Comparative phylogeography of West African amphibians and reptiles

Comparative phylogeographic studies often support shared divergence times for co-distributed species with similar life histories and habitat specializations. During the late Holocene, West Africa experienced aridification and the turnover of rain forest habitats into savannas. These fragmented rain forests harbor impressive numbers of endemic and threatened species. In this setting, populations of co-distributed rain forest species are expected to have diverged simultaneously, whereas divergence events for species adapted to savanna and forest-edge habitats should be absent or idiosyncratic. We conducted a Bayesian analysis of shared evolutionary events to test models of population divergence for 20 species of anurans (frogs) and squamates (lizards and snakes) that are distributed across the Dahomey Gap, a climate change-induced savanna barrier responsible for fragmenting previously contiguous rain forests of Ghana into two regions: the Togo-Volta Hills and the Southwestern Forests. A model of asynchronous diversification is supported for anurans and squamates, suggesting that drivers of diversification are not specifically related to ecological and life history associations with habitat types. Instead, the wide variability of genetic divergence histories exhibited by these species suggests that biodiversity in this region has been shaped by diversification events that extend beyond the Holocene. Comparisons of the genealogical divergence index, a measure of the genetic divergence between populations due to the combined effects of genetic isolation and gene flow, illustrate that these populations represent a broad sampling of the speciation continuum.     

Cryptic vicariance in Gulf of California fishes parallels vicariant patterns found in Baja California mammals and reptiles

Comparisons across multiple taxa can often clarify the histories of biogeographic regions. In particular, historic barriers to movement should have affected multiple species and, thus, result in a pattern of concordant intraspecific genetic divisions among species. A striking example of such comparative phylogeography is the recent observation that populations of many small mammals and reptiles living on the Baja California peninsula have a large genetic break between northern and southern peninsular populations. In the present study, I demonstrate that five species of near-shore fishes living on the Baja coastline of the Gulf of California share this genetic pattern. The simplest explanation for this concordant genetic division within both terrestrial and marine vertebrates is that the Baja Peninsula was fragmented by a Plio-Pleistocene marine seaway and that this seaway posed a substantial barrier to movement for near-shore fishes. For some fish species, the signal of this vicariance in mtDNA has been eroded by gene flow and is not evident with classic, equilibrium measures of population structure. Yet, significant divisions are apparent in coalescent analyses that jointly estimate divergence with gene flow. The genetic divisions within Gulf of California fishes also coincide with recognized biogeographic regions based on fish community composition and several environmental factors. It is likely that adaptation to regional environments and present-day oceanographic circulation limit gene exchange between biogeographic regions and help maintain evidence of past vicariance.     

Cryptic lineages and Pleistocene population expansion in a Brazilian Cerrado frog

Diversification of South American species endemic to open habitats has been attributed to both Tertiary events and Pleistocene climatic fluctuations. Nonetheless, phylogeographical studies of taxa in these regions are few, precluding generalizations about the timing and processes leading to differentiation and speciation. We inferred population structure of Hypsiboas albopunctatus, a frog widely distributed in the Brazilian Cerrado. Three geographically distinct lineages were recovered in our phylogeny. The Chapada dos Guimarães (CG) clade was the first to diverge from other populations and contains multiple haplotypes from a single population in western Cerrado, probably representing a cryptic species. The southeast clade (SE) includes populations along the southeastern limit of the range within the historical distribution of the Brazilian Atlantic forest. Finally, the Central Cerrado (CC) group includes haplotypes from the interior of Brazil that are paraphyletic relative to the SE clade. Analyses of historical demography indicate significant population expansion in the CC and SE populations, likely associated with colonization of newly formed open habitats. The divergence of populations in the CG clade occurred in the late Miocene, concordant with the uplift of the central Brazilian plateau. Divergence of the SE clade from the CC occurred during the mid‐Pleistocene. Thus, both Tertiary geological events and Pleistocene climatic fluctuations promoted divergences among lineages. Our study reveals a complex history of diversification in the Cerrado, a morphoclimatic domain highly threatened because of anthropogenic habitat alteration. We identified surprisingly deep divergences in a widely distributed frog, indicating that the Cerrado is not a barrier‐free habitat and that its diversity is likely underestimated.     

Not just vicariance: phylogeography of a Sonoran Desert euphorb indicates a major role of range expansion along the Baja peninsula

To examine the generality of population-level impacts of ancient vicariance identified for numerous arid-adapted animal taxa along the Baja peninsula, we tested phylogeographical hypotheses in a similarly distributed desert plant, Euphorbia lomelii (Euphorbiaceae). In light of fossil data indicating marked changes in the distributions of Baja floristic assemblages throughout the Holocene and earlier, we also examined evidence for range expansion over more recent temporal scales. Two classes of complementary analytical approaches — hypothesis-testing and hypothesis-generating — were used to exploit phylogeographical signal from chloroplast DNA sequence data and genotypic data from six codominant nuclear intron markers. Sequence data are consistent with a scenario of mid-peninsular vicariance originating c. 1 million years ago (Ma). Alternative vicariance scenarios representing earlier splitting events inferred for some animals (e.g. Isthmus of La Paz inundation, c. 3 Ma; Sea of Cortez formation, c. 5 Ma) were rejected. Nested clade phylo-geographical analysis corroborated coalescent simulation-based inferences. Nuclear markers broadened the temporal spectrum over which phylogeographical scenarios could be addressed, and provided strong evidence for recent range expansions along the north–south axis of the Baja peninsula. In contrast to previous plant studies in this region, however, the expansions do not appear to have been in a strictly northward direction. These findings contribute to a growing appreciation of the complexity of organismal responses to past climatic and geological changes — even when taxa have evolved in the same landscape context.     

The phylogeny,phylogeography, and diversification history of the westernmost Asian cobra (Serpentes: Elapidae: Naja oxiana) in the Trans‐Caspian region

We conducted a comprehensive analysis of the phylogenetic, phylogeographic, and demographic relationships of Caspian cobra (Naja oxiana; Eichwald, 1831) populations based on a concatenated dataset of two mtDNA genes (cyt b and ND4) across the species'' range in Iran, Afghanistan, and Turkmenistan, along with other members of Asian cobras (i.e., subgenus Naja Laurenti, 1768). Our results robustly supported that the Asiatic Naja are monophyletic, as previously suggested by other studies. Furthermore, N. kaouthia and N. sagittifera were recovered as sister taxa to each other, and in turn sister clades to N. oxiana. Our results also highlighted the existence of a single major evolutionary lineage for populations of N. oxiana in the Trans‐Caspian region, suggesting a rapid expansion of this cobra from eastern to western Asia, coupled with a rapid range expansion from east of Iran toward the northeast. However, across the Iranian range of N. oxiana, subdivision of populations was not supported, and thus, a single evolutionary significant unit is proposed for inclusion in future conservation plans in this region.     

Phylogeography of Diadophis punctatus: extensive lineage diversity and repeated patterns of historical demography in a trans-continental snake

Dynamic climatic oscillations during the Pleistocene had profound effects on the distributions of species across North America. Although the role of historical climate change on speciation remains controversial, the impact on genetic variation within species has been well documented. We examined mtDNA sequences from the cytochrome b gene (1117 bp) and a portion of the NADH-4 gene (659 bp) for 286 individuals of Diadophis punctatus to infer phylogeographic patterns and population structure and to examine historical demographic patterns in both glaciated and unglaciated regions of North America. We inferred 14 lineages that replace each other geographically across the United States. Several of these lineages appear to be confined to specific habitats (floodplains, grasslands, montane environments) and traverse previously identified genetic barriers for terrestrial vertebrates including the Mississippi and Apalachicola Rivers, the Appalachian Mountains, and the western continental divide. We also observed overlapping ranges between some haplotype groups and several instances of secondary contact associated with ecological transition zones in eastern South Carolina, southern Oklahoma and central California. Within the US, diversification began during the late Miocene and continued into the mid-Pleistocene, suggesting these lineages pre-dated the last glacial maximum. Coalescent and non-coalescent demographic analyses indicate that independent lineages currently occupying previously glaciated or unsuitable areas in eastern, central and western US underwent post-glacial population expansion likely from southern refugia during the late Pleistocene/early Holocene. Conversely, southern lineages display patterns consistent with long-term population stability. Such long-term persistence of genetic structure may be due to the competitive effects between lineages or ecosystem stability in more southern latitudes.     

Colonization, population expansion, and lineage turnover: phylogeography of Mesoamerican characiform fish

We present a phylogeographical analysis of four genera of Mesoamerican primary freshwater fish ( Brycon , Bryconamericus , Eretmobrycon , and Cyphocharax ). Three hundred and thirty-nine individuals were genotyped into one of 31 operational taxonomic units (OTUs) based on the nucleotide sequence of their mitochondrial ATPase 6 & 8 genes (842–839 bp). Contrary to inference based on the species-level taxonomy of these genera, molecular data identified only a single case of sympatry between closely related OTUs, despite extensive parapatry. Polytomies dominate the mtDNA-based phylogenies and demonstrate multiple, noncontemporaneous waves of rapid expansion across Mesoamerica from South American sources. Analyses based on genetic distances observed among congeneric species of Mesoamerican primary freshwater fishes in comparison to divergence between transisthmian marine fishes permit the strong inference that the Pliocene rise of the Panama land bridge provided the first opportunity for the colonization of Mesoamerica by Characiform fishes. We develop a priority-effect model, based on the assumption that genetically closely related OTUs share similar ecological niches, to reconcile the general lack of contemporary sympatry between closely related OTUs with the substantial historical connectivity among Mesoamerican drainages demonstrated by the rapid expansion of Brycon , Bryconamericus , and Cyphocharax . Finally, in most cases, we infer that the westerly limits of freshwater fish distributions in Mesoamerica are more consistent with being defined by ecological factors rather than by dispersal limitation.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 235–255.     

A species assemblage approach to comparative phylogeography of birds in southern Australia

We present a novel approach to investigating the divergence history of biomes and their component species using single-locus data prior to investing in multilocus data. We use coalescent-based hierarchical approximate Bayesian computation (HABC) methods (MsBayes) to estimate the number and timing of discrete divergences across a putative barrier and to assign species to their appropriate period of co-divergence. We then apply a coalescent-based full Bayesian model of divergence (IMa) to suites of species shown to have simultaneously diverged. The full Bayesian model results in reduced credibility intervals around divergence times and allows other parameters associated with divergence to be summarized across species assemblages. We apply this approach to 10 bird species that are wholly or patchily discontinuous in semi-arid habitats between Australia's southwest (SW) and southeast (SE) mesic zones. There was substantial support for up to three discrete periods of divergence. HABC indicates that two species wholly restricted to more mesic habitats diverged earliest, between 594,382 and 3,417,699 years ago, three species from semi-arid habitats diverged between 0 and 1,508,049 years ago, and four diverged more recently, between 0 and 396,843 years ago. Eight species were assigned to three periods of co-divergence with confidence. For full Bayesian analyses, we accounted for uncertainty in the two remaining species by analyzing all possible suites of species. Estimates of divergence times from full Bayesian divergence models ranged between 429,105 and 2,006,355; 67,172 and 663,837; and 24,607 and 171,085 for the earliest, middle, and most recent periods of co-divergence, respectively. This single-locus approach uses the power of multitaxa coalescent analyses as an efficient means of generating a foundation for further, targeted research using multilocus and genomic tools applied to an understudied biome.     

The molecular phylogenetics of endangerment: cryptic variation and historical phylogeography of the California tiger salamander, Ambystoma californiense

A primary goal of conservation genetics is the discovery, delimitation and protection of phylogenetic lineages within sensitive or endangered taxa. Given the importance of lineage protection, a combination of phylogeography, historical geology and molecular clock analyses can provide an important historical context for overall species conservation. We present the results of a range-wide survey of genetic variation in the California tiger salamander, Ambystoma californiense, as well as a summary of the past several million years of inundation and isolation of the Great Central Valley and surrounding uplands that constitute its limited range. A combination of population genetic and phylogenetic analyses of mitochondrial DNA variation among 696 samples from 84 populations revealed six well-supported genetic units that are geographically discrete and characterized by nonoverlapping haplotype distributions. Populations from Santa Barbara and Sonoma Counties are particularly well differentiated and geographically isolated from all others. The remaining units in the Southern San Joaquin Valley, Central Coast Range, Central Valley and Bay Area are separated by geological features, ecological zone boundaries, or both. The geological history of the California landscape is consistent with molecular clock evidence suggesting that the Santa Barbara unit has been isolated for at least 0.74-0.92 Myr, and the Sonoma clade is equally ancient. Our work places patterns of genetic differentiation into both temporal- and landscape-level contexts, providing important insights into the conservation genetics of the California tiger salamander.     

Seasonal patterns of nutrient deposition in a Quercus douglasii woodland in central California

The monthly deposition of total nitrogen, phosphorus, potassium, calcium and magnesium via canopy throughfall, and various components of the litterfall was measured for 31 months under mature Quercus douglasii and in the bulk precipitation in the surrounding open grassland. Seasonal patterns of nutrient concentration in leaf litter, throughfall, and precipitation were also measured. Total annual subcanopy deposition exceeded open precipitation deposition by approximately 45–60x for nitrogen, 5–15x for phosphorus, 30–35x for potassium, 25–35x for calcium, and 5–10x for magnesium. Total annual subcanopy deposition was low in comparison to other oak woodland sites reported in the literature. Throughfall and leaf litter were the primary sources of nutrients and thus determined the seasonal peaks of nutrient deposition. The first autumn rains and leaf fall were associated with one peak in nutrient deposition, and throughfall during early spring leaf emergence was associated with a second peak in potassium, magnesium and phosphorus. Non-leaf plant litter (excluding acorns) provided approximately 15–35% of most nutrients, with twigs and bark depositing over 12% of the annual calcium flux in 1987–1988, and flower litter depositing over 8% of the annual nitrogen flux in 1986–1987. Acorns had high concentrations of phosphorus and nitrogen and during the mast season of 1987–1988 they contained a large proportion of the total subcanopy annual flux of these elements. With acorns excluded, total annual nutrient deposition was similar between years, but timing of nutrient deposition differed. Late summer leaf fall associated with drought, variation in precipitation, and variation in deposition of non-leaf parts were associated with seasonal differences in nutrient deposition between years.     

Comparative phylogeography of codistributed aquatic insects in western North America: insights into dispersal and regional patterns of genetic structure

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Molecular systematics and phylogeography of the Plethodon elongatus species group: combining phylogenetic and population genetic methods to investigate species history

Plethodon elongatus and P. stormi (Caudata: Plethodontidae) are Pacific Northwest endemic species which occur in northwestern California and southwestern Oregon. Studies on these salamanders have resulted in differing taxonomic conclusions, but the underlying historical hypotheses, at both inter- and intraspecific levels, have never been examined in a molecular framework. Here, representatives of 81 populations from throughout the range of both taxa are sequenced. Portions of three mitochondrial protein-coding genes (cytochrome b, NADH dehydrogenase subunit 4, and ATPase 6) were sequenced. Four haplotype groups with nonoverlapping geographical ranges were recovered in separate and combined analyses of the data. One clade corresponds to the distribution of P. stormi, while the remaining three comprise P. elongatus. Phylogenetic relationships among haplotype groups differ in separate analyses of the genes but converge on a well-supported topology, with P. elongatus and P. stormi as monophyletic sister taxa, in combined Maximum Parsimony and Maximum Likelihood analyses. Population genetic analyses of mismatch distributions and Tajima's D-statistic are consistent with range expansion for the largest clade within P. elongatus, covering the northern two-thirds of the species range. In contrast, the P. stormi haplotype clade and the P. elongatus clade from the southern third of the species range may have been relatively stable. Morphological boundaries between P. elongatus and P. stormi are largely congruent with mitochondrial DNA breaks and continued treatment as sister taxa is supported. Although mitochondrial DNA haplotype groups may reflect historical separation within P. elongatus, genetic barriers are incongruent with intraspecific patterns of morphological variation.     

Comparative phylogeography of Nearctic and Palearctic fishes

Combining phylogeographic data from mitochondrial DNA (mtDNA) of Nearctic and Palearctic freshwater and anadromous fishes, we used a comparative approach to assess the influence of historical events on evolutionary patterns and processes in regional fish faunas. Specifically, we (i) determined whether regional faunas differentially affected by Pleistocene glaciations show predictable differences in phylogeographic patterns; (ii) evaluated how processes of divergence and speciation have been influenced by such differential responses; and (iii) assessed the general contribution of phylogeographic studies to conservation issues. Comparisons among case studies revealed fundamental differences in phylogeographic patterns among regional faunas. Tree topologies were typically deeper for species from nonglaciated regions compared to northern species, whereas species with partially glaciated ranges were intermediate in their characteristics. Phylogeographic patterns were strikingly similar among southern species, whereas species in glaciated areas showed reduced concordance. The extent and locations of secondary contact among mtDNA lineages varied greatly among northern species, resulting in reduced intraspecific concordance of genetic markers for some northern species. Regression analysis of phylogeographic data for 42 species revealed significant latitudinal shifts in intraspecific genetic diversity. Both relative nucleotide diversity and estimates of evolutionary effective population size showed significant breakpoints matching the median latitude for the southern limit of the Pleistocene glaciations. Similarly, analysis of clade depth of phylogenetically distinct lineages vs. area occupied showed that evolutionary dispersal rates of species from glaciated and nonglaciated regions differed by two orders of magnitude. A negative relationship was also found between sequence divergence among sister species as a function of their median distributional latitude, indicating that recent bursts of speciation events have occurred in deglaciated habitats. Phylogeographic evidence for parallel evolution of sympatric northern species pairs in postglacial times suggested that differentiation of cospecific morphotypes may be driven by ecological release. Altogether, these results demonstrate that comparative phylogeography can be used to evaluate not only phylogeographic patterns but also evolutionary processes. As well as having significant implications for conservation programs, this approach enables new avenues of research for examining the regional, historical, and ecological factors involved in shaping intraspecific genetic diversity.     

Quaternary range and demographic expansion of Liolaemus darwinii (Squamata: Liolaemidae) in the Monte Desert of Central Argentina using Bayesian phylogeography and ecological niche modelling

Until recently, most phylogeographic approaches have been unable to distinguish between demographic and range expansion processes, making it difficult to test for the possibility of range expansion without population growth and vice versa. In this study, we applied a Bayesian phylogeographic approach to reconstruct both demographic and range expansion in the lizard Liolaemus darwinii of the Monte Desert in Central Argentina, during the Late Quaternary. Based on analysis of 14 anonymous nuclear loci and the cytochrome b mitochondrial DNA gene, we detected signals of demographic expansion starting at ~55 ka based on Bayesian Skyline and Skyride Plots. In contrast, Bayesian relaxed models of spatial diffusion suggested that range expansion occurred only between ~95 and 55 ka, and more recently, diffusion rates were very low during demographic expansion. The possibility of population growth without substantial range expansion could account for the shared patterns of demographic expansion during the Last Glacial Maxima (OIS 2 and 4) in fish, small mammals and other lizards of the Monte Desert. We found substantial variation in diffusion rates over time, and very high rates during the range expansion phase, consistent with a rapidly advancing expansion front towards the southeast shown by palaeo‐distribution models. Furthermore, the estimated diffusion rates are congruent with observed dispersal rates of lizards in field conditions and therefore provide additional confidence to the temporal scale of inferred phylogeographic patterns. Our study highlights how the integration of phylogeography with palaeo‐distribution models can shed light on both demographic and range expansion processes and their potential causes.     

A multilocus perspective on refugial isolation and divergence in rainforest skinks (Carlia)

To explore the evolutionary consequences of climate-induced fluctuations in distribution of rainforest habitat we contrasted demographic histories of divergence among three lineages of Australian rainforest endemic skinks. The red-throated rainbow skink, Carlia rubrigularis, consists of morphologically indistinguishable northern and southern mitochondrial DNA (mtDNA) lineages that are partially reproductively isolated at their parapatric boundary. The third lineage (C. rhomboidalis) inhabits rainforests just to the south of C. rubrigularis, has blue, rather than red-throated males, and for mtDNA is more closely related to southern C. rubrigularis than is northern C. rubrigularis. Multigene coalescent analyses supported more recent divergence between morphologically distinct lineages than between morphologically conservative lineages. There was effectively no migration and therefore stronger isolation between southern C. rubrigularis and C. rhomboidalis, and low unidirectional migration between morphologically conservative lineages of C. rubrigularis. We found little or no evidence for strong differences in effective population size, and hence different contributions of genetic drift in the demographic history of the three lineages. Overall the results suggest contrasting responses to long-term fluctuations in rainforest habitats, leading to varying opportunities for speciation.     

Two waves of diversification in mammals and reptiles of Baja California revealed by hierarchical Bayesian analysis

Many species inhabiting the Peninsular Desert of Baja California demonstrate a phylogeographic break at the mid-peninsula, and previous researchers have attributed this shared pattern to a single vicariant event, a mid-peninsular seaway. However, previous studies have not explicitly considered the inherent stochasticity associated with the gene-tree coalescence for species preceding the time of the putative mid-peninsular divergence. We use a Bayesian analysis of a hierarchical model to test for simultaneous vicariance across co-distributed sister lineages sharing a genealogical break at the mid-peninsula. This Bayesian method is advantageous over traditional phylogenetic interpretations of biogeography because it considers the genetic variance associated with the coalescent and mutational processes, as well as the among-lineage demographic differences that affect gene-tree coalescent patterns. Mitochondrial DNA data from six small mammals and six squamate reptiles do not support the perception of a shared vicariant history among lineages exhibiting a north-south divergence at the mid-peninsula, and instead support two events differentially structuring genetic diversity in this region.     

Comparative phylogeography in a genus of coral reef fishes: biogeographic and genetic concordance in the Caribbean

Geographic barriers that limit the movement of individuals between populations may create or maintain phylogenetically discrete lineages. Such barriers are often inferred from geographic surveys of a single mitochondrial marker to identify phylogenetic splits. Mitochondrial DNA, however, has an effective population size one-fourth that of nuclear DNA, which can facilitate the rapid evolution of monophyletic mtDNA lineages in the absence of geographic barriers. The identification of geographic barriers will thus be more robust if barriers are proposed a priori, and tested with multiple independent genetic markers in multiple species. Here, we tested two proposed marine biogeographic breaks located at the Mona Passage in the Caribbean Sea and at the southern end of Exuma Sound in the Bahamas. We sequenced mitochondrial cytochrome b (400 bp) and nuclear rag1 (573 bp) for nine species and colour forms (183 individuals total) within the teleost genus Elacatinus (Gobiidae) that span the proposed breaks. Our results showed that Mona Passage separated mtcyb and rag1 lineages, with no genetic exchange between populations separated by just 23 km. However, the Central Bahamas barrier was only weakly supported by our data. Importantly, neither barrier coincided with deep genetic splits. This suggests that these two barriers did not initially isolate regional populations, but instead disrupt ongoing gene flow between regions. Our inferred relationships further suggested a division of the Caribbean region into northwestern and southeastern regions, a pattern reflected by some freshwater and terrestrial vertebrates. Our results, coupled with genetic and demographic data from other reef fishes and corals, provide robust support for the Mona Passage as a long-term biogeographic barrier for Caribbean animals.     

Post‐glacial population expansion of the Monterey Spanish mackerel Scomberomorus concolor in the Gulf of California

The level of genetic homogeneity and demographic history of the Monterey Spanish mackerel Scomberomorus concolor was assessed by analyses using sequences of the mitochondrial (mt)DNA‐control region of samples from the two oceanographic regions of the Gulf of California in order to define the stock structure for this exploited vulnerable species. The data were consistent with a single homogeneous population and revealed the hallmark of fluctuations in population size; these fluctuations appear to have occurred during glacial events of the middle to late Pleistocene, which may in turn be related to the colonization and expansion of S. concolor populations in the gulf.