Identify Management Units Research Articles

Cats, connectivity and conservation: incorporating data sets and integrating scales for wildlife management

Summary Understanding resource selection and quantifying habitat connectivity are fundamental to conservation planning for both land‐use and species management plans. However, data sets available to management authorities for resource selection and connectivity analyses are often highly limited and fragmentary. As a result, measuring connectivity is challenging, and often poorly integrated within conservation planning and wildlife management. To exacerbate the challenge, scale‐dependent resource use makes inference across scales problematic, resource use is often modelled in areas where the species is not present, and connectivity is typically measured using a source‐to‐sink approach, erroneously assuming animals possess predefined destinations. Here, we used a large carnivore, the leopard Panthera pardus, to characterise resource use and landscape connectivity across a vast, biodiverse region of southern Africa. Using a range of data sets to counter data deficiencies inherent in carnivore management, we overcame methodological limitations by employing occupancy modelling and resource selection functions across three orders of selection, and estimated landscape‐scale habitat connectivity – independent of a priori source and sink locations – using circuit theory. We evaluated whether occupancy modelling on its own was capable of accurately informing habitat connectivity, and identified conservation priorities necessary for applied management. We detected markedly different scale‐dependent relationships across all selection orders. Our multi‐data, multi‐scale approach accurately predicted resource use across multiple scales and demonstrates how management authorities can more suitably utilise fragmentary data sets. We further developed an unbiased landscape‐scale depiction of habitat connectivity, and identified key linkages in need of targeted management. We did not find support for the use of occupancy modelling as a proxy for landscape‐scale habitat connectivity and further caution its use within a management context. Synthesis and applications. Maintaining habitat connectivity remains a fundamental component of wildlife management and conservation, yet data to inform these biological and ecological processes are often scarce. We present a robust approach that incorporates multi‐scale fragmentary data sets (e.g. mortality data, permit data, sightings data), routinely collected by management authorities, to inform wildlife management and land‐use planning. We recommend that management authorities employ a multi‐data, multi‐scale connectivity approach – as we present here – to identify management units at risk of low connectivity.

Distribution and Abundance of the Central American River Turtle, Dermatemys Mawii, in Southern Quintana Roo, Mexico: Implications for a Regional Conservation Strategy

We estimated the distribution and abundance of the Central American River Turtle, Dermatemys mawii, in four aquatic systems in southern Quintana Roo, Mexico. Using nets and free diving we captured 52 individuals D. mawii among the winter, dry and rainy seasons. We recorded 12 variables to characterize the habitat and correlated these with the abundance of D. mawii. Using catching per unit effort, we evaluated the species’ relative abundance for each aquatic system. Using Maxent, we modeled the potential distribution of D. mawii using historical and present locality data. We recorded 81 D. mawii individuals using systematic sampling and casual observations. La Union was the site with the highest relative abundance (~4 ind.-net). We found a negative correlation between D. mawii abundance and salinity. The model of potential distribution identified sites with ecological conditions suitable for the species where it is undocumented. Information about the ecology of this species remains scarce, but we propose that identifying management units could improve conservation of the species at local and regional levels.

Geographic extent of introgression in Sebastesmentella and its effect on genetic population structure.

Genetic population structure is often used to identify management units in exploited species, but the extent of genetic differentiation may be inflated by geographic variation in the level of hybridization between species. We identify the genetic population structure of Sebastes mentella and investigate possible introgression within the genus by analyzing 13 microsatellites in 2,562 redfish specimens sampled throughout the North Atlantic. The data support an historical divergence between the “shallow” and “deep” groups, beyond the Irminger Sea where they were described previously. A third group, “slope,” has an extended distribution on the East Greenland Shelf, in addition to earlier findings on the Icelandic slope. Furthermore, S. mentella from the Northeast Arctic and Northwest Atlantic waters are genetically different populations. In both areas, interspecific introgression may influence allele frequency differences among populations. Evidence of introgression was found for almost all the identified Sebastes gene pools, but to a much lower extent than suggested earlier. Greenland waters appear to be a sympatric zone for many of the genetically independent Sebastes groups. This study illustrates that the identified groups maintain their genetic integrity in this region despite introgression.

Managing catch of marine megafauna: Guidelines for setting limit reference points

Limit reference points (LRPs) for catch, which correspond to thresholds to undesirable population or ecosystem states, offer a consistent, objective approach to management evaluation and prioritization across fisheries, species, and jurisdictions. LRPs have been applied successfully to manage catch of some marine megafauna (elasmobranchs, marine reptiles, seabirds, and marine mammals) in some jurisdictions, such as the use of Potential Biological Removal (PBR) to manage incidental mortality of marine mammals under the U.S. Marine Mammal Protection Act. However, implementation of ecosystem-based management is still in its infancy globally, and LRPs have not yet been widely adopted for marine megafauna, particularly for incidental catch. Here, guidelines are proposed for estimating catch LRPs for marine megafauna, with particular attention to resolving common technical and political challenges, including (1) identifying management units, population thresholds, and risk tolerances that align with common conservation goals and best practices, (2) choosing catch LRP estimators, (3) estimating input parameters such as abundance and productivity, (4) handling uncertainty, and (5) dealing with mismatches between management jurisdictions and population boundaries. The problem of cumulative impacts across sectors is briefly addressed. These guidelines, grounded in marine policy, science, precedent, and lessons learned, should facilitate wider application of catch LRPs in evaluation and management of fisheries impacts on marine megafauna, in support of global commitments to conserve biodiversity and manage fisheries responsibly.

Evidence for Bergmann's Rule and Not Allopatric Subspeciation in the Threatened Kaka (Nestor meridionalis).

Species of conservation concern characterized by small and declining populations greatly benefit from proactive management approaches such as population translocations. Because they often show intra-specific genetic and phenotypic variation, which can result from drift or differential selective pressures between habitats, understanding the distribution of such variation and its underlying processes is a prerequisite to develop effective management guidelines. Indeed, translocations among genetically differentiated populations potentially locally adapted are discouraged in order to avoid outbreeding depression, while translocations among populations characterized by high gene flow with no evidence for local adaptation are encouraged. Here, we first test whether 2 recognized subspecies, the North Island kaka (Nestor meridionalis septentrionalis) and South Island kaka (Nestor meridionalis meridionalis) of New Zealand fit a scenario of allopatric subspeciation following the separation of the North and South Islands at the end of the Pleistocene using 1 mtDNA (n = 96) and 9 microsatellite markers (n = 126). We then test whether morphological differences among the 2 subspecies support a pattern of local adaptation, comparing phenotypic divergence (P ST) and the level of divergence by drift alone (F ST) among populations. We find little population structure between islands, ruling out allopatric subspeciation in kaka. Further, P ST exceeds F ST, supporting an adaptive latitudinal size cline consistent with Bergmann's rule. These results therefore suggest that using neutral genetic diversity alone can be misleading when identifying management units and that the nature of phenotypic variation should be considered in translocations efforts. We finally discuss North and South Island management units but suggest that cross-island translocation be allowed.

From refugia to rookeries: Phylogeography of Atlantic green turtles

Investigating species' distribution and abundance over time is central to evolutionary biology, and provides important context for conservation and management. With respect to population genetic structure in green sea turtles (Chelonia mydas), certain processes such as female philopatry to natal rookeries are well understood, while others, such as male philopatry and historical changes in distribution and abundance, remain relatively understudied. Further, although inferences from mitochondrial DNA and nuclear microsatellites have both been critical in identifying management units, comparisons of these units based on both markers are still rare. Here we analyzed novel data from fifteen microsatellite markers gathered at six green turtle rookeries in the western Atlantic as well as previously published mitochondrial sequences from 13 regional rookeries. We detected low, but significant, population structure at microsatellite loci, which coincides with previous delineations of local and regional management units as well as reports of male philopatry. However, we also detected a discord between nuclear and mitochondrial data, in which two tropical rookeries (Aves Island, Venezuela; and Matapica, Surinam) clustered with the Caribbean and Mediterranean based on microsatellite data, but displayed a mitochondrial lineage characteristic of the southern Atlantic and Africa. To investigate the possible causes of this discord, we used both classical and Bayesian methods to estimate historical migration rates and the timing and magnitude of changes in population size. We detected a strong barrier to dispersal between the northern and southern Atlantic, as well as an expansion in the southern mitochondrial lineage during the Wisconsin glacial period and a later expansion in the northern lineage following the Last Glacial Maximum. We propose that the Aves and Surinam rookeries were colonized by females from a southern glacial refugium, after which they experienced male-biased gene flow from the Caribbean. This study highlights the utility of incorporating data from multiple types of molecular markers in accurately identifying conservation units and in elucidating the complex historical and contemporary processes underlying population genetic structure in marine species.

Limited genetic diversity in the critically endangered Mexican howler monkey (Alouatta palliata mexicana) in the Selva Zoque, Mexico

The Mexican howler monkey (Alouatta palliata mexicana) is a critically endangered primate, which is paleoendemic to Mexico. However, despite the potential significance of genetic data for its management and conservation, there have been no population genetic studies of this subspecies. To examine genetic diversity in the key remaining forest refuge for A. p. mexicana, the Selva Zoque, we amplified full-length mitochondrial control region sequences (1,100 bp) from 45 individuals and found 7 very similar haplotypes. Haplotype diversity (h = 0.486) and nucleotide diversity (π = 0.0007) were extremely low compared to other Neotropical primates. Neutrality tests, used to evaluate demographic effects (Tajima's D = -1.48, p = 0.05; Fu's F s = -3.33, p = 0.02), and mismatch distribution (sum of squares deviation = 0.006, p = 0.38; raggedness index = 0.12, p = 0.33) were consistent with a recent and mild population expansion and genetic diversity appears to be historically low in this taxon. Future studies should use a combination of mitochondrial and nuclear markers to fully evaluate genetic diversity and to better understand demographic history in A. p. mexicana. These studies should be undertaken throughout its geographic range in order to evaluate population structure and identify management units for conservation. Due to the limited distribution and population size of A. p. mexicana, future conservation strategies may need to consider genetic management. However, a more detailed knowledge of the population genetics of the subspecies is urgently recommended to maximise the conservation impact of these strategies.

The use of carcasses for the analysis of cetacean population genetic structure: a comparative study in two dolphin species.

Advances in molecular techniques have enabled the study of genetic diversity and population structure in many different contexts. Studies that assess the genetic structure of cetacean populations often use biopsy samples from free-ranging individuals and tissue samples from stranded animals or individuals that became entangled in fishery or aquaculture equipment. This leads to the question of how representative the location of a stranded or entangled animal is with respect to its natural range, and whether similar results would be obtained when comparing carcass samples with samples from free-ranging individuals in studies of population structure. Here we use tissue samples from carcasses of dolphins that stranded or died as a result of bycatch in South Australia to investigate spatial population structure in two species: coastal bottlenose (Tursiops sp.) and short-beaked common dolphins (Delphinus delphis). We compare these results with those previously obtained from biopsy sampled free-ranging dolphins in the same area to test whether carcass samples yield similar patterns of genetic variability and population structure. Data from dolphin carcasses were gathered using seven microsatellite markers and a fragment of the mitochondrial DNA control region. Analyses based on carcass samples alone failed to detect genetic structure in Tursiops sp., a species previously shown to exhibit restricted dispersal and moderate genetic differentiation across a small spatial scale in this region. However, genetic structure was correctly inferred in D. delphis, a species previously shown to have reduced genetic structure over a similar geographic area. We propose that in the absence of corroborating data, and when population structure is assessed over relatively small spatial scales, the sole use of carcasses may lead to an underestimate of genetic differentiation. This can lead to a failure in identifying management units for conservation. Therefore, this risk should be carefully assessed when planning population genetic studies of cetaceans.

Population structure of the climbing perch, Anabas testudineus, in the lower Mekong River basin

Abstract Genetic variation in the climbing perch Anabas testudineus (Bloch) was investigated by sequencing 1047 base pairs of the mitochondrial ND2 gene. A total of 367 fish samples were collected from the Mekong River. The samples were separated into two genetically differentiated intra-specific groups, the Laotian and Cambodian group, showing a population structure roughly in accordance with geographical location. Genetic differentiation between groups was confirmed by high pairwise F-statistic values (0.52–0.98). Molecular clock analysis indicated that both populations were separated approximately 240 000 years ago. Additionally, samples within both groups could be divided into several regional small populations. Their genetic variation might have been supported not only by environmental factors including physical barriers, but also by historical events such as migration routes and/or timing of invasions into the Mekong River. These results could be valuable in identifying management units for the conservation of the species and its resource.

Dynamics of Fishing Gear and Spatial Allocation of Fishing Effort in a Multispecies Fleet

AbstractOptimization of fishing effort allocation and efficient deployment of fishing gear are necessary for successful management of multispecies fisheries. Campeche Bank, located in the southwestern Gulf of Mexico, provides an opportunity to understand fishing effort and fishing gear dynamics through the analysis of the fishing operations of a semi‐industrial fleet and obtain insights into how to identify management units for these types of fisheries. We analyzed the operation of this fleet over 4 years by splitting it into groups and then fully describing the behavior of each one. Our analysis was based on two data sets, including records from logbooks (8,390 fishing trips) and interviews with skippers from fishing vessels at the landing ports (882 trips). We used multivariate statistical techniques (SIMPER, hierarchical cluster analysis, and nonmetric multidimensional scaling analysis) to define targeted species and define the groups (métiers). Geographical information systems tools helped us to identify the spatial distribution of fishing effort by gear on an annual and monthly basis. We identified four different groups that resulted from the combination of fishing gear, target species, and fishing zones. Shifting behavior between gears and target species was a fishing strategy developed by several vessels, and technological interactions were evident between two gear types that employ longlines. Spatial allocation of fishing effort indicated a preference for certain fishing zones by vessels that operated two of the four gears. This pattern was consistent throughout the years studied; however, monthly differences did exist. The results provide information to identify management units in multispecies fisheries through the identification of métiers and the understanding of fishing strategies.

Twelve new microsatellite loci for the shortbeard grenadier (Coryphaenoides brevibarbis)

We isolated 12 new microsatellites for the deep-sea fish Coryphaenoides brevibarbis. These loci are highly polymorphic, with allele number ranging from 2 to 17 and heterozygosity ranging from 0.231 to 0.938. These new loci will aid in identifying management units for this species.

Nineteen new microsatellite loci for the blue hake (Antimora rostrata)

We isolated nineteen new microsatellites for the deep-sea fish Antimora rostrata. These loci are highly polymorphic, with allele number ranging from 4 to 22 and heterozygosity ranging from 0.525 to 0.958. These new loci will aid in identifying management units for this species, which has recently suffered massive declines in abundance due to overfishing.

A method for defining management units based on genetically determined close relatives

AbstractØkland, J-M., Haaland, Ø. A., and Skaug, H. J. 2010. A method for defining management units based on genetically determined close relatives. – ICES Journal of Marine Science, 67: 551–558. We propose a new method for identifying management units from genetic samples (DNA profiles). The main idea is to look at the geographic distribution of genetically determined close relatives and to use these to separate different breeding populations. The method has the potential to detect population structure emerging on a demographic time-scale, as opposed to classical population genetic methods. It is not required that the breeding populations have different allele frequencies. Using simulated datasets, the proposed method has good statistical properties throughout the range of migration rates considered. This may be a powerful method for setting management boundaries.

Population genetic structure of the blue-fronted Amazon (Amazona aestiva, Psittacidae: Aves) based on nuclear microsatellite loci: implications for conservation

The blue-fronted Amazon (Amazona aestiva) is a widely distributed Neotropical parrot and one of the most captured parrots in nature to supply the illegal trade of wild animals. The objectives of the present study were to analyze the genetic structure of A. aestiva to identify management units and support conservation planning and to verified if A. aestiva populations have undergone a recent bottleneck due to habitat loss and capture for the pet trade. The genetic structure was accessed by analyzing six microsatellite loci in 74 individuals of A. aestiva, including samples from the two subspecies (A. a. aestiva and A. a. xanthopteryx), from five populations: four in Brazil and one in Argentina. A significant genetic differentiation (theta = 0.007, p = 0.005) could be detected only between the most distant populations, Tocantins and Argentina, localized at the northeast and southwest limits of the sample sites, respectively. There was no evidence of inbreeding within or between populations, suggesting random mating among individuals. These results suggest a clinal distribution of genetic variability, as observed for variation in plumage color of the two A. aestiva subspecies. Bottleneck analysis did not show a recent reduction in population size. Thus, for the management and conservation of the species, the populations from Argentina and Tocantins should be considered as different management units, and the other populations from the center of the geographical distribution as another management unit.

Comparative studies of quantitative trait and neutral marker divergence: a meta‐analysis

Comparative studies of quantitative genetic and neutral marker differentiation have provided means for assessing the relative roles of natural selection and random genetic drift in explaining among-population divergence. This information can be useful for our fundamental understanding of population differentiation, as well as for identifying management units in conservation biology. Here, we provide comprehensive review and meta-analysis of the empirical studies that have compared quantitative genetic (Q(ST)) and neutral marker (F(ST)) differentiation among natural populations. Our analyses confirm the conclusion from previous reviews - based on ca. 100% more data - that the Q(ST) values are on average higher than F(ST) values [mean difference 0.12 (SD 0.27)] suggesting a predominant role for natural selection as a cause of differentiation in quantitative traits. However, although the influence of trait (life history, morphological and behavioural) and marker type (e.g. microsatellites and allozymes) on the variance of the difference between Q(ST) and F(ST) is small, there is much heterogeneity in the data attributable to variation between specific studies and traits. The latter is understandable as there is no reason to expect that natural selection would be acting in similar fashion on all populations and traits (except for fitness itself). We also found evidence to suggest that Q(ST) and F(ST) values across studies are positively correlated, but the significance of this finding remains unclear. We discuss these results in the context of utility of the Q(ST)-F(ST) comparisons as a tool for inferring natural selection, as well as associated methodological and interpretational problems involved with individual and meta-analytic studies.

Phylogeography and the conservation of coral reef fishes

Here we present a review of how the study of the geographic distribution of genetic lineages (phylogeography) has helped identify management units, evolutionary significant units, cryptic species, and areas of endemism, and how this information can help efforts to achieve effective conservation of coral reefs. These studies have confirmed the major biogeographic barriers that were originally identified by tropical species distributions. Ancient separations, identified primarily with mtDNA sequence comparisons, became apparent between populations on each side of the barriers. The general lack of correlation between pelagic larval duration and genetic connectivity across barriers indicates that life history and ecology can be as influential as oceanography and geography in shaping evolutionary partitions within ocean basins. Hence, conservation strategies require a recognition of ecological hotspots, those areas where habitat heterogeneity promotes speciation, in addition to more traditional approaches based on biogeography. Finally, the emerging field of genomics will add a new dimension to phylogeography, allowing the study of genes that are pertinent to recent and ongoing differentiation, and ultimately providing higher resolution to detect evolutionary significant units that have diverged in an ecological time scale.

Defining units for savanna management in Sudano-sahelian areas

Management-oriented identification of vegetation types is needed in Mali for production savannas devoted to fuel-wood and charcoal production. This study seeks to determine which factor can be used to identify management units in relation to vegetation characteristics. Three production savannas, covering 1404 ha, were inventoried in the Zan Coulibaly district near Bamako. Structural variables on each inventoried plot, e.g. basal area or tree density, were measured to characterize the vegetation. Site variables such as soil depth and toposequence phase (plain, hillside or plateau) were determined to characterize the environment and anthropic pressure. Multivariate analyses were used to define vegetation units from structural variables, and to relate these to site variables. Five vegetation units were identified. A significant relationship was detected between these units and site variables. Significant differences were found in terms of structural variables between toposequence phases and between the three savannas. The results were consistent with a gradient from plain to plateau with decreasing logging intensity and decreasing soil depth. The vegetation in each toposequence phase was made up of a mosaic of vegetation units. In conclusion, toposequence phases can be used as the basis for stratifying production savannas in management units.

Effect of nitrogen fertilization and topography on soft red winter wheat yield and protein content in two Ontario landscapes

Identification of suitable management units for the variable application of fertilizer N is an essential component of a site-specific N management program. Topography and/or soil N test results are examples of two parameters that could potentially delineate N management units for improved grain yield or protein concentration. Field studies were conducted on soft red winter wheat (Triticum aestivum L.) to examine the effects of mineral soil N, soil organic carbon (SOC), and N fertilization on grain yields and protein concentrations in two variable landscapes in southwestern Ontario, Canada. Six N rates (0 to 145 kg N ha-1) were applied to plots (3 × 400 m long), arranged in a randomized complete split block design with four replicates. Sampling on a 3 × 20 m grid indicated slope position affected soil nitrate (NO3-N) and SOC levels at site 1, but not at site 2. The range of spatial correlation for NO3-N was 11.5 m at both sites and for SOC was 16.0 m and 32.4 m at site 1 and 2, respectively. Yields decreased and protein concentrations increased while moving upslope at both sites. Yield response to applied fertilizer N was characterized using a quadratic model. The most economic rate of N (MERN) for site 1 was 105 kg ha-1, and did not vary with topography. At site 2, yield response to applied fertilizer N varied with topography and MERN increased while moving downslope (91, 104, 120 kg N ha-1 for upper, mid, and lower, respectively). Protein concentration responses to applied N were fitted to cubic models, and the nature of the response to applied N did not vary with slope position. Based simply on grain yield, the potential to use topography and/or mineral N in the soil to identify management units for variable application of N was limited at these two sites; however, variably applying N may reduce the risk of exceeding the protein limits for export markets on the upper slope positions without sacrificing yield. Key words: Site-specific crop management, nitrogen application, N fertilizer, variogram, topography

Spatial genetic structure of northern pike (Esox lucius) in the Baltic Sea

The genetic relationships among 337 northern pike (Esox lucius) collected from the coastal zone of the central Baltic region and the Finnish islands of Aland were analysed using five microsatellite loci. Spatial structure was delineated using both traditional F-statistics and individually based approaches including spatial autocorrelation analysis. Our results indicate that the observed genotypic distribution is incompatible with that of a single, panmictic population. Isolation by distance appears important for shaping the genetic structure of pike in this region resulting in a largely continuous genetic change over the study area. Spatial autocorrelation analysis (Moran's I) of individual pairwise genotypic data show significant positive genetic correlation among pike collected within geographical distances of less than c. 100-150 km (genetic patch size). We suggest that the genetic patch size may be used as a preliminary basis for identifying management units for pike in the Baltic Sea.

Genetic Diversity in a Morphologically Conservative Invasive Taxon: Multiple Introductions of Swamp Eels to the Southeastern United States

Abstract: Genetic analysis of introduced populations, especially in morphologically conservative taxa, can clarify introduction histories, identify management units and source populations, provide a more realistic estimate of the frequency of successful invasion, and suggest strategies for preventing further introductions. In the last 7 years, populations of swamp eels, referred to the Asian genus Monopterus ( Family Synbranchidae) on the basis of external morphology, have been discovered in aquatic habitats near Atlanta, Georgia; Tampa, Florida; North Miami, Florida; and most recently in close proximity to Everglades National Park in Homestead, Florida. Swamp eels are large predators capable of dispersal over land and have the potential to disrupt already threatened ecosystems. We analyzed mitochondrial DNA sequences from four known populations in the continental United States and samples from Malaysia, Indonesia, Vietnam, and two locations in China to determine introduction histories, source populations, genetic diversity, and relationships among populations. Our results indicate that there have been at least three independent introductions of genetically distinct forms. Introduced populations in close proximity (separated by <40 km) are genetically distinct. The level of sequence difference among introduced populations reaches levels seen among sister families of teleost fishes for the same region of the mitochondrial genome. These genetically distinct introduced populations in all likelihood represent at least two and possibly three species. Regardless of species status, these genetically distinct lineages may be expected to vary in ecological or life‐history traits, representing different potential threats to the ecosystems where they have been introduced. Given the success of swamp eels in invading many habitats around the world, further study of these eels is warranted to elucidate the characteristics of successful invaders and invasions.