Recent origin,active speciation and dispersal for the lichen genus Nephroma (Peltigerales) in Macaronesia

Aim We reconstructed the phylogeny of the lichen genus Nephroma (Peltigerales) to assess the relationships of species endemic to Macaronesia. We estimated dates of divergences to test the hypothesis that the species arose in Macaronesia (neo‐endemism) versus the oceanic archipelagos serving as refugia for formerly widespread taxa (palaeo‐endemism). Location Cosmopolitan with a special focus on the archipelagos of the Azores, Madeira and the Canary Islands. Methods DNA sequences were obtained from 18 species for three loci and analysed using maximum parsimony, maximum likelihood and Bayesian inferences. Divergence dates were estimated for the internal transcribed spacer (ITS)‐based phylogeny using a relaxed molecular clock. Reconstruction of the ancestral geographical range was conducted using the Bayesian 50% majority rule consensus tree under a parsimony method. Results The backbone phylogenetic tree was fully supported, with Nephroma plumbeum as sister to all other species. Four strongly supported clades were detected: the Nephroma helveticum, the N. bellum, the N. laevigatum and the N. parile clades. The latter two share a common ancestor and each includes a widespread Holarctic species (N. laevigatum and N. parile, respectively) and all species endemic to Macaronesia. The data suggest a neo‐endemic origin of Macaronesian taxa, a recent range expansion from Macaronesia of both widespread species, a range expansion limited to the Mediteranean Basin and south‐western Europe for another taxon, and a long dispersal event that resulted in a speciation event in the western parts of North America. Main conclusions The Macaronesian endemic species belong to two sister clades and originated from a most recent common ancestor (MRCA) shared with one widely distributed taxon, either N. parile or N. laevigatum. Estimates of the mean divergence dates suggest that the endemics originated in the archipelagos after the rise of the volcanic islands, along with the ancestor to the now widespread species, which probably expanded their range beyond Macaronesia via long‐distance dispersal. This study provides the first phylogenetic evidence of Macaronesian neo‐endemism in lichenized fungi and provides support for the hypothesis that oceanic islands may serve as a source for the colonization of continents. However, further data are needed to properly assess the alternative hypothesis, namely colonization from western North America.     

Generalized Verlet Algorithm for Efficient Molecular Dynamics Simulations with Long-range Interactions

For the purpose of molecular dynamics simulations of large biopolymers we have developed a new method to accelerate the calculation of long-range pair interactions (e.g. Coulomb interaction). The algorithm introduces distance classes to schedule updates of non-bonding interactions and to avoid unnecessary computations of interactions between particles which are far apart. To minimize the error caused by the updating schedule, the Verlet integration scheme has been modified. The results of the method are compared to those of other approximation schemes as well as to results obtained by numerical integration without approximation. For simulation of a protein with 12 637 atoms our approximation scheme yields a reduction of computer time by a factor of seven. The approximation suggested can be implemented on sequential as well as on parallel computers. We describe an implementation on a (Transputer-based) MIMD machine with a systolic ring architecture.     

Low genetic diversity and limited genetic structure across the range of the critically endangered Mexican howler monkey (Alouatta palliata mexicana)

Genetic diversity provides populations with the possibility to persist in ever-changing environments, where selective regimes change over time. Therefore, the long-term survival of a population may be affected by its level of genetic diversity. The Mexican howler monkey (Alouatta palliata mexicana) is a critically endangered primate restricted to southeast Mexico. Here, we evaluate the genetic diversity and population structure of this subspecies based on 83 individuals from 31 groups sampled across the distribution range of the subspecies, using 29 microsatellite loci. Our results revealed extremely low genetic diversity (H_O = 0.21, H_E = 0.29) compared to studies of other A. palliata populations and to other Alouatta species. Principal component analysis, a Bayesian clustering method, and analyses of molecular variance did not detect strong signatures of genetic differentiation among geographic populations of this subspecies. Although we detect small but significant F_ST values between populations, they can be explained by a pattern of isolation by distance. These results and the presence of unique alleles in different populations highlight the importance of implementing conservation efforts in multiple populations across the distribution range of A. p. mexicana to preserve its already low genetic diversity. This is especially important given current levels of population isolation due to the extreme habitat fragmentation across the distribution range of this primate.     

Using density surface models to estimate spatio-temporal changes in population densities and trend

Precise measures of population abundance and trend are needed for species conservation; these are most difficult to obtain for rare and rapidly changing populations. We compare uncertainty in densities estimated from spatio–temporal models with that from standard design-based methods. Spatio–temporal models allow us to target priority areas where, and at times when, a population may most benefit. Generalised additive models were fitted to a 31-year time series of point-transect surveys of an endangered Hawaiian forest bird, the Hawai‘i ‘ākepa Loxops coccineus. This allowed us to estimate bird densities over space and time. We used two methods to quantify uncertainty in density estimates from the spatio–temporal model: the delta method (which assumes independence between detection and distribution parameters) and a variance propagation method. With the delta method we observed a 52% decrease in the width of the design-based 95% confidence interval (CI), while we observed a 37% decrease in CI width when propagating the variance. We mapped bird densities as they changed across space and time, allowing managers to evaluate management actions. Integrating detection function modelling with spatio–temporal modelling exploits survey data more efficiently by producing finer-grained abundance estimates than are possible with design-based methods as well as producing more precise abundance estimates. Model-based approaches require switching from making assumptions about the survey design to assumptions about bird distribution. Such a switch warrants consideration. In this case the model-based approach benefits conservation planning through improved management efficiency and reduced costs by taking into account both spatial shifts and temporal changes in population abundance and distribution.     

救护白鹤与野生白鹤迁徙路线和活动规律差异分析

受伤和体弱白鹤的救护及放归是白鹤保护的重要方式之一。2014—2016年间,先后对8只救护白鹤和2只野生白鹤进行环志并安装卫星跟踪器,根据所获得的卫星跟踪数据来分析比较救护白鹤与野生白鹤在秋季迁徙路线和在重要中途停歇地的最大日活动距离、活动区分布和面积、生境类型等方面的异同。结果显示,救护白鹤放归当年与放归次年以及救护白鹤放归当年与野生白鹤的秋季迁徙路线和活动规律之间存在明显差异,但救护白鹤放归次年与野生白鹤之间差异不明显。(1)放归当年,4只救护白鹤在农田和水塘停歇1个月左右,停歇时长明显高于野生白鹤和放归次年的救护白鹤。(2)救护白鹤放归当年在跨海方式、登陆地点、停歇地点以及登陆后的迁徙方向上表现出多样性和不确定性,其中部分个体在迁徙过程中有停顿徘徊、迷失迁徙方向的现象,且跨越渤海和大别山的距离大于放归次年的救护白鹤和野生白鹤。(3)救护白鹤放归后4天内每日最大活动距离小,而后高低分化明显,无明显规律,而救护白鹤放归次年的每日最大活动距离规律变化与野生白鹤较一致。(4)与救护白鹤放归次年以及野生白鹤的活动规律相比,救护白鹤放归当年的栖息地位点变化频繁,具体表现为生境类型选择的多样化,且无明显规律,同时活动区面积较小。探索救护白鹤放归野外后与野生白鹤迁徙路线和活动规律的差异,对救护白鹤的科学放归具有指导意义。     

Genetic variation in an ephemeral mudflat species: The role of the soil seed bank and dispersal in river and secondary anthropogenic habitats

Many ephemeral mudflat species, which rely on a soil seed bank to build up the next generation, are endangered in their natural habitat due to the widespread regulation of rivers. The aim of the present study was to elucidate the role of the soil seed bank and dispersal for the maintenance of genetic diversity in populations of near‐natural river habitats and anthropogenic habitats created by traditional fish farming practices using Cyperus fuscus as a model. Using microsatellite markers, we found no difference in genetic diversity levels between soil seed bank and above‐ground population and only moderate differentiation between the two fractions. One possible interpretation is the difference in short‐term selection during germination under specific conditions (glasshouse versus field) resulting in an ecological filtering of genotypes out of the reservoir in the soil. River populations harbored significantly more genetic diversity than populations from the anthropogenic pond types. We suggest that altered levels and patterns of dispersal together with stronger selection pressures and historical bottlenecks in anthropogenic habitats are responsible for the observed reduction in genetic diversity. Dispersal is also supposed to largely prohibit genetic structure across Europe, although there is a gradient in private allelic richness from southern Europe (high values) to northern, especially north‐western, Europe (low values), which probably relates to postglacial expansion out of southern and/or eastern refugia.     

Pollen limitation in the endangered Chinese endemic species Sinocalycanthus chinensis

Pollen limitation negatively impacts endangered and endemic plants with small fragmented populations, such as Sinocalycanthus chinensis, an endangered plant endemic to China. In this study, we analyzed the pollen limitation of the S. chinensis Damingshan (DMS) population in 2006, 2009, and 2010, and crossed plants with mates separated by different distances, both within and between populations. The DMS population exhibited strong pollen limitation in fruit set, seed set, and seeds per fruit in 2006, 2009, and 2010. The average accumulated pollen limitation (for fruit set times seeds per fruit) was 0.510 ± 0.180. Progeny crossed with pollen from intermediate neighboring plants within the same population (separated by 30–50 m from pollen recipients) had the lowest fitness. No optimal outcrossing distance was found within the DMS population. Progeny from crosses with the Shunxiwu (SXW) and Daleishan (DLS) populations performed relatively better, while those from crosses with Qingliangfeng (QLF) and Longxushan (LXS) populations performed worse. Compared with average reproductive success, outbreeding depression was found in progeny from crosses with the LXS and QLF populations. Reproductive success from pure self‐pollination indicated S. chinensis is self‐compatible. Geitonogamous selfing increased reproductive success. Based on geitonogamous selfing, the proportion of selfed offspring was relatively high. These results provide basic references for the conservation of this species.     

Movement of sturgeons (Acipenser oxyrinchus oxyrinchus and A. fulvescens) in the St. Lawrence Estuary: A 35-year tagging study

Movement of Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus) and lake sturgeon (A. fulvescens) in the St. Lawrence Estuary (Québec, Canada) are not fully understood. To assess the movement extent of both species, a mark–recapture study was conducted in collaboration with commercial fishermen operating in the St. Lawrence Estuary. Between 1981 and 2015, 3,367 Atlantic sturgeon (fork length 21.8–199.5 cm) and 3,180 lake sturgeon (fork length 17.8–190.8 cm) were tagged and released. Of these, 673 Atlantic sturgeon and 42 lake sturgeon were recaptured. The maximum distances traveled between capture and recapture locations were 1,307 km for Atlantic sturgeon (8 years after initial capture) and 252 km for lake sturgeon (less than 1 year after initial capture). Statistical analyses identified differences in the dispersal distance of both species as revealed by a first component characterized by individuals with short dispersal distances (98% and <35 km for Atlantic sturgeon; 58% and <1 km for lake sturgeon) and a second component characterized by individuals with longer dispersal distances (2% and >600 km for Atlantic sturgeon; 42% and >190 km for lake sturgeon). We suggest that the short dispersal distances detected in the vast majority of Atlantic sturgeon recaptures likely reflect strong site fidelity, highlighting the importance of the St. Lawrence Estuary as a preferred habitat for juveniles and subadults. Although recaptures were low for lake sturgeon because this species is only marginally targeted by commercial fishermen in the St. Lawrence Estuary, our results also showed that this species uses estuarine habitats and that half of the population seems to exhibit strong site fidelity (67% of individuals were recaptured within 2 km).