Cryptic species of cardinalfish with evidence for old and new divergence

Larval dispersal and limited knowledge of physical boundaries challenge our understanding of the processes that drive genetic divergence and potential speciation in the marine environment. Divergence, both within and between populations of marine taxa, is not uncommon, but spatial and temporal stability of observed genetic structure is not well known. Previously, we detected large genetic differences among populations of the cardinalfish species Ostorhinchus doederleini inhabiting adjacent coral reefs. Here, we determined the spatial and temporal persistence of these genetic structures over the course of ten consecutive generations. Using microsatellite markers, we detected large changes (genetic population distance, D _est, ranged from 0.04 to 0.46) in the genetic structure in some years, but some reefs maintained the same populations for nearly all sampling years. As this species’ life span does not exceed 1 yr, persistence of distinct reef populations suggests natal homing. Mitochondrial identity based on two mtDNA markers corroborates the nuclear genetic evidence for genetic differences large enough to constitute different clades and even cryptic species in O. doederleini, which, based on gross morphology, was thought to be a single taxon. Habitat specialization was observed in one clade that exclusively inhabited reef lagoons, while all clades could be observed on reef slopes. We suggest that local habitat recognition combined with local population recognition and selection against hybrids can form barriers that maintain a cryptic species complex.     

Unraveling hierarchical genetic structure in a marine metapopulation: A comparison of three high‐throughput genotyping approaches

Marine metapopulations often exhibit subtle population structure that can be difficult to detect. Given recent advances in high‐throughput sequencing, an emerging question is whether various genotyping approaches, in concert with improved sampling designs, will substantially improve our understanding of genetic structure in the sea. To address this question, we explored hierarchical patterns of structure in the coral reef fish Elacatinus lori using a high‐resolution approach with respect to both genetic and geographic sampling. Previously, we identified three putative E. lori populations within Belize using traditional genetic markers and sparse geographic sampling: barrier reef and Turneffe Atoll; Glover's Atoll; and Lighthouse Atoll. Here, we systematically sampled individuals at ~10 km intervals throughout these reefs (1,129 individuals from 35 sites) and sequenced all individuals at three sets of markers: 2,418 SNPs; 89 microsatellites; and 57 nonrepetitive nuclear loci. At broad spatial scales, the markers were consistent with each other and with previous findings. At finer spatial scales, there was new evidence of genetic substructure, but our three marker sets differed slightly in their ability to detect these patterns. Specifically, we found subtle structure between the barrier reef and Turneffe Atoll, with SNPs resolving this pattern most effectively. We also documented isolation by distance within the barrier reef. Sensitivity analyses revealed that the number of loci (and alleles) had a strong effect on the detection of structure for all three marker sets, particularly at small spatial scales. Taken together, these results illustrate empirically that high‐throughput genotyping data can elucidate subtle genetic structure at previously‐undetected scales in a dispersive marine fish.     

Past lake shore dynamics explain present pattern of unidirectional introgression across a habitat barrier

Introgression patterns between divergent lineages are often characterized by asymmetry in the direction and among-marker variation in the extent of gene flow, and therefore inform on the mechanisms involved in differentiation and speciation. In the present study, we test the hypothesis that unidirectional introgression between two phenotypically and genetically distinct lineages of the littoral, rock-dwelling cichlid fish Tropheus moorii across a wide sandy bay is linked to observed differences in mate preferences between the two lineages. This hypothesis predicts bi-directional nuclear gene flow and was rejected by congruent patterns of introgression in mtDNA, AFLP and microsatellite markers, with admixture confined to the populations west of the bay. This pattern can be explained on the basis of habitat changes in the course of lake level fluctuations, which first facilitated the development of a symmetric admixture zone including the area corresponding to the present sand bay and then shaped asymmetry by causing local extinctions and cessation of gene flow when this area became once more inhabitable. This conforms with previous assumptions that habitat dynamics are a primary determinant of population-level evolution in Tropheus. In this respect, Tropheus may be representative of species whose preferred habitat is subject to frequent re-structuring.     

Discordant patterns of introgression across a narrow hybrid zone between two cryptic lineages of an Iberian endemic newt

The study of natural hybrid zones can illuminate aspects of lineage divergence and speciation in morphologically cryptic taxa. We studied a hybrid zone between two highly divergent but morphologically similar lineages (south‐western and south‐eastern) of the Iberian endemic Bosca's newt (Lissotriton boscai) in SW Iberia with a multilocus dataset (microsatellites, nuclear and mitochondrial genes). STRUCTURE and NEWHYBRIDS analyses retrieved few admixed individuals, which classified as backcrosses involving parental individuals of the south‐western lineage. Our results show asymmetric introgression of mtDNA beyond the contact from this lineage into the south‐eastern lineage. Analysis of nongeographic introgression patterns revealed asymmetries in the direction of introgression, but except for mtDNA, we did not find evidence for nonconcordant introgression patterns across nuclear loci. Analysis of a 150‐km transect across the hybrid zone showed broadly coincident cline widths (ca. 3.2–27.9 km), and concordant cline centres across all markers, except for mtDNA that is displaced ca. 60 km northward. Results from ecological niche modelling show that the hybrid zone is in a climatically homogenous area with suitable habitat for the species, suggesting that contact between the two lineages is unlikely to occur further south as their distributions are currently separated by an extensive area of unfavourable habitat. Taken together, our findings suggest the genetic structure of this hybrid zone results from the interplay of historical (biogeographic) and population‐level processes. The narrowness and coincidence of genetic clines can be explained by weak selection against hybrids and reflect a degree of reproductive isolation that is consistent with cryptic speciation.     

Geographic genetic structure of Iberian columbines (gen. <Emphasis Type="Italic">Aquilegia</Emphasis>)

Southern European columbines (genus Aquilegia) are involved in active processes of diversification, and the Iberian Peninsula offers a privileged observatory to witness the process. Studies on Iberian columbines have provided significant advances on species diversification, but we still lack a complete perspective of the genetic diversification in the Iberian scenario. This work explores how genetic diversity of the genus Aquilegia is geographically structured across the Iberian Peninsula. We used Bayesian clustering methods, principal coordinates analyses, and NJ phenograms to assess the genetic relationships among 285 individuals from 62 locations and detect the main lineages. Genetic diversity of Iberian columbines consists of five geographically structured lineages, corresponding to different Iberian taxa. Differentiation among lineages shows particularly complex admixture patterns at Northeast and highly homogeneous toward Northwest and Southeast. This geographic genetic structure suggests the existence of incomplete lineage sorting and interspecific hybridization as could be expected in recent processes of diversification under the influence of quaternary postglacial migrations. This scenario is consistent with what is proposed by the most recent studies on European and Iberian columbines, which point to geographic isolation and divergent selection by habitat specialization as the main diversification drivers of the Iberian Aquilegia complex.     

Population genetics information for the regional conservation of a tropical seagrass, <Emphasis Type="Italic">Enhalus acoroides</Emphasis>, around the Guimaras Strait,Philippines

Seagrasses are marine angiosperms and play an essential ecological role in coastal ecosystems; however, seagrass meadows are threatened locally by anthropogenic disturbances. Understanding the dispersal patterns of seagrasses is essential for appropriate ecosystem management and establishment of marine protected areas (MPAs) in coastal ecosystems. In the Guimaras Strait in the Philippines, Banate (BAN) has been established as an MPA. However, there is a lack of information on the genetic diversity of seagrasses in BAN and the surrounding areas. In the present study, population genetics analysis of Enhalus acoroides was performed by using polymorphic microsatellite markers, for the estimation of genetic diversity, differentiation, and migration patterns of seagrasses within the regional geographical scale (~200 km) around the Guimaras Strait. The results showed that the genetic diversity of BAN is extremely low, although the Guimaras Strait is located in the tropical central habitat. Guimaras Island geographically divides the populations of E. acoroides into south and north. However, the genetic structure did not show any relationship between the geographical location and distance. The floating, buoyant fruits of E. acoroides may play a role in their long-distance dispersal; however, such dispersal is not frequent. Almost all of the seeds and fruits are derived from self-recruitment in the natal meadow. This study suggests that E. acoroides populations possess a weak genetic connectivity, and that the persistence of the meadow is threatened due to the low genetic diversity and high degree of population isolation in BAN. To maintain and enhance the genetic diversity of seagrasses within the MPA, the seagrass meadows in the surrounding areas should also be conserved.     

Phylogeographic pattern of range expansion provides evidence for cryptic species lineages in Silene nutans in Western Europe

As a result of recent or past evolutionary processes, a single species might consist of distinct Evolutionary Significant Units (ESUs), even corresponding to cryptic species. Determining the underlying mechanisms of range shifts and the processes at work in the build-up of divergent ESUs requires elucidating the factors that contribute to population genetic divergence across a species'' range. We investigated the large-scale patterns of genetic structure in the perennial herbaceous plant species Silene nutans (Caryophyllaceae) in Western Europe. We sampled and genotyped 111 populations using 13 nuclear microsatellite loci and 6 plastid single-nucleotide polymorphisms. Broad-scale spatial population genetic structure was examined using Bayesian clustering, spatial multivariate analyses and measures of hierarchical genetic differentiation. The genotypic structure of S. nutans was typical of a predominantly allogamous mating system. We also identified plastid lineages with no intra-population polymorphism, mirroring two genetically differentiated nuclear lineages. No evidence of admixture was found. Spatial trends in genetic diversity further suggested independent leading-edge expansion associated with founding events and subsequent genetic erosion. Overall, our findings suggested speciation processes in S. nutans and highlighted striking patterns of distinct stepwise recolonisation of Western Europe shaped by Quaternary climate oscillations. Two main potential ESUs can be defined in Western Europe, corresponding to Eastern and Western nuclear-plastid lineages. In situ preservation of populations and genetic rescue implying ex situ conservation techniques should take the lineage identity into account. This is particularly true in Great Britain, northern France and Belgium, where S. nutans is rare and where distinct lineages co-occur in close contact.     

Diversity and succession of pelagic microorganism communities in a newly restored Illinois River floodplain lake

Stenotopic specialization to a fragmented habitat promotes the evolution of genetic structure. It is not yet clear whether small-scale population structure generally translates into large-scale intraspecific divergence. In the present survey of mitochondrial genetic structure in the Lake Tanganyika endemic Altolamprologus (Teleostei, Cichlidae), a rock-dwelling cichlid genus comprising A. compressiceps and A. calvus, habitat-induced population fragmentation contrasts with weak phylogeographic structure and recent divergence among genetic clades. Low rates of dispersal, perhaps along gastropod shell beds that connect patches of rocky habitat, and periodic secondary contact during lake level fluctuations are apparently sufficient to maintain genetic connectivity within each of the two Altolamprologus species. The picture of genetic cohesion was interrupted by a single highly divergent haplotype clade in A. compressiceps restricted to the northern part of the lake. Comparisons between mitochondrial and nuclear phylogenetic reconstructions suggested that the divergent mitochondrial clade originated from ancient interspecific introgression. Finally, ‘isolation-with-migration’ models indicated that divergence between the two Altolamprologus species was recent (67–142 KYA) and proceeded with little if any gene flow. As in other rock-dwelling cichlids, recent population expansions were inferred in both Altolamprologus species, which may be connected with drastic lake level fluctuations.     

Cryptic barriers to dispersal within a lake allow genetic differentiation of Eurasian perch

Gene flow between coexisting or nearby populations normally prevents genetic divergence and local adaptation. Despite this, there are an increasing number of reports of sympatric sister taxa, indicating potential divergence and speciation in the face of gene flow. A large number of such reported cases involve lake-dwelling fish, which are expected to run into few physical barriers to dispersal within their aquatic habitat. However, such cases may not necessarily reflect sympatric speciation if cryptic dispersal barriers are common in lakes and other aquatic systems. In this study, we examined genetic differentiation in perch (Perca fluviatilis L.) from nine locations in a single, small lake (24 km(2)), using microsatellites. We detected significant genetic differentiation in all but two pairwise comparisons. These patterns were not consistent with divergence by distance or the existence of kin groups. Instead, they suggest that cryptic barriers to dispersal exist within the lake, allowing small-scale genetic divergence. Such an observation suggests that allopatric (or parapatric) divergence may be possible, even in small, apparently homogenous environments such as lakes. This has important consequences for how we currently view evidence from nature for sympatric speciation.     

Molecular Comparisons of Freshwater and Marine Isolates of the Same Morphospecies of Heterotrophic Flagellates

Heterotrophic flagellates are key components of all ecosystems. Understanding the patterns of biodiversity of these organisms is thus particularly important. Here we analyzed the intraspecific diversity of 10 morphospecies of heterotrophic flagellates comprising representatives of the Apusozoa (2 morphospecies) and Kinetoplastea (8 morphospecies), all belonging to the most common flagellates with worldwide distribution. Most morphospecies showed a mixing of lineages isolated from diverse habitats, indicating that some lineages of these morphospecies had been able to colonize different habitats several times. Furthermore, our results revealed remarkable levels of genetic divergence within most of the morphospecies studied, underlining the difficulty of correctly determining species by means of morphology alone. Many cryptic or pseudocryptic species seem to occur. Our results revealed clear divergence between marine and freshwater lineages of the morphospecies Ancyromonas sigmoides, showing that freshwater lineages have not been able to colonize marine environments and marine lineages have not been able to colonize freshwater environments for a long time.     

Population Genomics Reveals Genetic Divergence and Adaptive Differentiation of Chinese Sea Bass (<Emphasis Type="Italic">Lateolabrax maculatus</Emphasis>)

The marine species usually show high dispersal capabilities accompanied by high levels of gene flow. On the other hand, many physical barriers distribute along the continental marginal seas and may prevent dispersals and increase population divergence. These complexities along the continental margin generate serious challenges to population genetic studies of marine species. Chinese sea bass Lateolabrax maculatus distributes broad latitudinal gradient spanning from the tropical to the mid-temperate zones in the continental margin seas of the Northwest Pacific Ocean. Using the double digest restriction-site-associated DNA tag sequencing (ddRAD) approach, we genotyped 10,297 SNPs for 219 Chinese seabass individuals of 12 populations along the Chinese coast in the Northwest Pacific region. Genetic divergence among these populations was evaluated, and population structure was established. The results suggested that geographically distant populations in the Bohai Gulf and the Beibu Gulf retain significant genetic divergence, which are connected by a series of intermediate populations in between. The results also suggested that Leizhou Peninsula, Hainan Island, and Shandong Peninsula are major physical barriers and substantially block gene flow and genetic admixture of L. maculatus. We also investigated the potential genetic basis of local adaptation correlating with population differentiation of L. maculatus. The sea surface temperature is a significantly differentiated environmental factor for the distribution of L. maculatus. The correlation of water temperature and genetic variations in extensively distributed populations was investigated with Bayesian-based approaches. The candidate genes underlying the local selection in geographically divergent populations were identified and annotated, providing clues to understand the potential mechanisms of adaptive evolution. Overall, our genome scale population genetic analysis provided insight into population divergence and local adaptation of Chinese sea bass in the continental marginal seas along Chinese coast.     

Rising the Persian Gulf Black-Lip Pearl Oyster to the Species Level: Fragmented Habitat and Chaotic Genetic Patchiness in <Emphasis Type="Italic">Pinctada persica</Emphasis>

Marine organisms with long pelagic larval stages are expected to exhibit low genetic differentiation due to their potential to disperse over large distances. Growing body of evidence, however, suggests that marine populations can differentiate over small spatial scales. Here we focused on black-lip pearl oysters from the Persian Gulf that are thought to belong to the Pinctada margaritifera complex given their morphological affinities. This species complex includes seven lineages that show a wide distribution ranging from the Persian Gulf (Pinctada margaritifera persica) and Indian Ocean (P. m. zanzibarensis) to the French Polynesia (P. m. cumingii) and Hawai’i (P. m. galtsoffi). Despite the long pelagic larval phase of P. m. persica, this lineage is absent from continental locations and can only be found on a few islands of the Persian Gulf. Mitochondrial COI-based analyses indicated that P. m. persica belongs to a clearly divergent ESU and groups with specimens from Mauritius (P. m. zanzibarensis). Microsatellite data, used here to assess the spatial scale of realized dispersal of Persian Gulf black-lip pearl oysters, revealed significant genetic structure among islands distant of only a few dozen kilometres. The scantiness of suitable habitats most likely restricted the distribution of this lineage originating the observed chaotic genetic patchiness. The hatchery-based enhancement performed in one of the sampled islands may also have affected population genetic structure. The long-term accumulation of genetic differences likely resulted from the allopatric divergence between P. m. persica and the neighbouring Indian Ocean black-lip pearl oysters.     

A Passerine Bird's evolution corroborates the geologic history of the island of New Guinea

New Guinea is a biologically diverse island, with a unique geologic history and topography that has likely played a role in the evolution of species. Few island-wide studies, however, have examined the phylogeographic history of lowland species. The objective of this study was to examine patterns of phylogeographic variation of a common and widespread New Guinean bird species (Colluricincla megarhyncha). Specifically, we test the mechanisms hypothesized to cause geographic and genetic variation (e.g., vicariance, isolation by distance and founder-effect with dispersal). To accomplish this, we surveyed three regions of the mitochondrial genome and a nuclear intron and assessed differences among 23 of the 30 described subspecies from throughout their range. We found support for eight highly divergent lineages within C. megarhyncha. Genetic lineages were found within continuous lowland habitat or on smaller islands, but all individuals within clades were not necessarily structured by predicted biogeographic barriers. There was some evidence of isolation by distance and potential founder-effects. Mitochondrial DNA sequence divergence among lineages was at a level often observed among different species or even genera of birds (5-11%), suggesting lineages within regions have been isolated for long periods of time. When topographical barriers were associated with divergence patterns, the estimated divergence date for the clade coincided with the estimated time of barrier formation. We also found that dispersal distance and range size are positively correlated across lineages. Evidence from this research suggests that different phylogeographic mechanisms concurrently structure lineages of C. megarhyncha and are not mutually exclusive. These lineages are a result of evolutionary forces acting at different temporal and spatial scales concordant with New Guinea's geological history.     

Fish with Chips: Tracking Reef Fish Movements to Evaluate Size and Connectivity of Caribbean Marine Protected Areas

Coral reefs and associated fish populations have experienced rapid decline in the Caribbean region and marine protected areas (MPAs) have been widely implemented to address this decline. The performance of no-take MPAs (i.e., marine reserves) for protecting and rebuilding fish populations is influenced by the movement of animals within and across their boundaries. Very little is known about Caribbean reef fish movements creating a critical knowledge gap that can impede effective MPA design, performance and evaluation. Using miniature implanted acoustic transmitters and a fixed acoustic receiver array, we address three key questions: How far can reef fish move? Does connectivity exist between adjacent MPAs? Does existing MPA size match the spatial scale of reef fish movements? We show that many reef fishes are capable of traveling far greater distances and in shorter duration than was previously known. Across the Puerto Rican Shelf, more than half of our 163 tagged fish (18 species of 10 families) moved distances greater than 1 km with three fish moving more than 10 km in a single day and a quarter spending time outside of MPAs. We provide direct evidence of ecological connectivity across a network of MPAs, including estimated movements of more than 40 km connecting a nearshore MPA with a shelf-edge spawning aggregation. Most tagged fish showed high fidelity to MPAs, but also spent time outside MPAs, potentially contributing to spillover. Three-quarters of our fish were capable of traveling distances that would take them beyond the protection offered by at least 40–64% of the existing eastern Caribbean MPAs. We recommend that key species movement patterns be used to inform and evaluate MPA functionality and design, particularly size and shape. A re-scaling of our perception of Caribbean reef fish mobility and habitat use is imperative, with important implications for ecology and management effectiveness.     

A geometric morphometric and microsatellite analyses of <Emphasis Type="Italic">Scaptotrigona mexicana</Emphasis> and <Emphasis Type="Italic">S. pectoralis</Emphasis> (Apidae: Meliponini) sheds light on the biodiversity of Mesoamerican stingless bees

Geometric morphometrics and molecular methods are effective tools to study the variability of stingless bee populations and species that merit protection given their worldwide decline. Based on previous evidence of cryptic lineages within the Scaptotrigona genus, we tested the existence of multiple evolutionary lineages within the species S. mexicana and we investigated the status of S. pectoralis. By analyzing their population structure, we found differences between the Pacific and Atlantic populations of each of these species, although geometric morphometrics of the wing only confirmed these results in S. mexicana. There was a tendency towards enhanced genetic differentiation over larger distances in the Atlantic populations of both species but not in the Pacific populations. These results revealed a pattern of differentiation among evolutionary units and a specific distribution of genetic diversity within these Scaptotrigona species in Mesoamerica, suggesting the need for future taxonomic revisions, as well as activities aimed at management and conservation.     

Seascape continuity plays an important role in determining patterns of spatial genetic structure in a coral reef fish

Detecting patterns of spatial genetic structure (SGS) can help identify intrinsic and extrinsic barriers to gene flow within metapopulations. For marine organisms such as coral reef fishes, identifying these barriers is critical to predicting evolutionary dynamics and demarcating evolutionarily significant units for conservation. In this study, we adopted an alternative hypothesis‐testing framework to identify the patterns and predictors of SGS in the Caribbean reef fish Elacatinus lori. First, genetic structure was estimated using nuclear microsatellites and mitochondrial cytochrome b sequences. Next, clustering and network analyses were applied to visualize patterns of SGS. Finally, logistic regressions and linear mixed models were used to identify the predictors of SGS. Both sets of markers revealed low global structure: mitochondrial Φ_ST = 0.12, microsatellite F_ST = 0.0056. However, there was high variability among pairwise estimates, ranging from no differentiation between sites on contiguous reef (Φ_ST = 0) to strong differentiation between sites separated by ocean expanses ≥ 20 km (maximum Φ_ST = 0.65). Genetic clustering and statistical analyses provided additional support for the hypothesis that seascape discontinuity, represented by oceanic breaks between patches of reef habitat, is a key predictor of SGS in E. lori. Notably, the estimated patterns and predictors of SGS were consistent between both sets of markers. Combined with previous studies of dispersal in E. lori, these results suggest that the interaction between seascape continuity and the dispersal kernel plays an important role in determining genetic connectivity within metapopulations.     

Divergent lineages and conserved niches: using ecological niche modeling to examine the evolutionary patterns of the Nile monitor (<Emphasis Type="Italic">Varanus niloticus</Emphasis>)

Ecological niche modeling is a useful tool that can support phylogeographic analyses, offering insight into the evolutionary processes that have generated present-day patterns of biodiversity. Findings of ecological divergence across evolutionary lineages can be utilized to bolster inferences of parapatric or sympatric modes of speciation, and provide support for species-level classifications. Conversely, conserved ecological niches across evolutionary timescales are thought to have facilitated allopatric speciation. Here, we examined the climatic niche of three genetic lineages of the Nile monitor (Varanus niloticus) to better understand the processes involved in generating patterns of genetic variation, and to potentially clarify their taxonomic status. We built ecological niche models using genetically confirmed occurrence points from the three evolutionary lineages of V. niloticus, occupying the western, northern, and southern regions of Africa. Pairwise comparisons of climatic niche overlap provided evidence in support of niche conservatism across all V. niloticus lineages. These findings are consistent with an allopatric mode of differentiation. Furthermore, climatic niche conservatism could have played a role in isolating V. niloticus populations during historic climate oscillations, generating the observed genetic patterns across Africa.     

Cryptic diversity in the pen shell Atrina pectinata (Bivalvia: Pinnidae): high divergence and hybridization revealed by molecular and morphological data

Cryptic species have been increasingly revealed in the marine realm through an analytical approach incorporating multiple lines of evidence (e.g., mtDNA, nuclear genes and morphology). Illustrations of cryptic taxa improve our understanding of species diversity and evolutionary histories within marine animals. The pen shell Atrina pectinata is known to exhibit extensive morphological variations that may harbour cryptic diversity. In this study, we investigated A. pectinata populations along the coast of China and one from Japan to explore possible cryptic diversity and hybridization using a combination of mitochondrial (cytochrome c oxidase subunit I, mtCOI) and nuclear (ribosomal internal transcribed spacer, nrITS) genes as well as morphology. Phylogenetic analyses of mtCOI ‘DNA barcoding gene’ sequences resolved six divergent lineages with intralineage divergences between 0.4% and 0.8%. Interlineage sequence differences ranged from 4.3% to 22.0%, suggesting that six candidate cryptic species are present. The nrITS gene revealed five deep lineages with Kimura 2‐parameter distances of 3.7–30.3%. The five nuclear lineages generally corresponded to mtCOI lineages 1–4 and (5 + 6), suggestive of five distinct evolutionary lineages. Multiple nrITS sequences of significant variance were found within an individual, clearly implying recent hybridization events between/among the evolutionary lineages, which contributed to cytonuclear discordance. Morphologically, five morphotypes matched the five genetic lineages, although the intermediates may well blur the boundaries of different morphotypes. This study demonstrates the importance of combining multiple lines of evidence to explore species cryptic diversity and past evolutionary histories.