Extensive Cryptic Diversity Research Articles

Multi-locus phylogeny and species delimitation of Australo-Papuan blacksnakes (Pseudechis Wagler, 1830: Elapidae: Serpentes)

Genetic analyses of Australasian organisms have resulted in the identification of extensive cryptic diversity across the continent. The venomous elapid snakes are among the best-studied organismal groups in this region, but many knowledge gaps persist: for instance, despite their iconic status, the species-level diversity among Australo-Papuan blacksnakes (Pseudechis) has remained poorly understood due to the existence of a group of cryptic species within the P. australis species complex, collectively termed “pygmy mulga snakes”. Using two mitochondrial and three nuclear loci we assess species boundaries within the genus using Bayesian species delimitation methods and reconstruct their phylogenetic history using multispecies coalescent approaches. Our analyses support the recognition of 10 species, including all of the currently described pygmy mulga snakes and one undescribed species from the Northern Territory of Australia. Phylogenetic relationships within the genus are broadly consistent with previous work, with the recognition of three major groups, the viviparous red-bellied black snake P. porphyriacus forming the sister species to two clades consisting of ovoviviparous species.

Species delimitation and phylogeography of the studfishFundulus catenatusspecies group (Ovalentaria: Cyprinodontiformes)

The Central Highlands of North America have an old and complex geological and biological history, with extensive unexplored cryptic diversity. We examined the species limits of the Fundulus catenatus species group (F. catenatus, Fundulus bifax, and Fundulus stellifer) using two phylogenetic approaches. Fundulus catenatus was densely sampled from five geographically disjunct regions across the eastern USA. We sequenced four nuclear introns and used species tree analyses and two species delimitation methods to determine historical relationships and investigate species diversity within the group. Both methods strongly supported the presence of two reciprocally monophyletic species within F. catenatus. Species tree analysis of four nuclear introns (stx5a, ncl1, rpsa, and rps3) from the F. catenatus species group (including a tip for F. sp. cf. catenatus) recovered the two Mobile Basin species as sister to a strongly supported clade of F. catenatus and F. sp. cf. catenatus. Cytochrome b sequences were used in phylogeographical analyses of the two putative species. In one species we identified signatures of population expansion whereas the other exhibited genetic structure consistent with isolation of populations.

Biogeography, cryptic diversity, and queen dimorphism evolution of the Neotropical ant genus Ectatomma Smith, 1958 (Formicidae, Ectatomminae)

Due to its high biodiversity and its complex climatic and geological history, the Neotropical region has caught the attention of evolutionary and conservation biologists. The Neotropics have an understudied and probably extensive cryptic diversity, stemming from old lineages that have persisted through time with highly similar morphology or from new morphologically undifferentiated sibling species. The wide-ranging Neotropical ant genus Ectatomma currently has only 15 described species, some of which present limited distribution. These ants provide an excellent system for the study of diversification and cryptic diversity in the Neotropics. Ectatomma also displays queen-size dimorphism in some northern populations of its two most common species: a case of true microgyny and a recently described parasitic species. We performed a phylogenetic and biogeographic analysis of Ectatomma species using two mitochondrial genes and one nuclear gene. We also explored the relationship between the history of the genus and the appearance of miniaturized queens. Our analysis recovered a monophyletic Ectatomma that originated in the Parana region of South America. We recorded three likely events of colonization of the Caribbean–Mesoamerican region. We also detected ample evidence of cryptic divergence that deserves a full taxonomic revision of the genus. Miniature queens—microgynes and parasites—represent two independent evolutionary events that appeared in the recent history of the genus.

Cryptic diversity, diversification and vicariance in two species complexes ofTomocerus(Collembola,Tomoceridae) fromChina

Springtails (Collembola) are a group of arthropods that are found in terrestrial ecosystems throughout the world. Two species complexes,Tomocerus ocreatusandT. nigruscomplexes, are widely distributed in the southern and northern parts of easternChina, 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 mixedYule coalescent model and aBayesian multilocus approach recognized 22DNA‐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 thatocreatusandnigruscomplexes originated in southern and northernChina, respectively. We estimated their divergence at 27.8–44.9 Mya during theEocene–Oligocene, at the time when the transmeridionalQinling–DabieMountains uplifted and formed the north–south geographical boundary of easternChina. Diversification analyses suggest that the subsequent orogenesis of theQinghai–TibetanPlateau in westernChina 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 theQinling–Dabie Mountains on patterns of animal speciation and distribution inChina.

Extensive cryptic species diversity and fine-scale endemism in the marine red alga Portieria in the Philippines

We investigated species diversity and distribution patterns of the marine red alga Portieria in the Philippine archipelago. Species boundaries were tested based on mitochondrial, plastid and nuclear encoded loci, using a general mixed Yule-coalescent (GMYC) model-based approach and a bayesian multilocus species delimitation method. The outcome of the GMYC analysis of the mitochondrial encoded cox2-3 dataset was highly congruent with the multilocus analysis. In stark contrast with the current morphology-based assumption that the genus includes a single, widely distributed species in the Indo-West Pacific (Portieria hornemannii), DNA-based species delimitation resulted in the recognition of 21 species within the Philippines. Species distributions were found to be highly structured with most species restricted to island groups within the archipelago. These extremely narrow species ranges and high levels of intra-archipelagic endemism contrast with the wide-held belief that marine organisms generally have large geographical ranges and that endemism is at most restricted to the archipelagic level. Our results indicate that speciation in the marine environment may occur at spatial scales smaller than 100 km, comparable with some terrestrial systems. Our finding of fine-scale endemism has important consequences for marine conservation and management.

River barriers and cryptic biodiversity in an evolutionary museum.

The Riverine Barriers Hypothesis (RBH) posits that tropical rivers can be effective barriers to gene flow, based on observations that range boundaries often coincide with river barriers. Over the last 160 years, the RBH has received attention from various perspectives, with a particular focus on vertebrates in the Amazon Basin. To our knowledge, no molecular assessment of the RBH has been conducted on birds in the Afrotropics, despite its rich avifauna and many Afrotropical bird species being widely distributed across numerous watersheds and basins. Here, we provide the first genetic evidence that an Afrotropical river has served as a barrier for birds and for their lice, based on four understory bird species collected from sites north and south of the Congo River. Our results indicate near-contemporaneous, Pleistocene lineage diversification across the Congo River in these species. Our results further indicate differing levels of genetic variation in bird lice; the extent of this variation appears linked to the life-history of both the host and the louse. Extensive cryptic diversity likely is being harbored in Afrotropical forests, in both understory birds and their lice. Therefore, these forests may not be “museums” of old lineages. Rather, substantial evolutionary diversification may have occurred in Afrotropical forests throughout the Pleistocene, supporting the Pleistocene Forest Refuge Hypothesis. Strong genetic variation in birds and their lice within a small part of the Congo Basin forest indicates that we may have grossly underestimated diversity in the Afrotropics, making these forests home of substantial biodiversity in need of conservation.

Mitochondrial sequence variation suggests extensive cryptic diversity within the Western Palearctic Daphnia longispina complex

We report on a discovery of six divergent lineages within the European Daphnia longispina complex from various localities in central to northeast Europe. The levels of divergence from well‐known species of the complex suggest that they represent as yet unrecognized distinct taxa. These newly recognized lineages always coexisted in syntopy with widespread species of the complex. Particularly rich in cryptic diversity (with four of the six lineages present) was the delta of the River Pechora in northern European Russia, a region not covered by an ice sheet during most of the last glacial period. We suggest that ice‐free regions of northeastern Europe may have been important refugia for planktonic species, and still are overlooked hot spots of diversity. Our findings confirm that the real diversity within widespread crustacean planktonic taxa is much higher than presently recognized. The potential presence of cryptic species should be considered in ecological studies.

Phylogenetic analysis of New Zealand earthworms (Oligochaeta: Megascolecidae) reveals ancient clades and cryptic taxonomic diversity

We have constructed the first ever phylogeny for the New Zealand earthworm fauna (Megascolecinae and Acanthodrilinae) including representatives from other major continental regions. Bayesian and maximum likelihood phylogenetic trees were constructed from 427 base pairs from the mitochondrial large subunit (16S) rRNA gene and 661 base pairs from the nuclear large subunit (28S) rRNA gene. Within the Acanthodrilinae we were able to identify a number of well-supported clades that were restricted to continental landmasses. Estimates of nodal support for these major clades were generally high, but relationships among clades were poorly resolved. The phylogenetic analyses revealed several independent lineages in New Zealand, some of which had a comparable phylogenetic depth to monophyletic groups sampled from Madagascar, Africa, North America and Australia. These results are consistent with at least some of these clades having inhabited New Zealand since rifting from Gondwana in the Late Cretaceous. Within the New Zealand Acanthodrilinae, major clades tended to be restricted to specific regions of New Zealand, with the central North Island and Cook Strait representing major biogeographic boundaries. Our field surveys of New Zealand and subsequent identification has also revealed extensive cryptic taxonomic diversity with approximately 48 new species sampled in addition to the 199 species recognized by previous authors. Our results indicate that further survey and taxonomic work is required to establish a foundation for future biogeographic and ecological research on this vitally important component of the New Zealand biota.

Who is Oxyrrhis marina? Morphological and phylogenetic studies on an unusual dinoflagellate

Oxyrrhis marina is an extensively studied morphospecies and a common protist model used to examine a range of ecological processes. Further, as a result of a number of unusual cytological and genetic features, Oxyrrhis is increasingly a target for the study of evolutionary patterns and genome organization within the Alveolata. However, a small number of early morphological studies and recent phylogenetic data suggest that O. marina represents more than one species. As different research groups employ different O. marina isolates (which are potentially highly divergent strains or different species), the context in which comparisons between isolates can be made is difficult to assess. In this paper, we explore the literature that has contributed to the definition of O. marina, highlighting the unusual characteristics possessed by O. marina that have motivated much of the study on this organism and informed its key phylogenetic position. In addition, we assess historical and contemporary evidence for multiple Oxyrrhis species. Based on this assessment, in particular recent molecular genetic data, we assert that O. marina represents two species: O. marina and O. maritima. Based on historical observations, we also indicate that a third species (O. tenticulifera) may occur, although there are no contemporary data to support or refute this designation. Extensive cryptic diversity has important implications for researchers studying Oxyrrhis: caution must be exercised in characterizing Oxyrrhis isolates for experimental study (i.e. it is inappropriate to report assessments concerning poorly characterized isolates), and comparative studies of multiple isolates are required to assess individual, population and species level variation in the genus. Finally, in a broader context, the ecological and evolutionary processes driving diversity in free-living protists remains poorly understood. Model protists such as O. marina and O. maritima for which we are beginning to recognize and characterize an extensive pool of variation present ideal opportunities to unravel these fundamental processes.

Evolutionary diversification of the gall midge genus Asteromyia (Cecidomyiidae) in a multitrophic ecological context

Gall-forming insects provide ideal systems to analyze the evolution of host-parasite interactions and understand the ecological interactions that contribute to evolutionary diversification. Flies in the family Cecidomyiidae represent the largest radiation of gall-forming insects and are characterized by complex trophic interactions with plants, fungal symbionts, and predators. We analyzed the phylogenetic history and evolutionary associations of the North American cecidomyiid genus Asteromyia, which is engaged in a complex and perhaps co-evolving community of interactions with host-plants, fungi, and parasitoids. Mitochondrial gene trees generally support current classifications, but reveal extensive cryptic diversity within the eight named species. Asteromyia likely radiated after their associated host-plants in the Astereae, but species groups exhibit strong associations with specific lineages of Astereae. Evolutionary associations with fungal mutualists are dynamic, however, and suggest rapid and perhaps coordinated changes across trophic levels.