Recent Reduction In Population Size Research Articles

Temporal Changes in Geographic Range and Population Size of the Santa Cruz Black Salamander

Abstract The Santa Cruz black salamander Aneides niger is a priority 3 California species of special concern with a restricted geographic range confined to the Santa Cruz Mountains. Anecdotal observations suggest that the species was relatively abundant in the early 1900s, but it has become more difficult to find in the past few decades. To better understand if the species has undergone population size fluctuations, we analyzed mitochondrial and nuclear sequence data to examine levels of genetic variation and phylogeographic structure, and test for signatures of population size change. We then reconstructed the climatic suitability for the species to 1) determine if past climate fluctuations could have influenced range size and genetic diversity, and 2) estimate the effects of future climate change on geographic range suitability as a proxy for possible future population size change. Genetic analyses detected low levels of genetic variation and a general lack of genetic structuring, suggesting a recent genetic bottleneck. While neutrality tests of individual loci were nonsignificant, skyline plot and isolation-with-migration analyses detected a relatively recent reduction in population size. Interpretation of these genetic results should consider the limited number of localities and individuals sampled for this species. Climatic suitability for Santa Cruz black salamanders was much lower during the last glacial maximum, which could be the cause of the detected historical change in population size. Future projections of climatic suitability under a high-emission scenario suggest a dramatic geographic range restriction to coastal areas. These projections highlight the need for the protection of coastal habitat patches to preserve existing coastal populations, and to maintain connectivity between coastal and inland habitats to allow the westward movement of populations and genes in response to climate change.

Population genetics of the critically endangered three-striped turtle, Batagur dhongoka, from the Ganga river system using mitochondrial DNA and microsatellite analysis

The three-striped roofed (Batagur dhongoka) is a semi-aquatic turtle that belongs to family Geoemydidae. Due to anthropogenic pressure, it has been facing an intense decline of over 80% in its distribution range in the past 50 years. It is considered as 'Critically Endangered' so effective conservation strategies are needed to protect the species by determining their genetic diversity and population genetic structure. This study investigates the genetic diversity, population structure and demographic pattern of B. dhongoka from two Turtle Rescue and Rehabilitation Centre established near Ganga river using mitochondrial cytochrome b (Cyt b: 1140 bp) ; control region (CR: 451 bp) and ten nuclear microsatellite loci. mtDNA results show low levels of nucleotide diversity (π = 0.0022) in B. dhongoka haplotypes and provide evidence for a low substitution rate. The demographic pattern estimated by the Bayesian skyline plot (BSP) analysis indicates historical stability followed by growth in the effective population size, with a recent reduction in population size from ~ 2 thousand years ago. The microsatellite findings show a moderate level of observed heterozygosity (Ho: 0.49). Bayesian-based clustering analysis revealed weak genetic structures in B. dhongoka and presence of admixed assignations suggesting close genetic relationships. These findings shed light on B. dhongoka's genetic status and underline the necessity of comprehensive rehabilitation and relocation programs and conservation and management techniques to ensure the species' long-term survival. In order to ensure the effective protection and conservation of B. dhongoka, the Government of India has taken a proactive measure by incorporating it into Schedule I of the Wildlife (Protection) Act, 1972, as amended in 2022.

Impacts of Chronic Habitat Fragmentation on Genetic Diversity of Natural Populations of Prunus persica in China.

Wild peach is an important resource for improving existing peach varieties. However, the extant populations of wild peach show fragmented distribution due to human disturbance and geographic isolation. In this study, we used natural populations (or wild populations) of Prunus persica (Rosaceae) to assess the genetic effects of habitat fragmentation. A total of 368 individuals sampled from 16 natural populations were analyzed using 23 polymorphic simple sequence repeat (SSR) markers. Prunus persica maintained low within-population genetic variation and high level of genetic differentiation. Two genetic clusters were revealed based on three different methods (UPGMA, PCoA, and STRUCTURE). All populations showed a significant heterozygosity deficiency and most extant populations experienced recent reduction in population size. A significant isolation by distance (IBD) was observed with Mantel’s test. Compared to historical gene flow, contemporary gene flow was restricted among the studied populations, suggesting a decrease in gene flow due to habitat fragmentation. Habitat fragmentation has impacted population genetic variation and genetic structure of P. persica. For breeding and conservation purpose, collecting as many individuals as possible from multiple populations to maximize genetic diversity was recommended during the process of germplasm collection. In addition, populations from central China had higher genetic diversity, suggesting these populations should be given priority for conservation and germplasm collection.

A revised Red List of British butterflies

Abstract Regular reassessment of extinction risk is critical to prioritise conservation action during the current period of rapid, anthropogenic biodiversity change. Butterflies are a flagship group for insect monitoring and conservation, as they are highly visible, well studied and exhibit rapid responses to environmental change. Here, we use systematic population monitoring data from the UK Butterfly Monitoring Scheme and citizen‐science derived occurrence records to provide an updated assessment of extinction risk in Great Britain (GB) by applying current International Union for Conservation of Nature (IUCN) criteria to 62 butterfly species. The resulting regional Red List categorises four species as Regionally Extinct, 24 (41% of the remaining, extant species) as threatened (8 Endangered and 16 Vulnerable), 5 (9%) as Near Threatened and 29 (50%) as Least Concern. Recent reduction in population size (Criterion A) based on smoothed, long‐term time series of abundance and occurrence data, was responsible for most of the threatened or Near Threatened categorisations. While the status of some species improved, likely due to conservation efforts, the revised Red List demonstrates an ongoing deterioration in the status of GB butterflies, with a 26% increase in threatened species since the previous assessment. A greater proportion of butterflies was classed as threatened than for most other GB taxa. While this may stem from greater data availability for butterflies than most other groups (thus allowing tests of extinction risk against more criteria), it highlights the need to reinvigorate conservation efforts for these charismatic insects.

Historical persistence and isolation by distance of

Context Empirical studies of intraspecific genetic diversity and population structure can inform the evolutionary and demographic history of individual species and of landscapes at the bioregional level. Aims We aimed to assess intraspecific genetic variation at macroevolutionary and microevolutionary temporal scales for Mirbelia viminalis, a key species present on the Hamersley Range in the ancient and highly diverse landscape of the Pilbara bioregion of northwest Western Australia. Methods We sampled extant populations and assessed diversity and structure using sequences (chloroplast DNA, 1759 base pairs) and microsatellite markers (nuclear DNA, 15 loci) data. Key results Significant phylogeographic structure and a lack of historical demographic signals of population contraction or expansion suggest historical population persistence. Moderate chloroplast haplotype diversity (h = 15) and moderate divergence among extant haplotypes indicates a degree of historical connectivity via seed dispersal across central populations on the Hamersley Range. Levels of nuclear genetic diversity were low to moderate (allelic richness = 3.554, expected heterozygosity = 0.489, observed heterozygosity = 0.462) and depauperate compared to another member of the Mirbelia genus present further south in the Midwest region. Nuclear diversity revealed a strong signal of isolation by distance with localised admixture among populations and some contemporary genetic clustering along a north-west to south-east transect of the Hamersley Range. Conclusions Low nuclear genetic diversity may be related to recent reductions in population size for M. viminalis. Historical population persistence with few barriers to dispersal other than geographic distance may be common for members of the Fabaceae across the Hamersley Range.

Genetic Diversity and Conservation Status of Helianthus verticillatus, an Endangered Sunflower of the Southern United States.

Evaluating species diversity and patterns of population genetic variation is an essential aspect of conservation biology to determine appropriate management strategies and preserve the biodiversity of native plants. Habitat fragmentation and potential habitat loss are often an outcome of a reduction in naturally occurring wildfires and controlled prescribed burning, as seen in Helianthus verticillatus (whorled sunflower). This endangered, wild relative of the common sunflower, Helianthus annuus, is endemic to four locations in Alabama, Georgia, and Tennessee, United States. Despite its endangered status, there is no recovery plan for H. verticillatus, and knowledge related to its basic plant biology and importance in ecosystem services is mostly unknown. In this study, we utilized 14 microsatellite loci to investigate fine-scale population structure and genetic diversity of H. verticillatus individuals found on two sampling sites within the Georgia population. Our results indicated moderate genetic diversity and the presence of two distinct genetic clusters. Analyses of molecular variance indicated that the majority of variance was individually based, thus confirming high genetic differentiation and limited gene flow between H. verticillatus collection sites. The evidence of a population bottleneck in these sites suggests a recent reduction in population size that could be explained by habitat loss and population fragmentation. Also, high levels of linkage disequilibrium were detected, putatively suggesting clonal reproduction among these individuals. Our study provides a better understanding of fine-scale genetic diversity and spatial distribution of H. verticillatus populations in Georgia. Our results can underpin an original recovery plan for H. verticillatus that could be utilized for the conservation of this endangered species and to promote its persistence in the wild.

Population Genetic Structure and Diversity of the Invasive Island Apple Snail Pomacea maculata (Perry, 1810) in South Carolina and Georgia

Population genetics is a valuable tool in understanding various aspects of biological invasions, such as pathways of invasions, predicting invasion success, and determining dispersal capabilities. The island apple snail (Pomacea maculata), which is native to South America, is an invasive gastropod currently established in several southeastern states in the United States, including South Carolina and Georgia. Despite its known negative impacts in invaded regions, knowledge of P. maculata specific to South Carolina is limited, and an in-depth analysis of the population genetic structure of P. maculata in South Carolina and Georgia has not been conducted. The present study aimed to genetically characterize P. maculata individuals from three locations in South Carolina and five locations in Georgia using a suite of 14 microsatellite markers. Population genetic structure was determined using pairwise FST comparisons, isolation by distance analysis, and a likelihood-based approach. Genetic diversity indices, effective population size, inbreeding coefficients, and Garza–Williamson indices, which is the mean ratio of number of alleles to the range in allele size in a population and can be used to detect recent reductions in population size, were all calculated. Significant genetic structure was observed in all sampling locations, apart from the two sites in Kingsland, GA; a weak correlation was found between genetic distance and geographic distance across all the sites; and genetic diversity was low across all loci at the eight sites. Garza–Williamson indices all showed likely recent reductions in population size. These results indicate that the populations in South Carolina and Georgia were probably the result of separate introduction events and that these populations are genetically isolated. The low genetic diversity observed could indicate that these populations are susceptible to eradication efforts and/or stochastic environmental changes.

Low genetic diversity and shallow population structure in the endangered vulture, Gyps coprotheres

Globally, vulture species are experiencing major population declines. The southern African Cape vulture (Gyps coprotheres) has undergone severe population collapse which has led to a listing of Endangered by the IUCN. Here, a comprehensive genetic survey of G. coprotheres is conducted using microsatellite markers. Analyses revealed an overall reduction in heterozygosity compared to other vulture species that occur in South Africa (Gypaetus barbatus, Necrosyrtes monachus, and Gyps africanus). Bayesian clustering analysis and principal coordinate analysis identified shallow, subtle population structuring across South Africa. This provides some support for regional natal philopatry in this species. Despite recent reductions in population size, a genetic bottleneck was not detected by the genetic data. The G. coprotheres, however, did show a significant deficiency of overall heterozygosity. This, coupled with the elevated levels of inbreeding and reduced effective population size, suggests that G. coprotheres is genetically depauperate. Given that genetic variation is considered a prerequisite for adaptation and population health, the low genetic diversity within G. coprotheres populations is of concern and has implications for the future management and conservation of this species.

Genetic Variation and Structure in Natural Populations of a Medicinal Vegetable, Satureja bachtiarica, Inferred from Microsatellite Markers Developed Using Next-Generation Sequencing

Satureja bachtiarica Bunge (Lamiaceae) is a medicinal plant native to Iran which is widely used in traditional medicine, as a spice and as a vegetable. Understanding the patterns of genetic variation and structure of natural populations of the plant will be crucial for breeding and management purposes. However, until now, there has been no molecular tool with codominance inheritance available for studying genetic variation in this plant. In this study, we developed microsatellite markers for S. bachtiarica using a next-generation sequencing technique, and applied these markers to quantify the genetic variation and structure of natural populations. Sixty individuals collected from five natural populations were tested with 15 markers, 11 of which were fund to be polymorphic. The number of alleles per locus ranged from 4 to 17, with an average of 7.5 alleles per locus. The polymorphic information content of loci ranged from 0.41 to 0.89, with an average of 0.63. The average observed and expected heterozygosities over all populations were 0.62 (range 0.58 to 0.69) and 0.61 (range 0.60 to 0.63), respectively, and a low level of inbreeding (FIS) was observed in all populations (ranging from − 0.08 to 0.10) except Boli. None of the populations revealed any signature of recent reduction in population size. Private allelic richness was positively correlated with elevation (P < 0.05). The mean pairwise FST (± SD) among populations was 0.07 ± 0.01 (range 0.05 to 0.10). The clustering and Bayesian structure analyses exhibited genetic admixture between populations as supported by a weak population differentiation. The results of this study show the high efficiency of developed markers to investigate the genetics of natural populations of S. bachtiarica. The developed markers can also help to screen natural variation in diverse populations of closely related species, and can consequently be applied in conservation genetic and breeding programs.

Conservation genetics of the threatened catfish Conorhynchos conirostris (Siluriformes: incertae sedis), an evolutionary relict endemic to the São Francisco River Basin, Brazil

Analysis of genetic datasets can be particularly useful in providing guidelines for conservation management of understudied species targeted by commercial activities. Here we used population genetic approaches to inform on the conservation status of the Neotropical long-nose pira catfish, Conorhynchos conirostris. Pira is a large migratory fish endemic to the Sao Francisco River Basin (SFRB). It is an evolutionarily divergent and relict species, being the sole representative of an incertae sedis family. The species is considered locally extinct in the upper and lower SFRB, listed as vulnerable on the IUCN Red List and as endangered on the Brazilian Red List (ICMBIO). Fishing prohibition has received severe criticism from middle SFRB fisheries that claim that this understudied species is relatively abundant in that region. We used information from 13 microsatellite markers and COI mitochondrial sequences to clarify the genetic diversity of this enigmatic species in the middle SFRB, to estimate contemporary effective population size (Ne), and to assess its conservation status. Results from bottleneck analyses indicated that the species has experienced recent reductions in population size, which is consistent with small estimates of contemporary Ne. The predicted amount of heterozygosity loss (Ht) in t generations ranged from 0.1152 (for an estimated Ne of 26.4; t = 100) to 0.7573 (for an estimated Ne of 169.9; t = 10). Our study supports the conservation status proposed by the ICMBIO to the remaining pira population. Moreover, we highlight the need for demographic data and the re-assessment of the current IUCN classification for this evolutionary relict lineage.

Hyrcanian forests—Stable rear‐edge populations harbouring high genetic diversity ofFraxinus excelsior,a common European tree species

AbstractAimThe Hyrcanian forests, in a region of lowland and montane temperate pure and mixed broadleaf forests located in Iran, near the southern shores of the Caspian Sea, form part of the Caucasus biodiversity hotspot. In this region, species experienced suitable and stable environmental conditions over historic periods and even some Arcto‐Tertiary relict species could survive. Although the ranges of several European tree species expand to the Hyrcanian forests, its role has mostly been overlooked in phylogeographic studies so far. Here, we used common ash (Fraxinus excelsior) to study the genetic diversity, population genetic structure and time of divergence between European and Hyrcanian populations.LocationSix populations from the Hyrcanian forests at the southern shore of the Caspian Sea (Iran) and three selected populations in Europe (Norway, Denmark and Italy).MethodWe amplified four genomic, seven genic and four plastidSSR(simple sequence repeat) markers in 268Fraxinus excelsiorsamples.ResultsIn particular,EST‐SSRs (expressed sequence tag–SSRs), that is genic markers, showed significantly higher genetic diversity in the Hyrcanian forests than in European populations. Population divergence between European and Hyrcanian populations dated back to the end of the middle to upper Pleistocene. A recent reduction in population size was detected in all study populations. Within the Hyrcanian region, a substructure was detected at nuclear and plastidSSRs, with a western to central and a smaller eastern subcluster. Two new plastid haplotypes were described in the easternmost Hyrcanian populations.Main conclusionsOur results confirm that the Hyrcanian forests harbour high genetic diversity that might be of great value for the evolutionary potential ofFraxinus excelsiorcurrently facing global climate change and ash dieback. We argue that the Hyrcanian forests could be an important genetic reservoir also for other European tree species.

Genetic Evidence of a Population Bottleneck and Inbreeding in the Endangered New Zealand Sea Lion, Phocarctos hookeri.

The New Zealand sea lion (NZSL) is of high conservation concern due to its limited distribution and its declining population size. Historically, it occupied most of coastal New Zealand, but is now restricted to a few coastal sites in southern mainland New Zealand and the sub-Antarctic Islands. NZSLs have experienced a recent reduction in population size due to sealing in the 1900s, which is expected to have resulted in increased inbreeding and a loss of genetic variation, potentially reducing the evolutionary capacity of the species and negatively impacting on its long-term prospects for survival. We used 17 microsatellite loci, previously shown to have cross-species applications in pinnipeds, to determine locus- and population-specific statistics for 1205 NZSLs from 7 consecutive breeding seasons. We show that the NZSL population has a moderate level of genetic diversity in comparison to other pinnipeds. We provide genetic evidence for a population reduction, likely caused by historical sealing, and a measure of allele sharing/parental relatedness (internal relatedness) that is suggestive of increased inbreeding in pups that died during recent epizootic episodes. We hypothesize that population bottlenecks and nonrandom mating have impacted on the population genetic architecture of NZSLs, affecting its population recovery.

Indigenous forests of European black poplar along the Danube River: genetic structure and reliable detection of introgression

The European black poplar (Populus nigra L.) is a tree species that once had the central role in the development of riparian ecosystems in a great part of Europe and Asia. During centuries, it is harassed by the riverside’s urbanization, drainage of wetlands, and controlled river management, and compromised by intercrossing with other poplar species and cultivated hybrids. With the aim to perceive its genetic diversity and integrity along the Danube River, 12 natural P. nigra forests from corresponding protected areas were assessed using eight highly polymorphic microsatellite loci and win3 genetic marker. In the sample set, among individuals morphologically recognized as P. nigra, 2.28 % were identified as P. × euramericana hybrids and those were excluded from further analyses. High number of alleles and high heterozigosity have been observed in all populations. Only 2.95 % of total genetic variance was recorded among populations, while the pattern of genetic differentiation corresponds to the isolation by geographic distance. It was found that one population had experienced a recent reduction in population size. We infer that genetic integrity and variation of European black poplar is not compromised within the studied areas which are, therefore, able to provide high-quality genetic material of non-hybrid P. nigra for maintaining and promoting metapopulations along the Danube River.

Left-right dewlap asymmetry and phylogeography ofAnolis lineatuson Aruba and Curaçao

Anolis lizards exhibit a remarkable degree of diversity in the shape, colour, pattern and size of their dewlaps. Asymmetry, where one side of the dewlap differs in pattern or colour from the other, has only been reported in one species, Anolis lineatus, and then on only one of the two islands from which it occurs. Given the importance of the dewlap in intra- and interspecific signalling, we expanded on previous work by (1) investigating whether the reported asymmetry actually occurs and, if so, whether it occurs on animals from both Aruba and Curaçao; (2) examining whether populations differ in other aspects of their morphology or ecology; and (3) resolving the evolutionary relationships and the history of the two populations. We confirmed the presence of the asymmetrical dewlap on Curaçao and found that the asymmetry extends to populations on Aruba as well. Animals on Curaçao were smaller overall than populations from Aruba with relatively shorter metatarsals, radii, and tibias but relatively deeper heads, longer jaws, and wider and more numerous toepads on fore and hind feet. Habitat use did not differ significantly between the islands. We found populations on Aruba and Curaçao to be reciprocally monophyletic with an early Pleistocene divergence of populations on the two islands. Neutrality tests indicate that neither population has seen any recent reduction in population size, making it unlikely that the asymmetry is a result of founder effects or is some other consequence of reduced genetic variation. A variety of factors likely account for the remarkable and unique dewlap morphology exhibited by this species, although more detailed field studies are required to test these hypotheses. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110, 409–426.

Recent population decline and selection shape diversity of taxol‐related genes

Taxanes are defensive metabolites produced by Taxus species (yews) and used in anticancer therapies. Despite their medical interest, patterns of natural diversity in taxane-related genes are unknown. We examined variation at five main genes of Taxus baccata in the Iberian Peninsula, a region where unique yew genetic resources are endangered. We looked at several gene features and applied complementary neutrality tests, including diversity/divergence tests, tests solely based on site frequency spectrum (SFS) and Zeng's compound tests. To account for specific demography, microsatellite data were used to infer historical changes in population size based on an Approximate Bayesian Computation (ABC) approach. Polymorphism-divergence tests pointed to positive selection for genes TBT and TAT and balancing selection for DBAT. In addition, neutrality tests based on SFS found that while a recent reduction in population size may explain most statistics' values, selection may still be in action in genes TBT and DBAT, at least in some populations. Molecular signatures on taxol genes suggest the action of frequent selective waves with different direction or intensity, possibly related to varying adaptive pressures produced by the host-enemy co-evolution on defence-related genes. Such natural selection processes may have produced taxane variants still undiscovered.

Genetic variation and structuring in the threatened koala populations of Southeast Queensland

Habitat fragmentation can act to cause reproductive isolation between conspecifics and undermine species’ persistence, though most studies have reported the genetic condition of populations that have already declined to a very small size. We examined genetic diversity within the vulnerable, declining koala (Phascolarctos cinereus) population in Southeast Queensland, Australia to determine the genetic impact of ongoing threatening processes. Five hundred and twelve koalas from ten Southeast Queensland Local Government Areas on the mainland and one island were genotyped at six polymorphic microsatellite loci. Based on Bayesian cluster analysis incorporating spatial data, the regional koala population was subdivided into six clusters, with location of major roads and rivers appearing to be consistent with being barriers to gene flow. The distribution of mtDNA control region haplotypes identified distinct coastal and inland clades suggesting that historically there was gene flow between koalas along the coast (though little interchange between coastal and inland animals). In contrast, koalas from the Koala Coast (Brisbane City, Logan City and Redland Shire) were shown by microsatellite analysis to be genetically distinct from adjacent areas. It is likely, therefore, that more recent reductions in population size and restricted gene flow through urbanisation have contributed to the genetic differentiation of koalas in the Koala Coast region.

Effects of founder events on the genetic variation of translocated island populations: implications for conservation management of the northern quoll

Translocation is a strategy commonly used to maximize the persistence of threatened species, but it may sometimes lead to undesirable genetic consequences. The northern quoll (Dasyurus hallucatus) is a carnivorous marsupial that is critically endangered in Australia’s Northern Territory due to rapid population declines in areas recently colonized by the exotic cane toad Chaunus [Bufo] marinus. In 2003, 64 quolls were translocated to two offshore islands to establish insurance populations and reduce the species’ risk of extinction. In this study, we assessed genetic diversity at five microsatellite loci in the translocated populations, two endemic islands and three mainland populations. In the short-term (three generations), the translocated populations showed a slight but non-significant reduction in genetic diversity (A = 4.1–4.2; He = 0.56–0.59) compared to the mainland source populations (A = 5.0–8.4; He = 0.56–0.71). In comparison, high genetic erosion was observed in the endemic island populations (A = 1.5–2.9; He = 0.11–0.34). Genetic bottlenecks were detected on both endemic islands and in one mainland population, indicating recent reductions in population size. Our results are consistent with previous studies describing greater losses of genetic diversity on islands compared to mainland populations. Divergence from ancestral allele frequencies in the translocated populations also suggests effects due to founder events. This study, although short-term, highlights the importance of continued monitoring for detecting changes in genetic diversity over time and makes a significant contribution to our understanding of the effects of founder events on island populations.

Genetic structure of an isolated population of mantled howler monkeys (Alouatta palliata) on Barro Colorado Island, Panama

Habitat fragmentation may influence genetic variability through reductions in population size and the physical isolation of conspecifics. We explored the effects of these factors on genetic diversity in a population of mantled howler monkeys (Alouatta palliata) on Barro Colorado Island (BCI), Panama. The study population was established in 1914 when an unknown number of resident individuals were isolated from the surrounding mainland by damming of the Rio Chagres to create the Panama Canal. Analyses of 10 microsatellite loci indicated that, despite this isolation, the howler monkeys on BCI exhibit levels of genetic diversity (H S = 0.584 ± 0.063) among the highest reported for any species of Alouatta. These data also revealed that although relatedness among adults in a social group was significantly greater than zero, the BCI population is not highly genetically structured. Tests for genetic bottlenecks based on departures from equilibrium expectations failed to reveal evidence of a recent reduction in population size. In contrast, coalescent modeling indicated that this population has likely experienced a marked decline within the last few 100 years. These findings generate new insights into the genetic structure of A. palliata and suggest that while the formation of BCI may not have substantially reduced genetic variation in these animals, genetic diversity has been influenced by historical changes in population size.

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

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

Detection of reduction in population size using data from microsatellite loci.

We demonstrate that the mean ratio of the number of alleles to the range in allele size, which we term M, calculated from a population sample of microsatellite loci, can be used to detect reductions in population size. Using simulations, we show that, for a general class of mutation models, the value of M decreases when a population is reduced in size. The magnitude of the decrease is positively correlated with the severity and duration of the reduction in size. We also find that the rate of recovery of M following a reduction in size is positively correlated with post-reduction population size, but that recovery occurs in both small and large populations. This indicates that M can distinguish between populations that have been recently reduced in size and those which have been small for a long time. We employ M to develop a statistical test for recent reductions in population size that can detect such changes for more than 100 generations with the post-reduction demographic scenarios we examine. We also compute M for a variety of populations and species using microsatellite data collected from the literature. We find that the value of M consistently predicts the reported demographic history for these populations. This method, and others like it, promises to be an important tool for the conservation and management of populations that are in need of intervention or recovery.