Coalescent Method in Conjunction with Niche Modeling Reveals Cryptic Diversity among Centipedes in the Western Ghats of South India

Background: There has been growing interest in integrative taxonomy that uses data from multiple disciplines for species delimitation. Typically, in such studies, monophyly is taken as a proxy for taxonomic distinctiveness and these units are treated as potential species. However, monophyly could arise due to stochastic processes. Thus here, we have employed a recently developed tool based on coalescent approach to ascertain the taxonomic distinctiveness of various monophyletic units. Subsequently, the species status of these taxonomic units was further tested using corroborative evidence from morphology and ecology. This inter-disciplinary approach was implemented on endemic centipedes of the genus Digitipes (Attems 1930) from the Western Ghats (WG) biodiversity hotspot of India. The species of the genus Digitipes are morphologically conserved, despite their ancient late Cretaceous origin. Principal Findings: Our coalescent analysis based on mitochondrial dataset indicated the presence of nine putative species. The integrative approach, which includes nuclear, morphology, and climate datasets supported distinctiveness of eight putative species, of which three represent described species and five were new species. Among the five new species, three were morphologically cryptic species, emphasizing the effectiveness of this approach in discovering cryptic diversity in less explored areas of the tropics like the WG. In addition, species pairs showed variable divergence along the molecular, morphological and climate axes. Conclusions: A multidisciplinary approach illustrated here is successful in discovering cryptic diversity with an indication that the current estimates of invertebrate species richness for the WG might have been underestimated. Additionally, the importance of measuring multiple secondary properties of species while defining species boundaries was highlighted given variable divergence of each species pair across the disciplines.

Ecological niche modeling, cytogenetics and phylogeography of the genera Geomalacus and Letourneuxia (Gastropoda, Pulmonata) from the Iberian-Moroccan region

First described more that 150 years ago, the systematics of the genera Geomalacus and Letourneuxia (Arionidae, Gastropoda, Pulmonata) is still challenging. The taxonomic classification of arionid species is based on extremely labile characters such as body size or color that depends both on diet and environment, as well as age. Moreover, there is little information on the genetic diversity and population structure of the Iberian slugs that could provide extra clues to disentangle their problematic classification. The present work uses different analytical tools such as habitat suitability (Ecological Niche Modeling - ENM), cytogenetic analysis and phylogeography to establish the geographical distribution and evolutionary history of these pulmonate slugs. The potential distribution of the four Geomalacus species was modeled using ENM, which allowed the identification of new locations for G. malagensis, including a first report in Portugal. Also, it was predicted a much wider distribution for G. malagensis and G. oliveirae than previously known. Classical cytogenetic analyses were assayed with reproductive and a novel use of somatic tissues (mouth and tentacles) returning the number of chromosomes for the four Geomalacus species and L. numidica (n = 31, 2n = 62) and the respective karyotypes. G. malagensis and L. numidica present similar chromosome morphologies and karyotypic formulae, being more similar to each other than the Geomalacus among themselves. We further reconstructed the phylogeny of the genera Geomalacus and Letourneuxia using partial sequences of the mitochondrial cytochrome oxidase subunit I (COI) and the nuclear ribosomal small subunit (18S rRNA), and applied an independent evolutionary rate method, the indicator vectors correlation, to evaluate the existence of cryptic diversity within species. The five nominal species of Geomalacus and Letourneuxia comprise 14 well-supported cryptic lineages. Letourneuxia numidica was retrieved as a sister group of G. malagensis. G. oliveirae is paraphyletic with respect to G. anguiformis. According to our dating estimates, the most recent common ancestor of Geomalacus dates back to the Middle Miocene (end of the Serravallian stage). The major lineage splitting events within Geomalacus occurred during the dry periods of the Zanclean stage (5.3-3.6 million years) and some lineages were confined to more humid mountain areas of the Iberian Peninsula, which lead to a highly geographically structured mitochondrial genetic diversity. The major findings of this are the following: (1) provides updated species distribution maps for the Iberian Geomalacus expanding the known geographic distribution of the concerned species, (2) unravels the cryptic diversity within the genera Geomalacus and Letourneuxia, (3) Geomalacus oliveirae is paraphyletic with G. anguiformis and (4) Letourneuxia numidica is sister group of G. malagensis.

Ecological niche modeling and geographical distribution of pollinator and plants: A case study of Peponapis fervens (Smith, 1879) (Eucerini: Apidae) and Cucurbita species (Cucurbitaceae)

The bees of the Peponapes genus (Eucerini, Apidae) have a Neotropical distribution with the center of species diversity located in Mexico and are specialized in Cucurbita plants. which have many species of economic importance. such as squashes and pumpkins Peponapis fervens is the only species of the genus known from southern South America The Cucurbita species occurring in the same area as P fervens Include four domesticated species (C ficifolia, C maxima maxima, C moschata and C pepo) and one non-domesticated species (Cucurbita maxima andreana) It was suggested that C. in andreana was the original pollen source to P fervens, and this bee expanded its geographical range due to the domestication of Cucurbita The potential geographical areas of these species were determined and compared using ecological niche modeling that was performed with the computational system openModeller and GARP with best subsets algorithm The climatic variables obtained through modeling were compared using Cluster Analysis Results show that the potential areas of domesticated species practically spread all over South America The potential area of P fervens Includes the areas of C m andreana but reaches a larger area, where the domesticated species of Cucurbita also Occur The Cluster Analysis shows a high climatic similarity between P fervens and C. m. andreana Nevertheless. P fervens presents the ability to occupy areas with wider ranges of climatic variables and to exploit resources provided by domesticated species (C) 2009 Elsevier B V All rights reserved

Ecological niche modeling and principal component analysis of Krameria Loefl. (Krameriaceae)

Krameria plants are found in arid regions of the Americas and present a floral system that attracts oil-collecting bees. Niche modeling and multivariate tools were applied to examine ecological and geographical aspects of the 18 species of this genus, using occurrence data obtained from herbaria and literature. Niche modeling showed the potential areas of occurrence for each species and the analysis of climatic variables suggested that North American species occur mostly in deserted or xeric ecoregions with monthly precipitation below 140 mm and large temperature ranges. South American species are mainly found in deserted ecoregions and subtropical savannas where monthly precipitation often exceeds 150 mm and temperature ranges are smaller. Principal Component Analysis (PCA) performed with values of temperature and precipitation showed that the distribution limits of Krameria species are primarily associated with maximum and minimum temperatures. Modeling of Krameria species proved to be a useful tool for analyzing the influence of the ecological niche variables in the geographical distribution of species, providing new information to guide future investigations. (C) 2011 Elsevier Ltd. All rights reserved.

Distributional potential of the Triatoma brasiliensis species complex at present and under scenarios of future climate conditions

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Delineating Ecological Boundaries of Hanuman Langur Species Complex in Peninsular India Using MaxEnt Modeling Approach

Hanuman langur is one of the widely distributed and extensively studied non-human diurnal primates in India. Until recently it was believed to be a single species - Semnopithecus entellus. Recent molecular and morphological studies suggest that the Hanuman langurs consists of at least three species S. entellus, S. hypoleucos and S. priam. Furthermore, morphological studies suggested that both S. hypoleucos and S. priam have at least three subspecies in each. We explored the use of ecological niche modeling (ENM) to confirm the validity of these seven taxa and an additional taxon S. johnii belonging to the same genus. MaxEnt modeling tool was used with 19 bioclimatic, 12 vegetation and 6 hydrological environmental layers. We reduced total environmental variables to 14 layers after testing for collinearity and an independent test for model prediction was done using ENMTools. A total of 196 non-overlapping data points from primary and secondary sources were used as inputs for ENM. Results showed eight distinct ecological boundaries, corroborating the eight taxa mentioned above thereby confirming validity of these eight taxa. The study, for the first time provided ecological variables that determined the ecological requirements and distribution of members of the Hanuman langur species complex in the Indian peninsula.

Delineating Ecological Boundaries of Hanuman Langur Species Complex in Peninsular India Using MaxEnt Modeling Approach

Hanuman langur is one of the widely distributed and extensively studied non-human diurnal primates in India. Until recently it was believed to be a single species - Semnopithecus entellus. Recent molecular and morphological studies suggest that the Hanuman langurs consists of at least three species S. entellus, S. hypoleucos and S. priam. Furthermore, morphological studies suggested that both S. hypoleucos and S. priam have at least three subspecies in each. We explored the use of ecological niche modeling (ENM) to confirm the validity of these seven taxa and an additional taxon S. johnii belonging to the same genus. MaxEnt modeling tool was used with 19 bioclimatic, 12 vegetation and 6 hydrological environmental layers. We reduced total environmental variables to 14 layers after testing for collinearity and an independent test for model prediction was done using ENMTools. A total of 196 non-overlapping data points from primary and secondary sources were used as inputs for ENM. Results showed eight distinct ecological boundaries, corroborating the eight taxa mentioned above thereby confirming validity of these eight taxa. The study, for the first time provided ecological variables that determined the ecological requirements and distribution of members of the Hanuman langur species complex in the Indian peninsula.

Thesis abstract. Applying species distribution modeling for the conservation of Iberian protected invertebrates

This article outlines the approaches to modeling the distribution of threatened invertebrates using data from atlases, museums and databases. Species Distribution Models (SDMs) are useful for estimating species’ ranges, identifying suitable habitats, and identifying the primary factors affecting species’ distributions. The study tackles the strategies used to obtain SDMs without reliable absence data while exploring their applications for conservation. I examine the conservation status of Copris species and Graellsia isabelae by delimiting their populations and exploring the effectiveness of protected areas. I show that the method of pseudo‐absence selection strongly determines the model obtained, generating different model predictions along the gradient between potential and realized distributions. After assessing the effects of species’ traits and data characteristics on accuracy, I found that species are modeled more accurately when sample sizes are larger, no matter the technique used.

Modeling the suitable habitat of a structural red gorgonian species in the Mediterranean/east Atlantic regions predicts a wider distribution than previously known

Dissertação de mestrado, Biologia Marinha, Faculdade de Ciências e Tecnologia, Univerdade do Algarve, 2015

Ecological niche similarities of Peponapis bees and non-domesticated Cucurbita species

Peponapis bees are considered specialized pollinators of Cucurbita flowers, a genus that presents several species of economic value (squashes and pumpkins). Both genera originated in the Americas, and their diversity dispersion center is in Mexico. Ten species of Peponapis and ten species of Cucurbita (only non-domesticated species) were analyzed considering the similarity of their ecological niche characteristics with respect to climatic conditions of their occurrence areas (abiotic variables) and interactions between species (biotic variables). The similarity of climatic conditions (temperature and precipitation) was estimated through cluster analyses. The areas of potential occurrence of the most similar species were obtained through ecological niche modeling and summed with geographic information system tools. Three main clusters were obtained: one with species that shared potential occurrence areas mainly in deserts (P. pruinosa, P. timberlakei, C. digitata, C. palmata, C. foetidissima), another in moist forests (P. limitaris, P. atrata, C. lundelliana, C. o. martinezii) and a third mainly in dry forests (C. a. sororia, C. radicans, C. pedatifolia, P. azteca, P. smithi, P. crassidentata, P. utahensis). Some species with similar ecological niche presented potential shared areas that are also similar to their geographical distribution, like those occurring predominantly on deserts. However, some clustered species presented larger geographical areas, such as P. pruinosa and C. foetidissima suggesting other drivers than climatic conditions to shape their distributions. The domestication of Cucurbita and also the natural history of both genera were considered also as important factors. (C) 2011 Elsevier B.V. All rights reserved.

Modeling the Potential Geographic Distribution of Black Pepper (Piper nigrum) in Asia Using GIS Tools

Known as the "king of spices", black pepper (Piper nigrum), a perennial crop of the tropics, is economically the most important and the most widely used spice crop in the world. To understand its suitable bioclimatic distribution, maximum entropy based on ecological niche modeling was used to model the bioclimatic niches of the species in its Asian range. Based on known occurrences, bioclimatic areas with higher probabilities are mainly located in the eastern and western coasts of the Indian Peninsula, the east of Sumatra Island, some areas in the Malay Archipelago, and the southeast coastal areas of China. Some undocumented places were also predicted as suitable areas. According to the jackknife procedure, the minimum temperature of the coldest month, the mean monthly temperature range, and the precipitation of the wettest month were identified as highly effective factors in the distribution of black pepper and could possibly account for the crop's distribution pattern. Such climatic requirements inhibited this species from dispersing and gaining a larger geographical range.

Environmental niche variation and evolutionary diversification of the Brachypodium distachyon grass complex species in their native circum-Mediterranean range

PREMISE OF THE STUDY: We conducted environmental niche modeling (ENM) of the Brachypodium distachyon s.l. complex, a model group of two diploid annual grasses ( B. distachyon , B. stacei ) and their derived allotetraploid ( B. hybridum) , native to the circum-Mediterranean region. We (1) investigated the ENMs of the three species in their native range based on present and past climate data; (2) identifi ed potential overlapping niches of the diploids and their hybrid across four Quaternary windows; (3) tested whether speciation was associated with niche divergence/conservatism in the complex species; and (4) tested for the potential of the polyploid outperforming the diploids in the native range. M ETHODS: Geo-referenced data, altitude, and 19 climatic variables were used to construct the ENMs. We used paleoclimate niche models to trace the potential existence of ancestral gene fl ow among the hybridizing species of the complex. KEY RESULTS: Brachypodium distachyon grows in higher, cooler, and wetter places, B. stacei in lower, warmer, and drier places, and B. hybridum in places with intermediate climatic features. Brachypodium hybridum had the largest niche overlap with its parent niches, but a similar distribution range and niche breadth. C ONCLUSIONS: Each species had a unique environmental niche though there were multiple niche overlapping areas for the diploids across time, suggesting the potential existence of several hybrid zones during the Pleistocene and the Holocene. No evidence of niche divergence was found, suggesting that species diversifi cation was not driven by ecological speciation but by evolutionary history, though it could be associated to distinct environmental adaptations.

The role of environmental factors in the spatial distribution of Japanese encephalitis in mainland China

Japanese encephalitis (JE) is the most common cause of viral encephalitis and an important public health concern in the Asia-Pacific region, particularly in China where 50% of global cases are notified. To explore the association between environmental factors and human JE cases and identify the high risk areas for JE transmission in China, we used annual notified data on JE cases at the center of administrative township and environmental variables with a pixel resolution of 1 km×1 km from 2005 to 2011 to construct models using ecological niche modeling (ENM) approaches based on maximum entropy. These models were then validated by overlaying reported human JE case localities from 2006 to 2012 onto each prediction map. ENMs had good discriminatory ability with the area under the curve (AUC) of the receiver operating curve (ROC) of 0.82-0.91, and low extrinsic omission rate of 5.44-7.42%. Resulting maps showed JE being presented extensively throughout southwestern and central China, with local spatial variations in probability influenced by minimum temperatures, human population density, mean temperatures, and elevation, with contribution of 17.94%-38.37%, 15.47%-21.82%, 3.86%-21.22%, and 12.05%-16.02%, respectively. Approximately 60% of JE cases occurred in predicted high risk areas, which covered less than 6% of areas in mainland China. Our findings will help inform optimal geographical allocation of the limited resources available for JE prevention and control in China, find hidden high-risk areas, and increase the effectiveness of public health interventions against JE transmission.

伞形科囊瓣芹属的系统学研究

囊瓣芹属Pternopetalum Franchet是伞形科Apiaceae/Umbelliferae芹亚科Apioideae芹族Apieae重要成员。全属包括约32个分类群（包括变种），分布于南朝鲜、日本、中国的西南部和邻近的喜马拉雅地区，中国西南部的横断山区是其多样性中心。典型的东亚特有格局和对东亚亚热带森林环境的偏爱是其东亚区系故有份子的特征。 基于19个标本馆标本材料、野外调查以及相应的实验证据，本博士论文从三个研究主题对囊瓣芹属展开了全面而系统的研究。一是通过标本观察和野外调查，利用标本管理系统BRAHMS和表型分析软件包DELTA系统，完成了囊瓣芹属的世界性分类修订；二是基于上述的分类方案，选择伞形科其它属的44个种作为参考性类群（Reference taxa），利用Winclada, NONA和MESQUITE软件包开展了分支系统学研究；三是基于坐标化的点分布数据，利用DIVA-GIS系统的生态位模型，进行潜在分布预测和生态地理分布特征的分析。研究的主要初步结论如下： 一、分类修订 根据对19个标本馆标本材料（包括85个模式采集）的考证，以及对云南、四川、贵州等地野外居群的观察，结合DELTA系统的表型分析，本研究确认囊瓣芹属包含14个种，提出了14个新异名，属下分为东亚囊瓣芹组Sect. I. Pteridophyllae H. Wolff和囊瓣芹组Sect. II. Pternopetalum H. Wolff两个组的分类方案。前者包括东亚囊瓣芹P. tanakae (Sav. & Franchet) Hand.-Mazz.、高山囊瓣芹P. subalpinum Hand.-Mazz.、洱源囊瓣芹P. molle (Franchet) Hand.-Mazz.等5个种；后者包括五匹青P. vulgare (Dunn) Hand.-Mazz.、囊瓣芹P. davidii Franchet和澜沧囊瓣芹P. delavayi (Franchet) Hand.-Mazz.等9个种。萼齿、花柱基、和花柱的形态是区别两个组比较好的形态学特征。叶的着生位置、最终末回裂片的形状（是否异形）、分裂回数以及伞形花序着生的位置和果棱表面的附属构造是种间识别有用的检索特征。 二、系统发育分析 根据如上的14个种的分类方案，另外选取了伞形科小芹属Sinocarum H. Wolff、丝瓣芹属Acronema Falc. ex Edgew.和鸭儿芹属Cryptotaenia L.等10个属共44种作为参考类群，基于63个广义形态学性状和58个种的形态学矩阵，利用最大简约法对囊瓣芹属进行了分支分析。结果表明，囊瓣芹属的14个种与日本特有单型的仙洞草Chamaele decumbens (Thunb.)Makino.形成一个单独分支，处于分支图的基部位置。表明囊瓣芹属与鸭儿芹属有较近的亲缘关系。长枝吸引可能是造成Chamaele Miq.与东亚囊瓣芹分支的非正常聚合的原因。囊瓣芹属可能是单系内群，但它与Chamaele Miq.属间关系需要进一步研究。属下形成以五匹青P. vulgare和东亚囊瓣芹P. tanakae为代表的两个主干演化线。分支进化（Cladogenesis）在两个主干演化线形成了形态和地理上对称分布的“种对”。根据形态特征的变异和地理分布，这些“种对”分为三种类型：1、形态上多变而地理上广布的类型，以东亚囊瓣芹P. tanakae和五匹青P. vulgare为代表；2、形态上稳定地理上狭域特有的类型，以薄叶囊瓣芹P. leptophyllum (Dunn)Hand.-Mazz. 和川鄂囊瓣芹P. rosthornii (Diels) Hand.-Mazz.为代表；3、形态上趋同而多变，地理分布上几乎完全重叠的类型，以洱源囊瓣芹P. molle和澜沧囊瓣芹P. delavayi为代表。 性状状态的分析显示，属下形态特征的趋异具有较强的同朔性。不等长的伞辐和花梗，以及囊状的花瓣基部三个形态学特征可以标识包括仙洞草在内的囊瓣芹分支。祖征状态的重建表明，东亚囊瓣芹分支相对保留了更多的祖征，是属下相对原始的类型；五匹青分支是后期生境需求的特化，适应潮湿和荫蔽环境的衍生类型。 三、生态地理分布 基于1128个坐标化的点分布数据和生态位模型，利用地理信息系统软件包DIVA-GIS对囊瓣芹属的物种多样性、现代地理分布、潜在分布进行了分析。结果表明，二郎山-峨眉山地区以及重庆金佛山及其临近地区是囊瓣芹属的两个主要的多样性中心。分布区内局部尺度上的异常性多样性（Diversity abnormalies）可能有两个来源：一是高的异质性生境条件下物种形成速率的差异；二是中国西南山地的“冰原岛峰效应”（Nunataks），比如峨眉山和金佛山，对属的早期演化线成员所起到的“避难所”（Refuge）的作用。 所预测的潜在分布范围与观察到的地理分布范围是一致的，说明对特化的气候忍耐性是限制囊瓣芹属物种地理分布的主要因素。温度和降水的季节性变化对囊瓣芹属代表中的地理分布限制作用比较大。亚热带-高山针阔常绿林是属下物种比较适宜的生境。属的地理分布可能形成于中新世以后，生态位的保守性是解释囊瓣芹属东亚本土就地分化和多样化的原因。属的分布范围的形成可能经历了一个早期南退西进的过程，后期分布范围变化可能主要是东西方向上的迁移和扩展。喜马拉雅—横断山—峨眉山/金佛山/神农架—日本、南朝鲜一线是囊瓣芹属多样化过程中分布范围东西延伸的重要通道。喜马拉雅—中国西南—日本朝鲜亚热带森林植被的完整性和连续性是囊瓣芹属演化和分布区形成的基本条件。

白豆杉的地理分布格局及潜在分布区估计

　　根据物种的分布信息结合环境因子估计物种的分布区对珍稀濒危物种的保护有着重要的意义。白豆杉Pseudotaxus chienii为第三纪孑遗植物，我国东南部地区特有，分布区狭窄。本文通过对白豆杉的标本记录研究它的地理分布，找出影响其分布的关键因子并对其潜在分布区进行估计，并解释其分布区形成的原因。全球升温将对物种分布造成重要影响，通过温度升高情况下2100年的气候数据模拟白豆杉未来的潜在分布区，估计温度升高对白豆杉的影响，将对白豆杉的保护有着重要的意义。 　　根据白豆杉的标本信息结合Diva-Gis软件对白豆杉的地理分布进行研究。以海拔图层和植被图层为底图对白豆杉的分布格局进行研究，并对白豆杉种群的多度进行统计分析。用Diva-Gis软件的气候数据提取功能提取白豆杉分布点的气候信息，并运用主成分分析对影响白豆杉分布的气候因子进行分析，找出影响白豆杉分布的主要环境因子。根据白豆杉的分布信息和气候数据，运用Diva-Gis内嵌的BIOCLIM模型和DOMAIN模型对白豆杉在不同气候条件下的潜在分布区进行估计，评价温度升高对白豆杉分布区的影响。 　　白豆杉分布格局研究结果表明，白豆杉分布在我国东南部地区中低海拔山区，白豆杉的分布和植被类型及海拔有着密切的关系。白豆杉的分布与海拔的关系表现为，由东到西，分布的最低海拔升高，海拔范围缩小。白豆杉分布地的植被类型为常绿灌木林，常绿阔叶林及针、阔叶混交林。白豆杉由东向西的海拔变化趋势与植被类型的由东向西的海拔变化趋势相一致。PCA分析结果表明白豆杉的分布与温度相关因子有着密切的关系。 　　现在气候对潜在分布区的估计表明,白豆杉的潜在分布区散布于浙、闽、粤、赣、湘，桂及黔几省各自交界之处即从浙江南部山区沿武夷山山系至南岭山系（向北到沿湘赣交界的罗宵山系）至大瑶山山系（向北沿雪峰山）。潜在分布区南部有三处分布的热点地区，即浙江南部、湖南南部和广西北部地区。三个主要分布区之间仅有有星散的潜在分布区存在，或没有潜在分布区出现，处在一种高度的隔离状态。造成这种潜在分布格局形成的原因可能有二，一是第四纪冰期的到来使白豆杉的分布区向南迁移，局部性气候的变化和地质变化可能导致了部分白豆杉的生境的消失，从而使得原来连续的分布区破碎化，形成了现在的星散分布；二是白豆杉的潜在分布区预测结果与中国东南部地区的山脉走势非常一致，山脉地带小生境多样化能够为白豆杉在垂直地带上的迁移提供更大的可能性。 　　未来气候数据对白都杉的潜在分布区估计表明，温度升高后白豆杉最适生分布区显著缩小。白豆杉的潜在分布区的地理分布格局发生了明显的变化，原来在南部的适生区明显缩小，星散程度更高。除已知的分布地外，在江西西南部武夷山、南岭山脉的湖南、广西、广东三省交界的地方都是白豆杉的适生区。江西和湖南交界的罗宵山山脉北部到井冈山都有白豆杉分布可能性较大，可以作为野外调查的重点地区。气候变化会使白豆杉在浙江、湖南南部的最适生境破碎化从而影响白豆杉的分布。生境保护对白豆杉的保护起着关键作用。