Phylogeny and phylogeography of critically endangered Gyps species based on nuclear and mitochondrial markers

Populations of Oriental White-backed Vulture (Gyps bengalensis) and Long-billed Vulture (Gyps indicus) dramatically declined by 95–100% on the Indian subcontinent in mid-1990s. The present study was conducted to discover the phylogeny and phylogeography of Gyps species based on nuclear (recombination activating gene, RAG-1) and mitochondrial (cytochrome b, cytb) markers. Gyps species showed monophyly and no geographic partition was observed within the three groups of Gyps species (G. bengalensis, G. indicus and G. fulvus) despite the large sample size available (n = 149). Our study supports the treatment of G. indicus and G. tenuirostris as separate species. In all analyses, the earliest divergence separated G. bengalensis from all other Gyps taxa while a sister relationship was supported between G. fulvus and G. rueppellii, and these two taxa together were sister group to a clade consisting of G. indicus, G. tenuirostris and G. coprotheres. Molecular clock estimates of both nuclear and mitochondrial (RAG-1, cytb) genes indicated a rapid and recent diversification within the Gyps species. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Inconsistent estimates of diversity between traditional and DNA taxonomy in bdelloid rotifers

Microscopic animals offer great potential in the analysis of spatial patterns of diversity, as they may provide different scenarios for biogeography and macroecology, but understanding diversity of microscopic animals is hampered by lack of comprehensive data on species distribution and by unreliable taxonomy. DNA taxonomy may prove useful in obtaining reliable data in the future, but we still do not know to what extent traditional and DNA taxonomy can be comparable for microscopic organisms. In this paper, we compare analyses and estimates of diversity at the level of species assemblage between traditional and DNA taxonomy for a group of moss-dwelling microscopic animals, bdelloid rotifers. The results are straightforward: Traditional species identification underestimates diversity by factors of 2 at the local and 2.5 at the regional scale. We discuss the results in the framework of current hypotheses on the distribution of microscopic animals.     

Cryptic diversity in a Eurasian water snake (Natrix tessellata, Serpentes: Colubridae): Evidence from mitochondrial sequence data and nuclear ISSR-PCR fingerprinting

The dice snake, Natrix tessellata (Laurenti, 1768), is a suitable study organism to address questions of Eurasian phylogeography due to its wide Palearctic distribution. We analysed complete mitochondrial cytochrome b sequences and nuclear ISSR-PCR fingerprints of more than 300 specimens representing nearly the entire geographic range. Nine major mitochondrial lineages were discovered based on mtDNA sequences. The three most basal lineages comprised populations from Iran, Jordan–Egypt, and Greece, respectively. Other lineages were associated with samples from the Turkish peninsula, the Caucasus, the Aral Sea, and eastern Kazakhstan. A sister-group relationship was found between two lineages from Crete and the European mainland. Assuming an evolutionary rate of 1.35% sequence divergence per million years, among-lineage p-distances of 1.7–8.4% suggest that intraspecific differentiation might date back as far as the Miocene/Pliocene transition 5–6 million years ago. The pattern of genetic differentiation in mitochondrial phylogeny with regard to Asia Minor and the region of the Aral Sea was not congruent with the results of the nuclear ISSR-PCR analyses, and suggests admixing within some mtDNA clades at contact zones. The taxonomic implications of the high intraspecific variation in the dice snake are discussed.     

Mitochondrial diversity of European pond turtles (Emys orbicularis) in Anatolia and the Ponto-Caspian Region: Multiple old refuges, hotspot of extant diversification and critically endangered endemics

The European pond turtle, Emys orbicularis (Linnaeus, 1758), is one of the world's most widely distributed chelonian species. We investigated its mitochondrial phylogeography and demography using ∼1300 cyt b sequences from the entire range, with a focus on the eastern part, in particular on Turkey, where the species currently suffers massive losses. Coloration data from >1450 turtles were compared with mtDNA differentiation to assess the validity of the currently accepted subspecies from Turkey, the Black Sea Region, the Transcaucasus, and Iran. Our study region harbors considerable part of the mtDNA diversity of Emys, including a newly discovered lineage and 16 new haplotypes. In this area corresponding to approximately one-third of the entire distribution range, six out of the ten mitochondrial lineages and about half of all 72 haplotypes occur. Two mitochondrial lineages (VIII, X) are confined to small ranges along the southern coast of Turkey, another lineage (I) occupies the remainder of Turkey, the entire Black Sea Region, and the north-eastern part of the species’ range. In the south-western corner of the Black Sea and in the Aegean Region, two lineages (II, IV) occur that have their main distribution areas farther west. In the Transcaucasus and northern Iran, another endemic lineage (VII) is found. Lineage I is the largest and most diverse of all lineages and has its greatest diversity in Anatolia. Phylogeographic and demographic data suggest Anatolia as an ancient glacial refuge for turtles harboring mitochondrial lineages I, VIII and X, and that Anatolia and the Black Sea coasts constitute a hotspot for a younger burst of diversification within lineage I. These two regions correspond to the glacial refuge from which lineage I turtles recolonized more northerly parts of the range in the Holocene; lineage II represents an off-shoot of lineage I that became isolated in a westward-located refuge in the south-eastern Balkans during a previous Pleistocene glacial. Our data on coloration indicate that such characters have only limited value for delineating evolutionarily significant units. We propose to reduce the number of subspecies using mtDNA lineages as arbiter, and to recognize three subspecies as valid in Turkey, the Black Sea Region, the Transcaucasus and Iran: Emys orbicularis orbicularis (mtDNA lineage I); E. o. eiselti Fritz et al., 1998 (X); and E. o. persica Eichwald, 1831 (VII). However, the southern Turkish lineage VIII most probably represents an additional undescribed subspecies. Both southern Turkish endemics are critically endangered, with only three surviving populations of fewer than 30 adults each. We recommend establishing sanctuaries for them, and including them in the IUCN Red List.     

Phylogeographical Study on Eriophyton wallichii (Labiatae) from Alpine Scree of Qinghai Tibetan Plateau

In this study, we examined the nuclear ribosomal DNA internal transcribed spacer (ITS) sequence variation of Eriophyton wallichii, a perennial endemic to alpine scree of the Qinghai Tibetan Plateau. Nineteen haplotypes were detected by analyzing 187 individuals from 20 populations of E.wallichii. Most populations hold the unique haplotype, which showed different population with different haplotype. An analysis of molecular variance (AMOVA) for populations showed that the genetic variation mainly resided among populations (89.54%), the level of differentiation among populations was very high (GST=0.863; NST=0.957) but didn’t show a significant phylogeographical structure. It is different from foregoing other species reported in Qinghai Tibetan Plateau that the haplotypes of E.wallichii showed a distribution pattern that almost one population hold one unique haplotype, hardly share same halotype among populations.We hypothesized the unique genetic structure of E.wallichii might result from allopatric fragmentation in the “islands of alpine” due to the extremely isolated alpine scree and rough topography of the region, through the Quaternary climate oscillation dramatically caused population expanding or shrinking.     

青藏高原高山流石滩特有植物绵参的谱系地理学研究

绵参(Eriophyton wallichii)是中国青藏高原地区高山流石滩特有植物.为探讨第四纪冰期气候波动对青藏高原高山流石滩植物居群遗传结构以及谱系历史的影响,检测了绵参20个居群187个个体的核糖体内转录间隔区(ITS)的序列变异,共发现19个单倍型,且结果表明大部分居群拥有独自的单倍型.AMOVA分析表明,居群间的变异占了总变异量的89.54％,居群遗传分化指数很高(GST=0.863,NST=0.957),但无明显的谱系结构.我们推测这种独特的谱系地理结构可能主要是由于高山流石滩独特的地形和环境及“孤岛效应”形成的,与先前研究过的青藏高原植物不同,绵参呈现出高度分化的遗传结构,常常呈现出“一个居群,一种单倍型”的模式,这可能是由于第四纪冰期及间冰期尽管绵参的分布范围有扩大和收缩,但始终由于特殊的高山生境和流石滩基质,导致了该物种长期以来居群间很少有基因交流并一直处于隔离状态,造成了现在这样的谱系地理结构.     

Genetic structure of Pseudo-nitzschia pungens (Bacillariophyceae) populations: Implications of a global diversification of the diatom

Pseudo-nitzschia pungens is a planktonic marine diatom known to be widespread in tropical and temperate coastal waters. We examined the population genetic structure of tropical Southeast Asian populations of P. pungens and compared it with those of northern and southern temperate populations. The secondary structures of the nuclear encoded internal transcribed spacer (ITS) region of 164 strains of P. pungens were modeled and analyzed. The tree revealed three ITS entities: clade I (comprised of P. pungens var. pungens) was distributed mainly in northern temperate waters; clade II (comprised of both P. pungens var. pungens and var. cingulata) was mainly from the NE Pacific; and clade III (comprised of both P. pungens var. pungens and var. aveirensis) was restricted to tropical and warm-temperate waters. Hybrids of both P. pungens var. pungens and var. cingulata co-occurred in clades I and II. Sixty haplotypes were revealed from the sequences of 164 strains. Haplotype diversity inferred from the median-joining network was in accordance with phylogenetic analysis, further supporting the grouping of the P. pungens haplogroups. Our results revealed limited gene flow between P. pungens from tropical and temperate waters, and significant population structure, as estimated by an analysis of molecular variance (AMOVA), with 75% of the total ITS variation found among populations (Ф_ST = 0.75). This study suggests that distinct environmental clines, such as ocean thermohaline circulation, have a potential for fragmenting and dispersing global populations of P. pungens. Formation of the Isthmus of Panama, in particular, is speculated to play a role in this allopatric differentiation in P. pungens populations worldwide.     

Mitochondrial DNA phylogeography reveals the existence of an Evolutionarily Significant Unit of the sand goby Pomatoschistus minutus in the Adriatic (Eastern Mediterranean)

The sand goby Pomatoschistus minutus is a major component of marine shelf and estuarine food webs and an important study organism in behavioural research. Yet, despite the sand goby’s significance, its past and present patterns of migration and gene flow are poorly understood. Here we use the mtDNA control region and parts of the flanking tRNA genes of 63 fish from six localities in the Adriatic (Eastern Mediterranean), Western Mediterranean, Atlantic, and North Sea to investigate the phylogeography of this gobiid. Phylogenetic analyses and population genetics statistics reveal the existence of an Evolutionarily Significant Unit, sensu Moritz (1994), in the Adriatic and another in the Western Mediterranean, Atlantic, and North Sea. A possible biogeographical scenario for the separation of the ancestral population is that sand gobies in the Adriatic and Western Mediterranean split between 10,000 and 5000 years ago when due to the rise in sea temperature they migrated northwards and were bisected by the Italian peninsula. A testable prediction of this scenario is that sand gobies from the Western Mediterranean, Adriatic, and Aegean form three reciprocally monophyletic groups which are the descendants of a three-way diversification event.     

Russula velenovskyi new to Japan,with phylogenetic implications of Russula species between Japanese subalpine forests and Northern Europe

To compare morphological characters and phylogenetic placement between Japanese and European Russula, 32 specimens of 12 species were collected from Japanese subalpine forests and Northern Europe. Several sequences of nrDNA ITS region (ITS) of these Russula species were obtained. High homological similarities were shown between ITS sequences of several Russula samples collected from Japanese subalpine forests, Europe and North America. These facts show distribution of the same Russula species among these areas. From morphological observations and phylogenetic analyses, two same Russula species, R. velenovskyi, and R. decolorans are found in Japan, Europe and North America. Of these, R. velenovskyi collected from Mt. Fuji, Mt. Nyukasa and Mt. Tateshina in mountainous area of central Honshu is reported as a new Japanese record.     

Assessing global range expansion in a cryptic species complex: insights from the red seaweed genus Asparagopsis (Florideophyceae)

The mitochondrial genetic diversity, distribution and invasive potential of multiple cryptic operational taxonomic units (OTUs) of the red invasive seaweed Asparagopsis were assessed by studying introduced Mediterranean and Hawaiian populations. Invasive behavior of each Asparagopsis OTU was inferred from phylogeographic reconstructions, past historical demographic dynamics, recent range expansion assessments and future distributional predictions obtained from demographic models. Genealogical networks resolved Asparagopsis gametophytes and tetrasporophytes into four A. taxiformis and one A. armata cryptic OTUs. Falkenbergia isolates of A. taxiformis L3 were recovered for the first time in the western Mediterranean Sea and represent a new introduction for this area. Neutrality statistics supported past range expansion for A. taxiformis L1 and L2 in Hawaii. On the other hand, extreme geographic expansion and an increase in effective population size were found only for A. taxiformis L2 in the western Mediterranean Sea. Distribution models predicted shifts of the climatically suitable areas and population expansion for A. armata L1 and A. taxiformis L1 and L2. Our integrated study confirms a high invasive risk for A. taxiformis L1 and L2 in temperate and tropical areas. Despite the differences in predictions among modelling approaches, a number of regions were identified as zones with high invasion risk for A. taxiformis L2. Since range shifts are likely climate‐driven phenomena, future invasive behavior cannot be excluded for the rest of the lineages.