Twenty polymorphic microsatellites in two of North Africa's most threatened ungulates: Gazella dorcas and Ammotragus lervia (Bovidae; Artiodactyla)

During the last century, North African ungulate species have suffered from habitat loss and over‐hunting. Gazella dorcas (Antilopidae subfamily) and Ammotragus lervia (Caprinae subfamily) are among the ungulates that have suffered most. To help to protect these species, conservation programs and population genetics studies are being implemented. Here, we tested 30 published microsatellite primer‐pairs from Bovids (cattle, sheep and goat) on eight individuals from each species. From the 30 loci tested, 20 amplified well and showed moderate allelic richness (3.75 and 4.65 mean number of alleles per species, respectively, for G. dorcas and A. lervia), and moderatly high heterozygosity (0.53 and 0.63 per species, respectively). These 20 polymorphic markers will facilitate conservation and genetic studies in these two species, and promise to be widely useful across divergent ungulate taxa.     

Re-sequencing regions of the ovine Y chromosome in domestic and wild sheep reveals novel paternal haplotypes

The male-specific region of the ovine Y chromosome (MSY) remains poorly characterized, yet sequence variants from this region have the potential to reveal the wild progenitor of domestic sheep or examples of domestic and wild paternal introgression. The 5' promoter region of the sex-determining gene SRY was re-sequenced using a subset of wild sheep including bighorn ( Ovis canadensis ), thinhorn ( Ovis dalli spp.), urial ( Ovis vignei ), argali ( Ovis ammon ), mouflon ( Ovis musimon ) and domestic sheep ( Ovis aries ). Seven novel SNPs ( oY 2– oY 8) were revealed; these were polymorphic between but not within species. Re-sequencing and fragment analysis was applied to the MSY microsatellite SRYM18 . It contains a complex compound repeat structure and sequencing of three novel size fragments revealed that a pentanucleotide element remained fixed, whilst a dinucleotide element displayed variability within species. Comparison of the sequence between species revealed that urial and argali sheep grouped more closely to the mouflon and domestic breeds than the pachyceriforms (bighorn and thinhorn). SNP and microsatellite data were combined to define six previously undetected haplotypes. Analysis revealed the mouflon as the only species to share a haplotype with domestic sheep, consistent with its status as a feral domesticate that has undergone male-mediated exchange with domestic animals. A comparison of the remaining wild species and domestic sheep revealed that O. aries is free from signatures of wild sheep introgression.     

Evidence for Introgressive Hybridization of Captive Markhor (Capra falconeri) with Domestic Goat: Cautions for Reintroduction

Markhors (Capra falconeri) are among the most endangered mammal species, and several conservation measures, including ex situ breeding, are implemented to prevent their extinction. We studied sequence diversity and differentiation of the first hypervariable segment of the mitochondrial DNA control region among C. f. heptneri and C. f. megaceros kept in four zoos in relationship to lineages of other wild and domestic goats, to assess for the first time the level of molecular distinctness and variability among those subspecies, and to check for possible introgression by related Capra taxa, such as domestic goats. Levels of differentiation between some Capra falconeri lineages and modern domestic goats were similar to levels between other wild goat species (i.e., Capra aegagrus, Capra ibex) and domestic goats. Among pure markhor lineages, paraphyly was observed for C. f. heptneri, suggesting occurrence of shared ancestral polymorphism among markhor subspecies and/or ancient or recent gene exchange between subspecies. Interestingly, 35.7% of all studied markhors from three zoos are introgressed by the domestic goat. Furthermore, despite relatively small breeding group sizes, markhors have maintained a relatively high proportion of mtDNA variation within zoo groups. In any case, the existence of markhors introgressed with domestic goat DNA in zoos should be considered when selecting markhors for ex situ breeding programs with the aim of building up a stock for later reintroduction into the wild.     

Sexual size dimorphism in domestic goats,sheep, and their wild relatives

Sexual size dimorphism (SSD) is a widespread phenomenon in different animal taxa, including the subfamily of goats and sheep (Caprinae), which belongs to the most dimorphic mammalian groups. Rensch's rule describes the pattern of SSD, claiming that larger species generally exhibits higher male to female body size ratio. Agreement with Rensch's rule is manifested by slope of the allometric relationship between male and female body size exceeding one. To test this rule, we analysed the data available in the literature on adult body mass of males and females in domestic goat and sheep breeds (169 and 303, respectively) and 37 wild species/subspecies of the subfamily Caprinae. According to the current phylogenetical hypotheses, there are six distinct monophyletic groups with different levels of SSD (expressed as M/F): (1) wild goats (1.83); (2) wild sheep (1.67); (3) non‐European chamoises, including Ovibos moschatus (1.18); (4) European chamoises (1.27); (5) Budorcas taxicolor (1.01); and (6) Pantholops hodgsonii (1.65). Domestication has led to a remarkable decline in SSD of both domestic goats (1.36) and sheep (1.41). The highest regression slope of the relationship between male and female body size is that estimated for wild goats (1.32), followed by wild sheep (1.24), non‐European chamoises (1.14), domestic sheep (1.13), and domestic goats (1.10). Nevertheless, only the last two values are statistically different from one and thus corroborate Rensch's rule. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98 , 872–883.     

Genome-wide cross-amplification of domestic sheep microsatellites in bighorn sheep and mountain goats

We tested for cross‐species amplification of microsatellite loci located throughout the domestic sheep (Ovis aries) genome in two north American mountain ungulates (bighorn sheep, Ovis canadensis, and mountain goats, Oreamnos americanus). We identified 247 new polymorphic markers in bighorn sheep (≥ 3 alleles in one of two study populations) and 149 in mountain goats (≥ 2 alleles in a single study population) using 648 and 576 primer pairs, respectively. Our efforts increased the number of available polymorphic microsatellite markers to 327 for bighorn sheep and 180 for mountain goats. The average distance between successive polymorphic bighorn sheep and mountain goat markers inferred from the Australian domestic sheep genome linkage map (mean ± 1 SD) was 11.9 ± 9.2 and 15.8 ± 13.8 centimorgans, respectively. The development of genomic resources in these wildlife species enables future studies of the genetic architecture of trait variation.     

Foods,macronutrients and fibre in the diet of blue sheep (Psuedois nayaur) in the Annapurna Conservation Area of Nepal

Food resources are often critical regulating factors affecting individual fitness and population densities. In the Himalayan Mountains, Bharal “blue sheep” (Pseudois nayaur) are the main food resource for the endangered snow leopard (Panthera uncia), as well as being preyed upon by other predators. Blue sheep, however, may face a number of challenges including food resource competition with other wild and domestic ungulates, and hunting pressure. Here, we characterized the diet of blue sheep in the Annapurna Conservation Area (ACA) of Nepal and conducted proximate nutritional analysis on a limited number of plants identified as foods. Furthermore, we investigated the macronutrient and fiber balance of these plants using nutritional geometry which is a state‐space approach to modeling multidimensional and interactive nutritional aspects of foraging. A total of 19 plant species/genera were identified in blue sheep pellets using microhistological analysis. On average, across seasons and regions of the study area, the two most frequently occurring plants in pellets were graminoids: Kobressia sp. and Carex spp. The macronutrient balance of Kobresia sp. was relatively high in carbohydrate and low in protein, while other plants in the diet were generally higher in protein and lipid content. Analysis of fiber balance showed that the two most consumed plants of blue sheep (i.e., Kobresia spp. and Carex spp.) contained the highest concentration of hemicellulose, which is likely digestible by blue sheep. The hemicellulose and lignin balance of plants ranged relatively widely, yet their cellulose contents showed less variation. Foraging by blue sheep may therefore be a balance between consuming highly digestible high‐carbohydrate plants and plants less‐digestible but higher in protein and/or lipid.     

Latitudinal gradients in the species richness of Australian termites (Isoptera)

Abstract Using data on the geographic range of 260 described species in the Atlas of Australian Termites, seven ‘regions’ with more complete data, across a wide range of latitudes were selected for further analysis. For these regions, mean species richness (± SE) was calculated for (i) all species from all families, (ii) Termitidae (197 spp.), (iii) Amitermes spp. (Termitidae, 58 spp.), (iv) all families excluding Amitermes spp. (139 spp.), (v) Termopsidae (5 spp.), (vi) Kalotermitidae (32 spp.) and (vii) Rhinotermitidae (25 spp.). In addition, we compared the Atlas data with species richness for five regions, across a comparable range of latitudes, based on the pooled species richness of described and un-described species given in community studies. No group of termites showed a consistent decline in species richness from tropical to temperate latitudes for either data set. The Atlas data showed similar total species richness from the tropics to the mediterranean southwest, before declining to lowest species richness at the highest latitudes. Species richness of Amitermes spp. and Rhinotermitidae was highest in the southwest. Termopsidae and Kalotermitidae showed no latitudinal pattern in species richness. Community studies showed highest and lowest total species richness in the southwest and at the highest latitudes (south-coastal Western Australia), respectively, and similar species richness from the tropics to arid central Australia. Species richness of. Amitermes spp. was highest in the southwest (31 spp.). Kalotermitidae and Rhinotermitidae showed no clear latitudinal pattern. The latitudinal patterns of species richness for the Australian termites is consistent with that for the Australian vertebrates and ants in that they differ from patterns established for these taxa on other continents.     

Characterization of polymorphic microsatellite loci for the polychaete tubeworm Hobsonia florida

Eight dinucleotide microsatellite loci were isolated and characterized from Hobsonia florida, a tube‐dwelling ampharetid polychaete. The identified loci were highly polymorphic, with allelic diversity ranging from six to 11 alleles. Levels of expected heterozygosity were 0.52 or greater in all cases, averaging 0.78 across the complete set of loci. Cross‐species amplification was successful in three of the eight loci for one or both of the other species (Melinna cristata and Ampharete acutifrons) tested. Although these novel loci were designed for immediate utility in H. florida population‐level research, these results indicate they may prove useful in studies of other related taxa.     

Reclassification of the serows and gorals: the end of a neverending story?

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Biodiversity within urban areas: A case study on bryophytes of the city of Cologne (NRW,Germany)

In this study, the urban bryophyte flora of the city of Cologne (W. Germany) was studied. A total of 143 bryophyte taxa (17 hepatics and 126 mosses) were recorded within the metropolitan area of Cologne. Three species were newly recorded for North Rhine‐Westphalia: Hannediella heimii, Schistidium helveticum and Tortula schimperi. Thirteen species red‐listed in NRW were recorded, among them hardly endangered: Bryum intermedium and Syntrichia laevipila and extinction endangered: Syntrichia papillosa. The temperate biogeographic element prevails among Cologne bryophytes. According to frequency of recordance, only 11 species are widespread over the urban area of which three are hepatics.     

Shallow genetic divergence and species delineations in the endemic Labeobarbus species flock of Lake Tana,Ethiopia

To assess whether the species distinctions of Lake Tana's Labeobarbus spp. are supported by genetic information, microsatellite markers were used. A total of 376 Labeobarbus spp., belonging to 24 populations of 11 species from three regions of the lake (north, south and east), were sampled. Eight microsatellite markers were analysed. In general, differences between conspecific populations were smaller than differences between populations of different species. For six species, conspecific populations from different regions in the lake were consistently more similar than populations of other species from the same region. For four species this was not the case, while for one species two populations were similar, but different from the third population. River‐spawning species appeared to be more distinct than presumed lake spawners. On the species level, there was a significant correlation between genetic and morphological differentiation, especially in morphological aspects associated with ecological functioning. This suggests that genetic differentiation arose together with adaptive radiation, although the overall genetic differentiation among the Lake Tana Labeobarbus spp. is small.     

Last exit before the brink: Conservation genomics of the Cambodian population of the critically endangered southern river terrapin

The southern river terrapin, Batagur affinis is one of the world's 25 most endangered freshwater turtle species. The major portion of the global population is currently found in peninsular Malaysia, with the only remnant Indochinese population in southern Cambodia. For more than a decade, wild nests in this remnant Cambodian population have been fenced and hatchlings reared in captivity. Here we amplified 10 microsatellite markers from all 136 captive individuals, obtained 2,658 presumably unlinked and neutral single nucleotide polymorphisms from 72 samples with ddRAD‐seq, and amplified 784 bp of mtDNA from 50 samples. Our results reveal that the last Indochinese population comprised only four kinship groups as of 2012, with all offspring sired from <10 individuals in the wild. We demonstrate an obvious decrease in genetic contributions of breeders in the wild from 2006–2012 and identify high‐value breeders instrumental for ex‐situ management of the contemporary genetic stock of the species.     

Conservation of microsatellite loci within the genus Vitis

Eleven microsatellites isolated from grapevine (Vitis vinifera) were used to study the degree of conservation of these sequences across different Vitis species. Nine microsatellites were newly isolated, the remaining two (VVS2 and VVS5) came from the literature. A preliminary assay on the conservation of priming sites was carried out on 14 non-V. vinifera species, including relevant taxa for breeding. Parthenocissus quinquefolia was added as representative of a related genus. Cross-species amplification was obtained in 94% of the 176 genotype×locus tested combinations. Three microsatellite loci were then cloned and sequenced in ten species. The microsatellite repeat was found present in all cases. The repeat region was often longer in V. vinifera than in the other species. Furthermore the non-source species showed interruptions in the repeat. In spite of these constraints, which could reduce the polymorphism of microsatellites in non-source species, the results demonstrate the possibility of extending the use of microsatellite markers to wild germplasm and inter-specific hybrids. Point mutations have been found in microsatellite flanking regions and these variations have been used to investigate the genetic relationship among taxa. The Neighbor-joining tree that was obtained on the basis of ten nucleotide variations, showed that there is not a clear cut difference between American, Asian and European species and that the actual taxonomy which reflects the geographical distribution of species must most likely be revised. Moreover, in general, nucleotide variations which occur in microsatellite flanking regions provide new molecular tools for investigating the evolution of species. Received: 24 October 1999 / Accepted: 11 November 1999     

Development of sequence‐tagged microsatellite site markers for chickpea (Cicer arietinum L.)

Microsatellite loci were identified from chickpea (Cicer arietinum L.), the third most important grain legume crop in the world. A total of 13 sequence‐tagged microsatellite markers were developed using two different approaches: (i) amplification using degenerate primers and (ii) cloning of intersimple sequence repeat (ISSR)‐amplified fragments. Thirty‐five chickpea accessions were analysed, which resulted in a total of 30 alleles at the 13 loci. The observed heterozygosity ranged from 0.1143 to 0.4571 with an average of 0.2284. The cross‐species transferability of the sequence‐tagged microsatellite site (STMS) markers was checked in Cicer reticulatum, the wild annual progenitor of chickpea. These microsatellite markers will be useful for assessing the genetic diversity patterns within chickpea as well as aid in construction of intra‐ and interspecific genetic linkage maps.     

Indicator taxa revisited: useful for conservation planning?

Aim Indicators for biodiversity are needed to facilitate the identification of complementary reserve networks for biodiversity conservation. One widely adopted approach is to use indicator taxa, i.e. a single taxon such as birds or butterflies, despite the ongoing debate regarding their usefulness as indicators of broader biodiversity. Here we assess several aspects, such as influence of species number, of indicator taxa for three extensive data sets to improve our insight into the effectiveness of indicator taxa. Location Denmark, sub‐Saharan Africa and Uganda. Methods First, we investigate to what extent variation in species number between indicator taxa (e.g. 488 mammal spp. vs. 210 snake spp.) is causing the differences in effectiveness between indicator taxa. Second, we investigate whether indicator taxa are capable of outperforming indicator groups composed of random sets of species chosen among all taxa. Finally, we assess the correlation of specific properties such as mean range size of the indicator taxa to their effectiveness. We investigate these aspects of the effectiveness of indicator taxa through the separate analysis of three distinct distributional species data sets: sub‐Saharan Africa (4,039 spp.), Denmark (847 spp.) and Uganda (2,822 spp.). Results We overall found that indicator taxa comprising a greater number of species tend to perform better than indicator taxa with fewer species (e.g. 488 mammal spp. outperform 210 snake spp.), although there are some exceptions. Second, we found most indicator taxa to perform worse than indicator groups consisting of a comparable number of species selected among all taxa. Finally, the effectiveness of indicator taxa was seen to correlate poorly with selected distributional properties such as mean range size of the indicator taxa, suggesting that it is difficult to predict which taxa are efficient biodiversity indicators. Main conclusions Overall, these findings might suggest that focus should simply be on increasing the number of species among all taxa as basis for priority setting, rather than striving to obtain the ‘perfect’ indicator taxa.     

Influence of plant domestication on plant-pollinator interactions: Floral attributes and floral visitor communities in wild and cultivated squash plants

Premise

Domestication of plant species results in phenotypic modifications and changes in biotic interactions. Most studies have compared antagonistic plant-herbivore interactions of domesticated plants and their wild relatives, but little attention has been given to how domestication influences plant-pollinator interactions. Floral attributes and interactions of floral visitors were compared between sister taxa of the genus Cucurbita (Cucurbitaceae), the domesticated C. moschata, C. argyrosperma ssp. argyrosperma and its wild progenitor C. argyrosperma ssp. sororia in the place of origin.

Methods

We conducted univariate and multivariate analyses to compare floral morphological traits and analyzed floral reward (nectar and pollen) quantity and quality between flowers of wild and domesticated Cucurbita taxa. Staminate and pistillate flowers of all three taxa were video recorded, and visitation and behavior of floral visitors were registered and analyzed.

Results

Most floral morphological characteristics of flowers of domesticated taxa were larger in both staminate and pistillate flowers. Staminate and pistillate flowers presented distinct correlations between floral traits and integration indices between domesticated and wild species. Additionally, pollen quantity and protein to lipid ratio were greater in domesticated species. Cucurbit pollen specialists, Eucera spp., had the highest probability of visit for all Cucurbita taxa.

Conclusions

We provide evidence that floral traits of domesticated and wild Cucurbita species experienced different selection pressures. Domesticated Cucurbita species may have more resources invested towards floral traits, thereby increasing attractiveness to pollinators and potentially plant reproductive success. Wild ancestor plant populations should be conserved in their centers of origin to preserve plant-pollinator interactions.     

Characterization,multiplex conditions,and cross‐species utility of tetranucleotide microsatellite loci for Blanchard's cricket frog (Acris crepitans blanchardi)

We have isolated and characterized 17 tetranucleotide microsatellite loci for Blanchard's cricket frog (Acris crepitans blanchardi), an anuran common in the central USA. Sixteen loci were organized into four multiplex amplification reactions. These loci were highly polymorphic when screened in 55 individuals from two distant populations, with 11–48 alleles per locus (average = 24.8). Observed and expected heterozygosities ranged from 0.18 to 0.97 and from 0.17 to 0.96, respectively. Nine loci were also polymorphic in Acris crepitans crepitans, with seven polymorphic in Acris gryllus. Five loci amplified in all three taxa. These loci will be useful for population‐ and species‐level investigations of this widespread group.     

Genetic depletion at adaptive but not neutral loci in an endangered bird species

Many endangered species suffer from the loss of genetic diversity, but some populations may be able to thrive even if genetically depleted. To investigate the underlying genetic processes of population bottlenecks, we apply an innovative approach for assessing genetic diversity in the last known population of the endangered Pale‐headed Brushfinch (Atlapetes pallidiceps) in Ecuador. First, we measure genetic diversity at eleven neutral microsatellite loci and adaptive SNP variation in five Toll‐like receptor (TLR) immune system genes. Bottleneck tests confirm genetic drift as the main force shaping genetic diversity in this species and indicate a 99 % reduction in population size dating back several hundred years. Second, we compare contemporary microsatellite diversity with historic museum samples of A. pallidiceps, finding no change in genetic diversity. Third, we compare genetic diversity in the Pale‐headed Brushfinch with two co‐occurring‐related brushfinch species (Atlapetes latinuchus, Buarremon torquatus), finding a reduction of up to 91% diversity in the immune system genes but not in microsatellites. High TLR diversity is linked to decreased survival probabilities in A. pallidiceps. Low TLR diversity is thus probably an adaptation to the specific selection regime within its currently very restricted distribution (approximately 200 ha), but could severely restrict the adaptive potential of the species in the long run. Our study illustrates the importance of investigating both neutral and adaptive markers to assess the effect of population bottlenecks and for recommending specific management plans in endangered species.     

Haemopexin in sheep,mouflon and goat: genetic polymorphism,heterogeneity and partial characterization*

Benzidine staining of starch gels after electrophoresis of sera to which haematin was added revealed polymorphism of haemopexin in sheep, mouflon and goat. In sheep three phenotypes were observed, Hpx A, Hpx AB and Hpx B. Pedigree data support the hypothesis of codominant inheritance from a single locus by two alleles, Hpx^A and Hpx^B. Neuraminidase treatment of haemopexin preparations showed that Hpx B covered two variants, B1 and B2, thus indicating genetic control by three alleles (Hpx^A, Hpx^B1 and Hpx^B2). In sheep populations the frequency of Hpx^B is low. In mouflon, in addition to the two variants that are like those of sheep, absence of haemopexin was observed in some animals, by using starch gel electrophoresis as well as immunoelectrophoresis. In goat, three phenotypes were detected, Hpx A, Hpx AB and Hpx B, differing in migration from those of sheep. Haemopexins of the studied species are heterogeneous. Sialic acid is responsible for electrophoretic heterogeneity of sheep haemopexin. Chemical. composition (amino acid and carbohydrate), molecular weight (56 060) and N-terminal sequence (Leu-Pro-Pro-) of sheep haemopexin were also determined.     

Characterization of microsatellite markers in the endangered Sinojackia xylocarpa (Styracaceae) and cross‐species amplification in closely related taxa

Twenty‐four polymorphic microsatellite loci were isolated and characterized from an AAG‐enriched genomic library of Sinojackia xylocarpa. The average allele number of these microsatellites was 3.3 per locus, ranging from two to seven. The observed and expected heterozygosities at population level were 0.10–0.83 and 0.10–1.00, respectively. In addition, successful cross‐species amplification of this set of microsatellites in three other species of Sinojackia and a closely related taxon, Changiostyrax dolichocarpa, suggested that this set of microsatellite markers should provide a useful tool for genetic and conservation studies of Sinojackia species and other closely related taxa in the Styracaceae.