Environmental heterogeneity and not vicariant biogeographic barriers generate community-wide population structure in desert-adapted snakes.

Genetic structure can be influenced by local adaptation to environmental heterogeneity and biogeographic barriers, resulting in discrete population clusters. Geographic distance among populations, however, can result in continuous clines of genetic divergence that appear as structured populations. Here, we evaluate the relevant importance of these three factors over a landscape characterized by environmental heterogeneity and the presence of a hypothesized biogeographic barrier in producing population genetic structure within 13 codistributed snake species using a genomic data set. We demonstrate that geographic distance and environmental heterogeneity across western North America contribute to population genomic divergence. Surprisingly, landscape features long thought to contribute to biogeographic barriers play little role in divergence community wide. Our results suggest that isolation by environment is the most important contributor to genomic divergence. Furthermore, we show that models of population clustering that incorporate spatial information consistently outperform nonspatial models, demonstrating the importance of considering geographic distances in population clustering. We argue that environmental and geographic distances as drivers of community-wide divergence should be explored before assuming the role of biogeographic barriers.

The evolutionary history of the goby Elacatinus puncticulatus in the tropical eastern pacific: Effects of habitat discontinuities and local environmental variability.

Habitat discontinuities, temperature gradients, upwelling systems, and ocean currents, gyres and fronts, can affect distributions of species with narrow environmental tolerance or motility and influence the dispersal of pelagic larvae, with effects ranging from the isolation of adjacent populations to connections between them. The coast of the Tropical Eastern Pacific (TEP) is a highly dynamic environment, with various large gyres and upwelling systems, alternating currents and large rocky-habitat discontinuities, which may greatly influence the genetic connectivity of populations in different parts of the coast. Elacatinus puncticulatus is a cryptic, shallow-living goby that is distributed along the continental shore of virtually the entire TEP, which makes it a good model for testing the influence of these environmental characteristics in the molecular evolution of widespread species in this region. A multilocus phylogeny was used to evaluate the influence of habitat gaps, and oceanographic processes in the evolutionary history of E. puncticulatus throughout its geographical range in the TEP. Two well-supported allopatric clades (one with two allopatric subclades) were recovered, the geographic distribution of which does not correspond to any previously proposed major biogeographic provinces. These populations show strong genetic structure and substantial genetic distances between clades and sub-clades (cytb 0.8-7.3%), with divergence times between them ranging from 0.53 to 4.88 Mya, and recent population expansions dated at 170-130 Kya. The ancestral area of all populations appears to be the Gulf of Panama, while several isolation events have formed the phylogeographic patterns evident in this species. Local and regional oceanographic processes as well as habitat discontinuities have shaped the distribution patterns of the genetic lineages along the continental TEP. Large genetic distances, high genetic differentiation, and the results of species-tree and phylogenetic analyses indicate that E. puncticulatus comprises a complex of three allopatric species with an unusual geographic arrangement.

Ice ages and butterflyfishes: Phylogenomics elucidates the ecological and evolutionary history of reef fishes in an endemism hotspot.

For tropical marine species, hotspots of endemism occur in peripheral areas furthest from the center of diversity, but the evolutionary processes that lead to their origin remain elusive. We test several hypotheses related to the evolution of peripheral endemics by sequencing ultraconserved element (UCE) loci to produce a genome-scale phylogeny of 47 butterflyfish species (family Chaetodontidae) that includes all shallow water butterflyfish from the coastal waters of the Arabian Peninsula (i.e., Red Sea to Arabian Gulf) and their close relatives. Bayesian tree building methods produced a well-resolved phylogeny that elucidated the origins of butterflyfishes in this hotspots of endemism. We show that UCEs, often used to resolve deep evolutionary relationships, represent an important tool to assess the mechanisms underlying recently diverged taxa. Our analyses indicate that unique environmental conditions in the coastal waters of the Arabian Peninsula probably contributed to the formation of endemic butterflyfishes. Older endemic species are also associated with narrow versus broad depth ranges, suggesting that adaptation to deeper coral reefs in this region occurred only recently (<1.75 Ma). Even though deep reef environments were drastically reduced during the extreme low sea level stands of glacial ages, shallow reefs persisted, and as such there was no evidence supporting mass extirpation of fauna in this region.

Phylogeography of the antilopine wallaroo (Macropus antilopinus) across tropical northern Australia.

The distribution of antilopine wallaroo, Macropus antilopinus, is marked by a break in the species' range between Queensland and the Northern Territory, coinciding with the Carpentarian barrier. Previous work on M. antilopinus revealed limited genetic differentiation between the Northern Territory and Queensland M. antilopinus populations across this barrier. The study also identified a number of divergent lineages in the Northern Territory, but was unable to elucidate any geographic structure. Here, we re-examine these results to (1) determine phylogeographic patterns across the range of M. antilopinus and (2) infer the biogeographic barriers associated with these patterns. The tropical savannahs of northern Australia: from the Cape York Peninsula in the east, to the Kimberley in the west. We examined phylogeographic patterns in M. antilopinus using a larger number of samples and three mtDNA genes: NADH dehydrogenase subunit 2, cytochrome b, and the control region. Two datasets were generated and analyzed: (1) a subset of samples with all three mtDNA regions concatenated together and (2) all samples for just control region sequences that included samples from the previous study. Analysis included generating phylogenetic trees based on Bayesian analysis and intraspecific median-joining networks. The contemporary spatial structure of M. antilopinus mtDNA lineages revealed five shallow clades and a sixth, divergent lineage. The genetic differences that we found between Queensland and Northern Territory M. antilopinus samples confirmed the split in the geographic distribution of the species. We also found weak genetic differentiation between Northern Territory samples and those from the Kimberley region of Western Australia, possibly due to the Kimberley Plateau-Arnhem Land barrier. Within the Northern Territory, two clades appear to be parapatric in the west, while another two clades are broadly sympatric across the Northern Territory. MtDNA diversity of M. antilopinus revealed an unexpectedly complex evolutionary history involving multiple sympatric and parapatric mtDNA clades across northern Australia. These phylogeographic patterns highlight the importance of investigating genetic variation across distributions of species and integrating this information into biodiversity conservation.

Regal phylogeography: Range-wide survey of the marine angelfish Pygoplites diacanthus reveals evolutionary partitions between the Red Sea, Indian Ocean, and Pacific Ocean.

The regal angelfish (Pygoplites diacanthus; family Pomacanthidae) occurs on reefs from the Red Sea to the central Pacific, with an Indian Ocean/Rea Sea color morph distinct from a Pacific Ocean morph. To assess population differentiation and evaluate the possibility of cryptic evolutionary partitions in this monotypic genus, we surveyed mtDNA cytochrome b and two nuclear introns (S7 and RAG2) in 547 individuals from 15 locations. Phylogeographic analyses revealed four mtDNA lineages (d=0.006-0.015) corresponding to the Pacific Ocean, the Red Sea, and two admixed lineages in the Indian Ocean, a pattern consistent with known biogeographic barriers. Christmas Island in the eastern Indian Ocean had both Indian and Pacific lineages. Both S7 and RAG2 showed strong population-level differentiation between the Red Sea, Indian Ocean, and Pacific Ocean (ΦST=0.066-0.512). The only consistent population sub-structure within these three regions was at the Society Islands (French Polynesia), where surrounding oceanographic conditions may reinforce isolation. Coalescence analyses indicate the Pacific (1.7Ma) as the oldest extant lineage followed by the Red Sea lineage (1.4Ma). Results from a median-joining network suggest radiations of two lineages from the Red Sea that currently occupy the Indian Ocean (0.7-0.9Ma). Persistence of a Red Sea lineage through Pleistocene glacial cycles suggests a long-term refuge in this region. The affiliation of Pacific and Red Sea populations, apparent in cytochrome b and S7 (but equivocal in RAG2) raises the hypothesis that the Indian Ocean was recolonized from the Red Sea, possibly more than once. Assessing the genetic architecture of this widespread monotypic genus reveals cryptic evolutionary diversity that merits subspecific recognition. We recommend P.d. diacanthus and P.d. flavescens for the Pacific and Indian Ocean/Red Sea forms.

Inventory of the fish fauna from Ivaí River basin, Paraná State, Brazil / Inventário da ictiofauna da bacia do rio Ivaí, Paraná, Brasil

Abstract We compiled data on fish fauna of the Ivaí River basin from recent specialised literature, standardised sampling and records of species deposited in fish collections. There were 118 fish species of eight orders and 29 families. Of these, 100 species are autochthonous (84.8%), 13, allochthonous (11.0%) and five, exotic (4.2%). The main causes for the occurrence of non-native species are escapes from aquaculture, introduction for fishing purposes and the construction of the Itaipu hydroelectric plant. The predominance of small and medium-sized Characiformes and Siluriformes, including 13 species new to science, accounts for approximately 11.0% of all species and 13.0% of all native species. About 10.2% of all species and 12.0% of all native species are endemic to the upper stretch of the Ivaí River, isolated by numerous waterfalls in tributary rivers and streams. The Ivaí River basin is subjected to various anthropogenic interferences such as pollution, eutrophication, siltation, construction of dams, flood control, fisheries, species introduction and release of fingerlings. These activities raise concerns about biodiversity of Brazilian inland waters especially regarding the fish fauna; the basin of the Ivaí River already has species classified in categories of extinction risk: Brycon nattereri and Apareiodon vladii (Vulnerable) and Characidium heirmostigmata and Steindachneridion scriptum (Endangered). The high species richness of native fish, endemism of some, high environmental heterogeneity, high risk of extinction and lack of knowledge of several other species along with the eminent human activities raise the need to enrich the scientific knowledge for future conservation efforts for the studied basin.

Resumo Nós compilamos dados sobre a diversidade da ictiofauna da bacia do rio Ivaí proveniente de recentes informações contidas em estudos divulgados na literatura especializada, coletas padronizadas e registros das espécies depositadas em coleções ictiológicas. Foram registradas 118 espécies de peixes pertencentes a oito ordens e 29 famílias. Dessas, 100 são autóctones, (84.8%), 13 são alóctones (11.0%) e cinco são exóticas (4.2%). As principais causas da ocorrência de espécies não nativas são escapes da piscicultura, introduções para pesca e a construção da usina hidrelétrica de Itaipu. Ocorre o predomínio de espécies de Characiformes e Siluriformes com porte pequeno e médio, sendo que 13 espécies são novas, o que representa aproximadamente 11.0% do total de espécies e 13.0% do total de espécies nativas. Ainda, aproximadamente 10.2% do total de espécies e 12.0% do total de espécies nativas correspondem a espécies endêmicas, isoladas pela presença de inúmeras cachoeiras em rios e riachos afluentes no trecho superior do rio Ivaí. A bacia do rio Ivaí está sujeita a uma variedade de interferências antrópicas como poluição, eutrofização, assoreamento, construção de represas, controle do regime de cheias, pesca, introduções de espécies e soltura de alevinos. Tais atividades apontam alarmantes preocupações com a biodiversidade das águas continentais brasileiras sobretudo para a ictiofauna, sendo que a bacia do rio Ivaí já apresenta espécies listadas em categorias de ameaças de extinção como Brycon nattereri e Apareiodon vladii (Vulneráveis) e Characidium heirmostigmata e Steindachneridion scriptum (Em Perigo). Devido à alta riqueza de espécies de peixes nativos, endemismo de algumas, alta heterogeneidade ambiental, sérios riscos de extinções e desconhecimento de várias outras espécies somados às eminentes ações antrópicas deve-se enriquecer o aporte científico de futuros apelos conservacionistas para a bacia aqui inventariada.