Article

Assembly of tropical plant diversity on a local scale: Cyrtandra (Gesneriaceae) on Mount Kerinci, Sumatra

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Abstract

At a regional scale, the high species numbers (gamma diversity) of tropical forests have been explained by either a gradual accumulation of species through time (museum hypothesis) or, by contrast, rapid recent speciation in large genera. However, the origins of local rain forest diversity (alpha diversity) have been given little attention. Cyrtandra (Gesneriaceae), an understorey genus in the highly species-rich Indo-Malayan rain forest, has considerable capacity for producing local endemics, making it particularly suitable for studying diversity on a local scale. We sampled Cyrtandra species from one community on Mount Kerinci, Sumatra, and phylogenetic analyses of ITS sequences suggest that this community is an assembly of three distinct phyletic lineages: (1) a group of herbaceous or subshrub plants of Bornean affinity, (2) one member of a group of widespread shrubs forming Cyrtandra section Dissimiles and (3) a second group of shrubs. The evolutionary origin of this community is therefore not a result of rapid and recent speciation: it is assembled from species resulting from a gradual accumulation of diversity through time (museum hypothesis), although one lineage shows evidence of more recent, continuing speciation than the other two. The community includes two distantly related, apparently endemic species, but there is no evidence for a local adaptive radiation. The protection of representative species from each lineage would allow the conservation of genetic diversity. © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 81, 49–62.

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... Centres of diversity for the genus in Southeast Asia are Borneo (~200 spp.), the Philippines (~150 spp.), and New Guinea (~120 spp.) (Atkins et al. 2013). Its high species diversity, large number of narrow endemic species, and wide distribution make it an ideal genus for examining biogeographic patterns , Cronk et al. 2005, Clark et al. 2008, Johnson et al. 2017) and investigating the processes which underlie current patterns of biodiversity (Bramley et al. 2004a, Johnson et al. 2015, 2019. The genus is characterised by a combination of two fertile stamens and an indehiscent fruit, which varies from a tough-walled green or brown capsule in the west to a fleshy berry that ripens white or rarely orange in the east of its distribution, particularly in New Guinea and the Pacific ( 2019). ...
... Earlier phylogenetic studies of Southeast Asian Cyrtandra have focused on particular localities with dense sampling from a small number of locations , Bramley et al. 2004a. Larger scale studies have focused on Cyrtandra diversification across the Pacific (Cronk et al. 2005, Clark et al. 2008, Johnson et al. 2017, and these studies have signalled that the origin of the genus is within the Malesian region. ...
... widespread. In contrast, sympatric Malesian Cyrtandra are more likely to be from distantly related lineages (Bramley et al. 2004a), and this is reflected by the higher level of floral divergence (Fig. 2) and apparent lack of hybridisation amongst sympatric species, all of which is congruent with pre-zygotic barriers playing a large role in maintaining species boundaries. The majority of the 36 named taxa that were represented by more than one sample resolved as monophyletic with strong support, including two species with multi-island distributions, C. umbellifera from Taiwan and the northern Philippines (Clade J, Fig. 5) and C. sandei from Java and Sumatra (Clade F, Fig. 5). ...
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The islands of Southeast Asia comprise one of the most geologically and biogeographically complex areas in the world and are a centre of exceptional floristic diversity, harbouring 45,000 species of flowering plants. Cyrtandra, with over 800 species of herbs and shrubs, is the largest genus in the family Gesneriaceae and is one of the most emblematic and species-rich genera of the Malesian rainforest understorey. The high number of species and tendency to narrow endemism make Cyrtandra an ideal genus for examining biogeographic patterns. We sampled 128 Cyrtandra taxa from key localities across Southeast Asia to evaluate the geo-temporal patterns and evolutionary dynamics of this clade. One nuclear and four chloroplast regions were used for phylogenetic reconstruction, molecular dating, and ancestral range estimation. Results from the dating analysis suggest that the great diversity of Cyrtandra seen in the Malesian region results from a recent radiation, with most speciation taking place in the last five million years. Borneo was recovered as the most likely ancestral range of the genus, with the current distribution of species resulting from a west to east migration across Malesia that corresponds with island emergence and mountain building. Lastly, our investigation into the biogeographic history of the genus indicates high levels of floristic exchange between the islands on the Sunda shelf and the important role of the Philippines as a stepping stone to Wallacea and New Guinea. These patterns underlie much of the plant diversity in the region and form an emerging paradigm in Southeast Asian plant biogeography.
... & G.Forst. (Atkins et al., 2001;Bramley et al., 2004) and Agalmyla Blume (Chapman, 2003). Given the widespread and successful use of ITS in phylogenetic studies at the species level in Gesneriaceae it seemed the most appropriate region for this study. ...
... This value is known to be consistent for related groups of plants but can vary between lineages (Hershkovitz et al., 1999). Didymocarpus, however, had relatively low values (48%) for its ITS sequences, significantly lower than those of other Gesneriaceae, for example Aeschynanthus, 55% (Denduangboripant et al., 2001); Streptocarpus, 56.1% (Möller & Cronk, 1997a); Cyrtandra, 58% (Atkins et Bramley et al., 2004) or Agalmyla, 63.4% (Chapman, 2003). The significance of this finding is not known. ...
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Until recently the genus Didymocarpus Wall. (Gesneriaceae) was used in an unwarrantably wide sense and included more than 180 species. It has now been remodelled and restricted to around 70 species. Of these, 18 species and one variety are known to occur in Thailand. To clarify the relationships among Thai species of Didymocarpus we sequenced the internal transcribed spacers (ITS) of nuclear ribosomal DNA (nrDNA) from a sample of 23 taxa, including 15 from Thailand, four from China, three from Malaysia and one from Bhutan. Seventeen morphological characters were coded for all 23 taxa and optimized onto a retention index (RI) reweighted maximum parsimony (MP) tree. The phylogenetic analyses suggested that Didymocarpus taxa formed a strongly supported monophyletic clade, with several supported subclades. The combination of molecular phylogeny and optimization of morphological characters suggests the presence of three distinct groups: the first, corresponding to Didymocarpus sect. Elati Ridl., includes plants with tall stems, yellow or white flowers and one-celled conoid or two-celled headed pigment glands; the other two groups, which represent Didymocarpus sect. Didymocarpus, both contain plants with dwarfed stems and violet or purple flowers, but are distinguished by the presence of both four-celled conoid or onecelled globose glands in one, and the absence in the other. Optimization of geographical locality onto the phylogeny led us to propose the hypothesis that, based on this sample, the geographical origin of Didymocarpus is the Malay Peninsula, and the ancestral corolla colour is white/yellow. Subsequent dispersal northward through southern and northern Thailand to China and Bhutan was accompanied by the evolution of a purple/violet corolla colour.
... This is particularly true for the genus Cyrtandra; despite the exceptional geographic range for the genus, frequently species are regionally restricted endemics rarely extending beyond archipelagos (Samuel et al. 1997). More often, species of Cyrtandra are restricted to single islands or even confined areas within islands (Atkins et al. 2001;Bramley et al. 2003Bramley et al. , 2004aBramley et al. , 2004bBramley 2005;Cronk et al. 2005). As such, many species of Cyrtandra are threatened and can be summarily eliminated through destructive practices such as logging. ...
... Despite a concerted recent effort to sample Cyrtandra across its range (principally by authors in this paper), sampling is far from comprehensive and many clades are only partially or not at all sampled. Even when sampling is near complete, species-level relationships cannot be resolved using commonly used markers (Atkins et al. 2001;Bramley et al. 2004aBramley et al. , 2004bClark et al. 2008Clark et al. , 2009. A recent study suggests using nextgeneration sequencing and a large number of genic regions is also unsuccessful in finding molecular solutions to resolving these relationships (Pillon et al. 2013). ...
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The objective of this study was to build on a previously published molecular phylogenetic hypothesis for Cyrtandra to identify major clades of the genus in the Solomon Islands. Species of Cyrtandra in the Pacific are represented by locally uncommon, poorly known and rarely collected taxa, a large number of which are at particular risk of extinction due to high rates of deforestation. We propose that research in Cyrtandra has progressed to the point that regional taxonomic revisions can be conducted effectively following procedures developed for Cyrtandra in Malesia and Hawaii. We identify four distinct clades in the Solomon Islands, each characterized by suites of morphological characters that can be used to circumscribe taxa for revision. Both genetically sampled taxa for the phylogenetic analysis and unsampled taxa are evaluated based on morphological traits that differentiate these four clades. A hypothesis of relationship is proposed as a model for future taxonomic revision of the genus in this region that includes 24 species and two additional taxa possibly new to science. A diagnostic key to the clades currently recognized in the Solomons and an annotated checklist of recognized species are also included as a foundation for future work in the archipelago.
... The western part of this island is dominated by the Barisan mountain range, running along the whole length of Sumatra [16]. A major part of the Barisan Mountains is covered by the Kerinci Seblat National Park (KSNP), a biodiversity hotspot, and the largest national park in Sumatra [17]. ...
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Understanding past forest dynamics and human influence is essential for future forest management and ecosystem conservation. This study aims to provide insights into the forest dynamics and agroforestry history in the highlands of Sumatra for the last 1800 years. We carried out palaeoecological multi-proxy analyses of pollen, spores, non-pollen palynomorphs, macro-charcoal, and X-ray fluorescence on a limnic sediment core taken from Danau Kecil in the submontane area of Kerinci Seblat National Park in Sumatra, Indonesia. Our results provide an 1800-year record of forest dynamics under climate change and human influence including the transition from forest opening to shifting cultivation and eventually permanent agroforestry. Indicators for forest openings and secondary forest formation have been present since the beginning of records (AD 200). This is followed by the possible initiation of sugar palm (Arenga) cultivation (AD 400). Since AD 500, potential agroforestry and forest gardening practices have promoted major timber trees such as Lithocarpus/Castanopsis, Bischofia, and Dipterocarpaceae combined with sugar palm (Arenga). Permanent agroforestry systems were possibly established since AD 1760, evinced by an increase in commodity trees such as Dipterocarpaceae for resin production. With the Dutch invasion ca. AD 1900, agroforestry intensified and expanded to the Kerinci Valley. This was followed by land use intensification and potential rice cultivation around Danau Kecil since the 1940s. This study provides the first details on past forest dynamics around Danau Kecil since AD 200, showing among others how appropriate forest management and a closed canopy could reduce fire vulnerability in submontane rainforest.
... Cyrtandra is found predominantly in the forest, from sea level to 3000 m (Burtt 2001;Atkins et al. 2013). This high diversity, large number of endemic species, and wide distribution make it an ideal genus for examining biogeographic patterns Cronk et al. 2005;Clark et al. 2009;Johnson et al. 2017) and investigating the processes which underlie current patterns of biodiversity (Bramley et al. 2004;Johnson et al. 2015Johnson et al. , 2019. Its large size, however, also poses major taxonomic challenges (Burtt 2001;Bramley 2003;Atkins et al. 2013). ...
Article
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Cyrtandra (Gesneriaceae), with over 800 species, is a mega-diverse genus which presents considerable taxonomic challenges due to its size. A well-sampled phylogeny of the genus across Southeast Asia has confirmed that all but one of the sections within Clarke’s 1883 genus-wide infrageneric classification are polyphyletic. It also shows that there are high levels of homoplasy in key morphological characters, although it is possible to use morphological characters to define clades in parts of the phylogenetic tree. There is some geographic structure in the phylogeny, but there is also evidence of dispersal between islands. A practical approach for tackling the taxonomy of Cyrtandra in the region, through phylogenetically informed taxonomic revisions of geographic areas, an approach which combines evidence from molecular, morphological and distribution data, is discussed. Completing our understanding of species diversity and delimitation in this genus will allow us to maximise the use of Cyrtandra as a tool for studying biogeography, speciation, diversification and conservation prioritisation in the rainforests of Southeast Asia.
... On a global scale, they are permitting a re-evaluation of the relative roles of plate tectonics and long-distance dispersal in the assembly of continental biota (Crisp et al ., 2004; Linder & Hardy, 2004; Pennington & Dick, 2004; Renner, 2004 Renner, , 2005). On a local and more recent timescale, they give insights into the assembly of communities within species rich biomes (Webb et al ., 2002; Bramley et al ., 2004). An exciting future direction of research that promises to link more closely phylogenetics and ecology, and increase our knowledge of biome history, uses the framework of phylogenetic community structure (Webb, 2000) and neutral ecological theory (Hubbell, 2001). ...
Article
Summary 605 Acknowledgements 614 References 614 Analytical methods are now available that can date all nodes in a molecular phylogenetic tree with one calibration, and which correct for variable rates of DNA substitution in different lineages. Although these techniques are approximate, they offer a new tool to investigate the historical construction of species-rich biomes. Dated phylogenies of globally distributed plant families often indicate that dispersal, even across oceans, rather than plate tectonics, has generated their wide distributions. By contrast, there are indications that animal lineages have undergone less long distance dispersal. Dating the origin of biome-specific plant groups offers a means of estimating the age of the biomes they characterize. However, rather than a simple emphasis on biome age, we stress the importance of studies that seek to unravel the processes that have led to the accumulation of large numbers of species in some biomes. The synthesis of biological inventory, systematics and evolutionary biology offered by the frameworks of neutral ecological theory and phylogenetic community structure offers a promising route for future work.
... Here we included seven species right across the distribution range of the genus, from Peninsula Malaysia to Hawaii. There is no suggestion for the genus not to represent a single natural lineage, though no analysis exists to specifically test this (previous phylogenetic analyses included as outgroup only one or two species of Aeschynanthus (Atkins et al. 2001;Bramley et al. 2004;Cronk et al. 2005;Clark et al. 2008, respectively). Perhaps adding more Cyrtandra species might stabilise the analysis with respect to the monophyly of the genus. ...
Article
Based on a considerably enlarged sampling, a phylogenetic analysis of the largest group of didymocarpoid Gesneriaceae, the “advanced Asiatic and Malesian genera”, was performed, covering all but 3 of the 60 genera presently recognised in this group (20 of these, mostly from China, are monotypic). The results suggest that no fewer than 17 out of the 57 genera examined are poly- (or rarely para-)phyletic. Highly polyphyletic are Briggsia, Chirita, Henckelia and Raphiocarpus. Only a dozen of the non-monotypic genera (including the three species-richest genera, Cyrtandra, Aeschynanthus and Agalmyla) are confirmed as monophyletic entities, though some exhibit considerable genetic variation. For eight genera, no statement can be made, as only one (of two or several) species was included in the analysis. For a dozen of the (particularly Chinese) monotypic genera a close relationship (or possible congenerity) with other genera was found. In China, only Allostigma, Cathayanthe, Conandron and Metapetrocosmea seem to have no strong affinities to other genera, indicating that they represent phylogenetically isolated lineages or represent remnants of previously larger and earlier diversified groups. The present study forms the foundation for targeted molecular, morphological and phytogeographic studies of the polyphyletic and monotypic genera and particular of clades of genera with interrelations uncovered here for the first time. KeywordsBayesian inference analysis–ITS–Maximum parsimony–Molecular phylogeny–Monotypic genera–Old World didymocarpoid Gesneriaceae–Taxonomy– trnL-F intron-spacer
... The internal transcribed spacer (ITS) region of 18-26S nuclear ribosomal DNA has been widely used at the species level in a number of studies within the Lamiaceae (e.g., Steane & al., 1999; Trusty & al., 2004), as well as in other closely related families e.g., Gesneriaceae (Atkins & al., 2001; Bramley & al., 2004). Within the Lamiales the chloroplast gene ndhF has been most widely used at a higher level, either within a family (e.g., Wagstaff & al., 1998; Olmstead & al., 2001) or within a subfamily to establish generic delimitations (e.g., Clerodendrum and allies, Steane & al., 2004; Gesneriaceae tribes, Smith, 2000). ...
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The relationships of Vitex and genera historically placed in Lamiaceae subfamily Viticoideae were investigated. Particular focus was given to some South East Asian genera traditionally allied to Vitex (Paravitex, Tsoongia, Viticipremna, Teijsmanniodendron) since progress with South East Asian Floras is being hampered by a lack of clarity in current generic delimitation. On the basis of maximum parsimony and Bayesian phylogenetic analyses of ITS and ndhF sequence data we provide evidence that the Viticoideae is not monophyletic, its members being spread between a number of clades which include genera currently recognised as incertae sedis (Peronema, Hymenopyramis, Petraeovitex, Tectona). The most well supported clade, the Vitex group, contains Vitex, Paravitex, Tsoongia, Viticipremna, Petitia and Teijsmanniodendron. Morphological similarities of the genera included in this group are also discussed. In light of this evidence Paravitex, Viticipremna and Tsoongia are reduced to synonymy with Vitex, the new combinations being made here. The position of Teijsmanniodendron is not resolved and its generic status is therefore upheld. Similarly, Petitia is upheld due to a lack of neotropical taxa within the sample.
... The relatively unsculptured tricolp(or)ate pollen characteristics of the New World taxa are too generic to reliably assign fossil pollen to Gesneriaceae , although one report of gesneriaceous pollen has been attributed to a New Zealand sample of Quaternary age (Mildenhall 1980). Ideally, a molecular clock would allow us to use a single global substitution rate (Richardson et al. 2001; Bramley et al. 2004; Bartish et al. 2005; Rutschmann 2006). However, a likelihood ratio test indicated that our data are not evolving at a clocklike rate (P < 0:005); therefore, we could not rely on this method. ...
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... It seems therefore of interest to subsequently be able to test the hypothesis that E. balgooyi is a derivative of the more common E. bengalensis. Relicts from other lineages have likewise persisted and radiated on high mountains in western Malesia (Bramley et al. 2004). ...
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... They showed ancient and recent dispersal events transgressing the line, suggesting ongoing dispersals in the region. Bramley et al. (2004) used molecular phylogenies and a regional taxonomic treatment approach to tackle Cyrtandra species on Mt Kerinci, Sumatra. Their phylogeny gave an insight into the mode of species assemblage, resulting from a gradual accumulation of species over time (the museum hypothesis, cf. ...
Article
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... Because most scaly tree ferns are adapted to and dependent on the rainforest habitat and because these ferns often constitute dominant elements in Madagascar's rainforest vegetation, we believe that insight in the evolutionary mechanisms of these plants may be applicable to the evolution of the rainforest biome. Identification of prevalent mechanisms of accumulation of rainforest diversity, such as contrasting hypotheses of continuous diversification (Stebbins 1974;Gaston and Blackburn 1996;Bramley et al. 2004;Mittelbach et al. 2007;Wilson et al. 2007) over extended periods of time with hypotheses of recent origin of diversity in rapid radiations (Richardson et al. 2001;Kocher 2004;Schneider et al. 2005) is essential to developing conservation strategies (Moritz et al. 2000). From our study, it is obvious that short-term climatic events may lead to a quick accumulation of biological diversity and significantly alter the composition of rainforest habitats. ...
... The markers used in the phylogenetic analyses were chosen based on previous work on the Didymocarpoideae (e.g., Atkins & al., 2001;Bramley & al., 2004;Puglisi & al., 2011a, b;Puglisi, 2014). These were the nuclear ITS and the plastid regions trnL-trnF (including both the trnL intron and the trnL-trnF spacer) and ndhF-trnL UAG (ndhF-rpl32 and rpl32-trnL UAG spacers). ...
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... The most rigorous assessments of the pattern of ecological character evolution use standard methods of phylogenetic ancestral state reconstruction (or divergent tendency; see Moles et al. 2005) for niche-related characters (see Linder and Hardy 2005 for a good example). There are now a handful of phylogenetically based studies of ecological character evolution in tropical and subtropical forest plant genera (Davies 1996, Givnish et al. 2000, Dubuisson et al. 2003, Bramley et al. 2004, Cavender-Bares et al. 2004, Fine et al. 2004, Fine et al. 2005, Plana et al. 2004), but none that we know of that has attempted to sample all the extant species in a lineage. There is no consensus view arising from these studies. ...
... A significant part of this mountain is located within the boundaries of the largest national park in Sumatra, the Kerinci Seblat National Park (KSNP; ca. 1.4 million hectares; Bramley et al., 2004). ...
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... Our provisional identification is that this description refers to a Cyrtandra species, possibly Cyrtandra peltata and/ or Cyrtandra pendula which are relatively widespread in the understorey of wet forest in Sumatra. Cyrtandra (Gesneriaceae), with over 600 species, is as an important understorey fleshy herb in primary rain forest, in Sundaland with growth habits ranging from epiphytes, herbs and shrubs, to small trees (Bramley et al. 2004). Flux (1990) reported that Cyrtandra was the preferred diet of N. netscheri, where 35 species of Cyrtandra occur on Sumatra and 10 on Mount Kerinci where this species live. ...
... Our provisional identification is that this description refers to a Cyrtandra species, possibly Cyrtandra peltata and/ or Cyrtandra pendula which are relatively widespread in the understorey of wet forest in Sumatra. Cyrtandra (Gesneriaceae), with over 600 species, is as an important understorey fleshy herb in primary rain forest, in Sundaland with growth habits ranging from epiphytes, herbs and shrubs, to small trees (Bramley et al. 2004). Flux (1990) reported that Cyrtandra was the preferred diet of N. netscheri, where 35 species of Cyrtandra occur on Sumatra and 10 on Mount Kerinci where this species live. ...
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The Sumatran striped rabbit ( Nesolagus netscheri Schlegel 1880), endemic to the Indonesian island of Sumatra, is one of the rarest and least known lagomorph in the World. On 2 February 2017, N. netscheri was sighted in the forested Gunung Raya Wildlife Reserve, South Sumatra Province, Indonesia. An immediate follow up survey of local coffee farmers and hunters provided new data on the occurrence and ecology of N. netscheri.
... The west coast of Sumatra Island is dominated by the Barisan Mountains that run the whole length of Sumatra (Whitten et al. 2000). A significant part of this mountain range falls within the boundaries of Kerinci Seblat National Park (KSNP), the largest national park and one of biodiversity hotspots in Sumatra (ca.1.4 million ha, Bramley et al. 2004). The national park area consists of steeply sloping land and numerous active volcanoes, including the highest peak in Sumatra, Mount Kerinci (3,805 m, Ohsawa et al. 1985). ...
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... Species of Cyrtandra are important rainforest elements, thriving in habitats with high humidity, low light intensity, and constant moisture supply (Gillett 1967). Despite a continuous distributional range, the genus shows high levels of local endemism exhibiting high degrees of ecological specialization, making it an ideal candidate to address hypotheses on speciation, patterns of diversification, and community assembly Bramley et al. 2004;Clark et al. 2009;Johnson et al. 2019). ...
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Cyrtandra argentii Olivar, H.J.Atkins & Muellner sp. nov., endemic to the Philippines and named after George Argent, is herein described and illustrated. Collections associated with this new species are often confused with three other species, namely C. ferruginea Merr., C. villosissima Merr., and C. hirtigera H.J.Atkins & Cronk. Distinguishing characters including keys, updated descriptions, distribution maps, and photos of live specimens are provided to aid identification of the four species. Following the International Union for the Conservation of Nature (IUCN) criteria, C. argentii sp. nov. is considered to be Near Threatened (NT) due to its distribution in a zone susceptible to anthropogenic pressure and the lack of any formal protection.
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The phylogeny of a representative group of genera and species from the Sapotaceae tribe Chrysophylleae, mainly from Australia and New Caledonia, was studied by jackknife analyses of sequences of nuclear ribosomal DNA. The phylogeny conflicts with current opinions on generic delimitation in Sapotaceae. Pouteria and Niemeyera, as presently circumscribed, are both shown to be nonmonophyletic. In contrast, all species currently assigned to these and other segregate genera confined to Australia, New Caledonia, or neighboring islands, form a supported clade. Earlier classifications in which more genera are recognized may better reflect relationships among New Caledonian taxa. Hence, there is need for a revision of generic boundaries in Chrysophylleae, and particularly within the Pouteria complex, including Leptostylis, Niemeyera, Pichonia, Pouteria pro parte (the main part of section Oligotheca), and Pycnandra. Section Oligotheca have been recognized as the separate genus Planchonella, a monophyletic group that needs to be resurrected. Three clades with strong support in our jackknife analysis have one Australian species that is sister to a relatively large group of New Caledonian endemics, suggesting multiple dispersal events between this small and isolated tropical island and Australia. The phylogeny also suggests an interesting case of a relatively recent and rapid radiation of several lineages of Sapotaceae within New Caledonia.
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The revision of species-rich genera underpins research and supports the sustainable use and monitoring of biological diversity. One fifth to one quarter of the diversity of all seed plant species occurs in such genera, but difficulties with the revision of species-rich genera has resulted in many of them being ignored since the late 1800s. Pilea, with 600-715 species is in need of revision. The only realistic approach is in manageable subunits, which requires confirmation of monophyly and identification of monophyletic subdivisions. Parsimony analyses of trnL-F, ITS, and morphology data were used to test the monophyly of, and explore intrageneric relationships within, Pilea. Analysis of trnL-F data confirms and recovers two morphologically diagnosable monophyletic clades that include all of the taxa within Pilea. Overlaying geographic distribution on a most parsimonious tree indicates a strong association between geography and phylogenetic relatedness. It is suggested that a strategic revision within the framework of morphologically and geographically diagnosable units might enable the revision of the group using an iterative approach. Analysis of the outgroup taxa supports the inclusion of Poikilospermum within the Urticaceae and suggests that the Urticaceae tribes could be placed into two clades that are supported by floral morphology.
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Tropical forests contain the majority of extant plant diversity and their role as a cradle and/or museum of biodiversity is an important issue in our attempts to assess the long-term consequences of global climate change for terrestrial biomes. Highly diverse groups of liverworts are an often ignored but extremely common element in rainforests, and thus their evolution may shed light on the ecological robustness of rainforest biomes to climate fluctuations. We record a remarkable constant accumulation of diversity through time for the most species-rich family of liverworts, Lejeuneaceae, inferred by divergence time estimates. The observed pattern supports the recently developed concept of a dual role of the tropics as both a museum and a cradle of biodiversity.
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A brief review is given of evidence for changes in sea levels, degree of seasonality in precipitation, and variations in temperature during the late Tertiary and Quaternary in the Malay Archipelago. Also, new evidence is presented for a seasonal climate within the Malay Peninsula during the middle Pleistocene.
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The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo. Availability: MRBAYES, including the source code, documentation, sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html. Contact: johnh{at}brahms.biology.rochester.edu
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Examining the pattern of nucleotide substitution for the control region of mitochondrial DNA (mtDNA) in humans and chimpanzees, we developed a new mathematical method for estimating the number of transitional and transversional substitutions per site, as well as the total number of nucleotide substitutions. In this method, excess transitions, unequal nucleotide frequencies, and variation of substitution rate among different sites are all taken into account. Application of this method to human and chimpanzee data suggested that the transition/transversion ratio for the entire control region was approximately 15 and nearly the same for the two species. The 95% confidence interval of the age of the common ancestral mtDNA was estimated to be 80,000-480,000 years in humans and 0.57-2.72 Myr in common chimpanzees.
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The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data. AVAILABILITY: The MODELTEST package, including the source code and some documentation is available at http://bioag.byu. edu/zoology/crandall_lab/modeltest.html.
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Species richness in the tropics has been attributed to the gradual accumulation of species over a long geological period in stable equatorial climates or, conversely, to speciation in response to late Tertiary geological events and unstable Pleistocene climates. DNA sequence data are consistent with recent diversification inInga, a species-rich neotropical tree genus. We estimate that speciation was concentrated in the past 10 million years, with many species arising as recently as 2 million years ago. This coincides with the more recent major uplifts of the Andes, the bridging of the Isthmus of Panama, and Quaternary glacial cycles. Inga may be representative of other species-rich neotropical genera with rapid growth and reproduction, which contribute substantially to species numbers in the world's most diverse flora.
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The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data. In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.
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Amino acid sequence data are available for ribulose biphosphate carboxylase, plastocyanin, cytochrome c, and ferredoxin for a number of angiosperm families. Cladistic analysis of the data, including evaluation of all equally or almost equally parsimonious cladograms, shows that much homoplasy (parallelisms and reversals) is present and that few or no well supported monophyletic groups of families can be demonstrated. In one analysis of nine angiosperm families and 40 variable amino acid positions from three proteins, the most parsimonious cladograms were 151 steps long and contained 63 parallelisms and reversals (consistency index = 0.583). In another analysis of six families and 53 variable amino acid positions from four proteins, the most parsimonious cladogram was 161 steps long and contained 50 parallelisms and reversals (consistency index = 0.689). Single changes in both data matrices could yield most parsimonious cladograms with quite different topologies and without common monophyletic groups. Presently, amino acid sequence data are not comprehensive enough for phylogenetic reconstruction among angiosperms. More informative positions are needed, either from sequencing longer parts of the proteins or from sequencing more proteins from the same taxa.
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The limits of Cyrtandra, its synonyms and the characters used for its division into subgenera and sections are surveyed chronologically. Additional features, known as yet for only a few groups, are discussed.
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At Danau di Atas (DDA) the pollen record extends back to c31 000 BP. At Telago the record extends back to c9000 BP. In the Late Pleistocene, vegetation zones were depressed, and a gymnosperm-rich rainforest, now found only >1800 m, surrounded DDA. At times upper montane forest may have been close to the site, suggesting a vegetational depression of c800 m. Mean annual temperature may have been 1.6°-5.2°C cooler than now. There is no direct evidence of formerly drier climates, although a possible reduction of water levels in the Late Pleistocene is suggested. During the Holocene, there is evidence for disturbance of rainforests, possibly by man, from a date some time after c8200 BP. Extensive recent forest clearance is demonstrated. -from Authors
Article
Amino acid sequence data are available for ribulose biphosphate carboxylase, plastocyanin, cytochrome c, and ferredoxin for a number of angiosperm families. Cladistic analysis of the data, including evaluation of all equally or almost equally parsimonious cladograms, shows that much homoplasy (parallelisms and reversals) is present and that few or no well supported monophyletic groups of families can be demonstrated. In one analysis of nine angiosperm families and 40 variable amino acid positions from three proteins, the most parsimonious cladograms were 151 steps long and contained 63 parallelisms and reversals (consistency index = 0.583). In another analysis of six families and 53 variable amino acid positions from four proteins, the most parsimonious cladogram was 161 steps long and contained 50 parallelisms and reversals (consistency index = 0.689). Single changes in both data matrices could yield most parsimonious cladograms with quite different topologies and without common monophyletic groups. Presently, amino acid sequence data are not comprehensive enough for phylogenetic reconstruction among angiosperms. More informative positions are needed, either from sequencing longer parts of the proteins or from sequencing more proteins from the same taxa.
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A biogeographic and phylogenetic study of Cyrtandra (Gesneriaceae) in the Sundaland region (Borneo and Peninsular Malaysia) and the Philippines using nuclear ribosomal (ITS) DNA sequence data reveals a major division between the Cyrtandra floras of Sundaland and the Philippines. Palawan, the most westerly of the Philippine islands, emerges as an area of mixing between these two. The Bornean element in the Cyrtandra flora of Palawan (two species in our sample) appears to result from recent (i.e. Pleistocene) dispersal from Borneo. The remaining seven species sampled from Palawan are most closely related to those from elsewhere in the Philippines. However, the Palawan clade is sister to the other Philippine taxa, suggesting an ancient (possibly Pliocene) vicariance event. Huxley's line—a zoogeographic boundary placing Palawan and Borneo together—receives some support from this study as there is evidence of recent dispersal of Bornean flora into Palawan. However, in terms of more ancient biogeographic patterning of the region, Palawan has stronger links with the other Philippine islands.
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— We studied sequence variation in 16S rDNA in 204 individuals from 37 populations of the land snail Candidula unifasciata (Poiret 1801) across the core species range in France, Switzerland, and Germany. Phylogeographic, nested clade, and coalescence analyses were used to elucidate the species evolutionary history. The study revealed the presence of two major evolutionary lineages that evolved in separate refuges in southeast France as result of previous fragmentation during the Pleistocene. Applying a recent extension of the nested clade analysis (Templeton 2001), we inferred that range expansions along river valleys in independent corridors to the north led eventually to a secondary contact zone of the major clades around the Geneva Basin. There is evidence supporting the idea that the formation of the secondary contact zone and the colonization of Germany might be postglacial events. The phylogeographic history inferred for C. unifasciata differs from general biogeographic patterns of postglacial colonization previously identified for other taxa, and it might represent a common model for species with restricted dispersal.
Article
Collections of Cyrtandra from the island of Palawan in the Philippines are reviewed. Twelve species are present, of which only five species are already described. A further three species and one variety are described here: C.cleopatrae H.J. Atkins & Cronk sp.nov.,C.pulgarensis [Elmer ex] H.J. Atkins & Cronk sp.nov.,C.hirtigera H.J. Atkins & Cronk sp.nov., and C.hirtigera var. chlorina H.J. Atkins & Cronk var.nov. Further material of the remaining four taxa (spp. B, C, D, E) will be needed before these can be formally named, although descriptions are provided here. All species are endemic except C.elatostemoides Elmer and C.hypochrysoides Kränzl., which also occur in Borneo and Luzon respectively. The pattern of narrow endemism shown by the cyrtandras of Palawan is commented on briefly.
Article
The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data, In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.
Article
Cyrtandra sect. Dissimiles C. B. Cl., sect. Radicicaules Kraenzlin and sect. Radiciflorae Kraenzlin are lectotypified. Two varieties are raised to specific rank: C. dispar var. glabriflora B. C. Stone to C. stonei (Malay Peninsula), C. decurrens var. polyneura C. B. Cl. to C. polyneura (Sulawesi). Nineteen new species are described (11 from Sarawak, 1 from Sarawak and Kalimantan, 7 from Sabah—6 of them from Mt Kinabalu). Annotations are provided on 6 previously known species: C. calycina Benth. (New Guinea), C. debilis Kraenzlin (Kalimantan), C. farinosa C. B. Cl. (Sarawak), C. ligulifera C. B. Cl. (New Guinea), C. rubropicta Kraenzlin (Kalimantan and Sarawak), and C. russa C. B. Cl. (Sarawak).
Article
A new method for estimating divergence times when evolutionary rates are variable across lineages is proposed. The method, called nonparametric rate smoothing (NPRS), relies on minimization of ancestor-descendant local rate changes and is motivated by the likelihood that evolutionary rates are autocorrelated in time. Fossil information pertaining to minimum and/or maximum ages of nodes in a phylogeny is incorporated into the algorithms by constrained optimization techniques. The accuracy of NPRS was examined by comparison to a clock-based maxi-mum-likelihood method in computer simulations. NPRS provides more accurate estimates of divergence times when (1) sequence lengths are sufficiently long, (2) rates are truly nonclocklike, and (3) rates are moderately to highly autocorrelated in time. The algorithms were applied to estimate divergence times in seed plants based on data from the chloroplast rbcL gene. Both constrained and unconstrained NPRS methods tended to produce divergence time estimates more consistent with paleobotanical evidence than did clock-based estimates.
Article
 Aeschynanthus Jack, an epiphytic genus with c.160 species, is widespread in SE Asia. We selected 50 species for ITS nrDNA sequencing, to include all biogeographic areas and all infrageneric groupings, which are currently based on seed morphology. Some species were sequenced directly from PCR product; others cloned because of ITS length polymorphisms. The clone sequences were analysed individually and combined in an elision matrix. Results extend earlier findings that Aeschynanthus is divided into two clades, one occurring primarily in mainland SE Asia and the other in Malesia. This pattern is interpreted as indicating an ancient vicariance event followed by dispersal and plate fusion. Clade I has straight or clockwise spiral orientation of the testa cells and clade II anticlockwise spiral orientation. In clade I some species of section Microtrichium form a basal group with other sections being polyphyletic or paraphyletic. In clade II the monophyletic section Aeschynanthus is nested within the paraphyletic basal Microtrichium.
Article
The application of maximum likelihood techniques to the estimation of evolutionary trees from nucleic acid sequence data is discussed. A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available. This method has advantages over the traditional parsimony algorithms, which can give misleading results if rates of evolution differ in different lineages. It also allows the testing of hypotheses about the constancy of evolutionary rates by likelihood ratio tests, and gives rough indication of the error of ;the estimate of the tree.
Article
Conservationists are far from able to assist all species under threat, if only for lack of funding. This places a premium on priorities: how can we support the most species at the least cost? One way is to identify 'biodiversity hotspots' where exceptional concentrations of endemic species are undergoing exceptional loss of habitat. As many as 44% of all species of vascular plants and 35% of all species in four vertebrate groups are confined to 25 hotspots comprising only 1.4% of the land surface of the Earth. This opens the way for a 'silver bullet' strategy on the part of conservation planners, focusing on these hotspots in proportion to their share of the world's species at risk.
Article
Rates of molecular evolution vary widely between lineages, but quantification of how rates change has proven difficult. Recently proposed estimation procedures have mainly adopted highly parametric approaches that model rate evolution explicitly. In this study, a semiparametric smoothing method is developed using penalized likelihood. A saturated model in which every lineage has a separate rate is combined with a roughness penalty that discourages rates from varying too much across a phylogeny. A data-driven cross-validation criterion is then used to determine an optimal level of smoothing. This criterion is based on an estimate of the average prediction error associated with pruning lineages from the tree. The methods are applied to three data sets of six genes across a sample of land plants. Optimally smoothed estimates of absolute rates entailed 2- to 10-fold variation across lineages.
Article
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