Drivers of jaguar (Panthera onca) and puma (Puma concolor) predation on endangered primates within a transformed landscape in southern Mexico

Human pressures have increasingly placed keystone species, such as large cats, under threat. Together with forest loss, prey depletion is one of the main threats to the survival of jaguars (Panthera onca) and pumas (Puma concolor) throughout the Neotropics. Generally, primates are not considered main prey for jaguar and puma, and their inclusion in the diet could be indicative of ongoing prey species decline. Here, we investigate the effect of habitat type and disturbance on primate predation by large cats. Surveys took place during the dry seasons (March to June) of 2010 and 2011, covering a total of 608.5 km across 24 localities in the Uxpanapa Valley, Mexico. We found 65 felid scat samples with the aid of a wildlife scat detection dog, and then examined them to identify predator species and classify the prey remains they contained. Primates represented the most frequent prey (35%) for both jaguar and puma in our study site and constituted approximately half of the biomass consumed by these felines in the area. Primate remains were more likely to be found in scats surrounded by the lowest percentage of conserved forest or in areas surrounded by more villages, showing the potential effects of human activities on these species' populations. The high proportion of primates found in scats within our study site could be an early indication that populations of ungulates and other “typical” prey are beginning to collapse, and urgent conservation interventions are needed for both large cats and primates before they become locally extinct. Abstract in Spanish is available with online material.     

Using occupancy models to investigate space partitioning between two sympatric large predators, the jaguar and puma in central Brazil

Coexistence of sympatric species is mediated by resource partitioning. Pumas occur sympatrically with jaguars throughout most of the jaguar's range but few studies have investigated space partitioning between both species. Here, camera trapping and occupancy models accounting for imperfect detection were employed in a Bayesian framework to investigate space partitioning between the jaguar and puma in Emas National Park (ENP), central Brazil. Jaguars were estimated to occupy 54.1% and pumas 39.3% of the sample sites. Jaguar occupancy was negatively correlated with distance to water and positively correlated with the amount of dense habitat surrounding the camera trap. Puma occupancy only showed a weak negative correlation with distance to water and with jaguar presence. Both species were less often present at the same site than expected under independent distributions. Jaguars had a significantly higher detection probability at cameras on roads than at off-road locations. For pumas, detection was similar on and off-road. Results indicate that both differences in habitat use and active avoidance shape space partitioning between jaguars and pumas in ENP. Considering its size, the jaguar is likely the competitively dominant of the two species. Owing to its habitat preferences, suitable jaguar habitat outside the park is probably sparse. Consequently, the jaguar population is likely largely confined to the park, while the puma population is known to extend into ENP's surroundings.     

Gene flow and genetic structure of the aquatic macrophyte Sparganium emersum in a linear unidirectional river

1. River systems offer special environments for the dispersal of aquatic plants because of the unidirectional (downstream) flow and linear arrangement of suitable habitats.
2. To examine the effect of this flow on microevolutionary processes in the unbranched bur-reed ( Sparganium emersum ) we studied the genetic variation within and among nine (sub)populations along a 103 km stretch of the Niers River (Germany–The Netherlands), using amplified fragment length polymorphisms.
3. Genetic diversity in S. emersum populations increased significantly downstream, suggesting an effect of flow on the pattern of intrapopulation genetic diversity.
4. Gene flow in the Niers River is asymmetrically bidirectional, with gene flow being approximately 3.5 times higher in a downstream direction. The observed asymmetry is probably caused by frequent hydrochoric dispersal towards downstream locations on the one hand, and sporadic zoochoric dispersal in an upstream direction on the other. The spread of vegetative propagules (leaf and stem fragments) is probably not an important mode of dispersal for S. emersum , suggesting that gene flow is mainly via seed dispersal. Realized dispersal distances exceeded 60 km, revealing a potential for long-distance dispersal in S. emersum .
5. There was no correlation between geographical and genetic distances among the nine S. emersum populations (i.e. no isolation by distance), which may be due to the occurrence of long-distance dispersal and/or colonization and extinction dynamics in the Niers River.
6. Overall, the genetic population structure and regional dispersal patterns of S. emersum in the Niers River are best explained by a linear metapopulation model. Our study shows that flow can exert a strong influence on population genetic processes of plants inhabiting stream systems.     

Gene flow and genetic drift in urban environments

Evidence is growing that human modification of landscapes has dramatically altered evolutionary processes. In urban population genetic studies, urbanization is typically predicted to act as a barrier that isolates populations of species, leading to increased genetic drift within populations and reduced gene flow between populations. However, urbanization may also facilitate dispersal among populations, leading to higher genetic diversity within, and lower differentiation between, urban populations. We reviewed the literature on nonadaptive urban evolution to evaluate the support for each of these urban fragmentation and facilitation models. In a review of the literature with supporting quantitative analyses of 167 published urban population genetics studies, we found a weak signature of reduced within‐population genetic diversity and no evidence of consistently increased between‐population genetic differentiation associated with urbanization. In addition, we found that urban landscape features act as barriers or conduits to gene flow, depending on the species and city in question. Thus, we speculate that dispersal ability of species and environmental heterogeneity between cities contributes to the variation exhibited in our results. However, >90% of published studies reviewed here showed an association of urbanization with genetic drift or gene flow, highlighting the strong impact of urbanization on nonadaptive evolution. It is clear that species biology and city heterogeneity obscure patterns of genetic drift and gene flow in a quantitative analysis. Thus, we suggest that future research makes comparisons of multiple cities and nonurban habitats, and takes into consideration species' natural history, environmental variation, spatial modelling and marker selection.     

Corridors for jaguar (Panthera onca) in Mexico: Conservation strategies

Several species of carnivores, as jaguar, live in low densities and require extent habitat areas for survive. One of their main threats is fragmentation and demographic isolation. Identifying the habitat corridors, we can help the conservation of these species. We identified the viable and potential corridors between jaguar management and conservation areas for Panthera onca in Mexico. We considerate an ensemble model of the potential distribution of P. onca in Mexico, from which were identified jaguar management and conservation areas (JCMA). According to these attributes, we identified the possible habitat corridors between the JCMA with Corridor Designer. Thirteen habitat corridors were between all JCMA. However only seven were viable corridors and six were potential corridors. Also, in two areas of potential corridors were identified Stepping Stones that can help the jaguar movement between large fragments. In the thirteen habitat corridors, the main threats for jaguars are habitat fragmentation, roads, highway and possible conflict human-wildlife (livestock predation). The results from this work can provide the bases to take actions on the protection of connecting zones and alleviate the mortality of wildlife in these areas.     

Gene flow and fine-scale genetic structure in a wind-pollinated tree species, Quercus lobata (Fagaceaee)

California Valley oak (Quercus lobata), one of the state's most distinctive oak species, has experienced serious demographic attrition since the 19th century, due to human activities. Recent estimates of pollen dispersal suggest a small reproductive neighborhood. Whether small neighborhood size is a recent phenomenon, a consequence of reduced gene flow caused by demographic changes, or whether it has been historically restricted, remains unclear. To examine this question, we have characterized the spatial genetic structure of N = 191 Q. lobata individuals, spread over an area of 230 ha, using eight microsatellite loci. The observed autocorrelogram suggests an historical standard deviation of gene flow distance of about 350 m per generation, higher than contemporary pollen dispersal estimates. To determine whether our estimates were affected by strong prevailing winds from the west-northwest, we developed and utilized a novel anisotropic autocorrelation analysis. We detected no more than a hint of anisotropy, and we concluded that adult spatial structure is indicative of strong historical signature of "isolation by distance." This historical estimate provides a useful reference value against which to gauge the future gene flow consequences of ongoing anthropogenic disturbance.     

Gene flow and genetic structure of Sicyopterus lagocephalus in the south-western Indian Ocean, assessed by intron-length polymorphism

Sicyopterus lagocephalus is the most abundant sicydiine (amphidromous gobiid) in the rivers of volcanic islands in the south-western Indian Ocean. The species occurs in the Mascarene (Mauritius and La Réunion) and Comoros islands (Anjouan, Mayotte, etc.) and the post-larvae supply an economically important fishery. Because of the scarcity of available ecological and biological data, a genetic survey has been undertaken at the scale of the south-western Indian Ocean using intron-length polymorphism. Samples from La Réunion, Mauritius and Mayotte were used to assess the population genetic structure within islands and between nearby and remote islands. No genetic divergences were observed in samples at these different geographical scales. A lower number of rare alleles were observed in Mayotte samples suggesting a slight effect of their peripheral geographical position. However, no recent bottleneck was evidenced for these populations. High temporal divergences have been demonstrated in La Réunion as in previous studies indicating a temporal Wahlund effect. In the light of these results, the dispersion abilities, the connectivity of populations and the metapopulation functioning are discussed in relation to the regional environmental factors (dispersal barriers, habitat colonization, cyclones, long distance dispersal).     

群体遗传结构中的基因流

群体遗传结构上的差异是遗传多样性的一种重要体现,对群体遗传结构的研究已有较久的历史,而其中的基因流研究近些年来越来越受到重视。它对群体遗传学、进化生物学、保护生物学、生态学有着极其重要的作用。虽然传统的群体遗传学能估测基因流大小,但它的精确性还有很大局限性。随着生物技术的进步,对基因流的研究逐渐向分子水平过渡,应用蛋白质电泳技术、分子标记技术(RAPD、RFLP、VNTR、ISSR、DNA测序等)方法对群体间基因流的流动水平进行了深入细致的研究。通过综述群体遗传结构的几种模式:陆岛模式、海岛模式、阶石模式、距离隔离模式、层次模式,以及在群体遗传结构的几种模式基础上的基因流的研究方法、作用、地位和近些年来研究者的研究成果,并指出了这些方法的局限性。     

群体遗传结构中的基因流

群体遗传结构上的差异是遗传多样性的一种重要体现,对群体遗传结构的研究已有较久的历史,而其中的基因流研究近些年来越来越受到重视。它对群体遗传学、进化生物学、保护生物学、生态学有着极其重要的作用。虽然传统的群体遗传学能估测基因流大小,但它的精确性还有很大局限性。随着生物技术的进步,对基因流的研究逐渐向分子水平过渡,应用蛋白质电泳技术、分子标记技术(RAPD、RFLP、VNTR、ISSR、DNA测序等)方法对群体间基因流的流动水平进行了深入细致的研究。本文综述了群体遗传结构的几种模式：陆岛模式、海岛模式、阶石模式、距离隔离模式、层次模式,以及在群体遗传结构的几种模式基础上的基因流的研究方法、作用、地位和近些年来研究者的研究成果,并指出了这些方法的局限性。Abstract: The difference of population genetic structure is one of the important embodiments of genetic diversity. There is a long history of the study of population genetic structure, and the study of gene flow of population genetic structure is aroused more and more importance. It has an important effect on population genetics, evolution biology, conservation biology and ecology. Although the level of gene flow is estimated by traditional population genetics, there is a large restriction in its precision. With the development of biological technology, the methods of the research on gene flow reach the molecular level. Methods of protein electrophoresis and molecular markers (RAPD, RFLP, VNTR, ISSR and mitochondrial DNA) are used to research gene flow among populations. This paper introduces not only some models of population genetic structure: Continent-Island Model, Island Model, Stepping-Stone Model, Isolation-By-Distance Model and Hierarchical Model; but also the study methods, function and role of gene flow is based on models of population genetic structure, research achievements in recent years and the restriction of the methods.     

Gene flow and inbreeding depression inferred from fine-scale genetic structure in an endangered heterostylous perennial, Primula sieboldii

We estimated the gene dispersal distance and the magnitude of inbreeding depression from the fine-scale genetic structure in the endangered heterostylous perennial Primula sieboldii. We indirectly estimated the neighbourhood size (Nb) and the standard deviation of gene dispersal distance (sigma(g)) from the detected genetic structure by using 10 microsatellite markers. We also estimated the fitness reduction in mating among neighbouring individuals caused by biparental inbreeding according to the genetic structure. We found clear fine-scale genetic structure (a significantly positive kinship coefficient within 42.3 m), and the indirect estimates of sigma(g) and Nb were 15.7 m and 50.9, respectively. These indirect estimates were similar to the direct estimates (18.4 m and 44.0). The slightly larger indirect estimate of Nb may reflect that inbreeding depression and genetic structure or rare long-distance dispersal that were overlooked in the direct estimate have elongated the long-term average of gene dispersal distance. P. sieboldii is also likely to suffer about 19% fitness reduction in progenies from mating among individuals 5 m apart. Our results suggest that biparental inbreeding and genetic structure can affect the range of gene dispersal and seed reproductive success in P. sieboldii.     

Marital structure and genetic isolation in a rural Hispanic population in Northern New Mexico

An investigation of the mating structure of the rural Hispanic population of the village of Abiquiu in northern New Mexico was carried out using village marriage registers. Marital movement and departure from random mating were analyzed by the distribution of birth places of marriage partners and by surname isonymy. The time periods studied were 1882 to 1910 and 1947 to 1977. The results of these analyses show marked marital isolation (median marital distances by birthplace of 11.5 and 20.0 miles, respectively) and a significant departure from random mating (F = 0.0556 and F = 0.0495, respectively). In each case the non-random component of the isonymy coefficient (F_n) greatly exceeds the random, or expected, component. Assortative mating for culture and proximity governed by the historical settlement pattern is indicated as the process producing these results. Isolation has begun to break down in recent years but as yet has had no great effect on the genetic structure of the Abiquiu population.     

Taxonomic re-evaluation of the jaguar

The purpose of this report is to re-examine jaguar (Panthera onca) subspecies using morphometric skull characters and multivariate statistical methods to analyze differences. Eleven skull characters used historically to define jaguar subspecies were measured on 170 specimens in U.S. natural history museums. Relationships among the eight recognized subspecies of jaguar were examined. using Multigroup Discriminant Analysis (MDA) and univarite statistics. Discriminant analyses of these skull characteristics does not indicate distinct groups, supporting the null hypothesis. This analysis was conducted to add to systematic studies such as DNA analysis to assist the Felid Taxon Advisory Group (Felid TAG) and the American Zoo and Aquarium Association (AZA) establish valid taxonomic differences in the jaguar. Zoo Biol 16:107–120, 1997. © 1997 Wiley-Liss, Inc.     

Gene algebra from a genetic code algebraic structure

By considering two important factors involved in the codon-anticodon interactions, the hydrogen bond number and the chemical type of bases, a codon array of the genetic code table as an increasing code scale of interaction energies of amino acids in proteins was obtained. Next, in order to consecutively obtain all codons from the codon AAC, a sum operation has been introduced in the set of codons. The group obtained over the set of codons is isomorphic to the group (Z₆₄, +) of the integer module 64. On the Z₆₄-algebra of the set of 64^N codon sequences of length N, gene mutations are described by means of endomorphisms f:(Z₆₄)^N→(Z₆₄)^N. Endomorphisms and automorphisms helped us describe the gene mutation pathways. For instance, 77.7% mutations in 749 HIV protease gene sequences correspond to unique diagonal endomorphisms of the wild type strain HXB2. In particular, most of the reported mutations that confer drug resistance to the HIV protease gene correspond to diagonal automorphisms of the wild type. What is more, in the human beta-globin gene a similar situation appears where most of the single codon mutations correspond to automorphisms. Hence, in the analyses of molecular evolution process on the DNA sequence set of length N, the Z₆₄-algebra will help us explain the quantitative relationships between genes.