Population Assignment Research Articles

Genetic homogeneity and weak signatures of local adaptation in the marine mussel Mytilus chilensis

The natural populations of the marine mussel Mytilus chilensis and the associated aquaculture industry forms a sensitive social-ecological system that relies on the released propagules for cultivation in the highly heterogeneous environment (temperature, productivity, and salinity) of northern Patagonia (42–44 °S). We assessed spatial genetic structure, signals of local adaptation, and population assignment of M. chilensis analyzing 5963 SNPs from 125 individuals across six natural populations sampled over two consecutive years along the southeast Pacific coast (39° 25′ to 43° 07′ S, ~ 430 km). Neutral and putatively adaptive loci revealed high genetic diversity and low genetic differentiation among populations. Of the whole dataset, less than 1% (50) of loci were identified as putatively adaptive through multiple approaches, with only 0.1% detected in by all of them, and only two loci of them were correlated with environmental variables. No evidence of Isolation by Environment (IBE) was found, albeit a slight differentiation in the southern sampling location (Yaldad). These results suggest that the genetic structure observed is primarily shaped by neutral processes with weak signals of local adaptation. Gene-flow appears to be the main evolutionary force influencing the species’ population genetic structure. Because of the importance for the industry, the probability of correct assignment of individuals to their population of origin using allelic frequencies was evaluated. Analyses exhibited relatively low probabilities (< 50% for four out of six sites) of accurately assigning individuals to their geographic origin, with a limited success of SNP markers the for such purposes. Likely, species' high dispersal capacity, seed translocation, and the spill-over effect of mussel aquaculture prevents population genetic differentiation through high effective gene flow, hindering local genetic adaptation.

Current species protection does not serve its porpoise-Knowledge gaps on the impact of pressures on the Critically Endangered Baltic Proper harbour porpoise population, and future recommendations for its protection.

Successful management requires information on pressures that threaten a species and areas where conservation actions are needed. The Baltic Proper harbour porpoise population was first listed as Critically Endangered by the International Union for the Conservation of Nature in 2008. Now, 16 years later, there is no change in conservation status despite ample conservation policy calling for its protection and an urgent need for management action to protect this population. Here, we provide an overview of the current status of the population, highlight knowledge gaps on the impact of pressures, and make recommendations for management of anthropogenic activities. Based on an exceeded limit for anthropogenic mortality, the high concentrations of contaminants in the Baltic Sea, combined with reductions in prey availability and increases in underwater noise, it is inferred that this population is likely still decreasing in size and conservation action becomes more urgent. As bycatch and unprotected underwater explosions result in direct mortality, they must be reduced to zero. Inputs of contaminants, waste, and existing and emerging noise sources should be minimised and regulated. Additionally, ecosystem-based sustainable management of fisheries is paramount in order to ensure prey availability, and maintain a healthy Baltic Sea. Stranding networks to routinely assess individuals for genetic population assignment and health need to be expanded, to identify rare samples from this population. Knowledge is still scarce on the population-level impact of each threat, along with the cumulative impact of multiple pressures on the population. However, the current knowledge and management instruments are sufficient to apply effective protection for the population now. While bycatch is the main pressure impacting this population, urgent conservation action is needed across all anthropogenic activities. Extinction of the Baltic Proper harbour porpoise population is a choice: decision-makers have the fate of this genetically and biologically distinct marine mammal population in their hands.

Two-stage differential evolution with dynamic population assignment for constrained multi-objective optimization

Using infeasible information to balance objective optimization and constraint satisfaction is a very promising research direction to address constrained multi-objective problems (CMOPs) via evolutionary algorithms (EAs). The existing constrained multi-objective evolutionary algorithms (CMOEAs) still face the issue of striking a good balance when solving CMOPs with diverse characteristics. To alleviate this issue, in this paper we develop a two-stage different evolution with a dynamic population assignment strategy for CMOPs. In this approach, two cooperative populations are used to provide feasible driving forces and infeasible guiding knowledge. To adequately utilize the infeasibility information, a dynamic population assignment model is employed to determine the primary population, which is used as the parents to generate offspring. The entire search process is divided into two stages, in which the two populations work in weak and strong cooperative ways, respectively. Furthermore, multistrategy-based differential evolution operators are adopted to create aggressive offspring. The superior exploration and exploitation ability of the proposed algorithm is validated via some state-of-the-art CMOEAs over artificial benchmarks and real-world problems. The experimental results show that our proposed algorithm gained a better, or more competitive, performance than the other competitors, and it is an effective approach to balancing objective optimization and constraint satisfaction.

Timber DNA release using focused ultrasound extraction (FUSE) for genetic species identification

The use of genetic data for timber species and population assignment is a powerful tool for combating the illegal timber trade, but the challenges of extracting DNA from timber have prevented the routine use of genetics as a supply chain management tool. To overcome these challenges, we explored the feasibility of focused ultrasound extraction (FUSE) for rapid DNA release from timber. Using high-pressure ultrasound pulses, FUSE generates a cavitation bubble cloud that disintegrates samples into acellular debris, resulting in the mechanical release of DNA. In this work, FUSE was applied to white oak (Quercus alba) timber shavings to test the feasibility of using FUSE for timber DNA extraction for the first time. Results showed that FUSE processing disintegrated the tissue samples and released significant quantities of DNA. After five minutes of tissue processing DNA quantities of 0.21 ± 0.02 ng/mg, 0.99 ± 0.32 ng/mg, and 0.14 ± 0.01 ng/mg, were released from medium, coarse, and combination shaving groups, respectively. Amplification and sequencing of regions within the matK and rbcL chloroplast genes confirmed that the quality of DNA prepared with FUSE was suitable for PCR and short-read sequencing applications. Overall, these results show that FUSE can serve as a DNA sample preparation method capable of releasing high-quality DNA from timber in a fraction of the time required by conventional extraction methods. Based on the improved efficiency of DNA release with FUSE, ongoing work aims to develop this technology into portable systems that can be used to rapidly prepare timber samples for genetic species identification.

SnpAIMeR: R package for evaluating ancestry informative marker contributions in non-model population diagnostics.

Single nucleotide polymorphism (SNP) markers are increasingly popular for population genomics and inferring ancestry for individuals of unknown origin. Because large SNP datasets are impractical for rapid and routine analysis, diagnostics rely on panels of highly informative markers. Strategies exist for selecting these markers, however, resources for efficiently evaluating their performance are limited for non-model systems. snpAIMeR is a user-friendly R package that evaluates the efficacy of genomic markers for the cluster assignment of unknown individuals. It is intended to help minimize panel size and genotyping effort by determining the informativeness of candidate diagnostic markers. Provided genotype data from individuals of known origin, it uses leave-one-out cross-validation to determine population assignment rates for individual markers and marker combinations. snpAIMeR is available on CRAN (https://CRAN.R-project.org/package=snpAIMeR).

An Exhaustive Examination of the Integration of Literature into Teaching/Learning Strategies for Advancing English Reading Comprehension: A Systematic Literature Review

This study aims to provide an extensive literature review of previous studies conducted to demonstrate and investigate the effectiveness of using literature in teaching and learning reading comprehension at the middle education level. Consequently, this literature review was conducted using a systematic approach, involving searches across multiple academic databases on the addressed topic, which resulted in highlighting twenty articles conducted between 2010 and 2021. The systematic review method included identifying relevant studies, evaluating their quality, and synthesizing their findings. Furthermore, the researchers divided the main findings into two groups: the first one focused on using short stories, and the second group included all other literary genres. Both groups showed the positive effect of using short stories, comic stories, or novels as an efficacious method in developing, teaching, and learning reading comprehension skills, especially for adolescents and children. Therefore, this study suggests using different literary genres such as children’s short stories, fiction, and plays in middle education classrooms and employing new reading techniques and strategies to further motivate students. In addition, it recommends using a larger population and random assignment when selecting samples for future studies.

Population assignment of migratory Westslope Cutthroat Trout (WCT) in the Clark Fork–Pend Oreille River basin

AbstractObjectiveThe Clark Fork–Pend Oreille River basin of northeastern Washington and the Idaho Panhandle historically supported a robust metapopulation of the Westslope Cutthroat Trout (WCT) Oncorhynchus lewisi, a western native salmonid of high cultural and economic value. The construction of impassible hydroelectric dams and smaller instream barriers has prevented the return of migratory WCT to spawning tributaries, leading to the fragmentation of this metapopulation over the past 100 years. One such impassible barrier is Albeni Falls Dam (AFD) near Newport, Washington, which was completed without fish passage capabilities in 1955. We sought to examine large‐scale genetic patterns in the study area and determine the most likely spawning tributary of origin for migratory WCT captured below AFD.MethodsWe created a genetic baseline representative of populations within the Clark Fork–Pend Oreille River basin from upstream and downstream of the dam using 191 biallelic single‐nucleotide polymorphism genetic markers. Our data set included 124 collections, which allowed for an examination of population structure and hatchery influence across the study area and provided a robust tool for population assignment. Population assignment tests were conducted using the program RUBIAS.ResultPopulation assignment tests were successful for all pure WCT of unknown origin despite potential influence from hatchery lineages across the study area. Of 83 migratory WCT captured below AFD, approximately 80% were assigned to tributaries upstream of AFD with a posterior assignment probability of at least 90%. Only one fish was assigned to a tributary downstream of AFD.ConclusionOur results indicate that AFD disrupts the natural metapopulation dynamics of WCT populations in the basin. Passage for WCT at this barrier would reestablish metapopulation connectivity within the basin by allowing migratory individuals to make genetic contributions to populations upstream of the dam.

Ngāokeoke Aotearoa: The Peripatoides Onychophora of New Zealand.

(1) Background: Originally described as a single taxon, Peripatoides novaezealandiae (Hutton, 1876) are distributed across both main islands of New Zealand; the existence of multiple distinct lineages of live-bearing Onychophora across this spatial range has gradually emerged. Morphological conservatism obscured the true endemic diversity, and the inclusion of molecular tools has been instrumental in revealing these cryptic taxa. (2) Methods: Here, we review the diversity of the ovoviviparous Onychophora of New Zealand through a re-analysis of allozyme genotype data, mitochondrial DNA cytochrome oxidase subunit I sequences, geographic information and morphology. (3) Results: New analysis of the multilocus biallelic nuclear data using methods that do not require a priori assumptions of population assignment support at least six lineages of ovoviviparous Peripatoides in northern New Zealand, and mtDNA sequence variation is consistent with these divisions. Expansion of mitochondrial DNA sequence data, including representation of all existing taxa and additional populations extends our knowledge of the scale of sympatry among taxa and shows that three other lineages from southern South Island can be added to the Peripatoides list, and names are proposed here. In total, 10 species of Peripatoides can be recognised with current data.

Abstract 789: GrafGen: Distance-Based Inference of Population Ancestry for Helicobacter pylori Genomes

Abstract BACKGROUND: The 1.67 megabase H. pylori genome contains ~143,000 biallelic single-nucleotide polymorphisms (SNP) with minor allele frequency &amp;gt; 1%. Confounding by population stratification is a major source of bias requiring adjustment in genome-wide association studies (GWAS). Previous model- and distance-based methods for bacterial genomes yield varying results depending upon which strains are included for comparison in analyses. We therefore developed a robust classification of H. pylori ancestry to facilitate generalizable inferences about disease associations. METHODS: GrafGen is an R software package adapted from the GrafPop tool for human ancestry (Jin et al., 2017; Jin et al., 2019). The underlying classification algorithm compares SNPs of an individual genome with frequencies in reference populations to estimate subject ancestry and ancestral proportions based on calculated genetic distances. Outputs incorporate visualization tools that provide natural geometric interpretation of population structure. RESULTS: Training data were obtained from the H. pylori Genome Project (HpGP), a global survey of 1011 H. pylori genomes collected across 51 countries (Thorell et al., 2023). Based on genetic distances, HpGP sequences clustered into nine mutually exclusive populations designated by their predominant geographic source. Previously published population assignments for a test set of 255 sequences obtained from GenBank mapped to specific GrafGen classifications (Table). GrafGen assignments based on randomly selected sets of 14,300 and 1430 SNPs were &amp;gt;97% and &amp;gt;90% identical, respectively, to those based on all 143,000 SNPs. CONCLUSIONS: GrafGen's universal categorization of H. pylori ancestry has utility for bacterial GWAS. The software code is publicly available for research on this important pathogen. Theoretically, the same algorithm can be implemented to infer ancestry of any single chromosome haploid species that has sufficient sequence data for references. Citation Format: William Wheeler, Difei Wang, Isaac Zhao, Yumi Jin, Charles S. Rabkin. GrafGen: Distance-Based Inference of Population Ancestry for Helicobacter pylori Genomes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 789.

Rare, long-distance dispersal underpins genetic connectivity in the pink sea fan, Eunicella verrucosa.

Characterizing patterns of genetic connectivity in marine species is of critical importance given the anthropogenic pressures placed on the marine environment. For sessile species, population connectivity can be shaped by many processes, such as pelagic larval duration, oceanographic boundaries and currents. This study combines restriction-site associated DNA sequencing (RADseq) and passive particle dispersal modelling to delineate patterns of population connectivity in the pink sea fan, Eunicella verrucosa, a temperate octocoral. Individuals were sampled from 20 sites covering most of the species' northeast Atlantic range, and a site in the northwest Mediterranean Sea to inform on connectivity across the Atlantic-Mediterranean transition. Using 7510 neutral SNPs, a geographic cline of genetic clusters was detected, partitioning into Ireland, Britain, France, Spain (Atlantic), and Portugal and Spain (Mediterranean). Evidence of significant inbreeding was detected at all sites, a finding not detected in a previous study of this species based on microsatellite loci. Genetic connectivity was characterized by an isolation by distance pattern (IBD) (r 2 = 0.78, p < 0.001), which persisted across the Mediterranean-Atlantic boundary. In contrast, exploration of ancestral population assignment using the program ADMIXTURE indicated genetic partitioning across the Bay of Biscay, which we suggest represents a natural break in the species' range, possibly linked to a lack of suitable habitat. As the pelagic larval duration (PLD) is unknown, passive particle dispersal simulations were run for 14 and 21 days. For both modelled PLDs, inter-annual variations in particle trajectories suggested that in a long-lived, sessile species, range-wide IBD is driven by rare, longer dispersal events that act to maintain gene flow. These results suggest that oceanographic patterns may facilitate range-wide stepping-stone genetic connectivity in E. verrucosa and highlight that both oceanography and natural breaks in a species' range should be considered in the designation of ecologically coherent MPA networks.

Atlantic bonito (Sarda sarda) genomic analysis reveals population differentiation across Northeast Atlantic and mediterranean locations: Implications for fishery management

The Atlantic bonito (Sarda sarda, family Scombridae) is a pelagic species and one of the most exploited small tuna species. Despite its economic importance, biological information is scarce with no associated management directives. In this study, using a population genomic approach resulted in a lack of panmixia of two genetic pools with different effective population sizes (east central-tropical Atlantic and northeast Atlantic-Mediterranean) and an intermixing zone in Atlantic Morocco. The absence of genetic heterogeneity between the locations in Atlantic - Mediterranean transitional zone adds new evidence that challenges the Strait of Gibraltar as a phylogeographic barrier for marine pelagic species. These results are proposed to the ICCAT Commission to establish management areas for this species, although they are not consistent with the recently adopted pelagic ecoregions. Finally, a panel of highly informative SNPs was developed for efficient and low-cost population assignment and the analysis of unresolved population structures.

Population assignment from genotype likelihoods for low‐coverage whole‐genome sequencing data

Abstract Low‐coverage whole‐genome sequencing (WGS) is increasingly used for the study of evolution and ecology in both model and non‐model organisms; however, effective application of low‐coverage WGS data requires the implementation of probabilistic frameworks to account for the uncertainties in genotype likelihoods. Here, we present a probabilistic framework for using genotype likelihoods for standard population assignment applications. Additionally, we derive the Fisher information for allele frequency from genotype likelihoods and use that to describe a novel metric, the effective sample size, which figures heavily in assignment accuracy. We make these developments available for application through WGSassign, an open‐source software package that is computationally efficient for working with whole‐genome data. Using simulated and empirical data sets, we demonstrate the behaviour of our assignment method across a range of population structures, sample sizes and read depths. Through these results, we show that WGSassign can provide highly accurate assignment, even for samples with low average read depths (&lt;0.01X) and among weakly differentiated populations. Our simulation results highlight the importance of equalizing the effective sample sizes among source populations in order to achieve accurate population assignment with low‐coverage WGS data. We further provide study design recommendations for population assignment studies and discuss the broad utility of effective sample size for studies using low‐coverage WGS data.

Genome-wide analysis of the harbour porpoise (Phocoena phocoena) indicates isolation-by-distance across the North Atlantic and potential local adaptation in adjacent waters

The harbour porpoise (Phocoena phocoena), a highly mobile cetacean species of the Northern Hemisphere, inhabits basins that vary broadly in salinity, temperature, and food availability; such variation can drive divergent adaptation among local populations. To shed light on range-wide population structure and local adaptation, we generated ddRAD sequencing data spanning the entire North Atlantic and the Baltic Sea, as well as the Black Sea as an outgroup, and mapped this data to the high-quality draft genome of the species. We identified 11,978 genome-wide SNPs from 150 individuals, which we used for population genetic inferences. Our results support genetic differentiation between North Atlantic and Baltic Sea populations, with Kattegat as a transition zone. Across the North Atlantic the population differentiation is subtle from west to east, congruent with an isolation-by-distance pattern, but indicates a separation of southern North Sea harbour porpoises. We identified genomic outlier regions, i.e., scaffold regions where SNPs with high FST across North Atlantic populations co-occur. Together with the draft genome annotation, these regions could point towards candidate genes for differential local adaptation processes among populations. Furthermore, they enable the development of a SNP panel for routine population assignment which will be useful in a conservation and management context. We identified six outlier loci putatively under positive selection, based on the population structure inferred from the complete SNP set. Our study highlights the value of genome resources in conservation and management and provides a crucial additional resource for the study of harbour porpoise evolution and phylogeny.

Natal origin and dispersal of problem saltwater crocodiles in the Darwin Harbor, Australia

AbstractManagement programs that successfully recovered wild saltwater crocodile (Crocodylus porosus) populations in the Northern Territory of Australia did so with an expanding commitment to maintaining public safety. One aspect of the program is the ongoing removal of resident and immigrant crocodiles within Darwin Harbor (since 1979), the main urban center. We determined the likely sources of crocodiles caught as problem animals between 2015–2017 by comparing recently developed methods for population assignment. Depending on the assignment model used, we estimated that between 30% and 50% of crocodiles in Darwin Harbor originated from the Adelaide and Mary rivers, and the Kakadu region east of Darwin, and between 20% and 30% of crocodiles originated from the Finniss, Reynolds, and Daly rivers southwest of Darwin. Saltwater crocodiles occur at particularly high densities in these catchments. The remainder came from a mixture of different sources across the Northern Territory. The most common animals captured were immature (150–180 cm) males that have traveled 100–200 km. We did not identify any relationships between the distance from the inferred origin to Darwin Harbor and the size and sex of the crocodiles, or the year of capture. The targeted removal of crocodiles from specific sites such as Darwin Harbor, near where most people live, improves public safety in the highest risk areas, without compromising abundant source populations in most areas.

Transcriptome-derived SNP markers for population assignment of sandfish, Holothuria (Metriatyla) scabra

The sandfish, Holothuria scabra is a commercially important fishery and aquaculture species contributing to the high-value sea cucumber industry. Overexploited across many areas throughout its distributional range, natural populations are considered in decline. Accurate genetic assignment to population of origin is becoming increasingly important for genetics-based marine fisheries management and monitoring, especially for species experiencing depletion of natural stocks and decline in fisheries productivity due to overfishing and illegal, unreported, and unregulated (IUU) fishing. Initiatives for genetics-based applications on economically important seafood such as H. scabra have been limited by the lack of comprehensive genome or transcriptome resources. The present study developed and evaluated the use of gene-associated single nucleotide polymorphism (SNP) markers to assign sandfish to three locations in the Philippines, in the proximity of existing and emerging hatchery production centers. In silico SNP discovery pipeline using pooled RNA-Seq libraries and medium-throughput genotyping approach generated a dataset comprising 115 individuals genotyped at 88 SNPs. Population assignment using machine-learning analysis and Bayesian approach revealed that the 88 transcriptome-derived SNPs allowed the assignment of sandfish individuals to population of origin, with an overall assignment accuracy of >80%. The novel SNPs developed could find their utility in facilitating the development of geographic traceability tools applicable in the context of sandfish aquaculture, fisheries management and conservation.

Low-coverage whole genome sequencing for highly accurate population assignment: Mapping migratory connectivity in the American Redstart (Setophaga ruticilla).

Understanding the geographic linkages among populations across the annual cycle is an essential component for understanding the ecology and evolution of migratory species and for facilitating their effective conservation. While genetic markers have been widely applied to describe migratory connections, the rapid development of new sequencing methods, such as low-coverage whole genome sequencing (lcWGS), provides new opportunities for improved estimates of migratory connectivity. Here, we use lcWGS to identify fine-scale population structure in a widespread songbird, the American Redstart (Setophaga ruticilla), and accurately assign individuals to genetically distinct breeding populations. Assignment of individuals from the nonbreeding range reveals population-specific patterns of varying migratory connectivity. By combining migratory connectivity results with demographic analysis of population abundance and trends, we consider full annual cycle conservation strategies for preserving numbers of individuals and genetic diversity. Notably, we highlight the importance of the Northern Temperate-Greater Antilles migratory population as containing the largest proportion of individuals in the species. Finally, we highlight valuable considerations for other population assignment studies aimed at using lcWGS. Our results have broad implications for improving our understanding of the ecology and evolution of migratory species through conservation genomics approaches.

Pitfalls and challenges with population assignments of individuals from admixed populations: Applying Genogeographer on Brazilian individuals

The assignment of individuals to a population can be of importance for the identification of mass disaster victims or criminal offenders in the field of forensic genetics. This assignment is based on biostatistical methods that process data of ancestry informative markers (AIMs), which are selected based on large allele frequency differences between the populations of interest.However, population assignments of individuals with an admixed genetic background are challenging. Admixed individuals are genetic mosaics of chromosomal segments from the parental populations, which may lead to ambiguous or no population assignment. This is problematic since admixture events are a substantial part of human history.In this study, we present challenges of interpreting the evidential weight of population assignments. We used Genogeographer for likelihood ratio (LR) calculations and Brazilians as examples of admixed individuals. Brazilians are a very heterogenous population representing a three-way admixture between Native Americans, Europeans, and Africans. Ancestry informative markers were typed in a total of 589 individuals from Brazil using the Precision ID Ancestry Panel. The Brazilians were assigned to six metapopulations (East Asia, Europe, Middle East, North Africa, South-Central Asia, Sub-Saharan Africa) defined in the Genogeographer software and LRs were calculated if the AIM profile was not an outlier in all metapopulations and simulated two-way (1:1) admixtures of the six metapopulations.Population assignments failed for 55% of the samples. These samples had significantly higher genetic contributions from East Asia, South-Central Asia and Sub-Saharan Africa, and significantly lower genetic contributions from Europe. Most of the individuals with population assignments were assigned to the metapopulations of Middle East (58%) or North Africa (36%), followed by Europe (4%), South-Central Asia (1%), and Sub-Saharan Africa (1%). For 8% of the samples, population assignments were only possible when assignments to simulated two-way (1:1) admixtures of the six metapopulations were considered. Most of these individuals were assigned to two-way admixtures of North Africa, South-Central Asia, or Sub-Saharan Africa.Relatively low median likelihood ratios (LRs<1000) were observed when comparing population likelihoods for Europe, Middle East, North Africa, South-Central Asia, or simulated 1:1 admixtures of these metapopulations. Comparisons including East Asian or Sub-Saharan African populations resulted in larger median LRs (LR>1010).The results suggested that the Precision ID Ancestry Panel provided too little information and that additional markers specifically selected for sub-continental differentiation may be required for accurate population assignment of admixed individuals. Furthermore, a Genogeographer database with additional populations including admixed populations would be advantageous for interpretation of admixed AIM profiles. It would likely increase the number of population assignments and illustrate alternatives to the most likely population, which would be valuable information for the case officer when writing the case report.

Origins of green turtle fishery bycatch in the central pacific revealed by mixed genetic markers

Longline fishing vessels, such as those that target tuna or billfish, also unintentionally catch endangered marine turtle species on the high seas. The stock composition of this bycatch is often unknown but potentially complex, with individuals coming from many possible origins on an ocean-basin scale. To better understand the stock composition of green turtle (Chelonia mydas) bycatch we obtained 46 turtles, 27-91 cm in curved carapace length, caught by Hawaii- and American Samoa-based pelagic longline fishing vessels across large areas of the North- and South-central Pacific. We genotyped these at nine microsatellite loci and one mitochondrial DNA marker, and used a baseline of 1,043 nesting female green turtles from beaches across the Pacific for population assignment and mixed-stock analysis. By analyzing both marker types jointly we were able to increase power and genetically resolve ten baseline stocks of nesting females with mean self-assignment and simulated accuracies of 75-97%. Above the Equator, green turtle bycatch was composed mostly of individuals from Hawaiian and Eastern Pacific stocks, with a small number from the Western Pacific. Below the Equator, the most common stocks in the bycatch were from Australia and the Coral Sea, American Samoa and French Polynesia, and the Galápagos Islands. Overall, turtles originating from East, West, and Central Pacific breeding populations were major components of the bycatch, suggesting that the geographic ranges of these populations overlap across large tracts of ocean during the pelagic life history stages.

An expanded description of Cnemaspis gracilis (Beddome 1870) (Squamata: Gekkonidae) based on recent material.

Cnemaspis gracilis is a poorly known species that has been reported from across southern India, with 11 named species within the clade. The species is known only from the type series, as many other records from areas outside the type locality have turned out to represent distinct species. We provide an expanded morphological description of the species based on topotypic material and other samples that were assigned using genetic data. Cnemaspis gracilis is now known with certainty from three localities in the vicinity of Palakkad, Palakkad District, Kerala, and Valparai town, Coimbatore district, Tamil Nadu, besides from an introduced population in the Timber Market, Kolhapur city, Kolhapur district, Maharashtra, India. The species is 7.6-15.8 % divergent on the ND2 gene from described members of the gracilis clade and can be diagnosed by a combination of morphological characters including body size, number of paravertebral tubercles between limb insertions, number of dorsal tubercle rows, number of ventral scale rows across the belly, number of femoral and precloacal pores and poreless scales separating these series in males, and the presence of a single central black ocellus on the neck and a smaller one on the occiput. The assignment of extant populations to the species, a detailed morphological description and genetic data will allow the description of many more species from within this diverse clade of diurnal geckos.

Genetic diversity and differentiation of Thutho cattle from northeast India using microsatellite markers

Cattle are losing maximum breeds among the world’s livestock. Genetic variability data is essentially required for conservation decision-making. Thutho is a recently registered Indian cattle breed (INDIA_CATTLE_1400_THUTHO_03047) from the northeast region (NE), a biodiversity hotspot. Genetic diversity in the Thutho population and its differentiation from the only other cattle breed of NE (Siri) and cattle (Bachaur) of the neighboring region was established using highly polymorphic, FAO-recommended microsatellite markers. Numerous alleles (253) were detected across the 25 loci. The mean observed and expected numbers of alleles in the population were 10.12 ± 0.5 and 4.5 ± 0.37, respectively. The observed heterozygosity (0.67 ± 0.04) was lower than the expected heterozygosity (0.73 ± 0.03) which indicated a departure from the Hardy–Weinberg equilibrium. A positive FIS value (0.097) confirmed the heterozygote deficiency in the Thutho population. Genetic distance, phylogenetic relationships, differentiation parameters, population assignment, and Bayesian analysis explicitly ascertained the unique genetic identity of the Thutho cattle. The population did not suffer any bottlenecks in the past. Thutho has minimum diversity among the three populations; hence, its scientific management needs to be initiated immediately. Interestingly, genetic variation is enough for formulating breeding programs for managing, improving, and conserving this precious indigenous cattle germplasm.