Quantifying “demographic independence” is a vital step in establishing potential conservation units for a species in that it effectively distinguishes migration from within‐population reproduction. ...This is an important aspect because it allows for an accurate estimate of recruitment. For example, populations may be designated as 'management units' (=MUs) if indeed population growth results from local demography rather than immigration. Of additional interest is the calculation of immigrant ancestry and ascertainment of the temporal context over which immigration occurred. This is because MUs depend largely upon local (self‐sustaining) birth and death rates, and the quantification of ancestry is necessary to validate demographic independence. Dispersal rate is also of immediate interest to conservation biologists, and can be assessed by quantifying genetic divergence among populations. The capacity with which to gauge these benchmarks has now been extended herein to genome‐wide molecular data, in an attempt to adjust an analytical tool that was until now intractable for the next generation sequencing data.
In this study, a popular legacy program for migrant detection (i.e. BayesAss3) has been modified to accept SNP (single nucleotide polymorphism) data. We validated BA3‐SNPs using empirical data to demonstrate its suitability for both high‐performance and desktop computing environments. We also facilitate high analytical throughput by presenting a binary search algorithm that automates MCMC (Markov chain Monte Carlo) parameter tuning.
Our BA3‐SNPs‐autotune program required five or fewer rounds of optimization for 99% of input files, with acceptable mixing parameters derived in 100% of our test cases. Runtime for BA3‐SNPs is a function of the number of loci analysed. Benchmarking yielded an average runtime <32 hr (10 million MCMC generations) for datasets containing thousands of SNPs.
The BA3 algorithm remains a viable option for analysing modern SNP datasets. Source code (C++ and Python) is released publicly under the GNU General Public License v3.0, and is available for download (Linux and Mac OSX) from the following URL: https://github.com/stevemussmann/.
Abstract
Background
Research on the molecular ecology of non-model organisms, while previously constrained, has now been greatly facilitated by the advent of reduced-representation sequencing ...protocols. However, tools that allow these large datasets to be efficiently parsed are often lacking, or if indeed available, then limited by the necessity of a comparable reference genome as an adjunct. This, of course, can be difficult when working with non-model organisms. Fortunately, pipelines are currently available that avoid this prerequisite, thus allowing data to be a priori parsed. An oft-used molecular ecology program (i.e., S
tructure
), for example, is facilitated by such pipelines, yet they are surprisingly absent for a second program that is similarly popular and computationally more efficient (i.e., A
dmixture
). The two programs differ in that A
dmixture
employs a maximum-likelihood framework whereas S
tructure
uses a Bayesian approach, yet both produce similar results. Given these issues, there is an overriding (and recognized) need among researchers in molecular ecology for bioinformatic software that will not only condense output from replicated A
dmixture
runs, but also infer from these data the optimal number of population clusters (
K
).
Results
Here we provide such a program (i.e., A
dmix
P
ipe
) that (a) filters SNPs to allow the delineation of population structure in A
dmixture
, then (b) parses the output for summarization and graphical representation via C
lumpak
. Our benchmarks effectively demonstrate how efficient the pipeline is for processing large, non-model datasets generated via double digest restriction-site associated DNA sequencing (ddRAD). Outputs not only parallel those from S
tructure
, but also visualize the variation among individual A
dmixture
runs, so as to facilitate selection of the most appropriate
K
-value.
Conclusions
A
dmix
P
ipe
successfully integrates A
dmixture
analysis with popular variant call format (VCF) filtering software to yield file types readily analyzed by C
lumpak
. Large population genomic datasets derived from non-model organisms are efficiently analyzed via the parallel-processing capabilities of A
dmixture
. A
dmix
P
ipe
is distributed under the GNU Public License and freely available for Mac OSX and Linux platforms at:
https://github.com/stevemussmann/admixturePipeline
.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Despite its imperative, biodiversity conservation is chronically underfunded, a deficiency that often forces management agencies to prioritize. Single-species recovery thus becomes a focus (often ...with socio-political implications), whereas a more economical approach would be the transition to multi-targeted management (= MTM). This challenge is best represented in Midwestern North America where biodiversity has been impacted by 300+ years of chronic anthropogenic disturbance such that native tall-grass prairie is now supplanted by an agroecosystem. Here, we develop an MTM with a population genetic metric to collaboratively manage three Illinois upland gamebirds: common pheasant (Phasianus colchicus; pheasant), northern bobwhite quail (Colinus virginianus; quail), and threatened-endangered (T&E) greater prairie chicken (Tympanuchus cupido pinnatus; prairie chicken). We first genotyped our study pheasant at 19 microsatellite DNA loci and identified three captive breeding stocks (N = 143; IL Department of Natural Resources) as being significantly bottlenecked, with relatedness >1st-cousin (μR = 0.158). 'Wild' (non-stocked) pheasant N = 543; 14 Pheasant-Habitat-Areas (PHAs) were also bottlenecked, significantly interrelated (μR = 0.150) and differentiated (μFST = 0.047), yet distinct from propagation stock. PHAs that encompassed significantly with larger areas also reflected greater effective population sizes (μNE = 43; P<0.007). We juxtaposed these data against previously published results for prairie chicken and quail, and found population genetic structure driven by drift, habitat/climate impacts, and gender-biased selection via hunter-harvest. Each species (hunter-harvested or T&E) is independently managed, yet their composite population genetic baseline provides the quantitative criteria needed for an upland game bird MTM. Its implementation would require agricultural plots to be rehabilitated/reclaimed using a land-sharing/sparing portfolio that differs markedly from the Conservation Reserve Program (CRP), where sequestered land decreases as agricultural prices escalate. Cost-savings for an MTM would accrue by synchronizing single-species management with a dwindling hunter-harvest program, and by eliminating propagation/stocking programs. This would sustain not only native grasslands and their resident species, but also accelerate conservation at the wildlife-agroecosystem interface.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Ecological restoration can promote biodiversity conservation in anthropogenically fragmented habitats, but effectiveness of these management efforts need to be statistically validated to determine ...'success.' One such approach is to gauge the extent of recolonization as a measure of landscape permeability and, in turn, population connectivity. In this context, we estimated dispersal and population connectivity in prairie vole (Microtus ochrogaster; N = 231) and meadow vole (M. pennsylvanicus; N = 83) within five tall-grass prairie restoration sites embedded within the agricultural matrix of midwestern North America. We predicted that vole dispersal would be constrained by the extent of agricultural land surrounding restored habitat patches, spatially isolating vole populations and resulting in significant genetic structure. We first employed genetic assignment tests based on 15 microsatellite DNA loci to validate field-derived species-designations, then tested reclassified samples with multivariate and Bayesian clustering to assay for spatial and temporal genetic structure. Population connectivity was further evaluated by calculating pairwise FST, then potential demographic effects explored by computing migration rates, effective population size (Ne), and average relatedness (r). Genetic species assignments reclassified 25% of initial field identifications (N = 11 M. ochrogaster; N = 67 M. pennsylvanicus). In M. ochrogaster population connectivity was high across the study area, reflected in little to no spatial or temporal genetic structure. In M. pennsylvanicus genetic structure was detected, but relatedness estimates identified it as kin-clustering instead, underscoring social behavior among populations rather than spatial isolation as the cause. Estimates of Ne and r were stable across years, reflecting high dispersal and demographic resilience. Combined, these metrics suggest the agricultural matrix is highly permeable for voles and does not impede dispersal. High connectivity observed confirms that the restored landscape is productive and permeable for specific management targets such as voles and also demonstrates population genetic assays as a tool to statistically evaluate effectiveness of conservation initiatives.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Porous species boundaries can be a source of conflicting hypotheses, particularly when coupled with variable data and/or methodological approaches. Their impacts can often be magnified when non-model ...organisms with complex histories of reticulation are investigated. One such example is the genus Catostomus (Osteichthys, Catostomidae), a freshwater fish clade with conflicting morphological and mitochondrial phylogenies. The former is hypothesized as reflecting the presence of admixed genotypes within morphologically distinct lineages, whereas the latter is interpreted as the presence of distinct morphologies that emerged multiple times through convergent evolution. We tested these hypotheses using multiple methods, to including multispecies coalescent and concatenated approaches. Patterson's D-statistic was applied to resolve potential discord, examine introgression, and test the putative hybrid origin of two species. We also applied naïve binning to explore potential effects of concatenation.
We employed 14,007 loci generated from ddRAD sequencing of 184 individuals to derive the first highly supported nuclear phylogeny for Catostomus. Our phylogenomic analyses largely agreed with a morphological interpretation,with the exception of the placement of Xyrauchen texanus, which differs from both morphological and mitochondrial phylogenies. Additionally, our evaluation of the putative hybrid species C. columbianus revealed a lack introgression and instead matched the mitochondrial phylogeny. Furthermore, D-statistic tests clarified all discrepancies based solely on mitochondrial data, with agreement among topologies derived from concatenation and multispecies coalescent approaches. Extensive historic introgression was detected across six species-pairs. Potential endemism in the Virgin and Little Colorado Rivers was also apparent, and the former genus Pantosteus was derived as monophyletic, save for C. columbianus.
Complex reticulated histories detected herein support the hypothesis that introgression was responsible for conflicts that occurred within the mitochondrial phylogeny, and explains discrepancies found between it and previous morphological phylogenies. Additionally, the hybrid origin of C. columbianus was refuted, but with the caveat that more fine-grain sampling is still needed. Our diverse phylogenomic approaches provided largely concordant results, with naïve binning useful in exploring the single conflict. Considerable diversity was found within Catostomus across southwestern North America, with two drainages Virgin River (UT) and Little Colorado River (AZ) reflecting unique composition.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Background
Gila topminnow (
Poeciliopsis occidentalis occidentalis
) was once highly abundant throughout the Lower Colorado River Basin of the southwestern United States. However, this Sonoran Desert ...endemic suffered extreme population declines over the past century because of habitat degradation and nonnative species introductions. Much of the prior conservation genetic work conducted on the species relied upon a small number of microsatellite loci; many exhibiting low variability in extant populations. Consequently, there was a need for additional microsatellite loci to provide high-resolution delimitation of populations for conservation purposes.
Methods and results
Paired-end Illumina sequencing was utilized to screen the Gila topminnow genome for novel microsatellite loci. We identified 21 novel loci that exhibited no deviations from expectations of genetic equilibrium, and cross-amplified in Yaqui topminnow (
P. o. sonoriensis
). These loci were amplified from 401 samples representing eight populations of Gila topminnow and Yaqui topminnow. Although diversity was low for all populations (observed heterozygosity = 0.12 to 0.45), these novel markers provided ample power to identify population of origin for each individual in Bayesian assignment tests.
Conclusions
This novel set of microsatellite loci provide a useful genetic tool to assess population genetic parameters of the endangered Gila topminnow and delineate populations for identifying conservation priorities. The cross-amplification of these loci in Yaqui topminnow shows promise for application to other
Poeciliopsis
species of Mexico and Central America.
The tips in the tree of life serve as foci for conservation and management, yet clear delimitations are masked by inherent variance at the species–population interface. Analyses using thousands of ...nuclear loci can potentially sort inconsistencies, yet standard categories applied to this parsing are themselves potentially conflicting and/or subjective e.g., DPS (distinct population segments); DUs (Diagnosable Units‐Canada); MUs (management units); SSP (subspecies); ESUs (Evolutionarily Significant Units); and UIEUs (uniquely identified evolutionary units). One potential solution for consistent categorization is to create a comparative framework by accumulating statistical results from independent studies and evaluating congruence among data sets. Our study illustrates this approach in speckled dace (Leuciscidae: Rhinichthys osculus) endemic to two basins (Owens and Amargosa) in the Death Valley ecosystem. These fish persist in the Mojave Desert as isolated Plio‐Pleistocene relicts and are of conservation concern, but lack formal taxonomic descriptions/designations. Double digest RAD (ddRAD) methods identified 14,355 SNP loci across 10 populations (N = 140). Species delimitation analyses multispecies coalescent (MSC) and unsupervised machine learning (UML) delineated four putative ESUs. FST outlier loci (N = 106) were juxtaposed to uncover the potential for localized adaptations. We detected one hybrid population that resulted from upstream reconnection of habitat following contemporary pluvial periods, whereas remaining populations represent relics of ancient tectonism within geographically isolated springs and groundwater‐fed streams. Our study offers three salient conclusions: a blueprint for a multifaceted delimitation of conservation units; a proposed mechanism by which criteria for intraspecific biodiversity can be potentially standardized; and a strong argument for the proactive management of critically endangered Death Valley ecosystem fishes.
The tips in the tree of life serve as foci for conservation and management, yet clear conservation unit delimitations are masked by inherent variance at the species‐population interface, and modern genomic applications can be difficult to parse for this purpose. Here, we present a study that provides a framework for parsing these data using speckled dace (Cyprinidae: Rhinichthys osculus), an endemic to two basins (Owens and Amargosa) in the Death Valley ecosystem (DVE). Our study offers three salient conclusions: a blueprint for a multi‐faceted delimitation of conservation units; a proposed mechanism by which criteria for intraspecific biodiversity can be potentially standardized; and a strong argument for the proactive management of critically endangered DVE fishes.
Fishes with periodic life histories are long‐lived, slow to mature, and have intermittent periods of successful recruitment, limiting the ability of managers to recover their populations rapidly.
...Endangered razorback sucker (Xyrauchen texanus) in the Colorado River Basin, USA, is a periodic strategist whose persistence is largely dependent on hatchery augmentation. Stocking efforts have increased population sizes in the basin; however, natural recruitment remains extremely limited.
Annual reproductive output of a reintroduced population of razorback sucker was evaluated over a 10‐year period in a Colorado River tributary by estimating the effective number of breeders (Nb) and numbers of repeat spawning adults through genetic analysis of wild‐spawned larval cohorts. Comparative estimates were also obtained for a self‐sustaining sympatric periodic strategist, flannelmouth sucker (Catostomus latipinnis).
Given known trade‐offs between delayed maturation and long lifespan, population size and age‐structure of razorback sucker was quantified to assess potential demographic constraints to reproductive output.
The results showed consistently low annual Nb estimates for razorback sucker (
x¯h = 127), compared with flannelmouth sucker (
x¯h= 3,022) and within the same period (2013–2018) an order of magnitude more repeat spawning individual razorback sucker (n = 41) were detected compared with flannelmouth sucker (n = 4). Given the relatively young age structure of the razorback sucker population (median = age 4), the results indicate that successful recruitment may be limited by the number of spawning adults.
These results highlight the importance of understanding how life history characteristics may affect the rate and success of reintroductions and where life‐stage specific bottlenecks to reproduction and recruitment may occur. Given the increasing necessity of stocking for most reintroductions, management of periodic strategists may need to aim at increasing the relative age‐structure of adults to bolster reproductive output in addition to increasing juvenile survival.
Environmental change is intensifying the biodiversity crisis and threatening species across the tree of life. Conservation genomics can help inform conservation actions and slow biodiversity loss. ...However, more training, appropriate use of novel genomic methods and communication with managers are needed. Here, we review practical guidance to improve applied conservation genomics. We share insights aimed at ensuring effectiveness of conservation actions around three themes: (1) improving pedagogy and training in conservation genomics including for online global audiences, (2) conducting rigorous population genomic analyses properly considering theory, marker types and data interpretation and (3) facilitating communication and collaboration between managers and researchers. We aim to update students and professionals and expand their conservation toolkit with genomic principles and recent approaches for conserving and managing biodiversity. The biodiversity crisis is a global problem and, as such, requires international involvement, training, collaboration and frequent reviews of the literature and workshops as we do here.
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