Management Units For Conservation Research Articles

Unraveling the genetic diversity of Ceiba pubiflora (Malvaceae) in isolated limestone outcrops: Conservation strategies.

Seasonally Dry Tropical Forests (SDTFs) located on limestone outcrops are vulnerable to degradation caused by timber logging and limestone extraction for cement production. Some of these forests represent the last remnants of native vegetation cover, functioning as isolated islands. Ceiba pubiflora (Malvaceae) is a tree frequently found on limestone outcrops in the central region of Brazil. This study aimed to evaluate the genetic diversity and identify suitable populations for the establishment of Management Units (MUs) for conservation. Inter-simple sequence repeat markers were employed to assess the genetic diversity in ten populations sampled from the Caatinga, Cerrado, and Atlantic Forest biomes. The species exhibited substantial genetic diversity (HT = 0.345; PLP = 97.89%). Populations SAH, JAN, and MON demonstrated elevated rates of polymorphic loci (> 84.2%) along with notable genetic diversity (He > 0.325). Additionally, these populations were the primary contributors to gene flow. The analysis of molecular variance (AMOVA) indicated that most genetic variation occurs within populations (91.5%) than between them. In the Bayesian analysis, the ten populations were clustered into five groups, revealing the presence of at least three barriers to gene flow in the landscape: 1) the Central Plateau or Paranã River valley; 2) near the Espinhaço mountains or the São Francisco River valley; and 3) around the Mantiqueira mountain range, Chapada dos Veadeiros plateau, and disturbed areas. A positive and statistically significant correlation was observed between genetic (θB) and geographic distances (r = 0.425, p = 0.008). Based on these findings, we propose the establishment of Management Units in Minas Gerais state, encompassing the (1) southern region (MIN population), (2) central region (SAH population), and (3) north region (MON population), as well as in Goiás state, covering the (4) Central Plateau region. These units can significantly contribute to preserving the genetic diversity of these trees and protecting their habitat against ongoing threats.

Low but highly geographically structured genomic diversity of East Asian Eurasian otters and its conservation implications.

Populations of Eurasian otters Lutra lutra, one of the most widely distributed apex predators in Eurasia, have been depleted mainly since the 1950s. However, a lack of information about their genomic diversity and how they are organized geographically in East Asia severely impedes our ability to monitor and conserve them in particular management units. Here, we re-sequenced and analyzed 20 otter genomes spanning continental East Asia, including a population at Kinmen, a small island off the Fujian coast, China. The otters form three genetic clusters (one of L. l. lutra in the north and two of L. l. chinensis in the south), which have diverged in the Holocene. These three clusters should be recognized as three conservation management units to monitor and manage independently. The heterozygosity of the East Asian otters is as low as that of the threatened carnivores sequenced. Historical effective population size trajectories inferred from genomic variations suggest that their low genomic diversity could be partially attributed to changes in the climate since the mid-Pleistocene and anthropogenic intervention since the Holocene. However, no evidence of genetic erosion, mutation load, or high level of inbreeding was detected in the presumably isolated Kinmen Island population. Any future insitu conservation efforts should consider this information for the conservation management units.

Genetic Evaluation of the Refuge Program for Sonoyta Pupfish Cyprinodon eremus (Cyprinodontidae) in Mexico

Cyprinodon eremus is endemic to the Sonoyta River system, where wild populations comprise two conservation management units, one in Quitobaquito Springs, Arizona, and another small segment of the Sonoyta River, Sonora. Declining habitat from overmining of groundwater threatens both populations. Because of concern for the Sonoyta River population, refuges were built in Sonora and stocked with individuals from the river. Using seven microsatellite loci, we evaluated the genetic diversity of the wild population and three refuge populations. Comparison with earlier results for the wild population suggests that diversity changed little over the 12 years between collections. Two refuge populations established in 2007–2008 had levels of diversity comparable to that of the wild population. This reflects the relatively recent origins and exchange with the wild population. Notably lower measures of diversity occurred in an older refuge population that was established in 1988 and has no history of exchange with other populations. Suggestions for a program of genetic exchange are presented to inform future management.

FOOD SUPPLEMENTATION INCREASES MULE DEER (Odocoileus hemionus eremicus) RETENTION AT THE RANCHO SAN HUBERTO WILDLIFE CONSERVATION MANAGEMENT UNIT, SONORA, MEXICO

Artificial food and water supplementation programs are common in Wildlife Conservation Management Units (UMAs) in arid northern Mexico to attract and retain mule deer as quality trophies. However, implementing these actions represents a high economic cost, and there is no convincing evidence of their effectiveness. This study evaluated the effect of food and water supplementation by capture-mark-recapture using camera traps at the UMA San Huberto, Sonora, Mexico. During the winter of 2015-2016, male mule deer counts and detection histories were collected at 62 photo-trapping stations spread across four supplementation treatments: 1) water and food, 2) water, 3) food, and 4) no supplementation. In addition, to assess the impact of natural vegetation on trough and feeder utilization on the ranch, the Normalized Difference Vegetation Index was calculated using Landsat 8 satellite images. A log-Poisson regression model for deer counts per photo-trapping station found that food supplementation increased mule deer numbers by 42 % when compared to stations without food supplementation. Vegetation biomass had no effect on the frequency of use of feeders and waterers in any of the treatments. According to the multistate model for detection histories, male mule deer at waterers receiving food-only supplementation are more likely to remain in that treatment than to move to either of the other two treatments (water and feed or water). This finding suggests that food-only supplementation is more effective in retaining male mule deer.

Conservation Genetics of Clinch Dace Chrosomus sp. cf. saylori

Clinch Dace (Chrosomus sp. cf. saylori) is a newly recognized and yet-undescribed species of minnow with a restricted and fragmented distribution in the upper Tennessee River basin in southwestern Virginia, USA. We collected Clinch Dace from seven streams and observed variations at nine selectively neutral microsatellite DNA loci to infer population genetic processes and identify units for conservation management. Bayesian cluster analysis showed that three of the seven surveyed populations were genetically distinct, while the other four populations showed signs of recent admixture. Estimated effective population sizes and m-ratios were low within most populations, suggesting loss of alleles due to recent genetic drift. Positive FIS values, high average individual inbreeding coefficients, and high degrees of inferred relatedness among individuals suggested that inbreeding is taking place in some populations. FST values were high, and analysis of molecular variance indicated genetic divergence among populations. These indicators suggest that Clinch Dace populations are subject to the genetic processes that are characteristic of small and isolated populations.

Landscape genomics reveals signals of climate adaptation and a cryptic lineage in Arthropodium fimbriatum

Habitat loss and fragmentation are critical threats to biodiversity. Consequent decreases in population size and connectivity can impact genetic diversity and, thus, future adaptability and resilience to environmental change. Understanding landscape patterns of genetic diversity, including patterns of adaptive variation, can assist in developing conservation strategies that maximise population persistence and adaptability in the face of environmental change. Using a reduced-representation genomic approach, we investigated genetic diversity, structure, and adaptive variation across an aridity gradient in the woodland forb Arthropodium fimbriatum. Moderate levels of genetic diversity (HS = 0.14–0.23) were found in all 13 sampled provenances. Inbreeding varied among provenances (FIS = 0.08–0.42) but was not associated with estimated population size. Four genetic clusters were identified, including one highly differentiated cluster. Higher pairwise FST (0.23–0.42) between the three provenances of this cluster and the remaining 10 provenances (pairwise FST between 10 provenances 0.02–0.32) suggested two highly divergent lineages or potentially a cryptic species. After excluding the three highly differentiated populations, outlier and genotype-environment association analysis identified 275 putatively adaptive loci suggesting genomic signatures of climate adaptation in A. fimbriatum is primarily associated with changes in aridity. Combined, these results suggest that all provenances have conservation value, contributing to the maintenance of genetic diversity and adaptive variation in this species. The uncovering of a potential cryptic taxon highlights the power of genomics approaches in conservation genetics and the importance of understanding the role of landscape variation shaping genetic variation to effectively define conservation management units in an era of rapid biodiversity decline.

Assessment of population genetic diversity and genetic structure of the North Chinese leopard (Panthera pardus japonensis) in fragmented habitats of the Loess Plateau, China

Leopard (Panthera pardus) populations on the Chinese Loess Plateau have experienced severe declines and were once on the verge of extinction. Currently, leopards in the Loess Plateau region are mainly scattered in human-dominated fragmented habitats in Shanxi, Shaanxi and Ningxia. The lack of information on the genetic diversity and genetic structure makes difficult to assess the resistance and persistence of this metapopulation to various factors. In this study, we used mitochondrial ND-5 gene sequences and eight microsatellite loci to genetically analyze 97 faecal samples collected from three leopard ranges on the Loess Plateau of China. Among these samples, 62 feces were successfully identified from 22 individuals (6 females, 16 males). Mitochondrial haplotypes showed four different haplotypes and the genetic diversity was moderate (Hd = 0.331, Pi = 0.0036), while SSR showed high diversity (PIC = 0.673). STRUCTURE and TESS analyses revealed that leopard populations on the Loess Plateau appeared to have a distinct population boundary (K = 2) associated with a spatial-geographic barrier (the Yellow River). We estimate that the time of population divergence occurred between 8700 and 8300 years BP. Based on this research, we suggest that the leopard population on both sides of the Yellow River should be divided into two conservation management units to improve the efficiency of conservation management and contribute to the better recovery of the North Chinese leopard population.

Genetic Relationship Between Founders of a Threatened Freshwater Turtle in a Mexican Wildlife Management Unit. A Conservation Strategy

Management Units for Wildlife Conservation (UMAs according to its Spanish acronym), are used for the ex-situ reproduction of freshwater turtles. These areas, often administered by local communities, are dedicated to conservation and sustainable management. The critically endangered freshwater turtle Dermatemys mawii has been successfully reproduced in several UMAs; however, no genetic management plan has been developed to maintain offspring genetic variability. Therefore, this study aims to determine the kinship relationship and homozygosity through the loci index of founder individuals in three UMAs devoted to the reproduction of D. mawii for the establishment of breeding groups. We collected skin samples of D. mawii in 2017 from 117 founder individuals from three UMAs located in the state of Tabasco, southeast Mexico. Ten specific D. mawii microsatellite markers were used for genotyping the founder individuals. We estimated the pedigree relationship between founders and proposed the formation of three breeding groups to optimize the use of related and non-related individuals to meet UMA-specific objectives and evaluated the genetic diversity retention of the breeding groups. The breeding groups were integrated as follows: 1) conservation breeding group consisting of 16 unrelated females and 7 unrelated males that presented a lower level of homozygosity (< 0.4); 2) research breeding group consisting of 45 females and 16 males that were unrelated or presented a half-sibling relationship and with a medium level of homozygosity (<0.6); and 3) a sustainable breeding group comprising 29 females and 4 males that were not necessarily unrelated and with a high level of homozygosity (> 0.6). Genetic diversity retention (Ho, He) was highest for the conservation breeder group and research breeder group. UMAs can create 3 breeding groups with different objectives: 1) species conservation, 2) research, and 3) sustainable use of species. All breeding groups can retain genetic diversity. Our proposal can enrich conservation actions and sustainable use for D. mawii at both national and international levels, specifically within the Mesoamerican corridor.

Perishing rich, expanding poor: Demography and population genetic patterns in two congeneric butterflies.

In human-altered landscapes, specialist butterflies typically form spatially restricted populations, genetically differentiated due to dispersal restrictions. Generalists, in contrast, display minimum differentiation but high genetic diversity. While local-level actions suffice to conserve specialists and landscape-level actions are necessary for generalists, minimum information exists regarding conservation of species with intermediate features. We targeted two congeneric butterflies, the recently re-expanding Argynnis adippe and the strongly declining A.niobe, co-occurring in the pastoral landscape of the Carpathian Mountains, Czech Republic. We integrated species distribution models, mark-recapture and microsatellite analysis to compare their habitat requirements, adult demography, dispersal and genetic patterns, and expanded the genetic analysis across the Carpathian Arc and beyond to delimit spatial conservation units. In two mountain valleys, both species formed interconnected populations numbering thousands of individuals. Mobility patterns suggested the populations' interconnection across the Czech Carpathians. Genetic diversity was extremely poor in the nonthreatened A.adippe and moderate in the declining A.niobe. No population differentiation was detected within the Czech Carpathians (~1500 km2 ). Low genetic diversity and no differentiation was preserved in A.adippe across East Central Europe, whereas in A.niobe, populations from Serbia were differentiated from the Carpathian Arc + Alps. The high adult mobility linked to low differentiation probably reflects the distribution of larval resources, historically widespread but sparse and currently declining for A.niobe (grazing-disturbed grounds), while currently increasing for A.adippe (abandonment scrub, disturbed woodlands). Units as large as entire mountain systems define population boundaries, and hence conservation management units, for both species.

Genetic patterns of Magnolia in the Lesser Antilles: Stepwise colonisation leading to highly inbred island ‘populations’

AbstractAimIslands are ‘nature's laboratories of evolution’. Most island biogeographical studies have focussed on remote volcanic island chains. Here, we challenge island biogeographical patterns using a slowly evolving recent colonist present on five islands in a nonlinear chronosequence island chain.LocationThe Lesser Antilles (Caribbean).TaxonMagnolia dodecapetala (Magnoliaceae).MethodsGenetic diversity was characterised using Sanger sequencing of 21 individuals amplified for 11 DNA markers, plus microsatellite data of 195 individuals genotyped with 19 simple sequence repeat (SSR) markers. Sanger sequencing data were used to construct a Bayesian phylogenetic hypothesis, while SSR markers were used to run approximate Bayesian computation (ABC) demographic analyses and calculate population statistics.ResultsBoth types of molecular data support stepwise colonisation, decoupled from known island ages. The ABC analyses support a north to south migration while the Sanger sequencing data indicate a mixture of island progression rule and stepping stone dispersal. The SSR data show strong genetic structuring per island and significant inbreeding in all populations except in Saint Lucia. The lowest genetic diversity is found in the population from Saint Vincent. A high amount of genetic linkage occurs in a subpopulation from Dominica.Main ConclusionsBiogeographical patterns in the complex geological setting of the Lesser Antilles are uncovered using a slowly evolving study species. All genetic data support treating each island as distinct Management Units for conservation and call for a re‐evaluation of the species limits. Inbreeding threatens the survival of island populations and the populations of Saint Vincent and Dominica represent conservation priorities.

Population Structure of Wild Schizothorax kozlovi in the Upper Yangtze River Based on mtDNA and Stable Isotopes, and Their Relationship with Ambient Temperature

Schizothorax kozlovi, as an endemic and vulnerable fish of the upper Yangtze River in China, faces many threats. In order to expose the population structure of wild S. kozlovi, the carbon and oxygen isotopic ratios in the otoliths, and the gene sequences of two common mitochondrial markers (Cytb and COI) were investigated in four sampling locations, and then their relationship with ambient temperature was further investigated. In general, it exhibits limited geographic population structuring of S. kozlovi in the upper Yangtze River by both mtDNA and stable isotopes. The values of otolith stable isotope ratios varied from −15.30‰ to −12.37‰ for δ18O and from −10.10‰ to −6.13‰ for δ13C. Significant relationships were revealed between stable isotope ratios and specific mean monthly water temperature variables (from November to March), indicating low temperature effect on otolith stable isotope ratios. Haplotype diversity and nucleotide diversity were 0.928 and 0.00778, both exhibiting high levels. A median-joining haplotype network indicated a mixture of geographical distribution but exhibited two distinct haplotype lineages (Clade I and Clade II). AMOVA detected that the higher percentage of genetic variance was within sampling locations (96.94%) and between two haplotype lineages (72.82%). Most FST values between sampling locations showed small levels of genetic differentiation except the differentiation between population SJ (Sanjiangkou) and JP (Jinping). Therefore, two haplotype lineages and population JP of S. kozlovi in the upper Yangtze River are suggested as three management units for conservation due to their moderate-to-great genetic differentiation and isolated habitat.

Chemodiversity is closely linked to genetic and environmental diversity: Insights into the endangered populations of the local endemic plant Sideritis euboea Heldr. of Evia Island (Greece)

Sideritis euboea is a perennial medicinal, local endemic species to mountainous areas of Central and Southern Evia Island (Greece) with isolated populations threatened with extinction. In this context, a genetic and phytochemical survey has been performed to evaluate the present status of S. euboea inter- and intra-population diversity in three mountainous areas (Dirfis, Xerovouni, Ochi) of Evia, while its occurrence data have been used to define the species-specific climate requirements and to simulate the habitat suitability. Our analysis revealed differences between the populations concerning their polymorphism and genetic homogenity, resulting in a clear clustering of the main three populations based on PCA analysis. An admixture of individuals was identified between distant populations, indicating a possible gene flow between them. The phytochemical analysis revealed significant differences concerning their content in species-specific polyphenolic metabolites, especially isoscutellarein and hypolaetin derivatives; based on the PCA analysis of the cumulative polyphenolic groups’ pattern, two populations were the more distinctive, while different functional groups of metabolites could result to more clear clustering. The ecological profile analysis revealed that the more diverse S. euboea populations in terms of genetics and cumulative polyphenolics are found under comparatively wetter conditions with lower annual temperature and higher annual precipitation. The findings herein support the distinct climate in the habitats of the main populations of S. euboea from the three mountains, suggesting that all three populations should be considered as distinct units for conservation management with Mt. Ochi’s population firstly prioritized.

POPULATIONAL ATTRIBUTES OF THE CENTRAL AMERICAN RED BROCKET DEER (Mazama temama) IN THE SIERRA DE ZONGOLICA, VERACRUZ, MEXICO

The Sierra de Zongolica is a biogeographic region with ecosystems and species of nearctic and neotropical affinity in the state of Veracruz, Mexico. However, no studies have been conducted on populations of the red brocket deer (Mazama temama Erxleben 1777) in this region. Such type of studies is essential to propose actions for sustainable management of the species and the habitat by the rural communities. The objective of this study was to describe the populational attributes of M. temama (distribution, population abundance, and patterns of activity) in the Sierra de Zongolica. Information was gathered through interviews, spoor detection and camera trapping from September 2014 to May 2015. To identify the sites where the deer is present, 76 inhabitants of four municipalities of the Sierra de Zongolica were interviewed. In the localities described with presence of the deer, 20 walking trails 300 m long by 1 m wide were identified. Six of the trails were in primary vegetation (1.8 km), 10 in secondary vegetation (3 km), and four in the area of cultivation (1.2 km) where 54 spoors were recorded (45 hoofprints and nine droppings), equivalent to nine signs of deer per km. The population of M. temama was higher in the farming area than in primary or secondary vegetation. In the 43 stations of camera traps, 71 independent images of M. temama were obtained. Of these images, 79 % were between 18:00 and 05:00 h, indicating a pattern of crepuscular and nocturnal activity. This species had a relative abundance index of 2.5 brockets per km2 in the Sierra de Zongolica, suggesting a population susceptible to management under the system of Management Units for Conservation and Sustainable Use of Wildlife (in Mexico, UMAs).

Rapid genetic divergence and mitonuclear discordance in the Taliang knobby newt ( Liangshantriton taliangensis, Salamandridae, Caudata) and their driving forces.

The Hengduan Mountains Region (HMR) is the largest “evolutionary frontier” of the northern temperate zone, and the origin and maintenance of species in this area is a research hotspot. Exploring species-specific responses to historical and contemporary environmental changes will improve our understanding of the role of this region in maintaining biodiversity. In this study, mitochondrial and microsatellite diversities were used to assess the contributions of paleogeological events, Pleistocene climatic oscillations, and contemporary landscape characteristics to the rapid intraspecific diversification of Liangshantriton taliangensis, a vulnerable amphibian species endemic to several sky-island mountains in the southeastern HMR. Divergence date estimations suggested that the East Asian monsoon, local uplifting events (Xigeda Formation strata), and Early-Middle Pleistocene transition (EMPT) promoted rapid divergence of L. taliangensis during the Pleistocene, yielding eight mitochondrial lineages and six nuclear genetic lineages. Moreover, population genetic structures were mainly fixed through isolation by resistance. Multiple in situ refugia were identified by ecological niche models and high genetic diversity, which played crucial roles in the persistence and divergence of L. taliangensis during glacial-interglacial cycles. Dramatic climatic fluctuations further promoted recurrent isolation and admixing of populations in scattered glacial refugia. The apparent mitonuclear discordance was likely the result of introgression by secondary contact and/or female-biased dispersal. Postglacial expansion generated two major secondary contact zones (Ganluo (GL) and Chuhongjue (CHJ)). Identification of conservation management units and dispersal corridors offers important recommendations for the conservation of this species.

Spatial Autocorrelation Analysis Using MIG-seq Data Indirectly Estimated the Gamete and Larval Dispersal Range of the Blue Coral, Heliopora coerulea, Within Reefs

Spatial autocorrelation analysis is a well-established technique for detecting spatial structures and patterns in ecology. However, compared to inter-population genetic structure, much less studies examined spatial genetic structure (SGS) within a population by means of spatial autocorrelation analysis. More SGS analysis that compares the robustness of genome-wide single nucleotide polymorphisms (SNPs) and traditional population genetic markers in detecting SGS, and direct comparison between the estimated dispersal range based on SGS and the larval dispersal range of corals directly surveyed in the field would be important. In this study, we examined the SGS of a reef-building coral species, Heliopora coerulea, in two different reefs (Shiraho and Akaishi) using genome-wide SNPs derived from Multiplexed inter-simple sequence repeat (ISSR) genotyping by sequencing (MIG-seq) analysis and nine microsatellite loci for comparison. Microsatellite data failed to reveal significant spatial patterns when using the same number of samples as MIG-seq, whereas MIG-seq analysis revealed significant spatial autocorrelation patterns up to 750 m in both Shiraho and Akaishi reefs based on the maximum significant distance method. However, detailed spatial genetic analysis using fine-scale distance classes (25–200 m) found an x-intercept of 255–392 m in Shiraho and that of 258–330 m in Akaishi reef. The latter results agreed well with a previously reported direct field observation of larval dispersal, indicating that the larvae of H. coerulea settled within a 350 m range in Shiraho reef within one generation. Overall, our results empirically demonstrate that the x-intercept of the spatial correlogram agrees well with the larval dispersal distance that is most frequently found in field observations, and they would be useful for deciding effective conservation management units for maintenance and/or recovery within an ecological time scale.

Using biophysical modelling and population genetics for conservation and management of an exploited species, Pecten maximus L.

AbstractConnectivity between populations is important when considering conservation or the management of exploitation of vulnerable species. We investigated how populations of a broadcast‐spawning marine species (scallop, Pecten maximus) that occur in discrete geographic locations were connected to each other. Population genetic insights were related to the outputs from a three‐dimensional hydrodynamic model implemented with scallop larval behaviour to understand the extent to which these areas were linked by oceanographic processes and how this was altered by season and two contrasting years that had strongly different average temperature records (warm vs cold) to provide contrasting oceanographic conditions. Our results span from regional to shelf scale. Connectivity was high at a regional level (e.g. northern Irish Sea), but lower at scales >100 km between sites. Some localities were possibly isolated thus dependent on self‐recruitment to sustain local populations. Seasonal timing of spawning and inter‐annual fluctuations in seawater temperature influenced connectivity patterns, and hence will affect spatial recruitment. Summer rather than spring spawning increased connectivity among some populations, due to the seasonal strengthening of temperature‐driven currents. Furthermore, the warm year resulted in higher levels of modelled connectivity than the cold year. The combination of genetic and oceanographic approaches provided valuable insights into the structure and connectivity at a continental shelf scale. This insight provides a powerful basis for defining conservation management units and the appropriate scale for spatial management. Temporal fluctuations in temperature impact upon variability in connectivity, suggesting that future work should account for ocean warming when investigating population resilience.

Genetic support for the current discrete conservation unit of the Central European wolf population

The gray wolf Canis lupus range in central Europe is dynamically expanding, reconnecting previously isolated populations. Thus, a recent paper has proposed to merge the current Baltic and Central European (CE) wolf management units, which are no longer isolated by distance. However, recent genetic findings indicate that these two populations are not genetically homogenous. Here we review the most recent data on wolf genetic structure in central Europe and show that even though the CE and Baltic wolves represent the same phylogeographic lineage, their demographic history has resulted in significant genetic structure between these two populations. While the groups are interconnected by moderate gene flow, it is not high enough to reduce the strong founder signal observed in the CE population, suggesting that population dynamics within the CE wolf range are largely independent from those of its source (Baltic) population. Consequently, a management unit combining the CE and Baltic wolves would not form a demographically coherent entity. Thus, we recommend that conservation management units maintain their separate status.

Large Differentiation of Extremely Threatened Chinese Pangolins Provide New Genomic Cues for Their Conservation

Human-induced poaching and trafficking has a substantial negative impact on the population growth and range expansion of the Chinese pangolin. However, recently reported activities of Chinese pangolins in several sites of Guangdong province in China indicates a promising sign for the recovery of this threatened species. Therefore, to ascertain population structure and genetic status of this species, we re-sequenced genomes of 15 individuals in Guangdong province and performed a comprehensive population genomics analyses with previously published 21 individuals of Yunnan province. These Chinese pangolins were divided into three distinct populations, with one population consisted of only individuals from Guangdong (CPA), one mixed with Guangdong and Yunnan individuals (CPB) and one Yunnan specific population (CPC). Especially, the CPC population is genetically distinct from the other two population with an extremely large fixation index ( FST ≈ 0.5), which we suggested an independent management unit for future protection and conservation. Further, all these three populations had low genome-wide diversity, high proportion of runs of homozygosity (ROH) in genomes, and a considerable amount of mutation load, which could pose serious threats to the long-term persistence of this species. However, the CPC population showed lower level of genetic load and less long ROH than the other two populations, indicating a potential resource for genetic rescue of other Chinese pangolin populations.

New management unit for conservation of the Endangered green turtle Chelonia mydas at the Xisha (Paracel) Islands, South China Sea

The Qilianyu cluster of the Xisha (Paracel) Islands has one of the few remaining green turtle Chelonia mydas rookeries in the China region. Genetic samples were obtained from dead green turtle embryos and hatchlings salvaged from post-hatched nests at Middle Island (n = 3), North Island (n = 9) and South Sand (n = 1) of the Qilianyu cluster in 2017-2019. The ~800 bp mitochondrial DNA control region was sequenced from the samples, and 5 haplotypes were identified belonging to 2 documented clades (clades III and VIII), including 2 new haplotypes (CmP243.1 and CmP244.1) and 3 previously reported haplotypes (CmP18.1, CmP19.1, CmP20.1). These results were combined with previously published mtDNA data for the Qilianyu cluster and nearby (~93 km) Yongle Islands indicating a lack of differentiation based on truncated 384 bp control region sequences (exact test, p = 0.0997; FST = 0.015, p = 0.2760), to represent a single Xisha Islands rookery. The rookery at the Xisha Islands was significantly differentiated (p < 0.01) from all 19 management units (MUs) documented in the Indo-Pacific and Japan regions, supporting recognition of the Xisha Islands rookery as a new independent MU. The results will help inform national and international conservation action plans by China and the countries around the South China Sea to protect green turtles in the West Pacific Ocean.

Genetic diversity and restricted genetic connectivity in an endangered marine fish (

Determining the genetic diversity and differentiation among populations is a critical element of conservation biology, but for many aquatic, data-deficient species with small population sizes, this is not possible. Closely related species may therefore provide a model. For the first time, using over 4000 single-nucleotide polymorphism loci, we characterise the population genetic diversity and structure of one of the world’s rarest marine fish, the spotted handfish (Brachionichthys hirsutus), a species which is also a member of the most threatened marine bony fish family (Brachionichthyidae). Fin clips were taken from 170 live spotted handfish across seven disjunct sites within the only known estuary (in Tasmania, Australia) where multiple populations of the species are found. Spatially discrete populations clustered into three genetic groupings and a significant variance in allele frequencies among populations (overall FST = 0.043), even at the small scale of the estuary, was observed. Furthermore, low contemporary migration rate estimates suggest low genetic homogeneity between locations. Because of the low genetic connectivity, population clusters of spotted handfish within the estuary should be considered as separate conservation management units. This insight should be considered for management and conservation strategies of other data-deficient and threatened species in the family.