Landscape genetics of California mule deer (Odocoileus hemionus): the roles of ecological and historical factors in generating differentiation

Landscape genetics is an emerging discipline that utilizes environmental and historical data to understand geographic patterns of genetic diversity. Niche modelling has added a new dimension to such efforts by allowing species–environmental associations to be projected into the past so that hypotheses about historical vicariance can be generated and tested independently with genetic data. However, previous approaches have primarily utilized DNA sequence data to test inferences about historical isolation and may have missed very recent episodes of environmentally mediated divergence. We type 15 microsatellite loci in California mule deer and identify five genetic groupings through a Structure analysis that are also well predicted by environmental data. We project the niches of these five deer ecotypes to the last glacial maximum (LGM) and show they overlap to a much greater extent than today, suggesting that vicariance associated with the LGM cannot explain the present-day genetic patterns. Further, we analyse mitochondrial DNA (mtDNA) sequence trees to search for evidence of historical vicariance and find only two well-supported clades. A coalescence-based analysis of mtDNA data shows that the genetic divergence of the mule deer genetic clusters in California is recent and appears to be mediated by ecological factors. The importance of environmental factors in explaining the genetic diversity of California mule deer is unexpected given that they are highly mobile species and have a broad habitat distribution. Geographic differences in the timing of reproduction and peak vegetation as well as habitat choice reflecting natal origin may explain the persistence of genetic subdivision.     

黑龙江省胜山林场冬季驼鹿、马鹿和狍的种间关系

1987—1989年的两个冬季在黑龙江省黑河市胜山林场,对驼鹿、马鹿和狍的食性、采食高度和栖息地进行了研究。驼鹿的主要食物是柳(22.4％)、榛(16.0％)、红松(14.3％)和桦(13.8％);马鹿为杨(36.0％)、桦(22.7％)和红松(17.3％);狍为桦(26.5％)、柳(19.0％)、杨(12.7％)。三种动物采食高度的频次为正态分布。驼鹿的采食高度(标准差)为137.4(±39.0)厘米;马鹿为136.2(±37.0)厘米;狍为84.2(±29.2)厘米。驼鹿和马鹿对红松林的利用程度最高,而狍主要利用沼泽植物和红松林。驼鹿与狍在食物维和栖息地维上的生态位重叠最大,驼鹿与马鹿在采食高度维上的重叠最大。三种动物在食物、采食高度和栖息地三维生态位上的重叠大小的顺序为:驼鹿和马鹿>驼鹿和狍>马鹿和狍。     

Selenium concentration in liver and kidney of free living animals (roe and red deer) from West Pomerania (Poland)

The aim of this study was to determine concentrations of selenium in the liver and kidneys of roe deer and red deer from West Pomerania, depending on the season. Altogether, samples from 169 animals were collected (96 from roe deer and 73 from red deer) in 2003–2007. The mean concentration of selenium in the liver of red deer and roe deer was 0.37 μg/g and 0.62 μg/g dry weight, respectively. In kidneys, Se concentration was 2.72 μg/g d.w. in red deer and 2.99 μg/g d.w. in roe deer. In roe deer, liver selenium concentration in autumn was significantly higher than in winter (P < 0.05) and spring (P < 0.01) and significantly lower in spring than in summer (P < 0.05); likewise, kidney selenium concentration was higher in autumn than in summer. In deer, no statistically significant season-related differences were observed for liver selenium concentrations. In red deer kidneys, selenium concentration was the lowest in summer, significantly lower than in autumn and winter. Low selenium concentrations in the analyzed tissues show that the animals live in areas deficient in this element.     

Recovery of a dwarf birch (Betula nana) population following reduction in grazing by red deer (Cervus elaphus)

Summary

In Britain Betula nana is a nationally scarce plant, its distribution being limited by climate, heather burning and grazing by deer and sheep. The recovery of a population of B. nana was monitored for several years inside a Scots pine regeneration exclosure in N.E. Scotland. Browsing pressure was reduced in the exclosure but a few red deer (amounting to 3–4 km^?2) were deliberately retained. B. nana stem density increased after red-deer density was reduced. Over the same period there was a reduction in browsing inside the exclosure. B. nana stem density was negatively related to heather height, deer presence and tree canopy cover. Comparisons of growth were made with plants outside the exclosure between 1998 and 2000, the mean annual increment of stems, allowing for browsing loss, being respectively 1.25 and 0.45 cm for inside and outside the exclosure. Most stem basal diameters inside the exclosure were smaller than outside. Reducing red deer density to 3–4 km^?2 on similar upland sites with peaty soils could lead to regeneration of B. nana.     

An Evaluation of Sex-Age-Kill (SAK) Model Performance

ABSTRACT The sex-age-kill (SAK) model is widely used to estimate abundance of harvested large mammals, including white-tailed deer (Odocoileus virginianus). Despite a long history of use, few formal evaluations of SAK performance exist. We investigated how violations of the stable age distribution and stationary population assumption, changes to male or female harvest, stochastic effects (i.e., random fluctuations in recruitment and survival), and sampling efforts influenced SAK estimation. When the simulated population had a stable age distribution and λ > 1, the SAK model underestimated abundance. Conversely, when λ < 1, the SAK overestimated abundance. When changes to male harvest were introduced, SAK estimates were opposite the true population trend. In contrast, SAK estimates were robust to changes in female harvest rates. Stochastic effects caused SAK estimates to fluctuate about their equilibrium abundance, but the effect dampened as the size of the surveyed population increased. When we considered both stochastic effects and sampling error at a deer management unit scale the resultant abundance estimates were within ±121.9% of the true population level 95% of the time. These combined results demonstrate extreme sensitivity to model violations and scale of analysis. Without changes to model formulation, the SAK model will be biased when λ ≠ 1. Furthermore, any factor that alters the male harvest rate, such as changes to regulations or changes in hunter attitudes, will bias population estimates. Sex-age-kill estimates may be precise at large spatial scales, such as the state level, but less so at the individual management unit level. Alternative models, such as statistical age-at-harvest models, which require similar data types, might allow for more robust, broad-scale demographic assessments.     

Phylogenetic relationships and ecological niche conservatism in killifish (Profundulidae) in Mesoamerica

The family Profundulidae is a group of small-sized fish species distributed between southern Mexico and Honduras, where they are frequently the only fish representatives at higher elevations in the basins where they occur. We characterized their ecological niche using different methods and metrics drawn from niche modelling and by re-examining phylogenetic relationships of a recently published molecular phylogeny of this family to gain a better understanding of its biogeographic and evolutionary history. We assessed both lines of evidence from the perspective of niche conservatism to set a foundation for discussing hypotheses about the processes underlying the distribution and evolution of the group. In fish clades where the species composition is not clear, we examined whether niche classification could be informative to discriminate groups geographically and ecologically consistent with any of the different hypotheses of valid species. The characterization of the ecological niche was carried out using the Maxent algorithm under different parameterizations and the projection of the presence on the main components of the most relevant environmental coverage, and the niche comparison was calculated with two indices (D and I), both in environmental space and in that projected geographically. With the molecular data, a species tree was generated using the *BEAST method. The comparison of these data was calculated with an age-overlap correlation test. Based on the molecular phylogeny and on niche overlap analyses, we uncovered strong evidence to support the idea that ecologically similar species are not necessarily sister species. The correlation analysis for genetic distance and niche overlap was not significant (P > 0.05). In clades with taxonomic conflicts, we only identified Profundulus oaxacae as a geographically and ecologically distinct group from P. punctatus. All the evidence considered leads us to propose that Profundulidae do not show evidence of niche conservatism and that there are reasons to consider P. oaxacae as a valid species. Our study suggests that niche divergence is a driving evolutionary force that caused the diversification and speciation processes of the Profundulidae, along with the geological and climatic events that promoted the expansion or contraction of suitable environments.     

Five (or so) challenges for species distribution modelling

Species distribution modelling is central to both fundamental and applied research in biogeography. Despite widespread use of models, there are still important conceptual ambiguities as well as biotic and algorithmic uncertainties that need to be investigated in order to increase confidence in model results. We identify and discuss five areas of enquiry that are of high importance for species distribution modelling: (1) clarification of the niche concept; (2) improved designs for sampling data for building models; (3) improved parameterization; (4) improved model selection and predictor contribution; and (5) improved model evaluation. The challenges discussed in this essay do not preclude the need for developments of other areas of research in this field. However, they are critical for allowing the science of species distribution modelling to move forward.     

Realized niche shift associated with Galinsoga quadriradiata (Asteraceae) invasion in China

粗毛牛膝菊在中国的入侵与生态位漂移有关 在外来物种入侵和扩散过程中,生态位的漂移可能起到了重要作用。粗毛牛膝菊(Galinsoga quadriradiata) 在中国已造成了较为严重的入侵,占据了许多与其原产地不同的气候区。为此,本研究力图揭示粗毛牛膝菊入侵过程中的气候生态位漂移,分析其在该物种入 侵中国过程中可能发挥的作用。本研究结合粗毛牛膝菊原 产地和入侵地的分布点与气候数据, 采用Maxent模型预测了其在中国潜在的分布,并采用主成分分析的方法评估 了在入侵中国过程中粗毛牛膝菊气候生态位的漂移。模型结果显示,该物种原产地种群和入侵地种群之间只 有32.7%的生态位重叠,两个种群的生态位相似性较低(Schoener's D = 0.093, P < 0.005),这暗示了在其入侵过程中发生了生态位漂移。相比于其原产地种群,其在中国的入侵种群气候生态位的整体范围和中心都明 显地漂移向了温度更低、降水更少的区域;中国南方大部分区域属于粗毛牛膝菊的稳定适生区,而位于入侵 前沿的北方地区则存在局域适应和潜在拓殖区域。这些研究结果说明,粗毛牛膝菊在中国的入侵种群仍处于准平衡阶段,未来有可能继续向新的适生区扩散入侵,其生态位的变化有力地解释了为什么该物种在中国的入侵性强、危害范围大。     

The establishment of a hybrid zone between red and sika deer (genus Cervus)

Japanese sika deer ( Cervus nippon nippon ) were introduced to Scotland around 80 years (20 generations) ago. The sika phenotype is expanding its range and hybridizing extensively with native red deer ( Cervus elaphus ) leading to the establishment of a hybrid zone. This zone is currently moving and cannot be considered to be at equilibrium. Cervid genotypes and mitochondrial haplotypes were mapped across the sika phenotype range, using diagnostic protein isozymes, microsatellite nuclear DNA markers and RFLPs in mtDNA. These were analysed to estimate heterozygote deficits and nuclear linkage disequilibria and cytonuclear disequilibria in relation to gene frequencies and time since contact. Introgression was found in both taxa and strong linkage disequilibria and heterozygote deficits characterize the populations longest exposed to hybridization. Populations further from the introduction site, where hybridization is facilitated by the dispersal of sika-like stags, show low values for linkage disequilibria and heterozygote deficit. The observed patterns in genotype are explained in terms of assortative mating and a selective advantage of the sika genotype. The genetic integrity of the Scottish mainland red deer is shown to be at risk from the invasion of sika.     

贺兰山同域分布高山麝和阿拉善马鹿秋季食性的比较研究

对贺兰山同域分布的高山麝和阿拉善马鹿秋季的粪便进行采集,利用粪便显微分析法对二者秋季食性进行了研究。分别采集高山麝和阿拉善马鹿活动区域内粪样和植物样本,分别获得两种动物40个复合粪便样本,采用频率转换法对数据处理计算,得到贺兰山同域分布的高山麝和阿拉善马鹿秋季的食性组成及组成比例。结果显示,高山麝秋季共取食植物20科30种(属),其中蓝锭果忍冬(11.96%)、秦氏黄芪(10.17%)、密齿柳(8.32%)、折枝绣线菊(6.82%)、内蒙野丁香(6.18%)组成了高山麝的主要食物;阿拉善马鹿秋季共取食植物12科29种(属),其中针茅(22.15%)、灰榆(21.14%)、早熟禾(16.90%)、小叶金露梅(11.62%)、山杨(10.00%)为阿拉善马鹿秋季的主要食物。高山麝和阿拉善马鹿共有9种食物重叠,生态位重叠指数为83.75%。秋季高山麝取食的Shannon-Wiener指数、Pieou均匀性指数、食物生态位宽度指数和最大的物种多样性指数均高于阿拉善马鹿。     

内蒙古草原布氏田鼠与绵羊的营养生态位研究

放牧活动对小型啮齿动物种群数量的影响是草原生态系统研究中的热点问题,确定绵羊和小型啮齿动物的营养生态位关系对于草原生态系统的管理具有重要的作用。运用粪便显微分析法分析了内蒙古草原动物生态研究站大型野外围栏内布氏田鼠和绵羊在6—9月份的食谱组成,确定两种草食动物食性选择和营养生态位的变化,从食物利用途径揭示放牧活动对布氏田鼠种群数量的影响方式及二者之间的竞争与共存关系。研究结果表明：围栏中共有23种植物,其中糙隐子草、克氏针茅、羊草和刺藜是围栏中的优势植物;布氏田鼠共取食10种植物,绵羊共取食8种植物,禾本植物为两种动物的主要采食植物。布氏田鼠和绵羊的喜食植物种类都存在季节性变化;除7月外,两种动物的食物多样性与围栏植物多样性有显著的正相关关系,表明动物的食性选择受植物资源变化的影响。布氏田鼠和绵羊具有很高的营养生态位重叠度,除8月(0.691)外,6、7、9月份的营养生态位重叠度均高于0.9,表明二者之间存在激烈的食物竞争;放牧活动极显著地降低了禾本科植物的地上生物量,导致布氏田鼠的食物数量减少;放牧处理下布氏田鼠的喜食植物的物种数和营养生态位宽度(除9月)增加,导致布氏田鼠的食物质量...     

Niche-tracking migrants and niche-switching residents: evolution of climatic niches in New World warblers (Parulidae)

Differences in life-history traits between tropical and temperate lineages are often attributed to differences in their climatic niche dynamics. For example, the more frequent appearance of migratory behaviour in temperate-breeding species than in species originally breeding in the tropics is believed to have resulted partly from tropical climatic stability and niche conservatism constraining tropical species from shifting their ranges. However, little is known about the patterns and processes underlying climatic niche evolution in migrant and resident animals. We evaluated the evolution of overlap in climatic niches between seasons and its relationship to migratory behaviour in the Parulidae, a family of New World passerine birds. We used ordination methods to measure seasonal niche overlap and niche breadth of 54 resident and 49 migrant species and used phylogenetic comparative methods to assess patterns of climatic niche evolution. We found that despite travelling thousands of kilometres, migrants tracked climatic conditions across the year to a greater extent than tropical residents. Migrant species had wider niches than resident species, although residents as a group occupied a wider climatic space and niches of migrants and residents overlapped extensively. Neither breeding latitude nor migratory distance explained variation among species in climatic niche overlap between seasons. Our findings support the notion that tropical species have narrower niches than temperate-breeders, but does not necessarily constrain their ability to shift or expand their geographical ranges and become migratory. Overall, the tropics may have been historically less likely to experience the suite of components that generate strong selection pressures for the evolution of migratory behaviour.     

马鹿东北亚种被毛形态结构的季节性差异

被毛作为哺乳动物特有的组织,具有保护和保温功能,一些季节性换毛动物需要通过更换被毛以适应冬季和夏季的不同环境（王泽长,1963;景松岩和张伟,1993）。因此,研究动物被毛结构与功能的季节性特征,对揭示被毛在物种生存和进化过程中的作用具有重要意义（张伟和徐艳春,2003）。对毛的结构多态性和功能多样性研究是国际毛发形态学研究中的前沿领域（Yalden,1985;Gaudette,1985;syred,1991;甘雅玲和郭中伟,2003;张伟和徐艳春,2003）。以往的毛发形态学研究多限于反映物种的特异性,并应用于分类鉴别方面（朱小曼,1987;张伟,1994;金煜,1995）。在强调毛发结构物种特异性的同时,忽略或淡化了其变异性,更缺少对结构和功能关系的研究。马鹿东北亚种（Cervus elaphus xanthopygus）为季节性换毛动物,绒毛退化,其被毛主要由上毛构成。本选择马鹿东北亚种的冬季和夏季上毛作为研究对象,初步测量了冬季和夏季其臀部、后肢上部、后肢下部及蹄部上毛的形态和微观结构数据,比较其季节性差异和部位差异。     

Testing the role of climate in speciation: New methods and applications to squamate reptiles (lizards and snakes)

Climate may play important roles in speciation, such as causing the range fragmentation that underlies allopatric speciation (through niche conservatism) or driving divergence of parapatric populations along climatic gradients (through niche divergence). Here, we developed new methods to test the frequency of climate niche conservatism and divergence in speciation, and applied it to species pairs of squamate reptiles (lizards and snakes). We used a large‐scale phylogeny to identify 242 sister species pairs for analysis. From these, we selected all terrestrial allopatric pairs with sufficient occurrence records (n = 49 pairs) and inferred whether each originated via climatic niche conservatism or climatic niche divergence. Among the 242 pairs, allopatric pairs were most common (41.3%), rather than parapatric (19.4%), partially sympatric (17.7%), or fully sympatric species pairs (21.5%). Among the 49 selected allopatric pairs, most appeared to have originated via climatic niche divergence (61–76%, depending on the details of the methods). Surprisingly, we found greater climatic niche divergence between allopatric sister species than between parapatric pairs, even after correcting for geographic distance. We also found that niche divergence did not increase with time, further implicating niche divergence in driving lineage splitting. Overall, our results suggest that climatic niche divergence may often play an important role in allopatric speciation, and the methodology developed here can be used to address the generality of these findings in other organisms.     

Complex patterns of environmental niche evolution in Iberian columbines (genus Aquilegia,Ranunculaceae)

Aims This study explores the patterns of niche differentiation in a group of seven closely related columbines (genus Aquilegia, Ranunculaceae) from the Iberian Peninsula. Populations of these columbines are subject to complex patterns of divergent selection across environments, which partly explain the taxonomic structure of the group. This suggests the hypothesis that niche divergence must have occurred along the process of diversification of the group.Methods We used MaxEnt to build environmental niche models of seven subspecies belonging to the three species of Aquilegia present in the Iberian Peninsula. From these models, we compared the environmental niches through two different approaches: ENMtools and multivariate methods.Important findings MaxEnt distributions conformed closely to the actual distribution of the study taxa. ENMtools methods failed to uncover any clear patterns of niche differentiation or conservatism in Iberian columbines. Multivariate analyses indicate the existence of differentiation along altitudinal gradients and along a gradient of climatic conditions determined by the summer precipitation and temperatures. However, climatic conditions related to winter temperature and precipitation, as well as soil properties, were equally likely to show conservatism or divergence. The complex patterns of niche evolution we found suggest that Iberian Columbines have not been significantly constrained by forces of niche conservatism, so they could respond adaptively to the fast and profound climate changes in the Iberian Peninsula through the glacial cycles of the Pleistocene.     

Climatic‐niche evolution with key morphological innovations across clades within Scutiger boulengeri (Anura: Megophryidae)

The studies of climatic‐niche shifts over evolutionary time accompanied by key morphological innovations have attracted the interest of many researchers recently. We applied ecological niche models (ENMs), ordination method (environment principal component analyses; PCA‐env), combined phylogenetic comparative methods (PCMs), and phylogenetic generalized least squares (PGLS) regression methods to analyze the realized niche dynamics and correspondingly key morphological innovations across clades within Scutiger boulengeri throughout their distributions in Qinghai–Tibet Plateau (QTP) margins of China. Our results show there are six clades in S. boulengeri and obvious niche divergences caused by niche expansion in three clades. Moreover, in our system, niche expansion is more popular than niche unfilling into novel environmental conditions. Annual mean temperature, annual precipitation, and precipitation of driest month may contribute to such a shift. In addition, we identified several key climatic factors and morphological traits that tend to be associated with niche expansion in S. boulengeri clades correspondingly. We found phenotypic plasticity [i.e., length of lower arm and hand (LAHL), hind‐limb length (HLL), and foot length (FL)] and evolutionary changes [i.e., snout–vent length (SVL)] may together contribute to niche expansion toward adapting novel niche, which provides us a potential pattern of how a colonizing toad might seed a novel habitat to begin the process of speciation and finally adaptive radiation. For these reasons, persistent phylogeographic divisions and accompanying divergences in niche occupancy and morphological adaption suggest that for future studies, distinct genetic structure and morphological changes corresponding to each genetic clade should be included in modeling niche evolution dynamics, but not just constructed at the species level.     

Temperature dependence of germination and growth in Anthurium (Araceae)

• By the year 2100, temperatures are predicted to increase by about 6 °C at higher latitudes and about 3 °C in the tropics. In spite of the smaller increase in the tropics, consequences may be more severe because the climatic niches of tropical species are generally assumed to be rather narrow due to a high degree of climate stability and higher niche specialisation. However, rigorous data to back up this notion are rare.
• We chose the megadiverse genus Anthurium (Araceae) for study. Considering that the regeneration niche of a species is crucial for overall niche breadth, we focused on the response of germination and early growth through a temperature range of 24 °C of 15 Anthurium species, and compared the thermal niche breadth (TNB) with the temperature conditions in their current range, modelled from occurrence records.
• Surprisingly, an increase of 3 °C would lead to a larger overlap of TNB of germination and modelled in situ temperature conditions, while the overlap of TNB of growth with in situ conditions under current and future conditions is statistically indistinguishable.
• We conclude that future temperatures tend to be closer to the thermal optima of most species. Whether this really leads to an increase in performance depends on other abiotic and biotic factors, most prominently potentially changing precipitation patterns.

     

Genetic admixture in multidimensional environmental space: asymmetrical niche similarity promotes gene flow in armadillos (Dasypus novemcinctus)

We unite genetic data with a robust test of niche divergence to test the hypothesis that patterns of gene flow between two lineages of the nine-banded armadillo are influenced by their climatic niches. We collected Geographical Information System (GIS) data on climate using locality information from 111 individuals from two lineages that had associated genetic material. We tested whether niches of these lineages were more conserved or divergent than the background environments of their geographic ranges and found evidence for niche conservatism on two axes and no evidence for divergence on any axis. To address the role of niche similarity in gene flow, we genotyped the 111 individuals at five microsatellite loci and tested whether admixed individuals tended to be located in parts of multidimensional environmental space (E-space) shared between the two lineages. We observed an asymmetrical pattern of overlap, in which the West lineage's E-space was almost completely included inside East lineage's E-space. Genetic admixture levels were significantly higher in the West lineage and, for both lineages, in shared portions of E-space. This suggests that niche similarity can facilitate gene flow among disjunct groups with moderate-to-good dispersal capabilities, contrasting with the prevailing view of niche conservatism as a diversifying force.