Population Structure Parameters Research Articles

Ecological dynamics and conservation implications of Indo-Pacific Tarpon (Megalops cyprinoides) in Lake Siombak, North Sumatra, Indonesia

This study presents a comprehensive examination of the Indo-Pacific Tarpon (IPT) population in Lake Siombak, North Sumatra Province, Indonesia. Through a year-long investigation, we analyzed various facets of IPT ecology, encompassing population structure, growth dynamics, reproductive behavior, feeding habits, and mortality parameters. Male dominance in collected specimens, coupled with consistently immature gonads in females, suggests a unique reproductive pattern influenced by the brackish nature of Lake Siombak. Utilizing the von Bertalanffy method, we determined a moderate growth rate in IPT, with a predominance of medium-sized, sexually immature individuals. The dietary analysis revealed an omnivorous nature, with a notable reliance on zooplankton, particularly Cladocera and Copepods. However, the most significant concern arises from the estimation of the exploitation rate (E), surpassing the annual optimum exploitation threshold, indicating a state of overexploitation. This underscores the urgent need for regulatory measures to ensure the sustainability of IPT resources in Lake Siombak. Our findings contribute to a nuanced understanding of IPT ecology in this specific ecosystem, emphasizing the importance of balanced conservation and management practices. The documented reproductive, growth, and feeding patterns provide crucial insights for informing targeted conservation strategies and safeguarding the enduring viability of the IPT population in Lake Siombak. This research serves as a foundational contribution to the broader field of fisheries science, advocating for evidence-based management to preserve the ecological balance of aquatic ecosystems.

Adaptation Centers for Migrants in the Context of Russian Migration Policy

Migration has become an integral part of sociocultural and economic dynamics, but the successful adaptation of migrants remains a priority to ensure the stability and development of society. As international migration continues to increase, greater understanding is needed of how migrant adaptation measures affect a country’s demographic indicators and prospects. In this connection, the need to create migration adaptation centers and to identify their role in the demographic development of the state is becoming urgent. This aspect of the study represents scientific novelty and complements knowledge about migration and demographic changes. The purpose of this research is to study the attitude of state and municipal employees to the problems of regulating migration processes and the creation of migration adaptation centers, identifying the main trends that require systemic changes and new approaches to migration. The concept of “demographic integration” is substantiated, reflecting the relationship and influence of successful adaptation of migrants on the demographic development of society, covering such aspects as changes in population structure, fertility, labor force and other demographic parameters that may be directly or indirectly related to the process of adaptation of migrants. Initial data: a pilot sociological study conducted among state and municipal employees who were trained under a professional development program in different regions of Russia. Data collection was carried out using the method of expert survey. The results of the study showed a multidirectional approach of state and municipal employees to key aspects of migration processes. The majority of respondents expressed support for the creation of migration adaptation centers, which indicates the need to provide migrants with knowledge and skills that would contribute to their more successful adaptation to Russian society. This factor emphasizes the importance of carefully developing adaptation educational programs and services of migration centers. Scientific contribution: the concept of “demographic integration” is introduced, in the context of which the role of migration adaptation centers in the demographic development of Russia is assessed and the need to take into account the social and demographic aspects of migration processes is emphasized. Scope of application: the results of the study can be used to develop and improve policies in the field of migration and adaptation of migrants, as well as to study the dynamics of demographic processes in Russia.

Microbial assessment of foaming dynamics in full-scale WWTP anaerobic digesters

Research on foaming processes in wastewater treatment plants (WWTPs) anaerobic digesters is increasing since it is a common phenomenon that can seriously affect digesters performance and treatment cost. This paper presents data from a full-scale experience of foam monitoring and antifoam reagents dosing as well as microbial community structure. The association of foaming episodes with microbial population structure and operational parameters has improved understanding of foaming episodes and their causes. During this long-term study (273 days), two foaming episodes occurred in the anaerobic digesters under study. Microbial community analysis showed that the first foaming episode is correlated with the proliferation of ST-12K33 (midas_s_22), which could be related to variations in the hydraulic retention time, a decrease in inflow solids concentration, and a decrease in digesters total alkalinity. The second foaming episode coincide with a clear migration of Ca. Microthrix parvicella from the activated sludge (bulking episodes) to the anaerobic digesters and its capacity to metabolize substrate under anaerobic conditions. Laboratory experiments showed that an increase in anaerobic digestion temperature and sludge pre-treatments have a positive impact on foam biodegradability and, therefore, they could be used as foam mitigation strategies. Finally, a techno-economic analysis showed that foaming episodes had an over cost of about 250 € d−1 and dropped the WWTP energy self-sufficiency from 67 to 63 %.

Population Index and Growth Estimation Based On SLW Index of the Sea Cucumber (Holothuria arguinensis Koehler & Vaney, 1906) in the Moroccan Waters of the Atlantic Coast

The population structure and growth parameters of the commercially important species of sea cucumber Holothuria arguinensis in Moroccan waters was studied, being the first study reported along these waters. We collected 455 individuals of H. arguinensis at Skhirat, and 209 at Souiria K’dima, Northern and center Atlantic of Morocco. To avoid deviation from the accurate measurements in sea cucumber related to statistical estimation because of the elasticity of the body wall, we used a compound index which merged length and width to give the SLW index (square root of length multiplied by width) and its related modifications such as Le (recalculated length) were assessed and different morphometric relationships were also explored, the results indicate that recalculated length appears to be more valuable and helpful in obtaining an accurate length of sea cucumber. The student’s t-test revealed that H. arguinensis has allometric growth (b ≠ 1 or b ≠ 3, P < 0.05). The von Bertalanffy growth function including L∞, K and t0 were estimated to be L∞ = 25.96 cm, K = 0.17 yr.−1, t0 = –1.55 year at Skhirat, and L∞ = 25.44 cm, K = 0.29 yr−1, t0 = –1.02 year at Souiria K’dima. The longevity in H. arguinensis was high (8.51 years at Skhirat and 6.81 years at Souiria k’dima) and the estimated natural mortality of H. arguinensis was low (0.47 year−1 at Skhirat and 0.67 year−1 at Souiria k’dima) when analyzed against other sea cucumber species, which indicated that this organism might be resistant to predation. Similarly, these findings will be used to establish a sustainable management strategy to exploit this marine resource and support the fishery development plans and aquaculture.

Population structure of Indian scad fish (Decapterus russelli) that was landed at the Nusantara Fishing Port of Ternate, North Maluku, Indonesia

Indian scad fish (Decapterus russelli) is a small pelagic fish species commonly caught in Indonesian seas. Excessive fishing efforts can cause population degradation, so it is necessary to understand its population structure. The purpose of this study was to analyze the population structure parameters of Indian scad fish, including growth parameters, cohort, and mortality. Sampling was done by Stratified Random Sampling method. Data analysis used the FISAT II application. Study results showed that there were 4 cohorts. The growth parameters of Indian scad fish obtained asymptote length (L∞) of 296.15 mm, coefficient of growth rate (K) of 0.60 per year, and initial age (t0) of -0.66 years. Value of coefficient of growth rate (K) indicated that growth of scad was relatively slow. The total mortality value (Z) was 0.51 per year, natural mortality (M) was 0.0034 per year, and fishing mortality (F) was 0.51 per year. So that the highest Indian scad fish mortality was caused by fishing mortality. The exploitation rate (E) was 1 per year, indicating that the Indian scad fish resources have been overexploited.

Population structure of a newly recorded (Halodule uninervis) and native seagrass (Halophila ovalis) species from an intertidal creek ecosystem

AbstractThe presence of the seagrass Halodule uninervis was documented for the first time outside the Chilika lagoon at Haripur creek, along with previously documented Halophila ovalis from the same region. The population structure (density; biomass; leaf growth rate; and morphometrics) and environmental parameters was assessed for both seagrass species. The pH levels of the water column above both seagrass meadows were lower than the standard oceanic pH of 8.2, likely attributable to upstream freshwater influences. Halophila ovalis grew on sandy and H. uninervis on silty substrates. High nutrient (nitrate and phosphate) concentrations in the water column of the creek influenced the growth of macroalgae (Ceramium sp. and Gracilaria verrucosa) on the leaves of H. uninervis. Leaf reddening was only observed in H. ovalis leaves. Under similar environmental conditions, the shoot density and biomass (above‐ and below‐ground) of H. ovalis were 2‐fold lower that for H. uninervis. The leaves of H. uninervis were 9‐fold longer than H. ovalis, whereas H. ovalis had 5‐fold wider leaves than H. uninervis. The leaf plastochrone interval of H. ovalis (2.3 days) and H. uninervis (9.6 days) was similar for the Indian Ocean region. Consequently, the H. ovalis leaf growth rate was 2‐fold lower than that for H. uninervis. H. ovalis shoot internodes were 2.6‐fold longer than for H. uninervis, whereas the root lengths of H. uninervis were longer than for H. ovalis. The shorter root length of H. ovalis resulted in a higher branching frequency than for H. uninervis. The total C and N content were higher in the H. ovalis leaves than those of H. uninervis. This study suggest seagrass responses to similar environmental conditions are species‐specific. Regular assessment of the seagrass population structure and water quality monitoring of Haripur creek are essential for better management and conservation of these important seascapes.

Improved normalization of species count data in ecology by scaling with ranked subsampling (SRS): application to microbial communities.

BackgroundAnalysis of species count data in ecology often requires normalization to an identical sample size. Rarefying (random subsampling without replacement), which is the current standard method for normalization, has been widely criticized for its poor reproducibility and potential distortion of the community structure. In the context of microbiome count data, researchers explicitly advised against the use of rarefying. Here we introduce a normalization method for species count data called scaling with ranked subsampling (SRS) and demonstrate its suitability for the analysis of microbial communities.MethodsSRS consists of two steps. In the scaling step, the counts for all species or operational taxonomic units (OTUs) are divided by a scaling factor chosen in such a way that the sum of scaled counts equals the selected total number of counts Cmin. The relative frequencies of all OTUs remain unchanged. In the subsequent ranked subsampling step, non-integer count values are converted into integers by an algorithm that minimizes subsampling error with regard to the population structure (relative frequencies of species or OTUs) while keeping the total number of counts equal Cmin. SRS and rarefying were compared by normalizing a test library representing a soil bacterial community. Common parameters of biodiversity and population structure (Shannon index H’, species richness, species composition, and relative abundances of OTUs) were determined for libraries normalized to different size by rarefying as well as SRS with 10,000 replications each. An implementation of SRS in R is available for download (https://doi.org/10.20387/BONARES-2657-1NP3).ResultsSRS showed greater reproducibility and preserved OTU frequencies and alpha diversity better than rarefying. The variance in Shannon diversity increased with the reduction of the library size after rarefying but remained zero for SRS. Relative abundances of OTUs strongly varied among libraries generated by rarefying, whereas libraries normalized by SRS showed only negligible variation. Bray–Curtis index of dissimilarity among replicates of the same library normalized by rarefying revealed a large variation in species composition, which reached complete dissimilarity (not a single OTU shared) among some libraries rarefied to a small size. The dissimilarity among replicated libraries normalized by SRS remained negligibly low at each library size. The variance in dissimilarity increased with the decreasing library size after rarefying, whereas it remained either zero or negligibly low after SRS.ConclusionsNormalization of OTU or species counts by scaling with ranked subsampling preserves the original community structure by minimizing subsampling errors. We therefore propose SRS for the normalization of biological count data.

Flood disturbance and shade stress shape the population structure of açaí palm Euterpe precatoria, the most abundant Amazon species

Euterpe precatoria Mart. is the most abundant plant species in the Amazon basin, and one of the main non-timber forest products on the continent. A thorough understanding of the ecology of this species is needed to support sustainable management initiatives. Resource availability, disturbance regime, and human management are some of the main factors influencing population structure. We described the species’ life stages, evaluated its allometric relationships, and assessed the effects of habitat type (floodplain and upland) and proximity to human settlements on population size distribution in the Central Amazon near the Purus River. The height:diameter ratio increased from Seedlings to Juvenile 2, but decreased from Juvenile 2 to Reproductive 2, indicating changing height investment for any given diameter along these life stages. There was a marked habitat dependency in both the density and population size distribution, with populations in upland forests dominated by juveniles, whereas populations in the floodplains were dominated by reproductive palms. Proximity to human settlements was not related to population structure parameters. Our results suggest that the disturbance regime may have opposite meanings in várzea forests, where it limits recruitment under increased light levels, and in terra firme forests, where it may stimulate recruitment under limited light conditions.

Metapop2: Re-implementation of software for the analysis and management of subdivided populations using gene and allelic diversity.

Management programmes often have to make decisions based on the analysis of the genetic properties and diversity of populations. Expected heterozygosity (or gene diversity) and population structure parameters are often used to make recommendations for conservation, such as avoidance of inbreeding or migration across subpopulations. Allelic diversity, however, can also provide complementary and useful information for conservation programmes, as it is highly sensitive to population bottlenecks, and is more related to long-term selection response than heterozygosity. Here we present a completely revised and updated re-implementation of the software metapop for the analysis of diversity in subdivided populations, as well as a tool for the management and dynamic estimation of optimal contributions in conservation programmes. This new update includes computation of allelic diversity for population analysis and management, as well as a simulation mode to forecast the consequences of taking different management strategies over time. Furthermore, the new implementation in C++ includes code optimization and improved memory usage, allowing for fast analysis of large data sets including single nucleotide polymorphism markers, as well as enhanced cross-software and cross-platform compatibility.

Evidence of high genetic diversity and significant population structuring in Vachellia tortilis (Forsk.) Galasso & Banfi population in Kenya

High genetic diversity and significant population structure of Vachellia tortilis population in Kenya has been determined using nuclear microsatellite markers. Despite wide distribution and long-distance gene dispersal of the species, geographic barriers affect its gene flow patterns. The Gregorian Rift Valley that cuts across the country is suggested to have differentiated the populations into eastern and western clusters. Vachellia tortilis is an important dryland tree species valued for fuelwood and fodder production; however, no strategy has been put in place for sustainable management of the species genetic resources. Furthermore, there is inadequate information on the species population genetics to aid the development of such strategies. We evaluated the amount and structure of neutral genetic diversity of V. tortilis population in Kenya and provided recommendations necessary for improvement and conservation of the species genetic resources. We hypothesized that the current genetic diversity of V. tortilis is high because of its demographic history and that no population structuring was expected to occur due to the presumed long-distance and effective gene flow patterns within the species. Leaf tissues were collected from 15 putative natural populations of V. tortilis covering the whole distribution range in Kenya. DNA was isolated from the leaf tissues and analyzed using microsatellite markers. In total, 450 trees were genotyped using ten polymorphic nuclear microsatellite loci, and genetic diversity and population structure parameters were determined. We found high levels of genetic diversity within the populations with a mean gene diversity at 0.85. However, significant population differentiation was evident (FST = 0.026, P = 0.007; RST = 0.032, P = 0.004) despite a large number of migrants per generation (Nm = 5.3). Population structure detected suggests the presence of two clusters, although many individuals showed mixed ancestry. The groups reflect the influence of geographic patterns and historical population gene flow. There exists high genetic diversity in V. tortilis in Kenya with significant population structuring into two clusters. We recommend the consideration of the two distinct groups in the development of the species improvement, breeding, and conservation programs. Such programs should ensure maintenance of the majority of the extant genetic diversity.

Population structure and morphology of South African deep‐water parapagurid hermit crabs

AbstractThe parapagurid hermit crabs Sympagurus dimorphus (Studer, 1883) and Parapagurus bouvieri (Stebbing, 1910) form dominant components of South African deeper‐water benthic invertebrate communities and, as adults, forego the use of “traditional” gastropod shells in favour of symbiotically associated Epizoanthus carcinoecia. A total of 1,122 adult S. dimorphus and 549 adult P. bouvieri derived from demersal research trawl surveys were examined to investigate parameters of population structure, carcinoecia association and morphology. S. dimorphus had a female‐biased sex ratio of 1:1.5, and P. bouvieri an equal sex ratio of 1:1. The proportion of males of both species increased with cephalothoracic shield length (CL). The lengths of the major right chelipeds of both S. dimorphus males and females, and P. bouvieri males were positively allometric, and negatively allometric in P. bouvieri females. All P. bouvieri inhabited carcinoecia, while 3.39% (n = 38) of S. dimorphus specimens occupied gastropod shells. There was a positive relationship between S. dimorphus CL and rate of gastropod shell occupation (r2 = 0.96). In S. dimorphus, number of zoanthid polyps forming the carcinoecia pseudoshell increased with both total shell volume (R2 = 0.73) and colony height (R2 = 0.61), but no such relationships were found for P. bouvieri. Euspira napus was the most common original shell around which carcinoecia developed in both S. dimorphus (45.45%) and P. bouvieri (39.00%). We speculate that these hermit species exist along an evolutionary continuum of carcinoecia use. Sympagurus dimorphus retains the ability to occupy both gastropod shells and pseudoshells and, like most other hermit crabs, continue to use shells/carcinoecia as shelters to protect the entire body. In contrast, adult P. bouvieri appear to be totally reliant on carcinoecia, which they use more as a brood pouch covering only the abdomen, rather than as a shelter into which they can fully retract to escape predation.

Assessment of genetic diversity of some Siberian and Far Eastern species of the genus Spiraea (Rosaceae) by newly developed multiplex panels of nuclear SSR loci

Taxonomic and population genetic studies of the genus Spiraea (Rosaceae) species require new informative genetic markers. We screened 37 previously published heterologous oligonucleotide primer pairs for nuclear microsatellite loci and selected eight polymorphic and most reproducible of them for PCR multiplexing which substantially increases performance of routine mass genotyping. Three multiplex sets of 3, 3 and 2 loci, respectively, were developed and tested for ability to estimate the parameters of genetic variability and population structure in closely related species Spiraea ussuriensis, S. f lexuosa, S. chamaedryfolia representing seven natural populations of the Russian Far East and Siberia. Allele number ranged among loci from twelve (Spth20) to three. Among 41 alleles found, 7 were unique in some species/populations. Analysis of parameters of genetic variability in Spiraea spp. showed similar values of allele number per locus and observed heterozygosity among populations and slightly greater estimates of expected hete rozygosity in the samples of S. f lexuosa (NA = 2.387; HO = 0.387 ± ± 0.052; HE = 0.540 ± 0.055) as compared to S. ussuriensis (NA = = 2.781; HO = 0.385 ± 0.079; HE = 0.453 ± 0.072) and S. chamaedryfolia (NA = 2.875; HO = 0.331 ± 0.071; HE = 0.505 ± 0.069). The observed values of genetic polymorphism parameters indicate the average level of genetic diversity of the studied species typical to previous studies in Spiraea. About 19 % of the observed variability occurred among populations (FST = 0.191) while 81 % of the total genetic variation concentrated within the populations. The loci VS11, VS12, VS2, and VS6 contributed most to the observed differentiation. Nei genetic distances between populations ranged from 0.049 to 0.585. Genetic differentiation patterns among studied populations based on allele frequencies of nuclear microsatellite loci correspond with their geographical location. Genetic composition of some samples contradicted with their provisional species identification.

An unexpected world population variation of MCT1 polymorphism 1470T > A involved in lactate transport

ABSTRACTA common missense mutation (1470T > A) in gene SLC16A1 responsible for an amino acid substitution in protein MCT1 has been associated with differential lactate transport and hence, differences in physical performance and muscle injuries in relation to physical exercise. This study describes, for the first time, the worldwide variation of MCT1 variant 1470T > A at an intra- and inter-continental level. Two thousand five hundred and four individual genotypes of 26 populations clustered in 5 population groups have been analysed with data downloaded from the public database 1000 Genomes Phase 3 Browser. Several parameters of population differentiation and structure have been explored as well as selection signatures in the whole gene. Allele T, the common variant, shows extremely high values in Sub-Saharan African groups (frequencies 86–91%) as compared with the remaining world regions (69–49%). TT genotype also predominates in African groups, showing significant differences with the rest of world populations. In view of the evidence that the TT genotype is associated with clinical implications and a better predisposition to sprint/power performances, we suggest that the high presence of the TT genotype in African populations should be taken into account in future association studies at both medical and sports fields.

A snapshot of a high density seahorse population in a tropical rocky reef

ABSTRACTSeahorses are fishes that suffer high trading pressure in the international market. Three species have been recorded in Brazil, Hippocampus reidi, Hippocampus erectus and Hippocampus patagonicus, already classified as threatened or data deficient. Guaíba Island is an ecologically relevant site due to its position between two bays in Rio de Janeiro state. The present study aimed to survey the seahorse population of Guaíba Island, verifying several population structure parameters. Eight diving sites were selected around the island. Only the longsnout seahorse H. reidi was recorded. The population showed the largest density ever recorded in the world for the species. Sex ratio was 1:1 and seahorses were reproductively active. We observed three juveniles. The mean length recorded was 8.9 ± 1.64 cm. The population structure was similar to others populations studied throughout the Brazilian coast.

Genetic diversity, effective population size, and structure among black bear populations in the Lower Mississippi Alluvial Valley, USA

Multiple small populations of American black bears Ursus americanus, including the recently delisted Louisiana black bear subspecies U. a. luteolus, occupy a fragmented landscape in the Lower Mississippi Alluvial Valley, USA (LMAV). Populations include bears native to the LMAV, bears translocated from Minnesota during the 1960s, and recently reintroduced and colonizing populations sourced from within the LMAV. We estimated population structure, gene flow, and genetic parameters important to conservation of small populations using genotypes at 23 microsatellite markers for 265 bears from seven populations. We inferred five genetic clusters corresponding to the following populations: White River and western Mississippi, Tensas River and Three Rivers, Upper Atchafalaya, Lower Atchafalaya, and Minnesota. Upper Atchafalaya was suggested as the product of Minnesota-sourced translocations, but those populations have since diverged, likely because of a founder effect followed by genetic drift and isolation. An admixture zone recently developed in northeastern Louisiana and western Mississippi between migrants from White River and Tensas River, resulting in a Wahlund effect. However, gene flow among most populations has been limited and considerable genetic differentiation accumulated (global FST = 0.22), particularly among the three Louisiana black bear populations that existed when federal listing occurred. Consistent with previous bottlenecks, founder effects, and persisting isolation, all LMAV bear populations had low genetic diversity (AR = 2.08–4.81; HE = 0.36–0.63) or small effective population size (NE = 3–49). Translocating bears among populations as part of a regional genetic restoration program may help improve genetic diversity and increase effective population sizes.

Population genetics and distribution data reveal conservation concerns to the sky island endemic Pithecopus megacephalus (Anura, Phyllomedusidae)

Pithecopus megacephalus is a reticulated monkey–frog species endemic to the highlands of the Espinhaco Mountain Range in southeastern Brazil, an important centre of endemism in South America. This species has a discontinuous distribution and is considered “data-deficient” by the IUCN Red List, raising concerns about its conservation. Understanding the historical dynamics and connectivity of P. megacephalus populations can provide guidelines for preservation of this species in the wild. To investigate the population dynamics of P. megacephalus, we obtained multilocus DNA data for 55 individuals from different locations along the species’ known distribution. Spatial population structure, genetic diversity and demographic parameters were evaluated using population genetic and phylogeographical tools. We also evaluated its extent of occurrence and area of occupancy to investigate extinction risk of this species. We found genetic structure along P. megacephalus’ spatial distribution in the South Espinhaco Mountain Range corresponding to three population groups: northern, central and southern. Our results could provide important data on geographic distribution and population dynamics for a Data Deficient species. Therefore, we suggest these population data, together with the species’ limited occurrence in sky island environments could be used for a more accurate classification of P. megacephalus in the IUCN list, and conservation strategies for the species should be planned accordingly.

Understanding the demographic drivers of realized population growth rates.

Identifying the demographic parameters (e.g., reproduction, survival, dispersal) that most influence population dynamics can increase conservation effectiveness and enhance ecological understanding. Life table response experiments (LTRE) aim to decompose the effects of change in parameters on past demographic outcomes (e.g., population growth rates). But the vast majority of LTREs and other retrospective population analyses have focused on decomposing asymptotic population growth rates, which do not account for the dynamic interplay between population structure and vital rates that shape realized population growth rates (λt=Nt+1/Nt) in time-varying environments. We provide an empirical means to overcome these shortcomings by merging recently developed "transient life-table response experiments" with integrated population models (IPMs). IPMs allow for the estimation of latent population structure and other demographic parameters that are required for transient LTRE analysis, and Bayesian versions additionally allow for complete error propagation from the estimation of demographic parameters to derivations of realized population growth rates and perturbation analyses of growth rates. By integrating available monitoring data for Lesser Scaup over 60yr, and conducting transient LTREs on IPM estimates, we found that the contribution of juvenile female survival to long-term variation in realized population growth rates was 1.6 and 3.7 times larger than that of adult female survival and fecundity, respectively. But a persistent long-term decline in fecundity explained 92% of the decline in abundance between 1983 and 2006. In contrast, an improvement in adult female survival drove the modest recovery in Lesser Scaup abundance since 2006, indicating that the most important demographic drivers of Lesser Scaup population dynamics are temporally dynamic. In addition to resolving uncertainty about Lesser Scaup population dynamics, the merger of IPMs with transient LTREs will strengthen our understanding of demography for many species as we aim to conserve biodiversity during an era of non-stationary global change.

Genetic diversity of a New Zealand multi-breed sheep population and composite breeds\u2019 history revealed by a high-density SNP chip

BackgroundKnowledge about the genetic diversity of a population is a crucial parameter for the implementation of successful genomic selection and conservation of genetic resources. The aim of this research was to establish the scientific basis for the implementation of genomic selection in a composite Terminal sheep breeding scheme by providing consolidated linkage disequilibrium (LD) measures across SNP markers, estimating consistency of gametic phase between breed-groups, and assessing genetic diversity measures, such as effective population size (Ne), and population structure parameters, using a large number of animals (n = 14,845) genotyped with a high density SNP chip (606,006 markers). Information generated in this research will be useful for optimizing molecular breeding values predictions and managing the available genetic resources.ResultsOverall, as expected, levels of pairwise LD decreased with increasing distance between SNP pairs. The mean LD r2 between adjacent SNP was 0.26 ± 0.10. The most recent effective population size for all animals (687) and separately per breed-groups: Primera (974), Lamb Supreme (380), Texel (227) and Dual-Purpose (125) was quite variable. The genotyped animals were outbred or had an average low level of inbreeding. Consistency of gametic phase was higher than 0.94 for all breed pairs at the average distance between SNP on the chip (~4.74 kb). Moreover, there was not a clear separation between the breed-groups based on principal component analysis, suggesting that a mixed-breed training population for calculation of molecular breeding values would be beneficial.ConclusionsThis study reports, for the first time, estimates of linkage disequilibrium, genetic diversity and population structure parameters from a genome-wide perspective in New Zealand Terminal Sire composite sheep breeds. The levels of linkage disequilibrium indicate that genomic selection could be implemented with the high density SNP panel. The moderate to high consistency of gametic phase between breed-groups and overlapping population structure support the pooling of the animals in a mixed training population for genomic predictions. In addition, the moderate to high Ne highlights the need to genotype and phenotype a large training population in order to capture most of the haplotype diversity and increase accuracies of genomic predictions. The results reported herein are a first step toward understanding the genomic architecture of a Terminal Sire composite sheep population and for the optimal implementation of genomic selection and genome-wide association studies in this sheep population.

Population genetics of immune-related multilocus copy number variation in Native Americans.

While multiallelic copy number variation (mCNV) loci are a major component of genomic variation, quantifying the individual copy number of a locus and defining genotypes is challenging. Few methods exist to study how mCNV genetic diversity is apportioned within and between populations (i.e. to define the population genetic structure of mCNV). These inferences are critical in populations with a small effective size, such as Amerindians, that may not fit the Hardy-Weinberg model due to inbreeding, assortative mating, population subdivision, natural selection or a combination of these evolutionary factors. We propose a likelihood-based method that simultaneously infers mCNV allele frequencies and the population structure parameter f, which quantifies the departure of homozygosity from the Hardy-Weinberg expectation. This method is implemented in the freely available software CNVice, which also infers individual genotypes using information from both the population and from trios, if available. We studied the population genetics of five immune-related mCNV loci associated with complex diseases (beta-defensins, CCL3L1/CCL4L1, FCGR3A, FCGR3B and FCGR2C) in 12 traditional Native American populations and found that the population structure parameters inferred for these mCNVs are comparable to but lower than those for single nucleotide polymorphisms studied in the same populations.

Diversity and genetic origin of introduced channel catfish (Ictalurus punctatus Rafinesque, 1818) to central-west Mexico

The channel catfish is an important aquaculture species in Mexico mostly managed in traditional production systems. The state of Tamaulipas has been the source of diverse populations of channel catfish in the country, however there is no documentary evidence of this. Therefore, the objective of this study was to confirm the genetic origin of populations of channel catfish (Ictalurus punctatus) of west central Mexico by microsatellite DNA markers. The study included four domestic populations from Michoacán, Zacatecas and Jalisco and two reference founder populations from Tamaulipas and Coahuila. The analysis was performed with a panel of 13 microsatellites. Some parameters of diversity and population structure were evaluated. The six populations showed excess of heterozygotes and a coefficient endogamy FIS ≤ -0.014. The analysis of gene structure was determined by a paired comparison populations, and indicated the 5.92% of variation among populations (FST= 0.059, P &lt; 0.001). The assessment approaches identified the population of Tamaulipas as the most likely genetic origin of channel catfish populations currently used in the evaluated states.