Phylogeny and biogeography of Chinese sisorid catfishes re-examined using mitochondrial cytochrome b and 16S rRNA gene sequences

The family Sisoridae is one of the largest and most diverse Asiatic catfish families, most species occurring in the water systems of the Qinhai-Tibetan Plateau and East Himalayas. To date published morphological and molecular phylogenetics hypotheses of sisorid catfishes are part congruent, and there are some areas of significant disagreement with respect to intergeneric relationships. We used mitochondrial cytochrome b and 16S rRNA gene sequences to clarify existing gaps in phylogenetics and to test conflicting vicariant and dispersal biogeographical hypotheses of Chinese sisorids using dispersal-vicariance analysis and weighted ancestral area analysis in combination with palaeogeographical data as well as molecular clock calibration. Our results suggest that: (1) Chinese sisorid catfishes form a monophyletic group with two distinct clades, one represented by (Gagata (Bagarius, Glyptothorax)) and the other by (glyptosternoids, Pseudecheneis); (2) the glyptosternoid is a monophyletic group and Glyptosternum, Glaridoglanis, and Exostoma are three basal species having a primitive position among it; (3) a hypothesis referring to Pseudecheneis as the sister group of the glyptosternoids, based on morphological evidence, is supported; (4) the genus Pareuchiloglanis, as presently defined, is not monophyletic; (5) congruent with previous hypotheses, the uplift of Qinghai-Tibetan Plateau played a primary role in the speciation and radiation of the Chinese sisorids; and (6) an evolutionary scenario combining aspects of both vicariance and dispersal theory is necessary to explain the distribution pattern of the glyptosternoids. In addition, using a cytochrome b substitution rate of 0.91% per million years and 0.23% for 16S rRNA, we tentatively date that the glyptosternoids most possibly originated in Oligocene-Miocene boundary (19-24Myr), and radiated from Miocene to Pleistocene, along with a center of origin in the Irrawaddy-Tsangpo drainages and several rapid speciation in a relatively short time. (c) 2005 Elsevier Inc. All rights reserved.

澜沧江姬鼠（Apodemus ilex）种群遗传结构及其生物地理分析

澜沧江姬鼠（Apodemus ilex）为小型啮齿类动物，长期以来常被认为是中华姬鼠（A. draco）或长尾姬鼠（A. orestes）的同物异名，但近年基于线粒体Cyt b 的研究证明，该类群与中华姬鼠的遗传距离达到了种间水平，并被认为是一个独立种。本文提取、扩增并测定了来自云南14个地区42个产地156个澜沧江姬鼠的Cyt b 全序列，并将GenBank中的3条澜沧江姬鼠的Cyt b 全序列纳入分析，选取福建武夷山与四川峨眉山的2个中华姬鼠样品的Cyt b 全序列，以及台湾姬鼠、大耳姬鼠、高山姬鼠Cyt b 全序列作为外群，利用贝叶斯法和最大似然法构建系统发育树，并使用Network分析，分子变异分析（AMOVA）分析、错配分析（Mismatch analysis）与Fu`Fs检验等方法，探讨了这些地区澜沧江姬鼠的种群遗传结构，种群动态及生物地理格局。结果表明：云南地区过去被鉴定为中华姬鼠的样品均属于澜沧江姬鼠，澜沧江姬鼠与中华姬鼠间的遗传距离（K2P-ds+v）达到0.091，显著超过姬鼠属内种间差距（0.080），支持澜沧江姬鼠独立种的地位；该种不同地理种群可大致以澜沧江为界分为两大支系，且每个支系又各分为两个亚支系；进一步的AMOVA分析表明遗传变异主要来源于两大支系之间，而错配分析与Fu`Fs检验表明澜沧江姬鼠各地理种群及其两个支系都经历过多次扩张事件，这可能是和冰期与间冰期的轮回交替有关；分子系统树和中介网络图表明地理环境的隔离对于澜沧江姬鼠种群分化存在明显影响，其中澜沧江的阻隔作用最为显著。基于松散分子钟（Relax molecular clock）分析，中华姬鼠和澜沧江姬鼠的分歧时间大约在2.98 Ma（95％HPD: 4.32-1.88），而澜沧江姬鼠则在1.13 Ma（95％HPD: 1.95-0.65）分成两个支系。按照平均分歧时间来看，澜沧江姬鼠两个支系的的分歧事件发生在鄱阳冰期（1.2-0.9 Ma），两个支系内部进一步分化为两支的时间非常接近，分别为：Clade 1中为0.67 Ma （95％HPD: 1.17-0.34）和Clade 2 中为0.64 Ma (95％HPD: 1.17-0.36)，这种隔离种群各自产生分化的时间却非常接近，这提示其分化事件可能是受到古气候如冰期或间冰期的影响所产生。

隆肛蛙属Feirana种群的系统学与动物地理学研究

对隆肛蛙属的物种构成进行了订正，建立新属肛刺蛙属Yerana gen. nov.；订正后的隆肛蛙属现仅隶2种， 即隆肛蛙F. quadrana和太行隆肛蛙F. taihangnicus。运用形态学分析探讨了隆肛蛙属物种及种群的形态差异和分类关系，通过分子系统学研究探讨了隆肛蛙属物种及种群的分类和系统发育关系，运用动物地理学方法结合系统发育关系探讨了隆肛蛙属种群的地理分布格局成因与历史过程。主要结果和推论如下： 1．隆肛蛙属物种构成的订正及一新属建立 建立新属肛刺蛙属，将隆肛蛙属中的原叶氏隆肛蛙F. yei归隶新属肛刺蛙属并更名为叶氏肛刺蛙Y. yei，，新属建立的主要依据为：（1）雄性肛部隆起，肛孔下方有两个布满黑刺的大的白色球形隆起，具单咽下内声囊， 第一指具婚刺；（2）形态量度分析表明叶氏肛刺蛙与隆肛蛙和太行隆肛蛙的形态差异远大于后两者之间的差异；（3）叶氏肛刺蛙的分布区与隆肛蛙和太行隆肛蛙的分布区距离较远且呈隔离状态；（4）分子系统学研究资料（Jiang et al.,2005）证明叶氏肛刺蛙与隆肛蛙和太行隆肛蛙非单系发生；叶氏肛刺蛙在第二支中位于基部。因此，隆肛蛙属现仅隶2种，即隆肛蛙和太行隆肛蛙。 2．隆肛蛙属种群形态学研究 对隆肛蛙属中隆肛蛙和太行隆肛蛙的15个地理种群565只标本的28项形态性状进行了测量，运用典型判别分析法对其分析的结果表明：（1）太行隆肛蛙与隆肛蛙形态差异明显，支持其为不同的物种；（2）原隆肛蛙河南伏牛山种群和山西中条山种群应为太行隆肛蛙的地理种群；（3）隆肛蛙不同地理种群之间形态差异明显，其中四川安县种群、陕西周至种群和湖北利川种群与模式产地重庆巫山种群的差异可能达到了亚种或亚种以上分化水平。对隆肛蛙属量度分析的15个种群进行定性形态分析表明其分为三种形态型，对应隆肛蛙、过渡型和太行隆肛蛙，其变异特征主要为内跗褶、雄性肛部隆起及疣粒分布、第五趾外侧缘膜等，这与量度分析结果相似。 3．隆肛蛙属种群分子系统学研究 测定隆肛蛙属Feirana的2种19种群的线粒体12S rRNA和16S rRNA基因片段、ND2基因的DNA序列，比对后共计1953bps。（1）遗传多样性与距离分析：结果表明，隆肛蛙属种群具很高的遗传多样性，19个种群样品表现出19种单倍型（遗传多样性指数Hd＝1.0）； ND2基因的进化信息含量远高于12SrRNA和16SrRNA。隆肛蛙属2种群组内的种群间的遗传距离远小于两种群组间的距离，种群在不同基因上的遗传距离表现的关系与对应的系统树一致。（2）系统发育关系分析：结果表明，不同基因片断基于不同方法构建的隆肛蛙属种群系统发育树结构基本一致，基本表明隆肛蛙属种群为单系发生；它们在系统树中分为两大支，分别对应于隆肛蛙和太行隆肛蛙；支持中条山种群（沁水、历山和济源种群）和伏牛山种群（栾川和内乡种群）为太行隆肛蛙的地理种群，而原隆肛蛙秦岭中东段的部分种群（柞水、宁陕、长安大坝沟种群）也应为太行隆肛蛙的地理种群。（3）亚种分化分析：根据遗传距离分析和系统发育关系分析结果，并考虑形态上的差异情况以及地理分布信息，隆肛蛙所隶种群组可分为2亚种，即隆肛蛙指名亚种F. quadrana quadrana包括四川盆地东缘大巴山东段-巫山-武陵山北麓种群和秦岭中段（周至板房子和长安广货街）种群，他们在系统关系树上聚为一支；安县亚种F. quadrana anxianensis包括四川盆地西缘岷山东麓-龙门山-大巴山和秦岭西段的种群（安县、青川、文县、南江和凤县种群），他们在系统关系树上聚为一支。太行隆肛蛙所隶种群组也可分为2亚种，即太行隆肛蛙指名亚种F. taihangnicus taihangnicus包括中条山的种群（沁水、历山和济源种群）和中东秦岭的部分种群（柞水、长安大坝沟和宁陕种群），他们在系统关系树上聚为一支；太行隆肛蛙伏牛亚种F. taihangnicus funiuensis，为伏牛山地区的种群（栾川和内乡种群），他们在系统关系树上聚为一支。 4．隆肛蛙属种群动物地理学研究 隆肛蛙属19种群的分歧年代分析： 以长江巫山段和黄河三门峡段的形成历史时期为参考点，根据已测隆肛蛙属19种群及其外群包括N. pleski、P. yunnanesis、P. robertingeri、F. limnocharis的1953bps DNA序列构建分子钟，获得各支系的分歧年代。结果表明：①棘蛙族在70Ma左右开始其独立演化历程，这与Roelants et al.（2004）的分析结果～60±15Ma左右开始分化基本一致，后者印证了本文的分子钟。②隆肛蛙属的起始分化年代较早，隆肛蛙和太行隆肛蛙两种群组的最近祖先种群大概在46Ma～50Ma左右；隆肛蛙和太行隆肛蛙种群组内的种群分化年代相对两种群组间晚得多， 隆肛蛙种群组内两亚种分化起始年代约为10Ma左右，而太行隆肛蛙种群组内两亚种分化起始年代约为6Ma。 隆肛蛙属种群分布格局形成过程分析： ①隆肛蛙属的系统关系与地理分布格局密切相关，大部分系统分支分级与地理距离成正比；②隆肛蛙属最近祖先种群的分化中心可能位于秦岭中部地区， 隆肛蛙属的种群分布格局的形成表现为隔离分化与扩散相结合的机制，由隔离分化产生的隆肛蛙祖先种群主要从秦岭中部向西南方向扩散，后隔离分化为两亚种；太行隆肛蛙祖先种群向东北方向扩散也分化为两亚种。 隆肛蛙属种群分布区域地质历史的探讨：本文所建分子钟和种群分化方式印证了该区域的几次主要地质事件，包括岷山-龙门山-西秦岭等地区的快速差异隆起、第四纪冰期等。 The specific composition of the genus Feirana should be revised. A new genus Yerana gen. nov.（Ranidae：Dicroglossinae）was established based on morphological data-set and molecular phylogeny, as a result, only two species F. quadrana and F. taihangnicus are classified into Feirana now. Morphological differences and taxonomy of populations of Feirana were investigated based on morphological and morphometric data; phylogenetic relationships and taxonomy of populations of Feirana were elucidated using molecular data, and then the proceeding of the distribution pattern of populations of Feirana were discussed. The main results and conclusions and proposals were presented as following: 1. Revising of the specific composition of the genus Feirana and establishment of a new genus The new genus Yerana, only containing the type species Y. yei, was established based on the following evidences: (1) In adult male, distinct up-heaved circular vesicle presents around the anal, and under anal there are two white balls on which black spines exist, black horny spines scatter on the upper side of first finger, and internal single subgular vocal sac presents; (2) there is obvious morphometric differences between Yerana and Feirana; (3) Yerana is distributed far from Feirana; (4) evidences of molecular phylogeny（Jiang et al.,2005）suggested that Yerana take a special phylogenetic clade which is different from other genus included in the tribe Paini. As a result, there are only two species in Feirana, i.e., F. quadrana and F. taihangnicus. 2. Morphological research of populations of Feirana Twenty-eight characters of 565 individuals of 15 populations of the genus Feirana were measured, the results of Canonical Discriminant analysis of the morphometric data-set indicated that: (1) there are very prominent differences between the two species F. quadrana and F. taihangnicus. The validity of species F. taihangnicus was approved here; (2) Mt. Funiu population and Mt. Zhongtiao population should belong to the species F. taihangnicus; (3) Obvious differences exist among 12 populations of F. quadrana, the differentiation among Zhouzhi population, Anxian population, Lichuan population, and Wushan population together with the others probably reach sub-specific or specific level. Result of morphological comparison between 15 different populations show that 3 morphological types are recogenized in according with F. quadrana, F. taihangnicus and intergradation, this result conform to the result of morphometric analysis. 3. Molecular phylogenetic study on populaions of Feirana Fragment of 12SrRNA and 16SrRNA genes, and ND2 gene of 19 populations of two species of Feirana were sequenced and aligned, from which 1953 bps were received. (1) analyses of genetic distance and hereditary diversity indicated that: genetic distance between populations in each group were less than distance between two groups of Feirana, 19 haplotypes were recognized from 19 samples of 19 populations, so the hereditary diversity of populations of Feirana was very high (Hd=1.0), phylogenetic information in ND2 gene is more than fragment sequence of 12SrRNA and 16SrRNA genes. (2) Result of molecular phylogeny indicate that the phylogenetic trees constructed using different methods based on different sequence data sets showed the revised genus Feirana is monophyletic since the 19 populations of Feirana were firstly clustered together as one large clade, which was further clustered into two major clades, corresponding to F. quadrana(GroupⅠ) and F. taihangnicus(GroupⅡ), respectively. So populations of Qinshui and Lishan in Mt. Zhongtiao, populations of Luanchuan and Neixiang in Mt. Funiu, and populations of Zhashui, Dabagou of Chang’an and Ningshan in eastern Mt. Qinling should belong to the species F. taihangnicus; (3) Subspecific differentiation. on the basis of genetic distance, phylogenetic trees and geographical distribution, F. quadrana should have two subspecies, i.e., F. quadrana qudadrana, consisting of the populations Guanghuojie of Chang’an and Zhouzhi in Mid-Mt. Qinling, populations in Wushan area and northern Mt. Wuling (Lichuan), and F. qudadrana anxianensis, consisting of the populations in eastern Mt. Ming shan-Mt. Longmen-western Mt. Daba-western Mt. Qinling (Anxian, Qingchuan, Wenxian, Nanjiang and Fengxian); F. taihangnicus should also has two subspecies, i.e., F. taihangnicus taihangnicus, consisting of the populations in Mt. Zhongtiao and eastern Mt. Qinling, and F. taihangnicus funiuensis, consisting of the populations in Mt. Funiu. 4. Zoogeography of populaions of Feirana Analysis for divergent time of 19 populations of Feirana: Using the dates of run-through of Wushan segment of Changjiang River as the time when the population of Lichuan started differentiated from the populations of Wushan and Shennongjia, and the dates of Sanmenxia segment of Yellow River as the time when the populations in Mt. Zhongtiao started differentiated from the population of Dabagou in Chang’an, molecular clock was established using sequences with 1953 bps of 19 populations of Feirana and outgroup including N. pleski, P. yunnanesis, P. robertingeri, F. limnocharis in order to estimate divergent time of all clades. Result of that indicated that: ① the tribe Paini started to evolve independently at about 70Ma when is in consistent with that estimated by Roelants et al.（2004）with result of about ～60±15Ma, they were corroborated by each other, this confirms the validity of this molecular clock; ② divergent time for speciation of Feriana is early, ancestral populations of F. quadrana and F. taihangnicus were found about 46Ma～50Ma; differentiation of populations within species is greatly late to the divergence of the two species, divergent time for F. quadrana is 10Ma and divergent time for F. taihangnicus is 6Ma. Proceeding of distribution pattern of Feirana. Phylogenetic relationships of populations of Feirana matched quite with distribution pattern of them, the relationships among clades showed in phylogenetic trees is direct ratio to geographical distance of them; the estimated date of speciation between two species of Feirana was as early as speciation of Paa yunnanesis and Nanara pleski; middle part of Mt. Qinling is the center of speciation of Feirana, combination of mult-events of dispersal and vicariance are probably the mechanism of speciation of Feirana, F. quadrana colonized the mid-Mt. Qinling and then differentiated into two subspecies in southwest direction, ancestral population of F. taihangnicus colonized the mid-Mt. Qinling and then differentiated into two subspecies in northeast direction. On geological history of the distribution of Feirana. According to molecular clock and speciation model of populations of Feirana, some geological events are confirmed, including special rise of Mt. Minshan- Mt. Longmen-western Mt. Qinling, glacial age.

Origin of mitochondrial DNA diversity of domestic yaks

Background: The domestication of plants and animals was extremely important anthropologically. Previous studies have revealed a general tendency for populations of livestock species to include deeply divergent maternal lineages, indicating that they were domesticated in multiple, independent events from genetically discrete wild populations. However, in water buffalo, there are suggestions that a similar deep maternal bifurcation may have originated from a single population. These hypotheses have rarely been rigorously tested because of a lack of sufficient wild samples. To investigate the origin of the domestic yak (Poephagus grunnies), we analyzed 637 bp of maternal inherited mtDNA from 13 wild yaks (including eight wild yaks from a small population in west Qinghai) and 250 domesticated yaks from major herding regions.Results: The domestic yak populations had two deeply divergent phylogenetic groups with a divergence time of > 100,000 yrs BP. We here show that haplotypes clustering with two deeply divergent maternal lineages in domesticated yaks occur in a single, small, wild population. This finding suggests that all domestic yaks are derived from a single wild gene pool. However, there is no clear correlation of the mtDNA phylogenetic clades and the 10 morphological types of sampled yaks indicating that the latter diversified recently. Relatively high diversity was found in Qinghai and Tibet around the current wild distribution, in accordance with previous suggestions that the earliest domestications occurred in this region. Conventional molecular clock estimation led to an unrealistic early dating of the start of the domestication. However, Bayesian estimation of the coalescence time allowing a relaxation of the mutation rateConclusion: The information gathered here and the previous studies of other animals show that the demographic histories of domestication of livestock species were highly diverse despite the common general feature of deeply divergent maternal lineages. The results further suggest that domestication of local wild prey ungulate animals was a common occurrence during the development of human civilization following the postglacial colonization in different locations of the world, including the high, arid Qinghai-Tibetan Plateau.

Radiation and diversification within the Ligularia-Cremanthodium-Parasenecio complex (Asteraceae) triggered by uplift of the Qinghai-Tibetan Plateau

The Ligularia-Cremanthodium-Parasenecio (L-C-P) complex of the Tussilagininae (Asteraceae: Senecioneae) contains more than 200 species that are endemic to the Qinghai-Tibetan Plateau in eastern Asia. These species are morphologically distinct; however, their relationships appear complex. A phylogenetic analysis of members of the complex and selected taxa, of the tribe Senecioneae was conducted using chloroplast (ndhF and trnL-F) and nuclear (ITS) sequences. Phylogenetic trees were constructed from individual and combined datasets of the three different sequences. All analyses suggested that Doronicum, a genus that has been included in the Tussilagininae, should be excluded from this subtribe and placed at the base of the tribe Senecioneae. In addition, the Tussilagininae should be broadly circumscribed to include the Tephroseridinae. Within the expanded Tussilagininae containing all 13 genera occurring in eastern Asia, Tussilago and NSPetasites diverged early as a separate lineage, while the remaining I I genera comprise an expanded L-C-P complex clade. We suggest that the L-C-P clade, which is largely unresolved, most likely originated as a consequence of an explosive radiation. The few monophyletic subclades identified in the L-C-P clade with robust support further suggest that some genera of Tussilagininae from eastern Asia require generic re-circumscriptions given the occurrence of subclades containing species of the same genus in different parts of the phylogentic tree due to homoplasy of important morphological characters used to delimit them. Molecular-clock analyses suggest that the explosive radiation of the L-C-P complex occurred mostly within the last 20 million years, which falls well within the period of recent major uplifts of the Qinghai-Tibetan Plateau between the early Miocene to the Pleistocene. It is proposed that significant increases in geological and ecological diversity that accompanied such uplifting, most likely promoted rapid and continuous allopatric speciation in small and isolated populations, and allowed fixation or acquisition of similar morphological characters within unrelated lineages. This phenomenon, possibly combined with interspecific diploid hybridization because of secondary sympatry during relatively stable stages between different uplifts, could be a major cause of high species diversity in the Qinghai-Tibetan Plateau and adjacent areas of eastern Asia. (c) 2005 Elsevier Inc. All rights reserved.

Biogeography in deep time - What do phylogenetics, geology, and paleoclimate tell us about early platyrrhine evolution?

Molecular data have converged on a consensus about the genus-level phylogeny of extant platyrrhine monkeys, but for most extinct taxa and certainly for those older than the Pleistocene we must rely upon morphological evidence from fossils. This raises the question as to how well anatomical data mirror molecular phylogenies and how best to deal with discrepancies between the molecular and morphological data as we seek to extend our phylogenies to the placement of fossil taxa. Here I present parsimony-based phylogenetic analyses of extant and fossil platyrrhines based on an anatomical dataset of 399 dental characters and osteological features of the cranium and postcranium. I sample 16 extant taxa (one from each platyrrhine genus) and 20 extinct taxa of platyrrhines. The tree structure is constrained with a "molecular scaffold" of extant species as implemented in maximum parsimony using PAUP with the molecular-based 'backbone' approach. The data set encompasses most of the known extinct species of platyrrhines, ranging in age from latest Oligocene (∼26 Ma) to the Recent. The tree is rooted with extant catarrhines, and Late Eocene and Early Oligocene African anthropoids. Among the more interesting patterns to emerge are: (1) known early platyrrhines from the Late Oligocene through Early Miocene (26-16.5Ma) represent only stem platyrrhine taxa; (2) representatives of the three living platyrrhine families first occur between 15.7 Ma and 13.5 Ma; and (3) recently extinct primates from the Greater Antilles (Cuba, Jamaica, Hispaniola) are sister to the clade of extant platyrrhines and may have diverged in the Early Miocene. It is probable that the crown platyrrhine clade did not originate before about 20-24 Ma, a conclusion consistent with the phylogenetic analysis of fossil taxa presented here and with recent molecular clock estimates. The following biogeographic scenario is consistent with the phylogenetic findings and climatic and geologic evidence: Tropical South America has been a center for platyrrhine diversification since platyrrhines arrived on the continent in the middle Cenozoic. Platyrrhines dispersed from tropical South America to Patagonia at ∼25-24 Ma via a "Paraná Portal" through eastern South America across a retreating Paranense Sea. Phylogenetic bracketing suggests Antillean primates arrived via a sweepstakes route or island chain from northern South America in the Early Miocene, not via a proposed land bridge or island chain (GAARlandia) in the Early Oligocene (∼34 Ma). Patagonian and Antillean platyrrhines went extinct without leaving living descendants, the former at the end of the Early Miocene and the latter within the past six thousand years. Molecular evidence suggests crown platyrrhines arrived in Central America by crossing an intermittent connection through the Isthmus of Panama at or after 3.5Ma. Any more ancient Central American primates, should they be discovered, are unlikely to have given rise to the extant Central American taxa in situ.

Chaetopterid tubes from vent and seep sites: Implications for fossil record and evolutionary history of vent and seep annelids

Vestimentiferan tube worms living at deep-sea hydrothermal vents and cold seeps have been considered as a clade with a long and continuing evolutionary history in these ecosystems. Whereas the fossil record appears to support this view, molecular age estimates do not. The two main features that are used to identify vestimentiferan tubes in the fossil record are longitudinal ridges on the tube's surface and a tube wall constructed of multiple layers. It is shown here that chaetopterid tubes from modern vents and seeps—as well as a number of fossil tubes from shallow-water environments—also show these two features. This calls for a more cautious interpretation of tubular fossils from ancient vent and seep deposits. We suggest that: current estimates for a relatively young evolutionary age based on molecular clock methods may be more reliable than the inferences of ancient “vestimentiferans” based on putative fossils of these worms; not all of these putative fossils actually belong to this group; and that tubes from fossil seeps should be investigated for chitinous remains to substantiate claims of their potential siboglinid affinities.

Species boundaries and phylogenetic relationships within the green algal genus Codium (Bryopsidales) based on plastid DNA sequences

Despite the potential model role of the green algal genus Codium for studies of marine speciation and evolution, there have been difficulties with species delimitation and a molecular phylogenetic framework was lacking. In the present study, 74 evolutionarily significant units (ESUs) are delimited using 227 rbcL exon 1 sequences obtained from specimens collected throughout the genus' range. Several morpho-species were shown to be poorly defined, with some clearly in need of lumping and others containing pseudo-cryptic diversity. A phylogenetic hypothesis of 72 Codium ESUs is inferred from rbcL exon 1 and rps3-rp/16 sequence data using a conventional nucleotide substitution model (GTR + Gamma + I), a codon position model and a covariotide (covarion) model, and the fit of a multitude of substitution models and alignment partitioning strategies to the sequence data is reported. Molecular clock tree rooting was carried out because out-group rooting was probably affected by phylogenetic bias. Several aspects of the evolution of morphological features of Codium are discussed and the inferred phylogenetic hypothesis is used as a framework to study the biogeography of the genus, both at a global scale and within the Indian Ocean. (c) 2007 Elsevier Inc. All rights reserved.

The Continuing Debate on Deep Molluscan Phylogeny: Evidence for Serialia (Mollusca, Monoplacophora + Polyplacophora)

Molluscs are a diverse animal phylum with a formidable fossil record. Although there is little doubt about the monophyly of the eight extant classes, relationships between these groups are controversial.We analysed a comprehensive multilocus molecular data set for molluscs, the first to include multiple species from all classes, including five monoplacophorans in both extant families. Our analyses of fivemarkers resolve two major clades: the first includes gastropods and bivalves sister to Serialia (monoplacophorans and chitons), and the second comprises scaphopods sister to aplacophorans and cephalopods. Traditional groupings such as Testaria, Aculifera, and Conchifera are rejected by our data with significant Approximately Unbiased (AU) test values. A new molecular clock indicates that molluscs had a terminal Precambrian origin with rapid divergence of all eight extant classes in the Cambrian. Therecovery of Serialia as a derived, Late Cambrian clade is potentially in line with the stratigraphic chronology of morphologically heterogeneous early mollusc fossils. Serialia is in conflict with traditional molluscan classifications and recent phylogenomic data. Yet our hypothesis, as others from molecular data, implies frequent molluscan shell and body transformations by heterochronic shifts in development and multiple convergent adaptations, leading to the variable shells and body plans in extant lineages.

Origin of British and Irish mammals: disparate post-glacial colonisation and species introductions

Global climate changes during the Quaternary reveal much about broader evolutionary effects of environmental change. Detailed regional studies reveal how evolutionary lineages and novel communities and ecosystems, emerge through glacial bottlenecks or from refugia. There have been significant advances in benthic imaging and dating, particularly with respect to the movements of the British (Scottish) and Irish ice sheets and associated changes in sea level during and after the Last Glacial Maximum (LGM). Ireland has been isolated as an island for approximately twice as long as Britain with no evidence of any substantial, enduring land bridge between these islands after ca 15 kya. Recent biogeographical studies show that Britain's mammal community is akin to those of southern parts of Scandinavia, The Netherlands and Belgium, but the much lower mammal species richness of Ireland is unique and needs explanation. Here, we consider physiographic, archaeological, phylogeographical i.e. molecular genetic, and biological evidence comprising ecological, behavioural and morphological data, to review how mammal species recolonized western Europe after the LGM with emphasis on Britain and, in particular, Ireland. We focus on why these close neighbours had such different mammal fauna in the early Holocene, the stability of ecosystems after LGM subject to climate change and later species introductions.

There is general concordance of archaeological and molecular genetic evidence where data allow some insight into history after the LGM. Phylogeography reveals the process of recolonization, e.g. with respect to source of colonizers and anthropogenic influence, whilst archaeological data reveal timing more precisely through carbon dating and stratigraphy. More representative samples and improved calibration of the ‘molecular clock’ will lead to further insights with regards to the influence of successive glaciations. Species showing greatest morphological, behavioural and ecological divergence in Ireland in comparison to Britain and continental Europe, were also those which arrived in Ireland very early in the Holocene either with or without the assistance of people. Cold tolerant mammal species recolonized quickly after LGM but disappeared, potentially as a result of a short period of rapid warming. Other early arrivals were less cold tolerant and succumbed to the colder conditions during the Younger Dryas or shortly after the start of the Holocene (11.5 kya), or the area of suitable habitat was insufficient to sustain a viable population especially in larger species. Late Pleistocene mammals in Ireland were restricted to those able to colonize up to ca 15 kya, probably originating from adjacent areas of unglaciated Britain and land now below sea level, to the south and west (of Ireland). These few, early colonizers retain genetic diversity which dates from before the LGM. Late Pleistocene Ireland, therefore, had a much depleted complement of mammal species in comparison to Britain.

Mammal species, colonising predominantly from southeast and east Europe occupied west Europe only as far as Britain between ca 15 and 8 kya, were excluded from Ireland by the Irish and Celtic Seas. Smaller species in particular failed to colonise Ireland. Britain being isolated as an island from ca. 8 kya has similar species richness and composition to adjacent lowland areas of northwest continental Europe and its mammals almost all show strongest genetic affinity to populations in neighbouring continental Europe with a few retaining genotypes associated with earlier, western lineages.

The role of people in the deliberate introduction of mammal species and distinct genotypes is much more significant with regards to Ireland than Britain reflecting the larger species richness of the latter and its more enduring land link with continental Europe. The prime motivation of early people in moving mammals was likely to be resource driven but also potentially cultural; as elsewhere, people exploring uninhabited places introduced species for food and the materials they required to survive. It is possible that the process of introduction of mammals to Ireland commenced during the Mesolithic and accelerated with Neolithic people. Irish populations of these long established, introduced species show some unique genetic variation whilst retaining traces of their origins principally from Britain but in some cases, Scandinavia and Iberia. It is of particular interest that they may retain genetic forms now absent from their source populations. Further species introductions, during the Bronze and late Iron Ages, and Viking and Norman invasions, follow the same pattern but lack the time for genetic divergence from their source populations. Accidental introductions of commensal species show considerable genetic diversity based on numerous translocations along the eastern Atlantic coastline. More recent accidental and deliberate introductions are characterised by a lack of genetic diversity other than that explicable by more than one introduction.

The substantial advances in understanding the postglacial origins and genetic diversity of British and Irish mammals, the role of early people in species translocations, and determination of species that are more recently introduced, should inform policy decisions with regards to species and genetic conservation. Conservation should prioritise early, naturally recolonizing species and those brought in by early people reflecting their long association with these islands. These early arrivals in Britain and Ireland and associated islands show genetic diversity that may be of value in mitigating anthropogenic climate change across Europe. In contrast, more recent introductions are likely to disturb ecosystems greatly, lead to loss of diversity and should be controlled. This challenge is more severe in Ireland where the number and proportion of invasive species from the 19th century to the present has been greater than in Britain.

Are there two species of Pygmy Shrews (Sorex)? Revisiting the question using DNA sequence data

Pygmy Shrews in North America have variously been considered to be one species (Sorex hoyi) or two species (S. hoyi and S. thompsoni). Currently, only S. hoyi is recognized. In this study, we examine mitochondrial DNA sequence data for the cytochrome b gene to evaluate the level of differentiation and phylogeographic relationships among eleven samples of Pygmy Shrews from across Canada. Pygmy Shrews from eastern Canada (i.e., Ontario, Quebec, New Brunswick, Nova Scotia, and Prince Edward Island) are distinct from Pygmy Shrews from western Canada (Alberta, Yukon) and Alaska. The average level of sequence divergence between these clades (3.3%) falls within the range of values for other recognized pairs of sister species of shrews. A molecular clock based on third position transversion substitutions suggests that these two lineages diverged between 0.44 and 1.67 million years ago. These molecular phylogenetic data. combined with a reinterpretation of previously published morphological data, are suggestive of separate species status for S. hoyi and S. thompsoni as has been previously argued by others. Further analysis of specimens from geographically intermediate areas (e.g., Manitoba. northern Ontario) is required to determine if there is secondary contact and/or introgression between these two putative species.

Discordances between phylogenetic and morphological patterns in alpine leaf beetles attest to an intricate biogeographic history of lineages in postglacial Europe.

Pleistocene glacial and interglacial periods have moulded the evolutionary history of European cold-adapted organisms. The role of the different mountain massifs has, however, not been accurately investigated in the case of high-altitude insect species. Here, we focus on three closely related species of non-flying leaf beetles of the genus Oreina (Coleoptera, Chrysomelidae), which are often found in sympatry within the mountain ranges of Europe. After showing that the species concept as currently applied does not match barcoding results, we show, based on more than 700 sequences from one nuclear and three mitochondrial genes, the role of biogeography in shaping the phylogenetic hypothesis. Dating the phylogeny using an insect molecular clock, we show that the earliest lineages diverged more than 1 Mya and that the main shift in diversification rate occurred between 0.36 and 0.18 Mya. By using a probabilistic approach on the parsimony-based dispersal/vicariance framework (MP-DIVA) as well as a direct likelihood method of state change optimization, we show that the Alps acted as a cross-roads with multiple events of dispersal to and reinvasion from neighbouring mountains. However, the relative importance of vicariance vs. dispersal events on the process of rapid diversification remains difficult to evaluate because of a bias towards overestimation of vicariance in the DIVA algorithm. Parallels are drawn with recent studies of cold-adapted species, although our study reveals novel patterns in diversity and genetic links between European mountains, and highlights the importance of neglected regions, such as the Jura and the Balkanic range.

Filogenia y genética poblacional del género Androcymbium (Colchiceae)

En este trabajo se ha estudiado el género Androcymbium (Colchicaceae) a dos niveles: macro- y micro- evolutivo. A nivel microevolutivo se ha obtenido que para las especies de Sudáfrica oriental la componente interpoblacional es muy importante para explicar la distribución de la variabilidad genética, igual que en Sudáfrica occidental. Para las especies de Namibia, la componente mas importante es la intrapoblacional, igual que en el norte de África. A nivel macroevolutivo se ha obtenido que el origen del género se sitúa en Sudáfrica occidental, datándose en 11,22 ma. Este género ha resultado ser parafilético, dada la aparición conjunta en un mismo clado de especies de Androcymbium y Colchicum, y las especies del norte de África derivan de un taxa de Namibia que llegó a la cuenca Mediterránea a principios del Plioceno gracias a la formación de un corredor árido entre las zonas áridas del suroeste y este de África.

Detecting the node-density artifact in phylogeny reconstruction

The node-density effect is an artifact of phylogeny reconstruction that can cause branch lengths to be underestimated in areas of the tree with fewer taxa. Webster, Payne, and Pagel (2003, Science 301:478) introduced a statistical procedure (the "delta" test) to detect this artifact, and here we report the results of computer simulations that examine the test's performance. In a sample of 50,000 random data sets, we find that the delta test detects the artifact in 94.4% of cases in which it is present. When the artifact is not present (n = 10,000 simulated data sets) the test showed a type I error rate of approximately 1.69%, incorrectly reporting the artifact in 169 data sets. Three measures of tree shape or "balance" failed to predict the size of the node-density effect. This may reflect the relative homogeneity of our randomly generated topologies, but emphasizes that nearly any topology can suffer from the artifact, the effect not being confined only to highly unevenly sampled or otherwise imbalanced trees. The ability to screen phylogenies for the node-density artifact is important for phylogenetic inference and for researchers using phylogenetic trees to infer evolutionary processes, including their use in molecular clock dating. [Delta test; molecular clock; molecular evolution; node-density effect; phylogenetic reconstruction; speciation; simulation.]

An extreme case of plant-insect co-diversification: figs and fig-pollinating wasps

It is thought that speciation in phytophagous insects is often due to colonization of novel host plants, because radiations of plant and insect lineages are typically asynchronous. Recent phylogenetic comparisons have supported this model of diversification for both insect herbivores and specialized pollinators. An exceptional case where contemporaneous plant insect diversification might be expected is the obligate mutualism between fig trees (Ficus species, Moraceae) and their pollinating wasps (Agaonidae, Hymenoptera). The ubiquity and ecological significance of this mutualism in tropical and subtropical ecosystems has long intrigued biologists, but the systematic challenge posed by >750 interacting species pairs has hindered progress toward understanding its evolutionary history. In particular, taxon sampling and analytical tools have been insufficient for large-scale co-phylogenetic analyses. Here, we sampled nearly 200 interacting pairs of fig and wasp species from across the globe. Two supermatrices were assembled: on average, wasps had sequences from 77% of six genes (5.6kb), figs had sequences from 60% of five genes (5.5 kb), and overall 850 new DNA sequences were generated for this study. We also developed a new analytical tool, Jane 2, for event-based phylogenetic reconciliation analysis of very large data sets. Separate Bayesian phylogenetic analyses for figs and fig wasps under relaxed molecular clock assumptions indicate Cretaceous diversification of crown groups and contemporaneous divergence for nearly half of all fig and pollinator lineages. Event-based co-phylogenetic analyses further support the co-diversification hypothesis. Biogeographic analyses indicate that the presentday distribution of fig and pollinator lineages is consistent with an Eurasian origin and subsequent dispersal, rather than with Gondwanan vicariance. Overall, our findings indicate that the fig-pollinator mutualism represents an extreme case among plant-insect interactions of coordinated dispersal and long-term co-diversification.