Genetic Management Units Research Articles

Assessing the population genetic structure of yellow croaker in China: Insights into the ecological and genetic consequences of artificial breeding on natural populations

The large yellow croaker, a crucial marine economic fish in China, experienced a drastic decline in wild resource in the early 1980s due to overfishing and habitat degradation. Since the year 2000, the government has implemented habitat protection measures and initiated long-term, large-scale releases aimed at restoring this ecologically and economically important fish resource. Despite these efforts, there has been no definitive success in increasing the biomass of this overexploited species, and the underlying reasons for this lack of success remain elusive. Leveraging whole-genome resequencing data from a large number of samples encompassing both cultured and wild populations, this study offers the most exhaustive analysis of the genetic structure of large yellow croaker to date. The results revealed no significant geographical structure among the wild populations along the coast of China, overturning the long-held belief that designated them into three genetic management units. Additionally, it highlighted the absence of genetic introgression from cultured to wild populations. Furthermore, this study identified adaptive changes in cultured populations due to artificial selection and aquaculture environments, potentially reducing their adaptability to natural environments. This reduced adaptability may impact the survival rate of released populations and their hybridization with wild populations, providing insights into the limited success of previous release efforts. In light of these findings, this study recommends implementing conservation and management strategies based on a single genetic management unit for the large yellow croaker. When selecting breeding populations for hatchery releases, emphasis should be placed on genetic background considerations rather than solely relying on the origin of individuals captured in the sea. These insights hold significant implications for conservation and restoration of the large yellow croaker resource, particularly in the management of germplasm resources.

Genetic Diversity and Structure Revealed by Genomic Microsatellite Markers of Mytilus unguiculatus in the Coast of China Sea.

The hard-shelled mussel Mytilus unguiculatus plays an important role in mussel aquaculture in China due to its characteristic and nutritive value. In this study, 10 microsatellite loci are used to study the genetic diversity and genetic structure of seven location populations of M. unguiculatus in coastal areas of China. The results of amplification and genotyping show that the observed heterozygosity (Ho) and the expected heterozygosity (He) are 0.61~0.71 and 0.72~0.83, respectively. M. unguiculatus has high genetic diversity. The inbreeding index (FIS) of M. unguiculatus is significantly positive (FIS: 0.14~0.19), indicating that inbreeding might exist within populations. The genetic structure of M. unguiculatus is weak within populations from the East China Sea All results showed that genetic differences existed between the Qingdao population from the Yellow Sea and other populations from the East China Sea. It does not detect a population bottleneck event or expansion event in the populations. The results from this study can be used to provide important insights in genetic management units and sustainable utilization of M. unguiculatus resources and provide a better understand of genetic structure of marine bivalve with similar planktonic larval stage in the China Sea.

High Levels of Genetic Divergence Detected in Sacramento Perch Suggests Two Divergent Translocation Sources

AbstractTranslocation has been used to conserve imperiled fishes and create new fisheries. One species for which translocation has played a significant role is the Sacramento Perch Archoplites interruptus. Extirpated from its native range, the Sacramento Perch has been introduced throughout California and Nevada through multiple translocation events, though historical records are incomplete. Recent assessments of eight previously uncharacterized Sacramento Perch populations have prompted reevaluation of range‐wide population structure to inform a genetic management plan for long‐term resiliency of this species. We examined Sacramento Perch genetic diversity and population structure across the current range of the species using 12 microsatellite markers. We analyzed samples from the eight uncharacterized populations and seven populations previously studied by Schwartz and May (2008). Bayesian clustering supported two distinct clusters of Sacramento Perch herein designated as A and B. Within these two clusters we detected hierarchical substructure, likely due to genetic drift after population founding. Genetic differentiation among populations within the same cluster was relatively low (FST = 0.023–0.176), while differentiation among populations from different clusters was higher (FST = 0.190–0.320). The existence of two strongly divergent genetic clusters in Sacramento Perch suggests two distinct translocation sources, and we recommend that these clusters be treated as genetic management units (GMUs). The B GMU populations had fairly low levels of genetic diversity relative to the A GMU populations. All populations showed evidence of past bottlenecks, and most had effective population sizes placing them at risk for inbreeding depression. Human‐facilitated gene flow is recommended to prevent further genetic diversity loss. Due to uncertainty surrounding Sacramento Perch translocation history and strong levels of divergence between the two GMUs, translocations should be facilitated only between populations within the same GMU.

Delineating genetic management units of sambar deer (

Abstract Context Invasive species are major drivers of biodiversity loss, requiring management to reduce their ecological impacts. Population genetics can be applied to delineate management units, providing information that can help plan and improve control strategies. Aim The present study aims to use a genetic approach to test the existence of three previously proposed sambar deer populations in south-eastern Australia. In doing so, the study aims to delineate management units of sambar deer in south-eastern Australia. Methods Sambar deer DNA was sourced opportunistically from tissue samples and targeted scat collection. Samples were collected from three areas in Victoria, south-eastern Australia: Mt Cole (MC), French Island (FI) and eastern Victoria (EV). Contemporary population structure was assessed using a suite of 11 polymorphic microsatellite markers. The number of maternal sambar deer lineages in south-eastern Australia was investigated through sequencing of the mitochondrial (mt)DNA control region. Key results Three distinct genetic clusters were identified. Differentiation among inferred clusters was found to be high, with FST ranging from 0.24 between EV and FI clusters and 0.48 between MC and FI clusters. Two mtDNA haplotypes were identified; R.u1 was found throughout EV and FI, and R.u2 was unique to MC. DNA isolated from scats provided reliable data and proved critical for sampling areas where hunting and culling of deer are not generally undertaken. Conclusions Three genetically distinct sambar deer management units in south-eastern Australia are defined – MC, FI and EV. Sambar deer control strategies should be applied to each management unit independently. This may be difficult or infeasible for the EV management unit, which is large and geographically complex. Further research may help identify additional fine-scale genetic structure in EV, allowing smaller, more practicable management units to be identified. Implications Genetic data can be used to identify management units for invasive species, which will be critical for the development of future management strategies and improving control operations. The approach outlined here could also be applied to improve the management of other introduced deer species in south-eastern Australia.

Describing Fine‐Scale Patterns of Genetic Structure and Introgression of Redband Trout in a Complex River System

AbstractThe conservation status of Redband Trout Oncorhynchus mykiss gairdneri has been an increasing concern of fish managers. Effective fish management first requires an understanding of the spatial distribution of distinct populations and the processes influencing gene flow. We performed a genetic analysis of Redband Trout from the Deschutes River basin in central Oregon to discern population genetic structure and the genetic impacts of an extensive hatchery stocking program and several potential barriers to dispersal. Conducting surveys in lateral habitats, we sampled over 1,400 young‐of‐the‐year Redband Trout and genotyped them at a panel of 269 SNPs using genotyping‐in‐thousands by sequencing. We found that within this section of the Deschutes River basin there were multiple distinct genetic groups of Redband Trout, with an irrigation diversion dam and only one of eight waterfalls in the study area acting as complete barriers to gene flow. Within these distinct genetic groups there was a strong signal of isolation by distance. Despite the extensive stocking of large numbers out‐of‐basin hatchery Rainbow Trout Oncorhynchus mykiss, our results indicated that introgression of wild fish occurred only with a locally derived hatchery strain of Redband Trout. Hatchery influence was greatest in Fall River and in neighboring portions of the Deschutes River. The combination of spatially explicit sampling in lateral habitat with genotyping via high‐throughput sequencing provided an effective sampling design for this large river and its tributaries. Such an approach may be useful elsewhere for identifying genetic management units of Redband Trout and other widespread freshwater fishes.

Population Structure and Genetic Diversity of the Endangered South American Giant Otter (Pteronura brasiliensis) from the Orinoco Basin in Colombia: Management Implications and Application to Current Conservation Programs.

Endangered giant otters, Pteronura brasiliensis, are found along the Amazon and Orinoco rivers and most of their tributaries. Hunting in the mid-1970s pushed giant otter populations to the brink of extinction. We studied population structure and genetic diversity of giant otters from Colombia's Orinoco basin using analyses of partial mitochondrial DNA control region sequences obtained from scat material. We collected and analyzed 54 scat samples from 22 latrines, 2 tissue samples primarily from captive giant otters and 2 from hunted animals near Puerto Carreño and Puerto Inírida (Colombian Orinoco), as well as one tissue sample from Puerto Leguizamo (Colombian Amazon). Thirty-nine partial control region sequences were obtained (258bp), corresponding to 15 unique haplotypes. Most of these haplotypes, found in samples collected around Puerto Carreño, defined one phylogeographic group (phylogroup) not previously described. Higher genetic diversity in the Colombian Orinoco populations than in other South American populations suggests that this newly described phylogroup, as well as a second phylogroup defined from a few Colombian Orinoco and Amazon samples, should be considered distinct genetic management units. National conservation programs, particularly those aiming to establish protected areas, should manage these independently. Current Colombian confiscated animal reintroduction and captive reproduction programs should also consider such differentiation when determining reintroduction locations or improving husbandry practices.

Conservation of cattle genetic resources: the role of breeds

SUMMARYFocusing on cattle (Bos taurus, Bos indicus), the present paper discusses the concept of the breed in the context of the dynamic history of livestock domestication. A breed categorization is proposed on the basis of how the breeds came into existence. The online Appendix (available athttp://journals.cambridge.org/AGS) presents a survey of the cattle breeds of the world consisting of: (1) a list of breeds per country and then subdivided according to the proposed categories; (2) a list of breed names, including synonyms and translations, ordered according to a comprehensive breed classification; and (3) an alphabetical list of these names. The commonly accepted perceptions of breeds and how these are influenced by the nomenclature are described. Considering the history of breeds, it is argued that conservation of genetic diversity does not necessarily imply conservation of breeds. However, breeds are instrumental for the conservation of genetic diversity as independent genetic management units. These considerations may very well be extrapolated to other domestic species.

Mitochondrial genetic diversity and population structure of a vulnerable freshwater fish, rock carp (Procypris rabaudi) in upper Yangtze River drainage

Rock carp (Procypris rabaudi (Tchang)) is an endemic species in the upper Yangtze River drainage. The genetic variability and population structure of eight populations (Mudong (MD), Hejiang (HJ), Wanzhou (WZ), Xishui (XS), Nantan (NT), Cangxi (CX), Tongjiang (TJ) and Wulong (WL)) were investigated based on mitochondrial DNA control region. According to the river dimensions, MD, HJ, WZ, WL and CX were defined as large river populations, while TJ, XS and NT were defined as small. The total genetic diversity level of rock carp was moderate (h = 0.858, π = 0.0079). Genetic differentiations among populations in small rivers were greater than those among populations in large rivers, and small rivers showed significant differentiation from large rivers. Analysis from the coalescent-based method showed that there were asymmetric gene flows among four large river populations (CX, HJ, MD and WZ). Demographic analyses suggested that the species as a whole and the WZ population experienced population expansion, while the HJ, NT, and MD populations experienced bottlenecks. The analysis of genetic diversity and population structure suggested that the WL, TJ, CX, NT and XS populations should be protected and managed separately, and that the HJ, MD and WZ populations should be considered as a genetic management unit.

Balancing genetic uniqueness and genetic variation in determining conservation and translocation strategies: a comprehensive case study of threatened dwarf galaxias, Galaxiella pusilla (Mack) (Pisces: Galaxiidae)

Genetic markers are widely used to define and manage populations of threatened species based on the notion that populations with unique lineages of mtDNA and well-differentiated nuclear marker frequencies should be treated separately. However, a danger of this approach is that genetic uniqueness might be emphasized at the cost of genetic diversity, which is essential for adaptation and is potentially boosted by mixing geographically separate populations. Here, we re-explore the issue of defining management units, focussing on a detailed study of Galaxiella pusilla, a small freshwater fish of national conservation significance in Australia. Using a combination of microsatellite and mitochondrial markers, 51 populations across the species range were surveyed for genetic structure and diversity. We found an inverse relationship between genetic differentiation and genetic diversity, highlighting a long-term risk of deliberate isolation of G.pusilla populations based on protection of unique lineages. Instead, we adopt a method for identifying genetic management units that takes into consideration both uniqueness and genetic variation. This produced a management framework to guide future translocation and re-introduction efforts for G.pusilla, which contrasted to the framework based on a more traditional approach that may overlook important genetic variation in populations.

Minimal Genetic Structure in the Cerulean Warbler Despite Evidence for Ecological Differentiation among Populations

Abstract. The Cerulean Warbler (Setophaga cerulea) is one of the most rapidly declining warblers in North America. Our previous genetic work suggested that this migratory songbird has no significant population genetic structure in the northern and western parts of its breeding range, and for conservation purposes we assigned all sampled populations to a single genetic management unit. Here, we expand this work to include the entire breeding range of the Cerulean Warbler, given recent evidence for morphological and ecological differentiation between the northern and southern sections of that range. We assayed variation in four microsatellite loci and an 841-base-pair fragment of the mitochondrial control region, finding support for low but significant population-genetic structure in the mitochondrial marker. Estimates of population-genetic structure for pairs of sampling locations did not detect a clear geographic pattern of differentiation, and a hierarchical AMOVA did not reveal significant structure bet...

III-3. ホシガレイの管理単位と遺伝的リスク

III-3. ホシガレイの管理単位と遺伝的リスク

Lack of genetic differentiation among subpopulations of the black‐footed albatross on the Bonin Islands

The endangered black-footed albatross Phoebastria nigripes exhibits strong nest fidelity and natal philopatry. These biological features can strongly affect population dynamics and population genetic structure. Therefore, for its long-term conservation, it is important to estimate genetic diversity and population genetic structure. We performed genetic analyses, using 11 polymorphic microsatellite markers of 77 black-footed albatrosses from six breeding colonies on the Bonin Islands, an important breeding area in the western North Pacific. In the population-based analysis, AMOVA results showed that almost all genetic variations existed among individuals in each subpopulation. Most FST and RST values among the subpopulations were 0.000 and the migration rates were 3.0–5.3%. In the individual-based analysis, the results of structure analysis suggested that all the individuals were clustered into the same genetic group. In the principal coordinates analysis based on kinship among individuals, most of the individuals were distributed as a single group. Although albatross species are strongly philopatric, the present results indicate a lack of population genetic differentiation among six subpopulations and the presence of sufficient gene flow to maintain the genetic homogeneity. In the principal coordinates analysis, a few individuals were genetically different from most of the other individuals, indicating a probability of immigration. The black-footed albatrosses on the Bonin Islands are in a good condition to maintain genetic diversity and can be treated as a single genetic management unit.

Preliminary operational genetic management units of a highly fragmented forest tree species of southern South America

The management of the genetic resources of any wild species requires the definition of genetically homogeneous units about which practical decisions can be taken. To this end, a structure analysis was performed on the Patagonian cypress Austrocedrus chilensis (D.Don) Pic. Ser. et Bizzarri. A total of 746 seed trees corresponding to 27 natural populations sampled across its entire Argentinean range were genotyped at 12 isozyme gene markers. Genetic structure was analyzed following four successive steps: (1) proposal of different population groupings according to (a) environmental features, (b) cluster and principal coordinate analyses on genetic distances, (c) Bayesian inference utilizing BAPS program and (d) maximally differentiated groups by the software SAMOVA. (2) Evaluation of the proposed groupings with AMOVA, considering that best groupings were those with a proportion of covariance component due to inter-group differences higher than that due to intra-group differences. (3) New grouping proposition after a synthetic analysis. (4) Evaluation and characterization of the final structure proposed. Mean values of diversity parameters revealed a generally low level of allelic diversity ( A/ L = 1.52; A e = 1.163; r 18 = 1.436), with moderate expected and observed heterozygosities ( H e = 0.143; H o = 0.135). Differentiation at species level was low ( δ = 0.048 and F ST = 0.060). Grouping according to precipitation regimes and glacial patterns proved not to be significant. Cluster and principal coordinate analyses did not reveal any geographical pattern. A six-group structure was proposed considering AMOVA results with intuitive adjustments based on biological facts. Three out of the six groups include most of the Argentinean range of the species. Since they are latitudinal groups, a latitudinal pattern is the basis of this structure, onto which other effects seem to superimpose. The three remaining groups would be related to the glacial history of the region. One of them is composed of populations outside the glaciated area but close to the ice sheet border, which are probably related to the re-colonization process after last deglaciation. Populations forming the fifth group are extremely isolated patches far beyond the glacial border. It is possible that those populations are the remnants of a pre-glaciation distribution of the species that managed to last to the present without any profound change. The sixth one is a rather atypical single-population group, most likely determined by drift processes. Each group of this structure serves as a preliminary operational genetic management unit (OGMU). The addition of complementary genetic data on adaptive traits is necessary to delineate definitive OGMUs.

Genetic structure of lake whitefish (Coregonus clupeaformis) in Lake Michigan

Genetic relationships among lake whitefish ( Coregonus clupeaformis ) spawning aggregates in Lake Michigan were assessed and used to predict a stock or management unit (MU) model for the resource. We hypothesized that distinct spawning aggregates represented potential MUs and that differences at molecular markers underlie population differentiation. Genetic stock identification using 11 microsatellite loci indicated the presence of six genetic MUs. Resolved MUs corresponded to geographically proximate spawning aggregates clustering into genetic groups. Within MUs, analyses suggested that all but one delineated MU was a stable grouping (i.e., no between-population differences), with the exception being the Hog Island – Traverse Bay grouping. Elk Rapids was the most genetically divergent population within Lake Michigan. However, low Fstvalues suggested that moderate to high levels of gene flow occur or have occurred in the past between MUs. Significant tests of isolation by distance and low pairwise Fstvalues potentially led to conflicting results between traditional analyses and a Bayesian approach. This data set could provide baseline data from which a comprehensive mixed-stock analysis could be performed, allowing for more efficient and effective management of this economically and socially important resource.

Global phylogeography of the band-rumped storm-petrel ( Oceanodroma castro; Procellariiformes: Hydrobatidae)

Factors shaping population differentiation in low latitude seabirds are not well-understood. In this study, we examined global patterns of DNA sequence variation in the mitochondrial control region of the band-rumped storm-petrel ( Oceanodroma castro), a highly pelagic seabird distributed across the sub-tropical and tropical Atlantic and Pacific Oceans. Despite previous classification as a single, monotypic species, fixed haplotype differences occurred between Atlantic and Pacific populations, and among all Pacific populations. In addition, Cape Verde and Galapagos birds formed distinct clades, estimated to have diverged from all other populations at least 150,000 years ago. Azores hot season populations were also genetically distinct, lending support to previous phenotypic evidence that they be recognized as a separate species. Seasonal populations in Madeira probably represent separate genetic management units. The phylogeography of the band-rumped storm-petrel appears to have been shaped by both nonphysical barriers to gene flow and Pleistocene oceanographic conditions. Ancestral populations likely expanded through contiguous range expansion and infrequent long-distance colonization into their current breeding range. These findings suggest several possible revisions to the taxonomy of the band-rumped storm-petrel.

Population Genetic Structure and Conservation of the Galápagos Petrel (Pterodroma phaeopygia)

The Galapagos petrel (Pterodroma phaeopygia) is endemic to the Galapagos archipelago, where it is known to breed only on five islands. The species has been listed as critically endangered due to habitat deterioration and predation by introduced mammals. Significant morphological and behavioural differences among petrels nesting on different islands suggest that island populations may differ genetically. Furthermore, nesting phenology suggests that genetically differentiated seasonal populations may exist within at least one island. We analysed variation in six microsatellite loci and part of the mitochondrial ATPase 6/8 gene in 206 Galapagos petrels sampled from all five islands. No evidence of genetic structuring within islands was found, although statistical power was low. In contrast, significant differences occurred among island populations. For the microsatellite loci, private alleles occurred at all islands, sometimes at high frequency; global and pairwise estimates of genetic differentiation were all statistically significant; Bayesian analysis of genotypes frequencies provided strong support for three genetic populations; and most estimates of migration between populations did not differ significantly from zero. Only two ATPase haplotypes were found, but the geographic distribution of haplotypes indicated significant differentiation among populations. For conservation purposes, populations from Floreana, Santa Cruz, San Cristobal and Santiago should be regarded as separate genetic management units. Birds from Isabela appear to be derived recently from the Santiago population, and the population on San Cristobal appears to be a mixture of birds from other populations. However, considering ecological and behavioural differences among birds from different islands, we recommend that all five populations be protected.

Population genetic structure and conservation of marbled murrelets (Brachyramphus marmoratus)

Marbled murrelets (Brachyramphus marmoratus) are coastal seabirds that nest from California to the Aleutian Islands. They are declining and considered threatened in several regions. We compared variation in the mitochondrial control region, four nuclear introns and three microsatellite loci among194 murrelets from throughout their range except Washington and Oregon. Significant population genetic structure was found: nine private control region haplotypes and three private intron alleles occurred at high frequency in the Aleutians and California; global estimates of FST or ΦST and most pairwise estimates involving the Aleutians and/or California were significant; and marked isolation-by-distance was found. Given the available samples, murrelets appear to comprise five genetic management units: (1) western Aleutian Islands, (2) central Aleutian Islands, (3) mainland Alaska and British Columbia, (4) northern California, and (5) central California.

Population genetic structure and dispersal across a fragmented landscape in cerulean warblers (Dendroica cerulea)

Cerulean warblers (Dendroica cerulea) have experienced significant declines across their breeding range and presently exist in disjunct populations, largely because of extensive loss and fragmentation of their breeding and wintering habitat. Despite this overall decline, a recent north-eastern expansion of the breeding range has been proposed, and some researchers have suggested that the eastern Ontario population may be acting as a source population maintaining sink populations elsewhere. However, little is known about either the geographic distribution of genetic variation or dispersal in these birds. We assayed variation in five microsatellite loci and a 366 base-pair fragment of the mitochondrial control region among 154 cerulean warblers from five populations throughout the breeding range. No evidence of population genetic structure was found. Assignment tests suggested that six individuals were either inter-population migrants or descendants of recent migrants. The lack of population genetic structure is probably due to a combination of historical association and contemporary dispersal. Population decline does not appear to have reduced genetic variation yet. Overall results suggest that cerulean warblers from Ontario, Illinois, Arkansas and Tennessee should be considered a single genetic management unit for conservation.

Phylogeographic lineages and differentiation pattern of Atlantic salmon (Salmo salar) in the Baltic Sea with management implications

The genetic structure and isolation pattern of the Atlantic salmon (Salmo salar) throughout its range in the Baltic Sea were examined as a starting point for a conservation strategy for the species in this area. The allozyme variation in seven polymorphic loci was studied in 5125 salmon from 24 rivers in four countries. A clear dichotomy was observed between stock groups from southeastern (Russia, Estonia, Latvia, southern Sweden) and northwestern (northern Finland, northern Sweden) drainage regions, corresponding to the postglacial colonisation of the Baltic Sea by two phylogeographic lineages, one from the east (the Ice Lake lineage) and one from the west (the Atlantic lineage). The geographical and genetic distances between stocks fit the one-dimensional "isolation-by-distance" model (p < 0.001). The estimated gene flow ranged from 0 to10 migrants per generation. The total diversity of hatchery stocks was 72% of that of the wild stocks. Genetically similar stock groups, phylogeographic lineages, and drainage regions are recommended for use as genetic management units in addition to stock level.

Phylogeographic lineages and differentiation pattern of Atlantic salmon (<i>Salmo salar</i>) in the Baltic Sea with management implications

The genetic structure and isolation pattern of the Atlantic salmon (Salmo salar) throughout its range in the Baltic Sea were examined as a starting point for a conservation strategy for the species in this area. The allozyme variation in seven polymorphic loci was studied in 5125 salmon from 24 rivers in four countries. A clear dichotomy was observed between stock groups from southeastern (Russia, Estonia, Latvia, southern Sweden) and northwestern (northern Finland, northern Sweden) drainage regions, corresponding to the postglacial colonisation of the Baltic Sea by two phylogeographic lineages, one from the east (the Ice Lake lineage) and one from the west (the Atlantic lineage). The geographical and genetic distances between stocks fit the one-dimensional "isolation-by-distance" model (p < 0.001). The estimated gene flow ranged from 0 to10 migrants per generation. The total diversity of hatchery stocks was 72% of that of the wild stocks. Genetically similar stock groups, phylogeographic lineages, and drainage regions are recommended for use as genetic management units in addition to stock level.