Comparative phylogeography of unglaciated eastern North America

Regional phylogeographical studies involving co-distributed animal and plant species have been conducted for several areas, most notably for Europe and the Pacific Northwest of North America. Until recently, phylogeographical studies in unglaciated eastern North America have been largely limited to animals. As more studies emerge for diverse lineages (including plants), it seems timely to assess the phylogeography across this region: (i) comparing and contrasting the patterns seen in plants and animals; (ii) assessing the extent of pseudocongruence; and (iii) discussing the potential applications of regional phylogeography to issues in ecology, such as response to climatic change. Unglaciated eastern North America is a large, geologically and topographically complex area with the species examined having diverse distributions. Nonetheless, some recurrent patterns emerge: (i) maritime - Atlantic vs. Gulf Coast; (ii) Apalachicola River discontinuity; (iii) Tombigbee River discontinuity; (iv) the Appalachian Mountain discontinuity; (v) the Mississippi River discontinuity; and (vi) the Apalachicola River and Mississippi River discontinuities. Although initially documented in animals, most of these patterns are also apparent in plants, providing support for phylogeographical generalizations. These patterns may generally be attributable to isolation and differentiation during Pleistocene glaciation, but in some cases may be older (Pliocene). Molecular studies sometimes agree with longstanding hypotheses of glacial refugia, but also suggest additional possible refugia, such as the southern Appalachian Mountains and areas close to the Laurentide Ice Sheet. Many species exhibit distinct patterns that reflect the unique, rather than the shared, aspects of species' phylogeographical histories. Furthermore, similar modern phylogeographical patterns can result from different underlying causal factors operating at different times (i.e. pseudocongruence). One underemphasized component of pseudocongruence may result from the efforts of researchers to categorize patterns visually - similar patterns may, in fact, not fully coincide, and inferring agreement may obscure the actual patterns and lead to erroneous conclusions. Our modelling analyses indicate no clear spatial patterning and support the hypothesis that phylogeographical structure in diverse temperate taxa is complex and was not shaped by just a few barriers.     

报春花属的保育遗传学及亲缘地理学研究进展

现存物种的分布格局、遗传结构是当前因素和历史因素共同作用的结果。人类的过度开发、全球变暖等当前因素造成的生境片段化是目前许多报春花属植物濒危的一大原因。该文总结了近年来报春花属内的保育遗传学研究进展,期望以此为更好地保护报春花属植物提供一定的理论基础。应用亲缘地理学研究方法可以弥补古生物学难以研究报春花植物历史成因的不足,因此也总结该方法在报春花属内的研究进展,并初步整理不同地区间的报春花属植物的分化式样,同时期望这些研究成果能为为研究报春花属植物在应对全球气候变化的响应机制方面提供一些参考。     

Statistical phylogeography

While studies of phylogeography and speciation in the past have largely focused on the documentation or detection of significant patterns of population genetic structure, the emerging field of statistical phylogeography aims to infer the history and processes underlying that structure, and to provide objective, rather than ad hoc explanations. Methods for parameter estimation are now commonly used to make inferences about demographic past. Although these approaches are well developed statistically, they typically pay little attention to geographical history. In contrast, methods that seek to reconstruct phylogeographic history are able to consider many alternative geographical scenarios, but are primarily nonstatistical, making inferences about particular biological processes without explicit reference to stochastically derived expectations. We advocate the merging of these two traditions so that statistical phylogeographic methods can provide an accurate representation of the past, consider a diverse array of processes, and yet yield a statistical estimate of that history. We discuss various conceptual issues associated with statistical phylogeographic inferences, considering especially the stochasticity of population genetic processes and assessing the confidence of phylogeographic conclusions. To this end, we present some empirical examples that utilize a statistical phylogeographic approach, and then by contrasting results from a coalescent-based approach to those from Templeton's nested cladistic analysis (NCA), we illustrate the importance of assessing error. Because NCA does not assess error in its inferences about historical processes or contemporary gene flow, we performed a small-scale study using simulated data to examine how our conclusions might be affected by such unconsidered errors. NCA did not identify the processes used to simulate the data, confusing among deterministic processes and the stochastic sorting of gene lineages. There is as yet insufficient justification of NCA's ability to accurately infer or distinguish among alternative processes. We close with a discussion of some unresolved problems of current statistical phylogeographic methods to propose areas in need of future development.     

Re-examination of a proposed case of stasipatric speciation: phylogeography of the Australian morabine grasshoppers (Vandiemenella viatica species group)

Karyotypic differences have been used for delimiting populations or species, although whether these mutations provide strong barriers to gene flow between populations and promote speciation remains contentious. In this study, we assessed whether 11 chromosomal races of Australian morabine grasshoppers ( Vandiemenella viatica species group) represent genetically distinct populations by analyses of cytological and allozyme (35 loci) data and DNA sequences of the elongation factor-1 alpha ( EF -1α), anonymous Mvia11 , and mitochondrial cytochrome c oxidase subunit I ( COI ) loci. While the Vandiemenella chromosomal taxa generally represent genetically distinct units, a substantial portion of the total genetic variation in our samples was not explained by the chromosomal variation. Mantel tests indicated that Vandiemenella populations were spatially structured and have maintained gene flow at a local scale within each of the taxa. The group was subdivided into 13 genetic clusters; four chromosomal taxa comprised single exclusive clusters, while others comprised more than one cluster or clusters shared with other taxa. Boundaries of these cryptic population subdivisions correspond with several biogeographical barriers, such as straits, gulfs, the Murray River, and an ancient mega-lake, Lake Bungunnia. The viatica species group was previously proposed to have diversified without major geographical separation based on the stasipatric speciation model; however, the present study suggests the involvement of allopatric fragmentation. Given extensive nonmonophyly of chromosomal taxa and incomplete barriers to gene flow among taxa, all Vandiemenella chromosomal taxa and genetically distinct populations within chromosomal taxa, except Vandiemenella pichirichi , should be regarded as populations of one species: Vandiemenella viatica .     

The phylogeography of dusky dolphins (Lagenorhynchus obscurus): a critical examination of network methods and rooting procedures

We investigated the phylogeography and evolutionary history of dusky dolphins (Lagenorhynchus obscurus) using DNA sequences of the full mitochondrial cytochrome b gene in 124 individuals from the putative stocks off Peru, Argentina and Southwest Africa. While genetic differentiation within oceans is surprisingly low, there is no evidence for recent female gene flow between Atlantic and Pacific waters. Highest genetic variability in terms of sequence divergence and number of haplotypes is found in the Atlantic. Our analyses also indicate that the eastern South Pacific dusky dolphins stock should be considered a separate management unit. Given the high level of mortality experienced by the Peruvian dusky dolphin in local fishery activities, these findings have important implications for an objective management of the species. Furthermore, we analysed our mitochondrial sequence data with several widely used network estimation and rooting methods. The resulting intraspecific gene genealogies and rooting inferences exhibited substantial differences, underlying the limitations of some algorithms. Given that scientific hypotheses and management decisions depend strongly on inferred tree or network topologies, there is a clear need for a systematic comparative analysis of available methods. Finally, the present study indicates that (i) the dusky and the Pacific white-sided dolphins are sister species and (ii) not only the Westwind Drift hypothesis but also other models of dispersion are compatible with the current geographical distribution of dusky dolphins.     

Mitochondrial haplotype variation and phylogeography of Iberian brown trout populations

The biogeographical distribution of brown trout mitochondrial DNA haplotypes throughout the Iberian Peninsula was established by polymerase chain reaction-restriction fragment polymorphism analysis. The study of 507 specimens from 58 localities representing eight widely separated Atlantic-slope (north and west Iberian coasts) and six Mediterranean drainage systems served to identify five main groups of mitochondrial haplotypes: (i) haplotypes corresponding to non-native, hatchery-reared brown trout that were widely distributed but also found in wild populations of northern Spain (Cantabrian slope); (ii) a widespread Atlantic haplotype group; (iii) a haplotype restricted to the Duero Basin; (iv) a haplotype shown by southern Iberian populations; and (v) a Mediterranean haplotype. The Iberian distribution of these haplotypes reflects both the current fishery management policy of introducing non-native brown trout, and Messinian palaeobiogeography. Our findings complement and extend previous allozyme studies on Iberian brown trout and improve present knowledge of glacial refugia and postglacial movement of brown trout lineages.     

Molecular phylogeography of the Amazonian Chagas disease vectors Rhodnius prolixus and R. robustus

The phylogeographical structure of the closely related species Rhodnius prolixus and R. robustus is presented based on a 663-base pair (bp) fragment of the mitochondrial cytochrome b gene. Twenty haplotypes were recovered from 84 samples examined, representing 26 populations from seven Latin American countries. The resulting phylogenetic tree is composed of five major reciprocally monophyletic clades, one representing R. prolixus and four representing R. robustus. While R. prolixus is a very homogeneous assemblage, R. robustus has deeper clades and is paraphyletic, with the clade comprising R. robustus from Venezuela (Orinoco region) more closely related to the R. prolixus clade than to the other R. robustus populations from the Amazon region. The R. robustus paraphyly was supported further by the analysis of a nuclear gene (D2 region of the 28S RNA) for a subset of specimens. The data support the view that R. robustus represents a species complex. Levels of sequence divergence between clades within each region are compatible with a Pleistocene origin. Nucleotide diversity (pi) for all R. prolixus populations was extremely low (0.0008), suggesting that this species went through a recent bottleneck, and was subsequently dispersed by man.     

Mitochondrial phylogeography of the Woodmouse (Apodemus sylvaticus) in the Western Palearctic region

We sequenced 965 base pairs of the mitochondrial DNA cytochrome b from 102 woodmice (Apodemus sylvaticus) collected from 40 European localities. The aims of the study were to answer the following questions. (i) Did the Mediterranean peninsulas play a role as refuge for woodmice? (ii) Is genetic variability of A. sylvaticus higher in the Mediterranean region compared with northern Europe? (iii) Are the patterns of the postglacial colonization of Europe by woodmice similar to those presently recognized for other European species? The results provide a clear picture of the impact of the Quaternary glaciations on the genetic and geographical structure of the woodmouse. Our analyses indicate a higher genetic variability of woodmice in the Mediterranean peninsulas compared to northern Europe, suggesting a role of the former as refuge regions for this small mammal. An original pattern of postglacial colonization is proposed where the Iberian and southern France refuge populations colonized almost all European regions. The Sicilian population appears to be very differentiated and highly variable. This emphasizes the importance of this island as a ‘hot spot’ for the intraspecific genetic diversity of the woodmouse. Finally, woodmice in North Africa originated from southwestern Europe, most probably as a result of a recent anthropogenic introduction.     

Recognizing the temporal distinctions between landscape genetics and phylogeography

The steadily advancing fields of landscape genetics and phylogeography share many goals. However, there are some very distinct differences between these two disciplines, including the kinds of data and analyses commonly used, the timescale over which these data are informative, and the hypotheses the data are used to examine. Recently, a number of studies appear to have confused or synonymized phylogeography and landscape genetics. The difference is not merely semantic; understanding the distinctions between these fields is important for ensuring that researchers are aware of the temporal scale over which their data are informative.     

Comparative phylogeography in marginal seas of the northwestern Pacific

The maturation of marine phylogeography depends on integration of comparative information across different regions globally. The northwestern Pacific, characterized by unique tectonic setting, however, is still underrepresented. This study seeks to highlight its phylogeographical history based on the available population data, focusing on three seas: the East China Sea (ECS), the South China Sea (SCS) and the Sea of Japan (SOJ). We first conducted a literature survey to evaluate current research efforts and then reanalysed the population structure, historical demography and genealogy for two selections of studies (namely ‘the ECS category’ and ‘the multiple‐sea category’) to elucidate the evolutionary processes within and across the seas, respectively. For the ECS category, the meta‐analyses revealed most studies displayed a shallow phylogeny, indicating a single origin from the sea. Significant population structure was commonplace, particularly in molluck and crustacean studies, with proportions of 89% and 80%, respectively. Nearly all studies selected showed signals of population expansion: the times estimated were closely linked to a period of ~120–140 Kya rather than the last glacial maximum. For the latter category, divergent intraspecific lineages appeared among seas and overlapped in the adjacent regions, a pattern implying each sea had served as an independent refugium during glaciations. The genetic splits, however, were estimated to arise from separate events dating from late Miocene to middle Pleistocene. As phylogeography is still in its infancy in the region, more effort is needed to test and complement the general rules abstracted here. Finally, challenges and prospects were discussed to accelerate further research.     

Comparative phylogeography of salmonid fishes (Salmonidae) reveals late to post-Pleistocene exchange between three now-disjunct river basins in Siberia

Abstract. We use a comparative phylogeographical framework to evaluate the hypothesis of hydrological exchange during the Pleistocene among the now disjunct Lena, Amur, and Enisei basins in Siberia, and to provide evidence on the causal mechanism of their present day faunal dissimilarities. Approximately 600 bases of the mitochondrial control region were sequenced in five distinct lineages among three genera of salmonid fishes, Hucho, Brachymystax and Thymallus. All three basins were fixed for divergent (2–5.4%) lineages of Thymallus whereas a single shared haplotype was present in all three basins for Hucho taimen ( Pallas, 1773 ) and one shared haplotype between the Lena and Amur basins out of a total of five for blunt‐snouted and one out of five for sharp‐snouted Brachymystax lenok ( Pallas, 1773 ). For both blunt‐ and sharp‐snouted lenok the haplotypes found within each basin did not form clades, so no relationship between genotypes and geographical occurrence was found. Our data support relatively recent hydrological mixing of the major river drainage systems in eastern and far‐eastern Siberia, congruent with the hypothesis of large‐scale palaeo‐hydrological exchange stemming from glacial advance, retreat and melting during Pleistocene climate fluctuations. Furthermore, these results in conjunction with a comparison of overall faunal composition suggest that environmental differences rather than historical contingency may be responsible for the faunal dissimilarities of the Amur, Lena, and Enisei river basins.     

Relationships of Palearctic and Nearctic 'glacial relict' Myoxocephalus sculpins from mitochondrial DNA data

The relationships among Myoxocephalus quadricornis complex fish from Arctic coastal waters and from 'glacial relict' populations in Nearctic and Palearctic postglacial lakes were assessed using mtDNA sequence data (1978 bp). A principal phylogeographical split separated the North American continental deepwater sculpin (M. q. thompsonii) from a lineage of the Arctic marine and North European landlocked populations of the fourhorn sculpin (M. q. quadricornis). The North American continental invasion took place several glaciation cycles ago in the Early-to-Middle Pleistocene (0.9% sequence divergence); the divergence of the European and Arctic populations was somewhat later (0.5% divergence). The Nearctic-Palearctic freshwater vicariance in Myoxocephalus, however, appears clearly younger than in similarly distributed 'glacial relict' crustacean taxa; the phylogeographical structure is more similar to that in other northern Holarctic freshwater fish complexes.     

Comparative phylogeography and the history of endemic vertebrates in the Wet Tropics rainforests of Australia

We examine the effects of historical climate change on vertebrate differentiation in tropical rainforest by comparing phylogeographic patterns in six species of widespread rainforest-restricted herpetofauna from throughout the Wet Tropics of Australia. Qualitative and quantitative comparisons of phylogeographic structure reveal strikingly similar patterns of pre-Pleistocene vicariant population differentiation on either side of a previously identified biogeographic break (variously referred to as the Black Mountain Barrier or Corridor; BMC). While divergence across the BMC antedates the Pleistocene, the impact of Quaternary climate change is apparent in populations on either side of the BMC. Consistent with palaeoclimatological reconstructions for the region, the distribution and degree of mtDNA diversity suggests that populations were fragmented and reduced to multiple refugia during Pleistocene glacial periods, with expansion following Holocene rainforest recovery. This pattern is repeated on both sides of the BMC, but substantial differences in the amount and distribution of mtDNA diversity within species indicate the importance of species-specific ecological characteristics. The historical processes of extinction and (re)colonization revealed by the comparative phylogeographic analysis of mtDNA sequences substantiate earlier suggestions that current regional patterns of species distribution and diversity in the Wet Tropics are largely determined by local extinctions and subsequent recolonization driven by Quaternary climate changes.     

Mitochondrial DNA phylogeography of Glyptothorax fokiensis and Glyptothorax hainanensis in Asia

Whole mitochondrial DNA cytochrome b sequences in 62 fish from 13 locations in Southeast China identified two major clades corresponding to two allopatric taxa, Glyptothorax fokiensis fokiensis and Glyptothorax fokiensis hainanensis . Reciprocal monophyly and a molecular clock separation between these two taxa of 2·3 million years indicate these taxa should be elevated to species. Mismatch distributions and Fu's F _S statistic suggest that both G. fokiensis and G. hainanensis have experienced recent population expansions. Analysis of molecular variance indicates that most of the genetic variation resides among populations within both species, with Φ _ST= 0·645 for G. fokiensis and 0·801 for G. hainanensis , suggesting restricted gene flow among populations. Significant correlations between the geographic and the genetic distances provide support for the importance of geographic isolations between populations. Nested clade analysis also confirms low levels of genetic exchanges between the two major groups and between populations within each group. The phylogeographical pattern among populations of Glyptothorax in East Asia can be attributed to historical fragmentations, demographic expansions and occasional long-distance dispersals stimulated by tectonic activity and Ice Age climate changes.     

Separating historic events from recurrent processes in cryptic species: phylogeography of mud snails (Hydrobia spp.)

The present study combines methods that were designed to infer intraspecific relationships (e.g. nested-clade analysis (NCA), mismatch distributions and maximum likelihood gene flow analysis) to analyse historic events and recurrent processes in the cryptic mud snail species Hydrobia acuta and H. glyca. Specifically, we test the proposed allopatry of cryptic species and whether the peculiar range-subdivision of the putative subspecies H. a. acuta and H. a. neglecta is a result of long-distance dispersal or continuous range expansion. The NCA indicates a past fragmentation of the two H. acuta subspecies as well as past fragmentations within H. glyca. Gene-flow analyses show extensive gene flow in an E-W direction (towards the Atlantic) in the Mediterranean H. a. acuta, generally low gene flow in a W-E direction in the Atlantic H. a. neglecta and complex gene-flow pattern in a N-S but also in a S-N direction (against the Gulf Stream) in H. glyca. Based on these data and supportive ecological and oceanographical data, we hypothesize that the separation of the two H. acuta subspecies was not caused by long-distance dispersal but by a range shift and/or range expansion of the closely related competitor H. glyca as a result of an interglacial warming with a subsequent range shift in H. acuta. Moreover, our data do not show evidence for a long-term, stable sympatry of Hydrobia species, supporting the concept of allopatric relationships within cryptic radiations. NCA and gene-flow analyses indicate that the only sympatric population found in our study is the result of a recent dispersal event from the nearby Mediterranean. It is assumed that allopatric relationships in ephemeral Hydrobia populations constitute an evolutionary advantage relative to competition, recruitment and re-establishment of habitats. Mechanisms that could be of relevance for maintaining allopatry are discussed.     

Comparative phylogeography of two co‐distributed but ecologically distinct rainbowfishes of far‐northern Australia

Aim

To test the influence of historical and contemporary environment in shaping the genetic diversity of freshwater fauna we contrast genetic structure in two co‐distributed, but ecologically distinct, rainbowfish; a habitat generalist (Melanotaenia splendida) and a habitat specialist (M. trifasciata).

Location

Fishes were sampled from far northern Australia (Queensland and Northern Territory).

Methods

We used sequence data from one mitochondrial gene and one nuclear gene to investigate patterns of genetic diversity in M. splendida and M. trifasciata to determine how differences in habitat preference and historical changes in drainage boundaries affected patterns of connectivity.

Results

Melanotaenia splendida showed high levels of genetic diversity and little population structure across its range. In contrast, M. trifasciata showed high levels of population structure. Whereas phylogeographic patterns differed, both species showed a strong relationship between geographical distance and genetic differentiation between populations. Melanotaenia splendida showed a shallower relationship with geographical distance, and genetic differentiation was best explained by stream length and a lower scaled ocean distance (11.98 times coast length). For M. trifasciata, genetic differentiation was best explained by overwater distance between catchments and ocean distance scaled at 1.16 × 10⁶ times coast length.

Main conclusions

Connectivity of freshwater populations inhabiting regions periodically interconnected during glacial periods appears to have been affected by ecological differences between species. Species‐specific differences are epitomized here by the contrast between co‐distributed congeners with different habitat requirements: for the habitat generalist, M. splendida, there was evidence for greater historical genetic connectivity with oceans as a weaker barrier to gene exchange in contrast with the habitat specialist, M. trifasciata.