Search for lunar periodicity in the bannertail kangaroo rat (Dipodomys spectabilis)

Abstract

The endogenous activity cycle of the nocturnal bannertail kangaroo rat was investigated. Although bannertail activity is a function of the lunar day as well as the solar day, all ten subjects exhibited free‐running activity periods of solar‐day length; there was no evidence of an endogenous lunar‐day cycle. Animals were provided with a burrow system and a small pseudo‐desert, a laboratory facility in which animal activity data closely resembled measurements taken in the field. Several analytical techniques for quantifying the data were utilized, and one, the mean interval of activity, is recommended to other investigators.     

Recent demographic bottlenecks are not accompanied by a genetic signature in banner-tailed kangaroo rats (Dipodomys spectabilis)

Single-sample methods of bottleneck detection are now routine analyses in studies of wild populations and conservation genetics. Three common approaches to bottleneck detection are the heterozygosity excess, mode-shift, and M-ratio tests. Empirical groundtruthing of these methods is difficult, but their performances are critical for the accurate reconstruction of population demography. We use two banner-tailed kangaroo rat (Dipodomys spectabilis) populations from southeastern Arizona (USA) that are known to have experienced recent demographic reductions to search for genetic bottleneck signals with eight microsatellite loci. Over eight total sample-years, neither population showed a genetic bottleneck signature. M-ratios in both populations were large, stable, and never fell below a critical significance value (Mc). The mode shift test did not detect any distortion of allele frequencies, and tests of heterozygosity excess were not significant in postbottleneck samples when we used standard microsatellite mutation models. The genetic effects of bottlenecks like those experienced by our study populations should be strongly influenced by rates of mutation and migration. We used genetic parentage data to estimate a relatively high mutation rate in D. spectabilis (0.0081 mutants/generation/locus), but mutation alone is unlikely to explain the temporal distribution of rare alleles that we observed. Migration (gene flow) is a more likely explanation, despite prior mark-recapture analysis that estimated very low rates of interpopulation dispersal. We interpret our kangaroo rat data in light of the broader literature and conclude that in natural populations connected by dispersal, demographic bottlenecks may prove difficult to detect using molecular genetic data.     

Spatial and temporal variability in a butterfly population

Summary The dynamics of a butterfly (Plebejus argus) population were analysed at two levels, (i) the population as a whole and (ii) sections within the population. Some sections of the population fluctuated out of synchrony with others, such that the variability [SD Log(Density+1)] shown by the population as a whole was less than the variability shown by each part of the population — overall temporal variability was dampened by spatial asynchrony. Since observed population variability depends on the spatial scale that is sampled, comparisons of population variability among taxa should be carried out only with caution. Implications for island biogeography and conservation biology are discussed.     

Geographic patterns of genetic differentiation within the restricted range of the endangered Stephens' kangaroo rat Dipodomys stephensi

Using mtDNA variation in the kangaroo rat Dipodomys stephensi, we found no support for the hypothesis that a species with an historically restricted range will exhibit low levels of genetic polymorphism and little genetic structure. Dipodomys stephensi has long been restricted to a few interior coastal valleys in southern California encompassing an area of approximately 70 x 40 km; however, we found high levels of genetic variation over much of its range and significant genetic structure both within and between regions. We also found evidence for a recent range expansion. Dipodomys stephensi is a federally endangered species that is separated from D. panamintinus, its presumed sister taxon, by a mountain range to the north. We assessed genetic variation by sequencing 645 bases of the mitochondrial d-loop from 61 individuals sampled from 16 locations across the species range and rooted their relationship using two D. panamintinus individuals. Despite its limited geographic range, the level of mtDNA variation in D. stephensi is comparable to that of other rodents, including that of the more widely distributed D. panamintinus. This variation revealed significant regional differentiation. The northern, central, and southern regions of the range differ in both the level and the distribution of genetic variation. Phylogenetic analysis revealed that the center of the range contains the most diversity of lineages, including the most basal. In this region and in the north, most haplotypes were found at only a single location (25/29), or at a pair of nearby locations (3/29). In addition, related haplotypes clustered geographically. These results are consistent with long-term demographic stability characterized by limited dispersal and high local effective population size. Further support for this conclusion is the finding of unique diversity in two northern peripheral populations, Norco and Potrero Creek (PC). However, in sharp contrast, one haplotype (CC) was found at five of 11 central and northern locations and comprised 18% of individuals sampled. The atypical distribution of the CC haplotype reflected a pattern seen more strongly in the southern region. Here the CC haplotype comprised 69% of the sample and was found at all five sampling locations. Consequently, the southern region had very low genetic variability. We propose that this dominance of CC was probably due to a local population bottleneck that occurred during a recent range expansion into the southern region.     

Spatial structure of a leaf-removing crab population in a mangrove of North-Brazil

The leaf-removing decapod crab, Ucides cordatus plays a key role as ecological engineer in Brazilian mangrove ecosystems. We analyzed the spatial distribution of a specific population at two different scales to observe how individual behavior could alter spatial population structure. First, we conducted a spatial point pattern analysis of the burrow entrances and the Rhizophora mangle prop roots on the mangrove floor at a scale of few meters. Secondly, we analyzed at a large scale (10–100 m) the potential effects of surface elevation, light intensity, prop root coverage, species of neighboring tree (R. mangle, Laguncularia racemosa, Avicennia germinans) and pneumatophore density on the size and number of burrow entrances. At the same large scale, we conducted an analysis of clustering of the crabs around the R. mangle trees. At small scale, the burrow entrances, although aggregated around the prop roots, showed a regularly spaced distribution (∼25 cm) signaling an intraspecific competition among the crabs. At large scale, crabs preferred to install their burrows at an intermediate level of surface elevation and prop root coverage, and in R. mangle-dominated areas. At the same kind of habitats, the largest burrows, and thus potentially the largest crabs, were found in higher number than on other habitats. The R. mangle-dominated areas preference was confirmed by an aggregating around R. mangle trees in R. mangle-dominated forest, but only of large individuals in L. racemosa-dominated forest. These observations lead us to the definition of a preferred habitat for U. cordatus. Competition leading to the small-scale regular patterns was proposed as an explanation for exclusion of smaller crabs from preferred habitats seen at large scale. We hypothesize that this preferred habitat might explain at regional scale the variation of U. cordatus importance in Neotropical mangroves.     

Spatial and temporal population structure of Brevicoryne brassicae

Allozymes from individual aphids were used as markers to examine the structure of Brevicoryne brassicae colonies collected from field experiments at Horticulture Research International, Wellesbourne, during the summers of 1991, 1992 and 1993. Eighteen enzyme systems were examined using cellulose acetate electrophoresis, but only 6-phosphogluconate dehydrogenase (6-PGDH) showed polymorphism (three alleles) in the samples. There were significant differences in gene frequencies between populations at some sites within 1 kilometre and between times of sampling, with an increase in the proportion of the most common genotype AA later in the season, possibly due to selection during the summer of the best adapted clones. These changes in gene frequency might produce biased results in trials screening brassica crops against aphids.     

Spatial and temporal continuity of kangaroo rat populations shown by sequencing mitochondrial DNA from museum specimens

Summary The advent of direct sequencing via the polymerase chain reaction (PCR) has opened up the possibility of molecular studies on museum specimens. Here we analyze genetic variation in populations over time by applying PCR to DNA extracted from museum specimens sampled from populations of one species over the last 78 years. Included in this study were 43 museum specimens of the Panamint kangaroo ratDipodomys panamintinus from localities representing each of three geographically distinct subspecies. These specimens were originally collected and prepared as dried skins in 1911, 1917, or 1937. For each specimen, a 225-bp segment of the mitochondrial genome was sequenced. These mitochondrial DNA sequences were compared to those of 63 specimens collected at the same localities in 1988. The three subspecies were nearly completely distinct. Only 2 of the 106 individuals shared mitochondrial types between subspecies. For all three localities, the diversity levels were maintained between the two temporal samples. The concordance observed between the two temporally separate phylogenies supports the use of museum specimens for phylogenetic inference. This study demonstrates the accuracy and routine nature of the use of museum specimens in the analysis of mitochondrial sequence variation in natural populations and, importantly, that a temporal aspect can now be added to such studies.     

Population structure and genetic variation in the endangered Giant Kangaroo Rat (<Emphasis Type="Italic">Dipodomys ingens</Emphasis>)

Populations of the endangered giant kangaroo rat, Dipodomys ingens (Heteromyidae), have suffered increasing fragmentation and isolation over the recent past, and the distribution of this unique rodent has become restricted to 3% of its historical range. Such changes in population structure can significantly affect effective population size and dispersal, and ultimately increase the risk of extinction for endangered species. To assess the fine-scale population structure, gene flow, and genetic diversity of remnant populations of Dipodomys ingens, we examined variation at six microsatellite DNA loci in 95 animals from six populations. Genetic subdivision was significant for both the northern and southern part of the kangaroo rat’s range although there was considerable gene flow among southern populations. While regional gene diversity was relatively high for this endangered species, hierarchical F-statistics of northern populations in Fresno and San Benito counties suggested non-random mating and genetic drift within subpopulations. We conclude that effective dispersal, and therefore genetic distances between populations, is better predicted by ecological conditions and topography of the environment than linear geographic distance between populations. Our results are consistent with and complimentary to previous findings based on mtDNA variation of giant kangaroo rats. We suggest that management plans for this endangered rodent focus on protection of suitable habitat, maintenance of connectivity, and enhancement of effective dispersal between populations either through suitable dispersal corridors or translocations.     

Microsatellite variation, population structure, and bottlenecks in the threatened copperbelly water snake

Habitat loss and isolation is pervasive in the Midwest U.S. Wetlands are experiencing particularly dramatic declines, yet there is a paucity of information on the genetic impacts of these losses to obligate wetland vertebrates. We quantified the genetic variation of extant populations of a shallow wetland specialist and evaluated potential reductions in population size (i.e. bottlenecks) using seven polymorphic microsatellite DNA markers. We analyzed 228 copperbelly water snakes (Nerodia erythrogaster neglecta), representing populations from three states. Moderate genetic differentiation exists among all three regions (F _ST = 0.12, P < 0.001), with evidence for low levels of differentiation within the federally protected Ohio region (F _ST = 0.025, P = 0.007), and moderate to strong differentiation within the Indiana region (F _ST = 0.23, P < 0.001). Furthermore, Bayesian clustering (i.e. STRUCTURE) supports the separation of the Indiana sites, both from each other and from all other sampling sites. However, it does not support the separation of the Ohio sites from the Kentucky sites. Differentiation among sampling sites did not appear to be related to geographic distance, but rather depended on the quality of terrestrial corridors used for dispersal. Mode shifts in allele frequencies and excess heterozygosity tests were negative, while M-ratio tests were nearly all positive, indicating the likelihood of historical rather than contemporary population bottlenecks. However, potential subspecific intergradation in the Kentucky region may have artificially lowered the M-ratio, and we suggest caution when using the M-ratio approach if intergradation is suspected. Our results have conservation implications for wetland management and management of the copperbelly populations, and emphasizes the importance of protecting wetland complexes.     

Behavioural syndromes in Merriam's kangaroo rats (Dipodomys merriami): a test of competing hypotheses

Behavioural syndromes, correlations of behaviours conceptually analogous to personalities, have been a topic of recent attention due to their potential to explain trade-offs in behavioural responses, apparently maladaptive behaviour and limits to plasticity. Using Merriam's kangaroo rats (Dipodomys merriami), we assessed the explanatory power and generality of hypothesized syndrome structures derived from the literature and the natural history of the species. Several aspects of functionally distinct behavioural responses of D. merriami were quantified. Syndrome structures were compared using structural equation modelling and model selection procedures. A domain-general behavioural syndrome incorporating cross-functional relationships between measures of boldness, agonistic behaviour, flexibility and food hoarding best explained the data. This pattern suggests that D. merriami behaviours should not be viewed as discrete elements but as components of a multivariate landscape. Our results support arguments that a lack of independence between behaviours may be a general aspect of behavioural phenotypes and suggest that the ability of D. merriami's behaviour to respond to selection may be constrained by underlying connections.     

Spatial dynamics of colony interactions in young populations of the fire ant Solenopsis invicta

Newly founded colonies of the fire ant Solenopsis invicta compete intensely by brood raids, which result in a rapid reduction of colony density. Experimental plantings of colonies and analyses of sequential maps were used to examine the importance of spatial pattern in the dynamics of young populations. Colony positions were initially clumped in naturally founded cohorts, but were regular in most mature populations. Incipient colonies planted in clumped patterns were more likely to engage in brood raids than colonies planted in regular hexagonal patterns at the same average density. However, contrary to what would be expected if local crowding increased mortality, no significant increases in spatial regularity were observed during brood raiding either in the experimentally planted populations or in a natural population of more than 1200 incipient colonies. These results show that it may be difficult to infer the degree of past or current competition by passive analysis of spatial data even when field experiments show that the probability of mortality depends on local spacing.     

Population structure and dynamics of Pinus taiwanensis Hayata at Songyang county,Zhejiang Province,China

Pinus taiwanensis is a widely distributed species in the southeastern China (Zhejiang, Anhui, Hubei, Human, Jiangxi, Fujian, Taiwan provinces) at an elevation of 700–2000 m. This pine is a pioneer in forest succession and is often used as a species for afforestation in this region at an elevation above 700 m. This study was carried out at Guanshanyuan, Zhejiang province, at a latitude of N 28° 18, a longitude of E 119° 16 and an altitude of 800–1502 m above sea level. On the basis of a census of all individuals of Pinus taiwanensis at different successional stages and various habitats, age structure, spatial pattern, density, biomass of population and their dynamics were described. Considering the population dynamics throughout the successional process, three phases could be recognized. Until about 9–10 years after Pinus taiwanensis invaded the stands, the density of population was increased by the recruitments along with increase of the mean tree weight and population biomass (phase I). Thereafter, the population was in full density state, the biomass of population and the mean tree weight increased exponentially, while the density was decreased drastically by the self-thinning and the invasion of other broad-leaved trees (phase II). The –3/2 power law of natural thinning was applicable to the populations in this phase. When the broad-leaved trees reached the canopy, although the mean tree weight increased slowly, the density and biomass of Pinus taiwanensis population decreased gradually (phase III) until the population senesced and retreated from the successional series completely. The population dynamics of Pinus taiwanensis during the successional process was in common with pioneer species in forest succession. At some special habitats such as rocky steep slopes and ridges, however, Pinus taiwanensis population could form such an edaphic climax community that the population density, biomass and the mean tree weight in phase III could be in a stable state for very long period.     

Determinants of spatial distribution in a population of the subalpine butterfly Oeneis chryxus

Summary This paper describes temporally varying determinants of the spatial distribution of adults in an insect population and the relationship between that distribution and the mating system. Male Oeneis chryxus butterflies were distributed nonrandomly throughout a sloping Colorado meadow divided horizontally by a dirt road into an upper and lower slope. Over an eight-year period of intensive study, the proportion of males located on the road, the upper slope, and the lower slope varied as a function of population size and sex ratio. In each year, more than half of the male population aggregated on sections of the road in a distinct and recurring pattern that was not correlated with the distribution of any food resource or thermal regime. Females were usually extremely scarce and not distributed in any pattern apparent from the few observations of them. Areas densely occupied by males were associated with visual landmarks. We hypothesize that the male distribution is determined by a pattern of movement of receptive females toward these landmarks. The road offers a thermally favorable environment with an unobstructed view in which to await the passage of scarce females. The mating system in this population has several lek-like features and supports the prediction that landmark mating is a favored strategy under conditions of female scarcity and wide dispersal of resources.     

Status and structure of the griffon vulture (Gyps fulvus) population in Crete

Griffon vulture (Gyps fulvus) population surveys were conducted during 1996–2002 in the island of Crete (Greece) to document population status and structure. Fieldwork was carried out during the breeding period when birds could be monitored in their colonies. Total population size was estimated at 379 individuals (range = 341–417) with adult birds comprising 63%. The breeding population was estimated at 141 pairs, which were distributed on an average in 23 colonies per year (range = 16–30) while the mean number of breeding pairs that laid eggs was 98 (range= 64–126). Crete thus supports the largest insular population of the species in the world and hosts 70–80% of the breeding population of the species in Greece. Population density was estimated at 6.9 individuals/100 km², 2.6 breeding pairs/100 km² and 1.8 nesting pairs/100 km². The average home range of an occupied colony (i.e., breeding group) was estimated at ca. 204 km² producing a theoretical foraging range of 8 km radius around the breeding cliff. No trends in the total number of individuals and breeding pairs appeared to exist, although significant differences in population size of individual colonies occurred between the years. The majority of the population was concentrated in small-sized colonies, which showed a low occupancy rate. The number of abandoned sites and the colonization of new ones could represent a shift of breeding pairs to alternative colonies provoked by local food abundance and conspesific attraction.     

广西猫儿山鹅掌楸天然种群动态研究

为进一步探讨鹅掌楸濒危的机制,对广西桂林猫儿山鹅掌楸天然种群进行了调查,以种群生命表及生存分析理论为基础,以林木径级结构代表龄级结构,编制鹅掌楸种群静态生命表,分析种群结构的动态变化特点.结果表明:鹅掌楸种群龄级结构为金字塔型,幼龄个体数量较多,中龄个体数居中,而老龄个体则相对数量较少,表现为增长型种群;在第Ⅳ龄级时该种群出现死亡高峰,其种群存活曲线属Deevey-Ⅱ型;猫儿山鹅掌楸天然种群具有前期种群数量快速减少,中后期稳定,末期衰退的特点.该研究结果对鹅掌楸天然种群的保护提供参考依据.     

珍稀濒危植物黄杉种群结构与空间分布格局北大核心CSCD

为了解珍稀濒危植物黄杉种群的生存现状和更新机制,对贵州省威宁县黄杉自然保护区内天然分布的黄杉(Pseudotsuga sinensis)群落的结构特征和空间分布格局进行了研究。结果表明,黄杉种群的中龄级个体数较多,幼龄级和老龄级个体相对较少,呈典型的“∩”型结构。种群结构动态指数V_(pi)(13.49%)和V′_(pi)(0.05%)均大于0,种群属于增长型,但增长幅度逐渐降低,对外界干扰敏感度较高。种群存活曲线趋于Deevey-II型,生命期望值单调下降,死亡率呈“V”型,有2个死亡高峰,第1个出现在I龄级,第2个出现在IX龄级。黄杉种群除部分样地(Q2和Q7)呈均匀分布外,大部分样地呈集群分布;随龄级的增加,空间分布格局由集群分布逐渐趋向于均匀分布。因此,黄杉种群濒危的主要因素是幼树个体无法及时补充种群,建议加强对幼苗的抚育和通过适度干扰,促进黄杉种群的更新。     

Metapopulation structure in the lagoon cockle <Emphasis Type="Italic">Cerastoderma lamarcki</Emphasis> in the northern Wadden Sea

Benthic invertebrates in discontinuous inshore habitats and with short or no pelagic larval dispersal are likely to exhibit regional metapopulation dynamics with partially isolated local populations. Near the island of Sylt, the bivalve Cerastoderma (Cardium) lamarcki (Reeve, 1844, syn. in part with C. glaucum Bruguiére, 1789) was widespread in intertidal seagrass beds, coexisting with the sibling species C. edule (Linné, 1758). However, the last C. lamarcki in this habitat was found in 1980. At present the lagoon cockle is restricted to disjunct ditches, creeks and ponds within island salt marshes. There it differs in year-class structure between localities. Successful recruitment events did not coincide. At one locality, a period with regular recruitment was followed by 5 years of recruitment failure, resulting in an overaged population probably at the rim of extinction. In a nearby brackish pond, extinction was followed by recolonization 3 years later. Other lagoonal habitats which seem to be suitable are without cockles. It is speculated that small and isolated habitats occasionally receive colonizers by eggs and juveniles adhering to avian vectors. Electronic Publication     

Genetic diversity and population differentiation of chestnut blight fungus, Cryphonectria parasitica, in China as revealed by RAPD

Seventeen Cryphonectria parasitica populations sampled from six regions in China were investigated using RAPD. Across all 169 isolates from the 17 populations evaluated, 52 of the 71 markers (73%) were polymorphic, total genetic diversity (h) was 0.1463, and Shannon’s index was 0.2312. Diversity within populations accounted for 74% of total genetic diversity, and genetic differentiation among populations was 0.26 (G _ST = 0.26). Gene flow was 1.4 among the populations; higher gene flow was found among populations within regions and among regions [N _m (G _SR) = 2.8 and N _m (G _RT) = 3.5]. The unweighted pair group mean analysis (UPGMA) dendrogram revealed two distinct clusters: the northern China group and the southern China group. The spatial autocorrelation analysis revealed that the variation at most loci was randomly distributed and lacked spatial structure, but several loci and closer distances were spatially structured. Human activity and habitat could also be important factors affecting genetic structure among C. parasitica populations in China. Genetic diversity was highest in Southwest China, descending in an orderly fashion to Northeast China. This pattern indicated that Southwest China might be the center of origin of C. parasitica in China. The present study provides useful information for understanding the origin and spread of chestnut blight fungus in China and valuable data for formulating relevant strategies for controlling the disease in China.