Comparative phylogeographic summary statistics for testing simultaneous vicariance

Testing for simultaneous vicariance across comparative phylogeographic data sets is a notoriously difficult problem hindered by mutational variance, the coalescent variance, and variability across pairs of sister taxa in parameters that affect genetic divergence. We simulate vicariance to characterize the behaviour of several commonly used summary statistics across a range of divergence times, and to characterize this behaviour in comparative phylogeographic datasets having multiple taxon-pairs. We found Tajima's D to be relatively uncorrelated with other summary statistics across divergence times, and using simple hypothesis testing of simultaneous vicariance given variable population sizes, we counter-intuitively found that the variance across taxon pairs in Nei and Li's net nucleotide divergence (pi(net)), a common measure of population divergence, is often inferior to using the variance in Tajima's D across taxon pairs as a test statistic to distinguish ancient simultaneous vicariance from variable vicariance histories. The opposite and more intuitive pattern is found for testing more recent simultaneous vicariance, and overall we found that depending on the timing of vicariance, one of these two test statistics can achieve high statistical power for rejecting simultaneous vicariance, given a reasonable number of intron loci (> 5 loci, 400 bp) and a range of conditions. These results suggest that components of these two composite summary statistics should be used in future simulation-based methods which can simultaneously use a pool of summary statistics to test comparative the phylogeographic hypotheses we consider here.

Diversity in the sunflower: Puccinia helianthi pathosystem in Australia

Sunflower rust caused by Puccinia helianthi is the most important disease of sunflower in Australia with the potential to cause significant yield losses in susceptible hybrids. Rapid and frequent virulence changes in the rust fungus population limit the effective lifespan of commercial cultivars and impose constant pressure on breeding programs to identify and deploy new sources of resistance. This paper contains a synopsis of virulence data accumulated over 25 years, and more recent studies of genotypic diversity and sexual recombination. We have used this synopsis, generated from both published and unpublished data, to propose the origin, evolution and distribution of new pathotypes of P. helianthi. Virulence surveys revealed that diverse pathotypes of P. helianthi evolve in wild sunflower populations, most likely because sexual recombination and subsequent selection of recombinant pathotypes occurs there. Wild sunflower populations provide a continuum of genetically heterogeneous hosts on which P. helianthi can potentially complete its sexual cycle under suitable environmental conditions. Population genetics analysis of a worldwide collection of P. helianthi indicated that Australian isolates of the pathogen are more diverse than non-Australian isolates. Additionally, the presence of the same pathotype in different genotypic backgrounds supported evidence from virulence data that sexual recombination has occurred in the Australian population of P. helianthi at some time. A primary aim of the work described was to apply our knowledge of pathotype evolution to improve resistance in sunflower to sunflower rust. Molecular markers were identified for a number of previously uncharacterised sunflower rust R-genes. These markers have been used to detect resistance genes in breeding lines and wild sunflower germplasm. A number of virulence loci that do not recombine were identified in P. helianthi. The resistance gene combinations corresponding to these virulence loci are currently being introgressed with breeding lines to generate hybrids with durable resistance to sunflower rust.

Reduced genetic diversity and significant genetic differentiation after translocation: Comparison of the remnant and translocated populations of bridled nailtail wallabies (Onychogalea fraenata)

Loss of genetic diversity and increased population differentiation from source populations are common problems associated with translocation programmes established from captive-bred stock or a small number of founders. The bridled nailtail wallaby is one of the most endangered macropods in Australia, having been reduced to a single remnant population in the last 100 years. A translocated population of bridled nailtail wallabies was established using animals sourced directly from the remnant population (wild-released) as well as the progeny of animals collected for a captive breeding programme (captive-bred). The aims of this study were to compare genetic diversity among released animals and their wild-born progeny to genetic diversity observed in the remnant population, and to monitor changes in genetic diversity over time as more animals were released into the population. Heterozygosity did not differ between the translocated and remnant population; however, allelic diversity was significantly reduced across all released animals and their wild-born progeny. Animals bred in captivity and their wild-born progeny were also significantly differentiated from the source population after just four generations. Wild-released animals, however, were representative of the source population and several alleles were unique to this group. Both heterozygosity and allelic diversity among translocated animals decreased over time with the additional release of captive-bred animals, as no new genetic stock was added to the population. Captive breeding programmes can provide large numbers of animals for release, but this study highlights the importance of sourcing animals directly from remnant populations in order to maintain genetic diversity and minimise genetic drift.

What is a gene today?

Historians of genetics agree that multiple conceptions of the gene have coexisted at each stages in the history of genetics and that the resulting partial ambiguity has often contributed to the success of genetics, both because workers in different areas have needed to communicate and to draw on one another’s results despite wrestled with very different scientific challenges, and because empirical findings have often challenged the presuppositions of existing conceptions of the gene. Today, a number of different conceptions of the gene coexist in the biosciences. An ‘instrumental’ gene similar to that of classical genetics retains a critical role in the construction and interpretation of experiments in which the relationship between genotype and phenotype is explored via hybridization between organisms or directly between nucleic acid molecules. It also plays an important theoretical role in the foundations of disciplines such as quantitative genetics and population genetics. A ‘nominal’ gene, defined by the practice of genetic nomenclature, is a critical practical tool and allows communication between bioscientists in a wide range of fields to be grounded in welldefined sequences of nucleotides. This concept, however, does not embody major theoretical insights into genome structure or function. Instead, a ‘post-genomic’ conception of the gene embodies the continuing project of understanding how genome structure supports genome function, but with a deflationary picture of the gene as a structural unit. This final concept of the gene poses a significant challenge to earlier assumptions about the relationship between genome structure and function, and between genotype and phenotype.

Impression of the global climate change on the ornamental plant usage in Hungary

The climate modeling, which has adequate spatial and temporal resolution, shows that the future climate of the Carpathian Basin will be much more arid and hot than nowadays. The currently used and taught assortment of the ligneous ornamental plants should be urgently revised. It is aimed in my research to collect the species which will probably be introduced in the future. They can be gathered from the Hungarian botanical gardens and research centers and from the spatially analogous territories. The collected taxa should be examined with GIS software if they will really suffer our future climate.

The effect of climate change on the potential distribution of the European Phlebotomus species

Our study intended to explore the potential distributionshif of Phlebotomusariasi, P. neglectus, P. perfiliewi, P. perniciosus, and P. tobbi, and some other sandfly species: P. papatasi, P. sergenti, and P. similis. We used climate envelope modeling (CEM) method to determine the ecological requirements of the species and to model the potential distribution for three periods (1961-1990, 2011-2040, and 2041- 2070). We found that by the end of the 2060’s the Southern UK, Germany, entire France and also the western part of Poland can be colonized by sandfly species, mostly by P. ariasi and P. pernicosus. P. ariasishowe the greatest potential northward expansion, from 49°N to 59°N. For all of the studied sand fly species the entire Mediterranean Basin, the Balkan Peninsula, the Carpathian Basin, and northern coastline of the Black Sea are potentially suitable. The length of the predicted active period of the vectors will increase with one or two months.

Regional climate change impacts on wild animals' living territory in Central Europe

In this paper the projected future impact of climate change has been analyzed for the quality of living conditions of the European terrestrial vertebrates (amphibians, reptiles, birds, mammals) in the Carpathian Basin. According to the climate scenarios, warmer and drier climatic conditions are likely to occur in the Carpathian Basin by end of this century. Simultaneous analysis of climate parameters, climate simulations and animal range datasets enables us to evaluate the vulnerability of different European species to regional warming and climate change. The spatial climate analogy technique is used to analyze the estimated rapid change of the wild animals’ habitats and their northward migration. For the reference climate data of Debrecen is considered, and three spatial analogue regions are compared. The results suggest that generally a significant decline in habitats is very likely for most of the analyzed animal groups by the end of the 21st century. The largest rate of decline is estimated for birds. However, living conditions for reptiles may improve in the future due to the warmer and drier climatic conditions, which are favourable for these species.

Impact of climate change on the potential distribution of Mediterranean pines

The impact of climate change on the potential distribution of four Mediterranean pine species – Pinus brutia Ten., Pinus halepensis Mill., Pinus pinaster Aiton, and Pinus pinea L. – was studied by the Climate Envelope Model (CEM) to examine whether these species are suitable for the use as ornamental plants without frost protection in the Carpathian Basin. The model was supported by EUFORGEN digital area database (distribution maps), ESRI ArcGIS 10 software’s Spatial Analyst module (modeling environment), PAST (calibration of the model with statistical method), and REMO regional climate model (climatic data). The climate data were available in a 25 km resolution grid for the reference period (1961–1990) and two future periods (2011–2040, 2041–2070). The regional climate model was based on the IPCC SRES A1B scenario. While the potential distribution of P. brutia was not predicted to expand remarkably, an explicit shift of the distribution of the other three species was shown. Northwestern African distribution segments seem to become abandoned in the future. Current distribution of P. brutia may be highly endangered by the climate change. P. halepensis in the southern part and P. pinaster in the western part of the Carpathian Basin may find suitable climatic conditions in the period of 2041–2070.

Ornamental plants as climatic indicators of arthropod vectors

The importance and risk of vector-borne diseases (eg. leishmaniasis, West Nile Virus, Lyme borreliosis) is going to increase in the European temperate areas due to climate change. Our previous studies have shown that the potential distribution of Leishmania infantum and some Phlebotomus (sand fly) species – a parasite of leishmaniasis, and its vectors – may be expanded even to the southern coastline of the Baltic Sea by the end of the 21st century. The lowland areas of the Carpathian Basin and the main part of Hungary are projected to be suitable for the studied sand fly vectors in the near future. It is important to find some indicator plants to examine whether the sand flies are able to live in a certain climate at a certain time. We studied several Mediterranean and Sub-Mediterranean plant species, and we found that the aggregated distribution of three ligneous species (Juniperus oxycedrus L., Quercus ilex L. and Pinus brutia Ten.) shows high correlation with the union distribution of five sand flies (Phlebotomus ariasi Tonn., Ph. neglectus Tonn., Ph. perfiliewi Parrot, Ph. perniciosus Newst. and Ph. tobbi Adler, Theodor et Lourie). Since these Mediterranean species are highly tolerant of the edaphic characteristics of the planting site, they may prove to be good indicators. The present and upcoming climate of Hungary is seen to be suitable for the selected indicator plant species, and it draws attention to and verifies the potential of the expansion of sand flies, which has been proved by some recent observations of the vectors in Southern Hungary.

Ornamental plants as climatic indicators of arthropod vectors

The importance and risk of vector-borne diseases (e.g., leishmaniasis, West Nile Virus, Lyme borreliosis) is going to increase in the European temperate areas due to climate change. Our previous studies have shown that the potential distribution of Leishmania infantum and some Phlebotomus (sand fly) species – a parasite of leishmaniasis, and its vectors – may be expanded even to the southern coastline of the Baltic Sea by the end of the 21st century. The lowland areas of the Carpathian Basin and the main part of Hungary are projected to be suitable for the studied sand fly vectors in the near future. It is important to find some indicator plants to examine whether the sand flies are able to live in a certain climate at a certain time. We studied several Mediterranean and Sub-Mediterranean plant species, and we found that the aggregated distribution of three ligneous species (Juniperus oxycedrus L., Quercus ilex L. and Pinus brutia Ten.) shows high correlation with the union distribution of five sand flies (Phlebotomus ariasi Tonn., Ph. neglectus Tonn., Ph. perfiliewi Parrot, Ph. perniciosus Newst. and Ph. tobbi Adler, Theodor et Lourie). Since these Mediterranean species are highly tolerant of the edaphic characteristics of the planting site, they may prove to be good indicators. The present and upcoming climate of Hungary is seen to be suitable for the selected indicator plant species, and it draws attention to and verifies the potential of the expansion of sand flies, which has been proved by some recent observations of the vectors in Southern Hungary.

Potential urban distribution of Phlebotomus mascittii Grassi and Phlebotomus neglectus Tonn. (Diptera: Psychodidae) in 2021–50 in Budapest, Hungary

Background & Objective: The most northern populations of two sand fly species (Phlebotomus mascittii and Phlebotomus neclectus) in the Carpathian Basin are known from Central Hungary. The most important limiting factor of the distribution of Phlebotomus species in the region is the annual minimum temperature which may be positively affected by the urban heat island and the climate change in the future. Method: Based on the latest case reports of the species, Climate Envelope Model was done for the period 1961-1990 and 2025-2050 to project the potential urban distribution of the species. The climatic data were obtained from RegCM regional climate model and MODIS satellite images. Results: The recent occurrence of the species in Central Hungary indicates that Phlebotomus species can overwinter in non-heated shelters in the built environment. Interpretation & Conclusion: Jointly heat island and future climate change seem to be able to provide suitable environment for the studied species in urban areas in a great extent.

Are mangroves in the tropical Atlantic ripe for invasion? Exotic mangrove trees in the forests of South Florida

Abstract Two species of mangrove trees of Indo- Pacific origin have naturalized in tropical Atlantic mangrove forests in South Florida after they were planted and nurtured in botanic gardens. Two Bruguiera gymnorrhiza trees that were planted in the intertidal zone in 1940 have given rise to a population of at least 86 trees growing interspersed with native mangrove species Rhizophora mangle, Avicennia germinans and Laguncularia racemosa along 100 m of shoreline; the population is expanding at a rate of 5.6% year-1. Molecular genetic analyses confirm very low genetic diversity, as expected from a population founded by two individuals. The maximumnumber of alleles at any locus was three, and we measured reduced heterozygosity compared to native-range populations. Lumnitzera racemosa was introduced multiple times during the 1960s and 1970s, it has spread rapidly into a forest composed of native R. mangle, A. germinans, Laguncularia racemosa and Conocarpus erectus and now occupies 60,500 m2 of mangrove forest with stem densities of 24,735 ha-1. We estimate the population growth rate of Lumnitzera racemosa to be between 17 and 23% year-1. Populations of both species of naturalized mangroves are dominated by young individuals. Given the long life and water-dispersed nature of propagules of the two exotic species, it is likely that they have spread beyond our survey area. We argue that the species-depauperate nature of tropical Atlantic mangrove forests and close taxonomic relatives in the more species-rich Indo-Pacific region result in the susceptibility of tropical Atlantic mangrove forests to invasion by Indo-Pacific mangrove species.

Are mangroves in the tropical Atlantic ripe for invasion? Exotic mangrove trees in the forests of South Florida

Two species of mangrove trees of Indo- Pacific origin have naturalized in tropical Atlantic mangrove forests in South Florida after they were planted and nurtured in botanic gardens. Two Bruguiera gymnorrhiza trees that were planted in the intertidal zone in 1940 have given rise to a population of at least 86 trees growing interspersed with native mangrove species Rhizophora mangle, Avicennia germinans and Laguncularia racemosa along 100 m of shoreline; the population is expanding at a rate of 5.6% year-1. Molecular genetic analyses confirm very low genetic diversity, as expected from a population founded by two individuals. The maximumnumber of alleles at any locus was three, and we measured reduced heterozygosity compared to native-range populations. Lumnitzera racemosa was introduced multiple times during the 1960s and 1970s, it has spread rapidly into a forest composed of native R. mangle, A. germinans, Laguncularia racemosa and Conocarpus erectus and now occupies 60,500 m2 of mangrove forest with stem densities of 24,735 ha-1. We estimate the population growth rate of Lumnitzera racemosa to be between 17 and 23% year-1. Populations of both species of naturalized mangroves are dominated by young individuals. Given the long life and water-dispersed nature of propagules of the two exotic species, it is likely that they have spread beyond our survey area. We argue that the species-depauperate nature of tropical Atlantic mangrove forests and close taxonomic relatives in the more species-rich Indo-Pacific region result in the susceptibility of tropical Atlantic mangrove forests to invasion by Indo-Pacific mangrove species.

(Table 1) Individual codes, haplotype codes, GenBank accession numbers for DNA sequences and sample locality of the analysed Betamorpha fusiformis specimens from the ANDEEP III expedition

Based on our current knowledge about population genetics, phylogeography and speciation, we begin to understand that the deep sea harbours more species than suggested in the past. Deep-sea soft-sediment environment in particular hosts a diverse and highly endemic invertebrate fauna. Very little is known about evolutionary processes that generate this remarkable species richness, the genetic variability and spatial distribution of deep-sea animals. In this study, phylogeographic patterns and the genetic variability among eight populations of the abundant and widespread deep-sea isopod morphospecies Betamorpha fusiformis [Barnard, K.H., 1920. Contributions to the crustacean fauna of South Africa. 6. Further additions to the list of marine isopods. Annals of the South African Museum 17, 319-438] were examined. A fragment of the mitochondrial 16S rRNA gene of 50 specimens and the complete nuclear 18S rRNA gene of 7 specimens were sequenced. The molecular data reveal high levels of genetic variability of both genes between populations, giving evidence for distinct monophyletic groups of haplotypes with average p-distances ranging from 0.0470 to 0.1440 (d-distances: 0.0592-0.2850) of the 16S rDNA, and 18S rDNA p-distances ranging between 0.0032 and 0.0174 (d-distances: 0.0033-0.0195). Intermediate values are absent. Our results show that widely distributed benthic deep-sea organisms of a homogeneous phenotype can be differentiated into genetically highly divergent populations. Sympatry of some genotypes indicates the existence of cryptic speciation. Flocks of closely related but genetically distinct species probably exist in other widespread benthic deep-sea asellotes and other Peracarida. Based on existing data we hypothesize that many widespread morphospecies are complexes of cryptic biological species (patchwork hypothesis).