitat generalists elsewhere. Unexpectedly, population increases were seen in N. eha, which inhabits the highest elevation among Niviventer species. Genome scans of nuclear exons revealed that among the congeneric species, N. eha has the largest number of positively selected genes. Protein functions of these genes are mainly related to olfaction, taste, and tumor suppression. Extensive genetic modification presents a major strategy in response to global changes in these alpine species.     

Demographic and genetic interrelationships among the Gavlis of Dharwad

Lot of work has been done in recent years on the genetics of isolated and small population groups. But J. Sutter (1963) notes that these studies have not yielded satisfactory results, because these investigators have applied the formulae and models constructed by the mathematicians which are based on the assumption of panmixia, whereas panmixia cannot occur in human populations especially if the population is very small. Sometimes we speak of genetic drift and selection without taking into account the fact that the population at the same time is controlled by two most important demographic parameters of fertility and mortality which can alter genetic drift and selection. The geneticists are primarily interested in fertility. They want to determine, for any given couple, the number of offspring reaching the age of reproduction. One might therefore assume that the measurement of fertility should play a major role in population genetics. Thus, there is an urgent need for the establishment of meaningful relationship between demography and population genetics. In view of the above facts, an attempt is made in the present study to analyse the “Demographic and Genetic Interrelationships among the Gavlis of Dharwad” so as to throw light on some of the complex genetic issues like endogamy, inbreeding and selection potential.     

Genetic structure of the Danish red deer (Cervus elaphus)

The red deer (Cervus elaphus) population in Denmark became almost extinct in recent historical times due to over‐hunting. The species has subsequently recovered within remote areas, but non‐Danish individuals have been introduced at several localities. To assess genetic structure, past demographic history, and the possibility of a still existing original stock, we analysed 349 specimens from 11 geographically separate areas and from three enclosed areas, genotyping 11 microsatellite loci. Moreover, an 826‐bp fragment of the control region of the mitochondrial DNA was sequenced for 116 recent specimens and seven museum specimens. There was a significant difference in mean expected heterozygosity (H_E) between the three enclosed areas and the 11 unenclosed areas. Significant departures from Hardy–Weinberg equilibrium were observed in the three enclosed areas and in nine of the unenclosed areas. The overall degree of genetic differentiation among all 14 areas was significant (F_ST = 0.09, P < 0.01), primarily because the mean pairwise F_ST for the three enclosed areas was significantly higher than that for the 11 unenclosed areas. A Bayesian clustering procedure detected three genetically distinct populations and indicated reduced gene flow between the enclosed and unenclosed areas. The individuals in the unenclosed areas show genotypic mixture, presumably as a result of gene flow among them. Markov Chain Monte Carlo simulations, based on the genealogical history of the microsatellite alleles, suggest a drastic decline in the effective population size of the enclosed areas some 188–474 years ago. Mitochondrial DNA analysis of the recent specimens showed seven haplotypes. Individuals from the enclosed Jægersborg Dyrehave contain haplotypes that occur all over Denmark and also are found in Western Europe. A close relationship between Scandinavian and Western European red deer is most likely. Only individuals from the unenclosed Lindenborg Estate and the enclosed Tofte Skov did not group with any other Danish individuals. As six of seven museum specimens had haplotypes also found in modern Danish samples, the current population of red deer in Denmark is genetically close to the original Danish red deer. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 688–701.     

Effect of founding events on coat colour polymorphism of Apodemus speciosus (Rodentia: Muridae) on the Izu Islands

To infer the evolutionary mechanism of phenotypic variation among isolated island populations, we investigated coat colour and genetic variation in the large Japanese field mouse (Apodemus speciosus) on the Izu Islands (Ohshima, Niijima, Kouzushima, and Miyakejima). Coat colour in the most remote population (Miyakejima) was unique and significantly darker than that in the other populations. Ohshima that is closest to the source population showed variation in coat colour within its population. Phylogeographical analyses using mitochondrial and microsatellite markers suggested that the island populations (except Kouzushima) were founded sequentially from the closest Ohshima to remote Niijima and Miyakejima during or before the penultimate interglacial period. Secondary gene flow from the source population was rare and occurred only for the closest (Ohshima) population. In addition, we found that an amino acid mutation in the Agouti signalling protein gene (Asip) was associated with coat colour variation among the island populations. The mutation was rare in the source population but completely fixed in the Miyakejima population. The phenotypic and genetic variation suggested that severe reduction of genetic variation and changes in allele frequency as a result of sequential colonization (i.e. the founder effect) had significant effects on colour polymorphism. The findings of the present study suggest that the founder effect, in addition to natural selection, facilitated the morphological changes below the species level over a relatively long time scale. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 522–535.     

Demographic parameters of a free-ranging deep-diving cetacean,the long-finned pilot whale

Demographic parameters provide baselines to estimate future population trajectories which can then be used in management decisions. The aim here was to estimate demographic parameters of long-finned pilot whale (Globicephala melas) from the Strait of Gibraltar by fitting mark-recapture models to photo-identification data of primary and secondary marked individuals. These parameters were used to forecast the future population trajectories in a population viability analysis (PVA) given different scenarios of demographic rates. Survival rate increased with age from 0.629, 95% CI [0.409, 0.805] for calves, 0.869, 95% CI [0.758, 0.934] for juveniles, to 0.972, 95% CI [0.953, 0.983] for adults. A preliminary mean observed interval of viable calves was 4.5 years. The PVA estimated the population would persist over 100 years with a 100% probability for all scenarios except those with lower 95% CI survival values, for which the probability of extinction reached 100%. Population growth rate was negative in all scenarios except those with 95% CI upper survival values. Interbirth interval and juvenile survival were found most influential and depended on the correct identification of secondary marked (e.g., calves and juveniles) individuals on a long-term basis. This population was found in a precarious state prior to a morbillivirus outbreak that might even more endanger its long-term viability.     

Recent Demographic History and Present Fine-Scale Structure in the Northwest Atlantic Leatherback (Dermochelys coriacea) Turtle Population

The leatherback turtle Dermochelys coriacea is the most widely distributed sea turtle species in the world. It exhibits complex life traits: female homing and migration, migrations of juveniles and males that remain poorly known, and a strong climatic influence on resources, breeding success and sex-ratio. It is consequently challenging to understand population dynamics. Leatherbacks are critically endangered, yet the group from the Northwest Atlantic is currently considered to be under lower risk than other populations while hosting some of the largest rookeries. Here, we investigated the genetic diversity and the demographic history of contrasted rookeries from this group, namely two large nesting populations in French Guiana, and a smaller one in the French West Indies. We used 10 microsatellite loci, of which four are newly isolated, and mitochondrial DNA sequences of the control region and cytochrome b. Both mitochondrial and nuclear markers revealed that the Northwest Atlantic stock of leatherbacks derives from a single ancestral origin, but show current genetic structuration at the scale of nesting sites, with the maintenance of migrants amongst rookeries. Low nuclear genetic diversities are related to founder effects that followed consequent bottlenecks during the late Pleistocene/Holocene. Most probably in response to climatic oscillations, with a possible influence of early human hunting, female effective population sizes collapsed from 2 million to 200. Evidence of founder effects and high numbers of migrants make it possible to reconsider the population dynamics of the species, formerly considered as a metapopulation model: we propose a more relaxed island model, which we expect to be a key element in the currently observed recovering of populations. Although these Northwest Atlantic rookeries should be considered as a single evolutionary unit, we stress that local conservation efforts remain necessary since each nesting site hosts part of the genetic diversity and species history.     

Changes in Demographic Parameters of <Emphasis Type="Italic">Macaca fuscata</Emphasis> at Takasakiyama in Relation to Decrease of Provisioned Foods

Though researchers have studied population dynamics extensively in many free-ranging primate populations, information on the relationship between food abundance and demographic parameters based on long-term data is sparse. We examined changes in demographic parameters in relation to decreased provisioning of foods based on data gathered for >50 yr in a provisioned, free-ranging Japanese macaque (Macaca fuscata) population at Takasakiyama, Oita Prefecture, in the southern region of Japan. At Takasakiyama, population size increased linearly because of heavy provisioning in the 1950s and 1960s. The provisioning of food to macaques decreased from 1965. We examined changes in the physique index of full adult females, primiparous age, birth percentage, infant mortality rate, population density, and annual population growth rate relative to the decrease of provisioned foods between the 1970s and 1990s. As a result of the drastic decrease in the amount of foods provisioned, the physique index of full adult females decreased, primiparous age increased, birth percentage decreased, and infant mortality rate increased, such that annual population growth rate diminished substantially. Ours is the first study to demonstrate quantitatively the relationship between provisioned food abundance and demographic parameters based on long-term data.     

Dioecy derived from distyly and pollination in Psychotria rubra (Rubiaceae) occurring in the Ryukyu Islands,Japan

Floral morphology and breeding system were examined in natural populations of Psychotria rubra (Rubiaceae) occurring in the Ryukyu Islands in southwest Japan. This species is morphologically dimorphic with long‐ and short‐styled morphs; however, these morphs are functionally dioecious. All long‐styled morphs set fruits, but their short anthers completely lack pollen grains; thus, they function as pistillate flowers. Alternately, short‐styled morphs usually have fertile pollen and never set fruit, whether after open or obligate pollinations; thus, they function as staminate flowers. However, some short‐styled morphs in Mounts Katsuu‐dake and Oppa‐dake populations have no fertile pollens. No fruit was obtained from bagging experiments, indicating that P. rubra requires pollinators for its reproduction. In our pollinator observations, flies and short‐tongued wasps were the main visitors of the flowers of P. rubra. Thus, these insects are probably effective pollinators for P. rubra in the Ryukyu Islands. Considering the morphological features, the dioecy found in P. rubra is probably derived from distyly; however, no sufficient evidence is available showing that dioecy has evolved “directly” from distyly.     

The biogeography of Miniopterus bats (Chiroptera: Miniopteridae) from the Comoro Archipelago inferred from mitochondrial DNA

The endemic fauna of the Comoro Archipelago is composed of a mixture of taxa originating from Africa and Madagascar. Bats are the only native land dwelling mammals on this archipelago, but the biogeographical origins for the vast majority of species within this group are ambiguous. We report here genetic analyses based on two mitochondrial DNA markers to infer the origin of Comorian bats belonging to a reputed species complex of Miniopterus that is further distributed across Africa and Madagascar. Phylogenetic reconstructions show that east African M. minor are not closely related to the insular Miniopterus of Madagascar and the Comoros (Grande Comore and Anjouan). The latter cluster into two distinct, monophyletic clades (Clade 1 and Clade 2). Representatives of these clades occur sympatrically both on the Comoros and on Madagascar, and are distinguished by a large genetic distance (K2P: 9.9% for cytochrome b). No haplotypes are shared between any islands, suggesting the absence of contemporary gene flow. Populations of the widespread Clade 1 are furthermore characterized by a significant inter‐island structure (Φ_CT = 0.249), and by high haplotype and nucleotide diversities (h = 0.90–0.98, π = 0.04–0.06). Demographic analyses of Clade 1 suggest secondary contact between two distinct phylogroups (Subclade 1 A and 1B) that reached Grande Comore and Anjouan, and a large, stable population with a long evolutionary history on Madagascar. These results and the current distribution of related lineages suggest that the Comoros were colonized independently at least two or three times by ancestors from Madagascar.     

Allozyme diversity and history of distribution expansion in the maritime perennial plant Hedyotis strigulosa (Rubiaceae), distributed over the wide latitudes in the Japanese Archipelago

Allozyme diversity was examined in 30 populations of the maritime perennial plant Hedyotis strigulosa var. parviflora , which is distributed from subtropical islands to the central mainland of Japan. Genetic diversity within populations tended to be larger in southern island populations than in northern mainland populations. In the southern part of the distribution, the population size is generally large and populations are distributed more continuously than in the northern area, resulting in the larger effective size of southern populations as a whole. These factors play a major role in maintaining greater genetic diversity in the southern populations. By contrast, genetic diversity in the northern populations is very low, probably resulting from bottlenecks of population establishments during recolonization from refugial area to the northern areas. Geographically close populations were located near each other in the multidimensional scaling and the phenogram based on genetic distances, suggesting that gene flow among remote populations is rather limited. The pattern of genetic diversity in H. strigulosa var. parviflora is likely caused by the distribution expansion of the species; in the last glacier era, the species was restricted to the southern area; its advance to the northern area is relatively recent. Another variety endemic only to the Daito Islands, H. strigulos a var. luxurians , has lower genetic diversity than H. strigulosa var. parviflora and has genetically diverged from H. strigulosa var. parviflor a.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 679–688.