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1.
The north‐western Mediterranean Sea's high biodiversity originates from a mixture of temperate and subtropical species. Large‐scale warming has been detected through northward range shifts of ‘warm‐water’ species, and mass‐mortality events for ‘cold‐water’ invertebrates. Marine caves are affected in a more subtle way. By monitoring endemic species of cave mysids (Crustacea) and comparing our results with data in the literature, we observed a strong decline in one species, coupled with the success of another. Near Marseille (France), this phenomenon began while two major thermal anomalies were reported. Different tolerances to temperature were demonstrated by both the species distribution ranges and laboratory experimentation. We provide a possible physiological explanation for populations of cold stenothermal species of endemic cave mysids being replaced by congeners of warmer affinities, with a high risk of extinction. We also found strong support for the view that Mediterranean marine biodiversity is already under the threat of global warming. 相似文献
2.
Melody Puckridge Peter R. Last William T. White Nikos Andreakis 《Ecology and evolution》2013,3(2):217-232
Maskrays of the genus Neotrygon (Dasyatidae) have dispersed widely in the Indo‐West Pacific being represented largely by an assemblage of narrow‐ranging coastal endemics. Phylogenetic reconstruction methods reproduced nearly identical and statistically robust topologies supporting the monophyly of the genus Neotrygon within the family Dasyatidae, the genus Taeniura being consistently basal to Neotrygon, and Dasyatis being polyphyletic to the genera Taeniurops and Pteroplatytrygon. The Neotrygon kuhlii complex, once considered to be an assemblage of color variants of the same biological species, is the most derived and widely dispersed subgroup of the genus. Mitochondrial (COI, 16S) and nuclear (RAG1) phylogenies used in synergy with molecular dating identified paleoclimatic fluctuations responsible for periods of vicariance and dispersal promoting population fragmentation and speciation in Neotrygon. Signatures of population differentiation exist in N. ningalooensis and N. annotata, yet a large‐scale geological event, such as the collision between the Australian and Eurasian Plates, coupled with subsequent sea‐level falls, appears to have separated a once homogeneous population of the ancestral form of N. kuhlii into southern Indian Ocean and northern Pacific taxa some 4–16 million years ago. Repeated climatic oscillations, and the subsequent establishment of land and shallow sea connections within and between Australia and parts of the Indo‐Malay Archipelago, have both promoted speciation and established zones of secondary contact within the Indian and Pacific Ocean basins. 相似文献
3.
J. Paupério J. S. Herman J. Melo‐Ferreira M. Jaarola P. C. Alves J.B. Searle 《Molecular ecology》2012,21(24):6015-6032
Species are generally described from morphological features, but there is growing recognition of sister forms that show substantial genetic differentiation without obvious morphological variation and may therefore be considered ‘cryptic species’. Here, we investigate the field vole (Microtus agrestis), a Eurasian mammal with little apparent morphological differentiation but which, on the basis of previous sex‐linked nuclear and mitochondrial DNA (mtDNA) analyses, is subdivided into a Northern and a Southern lineage, sufficiently divergent that they may represent two cryptic species. These earlier studies also provided limited evidence for two major mtDNA lineages within Iberia. In our present study, we extend these findings through a multilocus approach. We sampled 163 individuals from 46 localities, mainly in Iberia, and sequenced seven loci, maternally, paternally and biparentally inherited. Our results show that the mtDNA lineage identified in Portugal is indeed a distinct third lineage on the basis of other markers as well. In fact, multilocus coalescent‐based methods clearly support three separate evolutionary units that may represent cryptic species: Northern, Southern and Portuguese. Divergence among these units was inferred to have occurred during the last glacial period; the Portuguese lineage split occurred first (estimated at c. 70 000 bp ), and the Northern and Southern lineages separated at around the last glacial maximum (estimated at c. 18 500 bp ). Such recent formation of evolutionary units that might be considered species has repercussions in terms of understanding evolutionary processes and the diversity of small mammals in a European context. 相似文献
4.
Patricia A. Warner Madeleine J. H. van Oppen Bette L. Willis 《Molecular ecology》2015,24(12):2993-3008
Mounting evidence of cryptic species in a wide range of taxa highlights the need for careful analyses of population genetic data sets to unravel within‐species diversity from potential interspecies relationships. Here, we use microsatellite loci and hierarchical clustering analysis to investigate cryptic diversity in sympatric and allopatric (separated by 450 km) populations of the widespread coral Seriatopora hystrix on the Great Barrier Reef. Structure analyses delimited unique genetic clusters that were confirmed by phylogenetic and extensive population‐level analyses. Each of four sympatric yet distinct genetic clusters detected within S. hystrix demonstrated greater genetic cohesion across regional scales than between genetic clusters within regions (<10 km). Moreover, the magnitude of genetic differentiation between different clusters (>0.620 G”ST) was similar to the difference between S. hystrix clusters and the congener S. caliendrum (mean G”ST 0.720). Multiple lines of evidence, including differences in habitat specificity, mitochondrial identity, Symbiodinium associations and morphology, corroborate the nuclear genetic evidence that these distinct clusters constitute different species. Hierarchical clustering analysis combined with more traditional population genetic methods provides a powerful approach for delimiting species and should be regularly applied to ensure that ecological and evolutionary patterns interpreted for single species are not confounded by the presence of cryptic species. 相似文献
5.
Jun Zhao Po‐Hsun Kuo Teh‐Wang Lee Kui‐Ching Hsu 《Journal of Zoological Systematics and Evolutionary Research》2013,51(4):316-326
Little has been known about the impacts of past vicariance events on the phylogeography and population structure of freshwater fishes in East Asia. The aims of this study are to assess the genetic variability with extensive sampling throughout the range of Chinese spiny loach, Cobitis sinensis, and to infer the genetic structure and evolutionary history of populations. Cobitis sinensis in China may have initiated from two ancestral populations, namely Yangtze and Pearl Rivers, which diverged about 7.24 MYA likely due to drainage systems alteration. In the phylogroup I, a southward dispersal event occurred from East China (Yangtze River) to south ZheMin and Hainan subregions, followed by eastward dispersal from ZheMin to south Taiwan. In the phylogroup II, eastward colonization took place from Pearl River to north Taiwan in the late Pliocene, coupled with loss of genetic diversity in the island populations. This study showed that Cenozoic tectonic movements and climatic and sea‐level fluctuations may have shaped the genetic structure of C. sinensis in concert. Highly diverged mtDNA sequences suggest existence of cryptic species in morphospecies C. sinensis. 相似文献
6.
Amidst the rapid advancement in next‐generation sequencing (NGS) technology over the last few years, salamanders have been left behind. Salamanders have enormous genomes—up to 40 times the size of the human genome—and this poses challenges to generating NGS data sets of quality and quantity similar to those of other vertebrates. However, optimization of laboratory protocols is time‐consuming and often cost prohibitive, and continued omission of salamanders from novel phylogeographic research is detrimental to species facing decline. Here, we use a salamander endemic to the southeastern United States, Plethodon serratus, to test the utility of an established protocol for sequence capture of ultraconserved elements (UCEs) in resolving intraspecific phylogeographic relationships and delimiting cryptic species. Without modifying the standard laboratory protocol, we generated a data set consisting of over 600 million reads for 85 P. serratus samples. Species delimitation analyses support recognition of seven species within P. serratus sensu lato, and all phylogenetic relationships among the seven species are fully resolved under a coalescent model. Results also corroborate previous data suggesting nonmonophyly of the Ouachita and Louisiana regions. Our results demonstrate that established UCE protocols can successfully be used in phylogeographic studies of salamander species, providing a powerful tool for future research on evolutionary history of amphibians and other organisms with large genomes. 相似文献
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8.
Hai‐Guang Zhang Min‐Hua Lv Wen‐Bo Yi Wei‐Bing Zhu Wen‐Jun Bu 《Molecular ecology resources》2017,17(2):314-323
The use of genetic distances to identify species within the framework of DNA barcoding has to some extent improved the development of biodiversity studies. However, using a fixed empirical threshold to delimit species may lead to overestimating species diversity. In this study, we use a new data set of COI sequences for 366 specimens within the genus of Cletus as well as conduct an analysis on the same genetic data for collected morphologically defined species from previous phylogeographical studies, to test whether high intraspecific genetic divergences are common with the premises of comprehensive sampling. The results indicate C. graminis Hsiao & Cheng 1964 , is the same species with C. punctiger (Dallas, 1852) and should be synonymized and that the distributional record of C. pugnator (Fabricius, 1787) in China is correct. High intraspecific genetic differentiations (0%–4.35%) were found in C. punctiger. Furthermore, as to the mined data, the maximum intraspecific K2P distances of 186 species (48.44% of 384) exceed 3%, and 101 species (26.30%) can be divided into two or more clusters with a threshold of 3% in cluster analysis. If genetic distance is used to delimit species boundaries, the minimum interspecific K2P distance of the congeneric species should be considered rather than only using the fixed empirical value; otherwise, the species richness may be overestimated in some cases. 相似文献
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10.
Ullasa Kodandaramaiah Thomas J. Simonsen Sean Bromilow Niklas Wahlberg Felix Sperling 《Ecology and evolution》2013,3(16):5167-5176
The satyrine butterfly Coenonympha tullia (Nymphalidae: Satyrinae) displays a deep split between two mitochondrial clades, one restricted to northern Alberta, Canada, and the other found throughout Alberta and across North America. We confirm this deep divide and test hypotheses explaining its phylogeographic structure. Neither genitalia morphology nor nuclear gene sequence supports cryptic species as an explanation, instead indicating differences between nuclear and mitochondrial genome histories. Sex‐biased dispersal is unlikely to cause such mito‐nuclear differences; however, selective sweeps by reproductive parasites could have led to this conflict. About half of the tested samples were infected by Wolbachia bacteria. Using multilocus strain typing for three Wolbachia genes, we show that the divergent mitochondrial clades are associated with two different Wolbachia strains, supporting the hypothesis that the mito‐nuclear differences resulted from selection on the mitochondrial genome due to selective sweeps by Wolbachia strains. 相似文献
11.
Melissa B. DeBiasse Vincent P. Richards Mahmood S. Shivji Michael E. Hellberg 《Journal of Biogeography》2016,43(11):2136-2146
12.
Nikos Andreakis Paul Costello Marianela Zanolla Gary W. Saunders Leonardo Mata 《Journal of phycology》2016,52(1):141-147
The red seaweed Asparagopsis taxiformis embodies five cryptic mitochondrial lineages (lineage 1–5) introduced worldwide as a consequence of human mediated transport and climate change. We compared globally collected mitochondrial cox2‐3 intergenic spacer sequences with sequences produced from multiple Australian locations and South Korea to identify Asparagopsis lineages and to reveal cryptic introductions. We report A. taxiformis lineage 4 from Cocos (Keeling) Islands, Australia, and the highly invasive Indo‐Pacific Mediterranean lineage 2 from South Korea and Lord Howe Island, Australia. Phylogeographic analysis showed a clear haplotype and geographic separation between western Australian and Great Barrier Reef (GBR) isolates belonging to the recently described lineage 5. The same lineage, however, was characterized by a substantial genetic and geographic break between the majority of Australian specimens and Asparagopsis collections from South Solitary Island, Southern GBR, Lord Howe Island, Kermadec Islands, Norfolk Island, New Caledonia and French Polynesia. The disjunct geographic distribution and sequence divergence between these two groups supports the recognition of a sixth cryptic A. taxiformis mitochondrial lineage. As climatic changes accelerate the relocation of biota and offer novel niches for colonization, periodic surveys for early detection of cryptic invasive seaweeds will be critical in determining whether eradication or effective containment of the aliens are feasible. 相似文献
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14.
Felipe Torquato Pedro Range Radhouane Ben‐Hamadou Eva E. Sigsgaard Philip F. Thomsen Rodrigo Riera Michael L. Berumen John A. Burt David A. Feary Alyssa Marshell Daniele D'Agostino Joseph D. DiBattista Peter R. Mller 《Ecology and evolution》2019,9(19):11215-11226
Ocean circulation, geological history, geographic distance, and seascape heterogeneity play an important role in phylogeography of coral‐dependent fishes. Here, we investigate potential genetic population structure within the yellowbar angelfish (Pomacanthus maculosus) across the Northwestern Indian Ocean (NIO). We then discuss our results with respect to the above abiotic features in order to understand the contemporary distribution of genetic diversity of the species. To do so, restriction site‐associated DNA sequencing (RAD‐seq) was utilized to carry out population genetic analyses on P. maculosus sampled throughout the species’ distributional range. First, genetic data were correlated to geographic and environmental distances, and tested for isolation‐by‐distance and isolation‐by‐environment, respectively, by applying the Mantel test. Secondly, we used distance‐based and model‐based methods for clustering genetic data. Our results suggest the presence of two putative barriers to dispersal; one off the southern coast of the Arabian Peninsula and the other off northern Somalia, which together create three genetic subdivisions of P. maculosus within the NIO. Around the Arabian Peninsula, one genetic cluster was associated with the Red Sea and the adjacent Gulf of Aden in the west, and another cluster was associated with the Arabian Gulf and the Sea of Oman in the east. Individuals sampled in Kenya represented a third genetic cluster. The geographic locations of genetic discontinuities observed between genetic subdivisions coincide with the presence of substantial upwelling systems, as well as habitat discontinuity. Our findings shed light on the origin and maintenance of genetic patterns in a common coral reef fish inhabiting the NIO, and reinforce the hypothesis that the evolution of marine fish species in this region has likely been shaped by multiple vicariance events. 相似文献
15.
Tahani El Ayari Najoua Trigui El Menif Carlos Saavedra David Cordero Frédérique Viard Nicolas Bierne 《Ecology and evolution》2017,7(21):9016-9026
Molecular approaches have proven efficient to identify cryptic lineages within single taxonomic entities. Sometimes these cryptic lineages maybe previously unreported or unknown invasive taxa. The genetic structure of the marine gastropod Stramonita haemastoma has been examined in the Western Mediterranean and North‐Eastern Atlantic populations with mtDNA COI sequences and three newly developed microsatellite markers. We identified two cryptic lineages, differentially fixed for alternative mtDNA COI haplogroups and significantly differentiated at microsatellite loci. The mosaic distribution of the two lineages is unusual for a warm‐temperate marine invertebrate with a teleplanic larval stage. The Atlantic lineage was unexpectedly observed as a patch enclosed in the north of the Western Mediterranean Sea between eastern Spain and the French Riviera, and the Mediterranean lineage was found in Macronesian Islands. Although cyto‐nuclear disequilibrium is globally maintained, asymmetric introgression occurs in the Spanish region where the two lineages co‐occur in a hybrid zone. A first interpretation of our results is mito‐nuclear discordance in a stable postglacial hybrid zone. Under this hypothesis, though, the location of genetic discontinuities would be unusual among planktonic dispersers. An alternative interpretation is that the Atlantic lineage, also found in Senegal and Venezuela, has been introduced by human activities in the Mediterranean area and is introgressing Mediterranean genes during its propagation, as theoretically expected. This second hypothesis would add an additional example to the growing list of cryptic marine invasions revealed by molecular studies. 相似文献
16.
Ulva Linnaeus (Ulvophyceae, Ulvales) is a genus of green algae widespread in different aquatic environments. Members of this genus show a very simple morphology and a certain degree of phenotypic plasticity, heavily influenced by environmental conditions, making difficult the delineation of species by morphological features alone. Most studies dealing with Ulva biodiversity in Mediterranean waters have been based only on morphological characters and a modern taxonomic revision of this genus in the Mediterranean is not available. We report here the results of an investigation on the diversity of Ulva in the North Adriatic Sea based on molecular analyses. Collections from three areas, two of which subject to intense shipping traffic, were examined, as well as historical collections of Ulva stored in the Herbarium Patavinum of the University of Padova, Italy. Molecular analyses based on partial sequences of the rbcL and tufA genes revealed the presence of six different species, often with overlapping morphologies: U. californica Wille, U. flexuosa Wulfen, U. rigida C. Agardh, U. compressa Linnaeus, U. pertusa Kjellman, and one probable new taxon. U. californica is a new record for the Mediterranean and U. pertusa is a new record for the Adriatic. Partial sequences obtained from historical collections show that most of the old specimens are referable to U. rigida. No specimens referable to the two alien species were found among the old herbarium specimens. The results indicate that the number of introduced seaweed species and their impact on Mediterranean communities have been underestimated, due to the difficulties in species identification of morphologically simple taxa as Ulva. 相似文献
17.
Ashleigh Marie Watts Grant A. Hopkins Sharyn Jane Goldstien 《Ecology and evolution》2019,9(6):3089-3104
Disentangling pathways by which nonindigenous species expand and spread regionally remains challenging. Molecular ecology tools are often employed to determine the origins and spread of introduced species, but the complexities of some organisms may be reducing the efficacy of these tools. Some colonial species exhibit complexities by way of chimerism and winter colony regression, which may alter the genetic diversity of populations and mask the connectivity occurring among them. This study uses nuclear microsatellite data and simple GIS‐based modeling to investigate the influence of chimerism and winter regression on the genetic diversity and patterns of genetic population connectivity among colonies of Didemnum vexillum on artificial substrates. Colonies sampled in summer were shown to form a metapopulation, with high levels of admixture, extreme outcrossing, and some substructure. These patterns were consistent within the subsampled winter colonies and with the inclusion of chimeric data. However, allelic richness and diversity were significantly different between winter and summer samples, altering interpretations relating to population connectivity and pelagic larval duration. This study demonstrates the importance of including seasonal sampling and imperative life history traits in genetic studies for clear interpretations and the successful management of introduced species. 相似文献
18.
John R. Hyde Karen E. Underkoffler Meagan A. Sundberg 《Molecular ecology resources》2014,14(6):1239-1247
The cornerstone of fisheries management relies on a solid taxonomic base and an understanding of how animals can be grouped into coherent management units. Surprisingly, little is known about the basic biology and ecology of opah (Lampris guttatus), a globally distributed species that is commercially exploited and regionally common in the North Pacific. Recent efforts to collect life history data on this species uncovered evidence of two North Pacific morphotypes. Sequencing of the mitochondrial cytochrome c oxidase I gene (655 bp) for these morphotypes and other specimens collected worldwide (n = 480) produced five strongly diverged and well‐supported clades. Additional sequence data from the cytochrome b gene (1141 bp) as well as the nuclear recombination activating gene 1 (1323 bp) corroborated these results, suggesting these five clades probably represent separate species. Our conclusion that opah is a complex of five separate species has implications for management and indicates a need to gather additional data on these poorly understood fishes. 相似文献
19.
Jim N. Underwood Zoe Richards Oliver Berry Daniel Oades Azton Howard James P. Gilmour 《Evolutionary Applications》2020,13(9):2404-2421
Management strategies designed to conserve coral reefs threatened by climate change need to incorporate knowledge of the spatial distribution of inter‐ and intra‐specific genetic diversity. We characterized patterns of genetic diversity and connectivity using single nucleotide polymorphisms (SNPs) in two reef‐building corals to explore the eco‐evolutionary processes that sustain populations in north‐west Australia. Our sampling focused on the unique reefs of the Kimberley; we collected the broadcast spawning coral Acropora aspera (n = 534) and the brooding coral Isopora brueggemanni (n = 612) across inter‐archipelago (tens to hundreds of kilometres), inter‐reef (kilometres to tens of kilometres) and within‐reef (tens of metres to a few kilometres) scales. Initial analysis of A. aspera identified four highly divergent lineages that were co‐occurring but morphologically similar. Subsequent population analyses focused on the most abundant and widespread lineage, Acropora asp‐c. Although the overall level of geographic subdivision was greater in the brooder than in the spawner, fundamental similarities in patterns of genetic structure were evident. Most notably, limits to gene flow were observed at scales <35 kilometres. Further, we observed four discrete clusters and a semi‐permeable barrier to dispersal that were geographically consistent between species. Finally, sites experiencing bigger tides were more connected to the metapopulation and had greater gene diversity than those experiencing smaller tides. Our data indicate that the inshore reefs of the Kimberley are genetically isolated from neighbouring oceanic bioregions, but occasional dispersal between inshore archipelagos is important for the redistribution of evolutionarily important genetic diversity. Additionally, these results suggest that networks of marine reserves that effectively protect reefs from local pressures should be spaced within a few tens of kilometres to conserve the existing patterns of demographic and genetic connectivity. 相似文献
20.
Peanut worm (Sipunculus nudus) is a cosmopolitan species mainly distributed in tropical and subtropical coastal waters. Analysis of the mitochondrial cytochrome c oxidase subunit I (COI) gene sequences among S. nudus from GenBank revealed high genetic variation (p‐distance, 0.115–0.235; k2p, 0.128–0.297) and paraphyletic relationships. These indicated misidentification and/or cryptic diversity may be present in the genus Sipunculus. To understand the genetic diversity and to manage the recourse of S. nudus, we collected specimens from coastal waters of southern China and Taiwan. In the phylogenetic topology, specimens can be separated into four distinct clades; three of these clades (clade A, B and C) were only represented from this region (southern China and Taiwan), but the clade D grouped with individuals from Central America (Atlantic coast). Furthermore, individuals of clades A and D were collected at the same location, which does not support the hypothesis that this genetic break reflects contemporary geographical isolation. The four distinct clades observed among coastal waters of southern China and Taiwan indicated underestimated diversity. It is noteworthy that the cryptic diversity is vulnerable under high pressure of human activity. 相似文献