Marine incursion into East Asia: a forgotten driving force of biodiversity

Yang, Lü; Hou, Zhonge; Li, Shuqiang

doi:10.1098/rspb.2012.2892

Cited by 22 publications

(15 citation statements)

References 38 publications

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“…For the second approach to estimate divergence times, we used the COI clock rate of 0.0115 substitutions per site per million years, which has been shown as a useful surrogate value in linking contemporary distributions with historical vicariance in amphipod crustaceans (Yang et al . ; Hou et al . ; Rewicz et al .…”

Section: Methodsmentioning

confidence: 99%

The southwestern Carpathians as an ancient centre of diversity of freshwater gammarid amphipods: insights from the Gammarus fossarum species complex

Copilaş‐Ciocianu

Petrusek

2015

Molecular Ecology

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Gammarus fossarum is a diverse species complex of epigean freshwater amphipods throughout Europe. Due to their poor dispersal capabilities and ubiquity, these crustaceans may serve as a model for investigating the influence of historical factors on the contemporary distribution and diversity patterns of freshwater macrozoobenthos. Here, we investigate the fine-scale phylogeographic structure of this complex across its range in the southwestern Carpathian Mountains, which comprises two areas that are geographically isolated from its main European distribution area as well as from each other. Given the Tertiary age of many freshwater Gammarus species, we hypothesize that the southwestern Carpathian populations reflect a relict distribution pattern. We used two mitochondrial and three nuclear markers from 32 localities to reconstruct phylogenetic relationships and estimate the timings of divergence among southwestern Carpathian and non-Carpathian lineages. Cryptic diversity was evaluated from mitochondrial markers by employing phylogenetic and distance-based methods. We distinguished at least 16 cryptic microendemic taxa, some of them coexisting, distributed in the southwestern Carpathians in a mosaic-like pattern. These lineages form a monophyletic group together with several lineages from southeastern Europe. Estimated divergence times indicate a Middle Miocene origin of this clade, with many deep splits dating back to more than 10 Ma. This time frame corresponds with a period of intense geological subsidence in the region that gave birth to the Pannonian Basin. We conclude that subsidence could have been an important driver of diversification in freshwater Gammarus and that the southwestern Carpathians represent an ancient centre of diversity for these crustaceans.

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Section: Methodsmentioning

confidence: 99%

The southwestern Carpathians as an ancient centre of diversity of freshwater gammarid amphipods: insights from the Gammarus fossarum species complex

Copilaş‐Ciocianu

Petrusek

2015

Molecular Ecology

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“…This proportion is probably a low estimate because detection of convergence depends on completeness of taxon sampling. Cases of morphological convergence among cryptic species were documented in several amphipod genera, where species from the same cryptic complex independently colonized freshwater‐semiterrestrial (Yang, Hou, & Li, ) or subterranean habitats (Villacorta, Jaume, Oromí, & Juan, ) or microhabitats within the subterranean realm (Trontelj, Blejec, & Fišer, ; Trontelj et al., ).…”

Section: Mechanisms Causing Cryptic Diversitymentioning

confidence: 99%

“…There was a substantial lag in the application of tree‐based methods. The generalized mixed Yule‐coalescent (Pons et al., ), multilocus coalescent (Rannala & Yang, ; Yang & Rannala, ) and Poisson tree process models (Zhang et al., ) were used in only seven studies (Copilaş‐Ciocianu & Petrusek, ; Esmaeili‐Rineh, Sari, Delić, Moškrič, & Fišer, ; Katouzian et al., ; King & Leys, ; Murphy, King, & Delean, ; Weiss, Niklas, Anna, & Florian, ; Yang et al., ). This lag in the use of tree‐based methods occurred despite 78% of the studies inferring molecular phylogenies (supporting information ).…”

Section: Taxonomic Practices In Delimiting Cryptic Speciesmentioning

confidence: 99%

“…Such clusters, referred to as molecular operational taxonomic units (OTUs, also referred as MOTUs), are delimited using methods presented in Section 2. In the amphipod literature, OTUs were used to explore determinants of diversification rates (Hou, Sket, Fi ser, & Li, 2011;Mamos, Wattier, Burzy nski, & Grabowski, 2016;Yang et al, 2013), the geographic origin of European groundwater fauna (McInerney et al, 2014), and species diversity-environment relationships of local assemblages (Knox et al, 2012). Importantly, failing to account for cryptic diversity in these studies is equivalent to omitting known species, thereby underestimating diversification rates, incorrectly reconstructing ancestral ranges and undervaluing local diversity (Morvan et al, 2013;Pyron & Burbrink, 2013).…”

Section: Molecular Operational Taxonomic Unitsmentioning

confidence: 99%

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Cryptic species as a window into the paradigm shift of the species concept

2018

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The species concept is the cornerstone of biodiversity science, and any paradigm shift in the delimitation of species affects many research fields. Many biologists now are embracing a new "species" paradigm as separately evolving populations using different delimitation criteria. Individual criteria can emerge during different periods of speciation; some may never evolve. As such, a paradigm shift in the species concept relates to this inherent heterogeneity in the speciation process and species category-which is fundamentally overlooked in biodiversity research. Cryptic species fall within this paradigm shift: they are continuously being reported from diverse animal phyla but are poorly considered in current tests of ecological and evolutionary theory. The aim of this review is to integrate cryptic species in biodiversity science. In the first section, we address that the absence of morphological diversification is an evolutionary phenomenon, a "process" counterpart to the long-studied mechanisms of morphological diversification. In the next section regarding taxonomy, we show that molecular delimitation of cryptic species is heavily biased towards distance-based methods. We also stress the importance of formally naming of cryptic species for better integration into research fields that use species as units of analysis. Finally, we show that incorporating cryptic species leads to novel insights regarding biodiversity patterns and processes, including large-scale biodiversity assessments, geographic variation in species distribution and species coexistence. It is time for incorporating multicriteria species approaches aiming to understand speciation across space and taxa, thus allowing integration into biodiversity conservation while accommodating for species uncertainty.

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“…Consequently, dating analysis was performed using a relaxed model. The crustacean mitochondrial COI clock of 0.0115 substitutions per site per million years was applied as calibration (Lefébure et al ., ; Yang, Hou & Li, ). The analysis was carried out in BEAST v. 1.7.5 (Drummond & Rambaut, ) under an uncorrelated lognormal relaxed molecular model and Yule speciation prior.…”

Section: Methodsmentioning

confidence: 99%

Diversification of low dispersal crustaceans through mountain uplift: a case study ofGammarus(Amphipoda: Gammaridae) with descriptions of four novel species

Hou

2014

Zool J Linn Soc

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Lineages with low dispersal ability are geographically restricted. We used freshwater Gammarus to test this hypothesis. Sequences of two mitochondrial (cytochrome c oxidase subunit I and 16S) and two nuclear (28S and cytosolic heat‐shock protein) genes were obtained for seven species distributed in 28 localities along the Lüliang and Taihang mountains in China. Phylogenetic analyses showed that Gammarus species were grouped into two clades, one from the Lüliang range and the other from the Taihang range. Each clade was further divided into three or four species, showing a congruent pattern with geographical vicariance. Divergence time estimation indicated that the split between the two clades coincided with the uplift of the Taihang Mountains at the boundary of Oligocene/Miocene. Most speciation events may have been driven by massive uplifting of the Lüliang and Taihang mountains from the late Miocene to early Pliocene. Additionally, four new species are described: Gammarus incoercitus sp. nov., Gammarus benignus sp. nov., Gammarus monticellus sp. nov., and Gammarus pisinnus sp. nov. The new species are compared with related species in this area and a key to these species is provided. © 2014 The Linnean Society of London

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Marine incursion into East Asia: a forgotten driving force of biodiversity

Cited by 22 publications

References 38 publications

The southwestern Carpathians as an ancient centre of diversity of freshwater gammarid amphipods: insights from the Gammarus fossarum species complex

The southwestern Carpathians as an ancient centre of diversity of freshwater gammarid amphipods: insights from the Gammarus fossarum species complex

Cryptic species as a window into the paradigm shift of the species concept

Diversification of low dispersal crustaceans through mountain uplift: a case study ofGammarus(Amphipoda: Gammaridae) with descriptions of four novel species

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