Pronounced differences in genetic structure despite overall ecological similarity for two Ambystoma salamanders in the same landscape

Studies linking genetic structure in amphibian species with ecological characteristics have focused on large differences in dispersal capabilities. Here, we test whether two species with similar dispersal potential but subtle differences in other ecological characteristics also exhibit strong differences in genetic structure in the same landscape. We examined eight microsatellites in marbled salamanders (Ambystoma opacum) from 29 seasonal ponds and spotted salamanders (Ambystoma maculatum) from 19 seasonal ponds in a single geographic region in west-central Massachusetts. Despite overall similarity in ecological characteristics of spotted and marbled salamanders, we observed clear differences in the genetic structure of these two species. For marbled salamanders, we observed strong overall genetic differentiation (F _ST = 0.091, F′ _ST = 0.375), three population-level clusters of populations (K = 3), a strong pattern of isolation by distance (r = 0.58), and marked variation in family-level structure (from 1 to 23 full-sibling families per site). For spotted salamanders, overall genetic differentiation was weaker (F _ST = 0.025, F′ _ST = 0.102), there was no evidence of population-level clustering (K = 1), the pattern of isolation by distance (r = 0.17) was much weaker compared to marbled salamanders, and there was less variation in family-level structure (from 10 to 36 full-sibling families per site). We suspect that a combination of breeding site fidelity, effective population size, and generation interval is responsible for these marked differences. Our results suggest that marbled salamanders, compared to spotted salamanders, are more sensitive to fragmentation from various land-use activities and would be less likely to recolonize extirpated sites on an ecologically and conservation-relevant time frame.     

The influence of breeding phenology on the genetic structure of four pond‐breeding salamanders

Understanding metapopulation dynamics requires knowledge about local population dynamics and movement in both space and time. Most genetic metapopulation studies use one or two study species across the same landscape to infer population dynamics; however, using multiple co‐occurring species allows for testing of hypotheses related to different life history strategies. We used genetic data to study dispersal, as measured by gene flow, in three ambystomatid salamanders (Ambystoma annulatum , A. maculatum , and A. opacum ) and the Central Newt (Notophthalmus viridescens louisianensis ) on the same landscape in Missouri, USA . While all four salamander species are forest dependent organisms that require fishless ponds to reproduce, they differ in breeding phenology and spatial distribution on the landscape. We use these differences in life history and distribution to address the following questions: (1) Are there species‐level differences in the observed patterns of genetic diversity and genetic structure? and (2) Is dispersal influenced by landscape resistance? We detected two genetic clusters in A. annulatum and A. opacum on our landscape; both species breed in the fall and larvae overwinter in ponds. In contrast, no structure was evident in A. maculatum and N. v. louisianensis , species that breed during the spring. Tests for isolation by distance were significant for the three ambystomatids but not for N. v. louisianensis . Landscape resistance also contributed to genetic differentiation for all four species. Our results suggest species‐level differences in dispersal ability and breeding phenology are driving observed patterns of genetic differentiation. From an evolutionary standpoint, the observed differences in dispersal distances and genetic structure between fall breeding and spring breeding species may be a result of the trade‐off between larval period length and size at metamorphosis which in turn may influence the long‐term viability of the metapopulation. Thus, it is important to consider life history differences among closely related and ecologically similar species when making management decisions.     

AFLP and breeding system studies indicate vicariance origin for scattered populations and enigmatic low fecundity in the Moroccan endemic Hypochaeris angustifolia (Asteraceae), sister taxon to all of the South American Hypochaeris species

We used Amplified Fragment Length Polymorphism markers (AFLP) and breeding system studies to investigate the population structure and reproductive biology of Hypochaeris angustifolia (Asteraceae: Cichorieae). This species is endemic to altiplanos of the Atlas Mountains (Morocco) where it occurs in scattered populations, and it is the sister species to c. 40 species of this genus in South America. PCoA, NJ, and Bayesian clustering, revealed that the populations are very isolated whilst AFLP parameters show that almost all populations have marked genetic divergence. We contend that these features are more in accord with a vicariance origin for the scattered populations of H. angustifolia, rather than establishment by long-distance dispersal. The breeding system studies revealed that H. angustifolia is a self-incompatible species, with low fecundity in natural and in experimental crosses, probably due to a low frequency of compatible phenotypes within and between the populations.     

Macrogeographic variation of a pond predator's top-down effects in a common garden environment

Geographic variation in species behavior and life history has been well documented in biology. Species with wide geographic distributions (i.e., across a continent) but small home ranges (i.e., <1 km²) likely experience wide variability in abiotic environments across the entirety of their range, possibly exhibiting strong local adaptation. Understanding variation across a large geographic scale is especially important when considering species that have strong ecological importance, such as keystone species. Yet, few studies have compared the potential cascading ecological effects of a predator with a keystone role in at least part of its range. To understand how keystone ability in pond food webs can vary across a large geographic range, we conducted an artificial pond experiment with a known keystone predator in at least part of its range, the marbled salamander (Ambystoma opacum). To do so, we collected size-matched salamander larvae from three geographically distant populations (>650 km apart) in Ohio, Mississippi, and North Carolina and placed them in mesocosms with a suite of spring breeding amphibian prey species. We observed differential survival of some prey species leading to differences in spring-breeding amphibian diversity among the three predator populations, indicating that keystone predation may vary at a geographic scale. Prey diversity was lowest with predators from northern (Ohio) populations of salamanders. Further understanding of large-scale variability in ecologically important predators and the potential effects of translocating wide-ranging ambystomatid species is needed to direct future conservation efforts and preserve biodiversity.     

Habitat Selection and Movement of Pond-Breeding Amphibians in Experimentally Fragmented Pine Forests

ABSTRACT Population-level responses of amphibians to forest management regimes are partly dictated by individual behavioral responses to habitat alteration. We examined the short-term (i.e., 24-hr) habitat choices and movement patterns of 3 amphibian species—southern leopard frogs (Rana sphenocephala), marbled salamanders (Ambystoma opacum), and southern toads (Bufo terrestris)—released on edges between forest habitats and recent clear-cuts in the Upper Coastal Plain of South Carolina, USA. We predicted that adult frogs and salamanders would preferentially select forest using environmental cues as indicators of habitat suitability. We also predicted that movement patterns would differ in clear-cuts relative to forests, resulting in lower habitat permeability of clear-cuts for some or all of the species. Using fluorescent powder tracking, we determined that marbled salamanders selected habitat at random, southern toads preferred clear-cuts, and southern leopard frogs initially selected clear-cuts but ultimately preferred forests. Frogs exhibited long-distance, directional movement with few turns. In contrast, toads exhibited wandering behavior and salamanders moved relatively short distances before locating cover. Southern toads and southern leopard frogs moved farther in forests, and all 3 species made more turns in clear-cuts than in forests. Habitat selection by southern toads did not vary according to body size, sex, or the environmental cues we measured. However, marbled salamanders were more likely to enter clear-cuts when soil moisture was high, and southern leopard frogs were more likely to enter clear-cuts when relative humidity and air temperature were higher in the clear-cut than in adjacent forest. Although we found evidence of reduced habitat permeability of clear-cuts for southern leopard frogs and southern toads, none of the species exhibited strong behavioral avoidance of the small (4-ha) clear-cuts in our study. Further studies of long-term habitat use and the potential physiological and other costs to individuals in altered forests are needed to understand the effects of forest management on population persistence. To reduce potentially detrimental effects of clear-cutting on amphibians in the Southeast, wildlife managers should consider the vagility and behavior of species of concern, especially in relation to the size of planned harvests adjacent to breeding sites.     

High levels of genetic structuring as a result of population fragmentation in the tropical tree species <Emphasis Type="Italic">Caesalpinia echinata</Emphasis> Lam.

We have investigated levels of genetic diversity within and among seven remnant populations of Caesalpinia echinata Lam., an endangered species found as fragmented populations in three major areas around the coastal regions of Brazil. Using amplified fragment length polymorphism (AFLP) genetic markers, we detected levels of within-population genetic diversity ranging from 0.092 to 0.163, with the lowest values generally being found in the smallest populations. Estimates of between-population genetic differentiation were strongly correlated with geographical distance (r = 0.884, p < 0.001), which,along with a neighbour-joining phylogenetic analysis, strongly suggested high levels of genetic isolation by distance. Over half (62%) of the total genetic diversity was partitioned between populations, further highlighting the genetic distinctness of individual populations. Taken together, these results suggest that fragmentation has led to an increase in population differentiation between fragments of C. echinata. These formations will be of great value in the development of conservation plans for species exhibiting high levels of genetic differentiation due to fragmentation, such as indication of conservation unit size, which populations should be chosen as priority in conservation plans and which samples should be introduced in areas with a low number of individuals of brazilwood.     

Habitat alteration increases invasive fire ant abundance to the detriment of amphibians and reptiles

Altered habitats have been suggested to facilitate red imported fire ant (Solenopsis invicta) colonization and dispersal, possibly compounding effects of habitat alteration on native wildlife. In this study, we compared colonization intensity of wood cover boards by S. invicta among four forest management treatments in South Carolina, USA: an unharvested control (>30 years old); a partially thinned stand; a clearcut with coarse woody debris retained; and a clearcut with coarse woody debris removed. Additionally, we compared dehydration rates and survival of recently metamorphosed salamanders (marbled salamanders, Ambystoma opacum, and mole salamanders, A. talpoideum) among treatments. We found that the number of wood cover boards colonized by S. invicta differed significantly among treatments, being lowest in the unharvested forest treatments and increasing with the degree of habitat alteration. Salamanders that were maintained in experimental field enclosures to study water loss were unexpectedly subjected to high levels of S. invicta predation that differed among forest treatments. All known predation by S. invicta was restricted to salamanders in clearcuts. The amount of vegetative ground cover was inversely related to the likelihood of S. invicta predation of salamanders. Our results show that S. invicta abundance increases with habitat disturbance and that this increased abundance has negative consequences for amphibians that remain in altered habitats. Our findings also suggest that the presence of invasive S. invicta may compromise the utility of cover boards and other techniques commonly used in herpetological studies in the Southeast.     

An AFLP analysis of genetic diversity and structure of Caragana microphylla populations in Inner Mongolia steppe, China

Genetic diversity and structure of five natural populations of Caragana microphylla from the Inner Mongolia steppe were estimated using AFLP markers. Five pairs of primers generated a total of 312 bands among 90 individuals, with percentage of polymorphic bands (PPB) being 63% at the population level and 76% at the species level, respectively. The genetic diversity within populations was correlated significantly with the soil N:P ratio. AMOVA analysis revealed high genetic variations within populations (95.5%). The estimated number of migrants per generation (Nm) was 10.72, indicating a high level of gene flow among populations. There was no significant correlation (r = 0.36) between genetic distance and geographical distance. These results were discussed in terms of eco-geographical variations among populations, together with the life history traits and breeding system of the species. The knowledge obtained may have important implications for better conservation and wise use of the vegetation dominate by C. microphylla.     

陕西唐棣遗传多样性和遗传分化的AFLP分析

采用扩增片段长度多态性分子标记技术对陕西省分布的6个野生唐棣居群的96个个体进行了遗传多样性分析, 以明确野生唐棣资源的亲缘关系,为唐棣资源的保护、良种选育和开发利用提供理论依据。结果显示：(1)从64对引物组合中筛选出8对扩增条带清晰、多态性高的引物组合,共扩增出277条清晰条带,其中多态性条带116条,多态性位点百分率为42.86%。(2)UPGMA聚类、主坐标分析(PCoA)和遗传结构分析结果相似,将6个陕西野生唐棣居群分成2大支,秦岭南北居群间遗传分化明显,且群体间存在一定基因流。(3)分子方差分析(AMOVA)结果显示遗传变异主要存在于居群内(63%),居群间遗传变异为37%。Mantel检验表明陕西唐棣居群地理距离与遗传距离之间无明显相关性(r = 0.192,P = 0.220)。研究表明,AFLP分子标记可以准确、有效地用于唐棣遗传多样性分析;唐棣遗传变异主要来源于居群内,居群间的基因交流有限;陕西野生唐棣遗传多样性水平较低,但部分居群的遗传多样性较高。该研究结果可为野生唐棣资源的保护、良种选育和开发利用提供理论依据。     

A comparison of genetic structuring of Yellowcheek Darters (Etheostoma moorei) using AFLPs and allozymes

The goals of this study were to characterize the genetic structure of 6 populations of Etheostoma moorei (Yellowcheek Darter), endemic to the Little Red River watershed of central Arkansas, to estimate the levels of gene flow within isolated streams, and to compare AFLP genetic diversity and distance data to our previously published allozyme data. The Yellowcheek Darter is a candidate species for listing under the Endangered Species Act. This darter is found in previously connected headwater streams presently isolated and partially inundated downstream by Greers Ferry Reservoir. AFLP data for the Yellowcheek Darter was concordant with previous work utilizing allozymes (r_s = 0.682; p < 0.01), yet genetic differences among populations were greater in magnitude. Genetic diversity (polymorphism = 92.7; heterozygosity = 0.496) is higher for the Yellowcheek Darter than would be expected for a species in decline, and greater for AFLP versus allozyme data. Genetic structuring among streams was also more evident using AFLP data. Gene flow levels are indicative of a metapopulation structure within streams (F_ST = 0.003 − 0.010), with genetic structuring indicating distinct populations among streams.     

Effects of Timber Management on Pond-Breeding Salamanders

Abstract: Pond-breeding salamanders spend most of their lives in forested habitat surrounding the vernal pools where they breed. Timber harvesting has been demonstrated to have negative impacts on salamander populations due to changes in soil temperature, soil compaction, and general degradation of habitat. However, little is known about how long it takes for harvested forest habitat to once again become suitable for salamanders. Questions also remain as to whether salamanders will use an area that has been harvested in recent years if an older intact forest area is available. We used drift fences and pitfall traps to capture adult spotted salamanders (Ambystoma maculatum) and marbled salamanders (A. opacum) migrating to 3 vernal ponds during their breeding seasons. The study area contained tracts of forest that were clear-cut 11–12 years prior to the study. All 3 ponds were surrounded by areas of clear-cut and intact forest and drift fences were placed in both habitat types. Similar numbers of spotted salamanders entered the ponds from clear-cut and intact forest areas. The number of marbled salamanders migrating to the ponds did not differ between areas of clear-cut and intact forest. These results suggest that clear-cut habitats may become suitable for adult pond-breeding salamanders after a relatively short regeneration period.     

Conservation and genetics of the frosted flatwoods salamander (Ambystoma cingulatum) on the Atlantic coastal plain

The federally threatened frosted flatwoods salamander, Ambystoma cingulatum, occurs in isolated populations on the coastal plain of northern Florida, Georgia and South Carolina. An earlier phylogeographic study based primarily on mitochondrial DNA (mtDNA) and morphometrics demonstrated that the previously recognized species A. cingulatum contained two cryptic species, and that two distinct mtDNA clades were contained within the newly restricted A. cingulatum. However, salamanders from the northern extent of the species range in South Carolina were not previously available for analysis. Here, we used individuals from a newly discovered South Carolina breeding site to determine whether A. cingulatum from South Carolina are genetically distinct from their more southerly conspecifics. These analyses included the mitochondrial gene studied previously as well as broad geographic sampling of three rapidly evolving nuclear genes that allowed us to further investigate lineage diversification of flatwoods salamanders. The mitochondrial and nuclear results are largely congruent, yielding strong support for two distinct species of flatwoods salamanders and also two lineages within the eastern species. Further, the South Carolina specimens are closely related to other haplotypes found in eastern Georgia and Florida. Our summary of field surveys over the past 20 years indicates that this South Carolina population may be one of only three remaining in the entire Atlantic coastal plain distribution of this rare and declining amphibian species.     

Genetic differentiation within metapopulations of Euphydryas aurinia and Melitaea phoebe in China

We analyzed genetic differentiation within metapopulations of two species of checkerspot butterfly, Euphydryas aurinia and Melitaea phoebe, in China. To generate genetic information, we used a new molecular technique, DALP – direct amplified length polymorphism. AMOVA results showed that most of the variation occurred among individuals within local populations of both E. aurinia and M. phoebe. However, while there was differentiation among local population in E. aurinia (P < 0.001), there was no subdivision in metapopulation of M. phoebe (P = 0.210). This is consistent with the behavior of M. phoebe adults being more dispersive than E. aurinia. Within the M. phoebe metapopulation, three neighboring patches were always occupied during the observation period (1998–2000). In addition, the number of individuals in these three populations accounted for the majority of M. phoebe larvae, and hence we conclude that the M. phoebe metapopulation might exist as a source-sink metapopulation. On the other hand, the E. aurinia metapopulation is an example of a classical metapopulation. Therefore, the conservation management of these two species should reflect these differences.     

A Comparison of Hybridization between Mottled Ducks (<Emphasis Type="Italic">Anas fulvigula</Emphasis>)and Mallards (<Emphasis Type="Italic">A. platyrhynchos</Emphasis>) in Florida and South Carolina using Microsatellite DNA Analysis

Interspecific hybridization has been implicated in population declines for some waterfowl species within the mallard complex, and hybridization with mallards (Anas platyrhynchos) is currently considered the largest threat to mottled ducks (A. fulvigula), one North American member of that complex. We assessed genetic variation among 225 mottled ducks and mallards using five microsatellite loci, and detected significant overall differences between these species within two geographic areas. We characterized hybridization in Florida, where mottled ducks are endemic and mallards are beginning to appear on the breeding grounds, and in South Carolina, where mottled ducks were introduced outside their native range. We used Bayesian genetic mixture analysis in an attempt to distinguish between these closely related species. In Florida, we detected two distinct genetic groups, and 10.9% of our samples from Florida mottled ducks were inferred to have been hybrids. In contrast only 3.4% of Florida mallards were inferred to have been hybrids, suggesting asymmetric hybridization. Populations from different geographic areas within Florida exhibited hybridization rates ranging from 0% to 24%. These data indicate a genetic component would be appropriate in actively managing interspecific hybridization in Florida mottled ducks. In contrast, South Carolina mottled ducks and mallards cannot be differentiated.     

硬核资源遗传多样性的AFLP分析

为了解云南省硬核[Scleropyrum wallichianum（Wight et Arn.）Arn.]的遗传多样性,采用AFLP标记分析了7个居群84份种质材料的遗传变异。结果表明,从64对引物组合中挑选出多态性较好的引物8对,共扩增出1 728条带,其中多态性条带1 388条,多态性百分率为80.14%。硬核在物种水平的多样性指数分别为Na=1.416,Ne=1.179,H=0.137,I=0.225,在居群水平上分别为H=0.111,I=0.175;在遗传相似性系数为0.52时,这些种质材料可分为3组,其中易武居群具有丰富的遗传变异,大部分的遗传变异存在于居群内,而在0.05置信区间内居群间遗传变异仅为11.5%;居群间的遗传距离和地理距离无显著相关性（r=0.0323,P=0.5820）。因此,硬核资源可采用就地和迁地保护策略,以增加其遗传多样性。     

Genetic Variation in the Endangered Endemic Species Cycas fairylakea (Cycadaceae) in China and Implications for Conservation

Cycas fairylakea is an endangered endemic species in China. Genetic diversity within and among four natural populations of this species in China was investigated using amplified fragments length polymorphism (AFLP). A moderate to low level of intraspecific genetic diversity was detected in this species (at population level: P = 39.57 %, H₀ = 0.244; at species level: P = 60.22%, H₀ = 0.356). The among-population component accounted for, respectively, 25.7 and 31.5% of the genetic variation, according to AMOVA and Shannon’s index, indicating most of the genetic variation was found between individuals within populations. All four populations have opposite pyramid age structure, and few coning individuals, which is still decreasing. Possibly because of habitat degradation and environmental pollution, plant diseases and insect pests in the populations were extremely serious, suggesting that the main factors threatening the survival of C. fairylakea populations were not genetic variation, but human activities and the breeding system of this species.     

琴叶风吹楠资源遗传多样性的AFLP分析

为研究濒危植物琴叶风吹楠(Horsfieldia pandurifolia)的遗传多样性,利用AFLP分子标记技术,对采自云南省西双版纳州、临沧市的8个居群共56份琴叶风吹楠样品进行了分析。结果表明,琴叶风吹楠在物种水平的多态性较高,多态性百分率为75.16%;在居群水平,平均多态性百分率为36.20%;AMOVA分析表明,琴叶风吹楠的遗传变异主要存在于居群内(75.45%),而居群间的变异仅为24.55%;mantel检验结果表明,地理距离和遗传距离存在不显著的正相关(r=0.119 7, P=0.321 0);基于遗传相似性系数,对8个居群进行了UPGMA聚类分析,在遗传相似性系数0.951处可将8个居群聚为3组。这些为琴叶风吹楠的保护和开发利用提供了理论依据,并提出了保护建议。     

‘Good-genes’ and ‘compatible-genes’ effects in an Alpine whitefish and the information content of breeding tubercles over the course of the spawning season

Abies ziyuanensis is a highly endangered fir species endemic to South China. Unlike other Abies species that are distributed in areas with cold climates, A. ziyuanensis is restricted to several isolated island-like localities at subtropical mountains. In this study, we used dominant amplified fragment length polymorphism (AFLP) and co-dominant simple sequence repeats (SSR) markers to infer the genetic structure of A. ziyuanensis. Seven populations consisting of 139 individuals were sampled across their whole distribution. A. ziyuanenesis has a relatively low level of genetic variation, with a mean genetic diversity per population (He) of 0.136 (AFLP) and 0.337 (SSR), which is lower than that of other reported endemic species based on the same kind of marker. We observed high population differentiation, with Gst = 0.482 (AFLP) and Fst = 0.250 (SSR), among the seven populations. AMOVA also detected significant differentiation among populations (Φst (AFLP) = 0.550 and Φst (SSR) = 0.289) and among regions (Φct (AFLP) = 0.139 and Φct (SSR) = 0.135) in both marker types. Both ongoing evolutionary forces (e.g., genetic drift resulting from small population size) and historical events (e.g., population contraction and fragmentation during and after the Quaternary glacial cycles) may have contributed to the genetic structure in A. ziyuanensis.     

Genetic diversity and phylogenetic relationships in alder,Alnus firma, revealed by AFLP

Molecular markers for alder,Alnus firma Sieb. et Zucc, have not been studied extensively. Here, we used amplified fragment length polymorphism (AFLP) to investigate genetic relationships among 15 natural populations. EcoRI-ACG + Msel-CTG combinations revealed the highest polymorphism (62.2%). A total of 171 DNA fragments were identified. On average, 58.1% of the AFLP markers that were generated using four primer pairs were polymorphic. Diversity was insignificant among the populations. The combination of a wind-pollinated, outcrossing breeding system along with large population sizes, and the ability to regenerate by stump sprouting may explain the high level of genetic diversity within this species. The majority (98%) of the genetic variance resided within populations. The average number of individuals that were exchanged between populations per generation was very high (N _em = 12.3). Gene dispersal in alder is apparently by seed dispersalvia water and human activity as well as through pollen. Five individuals per population were claded in the same cluster.