Population Structure of the Endangered Franciscana Dolphin (Pontoporia blainvillei): Reassessing Management Units

Franciscanas are the most endangered dolphins in the Southwestern Atlantic. Due to their coastal and estuarine habits, franciscanas suffer from extensive fisheries bycatch, as well as from habitat loss and degradation. Four Franciscana Management Areas (FMA), proposed based on biology, demography, morphology and genetic data, were incorporated into management planning and in the delineation of research efforts. We re-evaluated that proposal through the analysis of control region sequences from franciscanas throughout their distribution range (N = 162), including novel sequences from the northern limit of the species and two other previously unsampled localities in Brazil. A deep evolutionary break was observed between franciscanas from the northern and southern portions of the species distribution, indicating that they must be managed as two Evolutionarily Significant Units (ESU). Furthermore, additional FMAs should be recognised to accommodate the genetic differentiation found in each ESU. These results have immediate consequences for the conservation and management of this endangered species.     

Phylogeography of the Sponge Suberites diversicolor in Indonesia: Insights into the Evolution of Marine Lake Populations

The existence of multiple independently derived populations in landlocked marine lakes provides an opportunity for fundamental research into the role of isolation in population divergence and speciation in marine taxa. Marine lakes are landlocked water bodies that maintain a marine character through narrow submarine connections to the sea and could be regarded as the marine equivalents of terrestrial islands. The sponge Suberites diversicolor (Porifera: Demospongiae: Suberitidae) is typical of marine lake habitats in the Indo-Australian Archipelago. Four molecular markers (two mitochondrial and two nuclear) were employed to study genetic structure of populations within and between marine lakes in Indonesia and three coastal locations in Indonesia, Singapore and Australia. Within populations of S. diversicolor two strongly divergent lineages (A & B) (COI: p = 0.4% and ITS: p = 7.3%) were found, that may constitute cryptic species. Lineage A only occurred in Kakaban lake (East Kalimantan), while lineage B was present in all sampled populations. Within lineage B, we found low levels of genetic diversity in lakes, though there was spatial genetic population structuring. The Australian population is genetically differentiated from the Indonesian populations. Within Indonesia we did not record an East-West barrier, which has frequently been reported for other marine invertebrates. Kakaban lake is the largest and most isolated marine lake in Indonesia and contains the highest genetic diversity with genetic variants not observed elsewhere. Kakaban lake may be an area where multiple putative refugia populations have come into secondary contact, resulting in high levels of genetic diversity and a high number of endemic species.     

Pangaea and the Out-of-Africa Model of Varicella-Zoster Virus Evolution and Phylogeography

The goal of this minireview is to provide an overview of varicella-zoster virus (VZV) phylogenetics and phylogeography when placed in the broad context of geologic time. Planet Earth was formed over 4 billion years ago, and the supercontinent Pangaea coalesced around 400 million years ago (mya). Based on detailed tree-building models, the base of the phylogenetic tree of the Herpesviridae family has been estimated at 400 mya. Subsequently, Pangaea split into Laurasia and Gondwanaland; in turn, Africa rifted from Gondwanaland. Based on available data, the hypothesis of this minireview is that the ancestral alphaherpesvirus VZV coevolved in simians, apes, and hominins in Africa. When anatomically modern humans first crossed over the Red Sea 60,000 years ago, VZV was carried along in their dorsal root ganglia. Currently, there are five VZV clades, distinguishable by single nucleotide polymorphisms. These clades likely represent continued VZV coevolution, as humans with latent VZV infection left Arabia and dispersed into Asia (clades 2 and 5) and Europe (clades 1, 3, and 4). The prototype VZV sequence contains nearly 125,000 bp, divided into 70 open reading frames. Generally, isolates within a clade display >99.9% identity to one another, while members of one clade compared to a second clade show 99.8% identity to one another. Recently, four different VZV genotypes that do not segregate into the previously defined five clades have been identified, a result indicating a wider than anticipated diversity among newly collected VZV strains around the world.     

濒危植物连香树居群的遗传多样性和遗传分化研究

利用ISSR分子标记技术对濒危植物连香树10个居群的遗传多样性和遗传变异进行了分析,结果表明:连香树物种水平遗传多样性较高,多态位点百分率(PPB)达到69.59%,Nei’s基因多样性指数(H)和Shannon信息指数(I)分别为0.231 3和0.351 4;而在居群水平上,多态位点百分率(PPB)为30.61%,Nei’s基因多样性指数(H)和Shannon信息指数(I)分别为0.115 6和0.173 3。遗传变异分析表明,居群间遗传分化程度高,遗传分化系数(GST)为0.500 3,居群间基因流Nm为0.527 3。Mantel检测,居群间的遗传距离和地理距离之间不存在显著的相关性。生境的片断化使居群间的基因流受阻,可能是导致居群间高遗传分化和居群水平低遗传多样性的主要原因。     

Intraspecific Phylogeography of Lacerta vivipara and the Evolution of Viviparity

The lacertid lizard Lacerta vivipara is one of the few squamate species with two reproductive modes. We present the intraspecific phylogeny obtained from neighbor-joining and maximum-parsimony analyses of the mtDNA cytochrome b sequences for 15 individuals from Slovenian oviparous populations, 34 individuals from western oviparous populations of southern France and northern Spain, 92 specimens from European and Russian viviparous populations, and 3 specimens of the viviparous subspecies L. v. pannonica. The phylogeny indicates that the evolutionary transition from oviparity to viviparity probably occurred once in L. vivipara. The western oviparous group from Spain and southern France is phylogenetically most closely related to the viviparous clade. However, the biarmed W chromosome characterizing the western viviparous populations is an apomorphic character, whereas the uniarmed W chromosome, existing both in the western oviparous populations and in the geographically distant eastern viviparous populations, is a plesiomorphic character. This suggests an eastern origin of viviparity. Various estimates suggest that the oviparous and viviparous clades of L. vivipara split during the Pleistocene. Our results are discussed in the framework of general evolutionary models: the concept of an oviparity–viviparity continuum in squamates, the cold climate model of selection for viviparity in squamates, and the contraction–expansion of ranges in the Pleistocene resulting in allopatric differentiation.     

Spatial Genetic Structure and Mitochondrial DNA Phylogeography of Argentinean Populations of the Grasshopper Dichroplus elongatus

Many grasshopper species are considered of agronomical importance because they cause damage to pastures and crops. Comprehension of pest population dynamics requires a clear understanding of the genetic diversity and spatial structure of populations. In this study we report on patterns of genetic variation in the South American grasshopper Dichroplus elongatus which is an agricultural pest of crops and forage grasses of great economic significance in Argentina. We use Direct Amplification of Minisatellite Regions (DAMD) and partial sequences of the cytochrome oxydase 1 (COI) mitochondrial gene to investigate intraspecific structure, demographic history and gene flow patterns in twenty Argentinean populations of this species belonging to different geographic and biogeographic regions. DAMD data suggest that, although genetic drift and migration occur within and between populations, measurable relatedness among neighbouring populations declines with distance and dispersal over distances greater than 200 km is not typical, whereas effective gene flow may occur for populations separated by less than 100 km. Landscape analysis was useful to detect genetic discontinuities associated with environmental heterogeneity reflecting the changing agroecosystem. The COI results indicate the existence of strong genetic differentiation between two groups of populations located at both margins of the Paraná River which became separated during climate oscillations of the Middle Pleistocene, suggesting a significant restriction in effective dispersion mediated by females and large scale geographic differentiation. The number of migrants between populations estimated through mitochondrial and DAMD markers suggest that gene flow is low prompting a non-homogeneous spatial structure and justifying the variation through space. Moreover, the genetic analysis of both markers allows us to conclude that males appear to disperse more than females, reducing the chance of the genetic loss associated with recent anthropogenic fragmentation of the D. elongatus studied range.     

High Connectivity of Animal Populations in Deep-Sea Hydrothermal Vent Fields in the Central Indian Ridge Relevant to Its Geological Setting

Dispersal ability plays a key role in the maintenance of species in spatially and temporally discrete niches of deep-sea hydrothermal vent environments. On the basis of population genetic analyses in the eastern Pacific vent fields, dispersal of animals in the mid-oceanic ridge systems generally appears to be constrained by geographical barriers such as trenches, transform faults, and microplates. Four hydrothermal vent fields (the Kairei and Edmond fields near the Rodriguez Triple Junction, and the Dodo and Solitaire fields in the Central Indian Ridge) have been discovered in the mid-oceanic ridge system of the Indian Ocean. In the present study, we monitored the dispersal of four representative animals, Austinograea rodriguezensis, Rimicaris kairei, Alviniconcha and the scaly-foot gastropods, among these vent fields by using indirect methods, i.e., phylogenetic and population genetic analyses. For all four investigated species, we estimated potentially high connectivity, i.e., no genetic difference among the populations present in vent fields located several thousands of kilometers apart; however, the direction of migration appeared to differ among the species, probably because of different dispersal strategies. Comparison of the intermediate-spreading Central Indian Ridge with the fast-spreading East Pacific Rise and slow-spreading Mid-Atlantic Ridge revealed the presence of relatively high connectivity in the intermediate- and slow-spreading ridge systems. We propose that geological background, such as spreading rate which determines distance among vent fields, is related to the larval dispersal and population establishment of vent-endemic animal species, and may play an important role in controlling connectivity among populations within a biogeographical province.     

Genetic Structure in Remnant Populations of an Endangered Andean Magnolia

By genetically characterizing adult individuals, we documented the presumed prefragmentation population structure of an endangered Andean tree, Magnolia espinalii. Our sample included all known surviving individuals for this species. Genetic diversity was high, but genetic distance was not related to geographic distance between sites. Magnolia espinalii apparently was originally distributed in numerous semi‐isolated demes. The lack of evidence of recruitment around most adults in this species suggests a fragmentation‐related disruption of their reproductive ecology. Artificial propagation projects should obviously attempt to involve all 23 known surviving trees.     

Response of Endangered Desert Fish Populations to a Constructed Refuge

The U.S. Bureau of Reclamation created a shallow, 110-m channel to provide habitat for two endangered fishes, Cyprinodon elegans (Comanche Springs pupfish) and Gambusia nobilis (Pecos gambusia), at the site of the fishes' former natural habitat. The ciénega (marsh) associated with Phantom Lake Spring in Jeff Davis County, Texas, was destroyed by the creation of an irrigation canal system. In 1993, the endangered fishes were stocked into the refuge with individuals from the irrigation canals, and in the case of C. elegans, hatchery stocks. The condition of habitat, status of fish populations, and fish ecology within the refuge were then monitored for two years. The abundance and density of both species increased in accordance with aquatic plant development. Cyprinodon elegans abundance peaked after one year and stabilized at an average density of 14.7/m² by the end of our study. Juvenile C. elegans were always rare, which may indicate that the population reached the refuge's carrying capacity and that recruitment is low. Gambusia nobilis was the most abundant fish in the refuge (average density 96/m²), used the entire refuge, and outcom-peted nonindigenous G. geiseri. The two Gambusia species used similar habitats but showed almost no dietary overlap. High densities of aquatic plants reduced the amount of open water areas necessary for C. elegans. The refuge will sustain the two endangered fishes at this historic site of endemism while maintaining flow to the irrigation system; however, the refuge is not equivalent to a restored ciénega.     

Non-Selective Evolution of Growing Populations

Non-selective effects, like genetic drift, are an important factor in modern conceptions of evolution, and have been extensively studied for constant population sizes (Kimura, 1955; Otto and Whitlock, 1997). Here, we consider non-selective evolution in the case of growing populations that are of small size and have varying trait compositions (e.g. after a population bottleneck). We find that, in these conditions, populations never fixate to a trait, but tend to a random limit composition, and that the distribution of compositions “freezes” to a steady state. This final state is crucially influenced by the initial conditions. We obtain these findings from a combined theoretical and experimental approach, using multiple mixed subpopulations of two Pseudomonas putida strains in non-selective growth conditions (Matthijs et al, 2009) as model system. The experimental results for the population dynamics match the theoretical predictions based on the Pólya urn model (Eggenberger and Pólya, 1923) for all analyzed parameter regimes. In summary, we show that exponential growth stops genetic drift. This result contrasts with previous theoretical analyses of non-selective evolution (e.g. genetic drift), which investigated how traits spread and eventually take over populations (fixate) (Kimura, 1955; Otto and Whitlock, 1997). Moreover, our work highlights how deeply growth influences non-selective evolution, and how it plays a key role in maintaining genetic variability. Consequently, it is of particular importance in life-cycles models (Melbinger et al, 2010; Cremer et al, 2011; Cremer et al, 2012) of periodically shrinking and expanding populations.     

Distinct and Diverse: Range-Wide Phylogeography Reveals Ancient Lineages and High Genetic Variation in the Endangered Okapi (Okapia johnstoni)

The okapi is an endangered, evolutionarily distinctive even-toed ungulate classified within the giraffidae family that is endemic to the Democratic Republic of Congo. The okapi is currently under major anthropogenic threat, yet to date nothing is known about its genetic structure and evolutionary history, information important for conservation management given the species'' current plight. The distribution of the okapi, being confined to the Congo Basin and yet spanning the Congo River, also makes it an important species for testing general biogeographic hypotheses for Congo Basin fauna, a currently understudied area of research. Here we describe the evolutionary history and genetic structure of okapi, in the context of other African ungulates including the giraffe, and use this information to shed light on the biogeographic history of Congo Basin fauna in general. Using nuclear and mitochondrial DNA sequence analysis of mainly non-invasively collected samples, we show that the okapi is both highly genetically distinct and highly genetically diverse, an unusual combination of genetic traits for an endangered species, and feature a complex evolutionary history. Genetic data are consistent with repeated climatic cycles leading to multiple Plio-Pleistocene refugia in isolated forests in the Congo catchment but also imply historic gene flow across the Congo River.     

生境破碎化后濒危植物缙云卫矛种群的数量动态

运用种群静态生命表、生殖力表和Leslie矩阵模型,研究了重庆特有濒危植物缙云卫矛在北温泉、鸡公山和东温泉3个片断生境中种群的数量动态。静态生命表结果显示3个种群的最大龄级分别为14、13、9龄;相对于其它两个种群,北温泉种群表现出数量较多的幼苗,但同时该样地幼苗种群表现出较高的种群消失率（K_x）。种群生殖力表显示3个种群的净增殖率（R₀）均大于1,内禀增长率（r_m）均大于0,表明缙云卫矛种群可以完成自我更新,种群表现出正增长。Leslie矩阵模型对缙云卫矛种群进行的数量预测结果显示缙云卫矛3个种群20年后均表现出数量的增长,这与生殖力表显示的结果一致。缙云卫矛的濒危可能是其生境破碎化引起的。     

Restoration Ecology of an Endangered Plant Species: Establishment of New Populations of Cirsium pitcheri

We determined the effects of shade, burial by sand, simulated herbivory, and fertilizers on the survival and growth of artificially planted population of Cirsium pitcheri—an endangered plant species of the sand dunes along Lake Huron. Sand burial experiments showed that greenhouse grown plants should optimally be transplanted into areas receiving 5 cm of sand deposition: burial at this depth maximized emergence, survivorship, and below‐ground biomass. Under field conditions, simulated herbivory of up to 50% of the plant height produced a slight increase in biomass after one year of growth. Field observations showed that when white‐tailed deer removed more than 50% of the transplant's leaf tissue, the plant died. The application of a 20:20:20 (N:P:K) water‐soluble fertilizer produced a significant increase in the dry leaf biomass, total leaf area, and total dry biomass relative to control plants. We also tested for the presence or absence of a persistent seed bank. Few seeds were recovered from soil samples collected from Pinery Provincial Park and Providence Bay. However, C. pitcheri has the ability to form a persistent seed bank under field conditions but only at soil depths of 15 cm. Cirsium pitcheri seeds are able to germinate and seedlings can emerge from a burial depth of up to 6 cm. Thus, seeds planted in open, sunny areas will probably maximize emergence, growth, and survivorship of seedlings. Populations of C. pitcheri can be restored by planting seeds at shallow depths, transplanting greenhouse‐grown plants, applying water soluble fertilizers, and protecting plants from herbivores.     

On the Evolution of Behavioral Heterogeneity in Individuals and Populations

A wide range of ecological and evolutionary models predict variety in phenotype or behavior when a population is at equilibrium. This heterogeneity can be realized in different ways. For example, it can be realized through a complex population of individuals exhibiting different simple behaviors, or through a simple population of individuals exhibiting complex, varying behaviors. In some theoretical frameworks these different realizations are treated as equivalent, but natural selection distinguishes between these two alternatives in subtle ways. By investigating an increasingly complex series of models, from a simple fluctuating selection model up to a finite population hawk/dove game, we explore the selective pressures which discriminate between pure strategists, mixed at the population level, and individual mixed strategists. Our analysis reveals some important limitations to the ESS framework often employed to investigate the evolution of complex behavior.     

极小种群野生植物海南风吹楠的遗传多样性研究

为探讨海南风吹楠(Horsfieldia hainanensis)的濒危原因,利用限制性酶切位点相关的DNA测序技术(RAD-seq)开发单核苷酸多态性(SNPs),评估居群的遗传多样性和遗传结构.结果表明,海南风吹楠的遗传多样性较低(Ho=0.167),其中BWL居群表现出最高的遗传多样性;居群间存在中等程度的遗传分...     

Conservation Genetics of the Critically Endangered Riverine Rabbit,Bunolagus monticularis: Structured Populations and High mtDNA Genetic Diversity

Journal of Mammalian Evolution - The riverine rabbit, Bunolagus monticularis, is regarded critically endangered. This endemic South African leporid is believed to have extremely low population...     

Evolution and Phylogeography of the Nonpathogenic Calicivirus RCV-A1 in Wild Rabbits in Australia

Despite its potential importance for the biological control of European rabbits, relatively little is known about the evolution and molecular epidemiology of rabbit calicivirus Australia 1 (RCV-A1). To address this issue we undertook an extensive evolutionary analysis of 36 RCV-A1 samples collected from wild rabbit populations in southeast Australia between 2007 and 2009. Based on phylogenetic analysis of the entire capsid sequence, six clades of RCV-A1 were defined, each exhibiting strong population subdivision. Strikingly, our estimates of the time to the most recent common ancestor of RCV-A1 coincide with the introduction of rabbits to Australia in the mid-19th century. Subsequent divergence events visible in the RCV-A1 phylogenies likely reflect key moments in the history of the European rabbit in Australia, most notably the bottlenecks in rabbit populations induced by the two viral biocontrol agents used on the Australian continent, myxoma virus and rabbit hemorrhagic disease virus (RHDV). RCV-A1 strains therefore exhibit strong phylogeographic separation and may constitute a useful tool to study recent host population dynamics and migration patterns, which in turn could be used to monitor rabbit control in Australia.Lagoviruses form a genus within the Caliciviridae family of RNA viruses (16). All representatives of this genus are highly species specific and infect only their respective hosts, i.e., rabbits and hares. The prototype species of the genus Lagovirus is rabbit hemorrhagic disease virus (RHDV), which was first described in China in 1984 when a severe infectious necrotizing hepatitis with mortality rates up to 90% was observed in angora rabbits (22). However, phylogenetic analysis indicates that the pathogenic strains of RHDV likely evolved from nonpathogenic lagoviruses several decades before they were initially described (20). Today, RHDV is found on most continents, causing ongoing damage to the rabbit meat industry (24) and threatening wild native rabbit populations in Europe. On the Iberian peninsula the rabbit is considered an endangered species and is itself a staple food of endangered predators, such as the imperial eagle and the Iberian lynx (10).In marked contrast, since 1995 Australia has been using RHDV as a successful viral biocontrol agent for rabbits (7), which cause severe environmental and economic damage in this country. The use of a viral biocontrol agent for a vertebrate species has been and remains controversial, but there is little doubt that since its release RHDV has generated close to $6 billion of savings to the Australian agricultural industry (41), as well as some much needed relief for the regeneration of many native plant species (35).Notably, RHDV-induced mortality is lower in certain areas of Australia, namely, the cooler and more humid southeast region of the continent, which is believed to be in part due to the presence of related but nonpathogenic lagoviruses circulating in the population (8). Recently, such a virus was identified in Australian wild rabbits (38). This new member of the genus Lagovirus, termed rabbit calicivirus Australia 1 (RCV-A1), is a nonpathogenic virus causing a predominantly enteric infection in rabbits. Other benign or moderately pathogenic RCV strains have also been described in the United States and Europe (1, 5, 14, 15). While the Italian nonpathogenic RCV provides complete cross-immunity to RHDV, only partial protection is conveyed by the Australian virus RCV-A1 (37) although this may be sufficient to reduce overall RHDV-induced mortality.Like all lagoviruses, RCV-A1 has a single-stranded positive-sense RNA genome of approximately 7.5 kb that is polyadenylated and has a viral protein (VpG) covalently bound to its 5′ end (25). The genome is organized into two open reading frames (ORFs) (6, 39). ORF1, which represents the majority (7 kb) of the genome, encodes a polyprotein that is auto-proteolytically cleaved during posttranslational processing into several smaller proteins, including the helicase, protease, and polymerase (26). In contrast, ORF2 is only 351 nucleotides (nt) long, and the function of its VP10 gene product is unknown although it is present in small amounts in the virion (39).Given the potential interactions between RCVs and pathogenic RHDV, which could impact rabbit survival in both Australia and Europe, it is clearly important to understand the evolutionary history, genetic diversity, and geographic distribution of RCV-A1 and other benign lagoviruses. In Australia, growing reports of rising rabbit numbers mean that there is a clear need for improved strategies to monitor and control rabbit populations. In addition, because RCV-A1 does not cause any fitness decrease in its rabbit host (37), it is possible that this virus could be used as a population genetic marker to track movements and changes in the distribution of the European rabbit across the Australian continent. Indeed, other microorganisms have proven to be useful indicators of the population dynamics of their hosts (3, 42). Microbial markers are particularly informative for the study of population processes in the very recent past since genetic changes will not have had sufficient time to be recorded in the more slowly evolving host genome (2).The host-pathogen interaction of Australian rabbits and their viruses is unique in that both were introduced only once (or possibly a few times in a limited period of time). In addition, 150 years of historical records are available documenting the introduction, spread, and control efforts of rabbits in Australia. Herein, we explore the evolutionary history and dynamics of RCV-A1 in Australia, with a particular focus on revealing the phylogeographic distribution of the virus across this continent, the evolutionary processes that have shaped its diversity, and its suitability as a marker to study host distribution and migration patterns.     

不同天然居群小蓬竹的遗传多样性

从分子水平探讨不同居群小蓬竹的遗传多样性以及与环境因子的相关性,揭示其濒危原因,为小蓬竹的保护和后续开发利用提供理论支撑,助力实施极危物种最佳保护策略。运用RAPD标记技术和POPGENE32对16个小蓬竹天然居群进行遗传多样性研究和遗传变异分析。结果表明,8个RAPD随机引物共扩增出105条清晰、重复性高的条带,其中多态性条带有98条,分子量300~2000bp;物种水平多态性位点百分率PPL=93.33%,有效等位基因数Ne=1.4942,Nei’s基因多样性H=0.3005,Shannon多样性指数I=0.4586;落湾(ZY1)居群的遗传多样性水平最高(PPL=60.95%,H=0.2329,I=0.3451),[JP3]桃坡(PT1)居群的最低(PPL=44.76%,H=0.1700,[JP]I=0.2523);16个天然居群的遗传分化系数Gst=0.3231,基因流Nm=1.0478,基于Shannon’s多样性指数的分化系数[(HSP-HPOP)/HSP]为0.3429。小蓬竹居群内存在丰富的遗传多样性,各个天然居群间具有一定的遗传分化但分化水平并不高,主要的遗传变异存在于居群内部。