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A zoogeographical boundary between the Palaearctic and Sino-Japanese realms documented by consistent north/south phylogeographical divergences in three woodland birds in eastern China
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.
... 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. ...
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. ...
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). ...
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. ...
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.
... Q. Liu, Duan, Hao, XuemgUn, & Sun, 2014;Qiu, Fu, & Comes, 2011). This region is characterized by northsouth peaks separated by valley bottoms (Song et al., 2016). From valleys situated approximately 1,000 m above sea level to the peakof Minya Konka at 7,556 m, the huge drop in altitude can form "sky islands" (Kai & Jiang, 2014;Qian, Ricklefs, & Thuiller, 2021). ...
Exploring the geological events and climate change in the Himalaya-Hengduan Mountains (HHM) region and the Qinghai-Tibet Plateau (QTP) is crucial for understanding the impact of environmental change on biogeographic distribution and biological evolution. To delve deeper into these mechanisms, we reconstructed the evolutionary history of three Notholirion species that span these regions. Here, we examined a total of 254 individuals from 31 populations of these three species, utilizing five chloroplast DNA (cpDNA) (matK, ndhA, ndhG-ndhI, petB-petD, and petL-petG), along with one nuclear DNA region (internal transcribed spacer, ITS). We identified 14 haplotypes from cpDNA and 27 haplotypes from the ITS, each specific to corresponding species. Robust haplotype trees were detected, and obvious discrepancies were found between the cpDNA and ITS trees. A total of 147 chloroplast genomes were used for divergence time estimation, of which 10 chloroplast genomes from distinct populations of Notholirion species provided a comprehensive representation of the genus. The divergence time estimation results suggested that species of Notholirion genus originated in the southern Himalayan region during the Late Oligocene period (25.05 Ma), and the three Notholirion species then diverged during the Late Pliocene period (7.43 Ma). Our maximum model forecasts that the overall distribution range of Notholirion over four different periods remains relatively stable，from LIG to the future. The origin of the genus Notholirion was triggered by sustained climate fluctuations during the Late Oligocene, with the uplift of the Himalayas and the subsequent orogenic movements intensifying climate changes and further promoting the species divergence of Notholirion. A long evolutionary history, coupled with sexual reproduction and habitat fragmentation, likely contributed to the higher genetic diversity of Notholirion. The higher genetic differentiation among Notholirion populations may be attributed to drastic changes in the external environment within their range, as well as their constrained capacity for seed production and dispersal.
... Similarly, Song et al. (2016) found a break (barrier) at ~40° N for three woodland passerine birds (Aegithalos caudatus, Poecile montanus and Poecile palustris), which is likely associated with the belt. These birds have much recent (Pleistocene) divergence. ...
Continental East Asia has a mild Pleistocene climate and a complex recent geological history. Phylogeographic studies of animals over the last 30 years have produced several distinctive patterns. Glaciation refugia are numerous and are not restricted to any particular regions. Most of them are localized and species-specific, although several large refugia, for example the mountains of SW China, are shared by multiple species and have refugia-within-refugia. Furthermore, postglaciation range expansion events vary greatly in time, scale and direction. Large-scale south-to-north post-LGM expansions are few and mostly occurred in the northern regions. Additionally, several unique geographic features, including the three-step terrain of China and the northern arid belt, have significant impacts on many species histories. Overall, the impacts of Pleistocene glaciations, particularly the LGM, on species history vary drastically from nondetectable to significant. The impacts are the least for species from the southwestern region and are most dominant for species from the north. Geological events play a more significant role in shaping species history than Pleistocene climatic changes. Phylogeographic patterns among animals species are highly consistent with those of plants. Future phylogeographic endeavour in East Asia should be hypothesis-driven and seek processes that underlie common patterns. The wide use of genomic data allow accurate estimates of historical population processes and exploration of older history beyond the Pleistocene.
... 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. ...
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. ...
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. ...
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). ...
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). ...
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). ...
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 ‐1α, ITS 1) 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 lineages 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. ...
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.
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.
Nuthatches of the Holarctic and partly Indo-Malayan genus Sitta have been subject to a number of phylogenetic analyses; however, the most complete phylogenetic hypothesis to date missed several Asian species-level taxa, was based on a limited sampling, and included only one sample per species. Other recent studies were mainly focused on phylogeographic patterns of single Asian species but failed to unam-biguously resolve their phylogenetic relationships. In this study, we provide a time-calibrated multi-locus phylogeny of nuthatches (Sitta) including 27 out of 28 currently recognized species. To account for intraspecific variation we included a number of subspecific taxa in our sampling, e.g. for the phenotypically diverse Eurasian nuthatch, S. europaea. Within the latter species (our clade X) three phenotypically distinct phylogroups started diversifying from the early Pleistocene on: (i) brown-bellied forms of the sinensis group from China and Tai-wan with smallest body size dimensions, (ii) white-bellied forms of the Central and Eastern Palearctic europaea group with average body size dimensions, and (iii) brown-bellied forms of the Western Palearctic and Caucasian caesia group with largest body size dimensions. The three phylogroups are connected by chains of phenotypically intermediate populations in Eastern Europe (e.g. ssp. homeyeri) and in Far East Russia and northeastern China (ssp. amurensis). The Eurasian nuthatch was sister to a monophyletic clade IX comprising five Sino-Himalayan species: S. nagaensis, S. cashmirensis, S. castanea, S. neglecta, and S. cinnamoventris. In the Sino-Himalayas, ecological segregation along the elevational gradient was established from the mid-Miocene onset of nuthatch diversification until the recent ecological segregation among chestnut-bellied forms of the S. castanea complex during the Pleistocene.
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 4 mya, and the ancestor of all North American chickadees colonized North America 3.5 mya.
Phylogénie chez la mésange (Paridés): II. Relations entre les espèces basées sur des séquences du gène mitochondrial cytochrome-b
Eurasia is a large continent characterized by heterogeneous environments. Glacial cycles during the late Pleistocene have had variable impacts on the avifauna across Eurasia. Bird populations from South-East Asia show stability through the Last Glacial Maximum (LGM), while populations from Europe exhibit evidence of post-LGM expansion. We investigated the phylogeography of the Long-tailed Tit (Aegithalos caudatus), which spans the longitudinal breadth of Eurasia to test how climatic history and regional topographical complexity affected populations and diversification within the species complex. Our results show that two lineages from central and southern China (lineages C and D) segregate geographically, while lineages across northern Eurasia (lineage A and B) show substantial sympatry. Bayesian estimates for the timing of diversification suggest that the four lineages diverged during the middle Pleistocene, splitting in parallel and undergoing concurrent demographic histories since divergence. A. caudatus lineages experienced similar and synchronous population size dynamics during glacial cycles before the LGM. We conclude that the difference in geo-topologic complexity may be an important factor that led to the variation in secondary admixture between northern Eurasian and eastern Asian lineages.
The Yanshan (Yan Mountains) of northern China extend westward at about lat 40°N from Bohai Bay and Liaoning province to the border between Hebei province and Inner Mongolia. It is likely, but not unequivocally demonstrated, that the Archean-floored Yanshan continue farther westward under a cover of Neogene strata to emerge as the Yinshan belt of Inner Mongolia. Mesozoic terrestrial sedimentation, magmatism and deformation-including multiple phases of folding and contractional, extensional, and strike-slip faulting-characterize the Yanshan fold and thrust belt. Field studies and radiometric dating (U-Pb, 40Ar-39Ar) of plutonic and volcanic rock units in Beijing Municipality and northern Hebei and western Liaoning provinces have revealed that the complexity of Mesozoic deformation in these areas is in large part (1) a consequence of profound earlier deformation of Permian(?) to early Mesozoic age, and (2) an unusual younger Mesozoic history of alternating northward and southward tectonic vergence of major structures. Major south-directed low-angle thrust faulting of pre-Middle Jurassic age (7180 Ma) in the Yanshan involved Archean basement rocks and their Proterozoic and Phanerozoic cover, and developed south of a Permian-Triassic magmatic arc. Thrusting could have been (1) a consequence of the collisional suturing of Paleozoic Mongolian arcs against an Andean-style continental arc along the northern margin of the North China plate, or (2) an expression of a backarc, foreland fold and thrust belt of U.S. Cordilleran type formed during southward subduction beneath the North China Archean "craton." This episode of thrusting and folding was followed by widespread erosion of upper plate rocks and subsequent terrestrial deposition of Middle Jurassic volcanic and sedimentary strata across both plates. Our studies indicate that Late Jurassic and Early Cretaceous contractional deformation in the Yanshan was also much more intense than generally believed, and that it followed a heretofore unrecognized phase of Middle Jurassic or early Late Jurassic east-west extension in northern Hebei province. Prior to our studies, popular views of east- to east-northeast- trending Yanshan contractional deformation proposed that (1) involvement of Archean basement rocks in faulting indicates a thickskinned tectonic style analogous to the U.S. Laramide Rocky Mountains; (2) thrust faults steepen downward into the basement; (3) vertical movements predominated in the development of the belt; and (4) Mesozoic contraction across the belt was only a few tens of percent; some workers have believed that the Yanshan developed independently of plate interactions. We question all of these assumptions. We have identified a major, synformally folded, thin-skinned thrust plate just south of Chengde, Hebei province, that is of Late Jurassic age and had a minimum northward displacement of &40 km. In earlier studies in the Yunmeng Shan area of the Yanshan north of Beijing we defined major south-vergent Late Jurassic-Early Cretaceous ductile structures involving Archean basement rocks and their cover. These structures include a recumbent, basement-cored anticlinal nappe and a lower limb ductile thrust fault within a 6-km-thick gneissic shear zone. The Jurassic-Cretaceous Yanshan belt, and its probable western continuation, the Yinshan belt of Inner Mongolia, appear to be reflect regional north-south intraplate shortening. However, some Yanshan patterns of deformation, e.g., ductile nappe formation in the Yunmeng Shan and northeast structural trends of the belt in Liaoning province, were influenced by thermal regimes related to magmatism (≤ 180-190 Ma) accompanying westward or northwestward Pacific plate subduction beneath eastern Asia. We thus believe it likely that two contrasting modes of plate interaction occurred synchronously in the Yanshan segment of the Yinshan-Yanshan belt during Middle Jurassic through Early Cretaceous time. Jurassic-Cretaceous collision of an amalgamated North China-Mongolian plate with the Siberian plate is widely believed to have accompanied closure of a Mongolo- Okhotsk sea more than 800-1100 km north of the Yanshan belt. This collision might have been responsible forYanshan (andYinshan) intraplate contractional deformation farther south, but such a hypothesis is severely complicated by reports of widespread, basin-forming Late Jurassic and Early Cretaceous extension in the terranes between the Mongolo-Okhotsk suture and the Yinshan-Yanshan belt. Following Early Cretaceous contraction in both the Yinshan and Yanshan belts, the northern margin of the Archean-floored plate was also the site of major northwest-southeast regional extension beginning soon after 120 Ma. Subducting plate rollback or postorogenic collapse are only two of several possible explanations for the development of extensional metamorphic core complexes in northern InnerMongolia and theYanshan belt farther east.
Little has been published to describe or interpret Asian biodiversity hotspots, especially the East Himalaya – Mountains of Southwest China (H-MSC) range, thus making necessary a review based on the current knowledge. The Pliocene and Pleistocene geological and glacial histories of the Asian continent is different from those of Europe and North America, suggesting different mechanisms of speciation and extinction, and thus different responses to climate changes during the Quaternary glaciations. This short review summarizes potential drivers in shaping and maintaining high species richness and endemism of birds in the H-MSC range. The geographical location at the junction of different biogeographical realms, wide range of habitats and climates along the extensive elevational range, complex topography, and distinct geological history of this region probably have contributed to the evolution of an exceptionally species-rich and endemic-rich, specialized montane avian fauna. The Mountain systems in the H-MSC may have provided refugia where species survived during the glacial periods and barriers for preventing species dispersal after the glacial periods. More studies are required to further test this refugia hypothesis by comparing more cold-tolerent and warm-tolerent species.This article is protected by copyright. All rights reserved
We present a new open source, extensible and flexible software platform for Bayesian evolutionary analysis called BEAST 2. This software platform is a re-design of the popular BEAST 1 platform to correct structural deficiencies that became evident as the BEAST 1 software evolved. Key among those deficiencies was the lack of post-deployment extensibility. BEAST 2 now has a fully developed package management system that allows third party developers to write additional functionality that can be directly installed to the BEAST 2 analysis platform via a package manager without requiring a new software release of the platform. This package architecture is showcased with a number of recently published new models encompassing birth-death-sampling tree priors, phylodynamics and model averaging for substitution models and site partitioning. A second major improvement is the ability to read/write the entire state of the MCMC chain to/from disk allowing it to be easily shared between multiple instances of the BEAST software. This facilitates checkpointing and better support for multi-processor and high-end computing extensions. Finally, the functionality in new packages can be easily added to the user interface (BEAUti 2) by a simple XML template-based mechanism because BEAST 2 has been re-designed to provide greater integration between the analysis engine and the user interface so that, for example BEAST and BEAUti use exactly the same XML file format.
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.
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) .
Different scales and frequencies of glaciations developed in Europe and Asia during the Pleistocene. Because species responses to climate change are influenced by interactive factors including ecology and local topography, the pattern and tempo of species diversification may vary significantly across regions. The great tit Parus major is a widespread Eurasian passerine with a range that encircles the central Asian desert and high-altitude areas of the Tibetan Plateau. A number of genetic studies have assessed the effect of paleo-climate changes on the distribution of the European population. However, none have comprehensively addressed how paleo-climate change affected the distribution of the great tit in China, an apparent hotspot of P. major subspecific diversity. Here, we describe likely paleo-climatic effects on P. major populations in China based on a combination of phylogeography and ecological niche models (ENMs). We sequenced three mitochondrial DNA markers from 28 populations (213 individuals), and downloaded 112 sequences from outside its Chinese range. As the first step in clarifying the intra-specific relationships among haplotypes, we attempted to clarify the divergence and demography of populations in China. Phylogeographic analysis revealed that P. major is comprised of five highly divergent clades with geographic breaks corresponding to steep mountains and dry deserts. A previously undescribed monophyletic clade with high genetic diversity, stable niches and a long and independent evolutionary history was detected in the mountainous areas of southwest China. The estimated times at which these clades diverged was traced back to the Early-Middle Pleistocene (2.190.61 mya). Contrary to the post-LGM (the Last Glacial Maximum) expansion of European populations, demographic history indicates that Asian populations expanded before the LGM after which they remained relatively stable or grew slowly through the LGM. ENMs support this conclusion and predict a similar distribution in the present and the LGM. Our genetic and ecological results demonstrate that Pleistocene climate changes shaped the divergence and demography of P. major in China.
Modern attempts to produce biogeographic maps focus on the distribution of species, and the maps are typically drawn without
phylogenetic considerations. Here, we generate a global map of zoogeographic regions by combining data on the distributions
and phylogenetic relationships of 21,037 species of amphibians, birds, and mammals. We identify 20 distinct zoogeographic
regions, which are grouped into 11 larger realms. We document the lack of support for several regions previously defined based
on distributional data and show that spatial turnover in the phylogenetic composition of vertebrate assemblages is higher
in the Southern than in the Northern Hemisphere. We further show that the integration of phylogenetic information provides
valuable insight on historical relationships among regions, permitting the identification of evolutionarily unique regions
of the world.
The world's zoogeographical regions were historically defined on an intuitive basis, with no or a limited amount of analytical testing. Here, we aimed (a) to compare analytically defined global zoogeographical clusters for the herpetofauna, birds, mammals, and all these groups taken together (tetrapod vertebrates); (b) to use commonalities among these groups to propose an updated global zoogeographical regionalization; and (c) to describe the resulting regions in terms of vertebrate diversity and characteristic taxa. The clusters were remarkably uniform across taxa and similar to previous intuitively defined regions. Eleven vertebrate-rich (Nearctic, Caribbean, Neotropical, Andean, Palearctic, Afrotropical, Madagascan, Indo-Malaysian, Wallacean, New Guinean, Australian) and three vertebrate-poor (Arctic, Antarctic, Polynesian) zoogeographical regions were derived; the Neotropical,- Afrotropical, and Australian had the highest numbers of characteristic tetrapod genera. This updated regionalization provides analytically accurate divisions of the world, relevant to conservation, biogeographical research, and geography education.
The Early-Middle Pleistocene transition (c. 1.2–0.5 Ma), sometimes known as the ‘mid-Pleistocene revolution’, represents a major episode in Earth history. Low-amplitude 41-ka obliquity-forced climate cycles of the earlier Pleistocene were replaced progressively in the later Pleistocene by high-amplitude 100-ka cycles. These later cycles are indicative of slow ice build-up and subsequent rapid melting, and imply a transition to a strongly non-linear forced climate system. Changes were accompanied by substantially increased global ice volume at 940 ka. These climate transformations, particularly the increasing severity and duration of cold stages, have had a profound effect on the biota and the physical landscape, especially in the northern hemisphere. This review assesses and integrates the marine and terrestrial evidence for change across this transition, based on the literature and especially the following 17 chapters in the present volume. Orbital and non-orbital climate forcing, palaeoceanography, stable isotopes, organic geochemistry, marine micropalaeontology, glacial history, loess-palaeosol sequences, pollen analysis, large and small mammal palaeoecology and stratigraphy, and human evolution and dispersal are all considered, and a series of discrete events is identified from Marine Isotope Stage (MIS) 36 (c. 1.2 Ma) to MIS 13 (c. 540–460 Ma). Of these, the cold MIS 22 (c. 880–870 ka) is perhaps the most profound. However, we here endorse earlier views that on practical grounds the Matuyama-Brunhes palaeomagnetic Chron boundary (mid-point at 773 ka, with an estimated duration of 7 ka) would serve as the best overall guide for establishing the Early-Middle Pleistocene Subseries boundary.
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.
Phylogeography has become a powerful approach for elucidating contemporary geographical patterns of evolutionary subdivision within species and species complexes. A recent extension of this approach is the comparison of phylogeographic patterns of multiple co-distributed taxonomic groups, or ‘comparative phylogeography.’ Recent comparative phylogeographic studies have revealed pervasive and previously unrecognized biogeographic patterns which suggest that vicariance has played a more important role in the historical development of modern biotic assemblages than current taxonomy would indicate. Despite the utility of comparative phylogeography for uncovering such ‘cryptic vicariance’, this approach has yet to be embraced by some researchers as a valuable complement to other approaches to historical biogeography. We address here some of the common misconceptions surrounding comparative phylogeography, provide an example of this approach based on the boreal mammal fauna of North America, and argue that together with other approaches, comparative phylogeography can contribute importantly to our understanding of the relationship between earth history and biotic diversification.
The phylogeography of four Apodemus species (Apodemus agrarius, Apodemus peninsulae, Apodemus latronum, and Apodemus draco) was studied in the Far East of Asia, based on sequences of the mitochondrial DNA cytochrome b gene. The results obtained show the existence of many different genetic lineages within the studied Apodemus species, suggesting the isolation and differentiation of populations in multiple refuge areas. Higher genetic diversities in some regions such as Yunnan, Sichuan (China), and eastern Russia suggest these areas are potential refuges for these species. The existence of such complex genetic structures could be linked to the presence of many biogeographic barriers (Himalaya Mountains, Tien-shan Mountains, Altai Mountains, Tibetan Plateau, Gobi desert, Yunnan Guizhou Plateau, Dzungaria basin, and others) in these regions, which were probably reinforced during the Quaternary climate changes. These barriers also played an important role concerning the low dispersal abilities of the two studied Apodemus species adapted to forest habitats (A. latronum and A. draco) with respect to colonizing regions other than China.
Aim Biogeographical regionalizations, such as zoogeographical regions, floristic kingdoms or ecoregions, represent categorizations central to many basic and applied questions in biogeography, ecology, evolution and conservation. Traditionally established by experts based on qualitative evidence, the lack of transparency and quantitative support has set constraints on their utility. The recent availability of global species range maps, novel multivariate techniques and enhanced computational power now enable a quantitative scrutiny and extension of biogeographical regionalizations that will facilitate new and more rigorous uses. In this paper we develop and illustrate a methodological roadmap for species‐level biogeographical regionalizations at the global scale and apply it to mammals.
Location Global.
Methods We explore the relative usefulness of ordination and clustering methods and validation techniques. The performance of nine different clustering algorithms is tested at different taxonomic levels. The grain of regionalization (i.e. the number of clusters) will usually be driven by the purpose of the study, but we present several approaches that provide guidance.
Results Non‐metric multidimensional scaling offers a valuable first step in identifying and illustrating biogeographical transition zones. For the clustering of regions, the nine different hierarchical clustering methods varied greatly in utility, with UPGMA (unweighted pair‐group method using arithmetic averages) agglomerative hierarchical clustering having consistently the best performance. The UPGMA approach allows a tree‐like phenetic representation of the relative distances of regions and can be applied at different levels of taxonomic resolution. We find that the new quantitative biogeographical regions exhibit both striking similarities to and differences from the classic primary geographical divisions of the world’s biota. Specifically, our results provide evidence that the Sahara, northern Africa, the Arabian Peninsula and parts of the Middle East should be regarded as part of the Afrotropics. Further, the position of the New Guinean continental shelf, Lydekker’s Line, is supported as an appropriate border to separate the Oriental and Australian regions.
Main conclusions We propose that this sort of new, quantitative delineation and relationship assessment across taxonomic and geographical grains is likely to offer opportunities for more rigorous inference in historical and ecological biogeography and conservation.
Genetic structuring of plant populations is strongly influenced by both common ancestry and current patterns of interpopulation genetic exchange. The interaction of these two forces is particularly confounding and hence interesting in plants. This complexity of plant genetic structures is due in part to a diversity of reproductive ecologies affecting genetic exchange and the fact that reproductive barriers are often weak between otherwise morphologically well-defined species. Phylogeographic methods provide a means of examining the history of genetic exchange among populations, with the potential to distinguish biogeographic patterns of genetic variation caused by gene flow from those caused by common ancestry. With regard to plants, phylogeography will be most useful when applied broadly across the entire spectrum of potential genetic exchange. Although current phylogeographic studies of plants show promise, widespread application of this approach has been hindered by a lack of appropriate molecular variation; this problem is discussed and possible solutions considered.
We present STRUCTURE HARVESTER (available at http://taylor0.biology.ucla.edu/structureHarvester/), a web-based program for collating results generated by the program STRUCTURE. The program provides a fast way to assess
and visualize likelihood values across multiple values of K and hundreds of iterations for easier detection of the number of genetic groups that best fit the data. In addition, STRUCTURE
HARVESTER will reformat data for use in downstream programs, such as CLUMPP.
KeywordsStructure–Population structure–Population genetics–Evanno method–Visualization–Clustering
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).
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.
We describe a model-based clustering method for using multilocus genotype data to infer population structure and assign individuals to populations. We assume a model in which there are K populations (where K may be unknown), each of which is characterized by a set of allele frequencies at each locus. Individuals in the sample are assigned (probabilistically) to populations, or jointly to two or more populations if their genotypes indicate that they are admixed. Our model does not assume a particular mutation process, and it can be applied to most of the commonly used genetic markers, provided that they are not closely linked. Applications of our method include demonstrating the presence of population structure, assigning individuals to populations, studying hybrid zones, and identifying migrants and admixed individuals. We show that the method can produce highly accurate assignments using modest numbers of loci—e.g., seven microsatellite loci in an example using genotype data from an endangered bird species. The software used for this article is available from http://www.stats.ox.ac.uk/~pritch/home.html.
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.
Springtails (Collembola) are a group of arthropods that are found in terrestrial ecosystems throughout the world. Two species complexes, Tomocerus ocreatus and T. nigrus complexes, are widely distributed in the southern and northern parts of eastern China, respectively. There is a poor understanding of the species diversity within these complexes and of the factors affecting their diversification and dispersal. Species delimitation using a general mixed Yule coalescent model and a Bayesian multilocus approach recognized 22 DNA-based species. This supports the presence of extensive cryptic diversity in species that are geographically widespread. In addition to genetic differences, we discovered corresponding morphological differences in jumping organs among the major clades. Analyses of divergence times and historical biogeographical processes revealed that ocreatus and nigrus complexes originated in southern and northern China, respectively. We estimated their divergence at 27.8–44.9 Mya during the Eocene–Oligocene, at the time when the transmeridional Qinling–Dabie Mountains uplifted and formed the north–south geographical boundary of eastern China. Diversification analyses suggest that the subsequent orogenesis of the Qinghai–Tibetan Plateau in western China had little impact on divergences within the two species complexes so that they maintained their geographical patterns from the Paleogene to the present day. Our findings also point to a potentially important influence of the Qinling–Dabie Mountains on patterns of animal speciation and distribution in China.
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.
Aim
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 L igia 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 .
Location
Eastern P acific coastline between southern O regon and the B aja C alifornia P eninsula.
Methods
We conducted a thorough sampling of L . occidentalis from the PC area to its northern range limit in southern O regon, and increased previous sampling coverage south of PC . We obtained sequences of the mitochondrial genes cytochrome c oxidase subunit I ( COI ) and 16S rDNA for the new localities and combined them with a previously published data set, resulting in a total of 58 sampling locations. We also obtained sequences of the nuclear gene sodium–potassium ATP ase α‐subunit ( NaK ). We conducted phylogenetic and population‐genetic analyses.
Results
The geographical limit between the two most divergent clades of L . occidentalis (20–25% divergence for COI ) distributed between southern O regon and the B aja C alifornia P eninsula occurs at the PC biogeographical boundary. Levels of allopatric genetic divergences were greatly reduced north of PC (≤ 3.0% divergence for COI ).
Main conclusions
The geographical limit between the two main L . occidentalis clades in C alifornia largely reflects the changes in sea surface temperature that define the PC biogeographical boundary. Reduced levels of genetic divergence among L . occidentalis lineages found north of PC suggest a recent expansion in the northern range of this isopod.
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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.
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.
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.
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.
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.
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.
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.
Cartwright, P. (2009). Phylogenetics and evolution of Capitata (Cnidaria: Hydrozoa), and the systematics of Corynidae. — Zoologica Scripta, **, ***–***. Generic-and family level classifications in Hydrozoa have been historically problematic due to limited morphological characters for phylogenetic analyses and thus taxonomy, as well as disagreement over the relative importance of polyp vs. medusa characters. Within the recently redefined suborder Capitata (Cnidaria: Hydrozoa: Hydroidolina), which includes 15 families and almost 200 valid species, family level relationships based on mor-phology alone have proven elusive, and there exist numerous conflicting proposals for the relationships of component species. Relationships within the speciose capitate family Cory-nidae also remain uncertain, for similar reasons. Here, we combine mitochondrial 16S, and nuclear 18S and 28S sequences from capitate hydrozoans representing 12 of the 15 valid capitate families, to examine family level relationships within Capitata. We further sample densely within Corynidae to investigate the validity of several generic-level classification schemes that rely heavily on the presence ⁄ absence of a medusa, a character that has been questioned for its utility in generic-level classification. We recover largely congruent tree topologies from all three markers, with 28S and the combined dataset providing the most resolution. Our study confirms the monophyly of the redefined Capitata, and provides res-olution for family level relationships of most sampled families within the suborder. These analyses reveal Corynidae as paraphyletic and suggest that the limits of the family have been underestimated. Our results contradict all available generic-level classification schemes for Corynidae. As classification schemes for this family have been largely based on reproductive characters such as the presence ⁄ absence of a medusa, our results suggest that these are not valid generic-level characters for the clade. We suggest a new taxonomic structure for the lineage that includes all members of the newly redefined Corynidae, based on molecular and morphological synapomorphies for recovered clades within the group.
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.
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.
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.
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.