Genetic evaluation of the Association of Zoos and Aquariums Matschie's tree kangaroo (Dendrolagus matschiei) captive breeding program

Matschie's tree kangaroo (Dendrolagus matschiei) is an endangered species that has been bred in captivity since the 1970s. In 1992, the Tree Kangaroo Species Survival Plan^® (TKSSP) was established to coordinate the captive management of Association of Zoos and Aquariums (AZA) D. matschiei. The TKSSP makes annual breeding recommendations primarily based on the mean kinship (MK) strategy. Captive breeding programs often use the MK strategy to preserve genetic diversity in small populations—to avoid the negative consequences of inbreeding and retain their adaptive potential. The ability of a captive breeding program to retain the population's genetic diversity over time can be evaluated by comparing the genetic diversity of the captive population to wild populations. We analyzed DNA extracted from blood and fecal samples from AZA (n = 71), captive (n = 28), and wild (n = 22) D. matschiei using eight microsatellite markers and sequenced the partial mitochondrial DNA control region gene. AZA D. matschiei had a similar expected heterozygosity (H_e = 0.595±0.184) compared with wild D. matschiei (H_e = 0.628±0.143), but they had different allelic frequencies (F_ST = 0.126; P<0.001). AZA D. matschiei haplotype diversity was almost two times lower than wild D. matschiei (). These data will assist management of AZA D. matschiei and serve as a baseline for AZA and wild D. matschiei genetic diversity values that could be used to monitor future changes in their genetic diversity. Zoo Biol 30:636–646, 2011. © 2010 Wiley Periodicals, Inc.     

Composition of browses consumed by Matschie's tree kangaroo (Dendrolagus matschiei) sampled from home ranges in Papua New Guinea

Twenty-six samples (n = 24 spp.) of foods eaten, including ferns, shrubs, vines, orchids, herbaceous plants, and tree leaves, were collected from the Yopno, Uruwa, and Som Conservation Area at approximately 1,800 m altitude on the Huon Peninsula, Papua New Guinea (PNG). Samples were weighed fresh in the field and transported to the Lae National Herbarium in PNG for drying and confirmed identification, before transporting to the US for analysis of primary nutrient composition and minerals. Water content averaged 76 ± 10% (mean ± standard deviation); on a dry matter (DM) basis, foods averaged moderate protein (11 ± 5%), and soluble carbohydrate (27 ± 8%) content, along with exceptionally low starch (1 ± 1%) and crude fat (3 ± 2%) values, and moderate to high values in fiber fractions (neutral detergent fiber 52 ± 13%, acid detergent fiber 39 ± 10%, lignin 15 ± 6%). Calculated metabolizable energy content of native forages averaged 1.9 ± 0.3 Mcal/kg DM (ruminant model). Macromineral concentrations (DM basis) were not exceptional (calcium 1.1 ± 1.0%, phosphorus 0.2 ± 0.1%, magnesium 0.3 ± 0.2%, potassium 1.8 ± 0.9%, sodium 0.02 ± 0.02%), and select trace minerals were within anticipated ranges for herbivores (copper 12 ± 13 mg/kg, iron 48 ± 26 mg/kg, zinc 34 ± 18 mg/kg) with the exception of manganese (268 ± 225 mg/kg), which could be considered on the high end of dietary adequacy for most herbivores. These data provide useful information that can be used to adjust nutrient targets for dietary development and feeding management of captive populations of tree kangaroos.     

A multiplex PCR assay to distinguish among three sympatric marsupial taxa from Huon Peninsula, Papua New Guinea, using the mitochondrial control region

Matschie’s tree kangaroo (Dendrolagus matschiei) is an endangered arboreal macropodid marsupial that is difficult to locate in the wild. The Tree Kangaroo Conservation Program noninvasively collected D. matschiei faecal samples, but a high percentage of samples were misidentified and belonged to two terrestrial macropods, New Guinea pademelon (Thylogale browni) and small dorcopsis (Dorcopsulus vanheurni). We developed species-specific primers that produced a unique sized mitochondrial DNA control region gene product for each taxon and achieved an 89% correct assignment rate. The species-specific primers can increase the accuracy of D. matschiei density estimates and facilitate additional genetic analyses of wild D. matschiei.     

Variation in food availability mediate the impact of density on cannibalism,growth, and survival in larval yellow spotted mountain newts (Neurergus microspilotus): Implications for captive breeding programs

In this study, we examined cannibalistic behavior, growth, metamorphosis, and survival in larval and post‐metamorph endangered yellow spotted mountain newts Neurergus microspilotus hatched and reared in a captive breeding facility. We designed a 2 × 2 factorial experiment, crossing two levels of food with two levels of density including high food/high density, high food/low density, low food/high density, and low food/low density. The level of cannibalistic behavior (including the loss of fore and hind limbs, missing toes, tail, gills, body damage, and whole body consumption) changed as the larvae grew, from a low level during the first 4 weeks, peaking from weeks 7 to 12, and then dropped during weeks 14–52. Both food level and density had a significant effect on cannibalism. The highest frequency of cannibalism was recorded for larvae reared in the low food/high density and lowest in high food/low density treatments. Growth, percent of larval metamorphosed, and survival were all highest in the high food/low density and lowest in low food/high density treatment. Food level had a significant effect on growth, metamorphosis, and survival. However, the two levels of density did not influence growth and metamorphosis but showed a significant effect on survival. Similarly, combined effects of food level and density showed significant effects on growth, metamorphosis, and survival over time. Information obtained from current experiment could improve productivity of captive breeding facilities to ensure the release of adequate numbers of individuals for reintroduction programs. Zoo Biol. 35:513–521, 2016. © 2016 The Authors. Zoo Biology published by Wiley Periodicals, Inc.     

Gm and Inv (Km) studies of melanesian people on the Huon Peninsula in northeast Papua New Guinea: Polymorphism for a Gm1,5,10,11,13,14,17,21,26 haplotype

Blood samples from 448 people living in six villages in the Huon Peninsula in northeast Papua, New Guinea, were tested for Gm(1,2,3,5,6,10,11,13,14,17,21,24,26) and Inv(1) [Km(1)]. All the people are non-Austronesian (NAN) speakers. As expected, there was a low frequency of the Gm^{1,3,5,10,11,13,14,26} haplotype, but in contradiction to expectations there was a complete absence of the Gm^1,2,17,21,26 haplotype. In addition, samples from people in one village (Yupna) and probably those for two other villages (Irumu 13 and 14) have the rare haplotype Gm^{1,5,10,11,13,14,21,26} at polymorphic frequencies. Two samples from people living in Yupna had the rare phenotype Gm(1,3,17,21,26), indicating the presence of any one of several rare haplotypes that had been observed in other populations. These are discussed.     

四川地区猕猴线粒体DNA 控制区遗传多样性及其种群遗传结构

猕猴是最理想的医学实验灵长类动物,并且是国家二级保护动物。四川地区的猕猴数量多、分布广,全面了解其遗传背景对于该地区猕猴资源的保护与合理利用具有重要的意义。本研究对来自四川8 个地理种群的231个不同猕猴个体的线粒体DNA 控制区部分序列进行了测定和群体分析,发现了110 个变异位点(22. 49% ),定义了56 种单倍型,其单倍型多样性(h)平均值为0. 686、核苷酸多样性(π)平均值为0. 01483,种群总体遗传多样性较高;进一步分析表明,8 个地理种群间存在着明显的遗传分化(F_st = 0. 70412,P < 0. 05),种群间基因交流较低(N_m < 1);系统发育树显示,四川猕猴8 个地理种群的单倍型基本上成簇分布在系统树上,与地理位置呈现一定的对应关系,说明四川猕猴具有明显的系统地理分布格局。地理隔离和人类活动可能是促使四川猕猴种群分化的主要因素。     

Genetic diversity of Setipinna taty (Engraulidae) populations from the China Sea based on mitochondrial DNA control region sequences

The genetic diversity of Setipinna taty, which is commercially fished in the China Sea, was studied based on mitochondrial DNA control region sequences. PCR was used to amplify the control region fragment in 100 individuals of S. taty collected from Weihai (WH), Yantai (YT), Zhoushan (ZS), Xiangshan (XS), and Ninghai (NH) in China. A control region fragment of 656 bp was successfully sequenced in these 100 individuals. The A+T content of this S. taty control region was 71.7%; 172 variable sites and 62 haplotypes were found. Nucleotide diversity in the WH, YT, ZS, XS, and NH groups was 0.0228, 0.0247, 0.0441, 0.0126, and 0.0238, respectively. The haplotype diversity was 0.984, 0.911, 0.989, 0.926, and 0.979, respectively. Analysis of molecular variance showed that 97.95% of genetic variation was within populations, and only 2.05% among populations. The neighbor-joining phylogenetic tree obtained based on genetic distance showed that no significant genealogical structure exists throughout this range of S. taty. These results indicate no apparent geographical differentiation in the comparison of Yellow Sea and East China Sea populations of S. taty. Within the control region, we identified an extended termination-associated sequence domain, a central conserved sequence block domain and a conserved sequence block domain; insertions of short tandem repeat sequence segments were found at the 5' end of the control region.     

Genetic diversity of silver pomfret (Pampus argenteus) populations from the China Sea based on mitochondrial DNA control region sequences

The genetic diversity of silver pomfret (Pampus argenteus) from the Bohai, East China, and South China Seas was investigated using mitochondrial DNA (mtDNA) control region sequence data. We found high levels of variation with 17 haplotypes among the 45 individuals (h = 0.88, π = 0.006). AMOVA analysis detected significant structuring among China Sea silver pomfret (P < 0.05, F_ST = 0.050), which indicates significant genetic differentiation. No significant differentiation between Bohai Sea and East China Sea samples was detected (P > 0.05). Whether silver pomfret from the South China Sea exhibit a different demographic history than those from the Bohai and East China Seas remains to be determined.     

Genetic diversity and phylogenetic relationships of Malayan tapir (Tapirus indicus) populations in the Malay Peninsula based on mitochondrial DNA control region

Biodiversity and Conservation - The Malayan tapir (Tapirus indicus) is an endangered species in Southeast Asia (SEA). Over the years, there has only been a few reports on its population genetic...     

Patterns of speciation in two sibling species of Graomys (Rodentia,Cricetidae) based on mtDNA sequences

To increase our understanding of the speciation process occurred in the sibling species Graomys griseoflavus and Graomys centralis, a phylogeographic study was conducted based on sequences of a hypervariable segment of the mtDNA D‐loop region. The resulting haplotype phylogenetic network showed two well‐defined clusters, one for each species. The clusters were connected by two haplotypes from localities that are almost 300 km apart, one situated in the Monte eco‐region and the other, in the Chaco. This result is in agreement with a previous hypothesis about the geographical context in which the cladogenetic process occurred. A divergence time of 0.15–0.28 million years was estimated, which is consistent with a process of recent speciation. An amova test confirmed that at present gene flow between species does not exist. The mismatch distribution analyses suggest that the geographical and demographic expansion undergone by the species is related to the climatic events that occurred in the region during the Quaternary.     

Phylogenetic relationships of Atherina hepsetus and Atherina boyeri (Pisces: Atherinidae) populations from Greece, based on mtDNA sequences

The genetic divergence and the phylogenetic relationships of six Atherina boyeri (freshwater and marine origin) and five Atherina hepsetus populations from Greece were investigated using partial sequence analysis of 12s rRNA, 16s rRNA and control region mtDNA segments. Three different well divergent groups were revealed; the first one includes A. boyeri populations living in the sea, the second includes A. boyeri populations living in the lakes and lagoons whereas the third one includes all A. hepsetus populations. Fifty-seven different haplotypes were detected among the populations studied. In all three mtDNA segments examined, sequence analysis revealed the existence of fixed haplotypic differences discriminating A. boyeri populations inhabiting the lagoon and the lakes from both the coastal A. boyeri and the A. hepsetus populations. The genetic divergence values estimated between coastal (marine) A. boyeri populations and those living in the lagoon and the lakes are of the same order of magnitude as those observed among coastal A. boyeri and A. hepsetus populations. The results obtained by different phylogenetic methods were identical. The deep sequence divergence with the fixed different haplotypes observed suggests the occurrence of a cryptic or sibling species within A. boyeri complex.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 151–161.     

Genetic diversity in the bronze gudgeon, <Emphasis Type="Italic">Coreius heterodon</Emphasis>, from the Yangtze River system based on mtDNA sequences of the control region

The bronze gudgeon, Coreius heterodon (Bleeker), is an economically important species, which only inhabits the Yangtze River. The stock declined drastically in recent years due to dam construction, over-fishing, and pollution. Little is known about its population genetic structure. In this study, the sequences of the mitochondrial DNA (mtDNA) control regions of natural bronze gudgeon was determined for fish collected from four sites in the Yangtze River (n = 102). The molecular data were used to estimate the genetic diversity and differentiation of the bronze gudgeon. The results showed that 28 haplotypes and 22 variable sites were found, and the haplotype diversity (π) and nucleotide diversity (h) were 0.849 and 0.00257, respectively. A low level of genetic diversity exists in the bronze gudgeon. Analysis of molecular variance (AMOVA) suggests that 98.8% of the genetic variability occurred within the populations; the site of collection had little influence on diversity. Future research should focus on investigating the genetic divergence of populations in different tributaries and using additional polymorphic markers, such as microsatellite DNA, to verify the results and improve interpretation.     

Patterns of molecular diversity in wild stocks of the redclaw crayfish (Cherax quadricarinatus) from northern Australia and Papua New Guinea: impacts of Plio-Pleistocene landscape evolution

1. Analysis of mitochondrial and nuclear DNA (microsatellites) in 379 individuals, collected from 15 localities in northern Australia and Papua New Guinea (PNG), demonstrated that wild redclaw crayfish ( Cherax quadricarinatus ) populations consist of two highly divergent Australian lineages and two PNG lineages.
2. The disjunction between the two Australian lineages occurs over a distance of approximately 200 km in the south-western corner of the Gulf of Carpenteria. These data conflict with an earlier study that detected no significant differentiation in 23 variable allozyme loci in redclaw sampled from northern Australia, but concur broadly with the previous recognition of two morphologically distinct species ( C. quadricarinatus and C. bicarinatus ) across northern Australia, and a third species in PNG ( C. albertsii ).
3. The inferred timing and patterns of divergence evident in the molecular data presented here closely align with a similar pattern reported in a co-distributed freshwater decapod crustacean, and broadly reflect patterns in some vertebrate taxa with similar distributions across northern Australia and PNG.
4. These congruent patterns most probably reflect periodic Plio-Pleistocene land and freshwater connections between Australia and New Guinea.     

Genetic diversity and population structure of the gizzard shad,Konosirus punctatus (Clupeidae,Pisces), in Korean waters based on mitochondrial DNA control region sequences

In this study, we clarified the population structure of the gizzard shad, Konosirus punctatus, in Korean waters. We analyzed 896 base pairs of the mitochondrial DNA control region in 182 individuals, which were sampled from eight localities between the East Sea and the Yellow Sea. The haplotype diversity (h) was very high (0.9662–1.0000) but the nucleotide diversity (π) was very low (0.0061–0.0434). A neighbor-joining tree showed that the population clustered into two reciprocal monophyletic groups, lineages A and B. Lineage A is distributed on all coasts of Korea, from the Yellow Sea to the East Sea, declining to the east, whereas lineage B is distributed in the East Sea and Korea Strait, disappearing completely from middle Korea Strait to the west. Analysis of molecular variance showed strong structuring (F _ST = 0.856; P < 0.0001) between the two lineages. Neutrality tests and mismatch distribution analyses showed that a recent rapid expansion event occurred only in lineage A. Our results suggest that the management unit of the Korean gizzard shad may be divided in two, lineage A and lineage B.     

Mesophyll cell‐sucking herbivores (Cicadellidae: Typhlocybinae) on rainforest trees in Papua New Guinea: local and regional diversity of a taxonomically unexplored guild

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A new genus (Borinken) and five new species (Borinken elyunque, Distigmoptera chamorrae, Kiskeya elyunque, Ulrica eltoro, and Ulrica iviei) from Puerto Rico are described and illustrated. A keyto all West Indian Monoplatini genera is provided, as are keys to all speciesof Kiskeya and to the speciesof Ulrica from Puerto Rico. A list of the flea beetle genera, along with the number of species and some of the faunal features is presented and discussed for the West Indies.     

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