Distribution and movement of juvenile and sub‐adult Chinese sturgeon (Acipenser sinensis Gray, 1835) in the Three Gorges Reservoir and the adjacent upstream free‐flowing Yangtze River section: a re‐introduction trial

The aim of this 2008–2012 study was to prove the hypothesis that the Three Gorges Reservoir (TGR) and the upper free‐flowing section can offer a habitat for restocking the Chinese sturgeon, Acipenser sinensis. Thus, 498 cultured A. sinensis (including 28 sub‐adults tagged with ultrasonic transmitters) were released into the TGR and the adjacent free‐flowing section of the Yangtze River. The distribution, movement and growth of the released fish were collected by acoustic telemetry and bycatch information. Results indicated that only three sub‐adults migrated upstream to the free‐flowing section where they remained for the three‐year observation (limited by the longevity of the transmitter battery). However, most sub‐adults migrated downstream after release, with a migration distance of 15–877 km as well as a tracking duration from 19 to 6063 h. The downstream traveling speed in the free‐flowing section (mean = 3.70 km h^?1, range = 1.51 – 8.25 km h^?1) was significantly faster than that in the reservoir section (mean = 1.05 km h^?1, range = 0.12 – 1.82 km h^?1; p < 0.05). Only three sub‐adults migrated to within 3 km of Three Gorges Dam (TGD) and stayed in the reservoir. Sub‐adults stayed obviously deeper within the reservoir (mean = 11.47 m) than in the free‐flowing section (mean = 3.63 m; p < 0.05). Juveniles were recaptured from 45 – 810 km downstream their release sites with a mean traveling speed of 1.05 km h^?1 (range = 0.13 – 1.82 km h^?1), lower than that of the sub‐adults released in the free‐flowing section. Twelve percent of juveniles released in one of the tributaries of the Yangtze River found the entrance and migrated downstream to the reservoir within the first 30 days. Average body weight of the recaptured juveniles increased by 10.3% (range = 2.3% – 15.3%) and some crustaceans (e.g. river shrimp) were found in the stomach and gut of two juveniles. The results demonstrate that the TGR and its adjacent upstream free‐flowing Yangtze River section can serve as reintroduction sites to support a certain quantity of Chinese sturgeon to remain and mature there.     

PERMANENT GENETIC RESOURCES: PCR primers for 100 microsatellites in red drum (Sciaenops ocellatus)

One hundred nuclear‐encoded microsatellites from a genomic library of red drum (Sciaenops ocellatus) were isolated and characterized. Eight microsatellites had tetranucleotide motifs; 92 had dinucleotide motifs. The average number of alleles per microsatellite (sample of 22–24 fish) was 17.7 (range = 2–30); gene diversity averaged 0.796 (range = 0.227–1.000). Following Bonferroni correction, genotype frequencies at 90 microsatellites did not deviate significantly from Hardy–Weinberg equilibrium expectations. Occurrence of null alleles was inferred at 15 microsatellites; alleles differing by only a single base were observed at 11 microsatellites. The microsatellites developed should prove useful for population‐genetic studies of ‘wild’ red drum and in construction of a genetic map.     

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Maternal investment in mammals may take many forms, including spatial relocation of offspring. Litter relocation behavior, in which a female moves her litter to a new location, has been reported for several species of carnivores and rodents but has received little study. We describe litter relocations during long-term studies of two species of ground-dwelling squirrels, yellow-bellied marmots (YBM, Marmota flaviventer) and golden-mantled ground squirrels (GMGS, Callospermophilus lateralis), to determine the distance and frequency of litter relocations and to explore possible explanations for litter relocation behavior. We observed 19 litters relocated by YBM mothers and 32 by GMGS mothers. Although YBM are much larger than GMGS, relocation distances for YBM (median = 46 m and range = 15–324 m) were not greater than those for GMGS (median = 79 m and range = 16–252 m), possibly because YBM home ranges in our study area were exceptionally small. Frequency of litter relocation was greater for GMGS (21% of litters produced) than for YBM (10%), perhaps because GMGS experience fewer social constraints or greater predation risk. We identified several possible costs (energy expenditure and vulnerability to predators while transporting young) and benefits (reduced exposure to predation risk, increased habitat quality, and social benefits) of litter relocation. Future studies should continue to explore litter relocations to better understand the ecological causes and consequences of this behavior.     

Population estimates of the Endangered Hawaiʻi ʻĀkepa (Loxops coccineus) in different habitats on windward Mauna Loa

Endangered Hawai‘i ?ākepas (Loxops coccineus) are endemic to Hawai‘i island, where they occur in five spatially distinct populations. Data concerning the status and population trends of these unique Hawaiian honeycreepers are crucial for assessing the effectiveness of recovery and management actions. In 2016, we used point‐transect distance sampling to estimate the abundance of Hawai‘i ?ākepas in portions of Hawai‘i Volcanoes National Park (HAVO) and the Ka?ū Forest Reserve (KFR) on Mauna Loa volcano. We then compiled the survey data from four other populations to provide a global population estimate. In our HAVO and KFR study area, we mapped habitat classes to determine the population densities in each habitat. Densities were highest (1.03 birds/ha) in open‐canopy montane ?ōhi?a (Metrosideros polymorpha) woodland. In contrast, densities of the largest ?ākepa population on Mauna Kea volcano were highest in closed‐canopy ?ōhi?a and koa (Acacia koa) forest where the species is dependent on nest cavities in tall (> 15 m), large (> 50‐cm diameter at breast height) trees. We surveyed potential nesting habitat in HAVO and KFR and found only one cavity in the short‐stature montane ?ōhi?a woodland and five cavities in the tall‐stature forest. Differences in densities between the Mauna Kea and Mauna Loa populations suggest that Hawai‘i ?ākepas may exhibit different foraging and nesting behaviors in the two habitats. The estimated overall population density in the HAVO and KFR study area was 0.52 birds/ha, which equates to 3663 (95% CI 1725–6961) birds in their 11,377‐ha population range. We calculated a global population of 16,428 (95% CI 10,065–25,198) birds, which is similar to an estimate of 13,892 (95% CI 10,315–17,469) birds made in 1986. Our results suggest that populations are stable to increasing in the two largest populations, but the three other populations are smaller (range = 77–1443 birds) and trends for those populations are unknown.     

Evidence for interannual variation in genetic structure of Dungeness crab (Cancer magister) along the California Current System

Using a combination of population‐ and individual‐based analytical approaches, we provide a comprehensive examination of genetic connectivity of Dungeness crab (Cancer magister) along ~1,200 km of the California Current System (CCS). We sampled individuals at 33 sites in 2012 to establish a baseline of genetic diversity and hierarchal population genetic structure and then assessed interannual variability in our estimates by sampling again in 2014. Genetic diversity showed little variation among sites or across years. In 2012, we observed weak genetic differentiation among sites (F_ST range = ?0.005–0.014) following a pattern of isolation by distance (IBD) and significantly high relatedness among individuals within nine sampling sites. In 2014, pairwise F_ST estimates were lower (F_ST range = ?0.014–0.007), there was no spatial autocorrelation, and fewer sites had significant evidence of relatedness. Based on these findings, we propose that interannual variation in the physical oceanographic conditions of the CCS influences larval recruitment and thus gene flow, contributing to interannual variation in population genetic structure. Estimates of effective population size (N_e) were large in both 2012 and 2014. Together, our results suggest that Dungeness crab in the CCS may constitute a single evolutionary population, although geographically limited dispersal results in an ephemeral signal of IBD. Furthermore, our findings demonstrate that populations of marine organisms may be susceptible to temporal changes in population genetic structure over short time periods; thus, interannual variability in population genetic measures should be considered.     

Microsatellite development suggests evidence of polyploidy in the social sponge-dwelling snapping shrimp Zuzalpheus brooksi

We isolated and characterized 33 novel, polymorphic microsatellite loci from the social sponge‐dwelling snapping shrimp Zuzalpheus brooksi. We screened all 33 loci in approximately 31 individuals from a population of Z. brooksi from the Florida Keys, USA and found an average of 16 alleles per locus. Approximately 25% of the loci showed more than two bands per individual, suggesting evidence of high gene duplication, or more likely, polyploidy, which is common in crustaceans. The 25 disomic loci had an observed heterozygosity of 0.57 (range = 0.03–1.00) and will be useful for studying the social organization in Zuzalpheus shrimp.     

Multi‐stage disruption of freshwater mussel reproduction by high suspended solids in short‐ and long‐term brooders

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Identifying growth parameters for two endemic species [Capoeta antalyensis (Battalgil, 1943) and Pseudophoxinus antalyae Bogutskaya, 1992] in Duden Creek,Antalya, Turkey

It is hypothesized that Capoeta antalyensis (Battalgil, 1943) and Pseudophoxinus antalyae (Bogutskaya, 1992) might display specific growth characteristics that differ from other species of their genus. Age and growth were described for species from Duden Creek (Antalya, Turkey) from February 2008 to January 2009. The length–weight relationship for all individuals were described by the parameters: a = 0.0143 and b = 2.946 for C. antalyensis and a = 0.0084 and b = 3.251 for P. antalyae. The von Bertalanffy growth parameters based on data from scales were L∞ = 35.78 cm, k = 0.251 year^?1 and t₀ = ?0.30 for C. antalyensis and L∞ = 22.59 cm, k = 0.232 year^?1 and t₀ = ?0.78 for P. antalyae. The growth characteristics for these two species are not much different from those of closely related species from the same genus.     

On the importance of g(0) for estimating bird population densities with standard distance-sampling: implications from a telemetry study and a literature review

Raw count data are often used to estimate bird population densities. However, such data do not consider detection probability. As an alternative, methods that model detection probability such as distance-sampling have been proposed. However, standard distance-sampling provides reliable estimates for absolute density only when the underlying assumptions are met. One of the most critical of these assumptions is that animals on a transect line or at an observation point have to be detected with certainty (the g (0) = 1 assumption). We radiotagged nine Orphean Warblers Sylvia hortensis and estimated their short-distance detection probability. Birds were radio-located in 264 cases in single bushes or trees. Their visual detection probability after a 5-min search was only 0.58 (sd = ±0.14, range = 0.38–0.80), although the observer knew the bird's location. Furthermore, we carried out a literature review to assess how the g (0) = 1 assumption is handled in practice. None of the 28 standard distance-sampling papers reviewed contained an estimation of g (0). In 57% of the papers, the g (0) = 1 assumption was not even mentioned. Nevertheless, none of the authors declared their estimates as being relative. Our empirical data show that the g (0) = 1 assumption would be severely violated for a foliage-gleaning bird species at a desert stopover site outside the breeding season. The literature review revealed that the testing of the g (0) = 1 assumption is largely ignored in practice. We strongly suggest that more attention should be paid to the testing of this key assumption, because results may not be reliable when it is violated. If it is not possible to test the g (0) = 1 assumption or g (0) is less than 1, alternative methods should be used. Another possibility is to estimate detection probability by the means of radiotagged individuals.     

Comparison of quantitative and molecular variation in agroforestry populations of the shea tree (Vitellaria paradoxa C.F. Gaertn) in Mali

In this study we investigated the within- and between-population genetic variation using microsatellite markers and quantitative traits of the shea tree, Vitellaria paradoxa, an important agroforestry tree species of the Sudano–Sahelian region in Africa. Eleven populations were sampled across Mali and in northern Côte d’Ivoire. Leaf size and form and growth traits were measured in a progeny test at the nursery stage. Eight microsatellites were used to assess neutral genetic variation. Low levels of heterozygosity were recorded (1.6–3.0 alleles/locus; H_E = 0.25–0.42) and the fixation index (F_IS = −0.227–0.186) was not significantly different from zero suggesting that Hardy–Weinberg equilibrium is encountered in all populations sampled. Quantitative traits exhibited a strong genetic variation between populations and between families within populations. The degree of population differentiation of the quantitative traits (Q_ST = 0.055–0.283, Q_STmean = 0.189) strongly exceeds that in eight microsatellite loci (F_ST = −0.011–0.142, F_STmean = 0.047). Global and pairwise F_ST values were very low and not significantly different from zero suggesting agroforestry practices are amplifying gene flow (Nm = 5.07). The population means for quantitative traits and the rainfall variable were not correlated, showing variation was not linked with this climatic cline. It is suggested that this marked differentiation for quantitative traits, independent of environmental clines and despite a high gene flow, is a result of local adaptation and human selection of shea trees. This process has induced high linkage disequilibrium between underlying loci of polygenic characters.     

New microsatellite loci for the endangered scalloped hammerhead shark, Sphyrna lewini

We isolated 15 microsatellite markers for the scalloped hammerhead shark, Sphyrna lewini. Loci were tested on 80 specimens of S. lewini from four Eastern Pacific samples. The number of alleles per locus ranged from 6 to 31 (mean = 14). Observed and expected levels of heterozygosity per locus ranged from 0.39 to 0.91 (mean = 0.70) and from 0.54 to 0.90 (mean = 0.76), respectively. No pairs of loci were in gametic disequilibrium after Bonferroni correction of α. One locus showed significantly lower heterozygosity than expected under Hardy–Weinberg proportions in two populations, possibly caused by null alleles.     

Difference in age,growth, and sexual demography of black‐spot tuskfish,Choerodon schoenleinii (Valenciennes, 1839), in two adjacent populations,Ryukyu Archipelago,southern Japan

To better understand the plasticity of life history traits in the blackspot tuskfish, Choerodon schoenleinii (Valenciennes, 1839), the characteristics of the population around the Yaeyama Islands (24°N, 124E) were examined and compared to those around Okinawajima Island (26°N, 128E) that had been investigated in a previous study. Age and growth of the Yaeyama population were examined based on 103 specimens collected at fish markets between 2006 and 2016. Specimens included 83 females (25.2–69.0 cm total length [TL]), and 20 males (43.1–71.8 cm TL). Ages determined from sectioned otoliths ranged from 1–9 for females, and 4–15 for males. Values for von Bertalanffy growth functions were L_t = 74.2 {1?exp[?0.23 (t + 0.38)]}, and the growth of the Yaeyama population was significantly faster than that of the previously studied population. Sexual demography of the two populations was compared using body length data on landings measured at the fish markets. In the Yaeyama population, females and males ranged from 24–65 cm TL and 39–75 cm TL, respectively; length at 50% individual sex change size was estimated at 54.7 ± 0.56 cm (±95% C.I.). In contrast, in the Okinawajima population, females and males ranged from 16–65 cm TL and 30–75 cm TL, respectively; meanwhile, 50% sex change size was estimated to be 50.0 ± 0.25 cm. There were thus significant differences in the size at sex change between the two populations. This difference may be related to the difference in population density between the sites.     

Epigenetic variation reflects dynamic habitat conditions in a rare floodplain herb

Variation of DNA methylation is thought to play an important role for rapid adjustments of plant populations to dynamic environmental conditions, thus compensating for the relatively slow response time of genetic adaptations. However, genetic and epigenetic variation of wild plant populations has not yet been directly compared in fast changing environments. Here, we surveyed populations of Viola elatior from two adjacent habitat types along a successional gradient characterized by strong differences in light availability. Using amplified fragment length polymorphisms (AFLP) and methylation‐sensitive amplification polymorphisms (MSAP) analyses, we found relatively low levels of genetic (H′_gen = 0.19) and epigenetic (H′_epi = 0.23) diversity and high genetic (?_ST = 0.72) and epigenetic (?_ST = 0.51) population differentiation. Diversity and differentiation were significantly correlated, suggesting that epigenetic variation partly depends on the same driving forces as genetic variation. Correlation‐based genome scans detected comparable levels of genetic (17.0%) and epigenetic (14.2%) outlier markers associated with site specific light availability. However, as revealed by separate differentiation‐based genome scans for AFLP, only few genetic markers seemed to be actually under positive selection (0–4.5%). Moreover, principal coordinates analyses and Mantel tests showed that overall epigenetic variation was more closely related to habitat conditions, indicating that environmentally induced methylation changes may lead to convergence of populations experiencing similar habitat conditions and thus may play a major role for the transient and/or heritable adjustment to changing environments. Additionally, using a new MSAP‐scoring approach, we found that mainly the unmethylated (?_ST = 0.60) and CG‐methylated states (?_ST = 0.46) of epiloci contributed to population differentiation and putative habitat‐related adaptation, whereas CHG‐hemimethylated states (?_ST = 0.21) only played a marginal role.     

Breeding biology of the Red Kite Milvus milvus in Corsica

The breeding biology of the Red Kite Milvus milvus is still little known in the southern part of its range (Mediterranean), despite recent conservation concerns and major declines in most insular populations (Sicily, Sardinia and Balearics). We report here on the breeding biology of the Red Kite in Corsica in 1996–99 and on recent population trends there. In a 42‐km² study area located in the northwest of the island (Balagne region), breeding density was locally high (1.17–1.78 breeding pairs/km²). Breeding dispersion ranged from loosely colonial to dispersed, with average nearest‐neighbour distance of 444 ± 316 m (range 50–2000) (all data as means ± sd). Kites established breeding territories in January–February, and 92.4% of territorial pairs laid a clutch (n = 238). Laying took place between February and May (mean lay date: 27 March ± 16 days, n = 147). Clutch size averaged 2.44 ± 0.71 (1–5 eggs, n = 96), hatching success 66.9% and fledging success 78.6%. Productivity averaged 1.33 ± 0.88 young per breeding attempt (n = 221) and 1.65 ± 0.65 young per successful breeding attempt (n = 173). Overall breeding success was 51.4 ± 38.0% (n = 88). We describe the growth of young (wing, weight, tarsus and bill) and show a marked seasonal decline in clutch size and breeding performance, with pairs laying earlier producing larger clutches and being more successful than later breeding pairs. Unlike most other insular Mediterranean Red Kite populations that have recently declined, the breeding population in the northwest of Corsica, which accounts for c. 25% of the whole island population, increased from 25 to 35 pairs in 1989 to a maximum of 80–90 pairs in 1997. This increase was probably related to the lack of persecution and a local increase in abundance of Rabbits Oryctolagus cuniculus, following their introduction in the late 1970s, which provided an important feeding resource for Kites. Finally, we compare our results with those from other Red Kite populations studied in Europe. We found that there is a latitudinal gradient in laying date and productivity across Western Europe populations, but no evidence of an insular syndrome in the Corsican population.     

Morphological adaptation of an invasive American mink population in Mediterranean areas of Spain

In this work we studied the morphology of an invasive population of American mink Mustela vison in Catalonia, Mediterranean Spain. Body weight, body length, tail length, hindfoot length and ear length were measured for four age–sex classes: subadult male (n = 17), subadult female (n = 16), adult male (n = 36) and adult female (n = 10). A General Linear Mixed Model was used to test the effect of year, sex, age and age–sex interaction, on each parameter. The morphological results differed from those of other introduced populations because of their different origin and their adaptation to different environments. Differences in sex and age were found, pointing to sexual dimorphism both in adults and subadults. The degree of dimorphism was lower than that of other populations, probably because of a lack of trophic niche separation between male and female mink because in the study area only small prey animals were available.     

PERMANENT GENETIC RESOURCES: Identification and characterization of 14 polymorphic microsatellite loci in the argasid tick Ornithodoros coriaceus

Fourteen polymorphic microsatellite loci (di, tetra and di‐tetra complexes) were developed for the argasid tick Ornithodoros coriaceus. Polymorphism was assessed for 56 individuals from two populations separated by ~95 km. All loci were polymorphic (X = 7, range 3–17 alleles). All loci were in Hardy–Weinberg equilibrium except for one locus (OrC 8) in a single population (P < 0.00119, after Bonferroni correction for multiple tests).     

Effects on river macroinvertebrate communities of tsunami propagation after the 2011 Great East Japan Earthquake

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PERMANENT GENETIC RESOURCES: Isolation of microsatellite loci from the endangered plant Sibara filifolia (Brassicaceae)

Sibara filifolia (Brassicaceae) is a federally endangered annual herb found on two of the California Channel Islands. Previous studies based on allozymes revealed little genetic variability on San Clemente Island. Nine polymorphic microsatellite loci were isolated from individuals on San Clemente Island. We found low levels of allelic variation (mean N_A = 2.3), with seven loci exhibiting significant deviations from Hardy–Weinberg equilibrium (P < 0.01) and 10 pairs of loci exhibiting significant linkage disequilibrium (P < 0.01). Most of the observed variability (mean H_O = 0.003) occurred among populations or in rare homozygous individuals.     

Genetic variation in skipjack tuna Katsuwonus pelamis(L.) using PCR‐RFLP analysis of the mitochondrial DNA D‐loop region

A high level of genetic diversity was observed in Katsuwonus pelamis populations from India ( h  = 0·952, ne  = 14·3) and Japan ( h  = 0·897, ne  = 8·9). The log‐likelihood ( G )‐based exact test revealed significant heterogeneity in the distribution of haplotypes between the two populations ( P  < 0·01, s . e . = 0·001). This result suggests that the two populations should now be treated as demographically independent and managed separately.     

Population genomics of local adaptation versus speciation in coral reef fishes (Hypoplectrus spp,Serranidae)

Are the population genomic patterns underlying local adaptation and the early stages of speciation similar? Addressing this question requires a system in which (i) local adaptation and the early stages of speciation can be clearly identified and distinguished, (ii) the amount of genetic divergence driven by the two processes is similar, and (iii) comparisons can be repeated both taxonomically (for local adaptation) and geographically (for speciation). Here, we report just such a situation in the hamlets (Hypoplectrus spp), brightly colored reef fishes from the wider Caribbean. Close to 100,000 SNPs genotyped in 126 individuals from three sympatric species sampled in three repeated populations provide genome‐wide levels of divergence that are comparable among allopatric populations (F_st estimate = 0.0042) and sympatric species (F_st estimate = 0.0038). Population genetic, clustering, and phylogenetic analyses reveal very similar patterns for local adaptation and speciation, with a large fraction of the genome undifferentiated (F_st estimate ≈ 0), a very small proportion of F_st outlier loci (0.05–0.07%), and remarkably few repeated outliers (1–3). Nevertheless, different loci appear to be involved in the two processes in Hypoplectrus, with only 7% of the most differentiated SNPs and outliers shared between populations and species comparisons. In particular, a tropomyosin (Tpm4) and a previously identified hox (HoxCa) locus emerge as candidate loci (repeated outliers) for local adaptation and speciation, respectively. We conclude that marine populations may be locally adapted notwithstanding shallow levels of genetic divergence, and that from a population genomic perspective, this process does not appear to differ fundamentally from the early stages of speciation.