Genetic diversity and molecular phylogeography of Chinese domestic goats by large-scale mitochondrial DNA analysis

Mitochondrial DNA (mtDNA) D-loop sequences of 666 individuals (including 109 new individuals, 557 individuals retrieved from GenBank) from 33 Chinese domestic goat breeds throughout China were used to investigate their mtDNA variability and molecular phylogeography. The results showed that all goat breeds in this study proved to be extremely diverse, and the average haplotype diversity and nucleotide diversity were 0.990 ± 0.001 and 0.032 ± 0.001, respectively. The 666 sequences gave 326 different haplotypes. Phylogenetic analyses revealed that there were 4 mtDNA haplogroups identified in Chinese domestic goats, in which haplogroup A was predominant and widely distributed. Our finding was consistent with archaeological data and other genetic diversity studies. Amova analysis showed there was significant geographical structuring. Almost 84.31 % of genetic variation was included in the within-breed variance component and only 4.69 % was observed among the geographic distributions. This genetic diversity results further supported the previous view of multiple maternal origins of Chinese domestic goats, and the results on the phylogenetic relationship contributed to a better understanding of the history of goat domestication and modern production of domestic goats.     

The influence of past and present climate on the biogeography of modern mammal diversity

Within most terrestrial groups of animals, including mammals, species richness varies along two axes of environmental variation, representing energy availability and plant productivity. This relationship has led to a search for mechanistic links between climate and diversity. Explanations have traditionally focused on single mechanisms, such as variation in environmental carrying capacity or evolutionary rates. Consensus, though, has proved difficult to achieve and there is growing appreciation that geographical patterns of species richness are a product of many interacting factors including biogeographic history and biological traits. Here, we review some current hypotheses on the causes of gradients in mammal richness and range sizes since the two quantities are intimately linked. We then present novel analyses using recent datasets to explore the structure of the environment-richness relationship for mammals. Specifically, we consider the impact of glaciation on present day mammalian diversity gradients. We conclude that not only are multiple processes important in structuring diversity gradients, but also that different processes predominate in different places.     

New insights into the past and recent evolutionary history of the Corsican mouflon (Ovis gmelini musimon) to inform its conservation

Human-mediated species dispersal across the Mediterranean stretches back at least 10,000 years and has left an indelible stamp on present-day biodiversity. Believed to be a descendant of the Asiatic mouflon (Ovis gmelini gmelinii), the Corsican mouflon (O. g. musimon) was translocated during the Neolithic as ancestral livestock by humans migrating from the Fertile Crescent to the Western Mediterranean. Today, two geographically limited and disconnected populations can be found in Corsica. Whether they originated from distinct founders or one ancestral population that later split remains unknown, although such information is pivotal for the species’ management on the island. We genotyped 109 and 176 individuals at the Cytochrome-b gene and 16 loci of the microsatellite DNA, respectively, to gain insights into the natural history of the Corsican mouflon. We found evidence confirming that the Asiatic was the ancestor of the Corsican mouflon, which should thus be unvaryingly referred to as O. g. musimon, i.e. as a subspecies of the Asiatic mouflon. Haplotype divergence dating and the investigation of genetic structure highlighted a strong and ancient genetic differentiation between the two Corsican populations. Approximate Bayesian Computation pointed to the introduction of a single group of founders as the most reliable scenario for the origin of the entire Corsican population. Later, this ancestral stock would have decreased in number, facing genetic bottlenecks and eventually resulting in two divergent demes. Splitting most likely occurred several hundred years ago. Their shared past notwithstanding, we discuss whether the two relic Corsican mouflon populations should be now considered as distinct management units.

     

Partitioning global patterns of freshwater fish beta diversity reveals contrasting signatures of past climate changes

Here, we employ an additive partitioning framework to disentangle the contribution of spatial turnover and nestedness to beta diversity patterns in the global freshwater fish fauna. We find that spatial turnover and nestedness differ geographically in their contribution to freshwater fish beta diversity, a pattern that results from contrasting influences of Quaternary climate changes. Differences in fish faunas characterized by nestedness are greater in drainage basins that experienced larger amplitudes of Quaternary climate oscillations. Conversely, higher levels of spatial turnover are found in historically unglaciated drainage basins with high topographic relief, these having experienced greater Quaternary climate stability. Such an historical climate signature is not clearly detected when considering the overall level of beta diversity. Quantifying the relative roles of historical and ecological factors in explaining present-day patterns of beta diversity hence requires considering the different processes generating these patterns and not solely the overall level of beta diversity.     

Surname analysis of the Corsican population reveals an agreement with geographical and linguistic structure

The surname is a cultural trait that is extremely useful for historical and linguistic studies and can effectively be used as a genetic marker. In many human populations the surname is inherited in the paternal lineage, and can therefore be considered a marker for the Y chromosome. In this study, surnames were recorded from the white pages of telephone directories in current use in Corsica in 1993. All surnames present in thirteen villages scattered over the whole island and covering the main historical regions were transcribed. Surname variability was found to be higher in coastal villages, and lower in more isolated communities. The isonymy detected among the thirteen villages allowed the calculation of kinship values, visualized in a tree showing two main clusters, one referring to the northern villages and one encompassing the villages of the south. The pattern reflects the administrative division of the island, with the exception of Vico, which belongs to the southern administrative region but is geographically close to the northern villages, and Ghisoni, which belongs to the northern district but is more similar to the village of Bastelica in the southern district. The data presented here show a structure in the surname distribution that is in substantial agreement with the geographical patterns. The kinship values are consistent with a moderated gene flow among villages producing a surname structure according to the geographic features of the territory.     

Approximate Bayesian computation reveals the factors that influence genetic diversity and population structure of foxsnakes

Contemporary geographical range and patterns of genetic diversity within species reflect complex interactions between multiple factors acting across spatial and temporal scales, and it is notoriously difficult to disentangle causation. Here, we quantify patterns of genetic diversity and genetic population structure using mitochondrial DNA sequences (101 individuals, cytochrome b) and microsatellites (816 individuals, 12 loci) and use Approximate Bayesian computation methods to test competing models of the demographic history of eastern and western foxsnakes. Our analyses indicate that post-glacial colonization and past population declines, probably caused by the infilling of deciduous forest and cooler temperatures since the mid-Holocene, largely underpin large-scale genetic patterns for foxsnakes. At finer geographical scales, our results point to more recent anthropogenic habitat loss as having accentuated genetic population structure by causing further declines and fragmentation.     

A large-scale phylogeny of Synodontis (Mochokidae,Siluriformes) reveals the influence of geological events on continental diversity during the Cenozoic

To explain the spatial variability of fish taxa at a large scale, two alternative proposals are usually evoked. In recent years, the debate has centred on the relative roles of present and historical processes in shaping biodiversity patterns. In Africa, attempts to understand the processes that determine the large scale distribution of fishes and exploration of historical contingencies have been under-investigated given that most of the phylogenetic studies focus on the history of the Great Lakes. Here, we explore phylogeographic events in the evolutionary history of Synodontis (Mohokidae, Siluriformes) over Africa during the Cenozoic focusing on the putative role of historical processes. We discuss how known geological events together with hydrographical changes contributed to shape Synodontis biogeographical history. Synodontis was chosen on the basis of its high diversity and distribution in Africa: it consists of approximately 120 species that are widely distributed in all hydrographic basins except the Maghreb and South Africa. We propose the most comprehensive phylogeny of this catfish genus. Our results provide support for the ‘hydrogeological’ hypothesis, which proposes that palaeohydrological changes linked with the geological context may have been the cause of diversification of freshwater fish deep in the Tertiary. More precisely, the two main geological structures that participated to shape the hydrographical network in Africa, namely the Central African Shear zone and the East African rift system, appear as strong drivers of Synodontis diversification and evolution.     

The influence of biodiversity-friendly ranching practices on dung beetle diversity in a Mexican mountainous tropical landscape

Journal of Insect Conservation - Tropical montane cloud forest (TMCF) has been reduced to riparian vegetation remnants, and small patches surrounded by different land uses and human settlements. In...     

Microsatellite and mitochondrial haplotype diversity reveals population differentiation in the tiger shrimp (Penaeus monodon) in the Indo-Pacific region

The black tiger shrimp (Penaeus monodon) is an ecologically and economically important penaeid species and is widely distributed in the Indo-Pacific region. Here we investigated the genetic diversity of P. monodon (n = 355) from eight geographical regions by genotyping at 10 microsatellite loci. The average observed heterozygosity at various loci ranged from 0.638 to 0.743, indicating a high level of genetic variability in this region. Significant departures from Hardy-Weinberg equilibrium caused by heterozygote deficiency were recorded for most loci and populations. Pairwise F(ST) and R(ST) values revealed genetic differentiation among the populations. Evidence from the assignment test showed that the populations in the West Indian Ocean were unique, whereas other populations examined were partially admixed. In addition, the non-metric multidimensional scaling analysis indicated the presence of three geographic groups in the Indo-Pacific region, i.e. the African populations, a population from western Thailand and the remaining populations as a whole. We also sequenced and analysed the mitochondrial control region (mtCR) in these shrimp stocks to determine whether the nuclear and mitochondrial genomes show a similar pattern of genetic differentiation. A total of 262 haplotypes were identified, and nucleotide divergence among haplotypes ranged from 0.2% to 16.3%. Haplotype diversity was high in all populations, with a range from 0.969 to 1. Phylogenetic analysis using the mtCR data revealed that the West Indian Ocean populations were genetically differentiated from the West Pacific populations, consistent with the microsatellite data. These results should have implications for aquaculture management and conservation of aquatic diversity.     

Phylogenetic analysis reveals the surprising diversity of an oxygenase class

As metalloenzymes capable of transforming a broad range of substrates with high stereo- and regiospecificity, the multicomponent Rieske oxygenases (ROs) have been studied in bacterial systems for applications in bioremediation and industrial biocatalysis. These studies include genetic and biochemical investigations, determination of enzyme structure, phylogenetic analysis, and enzyme classification. Although RO terminal oxygenase components (RO–Os) share a conserved domain structure, their sequences are highly divergent and present significant challenges for identification and classification. Herein, we present the first global phylogenetic analysis of a broad range of RO–Os from diverse taxonomic groups. We employed objective, structure-based criteria to significantly reduce the inclusion of erroneously aligned sequences in the analysis. Our findings reveal that RO biochemical studies to date have been largely concentrated in an unexpectedly narrow portion of the RO–O sequence landscape. Additionally, our analysis demonstrates the existence two distinct groups of RO–O sequences. Finally, the sequence diversity recognized in this study necessitates a new RO–O classification scheme. We therefore propose a P450-like naming system. Our results reveal a diversity of sequence and potential catalytic functionality that has been wholly unappreciated in the RO literature. This study also demonstrates that many commonly used bioinformatic tools may not be sufficient to analyze the vast amount of data available in current databases. These findings facilitate the expanded exploration of RO catalytic capabilities in both biological and technological contexts and increase the potential for practical exploitation of their activities.     

Probing into the diversity of trypanosomatid flagellates parasitizing insect hosts in South-West China reveals both endemism and global dispersal

Flagellates of the class Kinetoplastea are known to frequently parasitize insects. We have collected 67 isolates from 407 Heteroptera hosts captured in several locations of South-West China. Their splice leader (SL) RNA gene repeats and small subunit (SSU) rRNA genes were PCR amplified from the infected tissue samples. In most cases, parasites were found in the midgut, rarely the infection was confined to the Malpighian tubes. Phylogenetic analysis of the obtained sequences has significantly expanded the known diversity of these monoxenous parasites. Fifteen typing units were found among these isolates including 11 potentially new species. Four typing units matched the previously known typing units from the Neotropics indicating a global distribution of the respective parasite species. At the same time, new clades appeared, testifying for a certain level of endemism. The host record of the parasites found indicated a variable specificity level of the host–parasite association including several cases of a very broad host range. Our results disprove the “one host – one parasite” paradigm and show that although the global diversity of monoxenous parasites is high, it is not as enormous as suggested earlier. Moreover, phylogenetic analysis revealed the presence, among the isolated strains, of a new Phytomonas species, which is the first documentation of this potentially pathogenic dixenous parasite of plants in China.     

A phylometagenomic exploration of oceanic alphaproteobacteria reveals mitochondrial relatives unrelated to the SAR11 clade

Background

According to the endosymbiont hypothesis, the mitochondrial system for aerobic respiration was derived from an ancestral Alphaproteobacterium. Phylogenetic studies indicate that the mitochondrial ancestor is most closely related to the Rickettsiales. Recently, it was suggested that Candidatus Pelagibacter ubique, a member of the SAR11 clade that is highly abundant in the oceans, is a sister taxon to the mitochondrial-Rickettsiales clade. The availability of ocean metagenome data substantially increases the sampling of Alphaproteobacteria inhabiting the oxygen-containing waters of the oceans that likely resemble the originating environment of mitochondria.

Methodology/Principal Findings

We present a phylogenetic study of the origin of mitochondria that incorporates metagenome data from the Global Ocean Sampling (GOS) expedition. We identify mitochondrially related sequences in the GOS dataset that represent a rare group of Alphaproteobacteria, designated OMAC (Oceanic Mitochondria Affiliated Clade) as the closest free-living relatives to mitochondria in the oceans. In addition, our analyses reject the hypothesis that the mitochondrial system for aerobic respiration is affiliated with that of the SAR11 clade.

Conclusions/Significance

Our results allude to the existence of an alphaproteobacterial clade in the oxygen-rich surface waters of the oceans that represents the closest free-living relative to mitochondria identified thus far. In addition, our findings underscore the importance of expanding the taxonomic diversity in phylogenetic analyses beyond that represented by cultivated bacteria to study the origin of mitochondria.     

Impact of past management practices on the present status of the Muthupet mangrove ecosystem

Muthupet mangrove ecosystem (10° 25 N and 79° 30 E) is located at the southern end of the Cauvery delta on the east coast of India. The swamp is characterized by the presence of only 4 species of exclusive mangroves namelyAvicennia marina, Excoecaria agallocha, Aegiceras corniculatum andAcanthus ilicifolius.Community structure analysis carried out at four randomly selected quadrats showed that the relative density, relative dominance, relative frequency and importance value ofA. marina was relatively higher than for the other three species. Hence, Muthupet mangrove ecosystem is characterized by the mono-specific dominance ofA. marina. Earlier palynological studies indicate that species likeRhizophora were present in this swamp some 200 years ago. It is believed that the past management practices together with the present poor scientific policy of the decision makers and harsh environment conditions may be considered as a few factors responsible for the disappearance ofRhizophora from this mangrove swamp.     

The Mesobuthus martensii genome reveals the molecular diversity of scorpion toxins

Recent complete sequencing of the genome of the Asian scorpion, Mesobuthus martensii, highlights the molecular diversity of its venom neurotoxin/defensin genes and interesting features of their evolution.     

中国近海浮游动物多样性研究的过去和未来

中国是世界上南北纬度跨度最大的国家之一.复杂的气候、水文和地形因素形成了我国海洋环境的多样性,也造就了浮游动物多样性的格局.我国浮游动物多样性的研究经历了分类、分布为主、环境变化对浮游动物的影响和浮游动物环境适应研究等阶段.在我国,地形、季风和水团是形成海洋环境格局的三大驱动力,因此不同环境对浮游动物的影响是较为活跃的研究方面.无论在我国还足在世界上,浮游动物对环境适应的研究是薄弱环节,研究方法的缺乏是重要的原因.近年来,已经解决了利用现场调查获得的多学科观测数据和资料(field data)结合统计方法求得种类最适温度、最适温度区间等生态学参数的技术难点.yield-density函数模型,麦夸特(Marquardt)法曲线拟合,中值定理,龙贝格(Romberg)积分法计算等数学方法得到应用.这些研究方法应用在生态类群划分是一项创新,对于浮游动物多样性成因分析有重大意义,未来浮游动物多样性应从不同生境、不同时空尺度、不同分类单元、不同粒径谱、不同生态类群和不同测度方法等多个方向展开,而这些领域的应用研究是浮游动物多样性最具前景的方向.     

A pathogenic cytochrome b mutation reveals new interactions between subunits of the mitochondrial bc1 complex

Energy transduction in mitochondria involves five oligomeric complexes embedded within the inner membrane. They are composed of catalytic and noncatalytic subunits, the role of these latter proteins often being difficult to assign. One of these complexes, the bc1 complex, is composed of three catalytic subunits including cytochrome b and seven or eight noncatalytic subunits. Recently, several mutations in the human cytochrome b gene have been linked to various diseases. We have studied in detail the effects of a cardiomyopathy generating mutation G252D in yeast. This mutation disturbs the biogenesis of the bc1 complex at 36 degrees C and decreases the steady-state level of the noncatalytic subunit Qcr9p. In addition, the G252D mutation and the deletion of QCR9 show synergetic defects that can be partially bypassed by suppressor mutations at position 252 and by a new cytochrome b mutation, P174T. Altogether, our results suggest that the supernumerary subunit Qcr9p enhances or stabilizes the interactions between the catalytic subunits, this role being essential at high temperature.