Phylogeny and biogeography of the core babblers (Aves: Timaliidae)

The avian family Timaliidae is a species rich and morphologically diverse component of African and Asian tropical forests. The morphological diversity within the family has attracted interest from ecologists and evolutionary biologists, but systematists have long suspected that this diversity might also mislead taxonomy, and recent molecular phylogenetic work has supported this hypothesis. We produced and analyzed a data set of 6 genes and almost 300 individuals to assess the evolutionary history of the family. Although phylogenetic analysis required extensive adjustment of program settings, we ultimately produced a well-resolved phylogeny for the family. The resulting phylogeny provided strong support for major subclades within the family but extensive paraphyly of genera. Only 3 genera represented by more than 3 species were monophyletic. Biogeographic reconstruction indicated a mainland Asian origin for the family and most major clades. Colonization of Africa, Sundaland, and the Philippines occurred relatively late in the family's history and was mostly unidirectional. Several putative babbler genera, such as Robsonius, Malia, Leonardina, and Micromacronus are only distantly related to the Timaliidae.     

Molecular phylogenetics of babblers (Timaliidae): revaluation of the genera Yuhina and Stachyris

The babblers (Timaliidae) form a large songbird family, which achieves its highest diversity in South-East Asia. As part of an ongoing phylogenetic investigation of this group, we focus here on the systematic position of two Asian genera, Yuhina and Stachyris , using cytochrome b , 16S and 12S sequence data. The analysis suggests that the two genera, as defined by morphological characters, are not monophyletic. The white-bellied yuhina Yuhina zantholeuca , which has been placed among the typical yuhinas by most authors, is not a babbler. The other yuhinas studied, six continental species and a species endemic to Taiwan, form a clade that includes also three species of Stachyris endemic to the Philippines. The other Stachyris are not related to this clade, and can be divided into two groups that correspond to morphological and geographical differences among the species.     

Molecular systematics of the Malagasy babblers (Passeriformes: timaliidae) and warblers (Passeriformes: sylviidae), based on cytochrome b and 16S rRNA sequences

The phylogenetic relationships of the Timaliidae (babblers) and Sylviidae (warblers) have long challenged ornithologists. We focus here on three Malagasy genera currently assigned to the Timaliidae, Mystacornis, Oxylabes, and Neomixis, and on their relationships with other babblers and warblers using the sequences of two mitochondrial genes (cytochrome b and 16S rRNA). Maximum parsimony analyses show that the Malagasy "babblers" are not related to any of the other African and Asian babblers. The genus Mystacornis is neither a babbler nor a warbler. The other Malagasy "babblers" are members of warbler groups (the monophyly of the Sylviidae is not demonstrated). Oxylabes madagascariensis and Hartertula flavoviridis (we recognize Hartertula as a genus for the species flavoviridis, previously Neomixis flavoviridis) constitute, with two presumed sylviine taxa, Thamnornis chloropetoides and Cryptosylvicola randrianasoloi, a warbler radiation endemic to the island of Madagascar. The other Neomixis species (tenella, striatigula, and viridis) belong to another warbler group comprising cisticoline taxa. These results show that the Timaliidae did not disperse to Madagascar. Rather, the island has been colonized, independently, by at least two clades of warblers, probably originating from Africa, where the Sylviidae radiation has been the most extensive.     

Phylogeny of babblers (Aves, Passeriformes): major lineages, family limits and classification

Babblers, family Timaliidae, have long been subject to debate on systematic position, family limits and internal taxonomy. In this study, we use five molecular regions to estimate the relationships among a large proportion of genera traditionally placed in Timaliidae. We find good support for five main clades within this radiation, and propose a new classification, dividing the babblers into the families Sylviidae and Timaliidae. Within the latter family, four subfamilies are recognized: Zosteropinae, Timaliinae, Pellorneinae and Leiothrichinae. Several taxa, previously not studied with molecular data, are phylogenetically placed within Sylviidae or Timaliidae. This is, however, not the case for the genus Pnoepyga , for which we propose the family name Pnoepygidae fam. n.     

Molecular Systematics of the Malagasy Babblers (Passeriformes: Timaliidae) and Warblers (Passeriformes: Sylviidae), Based on Cytochrome b and 16S rRNA Sequences

The phylogenetic relationships of the Timaliidae (babblers) and Sylviidae (warblers) have long challenged ornithologists. We focus here on three Malagasy genera currently assigned to the Timaliidae, Mystacornis, Oxylabes, and Neomixis, and on their relationships with other babblers and warblers using the sequences of two mitochondrial genes (cytochrome b and 16S rRNA). Maximum parsimony analyses show that the Malagasy “babblers” are not related to any of the other African and Asian babblers. The genus Mystacornis is neither a babbler nor a warbler. The other Malagasy “babblers” are members of warbler groups (the monophyly of the Sylviidae is not demonstrated). Oxylabes madagascariensis and Hartertula flavoviridis (we recognize Hartertula as a genus for the species flavoviridis, previously Neomixis flavoviridis) constitute, with two presumed sylviine taxa, Thamnornis chloropetoides and Cryptosylvicola randrianasoloi, a warbler radiation endemic to the island of Madagascar. The other Neomixis species (tenella, striatigula, and viridis) belong to another warbler group comprising cisticoline taxa. These results show that the Timaliidae did not disperse to Madagascar. Rather, the island has been colonized, independently, by at least two clades of warblers, probably originating from Africa, where the Sylviidae radiation has been the most extensive.     

High plant endemism in an Indian hotspot – eastern Himalaya

A preliminary investigation in the Subansiri area of the eastern Himalaya recorded high plant endemism. As a regular exercise of field sampling of various forest types to map the biorich areas, the number of species observed was evaluated to analyze their endemic status in one of the important hotspot regions of the world. The total number of individuals, species, genera and families observed were recorded in various natural and semi-natural forest types. A total of 122 plots sampled randomly in various forest types recorded 764 plant species, of which 59 were found to be endemic. The overall species endemism is observed to be 13 per ha. These 59 species belong to 27 families and 46 genera. Fifty percent of species were from just five families, Rubiaceae, Lauraceae, Acanthaceae, Magnoliaceae and Rosaceae. Stem size class distribution of the most abundantly found endemic tree species in three primary forest types indicated a quantitative status. This study envisages the status of plant endemism carried out following a proportional stratified random sampling method for various classified vegetation cover types using satellite remote sensing data. Many primitive genera and families were recorded which are indicative of long evolutionary age and affinities of the area with respect to species endemism.     

THE TAXONOMIC SIGNIFICANCE OF THE HEAD-SCRATCHING METHODS OF BIRDS.

Birds scratch their heads in one only of two ways, either directly or indirectly, and one method is used by all members of the same family though not necessarily by all families in the same order. When related families have different head-scratching methods, then the behaviour can help in disentangling difficult relationships. Examples are given. In the case of the passerines, only the Timaliidae (babblers) scratch directly. The implications are briefly discussed; for example, on this evidence Picathartes is not a babbler. The Psittaciformes are a potentially rewarding group for future work.     

An integrative species delimitation approach reveals fine-scale endemism and substantial unrecognized avian diversity in the Philippine Archipelago

The Philippine archipelago is recognized as a biodiversity hotspot because of its high levels of endemism and numerous threatened species. Avian lineages in the Philippines feature morphologically distinct allopatric taxa, which have been variably treated either as species or subspecies depending on species concepts and recognition criteria. To understand how alternative species limits would alter diversity metrics and patterns of endemism in the Philippines, we selected 19 focal lineages of birds, each containing multiple described taxa within the Mindanao Island Group. We delimited species in an integrative, lineage-based framework using three operational criteria: species must (1) form well-supported, geographically circumscribed clades, (2) be monophyletic with significant genetic differentiation identified by a coalescent model, and (3) feature fixed differences in phenotypic characters. Our criteria identified 40 species from the original 19 focal lineages, a 50–74% increase over recent comprehensive taxonomic treatments. Genetic criteria in isolation identified an additional 10 populations that could be cryptic species in need of further study. We identified fine-scale endemism within the Mindanao Island Group, with multiple unrecognized avian endemics restricted to Samar/Leyte, Bohol Island, and the Zamboanga Peninsula. Genetic and phenotypic information support the hypothesis that polytypic bird species in the Philippines tend to be composed of evolutionarily distinct, range-restricted, allopatric replacements rather than widespread and variable “superspecies”. We conclude that lack of species recognition has resulted in underestimates of species diversity and overlooked fine-scale endemism in the Philippines. Recognizing this diversity would alter conservation priorities, shifting efforts to protect microendemics on smaller islands and finer scale endemic areas within larger islands.     

Endemism in the Flora of China—Studies on the Endemic Genera

China, under highly varied ecological conditions resulted from wide latitudinal and altitudinal ranges and from the adequate precipitation, has developed a very rich flora of great diversity. As far as flowering plants are concerned, there are 2980 genera, 214 of which, belonging to 64 families, are endemic. Among these endemic genera, there are 9 genera of taxads and conifers, 19 genera of monocots and others of dicots. Of the approximately 129 herbaceous endemic genera in the Chinese flora as a whole, about 22 (17%) are annual and 107 (83%) are biennial or perennial. In the present paper the ecological distribution, the nature of endemic genera and the centers of endemism are discussed. 1. Three types of endemic genera are distinguished, neoendemics, palaeoendemics and active epibiotics, The endemic genera in the flora of China are, for the most part, considered to be very old ones, and most of them are of temperate nature. 2. the degree of endemism in our 22 floristic regions is shown in Figure 1. The areas richest in endemic genera in the Chinese flora as a whole are the 13, 16 and 17 regions. The poorest are the 2, 4, 9 and 10 regions, and no one in the 1 and 3 regions These results on floristic richness are of general applicability. As shown in table 1, the difference in the degree of endemism among the seven Chinese floristic subkingdoms are most pronounced. 101 endemic genera are known to occur in one subkingdom, 72 to occur in two subkingdoms, and 3 to occur in four subkingdoms, only one genus widely distributed in five subkingdoms. However, there is no genus occurring in seven subkingdoms. The difference in the degree of endemism in each subkingdom reveals that the distribution of endemic genera is not well-distributed in the Chinese flora as a whole. Analysis of the vertical distribution of the 200 endemic genera of the Chinese flora bears out that there is no evident increase in endemism as a whole with altitude. 3. Three centers of endemism are found (Fig. 2). These are as follows: a). Eastern Sichuan-western Hubei center. b). Southeastern Yunnan-western Guangxi center. c). Western Sichuan-northwestern Yunnan center. The degree of endemism andcharacters of endemic genera in each center are discussed.     

Systematic revision of the avian family Cisticolidae based on a multi-locus phylogeny of all genera

The avian taxon Cisticolidae includes c. 110 species which are distributed throughout the tropical and subtropical parts of the Old World. We estimated the phylogeny of 47 species representing all genera assumed to be part of Cisticolidae based on sequence data from two mitochondrial and two nuclear markers, in total 3495 bp. Bayesian inference and maximum likelihood analyses resulted in a generally well-supported phylogeny which clarified the position of several previously poorly known taxa. The placement of Drymocichla, Malcorus, Micromacronus, Oreophilais, Phragmacia, Phyllolais, Poliolais and Urorhipis in Cisticolidae is corroborated, whereas Rhopophilus and Scotocerca are removed from Cisticolidae. Urorhipis and Heliolais are placed in the genus Prinia whereas Prinia burnesii is shown to be part of Timaliidae, and is placed in the genus Laticilla. Although not recovered by all single loci independently, four major clades were identified within Cisticolidae, and one of these is here described as a new taxon (Neomixinae).     

Endemic species of grasses in Mexico: a phytogeographic approach

The Poaceae family includes approximately 700 genera and 10000 species, and Mexico is considered one of its most important centers of diversity and endemism. A total of 256 taxa (including 16 subspecific taxonomic units), belonging to 65 genera, are endemic to Mexico. Some of them are close relatives of important crops, while others are used in different ways all over the country. The aim of this paper is to discuss the distribution patterns at state level of the Mexican endemic species of Poaceae. Using cluster strategies, the states are classified according to their floristic similarities. Later, hotspots of endemism are identified, in order to discuss their role in conservation strategies. To evaluate the importance of each state in the conservation of the Mexican endemic Poaceae, two iterative complementarity methods were also used. Our results show that the largest concentration of endemic taxa occurs in a few states, such as Jalisco, Mexico, Michoacán, Durango, Oaxaca, Veracruz, San Luis Potosi, Chiapas, Chihuahua, Puebla, and Coahuila. The results also show that there are some patterns in the relationship to its endemism that seem to reflect important diversification trends in the family. Accordingly, 31% of the grass genera of Mexico have at least one endemic species, and 16.7% of the genera have only one endemic species. In contrast, six genera contribute 47.2% of the total number of grass endemics in Mexico. The Chloridoideae contributes 42.9% of the total grass endemic species of Mexico, whereas the Panicoideae includes 24.6%, and the Pooideae 19.8%. Thus, these three subfamilies contribute about 87% of the species endemism. On the basis of the habitat and distribution patterns of these subfamilies, two main areas of endemicity can be identified. The first area is located in warm habitats, whereas the second is related to temperate and high regions. The cluster analyses indicate the occurrence of four state groups whose phytogeographical explanation is discussed on the basis of a floristic regionalization of Mexico. The results also indicate the need to establish a relatively high number of sites and states for the conservation of 256 endemic taxa. The elevated number of sites required to conserve the Mexican endemic Poaceae is mainly due to the fact that many taxa have a restricted distribution pattern. On the basis of the patterns obtained, a few proposals are presented for undertaking the establishment of conservation priorities of these taxa.     

Abrocomaphthirus hoplai, a new genus and species of sucking louse from Chile and its relevance to zoogeography

Both sexes of Abrocomaphthirus hoplai, new genus and new species (Anoplura: Polyplacidae), are described and illustrated. The endemic Chilean chinchilla rat Abrocoma bennetti Waterhouse (Rodentia: Abrocomidae) is the type host. The definition of the family Polyplacidae is amended to accommodate the new genus. Polyplax longa (Werneck), also referred to in the literature as Neohaematopinus longus Werneck, is reassigned to Abrocomaphthirus. The host of A. longus comb.n., is Abrocoma cinerea Thomas, another chinchilla rat, which inhabits parts of Argentina, Bolivia, Chile and Peru. The erection of Abrocomaphthirus as a distinct genus has important zoogeographical and evolutionary implications. The tenuous anomaly of P. longa being the sole native representative of the genus Polyplax in South America, possibly with African affinities, is now refuted. Instead, partial colonization of the neotropics by native species of both Polyplax and Neohaematopinus appears to have been relatively recent and from North America. The phylogenetic affinities of Abrocomaphthirus are unknown, but it appears to be closely related to other, more ancient, native South American polyplacid louse genera, such as Cuyana, Eulinognathus, Galeophthirus, and Lagidiophthirus. Arguments are presented in support of an ancestral zoogeographical link to Africa for these louse genera.     

无量山种子植物区系的特有现象

地处滇中南的无量山地区迄今计有种子植物２０７科,１０２６属,２５４０种,其中东亚特有科１０个,中国特有属２７个,无量山特有种子６７个,这一地区不仅植物种类丰富,而且特有现象较为显著,在对科级持有现象进行较细致的研究后,本文认国无量山具有较多的分类系统上隔离的东亚特有科反映了该地作为东亚古老植物区系的一部分,其地质历史与整个东亚是一致的,且与东亚植物区系的发端密切相关,属的特有现象表明,地处中国特有     

云南省小黑山自然保护区种子植物区系研究

小黑山自然保护区有野生种子植物170科787属2195种。分析表明该区种子植物区系的地理成分复杂,联系广泛。热带性质的属有506属,占总属数的68.6%,温带性质的属有224属,占总属数的30.4%。热带性质的种890种,占总种数的40.9%,温带性质的种有1267种,占总种数的58.3%。表明该地区植物区系具有明显的亚热带性质,同时深受热带植物区系的影响。植物区系来源主要由东亚成分、热带亚洲成分(印度—马来西亚成分)、中国特有成分三部分融合而成。特有现象明显,有东亚特有科5科,中国特有属6属,中国特有种778种,占种总数的35.8%,而云南特有种有355种,占中国特有种的45.6%。保护区还拥有众多的珍稀濒危植物。     

Molecular systematics and diversification of the Asian scimitar babblers (Timaliidae, Aves) based on mitochondrial and nuclear DNA sequences

The Asian scimitar babblers, including the genus Pomatorhinus and Xiphirhynchus, are a small group of babblers characterized by long down-curved bills and a distribution throughout East and Southeast Asia. To infer the molecular phylogeny of this group and their divergence time, we examined sequences of multiple fragments including two entire mitochondrial genes and four nuclear introns (4352 bp in total) from multiple samples of eight of the nine recognized species of Asian scimitar babblers. The phylogeny resulting from the concatenated multi-locus dataset suggests that Pomatorhinus is paraphyletic. Due to its paraphyly, we propose dividing the traditional genus Pomatorhinus into two morphologically and genetically diagnosable genera: Pomatorhinus and Erythrogenys. Results of the molecular dating based on the conventional mitochondrial DNA divergence rate indicates that the diversification of these babblers is likely congruent with the historical climatic events. Our findings shed light on the diversification of avian species in southern Asia, a poorly studied biodiversity hotspot.     

Spatio‐temporal history of the endemic genera of Madagascar

Madagascar is renowned for its unparalleled species richness and levels of endemism, which have led, in combination with species extinction caused by an unprecedented rate of anthropogenic deforestation, to its designation as one of the most important biodiversity hotspots. It is home to 10 650 species (84% endemic) of angiosperms in 1621 genera (19% endemic). During the last two centuries, botanists have focused their efforts on the provision of a taxonomic framework for the flora of the island, but much remains to be investigated regarding the evolutionary processes that have shaped Madagascan botanical diversity. In this article, we review the current state of phylogenetic and biogeographical knowledge of the endemic angiosperm genera. We also propose a new stratified biogeographical model, based on palaeogeographical evidence, allowing the inference of the spatio‐temporal history of Madagascan taxa. The implications of past climate change and extinction events on the evolutionary history of the endemic genera are also discussed in depth. Phylogenetic information was available for 184 of the 310 endemic genera (59.3%) and divergence time estimates were available for 67 (21.6%). Based on this evidence, we show the importance of phylogenetic clustering in the assemblage of the current Madagascan diversity (26% of the genera have a sister lineage from Madagascar) and confirm the strong floristic affinities with Africa, South‐East Asia and India (22%, 9.1% and 6.2% of the genera, respectively). The close links with the Comoros, Mascarenes and Seychelles are also discussed. These results also support an Eocene/Oligocene onset for the origin of the Madagascan generic endemic flora, with the majority arising in the Miocene or more recently. These results therefore de‐emphasize the importance of the Gondwanan break‐up on the evolution of the flora. There is, however, some fossil evidence suggesting that recent extinctions (e.g. Sarcolaenaceae, a current Madagascan endemic, in southern Africa) might blur vicariance patterns and favour dispersal explanations for current biodiversity patterns. © 2013 The Linnean Society of London     

云南怒江河谷种子植物区系的特有现象

怒江是我国西南地区重要的大河之一,研究其河谷植物区系特有现象对于认识该区植物区系的特点、发生和演变以及生物多样性保护等具有十分重要的意义。本文采用样方调查和样线调查法,沿怒江河谷从最南端的中缅边境(木城)到滇藏交界地区(秋那桶)对云南怒江河谷的种子植物进行了实地调查,并通过查阅文献和标本鉴定,统计得到该区域野生种子植物164科776属1718种。其中东亚特有科4科,中国特有属1属,中国特有种316种(含68种云南特有种,包括怒江河谷特有种3种)。对该区域种子植物区系及特有性研究结果显示,其种子植物区系地理成分复杂,与其他地区植物区系联系广泛,并具有强烈的热带性;该区域种子植物科、属、种的特有性均不显著,科级特有现象表明本区系属于东亚植物区系的一部分;本区域的中国特有种在云南层面与滇西南、滇西北联系密切,在全国层面与南方与西南关系密切,在东亚层面与中国-喜马拉雅地区联系最为紧密。     

Origin and differentiation of endemism in the flora of China

The present paper analyzed 239 endemic genera in 67 families in the flora of seed plants in China.The results showed that there are five families containing more than ten endemic genera,namely,Gesneriaceae (27),which hereafter refers to the number of endemic genera in China,Composite (20),Labiatae (12),Cruciferae (11),and Umbelliferae (10),15 families with two endemic genera,and another 30 families with only one endemic genus.Four monotypic families (Ginkgoaceae,Davidiaceae,Eucommiaceae and Acanthochlamydaceae)are the most ancient,relict and characteristic in the flora of seed plants in China.Based on integrative data of systematics,fossil history,and morphological and molecular evidence of these genera,their origin,evolution and relationships were discussed.In gymnosperms,all endemic genera are relicts of the Arctic-Tertiary flora,having earlier evolutionary history,and can be traced back to the Cretaceous or to the Jurassic and even earlier.In angiosperms,the endemic genera are mostly relicts,and are represented in all lineages in the"Eight-Class System ofClassification of Angiosperms",and endemism can be found in almost every evolutionary stage of extant angiosperms.The relict genera once occupied huge areas in the northern hemisphere in the Tertiary or the late Cretaceous,while neo-endemism mostly originated in the late Tertiary.They came from Arctic-Tertiary,Paleo-tropical-Tertiary and Tethys-Tertiary florisitic elements,and the blend of the three elements with many genera of autochthonous origin.The endemism was formed when some dispersal routes such as the North Atlantic Land Bridge,and the Bering Bridge became discontinuous during the Tertiary,as well as the climate change and glaciations in the late Tertiary and the Quaternary.Therefore,the late Tertiary is the starting point of extant endemism of the flora in China.     

Origin and differentiation of endemism in the flora of China

The present paper analyzed 239 endemic genera in 67 families in the flora of seed plants in China. The results showed that there are five families containing more than ten endemic genera, namely, Gesneriaceae (27), which hereafter refers to the number of endemic genera in China, Composite (20), Labiatae (12), Cruciferae (11), and Umbelliferae (10), 15 families with two endemic genera, and another 30 families with only one endemic genus. Four monotypic families (Ginkgoaceae, Davidiaceae, Eucommiaceae and Acanthochlamydaceae) are the most ancient, relict and characteristic in the flora of seed plants in China. Based on integrative data of systematics, fossil history, and morphological and molecular evidence of these genera, their origin, evolution and relationships were discussed. In gymnosperms, all endemic genera are relicts of the Arctic-Tertiary flora, having earlier evolutionary history, and can be traced back to the Cretaceous or to the Jurassic and even earlier. In angiosperms, the endemic genera are mostly relicts, and are represented in all lineages in the “Eight-Class System of Classification of Angiosperms”, and endemism can be found in almost every evolutionary stage of extant angiosperms. The relict genera once occupied huge areas in the northern hemisphere in the Tertiary or the late Cretaceous, while neo-endemism mostly originated in the late Tertiary. They came from Arctic-Tertiary, Paleo-tropical-Tertiary and Tethys-Tertiary florisitic elements, and the blend of the three elements with many genera of autochthonous origin. The endemism was formed when some dispersal routes such as the North Atlantic Land Bridge, and the Bering Bridge became discontinuous during the Tertiary, as well as the climate change and glaciations in the late Tertiary and the Quaternary. Therefore, the late Tertiary is the starting point of extant endemism of the flora in China. __________ Translated from Acta Botanica Yunnanica, 2005, 27(6): 577–604 [译自: 云南植物研究]     

Features and distribution patterns of Chinese endemic seed plant species

We compiled and identified a list of Chinese. endemic seed plant species based on a large number of published References and expert reviews. The characters of these seed plant species and their distribution patterns were described at length. China is rich in endemic seed plants, with a total of 14 939 species (accounting for 52.1%of its total seed plant species) belonging to 1584 genera and 191 families. Temperate families and genera have a significantly higher proportion of endemism than cosmopolitan and tropical ones. The most primitive and derived groups have significantly higher endemism than the other groups. The endemism of tree, shrub, and liana or vine is higher than that of total species; in contrast, the endemism of herb is lower than that of total species. Geographically,these Chinese endemic plants are mainly distributed in Yunnan and Sichuan provinces, southwest China. Species richness and proportion of these endemic plants decrease with increased latitude and have a unimodal response to altitude. The peak value of proportion of endemism is at higher altitudes than that of total species and endemic species richness. The proportions of endemic shrub, liana or vine, and herb increase with altitude and have a clear unimodal curve. In contrast, the proportion of tree increases with altitude, with a sudden increase at～4000 m and has a completely different model. To date, our study provides the most comprehensive list of Chinese endemic seed plant species and their basic composition and distribution features.