Inferring the late Quaternary phylogeography of Pseudopanax crassifolius using microsatellite analysis

<p>Geologic processes have shaped the New Zealand archipelago throughout its existence. The last major geologic event was the Pleistocene glaciations beginning around 2.5 million years ago. This cold period left its mark in the phylogeography (the geographic distribution of genetic variation) of New Zealand’s globally significant biota. Studies into the phylogeography of New Zealand have largely focused on species with limited distributions through rarity or ecological preferences. This study focuses on the ubiquitous species Pseudopanax crassifolius (Sol. Ex A. Cunn) K. Koch, also known commonly as Horoeka or Lancewood. This species is widespread and almost continuously distributed throughout New Zealand giving a broad scale look at the patterns and processes that have influenced the formation of New Zealand’s natural history. Seven microsatellite loci and two rps4 chloroplast haplotypes were utilised to study 247 Pseudopanax crassifolius and nine P. chathamicus individuals sampled from populations from around New Zealand. Pseudopanax crassifolius was found to have levels of genetic diversity and overall differentiation consistent with common widespread trees. The genetic structuring suggests P. crassifolius is not a single homogenous population across a southern cluster. The geographic structuring of genetic variation within these clusters is poor. The genetic patterns and the spatial distribution of these patterns may reflect the response of Pseudopanax crassifolius to changing environmental conditions during the late Quaternary following the maximum extent of the last glacial maximum (LGM) period. During the maximally cold periods of the LGM, P. crassifolius is likely to have been eliminated or at least greatly reduced in the south and west coast of the South Island. In the remainder of the South Island and throughout the North Island it remained widespread. The heterogeneous pattern of genetic variation with little geographic correlation in the northern cluster may reflect either the extent of the historic distribution of the species or the effect of gene flow between populations acting to inhibit population structuring from establishing. The reduction in genetic diversity and the homogeneity of structure in the south indicate a pattern of leading edge re-colonisation into southern areas as conditions became more favourable following the LGM. The leading edge mode is supported by asymmetric introgression of rps4 haplotype seen between P. crassifolius and P. ferox along the east coast of the South Island. This study also investigated levels of differentiation between Pseudopanax crassifolius and P. chathamicus. There is limited evidence of differentiation based on microsatellite markers. There is therefore no strong genetic evidence for either the support or rejection of the current species delimitation of the crassifolius group of Pseudopanax species. The two species are morphologically different and geographically isolated. This, alongside evidence from previous studies suggest that P. chathamicus is possibly an example of a group undergoing incipient allopatric speciation. A recent founder event is proposed with enough potential diversity carried in two individual fruit to account for the diversity seen in P. chathamicus.</p>

Inferring the late Quaternary phylogeography of Pseudopanax crassifolius using microsatellite analysis

<p>Geologic processes have shaped the New Zealand archipelago throughout its existence. The last major geologic event was the Pleistocene glaciations beginning around 2.5 million years ago. This cold period left its mark in the phylogeography (the geographic distribution of genetic variation) of New Zealand’s globally significant biota. Studies into the phylogeography of New Zealand have largely focused on species with limited distributions through rarity or ecological preferences. This study focuses on the ubiquitous species Pseudopanax crassifolius (Sol. Ex A. Cunn) K. Koch, also known commonly as Horoeka or Lancewood. This species is widespread and almost continuously distributed throughout New Zealand giving a broad scale look at the patterns and processes that have influenced the formation of New Zealand’s natural history. Seven microsatellite loci and two rps4 chloroplast haplotypes were utilised to study 247 Pseudopanax crassifolius and nine P. chathamicus individuals sampled from populations from around New Zealand. Pseudopanax crassifolius was found to have levels of genetic diversity and overall differentiation consistent with common widespread trees. The genetic structuring suggests P. crassifolius is not a single homogenous population across a southern cluster. The geographic structuring of genetic variation within these clusters is poor. The genetic patterns and the spatial distribution of these patterns may reflect the response of Pseudopanax crassifolius to changing environmental conditions during the late Quaternary following the maximum extent of the last glacial maximum (LGM) period. During the maximally cold periods of the LGM, P. crassifolius is likely to have been eliminated or at least greatly reduced in the south and west coast of the South Island. In the remainder of the South Island and throughout the North Island it remained widespread. The heterogeneous pattern of genetic variation with little geographic correlation in the northern cluster may reflect either the extent of the historic distribution of the species or the effect of gene flow between populations acting to inhibit population structuring from establishing. The reduction in genetic diversity and the homogeneity of structure in the south indicate a pattern of leading edge re-colonisation into southern areas as conditions became more favourable following the LGM. The leading edge mode is supported by asymmetric introgression of rps4 haplotype seen between P. crassifolius and P. ferox along the east coast of the South Island. This study also investigated levels of differentiation between Pseudopanax crassifolius and P. chathamicus. There is limited evidence of differentiation based on microsatellite markers. There is therefore no strong genetic evidence for either the support or rejection of the current species delimitation of the crassifolius group of Pseudopanax species. The two species are morphologically different and geographically isolated. This, alongside evidence from previous studies suggest that P. chathamicus is possibly an example of a group undergoing incipient allopatric speciation. A recent founder event is proposed with enough potential diversity carried in two individual fruit to account for the diversity seen in P. chathamicus.</p>

Analysis of Latvian and Belarusian Oak (Quercus robur L.) Population Provenance and Genetic Structure Using Chloroplast Markers

In this study, oak specific chloroplast simple sequence repeat (SSR) markers were used to analyse Latvian and Belarusian oak (Quercus robur L.) population provenance and genetic structure. Chloroplast haplotypes were compared between Latvian and Belarusian pedunculate oak, and several common haplotypes were identified. The SSR haplotypes were compared to previously reported PCR-RFLP haplotypes, and haplotypes from the A (eastern European) and C (central European) lineages were identified. C lineage haplotypes were only found in the western region of Latvia. Haplotypes shared between Latvia and Belarus were all from the A lineage. Despite the much smaller population size of oak in Latvia in comparison to Belarus, the level of genetic diversity identified using the chloroplast SSR markers is similar. Provenance trials will need to be established in order to determine the suitability of Belarusian oak reproductive material for deployment in Latvia. Based on the results from this comparison of chloroplast haplotypes, as well as climatic similarities, it is probable that Belarusian oak material will be better suited to the eastern regions of Latvia compared to the western regions of Latvia.

Geographic Patterns of Genetic Variation among Cacao (Theobroma cacao L.) Populations Based on Chloroplast Markers

The cacao tree (Theobroma cacao L.) is native to the Amazon basin and widely cultivated in the tropics to produce seeds, the valuable raw material for the chocolate industry. Conservation of cacao genetic resources and their availability for breeding and production programs are vital for securing cacao supply. However, relatively little is still known about the phylogeographic structure of natural cacao populations. We studied the geographic distribution of cpDNA variation in different populations representing natural cacao stands, cacao farms in Ecuador, and breeding populations. We used six earlier published cacao chloroplast microsatellite markers to genotype 233 cacao samples. In total, 23 chloroplast haplotypes were identified. The highest variation of haplotypes was observed in western Amazonia including geographically restricted haplotypes. Two observed haplotypes were widespread across the Amazon basin suggesting long distance seed dispersal from west to east in Amazonia. Most cacao genetic groups identified earlier using nuclear SSRs are associated with specific chloroplast haplotypes. A single haplotype was common in selections representing cacao plantations in west Ecuador and reference Trinitario accessions. Our results can be used to determine the chloroplast diversity of accessions and in combination with phenotypic assessments can help to select geographically distinctive varieties for cacao breeding programs.

Reticulate Evolution, Ancient Chloroplast Haplotypes, and Rapid Radiation of the Australian Plant Genus Adenanthos (Proteaceae)

Cytonuclear discordance, commonly detected in phylogenetic studies, is often attributed to hybridization and/or incomplete lineage sorting (ILS). New sequencing technologies and analytical approaches can provide new insights into the relative importance of these processes. Hybridization has previously been reported in the Australian endemic plant genus Adenanthos (Proteaceae). Like many Australian genera, Adenanthos is of relatively ancient origin, and provides an opportunity to examine long-term evolutionary consequences of gene flow between lineages. Using a hybrid capture approach, we assembled densely sampled low-copy nuclear and plastid DNA sequences for Adenanthos, inferred its evolutionary history, and used a Bayesian posterior predictive approach and coalescent simulations to assess relative contributions of hybridization and ILS to cytonuclear discordance. Our analyses indicate that strong incongruence detected between our plastid and nuclear phylogenies is not only the result of ILS, but also results from extensive ancient introgression as well as recent chloroplast capture and introgression between extant Adenanthos species. The deep reticulation was also detected from long-persisting chloroplast haplotypes shared between evolutionarily distant species. These haplotypes may have persisted for over 12 Ma in localized populations across southwest Western Australia, indicating that the region is not only an important area for old endemic lineages and accumulation of species, but is also characterized by persistence of high genetic diversity. Deep introgression in Adenanthos coincided with the rapid radiation of the genus during the Miocene, a time when many Australian temperate plant groups radiated in response to large-scale climatic change. This study suggests that ancient introgression may play an important role in the evolution of the Australian flora more broadly.

Genetic Distinctiveness Highlights the Conservation Value of a Sicilian Manna Ash Germplasm Collection Assigned to Fraxinus angustifolia (Oleaceae)

The cosmopolitan genus Fraxinus comprises about 40 species occupying several habitats in the Northern Hemisphere. With some species hybridizing and sharing genetic variants, questions remain on the species assignment of germplasm within the genus Fraxinus despite numerous species-specific assessments. A multidisciplinary approach was employed to provide a definitive insight into the genetics of an endangered Fraxinus “manna ash” collection, located in a rich plant biodiversity hotspot of the Madonie Mountains (Sicily). Although the collection size was small, genetic diversity, assessed by chloroplast (cpSSR) and nuclear (nSSR) microsatellites (SSR—Simple Sequence Repeats), allowed identifying three different chloroplast haplotypes, with one (H5) dominant, and several polymorphic loci, able to discriminate most of the local accessions studied. Molecular data were linked to cytofluorimetric and phenotypic evaluations and, contrary to popular belief that manna ash is Fraxinus ornus L., the germplasm currently used for manna production belongs to Fraxinus angustifolia Vahl. Interestingly, joint analysis of our genetic panel with a large European dataset of Fraxinus spp. suggested the presence of a possible glacial refuge in Sicily, confirming its importance as biodiversity source. Our results will be helpful for the design of long-term conservation programs for genetic resources, such as in situ and ex situ conservation, seed collection and tree reintroduction.

Tracing back the origin of pumpkins ( Cucurbita pepo ssp. pepo L.) in Mexico

Cucurbita pepo is an economically important crop, which consists of cultivated C. pepo ssp. pepo , and two wild taxa ( C. pepo ssp. fraterna and C. pepo ssp. ovifera ) . We aimed at understanding the domestication and the diversity of C. pepo in Mexico. We used two chloroplast regions and nine nuclear microsatellite loci to assess the levels of genetic variation and structure for C. pepo ssp. pepo 's landraces sampled in 13 locations in Mexico, five improved varieties, one C. pepo ssp. fraterna population and ornamental C. pepo ssp. ovifera . We tested four hypotheses regarding the origin of C. pepo ssp. pepo 's ancestor through approximate Bayesian computation: C. pepo ssp. ovifera as the ancestor; C. pepo ssp. fraterna as the ancestor; an unknown extinct lineage as the ancestor; and C. pepo ssp. pepo as hybrid from C. pepo ssp. ovifera and C. pepo ssp. fraterna ancestors. Cucurbita pepo ssp. pepo showed high genetic variation and low genetic differentiation. Cucurbita pepo ssp. fraterna and C. pepo ssp. pepo shared two chloroplast haplotypes. The three subspecies were well differentiated for microsatellite loci. Cucurbita pepo ssp. fraterna was probably C. pepo ssp. pepo 's wild ancestor, but subsequent hybridization between taxa complicate defining C. pepo ssp. pepo 's ancestor.

Taxonomic revision of the African genus Greenwayodendron (Annonaceae)

Greenwayodendron (Annonaceae) is a tropical African genus of trees occurring mainly in rain forests. Until recently, Greenwayodendron contained only two species: Greenwayodendronoliveri from West Africa and Greenwayodendronsuaveolens from Central and East Africa. Genetic data, using chloroplast haplotypes and nuclear microsatellites as well as morphometric analyses, provided important information on the delineation of species. Greenwayodendron now contains six species, including two new species (Greenwayodendronglabrum Lissambou, Hardy &amp; Couvreur, sp. nov. and Greenwayodendronlittorale Lissambou, Dauby &amp; Couvreur, sp. nov.). Greenwayodendronsuaveolensvar.gabonica and Greenwayodendronsuaveolenssubsp.usambaricum are recognised as distinct species: Greenwayodendrongabonicumcomb. nov. and Greenwayodendronusambaricumcomb. nov., respectively. A key, detailed descriptions of morphology and geographic distributions, as well as notes on their ecology and uses are presented for all species. Preliminary conservation assessments following IUCN criteria are also provided. Two species are preliminarily identified as threatened, one as Endangered and one as Vulnerable.