A story from the Miocene: Clock‐dated phylogeny of Sisymbrium L. (Sisymbrieae, Brassicaceae)

Abstract: Policy aimed at conserving biodiversity has focused on species diversity. Loss of genetic diversity, however, can affect population persistence, evolutionary potential, and individual fitness. Although mammals are a well‐studied taxonomic group, a comprehensive assessment of mammalian genetic diversity based on modern molecular markers is lacking. We examined published microsatellite data from populations of 108 mammalian species to evaluate background patterns of genetic variability across taxa and body masses. We tested for loss of genetic diversity at the population level by asking whether populations that experienced demographic threats exhibited lower levels of genetic diversity. We also evaluated the effect of ascertainment bias (a reduction in variability when microsatellite primers are transferred across species) on our assessment of genetic diversity. Heterozygosity did not vary with body mass across species ranging in size from shrews to whales. Differences across taxonomic groupings were noted at the highest level, between populations of marsupial and placental mammals. We documented consistently lower heterozygosity, however, in populations that had experienced demographic threats across a wide range of mammalian species. We also documented a significant (p = 0.01) reduction in heterozygosity as a result of ascertainment bias. Our results suggest that populations of both rare and common mammals are currently losing genetic diversity and that conservation efforts focused above the population level may fail to protect the breadth of persisting genetic diversity. Conservation policy makers may need to focus their efforts below the species level to stem further losses of genetic resources.

Litter decomposition is a fundamental ecosystem process and service that supplies nutrients to the soil. Although decomposition rate is influenced by litter quality, climatic conditions, the decomposer community and vegetation type in non-urban ecosystems, little is known about the degradation of different organic matter types in urban settings. We investigated the decomposition rates of recalcitrant (wood sticks for 4 years) and labile litter (green tea leaves in pyramid-shaped teabags for 3 years) in urban habitats that differed in level of management and disturbance. We found that recalcitrant woody material decomposed slower in urban habitat types (ca. 60–75% mass loss after 4 years in remnant spruce forests, park lawns, ruderal habitats) than in natural to semi-natural spruce forest soils (84% mass loss) outside the city. Labile tea litter, however, decomposed faster in typical open urban habitats (70% mass loss after 3 years in park lawns, ruderal habitats) than in forested habitats (60% mass loss in semi-natural and remnant spruce forests), with a remarkable dichotomy in decomposition rate between open and forested habitats. We suggest that the slower rate of wood decomposition in the city relates to its depauperate saprotrophic fungal community. The faster rate of labile litter decomposition in open habitats is difficult to explain, but is potentially a consequence of environmental factors that support the activity of bacteria over fungi in open habitats. We propose that the reintroduction of decaying woody material into the urban greenspace milieu could increase biodiversity and also improve the ability of urban soils to decompose an array of organic material entering the system. This reintroduction of decaying woody material could either occur by leaving cut logs – due to management – in urban remnant forests, which has been shown to be accepted as natural features by residents in Fennoscandian cities, and by placing logs in urban parks in ways that communicate their intentional use as part of urban landscape design and management.

ABSTRACTAim To assess how habitat affinities in the native distribution range influence the invasion success of 282 central European neophytes (alien plants introduced after ad 1500).Location Czech Republic.Methods Classification trees were used to determine which native habitats donate the most alien species, the correspondence between habitats occupied by species in their native and invaded distribution ranges, and invasion success of species originating from different habitats.Results The species most likely to naturalize in Central Europe are those associated with thermophile woodland fringes in their native range (81%), cultivated areas of gardens and parks (75%) and broad‐leaved deciduous woodlands (72%). The largest proportions of invasive species recruit from those that occur on riverine terraces and eroded slopes, or grow in both deciduous woodland and riverine scrub. When the relative role of habitats in the native range is assessed as a determinant of the probability that a species will become invasive in concert with other factors (the species’ residence time, life history, region of origin), the direct effect of habitat is negligible. However, the effect of native habitats on patterns of invasions observed in central Europe is manifested by large differences in the numbers of species they supply to the invaded region. More than 50 neophytes were recruited from each of the following habitats: dry grasslands, ruderal habitats, deciduous woodland, inland cliffs, rock pavements and outcrops, and tall‐herb fringes and meadows.Main conclusions Casual species recruit from a wider range of habitats in their native range than they occupy in the invaded range; naturalized but not invasive species inhabit a comparable spectrum of habitats in both ranges, and successful invaders occupy a wider range of habitats in the invaded than in the native range. This supports the idea that the invasive phase of the process is associated with changes in biological features that allow for extension of the spectrum of habitats invaded.

Assessing the genetic diversity of twenty one Colombo limon L. genotypes through multivariate and covariance matrix analysis

Cardiospermum grandiflorum

Suratman, Ari Pitoyo, Sri Mulyani, Suranto. 2015. Assessment of genetic diversity among soursop (Annona muricata)populations from Java, Indonesia using RAPD markers. Biodiversitas 16: 247-253. The objective of this study was to determine geneticdiversity of the soursop (Annona muricata L.) populations from Java (Indonesia) using RAPD markers. A total of 70 individuals werecollected from 7 soursop populations, distributed along the geographical range of natural distribution in Java. Genetic diversity wasestimated by RAPD technique using 6 arbitrary selected primers. Those primers produced 151 polymorphic bands with the percentageof polymorphism for each primer ranged from 95% to 100%. The genetic diversity value (h) within each population ranged from 0.0418to 0.0525. The highest h value (0.0525) was found in the KRA population whereas the lowest h value was observed in the PCTpopulation. The highest genetic distance value (0.0410) was observed in SKH-GKD populations pair whereas the lowest geneticdistance value (0.02448) was estimated in KRA-PCT populations pair. Based on the dendogram, the seven soursop populations weresegregated into three major clusters. The first cluster consisted of SKH, KRA, PCT, NGW, and KPG populations. The GKD populationwas then grouped into second cluster. In the third cluster, the BGR population was grouped separately and more genetically distant thanthe others. However, the relationship dendrogram showed that the grouping did not always indicate the geographical origins similarity,but possibly showed the genetic similarity.

The taxonomy of the yeast genus Metschnikowia has undergone profound changes over the past century. Major developments, from the capacity to obtain pure cultures of parasitic species to progress associated with the extensive use of molecular biology tools in yeast systematics, are briefly reviewed. Results from past work and new data are combined to evaluate evolutionary relationships and clarify the classification of both terrestrial and aquatic species. Recent physiological studies, including the utilization of non-conventional carbon and nitrogen sources, and characteristics like lipolytic activity and maximum temperatures for growth, are presented. The assessment of the genetic diversity within the genus by restriction analysis of the mitochondrial DNA and by the production of specific DNA probes has been explored. The results indicate the potential application of the latter in rapid identification procedures.

Japanese Black cattle are at risk for genetic homogeneity due to intensive use of a few sires. Therefore, assessment of the actual genetic diversity of this breed is important for future breeding plans. In the present study, we investigated the genetic diversity within and among eight subpopulations of Japanese Black cattle using 52 microsatellite markers. The parameters for genetic diversity of Japanese Black cattle were comparable to those of other cattle breeds, suggesting that the relatively high genetic diversity of the breed. However, upon comparison among the eight subpopulations, the Hyogo subpopulation showed markedly low genetic diversity. The results of the pairwise FST values, phylogenetic network and structure analysis indicated that the Hyogo population has remarkably high level of genetic differentiation from other populations, while Yamagata, Niigata, Hiroshima and Kagawa populations have low levels of genetic differentiation. Furthermore, multidimensional scaling plots indicated that individuals in some subpopulations were separated from individuals in the other subpopulations. We conclude that while the overall genetic diversity of Japanese Black cattle is still maintained at a relatively high level, that of a particular subpopulation is significantly reduced, and therefore the effective population size of the breed needs to be controlled by correct mating strategies.

BackgroundThe influence of introduction history and post-introduction dynamics on genetic diversity and structure has been a major research focus in invasion biology. However, genetic diversity and structure in the invasive range can also be affected by human-mediated processes in the native range prior to species introductions, an aspect often neglected in invasion biology. Here we aim to trace the native provenance of the invasive tree Acacia pycnantha by comparing the genetic diversity and structure between populations in the native Australian range and the invasive range in South Africa. This approach also allowed us to explore how human actions altered genetic structure before and after the introduction of A. pycnantha into South Africa. We hypothesized that extensive movement and replanting in A. pycnantha’s Australian range prior to its introduction to South Africa might result in highly admixed genotypes in the introduced range, comparable genetic diversity in both ranges, and therefore preclude an accurate determination of native provenance(s) of invasive populations.ResultsIn the native range Bayesian assignment tests identified three genetic clusters with substantial admixture and could not clearly differentiate previously identified genetic entities, corroborating admixture as a result of replantings within Australia. Assignment tests that included invasive populations from South Africa indicated similar levels of admixture compared to Australian populations and a lack of genetic structure. Invasive populations of A. pycnantha in South Africa are as genetically diverse as native populations, and could not be assigned to particular native range regions.ConclusionsOur results indicate that the genetic structure of A. pycnantha in Australia has been greatly altered through various planting initiatives. Specifically, there is little geographic structure and high levels of admixture. While numerous introduction history scenarios may explain the levels of admixture observed in South Africa, planting records of A. pycnantha in Australia suggest that populations were probably already admixed before propagules were introduced to South Africa. These findings have important implications for the management of invasive A. pycnantha populations in South Africa, especially for classical biological control, and more broadly, for studies that aim to understand the evolutionary dynamics of the invasion process.

Eryngium maritimum L. is a wild plant species threatened or endangered in most of Northern Europe, where species is on the northern margin of its distribution range. Recent studies have found reduction of size and even extinction of many populations. Assessment of genetic diversity in natural populations of endangered wild plant species can reflect condition and fitness of particular population and inform decisions on appropriate conservation measures. Application of inter simple sequence repeat markers and chloroplast DNA sequencing could not resolve genetic relationship between E. maritimum populations in Northern Europe. Therefore, the more sensitive retrotransposon-sequence-specific amplification polymorphism (SSAP) molecular marker system was developed. Six Ty1-copia long terminal repeat retrotransposons were isolated from E. maritimum genome (Tem1–Tem6) and assessed for their utility as molecular markers in this species. Two retrotransposons – Tem2 and Tem5 – were recognized as most informative based on the level of polymorphism and SSAP banding pattern quality. On average, 20.4% of SSAP bands were polymorphic for the five most informative primer combinations in a set of 150 Northern European E. maritimum plants from 13 locations, providing a useful tool for assessment of genetic diversity in this endangered species.

Meyer’s Parrot Poicephalus meyeri has the widest distributional range of any African parrot. There are six subspecies distributed throughout the African subtropics, all of which manage to breed successfully during the winter dry season when few other cavity-nesting birds are actively nesting. In 2004, we recorded Meyer’s Parrots feeding on four cryptic arthropod larvae incubating inside fruits and pods in their seasonal diet. All of these were previously unknown in the diet of African parrots. Nesting females and chicks were fed regurgitate almost exclusively comprising these arthropod larvae for the first 10 weeks after nest occupation. In 2007, we demonstrated that Meyer’s Parrots actively search for these protein-rich arthropod larvae and synchronized their breeding effort within our study area to coincide their hatching period with the period of highest relative abundance of these larvae, resulting in a breeding synchrony index value of 79.3 % between females in the population. In 2009, we recorded the consumption of similar arthropod larvae parasitizing similar tree species in northern Zambia and two locations in Tanzania, thus confirming this behaviour throughout their distributional range. Similar behaviour is expected in their closest congeners, the Brown-headed Parrot P. cryptoxanthus and Ruppell’s Parrot P. rueppellii. Poor land management practices (e.g. deforestation and frequent fires) most likely influence the abundance of these cryptic arthropod larvae and thus the breeding success of Meyer’s Parrot at population level.

The assessment of genetic diversity is essential for the conservation and breeding purposes. This study aimed to assess and evaluate the genetic diversity of 116 accessions of mango (Mangifera indica) germplasm using microsatellite markers. The DNA was extracted from young fresh leaf before genotyping using microsatellites to determine the allele size. The analysis of 20 polymorphic microsatellite markers revealed a total of 122 alleles ranging from two (MiIIHR10, MiIIHR21, and MiIIHR25) to 11 alleles per locus (MiIIHR28 and MiIIHR30) with an average of 6.1. The mean polymorphic information content (PIC) value was 0.4585 which ranged between 0.0081 (MiIIHR10) to 0.9573 (MiIIHR28). The UPGMA dendrogram indicated that the accessions were divided into two major clusters, which were divided into several sub-clusters based on their genetic distance matrix values. Some accessions were highly similar to each other, probably due to the duplication of collected accessions or insufficient microsatellite markers to differentiate them. The analysis of the population structure of the individuals also showed two subpopulations, suggesting that the accessions could be separated into two groups, which supported the generated dendrogram. The findings of this study facilitate improved conservation management of the germplasm and help to find strategies for future breeding activities.

Sunflower (Helianthus annuus L.) is one of the most important oilseed crops grown worldwide because of its supreme oil quality and commercial importance. Assessment of diversity among inbreds is a vital prerequisite to select parents for a hybridization programme. Hence, in the present investigation, the genetic divergence of 29 genotypes consisting of both maintainer and restorer inbreds was studied using Mahalanobis (D2) analysis. Genotypes were grouped into eight clusters, in which cluster I was the largest with 13 genotypes. Clusters IV, VI, VII and VIII were the smallest, with one genotype each. The maximum intracluster distance was observed in cluster I followed by II. Maximum inter cluster distance was recorded between clusters II and V followed by clusters II and VII. Days to 50% flowering had the maximum contribution (32.76%) for genetic divergence. Superior mean performance for head diameter, 100 - seed weight, seed yield per plant and oil content was observed in cluster VI whereas earliness in terms of days to 50% flowering and days to maturity was observed in cluster II. Cluster VIII recorded superior mean performance for volume weight and the lowest mean plant height was observed in cluster VII. Hence, hybridization between cluster II (CMS 10B, HA 89B, RHA-1-1) and cluster V (CMS 519B, HA 430B) could create more variability in the segregating generations. Key words: Sunflower, genetic diversity, inbreds, maintainer, restorer.

Lichia amia is an important coastal recreational fishery species with a cosmopolitan distribution in the eastern Atlantic. In southern Africa, it is distributed from southern Angola to northern KwaZulu-Natal in South Africa. A recent biological survey revealed differences between Angolan and South African individuals suggesting that they may represent separate stocks. As fishery management decisions should be based on accurate knowledge of population structure, an initial survey of the genetic substructuring of L. amia was conducted on samples collected in southern Angola and South Africa. Assessment of genetic diversity and population structure was conducted using a fragment of the mitochondrial Control Region. Obtained genetic diversity levels were within the expected range for marine teleosts (h = 0.867, π = 0.007), and two deeply divergent (southern Angolan and South African) populations were identified (average φ ST = 0.78) across the Benguela Current system. These results suggest that Angolan and South African L. amia should be managed as two independent stocks. This work represents the first assessment of population genetic substructuring across the Benguela Current of a valuable coastal fishery resource, and has application for future fisheries management.

Bluetongue (BT), a viral disease of ruminants, is endemic throughout South Africa, where outbreaks of different serotypes occur. The predominant serotypes can differ annually due to herd immunity provided by annual vaccinations using a live attenuated vaccine (LAV). This has led to both wild-type and vaccine strains co-circulating in the field, potentially leading to novel viral strains due to reassortment and recombination. Little is known about the molecular evolution of the virus in the field in South Africa. The purpose of this study was to investigate the genetic diversity of field strains of BTV in South Africa and to provide an initial assessment of the evolutionary processes shaping BTV genetic diversity in the field. Complete genomes of 35 field viruses belonging to 11 serotypes, collected from different regions of the country between 2011 and 2017, were sequenced. The sequences were phylogenetically analysed in relation to all the BTV sequences available from GenBank, including the LAVs and reference strains, resulting in the analyses and reassortment detection of 305 BTVs. Phylogenomic analysis indicated a geographical selection of the genome segments, irrespective of the serotype. Based on the initial assessment of the current genomic clades that circulate in South Africa, the selection for specific clades is prevalent in directing genome segment reassortment, which seems to exclude the vaccine strains and in multiple cases involves Segment-2 resulting in antigenic shift.