Robert W. Lamont

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 April 2010-31 May 2010

This article documents the addition of 396 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Anthocidaris crassispina, Aphis glycines, Argyrosomus regius, Astrocaryum sciophilum, Dasypus novemcinctus, Delomys sublineatus, Dermatemys mawii, Fundulus heteroclitus, Homalaspis plana, Jumellea rossii, Khaya senegalensis, Mugil cephalus, Neoceratitis cyanescens, Phalacrocorax aristotelis, Phytophthora infestans, Piper cordulatum, Pterocarpus indicus, Rana dalmatina, Rosa pulverulenta, Saxifraga oppositifolia, Scomber colias, Semecarpus kathalekanensis, Stichopus monotuberculatus, Striga hermonthica, Tarentola boettgeri and Thermophis baileyi. These loci were cross‐tested on the following species: Aphis gossypii, Sooretamys angouya, Euryoryzomys russatus, Fundulus notatus, Fundulus olivaceus, Fundulus catenatus, Fundulus majalis, Jumellea fragrans, Jumellea triquetra Jumellea recta, Jumellea stenophylla, Liza richardsonii, Piper marginatum, Piper aequale, Piper darienensis, Piper dilatatum, Rana temporaria, Rana iberica, Rana pyrenaica, Semecarpus anacardium, Semecarpus auriculata, Semecarpus travancorica, Spondias acuminata, Holigarna grahamii, Holigarna beddomii, Mangifera indica, Anacardium occidentale, Tarentola delalandii, Tarentola caboverdianus and Thermophis zhaoermii.

Heritability for body colour and its genetic association with morphometric traits in Banana shrimp ( Fenneropenaeus merguiensis )

BackgroundBanana shrimp Fenneropenaeus merguiensis has emerged as an important aquacultured shrimp species in South East Asia and Australia. However, the quantitative genetic basis of economically important traits in this species are currently not available, while for body colour, cooked or uncooked, there are no genetic parameter estimates for any shrimp or indeed any decapod crustacean. In this study, we report for banana shrimp genetic parameters for morphometric traits and, the first time for any shrimp, parameter estimates for body colour. Ten highly polymorphic microsatellite markers were developed from genomic sequences and used to construct a pedigree for 2000 offspring from approximately 60 female and 60 male parents that were sampled from a single routine commercial production pond.ResultsRestricted maximum likelihood method applied to a single trait mixed model was used to estimate heritabilities, while correlations were estimated using the multi-trait approach. The estimates of heritability for morphometric traits were moderate to high (h2 = 0.14 – 0.50). Body colour of uncooked shrimp showed a heritable additive genetic component (h2 = 0.03 – 0.55), and those estimates obtained for cooked shrimp were significantly different from zero. Genetic correlations among morphometric traits were all positive and very high (close to unity, rg = 0.85 – 0.99). The genetic correlations of body traits (weight, length and width) were positive with both colour after cooking (0.74 – 0.84) and body colour measured on live shrimp (0.59 to 0.70). The positive genetic correlations between the cooked body colour and uncooked body colour (0.64 ± 0.20) suggests these two traits can be simultaneously improved in practical selective breeding programs. This first ever report of genetic parameters for cooked or uncooked colour in crustacean indicates there is potential for genetic improvement of both growth and body colour through selection.ConclusionsIn the present study we demonstrated for banana shrimp that genetic parameters can be estimated from commercial samples (using pedigrees based on DNA markers), that selection for shrimp colour should be successful under such commercial conditions.

Genetic diversity and population genetic structure in three threatened Ocotea species (Lauraceae) from Brazil’s Atlantic Rainforest and implications for their conservation

The Atlantic Rainforest in Brazil is currently comprised of small fragments due to the history of conversion and degradation in the last five centuries. The rainforest trees, Ocotea catharinensis, O. odorifera and O. porosa have been heavily harvested because of the high economic value of their timber and essential oils. Their respective habitats have undergone substantial reduction in area due to continuing anthropogenic pressures. As a consequence, these species have suffered large declines in population size and are now considered to be potentially vulnerable to extinction. This study investigated the patterns and levels of genetic diversity and inbreeding of these species using eight microsatellite markers in order to define priority populations for conservation management actions focusing on population enhancement and ex situ germplasm collections. High genetic diversity was found for each of the species with moderate genetic differentiation among populations. Most populations displayed significant inbreeding and isolation by distance. The results provide important information to choose priority populations for both in situ and ex situ conservation measures.

The importance of genetic considerations for planning translocations of the rare coastal heath species Boronia rivularis (Rutaceae) in Queensland.

The Sunshine Coast of Queensland, Australia, is facing increasing pressure from rapid urban expansion. Because of the area’s high biodiversity, developers are facing pressure to translocate rare, endangered, and vulnerable plants to more protected areas. Translocation of turves, comprising sections of soil and intact aboveground vegetation, has been used as a strategy for reintroducing understory species where establishment from seed is difficult. Moving populations spatially can change levels and direction of gene flow. In what appears to be one of the largest reported translocations of a rare species, this study uses allozymes, which are variant forms of enzymes, to investigate the genetics of a population of the rare heath species Boronia rivularis, which is to be translocated to compensate for an urban development. The population on the development site was found to be significant due to its large size and high genetic diversity and distinctiveness. Diversity and inbreeding levels were not evenly distributed across the development site; inbreeding was highest where density was highest. It was found that retention of a significant portion of the population on the development site reduced the potential loss of connectivity. However, we found that ecological assessments based on density could have led to the loss of the most genetically diverse and least inbred parts of the population.

Population genetics of Philotheca sporadica (Rutaceae) to advise an offset translocation program

Philotheca sporadica (Rutaceae) is a vulnerable species restricted to a small geographic area, with very few populations protected in reserves. Environmental impact surveys identified some populations that will be impacted by gas pipeline construction. This study aimed to determine the genetic diversity of P. sporadica to advise an offset planting program. P. sporadica was found to have high population genetic diversity but all populations were genetically similar except two isolated genetically depauperate populations. Genetic diversity decreased with decreasing population size and increasing population isolation. Impacted populations were significant for the species viability, being among the largest and most genetically diverse, although a high percentage of populations were reproductively active and not inbred. A congeneric species P. difformis ssp. difformis that grows in the nearby vicinity was shown to be genetically distinct but some evidence of hybridisation was found suggesting that offset populations should not be located near known populations of this species to prevent further hybridisation.

How do rare Boronia species differ from their more widespread congeners

The vulnerable Boronia keysii Domin. (Rutaceae; BK) and the rare B. rivularis White. (BR), endemic to the Sunshine Coast region of Queensland, and the more widespread B. safrolifera Cheel. (BS) and B. falcifolia (BF), were studied. The taxonomic distinctiveness between the morphologically similar B. rivularis and its more southern congener B. safrolifera had previously been in question. This study clearly confirmed the long genetic separation of these two species. High levels of reproductive activity (%R) were observed in both of the threatened species (B. keysii: %R = 84; B. rivularis: %R = 66), which were also found to differ fundamentally in response to fire (obligate seed regenerators) from the more widespread species (facultative resprouters). Genetic diversity was not consistently related to rarity since B. keysii (vulnerable; He = 0.282) and B. falcifolia (common; He = 0.294) had significantly (P < 0.05) higher genetic diversity than did B. rivularis (rare; He = 0.155) and B. safrolifera (common; He = 0.197). There was no relationship between population differentiation and geographic distribution of species since B. keysii (FST = 0.293) and B. safrolifera (FST = 0.283) exhibited lower between-population diversity than did B. rivularis (FST = 0.360) and B. falcifolia (FST = 0.324). The average number of migrants per generation was less than one in all species (Nm = 0.604 for BK; 0.444 for BR; 0.634 for BS; 0.522 for BF). All four species are effectively inbred; however, B. keysii (F = 0.85) and B. falcifolia (F = 0.90) had significantly (P < 0.05) higher levels of inbreeding than did B. rivularis (F = 0.621) and B. safrolifera (F = 0.472), indicating that inbreeding was not determined by conservation status.

Ecological genetics of the wind-pollinated, tetraploid, Allocasuarina emuina L. Johnson (Casuarinaceae) from southeast Queensland reveals montane refugia for coastal heath during the last interglacial

Thesubtropical coastal heathlands of southeast Queensland contain many rareand threatened species and have undergone considerable habitat loss in recent years due to high levels of urbanisation. We used morphological and microsatellite markers to investigate the reproductive ecology, in relation to fire, and population genetic structure of the endangered shrub Allocasuarina emuina. Highly significant differences (P <0.001) were detected among populations for allcone-andseed-relatedmorphologicaltraits,whichrevealeddistinctnorthernandsoutherngroupsofpopulations,apattern repeated in the genetic component of the study. Results also indicated that the reproductive viability of A. emuina is more related to fire interval than population size and confirmed that seed viability declines with time since fire. The highest level of genetic diversity for the species was observed in the population on Mt Emu (AE4A; HE=0.688). Contrary to the expectations of population genetic theory, no relationship was found between the level of genetic variation and population size, density or degree of isolation, hinting that genetic diversity is being conserved as a result of polyploidy and apomixis. However, genetic signatures in the northern populations indicated that unidirectional dispersal of genetic material from the putatively refugial population on Mt Emu to the surrounding coastal plain has been occurring with recession of sea levels following the last interglacial. The findings of the study will aid in both the conservation of natural populations and translocations of A. emuina and have significant implications relating to the biogeographical history of a considerable number of co-occurring heathland taxa.

Genetics and species distribution modelling of Solanum johnsonianum (Solanaceae) reveal impacts of brigalow land clearing on this endemic species

Australia is one of the centres of diversity for Solanum and many species are found in the arid zone with a concentration in the Brigalow belt. This region has been significantly impacted by land clearing and Brigalow is now an endangered vegetation type. Recent gas pipeline developments have led to further impacts to endangered species within the region necessitating offset and translocation activities. Solanum johnsonianum was impacted by pipeline construction despite little knowledge of its ecology or genetics to guide translocation or restoration. This study conducted field surveys, habitat modelling, and genetic analysis in order to increase understanding of S. johnsonianum. The species has moderate to low genetic diversity across its localised geographic range. The populations are not inbred, with some exhibiting heterozygote excess. The populations that are located close to the pipeline were among those with the highest genetic diversity. Population size varies among populations and was not correlated with genetic diversity. Evidence of clonal spread was found in most populations however they also produce viable seeds and most plants are productively active. The results indicate that care should be taken to maintain provenance and that it is recommended to follow guidelines which limit mixing of plants from different populations.

A genetic, demographic and habitat evaluation of an endangered ephemeral species Xerothamnella herbacea from Australia’s Brigalow belt

Little remains of the Brigalow (Acacia harpophylla F.Muell. ex Benth.) woodlands of Australia, primarily due to land clearing for grazing and agriculture. Many threatened species in this region are poorly studied, and the life history traits of some herbaceous species such as ephemeral shoot systems, mean that conservation assessments are difficult. Recent gas pipeline developments have led to an increased need to understand the ecology and genetics of such taxa, in order to advise offset and translocation activities. Xerothamnella herbacea R.Baker is an endangered ephemeral herbaceous species from the Brigalow Belt region, which dies back during prolonged dry conditions. The aim of this study was to map the extent of potentially suitable habitat of this species, including determination of population extent within existing protected area estate. The species population sizes, reproductive activity and evidence of clonal spread, as well as the levels of genetic diversity and inbreeding, across the species range were also assessed to provide guidance for potential translocation and offsetting programs. The genetic results were related to the species suitable habitat distribution to test whether historic or recent habitat fragmentation most explains genetic patterns in this species. Most of the populations of this species were found to be small with less than 100 plants. The species appears not to be limited by its reproductive output, suggesting other factors may limit its abundance. The species populations have moderate to low genetic diversity suggesting the species is genetically viable in the medium term but are inbred which may be partially due to vegetative spread. Geographic proximity does not predict genetic similarity of populations and diversity is not correlated with population size. The results indicate potential translocation or offsetting programs need to account for genetic relationships in their planning. Resprouting ability has potentially assisted the species to slow the pace of genetic diversity loss due to anthropogenic fragmentation.

Conservation genetics and demographic analysis of the endangered cycad species Cycas megacarpa and the impacts of past habitat fragmentation

The limited seed dispersal range of cycads, longevity of individuals, including a long juvenile phase, coupled with dioecy, suggest that the impacts of habitat fragmentation are not straightforward. Cycas megacarpa K.D. Hill. is an endangered cycad that occurs in a highly fragmented landscape derived from past agricultural land clearing. Current threats continue to be land clearing for both urban and rural developments and major infrastructure development for coal seam gas. This study investigated the effect fragmentation has had on C. megacarpa populations across its entire range. Twelve microsatellite loci were developed with next generation sequencing and used to analyse 992 samples from 33 populations. Geographic information system (GIS) analysis of the total reduction in suitable regional ecosystem (RE) habitat in Queensland revealed a 69% loss between 1960s pre-clearing records and 2009 with only 29% of remaining habitat occurring in protected areas. Populations are highly variable with many small populations, and there is evidence of possible declining recruitment of seedlings. The relatively low proportion of adult sized plants that reproduce synchronously promotes outcrossing; however, there is some evidence that reduced population sizes may lead to inbreeding. Genetic diversity is not correlated with population size but it is weakly correlated with isolation. There is evidence of considerable historic gene flow among populations and little genetic differentiation among broad geographic regions. The results show genetic clustering and are consistent with hypotheses that C. megacarpa existed as a set of metapopulations historically linked by gene flow. This has maintained diversity in small populations but suggests that fragmentation that increases population isolation has and will continue to reduce the species viability. The persistence of adult cycads through multiple generations may allow rare alleles to remain within populations over a longer period of time.