Zoologica Scripta

Mongiardino Koch, Nicolás; Soto, Ignacio M.; Ramírez, Martín J.

doi: 10.1111/zsc.12120pmid: N/A

The use of quantitative morphometric information for phylogenetic inference has been an intensely debated topic for most of the history of phylogenetic systematics. Despite several drawbacks, the most common strategy to include this sort of data into phylogenetic studies is the use of ratios, that is quotients between morphometric variables. Here, we discuss one particular problem associated with such methodology: the fact that the often arbitrary election of which variable serves as numerator and which as denominator affects the phylogenetic outcome of the analysis. We describe the cause for such an effect, and study its implications with the use of several published data matrices. Alternative coding schemes for ratio characters result in very different phylogenetic hypotheses, an effect that may even be strong enough to affect studies that combine continuous and discrete morphological information. Some of the resulting incongruence is produced by the differences in magnitude of the continuous characters involved, although different rescaling techniques are shown to decrease, but not eliminate, the confounding effect. To eliminate such problematic effect, ratios should be either log‐transformed before their use or replaced by more effective ways to capture morphometric information.

Lu, Liang; Ge, Deyan; Chesters, Douglas; Ho, Simon Y. W.; Ma, Ying; Li, Guichang; Wen, Zhixin; Wu, Yongjie; Wang, Jun; Xia, Lin; Liu, Jingli; Guo, Tianyu; Zhang, Xiaolong; Zhu, Chaodong; Yang, Qisen; Liu, Qiyong

Mezzasalma, Marcello; Dall'Asta, Andrea; Loy, Anna; Cheylan, Marc; Lymberakis, Petros; Zuffi, Marco A. L.; Tomović, Ljiljana; Odierna, Gaetano; Guarino, Fabio M.

doi: 10.1111/zsc.12115pmid: N/A

We used a multidisciplinary approach to infer the taxonomy and historical biogeography of Hierophis viridiflavus and H. gemonensis, performing molecular analyses of mitochondrial (16S, Cyt‐b, ND4) and nuclear markers (PRLR), a landmark‐based morphometric study and a cytogenetic analysis. Our data distinguished three main groups in the studied species, corresponding to H. gemonensis and to two monophyletic clades (E and W) within H. viridiflavus. Clades E and W display a significant genetic (about 4% for Cyt‐b and ND4) and morphological divergence and a different morphology of the W sex chromosome (submetacentric in clade E and telocentric in clade W). Taking into account the existing divergence, these clades appear to represent independent phylogenetic units, deserving elevation to species status. Specific names should be H. viridiflavus (Lacépède, 1789) and H. carbonarius (Bonaparte 1833) for clades W and E, respectively. The phylogeography of the studied species is only partially concordant with a general pattern of ‘southern richness and northern purity’ of genetic diversity, whereas H. gemonensis exhibits high genetic diversity at low latitudes (especially in the Peloponnese), H. carbonarius shows a number of different haplotypes both at low (along the southern Italian Apennines and in Sicily) and high latitudes in Italy. Furthermore, a relaxed clock model hypothesizes the differentiation between H. gemonensis and H. viridiflavus sensu lato at about 7 Mya, in the Messinian. Subsequently, the speciation involving H. viridiflavus sensu stricto and H. carbonarius took place in the Quaternary, probably as a result of Pleistocene climatic oscillations. Furthermore, our results are consistent with the existence of several ‘refugia within refugia’ in Italy and in the Balkans and depict the major cladogenesis as allopatric events, mainly driven by paleoclimatic and geographical factors.

Meegaskumbura, Madhava; Senevirathne, Gayani; Biju, S. D.; Garg, Sonali; Meegaskumbura, Suyama; Pethiyagoda, Rohan; Hanken, James; Schneider, Christopher J.

doi: 10.1111/zsc.12121pmid: N/A

The Old World tree frogs (Anura: Rhacophoridae), with 387 species, display a remarkable diversity of reproductive modes – aquatic breeding, terrestrial gel nesting, terrestrial foam nesting and terrestrial direct development. The evolution of these modes has until now remained poorly studied in the context of recent phylogenies for the clade. Here, we use newly obtained DNA sequences from three nuclear and two mitochondrial gene fragments, together with previously published sequence data, to generate a well‐resolved phylogeny from which we determine major patterns of reproductive‐mode evolution. We show that basal rhacophorids have fully aquatic eggs and larvae. Bayesian ancestral‐state reconstructions suggest that terrestrial gel‐encapsulated eggs, with early stages of larval development completed within the egg outside of water, are an intermediate stage in the evolution of terrestrial direct development and foam nesting. The ancestral forms of almost all currently recognized genera (except the fully aquatic basal forms) have a high likelihood of being terrestrial gel nesters. Direct development and foam nesting each appear to have evolved at least twice within Rhacophoridae, suggesting that reproductive modes are labile and may arise multiple times independently. Evolution from a fully aquatic reproductive mode to more terrestrial modes (direct development and foam nesting) occurs through intermediate gel nesting ancestral forms. This suggests that gel nesting is not only a possible transitional state for the evolution of terrestriality, but also that it is a versatile reproductive mode that may give rise to other terrestrial reproductive modes. Evolution of foam nesting may have enabled rhacophorids to lay a larger number of eggs in more open and drier habitats, where protection from desiccation is important. Terrestrial direct development allows frogs to lay eggs independent of bodies of water, in a diversity of humid habitats, and may represent a key innovation that facilitated the evolution of nearly half of all known rhacophorid species.

Qi, Delin; Guo, Songchang; Chao, Yan; Kong, Qinghui; Li, Changzhong; Xia, Mingzhe; Xie, Baosheng; Zhao, Kai

doi: 10.1111/zsc.12116pmid: N/A

Freshwater fish belonging to the genus Schizopygopsis are widespread in drainages throughout the Qinghai‐Tibetan Plateau and, thus, a model group with which to investigate how paleo‐drainage changes linked to historical uplifting within the Qinghai‐Tibetan Plateau influence speciation. To date, the phylogenetic and taxonomic relationships within Schizopygopsis remain controversial. In this study, we constructed a comprehensive molecular phylogeny of Schizopygopsis based on six mitochondrial gene sequences. We compared the taxonomic relationships revealed by this phylogeny with those obtained from morphological data. We also used this phylogeny to assess the extent to which the evolution of Schizopygopsis has been driven by paleo‐drainage changes linked to uplifting of the Qinghai‐Tibetan Plateau. Results indicated that all Schizopygopsis taxa formed a monophyletic group comprising five major clades, which were inconsistent with the taxonomic relationships based on morphology for this group. Our results also strongly supported the validity of S. anteroventris and S. microcephalus as distinct species within Schizopygopsis. Molecular calibrations showed that species within the middle Yangtze species diverged earlier (~4.5 Mya) than species within the Indus River (~3.0 Mya), the Mekong River (~2.8 Mya) and the Tsangpo + Salween rivers (~2.5 Mya). The most recent evolutionary splits occurred among species from the upper and lower Yangtze River, the Yellow River and the Qiadam Basin at about 1.8 to 0.3 Mya. Our molecular evidence and use of the molecular clock calibration have allowed us to associate speciation events within the genus Schizopygopsis to the formation and separation of paleo‐drainage connections caused by tectonic events during the uplifting of the Qinghai‐Tibetan Plateau (~4.5 Mya). This work underlines the dominant role of vicariance in shaping the evolutionary history of the genus Schizopygopsis. Further research using multiple loci and more extensive sampling will reveal a more complete picture of the phylogenetic relationships and biogeography of Schizopygopsis fishes.

Çıplak, Battal; Kaya, Sarp; Boztepe, Zehra; Gündüz, İslam

doi: 10.1111/zsc.12118pmid: N/A

Although the high‐latitude range margins in Europe and North America are intensively studied, attention is gradually turned towards the taxa/populations inhabiting glacial refugia. Here, we evaluate the genealogical history of the cold‐adapted Anatolio‐Balkan genus Anterastes especially to test the possible effects of intrarefugial vertical range shifts during climatic oscillations of the Quaternary. Using concatenated data from sequences of COI+16S and ITS1–5.8S–ITS2, intrageneric relationships and the time of speciation events were estimated. Thirteen different demographic analyses were performed using a data set produced from sequences of 16S. Different phylogenetic analyses recovered similar lineages with high resolution. The molecular chronogram estimated speciation events in a period ranging from 5.60 to 1.22 Myr. Demographic analyses applied to 13 populations and five lineages suggested constant population size. Genetic diversity is significantly reduced in a few populations, while not in others. Fixation indices suggested extremely diverged populations. In the light of these data, the following main conclusions were raised: (i) although glacial refugia are the biodiversity hotspots, species level radiation of the cold‐adapted lineages is mainly prior to the Mid‐Pleistocene transition; (ii) heterogeneous topography provides refugial habitats and allows populations to survive through vertical range shifts during climatic fluctuations; (iii) prolonged isolation of refugial populations do not always result in reduced intrapopulation diversity, but in high level of genetic differentiation; (iv) the cold‐adapted lineages with low dispersal ability might have not colonised the area out of Anatolian refugium during interglacial periods; and (v) populations of invertebrates may have restricted ranges, but this does not mean that they have small effective population size.

Labarque, Facundo M.; Soto, Eduardo M.; Ramírez, Martín J.; Arnedo, Miquel A.

doi: 10.1111/zsc.12119pmid: N/A

The family Anyphaenidae, also known as ghost spiders, includes a diverse array of nocturnal cursorial spiders that actively hunt on vegetation. The family is mostly distributed in the Americas and has been traditionally divided into three subfamilies. The mostly tropical and North American Anyphaeninae and the Amaurobioidinae, primarily distributed in southern South America, hold the bulk of the diversity, while the Malenellininae includes a single Chilean species. Here, we use a combined morphological and molecular approach to infer the relationships of the subfamily Amaurobioidinae and examine the delimitation of contentious genera. The morphological characters include both genitalic and somatic morphology, whereas molecular data include four markers, two mitochondrial (COI, 16S) and two nuclear (28S, H3). All our analyses agree on the monophyly of Amaurobioidinae, Amaurobioidini, Gayennini, the genera Negayan, Amaurobioides, Josa, Araiya, Arachosia and Monapia, as well as the paraphyly of Anyphaeninae. The total evidence analysis supports the novel placement of Josa as the sister group of both tribes Amaurobioidini and Gayennini, most of the previously known intergeneric relationships within Gayennini, and a clade of Amaurobioidini with a projecting ocular area, including Aysenoides, Axyracrus, Amaurobioides and Aysenia. The sequence data solve the puzzling placement of Philisca puconensis, here transferred to Tomopisthes, and Tasata chiloensis, transferred to Oxysoma. The advantages of the total evidence phylogenetic approach and the evolution of the male copulatory organ are discussed.

Meksuwan, Phuripong; Pholpunthin, Pornsilp; Segers, Hendrik H.

doi: 10.1111/zsc.12114pmid: N/A

We test the hypothesis that conochilid rotifers represent an independent family‐level taxon within Superorder Gnesiotrocha, by analysing their phylogenetic position based on the 18S rDNA sequence of a large number of representatives of this taxon and its putative relatives. Both Bayesian and maximum likelihood analysis confirm a monophyletic clade of all gnesiotrochans with strong branch supports. Within Gnesiotrocha, Conochilidae form a strongly supported clade with representatives of all but some genera of Flosculariidae. These results refute Conochilidae as separate family‐level taxon within Gnesiotrocha. This finding is also supported by a phylogenetic analysis using morphology, in particular new observations on trophi morphology. Conochilid rotifers are likely specialized Flosculariidae, which evolved to a planktonic lifestyle and reduction of coloniality within the group, in contrast to other Flosculariidae. Furthermore, our analysis reveals that two genera of Flosculariidae, Beachampia and Limnias, form a single, strongly supported clade in a sister‐group relation to a clade consisting of representatives of Order Collothecacea. The present results, both regarding position of the conochild rotifers and of two genera of Flosculariidae, highlight the need for a more extensive analysis of relationships within Gnesiotrocha.

Wang, Pu; Gao, Feng; Huang, Jie; Strüder‐Kypke, Michaela; Yi, Zhenzhen

doi: 10.1111/zsc.12122pmid: N/A

Phylogenetic studies of ciliates are mainly based on the primary structure information of the nuclear genes. Some regions of the small subunit ribosomal RNA (SSU‐rRNA) gene have distinctive secondary structures, which have demonstrated value as phylogenetic/taxonomic characters. In the current work, we predict the secondary structures of four variable regions (V2, V4, V7 and V9) in the SSU‐rRNA gene of 45 urostylids. Structure comparisons indicate that the V4 region is the most effective in revealing interspecific relationships, while the V9 region appears suitable at the family level or higher. The V2 region also offers some taxonomic information, but is too conserved to reflect phylogenetic relationships at the family or lower level, at least for urostylids. The V7 region is the least informative. We constructed several phylogenetic trees, based on the primary sequence alignment and based on an improved alignment according to the secondary structures. The results suggest that including secondary structure information in phylogenetic analyses provides additional insights into phylogenetic relationships. Using urostylid ciliates as an example, we show that secondary structure information results in a better understanding of their relationships, for example generic relationships within the family Pseudokeronopsidae.