Article

A zoogeographical boundary between the Palaearctic and Sino-Japanese realms documented by consistent north/south phylogeographical divergences in three woodland birds in eastern China

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Abstract

Aim: The location of zoogeographical boundaries in eastern China has long been the subject of debate. To identify any north/south genetic divergence between the Palaearctic and Sino-Japanese realms proposed by previous studies, we conducted a comparative phylogeographical study involving three passerine species with wide latitudinal distributions in eastern China. Location: Eastern China. Methods: Two mitochondrial genes and three nuclear introns were amplified and sequenced. Population structures were analysed using intra-specific phylogeny, tcs networks, AMOVA and structure inferences. We tested for evidence of genetic barriers based on pairwise differences. Lineage divergences, demographic dynamics and gene flow between lineages were estimated using Bayesian methods. Results: A congruent north/south phylogeographical divergence was identified for three species. A geographical barrier was inferred at c. 40° N in eastern China. The population sizes of the northern and southern lineages have both been stable through the late Pleistocene, while multiple divergences were inferred during the early and middle Pleistocene. Main conclusions: Our results suggest a general phylogeographical break in north-eastern China, coinciding with the Palaearctic/Sino-Japanese boundary. Physical blocking of the Yan Mountains and fragmentation of suitable habitat during glacial stages between the north and south probably acted together to provide long-lasting barrier effects. Our comparative phylogeographical approach demonstrates that the Palaearctic/Sino-Japanese boundary may represent a gene-flow barrier even within widespread species.

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... In contrast, the azure-winged magpie, Cyanopica cyanus, which requires well-wooded habitat, shows a north-south genetic division in eastern China [3]. Multiple factors contribute to the observed phylogeographic patterns of divergence in China, including environmental features [4], geographical barriers [5], glacial periods [6], habitat preferences of organisms [3]. It is important to combine geo-climatical and ecological components in interpreting phylogeographical patterns we observed from empirical studies. ...
... However, the roles of mountain system in southwest China are not substantially illustrated (but see literatures by Song et al. [9] and Qu et.al. [10]), and few study to demonstrated the barrier effects of Qinling Mountains-Huai River line on lineage diversification in birds but questioned by Song et al. [5]. Therefore, it is necessary to evaluate the phylogeographical impacts of these geographic features and their related geological events on birds in central and south China. ...
... The average overall mean p distances of Cytb and the combined mtDNA were 0.02100 and 0.02140, respectively, which implied a substitution rate of combined mtDNA 1.0190 times greater than that of Cytb. Therefore, we obtained a substitution rate of 0.01055 per site per million years for the combined mtDNA sequences [5]. The analyses were implemented with a constant growth as a coalescent constant tree prior and a strict molecular clock. ...
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Background: Geological events and climatic changes played important roles in shaping population differentiation and distribution within species. In China, populations in many species have contracted and expanded responding to environmental changes with the uplift of the Qinghai-Tibet Plateau (QTP) and glacial cycles during Pleistocene. In this study, we analysed the population structure of Godlewski's Bunting, Emberiza godlewskii, to determine the effects of major historical events, geographic barriers and past climatic changes on phylogenetic divergence and historical demographic dynamics of this species. Results: A phylogeny based on concatenated mitochondrial and nuclear DNA datasets show two (northern and southern) clades approximately diverged 3.26 million years ago (Ma). The West Qinling Mountains serve as a dividing line between the two lineages. Both lineages experienced a recent demographic expansion during interglacial periods (marine isotope stages (MISs) 2-6). Bayesian skyline plots and the results of ecological niche modelling suggested a more intensive expansion of the northern lineage during the late Pleistocene, whereas the southern lineage was comparatively mild in population growth. Conclusions: Our results provide insights into the distribution patterns of avian taxa and the possible mechanisms for a south and north divergence model in China. The deep divergence may have been shaped by the uplift of the QTP. Habitat preferences might have facilitated the lineage divergence for E. godlewskii. Moreover, the West Qinling Mountains act as a dividing line between the two lineages, indicating a novel phylogeographic pattern of organisms in China. The difference in population expansion mode between two lineages resulted from different effects caused by the climate of the LGM and the subsequent habitat changes accompanying the arrival of a colder climate in northern and southern regions of China.
... Traditionally, the global biogeographical regionalization of China covers both the Oriental and Palearctic realms, which are bounded by the Qingling Mountain-Huai River, around 32-34N in the east of China (Sclater 1858, Wallace 1876, Zhen 1960, Zhang 1999, Cox 2001, Kreft and Jetz 2010, Morrone 2015, Song et al. 2016. In 2013, based on its zoological fauna, Holt added a Sino-Japanese realm standing between the Palearctic and Oriental realms, and from west of Tibet to east of the Japanese archipelago. ...
... Kreft and Jetz (2013) questioned the validity of this realm because they regarded it as just a biogeographical transition zone between the Palearctic and Oriental realms. According to their taxa ethoecological characteristics, the Sino-Japanese realm boundaries are generally clustered with the Oriental realm (Kreft and Jetz 2010, Song et al. 2016, He et al. 2018). (Feng et al. 2013, Ebersbach et al. 2017. ...
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Background: Cixiidae are small strictly phytophagous hemipteran insects worldwide distributed. Ecology and systematics of Chinese fauna remains poorly investigated. For instance, does their distribution follows the patterns of biogeogaphical distribution established for their host plants or other related-taxa because they are all obligatory phytophagous taxa? Do they follow the usual distributional Chinese realms and boundaries already recognized? Which zoogeographical Chinese regions and connections between them do they depict. To investigate these issues, we provide here a referenced and comprehensive checklist of the 250 cixiid species currently reported from China (77 new records), with their precise distribution at the regional level. In the 8 Chinese main zoogeographical regions usually recognized and 2 adjacent areas, we analyzed further their diversity at the tribal, generic, and specific levels using a non-metric multidimensional scaling and an unweighted pairwise group analysis using an arithmetic mean cluster analyses. The observed distribution patterns shown that an intercalary Sino-Japanese realm is recognisable between the Palaearctic and Oriental realms. At the regional level, the South China region clusters more closely with the Southwest, Central and North China regions. Taiwan, clearly separated from the South China region and mainland China, is more closely related to the Qinghai-Tibet region and Indochina countries. Although Central and South China regions remain close to each other, the Qinghai-Tibet region appears singularly different. New information: An updated checklist of the 250 Cixiidae species, known to occur in China and counting for 10% of the Chinese planthopper fauna, is presented based on literature, recent collections, and museum records. More than 400 records distributed among the 28 provinces and 8 regions in China are extensively provided, including 77 new records. Of these, more than 80% of the species (205 species, 82%) have been only reported from China, and most of them are endemic species, which could reflects the great diversity degree of the Chinese regions and local biotypes highlights the uniqueness of this fauna. These species are found in 8 Chinese zoogeographical regions: The Taiwan region is the most diversified with 161 species and the highest rate of endemic species (69.57%), followed by South China (78 species, 17.95%), Central China (60 species, 33.33%), Southwest China (43 species, 39.53%), North China (29 species, 34.48%), Qinghai-Tibet region (10 species, 20%), Northeast China (8 species, 12.5%), and 5 species found in the Inner Mongolia-Xinjiang region that are not endemic ones. Endemism was analyzed for each region and repeated for species distribution patterns across them, 9 being bi-regionally and tri-regionally distributed. The South China-Taiwan pattern is the most richest one, followed by the Central-South China-Taiwan pattern. Semonini and Pentastirini tribes are widespread among all the zoological regions, representing respectively 21.20% and 17.20% of all the species, while Cixiini being is the most common tribe with 45.20%, remains absent from the North-Eastern China region. Andini with only 5.20% of the species is distributed in the Sino-Japanese - Oriental Region; Eucarpini (6.40%) and Borysthenini (2.00%) are mainly concentrated in the south of the Qingling Mountain-Huai River. The remaining four tribes, Bennini (0.40%), Briixini (0.80%), Oecleini (1.20%) and Stenophlepsiini (0.40%) are relatively rare and restricted to Taiwan. At the generic level, Kuvera (7.2%) is the most widely distributed genus in China while Cixius, Betacixius, Kuvera, Oecleopsis and Andes are the more diversified. One genus (Oliparisca) is distributed only in the Tibet region, while 10 genera are distributed only in the Taiwan region. In addition, nearly half of the genera (16 genera, 48.48%) are distributed south of the Palearctic/Oriental boundary. A non-metric multidimensional scaling and an unweighted pairwise group method analysis using arithmetic mean clustering based on the Jaccard similarity coefficient matrix support a Palaearctic/Sino-Japanese boundary and a South China region closer to the Southwest, Central and North China regions. The Taiwan region appears clearly separated from the South China region and to mainland China, and more closely related to the Qinghai-Tibet region and Indochina countries. The Central and South China regions appear close to each other, but the Qinghai-Tibet region is singularly isolated.
... region has a unique mountainous topography and was impressive during the orogeny. This area is distinguished by north-south oriented high peaks separated by valley floors (Zhang et al., 2004;Cao et al., 2009;Sun et al., 2011;Song et al., 2016). Dramatic elevation variations ranging from ca. 1,000 m in some valleys to 7,556 m at the summit of Minya Konka can form "sky islands" (Lopez-Pujol et al., 2011;He and Jiang, 2014;Sklenar et al., 2014). ...
... In the late Miocene and later (10 Ma-present), QTP experienced further uplift and expansion, especially in the eastern margin region, which contains many mountain ranges, most notably the Hengduan biodiversity hotspot. Warm and moist air from the Indian Ocean is blocked by the Himalayas and the KailasRange, so it enters China from the Hengduan Mountains (Lopez-Pujol et al., 2011;He and Jiang, 2014;Sklenar et al., 2014;Song et al., 2016). This has brought plenty of rain to the southeastern part of QTP, which in turn has had a dramatic effect on species there, such as Allium section Sikkimensia, Cardiocrinum, Dolomiaea, Rheum, and Myricaria (Miehe et al., 2007;Sun et al., 2012;Zhang et al., 2014;Yang et al., 2016;Xie et al., 2018). ...
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Exploring the effects of orographic events and climatic shifts on the geographic distribution of organisms in the Himalayas-Hengduan Mountains (HHM) region and Qinghai-Tibetan Plateau (QTP) is crucial to understand the impact of environmental changes on organism evolution. To gain further insight into these processes, we reconstructed the evolutionary history of nine Chamaesium species distributed across the HHM and QTP regions. In total, 525 individuals from 56 populations of the nine species were analyzed based on three maternally inherited chloroplast fragments (rpl16, trnT-trnL, and trnQ-rps16) and one nuclear DNA region (internal transcribed spacer, ITS). Fifty-two chloroplast DNA (cpDNA) and 47 ITS haplotypes were identified in nine species. All of the cpDNA and ITS haplotypes were species-specific. Phylogenetic analysis suggested that all nine species form a monophyletic clade with high support. Dating analysis and ancestral area reconstruction revealed that the ancestral group of Chamaesium originated in the southern Himalayan region at the beginning of the Paleogene (60.85 Ma). The nine species of Chamaesium then separated well during the last 25 million years started in Miocene. Our maxent modeling indicated the broad-scale distributions of all nine species remained fairly stable from LIG to the present and predicted that it will remain stable into the future. The initial split of Chamaesium was triggered by climate changes following the collision of the Indian plate with the Eurasia plate during the Eocene. Subsequently, divergences within Chamaesium may have been induced by the intense uplift of the QTP, the onset of the monsoon system, and Central Asian aridification. Long evolutionary history, sexual reproduction, and habitat fragmentation could contribute to the high level of genetic diversity of Chamaesium. The higher genetic differentiation among Chamaesium populations may be related to the drastic changes of the external environment in this region and limited seed/pollen dispersal capacity.
... Other authors united all brownish-headed Asian willow tits and allies under the species name P. songarus (the ''songar tit" including Central Asian P. s. songarus and Chinese P. s. affinis, P. s. stoetzneri and P. s. weigoldicus; see Table 1), but so far this arrangement has not been corroborated by molecular phylogenetics (Kvist et al., 2001;Salzburger et al., 2002). A recent phylogeographic study by Song et al. (2016) compared Chinese marsh tit and willow tit populations only without considering their trans-Palearctic counterparts and thus did not provide a finite solution of the systematictaxonomic dilemma either. ...
... 47.1). In fact, our P. hypermelaenus lineage comprises all samples and sequences from Shaanxi and Shanxi (including specimens identified as P. m. hellmayri by Dai et al. 2010) and Song et al. (2016) identified further four populations from Shanxi, Shaanxi and Hubei that belonged to the mitochondrial P. hypermelaenus lineage. Considering the spatial distribution of mtDNA haplotypes the northern range limits of P. hypermelanus should at least extend across Shaanxi to adjacent southern Shanxi. ...
Article
A recent full species-level phylogeny of tits, titmice and chickadees (Paridae) has placed the Chinese endemic black-bibbed tit (Poecile hypermelaenus) as the sister to the Palearctic willow tit (P. montanus). Because this sister-group relationship is in striking disagreement with the traditional affiliation of P. hypermelaenus close to the marsh tit (P. palustris) we tested this phylogenetic hypothesis in a multi-locus analysis with an extended taxon sampling including sixteen subspecies of willow tits and marsh tits. As a taxonomic reference we included type specimens in our analysis. The molecular genetic study was complemented with an analysis of biometric data obtained from museum specimens. Our phylogenetic reconstructions, including a comparison of all GenBank data available for our target species, clearly show that the genetic lineage previously identified as P. hypermelaenus actually refers to P. weigoldicus because sequences were identical to that of a syntype of this taxon. The close relationship of P. weigoldicus and P. montanus – despite large genetic distances between the two taxa – is in accordance with current taxonomy and systematics. In disagreement with the previous phylogenetic hypothesis but in accordance with most taxonomic authorities, all our P. hypermelaenus specimens fell in the sister clade of all western and eastern Palearctic P. palustris. Though shared haplotypes among the Chinese populations of the two latter species might indicate mitochondrial introgression in this part of the breeding range, further research is needed here due to the limitations of our own sampling.
... Recent research in the QHL has focused on lineage divergence in non-aquatic species on both sides of the QHL, and its role as a major geographical barrier (e.g. Liu et al., 2017;Song et al., 2016;Yan et al., 2010). In contrast, aquatic species might be expected to have responded differently to past climate fluctuations (i.e. ...
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Aim The evolutionary importance of paleoclimate regimes has been noted in biogeographic studies. However, little is known about how paleoclimate differences shaped the biogeographic pattern and diversification history of the freshwater fauna in important zoogeographical boundary regions. Here, we aim to investigate how past regional climatic differences have shaped the biogeographic history of the inland aquatic fauna in China using an endemic freshwater crab species complex found on both sides of the Qinling Mountains–Huaihe River Line (QHL), a critical ecological boundary in eastern China, as a model system. Location Eastern China, the Qinling Mountains–Huaihe River Line. Taxon The Sinopotamon yangtsekiense species complex. Methods A total of 482 individuals of Sinopotamon yangtsekiense sensu lato were collected from 34 localities throughout its entire distributional range. The phylogeographic analyses of population structure, morphological and genetic variations, and demographic dynamics were made based on multiple mtDNA and nuDNA loci and on morphological traits. Fine‐tuned ecological niche modeling was used to reconstruct the location of climatically suitable areas that existed during the Last Glacial Maximum. Results The divergence of two freshwater crab lineages across the QHL correlated with significant past variations in monsoon intensity and with the location of multiple refuges. The divergence time was broadly consistent with the timing of the critical paleoclimate transition event in the mid‐Pleistocene (95% HPD, 0.48–1.06 Ma). Each freshwater crab lineage has evolved distinct male genital traits associated with their isolation in areas with different precipitation rates and temperatures in the past. The patterns of crab distribution observed today reflect past contractions of the two lineages in response to glacial and interglacial cycles during the Pleistocene, followed by their subsequent rapid expansion after the Last Glacial Maximum (~15 kya). Main conclusions Populations of the widespread species Sinopotamon yangtsekiense s.l. experienced a deep division in the past that led to the phylogeographical isolation observed today. The two main drivers of genetic isolation in this taxon were (a) differences in the intensity of the monsoons on each side of the QHL boundary during the mid‐Pleistocene, and (b) isolation of different populations of S. yangtsekiense s.l. in a number of separate refuges during the LGM.
... The current study further supports the validity of this recently suggested boundary. This boundary may reflect a combined effect of geographic isolation brought by the Yan mountains and the vegetational changes during the Pleistocene (Song et al. 2016b). This pattern contrasts with another typical pattern within the region, namely that of an east-west split at the Southern margin of QTP (Päckert et al. 2015), with a Chinese and/or Palearctic clade in the east and a Himalayan counterpart in the west (e.g. the Yellowish-bel- While there are no distinctive plumage or song divergences between the taxa within the two Carpodacus sibiricus clades, both show a significant phylogeographic pattern. ...
Article
The Long-tailed Rosefinch Carpodacus sibiricus breeds in two widely disjunct areas in East Asia. Five subspecies are usually recognized. The plumage differences between different subspecies groups within C. sibiricus are notable, suggesting it may actually comprise more than one species. However, proper taxonomic assessment has not been carried out, probably in part due to the scarcity and lack of museum specimens of some of these subspecies. In the current study, we re-evaluated the taxonomy of the C. sibiricus complex using molecular, acoustic and morphological data. Using mitochondrial DNA, the samples formed two clades, a northern clade (C. s. sibiricus, C. s. ussuriensis and C. s. sanguinolentus) and a southern clade (C. s. henrici and C. s. lepidus). We also revealed that C. s. ussuriensis and C. s. sanguinolentus are mostly indistinguishable based on mitochondrial markers. This north/south split pattern is congruent with the pattern of plumage differences among north and south taxa. However, no diagnosable differences were found in their songs. We propose synonymizing C. s. ussuriensis with C. s. sanguinolentus. At the species level, we suggest splitting the complex into two species, with Siberian Long-tailed Rosefinch C. sibiricus comprising C. s. sibiricus and C. s. sanguinolentus, and Chinese Long-tailed Rosefinch C. lepidus comprising C. l. henrici and C. l. lepidus.
... There is further evidence that lower elevations had a relatively mild Pleistocene climate, potentially including microclimatic zones capable of supporting various habitats and with relative stability (Hu et al., 2008). Several recent studies have also suggested that this region plays a significant role in shaping biodiversity in that it represents a significant barrier to the Yanshan mountains (Song et al., 2016), and that it provided a refuge for many species during the Last Glacial Maximum (Taihang mountains; Qiu, Fu, & Comes, 2011). In any case, the dominant biogeographical process shaping this region was the formation of the Yanshan and Taihang mountains. ...
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Understanding diversity patterns requires accounting for the roles of both historical and contemporary factors in the assembly of communities. Here, we compared diversity patterns of two moth assemblages sampled from Taihang and Yanshan mountains in Northern China and performed ancestral range reconstructions using the Multi‐State‐Speciation and Extinction model, to track the origins of these patterns. Further, we estimated diversification rates of the two moth assemblages and explored the effects of contemporary ecological factors. From 7788 specimens we identified 835 species belonging to 23 families, using both DNA barcode analysis and morphology. Moths in Yanshan mountains showed higher species diversity than in Taihang mountains. Ancestral range analysis indicated Yanshan as the origin, with significant historical dispersals from Yanshan to Taihang. Asymmetrical diversification, population expansion, along with frequent and considerable gene flow were detected between communities. Moreover, dispersal limitation or the joint effect of environment filtering and dispersal limitation were inferred as main driving forces shaping current diversity patterns. In summary, we demonstrate that a multi‐scale (community, population and species level) analysis incorporating both historical and contemporary factors can be useful in delineating factors contributing to community assembly and patterning in diversity.
... On the other hand, phylogeographic patterns at the eastern margin of the Tibetan Plateau are characterised by North-South divides (cf. Fig. 5B) that, according to a more finely-scaled zoogeographic classification, represent the boundary between the Palaearctic and the Sino-Japanese realm along the Yan mountains, and between the Palaearctic and the Oriental region along the Qinling mountains (Song et al. 2016). ...
Chapter
In the first half of the 20th century the German ornithologist Hugo Weigold was one of the pioneers in the emerging field of biogeography. As a member of Walther Stötzner’s expedition to Sichuan and Tibet (1913-1915) he was among the first Western researchers to study the immense species richness of the Chinese avifauna. Today, his rich collections of bird skins from China are housed in nearly equal parts at the Natural History Museums of Berlin and Dresden and from this material many taxa were described as new to science. Several of these are accepted as good species today and some are even representatives of the endemic avifauna of China. In his early work already Weigold hypothesized a Tibetan center of origin and diversification from where ancestors of extant species dispersed northwards and colonized the Northern and Western Palaearctic. This idea received recent support from genetic studies that found evidence of a Tibetan cradle of evolution for example in alpine plants and cold-adapted mammals. Furthermore, modern analytical methods allow for genetic analysis of the 100-year-old specimens collected by Weigold and his contemporaries. In this respect, type specimens are of utmost mportance for the authoritative assignment of taxon names to genetic lineages. When it was finally published after his death, Weigold’s monograph on the biogeography of Tibet and its forelands still featured some visionary thoughts on the evolutionary history of faunal assemblages of the Tibetan Plateau and the mountain ranges at its margins. Today, some of Weigold’s original ideas have received support from modern phylogenetic and phylogeographic studies, including examples from our own research group.
... Sequences were assembled in SeqMan (DNASTAR, Madison, WI, USA), and were aligned using CLUSTAL W (Thompson et al., 1994) in MEGA v6.0 (Tamura et al., 2013) with default parameters. As per Song et al. (2016), we used the PHI test in Splitstree4 (Huson and Bryant, 2006) and the GARD method (Pond et al., 2006) to search the signatures of recombination in the nuclear sequences. We used the PHASE algorithm (Stephens et al., 2001) in DnaSP v5.1 (Librado and Rozas, 2009) with default parameters to determine the gametic phase of heterozygous nuclear genes. ...
... Allopatric speciation shaped extant species distributions, including zones of secondary contact and hybridization (Himalaya: Martens & Eck 1995;Palearctic: Aliabadian et al. 2005). Typically, east-west phylogeographic disjunctions are observed in many species pairs along the southern Qinghai-Tibetan Plateau margins (Päckert et al. 2012(Päckert et al. , 2015aMartens 2015) and north-south disjunctions are seen in the Hengduan Shan and adjacent northern Chinese mountain ranges (Päckert et al. 2015b;Song et al. 2016). Strikingly, Pleistocene speciation processes were most commonly observed in higher-elevation species assemblages: in the upper forest belt below timberline, in the sub-alpine shrubs and alpine rocks and grasslands and to a lesser degree in the temperate and subtropical species assemblages at the lower elevations (Päckert et al. 2012). ...
Chapter
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The Tibeto-Himalayan region, also known as the “Third Pole”, is a unique, vast and fascinating area of Earth. Similar to the North and South Poles, the Tibeto-Himalayan region plays a major role in global climate dynamics including hemispheric-scale climate connections. In particular, the Tibeto-Himalayan highlands influence the Indian and East Asian monsoons. The region, with its humid and high relief mountains in the south and southeast, is characterised by a complex biological history and encompasses areas of remarkably high biodiversity. Here, we provide a short summary of the evolution of geo-biodiversity in the Tibeto-Himalayan region since its formation in the Eocene. We use a systemic approach considering both the local abiotic and biotic dynamics, thus integrating the available geological, climatic and biological information. Thereby, our focus is on the evolution of present-day biodiversity patterns for which we provide examples across a wide range of organisms. Based on dated molecular phylogenies of extant species, it appears that already during the early uplift phase in the Eocene to mid-Miocene, alpine lineages emerged that later diversified in the Tibeto-Himalayan region and thus contributed to existing patterns of biodiversity. These data further show three putative phases of high net diversification. The first peak of diversification of modern families and genera occurred during the mid-Miocene (20-15 Ma), with a second peak towards the Miocene-Pliocene boundary and a third peak between 2 Ma and 150,000 ka. To explain this pattern we propose the “mountain-geobiodiversity-hypothesis”. It postulates three boundary conditions that are required to maximise the impact of mountain formation and surface uplift on regional biodiversity patterns in mountainous regions: 1) presence of lowland, montane and alpine zones; 2) climatic oscillations that enable mountains to act as species pumps; and 3) high-relief terrain with environmental gradients that minimise migration distances during climate oscillations, providing refugia and geographical barriers that allow for survival of many species as well as allopatric speciation. We propose that the combination of these three boundary conditions is key for the origination of montane biodiversity hotspots.
... As there were no fossil records or geological calibration points available for molecular dating, we employed the substitution rate and accepted 0.004-0.008 site/million years for the COI gene in semiaquatic Heteroptera ( Damgaard & Zettel, 2003;Ye, Zhu, Chen, Zhang, & Bu, 2014), and we modified the value for the combined mitochondrial sequences (0.003-0.006 site/million years) using the p distances method ( Song et al., 2016). We ran the Markov chain Rambaut & Drummond, 2007). ...
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Aim: Palaeoclimatic and palaeogeological events have been identified as two main factors that influence the genetic structuring of extant organisms. We studied a montane stream-dwelling insect, Metrocoris sichuanensis, to explore the relative roles played by these two factors in population genetic connectivity. Location: Sichuan Basin, China. Methods: Mitochondrial (COI, COII, Cytb, 16S) and nuclear (EF-1a, ITS1) markers were sequenced from 208 individuals. Suitable habitat shifts from the Last Glacial Maximum (LGM) to the present were predicted through fine-tuned ecological niche modelling (ENM). Phylogenetic and phylogeographical analyses were conducted to reveal the population genetic structure. Intraspecific divergence and expansion times were estimated using BEAST. Finally, the least cost path (LCP) method coupled with migrate analysis was used to identify possible dispersal corridors and estimate the asymmetric gene flow. Results: Our ENM results suggested that population habitat connectivity did not change both in the LGM and current conditions. Whole haplotypes were separated into four highly supported clades/haplogroups that exhibited strong geographical structure. The splitting events between the four lineages likely date back to the Early Pleistocene. Bayesian skyline plot (BSP) indicated a moderate demographic growth from the LGM to the present. A putative dispersal corridor was detected along the Longmen Mountains thrust belt, with unidirectional gene flow from north to south. Main conclusion: Our findings support the geographical isolation of the genetic lin-eages and a deep early Pleistocene split in M. sichuanensis. Landscape connectivity analysis incorporating the genetic data and the ENM prediction revealed that population genetic connectivity was strongly associated with stable climatic habitats shaped by complex topography. The drainage system might have assisted the rapid movement of populations along the Longmen Mountains thrust belt. A strategy for researching the population genetic connectivity of narrow endemics, such as M. sichuanensis, in global biodiversity hotspots is proposed and discussed in this paper.
... In addition to climatic and environmental changes, geographical barriers in different parts of the Northern Hemisphere might also have had great influence on gene flow. Deep splits between the geographically close regions of Iberia and North Africa have been recorded in birds (Li et al. 2016, Pons et al. 2011, Stervander et al. 2015 and other organisms (Salicini et al. 2013, Veith et al. 2004 The clear split between the North Eurasian and East Asian clades has been recorded in previous studies on Pica (Haring et al. 2007, Lee et al. 2003, Zhang et al. 2012) as well as in other birds such as the Phylloscopus borealis, Motacilla alba and Aegithalos caudatus complexes (Saitoh et al. 2010, Li et al. 2016, Song et al. 2015, indicating a general geographical or climatic barrier blocking population dispersal and gene flow between the northern boreal zone and more mesic regions in eastern China and neighbouring areas (Song et al. 2016). The inferred dating suggests that this divergence began around 2.3 Ma in the magpies, concordant with the environmental cooling and drying at the early stage of the Pleistocene. ...
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Previous studies have suggested that bird populations in East Asia were less affected by Pleistocene climatic fluctuations than those in Europe and North America. However, this is mainly based on comparisons among species. It would be more relevant to analyse geographical populations of widespread species or species complexes. We analyzed two mitochondrial genes and two nuclear introns for all taxa of Pica to investigate 1) which Earth history factors have shaped the lineage divergence, and 2) whether different geographical populations were differently affected by the Pleistocene climatic changes. Our mitochondrial tree recovered three widespread lineages, 1) in East Asia, 2) across North Eurasia, and 3) in North America, respectively, with three isolated lineages in Northwest Africa, Arabia and the Qinghai-Tibet Plateau, respectively. Divergences among lineages took place 1.4–3.1 million years ago. The Northwest African population was sister to the others, which formed two main clades. In one of these, Arabia was sister to Qinghai-Tibet, and these formed the sister clade to the East Asia clade. The other main clade comprised the North American and North Eurasian clades. There was no or very slight structure within these six geographical clades, including a lack of differentiation between the two North American species Black-billed Magpie P. hudsonia and Yellow-billed Magpie P. nutalli. Demographic expansion was recorded in the three most widespread lineages after 0.06 Ma. Asymmetric gene flow was recorded in the North Eurasian clade from southwestern Europe eastward, whereas the East Asian clade was rooted in south central China. Our results indicate that the fragmentation of the six clades of Pica was related to climatic cooling and aridification during periods of the Pliocene–Pleistocene. Populations on both sides of the Eurasian continent were similarly influenced by the Pleistocene climate changes and expanded concomitantly with the expansion of steppes. Based on results we also propose a revised taxonomy recognising seven species of Pica.
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Background: Correct identification together with information on distribution range, geographical origin and evolutionary history are the necessary basis for the management and control of invasive species. The bean bug Megacopta cribraria is a crucial agricultural pest of soybean. Recently, M. cribraria has invaded the United States and spread rapidly, causing severe reductions in soybean yields. However, the species boundary and phylogeographical pattern of this invasive bean bug are still unclear. Results: The results of different species delimitation methods (Automatic Barcode Gap Discovery, Assemble Species by Automatic Partitioning, Bayesian Poisson Tree Processes and Bayesian Phylogenetics and Phylogeography) strongly demonstrated that M. cribraria and Megacopta punctatissima represent the same species. M. punctatissima should not be considered a distinct species but rather a variety of M. cribraria. Phylogenetic analyses revealed three well-supported clades (Southeast Asia [SEA], East Asia continent [EAC] and Japan [JA]) with distinct geographical structures in the M. cribraria-M. punctatissima complex. The SEA clade was at the base of the phylogenetic tree, and the sister relationship between the EAC clade and JA clade was strongly supported. The split between the EAC clade and JA clade occurred at approximately 0.71 Ma, corresponding to the submergence period of the East China Sea land bridge. Conclusion: This study clarified the species boundary between M. cribraria and its closely related species and revealed the phylogeographical pattern and evolutionary history of M. cribraria. The species delimitation and phylogeography results achieved in this study could provide new insights into the monitoring and management of this agricultural pest. © 2022 Society of Chemical Industry.
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Holt et al. (Report, 4 January 2013, p. 74) propose substantial modifications of Wallace’s long-standing zoogeographic regions based on clustering of a pairwise similarity matrix of vertebrate assemblages. We worry about their compromised use of phylogenies and show that a fundamental point of their analysis—i.e., the delineation of new realms—is only weakly supported by their results and conceptually flawed.
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Estimating genealogical relationships among genes at the population level presents a number of difficulties to traditional methods of phylogeny reconstruction. These traditional methods such as parsimony, neighbour-joining, and maximum-likelihood make assumptions that are invalid at the population level. In this note, we announce the availability of a new software package, TCS, to estimate genealogical relationships among sequences using the method of Templeton et al. (1992) .
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We present a phylogenetic hypothesis for 40 species in the bird family Paridae, based on comparisons of nucleotide sequences of the mitochondrial cytochrome-b gene. Parids, including tits and chickadees, are an older group than their morphological stereotypy suggests. The longest cytochrome-b distances between species reach 12% in uncorrected divergence. With the exception of one thrasher-like terrestrial tit species of the Tibetan plateau (Pseudopodoces humilis), morphological and ecological stasis have prevailed since the initial parid radiation in the Old World during the mid-Tertiary. All trees support monophyly of the family Paridae, which includes Parus (sensu lato) and the monotypic Oriental genera Sylviparus, Melanochlora, and Pseudopodoces. Within the clade of chickadees and gray tits (Parus, subgenus Poecile), three Old World species, Parus lugubris of the eastern Mediterranean and Balkan regions, P. superciliosus of high elevations in the Himalayas of western China, and P. varius of the Orient are sisters to all other species. The Eurasian crested titmice (subgenus Lophophanes) and North American crested titmice (subgenus Baeolophus) are sister groups. Our data suggest two colonizations of the New World by parids in the late Tertiary. The ancestor of modern Baeolophus colonized North America similar to 4 mya, and the ancestor of all North American chickadees colonized North America similar to 3.5 mya.
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Understanding the evolutionary history of living organisms is a central problem in biology. Until recently the ability to infer evolutionary relationships was limited by the amount of DNA sequence data available, but new DNA sequencing technologies have largely removed this limitation. As a result, DNA sequence data are readily available or obtainable for a wide spectrum of organisms, thus creating an unprecedented opportunity to explore evolutionary relationships broadly and deeply across the Tree of Life. Unfortunately, the algorithms used to infer evolutionary relationships are NP-hard, so the dramatic increase in available DNA sequence data has created a commensurate increase in the need for access to powerful computational resources. Local laptop or desktop machines are no longer viable for analysis of the larger data sets available today, and progress in the field relies upon access to large, scalable high-performance computing resources. This paper describes development of the CIPRES Science Gateway, a web portal designed to provide researchers with transparent access to the fastest available community codes for inference of phylogenetic relationships, and implementation of these codes on scalable computational resources. Meeting the needs of the community has included developing infrastructure to provide access, working with the community to improve existing community codes, developing infrastructure to insure the portal is scalable to the entire systematics community, and adopting strategies that make the project sustainable by the community. The CIPRES Science Gateway has allowed more than 1800 unique users to run jobs that required 2.5 million Service Units since its release in December 2009. (A Service Unit is a CPU-hour at unit priority).
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This paper emphasizes that the interactive constraints of geology and isotopic dating is the best approach to construct the geological event sequence, and has compiled 106 data of reasonable isotopic ages for the igneous rocks of the Yanshan belt. We propose a sequence of mgmatic-tectonic events in the Jurassic-Cretaceous Yanshan orogen of North China. Five orogenic episodes are divided, (1) pre-and initial orogenic episode (Early Jurassic); (2) early orogenic episode (Middle Jurassic); (3) peak orogenic episode (Late Jurassic); (4) late orogenic episode (early Early Cretaceous), and (5) post-orogenic episode. Each episode is a short cycle, all of the orogenic processes construct a longer cycle, and they, in general, followed a counter-clockwise (ccw) PTt path. Finally, it is suggested that the Yanshanian movement was so intensive that the magmatism and tectonic deformation had involved all the lithosphere thickness and the late-Achaean-formed cratonic lithosphere had been significantly reworked.
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Aim When dividing the world into zoogeographical regions, Alfred Russel Wallace stipulated a set of criteria by which regions should be determined, foremost the use of generic rather than species distributions. Yet, recent updates of Wallace’s scheme have not followed his reasoning, probably explain- ing in part the discrepancies found. Using a recently developed quantitative method, we evaluated the world’s zoogeographical regions following his criteria as closely as possible. Location Global. Methods We subjected presence–absence data from range maps of birds, mammals and amphibians to an innovative clustering algorithm, affinity prop- agation. We used genera as our taxonomic rank, although species and familial ranks were also assessed, to evaluate how divergence from Wallace’s criteria influences the results. We also accepted Wallace’s argument that bats and migratory birds should be excluded (although he was contradictory about the birds) and devised a procedure to determine the optimal number of regions to eliminate subjectivity in delimiting the number of regions. Results Regions attained using genera (eight for mammals and birds and six for amphibians) strongly coincided with the regions proposed by Wallace. The regions for amphibians were nearly identical to Wallace’s scheme, whereas we obtained two new ‘regions’ for mammals and two for birds that largely coin- cide with Wallace’s subregions. As argued by Wallace, there are strong reasons not to consider these as being equivalent to the six main regions. Species distri- butions generated many small regions related to contemporary climate and vegetation patterns, whereas at the familial rank regions were very broad. The differences between our generic maps and Wallace’s all involve areas which he identified as being uncertain in his regionalization. Main conclusions Despite more than 135 years of additional knowledge of distributions, the shuffling of generic concepts, and the development of com- puters and complex analytical techniques, Wallace’s zoogeographical regions appear to be no less valid than they were when he proposed them. Recent studies re-evaluating Wallace’s scheme should not be considered updates as such because they have not followed Wallace’s reasoning, and all computer- based analyses, including this one, are subject to the vagaries of the particular methods used.
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The Point Conception (PC) biogeographical boundary is defined by a transition between cold northern and warm southern water masses, accompanied by shifts in numerous ecological and environmental parameters. While these factors can potentially contribute to the genetic differentiation of lineages whose distributions span this boundary, few organisms exhibit genetic signatures of restricted gene flow across this region. We examine the effects of the PC boundary and other potential dispersal barriers on phylogeographical patterns in the rocky supralittoral isopod Ligia occidentalis. This isopod has a limited dispersal potential, its distribution spans the PC region, and it exhibits high levels of allopatric genetic differentiation south of PC.
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Nature is the international weekly journal of science: a magazine style journal that publishes full-length research papers in all disciplines of science, as well as News and Views, reviews, news, features, commentaries, web focuses and more, covering all branches of science and how science impacts upon all aspects of society and life.
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The avian family Paridae (tits and chickadees) contains c. 55 species distributed in the Palearctic, Nearctic, Afrotropic and Indomalaya. The group includes some of the most well-known and extensively studied avian species, and the evolutionary history, in particular the post-glacial colonization of the northern latitudes, has been comparably well-studied for several species. Yet a comprehensive phylogeny of the whole clade is lacking. Here, we present the first complete species phylogeny for the group based on sequence data from two nuclear introns and one mitochondrial gene for 67 taxa of Paridae. Our results strongly support the inclusion of the Fire-capped Tit (Cephalopyrus flammiceps), currently placed in the Remizidae, as the most basal member of the Paridae. The Yellow-browed Tit (Sylviparus modestus) and the Sultan Tit (Melanochlora sultanea) constitute the next two sequential branches whereas the remaining tits falls into two large clades, one of which contains the seed hoarding and nest excavating species. The indicated clades within these two groups are largely congruent with recent classifications, with several unforeseen relationships, such as non-monophyly of the Sombre Tit (Poecile lugubris) and the Marsh Tit (Poecile palustris), as well as non-monophyly of both the African grey and the African black tits. Further, our results support a close relationship between the White-fronted Tit (Parus semilarvatus) and the varied Tit (Poecile varius) as well as a close relationship between the White-naped Tit (Parus nuchalis) and the Yellow-cheecked and Black-lored tits (Parus spilonotus and P. xanthogenys). We propose a new classification that is in accordance with this phylogeny.
Article
Recent studies of intraspecific phylogeography have suggested that the geographic location of genetic discontinuities, or phylogeographic breaks, may frequently coincide with biogeographic boundaries. The concordance is hypothesized to reflect similarity in the processes governing species boundaries and intraspecific lineage boundaries. This concordance has not, however, been widely tested. In the case of the Point Conception biogeographic boundary between the Oregonian and Californian marine biotas, only the supralittoral copepod Tigriopus californicus has been found to have a coincident phylogeographic break. Here I show that the apparent relationship between this break and Point Conception was, in fact, an artifact of insufficient geographic sampling. Mitochondrial DNA analyses of T. californicus populations between Morro Bay and San Diego reveal at least five equally deep phylogeographic breaks in the region (where only one biogeographic boundary is recognized). Limited nuclear DNA sequence data and allozyme data also support the occurrence of multiple genetic discontinuities along this geographic range. Lack of one-to-one correspondence between intraspecific phylogeography and biogeographic boundaries indicates that the processes affecting the genetic differentiation of populations of T. californicus differ from those responsible for determining species distributional limits at the Point Conception biogeographic boundary. A review of genetic data from other species also fails to provide evidence for concordance of biogeography and intraspecific phylogeography across Point Conception. I suggest that the concordance of phylogeography with biogeography will only be pronounced where the biogeographic boundary separates biotas that are phylogenetically related. The numerous cases of interspecific hybrid zones in the region of Cape Canaveral, for example, indicate that many sister-species pairs occur across this biogeographic boundary. Such hybrid zones are not common at Point Conception, and there appears to be no cases of intraspecific phylogeographic breaks associated with this well-recognized biogeographic boundary.
Article
Aim Zoogeographic patterns in the Himalayas and their neighbouring Southeast Asian mountain ranges include elevational parapatry and ecological segregation, particularly among passerine bird species. We estimate timings of lineage splits among close relatives from the north Palaearctic, the Sino-Himalayan mountain forests and from adjacent Southeast Asia. We also compare phylogeographic affinities and timing of radiation among members of avian communities from different elevational belts. Location East Asia. Methods We reconstructed molecular phylogenies based on a mitochondrial marker (cytochrome b) and multilocus data sets for seven passerine groups: Aegithalidae, Certhiidae (Certhia), Fringillidae (Pyrrhula), Paridae (Periparus), Phylloscopidae, Regulidae and Timaliidae (Garrulax sensu lato). Molecular dating was carried out using a Bayesian approach applying a relaxed clock in beast. Time estimates were inferred from three independent calibrations based on either a fixed mean substitution rate or fixed node ages. The biogeographic history of each group was reconstructed using a parsimony-based approach. Results Passerine radiation in Southeast Asia can be divided into roughly three major phases of separation events. We infer that an initial Miocene radiation within the Southeast Asian region included invasions of (sub)tropical faunal elements from the Indo-Burmese region to the Himalayan foothills and further successive invasions to Central Asia and Taiwan towards the early Pliocene. During two further Pliocene/Pleistocene phases, the subalpine mountain belt of the Sino-Himalayas was initially invaded by boreal species with clear phylogenetic affinities to the north Palaearctic taiga belt. Most terminal splits between boreal Himalayan/Chinese sister taxa were dated to the Pleistocene. Main conclusions Extant patterns of elevational parapatry and faunal transition in the Sino-Himalayas originated from successive invasions from different climatic regions. The initiation of Southeast Asian passerine diversification and colonization of the Himalayan foothills in the mid-Miocene coincides with the postulated onset of Asian monsoon climate and the resulting floral and faunal turnovers. Patterns of elevational parapatry were established by southward invasions of boreal avifaunal elements to the subalpine Sino-Himalayan forest belt that were strongly connected to climate cooling towards the end of the Pliocene. Current patterns of allopatry and parapatry in boreal species (groups) were shaped through Pleistocene forest fragmentation in East Asia.
Article
Mitochondrial (mt) DNA data on the comparative phylogeographic patterns of 19 species of freshwater, coastal, and marine species in the southeastern U.S.A. are reviewed. Nearly all assayed species exhibit extensive mtDNA polymorphism, although still orders-of-magnitude less than predicted under neutrality theory if evolutionary effective population sizes of females are similar to current census sizes. In both the freshwater and marine realms, deep and geographically concordant forks in intraspecific mtDNA phylogenies commonly distinguish regional populations in the Atlantic versus Gulf Coast areas. These concordant phylogeographic patterns among independently evolving species provide evidence of similar vicariant histories of population separation, and can be related tentatively to episodic changes in environmental conditions during the Pleistocene. However, the heterogeneity of observed genetic distances and inferred separation times are difficult to accommodate under a uniform molecular clock. Additional population genetic structure within geographic regions is evidenced by species-specific shifts in frequencies of more closely related mtDNA haplotypes, and by high frequencies of private haplotypes in some species. The magnitude of local population structure appears partially related to the life history pattern and dispersal capability of a species. The mtDNA results indicate that conspecific populations can be structured at a wide variety of evolutionary depths. The deeper subdivisions in an intraspecific phylogeny reflect the major sources of evolutionary gene pool diversity within a species, while the shallower molecular separations evidence more recent population subdivisions that can be related to comparative dispersal and gene flow patterns. These molecular findings are relevant to the understanding of biogenetic diversity, and carry implications for conservation biology.
Article
The exceptionally broad species diversity of vascular plant genera in east Asian temperate forests, compared with their sister taxa in North America, has been attributed to the greater climatic diversity of east Asia, combined with opportunities for allopatric speciation afforded by repeated fragmentation and coalescence of populations through Late Cenozoic ice-age cycles1. According to Qian and Ricklefs1, these opportunities occurred in east Asia because temperate forests extended across the continental shelf to link populations in China, Korea and Japan during glacial periods, whereas higher sea levels during interglacial periods isolated these regions and warmer temperatures restricted temperate taxa to disjunct refuges. However, palaeovegetation data from east Asia2, 3, 4, 5, 6 show that temperate forests were considerably less extensive than today during the Last Glacial Maximum, calling into question the coalescence of tree populations required by the hypothesis of Qian and Ricklefs1.
Article
Abstract This paper emphasizes that the interactive constraints of geology and isotopic dating is the best approach to construct the geological event sequence, and has compiled 106 data of reasonable isotopic ages for the igneous rocks of the Yanshan belt. We propose a sequence of mgmatic-tectonic events in the Jurassic-Cretaceous Yanshan orogen of North China. Five orogenic episodes are divided, (1) pre-and initial orogenic episode (Early Jurassic); (2) early orogenic episode (Middle Jurassic); (3) peak orogenic episode (Late Jurassic); (4) late orogenic episode (early Early Cretaceous), and (5) post-orogenic episode. Each episode is a short cycle, all of the orogenic processes construct a longer cycle, and they, in general, followed a counter-clockwise (ccw) PTt path. Finally, it is suggested that the Yanshanian movement was so intensive that the magmatism and tectonic deformation had involved all the lithosphere thickness and the late-Achaean-formed cratonic lithosphere had been significantly reworked.
Article
We analysed variation of the mitochondrial control region from willow tits through its Palaearctic distribution range. Although we found high amount of genetic variation (π=1.114%), there was almost no differentiation between subspecies or geographical localities. This may be because of a combination of several ecological and genetic factors, including a relatively homogenic habitat through the distribution range, lack of geographical barriers, high gene flow and a large long-term effective population size. On the contrary, in the songar tit, which is sometimes considered to be conspecific with the willow tit, the mitochondrial lineages seem to correlate with the geographical locality and are clearly distinct from the willow tit. We concluded that the common ancestors of willow and songar tits existed some 1.5–2 Myr ago in the south-eastern Asia. After the last Ice Ages, the willow tit expanded all through the Palaearctic, whereas the songar tit remained in eastern Asia.
Article
Regionalization is the primary classification problem in geography, although other typologies are sometimes demanded by specific research endeavors. Groupings of area units can produce either contiguous or fragmented patterns. Dis-contiguous regionalizations may have the advantage of placing truly alike areal units in the same category and are obviously necessary when the similarity of distant places is sought. The same number of contiguous regions, on the other hand, will most likely produce a more regular map pattern, thereby facilitating the transferral of the printed map into a more coherent and more lasting mental image.' Furthermore, many problems, particularly those partitioning space for administrative purposes, demand contiguity. Although some within-group homo-geneity is often lost by imposing contiguity, this is a difficulty only for situations with relatively low spatial consistency.a This loss of homogeneity may well be offset by the perceptual advantage of simplicity. Previous quantitative approaches to regional clustering have largely achieved contiguity by prohibiting linkages from occurring unless the two places abut. This contiguity restriction has been employed most often with hierarchical grouping procedures in which the clustering of N places proceeds through N-1 levels of classification to the ultimate aggregation of all units into a single group? At * The author is grateful to the Research Foundation of the State University of New York for financial support and to Michael Dobson, Peter Gould, and Anthony Williams for helpful suggestions. 1 For a discussion of the perceptual advantages of regular map patterns, see Monmonier [PI. 2 Spence [I21 discusses this problem and gives an example in which the loss of homogeneity for M regions of N counties decreases as Af approaches both 1 and N. 8Two of the earliest users of this approach were Ray and Berry [ I l l. Mark S. Monmonier is associate professor of geography at Syracuse University.
Article
In analysis of multilocus genotypes from structured populations, individual coefficients of membership in subpopulations are often estimated using programs such as structure. distruct provides a general method for visualizing these estimated membership coefficients. Subpopulations are represented as colours, and individuals are depicted as bars partitioned into coloured segments that correspond to membership coefficients in the subgroups. distruct, available at http://www.cmb.usc.edu/~noahr/distruct.html, can also be used to display subpopulation assignment probabilities when individuals are assumed to have ancestry in only one group.
Article
Five species of Eurasian birds displayed a range of mitochondrial DNA phylogeographic structures, including a single widespread lineage (common sandpiper), two geographically unsorted and closely related lineages (long-tailed tit), three partially overlapping closely related lineages (reed bunting), and two divergent geographically isolated lineages that rival species distinction (red-breasted flycatcher and skylark). Only the red-breasted flycatcher and the skylark displayed congruent phylogeographic structures. These five species represent different stages of diversification and speciation. There was little evidence that natural selection had influenced mitochondrial NADH dehydrogenase subunit 2 (ND2) sequences. In several instances, population growth was hypothesized, based on haplotype distributions within populations.
Article
The sequence of marine and marginal-marine silts and sands of the U.S. Middle Atlantic Coastal Plain preserves a relatively complete record of Pliocene sea-level highstands. A general chronology for the deposition of these units has been developed previously from studies of the microfossil biostratigraphy complemented by a limited number of paleomagnetic and radiometric dates. Within this broad temporal framework it is currently difficult to assign ages to individual transgressive events with a resolution much better than 0.5 Ma.The age model proposed here attempts to refine the depositional history of the Atlantic Coastal Plain by correlation with the more continuous deep-ocean record. The model assigns probable ages to the Pliocene transgressions onto the Atlantic Coastal Plain based on evidence for sea-level highstands inferred from high-resolution deep-ocean δ18O records. At least five major transgressive-regressive events can be correlated with presumed eustatic fluctuations. The temporal resolution for the timing of the transgressive events is greatly improved over that of the biostratigraphy alone. Many aspects of the proposed chronology require verification by more detailed field study, but it is offered as a testable working hypothesis.
Article
Genetic clustering algorithms require a certain amount of data to produce informative results. In the common situation that individuals are sampled at several locations, we show how sample group information can be used to achieve better results when the amount of data is limited. New models are developed for the structure program, both for the cases of admixture and no admixture. These models work by modifying the prior distribution for each individual's population assignment. The new prior distributions allow the proportion of individuals assigned to a particular cluster to vary by location. The models are tested on simulated data, and illustrated using microsatellite data from the CEPH Human Genome Diversity Panel. We demonstrate that the new models allow structure to be detected at lower levels of divergence, or with less data, than the original structure models or principal components methods, and that they are not biased towards detecting structure when it is not present. These models are implemented in a new version of structure which is freely available online at http://pritch.bsd.uchicago.edu/structure.html.