Continental Clades Research Articles

Complex geographic- and habitat-based niche partitioning of an East Asian habitat generalist mayflyIsonychia japonica(Ephemeroptera:Isonychiidae) with reference to differences in genetic structure

AbstractWe focused on the genetic structure and evolutionary divergence of a typical habitat generalist mayfly, Isonychia japonica, inhabiting rivers widely distributed across eastern Asia. In the Japanese Archipelago, they are distributed across a wide range of environments, including up- and downstream areas in 1 river basin. We analyzed DNA sequences of this mayfly from both the mitochondrial (cytochrome oxidase c subunit I [COI] and 16S ribosomal RNA) and nuclear genomes (Histone H3 and ITS2) of specimens from populations across the eastern Asian region, with emphasis on the Japanese Archipelago. Isonychia japonica is genetically differentiated into 2 major clades (C = continental clade, J = Japanese Archipelago clade). Furthermore, clade J is composed of 2 subclades (clades J-U and J-D). Clade J is separated by environment, with specimens constituting clade J-U occurring in small-scale rivers of the upstream regions and specimens constituting clade J-D occurring in large-scale rivers of downstream re...

Phylogeography of the Vermilion Flycatcher species complex: Multiple speciation events, shifts in migratory behavior, and an apparent extinction of a Galápagos-endemic bird species

The Vermilion Flycatcher (Pyrocephalus rubinus) is a widespread species found in North and South America and the Galápagos. Its 12 recognized subspecies vary in degree of geographic isolation, phenotypic distinctness, and migratory status. Some authors suggest that Galápagos subspecies nanus and dubius constitute one or more separate species. Observational reports of distinct differences in song also suggest separate species status for the austral migrant subspecies rubinus. To evaluate geographical patterns of diversification and taxonomic limits within this species complex, we carried out a molecular phylogenetic analysis encompassing 10 subspecies and three outgroup taxa using mitochondrial (ND2, Cyt b) and nuclear loci (ODC introns 6 through 7, FGB intron 5). We used samples of preserved tissues from museum collections as well as toe pad samples from museum skins. Galápagos and continental clades were recovered as sister groups, with initial divergence at ∼1mya. Within the continental clade, North and South American populations were sister groups. Three geographically distinct clades were recovered within South America. We detected no genetic differences between two broadly intergrading North American subspecies, mexicanus and flammeus, suggesting they should not be recognized as separate taxa. Four western South American subspecies were also indistinguishable on the basis of loci that we sampled, but occur in a region with patchy habitat, and may represent recently isolated populations. The austral migrant subspecies, rubinus, comprised a monophyletic mitochondrial clade and had many unique nuclear DNA alleles. In combination with its distinct song, exclusive song recognition behavior, different phenology, and an isolated breeding range, our data suggests that this taxon represents a separate species from other continental populations. Mitochondrial and nuclear genetic data, morphology, and behavior suggest that Galápagos forms should be elevated to two full species corresponding to the two currently recognized subspecies, nanus and dubius. The population of dubius is presumed to be extinct, and thus would represent the first documented extinction of a Galápagos-endemic bird species. Two strongly supported mitochondrial clades divide Galápagos subspecies nanus in a geographic pattern that conflicts with previous hypotheses that were based on plumage color. Several populations of nanus have recently become extinct or are in serious decline. Urgent conservation measures should seek to preserve the deep mitochondrial DNA diversity within nanus, and further work should explore whether additional forms should be recognized within nanus. Ancestral states analysis based on our phylogeny revealed that the most recent common ancestor of extant Vermilion Flycatcher populations was migratory, and that migratory behavior was lost more often than gained within Pyrocephalus and close relatives, as has been shown to be the case within Tyrannidae as a whole.

Spatiotemporal diversification of a low‐vagility Neotropical vertebrate clade (short‐tailed opossums, Didelphidae: Monodelphis)

AbstractAimTo infer historical‐biogeographical patterns and processes in South America based on estimated divergence times and ancestral distributions for a diverse clade of small marsupials (Monodelphis).LocationSouth America.MethodsWe estimated a time‐scaled phylogeny using sequence data from four nuclear genes and one mitochondrial gene for most currently recognized species, which we also scored for biome occupancy. We used maximum‐likelihood methods that explicitly model historical‐biogeographical processes to estimate ancestral distributions.ResultsThe earliest cladogenetic events in the genus occurred in the late Miocene, with subsequent diversification from the early Pliocene to the late Pleistocene. Model selection suggests an important role for founder‐event speciation, a process seldom accounted for in previous biogeographical analyses of continental clades. Two equivalently optimal models that incorporate this process each reconstruct the most recent common ancestor of Monodelphis as occurring in both Amazonia and the Atlantic Forest, from which the Andes, the Arid Diagonal (Caatinga, Cerrado, Chaco) and other neighbouring biomes were colonized during the Pliocene and Pleistocene.Main ConclusionsThe diversification of Monodelphis was not restricted to a narrow time interval, suggesting that speciation cannot be attributed to a single leading factor such as tectonism or Pleistocene climatic fluctuations. In particular, speciation within the Atlantic Forest biome appears to have occurred in the Neogene, whereas most Amazonian speciation events are substantially younger. Amazonia and/or the Atlantic Forest hosted most diversification events within Monodelphis and were the historical sources of lineages that subsequently colonized other areas. Founder‐event speciation, a concept traditionally associated with long‐distance dispersal among islands, must sustain other interpretations in historical‐biogeographical analyses of non‐vagile organisms in continental contexts. Possible mechanisms for founder‐event speciation in Monodelphis include historically transient connections between currently disjunct biomes and rapid reproductive isolation of populations colonizing adjacent but ecologically disparate biomes.

Rates of karyotypic evolution in Estrildid finches differ between island and continental clades.

Reasons why chromosomal rearrangements spread to fixation and frequently distinguish related taxa remain poorly understood. We used cytological descriptions of karyotype to identify large pericentric inversions between species of Estrildid finches (family Estrildidae) and a time-dated phylogeny to assess the genomic, geographic, and phylogenetic context of karyotype evolution in this group. Inversions between finch species fixed at an average rate of one every 2.26 My. Inversions were twice as likely to fix on the sex chromosomes compared to the autosomes. A high repeat density on the sex chromosomes may increase mutation rates, but other explanations via mutagenic input are not supported, as the number of inversions on a chromosome does not correlate with its length or map size. Inversions have fixed 3.3× faster in three continental clades than in two island chain clades, and fixation rate correlates with both range size and the number of sympatric species pairs. These results point to adaptation as the dominant mechanism driving fixation and suggest a role for gene flow in karyotype divergence. A review shows that the rapid karyotype evolution observed in the Estrildid finches appears to be more general across birds, and by implication other understudied taxa.

Mitogenomic phylogenetics of the bank vole Clethrionomys glareolus, a model system for studying end-glacial colonization of Europe

We have revisited the mtDNA phylogeny of the bank vole Clethrionomys glareolus based on Sanger and next-generation Illumina sequencing of 32 complete mitochondrial genomes. The bank vole is a key study species for understanding the response of European fauna to the climate change following the Last Glacial Maximum (LGM) and one of the most convincing examples of a woodland mammal surviving in cryptic northern glacial refugia in Europe. The genomes sequenced included multiple representatives of each of the eight bank vole clades previously described based on cytochrome b (cob) sequences. All clades with the exception of the Basque – likely a misidentified pseudogene clade – were highly supported in all phylogenetic analyses and the relationships between the clades were resolved with high confidence. Our data extend the distribution of the Carpathian clade, the marker of a northern glacial refugium in the Carpathian Mountains, to include Britain and Fennoscandia (but not adjacent areas of continental Europe). The Carpathian sub-clade that colonized Britain and Fennoscandia had a somewhat different history from the sub-clade currently found in or close to the Carpathians and may have derived from a more north-westerly refugial area. The two bank vole populations that colonized Britain at the end of the last glaciation are for the first time linked with particular continental clades, the first colonists with the Carpathian clade and the second colonists with the western clade originating in a more southerly refugium in the vicinity of the Alps. We however found no evidence that a functional divergence of proteins encoded in the mitochondrial genome promoted the partial genetic replacement of the first colonists by the second colonists detected previously in southern Britain. We did identify one codon site that changed more often and more radically in the tree than expected and where the observed amino acid change may affect the reductase activity of the cytochrome bc1 complex, but the change was not specific to a particular clade. We also found an excess of radical changes to the primary protein structure for geographically restricted clades from southern Italy and Norway, respectively, possibly related to stronger selective pressure at the latitudinal extremes of the bank vole distribution. However, overall, we find little evidence of pervasive effects of deviation from neutrality on bank vole mtDNA phylogeography.

Microscale vicariance and diversification of Western Balkan caddisflies linked to karstification.

The karst areas in the Dinaric region of the Western Balkan Peninsula are a hotspot of freshwater biodiversity. Many investigators have examined diversification of the subterranean freshwater fauna in these karst systems. However, diversification of surface-water fauna remains largely unexplored. We assessed local and regional diversification of surface-water species in karst systems and asked whether patterns of population differentiation could be explained by dispersal-diversification processes or allopatric diversification following karst-related microscale vicariance. We analyzed mitochondrial cytochrome c oxidase subunit I (mtCOI) sequence data of 4 caddisfly species (genus Drusus) in a phylogeographic framework to assess local and regional population genetic structure and Pliocene/Pleistocene history. We used BEAST software to assess the timing of intraspecific diversification of the target species. We compared climate envelopes of the study species and projected climatically suitable areas during the last glacial maximum (LGM) to assess differences in the species climatic niches and infer potential LGM refugia. The haplotype distribution of the 4 species (324 individuals from 32 populations) was characterized by strong genetic differentiation with few haplotypes shared among populations (16%) and deep divergence among populations of the 3 endemic species, even at local scales. Divergence among local populations of endemics often exceeded divergence among regional and continental clades of the widespread D. discolor. Major divergences among regional populations dated to 2.0 to 0.5 Mya. Species distribution model projections and genetic structure suggest that the endemic species persisted in situ and diversified locally throughout multiple Pleistocene climate cycles. The pattern for D. discolor was different and consistent with multiple invasions into the region. Patterns of population genetic structure and diversification were similar for the 3 regional endemic Drusus species and consistent with microscale vicariance after the onset of intensified karstification in the Dinaric region. Karstification may induce microscale vicariance of running surface-water habitats and probably promotes allopatric fragmentation of stream insects at small spatial scales.

Microsatellites underestimate genetic divergence in the Green-backed Tit (Parus monticolus)

Although a growing number of both sequence-based and microsatellite nuclear loci have been used to infer genetic structures, their relative efficiencies remain poorly understood. In our study, we used the Green-backed Tit (<i>Parus monticolus</i>) to explore the resolving ability of these two types of markers. The south-western and central mitochondrial DNA (mtDNA) phylogroups were divergent to some extent in sequence-based nuclear data, while mixed together in microsatellites data. The <i>F</i>_ST values among clades were about four times lower in microsatellite loci than those in sequence-based nuclear loci. We are of the opinion that size homoplasy may have contributed to the inability of microsatellites to uncover differentiation. Our results suggest that sequence-based nuclear loci outperformed microsatellite loci in detecting population structures, especially those focused on populations with large effective population sizes. There was no significant correlation between <i>F</i>_ST values and allelic size variability, which suggested that the efficiency of microsatellite loci in detecting genetic structure may be independent of their polymorphism. <i>F</i>_ST is better than <i>R</i>_ST in detecting intraspecific divergence due to the high variance of <i>R</i>_ST. In agreement with sequence-based nuclear loci, microsatellite loci did resolve the genetic distinctness of the Taiwanese phylogroup. The genetic differentiation between the Taiwanese and continental clades may involve allopatric divergence without gene flow.

Small-scale genetic structure of American black bears illustrates potential postglacial recolonization routes

In the absence of obvious barriers to dispersal microsatellite studies of vagile mammalian carnivores frequently find panmictic-like genetic structure over wide scales, whereas high levels of differentiation at much finer scales are detected with mitochondrial DNA (mtDNA). Given the maternal inheritance of mtDNA, these differences are often attributed to male-biased dispersal, remnants of postglacial range expansion, or both. Based on such contrasting results, it is not always clear how to delineate contemporary populations. We investigated the genetic structure of American black bears (Ursus americanus) over a wide geographic area (.1,700 km) that has no obvious physiogeographic barriers to gene flow. We analyzed a 315-base pair fragment of the mtDNA control region from 660 individual bears from 23 regions of Ontario, Canada. Relative to black bear studies based on nuclear data, mitochondrial analyses revealed much stronger patterns of genetic structure among regions (0.09 , FST , 0.44), even at small-scale intervals (,150 km), which likely reflects strong female philopatry combined with male-biased dispersal. The patterns of genetic differentiation among regions were consistent with previously described historical patterns in black bears, specifically the division of the species into 2 phylogeographic clades (coastal and continental). We confirmed that further subdivision of the continental clade occurs in a region where obvious physiogeographic barriers do not exist. We postulate that this small-scale differentiation can be explained by residual patterns from postglacial recolonization routes on either side of the Great Lakes. We suggest that it was maintained through extreme female philopatry due to habitat saturation following the postglacial geographic expansion. Based on our results, we propose that a combination of several molecular markers can be more useful in defining population units for conservation and management decisions than biparentally inherited microsatellites.

Demographic and phylogeographic histories of two venomous North American snakes of the genus Agkistrodon

Many studies have revealed that lineages currently inhabiting formerly glaciated areas were pushed into southern glacial refugia and have expanded into their modern range since the last glacial maximum. There have been few studies that compare the effects of glacial cycles on lineage diversification and historical demography in closely related species with overlapping ranges. In this study we compare phylogeographic structure, historical demography, and approximate lineage age in two closely related and broadly co-occurring venomous snakes in eastern North America, the cottonmouth ( Agkistrodon piscivorus) and copperhead ( A. contortrix) using sequences from the mtDNA gene cytochrome b. We inferred three geographic lineages of A. contortrix and two of A. piscivorus with no common geographic or temporal pattern of lineage diversification identified for these species. Lineage diversification occurred in the Late Pliocene for A. piscivorus (∼2.5 mya) and in the Early Pleistocene for A. contortrix (∼1.5 mya). Demographic estimates revealed population expansion following the last glacial maximum (∼20,000 years ago) in two lineages of A. contortrix (the Central clade and Eastern clade) and one lineage of A. piscivorus (the Continental clade). The Florida clade of A. piscivorus is the only lineage for which constant population size through time was inferred, possibly due to stable populations persisting in areas unaffected by glacial advances. Our data suggest that unique habitat preferences may have shaped both the phylogeographic and demographic histories of each species.

Discovery of African roots for the Mesoamerican Chiapas catfish, Lacantunia enigmatica, requires an ancient intercontinental passage

ABSTRACT Mesoamerica is famous for its complex biota assembled from diverse sources. The recent discovery of a highly distinct freshwater catfish, Lacantunia enigmatica (Lacantuniidae), in Chiapas, Mexico, added an unresolved taxon to this biogeographic puzzle. Morphology has not resolved the relationships of Lacantunia among the >3000 species of Siluriformes. We added Lacantunia to an expanding phylogenetic study of family-level taxa of living catfishes using >3.6 kilobases of nuclear DNA. We find that Lacantunia is derived from within a multi–family clade of African freshwater catfishes. Without living or fossil intermediates marking a wider lacantuniid distribution, this is an extraordinary case of biogeographic disjunction. Continental clades distributed in the New and Old World tropics are often explained by vicariance of Gondwanan ancestors of deep Mesozoic age. However, our fossil-calibrated, relaxed-clock molecular analyses estimate lacantuniid divergence between 75 to 94 mya, after separation of ...

A phylogenetic analysis of the major groups of catfishes (Teleostei: Siluriformes) using rag1 and rag2 nuclear gene sequences

Higher-level relationships among catfishes were investigated by parsimony, maximum likelihood and Bayesian analyses of two nuclear genes across 110 catfish species representing 36 of 37 families and Conorhynchos (family incertae sedis). Analysis of 3660 aligned base pairs from the rag1 and rag2 genes confirms monophyly of Siluriformes, of most siluriform families and of a number of multifamily groups, some recognized, some novel. South American Loricarioidei are recovered as the sistergroup to other catfishes which are divided into Diplomystidae and Siluroidei. This result contrasts with the prevailing hypothesis that Diplomystidae is the sister to all other catfishes. Monophyly of Siluroidei is supported by rag data including a unique three-codon deletion from rag1. Deep within Siluroidei are 12 large, strongly supported groups with poorly resolved interrelationships. Five are single families: Cetopsidae, Plotosidae, Chacidae, Siluridae and Pangasiidae. Four others are monophyletic taxa ranked here as superfamilies: Clarioidea (Clariidae, Heteropneustidae), Arioidea (Ariidae, Anchariidae), Pimelodoidea (Pimelodidae, Pseudopimelodidae, Heptapteridae, Conorhynchos), Ictaluroidea (Ictaluridae, Cranoglanididae). South American Doradoidea (Doradidae, Auchenipteridae) and Aspredinidae are a sistergroup pair. Sisoroidea (without Aspredinidae), Ailia+Laides, Horabagridae, and Bagridae (without Rita) form a large, predominantly Asian clade, "Big Asia." Mochokidae, Malapteruridae, Amphiliidae, Claroteidae, and African schilbids are united as a species-rich African clade, "Big Africa." The three large continental clades, "Big Asia," "Big Africa" and Neotropical Loricarioidei suggest a prevalence of intracontinental diversification of catfishes. South America is the home of the Gymnotiformes, putative sistergroup of catfishes, plus two of the deepest siluriform clades, Loricarioidei and Diplomystidae, thus suggesting an ancient siluriform presence if not origin there. The rag phylogeny does not identify any African-South American catfish clade. The well-known African-Asian relationships within families Clariidae and Bagridae are confirmed, as is the recently found North American-Asian relationship between Ictaluridae and Cranoglanididae.

Cryptic Neogene vicariance and Quaternary dispersal of the red‐spotted toad (Bufo punctatus): insights on the evolution of North American warm desert biotas

We define the geographical distributions of mitochondrial DNA (mtDNA) lineages embedded within a broadly distributed, arid-dwelling toad, Bufo punctatus. These patterns were evaluated as they relate to hypothesized vicariant events leading to the formation of desert biotas within western North America. We assessed mtDNA sequence variation among 191 samples from 82 sites located throughout much of the species' range. Parsimony-based haplotype networks of major identified lineages were used in nested clade analysis (NCA) to further elucidate and evaluate shallow phylogeographic patterns potentially associated with Quaternary (Pleistocene-Holocene) vicariance and dispersal. Phylogenetic analyses provided strong support for three monophyletic lineages (clades) within B. punctatus. The geographical distributions of the clades showed little overlap and corresponded to the general boundaries of the Peninsular Desert, and two continental desert regions, Eastern (Chihuahuan Desert-Colorado Plateau) and Western (Mojave-Sonoran deserts), geographically separated along the Rocky Mountains and Sierra Madre Occidental. The observed divergence levels and congruence with postulated events in earth history implicate a late Neogene (latest Miocene-early Pliocene) time frame for separation of the major mtDNA lineages. Evaluation of nucleotide and haplotype diversity and interpretations from NCA reveal that populations on the Colorado Plateau resulted from a recent, likely post-Pleistocene, range expansion from the Chihuahuan Desert. Dispersal across historical barriers separating major continental clades appear to be recent, resulting in secondary contacts in at least two areas. Given the observed contact between major clades, we speculated as to why the observed deep phylogeographic structure has not been eroded during the multiple previous interglacials of the Pleistocene.

Evolutionary diversity and ecology of endemic small mammals of southeastern Alaska with implications for land management planning

The dynamic geological history and naturally fragmented landscapes of southeastern Alaska create an environment with a high potential for endemism. The temperate rainforest of the region regenerates and develops slowly, and old-forest characteristics do not appear until ≥300 years following disturbance. The challenges of managing forest resources are intensified in island archipelagos because of the increased sensitivity of indigenous biota to disturbance and higher rates of extinction, especially among endemic organisms. Early expeditions of the large islands of the Alexander Archipelago (≈1% of all named islands) documented 27 endemic mammalian taxa. More recent studies with modern techniques found that some reputed endemics showed nominal levels of genetic divergence from other conspecific populations, but more divergence existed among several taxa than was reflected in the current taxonomy. Furthermore, the mammal fauna of southeastern Alaska has a nested structure with complex phylogeographic patterns suggesting multiple colonization events. Of eight taxa examined through phylogeographic analyses, five species showed acute genetic variation and divergence in mitochondrial sequences. Four species were comprised of coastal and continental clades (i.e. populations of recent common descent), whereas the fifth species showed a third clade. Conversely, the northern flying squirrel ( Glaucomys sabrinus) and southern red-backed vole ( Clethrionomys gapperi) were represented by relatively shallow divergent lineages. Still, G. sabrinus showed a distinct mitochondrial lineage on 11 islands (Prince of Wales Island complex), which exhibited severely reduced genetic variation. Moreover, flying squirrels in southeastern Alaska are genetically distinct from populations in the Pacific Northwest; as different as each is from the southern flying squirrel ( G. volans). Recent ecological studies of endemic populations of the northern flying squirrel and the southern red-backed vole (reputed old-growth associates) suggest that risk of extirpation in managed landscapes is likely less than was presumed during recent land management planning in the region because: (1) abundant noncommercial forests apparently contribute to breeding populations of northern flying squirrels, which appear to have a more general lifestyle than populations in the Pacific Northwest; and (2) red-backed vole populations may be able to exist in managed young-growth stands that originated from clearcut logging. Still, there are essential questions for both species regarding the influence of annual population fluctuations on habitat distribution and population demography, stand and landscape features that restrict dispersal, and vegetative and structural characteristics of second-growth stands that will sustain breeding populations of both species.

Phylogeography of the dusky shrew, Sorex monticolus (Insectivora, Soricidae): insight into deep and shallow history in northwestern North America

Phylogenetic relationships among the dusky shrew (Sorexmonticolus) and eight related species (S. bairdi, S. bendirii, S. neomexicanus, S.ornatus, S. pacificus, S. palustris, S. sonomae and S.vagrans) were assessed using sequences from the mitochondrial cytochrome b gene (801 bp). Analyses using parsimony and maximum likelihood revealed significant molecular variation not reflected in previous morphological studies of these species. Conversely, three morphologically defined species (S.bairdi, S.neomexicanus and S.pacificus) were poorly differentiated. Sorexornatus and S.vagrans represented basal taxa for a more inclusive group that included: (i) a widespread Continental clade containing S.monticolus (Arizona to Alaska, including S. neomexicanus); (ii) a Coastal clade containing S.monticolus (Oregon to south-east Alaska, including S. bairdi and S. pacificus); (iii) the semiaquatic species (S. bendirii and S. palustris); and (iv) S.sonomae. Additional subdivision was observed within the Continental clade corresponding to populations from the northern and southern Rocky Mountains. Average uncorrected sequence divergence between the Coastal and Continental clades was 5.3% (range 4.5-6.2%), which exceeds many interspecific comparisons within this species complex and within the genus Sorex. Lack of resolution of internal nodes within topologies suggests a deep history of rapid diversification within this group. Late Pleistocene/Holocene glacial perturbations are reflected in the shallow phylogeographic structure within these clades in western North America. Our results suggest also that S. monticolus is not monophyletic under current taxonomic nomenclature. This perspective on phylogeographic history was developed within a growing comparative framework for other organisms in western North America.